Posts Tagged ‘Biochemistry and Molecular Biology’

Science Teaching in Math and Technology

Larry H. Bernstein, MD, FCAP, Curator


2015 Best High Schools for STEM Rankings Methodology

U.S. News looked at 500 public high schools to identify the best in math and science education.

By Robert Morse May 11, 2015

U.S. News & World Report’s Best High Schools for STEM rankings methodology is based on the key principle that students at the Best High Schools for STEM must participate in and pass a robust curriculum of college-level math and science courses. STEM stands for science, technology, engineering and math.

To be included in the U.S. News Best High Schools for STEM rankings, a public high school first had to be listed as a gold medal winner in the 2015 U.S. News Best High Schools rankings. That meant that the top 500 nationally ranked high schools were eligible for the STEM rankings.

Those eligible schools were next judged nationally on their level of math and science participation and success, using Advanced Placement STEM test data for 2013 graduates as the benchmark to conduct the analysis. The U.S. News Best High Schools for STEM rankings methodology does not rely on any data from the U.S. Department of Education.

AP is a College Board program that offers college-level courses at high schools across the country. College Board defines STEM Math as AP courses in Calculus AB, Calculus BC, Computer Science A and Statistics; and STEM Science as AP courses in Biology, Chemistry, Environmental Science, Physics B, Physics C: Electricity and Magnetism and Physics C: Mechanics.

Math and science success at the high school level was assessed by computing a STEM Achievement Index for each school that ranked in the top 500 of the 2015 Best High Schools. The index was based on the percentage of all the AP test-takers in a school’s 2013 graduating class who took and passed college-level AP STEM Math and AP STEM Science tests. The higher a high school scored on the STEM Achievement Index, the better it placed in the Best High Schools for STEM rankings.

The maximum STEM Achievement Index value is 100. No public high school evaluated achieved that top score. The highest index was 98.3.

The first step in the rankings process was to compute the STEM Math Achievement Index. It was derived from two variables. The first was the percentage of AP test-takers in the 2013 graduating class who took at least one AP STEM Math course during high school, which was weighted 25 percent. The second was the percentage of those AP STEM Math test-takers who passed at least one AP STEM Math test during high school, receiving an AP score of 3 or higher. This variable was weighted 75 percent.

The next step was to calculate a STEM Science Achievement Index. Much like the math index, it was derived from the percentage of AP test-takers in the 2013 graduating class who took at least one AP STEM Science course during high school – weighted 25 percent – and the percentage of those AP STEM Science test-takers who passed at least one AP STEM Science test during high school, receiving an AP score of 3 or higher – weighted 75 percent.

This means that the methodology weights students taking AP math and science STEM courses at the high school level at 25 percent and passing those same AP STEM courses at 75 percent. In other words, passing both AP math and science tests was three times as important in the rankings as simply taking AP math and science courses.

The final step in the rankings process was to calculate the overall STEM Achievement Index, a combination of the STEM Math Achievement Index and the STEM Science Achievement Index. Each index was weighted at 50 percent, and then added together to create a composite value that is the STEM Achievement Index score.

The STEM rankings were based on sorting the unrounded – to many decimal places – STEM Achievement Index in descending order, with the top-ranked schools having the highest index values. The STEM Achievement Index was then rounded to the nearest 10th for online publication.

The top 250 high schools that achieved a value of greater than or equal to 66.8 in their STEM Achievement Index scored high enough to be numerically ranked. That high index cutoff point was used since it meant that all the high schools in the STEM rankings had, on average, more than two-thirds of the AP test-takers in their 2013 graduating class take and pass at least one AP STEM Math and one AP STEM Science test.

AP® and Advanced Placement® are registered trademarks of the College Board. Used with permission.

Top 50 Science Teacher Blogs

Bringing the subject of science to life for students is the challenge shared by the teachers who author these 50 amazing and insightful science education blogs. Sharing narratives set within and beyond the classroom walls, these next generation educators embrace technology but are never so dazzled by it that they lose sight of their common goal.

Physics Teacher Frank Noschese discusses science education topics like whether Khan Academy is effective at teaching physics, applying Angry Birds in physics lessons, and the idea of pseudoteaching.

Teaching High School Psychology
Teaching High School Psychology is a joint collaboration that explores the deeper lesson of the Stanford Prison Experiment, Gamification and its implications as a behavioral motivator, and opportunities for teaching Operant Conditioning with TV’s Big Bang Theory.

Little Miss Hypothesis
Inspiring Kindergarten scientists and giving a too-often neglected subject its due is the aim of Little Miss Hypothesis, where Mrs. Coe chronicles activities with growing brains, harvesting Spirit Garden salads and the development of science centers in a classroom that is home to Bluebonnet the Betta fish and the crab shack’s resident hermits.

Science for Kids
Sue Cahalane shares her passion for teaching science to elementary students in grades PK-4 on Science for Kids with ideas for classroom experiments, tutorials for science lessons, updates on science education news, and photos of students engaged in science activities.

Science Education on the Edge
Chris Ludwig, a high school science teacher from Colorado, writes about improving assessment and instruction in science and education technology.

Teach Science for All
Kirk Robbins shares helpful resources and tools for science teachers including reports, useful websites, and online tools.

Teaching | chemistry
Ellena Bethea, a high school chemistry teacher, writes about grading practices, online tools, and lab activities.

Adventures with the Lower Level
Tracie Schroeder shares her experiences teaching science, teaching methods, and thoughts on learning.

Physics in Flux
Dan Fullerton provides a resource for teachers with details of his successes and failures, technology guides, and physics book reviews.

Think Thank Thunk
On his blog, Think Thank Thunk, Shawn Cornally celebrates the Merlin within every teacher, the need for repackaging education, the debate surrounding Standards Based Grading and the dread of being dull as he chronicles his plight as an educator.

Marine biology teacher Sean Nash gets inspired by WordFoto and invites educators to appreciate and aim for “Whoa” moments on his blog, nashworld.

Science Teacher
A science teacher and former pediatrican finds an exemplary model in Dr. Seuss, challenges technophiles to understand deeply, and explains why he has made a tradition of culminating each school year with a field trip to watch horseshoe crabs in the throes of romance.

Teach Science
At Teach Science, Ed Hitchcock muses on the DNA shared by Socrates and explains why science’s greatest appeal is the unexpected.

Quantum Progress
At Quantum Progress, 9th grade Atlanta physics teacher John Burk relives a childhood tradition at Physics Teacher Camp, promotes blogging as a tool for professional development, and ponders why physics buildings never win campus beauty contests.

Pedagogue Padawan
At Pedagogue Padawan, Geoff Schmit shares innovative ideas for using Sudoku to teach Circuit Analysis, Angry Birds as a lesson in holography, and wikispaces as a tool for science projects.

Re:thinking blends personal reflection with a challenge to rethink school culture and policy as 9th grade teacher Ben Wildeboer finds teachable moments in events like the Japanese quake and explains the importance of “hard fun” for students.

Journey in Technology
At Journey in Technology a Dallas Physics teacher discusses implementing Khan Academy, discovering community and deep connections at Educon, and transforming the pseudoteaching of “cookbook” lab projects into real learning in the classroom.

Always Formative
Jason Buell is a middle school science teacher from California who writes about standards-based grading, education conferences, education books and more.

Stretching Forward
At Stretching Forward, Earth science teacher Janelle Wilson shares experiences from the Space Academy for Educators, discusses class blogging, and shares thoughts on engaging students and parents in science.

Tearing Down Walls
Derrick Willard teaches AP Environmental Science and discusses using social media and online tools to extend lessons outside the walls of the physical classroom.

Teaching Computer Science
Alfred Thompson is a former high school computer science teacher who currently works at Microsoft and writes about computer science education and resources.

A+ Computer Science Blog
High school computer science teacher Stacey Armstrong discusses why computer science is cool, game programming, career options in computer science, and computer science resources.

Teaching CS in Dallas
Kathleen Weaver writes about teaching robotics, Android development, and computer science education topics on her blog.

In Need of a Base Case
This blog discusses the need for change in computer science education, computer science project ideas, and the value of learning computer science.

Hélène Martin
Hélène Martin muses on the power of childhood playthings to fuel tech career ambitions and describes how lost airport luggage is a reminder to look for ways to leverage computing to solve real-life problems in this blog from the perspective of a computer science teacher.

Garth’s CS Education Blog
A computer science and programming teacher at a private school writes about teaching fun and important concepts and preparing students for computer science careers.

The Blog of Phyz
The Blog of Phyz is California teacher Dean Baird’s platform for debunking “Magnet Boys” and magic wristbands, and touting a 75 cent investment guaranteed to wow even the most cynical student.

Mr. Gonzalez’s Classroom
An Olympic Odyssey customarily culminates the academic year for middle school teacher Alfonso Gonzalez, who explores the challenge of giving terms like “on-task” and “structured learning” 21st century relevance on his blog, Mr. Gonzalez’s Classroom.

Free/Libre Open Source Science Education
Pseudoteaching and trends like the “reverse lecture” are hot topics on Free/Libre Open Source Science Education, where Steve Dickie shares his own innovative methods, including cartooning with GoAnimate and creating his own textbooks.

The Science Classroom
Oklahoma physics teacher Jody Bowie reports on the thrill of seeing students connect classroom lessons in everyday life, explains why everyone needs a whetstone to hone their thinking and divulges his identification with the Wizard in Wicked on The Science Classroom blog.

Jacobs Physics
On his blog Greg Jacobs calls course evaluations brutal but vital and bucks a few trends by advocating daily work and disparaging summer assignments in favor of starting each year “from the ground up”.

New Physics Modeler
Bryan Battaglia explains the appeal of professional conferences, the career changing power of blogging, and reflects that teachers gain as many lessons by year’s end as their students.

Just Call Me Ms Frizzle
Becky offers a distinctive first-year teacher perspective on Just Call Me Ms Frizzle, contrasting the low of leaving the room in frustration with the high of a Friday classroom on its best behavior, along with the challenge of teaching a non-traditional class.

And Yet it Moves
On his blog, And Yet it Moves, Ben Chun explains why problem-solving skills trump smarts, tackles the debate over doing away with honors classes, and challenges the AP curriculum.

Reflections of a Science Teacher
Sandra McCarron dismisses the notion of a rubric for thinking, believes that a successful classroom starts out with a vision and ponders the merits of science fairs that have been sacrificed to make way for education reforms on her blog, Reflections of a Science Teacher.

Hurricane Maine
A veteran teacher discusses ideas in education and technology, interesting articles, and how to make school more like play rather than work.

The Physics of Learning
Doug Smith authors this physics education blog that discusses topics like whether to use iPads in the classroom, the myths of merit pay, and scientific literacy.

Room 611
Mr. Young teaches Earth science and other subjects in Canada and provides insights into class by outlining what is covered in class almost every school day.

Using Blogs in Science Education
Stacey Baker is a high school biology teacher and writes about how to use classroom blogs to help students learn science.

Physics! Blog!
Physics! Blog! shares results of The No Homework Experiment and discusses standards based grading, the goal of testing, and teaching students how to learn from mistakes.

Ideas for Teaching Computer Technology to Kids
A blog sharing ideas and resources for teaching computer technology including robots for computer science education, programming resources, and computer science teaching tools.

A physics teacher shares interesting science articles like Nobel prize winning sentences, things from movies that cannot exist, and cool science videos.

Teach. Brian. Teach.
Brian discusses what makes for a good science conversation, reflects on teaching, shares observations of students, and explains why it is important to point out when students are having fun doing science.

The Skeptical Teacher
A high school physics teacher discusses science education and promotes critical thinking on his blog.

Physics & Physical Science Demos, Labs, & Projects for High School Teachers
A physics teacher provides a resource for science teachers to share ideas for labs and demonstrations and commentary on what works.

The Art of Teaching Science
Jack Hassard is a professor of science education and explores issues in teaching science, shares resources for science teachers, and discusses why teaching science is important.

SuperFly Physics
At SuperFly Physics, Andy Rundquist shares ideas for teaching physics, fun science experiments, and interesting physics problems.

Newton’s Minions
A physics blog sharing student work, anecdotes from the classroom, thoughts on student assessment, and ideas for teaching complex physics lessons.

Mr. Barlow’s Blog
Mr. Barlow is a high school science teacher and podcaster from Melbourne, Australia who shares interesting science studies, cool science news, and optical illusions at his blog.


What is JASON?

We are a non-profit organization that connects students, in the classroom and out, to real science and exploration to inspire and motivate them to study and pursue careers in Science, Technology, Engineering and Math (STEM).

We embed exciting STEM professionals and cutting-edge research into award-winning, standards-aligned in and out-of-school curricula. Live webcasts connect students with inspirational STEM role models. Student materials include reading selections with read-to-me functionality, inquiry-based labs, videos, and online games. For teachers and informal educators, we provide lesson plans, assessments, and comprehensive professional development programs.


Ten Websites for Science Teachers

Originally Published: February 7, 2012 | Updated: October 10, 2014



We all know that the web is full of excellent web resources for science teachers and students. However, unless you live on the web, finding the best websites can become quite a challenge. This isn’t a “Top Ten” list — instead, it is a list of websites that I either use on a regular basis or just find interesting. From teaching resources for the nature of science and authentic field journals to wacky videos about numbers, I am sure that you will find something in the following list the works for you!

1) Understanding Science

UC Berkeley’s Understanding Science website is a “must use” for all science teachers. It is a great resource for learning more about the process of science. The resource goes much deeper than the standard “PHEOC” model of the scientific method by emphasizing peer review, the testing of ideas, a science flowchart and “what is science?” checklist. Understanding Science also provides a variety of teaching resources including case studies of scientific discoveries and lesson plans for every grade level.

2) Field Research Journals

The Field Book Project from the National Museum of Natural History and the Smithsonian Institution Archives intends to create a “one stop” archive for field research journals and other documentation. You can find plenty of examples from actual field research journals for your classes.

3) Evolution

Berkeley’s Understanding Evolution website is the precursor to their Understanding Science efforts. The Understanding Evolution website provides a plethora of resources, news items and lessons for teaching about evolution. Lessons provide appropriate “building blocks” to help students at any grade level work towards a deeper understanding of evolution. The Evo 101 tutorial provides a great overview of the science behind evolution and the multiple lines of evidence that support the theory.

4) PhET Simulations

PhET from the University of Colorado provides dozens of fantastic simulations for physics, chemistry and biology. The website also includes a collection of teacher contributed activities, lab experiences, homework assignments and conceptual questions that can be used with the simulations.

5) Earth Exploration

The Earth Exploration Toolbook provides a series of activities, tools and case studies for using data sets with your students.

6) EdHead Interactives

Edheads is an organization that provides engaging web simulations and activities for kids. Current activities focus on simulated surgical procedures, cell phone design (with market research), simple and compound machines, and weather prediction.

7) Plant Mentors

Do you teach about plants? Check out Planting Science to connect your middle or high school students to science mentors and a collaborative inquiry project. From the project:

Planting Science is a learning and research resource, bringing together students, plant scientists, and teachers from across the nation. Students engage in hands-on plant investigations, working with peers and scientist mentors to build collaborations and to improve their understanding of science.

8) Periodic Table of Videos

Check out The Periodic Table of Videos for a wide array of videos about the elements and other chemistry topics.

9) More Videos!

Students can read and watch video about 21 Smithsonian scientistsincluding a volcano watcher, fossil hunter, art scientist, germinator and zoo vet.

10) Even More Videos!

How many videos were watched on YouTube in 2010? If you said 22 billion, you are sort of correct… Those 22 billion views only represent the number of times education videos were watched! In addition to this list of science and math YouTube channels, here are two of my favorites:

  • SciShow is all about teaching scientific concepts in an accessible and easy-to-understand manner. This channel includes a variety of short (3 minute) and long (10 minute) videos. New videos are released weekly.
  • Former BBC journalist Brady Haran is crazy about math and science. If you love numbers, you will love his Numberphile channel, dedicated to exploring the stories behind numbers.
  • And let’s close with a particularly good SciShow on Climate Change:


Best High Schools


 School for the Talented and Gifted


DALLAS, TX 75203

Dallas Independent School District

GOLD Medal


Near National Avg

253 Students

17 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#2 BASIS Scottsdale

11440 NORTH 136TH ST


BASIS Schools Inc.

GOLD Medal



698 Students

N/A Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#3 Thomas Jefferson High School for Science and Technology



Fairfax County Public Schools

GOLD Medal


Near National Avg

1,846 Students

111 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#4 Gwinnett School of Mathematics, Science and Technology



Gwinnett County Public Schools

GOLD Medal


Near National Avg

851 Students

48 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)


School of Science and Engineering Magnet


DALLAS, TX 75203

Dallas Independent School District

GOLD Medal




Near National Avg

386 Students

24 Teachers



Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#6 Carnegie Vanguard High School

1501 TAFT


Houston Independent School District

GOLD Medal


Near National Avg

590 Students

34 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#7 Academic Magnet High School



Charleston County School District

GOLD Medal


Near National Avg

610 Students

44 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#8 University High School



Tolleson Union High School District

GOLD Medal


Larger than National Avg

460 Students

14 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#9 Lamar Academy

1009 NORTH 10TH ST


Mcallen Independent School District

GOLD Medal


Smaller than National Avg

106 Students

19 Teachers


Above National Avg

100% Tested (IB)

100% Passed (IB)

#10 Gilbert Classical Academy High School



Gilbert Unified District

GOLD Medal


Smaller than National Avg

220 Students

20 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#11 The High School of American Studies at Lehman College


BRONX, NY 10468

New York City Public Schools

GOLD Medal


Near National Avg

393 Students

25 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#12 American Indian Public High School



Oakland Unf

GOLD Medal


Larger than National Avg

243 Students

13 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#13 International Studies Charter High School

2480 SW 8TH ST

MIAMI, FL 33135

Miami-Dade County Public Schools

GOLD Medal


Near National Avg

359 Students

27 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#14 High School for Dual Language and Asian Studies


NEW YORK, NY 10002

New York City Public Schools

GOLD Medal


Near National Avg

392 Students

25 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#15 Northside College Preparatory High School



Chicago Public Schools

GOLD Medal


Near National Avg

1,069 Students

74 Teachers


Above National Avg

100% Tested (AP®)

100% Passed (AP®)

#16 Oxford Academy



Anaheim Union High

GOLD Medal


Larger than National Avg

1,152 Students

38 Teachers


Above National Avg

100% Tested (AP®)

99% Passed (AP®)

#17 University High School


TUCSON, AZ 85711

Tucson Unified School District

GOLD Medal


Larger than National Avg

934 Students

44 Teachers


Above National Avg

100% Tested (AP®)

99% Passed (AP®)

#18 Pacific Collegiate School



Santa Cruz County Office Of Education

GOLD Medal


Larger than National Avg

515 Students

28 Teachers


Above National Avg

100% Tested (AP®)

99% Passed (AP®)

#19 Biotechnology High School



Monmouth County Vocational School District

GOLD Medal


Near National Avg

311 Students

23 Teachers


Above National Avg

100% Tested (IB)

99% Passed (IB)

#20 High Technology High School



Monmouth County Vocational School District

GOLD Medal


Near National Avg

280 Students

22 Teachers


Above National Avg

99% Tested (AP®)

99% Passed (AP®)

The United States has developed as a global leader, in large part, through the genius and hard work of its scientists, engineers, and innovators. In a world that’s becoming increasingly complex, where success is driven not only by what you know, but by what youcan do with what you know, it’s more important than ever for our youth to be equipped with the knowledge and skills to solve tough problems, gather and evaluate evidence, and make sense of information. These are the types of skills that students learn by studying science, technology, engineering, and math—subjects collectively known as STEM.

Yet today, few American students pursue expertise in STEM fields—and we have an inadequate pipeline of teachers skilled in those subjects. That’s why President Obama has set a priority of increasing the number of students and teachers who are proficient in these vital fields.



The need

All young people should be prepared to think deeply and to think well so that they have the chance to become the innovators, educators, researchers, and leaders who can solve the most pressing challenges facing our nation and our world, both today and tomorrow. But, right now, not enough of our youth have access to quality STEM learning opportunities and too few students see these disciplines as springboards for their careers.expand/collapse

The goals

President Obama has articulated a clear priority for STEM education: within a decade, American students must “move from the middle to the top of the pack in science and math.” The Obama Administration also is working toward the goal of fairness between places, where an equitable distribution of quality STEM learning opportunities and talented teachers can ensure that all students have the chance to study and be inspired by science, technology, engineering, and math—and have the chance to reach their full potential.expand/collapse

The plan

The Committee on STEM Education (CoSTEM), comprised of 13 agencies—including all of the mission-science agencies and the Department of Education—are facilitating a cohesive national strategy, with new and repurposed funds, to increase the impact of federal investments in five areas: 1.) improving STEM instruction in preschool through 12th grade; 2.) increasing and sustaining public and youth engagement with STEM; 3.) improving the STEM experience for undergraduate students; 4.) better serving groups historically underrepresented in STEM fields; and 5.) designing graduate education for tomorrow’s STEM workforce.expand/collapse

Supporting Teachers and Students in STEM

At the Department of Education, we share the President’s commitment to supporting and improving STEM education. Ensuring that all students have access to high-quality learning opportunities in STEM subjects is a priority, demonstrated by the fact that dozens of federal programs have made teaching and learning in science, technology, engineering, and math a critical component of competitiveness for grant funding. Just this year, for the very first time, the Department announced that its Ready-to-Learn Television grant competition would include a priority to promote the development of television and digital media focused on science.

The Department’s Race to the Top-District program supports educators in providing students with more personalized learning—in which the pace of and approach to instruction are uniquely tailored to meet students’ individual needs and interests—often supported by innovative technologies. STEM teachers across the country also are receiving resources, support, training, and development through programs like Investing in Innovation (i3), the Teacher Incentive Fund, the Math and Science Partnershipsprogram, Teachers for a Competitive Tomorrow, and the Teacher Quality Partnerships program.

Because we know that learning happens everywhere—both inside and outside of formal school settings—the Department’s 21st Century Community Learning Centers program is collaborating with NASA, the National Park Service, and the Institute of Museum and Library Services to bring high-quality STEM content and experiences to students from low-income, high-need schools. This initiative has made a commitment to Native-American students, providing about 350 young people at 11 sites across six states with out-of-school STEM courses focused on science and the environment.

And in higher education, the Hispanic-Serving Institutions-STEM program is helping to increase the number of Hispanic students attaining degrees in STEM subjects.

This sampling of programs represents some of the ways in which federal resources are helping to assist educators in implementing effective approaches for improving STEM teaching and learning; facilitating the dissemination and adoption of effective STEM instructional practices nationwide; and promoting STEM education experiences that prioritize hands-on learning to increase student engagement and achievement.

Learn more

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A new ranking of how well the United States’ schools are preparing students for science and engineering careers shows that although there’s a small number of high performers, most states are doing a poor job of educating students in these subjects.

According to the ranking of schools teaching kindergarten through 12th grade, Massachusetts leads the pack with a score of 4.82 on a scale of 1 to 5, while Mississippi trails behind as “worst in the United States” with a 1.11 score. Twenty-one states in total, including California, earned what the ranking classified as “below average” or “far below average” scores, and only 10 states earned scores above the national average of 2.82.

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Liposomal encapsulated drug

Writer and Curator: Larry H. Bernstein, MD, FCAP 

7.2  Liposomal encapsulated drug

7.2.1 Curcumin-containing liposomes stabilized by thin layers of chitosan derivatives

7.2.2 Colloids and Surfaces B: Biointerfaces 1 Sep 2013; 109:307–316

7.2.3 Increasing the stability of curcumin in serum with liposomes or hybrid drug-in-cyclodextrin-in-liposome systems

7.2.4 Influence of curcumin-loaded cationic liposome on anticancer activity for cervical cancer therapy

7.2.5 Liposome encapsulation of curcumin

7.2.6 Gemcitabine and γ-cyclodextrin-docetaxel inclusion complex-loaded liposome for highly effective combinational therapy of osteosarcoma

7.2.7 Self-organized thermo-responsive hydroxypropyl cellulose nanoparticles for curcumin delivery

7.2.8 The enhancement of gene silencing efficiency with chitosan-coated liposome formulations of siRNAs targeting HIF-1α and VEGF

7.2.9 Interactions of nanomaterials and biological systems. Implications to personalized nanomedicine

7.2.1 Curcumin-containing liposomes stabilized by thin layers of chitosan derivatives

Anna Karewicz, Dorota Bielska, Agnieszka Loboda, Barbara Gzyl-Malcher, Jan Bednar, Alicja Jozkowicz, Jozef Dulak, Maria Nowakowska


    • Cationic, hydrophobic and cationic–hydrophobic derivatives of chitosan were obtained and characterized.• Curcumin-containing liposomes were successfully stabilized by effective coating with these derivatives.• Liposomes coated with cationic–hydrophobic chitosan are most promising for curcumin delivery.• Such coated liposomes easily penetrate cell membrane and release curcumin in a controlled manner.• These curcumin-loaded liposomal systems are non-toxic for normal cells, but toxic for murine melanoma.


Stable vesicles for efficient curcumin encapsulation, delivery and controlled release have been obtained by coating of liposomes with thin layer of newly synthesized chitosan derivatives. Three different derivatives of chitosan were obtained and studied: the cationic (by introduction of the stable, quaternary ammonium groups), the hydrophobic (by attachment of N-dodecyl groups) and cationic–hydrophobic one (containing both quaternary ammonium and N-dodecyl groups). Zeta potential measurements confirmed effective coating of liposomes with all these chitosan derivatives. The liposomes coated with cationic–hydrophobic chitosan derivative are the most promising curcumin carriers; they can easily penetrate cell membrane and release curcumin in a controlled manner. Biological studies indicated that such systems are non-toxic for murine fibroblasts (NIH3T3) while toxic toward murine melanoma (B16F10) cell line.

Graphical abstract

Full-size image (30 K)


7.2.2 Colloids and Surfaces B: Biointerfaces 1 Sep 2013; 109:307–316


  • Cationic, hydrophobic and cationic–hydrophobic derivatives of chitosan were obtained and characterized.
  • Curcumin-containing liposomes were successfully stabilized by effective coating with these derivatives.
  • Liposomes coated with cationic–hydrophobic chitosan are most promising for curcumin delivery.
  • Such coated liposomes easily penetrate cell membrane and release curcumin in a controlled manner.
  • These curcumin-loaded liposomal systems are non-toxic for normal cells, but toxic for murine melanoma.


Stable vesicles for efficient curcumin encapsulation, delivery and controlled release have been obtained by coating of liposomes with thin layer of newly synthesized chitosan derivatives. Three different derivatives of chitosan were obtained and studied: the cationic (by introduction of the stable, quaternary ammonium groups), the hydrophobic (by attachment of N-dodecyl groups) and cationic–hydrophobic one (containing both quaternary ammonium and N-dodecyl groups). Zeta potential measurements confirmed effective coating of liposomes with all these chitosan derivatives. The liposomes coated with cationic–hydrophobic chitosan derivative are the most promising curcumin carriers; they can easily penetrate cell membrane and release curcumin in a controlled manner. Biological studies indicated that such systems are non-toxic for murine fibroblasts (NIH3T3) while toxic toward murine melanoma (B16F10) cell line.


7.2.3 Increasing the stability of curcumin in serum with liposomes or hybrid drug-in-cyclodextrin-in-liposome systems

Matloob AH1Mourtas S1Klepetsanis P2Antimisiaris SG3.
Int J Pharm. 2014 Dec 10; 476(1-2):108-15

Curcumin (CURC) was incorporated in liposomes as free drug or after formation of hydropropyl-β- or hydroxypropyl-γ-cyclodextrin (HPβCD or HPγCD) complexes prepared by coprecipitation and characterized by X-ray diffractometry. Liposomes encapsulating CURC as free drug or CD-complexes (hybrid formulations) were prepared by the dehydration-rehydration vesicle (DRV) method followed by extrusion, and characterized for size, zeta-potential and CURC loading. CURC stability (at 0.01 and 0.05mg/mL) in 80% (v/v) fetal bovine serum (FBS) was evaluated at 37°C. Results demonstrate that HPβCD stabilizes CURC more than HPγCD, but liposome encapsulation provides substantially more protection, than CDs. CURC stabilization is similar, when encapsulated as free compound or CD-complex. However, the last method increases CURC loading by 23 times (depending on the lipid composition of liposomes and the CD used), resulting in higher solubility. The stability profile of CURC in serum depends on the composition of liposomes and CURC concentration, since at lower concentrations larger CURC fractions are protected due to protein binding. Compared to the corresponding CD complexes, hybrid formulations provide intermediate CURC solubility (comparable to HPβCD) but profoundly higher stabilization.

7.2.4 Influence of curcumin-loaded cationic liposome on anticancer activity for cervical cancer therapy

Saengkrit N1Saesoo S1Srinuanchai W1Phunpee S1Ruktanonchai UR2.
Colloids Surf B Biointerfaces. 2014 Feb 1; 114:349-56.


  • The delivery of curcumin using liposomes was explored in cervical cancer cell lines.
  • A critical role of DDAB in liposomes containing curcumin was investigated.
  • DDAB is a potent inducer of cell uptake, anticancer efficiency and cell death.
  • Anticancer efficiency of liposomal curcumin was more pronounced than free curcumin.

The delivery of curcumin has been explored in the form of liposomal nanoparticles to treat various cancer cells. Since curcumin is water insoluble and an effective delivery route is through encapsulation in liposomes, which were modified with three components of DDAB, cholesterol and non-ionic surfactant. The purpose of this study was to establish a critical role of DDAB in liposomes containing curcumin at cellular response against two types of cell lines (HeLa and SiHa). Here, we demonstrate that DDAB is a potent inducer of cell uptake and cell death in both cell lines. The enhanced cell uptake was found on DDAB-containing liposome, but not on DDAB-free liposome. However, the cytotoxicity of DDAB-containing liposomes was high and needs to be optimized. The cytotoxicity of liposomal curcumin was more pronounced than free curcumin in both cells, suggesting the benefits of using nanocarrier. In addition, the anticancer efficiency and apoptosis effect of the liposomal curcumin formulations with DDAB was higher than those of DDAB-free liposomes. Therefore curcumin loaded liposomes indicate significant potential as delivery vehicles for the treatment of cervical cancers.

Full-size image (19 K)


7.2.5 Liposome encapsulation of curcumin: physico-chemical characterizations and effects on MCF7 cancer cell proliferation.

Hasan M1Belhaj N1Benachour H2Barberi-Heyob M3Kahn CJ4Jabbari E5Linder M1Arab-Tehrany E6.
Int J Pharm. 2014 Jan 30; 461(1-2):519-28

The role of curcumin (diferuloylmethane), for cancer treatment has been an area of growing interest. However, due to its low absorption, the poor bioavailability of curcumin limits its clinical use. In this study, we reported an approach of encapsulation a curcumin by nanoliposome to achieve an improved bioavailability of a poorly absorbed hydrophobic compound. We demonstrated that liposomal preparations to deliver curcumin increase its bioavailability. Liposomes composed of salmon’s lecithin also improved curcumin bioavailability compared to those constituted of rapeseed and soya lecithins. A real-time label-free cell analysis system based on real-time cell impedance monitoring was used to investigate the in vitro cytotoxicity of liposomal preparations.

Fig. 1. Chemical structure of curcuminoids (curcumin, demethoxycurcumin, bis

Table 2 Membrane fluidity of nanoliposomes with and without curcumin.
Sample                                            Membrane fluidity
Salmon liposome                           3.19 ± 0.08a,b,*
Curcumin loaded
salmon liposome                           2.81 ± 0.05*
Rapeseed liposome                       3.53 ± 0.07a,*
Curcumin loaded
rapeseed liposome                        2.83 ± 0.04*
Soya liposome                                3.58 ± 0.10b,*
Curcumin loaded
soya liposome                                2.83 ± 0.02*
* Significant t-test                         (p < 0.05)
between salmon
and rapeseed
(a), salmon and soya
(b), curcumin loaded liposome
and liposome of the same lecithin.

Fig. 3. Transmission electron microscopic images of rapeseed
(a), soya
(b) and salmon
(c) nanoliposomes

Fig. 4. Cell index (CI) kinetics of the MCF-7 cells exposed to different concentrations of curcumin.
CI was monitored during 72 h after compounds exposure. Reported data are the means of three replicates.
Statistical differences were found after 24 h for 12 and 20 mM of curcumin vs. control cells (without curcumin)
and between 12 mM and 20 mM of curcumin.


7.2.6 Gemcitabine and γ-cyclodextrin-docetaxel inclusion complex-loaded liposome for highly effective combinational therapy of osteosarcoma

Int J Pharm. 2014 Nov 26; 478(1):308-317.

Fig.1. Schematic illustration of DTX and GEM loaded nanocarriers. First, DTX was complexed with HP-g-cyclodextrin to form a DTX/CD inclusion complex.
In the second step, GEM and DTX/CD complex was incorporated in a PEGylated liposome.

In vitro release study
The release study of DTX/GEM-L was performed in phosphate buffered saline (pH 7.4) at 37C. As shown in Fig. 3, no initial burst release phenomenon was
observed with both the drugs indicating that none of the drugs were present in the surface of liposome. As expected, hydrophilic GEM released faster than
that of DTX. 50% of GEM released within 16 h of study period and almost 90% of drug released during the 48 h study period. The faster release of drug was
attributed to the free diffusion of drug from the core of liposomes to the release media. On the other hand, DTX relatively released slowly from the liposome
system. It could be due to the presence of inclusion complex which delayed the release rate of DTX. Nearly 40% of DTX released from the CD/liposome
system at the end of 48 h study period. For this system, various factors decide the drug release patterns including nature of drug, interaction between drug
and lipid, diffusion path length. Moreover, difference in the hydrophobicity of drugs decides the drug release pattern. GEM is a highly hydrophilic drug
while DTX is a hydrophobic drug.

Cytotoxic effect of GEM and DTX against MG63 cancer cells
The in vitro antitumor potential of GEM and DTX (individually and combined) was evaluated in MG63 bone tumor cells. The cells were exposed to increasing
concentration of single as well as combined drug in a time-dependent manner. As shown in Fig. 4, both DTX and GEM inhibited the growth of the cancer cell
in a dose-dependent and time-dependent manner. As seen, DTX was more effective in controlling the cell growth rate compared to that of GEM. However,
combined DTX/GEM showed better antitumor potential than that of individual drugs. Most importantly, DTX/GEM-L showed a more pronounced tumor inhibiting
effect than the free drug combination. For example, at a fixed concentration of 1 mg/mL, free DTX/GEM showed 55% cell viability compared to 40% cell viability
for DTX/GEM-L at the end of 24 h. Notably, cellular viabilities of combinational drug were significantly lower than that of individual GEM or DTX. IC50 value
was calculated to quantitatively estimate the inhibitory levels. The IC50 for free GEM and free DTX were >10 mg/mL and 5.4 mg/mL.

Fig. 2. Transmission electron microscope (TEM) image of nanocarriers (A) blank liposome (B) DTX/GEM-loaded CD/liposome.

Fig. 3. In vitro release kinetics of DTX and GEM from DTX/GEM-L. The release study was performed in phosphate buffered saline (pH 7.4) at 37C. The nanoparticle
dispersions were kept in dialysis tube placed in tube containing media. The release samples were collected at predetermined time intervals. *p < 0.05 is the
statistical difference between release rate of GEM and DTX.

Fig. 4. In vitro cytotoxicity evaluation of formulations on MG63 cancer cells. The cells were treated with DTX, GEM, DTX/GEM, and DTX/GEM-L and incubated
for 24 h (a) and 48 h (b), respectively. Untreated cells were considered as control. (c) Cytotoxicity of blank nanoparticles. The free DTX and free GEM was
treated in respective concentrations while a molar ratio of 1:1 (two drugs) was used for DTX/GEM combinational cocktail as well as nanocarriers. *p < 0.05
and **p < 0.01 are the statistical difference between cytotoxicity of DTX/GEM-L and free GEM/DTX.

7.2.7 Self-organized thermo-responsive hydroxypropyl cellulose nanoparticles for curcumin delivery

European Polymer Journal Sep 2013; 49(9)9:2485–2494

A tunable temperature-responsive nanoparticulate system based on the ionic modifications of hydroxypropyl cellulose (HPC) was obtained. Two derivatives of HPC were successfully obtained and characterized: cationic (modified with trimethylammonium groups) and anionic (modified with styrenesulfonate groups). Due to the polycation-polyanion interactions they spontaneously self-assemble into nanoparticles in water. The size and surface charge of the nanoparticles can be controlled by the polycation/polyanion ratio. The resulting structures are spherical with diameters in the range from 150 to 250 nm, as confirmed by AFM, SEM, and DLS measurements. The size of the nanospheres increases in elevated temperatures. A model compound, curcumin, known for its anti-cancer and anti-inflammatory properties, was effectively entrapped inside nanospheres. Its release profile was found to be temperature-dependent.

Graphical abstract

Full-size image (10 K)


► Cationic and anionic derivatives of hydroxypropyl cellulose were synthesized. ► The polymers self-assemble forming spherical nanoparticles. ► The size of the nanoparticles is temperature-dependent. ► Curcumin could be efficiently entrapped within the nanospheres. ► No burst effect was observed for curcumin release.

7.2.8 The enhancement of gene silencing efficiency with chitosan-coated liposome formulations of siRNAs targeting HIF-1α and VEGF

Int J Pharm. 2014 Nov 13; 478(1):147-154.

RNA interference (RNAi) holds considerable promise as a novel therapeutic strategy in the silencing of disease-causing genes. The development of effective delivery systems is important for the use of small interfering RNA (siRNA) as therapy. In the present study, we investigated the effect on breast cancer cell lines and the co-delivery of liposomes containing siHIF1-α and siVEGF. In order to achieve the co-delivery of siHIF1-α and siVEGF and to obtain lower cytotoxicity, higher transfection and silencing efficiency, in this study, we used chitosan-coated liposomal formulation as the siRNA delivery system. The obtained particle size and zeta potential values show that the chitosan coating process is an effective parameter for particle size and the zeta potential of liposomes. The liposome formulations loaded with siHIF1-α and siVEGF showed good stability and protected siRNA from serum degradation after 24-h of incubation. The expression level of VEGF mRNA was markedly suppressed in MCF-7 and MDA-MB435 cells transfected with chitosan-coated liposomes containing HIF1-α and VEGF siRNA, respectively (95% and 94%). In vitro co-delivery of siVEGF and siHIF1-α using chitosan-coated liposome significantly inhibited VEGF (89%) and the HIF1-α (62%) protein expression when compared to other liposome formulations in the MDA-MB435 cell. The co-delivery of siVEGF and siHIF1-α was greatly enhanced in the vitro gene silencing efficiency. In addition, chitosan-coated liposomes showed 96% cell viability. Considering the role of VEGF and HIF1-α in breast cancer, siRNA-based therapies with chitosan coated liposomes may have some promises in cancer therapy.

Fig. 2. TEM photographs of  cationic (a) and chitosan-coated (b) liposomes.

As shown in Table 1, the particle sizes of the liposome formulations fluctuated from 131.25 2.76 nm to 641.75 + 5.24 nm. The particle size of the chitosan-coated liposomes was significantly larger
than the non-coated liposome formulations (between 510.65 + 49.71 nm and 641.75 + 25.24 nm). In addition, the particle sizes of the liposome formulations containing siVEGF and siHIF were
smaller than those containing either siVEGF or siHIF  only (Table 1). According to the net surface charge values, the prepared liposome formulations which are suitable for the methods used,
are determined to have the expected electrical charge type (anionic liposome 23.10 + 0.71 mV; cationic liposome 39.05  1.63 mV). It was determined that siRNA which was added to the
formulation and coating with the chitosan of  the liposomes affected their net surface charge. The surface charge values changed into negative directions with the amount of siRNA added
to the formulation (anionic liposome 26.60 + 0.14 mV; cationic liposome 29.95 + 0.64 mV). It was determined that the surface charge values changed into positive directions during the
coating process of the negatively charged liposomes with a natural cationic polymer chitosan (chitosan coated anionic liposome 27.0 + 0.57). These  data suggest the liposome exerts
a protective effect on the siRNA.

7.2.9 Interactions of nanomaterials and biological systems. Implications to personalized nanomedicine

Adv Drug Deliv Rev. 2012 Oct; 64(13):1363-84.

The application of nanotechnology to personalized medicine provides an unprecedented opportunity to improve the treatment of many diseases. Nanomaterials offer several advantages as therapeutic and diagnostic tools due to design flexibility, small sizes, large surface-to-volume ratio, and ease of surface modification with multivalent ligands to increase avidity for target molecules. Nanomaterials can be engineered to interact with specific biological components, allowing them to benefit from the insights provided by personalized medicine techniques. To tailor these interactions, a comprehensive knowledge of how nanomaterials interact with biological systems is critical. Herein, we discuss how the interactions of nanomaterials with biological systems can guide their design for diagnostic, imaging and drug delivery purposes. A general overview of nanomaterials under investigation is provided with an emphasis on systems that have reached clinical trials. Finally, considerations for the development of personalized nanomedicines are summarized such as the potential toxicity, scientific and technical challenges in fabricating them, and regulatory and ethical issues raised by the utilization of nanomaterials.

The application of nanotechnology to medicine has created an interdisciplinary research field, often referred to as nanomedicine, which has the potential to significantly improve the way many diseases are treated [1]. Within the nascent but rapidly growing field of nanomedicine, personalized medicine applications are among the most promising and exciting innovations [2]. Personalized medicine consists of a healthcare strategy where specific therapeutics are prescribed to patients on the basis of genetic, phenotypic, and environmental factors that influence the response to therapy [3]. It has long been recognized that individual patients respond differently to the same drug in terms of efficacy and safety due to the complexity and heterogeneity of diseases and patients [4]. For example, some drugs and dosages cause adverse health effects within a particular patient population while a different patient population responds well to the drug treatment with minimal side effects. Similarly, there may be marked variability in efficacy as well. With an increased understanding of genomics and the emergence of novel technologies for the investigation of molecular profiling and genetic mapping of a patient, personalized medicine is poised to begin reaching its full potential.

The application of nanomaterials to medical problems has already demonstrated a clinical impact in terms of delivery strategies for a range of bioactive molecules, including therapeutic agents, nucleic acids and imaging contrast agents [5]. Nanotechnology enables a combinatorial library of nanoparticles to be synthesized with precise control over surface modifications (e.g., targeting moieties, charge modification, stealth), size, shape, and other particle characteristics that can be screened in order to find the best particle properties for patient-specific therapeutics [6]. There are already examples of nanomedicine in the clinic. Doxil®, a PEGylated liposomal doxorubicin formulation, was the first nanosized therapeutic on the market in 1995 and was used as an effective treatment for metastatic breast cancer and recurrent ovarian cancer [7]. Other systems are in various stages of preclinical and clinical advancements. For example, a targeted therapeutic nanoparticle, named BIND-014, that accumulates in tumors while avoiding uptake by the healthy cells have shown promising results in an ongoing clinical trial [6]. Another example is a lipid nanoparticulate delivery system (Oncoprex®) containing plasmid DNA encoding the TUSC2 tumor suppressor that is being studied in combination with erlotinib, a human epidermal growth factor receptor (EGFR) inhibitor, in lung cancer patients unresponsive to erlotinib or lacking the EGFR mutation [8]. Preclinical studies in animals showed that intravenous TUSC2 nanoparticles work synergistically with erlotinib to overcome drug-induced resistance by simultaneously inactivating the EGFR pathway and by inducing apoptosis in resistant cells. A phase II clinical trial evaluating intravenous TUSC2 nanoparticles in combination with erlotinib will begin in 2012. This will provide two possible therapeutic options depending on the tumor EGFR expression: EGFR inhibitor monotherapy or in combination with the nanoparticles. Progress has also been made in the development of versatile nanocarriers placing emphasis upon patient-specific treatments. For example, Zhang and colleagues recently proposed red blood cell (RBC) membrane-coated nanoparticles to evade the immune system and exhibit longer retention time in the blood [9]. This approach suggests an elegant yet hard to clinically-implement methodology: the patient’s RBCs are collected and emptied to leave only the membranes, the latter are then fused with pre-formed polymeric nanoparticles. The resultant RBC-membrane coated nanoparticles are therefore decorated with the patient’s own proteins and cell membranes to evade the host’s defense mechanisms.

While personalized medicine can guide the design and use of nanocarriers, nanotechnology can also aid in the collection of genomic and molecular data necessary for personalized medicine. Advances in personalized medicine occur through the development of novel nanomaterials as well as technologies for the early detection, imaging, and identification of molecular signatures of diseases. The field of pharmacogenetics and “omics” technologies (e.g., pharmacogenomics, pharmacoproteomics and pharmacometabonomics) have enabled the investigation of an individual patient’s genetic and molecular profiles. This information have provided insights into the mechanisms of disease and how to appropriately combine therapeutics with specific disease profiles. Nanoscale materials and technologies have the ability to greatly expand the molecular and genetic information gathered from patients. For example, the GeneChip® microarray allows nanoscale patterning of biological molecules on surfaces with exquisite control over their spatial placement to obtain DNA sequencing [1, 10]. With the ability to control molecular deposition now in the nanometer range, a million-fold increase in information density could be packed in “nanoarrays” for the detection of nucleic acids or proteomic profiles [1113]. Another example is gold nanoparticles modified with biorecognition molecules that are used for high-throughput genomic detection and are currently approved for use by the FDA [1416].

A research report of commercialization efforts of nanomedicine from the Business Communications Company indicated that the global nanomedicine sales are projected to grow to over $100 billion by 2014 [17]. There are increasingly growing partnerships between biopharmaceutical companies and nanomedicine startups pursuing nanomedicine R&D projects due to the enormous potential applications of nanotechnology to healthcare. One of the predominant focuses is drug delivery applications. The other nanomedicine products include in vivo imaging agents, in vitro diagnostics, biomaterials, and active implants [18]. As our fundamental understanding of diseases increases, implementations of nanotechnology will offer an expanding toolbox to improve point-of-care diagnostics, enable integration of diagnostics with therapeutics, and treat patients with a more personal approach.

While nanomedicine starts to show much promise to the field of personalized medicine, further research is required to expand its impact. In particular, a fundamental understanding of the interactions between nanomaterial surfaces and complex proteins in biological fluids needs to be achieved. This would influence both in vivo delivery of therapeutics and ex vivo diagnostics. Likewise, interactions between nanomaterials and cells, through non-specific contacts or ligand-receptor interactions, as well as the intracellular mechanisms responsible for trafficking of a nanomaterial in the cell, must be more thoroughly characterized. There is a complex relationship between a nanomaterial’s physicochemical properties (e.g., size, charge, surface properties), and its interaction within a biological system. Small changes in size, charge, surface functionalization and chemical composition can lead to radically different interactions with living systems [19]. These interactions then determine the biocompatibility, stability, biological performance and side effects of the nanomaterial. In this regard, understanding the nano-bio interactions and the relationships between the nanomaterial properties/structure and activity will provide a conceptual basis for the rational design and safe use of personalized nanomedicines.

In the first section of this review, we will address different areas in which better comprehension is required and propose examples showing how nanomaterials interact with their environment in complex and subtle manners. Each subject will be discussed from the perspective of its implications for personalized medicine. The second section will highlight some examples that demonstrate current trends and novel concepts in the field of nanomedicine and its impact on personalized medicine. These include nano-sized platforms for the targeted delivery of therapeutics, contrast agents for diagnostic imaging, and theranostic nanoparticles. The use of nanoparticles for the discovery of biomarkers and molecular diagnostic will also be evaluated. Finally, the third section will present the scientific and technical challenges associated with developing personalized nanomedicines, various safety, political and ethical issues raised in the field, as well as the obstacles and limitations associated with personalized nanomedicine.

Interactions of nanomaterials in biological systems

As the role of nanomaterials in biology and medicine continues to grow, the number of situations in which they will be in contact with biological systems will indisputably increase. In this domain where the complexities of nanotechnology and human physiology combine, fundamental understanding is essential before one can think about intricate applications. In the following section, three different aspects of the interactions between nanomaterials and proteins will be presented. Their relevance to personalized medicine will be highlighted in the last section.


When nanoparticles are utilized for treatment, imaging a tumor, or aiding to establish a diagnosis upon systemic administration, the first tissue they encounter is the blood and all the proteins it contains within. Similarly, when diagnostic nanomaterials are used in vitro or ex vivo to analyze samples of biological fluids, they will come in contact with complex proteins mixtures. The adsorption of proteins on a substrate is a much more complex phenomenon when the surface possesses nanoscale dimensions as compared to that of larger proportions [20]. The relative surface area of nanomaterials is very large and their features are on the same order as proteins (1 to 20 nm) [21]. The interactions between proteins and materials of the nano- and meso- or macroscales are therefore both quantitatively and qualitatively different.

Upon contact with biological fluids (e.g., blood, interstitial fluid or mucosal secretions), nanoparticles are coated with proteins that may change their surface charge and properties. This biological coating can subsequently lead to the loss of performance due to an increase in hydrodynamic size or aggregation. The protein that binds most strongly to polymeric nanoparticles, liposomes, iron oxide nanoparticles and carbon nanotubes are albumin, immunoglobulins, fibrinogen, apolipoproteins and proteins from the complement cascade [20].

Decreasing the nonspecific protein interaction

When nanoparticles are administered systemically, the proteins that adhere to their surface will greatly affect their circulation and biodistribution [22, 23]. Complement and immunoglobulin binding promotes particle opsonization, leading to recognition by the mononuclear phagocyte system (MPS) and rapid clearance from the bloodstream [22]. MPS capture is dictated by macrophage phagocytosis (mostly in the sinusoids of the liver) and splenic filtration [23, 24]. Aggregation of nanoparticles in the blood can also lead to retention and embolism in the lung capillaries [25].

Short circulation half-life, low efficacy, and toxicity caused by accumulation of foreign materials in the liver and spleen are the primary limitation for the systemic administration of nanoparticles. These issues have led to the development of strategies aimed at increasing blood residence time. Among these, the use of poly(ethylene glycol) (PEG) for surface functionalization has been shown to dramatically reduce protein absorption, particularly apolipoprotein J and complement protein C3, through hydrophilicity and steric repulsion effects, therefore extending residence time in blood [2628]. This has allowed the “stealth” nanoparticle carriers to be present in the bloodstream long enough to reach or recognize their therapeutic site of action [29].

Examples of “stealth” nanocarriers include PEGylated liposomal doxorubicin (Doxil®) and the PLA-PEG micelle form of paclitaxel (Genexol-PM®, marketed in Korea in 2007). Encapsulating doxorubicin within PEGylated nanoparticles allows for extended circulation half-life in blood and higher tumor concentration of doxorubicin. The homing to the disease site is driven only by the particles’ nano-dimensions and PEGylated surface through the enhanced permeability and retention (EPR) effect [30], which results from enhanced vascular permeability and the absence of a functioning lymphatic system, and is not related to any specific recognition of the target.

In addition to causing quick clearance, nonspecific interactions of nanomaterials with proteins from complex biological samples (e.g., human blood serum, plasma and tissue extracts) hamper the full exploitation of ex vivo nano-based diagnostics and arrays [31]. Novel diagnostic nanomaterials are emerging for the detection and quantification of less abundant biomarkers in biological samples and are envisioned to provide ground-breaking tools for personalized nanomedicine [32]. These nanoparticles and nanostructures possess many unique and advantageous physical properties when applied as ultra-sensitive signal transducers and protein biosensors in the fields of molecular diagnostics and proteomics. Their nanoscale dimensions also result in increases in information quality, quantity and density. Major examples include nanocantilevers, nanowires, nanotube arrays and oligonucleotide-modified gold nanoparticle-based bio-barcode assays that enable multi-biomarker detection [1]. However, the development of these approaches with high sensitivity and selectivity faces several bottlenecks including deconvolution of noise from the signal, especially in regard to biofouling. For the analysis of proteomic signatures, a major challenge will be the identification of signatures from low-concentration molecular species, in the presence of extremely high concentrations of non-specific serum proteins. Nonspecific binding remains a major concern which may lead to false positive signals and low signal-to-noise ratios for a given assay. For various applications such as affinity biosensors or nanoarrays, it is critical to block possible sites for nonspecific binding and/or treat nanomaterials with surface coatings that combine an ultralow fouling background with abundant biorecognition elements. To solve this problem, nonfouling coating materials such as zwitterionic polymers, PEG and its derivates have been developed to prevent nonspecific protein adsorption when exposed to complex media [33, 34]. For example, combined with a surface plasma resonance (SPR) sensor, the protein arrays created using zwitterionic poly(carboxybetaine acrylamide) are able to detect specific cancer biomarkers and monitor the kinetics of antigen-antibody interactions from 100% human blood plasma with high specificity and sensitivity [33]. The background noise was very low due to significantly minimized total nonspecific protein adsorption on the functionalized zwitterionic surface.

Limiting the immunogenicity

Decreasing the immunogenicity of a nanomaterial is also of critical importance since therapeutic nanoconstructs have dimensions very similar to those of pathogens for which recognition signals were positively selected for evolution [35]. The understanding of the immune reactions to therapeutic and diagnostic nanomaterials is still poorly characterized and additional knowledge is required to ensure which characteristics warrant repeated systemic administration without adverse reactions.

For example, in preclinical studies, the phenomenon aptly named accelerated blood clearance (ABC) has been observed in animal models for various types of nanoconstructs [3638]. In this effect, an initial sensitization of the animals to the nanomaterial triggers a transient immune response and induction of Immunoglobulin M (IgM) antibody which prompts rapid clearance of the subsequently administered doses by increased capture in the liver and the spleen [1214]. The factors that impact the appearance of this phenomenon are multifaceted and include the nature of the payload of the nanomaterial [39, 40], the dose administered [3941], and other physicochemical characteristics of each nanoconstruct [41, 42]. The encapsulation of cytotoxic compounds seems to highly diminish the ABC effect, possibly through a deleterious effect on the B cells responsible for the secretion of IgM [39, 40]. In the current context where all nanomedicines on the market contain anticancer drugs, the manifestations of ABC have had limited significance. However, the future development of nanomedicines for all types of diseases and encapsulating a variety of drugs will certainly have to address that problem before nanomaterials can be repeatedly and consistently administered.

Understanding nanomaterial-protein interactions is also important for the development of safer and better tolerated nanomedicine. PEGylated liposomes are known to exhibit prolonged circulation time in blood and have had success in translation to the clinic. However, infusion of therapeutic liposomal drugs such as Doxil® as well as other amphiphilic lipids which have reached the bedside (e.g., Cremophor EL®) could lead to a hypersensitivity syndrome called complement activation-related pseudoallergy (CARPA). The CARPA syndrome differs from anaphylaxis since it does not involve IgE but arises as a consequence of activation of the complement (C) system. Also, CARPA improves upon subsequent exposure and can be mitigated in patients by reducing the infusion rate as opposed to anaphylaxis where re-exposition usually triggers a more serious reaction [43].

Moghimi et al. have demonstrated that liposomes prepared using anionic phospholipid-PEG conjugates caused CARPA, partly because the highly cationic region of the globular C1q protein binds with the anionic charge localized on the phosphate oxygen of the lipid-PEG conjugate through electrostatic interaction. This induces activation of the complement cascade, opsonization of the nanoparticle surface and anaphylatoxin production (reflected in significant rises in SC5b-9, C4d, C3a and C5a levels in human sera) [44]. CARPA is mostly mild and transient, but in some patients, it can be severe or even lethal. In addition, a main manifestation of complement activation is cardiopulmonary distress; therefore, CARPA may be a safety issue primarily in cardiac patients.

Several methods have been explored to circumvent the problem. A previous study revealed that removal of the negative charge by methylation of the phosphate oxygen of lipid-PEG conjugates totally prevented complement activation. Others have recently synthesized a range of neutral lipopolymers and variations thereof for liposome engineering [45]. Remarkably, preliminary investigations have demonstrated that such lipopolymer-incorporated liposomes are poor activators of the human and porcine complement system when compared to vehicles bearing anionic lipid-PEG conjugates [46]. The nanoformulations prepared with neutral lipopolymers may hold great potential to treat patients with severe CARPA response or cardiac disease. More studies have been conducted to test the CARPA concept and the immunological interactions of liposomal and amphiphilic polymeric nanoparticles [47, 48]. In addition to the CARPA reactions observed in the clinics, complement activation also leads to opsonisation of the nanomaterials and enhances their clearance by the MPS. Therefore, any measure to prevent its activation could translate into increased circulation times and efficiency. Figure 1 demonstrates the different pathways that trigger the complement system and how physicochemical properties of nanomaterials can switch the activation process from one pathway to another [4955].

pathways of complement cascade activation nihms-401532-f0001

pathways of complement cascade activation nihms-401532-f0001

The physicochemical properties of the nanomaterial surface can trigger the different pathways of complement cascade activation [4955]. The classical pathway is activated through deposition of specific proteins like antibodies and others. The lectin pathway is triggered by the recognition of the surface by a Mannose-binding Lectin (MBL) through pathogen-associated motifs. The lectin subsequently interacts with a serine protease (MASP) to elicit the formation of a C3-convertase (C4b2a) analogously to the classical pathway. The spontaneous tickover responsible for the alternative pathway activation is constantly present in plasma. When not properly regulated, the preferred deposition of the C3b products on the surface of the nanomaterial amplifies the cascade activation. All 3 pathways lead to C5-convertases that cleave C5 and lead to the deposition of the terminal membrane attack complex which can lyse pathogens and senescent cells, further releasing proinflammatory mediators. The release of proinflammatory chemoattractants is symbolized by the yellow outburst.

Exploiting the beneficial aspects of protein-binding

The nanomaterial-protein interactions should not only be viewed as being disadvantageous, as some preferential interactions can be used to guide the distribution of nanoparticles to specific tissues. For example, decoration of nanomaterial with specific proteins prior to injection has been exploited for particular targeting purposes [5658].

More recently, a possibly higher response rate in a subset of patients observed during the first clinical studies on albumin-coated paclitaxel (nab-PTX, Abraxane®) sparked a flash of enthusiasm in the drug delivery community. In this study, it was found that different response rates between individual patients receivingnab-PTX could be explained by degrees of expression in the extratumoral protein SPARC (secreted protein acidic and rich in cysteine) [59]. SPARC is a secreted matricellular glycoprotein with high binding affinity to albumin which functions to regulate cell-matrix interactions [60]. Its overexpression is associated with increased tumor invasion and metastasis, leading to poor prognosis in multiple tumor types including breast, prostate, and head and neck cancers [61]. In this context, the prospect that SPARC-positive patients would respond better to nab-PTX was particularly appealing.

Desai et al. tested this hypothesis by correlating the clinical response and SPARC tumor expression in a retrospective analysis of 60 patients receiving nab-PTX as monotherapy against head and neck cancer [59]. It was found that response to nab-PTX was higher for SPARC-positive patients (83%) than SPARC-negative patients (25%). As shown in Figure 2, a possible explanation for the positive correlations between SPARC expression and the drug is that the interactions of albumin and SPARC in the tumor interstitium could facilitate the accumulation of nab-PTX in the tumor. Furthermore, the albumin-drug interactions were thought to facilitate the transport of paclitaxel molecules across endothelial barriers via gp60 receptor and caveolin-1 mediated transcytosis [59].

Mechanisms for the transport and accumulation of albumin-bound paclitaxel in tumor nihms-401532-f0002

Mechanisms for the transport and accumulation of albumin-bound paclitaxel in tumor nihms-401532-f0002

Mechanisms for the transport and accumulation of albumin-bound paclitaxel in tumors. Binding of albumin-bound paclitaxel complexes to the gp60 receptor and subsequent caveolin-1 mediated transcytosis results in transport across the endothelial barrier of the tumor vasculature. SPARC, an albumin-binding protein present in the tumor interstitium, enhances accumulation of the complexes in tumor tissue. Figure taken from reference [59].

As further supporting evidence, a study in animals with multiple tumor xenografts also showed correlations between the relative efficacy of nab-PTX and SPARC expression. In this study, the albumin-containing formulation was compared to polysorbate-based docetaxel. In comparison with control groups, the effect ofnab-PTX in HER2-positive breast tumors with increasing SPARC expression seemed superior to that witnessed in MDA-MB-231/HER2-positive tumors with low SPARC expression [62]. It should be noted, however, that differences between the pharmacological agents used (paclitaxel vs. docetaxel) and the large discrepancies between the doses of drug administered in the different groups strongly limit the conclusions that can be drawn from this study.

To complicate matters, a recent study yielded confounding evidence about the implication of SPARC on the efficacy of nab-PTX. In animals bearing patient-derived non-small cell lung cancer (NSCLC) tumor xenografts, the response to nab-PTX could not be correlated to SPARC expression. In this study, the improved antitumor effect of the albumin-based formulation over solvent-solubilized PTX could also be observed in some SPARC-negative tumors and the induction of SPARC expression in low-responsive tumors could not enhance activity [63]. This implies the possibility of other mechanisms being implicated to explain the response to nab-PTX. In this study, the compared doses of drugs (30 mg/kg/day of nab-PTX vs. 13.4 mg/kg/day of solvent-formulated PTX) were reputedly equitoxic. However, these doses were ascertained based on the tolerability of the compound in mice [64]. Hence, it still remains difficult to address if the benefits of nab-PTX over solvent-formulated PTX are uniquely owed to improved tolerability or to real targeting manifestations.

In conclusion, more efforts are needed before we can ascertain the role of SPARC expression as a biomarker for personalized anticancer therapies using albumin-based formulations. For one, there is a current lack of understanding of the stability of the 130-nm albumin-encapsulated PTX nanoparticles once it is introduced in the blood. Some reports mention that, upon dilution, the nanoparticles dissolve into individual albumin-PTX complexes [65], but the nature of these interactions between the drug and proteins remain unclear. Finally, larger prospective clinical validations in multiple tumor types are required to investigate the correlations between SPARC expression and response to treatment. As of now, the only published clinical justification that establishes association between nab-PTX and SPARC expression is a retrospective analysis of a 60-patient clinical phase II study [59].

The impact of nanomaterial-protein interactions on personalized nanomedicine

From the preceding examples, it is clear that further understanding of the interactions between proteins and nanomaterials are required to further establish their potential for personalized medicine. The role of blood proteins on the clearance and immunological mechanisms must be better defined in order to more effectively implement nanoconstructs for therapeutic purposes. Patients display inter-individual variability in the circulating levels of various proteins (e.g., lipoproteins, immunoglobulins, cytokines). These differences can explain the variations in each patient’s response to therapeutics or their higher susceptibility to side effects (i.e., CARPA is observed only in a “reacting” subset of patient population) [43]. Similarly, the homeostasis of blood component can also be intensely affected by health conditions or diseases [66]. For example, physiological stress can trigger overexpression of acute-phase proteins and some of these proteins (e.g., C-reactive protein) can enhance complement activation and macrophage uptake when fixed on the surface of pathogens and senescent cells [67, 68]. The impact of such conditions on the fate of therapeutic nanomaterial must be ascertained before nanomedicine can be used efficiently in a variety of diseases.

In addition, nanomaterial-protein interactions must also be further understood to optimally exploit their beneficial effects on the activity or distribution of nanoconstructs. The example of SPARC is particularly relevant because if the protein is confirmed as a predictive biomarker of response to treatment, the albumin-based formulation would become the first nanomedicine approved for individualized therapy. However, extensive additional preclinical and clinical evidence is required before patients screened based on SPARC expression can receive personalized treatments.

2.2 Ligand-mediated interactions

Nanomaterials can be designed to specifically recognize a target with a surface ligand. These interactions can be utilized to preferentially concentrate a therapeutic nanoconstruct at a diseased tissue in vivo [69] or to bind and detect a biomarker for ex vivo diagnostic purposes [1]. The dimensions of the nanomaterials and the opportunity for polyvalent decoration of their surface with ligands contribute to their potential as effective homing and recognition devices. Throughout evolution, pathogens have exploited the multivalent patterning of a ligand on their surface to considerably enhance their affinity and tropism for their target [35, 70]. Likewise, on artificial constructs, a simple increase in the stoichiometry of a ligand can sometimes drastically enhance the ability to bind a substrate [71].

The decoration of a nanoparticle’s surface with a ligand can also trigger receptor-mediated endocytosis by cells expressing the right target on their membrane, a process that has considerable implications for targeted delivery [72]. Ligand-mediated interactions provide many opportunities for personalized medicine including differential spatial localization, intentional homing of nanoparticles to active diseased sites, and elimination of off-target adverse effects. Figure 3A and B illustrate the active binding of nanoparticles to cell surfaces for vascular targeting and tumor cell targeting. Ligand-functionalized nano-based therapeutic systems or imaging contrast agents therefore represent unrivaled platforms to improve the specificity and sensitivity of treatment and diagnostic tools.

Nanoparticles with ligands specific for endothelial cell surface markers nihms-401532-f0003

(A) Nanoparticles with ligands specific for endothelial cell surface markers allow for binding and accumulation to tumor vasculature. (B) Once in the tumor tissue, nanoparticles with ligands specific for tumor cell markers can actively bind to tumor cells,

The ligands used to decorate nanoparticles can include antibodies, engineered antibody fragments, proteins, peptides, small molecules, and aptamers [73]. For both applications, two types of targets exist: targets that are ubiquitously-expressed in all tissues and targets that are specific to diseased cells. Herein several examples of ligand-receptor interactions exploiting both categories will be presented, and special attention will be given to a few nanoplatforms that are targeted through ligand-receptor interactions and have made their way successfully to clinical trials [74].

2.2.1 Ubiquitous targets

The active targeting of drug delivery systems with transferrin (Tf), a 80-kDa blood-circulating glycoprotein, is a concept which dates back to the late-1980s [75]. Several characteristics make the targeting of transferrin receptors (TfR) attractive and an abundance of systems exploiting this internalization pathway have been designed. First, although the TfR is expressed in all types of tissue to satisfy the ferric (II) iron requirements of dividing cells, the hyper-proliferation of cancer cells makes it an attractive overexpressed target in tumors [76]. Secondly, the endocytosed TfR is very rapidly recycled to the cell surface after internalization [77, 78] which makes it an appealing, almost non-saturable, entryway into the cells. Thirdly, the TfR is believed to facilitate the transport of macromolecules and nanoconstructs across the blood-brain barrier [77], representing a rare opportunity to enable penetration to the central nervous system. For all these reasons, the targeting of therapeutic nanomaterials through Tf has been widely studied.

Recently, Davis et al. reported the first human trial of targeted siRNA delivery using polymeric nanoparticles containing Tf-modified cyclodextrin (CALAA-01) [79, 80]. In this study, human Tf was used as a targeting ligand for binding to TfR, which is typically upregulated on cancer cells and trigger cellular uptake via clathrin-coated pits. These targeted nanoparticles were administered intravenously to patients with melanoma where they circulated and localized in tumors (Figure 4). The Tf on the nanoparticle surface was able to bind to overexpressed TfR on cancer cells, and the nanoparticles were internalized via receptor-mediated endocytosis (Figure 4d). Tumor biopsies from melanoma patients obtained after treatment showed the presence of intracellularly localized nanoparticles in amounts that correlated with dose levels of the nanoparticles administered. Furthermore, a reduction was found in both the specific messenger RNA and the protein levels when compared to tissue obtained before dosing of the targeted nanoconstructs.

Figure 4

Assembly and function of targeted cyclodextrin nanoparticles containing siRNA. (a) Nanoparticles consist of four components: (i) a water-soluble, linear cyclodextrin-containing polymer (CDP), (ii) an adamantane (AD)-PEG conjugate (AD-PEG), (iii) the targeting

The receptor tyrosine kinase EGFR is another potent and well-studied target for anticancer drug delivery systems which is constitutively expressed on the surface of cells throughout the body. In response to the binding of its ligands (i.e., various growth factors), EGFR is significantly involved in cell signaling pathways associated with growth, differentiation and proliferation. EGFR exists on the cell surface and is overexpressed in multi-drug resistant (MDR) cancer cells [81, 82]. Milane et al. utilized this overexpression through the development of EGFR-targeted polymeric nanocarriers for the treatment of MDR cancer using paclitaxel (a common chemotherapeutic agent) and lonidamine (an experimental drug; mitochondrial hexokinase 2 inhibitor) [82]. The safety and efficacy of nanoparticle treatment were tested in a mouse orthotopic model of MDR human breast cancer. It was observed that this nanocarrier system demonstrated superior efficacy and safety relative to free drug combinations (paclitaxel/lonidamine solution) and single agent treatments in nanoparticle and solution forms. The targeted nanoparticles loaded with a combination of paclitaxel and lonidamine were the only treatment group that achieved sustained decrease in tumor volume. In addition, treatment with the EGFR-targeted lonidamine/paclitaxel nanoparticles decreased tumor density and altered the MDR phenotype of the tumor xenografts, decreasing the MDR character of the xenografts as evidenced by a drop in the expression of P-glycoprotein (Pgp) and EGFR. In another study, a versatile nanodiamond (ND) construct that incorporates anti-EGFR monoclonal antibodies (mAb), a fluorescent imaging agent and paclitaxel has been developed for multimodal imaging and the treatment of triple-negative subtype of breast cancer (TNBC) [83]. EGFR is expressed at high levels in at least 20% of breast cancers overall, but in 60-70% of patients with TNBC [84], which makes EGFR a potential treatment target. The enhanced cellular internalization of anti-EGFR mAb conjugated ND was only observed in the EGFR-overexpressing MDA-MB-231 cells but not in the basal EGFR expressing MCF7 cells. The data suggested that targeting through the mAb moiety increased specificity and internalization within EGFR-overexpressing breast cancer cells, which subsequently enhanced therapeutic activity of targeted conjugates. To monitor receptor-mediated endocytosis, Lidke et al. used quantum dots (QDs) conjugated to epidermal growth factor (EGF) to study erbB/HER receptor-mediated cellular response to EGF in living human epidermoid carcinoma A431 cells, assigning the mechanism of EGF-induced signaling to heterodimerization of erbB1 and erbB2 monomers and uncovering retrograde transport of endocytosed QD probes [85].

Finally, other examples of ubiquitously-occurring receptors being exploited for active targeting of ligand-functionalized therapeutics exist. For instance, various macromolecular drug conjugates and nanoparticulate systems were studied to take advantage of the overexpression of the folate receptor in tumor cells for the purpose of enhanced delivery as well as diagnosing and imaging malignant masses with improved specificity and sensitivity [86, 87]. Similarly, the retinol-binding protein, which is constitutively expressed in the brain, the spleen, the eyes, the genital organs and in lower quantities in the heart and lungs, was recently exploited to target stellate cells in the liver to alleviate cirrhotic fibrosis [88, 89]. In this approach, the favored non-specific distribution of the liposomes in the liver might contribute to enhancing the interactions between the nanomaterials and their target on the surface of the cells.

Cell-specific targets

Targeting to molecules that are differentially expressed at high levels by certain tissues offers a way to enhance accumulation at specific sites in the body. The exploitation of targets which are distinctively expressed in certain organs offers the possibility to further enhance the specificity of a treatment. The use of prostate-specific membrane antigen (PSMA) is a good example of a tissue-specific receptor that has been efficiently used to target anticancer drug-loaded nanoparticles. The first generation of prostate-specific nanoparticles incorporated PSMA-binding aptamers on their surface to promote internalization by cancer cells. In a mouse xenograft model, one single intratumoral injection of aptamer-functionalized nanoparticles loaded with docetaxel was able to show a considerably higher proportion of complete tumor regression and significantly prolonged survival rates [90]. Similar aptamer-decorated particles were also shown to be able to incorporate prodrugs of a hydrophilic platinum compound [91]. In order to translate these findings to the clinic, a formulation using a low molecular weight ligand with high affinity for PSMA was developed. These formulations using urea-based ligands provided the advantages of being easier to scale-up, while simultaneously not presenting the potential immunological problems associated with the presence of nucleic acids on the surface of the nanomaterial. A docetaxel-containing formulation functionalized with the PSMA-specific ligand, BIND-014, is currently in phase I clinical trials. Preliminary data showed stable disease in patients at doses below the commonly used regimen for the commercially-available, solvent-based docetaxel formulation [6].

Other specific targets have been investigated to optimize the interactions of therapeutic and diagnostic nanomaterials with diseased cells. For example, anti-CD33 monoclonal antibody has been successfully exploited to target leukemic cells since CD33 is a surface antigen expressed on over 80% of leukemia blast cells from acute myeloid leukemia (AML)-suffering patients but not on healthy cells [92]. Gemtuzumab, a monoclonal antibody to CD33 linked to a cytotoxic drug, was approved by the FDA in 2000 for use in patients over the age of 60 with relapsed AML. Upon the conjugation of anti-CD33 monoclonal antibody, the modified polymer/liposome hybrid nanovectors demonstrated enhanced internalization by CD33+ leukemic cell lines while limited interaction was found for nanovectors decorated with an isotype-matched control antibody [93]. In addition, the drug-loaded anti-CD33 nanoformulation exhibited the highest cytotoxicity against CD33+ leukemic cells, suggesting a promising targeted nanotherapeutics for the treatment of AML. The cancer cell-specific anti-nucleosome monoclonal antibody 2C5 (mAb 2C5), which recognizes the surface of various tumor cells (but not normal cells) via tumor cell surface-bound nucleosomes, was also attached to polymeric micelles, making the resulting micelles capable of specifically targeting a broad range of tumors [94]. Intravenous administration of tumor-specific 2C5 micelles loaded with paclitaxel into experimental mice bearing Lewis lung carcinoma resulted in an increased accumulation of paclitaxel in the tumor compared with free drug or paclitaxel in nontargeted micelles and in enhanced tumor growth inhibition.

The increasing availability of monoclonal antibodies for targeted therapy at large has fostered the interest of antibody-functionalized targeted nanomaterial for many years [9598]. However, the presence of these large biological macromolecules (Ab or Ab fragments) can seriously compromise their circulation times in the bloodstream, and their ability to traffic to their intended destination in vivo [99]. Therefore, large efforts have been put in the development of less immunogenic targeting moieties (e.g., peptides, small molecules) [100,101] which might possibly have brighter futures for in vivo applications.

2.2.3 Ligand-mediated in vitro diagnosis

In comparison, the immunologic properties of antibodies are much less of a hindrance for ex vivo diagnostic applications, and the field has benefited greatly from the specific-binding properties of these molecules to recognize and detect biomarkers of interest [1]. Several nanomaterials can be modified with different combinations of specific markers to rapidly screen molecular profiling of small populations of cancer cells at good signal-to-noise levels [102], which is of clinical importance for early cancer detection. An example of such technique named “bioorthogonal nanoparticle detection” (BOND) was developed by Weissleder and colleagues [102]. In this work, live cells were labeled with trans-cyclooctene-modified antibodies (anti-HER-2, EpCAM and EGFR, respectively) followed by coupling with tetrazine-modified fluorescent-labeled iron oxide nanoparticles (Figure 5A and B). The transverse relaxation rate (R2) was measured for ~ 1000 cells, a sample size in line with clinical specimens, using a miniaturized diagnostic magnetic resonance detector. As shown in Figure 5C, markers signals were nearly at normal levels for benign fibroblasts and leukocytes (except for CD45, naturally expressed in the latter) while tumor cells showed considerable heterogeneity in the expression of the different markers. The nuclear magnetic resonance (NMR) signals correlated well with the actual expression levels that were independently determined by flow cytometry using a larger sample size (Figure 5C). This BOND platform demonstrated its application in clinically-oriented molecular profiling by utilizing the polyvalent interactions between engineered nanomaterials and their targets of interest on cell surfaces.

Figure 5

(A and B) Two-step process for targeting biomarkers on cancer cells. Live cells are labeled with TCO-modified antibodies followed by covalent reaction with Tz-modified fluorescent0labeled iron oxide nanoparticles. (C) Cell profiling using a miniaturized

Similarly, small molecules can also be utilized for specific recognition. For example, the self-assembly properties of mannose-functionalized nanoobjects upon interactions with the lectin-coated E. Coli bacterial wall was utilized to detect the presence of the pathogen at different concentrations [103]. In this work, the material becomes highly fluorescent by spatially-rearranging itself in a polymeric fiber structure upon interaction with bacteria. Similarly, in a two-step approach, Weissleder et al. decorated the surface of gram-positive bacteria by targeting the surface D-Ala-D-Ala functional groups on the pathogen with vancomycin-trans-cyclooctene conjugates [104]. The presence of these conjugates is subsequently detected using tetrazine-functionalized magnetofluorescent nanoparticles which can attach covalently in situ with the cyclooctene moieties [102, 104].

Selection of ligands

Depending on the intended application, the ligands chosen in the nanomaterial design will highly influence the efficacy of the system. For ex vivo diagnosis, the nanoparticles are expected to immobilize on the cell surface via ligand-receptor interactions as a diagnostic tag. The high affinity and specificity of the ligands are of paramount importance for the reduction of false negatives and positives, respectively. In contrast, nanoparticles that serve as delivery vehicles for drugs will have other considerations. For example, considering that intracellular delivery of drug-loaded nanoparticles could provide enhanced therapeutic effects, selection techniques have been developed to distinguish internalizing ligands from non-internalizing ligands [105, 106]. Hild et al. elegantly showed that QDs modified with agonists binding to G protein-coupled receptors could be internalized whereas the same nanoparticles modified with antagonists could not [107]. The functionalization of the nanomaterial with the appropriate ligand dictates the fate of the nanoparticle, allowing for either simple flagging of the cell surface or further uptake to deliver a payload using the same target. Recently, Xiao et al. designed a cell-uptake selection strategy to isolate a group of cancer-cell specific internalizing RNA aptamers (Figure 6A) [108]. In this strategy, selection was carried out against prostate cancer cells using counter selection with non-prostate and normal prostate cells to remove non-specific strands. The internalizing ligands were preferentially collected by deleting non-internalizing, membrane-bound aptamers. The cell uptake properties of nanoparticles functionalized with the identified aptamers were confirmed to be highly specific and efficient (Figure 6B).

selection process for isolating RNA aptamers capable of cell-specific internalization in prostate cancer cells nihms-401532-f0006

selection process for isolating RNA aptamers capable of cell-specific internalization in prostate cancer cells nihms-401532-f0006

(A) Cell-uptake selection process for isolating RNA aptamers capable of cell-specific internalization in prostate cancer cells. (B) Visualization of aptamer-functionalized nanoparticle internalization by PC3 cells using confocal fluorescence microscopy.

Further efforts are now underway to identify ligands with the appropriate affinity and to apply these binding ligands to specifically engineer nanomaterials for diagnosis and targeted therapy [109]. One might note, however, that for a specific ligand, the internalizing properties of the nanomaterial can also depend on multiple physicochemical properties, like size [110] and surface density [111]. The biological processes emerging from successful internalization of the nanomaterials by the cells will be discussed in Section 2.3.

Considerations for personalized medicine

In the near future, the availability of ligand-functionalized therapeutic nanomaterial will have a clear impact on the individualized treatment of diseases. In this context, the detection and monitoring of the target expression before initiating therapy and during the whole treatment will clearly be of utmost importance. Similarly, multivalent nanoparticles are complex objects in which behavior depends on a variety of physicochemical properties [6, 112]. Presently, efforts should be made to better understand how ligand-functionalized nanomaterials interact with their targets. In parallel, a better comprehension of the correlations between target expression patterns and cancer prognosis is also required. When both of these aspects are addressed, the therapeutic targets to select for the rational design of nanomedicine will become clearer.

Interactions during intracellular processing

Once endocytosed, nanomaterials are internalized and remain entrapped in transport vesicles which traffic along the endolysosomal scaffold, thereby exerting key effects on subcellular organelles. Intracellular trafficking and the fate of nanomaterials are linked to their physicochemical properties and endocytic pathways [113116]. For example, nanoparticles taken up by clathrin-dependent receptor-mediated endocytosis (RME) are typically destined for lysosomal degradation; whereas, clathrin-independent RME internalization leads to endosomal accumulation and sorting to a nondegradative path [116]. While some drug delivery systems aim to avoid lysosomal degradation [117], recent studies have utilized directed delivery to this environment for the enzymatic release of therapeutics [116, 118]. Understanding the key intracellular interactions of nanoparticles has allowed researchers to engineer nanoparticles for highly specialized delivery. Appropriate design and engineering of nanocarriers could therefore allow for controlled intracellular delivery of therapeutics to individual intracellular compartments, which provides benefits to therapies associated with these unique organelles, including cancer therapy, gene therapy, and lysosomal storage disease (LSD) treatments. Furthermore, by offering an alternative to passive diffusion as an entryway into the cells, the design of nanomaterials that can be internalized by receptor-mediated endocytosis and thus release their active drugs inside subcellular organelles might provide a useful means to circumvent efflux pump-mediated drug resistance [119]. Here we briefly discuss several examples where the physiological endosomal and lysosomal environment can be exploited to develop responsive drug delivery systems.

Intracellular drug release

Polymer-drug conjugates were among the earliest formulations designed to preferentially release their payload inside the cell. Poly[N-(2-hydroxypropyl)methacrylamide] (HPMA) was the first synthetic polymer-drug conjugate to enter clinical trials in 1994. Others, like degradable polyglutamate (PGA), have also been widely clinically investigated as anticancer nanomedicines [118]. These nanosized drug delivery systems are based on the covalent conjugation of chemotherapeutics to hydrophilic polymers, which markedly improves solubility as well as alters drug biodistribution and pharmacokinetics. Conjugates have longer half-life (typically > 1 h) than free drug (< 5 min) when circulating in the blood, leading to significantly increased drug concentrations in tumors [120122]. Since most drugs need to be released from the macromolecule to exert their pharmacological effect, the nature of the linker between the drug and the polymer is therefore of crucial importance (Figure 7). Although the chemical reacting groups on both the macromolecule and the drug dictate the character of the linker available, various classes of bonds with passive or physiologically-triggered cleavage have been studied [123]. Clinical experience has shown that rapid degradation of ester bonds in the bloodstream could lead to suboptimal distribution of the drug in the tumor [124127]. Therefore, if the drug exerts its effects through an intracellular pharmacological receptor, it can be beneficial to design the conjugate with a lysosomally-degradable peptidyl linker (e.g., Gly-Phe-Leu-Gly). This type of linker is stable in the bloodstream but can be cleaved by the lysosomal protease cathepsin B once internalized over 24-48 h [114, 118, 128]. Lysosomes and lysosomal hydrolase malfunctions have been associated with several aspects of malignant transformation, including the loss of cell growth control, altered regulation of cell death, and acquisition of chemo-resistance and of metastatic potential [129]. Lysosomal protease-mediated drug release is thus a key conceptual design principle for the chemotherapy of cancer with nanomedicine [118]. An exciting clinical program is assessing a PGA-paclitaxel conjugate (CT-2103; Opaxio) using the Gly-Phe-Leu-Gly linker [120, 130]. In this system, paclitaxel is released to a small extent by slow hydrolytic release, but is released mainly through lysosomal cathepsin B degradation of the polymer backbone [131]. Experiments in cathepsin-B-homozygous knockout mice confirmed the importance of enzyme degradation and intracellular delivery. Clinical studies showed that a significant number of patients responded to stable disease profiles, particularly in patients with mesothelioma, renal cell carcinoma, NSCLC and in paclitaxel-resistant ovarian cancer [120]. In a recent randomized phase III clinical trial, PGA-paclitaxel demonstrated reduced severe side effects and superior therapeutic profiles compared with gemcitabine or vinorelbine as a first-line treatment for poor performance status NSCLC patients [132, 133]. Additionally, in comparison with men this trial showed increased survival in women treated with PGA-paclitaxel, specially marked in pre-menopausal women [134]. It should also be noted that activity might correlate with estrogen levels which increase expression of cathepsin B [135]. If these findings are confirmed in larger studies, PGA-paclitaxel could be used as a potential gender-specific first-line therapy to treat women with NSCLC.

Tumor cell internalization of polymer-drug conjugates nihms-401532-f0007

Tumor cell internalization of polymer-drug conjugates nihms-401532-f0007

Tumor cell internalization of polymer-drug conjugates occurs through several possible mechanisms, including fluid-phase pinocytosis (in solution), non-specific membrane binding (due to hydrophobic or charge interactions) resulting in receptor-mediated

In addition to lysosomally-cleavable peptide linkers, pH-sensitive cis-aconityl, hydrazone and acetal linkages that respond to changes in intracellular pH have also been used [115]. They can be hydrolyzed under the local acidic pH (6.5-4) within endosomal and lysosomal vesicles [136]. As such, pH-sensitive [137140] or reduction-specific [141, 142] nanoparticle formulations have been designed to facilitate the intracellular delivery of active components. Once low molecular weight drugs are released in the endosome, they are free to escape the intracellular vesicles by diffusion. However, for high molecular weight or charged compounds (e.g., proteins or nucleic acids), passive diffusion through the membrane is difficult and the formulation needs to further provide endosome-disruptive properties to allow for intracytosolic delivery.

Considerable effort has been made to design various types of endosomolytic formulations, especially for the delivery of siRNA and other therapeutic nucleic acids. siRNA must escape from endosome compartments before endosomal/lysosomal degradation occurs in order to exert their gene silencing activity. A wide range of delivery systems have been developed, including dendrimers, liposomes, cationic lipid-like compounds (lipidoids), cyclodextrin, polyethyleneimine (PEI) and others, to facilitate endosomal escape and ensure cytosolic delivery of the therapeutics. In these systems, membrane-disruptive properties can be obtained by using proteins and peptides [143, 144], polymers [145, 146] or simply by incorporating a high number of ionisable amine groups to exploit the proton sponge effect [117]. Figure 8 illustrates the mechanisms of the proton sponge effect, in which nucleic acids are released from polyamine-containing nanoparticles in acidic endosomes. The key to understanding the proton pump hypothesis is the lysosomal proton pump (v-ATPase), which is responsible for acidification of the lysosomal compartment. Within acidifying lysosomal compartments, unsaturated amines on the nanoparticle surface are capable of sequestering protons that are supplied by the proton pump, continuing pump activity and leading to the retention of one Cl- anion and one water molecule for each proton that enters the lysosome. Ultimately, this process causes lysosomal swelling and rupture, leading to siRNA-loaded particle deposition in the cytoplasm [20].

The proton sponge effect nihms-401532-f0008

The proton sponge effect nihms-401532-f0008

The proton sponge effect allows for cationic nanoparticles to escape endosomal and lysosomal vesicles and enter the cytoplasm. When cationic nanoparticles enter acidic vesicles, unsaturated amino groups sequester protons supplied by v-ATPase (proton pump).

Finally, increasing attention has been focused on the targeting of therapeutic agents to specific organelles. This can be achieved by attaching subcellular targeting ligands on the surface of nanomaterials to redirect their accumulation to desired compartments. For instance, Niemann-Pick type A and B are rare genetic LSDs associated with a deficiency of acid sphingomyelinase (ASM), a single enzyme required for the metabolism of lipids, glycoproteins or mucopolysaccharides [147]. A recent study demonstrated that the specific delivery of recombinant ASM to lysosomes by nanocarriers coated with antibody against intercellular adhesion molecule-1 (ICAM-1) could alleviate lysosomal lipid accumulation and improve the efficacy of enzyme replacement therapy [147].

Considerations for personalized medicine

The utilization of intracellular enzymes to trigger the therapeutic activity of nanoconstructs has considerable implications for personalized medicine. As differences in enzyme expression between individuals and pathologies are expected, the sophisticated systems described above might prove more beneficial in a certain subset of patient populations. For example, if the effect of gender-specific cathepsin B expression on the efficacy of PGA-paclitaxel is further confirmed in clinical trials, the appeal of the drug conjugate to treat women-specific cancer types (e.g., ovarian, breast) will certainly be strengthened. More generally, the linkers that can be cleaved by an intracellular protease of interest (e.g., Gly-Phe-Leu-Gly linker) might turn out to be very useful for the design of future drug delivery systems to treat patients overexpressing the target proteases.

The development of drug delivery systems which can effectively deliver their payload inside the cells is also crucial for the future of nucleic acid-based therapies. These therapies hold great promises as treatment and prevention methods for various diseases. For example, successful delivery of siRNA could inhibit the expression of MDR transporters and may restore tumors’ chemosensitivity to treatment [148, 149]. In this context, the combination of conventional chemotherapeutics with siRNA-based therapeutics represents a promising therapy for patients with chemoresistance malignancies.

Engineered nanomaterials for personalized medicine applications

Nanomaterials have evolved significantly over the last few years and nanomedicine has brought unprecedented advances in the diagnosis, imaging and treatment of a variety of diseases. Presently, nearly 250 nano-sized products exist in various stages of development, including nanomaterials with different compositions, physicochemical characteristics, surface functionality and geometry [150]. The following section will explore some examples of the applications of nanomaterials relevant to personalized medicine and the associated design features based on an understanding of nano-bio interactions.

Ex vivo diagnostics

The identification of biomarkers represents the first step in attaining an individually tailored medicine. Biomarkers could be mutant genes, RNAs, proteins, lipids or metabolites that are associated with a specific pathological stage or clinical outcome. Molecular profiling studies on biomarker discoveries have shown that gene expression patterns can be used to identify cancer classification, yielding new insights into tumor pathology such as stage, grade, clinical course and response to treatment [151]. Alizadeh et al. were the first to report the correlation between gene expression patterns and clinically distinct subtypes of cancer based on their study of diffuse large B-cell lymphoma [152]. The concept of a specific molecular profile for each patient’s tumor was later validated [153, 154]. By linking biomarkers with cancer behavior, it is possible to improve diagnosis, assess response to treatment and evaluate progression of cancer based on each patient’s molecular profile [155].

The enhanced interactions that occur between nanomaterials and biomacromolecules (e.g., proteins and nucleic acids) markedly improve the sensitivities of current detection methods. Nanomaterial surfaces can be tailored to selectively bind biomarkers and sequester them for subsequent high-sensitivity proteomic tests [156]. For example, nanoparticles containing DNA sequences complementary to messenger RNAs of biomarker genes can be used as simple and semi-quantitative beacons for the detection of the expression patterns of biomarkers in a single cell [157]. A bio-barcode assay has been recently developed based on oligonucleotide modified gold nanoparticles for high-throughput detection of nucleic acid and protein targets [15]. This approach utilizes gold nanoparticles functionalized with oligonucleotides and antibodies to target either a patient’s DNA or a protein sample and can detect multiple markers with high accuracy (95%). This nanoparticle-based bio-barcode assay has extraordinarily high sensitivity (10−18 M) similar to that of PCR-based assays but without the need for lengthy amplification procedures [14, 15]. Furthermore, this approach does not suffer from the problems often associated with conventional fluorescent probes for microarray labeling, such as photobleaching (loss of signal after exposure to light), which opens a new avenue for developing highly selective panel assays for early detection of a wide range of diseases. This technology has been approved by the FDA for genetic screening to determine drug sensitivity and to detect genetic mutations. It is currently being validated for the detection of proteins found in prostate cancer, ovarian cancer, and Alzheimer’s disease [16].

Likewise, the simultaneous use of nanomaterials with different ligands can allow concurrent detection and precise profiling of the epitopes present in cell specimens. Yezhelyev et al. demonstrated the detection and quantification of multiple biomarkers in human breast cancer cells and biopsies using QDs conjugated with primary antibodies against HER2, ER, PR, EGFR and mTOR [158]. The parallel evaluations of three specimens revealed distinct molecular profiles: one tumor biopsy over-expressed EGFR, another ER and PR, and the third one ER and HER2. This high throughput ex vivo screening analysis could be used to identify the molecular signatures of an individual patient’s tumor, and to correlate a panel of cancer biomarkers with the clinically distinct subset of biomarkers present in the patient’s tumor.

Nanomaterials can also be used to harvest disease-relevant biomarkers in the sample for early detection. Luchini et al. used Poly(N-isopropylacrylamide) hydrogel nanoparticles to harvest and concentrate low molecular weight (LMW) biomarkers (e.g., proteins and metabolites) from biological fluids via electrostatic interactions [159]. The hydrogel nanoparticles possessed defined porosity and negatively- and positively-charged groups for a rapid one-step sequestration and concentration of the ionized LMW fractions from complex serum molecules. The captured peptides or proteins were protected from further enzymatic degradation and were readily extracted from the particles by electrophoresis. When using the nanoporous sieves presented in this study, the proteins are denatured when eluted out of particles and then analyzed by MS for biomarker discovery. The denaturation step may hinder subsequent applications that require the analytes to be in their native state (e.g., immunoassays, enzymatic assays). Therefore, it is necessary to develop novel nanoparticles which preserve the conformational integrity of the isolated proteins. Combined with current proteomic technologies, these nanoparticles provide enormous enhancement of rare biomarkers associated with disease.

In vivo imaging

In recent years, several medical diagnostic technologies have been developed for clinical imaging and detection, including fluorescence imaging, positron emission tomography (PET), single-photon-emission computer tomography (SPET), and magnetic resonance imaging (MRI). These methods require injection of fluorescent trackers, radionuclides or contrast agents. The development of contrast agents able to target specific molecules could advance the molecular characterization of disease, from the identification of disease-associated molecular pathways to the clinical monitoring of relevant biomarkers before and after treatment [5]. Nanomaterials have been explored as platforms for the development of novel contrast agents because they are easily functionalized, possess high contrast, and have tunable physicochemical properties [5].

Various formulations of superparamagnetic iron oxide nanoparticles (SPIONs) are approved or are under clinical investigation for imaging. A key advantage of SPIONs in comparison to other inorganic or heavy metal-based MRI contrast agents is their innocuity. Particles can be degraded to iron and iron oxides molecules that are metabolized, stored in intracellular pools as ferritin, and incorporated into hemoglobin [160]. Administration of 100-200 mg iron/kg in rodent models elicited no detectable side effects [160, 161], a dose well above that used for MRI procedures (< 5 mg/kg). Ferumoxides (Feridex I.V.®) and ferucarbotan (Resovist®) are clinically approved as the first generation SPIONs and are suitable for T2- and T2*-weighted imaging. These contrast agents rely on passive targeting strategies to detect and evaluate lesions of the liver associated with an alteration in the MPS [162]. Their distinctive in vivo behavior dictates their utility in the clinic: ferumoxides, administered via slow infusion, for the detection of small focal lesions with high accuracy during delayed phase imaging [163] and ferocarbotan, which can be administered as a rapid bolus, to produce higher liver-to-tumor contrast during dynamic imaging [164]. Two other SPIONs formulations are currently in clinical trials as contrast agents for MR angiography (MRA). Supravist (Ferucarbotran, a T1-weighted reformulation of Resovist) and VSOP-C184 (7-nm, citrate-coated SPION formulation) have generated first-class images comparable to those using gadolinium (Gd) based agents but with favorable safety, tolerability, and efficacy data [165167]. These nanoparticle-based MRA agents will likely play an important role in advancing angiography as imaging modality for personalized medicine due to their advantages of long plasma half-life and ultra-small sizes that facilitate the detection of small vessels with slow and/or complex flow [165, 168]. SPIONs are now being developed to track cell movement in vivo following transplantation with the long-term goal of developing and monitoring personalized cell-based therapies [169].

For similar applications and as an alternative approach to the use of MRI, others have utilized QDs as probes for high resolution molecular imaging of cellular components and for tracking a cell’s activities and movements inside the body [170, 171]. With the capability of single-cell detection, these nanomaterials enable the real-time characterization of properties of certain cancer cells that distinguish them from closely related non-pathogenic cells.

Since targeted cancer treatments are selected on the basis of the expression patterns of specific biomarkers, there is an urgent need for detecting and monitoring the changes in biomarker expression in situ in a non-invasive manner. Nanoparticles are in development to maximize the specificity of contrast agents by exploiting receptor-ligand interactions. Targeted nanoparticles are able to accumulate at sites where the molecular target is expressed, increasing the local concentration of contrast agents.

One example is the 18F-labeled ABY-025 affibody, a compact three-helix bundle that binds HER-2 [5, 172]. When tested in animals, the 18F-labeled ABY-025 was able to directly assess HER-2 expression in vivousing PET and monitor changes in receptor expression in response to therapeutic interventions [172]. Lee and colleagues also reported that herceptin-conjugated magnetic nanoparticles that target HER-2 could significantly enhance MR sensitivity compared with currently available probes, enabling the detection of a tumor mass as small as 50 mg [173]. The correlation of the signal observed by non-invasive imaging modalities with receptor expression could be utilized to perform follow-up studies without the need for biopsies to evaluate treatment efficacy and direct therapy tailoring.

In the near future, in vivo imaging techniques using nanomaterials will go beyond the field of oncology. Monocrystalline iron oxide particles functionalized with anti-myosin Fab fragments are in preclinical development to detect myocardial infarcts [174]. Similarly, combination approaches using two or more imaging modalities are particularly appealing. Cross-linked iron oxide nanoparticles (CLION) activated by proteases were prepared by encapsulating iron oxide nanoparticles within polymer-Cy5.5 conjugates, combining fluorescence and MRI imaging to assess the enzymatic activity in plaques [175178]. In this system, the fluorescence of the multiple Cy5.5 molecules was quenched until the lysine-lysine bonds were cleaved by cathepsin B, which is upregulated in atherosclerotic lesions. The CLION developed initially for tomography was also able to image vulnerable plaques and infarcted lesions. Other multi-modal nanoparticle-based contrast agents include fluorescently labeled gadolinium-conjugated gold nanoparticles [179] and paramagnetic lipid-coated QDs [180].

Theranostic nanoparticles

Theranostic nanoparticles integrate molecular imaging and drug delivery, allowing the imaging of therapeutic delivery as well as follow-up studies to assess treatment efficacy [181183]. Theranostic nanoparticles can serve as useful tools to explore the fundamental process of drug release after cellular internalization of nanoparticles, which could provide key insights into the rational design of targeted nanocarriers for personalized treatment.

For example, a smart core-shell QD platform, namely QD-aptamer (doxorubicin), was engineered to sense drug release (Figure 9) [183]. A10 RNA aptamer was used to recognize the extracellular domain of PSMA. The intercalation of doxorubicin within the double-stranded “GC” dinucleotide segment of the A10 aptamer on the surface of QDs resulted in quenching of both QD and doxorubicin fluorescence (“OFF” state). Upon receptor-mediated endocytosis of targeted QD conjugates into PSMA-expressing prostate cancer cells, the released doxorubicin induced the recovery of fluorescence from both the QDs and doxorubicin (“ON” state). This system allowed sensing of the intracellular release of doxorubicin and enabled the synchronous fluorescent localization and killing of cancer cells.

QD-aptamer (doxorubicin) system

QD-aptamer (doxorubicin) system

(a) Schematic of a QD-aptamer (doxorubicin) system capable of fluorescence resonance energy transfer (FRET). Doxorubicin is able to intercalate with the A10 PSMA aptamer bound to the QD surface, quenching both QD and doxorubicin fluorescence through a

Another elegant design is the drug-containing paramagnetic nanoparticles targeted to various atherosclerotic plaque lesions components including the αvβ3 integrin [184], fibrin [185], and collagen type III [186], allowing both targeted MR imaging and drug delivery. Animal studies were performed using αvβ3-targeted nanoparticles containing the anti-angiogenesis drug fumagillin repeatedly administered to atherosclerotic rabbits [184]. The results demonstrated that nanoparticle accumulation enabled imaging of the atherosclerotic lesion and generated an anti-angiogenic effect. Advances in this field will pave the way for detecting disease, targeting therapies, and assessing response with one single nanoparticle agent.

Targeted therapies

One of the major avenues of personalized nanomedicine is the development of delivery platforms that can specifically target diseased tissues (i.e., tumor) [187]. In theory, drug targeting would not only ensure a more effective treatment of the target tissue, but also permit a much lower overall dose to be administered than conventional drug delivery, reducing adverse side effects and increasing patient compliance. Two approaches, both passive and active targeting, have been utilized to home nanoparticles to active sites in disease conditions.

Passive targeting takes advantage of the inherent biophysicochemical properties of the nanoparticles (size, shape, charge and flexibility etc.). This phenomenon is most often associated with EPR effects in tumors. A recent in vivo breast cancer study in rodents showed that the passive targeting approach can be used to personalize treatment [188]. Individualized therapy in its simplest form could be achieved by studying the intratumoral accumulation of iodine-containing liposomes by X-ray tomography to predict the deposition of therapeutic doxorubicin-loaded liposomes in the diseased tissue [188]. If tumor accumulation is found to correlate with the patient’s susceptibility to treatment, this approach could be used to identify individuals with lesions possessing leaky vasculature and who would benefit the most from nanosized formulation.

Actively targeted personalized therapies involve surface modification of drug carriers with ligands such as antibodies, peptides, aptamers, and small molecules that specifically bind to tissues of interest. The drug can then be delivered to the target cells through receptor-mediated internalizing interactions as presented in section 2.2 and 2.3. The binding targets of the modified nanocarriers include differentially overexpressed receptors/antigens on the plasma membrane of disease cells and the differentially overexpressed extra-cellular matrix proteins in diseased tissues. For instance, a peptide-conjugated nanoparticle was shown to target the vascular basement membrane exposed on injured vasculature [189]. The C-11 peptide decorating the nanoparticles showed high affinity for collagen IV, which represents 50% of the vascular basement membrane. This targeted nanoparticle platform holds particular promise for treatments of targeted blood vessel walls such as catheter or stent-induced cardiovascular injuries.

Intracellular organelles can also be targeted. Direct DNA delivery to the mitochondrial matrix has been suggested for the treatment of genetic diseases associated with mitochondrial genome defects [190]. Lee et al. conjugated the mitochondrial leader peptide, a peptide derived from the nucleocytosol-expressed but mitochondria-localized ornithine transcarbamylase, to polyethylenimine using a disulfide bond to render the resultant PEI-MLP conjugates mitochondriotropic [190]. In vitro delivery tests of rhodamine-labeled DNA into living cells demonstrated that PEI-MLP/DNA complexes were localized at mitochondrial sites. The data suggested that PEI-MLP can deliver DNA to the mitochondrial sites and may be useful for the development of direct mitochondrial gene therapy.

Combination therapies

The combination of multiple therapeutic agents in a single nanocarrier has been proposed as an alternative approach to increase the efficacy of anticancer treatments through synergistic interactions while mitigating drug resistance [191]. As a proof of concept, Kolishetti et al. developed a targeted therapeutic nanoparticle system for co-delivery of cisplatin and docetaxel, two drugs with different metabolic targets, to prostate cancer cells [192]. In this approach, a Pt(IV) cisplatin prodrug-polymer conjugate was blended with PLGA-PEG and docetaxel to form nanoparticles (Figure 10) [192]. The dual-drug encapsulated nanoparticles were then conjugated with the A10 aptamer to target PSMA overexpressing cancer cells. In vitro studies demonstrated that the aptamer targeted, dual-drug loaded nanoparticles were 5 to 10 times more cytotoxic than respective single drug encapsulating nanoparticles.

Pt(IV)-PLA drug conjugates were blended with PLGA-PEG and docetaxel to form nanoparticles  nihms-401532-f0010

Pt(IV)-PLA drug conjugates were blended with PLGA-PEG and docetaxel to form nanoparticles nihms-401532-f0010

Pt(IV)-PLA drug conjugates were blended with PLGA-PEG and docetaxel to form nanoparticles capable of delivering chemotherapy drug combinations. The nanoparticle surface was then functionalized with the A10 aptamer to target the nanoparticles to PSMA receptors.

The release of multiple payloads can also be tailored to enhance efficacy. Sengupta et al. synthesized a biphasic “nanocell” with a lipid layer containing combretastatin and a hydrophobic core containing PLGA-doxorubicin conjugates [193]. This construct enabled temporal release of the two drugs: combrestatin was released first to collapse the blood vessels and trap the particles inside the tumor, followed by the release of doxorubicin to kill the tumor cells focally without being diluted by the blood circulation. The polymeric nanocell was compared with liposomes co-encapsulating combretastatin and doxorubicin, which lack the differential drug release kinetics. In murine models bearing Lewis lung carcinoma and B16/F10 melanoma, the nanocell platform resulted in better tumor reduction, longer median survival time, and lower systemic toxicity. This study demonstrated that sequential delivery and scheduling of combinatorial drugs are important parameters that influence drug synergism and side effects.

Finally, combination strategies are particularly appealing in the case of siRNA delivery where the knockdown of specific genes can lead to tremendous improvement in the efficiency of drugs. For instance, MDR-1 gene silencing and paclitaxel co-therapy in PLGA nanoparticles was shown to significantly contribute in overcoming tumor multidrug resistance in vivo [194]. Taken together, the development of combination nanotherapeutic strategies that combine gene silencing and drug delivery could provide a more potent therapeutic effect, especially in refractory tumors.

Research on the development of combinational therapies is on the rise. However, this area will benefit from further investigations involving: (1) the discovery of efficacious molecular targets in cancer cells and better understanding of drug activity in these cells; (2) understanding the pharmacokinetics of different drugs by simultaneously delivering multiple therapeutic agents to the target site; (3) the demonstration of the contribution of each component of the combination to the treatment effect; (4) the development of nanocarriers that allow for precisely-controlled loading and release of two or more drugs with variable properties; and (5) the evaluation of responses to treatment among patients following the use of combination therapies.

Challenges with nanomaterials for personalized nanomedicine
Toxicity of nanomaterials

The uncertain health hazard potential of nanomaterials is probably the most significant hurdle for regulatory approval and commercialization of nanomedical products [195]. The unique physical and chemical properties of nanomaterials (i.e. small size, increased reactivity, high surface-to-volume ratio, etc.) while are likely to provide health benefits, may also be associated with deleterious effects on cells and tissues [187, 196]. Nanomaterials have dimensions similar to organelles found in the cell and have the potential to interfere with vital cellular functions, resulting in potential toxicity [197]. While engineered nanomaterials offer improved half-life circulation, this implies that the time required for clearance of loaded drug will also be prolonged. Accordingly, some nanoparticles may be retained in the body not only for days, but potentially for years. Some nanomaterials such as metal nanoparticles, metal oxide nanoparticles, QDs, fullerenes and fibrous nanomaterials were found to induce chromosomal fragmentation, DNA strand breakages, point mutations, oxidative DNA adducts and alterations in gene expression [198], sometimes even through cellular barriers [199]. In these cases, the safety profile becomes a major concern. Although there have been no reported examples of clinical toxicity due to nanomaterials thus far, early studies indicate that nanomaterials could initiate adverse biological interactions that can lead to toxicological outcomes [200]. Since the mechanisms and severity of nanotoxicity are not fully predictable or testable with current toxicological methods, the toxicity of nanomaterials is rapidly emerging as an important area of tangential study in the nanomedicine research field.

There are many different factors to consider when designing nanomaterials and an understanding of how different parameters affect toxicity can aid in designing safer nanomaterials for medical applications. Some important parameters to consider include size, shape, surface area, charge, state of aggregation, crystallinity, and the potential to generate reactive oxygen species (ROS) [200]. Size is a significant factor and can influence the distribution and toxicity of a material. Studies with gold nanoparticles (AuNPs) in four different cell lines demonstrated that both toxicity and the mechanism of cell death were size-dependent [201]. 1.4 nm AuNPs were 60-fold more toxic than 15 nm AuNPs and cell death from 1.4 nm AuNPs was due to necrosis while 1.2 nm AuNPs caused apoptosis of the cells [201]. The toxicity of the 1.4 nm AuNPs was due to the ability to intercalate with DNA while AuNPs of larger sizes were unable to intercalate with the DNA [202]. Size can affect both the distribution within the body as well as the distribution within a cell [203, 204]. Studies of QDs in macrophages have shown that QD size influences subcellular trafficking, with the smallest QDs able to target histones in the cell nucleus [204]. Composition is another factor that influences the toxicity of nanomaterials. QDs may create a health hazard due to toxic heavy metal elements such as cadmium that are incorporated into the QDs [205]. It may, however, be possible to reduce the potential toxicity of nanomaterials such as QDs by adding a coating or nanoshell [206].

Carbon nanotubes (CNTs) are a nanomaterial that has great potential in various medical applications. However, concerns have emerged over its toxicity due to its shape, which resembles asbestos fibers [207]. Longer CNTs have been shown to act like indigestible fibers that lead to frustrated phagocytosis and granuloma formation [208]. Studies in mice have shown that frustrated phagocytosis can lead to massive release of oxygen radicals by immune cells, which can result in chronic granulomatous inflammation and potentially mesothelioma if the CNTs are in the pleural cavity or peritoneum [209]. CNTs can cause mutagenic effects through the generation of inflammation and direct interaction with components of the cell. Exposure of mice to CNTs by inhalation increased the rate of mutation of the K-ras gene locus in the lung, with the mutations occurring during times of maximum inflammation in the tissue [210]. CNTs can also interact directly with the cellular cytoskeleton, including the microtubule system during the formation of the mitotic spindle apparatus, leading to aberrant cell division [211].

Nanomaterials such as titanium dioxide can cause toxicity based on crystalline structure. Cytotoxic studies showed that the anatase form of titanium dioxide was 100 times more toxic than the rutile form, and that the toxicity correlated with the generation of ROS under UV light [212]. Oxidative stress and the generation of ROS is a key injury mechanism that promotes inflammation and atherogenesis, resulting in adverse health events [213, 214]. The surface composition also plays a role in nanomaterial toxicity. Discontinuous crystal planes and material defects can act as sites for ROS generation [200]. The presence of transition metals or organic chemicals on the surface of nanomaterials can also result in oxygen radical formation and oxidative stress [215].

The degradability of a nanomaterial is another important parameter to consider for toxicity. If nondegradable nanomaterials have no mechanism of clearance from the body, they can accumulate in organs and cells and exert toxic effects. Injectable gold compounds have been used for the treatment of rheumatoid arthritis and the accumulation of gold compounds in the body over time may cause toxic effects in patients [216]. However, biodegradable materials may also cause toxic effects if the degraded components of the material are toxic [217].

In addition, the nanomaterial charge is a significant contributor to the toxicity of the material. Increased in vitro cytotoxicity and in vivo pulmonary toxicity has been observed for cationic polystyrene nanospheres when compared with anionic or neutral polystyrene [218, 219]. Interestingly, the mechanism of toxicity for cationic nanospheres was dependent on the cell type and uptake mechanism [219]. In macrophages, particles entered the cell through phagosomes and caused lysosomal rupture due to the proton sponge effect. Upon entry into the cytosol, the particles caused an increase in Ca2+ uptake by mitochondria and oxidative stress, leading to apoptosis. In epithelial cells, cationic particles entered through caveolae. The particles also induced an increase in mitochondrial Ca2+ uptake and oxidative stress, but cell death was by necrosis.

As new nanomaterials are developed, it is important to consider potential mechanisms of toxicity. Nanomaterials have the increased potential to cross biological barriers and obtain access to tissues and cells as a result of their physicochemical properties. As novel properties are introduced into nanomaterials resulting in new interactions with biological systems, it is possible that new mechanisms of injury and toxicological paradigms might emerge [200]. A further understanding of how nanomaterials interact with biological systems may provide better methods to engineer nanomaterials to minimize toxicity [20].

Mass transport

Efficient delivery of nanotherapeutics is another challenge encountered in regards to nanomaterials. The small size of nanoparticles may result in acceleration or delay in their intended action. They may also accumulate non-specifically in certain tissues after administration. Enormous efforts have been expended towards achieving targeted delivery through modification of nanoparticles with antibodies, small molecules, aptamers and/or peptides. However, the biodistribution of nanotherapeutical agents is primarily governed by their ability to negotiate through biological barriers including the mononuclear phagocyte system (MPS), endothelial/epithelial membranes, complex networks of blood vessels, and abnormal blood flow. In addition, drug delivery is further inhibited by barriers such as enzymatic degradation and molecular/ionic efflux pumps that expel drugs from target cells. A full understanding of the interactions between nanomaterials and biological systems will open the door to rational design of nanomedicines and hence improve their biodistribution.

Complexity of nanopharmaceuticals, characterization, stability and storage

To design therapeutics and diagnostics that are functional for personalized use, multiple components will be integrated into a single nanomaterial, requiring multiple steps such as chemical synthesis, formulation and purification. Those procedures will inevitably lower the yield and increase the production cost. In addition, scale-up and manufacturing under current good manufacturing practice (cGMP) will be challenging. In general, multifunctional nanotherapeutics have more variables within their physicochemical properties, which make it more difficult to predict the fate and action after administration. The characterization of nanotherapeutic agents also poses a challenge to manufacturers as well as regulators in terms of chemical, physical, magnetic, optical and biological properties. It would be difficult to monitor a wide range of physicochemical parameters including composition, structure, shape, size, size distribution, concentration, agglomeration, surface functionality, porosity, surface area, surface charge, and surface specification after nanotherapeutic agents are administered.

Stability and storage are also hurdles that must be addressed for clinical practice. For example, biodegradable polymers have been widely used as nanotherapeutic carriers. Depending on their chemical and morphological properties, a polymer will start degrading after nanoparticle formulation in aqueous/organic solvents, which usually results in a change in physicochemical properties (such as agglomeration, particle size, surface charge, drug loading, drug release profile), and can in turn affect the performance in vivo. As such, storage conditions may be critical to the shelf life of nanotherapeutics. For example, the measurement result of nanoparticle size, surface charge, polymer degradation rate and drug release profile may be quite different when nanotherapeutics are stored in deionized water, as opposed to phosphate buffered saline (PBS) or human blood serum.

Limitations and obstacles of personalized nanomedicine

While personalized nanomedicine holds much promise, there are also many challenges associated with it that need to be overcome in order for it to reach its full potential. Manipulating materials at the nanoscale level is difficult and complex due to novel nanoscale interactions, forces and effects that can complicate the reliability, predictability and utility of nanomedical products. Moreover, the potential risks of nanomedicine products and the uncertainties associated with those risks make it difficult to design and obtain consent in clinical trials to assess the clinical utility of such products.

Regulatory approval of nanomedicine products may present another major obstacle. Personalized treatment strategies are inherently not designed to be safe and efficacious for a population, but rather for an individual. Due to the complexity and differences among individual patients in terms of therapeutic response, clinical outcome, genetic profile and many other factors, it is inconceivable to evaluate and approve an exponentially large combinatorial library of possible nanoparticle configurations with various sizes, shapes, surface modifications and therapeutic payloads, especially when considering the long time and high cost associated with the development of an average therapeutic. On the other hand, as the nanomaterials involved in personalized medical applications become more advanced and multifunctional, they may increasingly challenge and eventually invalidate traditional regulatory categories and criteria. Thus, regulatory reform is necessary to facilitate the translation of nano-based medical products into clinical use. It will be critical for the Food and Drug Administration (FDA) to make adjustments and additional requirements to provide predictable and well-defined evaluation pathways for nanomedicine products, and to adapt regulatory requirements when appropriate to keep pace with rapidly emerging nanomaterials and nanotechnologies.

The incorporation of nanomaterials and nanotechnology into personalized medicine also brings up ethical issues. Nanodiagnostics and genetic testing offer the opportunity to collect more personal data on patients than ever before [220]. In particular, the use of point-of-care nanodevices that may bypass a health care professional will have a large impact on mass collection of personal data. This large volume of molecular-level data collected by such nanodevices will challenge the health care system in terms of storage and handling as well as privacy issues, and may raise questions for patients who will receive a torrent of medical information that will inevitably contain false positive and other misleading data [187].

The advances in nanomaterials and nanobiotechnology will play an important role in the development of cutting-edge diagnostic and therapeutic tools, which are an essential component of personalized medicine. While nanomedicine products face safety, scientific, regulatory and ethical issues, personalized medicine also encounters challenges and obstacles. A major obstacle with personalized approaches such as genetic testing is heterogeneity. A recent study demonstrated that a tumor’s genetic makeup can vary significantly within a single tumor [221]. The study showed that, within a single tumor, about 2/3 of the mutations found in a single biopsy was not uniformly detected throughout all the sampled regions of the same patient’s tumors. These results elucidated that a single biopsy cannot be considered representative of the landscape of genetic abnormalities in a tumor and that current practices may miss important genetic mutations that could affect the treatment of the disease [222]. Moreover, there were significant differences between mutations in the original tumor and the site of metastasis. The tumor discovered at diagnosis may be very different from the tumor that is growing or exposed to different treatments. However, getting additional biopsies from patients at different stages could be costly and inconvenient for patients. These findings represent a significant challenge for personalized medicine, as the use of genetic testing to direct therapy may be more complex than currently thought.

Economic considerations

The economical conundrums behind the advance of personalized nanomedicine are intricate. On the one hand, given the important resources devoted to the development of complex nanomaterial systems, the choice to focus only on the treatment of a subset of the population (i.e., HER-2 positive breast cancer patients) might be a difficult one to make. The aforementioned risks and challenges associated with the design of nanomaterial remain similar whether it is to treat all patients suffering from cancer or just a cohort showing a specific mutation. Therefore, the financial gain-to-risk ratio strongly leans towards applications which benefit larger populations. On the other hand, the proof of efficacy needed to obtain regulatory approval might be easier to obtain with a system rationally designed for a specific subpopulation where the prognosis with standard treatment is particularly grim. The evaluation of therapeutic candidates in patients that are more likely to benefit from it might speed up clinical trials and facilitate regulatory approval of the nanomaterial.

In this context, what makes nanomaterials remarkably appealing are their versatility and the ability to transfer the efforts dedicated to the development of one platform to other applications. The example of the CLION system, where the imaging platform was translated from oncology to cardiovascular applications was mentioned in section 3.2 [175178], but others also exist. For example, liposomes similar to the commercially-available doxorubicin liposomal formulations were recently proposed to act as scavenging nanomaterials for drug detoxification [223, 224]. Similarly, 2-hydroxypropyl-β-cyclodextrin, an excipient which forms nanosized complexes with multiple drugs, was shown to overcome cholesterol metabolism dysfunction in Niemann-Pick Type C [225, 226]. It was approved in 2011 for the intravenous and intrathecal treatment of this very rare LSD.

Finally, the development of treatments for orphan or “niche” diseases might provide attractive entryways to the clinic for nanomaterials. The favorable benefit-to-risk ratio expressly encountered in disorders for which no current treatment exist can prove an efficient way of showing the feasibility of an approach as well as the tolerability and safety of a novel material. In this perspective, scientists at the Children’s Hospital of Philadelphia have invested tremendous efforts in developing an adenovirus-based treatment for Leber Congenital Amaurosis (LCA), a very rare degenerative disease which irremediably leads to blindness [227229]. This gene delivery vector, which is now in phase II/III for LCA, was developed in parallel with an analogous formulation containing encoding DNA for the human coagulation factor IX, for the treatment of hemophilia B [230]. These examples, showcasing the versatility of drug delivery systems, offer strong support to the future contribution of nanomedicine to personalized medicine.


In summary, the application of nanomaterials in the realm of medicine has demonstrated tremendous potential from early diagnosis of disease to the development of highly effective targeted therapeutics. As our understanding of health and disease become more refined at the molecular level, the potential of nanomaterials to address the biological complexities of diseases will increase. Likewise, opportunities to develop patient- and disease-specific therapeutics or diagnostic modalities will emerge.

Contemporary chemistry and material science enable the fabrication of a virtually infinite library of nanomaterials. In the near future, these materials will be engineered to efficiently optimize interactions with biological systems for a range of medical applications. For the purpose of targeted therapy and diagnostic imaging, nanocarriers should possess improved stability, extended circulation half-life, favorable biodistribution profiles, lower immunotoxicity as well as targeting to specific tissues, cells and subcellular organelles. Proper ligands will also be chosen based on differential expression of molecular markers on diseased cells to produce patient-specific nanomedicines. When used for detection and diagnosis, nanomaterials should be engineered to avoid non-specific protein absorption and specifically recognize the targets of interest with high affinity. In this context, an in-depth understanding and thorough investigation of how nanomaterials interact with biological structures is required. In order to promote the development of nanomedicines into clinically feasible therapies, there is an urgent need for complete characterization of nanomaterial interactions with biological milieus that drive possible toxicological responses. Medical products must be demonstrated to not only be effective but also safe before they are approved for patient use. Some experimental studies have indicated that engineered nanomaterials could exhibit unique toxicological properties in cell culture and in animal models that may not be predicted from the toxicological assessment of the bulk version of the same materials. To establish a database and appropriated standardized protocols for toxicity assessment, the mechanism of nanomaterial-induced toxicity must be fully explored and nanomaterials must be investigated in vitro and in vivo (e.g., absorption, distribution, metabolism, excretion and toxicological studies) on a particle-by-particle basis.

In parallel, the concept of personalized medicine is also particularly appealing from the perspective of optimizing treatments for an individual patient. Nevertheless, this is a nascent field that has yet to reach its full potential. A potential error may be to succumb to over-enthusiasm and adopt personalized therapeutic practices without strong evidence that personalized treatment is superior to conventional approaches. Even in the field of antibody-based targeted anticancer treatments, which benefited from a head-start in individualized therapies, each clinical or genomic study brings new understanding of the intricate phenomena involved in treating the disease [231]. The understanding of all genomic components of complex diseases like cancer is still unraveling. One should therefore be careful before jumping to conclusions in identifying a particular biomarker as the new ubiquitous target that will eradicate the disease once and for all.

Although significant challenges exist, including regulatory issues and scientific challenges associated with manufacturing nanomedical products, the development and deployment of personalized nanomedicines holds enormous promise for the future treatment of complex diseases. Some nanomedicine products are already in clinical trials, and many others are in various phases of preclinical development. Critical and rational assessment of clinical needs coupled with an improved understanding of physicochemical parameters of nanomaterials that define their effects on the biological system will foster the development of efficient and safe nanomedicine. It is therefore practical to envision a future translation of personalized nanomedicine to the bedside.

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Depth Underwater and Underground

Writer and Curator: Larry H. Bernstein, MD, FCAP 



Deep diving for mammals is dangerous for humans and land based animals for too long, and it has dangerous consequences, most notable in nitrogen emboli  with very deep underwater diving. Other mammals live in water and have adapted to a water habitat.  This is another topic that needs further exploration.

Deep diving has different meanings depending on the context. Even in recreational diving the meaning may vary:

In recreational diving, a depth below about 30 metres (98 ft), where nitrogen narcosis becomes a significant hazard for most divers, may be considered a “deep dive”

In technical diving, a depth below about 60 metres (200 ft) where hypoxic breathing gas becomes necessary to avoid oxygen toxicity may be considered a “deep dive”.

Early experiments carried out by Comex S.A. (Compagnie maritime d’expertises) using hydrox and trimix attained far greater depths than any recreational technical diving. One example being the Comex Janus IV open-sea dive to 501 metres (1,644 ft) in 1977. The open-sea diving depth record was achieved in 1988 by a team of Comex divers who performed pipe line connection exercises at a depth of 534 metres (1,752 ft) in the Mediterranean Sea as part of the Hydra 8 program. These divers needed to breathe special gas mixtures because they were exposed to very high ambient pressure (more than 50 times atmospheric pressure).

Then there is the adaptation to the water habitat as a living environment. The two main types of aquatic ecosystems are marine ecosystems and freshwater ecosystems.


Marine ecosystems are part of the earth’s aquatic ecosystem. The habitats that make up this vast system range from the productive nearshore regions to the barren ocean floor. The marine waters may be fully saline, brackish or nearly fresh. The saline waters have a salinity of 35-50 ppt (= parts per thousand). The freshwater has a salinity of less than 0.5 ppt. The brackish water lies in between these 2. Marine habitats are situated from the coasts, over the continental shelf to the open ocean and deep sea. The ecosystems are sometimes linked with each other and are sometimes replacing each other in other geographical regions. The reason why habitats differ from another is because of the physical factors that influence the functioning and diversity of the habitats. These factors are temperature, salinity, tides, currents, wind, wave action, light and substrate.

Marine ecosystems are home to a host of different species ranging from planktonic organisms that form the base of the marine food web to large marine mammals. Many species rely on marine ecosystems for both food and shelter from predators. They are very important to the overall health of both marine and terrestrial environments. Coastal habitats are those above the spring high tide limit or above the mean water level in non-tidal waters.  They are close to the sea and include habitats such as coastal dunes and sandy shores, beaches , cliffs and supralittoral habitats. Coastal habitats alone account for approximately 30% of all marine biological productivity.


All plant and animal life forms are included from the microscopic picoplankton all the way to the majestic blue whale, the largest creature in the sea—and for that matter in the world. It wasn’t until the writings of Aristotle from 384-322 BC that specific references to marine life were recorded. Aristotle identified a variety of species including crustaceans, echinoderms, mollusks, and fish.
Today’s classification system was developed by Carl Linnaeus external link as an important tool for use in the study of biology and for use in the protection of biodiversity. Without very specific classification information and a naming system to identify species’ relationships, scientists would be limited in attempts to accurately describe the relationships among species. Understanding these relationships helps predict how ecosystems can be altered by human or natural factors.

Preserving biodiversity is facilitated by taxonomy. Species data can be better analyzed to determine the number of different species in a community and to determine how they might be affected by environmental stresses. Family, or phylogenetic, trees for species help predict environmental impacts on individual species and their relatives.


For generations, whales and other marine mammals have intrigued humans. 2,400 years ago, Aristotle, a Greek scientist and philosopher, recognized that whales are mammals, not fish, because they nurse their young and breathe air like other mammals. There are numerous myths and legends surrounding marine mammals. The Greeks believed that killing a dolphin was as bad as murdering a human. An Amazon legend said that river dolphins came to shore dressed as men to woo pretty girls during fiestas. During the Middle Ages, there were numerous legends surrounding the narwhals’ amazing tusk, which was thought to have come from the unicorn.

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Marine mammals evolved from their land dwelling ancestors over time by developing adaptations to life in the water. To aid swimming, the body has become streamlined and the number of body projections has been reduced. The ears have shrunk to small holes in size and shape. Mammary glands and sex organs are not part of the external physiology, and posterior (hind) limbs are no longer present.

Mechanisms to prevent heat loss have also been developed. The cylindrical body shape with small appendages reduces the surface area to volume ratio of the body, which reduces heat loss. Marine mammals also have a counter current heat exchange mechanism created by convergent evolution external link where the heat from the arteries is transferred to the veins as they pass each other before getting to extremities, thus reducing heat loss. Some marine mammals also have a thick layer of fur with a water repellent undercoat and/or a thick layer of blubber that can’t be compressed. The blubber provides insulation, a food reserve, and aids with buoyancy. These heat loss adaptations can also lead to overheating for animals that spend time out of the water. To prevent overheating, seals or sea lions will swim close to the surface with their front flippers waving in the air. They also flick sand onto themselves to keep the sun from directly hitting their skin. Blood vessels can also be expanded to act as a sort of radiator.

One of the major behavioral adaptations of marine mammals is their ability to swim and dive. Pinnipeds swim by paddling their flippers while sirenians and cetaceans move their tails or flukes up and down.

Some marine mammals can swim at relatively high speeds. Sea lions swim up to 35 kph and orcas can reach 50 kph. The fastest marine mammal, however, is the common dolphin, which reaches speeds up to 64 kph. While swimming, these animals take very quick breaths. For example, fin whales can empty and refill their huge lungs in less than 2 seconds. Marine mammals’ larynx and esophagus close automatically when they open their mouths to catch prey during dives. Oxygen is stored in hemoglobin in the blood and in myoglobin in the muscles. The lungs are also collapsible so that air is pushed into the windpipe preventing excess nitrogen from being absorbed into the tissues. Decreasing pressure can cause excess nitrogen to expand in the tissues as animals ascend to shallower depths, which can lead to decompression sickness,  aka “the bends.” Bradycardia, the reduction of heart rate by 10 to 20%, also takes place to aid with slowing respiration during dives and the blood flow to non-essential body parts. These adaptations allow sea otters to stay submerged for 4 to 5 minutes and dive to depths up to 55 m. Pinnipeds can often stay down for 30 minutes and reach average depths of 150-250 m. One marine mammal with exceptional diving skills is the Weddell seal, which can stay submerged for at least 73 minutes at a time at depths up to 600 m. The length and depth of whale dives depends on the species. Baleen whales feed on plankton near the surface of the water and have no need to dive deeply so they are rarely seen diving deeper than 100 m external link. Toothed whales seek larger prey at deeper depths and some can stay down for hours at depths of up to 2,250 m external link.


Human Experience

Albert Behnke: Nitrogen Narcosis

Casey A. Grover and David H. Grover
The Journal of Emergency Medicine, 2014; 46(2):225–227

As early as 1826, divers diving to great depths noted that descent often resulted in a phenomenon of intoxication and euphoria. In 1935, Albert Behnke discovered nitrogen as the cause of this clinical syndrome, a condition now known as nitrogen narcosis. Nitrogen narcosis consists of the development of euphoria, a false sense of security, and impaired judgment upon underwater descent using compressed air below 34 atmospheres (99 to 132 feet). At greater depths, symptoms can progress to loss of consciousness. The syndrome remains relatively unchanged in modern diving when compressed air is used. Behnke’s use of non-nitrogencontaining gas mixtures subsequent to his discovery during the 1939 rescue of the wrecked submarine USS Squalus pioneered the use of non-nitrogencontaining gas mixtures, which are used by modern divers when working at great depth to avoid the effects of nitrogen narcosis.

Behnke’s first duty station as a licensed physician was as assistant medical officer for Submarine Division 20 in San Diego, which was then commanded by one of the Navy’s rising stars, Captain Chester W. Nimitz of World War II fame.
In this setting, Dr. Behnke spent his free time constructively by learning to dive, using the traditional ‘‘hard-hat’’ gear aboard the USS Ortalon, a submarine rescue vessel to which he also rotated. Diving was not a notable specialty of the Navy at the time, and the service was slow in developing the infrastructure for it. Dr. Behnke devoted his efforts to research on the topic of diving medicine, as well as developing a more sound understanding of the biophysics of diving. In 1932, he wrote a letter to the Surgeon General describing some of his observations on arterial gas embolism, which earned him some accolades from the Navy and resulted in his transfer to Harvard’s School of Public Health as a graduate fellow. After 2 years at Harvard, the Navy assigned duty to Dr. Behnke at the Navy’s submarine escape training tower at Pearl Harbor. He worked extensively here on developing techniques for rescuing personnel from disabled submarines on the sea floor. In 1937, he was one of three Navy physicians assigned to the Navy’s Experimental Diving Unit. This team worked on improving the rescue system, plus updating the diving recompression tables originally developed by the British in 1908.

The intoxicating effects of diving were first described by a French physician named Colladon in 1826, who reported that descent in a diving bell resulted in his feeling a ‘‘state of excitement as though I had drunk some alcoholic liquor’’.
The etiology of this phenomenon remained largely unknown until the 1930s, when the British military researcher Damant again highlighted the issue, and reported very unpredictable behavior in his divers during descents as deep as 320 feet during the British Admiralty Deep Sea diving trials. Two initial theories arose as to the etiology for this effect, the first being from psychological causes by Hill and Phillip in 1932, and the second being from oxygen toxicity by Haldane in 1935.

Dr. Behnke and his colleagues at the Harvard School of Public Health had another idea as to the etiology of this phenomenon. In 1935, based on observation of individuals in experiments with a pressure chamber, Dr. Behnke published an article in the American Journal of Physiology in which he posited that nitrogen was the etiology of the intoxicating effects of diving.

Nitrogen narcosis, described as ‘‘rapture of the deep’’ by Jacques Cousteau, still remains a relatively common occurrence in modern diving, despite major advances in diving technology since Behnke’s initial description of the pathophysiologic cause of the condition in 1935. The development of symptoms of this condition varies from diver to diver, but usually begins when a depth of 4 atmospheres (132 feet) is reached in divers using compressed air. More sensitive divers can develop symptoms at only 3 atmospheres (99 feet), and other divers may not be affected up to depths as high as 6 atmospheres (198 feet). Interestingly, tolerance to nitrogen narcosis can be developed by frequent diving and exposure to the effects of compressed air at depth.

  1. Acott C. A brief history of diving and decompression illness. SPUMS J 1999;29:98–109.
    2. Bornmann R. Dr. Behnke, founder of UHMS, dies. Pressure 1992; 21:14.
    3. Behnke AR, Thomson RM, Motley P. The psychologic effects from breathing air at 4 atmospheric pressures. Am J Physiol 1935; 112:554–8.
    4. Behnke AR, Johnson FS, Poppen JR, Motley P. The effect of oxygen on man at pressures from 1 to 4 atmospheres. AmJ Physiol 1934; 110:565–72.

Exhaled nitric oxide concentration and decompression-induced bubble formation: An index of decompression severity in humans?

J.-M. Pontier, Buzzacott, J. Nastorg, A.T. Dinh-Xuan, K. Lambrechts
Nitric Oxide 39 (2014) 29–34

Introduction: Previous studies have highlighted a decreased exhaled nitric oxide concentration (FE NO) in divers after hyperbaric exposure in a dry chamber or following a wet dive. The underlying mechanisms of this decrease remain however unknown. The aim of this study was to quantify the separate effects of submersion, hyperbaric hyperoxia exposure and decompression-induced bubble formation on FE NO after a wet dive.
Methods: Healthy experienced divers (n = 31) were assigned to either

  • a group making a scuba-air dive (Air dive),
  • a group with a shallow oxygen dive protocol (Oxygen dive) or

a group making a deep dive breathing a trimix gas mixture (deep-dive).
Bubble signals were graded with the KISS score. Before and after each dive FE NO values were measured using a hand-held electrochemical analyzer.
Results: There was no change in post-dive values of FE NO values (expressed in ppb = parts per billion) in the Air dive group (15.1 ± 3.6 ppb vs. 14.3 ± 4.7 ppb, n = 9, p = 0.32). There was a significant decrease in post-dive values of FE NO in the Oxygen dive group (15.6 ± 6 ppb vs. 11.7 ± 4.7 ppb, n = 9, p = 0.009). There was an even more pronounced decrease in the deep dive group (16.4 ± 6.6 ppb vs. 9.4 ± 3.5 ppb, n = 13, p < 0.001) and a significant correlation between KISS bubble score >0 (n = 13) and percentage decrease in post-dive FE NO values (r = -0.53, p = 0.03). Discussion: Submersion and hyperbaric hyperoxia exposure cannot account entirely for these results suggesting the possibility that, in combination, one effect magnifies the other. A main finding of the present study is a significant relationship between reduction in exhaled NO concentration and dive-induced bubble formation. We postulate that exhaled NO concentration could be a useful index of decompression severity in healthy human divers.

Brain Damage in Commercial Breath-Hold Divers

Kiyotaka Kohshi, H Tamaki, F Lemaıtre, T Okudera, T Ishitake, PJ Denoble
PLoS ONE 9(8): e105006 http://dx.doi.org:/10.1371/journal.pone.0105006

Background: Acute decompression illness (DCI) involving the brain (Cerebral DCI) is one of the most serious forms of diving related injuries which may leave residual brain damage. Cerebral DCI occurs in compressed air and in breath-hold divers, likewise. We conducted this study to investigate whether long-term breath-hold divers who may be exposed to repeated symptomatic and asymptomatic brain injuries, show brain damage on magnetic resonance imaging (MRI).
Subjects and Methods: Our study subjects were 12 commercial breath-hold divers (Ama) with long histories of diving work in a district of Japan. We obtained information on their diving practices and the presence or absence of medical problems, especially DCI events. All participants were examined with MRI to determine the prevalence of brain lesions.
Results: Out of 12 Ama divers (mean age: 54.965.1 years), four had histories of cerebral DCI events, and 11 divers demonstrated ischemic lesions of the brain on MRI studies. The lesions were situated in the cortical and/or subcortical area (9 cases), white matters (4 cases), the basal ganglia (4 cases), and the thalamus (1 case). Subdural fluid collections were seen in 2 cases. Conclusion: These results suggest that commercial breath-hold divers are at a risk of clinical or subclinical brain injury which may affect the long-term neuropsychological health of divers.

Decompression illness

Richard D Vann, Frank K Butler, Simon J Mitchell, Richard E Moon
Lancet 2010; 377: 153–64

Decompression illness is caused by intravascular or extravascular bubbles that are formed as a result of reduction in environmental pressure (decompression). The term covers both arterial gas embolism, in which alveolar gas or venous gas emboli (via cardiac shunts or via pulmonary vessels) are introduced into the arterial circulation, and decompression sickness, which is caused by in-situ bubble formation from dissolved inert gas. Both syndromes can occur in divers, compressed air workers, aviators, and astronauts, but arterial gas embolism also arises from iatrogenic causes unrelated to decompression. Risk of decompression illness is
affected by immersion, exercise, and heat or cold. Manifestations range from itching and minor pain to neurological symptoms, cardiac collapse, and death. First aid treatment is 100% oxygen and definitive treatment is recompression to increased pressure, breathing 100% oxygen. Adjunctive treatment, including fluid administration and prophylaxis against venous thromboembolism in paralyzed patients, is also recommended. Treatment is, in most cases, effective although residual deficits can remain in serious cases, even after several recompressions.

Bubbles can have mechanical, embolic, and biochemical effects with manifestations ranging from trivial to fatal. Clinical manifestations can be caused by direct effects from extravascular (autochthonous) bubbles such as mechanical distortion of tissues causing pain, or vascular obstruction causing stroke-like signs and symptoms. Secondary effects can cause delayed symptom onset up to 24 h after surfacing. Endothelial damage by intravascular bubbles can cause capillary leak, extravasation of plasma, and haemoconcentration. Impaired endothelial function, as measured by decreased effects of vasoactive compounds, has been reported in animals and might occur in man. Hypotension can occur in severe cases. Other effects include platelet activation and deposition, leucocyte-endothelial adhesion, and possibly consequences of vascular occlusion believed to occur in thromboembolic stroke such as ischaemia-reperfusion injury, and apoptosis.

Classification of initial and of all eventual manifestations of decompression illness in 2346 recreational diving accidents reported to the Divers Alert Network from 1998 to 2004 For all instances of pain, 58% consisted of joint pain, 35% muscle pain, and 7% girdle pain. Girdle pain often portends spinal cord involvement. Constitutional symptoms included headache, lightheadedness, inappropriate fatigue, malaise, nausea or vomiting, and anorexia. Muscular discomfort included stiffness, pressure, cramps, and spasm but excluded pain. Pulmonary manifestations included dyspnoea and cough.

Other than depth and time, risk of decompression sickness is affected by other factors that affect inert gas exchange and bubble formation, such as immersion (vs dry hyperbaric chamber exposure), exercise, and temperature. Immersion decreases venous pooling and increases venous return and cardiac output. Warm environments improve peripheral perfusion by promoting vasodilation, whereas cool temperatures decrease perfusion through vasoconstriction. Exercise increases both peripheral perfusion and temperature. The effect of environmental conditions on risk of decompression sickness is dependent on the phase of the pressure exposure. Pressure, exercise, immersion, or a hot environment increase inert gas uptake and risk of decompression sickness. During decom-pression these factors increase inert gas elimination and therefore decrease the risk of decompression sickness. Conversely, uptake is reduced during rest or in a cold environment, hence a diver resting in a cold environment on the bottom has decreased risk of decompression sickness. Rest or low temperatures during decompression increase the risk. If exercise occurs after decompression when super-saturation is present, bubble formation increases and risk of decompression sickness rises.

Exercise at specific times before a dive can decrease the risk of serious decompression sickness in animals and incidence of venous gas emboli in both animals and man. The mechanisms of these effects are unknown but might involve modulation of nitric oxide production and effects on endothelium. Venous gas emboli and risk of decompression sickness increase slightly with age and body-mass index.

Arterial gas embolism should be suspected if a diver has a new onset of altered consciousness, confusion, focal cortical signs, or seizure during ascent or within a few minutes after surfacing from a compressed gas dive.

If the diver spends much time at depth and might have absorbed substantial inert gas before surfacing, arterial gas embolism and serious decompression sickness can coexist, and in such cases, spinal cord manifestations can predominate. Other organ systems, such as the heart, can also be affected, but the clinical diagnosis of gas embolism is not reliable without CNS manifestations. Arterial gas embolism is rare in altitude exposure; if cerebral symptoms occur after altitude exposure, the cause is usually decompression sickness.

Nondermatomal hypoaesthesia and truncal ataxia are common in neurological decompression sickness and can be missed by cursory examination. Pertinent information includes level of consciousness and mental status, cranial nerve function, and motor strength. Coordination can be affected disproportionately, and abnormalities can be detected by assessment of finger-nose movement, and, with eyes open and closed, ability to stand and walk and do heel-toe walking backwards and forwards. Many of these simple tests can be done on the scene by untrained companions.

Panel: Differential diagnosis of decompression illness
Inner-ear barotrauma
Middle-ear or maxillary sinus overinfl ation
Contaminated diving gas and oxygen toxic effects
Musculoskeletal strains or trauma sustained before, during, or after diving
Seafood toxin ingestion (ciguatera, pufferfish, paralytic shellfish poisoning)
Immersion pulmonary edema
Water aspiration
Decompression chamber

Decompression chamber

Decompression chamber. fluidic or pneumatic ventilator is shown at the left. The infusion pump is contained within a plastic cover, in which 100% nitrogen is used to decrease the fi re risk in the event of an electrical problem. The monitor screen is outside the chamber and can be seen through the viewing port. Photo from Duke University Medical Center, with permission.

Long-term outcomes of 69 divers with spinal cord decompressionsickness, by manifestation
n %
No residual symptoms 34 49·3
Any residual symptom 35 50·7
Mild paraesthesias, weakness, or pain 14 20·3
Some impairment of daily activities 21 30·4
Difficulty walking 11 15·9
Impaired micturition 13 18·8
Impaired defecation 15 21·7
Impaired sexual function 15 21·7

Decompression illness occurs in a small population but is an international problem that few physicians are trained to recognise or manage. Although its manifestations are often mild, the potential for permanent injury exists in severe cases, especially if unrecognised or inadequately treated. Emergency medical personnel should be aware of manifestations of decompression illness in the setting of a patient with a history of recent diving or other exposure to substantial pressure change, and should contact an appropriate consultation service for advice.

Diving Medicine: Contemporary Topics and Their Controversies

Michael B. Strauss and Robert C. Borer, Jr
Am J Emerg Med 2001; 19:232-238

SCUBA diving is a popular recreational sport. Although serious injuries occur infrequently, when they do knowledge of diving medicine and/or where to obtain appropriate consultation is essential. The emergency physician is likely to be the first physician contact the injured diver has. We discuss 8 subjects
in diving medicine which are contemporary, yet may have controversies associated with them. From this information the physician dealing primarily with the injured diver will have a basis for understanding and managing, as
well as where to find additional help, for his/her patients’ diving injuries.

Over the past 10 years, new knowledge and equipment improvements have made diving safer and more enjoyable. Estimates of actively participating sports divers show a striking increase over this time interval while the number of SCUBA diving deaths annually has remained nearly level at approximately 100. A further indicator of recreational diving safety is that reflected in the nearly constant number of diving injuries (1000 per annum) over the most recent 5 reported years, or approximately 0.53 to 3.4 incidents/10,000 dives.

Divers Alert Network.
The Divers Alert Network (DAN) is a nonprofit organization directed and staffed by experts in the specialty of diving medicine.6 DAN provides immediate consultation for both divers and physicians in the diagnosis and initial management of diving injuries. This 24-hour service is available free world-wide through a dedicated emergency telephone line: 1-919-684-4326. The DAN staff will also identify the nearest appropriate recompression treatment facility and knowledgeable physicians for an expedient referral. General diving medical inquiries can be answered during normal weekday hours either through an information telephone line: 1-919-684-2948 or through an interactive web site http://www.diversalertnetwork.org.

Use of 100% Oxygen for Initial, on the Scene, Management of Diving Accidents
The breathing of pure oxygen is crucial for the initial management of the diving related problems of arterial gas embolism (AGE), decompression sickness (DCS), pulmonary barotrauma (thoracic squeeze), aspiration pneumonitis, and hypoxic encephalopathy associated with near drowning. In 1985, Dick reported that in many cases the neurologic symptoms of AGE and DCS were resolved with the immediate breathing of pure oxygen on the surface. The breathing of pure oxygen reduces bubble size by increasing the differential pressure for the inert gas to diffuse out of the bubble and it also speeds the washout of inert gas from body tissues. The early elimination of the bubble prevents hypoxia and the interaction of the bubble with the blood vessel lining. This interaction leads to secondary problems of capillary leak, bleeding, inflammation, ischemia, and cell death. These secondary problems are the reasons not all DCS symptoms resolve with recompression chamber treatment. The immediate use of pure oxygen for the medical management of these diving problems is analogous to the use of cardiopulmonary resuscitation for the witnessed cardiac arrest; the sooner initiated the better the results.

Diving Education

Medical Fitness for Diving

Asthma has the potential risk for AGE. Neuman reviewed the subject of asthma and diving. He and his coauthors recommend that asthmatics who are asymptomatic, not on medications and have no exercised induced abnormality on pulmonary function studies be allowed to dive.

Conditions leading to loss of consciousness, such as insulin dependent diabetes and epilepsy, can result in drowning. Carefully controlled diving studies in diabetics, who are free from complications, are now defining the safe requirements for diving. Epilepsy remains as a disqualification except in individuals with a history of febrile seizures ending prior to 5 years of age.

Availability of Hyperbaric Oxygen Treatment Facilities

The availability of these chambers makes it possible for divers who become symptomatic after SCUBA diving to readily receive recompression treatment. This is important because the closer the initiation of recompression treatment to the onset of DCS (and AGE) signs and symptoms, the greater the likelihood of full recovery.

Improved Diving Equipment

Mixed and Rebreather Gas Diving
Mixed gas diving involves changing the breathing gas from air which has 20% oxygen to higher oxygen percentages (nitrox). As the amount of oxygen is increased in the gas mixture, the amount of the inert gas (nitrogen) is reduced. With oxygen enriched air there is less tissue deposition of inert gas per unit of time under water for any given depth. However, because of increased oxygen partial pressures, the seizure threshold for oxygen toxicity is lowered. For normal sports diving activities, oxygen toxicity with mixed gas diving is only a theoretical concern.

Decompression Illness is More Than Bubbles

When AGE occurs, DCS symptoms may be concurrent or appear during or after recompression treatment even though the decompression tables were not violated on the dive. When DCS occurs in this situation it appears resistant to recompression treatment (Neuman) perhaps because of the inflammatory reaction generated by the bubble-blood vessel interaction from the AGE. In cases of DCI where components of both DCS and AGE are suspected, the diver should be observed for a minimum of 24 hours after the recompression treatment is completed for the delayed onset of DCS.

No theory of DCS discounts the primary role of bubbles in this condition. However, new information suggests that there are precursors to bubble formation and post-bubbling events that occur as a consequence of the bubbles. As mentioned earlier, venous gas emboli are a common occurrence diving ascent and ordinarily are filtered out harmlessly by the lungs. Precursors to DCS include stasis, dehydration and too rapid of ascents. These conditions allow the ubiquitous VGE to enlarge, coalesce and occlude the venous side of the circulation. Massive venous bubbling to the lungs can cause pulmonary vessel obstruction described as the chokes. If right to left shunts occur in the heart, VGE can become AGE to the brain. If the arterial flow is slow enough and/or the gradients large enough, autochthonus (ie, spontaneous) bubbles can form in the arterial circulation and lead to any of the consequences of AGE. In such situations it could be difficult to determine whether the DCI event was from AGE or DCS even after careful analysis of the dive profile. Hollenbeck’s model for diving paraplegia includes the setting of venous stasis (Batson’s plexus of veins) in the spinal canal, bubble formation, bubble enlargement possibly from off gassing of the spinal cord, blood vessel occlusion, and venous side infarctions of the spinal cord.
Contemporary Management of DCS

Problem Intervention Effect
Bubble Recompression
with HBO
Reduce bubble size
1. Washout inert gas.
2. Change bubble composition by diffusion.
Stasis and dehydration Hydration: oral fluids if alert, IV fluids otherwise. Improve blood flow.
InflammationCell Ischemia ? Anti-inflammatory medicationsHBO Reduce interaction between bubble and blood vessel endothelium.
Improve oxygen availability to hypoxic tissues, reduce edema and also reduces the interaction between bubble and blood vessel endothelium.



We anticipate that in the future there will be further improvements for the safety and enjoyment of the recreational SCUBA diver. For example, the dive computer of the future will be able to individualize dive profiles for different personal medical parameters such as age, body composition and fitness level. Diver locators could quickly target a missing diver and save time and gas consumption as well as prevent serious diving mishaps. Drugs may be developed that would minimize the effect of bubbles interacting with body tissues and prevent DCS and AGE.

Extracorporeal membrane oxygenation therapy for pulmonary decompression illness

Yutaka Kondo, Masataka Fukami and Ichiro Kukita
Kondo et al. Critical Care 2014; 18:438 http://ccforum.com/content/18/3/438/10.1186/cc13935

Pulmonary decompression illness is rarely observed in clinical settings, and most patients die prior to hospitalization. We administered ECMO therapy to rescue a patient, even though this therapy has rarely been reported with good outcome in patients with decompression illness. In addition, we had to select venovenous ECMO even with the patient showing right ventricular failure. A lot of physicians may select venoarterial ECMO if the patient shows right ventricular failure, but the important physiological mechanism of pulmonary decompression illness is massive air embolism in the pulmonary arteries, and the bubbles diminish within the first 24 hours. The management of decompression illness therefore differs substantially from the usual right-sided heart failure.

Extremes of barometric pressure

Jane E Risdall, David P Gradwell
Anaesthesia and Intensive Care Medicine 16:2
Ascent to elevated altitude, commonly achieved through flight, by climbing or by residence in highland regions, exposes the individual to reduced ambient pressure. Although there are physical manifestations of this exposure as a consequence of Boyle’s law, the primary physiological challenge is of hypobaric hypoxia. The acute physiological and longer-term adaptive responses of the cardiovascular, respiratory, hematological and neurological systems to altitude are described, together with an outline of the presentation and management of acute mountain sickness, high-altitude pulmonary edema and high-altitude cerebral edema. While many millions experience modest exposure to altitude as a result of flight in pressurized aircraft, fewer individuals are exposed to increased ambient pressure. The pressure changes during diving and hyperbaric exposures result in greater changes in gas load and gas toxicity. Physiological effects include the consequences of increased work of breathing and redistribution of circulating volume. Neurological manifestations may be the direct result of pressure or a consequence of gas toxicity at depth. Increased tissue gas loads may result in decompression illness on return to surface or subsequent ascent in flight.

  • understand the physical effects of changes in ambient pressure and the physiological consequences on the cardiovascular respiratory and neurological systems
  • gain an awareness that exposure to reduced ambient pressure produces both acute and more chronic effects, with differing signs, symptoms and time to onset at various altitudes
  • develop an awareness of the toxic effects of ‘inert’ gases at increased ambient pressures and the pathogenesis and management of decompression illness

Decompression illness According to Henry’s law, at a constant temperature the amount of gas which dissolves in a liquid is proportional to the pressure of that gas or its partial pressure, if it is part of a mixture of gases. Breathing gases at increased ambient pressure will increase the amount of each gas dissolved in the fluid phases of body tissues. On ascent this excess gas has to be given up. If the ascent is controlled at a sufficiently slow rate, elimination will be via the respiratory system. If the ascent is too fast, excess gas may come out of solution and form free bubbles in the tissues or circulation. Bubbles may contain any of the gases in the breathing mixture, but it is the presence of inert gas bubbles (nitrogen or helium) that are thought most likely to give rise to problems, since the elimination of excess oxygen is achieved by metabolism as well as ventilation. These bubbles may act as venous emboli or may trigger inflammatory tissue responses giving rise to symptoms of decompression illness (DCI). Signs and symptoms of DCI may appear up to 48 hours after exposure to increased ambient pressure and include joint pains, motor and sensory deficits, dyspnoea, cough and skin rashes.

Neurological effects of deep diving

Marit Grønning, Johan A. Aarli
Journal of the Neurological Sciences 304 (2011) 17–21

Deep diving is defined as diving to depths more than 50 m of seawater (msw), and is mainly used for occupational and military purposes. A deep dive is characterized by the compression phase, the bottom time and the decompression phase. Neurological and neurophysiologic effects are demonstrated in divers during the compression phase and the bottom time. Immediate and transient neurological effects after deep dives have been shown in some divers. However, the results from the epidemiological studies regarding long term neurological effects from deep diving are conflicting and still not conclusive.

Possible immediate neurological effects of deep diving
Syndrome Pressure
Hyperoxia/oxygen seizures >152 kPa (5 msw)
Nitrogen narcosis >354 kPa (25 msw)
High pressure nervous syndrome >1.6 MPa (150 msw)
Neurological decompression sickness

Neurological effects have been demonstrated, both clinically and neurophysiologically in divers during the compression phase and the bottom time. Studies of divers before and after deep dives have shown immediate and transient neurological effects in some divers. However, the results from the epidemiological and clinical studies regarding long term neurological effects from deep diving are conflicting and still not conclusive. Prospective clinical studies with sufficient power and sensitivity are needed to solve this important issue.

Today deep diving to more than 100 msw is routinely performed globally in the oil- and gas industry. In the North Sea remote underwater intervention and maintenance is performed by the use of remotely operated vehicles (ROV), both in conjunction to and as an alternative to manned underwater operations. There will, however, always be a need for human divers in the technically more advanced underwater operations and for contingency repair operations.

P300 latency indexes nitrogen narcosis

Barry Fowler, Janice Pogue and Gerry Porlier
Electroencephalography, and clinical Neurophysiology, 1990, 75:221-229

This experiment investigated the effects of nitrogen narcosis on reaction time (RT) and P300 latency and amplitude, Ten subjects breathed either air or a non-narcotic 20% oxygen-80% helium (heliox) mixture in a hyperbaric chamber at 6.5, 8.3 and 10 atmospheres absolute (ATA), The subjects responded under controlled accuracy conditions to visually presented male or female names in an oddball paradigm. Single-trial analysis revealed a strong relationship between RT and P300 latency, both of which were slowed in a dose-related manner by hyperbaric air but not by heliox. A clear-cut dose-response relationship could not be established for P300 amplitude. These results indicate that P300 latency indexes nitrogen narcosis and are interpreted as support for the slowed processing model of inert gas narcosis.

Adaptation to Deep Water Habitat

Effects of hypoxia on ionic regulation, glycogen utilization and antioxidative ability in the gills and liver of the aquatic air-breathing fish Trichogaster microlepis

Chun-Yen Huang, Hui-Chen Lina, Cheng-Huang Lin
Comparative Biochemistry and Physiology, Part A 179 (2015) 25–34

We examined the hypothesis that Trichogaster microlepis, a fish with an accessory air-breathing organ, uses a compensatory strategy involving changes in both behavior and protein levels to enhance its gas exchange ability. This compensatory strategy enables the gill ion-regulatory metabolism to maintain homeostasis during exposure to hypoxia. The present study aimed to determinewhether ionic regulation, glycogen utilization and antioxidant activity differ in terms of expression under hypoxic stresses; fish were sampled after being subjected to 3 or 12 h of hypoxia and 12 h of recovery under normoxia. The air-breathing behavior of the fish increased under hypoxia. No morphological modification of the gills was observed. The expression of carbonic anhydrase II did not vary among the treatments. The Na+/K+-ATPase enzyme activity did not decrease, but increases in Na+/K+-ATPase protein expression and ionocyte levels were observed. The glycogen utilization increased under hypoxia as measured by glycogen phosphorylase protein expression and blood glucose level, whereas the glycogen content decreased. The enzyme activity of several components of the antioxidant system in the gills, including catalase, glutathione peroxidase, and superoxidase dismutase, increased in enzyme activity. Based on the above data, we concluded that T. microlepis is a hypoxia-tolerant species that does not exhibit ion-regulatory suppression but uses glycogen to maintain energy utilization in the gills under hypoxic stress. Components of the antioxidant system showed increased expression under the applied experimental treatments.

Divergence date estimation and a comprehensive molecular tree of extant cetaceans

Michael R. McGowen , Michelle Spaulding, John Gatesy
Molecular Phylogenetics and Evolution 53 (2009) 891–906

Cetaceans are remarkable among mammals for their numerous adaptations to an entirely aquatic existence, yet many aspects of their phylogeny remain unresolved. Here we merged 37 new sequences from the nuclear genes RAG1 and PRM1 with most published molecular data for the group (45 nuclear loci, transposons, mitochondrial genomes), and generated a supermatrix consisting of 42,335 characters. The great majority of these data have never been combined. Model-based analyses of the supermatrix produced a solid, consistent phylogenetic hypothesis for 87 cetacean species. Bayesian analyses corroborated odontocete (toothed whale) monophyly, stabilized basal odontocete relationships, and completely resolved branching events within Mysticeti (baleen whales) as well as the problematic speciose clade Delphinidae (oceanic dolphins). Only limited conflicts relative to maximum likelihood results were recorded, and discrepancies found in parsimony trees were very weakly supported. We utilized the Bayesian supermatrix tree to estimate divergence dates among lineages using relaxed-clock methods. Divergence estimates revealed rapid branching of basal odontocete lineages near the Eocene–Oligocene boundary, the antiquity of river dolphin lineages, a Late Miocene radiation of balaenopteroid mysticetes, and a recent rapid radiation of Delphinidae beginning [1]10 million years ago. Our comprehensive,  time calibrated tree provides a powerful evolutionary tool for broad-scale comparative studies of Cetacea.

Mitogenomic analyses provide new insights into cetacean origin and evolution

Ulfur Arnason, Anette Gullberg, Axel Janke
Gene 333 (2004) 27–34

The evolution of the order Cetacea (whales, dolphins, porpoises) has, for a long time, attracted the attention of evolutionary biologists. Here we examine cetacean phylogenetic relationships on the basis of analyses of complete mitochondrial genomes that represent all extant cetacean families. The results suggest that the ancestors of recent cetaceans had an explosive evolutionary radiation 30–35 million years before present. During this period, extant cetaceans divided into the two primary groups, Mysticeti (baleen whales) and Odontoceti (toothed whales). Soon after this basal split, the Odontoceti diverged into the four extant lineages, sperm whales, beaked whales, Indian river dolphins and delphinoids (iniid river dolphins, narwhals/belugas, porpoises and true dolphins). The current data set has allowed test of two recent morphological hypotheses on cetacean origin. One of these hypotheses posits that Artiodactyla and Cetacea originated from the extinct group Mesonychia, and the other that Mesonychia/Cetacea constitutes a sister group to Artiodactyla. The current results are inconsistent with both these hypotheses. The findings suggest that the claimed morphological similarities between Mesonychia and Cetacea are the result of evolutionary convergence rather than common ancestry.

The order Cetacea traditionally includes three suborders: the extinct Archaeoceti and the recent Odontoceti and Mysticeti. It is commonly believed that the evolution of ancestral cetaceans from terrestrial to marine (aquatic) life was accompanied by a fast and radical morphological adaptation. Such a scenario may explain why it was, for a long time, difficult to morphologically establish the position of Cetacea in the mammalian tree and even to settle whether Cetacea constituted a monophyletic group.

Biochemical analyses in the 1950s  and 1960s had shown a closer relationship between cetaceans and artiodactyls (even-toed hoofed mammals) than between cetaceans and any other eutherian order and karyological studies in the late 1960s and early 1970s unequivocally supported cetacean monophyly (Arnason, 1969, 1974). The nature of the relationship between cetaceans and artiodactyls was resolved in phylogenetic studies of mitochondrial (mt) cytochrome b (cytb) genes (Irwin and Arnason, 1994; Arnason and Gullberg, 1996) that placed Cetacea within the order Artiodactyla itself as the sister group of the Hippopotamidae (see also Sarich, 1993). The Hippopotamidae/ Cetacea relationship was subsequently supported in studies of nuclear data (Gatesy et al., 1996; Gatesy, 1997) and statistically established in analysis of complete mt genomes (Ursing and Arnason, 1998). The relationship has also been confirmed in analyses of combined nuclear and mt sequences (Gatesy et al., 1999; Cassens et al., 2000) and in studies of short interspersed repetitive elements (SINEs). Artiodactyla and Cetacea are now commonly referred to as Cetartiodactyla.

Previous analyses of the complete cytb gene of more than 30 cetacean species (Arnason and Gullberg, 1996) identified five primary lineages of recent cetaceans, viz., Mysticeti and the four odontocete lineages Physeteridae (sperm whales), Platanistidae (Indian river dolphins), Ziphiidae (beaked whales) and Delphinoidea (iniid river dolphins, porpoises, narwhals and dolphins). However, these studies left unresolved the relationships of the five lineages as well as those between the three delphinoid families Monodontidae (narwhals, belugas), Phocoenidae (porpoises) and Delphinidae (dolphins). Similarly, the relationships between the four mysticete families Balaenidae (right whales), Neobalaenidae (pygmy right whales), Eschrichtiidae (gray whales) and Balaenopteridae (rorquals) were not conclusively resolved in analyses of cytb genes.

Fig. (not shown). Cetartiodactyl relationships and the estimated times of their divergences. The tree was established on the basis of maximum likelihood analysis of the concatenated amino acid (aa) sequences of 12 mt protein-coding genes. Length of alignment 3610 aa. Support values for branches A–H are shown in the insert.
Cetruminantia (branch A) receives moderate support and Cetancodonta (B) strong support. Cetacea (C) splits into monophyletic Mysticeti (baleen whales) and monophyletic Odontoceti (toothed whales). Odontoceti has four basal lineages, Physeteridae (sperm whales: represented by the sperm and pygmy sperm whales), Ziphiidae (beaked whales: bottlenose and Baird’s beaked whales), Platanistidae (Indian river dolphins: Indian river dolphin) and Delphinoidea. Delphinoidea encompasses the families Iniidae (iniid river dolphins: Amazon river dolphin, La Plata dolphin), Monodontidae (narwhals/belugas: narwhal), Phocoenidae (porpoises: harbour porpoise) and Delphinidae (dolphins: white-beaked dolphin). The common odontocete branch and the branches separating the four cetacean lineages are short. These relationships are therefore somewhat unstable (cf. Section 3.1 and Table 1). Iniid river dolphins (F) are solidly nested within the Delphinoidea (E). Thus, traditional river dolphins (Platanistidae + Iniidae) do not form a monophyletic unit. Molecular estimates of divergence times (Sanderson 2002) were based on two calibration points, A/C-60 and O/M-35 (cf. Section 3.2). Due to the short lengths of internal branches, some estimates for these divergences overlap. NJ: neighbor joining; MP: maximum parsimony; LBP: local bootstrap probability; QP: quartet puzzling. The bar shows the number of aa substitutions per site.

The limited molecular resolution among basal cetacean lineages has been known for some time. Studies of hemoglobin and myoglobin (Goodman, 1989; Czelusniak et al., 1990) have either joined Physeteridae and Mysticeti to the exclusion of Delphinoidea (myoglobin data) or Mysticeti and Delphinoidea to the exclusion of Physeteridae (hemoglobin data). Thus, neither of the data sets identified monophyletic Odontoceti by joining the two odontocete lineages (Physeteridae and Delphinoidea) to the exclusion of Mysticeti. A similar instability was recognized and cautioned against in analyses of some mt data, notably, sequences of rRNA genes (Arnason et al., 1993b). The suggestion (Milinkovitch et al., 1993) of a sister group relationship between Physeteridae and the mysticete family Balaenopteridae (rorquals) was based on a myoglobin data set (which joins Physeteridae and Mysticeti to the exclusion of Delphinoidea) that was complemented with partial data of the mt 16S rRNA gene.

The cetancodont divergence times calculated using A/C-60 and O/M-35 as references have been included in Fig. 1. As a result of the short branches separating several cetacean lineages, the estimates of these divergences overlap. The same observation has been made in calculations based on SINE flanking sequences (Nikaido et al., 2001). There is a general consistency between the current and the flanking sequence datings, except for those involving the Balaenopteridae, which are somewhat younger in our analysis than in the SINEs study. The currently estimated age of the divergence between Hippopotamus and Cetacea (c53.5 MYBP) is consistent with the age (>50 MY) of the oldest archaeocete fossils identified so far (Bajpai and Gingerich, 1998). This suggests that the ages allocated to the two references, A/C-60 (the divergence between ruminant artiodactyls and cetancodonts) and O/M-35 (the divergence between odontocetes and mysticetes) are reasonably accurate.

The dating of the divergence between the blue and fin whales is of interest regarding hybridization between closely related mammalian species. Previous molecular analyses (Arnason et al., 1991b; Spilliaert et al., 1991) demonstrated the occurrence of hybridization between these two species. These studies, which were based on three hybrids (one female and two males), showed that either species could be the mother or father in these hybridizations. The two male hybrids had rudimentary testes, whereas the female hybrid was in her second pregnancy. This suggests that the blue and fin whales may be close to the limit for permissible species hybridization among mammals.

The current data set has allowed examination of the coherence between the molecular results and two prevalent morphological hypotheses related to cetacean evolution. The first hypothesis, which in essence originates from Van Valen (1966, 1968), postulates that monophyletic Artiodactyla and monophyletic Cetacea evolved separately from the extinct Palaeocene group Mesonychia. This hypothesis was recently reinforced in a morphological study (Thewissen et al., 2001) that included mesonychians, two archaeocete taxa (Ambuloocetus and Pakicetus) and some extant and fossil artiodactyls. The study of Thewissen et al. (2001) showed a sister group relationship between monophyletic Artiodactyla and monophyletic Cetacea, with Mesonychia as the basal sister group of Artiodactyla/Cetacea, a conclusion consistent with the palaeontological age of Mesonychia relative to that of Artiodactyla and Cetacea. The second hypothesis favours a sister group relationship between Mesonychia and Cetacea with the Mesonychia/Cetacea clade as the sister group of monophyletic Artiodactyla (O’Leary and Geisler, 1999; see also Gatesy and O’Leary, 2001).

Although the position of Mesonychia differs in the two morphological hypotheses, both correspond to a sister group relationship between Cetacea and monophyletic Artiodactyla among extant cetartiodactyls. Thus, both hypotheses can be tested against the current data set. The result of such a test has been included in Table 1, topology (m)(not shown). As evident, both these morphological hypotheses are incongruent with the mitogenomic findings.

Morphological studies have not provided an answer to the question whether mysticetes and odontocetes had separate origins among the archaeocetes (Fordyce and de Muizon, 2001). However, the long common cetacean branch and the short branches separating the five extant cetacean lineages strongly suggest an origin of modern cetaceans from the same archaeocete group (probably the Dorudontidae).

The limbs of Ambulocetus constitute somewhat of an evolutionary enigma. As evident in Thewissen et al.’s (1994) paper, Ambulocetus has very large hind limbs compared to its forelimbs, a difference that is less pronounced in later silhouette drawings of the animal. It is nevertheless evident that evolution from the powerful hindlimbs of Ambulocetus to their rudimentation in archaeocetes constitutes a remarkable morphological reversal if Ambulocetus is connected to the cetacean branch after the separation of the hippopotamid and cetacean lineages.

For natural reasons, systematic schemes have traditionally been based on external morphological characteristics. The rates of morphological and molecular evolution are rarely (if ever) strictly correlated, however, and this may give rise to inconsistency between traditional systematics and molecular findings. The emerging consensus that the order Cetacea resides within another traditional order, Artiodactyla, makes apparent the incongruity in cetartiodactyl nomenclature (Graur and Higgins, 1994). In this instance, a possible solution for maintaining reasonable consistency between nomenclature and phylogeny would be to recognize Cetartiodactyla as an order with three suborders: Suina, Tylopoda and Cetruminantia. According to such a scheme, Cetacea would (together with the Hippopotamidae) constitute a parvorder within the infraorder Cetancodonta.

Cytochrome b and Bayesian inference of whale phylogeny

Laura May-Collado, Ingi Agnarsson
Molecular Phylogenetics and Evolution 38 (2006) 344–354

In the mid 1990s cytochrome b and other mitochondrial DNA data reinvigorated cetacean phylogenetics by proposing many novel

and provocative hypotheses of cetacean relationships. These results sparked a revision and reanalysis of morphological datasets, and the collection of new nuclear DNA data from numerous loci. Some of the most controversial mitochondrial hypotheses have now become benchmark clades, corroborated with nuclear DNA and morphological data; others have been resolved in favor of more traditional views. That major conflicts in cetacean phylogeny are disappearing is encouraging. However, most recent papers aim specifically to resolve higher-level conflicts by adding characters, at the cost of densely sampling taxa to resolve lower-level relationships. No molecular study to date has included more than 33 cetaceans. More detailed molecular phylogenies will provide better tools for evolutionary studies. Until more genes are available for a high number of taxa, can we rely on readily available single gene mitochondrial data? Here, we estimate the phylogeny of 66 cetacean taxa and 24 outgroups based on Cytb sequences. We judge the reliability of our phylogeny based on the recovery of several deep-level benchmark clades. A Bayesian phylogenetic analysis recovered all benchmark clades and for the Wrst time supported Odontoceti monophyly based exclusively on analysis of a single mitochondrial gene. The results recover the monophyly, with the exception of only one taxa within Cetacea, and the most recently proposed super- and subfamilies. In contrast, parsimony never recovered all benchmark clades and was sensitive to a priori weighting decisions. These results provide the most detailed phylogeny of Cetacea to date and highlight the utility of both Bayesian methodology in general, and of Cytb in cetacean phylogenetics. They furthermore suggest that dense taxon sampling, like dense character sampling, can overcome problems in phylogenetic reconstruction.

Some long standing debates are all but resolved: our understanding of deeper level cetacean phylogeny has grown strong. However, the strong focus of most recent studies, aiming specifically to resolve these higher level conflicts by adding mostly characters rather than taxa, has left our understanding of lower level relationships among whale species lagging behind. Mitogenomic data, for example, is available only for 16 cetacean species, and no molecular study to date has included more than 33 cetaceans. It seems timely to focus on more detailed (genus, and species level) molecular phylogenies. These will provide better tools for detailed evolutionary studies, and are necessary to test existing morphological phylogenetic hypotheses, and current cetacean classification.

We judge the reliability of our phylogeny based on the recovery of the previously mentioned benchmark clades, in addition to the less controversial clades Perissodactyla, Euungulata (sensu Waddell et al., 2001; Perissodactyla+ Cetartiodactyla), Cetacea, and Mysticeti. Because Cytb is thought to be most reliable at lower taxonomic levels (due to high substitution rates), recovering ‘known’ deeper clades gives credibility to these new findings which have not been addressed by studies using few taxa. We compare the performance of Bayesian analyses versus parsimony under four different models, and briefly examine the sensitivity of the results to taxon sampling. We use our results to discuss agreement and remaining conflict in cetacean phylogenetics, and provide comments on current classification.

The Bayesian analysis recovered all seven benchmark clades. Support for five of the benchmark clades is high (100 posterior probabilities) but rather low for Cetancodonta (79) and marginal for the monophyly of Odontoceti. The analysis also recovered all but one family level, and most sub- and superfamily level cetacean taxa. The results broadly corroborate current cetacean classiffcation, while also pointing to some lower-level groups that may need redefinition.

Many recent cetacean phylogenetic studies include relatively few taxa, in part due to a focus on generating more characters to resolve higher level phylogenetics. While addressing crucial questions and providing the backbone for lower level phylogenies, such studies have limited utility for classification, and for comparative evolutionary studies. In some cases sparse taxon sampling may also confound the results. Of course, taxon sampling is usually simply constrained by the availability of character data, but for some reason many studies have opted to include only one, or a few outgroup taxa, even if many are available.

We find that as long as outgroup taxon sampling was extensive, Bayesian analyses of Cytb recovered all the a priori identified benchmark clades. When only a few outgroups were chosen, however, the Bayesian analysis negated Odontoceti monophyly, as have many previous parsimony analyses of mitochondrial DNA. Furthermore, in almost every detailed comparison possible our results mirror the findings O’Leary et al. (2004), the most ‘character-complete’ (but including relatively few cetacean taxa) analysis to date (37,000 characters from morphology, SINE, and 51 gene fragments). This result gives credibility to our findings, including previously untested lower level clades.

  • Monophyly and placement of Mysticeti (baleen whales).
  • Monophyly of Odontoceti (toothed whales)
  • Delphinoids
  • River Dolphins
  • Beaked and sperm whales

A major goal of phylogenetics is a phylogeny of life (i.e., many taxa), based on multiple lines of evidence (many characters of many types). However, when phylogenies based on relatively few characters can be judged reliable based on external evidence (taxonomic congruence with other phylogenies using many characters, but few taxa), they seem like very promising and useful ‘first guess’ hypotheses. The evolution of sexual dimorphism, echolocation, social behavior, and whistles and other communicative signals, and major ecological shifts (e.g., transition to fresh water) are among the numerous interesting questions in cetacean biology that this phylogeny can help answer.

Deep-diving sea lions exhibit extreme bradycardia in long duration dives

Birgitte I. McDonald1, and Paul J. Ponganis
The Journal of Experimental Biology (2014) 217, 1525-1534 http://dx.doi.org:/10.1242/jeb.098558

Heart rate and peripheral blood flow distribution are the primary determinants of the rate and pattern of oxygen store utilization and ultimately breath-hold duration in marine endotherms. Despite this, little is known about how otariids (sea lions and fur seals) regulate heart rate (fH) while diving. We investigated dive fH in five adult female California sea lions (Zalophus californianus) during foraging trips by instrumenting them with digital electrocardiogram (ECG) loggers and time depth recorders. In all dives, dive fH (number of beats/duration; 50±9 beats min−1) decreased compared with surface rates (113±5 beats min−1), with all dives exhibiting an instantaneous fH below resting (<54 beats min−1) at some point during the dive. Both dive fH and minimum instantaneous fH significantly decreased with increasing dive duration. Typical instantaneous fH profiles of deep dives (>100 m) consisted of:

(1) an initial rapid decline in fH resulting in the lowest instantaneous fH of the dive at the end of descent, often below 10 beats min−1 in dives longer than 6 min in duration;
(2) a slight increase in fH to ~10–40 beats min−1 during the bottom portion of the dive; and
(3) a gradual increase in fH during ascent with a rapid increase prior to surfacing.

Thus, fH regulation in deep-diving sea lions is not simply a progressive bradycardia. Extreme bradycardia and the presumed associated reductions in pulmonary and peripheral blood flow during late descent of deep dives should

(a) contribute to preservation of the lung oxygen store,
(b) increase dependence of muscle on the myoglobin-bound oxygen store,
(c) conserve the blood oxygen store and
(d) help limit the absorption of nitrogen at depth.

This fH profile during deep dives of sea lions may be characteristic of deep-diving marine endotherms that dive on inspiration as similar fH profiles have been recently documented in the emperor penguin, another deep diver that dives on inspiration.

The resting ƒH measured in this study (54±6 beats min−1) was lower than predicted for an animal of similar size (~80 beats min−1 for an 80 kg mammal). In part, this may be due to the fact that the sea lions were probably sleeping. The resting ƒH in our study was also lower than previous measurements in captive juvenile California sea lions (87±17 beats min−1, average mass 30 kg)  and wild Antarctic fur seals (78±5 beats min−1, body mass 30–50 kg). However, we found a significant negative relationship between mass and resting ƒH even with our small sample size of five sea lions (resting ƒH = –0.58 Mb +100.26, r2=0.81, F1,3=12.37, P=0.039). For a 30 kg sea lion, this equation predicts a resting ƒH of 83 beats min−1, which is similar to what was measured previously in juvenile sea lions, suggesting this equation may be useful in estimating resting ƒH in sea lions.

The sea lions exhibited a distinct sinus arrhythmia fluctuating between a minimum of 42±9 and a maximum of 87±12 beats min−1, comparable to the sinus arrhythmias described in other diving birds and mammals, including sea lions. The minimum instantaneous ƒH during the sinus arrhythmia was similar to the mean minimum ƒH in dives less than 3 min (37±7 beats min−1), indicating that in dives less than 3 min (estimated cADL), ƒH only decreased to levels observed during exhalation at rest. This is consistent with observations in emperor penguins and elephant seals, where it was proposed that in dives shorter than the aerobic dive limit (ADL) the reduction in ƒH is regulated by a mechanism of cardiorespiratory control similar to that governing the respiratory sinus arrhythmia, with a further reduction only occurring in dives longer than the ADL.

Fig. 3. (not shown) Instantaneous fH and dive depth profiles of a California sea lion (CSL12_2). Data are from (A) a short, shallow dive (1.3 min, 45 m), (B) a mid-duration dive (4.8 min, 239 m) and (C) a long-duration dive (8.5 min, 305 m). Minimum instantaneous fH reached 37 beats min−1 in the short dive
(A) 19 beats min−1 in the mid-duration dive
(B) and 7 beats min−1 in the long duration dive
(C) Prominent features typical of mid- and long-duration dives include

  • a surface interval tachycardia (pre- and post-dive);
  • a steady rapid decrease in fH during initial descent;
  • a gradual decline in fH towards the end of descent with the lowest fH of the dive at the end of descent;
  • a slight increase and sometimes variable fH during the bottom portion of the dive; and
  • a slow increase in fH during ascent,
  • often ending in a rapid increase just before surfacing.

We obtained the first diving ƒH data from wild sea lions on natural foraging trips, demonstrating how they regulate ƒH over a range of dive durations. Sea lions always decreased dive ƒH from surface ƒH values; however, individual sea lions exhibited different dive ƒH, accounting for a significant amount of the variation in the relationship between dive duration and ƒH (intra-individual correlation: 75–81%)). The individual differences in dive ƒH exhibited in this study suggest that different dive capacities of individual sea lions may partially account for the range of dive strategies exhibited in a previous study (Villegas-Amtmann et al., 2011). Despite the individual differences in ƒH, the pattern of the dive ƒH response was similar in all the sea lions. As predicted, sea lions only consistently displayed a true bradycardia on mid- to long- duration dives (>4 min) (Fig. 5A). Additionally, as seen in freely diving phocids, dive ƒH and minimum ƒH were negatively related to dive duration, with the longest duration dives having the lowest dive ƒH and displaying the most intense bradycardia, often below 10 beats min−1 (Fig. 5A,B).

Profiles of mean fH at 10 s intervals of dives

Profiles of mean fH at 10 s intervals of dives

Fig 4.  Profiles of mean fH at 10 s intervals of dives for (A) six duration categories and (B) five depth categories. Standard error bars are shown. Data were pooled from 461 dives performed by five sea lions. The number of dives in each category and the number of sea lions performing the dives in each category are provided in the keys.

The mild bradycardia and the dive ƒH profiles observed in the shorter duration dives (<3 min) were similar to those observed in trained juvenile California sea lions and adult Stellar sea lions, but much more intense than ƒH observed in freely diving Antarctic fur seals. Surprisingly, although dive ƒH of trained Steller sea lions was similar, Steller sea lions regularly exhibited lower minimum ƒH, with minimum ƒH almost always less than 20 beats min−1 in dives less than 2 min in duration. In the wild, California sea lions rarely exhibited a minimum ƒH less than 20 beats min−1 in similar duration dives (Fig. 5B), suggesting greater blood oxygen transport during these natural short-duration dives.

Fig. 5. (not shown)  fH decreases with increasing dive duration. Dive duration versus (A) dive fH (total number of beats/dive duration), (B) minimum instantaneous fH and (C) bottom fH (total beats at bottom of dive/bottom time) for California sea lions (461 dives from five sea lions).

Although California sea lions are not usually considered exceptional divers, they exhibited extreme bradycardia, comparable to that of the best diving phocids, during their deep dives. In dives greater than 6 min in duration, minimum ƒH was usually less than 10 beats min−1 and sometimes as low as 6 beats mins−1 (Fig. 5B), which is similar to extreme divers such as emperor penguins (3 beats min−1), elephant seals (3 beats min−1), grey seals (2 beats min−1) and Weddell seals (<10 beats min−1), and even as low as what was observed in forced submersion studies. Thus, similar to phocids, the extreme bradycardia exhibited during forced submersions is also a routine component of the sea lion’s physiological repertoire, allowing them to perform long-duration dives.

While the degree of bradycardia observed in long dives of California sea lions was similar to the extreme bradycardia observed in phocids, the ƒH profiles were quite different. In general, phocid ƒH decreases abruptly upon submergence. The intensity of the initial phocid bradycardia either remains relatively stable or intensifies as the dive progresses, and does not start to increase until the seal begins its ascent. In contrast, the ƒH profiles of sea lions were more complex, showing a more gradual decrease during descent, with the minimum ƒH of the dive usually towards the end of descent (Figs 3, 6). There was often a slight increase in ƒH during the bottom portion of the dive, and as soon as the sea lions started to ascend, the ƒH slowly started to increase, often becoming irregular during the middle of ascent, before increasing rapidly as the sea lion approached the surface.

Fig. 6. (not shown) Instantaneous fH and dive depth profiles of the longest dive (10.0 min, 385 m) from a California sea lion (CSL12_1). During this dive, instantaneous fH reached 7 beats min−1 and was less than 20 beats min−1 for over 5.5 min. Post-dive fH was high in the first 0.5–1 min after surfacing, but then declined to ~100 beats min−1 towards the end of the surface interval.

Implications for pulmonary gas exchange

The moderate dive ƒH in short, shallow dives compared with the much slower ƒH of deep long-duration dives suggests more pulmonary blood flow and greater potential for reliance on lung O2. Most of these dives were to depths of less than 100 m (well below the estimated depth of lung collapse near 200 m), so maintenance of a moderate ƒH during these dives may allow sea lions to maximise use of the potentially significant lung O2 stores (~16% of total body O2 stores) throughout the dive. This is supported by venous blood O2 profiles, where, occasionally, there was no decrease in venous blood O2 between the beginning and end of the dive; this can only occur if pulmonary gas exchange continues throughout the dive. Greater utilization of the lung O2 store in sea lions is consistent with higher dive ƒH in other species that both dive on inspiration and typically perform shallow dives (dolphins, porpoises, some penguin species), and in deeper diving species when they perform shallow dives (emperor penguins).

In deeper dives of sea lions, although ƒH was lower and bradycardia more extreme, the diving ƒH profiles suggest that pulmonary gas exchange is also important. In long-duration dives, even though ƒH started to decrease upon or shortly after submergence, the decrease was not as abrupt as in phocids. Additionally, in long deep dives, despite having overall low dive ƒH, there were more heart beats before resting ƒH was reached compared with short, shallow dives. In dives less than 3 min in duration, there were ~10–15 beats until instantaneous ƒH reached resting values. In longer duration dives (>3 min), there were usually ~30–40 beats before instantaneous ƒH reached resting values. We suggest the greater number of heart beats early in these deeper dives enables more gas exchange and blood O2 uptake at shallow depths, thus allowing utilisation of the postulated larger respiratory O2 stores in deeper dives The less abrupt decline in ƒH we observed in sea lions is similar to the more gradual declines documented in emperor penguins and porpoises, where it has also been proposed that the gradual decrease in ƒH allows them to maximise pulmonary gas exchange at shallower depths. However, as sea lions swam deeper, ƒH decreased further (Figs 3, 6), and by 200 m depth (the approximate depth of lung collapse, instantaneous ƒH was 14 beats min−1. Such an extreme decline in ƒH in conjunction with increased pulmonary shunting due to lung compression at greater depths will result in minimization of both O2 and N2 uptake by blood, even before the depth of full lung collapse (100% pulmonary shunt) is reached.

Implications for blood flow

ƒH is often used as a proxy to estimate blood flow and perfusion during diving because of the relative ease of its measurement. This is based on the assumption that stroke volume does not change during diving in sea lions, and, hence, changes in ƒH directly reflect changes in cardiac output. As breath-hold divers maintain arterial pressure while diving, changes in cardiac output should be associated with changes in peripheral vascular resistance and changes in blood flow to tissues. In Weddell seals, a decrease in cardiac output of ~85% during forced submersions resulted in an 80–100% decrease in tissue perfusion in all tissues excluding the brain, adrenal glands and lung. Sea lions exhibited extremely low instantaneous ƒH values that often remained low for significant portions of the dive (Figs 4, 6), suggesting severe decreases in tissue perfusion in dives greater than 5 min in duration. In almost all dives greater than 6 min in duration, instantaneous ƒH reached 10 beats min−1, and stayed below 20 beats min−1 for more than a minute. At a ƒH of 20 beats min−1, cardiac output will be ~36% of resting cardiac output and only about 18% of average surface cardiac output. At these levels of cardiac suppression, most of this flow should be directed towards the brain and heart.


We successfully obtained diving ƒH profiles from a deep-diving otariid during natural foraging trips. We found that

(1) ƒH decreases during all dives, but true and more intense bradycardia only occurred in longer duration dives and
(2) in the longest duration dives, ƒH and presumed cardiac output were as low as 20% of resting values.

We conclude that, although initial high ƒH promotes gas exchange early in deep dives, the extremely low ƒH in late descent of deep dives (a) preserves lung O2, (b) conserves blood O2, (c) increases the dependence of muscle on myoglobin-bound O2 and (d) limits N2 absorption at depth. This ƒH profile, especially during the late descent/early bottom phase of deep dives is similar to that of deep-diving emperor penguins, and may be characteristic of deep diving endotherms that dive on inspiration.

Dive duration was the fixed effect in all models, and to account for the lack of independence caused by having many dives from the same individual, individual (sea lion ID) was included as a random effect. Covariance and random effect structures of the full models were evaluated using Akaike’s information criterion (AIC) and examination of residual plots. AICs from all the tested models are presented with the best model in bold.

Additionally, dives were classified as short-duration (less than 3 min, minimum cADL), mid-duration (3–5 min, range of cADLs) or long-duration (>5 min) dives. Differences in pre-dive ƒH, dive ƒH, minimum ƒH, post-dive ƒH, and heart beats to resting between the categories were investigated using mixed effects ANOVA, followed by post hoc Tukey tests. In all models, dive duration category was the fixed effect and individual (sea lion ID) was included as a random effect. Model fit was accessed by examination of the residuals. All means are expressed ±s.d. and results of the Tukey tests were considered significant at P<0.05. Statistical analysis was performed in R.

Investigating Annual Diving Behaviour by Hooded Seals (Cystophora cristata) within the Northwest Atlantic Ocean

Julie M. Andersen, Mette Skern-Mauritzen, Lars Boehme
PLoS ONE 8(11): e80438. http://dx.doi.org:/10.1371/journal.pone.0080438

With the exception of relatively brief periods when they reproduce and molt, hooded seals, Cystophora cristata, spend most of the year in the open ocean where they undergo feeding migrations to either recover or prepare for the next fasting period. Valuable insights into habitat use and diving behavior during these periods have been obtained by attaching Satellite Relay Data Loggers (SRDLs) to 51 Northwest (NW) Atlantic hooded seals (33 females and 18 males) during icebound fasting periods (200422008). Using General Additive Models (GAMs) we describe habitat use in terms of First Passage Time (FPT) and analyze how bathymetry, seasonality and FPT influence the hooded seals’ diving behavior described by maximum dive depth, dive duration and surface duration. Adult NW Atlantic hooded seals exhibit a change in diving activity in areas where they spend .20 h by increasing maximum dive depth, dive duration and surface duration, indicating a restricted search behavior. We found that male and female hooded seals are spatially segregated and that diving behavior varies between sexes in relation to habitat properties and seasonality. Migration periods are described by increased dive duration for both sexes with a peak in May, October and January. Males demonstrated an increase in dive depth and dive duration towards May (post-breeding/pre-molt) and August–October (post-molt/pre-breeding) but did not show any pronounced increase in surface duration. Females dived deepest and had the highest surface duration between December and January (post-molt/pre-breeding). Our results suggest that the smaller females may have a greater need to recover from dives than that of the larger males. Horizontal segregation could have evolved as a result of a resource partitioning strategy to avoid sexual competition or that the energy requirements of males and females are different due to different energy expenditure during fasting periods.

Novel locomotor muscle design in extreme deep-diving whales

P. Velten, R. M. Dillaman, S. T. Kinsey, W. A. McLellan and D. A. Pabst
The Journal of Experimental Biology 216, 1862-1871

Most marine mammals are hypothesized to routinely dive within their aerobic dive limit (ADL). Mammals that regularly perform deep, long-duration dives have locomotor muscles with elevated myoglobin concentrations that are composed of predominantly large, slow-twitch (Type I) fibers with low mitochondrial volume densities (Vmt). These features contribute to extending ADL by increasing oxygen stores and decreasing metabolic rate. Recent tagging studies, however, have challenged the view that two groups of extreme deep-diving cetaceans dive within their ADLs. Beaked whales (including Ziphius cavirostris and Mesoplodon densirostris) routinely perform the deepest and longest average dives of any air-breathing vertebrate, and short-finned pilot whales (Globicephala macrorhynchus) perform high-speed sprints at depth. We investigated the locomotor muscle morphology and estimated total body oxygen stores of several species within these two groups of cetaceans to determine whether they

(1) shared muscle design features with other deep divers and
(2) performed dives within their calculated ADLs.

Muscle of both cetaceans displayed high myoglobin concentrations and large fibers, as predicted, but novel fiber profiles for diving mammals. Beaked whales possessed a sprinterʼs fiber-type profile, composed of ~80% fast-twitch (Type II) fibers with low Vmt. Approximately one-third of the muscle fibers of short-finned pilot whales were slow-twitch, oxidative, glycolytic fibers, a rare fiber type for any mammal. The muscle morphology of beaked whales likely decreases the energetic cost of diving, while that of short-finned pilot whales supports high activity events. Calculated ADLs indicate that, at low metabolic rates, both beaked and short-finned pilot whales carry sufficient onboard oxygen to aerobically support their dives.

Serial cross-sections of the m. longissimus dorsi of Mesoplodon densirostris

Serial cross-sections of the m. longissimus dorsi of Mesoplodon densirostris

Fig. Serial cross-sections of the m. longissimus dorsi of Mesoplodon densirostris (A–D) and Globicephala macrorhynchus (E–H). Scale bars, 50μm. Muscle sections stained for the alkaline (A,E) and acidic (B,F) preincubations of myosin ATPase were used to distinguish Type I and II fibers. Muscle sections stained for succinate dehydrogenase (C,G) and α-glycerophosphate dehydrogenase (D,H) were used to distinguish glycolytic (gl), oxidative (o) and intermediate (i) fibers.

Previous studies of the locomotor muscles of deep-diving marine mammals have demonstrated that these species share a suite of adaptations that increase onboard oxygen stores while slowing the rate at which these stores are utilized, thus extending ADL. Their locomotor muscles display elevated myoglobin concentrations and are composed predominantly of large Type I fibers. Vmt are also lower in deep divers than in shallow divers or athletic terrestrial species. The results of this study indicate that beaked whales and short-finned pilot whales do not uniformly display these characteristics and that each possesses a novel fiber profile compared with those of other deep divers.

The phylogeny of Cetartiodactyla: The importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies

Ingi Agnarsson, Laura J. May-Collado
Molecular Phylogenetics and Evolution 48 (2008) 964–985

We perform Bayesian phylogenetic analyses on cytochrome b sequences from 264 of the 290 extant cetartiodactyl mammals (whales plus even-toed ungulates) and two recently extinct species, the ‘Mouse Goat’ and the ‘Irish Elk’. Previous primary analyses have included only a small portion of the species diversity within Cetartiodactyla, while a complete supertree analysis lacks resolution and branch lengths limiting its utility for comparative studies. The benefits of using a single-gene approach include rapid phylogenetic estimates for a large number of species. However, single-gene phylogenies often differ dramatically from studies involving multiple datasets suggesting that they often are unreliable. However, based on recovery of benchmark clades—clades supported in prior studies based on multiple independent datasets—and recovery of undisputed traditional taxonomic groups, Cytb performs extraordinarily well in resolving cetartiodactyl phylogeny when taxon sampling is dense. Missing data, however, (taxa with partial sequences) can compromise phylogenetic accuracy, suggesting a tradeoff between the benefits of adding taxa and introducing question marks. In the full data, a few species with a short sequences appear misplaced, however, sequence length alone seems a poor predictor of this phenomenon as other taxa.

The mammalian superorder Cetartiodactyla (whales and eventoed ungulates) contains nearly 300 species including many of immense commercial importance (cow, pig, and sheep) and of conservation interest and aesthetic value (antelopes, deer, giraffe, dolphins, and whales) (MacDonald, 2006). Certain members of this superorder count among the best studied organisms on earth, whether speaking morphologically, behaviorally, physiologically or genetically. Understanding the interrelationships among cetartiodactyl species, therefore, is of obvious importance with equally short sequences were not conspicuously misplaced. Although we recommend awaiting a better supported phylogeny based on more character data to reconsider classification and taxonomy within Cetartiodactyla, the new phylogenetic hypotheses provided here represent the currently best available tool for comparative species-level studies within this group. Cytb has been sequenced for a large percentage of mammals and appears to be a reliable phylogenetic marker as long as taxon sampling is dense. Therefore, an opportunity exists now to reconstruct detailed phylogenies of most of the major mammalian clades to rapidly provide much needed tools for species-level comparative studies.

Our results support the following relationship among the four major cetartiodactylan lineages (((Tylopoda ((Cetancodonta (Ruminantia + Suina))), with variable support. This arrangement has not been suggested previously, to our knowledge (see review in O’Leary and Gatesy, 2008 and discussion).

Relationships among clades within Cetancodonta are identical to those found by May-Collado and Agnarsson (2006).

Within Ruminantia all our analyzes suggest the following relationships among families: (((((Tragulidae((((Antilocapridae(((Giraffidae(( Cervidae(Moschidae + Bovidae))))) with relatively high support, supporting the subdivision of Ruminantia into Tragulina and Pecora.
In the rare cases where our results are inconsistent with benchmark clades, ad hoc explanations seem reasonable. The placement of M. meminna (Tragulidae) within Bovidae is likely an artifact of missing data, although remarkably it is the only conspicuous misplacement of a species across the whole phylogeny at the family level (while three species appear to be misplaced at the subfamily level within Cervidae in the full analysis, see Fig. 5a). This is supported by the fact that the placement of Moschiola receives low support, and the removal of Moschiola prior to analysis increases dramatically the support for clades close to where it nested (not shown, analysis available from authors), suggesting it had a tendency to ‘jump around’. Two other possibilities cannot be ruled out, however. One, that possibly the available sequence in Genbank may be mislabeled. And second, it should be kept in mind that the validity of Tragulidae has never been tested with molecular data including more than two species.

Oxygen and carbon dioxide fluctuations in burrows of subterranean blind mole rats indicate tolerance to hypoxic–hypercapnic stresses

Imad Shams, Aaron Avivi, Eviatar Nevo
Comparative Biochemistry and Physiology, Part A 142 (2005) 376 – 382

The composition of oxygen (O2), carbon dioxide (CO2), and soil humidity in the underground burrows from three species of the Israeli subterranean mole rat Spalax ehrenbergi superspecies were studied in their natural habitat. Two geographically close populations of each species from contrasting soil types were probed. Maximal CO2 levels (6.1%) and minimal O2 levels (7.2%) were recorded in northern Israel in the breeding mounds of S. carmeli in a flooded, poor drained field of heavy clay soil with very high volumetric water content. The patterns of gas fluctuations during the measurement period among the different Spalax species studied were similar. The more significant differentiation in gas levels was not among species, but between neighboring populations inhabiting heavy soils or light soils: O2 was lower and CO2 was higher in the heavy soils (clay and basaltic) compared to the relatively light soils (terra rossa and rendzina). The extreme values of gas concentration, which occurred during the rainy season, seemed to fluctuate with partial flooding of the tunnels, animal digging activity, and over-crowded breeding mounds inhabited by a nursing female and her offspring. The gas composition and soil water content in neighboring sites with different soil types indicated large differences in the levels of hypoxic–hypercapnic stress in different populations of the same species. A growing number of genes associated with hypoxic stress have been shown to exhibit structural and functional differences between the subterranean Spalax and the aboveground rat (Rattus norvegicus), probably reflecting the molecular adaptations that Spalax went through during 40 million years of evolution to survive efficiently in the severe fluctuations in gas composition in the underground habitat.

map of the studied sites

map of the studied sites

Schematic map of the studied sites: S. galili (2n =52): 1— Rehania (chalk); 2— Dalton (basaltic); S. golani (2n =54): 3— Majdal Shams (terra tossa); 4—Masa’ada (basaltic soils); S. carmeli (2n =58): 5— Al-Maker (heavy clay); 6— Muhraqa (terra rossa).

Comparison of gas composition (O2 and CO2) and water content between light and heavy soils inhabited by S. carmeli

Comparison of gas composition (O2 and CO2) and water content between light and heavy soils inhabited by S. carmeli

Comparison of gas composition (O2 and CO2) and water content between light and heavy soils inhabited by S. carmeli, Al-Maker (heavy soil) and Muhraqa (light soil). AverageTSD of measurements in the burrows of approximately 10 animals at a given date is presented. **p <0.01, T-test and Mann– Whitney test).

Subterranean mammals, which live in closed underground burrow systems, experience an atmosphere that is different from the atmosphere above-ground. Gas exchange between these two atmospheres depends on diffusion through the soil, which in turn, depends on soil particle size, water content, and burrow depth. Heavy soils (clay and basaltic), hold water and have little air space for gas diffusion. A large deviation from external gas composition is found in the burrows of Spalax living in these soil types. The maximal measured concentration of CO2 was 6.1% in Spalax breeding mounds, which is one of the highest concentrations among studied mammals in natural conditions. At the same time 7.2% O2 was measured in water saturated heavy clay soil

seasonal variation from August to March in mean O2, CO2, and soil water content

seasonal variation from August to March in mean O2, CO2, and soil water content

Example of seasonal variation from August to March in mean O2, CO2, and soil water content (VWC) in the Al-Maker population (2n =58, heavy soil). Values are presented as mean TSD.

In this study new data were presented for a wild mammal that survives in an extreme hypoxic–hypercapnic environment. Interestingly, the very low concentrations of O2 experienced by Spalax are correlated with the expression pattern of hypoxia related genes.  So far, we have shown higher and longer-term mRNA expression of erythropoietin, the main factor that regulates the level of circulating red blood cells, in subterranean Spalax compared to the above-ground rat in response to hypoxic stress, as well as differences in the response of erythropoietin to hypoxia in different populations of Spalax experiencing different hypoxic stress in nature. We also demonstrated that erythropoietin pattern of expression is different in Spalax than in Rattus throughout development, a pattern suggesting more efficient hypoxic tolerance in Spalax starting as early as in the embryonic stages. Furthermore, vascular endothelial growth factor (VEGF), which is a critical angiogenic factor that responds to hypoxia, is constitutively expressed at maximal levels in Spalax muscles, the most energy consuming tissue during digging. This level is 1.6-fold higher than in Rattus muscles and is correlated with significantly higher blood vessel concentration in the Spalax muscles compared to the Rattus muscles. Likewise, myoglobin the globin involved in oxygen homeostasis in skeletal muscles, exhibits different expression pattern under normoxia and in response to hypoxia in Spalax muscles compared to rat muscles as well as between different populations of Spalax exposed to different hypoxic stress in nature (unpublished results). Similarly, neuroglobin, a brain-specific globin involved in reversible oxygen binding, i.e., presumably in cellular homeostasis, is expressed differently in the Spalax brain compared to Rattus brain. Like erythropoietin and myoglobin also neuroglobin is expressed differently in Spalax populations experiencing different oxygen supply (unpublished results). Furthermore, Spalax p53 harbors two amino acid substitutions in its binding domain, which are identical to mutations found in p53 of human cancer cells. These substitutions endow Spalax p53 with several-fold higher activation of cell arrest and DNA repair genes compared to human p53 and favor activation of DNA repair genes over apoptotic genes. The study of specific tumoral variants indicates that such preference of growth arrest over apoptosis possibly results as a response to the hypoxic environmental stress known in tumors. Differences in the structure of other molecules related to homeostasis, namely, hemoglobin, haptoglobin (Nevo, 1999), and cytoglobin (unpublished) were also observed in Spalax.

Stress, adaptation, and speciation in the evolution of the blind mole rat, Spalax, in Israel

Eviatar Nevo
Molecular Phylogenetics and Evolution 66 (2013) 515–525

Environmental stress played a major role in the evolution of the blind mole rat superspecies Spalax ehrenbergi, affecting its adaptive evolution and ecological speciation underground. Spalax is safeguarded all of its life underground from aboveground climatic fluctuations and predators. However, it encounters multiple stresses in its underground burrows including darkness, energetics, hypoxia, hypercapnia, food scarcity, and pathogenicity. Consequently, it evolved adaptive genomic, proteomic, and phenomic complexes to cope with those stresses. Here I describe some of these adaptive complexes, and their theoretical and applied perspectives. Spalax mosaic molecular and organismal evolution involves reductions or regressions coupled with expansions or progressions caused by evolutionary tinkering and natural genetic engineering. Speciation of Spalax in Israel occurred in the Pleistocene, during the last 2.00–2.35 Mya, generating four species associated intimately with four climatic regimes with increasing aridity stress southwards and eastwards representing an ecological speciational adaptive trend: (Spalax golani, 2n = 54?S. galili, 2n = 52?S. carmeli, 2n = 58?S. judaei, 2n = 60). Darwinian ecological speciation occurred gradually with relatively little genetic change by Robertsonian chromosomal and genic mutations. Spalax genome sequencing has just been completed. It involves multiple adaptive complexes to life underground and is an evolutionary model to a few hundred underground mammals. It involves great promise in the future for medicine, space flight, and deep-sea diving.

Stress is a major driving force of evolution (Parsons, 2005; Nevo, 2011). Parsons defined stress as the ‘‘environmental factor causing potential injurious changes to biological systems with a potential for impacts on evolutionary processes’’. The global climatic transition from the middle Eocene to the early Oligocene (45–35 Ma = Million years ago) led to extensive convergent evolution underground of small subterranean mammals across the planet (Nevo, 1999; Lacey et al., 2000; Bennett and Faulkes, 2000; Begall et al., 2007). The subterranean ecotope provided small mammals with shelter from predators and extreme aboveground climatic stressful fluctuations of temperature and humidity. However, they had to evolve genomic adaptive complexes for the immense underground stresses of darkness, energy for burrowing in solid soil, low productivity and food scarcity, hypoxia, hypercapnia, and high infectivity. These stresses have been described in Nevo (1999, 2011) and Nevo et al. (2001); and Nevo list of Spalax publication at http://evolution.haifa.ac.il with many cited references relevant to these stresses).

blind subterranean mole rat of the Spalax ehrenbergi superspecies

blind subterranean mole rat of the Spalax ehrenbergi superspecies

The blind subterranean mole rat of the Spalax ehrenbergi superspecies in Israel. An extreme example of adaptation to life underground

Circadian rhythm and genes

adaptive circadian genes. We identified the circadian rhythm of Spalax
(Nevo et al., 1982) and described, cloned, sequenced, and expressed several circadian genes in Spalax. These include Clock, MOP3, three Period (Per), and cryptochromes (Avivi et al., 2001, 2002, 2003). The Spalax circadian genes are differentially conserved, yet characterized by a significant number of amino acid substitutions. The glutamine-rich area of Clock, which is assumed to function in circadian rhythmicity, is expanded in Spalax compared with that of mice and humans and is different in amino acid composition from that of rats. All three Per genes of Spalax oscillate with a periodicity of 24 h in the suprachaismatic nucleus, eye, and Harderian gland and are expressed in peripheral organs. Per genes are involved in clock resetting. Spalax Per 3 is unique in mammals though its function is still unresolved. The Spalax Per genes contribute to the unique adaptive circadian rhythm to life underground. The cryptochrome (Cry) genes, found in animals and plants, act both as photoreceptors and as ingredients of the negative feedback mechanism of the biological Clock. The CRY 1 protein is significantly closer to the human homolog than to that of mice, as was also shown in parts of the immunogenetic system. Both Cry 1 and Cry 2 mRNAs were found in the SCN, eye, harderian gland, and in peripheral tissues. Remarkably, the distinctly hypertrophied harderian gland is central in Spalax’s unique underground circadian rhythmicity (Pevet et al., 1984).

  • Spalax eye mosaic evolution
  • Gene expression in the eye of Spalax
  • Brain evolution in Spalax to underground stresses
  • Spalax: four species in Israel

The morphological, physiological, and behavioral Spalax eye patterns are underlain by gene expression representing regressive and progressive associated transcripts. Regressive transcripts involve B-2 microglobulin, transketolase, four keratins, alpha enolase, and different heat shock proteins. Several proteins may be involved in eye degeneration. These include heat shock protein 90alpha (hsp90alpha), found also in the blind fish Astyanax mexicanus, two transcripts of programmed cell death proteins, oculospanin, and peripherin 2, both belonging to the Tetraspanin family, in which 60 different mutations cause eye degeneration in humans. Several progressive transcripts in the Spalax eye are found in the retina of many mammals involving gluthatione, peroxidase 4, B spectrin, and Ankyrin; the last two characterize rod cells in the retina. Some transcripts are involved in metabolic processing of retinal, a vertebrate key component in phototransduction, and a relative of vitamin A.

cross section of the developing eye of the mole rat

cross section of the developing eye of the mole rat

Light micrographs showing cross section of the developing eye of the mole rat Spalax ehrenbergi. (A) Optic cup and lens vesicle initially develop normally (x100). (B) Eye at a later embryonic stage. Note appearance of iris-ciliary body rudiment (arrows), and development of the lens nucleus (L). ON, optic nerve (x100). (C) Eye at a still later fetal stage. Note massive growth of the iris-ciliary body complex colobomatous opening (arrow) (x100). (D) Early postnatal stage. The iris-ciliary body complex completely fills the chamber. The lens is vascularized and vacuolated (x100). (E) Adult eye. Eyelids are completely closed and pupil is absent. Note atrophic appearance of the optic disc region (arrow) (x65). (F) Higher magnification of the adult retina. The different retinal layers are retained: PE, pigment epithelium: RE, receptor layer; ON, outer nuclear layer: IN, inner nuclear layer; GC, ganglion cell layer (x500) (from Sanyal et al., 1990, Fig. 1).

The brains of subterranean mammals underwent dramatic evolution in accordance with underground stresses for digging and photoperiodic perception associated with vibrational, tactile, vocal, olfactory, and magnetic communication systems replacing sight, as is seen in Spalax. The brain of Spalax is twice as large as that of the laboratory rat of the same body size. The somatosensory region in the isocortex of Spalax is 1.7 times, the thalamic nuclei 1.3 times, and the motor cortex 3.1 times larger than in the sighted laboratory rat Rattus norvegicus matched to body size.

The ecological stress determinant in Spalax brain evolution is highlighted by the four species of the Spalax ehrenbergi superspecies in Israel. They differentiated chromosomally (by means of Robertsonian mutations and fission), allopatrically, and clinally southwards into four species associated with different climatic regimes, following the gradient of increasing aridity stress and decreasing predictability southwards towards the desert: Spalax galili (2n = 52) ->S. golani (2n = 54)->S. carmeli (2n = 58)->S. judaei (2n = 60), and eastwards S. galili ->S. golani (2n = 52–>54) (Fig. 2). This chromosomal speciation trend southwards is associated with the regional aridity stress southwards (and eastwards) in Israel, budding new species adapted genomically, proteomically, and phenomically (i.e., in morphology, physiology, and behavior) to increasing stresses of higher solar radiation, temperature, and drought southwards (Nevo, 1999; Nevo et al., 2001; Nevo
list of Spalax at http://evolution.haifa.ac.il). A uniquely recent discovery of incipient sympatric ecological speciation at a microscale in Spalax triggered by local stresses occurs within Spalax galili.

retinal input to primary visual structures in Spalax

retinal input to primary visual structures in Spalax

Relative degree of retinal input to primary visual structures in Spalax, hamster, rat, and Spalacopus cyanus (South American Octodontidae, ‘‘coruro’’). These rodents are of similar body size (120–140 g). B. Relative degree of change in the proportions of retinal input to different primary visual structures in Spalax compared with measures obtained in other rodents. A relative progressive development in Spalax is seen in structures involved in photoperiodic and neuroendocrine functions (SCN, BNST).The main regressive feature is the drastic relative reduction of retinal input to the superior colliculus. The main regressive feature is the drastic reduction of retinal input to the superior colliculus. The relative size of other visual structures in Spalax is modified compared to that of the other species. c. Comparison of the absolute size (volume, mm3 x 10-4) of visual structures in Spalax and other rodents. The size of the SCN is equivalent in all species. The vLGN and dLGN are reduced by 87–93% in Spalax. The retino-recipient layers of the superior colliculus are reduced by 97%. Abbreviations: SCN: suprachiasmatic nucleus; BNST: bed nucleus of the stria terminalis; dLGN: dorsal lateral geniculate nucleus; SC: superior colliculus [From Cooper et al., 1993 (Fig 3)].

Subterranean life has a high energetic cost if an animal has to burrow in order to obtain its food. For a 150 g Thomomys bottae, burrowing 1 m may be 360–3400 times more expensive energetically than moving the same distance on the surface (Vleck, 1979). Mean rates of oxygen consumption during burrowing at 22 oC are from 2.8 to 7.1 times the RMR. Vleck developed a model examining the energetics of foraging by burrowing and found that, in the desert, Thomomys adjusts the burrow segment length to minimize the cost of burrowing. Since burrowing becomes less economic as body size increases, Vleck (1981) predicted that the maximum possible body size that a subterranean mammal can attain depends on a balance between habitat productivity and the cost of burrowing in local soils. Vleck’s cost of burrowing hypothesis has been verified in multiple cases. Heth (1989) demonstrated longer burrows in the rendzina soil and shorter ones in the terra rossa soil, associating lower productivity in the former for Spalax.

Food is a limiting factor for subterranean mammals. The abundance and distribution of food explain some of the ecological, physiological, and behavioral characteristics of subterranean mammals. In a field test of Spalax foraging strategy, we concluded that Spalax was a generalist due to the constraints of the subterranean ecotope. Restricted foraging time primarily during the winter when soil is wet, and the high energetic investment of tunneling to get to food items is significantly reduced than in summertime.
We also identified a decrease in the basic metabolic rate towards the desert, i.e., economizing energetics. The maintenance of adequate O2 transport in a subterranean mammal confronting hypoxia requires adaptation along the O2 transport system, achieved by increasing the flow of O2 in the convection systems (ventilation and perfusion) and by reduction of oxygen pressure (PO2) gradients at the diffusion barriers (lung blood, blood-tissue (Arieli, 1990). The PO2 gradient between blood capillaries and respiring mitochondria capillaries is large, and any adaptation at this level could be significant for O2 transport. Reduction of diffusion distance in a muscle can be achieved, like in Spalax, by increasing the number of capillaries that surround muscle fiber or by reducing fiber areas.

Geographic distribution in Israel of the four chromosomal species belonging to the S. ehrenbergi superspecies

Geographic distribution in Israel of the four chromosomal species belonging to the S. ehrenbergi superspecies

Geographic distribution in Israel of the four chromosomal species belonging to the S. ehrenbergi superspecies that are separated by narrow hybrid zones (2n = 52, 54, 58, and 60, now named as S. galili, S. golani, S. carmeli, and S. judaei, respectively; see Nevo et al., 2001).

Spalacid evolution, based on mtDNA, is driven by climatic oscillations and stresses. The underground ecotope provided subterranean mammals with shelter from extreme climate (temperature and humidity) fluctuations, and predators. However, they had to extensively and intensively adapt to the multiple underground stresses (darkness, energetic, low productivity and
food scarcity, hypoxia, hypercapnia, and high infectivity). All subterranean mammals, including spalacids as an extreme case, share convergent molecular and organismal adaptations to their shared unique underground ecotope. Evolution underground, as exemplified here in spalacids, led to mosaic molecular and organismal evolutionary syndromes to cope with multiple stresses.

Speciation involves all rates – from gradual to rapid. Subterranean mammals, with the spalacid example discussed above, provide uniquely rich evolutionary global tests of speciation and adaptation, convergence, regression, progression, and mosaic evolutionary processes. Adaptation and speciation underground was one of the most dramatic natural experiments verifying Darwinian evolution.

The Spalax genome sequencing has just been completed. It is being analyzed and will soon be published in 2012. This will be a milestone in understanding how numerous mammals across the globe, who found underground shelter from climatic fluctuations and stresses above ground, cope with the new suite of stresses they encountered underground, demanding a new engineering overhaul on all organizational levels, selecting for adaptive complexes to cope with the new underground stresses. The main current and future challenges are to compare and contrast genome sequences and identify the genomic basis of adaptation and speciation.

This global Cenozoic experiment could answer the following open questions: How heterozygous is the whole genome? How prevalent are retrotransposons and what is their functional role? How many genes are involved in the Spalax genome and how are they regulated? What are the genic and regulatory networks resisting the multiple stresses underground? How much of the Spalax genome is conserved and how much is reorganized to cope with the underground stresses? How is the solitary blind mole rat, Spalax, different from the social naked mole rat Heterocephalus? How are the processes of reduction, expansion, and genetic tinkering and engineering reflected across the genome? How effective is copy number variation in regulation? Is there similarity in the transcriptomes of subterranean mammals? How could we harness the rich genome repertoire of Spalax to revolutionize medicine, especially in the realm of hypoxia tolerance and the related major diseases of the western world, e.g., cancer, stroke, and cardiovascular diseases? What is the phylogenetic origin of Spalax? How much of the Spalax genome represents its phylogenetic roots and how much of coding and noncoding genomic regions are shared with other subterranean mammals across the globe in adapting to life underground?

The Atmospheric Environment of the Fossorial Mole Rat (Spalax Ehrenbergi): Effects of Season, Soil Texture, Rain, Temperature and Activity

  1. Arieli
    Comp Biochen Physiol. 1978; 63A:569-5151. The fossorial mole rat (Spalax ehrenbergi) may inhabit heavy soil with low gas permeability.
  2. Air composition in burrows in heavy soil deviates from atmospheric air more than that of burrows in light soil.
  3. In winter and spring O2 and CO2 concentrations in breeding mounds were 16.5% O2 and 2.5-3x CO2 and the extreme values measured were 14.0% O2 and 4.8% Cot.
  4. Hypoxia and hypercapnia in the burrow develop shortly after rain and when ambient temperature drops.
  5. Composition of the burrows air is influenced by the solubility of CO2 in soil water and by faster penetration of oxygen than outflowing of CO2.

Hypo-osmotic stress-induced physiological and ion-osmoregulatory responses in European sea bass (Dicentrarchus labrax) are modulated differentially by nutritional status

Amit Kumar Sinha, AF Dasan, R Rasoloniriana, N Pipralia, R Blust, G De Boeck
Comparative Biochemistry and Physiology, Part A 181 (2015) 87–99

We investigated the impact of nutritional status on the physiological, metabolic and ion-osmoregulatory performance of European sea bass (Dicentrarchus labrax)when acclimated to seawater (32 ppt), brackishwater (20 and 10 ppt) and hyposaline water (2.5 ppt) for 2 weeks. Following acclimation to different salinities, fish were either fed or fasted (unfed for 14 days). Plasma osmolality, [Na+], [Cl−] and muscle water contentwere severely altered in fasted fish acclimated to 10 and 2.5 ppt in comparison to normal seawater-acclimated fish, suggesting ion regulation and acid–base balance disturbances. In contrast to feed-deprived fish, fed fish were able to avoid osmotic perturbation more effectively. This was accompanied by an increase in Na+/K+-ATPase expression and activity, transitory activation of H+-ATPase (only at 2.5 ppt) and down-regulation of Na+/K+/2Cl− gene expression. Ammonia excretion rate was inhibited to a larger extent in fasted fish acclimated to low salinities while fed fish were able to excrete efficiently. Consequently, the build-up of ammonia in the plasma of fed fish was relatively lower. Energy stores, especially glycogen and lipid, dropped in the fasted fish at low salinities and progression towards the anaerobic metabolic pathway became evident by an increase in plasma lactate level. Overall, the results indicate no osmotic stress in both feeding treatments within the salinity range of 32 to 20 ppt. However, at lower salinities (10–2.5 ppt) feed deprivation tends to reduce physiological, metabolic, ion-osmo-regulatory and molecular compensatory mechanisms and thus limits the fish’s abilities to adapt to a hypo-osmotic environment.

The absence of ion-regulatory suppression in the gills of the aquatic air-breathing fish Trichogaster lalius during oxygen stress

Chun-Yen Huang, Hsueh-Hsi Lin, Cheng-Huang Lin, Hui-Chen Lin
Comparative Biochemistry and Physiology, Part A 179 (2015) 7–16

The strategy for most teleost to survive in hypoxic or anoxic conditions is to conserve energy expenditure, which can be achieved by suppressing energy-consuming activities such as ion regulation. However, an air-breathing fish can cope with hypoxic stress using a similar adjustment or by enhancing gas exchange ability, both behaviorally and physiologically. This study examined Trichogaster lalius, an air-breathing fish without apparent gill modification, for their gill ion-regulatory abilities and glycogen utilization under a hypoxic  treatment. We recorded air-breathing frequency, branchial morphology, and the expression of ion-regulatory proteins (Na+/K+-ATPase and vacuolar-type H+-ATPase) in the 1st and 4th gills and labyrinth organ (LO), and the expression of glycogen utilization (GP, glycogen phosphorylase protein expression and glycogen content) and other protein responses (catalase, CAT; carbonic anhydrase II, CAII; heat shock protein 70, HSP70; hypoxia-inducible factor-1α, HIF-1α; proliferating cell nuclear antigen, PCNA; superoxidase dismutase, SOD) in the gills of T. lalius after 3 days in hypoxic and restricted conditions. No morphological modification of the 1st and 4th gills was observed. The air breathing behavior of the fish and CAII protein expression both increased under hypoxia. Ion-regulatory abilities were not suppressed in the hypoxic or restricted groups, but glycogen utilization was enhanced within the groups. The expression of HIF-1α, HSP70 and PCNA did not vary among the treatments. Regarding the antioxidant system, decreased CAT enzyme activity was observed among the groups. In conclusion, during hypoxic stress, T. lalius did not significantly reduce energy consumption but enhanced gas exchange ability and glycogen expenditure.

The combined effect of hypoxia and nutritional status on metabolic and ionoregulatory responses of common carp (Cyprinus carpio)

Sofie Moyson, HJ Liew, M Diricx, AK Sinha, R Blusta, G De Boeck
Comparative Biochemistry and Physiology, Part A 179 (2015) 133–143

In the present study, the combined effects of hypoxia and nutritional status were examined in common carp (Cyprinus carpio), a relatively hypoxia tolerant cyprinid. Fish were either fed or fasted and were exposed to hypoxia (1.5–1.8mgO2 L−1) at or slightly above their critical oxygen concentration during 1, 3 or 7 days followed by a 7 day recovery period. Ventilation initially increased during hypoxia, but fasted fish had lower ventilation frequencies than fed fish. In fed fish, ventilation returned to control levels during hypoxia, while in fasted fish recovery only occurred after reoxygenation. Due to this, C. carpio managed, at least in part, to maintain aerobic metabolism during hypoxia: muscle and plasma lactate levels remained relatively stable although they tended to be higher in fed fish (despite higher ventilation rates). However, during recovery, compensatory responses differed greatly between both feeding regimes: plasma lactate in fed fish increased with a simultaneous breakdown of liver glycogen indicating increased energy use, while fasted fish seemed to economize energy and recycle decreasing plasma lactate levels into increasing liver glycogen levels. Protein was used under both feeding regimes during hypoxia and subsequent recovery: protein levels reduced mainly in liver for fed fish and in muscle for fasted fish. Overall, nutritional status had a greater impact on energy reserves than the lack of oxygen with a lower hepatosomatic index and lower glycogen stores in fasted fish. Fasted fish transiently increased Na+/K+-ATPase activity under hypoxia, but in general ionoregulatory balance proved to be only slightly disturbed, showing that sufficient energy was left for ion regulation.

The effect of temperature and body size on metabolic scope of activity in juvenile Atlantic cod Gadus morhua L.

Bjørn Tirsgaard, Jane W. Behrens, John F. Steffensen
Comparative Biochemistry and Physiology, Part A 179 (2015) 89–94

Changes in ambient temperature affect the physiology and metabolism and thus the distribution of fish. In this study we used intermittent flow respirometry to determine the effect of temperature (2, 5, 10, 15 and 20 °C) and wet body mass (BM) (~30–460 g) on standard metabolic rate (SMR, mg O2 h−1), maximum metabolic rate (MMR, mg O2 h−1) and metabolic scope (MS, mg O2 h−1) of juvenile Atlantic cod. SMR increased with BM irrespectively of temperature, resulting in an average scaling exponent of 0.87 (0.82–0.92). Q10 values were 1.8–2.1 at temperatures between 5 and 15 °C but higher (2.6–4.3) between 2 and 5 °C and lower (1.6–1.4) between 15 and 20 °C in 200 and 450 g cod. MMR increased with temperature in the smallest cod (50 g) but in the larger cod MMR plateaued between 10, 15 and 20 °C. This resulted in a negative correlation between the optimal temperature for MS (Topt) and BM, Topt being respectively 14.5, 11.8 and 10.9 °C in a 50, 200 and 450 g cod. Irrespective of BM cold water temperatures resulted in a reduction (30–35%) of MS whereas the reduction of MS at warm temperatures was only evident for larger fish (200 and 450 g), caused by plateauing of MMR at 10 °C and above. Warm temperatures thus seem favorable for smaller (50 g) juvenile cod, but not for larger conspecifics (200 and 450 g).

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Prefacing the e-Book Epilogue: Metabolic Genomics and Pharmaceutics

Author and Curator: Larry H. Bernstein, MD, FCAP


Adieu, adieu, adieu …

Sound of Music

Snoopy - Charlie happiness

Snoopy – Charlie happiness

This work has been a coming to terms with my scientific and medical end of career balancing in a difficult time after retiring, but it has been rewarding.  In the clinical laboratories, radiology, anesthesiology, and in pharmacy, there has been some significant progress in support of surgical, gynecological, developmental, medical practices, and even neuroscience directed disciplines, as well as epidemiology over a period of half a century.  Even then, cancer and neurological diseases have been most difficult because the scientific basic research has either not yet uncovered a framework, or because that framework has proved to be multidimensional.  In the clinical laboratory sciences, there has been enormous progress in instrumental analysis, with the recent opening of molecular methods not yet prepared for routine clinical use, which will be a very great challenge to the profession, which has seen the development of large sample volume, multianalite, high-throughput, low-cost support emerging for decades.  The capabilities now underway will also enrrich the the capabilities of the anatomic pathology suite and the capabilities of 3-dimensional radiological examination.  In both pathology and radiology, we have seen the division of the fields into major subspecialties.  The development of the electronic health record had to take lessons from the first developments in the separate developments of laboratory, radiology, and pharmacy health record systems, to which were added, full cardiology monitoring systems.  These have been unintegrated.  This made it difficult to bring forth a suitable patient health record because the information needed to support decision-making by practitioners was in separate “silos”.  The mathematical methods that are being applied to the -OMICS sciences, can be brought to bear on the simplification and amplification of the clinicians’ ability to make decisions with near “errorless” discrimination, still allowing for an element of “art” in carrying out the history, physical examination, and knowledge unique to every patient.

We are at this time opening a very large, complex, study of biology in relationship to the human condition.  This will require sufficient resources to be invested in the development of these for a better society, which I suspect, will go on beyond the life of my grandchildren.  Hopefully, the long-term dangers of climate change will be controlled in that time.  As a society, or as a group of interdependent societies, we have no long term interest in continuing self-destructive behaviors that have predominated in the history of mankind.  I now top off these discussions with some further elucidation of what lies before us.

Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery

Douglas B. Kell and Royston Goodacre
School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
Drug Discovery Today Feb 2014;19(2)  http://dx.doi.org/10.1016/j.drudis.2013.07.014

Metabolism represents the ‘sharp end’ of systems biology,

  • because changes in metabolite concentrations
  • are necessarily amplified relative to
  • changes in the transcriptome, proteome and enzyme activities,
  • which can be modulated by drugs.

To understand such behaviour, we therefore need
(and increasingly have)

  • reliable consensus (community) models of the human metabolic network
  • that include the important transporters.

Small molecule ‘drug’ transporters are in fact metabolite transporters,

  • because drugs bear structural similarities to metabolites known
  • from the network reconstructions and from measurements of the metabolome.

Recon2 represents the present state-of-the-art human metabolic
network reconstruction; it can predict inter alia:

  1. the effects of inborn errors of metabolism;
  2. which metabolites are exometabolites, and
  3. how metabolism varies between tissues and cellular compartments.

Even these qualitative network models are not yet complete. As our
understanding improves so do we recognize more clearly the need for a systems (poly)pharmacology.

Modelling biochemical networks – why we do so
There are at least four types of reasons as to why one would wish to model a biochemical network:

  1. Assessing whether the model is accurate, in the sense that it
    reflects – or can be made to reflect – known experimental facts.
  2. Establishing what changes in the model would improve the
    consistency of its behaviour with experimental observations
    and improved predictability, such as with respect to metabolite
    concentrations or fluxes.
  3. Analyzing the model, typically by some form of sensitivity
    analysis, to understand which parts of the system contribute
    most to some desired functional properties of interest.
  4. Hypothesis generation and testing, enabling one to analyse
    rapidly the effects of manipulating experimental conditions in
    the model without having to perform complex and costly
    experiments (or to restrict the number that are performed).

In particular, it is normally considerably cheaper to perform
studies of metabolic networks in silico before trying a smaller
number of possibilities experimentally; indeed for combinatorial
reasons it is often the only approach possible. Although
our focus here is on drug discovery, similar principles apply to the
modification of biochemical networks for purposes of ‘industrial’
or ‘white’ biotechnology.
Why we choose to model metabolic networks more than

  • transcriptomic or proteomic networks

comes from the recognition – made particularly clear

  • by workers in the field of metabolic control analysis

– that, although changes in the activities of individual enzymes tend to have

  • rather small effects on metabolic fluxes,
  • they can and do have very large effects on metabolite concentrations (i.e. the metabolome).

Modelling biochemical networks – how we do so

Although one could seek to understand the

  1. time-dependent spatial distribution of signalling and metabolic substances within indivi
    dual cellular compartments and
  2. while spatially discriminating analytical methods such as Raman spectroscopy and
    mass spectrometry do exist for the analysis of drugs in situ,
  • the commonest type of modelling, as in the spread of substances in
  • assumes ‘fully mixed’ compartments and thus ‘pools’ of metabolites.

Although an approximation, this ‘bulk’ modelling will be necessary for complex ecosystems such as humans where, in addition to the need for tissue- and cell-specific models, microbial communities inhabit this superorganism and the
gut serves as a source for nutrients courtesy of these symbionts.

Topology and stoichiometry of metabolic networks as major constraints on fluxes
Given their topology, which admits a wide range of parameters for
delivering the same output effects and thereby reflects biological

  • metabolic networks have two especially important constraints that assist their accurate modelling:

(i) the conservation of mass and charge, and
(ii) stoichiometric and thermodynamic constraints.

These are tighter constraints than apply to signalling networks.

New developments in modelling the human metabolic network
Since 2007, several groups have been developing improved but nonidentical models of the human metabolic network at a generalised level and in tissue-specific forms. Following a similar community-driven strategy in Saccharomyces cerevisiae, surprisingly similar to humans, and in Salmonella typhimurium,

we focus in particular on a recent consensus paper that provides a highly curated and semantically annotated model of the human metabolic network, termed

In this work, a substantial number of the major groups active in this area came together to provide a carefully and manually constructed/curated network, consisting of some 1789 enzyme-encoding genes, 7440 reactions and 2626 unique metabolites distributed over eight cellular compartments.  A variety of dead-end metabolites and blocked reactions remain (essentially orphans and widows). But Recon2 was able to

  • account for some 235 inborn errors of metabolism,
  • a variety of metabolic ‘tasks’ (defined as a non-zero flux through a reaction or through a pathway leading to the production of a metabolite Q from a metabolite P).
  • filtering based on expression profiling allowed the construction of 65 cell-type-specific models.
  • Excreted or exometabolites are an interesting set of metabolites,
  • and Recon2 could predict successfully a substantial fraction of those

Role of transporters in metabolic fluxes

The uptake and excretion of metabolites between cells and their macrocompartments

  • requires specific transporters and in the order of one third of ‘metabolic’ enzymes,
  • and indeed of membrane proteins, are in fact transporters or equivalent.

What is of particular interest (to drug discovery), based on their structural similarities, is the increasing recognition (Fig. 3) that pharmaceutical drugs also

  • get into and out of cells by ‘hitchhiking’ on such transporters, and not –

to any significant extent –

  • by passing through phospholipid bilayer portions
    of cellular membranes.

This makes drug discovery even more a problem of systems biology than of biophysics.

role of solute carriers and other transporters in cellular drug uptake

role of solute carriers and other transporters in cellular drug uptake

Two views of the role of solute carriers and other transporters in cellular drug uptake. (a) A more traditional view in which all so-called ‘passive’drug uptake occurs through any unperturbed bilayer portion of membrane that might be present.
(b) A view in which the overwhelming fraction of drug is taken up via solute transporters or other carriers that are normally used for the uptake of intermediary metabolites. Noting that the protein:lipid ratio of biomembranes is typically 3:1 to 1:1 and that proteins vary in mass and density (a typical density is 1.37 g/ml) as does their extension, for example, normal to the ca. 4.5 nm lipid bilayer region, the figure attempts to portray a section of a membrane with realistic or typical sizes and amounts of proteins and lipids. Typical protein areas when viewed normal to the membrane are 30%, membranes are rather more ‘mosaic’ than ‘fluid’ and there is some evidence that there might be no genuinely ‘free’ bulk lipids (typical phospholipid masses are 750 Da) in biomembranes that are uninfluenced by proteins. Also shown is a typical drug: atorvastatin (LipitorW) – with a molecular mass of 558.64 Da – for size comparison purposes. If proteins are modelled as
cylinders, a cylinder with a diameter of 3.6 nm and a length of 6 nm has a molecular mass of ca. 50 kDa. Note of course that in a ‘static’ picture we cannot show the dynamics of either phospholipid chains or lipid or protein diffusion.

‘Newly discovered’ metabolites and/or their roles

To illustrate the ‘unfinished’ nature even of Recon2, which concentrates on the metabolites created via enzymes encoded in the human genome, and leaving aside the more exotic metabolites of drugs and foodstuffs and the ‘secondary’ metabolites of microorganisms, there are several examples of interesting ‘new’ (i.e. more or less recently recognised) human metabolites or roles thereof that are worth highlighting, often from studies seeking biomarkers of various diseases – for caveats of biomarker discovery, which is not a topic that we are covering here, and the need for appropriate experimental design. In addition, classes of metabolites not well represented in Recon2 are oxidised molecules such as those caused by nonenzymatic reaction of metabolites with free radicals such as the hydroxyl radical generated by unliganded iron. There is also significant interest in using methods of determining small molecules such as those in the
metabolome (inter alia) for assessing the ‘exposome’, in other words all the potentially polluting agents to which an
individual has been exposed.

Recently discovered effects of metabolites on enzymes 

Another combinatorial problem reflects the fact that in molecular enzymology it is not normally realistic to assess every possible metabolite to determine whether it is an effector (i.e.activator or inhibitor) of the enzyme under study. Typical proteins are highly promiscuous and there is increasing evidence for the comparative promiscuity of metabolites
and pharmaceutical drugs. Certainly the contribution of individual small effects of multiple parameter changes can have substantial effects on the potential flux through an overall pathway, which makes ‘bottom up’ modelling an inexact science. Even merely mimicking the vivo (in Escherichia coli) concentrations of K+, Na+, Mg2+, phosphate, glutamate, sulphate and Cl significantly modulated the activities of several enzymes tested relative to the ‘usual’ assay conditions. Consequently, we need to be alive to the possibility of many (potentially major) interactions of which we are as yet ignorant. One class of example relates to the effects of the very widespread post-translational modification on metabolic
enzyme activities.

A recent and important discovery (Fig. 4) is that a single transcriptome experiment, serving as a surrogate for fluxes through individual steps, provides a huge constraint on possible models, and predicts in a numerically tractable way and
with much improved accuracy the fluxes to exometabolites without the need for such a variable ‘biomass’ term. Other recent and related strategies that exploit modern advances in ‘omics and network biology to limit the search space in constraint-based metabolic modelling.

Fig 4. Workflow for expression-profile-constrained metabolic flux estimation

  1. Genome-scale metabolic model with gene-protein-reaction relationships
  2. Map absolute gene expression levels to reactions
  3. Maximise correlation between absolute gene expression and metabolic flux
  4. Predict fluxes to exometabolites
  5. Compare predicted with experimental fluxes to exometabolites

Drug Discovery Today

The steps in a workflow that uses constraints based on (i) metabolic network stoichiometry and chemical reaction properties (both encoded in the model) plus, and (ii) absolute (RNA-Seq) transcript expression profiles to enable the
accurate modelling of pathway and exometabolite fluxes. .

Concluding remarks – the role of metabolomics in systems pharmacology

What is becoming increasingly clear, as we recognize that to understand living organisms in health and disease we must treat them as systems, is that we must bring together our knowledge of the topologies and kinetics of metabolic networks with our knowledge of the metabolite concentrations (i.e. metabolomes) and fluxes. Because of the huge constraints imposed on metabolism by reaction stoichiometries, mass conservation and thermodynamics, comparatively few well-chosen ‘omics measurements might be needed to do this reliably (Fig. 4). Indeed, a similar approach exploiting constraints has come to the fore in denovo protein folding and interaction studies.

What this leads us to in drug discovery is the need to develop and exploit a ‘systems pharmacology’ where multiple binding targets are chosen purposely and simultaneously. Along with other measures such as phenotypic screening, and the integrating of the full suite of e-science approaches, one can anticipate considerable improvements in the rate of discovery of safe and effective drugs.

Metabolomics: the apogee of the omics trilogy
Gary J.!Patti, Oscar Yanes and Gary Siuzdak

Metabolites, the chemical entities that are transformed during metabolism, provide a functional readout of cellular biochemistry. With emerging technologies in mass spectrometry, thousands of metabolites can now be
quantitatively measured from minimal amounts of biological material, which has thereby enabled systems-level analyses. By performing global metabolite profiling, also known as untargeted metabolomics, new discoveries linking cellular pathways to biological mechanism are being revealed and are shaping our understanding of cell biology, physiology and medicine.

Metabolites are small molecules that are chemically transformed during metabolism and, as such, they provide a functional readout of cellular state. Unlike genes and proteins, the functions of which are subject to epigenetic regulation and posttranslational modifications, respectively, metabolites serve as direct signatures of biochemical activity and are therefore easier to correlate with phenotype. In this context, metabolite profiling, or metabolomics, has become a powerful approach that has been widely adopted for clinical diagnostics.

The field of metabolomics has made remarkable progress within the past decade and has implemented new tools that have offered mechanistic insights by allowing for the correlation of biochemical changes with phenotype.

In this Innovation article, we first define and differentiate between the targeted and untargeted approaches to metabolomics. We then highlight the value of untargeted metabolomics in particular and outline a guide to performing such studies. Finally, we describe selected applications of un targeted metabolomics and discuss their potential in cell biology.

  • metabolites serve as direct signatures of biochemical activity
  1. In some instances, it may be of interest to examine a defined set of metabolites by using a targeted approach.
  2. In other cases, an untargeted or global approach may be taken in which as many metabolites as possible are measured and compared between samples without bias.
  3. Ultimately, the number and chemical composition of metabolites to be studied is a defining attribute of any metabolomic experiment and shapes experimental design with respect to sample preparation and choice of instrumentation.

The targeted and untargeted workflow for LC/MS-based metabolomics.

a | In the triple quadrupole (QqQ)-based targeted metabolomic workflow, standard compounds for the metabolites of interest are first used to set up selected reaction monitoring methods. Here, optimal instrument voltages are determined and response curves are generated for absolute quantification. After the targeted methods have been established
on the basis of standard metabolites, metabolites are extracted from tissues, biofluids or cell cultures and analysed. The data output provides quantification only of those metabolites for which standard methods have been built.

b | In the untargeted metabolomic workflow, metabolites are first isolated from biological samples and subsequently analysed by liquid chromatography followed by mass spectrometry (LC/MS). After data acquisition, the results are processed by using bioinformatic software such as XCMS to perform nonlinear retention time alignment and identify peaks that are changing between the groups of samples measured. The m/z value s for the peaks of interest are searched in metabolite databases to obtain putative identifications. Putative identifications are then confirmed
by comparing tandem mass spectrometry (MS/MS) data and retention time data to that of standard compounds. The untargeted workflow is global in scope and outputs data related to comprehensive cellular metabolism.

Metabolic Biomarker and Kinase Drug Target Discovery in Cancer Using Stable Isotope-Based Dynamic Metabolic Profiling (SIDMAP)

László G. Boros1*, Daniel J. Brackett2 and George G. Harrigan3
1UCLA School of Medicine, Harbor-UCLA Research and Education Institute, Torrance, CA. 2Department of Surgery, University of Oklahoma Health Sciences Center & VA Medical Center, Oklahoma City, OK, 3Global High Throughput
Screening (HTS), Pharmacia Corporation, Chesterfield, MO.
Current Cancer Drug Targets, 2003, 3, 447-455.

Tumor cells respond to growth signals by the activation of protein kinases, altered gene expression and significant modifications in substrate flow and redistribution among biosynthetic pathways. This results in a proliferating phenotype
with altered cellular function. These transformed cells exhibit unique anabolic characteristics, which includes increased and preferential utilization of glucose through the non-oxidative steps of the pentose cycle for nucleic acid synthesis but limited denovo fatty acid synthesis and TCA cycle glucose oxidation. This primarily nonoxidative anabolic profile reflects an undifferentiated highly proliferative aneuploid cell phenotype and serves as a reliable metabolic biomarker to determine cell proliferation rate and the level of cell transformation/differentiation in response to drug treatment. Novel drugs effective in particular cancers exert their anti-proliferative effects by inducing significant reversions of a few specific non-oxidative anabolic pathways. Here we present evidence that cell transformation of various mechanisms is sustained by a unique
disproportional substrate distribution between the two branches of the pentose cycle for nucleic acid synthesis, glycolysis and the TCA cycle for fatty acid synthesis and glucose oxidation. This can be demonstrated by the broad labeling and unique specificity of [1,2-13C2]glucose to trace a large number of metabolites in the metabolome. Stable isotope-based dynamic metabolic profiles (SIDMAP) serve the drug discovery process by providing a powerful new tool that integrates the metabolome into a functional genomics approach to developing new drugs. It can be used in screening kinases and their metabolic targets, which can therefore be more efficiently characterized, speeding up and improving drug testing, approval and labeling processes by saving trial and error type study costs in drug testing.

Navigating the HumanMetabolome for Biomarker Identification and Design of Pharmaceutical Molecules

Irene Kouskoumvekaki and Gianni Panagiotou
Department of Systems Biology, Center for Biological Sequence Analysis, Building 208, Technical University of Denmark, Lyngby, Denmark
Hindawi Publishing Corporation  Journal of Biomedicine and Biotechnology 2011, Article ID 525497, 19 pages

Metabolomics is a rapidly evolving discipline that involves the systematic study of endogenous small molecules that characterize the metabolic pathways of biological systems. The study of metabolism at a global level has the potential to contribute significantly to biomedical research, clinical medical practice, as well as drug discovery. In this paper, we present the most up-to-date metabolite and metabolic pathway resources, and we summarize the statistical, and machine-learning tools used for the analysis of data from clinical metabolomics.

Through specific applications on cancer, diabetes, neurological and other diseases, we demonstrate how these tools can facilitate diagnosis and identification of potential biomarkers for use within disease diagnosis. Additionally, we
discuss the increasing importance of the integration of metabolomics data in drug discovery. On a case-study based on the Human Metabolome Database (HMDB) and the Chinese Natural Product Database (CNPD), we demonstrate the close relatedness of the two data sets of compounds, and we further illustrate how structural similarity with human metabolites could assist in the design of novel pharmaceuticals and the elucidation of the molecular mechanisms of medicinal plants.

Metabolites are the byproducts of metabolism, which is itself the process of converting food energy to mechanical energy
or heat. Experts believe there are at least 3,000 metabolites that are essential for normal growth and development (primary metabolites) and thousands more unidentified (around 20,000, compared to an estimated 30,000 genes and 100,000 proteins) that are not essential for growth and development (secondary metabolites) but could represent prognostic, diagnostic, and surrogate markers for a disease state and a deeper understanding of mechanisms of disease.

Metabolomics, the study of metabolism at the global level, has the potential to contribute significantly to biomedical
research, and ultimately to clinical medical practice. It is a close counterpart to the genome, the transcriptome and the proteome. Metabolomics, genomics, proteomics, and other “-omics” grew out of the Human Genome Project, a massive research effort that began in the mid-1990s and culminated in 2003 with a complete mapping of all the genes in the human body. When discussing the clinical advantages of metabolomics, scientists point to the “real-world” assessment
of patient physiology that the metabolome provides since it can be regarded as the end-point of the “-omics” cascade. Other functional genomics technologies do not necessarily predict drug effects, toxicological response, or disease states at the phenotype but merely indicate the potential cause for phenotypical response. Metabolomics can bridge this information gap. The identification and measurement of metabolite profile dynamics of host changes provides the closest link to the various phenotypic responses. Thus it is clear that the global mapping of metabolic signatures pre- and postdrug treatment is a promising approach to identify possible functional relationships between medication and medical phenotype.

Human Metabolome Database (HMDB). Focusing on quantitative, analytic, or molecular scale information about
metabolites, the enzymes and transporters associated with them, as well as disease related properties the HMDB represents the most complete bioinformatics and chemoinformatics medical information database. It contains records for
thousands of endogenous metabolites identified by literature surveys (PubMed, OMIM, OMMBID, text books), data
mining (KEGG, Metlin, BioCyc) or experimental analyses performed on urine, blood, and cerebrospinal fluid samples.
The annotation effort is aided by chemical parameter calculators and protein annotation tools originally developed for

A key feature that distinguishes the HMDB from other metabolic resources is its extensive support for higher level database searching and selecting functions. More than 175 hand-drawn-zoomable, fully hyperlinked human
metabolic pathway maps can be found in HMDB and all these maps are quite specific to human metabolism and
explicitly show the subcellular compartments where specific reactions are known to take place. As an equivalent to
BLAST the HMDB contains a structure similarity search tool for chemical structures and users may sketch or
paste a SMILES string of a query compound into the Chem-Query window. Submitting the query launches a
structure similarity search tool that looks for common substructures from the query compound that match the
HMDB’s metabolite database. The wealth of information and especially the extensive linkage to metabolic diseases
to normal and abnormal metabolite concentration ranges, to mutation/SNP data and to the genes, enzymes, reactions
and pathways associated with many diseases of interest makes the HMDB one the most valuable tool in the hands
of clinical chemists, nutritionists, physicians and medical geneticists.

Metabolomics in Drug Discovery and Polypharmacology Studies

Drug molecules generally act on specific targets at the cellular level, and upon binding to the receptors, they exert
a desirable alteration of the cellular activities, regarded as the pharmaceutical effect. Current drug discovery depends
largely on ransom screening, either high-throughput screening (HTS) in vitro, or virtual screening (VS) in silico. Because
the number of available compounds is huge, several druglikeness filters are proposed to reduce the number of compounds that need to be evaluated. The ability to effectively predict if a chemical compound is “drug-like” or “nondruglike” is, thus, a valuable tool in the design, optimization, and selection of drug candidates for development. Druglikeness is a general descriptor of the potential of a small molecule to become a drug. It is not a unified descriptor
but a global property of a compound processing many specific characteristics such as good solubility, membrane
permeability, half-life, and having a pharmacophore pattern to interact specifically with a target protein. These
characteristics can be reflected as molecular descriptors such as molecular weight, log P, the number of hydrogen bond
donors, the number of hydrogen-bond acceptors, the number of rotatable bonds, the number of rigid bonds, the
number of rings in a molecule, and so forth.

Metabolomics for the Study of Polypharmacology of Natural Compounds

Internationally, there is a growing and sustained interest from both pharmaceutical companies and public in medicine
from natural sources. For the public, natural medicine represent a holistic approach to disease treatment, with
potentially less side effects than conventional medicine. For the pharmaceutical companies, bioactive natural products
constitute attractive drug leads, as they have been optimized in a long-term natural selection process for optimal interaction with biomolecules. To promote the ecological survival of plants, structures of secondary products have evolved to interact with molecular targets affecting the cells, tissues and physiological functions in competing microorganisms,
plants, and animals. In this, respect, some plant secondary products may exert their action by resembling endogenous
metabolites, ligands, hormones, signal transduction molecules, or neurotransmitters and thus have beneficial
effects on humans.

Future Perspectives

Metabolomics, the study of metabolism at the global level, is moving to exciting directions.With the development ofmore
sensitive and advanced instrumentation and computational tools for data interpretation in the physiological context,
metabolomics have the potential to impact our understanding of molecular mechanisms of diseases. A state-of-theart
metabolomics study requires knowledge in many areas and especially at the interface of chemistry, biology, and
computer science. High-quality samples, improvements in automated metabolite identification, complete coverage of
the human metabolome, establishment of spectral databases of metabolites and associated biochemical identities, innovative experimental designs to best address a hypothesis, as well as novel computational tools to handle metabolomics data are critical hurdles that must be overcome to drive the inclusion of metabolomics in all steps of drug discovery and drug development. The examples presented above demonstrated that metabolite profiles reflect both environmental and genetic influences in patients and reveal new links between metabolites and diseases providing needed prognostic,diagnostic, and surrogate biomarkers. The integration of these signatures with other omic technologies is of utmost importance to characterize the entire spectrum of malignant phenotype.

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Preface to Metabolomics as a Discipline in Medicine

Author: Larry H. Bernstein, MD, FCAP


The family of ‘omics fields has rapidly outpaced its siblings over the decade since
the completion of the Human Genome Project.  It has derived much benefit from
the development of Proteomics, which has recently completed a first draft of the
human proteome.  Since genomics, transcriptomics, and proteomics, have matured
considerably, it has become apparent that the search for a driver or drivers of cellular signaling and metabolic pathways could not depend on a full clarity of the genome. There have been unresolved issues, that are not solely comprehended from assumptions about mutations.

The most common diseases affecting mankind are derangements in metabolic
pathways, develop at specific ages periods, and often in adulthood or in the
geriatric period, and are at the intersection of signaling pathways.  Moreover,
the organs involved and systemic features are heavily influenced by physical
activity, and by the air we breathe and the water we drink.

The emergence of the new science is also driven by a large body of work
on protein structure, mechanisms of enzyme action, the modulation of gene
expression, the pH dependent effects on protein binding and conformation.
Beyond what has just been said, a significant portion of DNA has been
designated as “dark matter”. It turns out to have enormous importance in
gene regulation, even though it is not transcriptional, effected in a
modulatory way by “noncoding RNAs.  Metabolomics is the comprehensive
analysis of small molecule metabolites. These might be substrates of
sequenced enzyme reactions, or they might be “inhibiting” RNAs just
mentioned.  In either case, they occur in the substructures of the cell
called organelles, the cytoplasm, and in the cytoskeleton.

The reactions are orchestrated, and they can be modified with respect to
the flow of metabolites based on pH, temperature, membrane structural
modifications, and modulators.  Since most metabolites are generated by
enzymatic proteins that result from gene expression, and metabolites give
organisms their biochemical characteristics, the metabolome links
genotype with phenotype.

Metabolomics is still developing, and the continued development has
relied on two major events. The first is chromatographic separation and
mass  spectroscopy (MS), MS/MS, as well as advances in fluorescence
ultrasensitive optical photonic methods, and the second, as crucial,
is the developments in computational biology. The continuation of
this trend brings expectations of an impact on pharmaceutical and
on neutraceutical developments, which will have an impact on medical
practice. What has lagged behind, and may continue to contribute to the
lag is the failure to develop a suitable electronic medical record to
assist the physician in decisions confronted with so much as yet,
hidden data, the ready availability of which could guide more effective
diagnosis and management of the patient. Put all of this together, and
we can meet series challenges as the research community
interprets and integrates the complex data they are acquiring.


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Imaging-guided cancer treatment

Imaging-guided cancer treatment

Writer & reporter: Dror Nir, PhD

It is estimated that the medical imaging market will exceed $30 billion in 2014 (FierceMedicalImaging). To put this amount in perspective; the global pharmaceutical market size for the same year is expected to be ~$1 trillion (IMS) while the global health care spending as a percentage of Gross Domestic Product (GDP) will average 10.5% globally in 2014 (Deloitte); it will reach ~$3 trillion in the USA.

Recent technology-advances, mainly miniaturization and improvement in electronic-processing components is driving increased introduction of innovative medical-imaging devices into critical nodes of major-diseases’ management pathways. Consequently, in contrast to it’s very small contribution to global health costs, medical imaging bears outstanding potential to reduce the future growth in spending on major segments in this market mainly: Drugs development and regulation (e.g. companion diagnostics and imaging surrogate markers); Disease management (e.g. non-invasive diagnosis, guided treatment and non-invasive follow-ups); and Monitoring aging-population (e.g. Imaging-based domestic sensors).

In; The Role of Medical Imaging in Personalized Medicine I discussed in length the role medical imaging assumes in drugs development.  Integrating imaging into drug development processes, specifically at the early stages of drug discovery, as well as for monitoring drug delivery and the response of targeted processes to the therapy is a growing trend. A nice (and short) review highlighting the processes, opportunities, and challenges of medical imaging in new drug development is: Medical imaging in new drug clinical development.

The following is dedicated to the role of imaging in guiding treatment.

Precise treatment is a major pillar of modern medicine. An important aspect to enable accurate administration of treatment is complementing the accurate identification of the organ location that needs to be treated with a system and methods that ensure application of treatment only, or mainly to, that location. Imaging is off-course, a major component in such composite systems. Amongst the available solution, functional-imaging modalities are gaining traction. Specifically, molecular imaging (e.g. PET, MRS) allows the visual representation, characterization, and quantification of biological processes at the cellular and subcellular levels within intact living organisms. In oncology, it can be used to depict the abnormal molecules as well as the aberrant interactions of altered molecules on which cancers depend. Being able to detect such fundamental finger-prints of cancer is key to improved matching between drugs-based treatment and disease. Moreover, imaging-based quantified monitoring of changes in tumor metabolism and its microenvironment could provide real-time non-invasive tool to predict the evolution and progression of primary tumors, as well as the development of tumor metastases.

A recent review-paper: Image-guided interventional therapy for cancer with radiotherapeutic nanoparticles nicely illustrates the role of imaging in treatment guidance through a comprehensive discussion of; Image-guided radiotherapeutic using intravenous nanoparticles for the delivery of localized radiation to solid cancer tumors.

 Graphical abstract


One of the major limitations of current cancer therapy is the inability to deliver tumoricidal agents throughout the entire tumor mass using traditional intravenous administration. Nanoparticles carrying beta-emitting therapeutic radionuclides [DN: radioactive isotops that emits electrons as part of the decay process a list of β-emitting radionuclides used in radiotherapeutic nanoparticle preparation is given in table1 of this paper.) that are delivered using advanced image-guidance have significant potential to improve solid tumor therapy. The use of image-guidance in combination with nanoparticle carriers can improve the delivery of localized radiation to tumors. Nanoparticles labeled with certain beta-emitting radionuclides are intrinsically theranostic agents that can provide information regarding distribution and regional dosimetry within the tumor and the body. Image-guided thermal therapy results in increased uptake of intravenous nanoparticles within tumors, improving therapy. In addition, nanoparticles are ideal carriers for direct intratumoral infusion of beta-emitting radionuclides by convection enhanced delivery, permitting the delivery of localized therapeutic radiation without the requirement of the radionuclide exiting from the nanoparticle. With this approach, very high doses of radiation can be delivered to solid tumors while sparing normal organs. Recent technological developments in image-guidance, convection enhanced delivery and newly developed nanoparticles carrying beta-emitting radionuclides will be reviewed. Examples will be shown describing how this new approach has promise for the treatment of brain, head and neck, and other types of solid tumors.

The challenges this review discusses

  • intravenously administered drugs are inhibited in their intratumoral penetration by high interstitial pressures which prevent diffusion of drugs from the blood circulation into the tumor tissue [1–5].
  • relatively rapid clearance of intravenously administered drugs from the blood circulation by kidneys and liver.
  • drugs that do reach the solid tumor by diffusion are inhomogeneously distributed at the micro-scale – This cannot be overcome by simply administering larger systemic doses as toxicity to normal organs is generally the dose limiting factor.
  • even nanoparticulate drugs have poor penetration from the vascular compartment into the tumor and the nanoparticles that do penetrate are most often heterogeneously distributed

How imaging could mitigate the above mentioned challenges

  • The inclusion of an imaging probe during drug development can aid in determining the clearance kinetics and tissue distribution of the drug non-invasively. Such probe can also be used to determine the likelihood of the drug reaching the tumor and to what extent.

Note: Drugs that have increased accumulation within the targeted site are likely to be more effective as compared with others. In that respect, Nanoparticle-based drugs have an additional advantage over free drugs with their potential to be multifunctional carriers capable of carrying both therapeutic and diagnostic imaging probes (theranostic) in the same nanocarrier. These multifunctional nanoparticles can serve as theranostic agents and facilitate personalized treatment planning.

  • Imaging can also be used for localization of the tumor to improve the placement of a catheter or external device within tumors to cause cell death through thermal ablation or oxidative stress secondary to reactive oxygen species.

See the example of Vintfolide in The Role of Medical Imaging in Personalized Medicine


Note: Image guided thermal ablation methods include radiofrequency (RF) ablation, microwave ablation or high intensity focused ultrasound (HIFU). Photodynamic therapy methods using external light devices to activate photosensitizing agents can also be used to treat superficial tumors or deeper tumors when used with endoscopic catheters.

  • Quality control during and post treatment

For example: The use of high intensity focused ultrasound (HIFU) combined with nanoparticle therapeutics: HIFU is applied to improve drug delivery and to trigger drug release from nanoparticles. Gas-bubbles are playing the role of the drug’s nano-carrier. These are used both to increase the drug transport into the cell and as ultrasound-imaging contrast material. The ultrasound is also used for processes of drug-release and ablation.


Additional example; Multifunctional nanoparticles for tracking CED (convection enhanced delivery)  distribution within tumors: Nanoparticle that could serve as a carrier not only for the therapeutic radionuclides but simultaneously also for a therapeutic drug and 4 different types of imaging contrast agents including an MRI contrast agent, PET and SPECT nuclear diagnostic imaging agents and optical contrast agents as shown below. The ability to perform multiple types of imaging on the same nanoparticles will allow studies investigating the distribution and retention of nanoparticles initially in vivo using non-invasive imaging and later at the histological level using optical imaging.



Image-guided radiotherapeutic nanoparticles have significant potential for solid tumor cancer therapy. The current success of this therapy in animals is most likely due to the improved accumulation, retention and dispersion of nanoparticles within solid tumor following image-guided therapies as well as the micro-field of the β-particle which reduces the requirement of perfectly homogeneous tumor coverage. It is also possible that the intratumoral distribution of nanoparticles may benefit from their uptake by intratumoral macrophages although more research is required to determine the importance of this aspect of intratumoral radionuclide nanoparticle therapy. This new approach to cancer therapy is a fertile ground for many new technological developments as well as for new understandings in the basic biology of cancer therapy. The clinical success of this approach will depend on progress in many areas of interdisciplinary research including imaging technology, nanoparticle technology, computer and robot assisted image-guided application of therapies, radiation physics and oncology. Close collaboration of a wide variety of scientists and physicians including chemists, nanotechnologists, drug delivery experts, radiation physicists, robotics and software experts, toxicologists, surgeons, imaging physicians, and oncologists will best facilitate the implementation of this novel approach to the treatment of cancer in the clinical environment. Image-guided nanoparticle therapies including those with β-emission radionuclide nanoparticles have excellent promise to significantly impact clinical cancer therapy and advance the field of drug delivery.

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Proteomics, Metabolomics, Signaling Pathways, and Cell Regulation: a Compilation of Articles in the Journal http://pharmaceuticalintelligence.com

Compilation of References by Leaders in Pharmaceutical Business Intelligence in the Journal http://pharmaceuticalintelligence.com about
Proteomics, Metabolomics, Signaling Pathways, and Cell Regulation

Curator: Larry H Bernstein, MD, FCAP


  1. The Human Proteome Map Completed

Reporter and Curator: Larry H. Bernstein, MD, FCAP


  1. Proteomics – The Pathway to Understanding and Decision-making in Medicine

Author and Curator, Larry H Bernstein, MD, FCAP


3. Advances in Separations Technology for the “OMICs” and Clarification of Therapeutic Targets

Author and Curator, Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/10/22/advances-in-separations-technology-for-the-omics-and-clarification-         of-therapeutic-targets/

  1. Expanding the Genetic Alphabet and Linking the Genome to the Metabolome

Author and Curator, Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/09/24/expanding-the-genetic-alphabet-and-linking-the-genome-to-the-                metabolome/

5. Genomics, Proteomics and standards

Larry H Bernstein, MD, FCAP, Author and Curator


6. Proteins and cellular adaptation to stress

Larry H Bernstein, MD, FCAP, Author and Curator




  1. Extracellular evaluation of intracellular flux in yeast cells

Larry H. Bernstein, MD, FCAP, Reviewer and Curator


  1. Metabolomic analysis of two leukemia cell lines. I.

Larry H. Bernstein, MD, FCAP, Reviewer and Curator


  1. Metabolomic analysis of two leukemia cell lines. II.

Larry H. Bernstein, MD, FCAP, Reviewer and Curator


  1. Metabolomics, Metabonomics and Functional Nutrition: the next step in nutritional metabolism and biotherapeutics

Reviewer and Curator, Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/22/metabolomics-metabonomics-and-functional-nutrition-the-next-step-          in-nutritional-metabolism-and-biotherapeutics/

  1. Buffering of genetic modules involved in tricarboxylic acid cycle metabolism provides homeomeostatic regulation

Larry H. Bernstein, MD, FCAP, Reviewer and curator

https://pharmaceuticalintelligence.com/2014/08/27/buffering-of-genetic-modules-involved-in-tricarboxylic-acid-cycle-              metabolism-provides-homeomeostatic-regulation/

Metabolic Pathways

  1. Pentose Shunt, Electron Transfer, Galactose, more Lipids in brief

Reviewer and Curator: Larry H. Bernstein, MD, FCAP


  1. Mitochondria: More than just the “powerhouse of the cell”

Ritu Saxena, PhD


  1. Mitochondrial fission and fusion: potential therapeutic targets?

Ritu saxena


4.  Mitochondrial mutation analysis might be “1-step” away

Ritu Saxena


  1. Selected References to Signaling and Metabolic Pathways in PharmaceuticalIntelligence.com

Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/14/selected-references-to-signaling-and-metabolic-pathways-in-                     leaders-in-pharmaceutical-intelligence/

  1. Metabolic drivers in aggressive brain tumors

Prabodh Kandal, PhD


  1. Metabolite Identification Combining Genetic and Metabolic Information: Genetic association links unknown metabolites to functionally related genes

Writer and Curator, Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2012/10/22/metabolite-identification-combining-genetic-and-metabolic-                        information-genetic-association-links-unknown-metabolites-to-functionally-related-genes/

  1. Mitochondria: Origin from oxygen free environment, role in aerobic glycolysis, metabolic adaptation

Larry H Bernstein, MD, FCAP, author and curator

https://pharmaceuticalintelligence.com/2012/09/26/mitochondria-origin-from-oxygen-free-environment-role-in-aerobic-            glycolysis-metabolic-adaptation/

  1. Therapeutic Targets for Diabetes and Related Metabolic Disorders

Reporter, Aviva Lev-Ari, PhD, RD


10.  Buffering of genetic modules involved in tricarboxylic acid cycle metabolism provides homeomeostatic regulation

Larry H. Bernstein, MD, FCAP, Reviewer and curator

https://pharmaceuticalintelligence.com/2014/08/27/buffering-of-genetic-modules-involved-in-tricarboxylic-acid-cycle-              metabolism-provides-homeomeostatic-regulation/

11. The multi-step transfer of phosphate bond and hydrogen exchange energy

Larry H. Bernstein, MD, FCAP, Curator:

https://pharmaceuticalintelligence.com/2014/08/19/the-multi-step-transfer-of-phosphate-bond-and-hydrogen-                          exchange-energy/

12. Studies of Respiration Lead to Acetyl CoA


13. Lipid Metabolism

Author and Curator: Larry H. Bernstein, MD, FCAP


14. Carbohydrate Metabolism

Author and Curator: Larry H. Bernstein, MD, FCAP


15. Update on mitochondrial function, respiration, and associated disorders

Larry H. Bernstein, MD, FCAP, Author and Curator

https://pharmaceuticalintelligence.com/2014/07/08/update-on-mitochondrial-function-respiration-and-associated-                   disorders/

16. Prologue to Cancer – e-book Volume One – Where are we in this journey?

Author and Curator: Larry H. Bernstein, MD, FCAP


17. Introduction – The Evolution of Cancer Therapy and Cancer Research: How We Got Here?

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/04/04/introduction-the-evolution-of-cancer-therapy-and-cancer-research-          how-we-got-here/

18. Inhibition of the Cardiomyocyte-Specific Kinase TNNI3K

Author and Curator: Larry H. Bernstein, MD, FCAP


19. The Binding of Oligonucleotides in DNA and 3-D Lattice Structures

Author and Curator: Larry H. Bernstein, MD, FCAP


20. Mitochondrial Metabolism and Cardiac Function

Author and Curator: Larry H. Bernstein, MD, FCAP


21. How Methionine Imbalance with Sulfur-Insufficiency Leads to Hyperhomocysteinemia

Curator: Larry H. Bernstein, MD, FCAP


22. AMPK Is a Negative Regulator of the Warburg Effect and Suppresses Tumor Growth In Vivo

Author and Curator: Stephen J. Williams, PhD

https://pharmaceuticalintelligence.com/2013/03/12/ampk-is-a-negative-regulator-of-the-warburg-effect-and-suppresses-         tumor-growth-in-vivo/

23. A Second Look at the Transthyretin Nutrition Inflammatory Conundrum

Author and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/12/03/a-second-look-at-the-transthyretin-nutrition-inflammatory-                         conundrum/

24. Mitochondrial Damage and Repair under Oxidative Stress

Author and Curator: Larry H. Bernstein, MD, FCAP


25. Nitric Oxide and Immune Responses: Part 2

Author and Curator: Aviral Vatsa, PhD, MBBS


26. Overview of Posttranslational Modification (PTM)

Writer and Curator: Larry H. Bernstein, MD, FCAP


27. Malnutrition in India, high newborn death rate and stunting of children age under five years

Writer and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/07/15/malnutrition-in-india-high-newborn-death-rate-and-stunting-of-                   children-age-under-five-years/

28. Update on mitochondrial function, respiration, and associated disorders

Writer and Curator: Larry H. Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/07/08/update-on-mitochondrial-function-respiration-and-associated-                  disorders/

29. Omega-3 fatty acids, depleting the source, and protein insufficiency in renal disease

Larry H. Bernstein, MD, FCAP, Curator

https://pharmaceuticalintelligence.com/2014/07/06/omega-3-fatty-acids-depleting-the-source-and-protein-insufficiency-         in-renal-disease/

30. Introduction to e-Series A: Cardiovascular Diseases, Volume Four Part 2: Regenerative Medicine

Larry H. Bernstein, MD, FCAP, writer, and Aviva Lev- Ari, PhD, RN

https://pharmaceuticalintelligence.com/2014/04/27/larryhbernintroduction_to_cardiovascular_diseases-                                  translational_medicine-part_2/

31. Epilogue: Envisioning New Insights in Cancer Translational Biology
Series C: e-Books on Cancer & Oncology

Author & Curator: Larry H. Bernstein, MD, FCAP, Series C Content Consultant


32. Ca2+-Stimulated Exocytosis:  The Role of Calmodulin and Protein Kinase C in Ca2+ Regulation of Hormone                         and Neurotransmitter

Writer and Curator: Larry H Bernstein, MD, FCAP and
Curator and Content Editor: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/12/23/calmodulin-and-protein-kinase-c-drive-the-ca2-regulation-of-                    hormone-and-neurotransmitter-release-that-triggers-ca2-stimulated-exocy

33. Cardiac Contractility & Myocardial Performance: Therapeutic Implications of Ryanopathy (Calcium Release-                           related Contractile Dysfunction) and Catecholamine Responses

Author, and Content Consultant to e-SERIES A: Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC
Author and Curator: Larry H Bernstein, MD, FCAP
and Article Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/08/28/cardiac-contractility-myocardium-performance-ventricular-arrhythmias-      and-non-ischemic-heart-failure-therapeutic-implications-for-cardiomyocyte-ryanopathy-calcium-release-related-                    contractile/

34. Role of Calcium, the Actin Skeleton, and Lipid Structures in Signaling and Cell Motility

Author and Curator: Larry H Bernstein, MD, FCAP Author: Stephen Williams, PhD, and Curator: Aviva Lev-Ari, PhD, RN


35. Identification of Biomarkers that are Related to the Actin Cytoskeleton

Larry H Bernstein, MD, FCAP, Author and Curator

https://pharmaceuticalintelligence.com/2012/12/10/identification-of-biomarkers-that-are-related-to-the-actin-                           cytoskeleton/

36. Advanced Topics in Sepsis and the Cardiovascular System at its End Stage

Author: Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/08/18/advanced-topics-in-Sepsis-and-the-Cardiovascular-System-at-its-              End-Stage/

37. The Delicate Connection: IDO (Indolamine 2, 3 dehydrogenase) and Cancer Immunology

Demet Sag, PhD, Author and Curator

https://pharmaceuticalintelligence.com/2013/08/04/the-delicate-connection-ido-indolamine-2-3-dehydrogenase-and-               immunology/

38. IDO for Commitment of a Life Time: The Origins and Mechanisms of IDO, indolamine 2, 3-dioxygenase

Demet Sag, PhD, Author and Curator

https://pharmaceuticalintelligence.com/2013/08/04/ido-for-commitment-of-a-life-time-the-origins-and-mechanisms-of-             ido-indolamine-2-3-dioxygenase/

39. Confined Indolamine 2, 3 dioxygenase (IDO) Controls the Homeostasis of Immune Responses for Good and Bad

Curator: Demet Sag, PhD, CRA, GCP

https://pharmaceuticalintelligence.com/2013/07/31/confined-indolamine-2-3-dehydrogenase-controls-the-hemostasis-           of-immune-responses-for-good-and-bad/

40. Signaling Pathway that Makes Young Neurons Connect was discovered @ Scripps Research Institute

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/06/26/signaling-pathway-that-makes-young-neurons-connect-was-                     discovered-scripps-research-institute/

41. Naked Mole Rats Cancer-Free

Writer and Curator: Larry H. Bernstein, MD, FCAP


42. Late Onset of Alzheimer’s Disease and One-carbon Metabolism

Reporter and Curator: Dr. Sudipta Saha, Ph.D.


43. Problems of vegetarianism

Reporter and Curator: Dr. Sudipta Saha, Ph.D.


44.  Amyloidosis with Cardiomyopathy

Writer and Curator: Larry H. Bernstein, MD, FCAP


45. Liver endoplasmic reticulum stress and hepatosteatosis

Larry H Bernstein, MD, FACP


46. The Molecular Biology of Renal Disorders: Nitric Oxide – Part III

Curator and Author: Larry H Bernstein, MD, FACP


47. Nitric Oxide Function in Coagulation – Part II

Curator and Author: Larry H. Bernstein, MD, FCAP


48. Nitric Oxide, Platelets, Endothelium and Hemostasis

Curator and Author: Larry H Bernstein, MD, FACP


49. Interaction of Nitric Oxide and Prostacyclin in Vascular Endothelium

Curator and Author: Larry H Bernstein, MD, FACP


50. Nitric Oxide and Immune Responses: Part 1

Curator and Author:  Aviral Vatsa PhD, MBBS


51. Nitric Oxide and Immune Responses: Part 2

Curator and Author:  Aviral Vatsa PhD, MBBS


52. Mitochondrial Damage and Repair under Oxidative Stress

Curator and Author: Larry H Bernstein, MD, FACP


53. Is the Warburg Effect the cause or the effect of cancer: A 21st Century View?

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/10/17/is-the-warburg-effect-the-cause-or-the-effect-of-cancer-a-21st-                 century-view/

54. Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/10/30/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-                  proteolysis-and-cell-apoptosis/

55. Ubiquitin-Proteosome pathway, Autophagy, the Mitochondrion, Proteolysis and Cell Apoptosis: Part III

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2013/02/14/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-                   proteolysis-and-cell-apoptosis-reconsidered/

56. Nitric Oxide and iNOS have Key Roles in Kidney Diseases – Part II

Curator and Author: Larry H Bernstein, MD, FACP


57. New Insights on Nitric Oxide donors – Part IV

Curator and Author: Larry H Bernstein, MD, FACP


58. Crucial role of Nitric Oxide in Cancer

Curator and Author: Ritu Saxena, Ph.D.


59. Nitric Oxide has a ubiquitous role in the regulation of glycolysis -with a concomitant influence on mitochondrial function

Curator and Author: Larry H Bernstein, MD, FACP

https://pharmaceuticalintelligence.com/2012/09/16/nitric-oxide-has-a-ubiquitous-role-in-the-regulation-of-glycolysis-with-         a-concomitant-influence-on-mitochondrial-function/

60. Targeting Mitochondrial-bound Hexokinase for Cancer Therapy

Curator and Author: Ziv Raviv, PhD, RN 04/06/2013


61. Biochemistry of the Coagulation Cascade and Platelet Aggregation – Part I

Curator and Author: Larry H Bernstein, MD, FACP


Genomics, Transcriptomics, and Epigenetics

  1. What is the meaning of so many RNAs?

Writer and Curator: Larry H. Bernstein, MD, FCAP


  1. RNA and the transcription the genetic code

Larry H. Bernstein, MD, FCAP, Writer and Curator


  1. A Primer on DNA and DNA Replication

Writer and Curator: Larry H. Bernstein, MD, FCAP


4. Synthesizing Synthetic Biology: PLOS Collections

Reporter: Aviva Lev-Ari


5. Pathology Emergence in the 21st Century

Author and Curator: Larry Bernstein, MD, FCAP


6. RNA and the transcription the genetic code

Writer and Curator, Larry H. Bernstein, MD, FCAP


7. A Great University engaged in Drug Discovery: University of Pittsburgh

Larry H. Bernstein, MD, FCAP, Reporter and Curator


8. microRNA called miRNA-142 involved in the process by which the immature cells in the bone  marrow give                              rise to all the types of blood cells, including immune cells and the oxygen-bearing red blood cells

Aviva Lev-Ari, PhD, RN, Author and Curator

https://pharmaceuticalintelligence.com/2014/07/24/microrna-called-mir-142-involved-in-the-process-by-which-the-                   immature-cells-in-the-bone-marrow-give-rise-to-all-the-types-of-blood-cells-including-immune-cells-and-the-oxygen-             bearing-red-blood-cells/

9. Genes, proteomes, and their interaction

Larry H. Bernstein, MD, FCAP, Writer and Curator


10. Regulation of somatic stem cell Function

Larry H. Bernstein, MD, FCAP, Writer and Curator    Aviva Lev-Ari, PhD, RN, Curator


11. Scientists discover that pluripotency factor NANOG is also active in adult organisms

Larry H. Bernstein, MD, FCAP, Reporter

https://pharmaceuticalintelligence.com/2014/07/10/scientists-discover-that-pluripotency-factor-nanog-is-also-active-in-           adult-organisms/

12. Bzzz! Are fruitflies like us?

Larry H Bernstein, MD, FCAP, Author and Curator


13. Long Non-coding RNAs Can Encode Proteins After All

Larry H Bernstein, MD, FCAP, Reporter


14. Michael Snyder @Stanford University sequenced the lymphoblastoid transcriptomes and developed an
allele-specific full-length transcriptome

Aviva Lev-Ari, PhD, RN, Author and Curator

https://pharmaceuticalintelligence.com/014/06/23/michael-snyder-stanford-university-sequenced-the-lymphoblastoid-            transcriptomes-and-developed-an-allele-specific-full-length-transcriptome/

15. Commentary on Biomarkers for Genetics and Genomics of Cardiovascular Disease: Views by Larry H                                     Bernstein, MD, FCAP

Author: Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/07/16/commentary-on-biomarkers-for-genetics-and-genomics-of-                        cardiovascular-disease-views-by-larry-h-bernstein-md-fcap/

16. Observations on Finding the Genetic Links in Common Disease: Whole Genomic Sequencing Studies

Author an curator: Larry H Bernstein, MD, FCAP


17. Silencing Cancers with Synthetic siRNAs

Larry H. Bernstein, MD, FCAP, Reviewer and Curator


18. Cardiometabolic Syndrome and the Genetics of Hypertension: The Neuroendocrine Transcriptome Control Points

Reporter: Aviva Lev-Ari, PhD, RN


19. Developments in the Genomics and Proteomics of Type 2 Diabetes Mellitus and Treatment Targets

Larry H. Bernstein, MD, FCAP, Reviewer and Curator

https://pharmaceuticalintelligence.com/2013/12/08/developments-in-the-genomics-and-proteomics-of-type-2-diabetes-           mellitus-and-treatment-targets/

20. Loss of normal growth regulation

Larry H Bernstein, MD, FCAP, Curator


21. CT Angiography & TrueVision™ Metabolomics (Genomic Phenotyping) for new Therapeutic Targets to Atherosclerosis

Reporter: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/11/15/ct-angiography-truevision-metabolomics-genomic-phenotyping-for-           new-therapeutic-targets-to-atherosclerosis/

22.  CRACKING THE CODE OF HUMAN LIFE: The Birth of BioInformatics & Computational Genomics

Genomics Curator, Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2014/08/30/cracking-the-code-of-human-life-the-birth-of-bioinformatics-                      computational-genomics/

23. Big Data in Genomic Medicine

Author and Curator, Larry H Bernstein, MD, FCAP


24. From Genomics of Microorganisms to Translational Medicine

Author and Curator: Demet Sag, PhD

https://pharmaceuticalintelligence.com/2014/03/20/without-the-past-no-future-but-learn-and-move-genomics-of-                      microorganisms-to-translational-medicine/

25. Summary of Genomics and Medicine: Role in Cardiovascular Diseases

Author and Curator, Larry H Bernstein, MD, FCAP


 26. Genomic Promise for Neurodegenerative Diseases, Dementias, Autism Spectrum, Schizophrenia, and Serious                      Depression

Author and Curator, Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2013/02/19/genomic-promise-for-neurodegenerative-diseases-dementias-autism-        spectrum-schizophrenia-and-serious-depression/

 27.  BRCA1 a tumour suppressor in breast and ovarian cancer – functions in transcription, ubiquitination and DNA repair

Sudipta Saha, PhD

https://pharmaceuticalintelligence.com/2012/12/04/brca1-a-tumour-suppressor-in-breast-and-ovarian-cancer-functions-         in-transcription-ubiquitination-and-dna-repair/

28. Personalized medicine gearing up to tackle cancer

Ritu Saxena, PhD


29. Differentiation Therapy – Epigenetics Tackles Solid Tumors

Stephen J Williams, PhD


30. Mechanism involved in Breast Cancer Cell Growth: Function in Early Detection & Treatment

     Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/17/mechanism-involved-in-breast-cancer-cell-growth-function-in-early-          detection-treatment/

31. The Molecular pathology of Breast Cancer Progression

Tilde Barliya, PhD


32. Gastric Cancer: Whole-genome reconstruction and mutational signatures

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2012/12/24/gastric-cancer-whole-genome-reconstruction-and-mutational-                   signatures-2/

33. Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine –                                                       Part 1 (pharmaceuticalintelligence.com)

Aviva  Lev-Ari, PhD, RN


34. LEADERS in Genome Sequencing of Genetic Mutations for Therapeutic Drug Selection in Cancer                                         Personalized Treatment: Part 2

A Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/13/leaders-in-genome-sequencing-of-genetic-mutations-for-therapeutic-       drug-selection-in-cancer-personalized-treatment-part-2/

35. Personalized Medicine: An Institute Profile – Coriell Institute for Medical Research: Part 3

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/13/personalized-medicine-an-institute-profile-coriell-institute-for-medical-        research-part-3/

36. Harnessing Personalized Medicine for Cancer Management, Prospects of Prevention and Cure: Opinions of                           Cancer Scientific Leaders @http://pharmaceuticalintelligence.com

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/13/7000/Harnessing_Personalized_Medicine_for_ Cancer_Management-      Prospects_of_Prevention_and_Cure/

37.  GSK for Personalized Medicine using Cancer Drugs needs Alacris systems biology model to determine the in silico
effect of the inhibitor in its “virtual clinical trial”

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2012/11/14/gsk-for-personalized-medicine-using-cancer-drugs-needs-alacris-             systems-biology-model-to-determine-the-in-silico-effect-of-the-inhibitor-in-its-virtual-clinical-trial/

38. Personalized medicine-based cure for cancer might not be far away

Ritu Saxena, PhD


39. Human Variome Project: encyclopedic catalog of sequence variants indexed to the human genome sequence

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2012/11/24/human-variome-project-encyclopedic-catalog-of-sequence-variants-         indexed-to-the-human-genome-sequence/

40. Inspiration From Dr. Maureen Cronin’s Achievements in Applying Genomic Sequencing to Cancer Diagnostics

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/10/inspiration-from-dr-maureen-cronins-achievements-in-applying-                genomic-sequencing-to-cancer-diagnostics/

41. The “Cancer establishments” examined by James Watson, co-discoverer of DNA w/Crick, 4/1953

Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/01/09/the-cancer-establishments-examined-by-james-watson-co-discover-         of-dna-wcrick-41953/

42. What can we expect of tumor therapeutic response?

Author and curator: Larry H Bernstein, MD, FACP


43. Directions for genomics in personalized medicine

Author and Curator: Larry H. Bernstein, MD, FCAP


44. How mobile elements in “Junk” DNA promote cancer. Part 1: Transposon-mediated tumorigenesis.

Stephen J Williams, PhD

https://pharmaceuticalintelligence.com/2012/10/31/how-mobile-elements-in-junk-dna-prote-cancer-part1-transposon-            mediated-tumorigenesis/

45. mRNA interference with cancer expression

Author and Curator, Larry H. Bernstein, MD, FCAP


46. Expanding the Genetic Alphabet and linking the genome to the metabolome

Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2012/09/24/expanding-the-genetic-alphabet-and-linking-the-genome-to-the-               metabolome/

47. Breast Cancer, drug resistance, and biopharmaceutical targets

Author and Curator: Larry H Bernstein, MD, FCAP


48.  Breast Cancer: Genomic profiling to predict Survival: Combination of Histopathology and Gene Expression                            Analysis

Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2012/12/24/breast-cancer-genomic-profiling-to-predict-survival-combination-of-           histopathology-and-gene-expression-analysis

49. Gastric Cancer: Whole-genome reconstruction and mutational signatures

Aviva  Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2012/12/24/gastric-cancer-whole-genome-reconstruction-and-mutational-                   signatures-2/

50. Genomic Analysis: FLUIDIGM Technology in the Life Science and Agricultural Biotechnology

Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/2012/08/22/genomic-analysis-fluidigm-technology-in-the-life-science-and-                   agricultural-biotechnology/

51. 2013 Genomics: The Era Beyond the Sequencing Human Genome: Francis Collins, Craig Venter, Eric Lander, et al.

Aviva Lev-Ari, PhD, RD


52. Paradigm Shift in Human Genomics – Predictive Biomarkers and Personalized Medicine – Part 1

Aviva Lev-Ari, PhD, RD

https://pharmaceuticalintelligence.com/Paradigm Shift in Human Genomics_/

Signaling Pathways

  1. Proteins and cellular adaptation to stress

Larry H Bernstein, MD, FCAP, Curator


  1. A Synthesis of the Beauty and Complexity of How We View Cancer:
    Cancer Volume One – Summary

Author and Curator: Larry H. Bernstein, MD, FCAP


  1. Recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes in
    serous endometrial tumors

Sudipta Saha, PhD

https://pharmaceuticalintelligence.com/2012/11/19/recurrent-somatic-mutations-in-chromatin-remodeling-ad-ubiquitin-           ligase-complex-genes-in-serous-endometrial-tumors/

4.  Prostate Cancer Cells: Histone Deacetylase Inhibitors Induce Epithelial-to-Mesenchymal Transition

Stephen J Williams, PhD

https://pharmaceuticalintelligence.com/2012/11/30/histone-deacetylase-inhibitors-induce-epithelial-to-mesenchymal-              transition-in-prostate-cancer-cells/

5. Ubiquinin-Proteosome pathway, autophagy, the mitochondrion, proteolysis and cell apoptosis

Author and Curator: Larry H Bernstein, MD, FCAP

https://pharmaceuticalintelligence.com/2012/10/30/ubiquinin-proteosome-pathway-autophagy-the-mitochondrion-                   proteolysis-and-cell-apoptosis/

6. Signaling and Signaling Pathways

Larry H. Bernstein, MD, FCAP, Reporter and Curator


7.  Leptin signaling in mediating the cardiac hypertrophy associated with obesity

Larry H. Bernstein, MD, FCAP, Reporter and Curator

https://pharmaceuticalintelligence.com/2013/11/03/leptin-signaling-in-mediating-the-cardiac-hypertrophy-associated-            with-obesity/

  1. Sensors and Signaling in Oxidative Stress

Larry H. Bernstein, MD, FCAP, Reporter and Curator


  1. The Final Considerations of the Role of Platelets and Platelet Endothelial Reactions in Atherosclerosis and Novel

Larry H. Bernstein, MD, FCAP, Reporter and Curator

https://pharmaceuticalintelligence.com/2013/10/15/the-final-considerations-of-the-role-of-platelets-and-platelet-                      endothelial-reactions-in-atherosclerosis-and-novel-treatments

10.   Platelets in Translational Research – Part 1

Larry H. Bernstein, MD, FCAP, Reporter and Curator


11.  Disruption of Calcium Homeostasis: Cardiomyocytes and Vascular Smooth Muscle Cells: The Cardiac and
Cardiovascular Calcium Signaling Mechanism

Author and Curator: Larry H Bernstein, MD, FCAP, Author, and Content Consultant to e-SERIES A:
Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC and Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/09/12/disruption-of-calcium-homeostasis-cardiomyocytes-and-vascular-             smooth-muscle-cells-the-cardiac-and-cardiovascular-calcium-signaling-mechanism/

12. The Centrality of Ca(2+) Signaling and Cytoskeleton Involving Calmodulin Kinases and
Ryanodine Receptors in Cardiac Failure, Arterial Smooth Muscle, Post-ischemic Arrhythmia,
Similarities and Differences, and Pharmaceutical Targets

     Author and Curator: Larry H Bernstein, MD, FCAP, Author, and Content Consultant to
e-SERIES A: Cardiovascular Diseases: Justin Pearlman, MD, PhD, FACC and
Curator: Aviva Lev-Ari, PhD, RN

https://pharmaceuticalintelligence.com/2013/09/08/the-centrality-of-ca2-signaling-and-cytoskeleton-involving-calmodulin-       kinases-and-ryanodine-receptors-in-cardiac-failure-arterial-smooth-muscle-post-ischemic-arrhythmia-similarities-and-           differen/

13.  Nitric Oxide Signalling Pathways

Aviral Vatsa, PhD, MBBS


14. Immune activation, immunity, antibacterial activity

Larry H. Bernstein, MD, FCAP, Curator


15.  Regulation of somatic stem cell Function

Larry H. Bernstein, MD, FCAP, Writer and Curator    Aviva Lev-Ari, PhD, RN, Curator


16. Scientists discover that pluripotency factor NANOG is also active in adult organisms

Larry H. Bernstein, MD, FCAP, Reporter


Read Full Post »

Einstein Center Reaps $17M from NCI for Infrastructure, Research Support

Reporter: Aviva Lev-Ari, PhD, RN

September 27, 2013

NEW YORK (GenomeWeb News) – The Albert Einstein Cancer Center (AECC) at Yeshiva University has received a $16.7 million grant from the National Cancer Institute to provide for support and infrastructure of its research programs, which involve a range of molecular, genomics, imaging, and related disciplines.

The funding will bolster research projects in five major areas at AECC, including studies of the tumor microenvironment and metastasis; stem cells, differentiation and cancer; experimental therapeutics; cancer epidemiology; and the biology of colon cancer, AECC said yesterday.

Supporting these research programs are 14 specialized shared resource facilities involving genomics, proteomics, biostatistics and bioinformatics, structural biology, transgenic mouse resource, and others. The new funding also would provide for a new shared resource, a cancer biospecimen and acquisition biorepository.

AECC’s genomics facility provides a range of sequencing services , including massively-parallel assays for expression, resequencing and de novo sequencing; gene expression, exon, and SNP arrays from Affymetrix; SNP typing, CpG methylation, and gene expression from Sequenom; real-time PCR using Sybr Green and Taqman assays; DNA purification; pyrosequencing, and others.

The proteomics core lab provides protein identification services; analysis of small proteins; spatial localization of molecules by mass spectrometry; quantitative proteomics; confirmation of synthetic and recombinant molecules, and multiple reaction monitoring assays and pharmacokinetics, among others.

AECC said its location in the Bronx, New York, provides its researchers with access to samples from and studies of diverse ethnic and racial populations, making it “a national resource.”


Read Full Post »

The immune response

The immune response (Photo credit: Wikipedia)

Confined Indolamine 2, 3 dioxygenase (IDO) Controls the Hemeostasis of Immune Responses for Good and Bad

Curator: Demet Sag, PhD, CRA, GCP


The immune response mechanism is the holy grail of the human defense system for health.   IDO, indolamine 2, 3-dioxygenase, is a key gene for homeostasis of immune responses and producing an enzyme catabolizing the first rate-limiting step in tryptophan degradation metabolism. The hemostasis of immune system is complicated.  In this review we will discuss properties of IDO such as basic molecular genetics, biochemistry and genesis. IDO belongs to globin gene family to carry oxygen and heme.

The main function and genesis of IDO comes from the immune responses during host-microbial invasion and choice between tolerance and immunegenity. In addition IDO has a role in vascular tone as well.  In human there are three kinds of IDOs, which are IDO1, IDO2, and TDO, with distinguished mechanisms and expression profiles. , IDO mechanism includes three distinguished pathways: enzymatic acts through IFNgamma, non-enzymatic acts through TGFbeta-IFNalpha/IFNbeta and moonlighting acts through AhR/Kyn. These mechanisms and their relation with various health and disease will be presented. Overall our purpose is to find a method to manipulate IDO to correct/fix/modulate immune responses for clinical applications.

Our focus is on cancer prevention with DCvax.  The first study proving the connection between IDO and immune response came from, a very natural event, a protection of pregnancy in human. This led to discover that high IDO expression is a common factor in cancer tumors. Thus, attention promoted investigations on IDO’s role in various disease states, immune disorders, transplantation, inflammation, women health, mood disorders.  Many approaches, vaccines and adjuvants are underway to find new immunotherapies by combining the power of DCs in immune response regulation and specific direction of siRNA.  As a result, with this unique qualities of IDO, DCs and siRNA, we orchestrated a novel intervention for immunomodulation of IDO by inhibiting with small interference RNA, called siRNA-IDO-DCvax.  Proven that our DCvax created a delay and regression of tumor growth without changing the natural structure and characterization of DCs in melanoma and breast cancers in vivo.


IDO is a key homeostatic regulator and confined in immune system mechanism for the balance between tolerance and immunity.  This gene encodes indoleamine 2, 3-dioxygenase (IDO) – a heme enzyme (EC= that catalyzes the first rate-limiting step in tryptophan catabolism to N-formyl-kynurenine and acts on multiple tryptophan substrates including D-tryptophan, L-tryptophan, 5-hydroxy-tryptophan, tryptamine, and serotonin (1; 2; 3; 4).

The basic genetic information describes indoleamine 2, 3-dioxygenase 1 (IDO1, IDO, INDO) as an enzyme located at Chromosome 8p12-p11 (5; 6) that active at the first step of the Tryptophan catabolism.    The cloned gene structure showed that IDO contains 10 exons ad 9 introns (7; 8) producing 9 transcripts.  After alternative splicing only five of the transcripts encode a protein but the other four does not make protein products, three of transcripts retain intron and one of them create a nonsense code (7).  Based on IDO related studies 15 phenotypes of IDO is identified, of which, twelve in cancer tumor models of lung, kidney, endometrium, intestine, two in nervous system, and one HGMD- deletion.

The specific cellular location of IDO is in cytosol, smooth muscle contractile fibers and stereocilium bundle. The expression specificity shows that IDO is present very widely in all cell types but there is an elevation of expression in placenta, pancreas, pancreas islets, including dendritic cells (DCs) according to gene atlas of transcriptome (9).  Expression of IDO is common in antigen presenting cells (APCs), monocytes (MO), macrophages (MQs), DCs, T-cells, and some B-cells. IDO present in APCs (10; 11), due to magnitude of role play hierarchy and level of expression DCs are the better choice but including MOs during establishment of three DC cell subset, CD14+CD25+, CD14++CD25+ and CD14+CD25++ may increase the longevity and efficacy of the interventions.

IDO is strictly regulated and confined to immune system with diverse functions based on either positive or negative stimulations. The positive stimulations are T cell tolerance induction, apoptotic process, and chronic inflammatory response, type 2 immune response, interleukin-12 production (12).  The negative stimulations are interleukin-10 production, activated T cell proliferation, T cell apoptotic process.  Furthermore, there are more functions allocating fetus during female pregnancy; changing behavior, responding to lipopolysaccharide or multicellular organismal response to stress possible due to degradation of tryptophan, kynurenic acid biosynthetic process, cellular nitrogen compound metabolic process, small molecule metabolic process, producing kynurenine process (13; 14; 15).   IDO plays a role in a variety of pathophysiological processes such as antimicrobial and antitumor defense, neuropathology, immunoregulation, and antioxidant activity (16; 17; 18; 19).

Active site of IDO–PI complex. (A) Stereoview of the residues around the heme of IDO viewed from the side of heme plane. The proximal ligand H346 is H-bonded to wa1. The 6-propionate of the heme contacts with wa2 and R343 Nε. The wa2 is H-bonded to wa1, L388 O, and 6-propionate. Mutations of F226, F227, and R231 do not lose the substrate affinity but produce the inactive enzyme. Two CHES molecules are bound in the distal pocket. The cyclohexan ring of CHES-1 (green) contacts with F226 and R231. The 7-propionate of the heme interacts with the amino group of CHES-1 and side chain of Ser-263. The mutational analyses for these distal residues are shown in Table 1. (B) Top view of A by a rotation of 90°. The proximal residues are omitted. (http://www.pnas.org/content/103/8/2611/F3.expansion.html)

Active site of IDO–PI complex. (A) Stereoview of the residues around the heme of IDO viewed from the side of heme plane. The proximal ligand H346 is H-bonded to wa1. The 6-propionate of the heme contacts with wa2 and R343 Nε. The wa2 is H-bonded to wa1, L388 O, and 6-propionate. Mutations of F226, F227, and R231 do not lose the substrate affinity but produce the inactive enzyme. Two CHES molecules are bound in the distal pocket. The cyclohexan ring of CHES-1 (green) contacts with F226 and R231. The 7-propionate of the heme interacts with the amino group of CHES-1 and side chain of Ser-263. The mutational analyses for these distal residues are shown in Table 1. (B) Top view of A by a rotation of 90°. The proximal residues are omitted. (http://www.pnas.org/content/103/8/2611/F3.expansion.html)

Molecular genetics data from earlier findings based on reporter assay results showed that IDO promoter is regulated by ISRE-like elements and GAS-sequence at -1126 and -1083 region (20).

Two cis-acting elements are ISRE1 (interferon sequence response element 1) and interferon sequence response element 2 (ISRE2).    Analyses of site directed and deletion mutation with transfected cells demonstrated that introduction of point mutations at these elements decreases the IDO expression. Removing ISRE1 decreases the effects of IFNgamma induction 50 fold and deleting ISRE1 at -1126 reduced by 25 fold (3). Introducing point mutations in conserved t residues at -1124 and -1122 (from T to C or G) in ISRE consensus sequence NAGtttCA/tntttNCC of IFNa/b inducible gene ISG4 eliminates the promoter activity by 24 fold (21).

ISRE2 have two boxes, X box (-114/1104) and Y Box 9-144/-135), which are essential part of the IFNgamma response region of major histocompatibility complex class II promoters (22; 23).  When these were removed from ISRE2 or introducing point mutations at two A residues of ISRE2 at -111 showed a sharp decrease after IFNgamma treatment by 4 fold (3).  The lack of responses related to truncated or deleted IRF-1 interactions whereas IRF-2, Jak2 and STAT91 levels were similar in the cells, HEPg2 and ME180 (3). Furthermore, 748 bp deleted between these elements did not affect the IDO expression, thus the distance between ISRE1 and ISRE2 elements have no function or influence on IDO (3; 24)

There are three types of IDO in human genome:

IDO was originally discovered in 1967 in rabbit intestine (25). Later, in 1990 the human IDO gene is cloned and sequenced (7).  However, its importance and relevance in immunology was not created until prevention of allocation of fetal rejection and founding expression in wide range of human cancers (26; 27).  There are three types of IDO, pro-IDO like, IDO1, and IDO2.  In addition, another enzyme called TDO, tryptophan 2, 3, dehydrogenase solely degrade L-Trp at first-rate limiting mechanism in liver and brain.


IDO1 mechanism is the target for immunotherapy applications. The initial discovery of IDO in human physiology is protection of pregnancy (1) since lack of IDO results in premature recurrent abortion (28; 26; 29).   The initial rate-limiting step of tryptophan metabolism is catalyzed by either IDO or tryptophan 2, 3-dioxygenase (TDO).

Structural studies of IDO versus TDO presenting active site environments, conserved Arg 117 and Tyr113, found both in TDO and IDO for the Tyr-Glu motif, but His55 in TDO replaced by Ser167b in IDO (30; 2). As a result, they are regulated with different mechanisms (1; 2) (30).

 The short-lived TDO, about 2h, responds to level of tryptophan and its expression regulated by glucorticoids (31; 32).  Thus, it is a useful target for regulation and induced by tryptophan so that increasing tryptophan induces NAD biosynthesis. Whereas, IDO is not activated by the level of Trp presence but inflammatory agents with its interferon stimulated response elements (ISRE1 and ISRE2) in its (33; 34; 35; 36; 3; 10) promoter.

TDO promoter contains glucorticoid response elements (37; 38) and regulated by glucocorticoids and other available amino acids for gluconeogenesis. This is how IDO binds to only immune response cells and TDO relates to NAD biosynthesis mechanisms.

Furthermore, TDO is express solely in liver and brain (36).  NAD synthesis (39) showed increased IDO ubiquitous and TDO in liver and causing NAD level increase in rat with neuronal degeneration (40; 41).  NAM has protective function in beta-cells could be used to cure Type1 diabetes (40; 42; 43). In addition, knowledge on NADH/NAD, Kyn/Trp or Trp/Kyn ratios as well as Th1/Th2, CD4/CD8 or Th17/Threg are equally important (44; 40).

The third type of IDO, called IDO2 exists in lower vertebrates like chicken, fish and frogs (45) and in human with differential expression properties. The expression of IDO2 is only in DCs, unlike IDO1 expresses on both tumors and DCs in human tissues.  Yet, in lower invertebrates IDO2 is not inhibited by general inhibitor of IDO, D-1-methyl-tryptophan (1MT) (46).

Recently, two structurally unusual natural inhibitors of IDO molecules, EXIGUAMINES A and B, are synthesized (47).  LIP mechanism cannot be switch back to activation after its induction in IDO2 (46). Crucial cancer progression can continue with production of IL6, IL10 and TGF-beta1 to help invasion and metastasis.  Inclusion of two common SNPs affects the function of IDO2 in certain populations.  SNP1 reduces 90% of IDO2 catalytic activity in 50% of European and Asian descent and SNP2 produce premature protein through inclusion of stop-codon in 25% of African descent lack functional IDO2 (Uniport).

The Origin of IDO:

A: Structure of human IDO2 gene and transcripts. Complete coding region is 1260 bps encoding a 420 aa polypeptide. Alternate splice isoforms lacking the exons indicated are noted. Hatch boxes represent a frameshift in the coding region to an alternate reading frame leading to termination. Black boxes represent 3' untranslated regions. Nucleotide numbers, intron sizes, and positioning are based on IDO sequence files NW_923907.1 and GI:89028628 in the Genbank database. (reference: http://atlasgeneticsoncology.org/Genes/IDO2ID44387ch8p11.html)

A: Structure of human IDO2 gene and transcripts. Complete coding region is 1260 bps encoding a 420 aa polypeptide. Alternate splice isoforms lacking the exons indicated are noted. Hatch boxes represent a frameshift in the coding region to an alternate reading frame leading to termination. Black boxes represent 3′ untranslated regions. Nucleotide numbers, intron sizes, and positioning are based on IDO sequence files NW_923907.1 and GI:89028628 in the Genbank database.
(reference: http://atlasgeneticsoncology.org/Genes/IDO2ID44387ch8p11.html)

Knowing the evolutionary steps will helps us to identify how we can manage the regulator function to protect human health in cancer, immune disorders, diabetes, and infectious diseases.   Bacterial IDO has two types of IDOs that are group I and group II IDO (48)These are the earliest version of the IDO, pro-IDO like, proteins with a quite complicated function.  Each microorganism recognized by a specific set of receptors, called Toll-Like Receptors (TLR), to activate the IDO-like protein expression based on the origin of the bacteria or virus (49; 35).  

Thus, the genesis of human IDO originates from gene duplication of these early bacterial versions of IDO-like proteins after their invasion interactions with human host.  IDO1 only exists in mammals and fungi.  Fungi also has three types of IDO; IDOa, IDO beta, and IDO gamma (50) with different properties than human IDOs, perhaps multiple IDO is necessary for the world’s decomposers.

All globins, haemoglobins and myoglobins, destined to evolve from a common ancestor that is only 14-16kDa (51) length. Binding of a heme and being oxygen carrier are central to the enzyme mechanism of this family.  Globins are classified under three distinct origins; a universal globin, a compact globin, and IDO-like globin (52).  IDO like globin widely distributed among gastropodic mollusks (53; 51).

The indoleamine 2, 3-dioxygenase 1–like “myoglobin” (Myb) was discovered in 1989 in the buccal mass of the abalone Sulculus diversicolor (54).  The conserved region between Myb and IDO-like Myb existed for at least 600 million years (53).  Even though the splice junction of seven introns was kept intact, the overall homolog region between Myb and IDO is only about 35%.  No significant evolutionary relationship is found between them after their amino acid sequence of each exon is compared to usual globin sequences. This led the hint that molluscan IDO-like protein must have other functions besides carrying oxygen, like myoglobin.   Alignment of S. cerevisiae cDNA, mollusk and vertebrate IDO–like globins show the key regions for controlling IDO or myoglobin function (55). These data suggest that there is an alternative pathways of myoglobin evolution.  In addition, understanding the diversity of globin may help to design better protocols for interventions of diseases.

B: Amino acid alignment of IDO and IDO2. Amino acids determined by mutagenesis and the crystal structure of IDO that are critical for catalytic activity are positioned below the human IDO sequence. Two commonly occurring SNPs identified in the coding region of human IDO2 are shown above the sequence which alter a critical amino acid (R248W) or introduce a premature termination codon (Y359stop).

B: Amino acid alignment of IDO and IDO2. Amino acids determined by mutagenesis and the crystal structure of IDO that are critical for catalytic activity are positioned below the human IDO sequence. Two commonly occurring SNPs identified in the coding region of human IDO2 are shown above the sequence which alter a critical amino acid (R248W) or introduce a premature termination codon (Y359stop).

The Immune Cells and IDO in DCs:

DCs are the orchestrator of the immune response (56; 57; 58) with list of functions in uptake, processing, and presentation of antigens; activation of effector cells, such as T-cells and NK-cells; and secretion of cytokines and other immune-modulating molecules to direct the immune response. The differential regulation of IDO in distinct DC subsets is widely studied to delineate and correct immune homeostasis during autoimmunity, infection and cancer and the associated immunological outcomes.

Genesis of antigen presenting cells (APCs), eventually the immune system, require migration of monocytes (MOs), which is originated in bone marrow. Then, these MOs move from bloodstream to other tissues to become macrophages and DCs (59; 60). Initiation of immune response requires APCs to link resting helper T-cell with the matching antigen to protect body. DCs are superior to MQs and MOs in their immune action model. When DCs are first described (61) and classified, their role is determined as a highly potent antigen-presenting cell (APC) subset with 100 to 1000-times more effective than macrophages and B-cells in priming T-cells. Both MQs and monocytes phagocytize the pathogen, and their cell structure contains very large nucleus and many internal vesicles. However, there is a nuance between MQ and DCs, since DCs has a wider capacity of stimulation, because MQs activates only memory T cells, yet DCs can activate both naïve and memory T cells.

DCs are potent activators of T cells and they also have well controlled regulatory roles. DC properties determine the regulation regardless of their origin or the subset of the DCs.  DCs react after identification of the signals or influencers for their inhibitory, stimulatory or regulatory roles, before they express a complex repertoire of positive and negative cytokines, transmembrane proteins and other molecules. Thus, “two signal theory” gains support with a defined rule.

The combination of two signals, their interaction with types of cells and time are critical. In short, specificity and time are matter for a proper response.  When IDO mRNA expression is activated with CTL40 ligand and IFNgamma, IDO results inhibition of T cell production (4).  However, if DCs are inhibited by 1MT, an inhibitor of IDO, the response stop but IgG has no affect (10).  In addition, if the stimulation is started by a tryptophan metabolite, which is downstream of IDO, such as 3-hydroxyantranilic or quinolinic acids, it only inhibits Th1 but not Th2 subset of T cells (62). Furthermore, inclusion of signal molecules, such as Fas Ligand, cytochrome c, and pathways also differ in the T cell differentiation mechanisms due to combination, time and specificity of two-signals.  The co-culture experiments are great tool to identify specific stimuli in disease specific microenvironment (63; 12; 64) for discovering the mechanism and interactions between molecules in gene regulation, biochemical mechanism and physiological function during cell differentiation.

As a result, the simplest differential cell development from the early development of DCs impact the outcome of the data. For example, collection of MOs from peripheral blood mononuclear cells (PBMCs) with IL4 and GM-CSF leads to immature DCs (iDCs). On next step, treatment of iDCs with tumor necrosis factor (TNF) or other plausible cytokines (TGFb1, IFNgamma, IFNalpha,  IFNbeta, IL6 etc.) based on the desired outcome differentiate iDCs  into mature DCs (mDCs). DCs live only up to a week but MOs and generated MQs can live up to a month in the given tissue. B cells inhibit T cell dependent immune responses in tumors (65).

Mechanisms of IDO:

IDO mechanism for immune response

The dichotomy of IDO mechanism lead the discovery that IDO is more than an enzyme as a versatile regulator of innate and adaptive immune responses in DCs (66; 67; 68). Meantime IDO also involve with Th2 response and B cell mediated autoimmunity showing that it has three paths, short term (acute) based on enzymatic actions, long term (chronic) based on non-enzymatic role, and moonlighting relies of downstream metabolites of tryptophan metabolism (69; 70).

IFNgamma produced by DC, MQ, NK, NKT, CD4+ T cells and CD8+ T cells, after stimulation with IL12 and IL8.  Inflammatory cytokine(s) expressed by DCs produce IFNgamma to stimulate IDO’s enzymatic reactions in acute response.  Then, TDO in liver and tryptophan catabolites act through Aryl hydrocarbon receptor induction for prevention of T cell proliferation. This mechanism is common among IDO, IDO2 (expresses in brain and liver) and TDO (expresses in liver) provide an acute response for an innate immunity (30). When the pDCs are stimulated with IFNgamma, activation of IDO is go through Jak, STAT signaling pathway to degrade Trp to Kyn causing Trp depletion. The starvation of tryptophan in microenvironment inhibits generation of T cells by un-read t-RNAs and induce apoptosis through myc pathway.  In sum, lack of tryptophan halts T cell proliferation and put the T cells in apoptosis at S1 phase of cell division (71; 62).

 T-reg, regulatory T cells; Th, T helper; CTLA-4, cytotoxic T lymphocyte-associated antigen 4; TCR, T cell receptor; IDO, indoleamine 2,3-dioxygenase. (refernece: http://www.pnas.org/content/101/28/10398/suppl/DC)

T-reg, regulatory T cells; Th, T helper; CTLA-4, cytotoxic T lymphocyte-associated antigen 4; TCR, T cell receptor; IDO, indoleamine 2,3-dioxygenase. (refernece: http://www.pnas.org/content/101/28/10398/suppl/DC)

The intermediary enzymes, functioning during Tryptophan degradation in Kynurenine (Kyn) pathway like kynurenine 3-hydroxylase and kynureninase, are also induced after stimulation with liposaccaride and proinflammatory cytokines (72). They exhibit their function in homeostasis through aryl-hydrocarbon receptor (AhR) induction by kynurenine as an endogenous signal (73; 74).  The endogenous tumor-promoting ligand of AhR are usually activated by environmental stress or xenobiotic toxic chemicals in several cellular processes like tumorigenesis, inflammation, transformation, and embryogenesis (Opitz ET. Al, 2011).

Human tumor cells constitutively produce TDO also contributes to production of Kyn as an endogenous ligand of the AhR (75; 27).  Degradation of tryptophan by IDO1/2 in tumors and tumor-draining lymph nodes occur. As a result, there are animal studies and Phase I/II clinical trials to inhibit the IDO1/2 to prevent cancer and poor prognosis (NewLink Genetics Corp. NCT00739609, 2007).

Systemic inflammation (like in sepsis, cerebral malaria and brain tumor) creates hypotension and IDO expression has the central role on vascular tone control (63).  Moreover, inflammation activates the endothelial coagulation activation system causing coagulopathies on patients.  This reaction is namely endothelial cell activation of IDO by IFNgamma inducing Trp to Kyn conversion. After infection with malaria the blood vessel tone has decreases, inflammation induce IDO expression in endothelial cells producing Kyn causing decreased trp, lower arterial relaxation, and develop hypotension (Wang, Y. et. al 2010).  Furthermore, existing hypotension in knock out Ido mice point out a secondary mechanism driven by Kyn as an endogenous ligand to activate non-canonical NfKB pathway (63). Another study also hints this “back –up” mechanism by a significant outcome with a differential response in pDCs against IMT treatment.  Unlike IFN gamma conditioned pDC blocks T cell proliferation and apoptosis, methyl tryptophan fails to inhibit IDO activity for activating naïve T cells to make Tregs at TGF-b1 conditioned pDCs (77; 78).

The second role of the IDO relies on non-enzymatic action as being a signal molecule. Yet, IDO2 and TDO are devoid of this function. This role mainly for maintenance of microenvironment condition. DCs response to TGFbeta-1 exposure starts the kinase Fyn induce phosphorylation of IDO-associated immunoreceptor tyrosine–based inhibitory motifs (ITIMs) for propagation of the downstream signals involving non-canonical (anti-inflammatory) NF-kB pathway for a long term response.

When the pDCs are conditioned with TGF-beta1 the signaling (68; 77; 78) Phospho Inositol Kinase3 (PIK-3)-dependent and Smad independent pathways (79; 80; 81; 82; 83) induce Fyn-dependent phosphorylation of IDO ITIMs.  A prototypic ITIM has the I/V/L/SxYxxL/V/F sequence (84), where x in place of an amino acid and Y is phosphorylation sites of tyrosines (85; 86).  Smad independent pathway stimulates SHP and PIK3 induce both SHP and IDO phosphorylation. Then, formed SHP-IDO complex can induce non-canonical (non-inflammatory) NF-kB pathway (64; 79; 80; 82) by phosphorylation of kinase IKKa to induce nuclear translocation of p52-Relb towards their targets.  Furthermore, the SHP-IDO complex also may inhibit IRAK1 (68).  SHP-IDO complex activates genes through Nf-KB for production of Ido1 and Tgfb1 genes and secretion of IFNalpha/IFNbeta.  IFNa/IFNb establishes a second short positive feedback loop towards p52-RelB for continuous gene expression of IDO, TGFb1, IFNa and IFNb (87; 68).  However, SHP-IDO inhibited IRAK1 also activates p52-RelB.  Nf-KB induction at three path, one main and two positive feedback loops, is also critical.  Finally, based on TGF-beta1 induction (76) cellular differentiation occurs to stimulate naïve CD4+ T cell differentiation to regulatory T cells (Tregs).  In sum, TGF-b1 and IFNalpha/IFNbeta stimulate pDCs to keep inducing naïve T cells for generation of Treg cells at various stages, initiate, maintain, differentiate, infect, amplify, during long-term immune responses (67; 66).

Moonlighting function of Kyn/AhR is an adaptation mechanism after the catalytic (enzymatic) role of IDO depletes tryptophan and produce high concentration of Kyn induce Treg and Tr1 cell expansion leading Tregs to use TGFbeta for maintaining this environment (67; 76). In this role, Kyn pathway has positive-feedback-loop function to induce IDO expression.

TABLE 3- Kyn induced Genes

Table 2: Kyn induced genes based on the only microarray analysis (based on Opitz et. al 2011 data)
  Upregulators Phenotype Location
 Upregulators MYC Oncogene myc
avian myelocytomatosis viral oncogene homolog
protooncogene homologous to myelocytomatosis virus
NfKB complex Inappropriate activation of NF-kappa-B has been linked to inflammatory events associated with autoimmune arthritis, asthma, septic shock, lung fibrosis, glomerulonephritis, atherosclerosis, and AIDS. In contrast, complete and persistent inhibition of NF-kappa-B has been linked directly to apoptosis, inappropriate immune cell development, and delayed cell growth. 10q24.32POSSIBLE INDIRECTLY MANIPULATEDTARGET   4q24 


ALDH1A3(ALDEHYDE DEHYDROGENASE 1 FAMILY, MEMBER A3) An unique ALDH isozyme in human saliva 15q26.3
ARNT2,ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR 2 Member of a novel transcription factor family consisting of a conserved basic helix-loop-helix (bhlh) structural motif contiguous with a PAS domain. Members of this family include PER, the aryl hydrocarbon receptor,SIM1,and HIF1A. 15q25.1
C2CD2 Myogenesis in C2C12 mouse myoblasts by DUX4 and inhibited zebrafish development past gastrulation or caused severe developmental abnormalities in the surviving embryos. 4q35.2
CDC42EP2,CDC42 EFFECTOR PROTEIN 2 A small RHO gtpase, regulates the formation of F-actin-containing structures through its interaction with several downstream effector proteins.  11q13.1
 CDH1,CADHERIN 1;  Uvomorulin, a specific calcium ion-dependent cell adhesion molecule, expresses its adhesive function during the preimplantation stage of development and in epithelial cells,Endometrial carcinoma, somatic, Ovarian carcinoma, somatic, Gastric cancer, familial diffuse, with or without cleft lip and/or palate, Breast cancer, lobular, Prostate cancer, susceptibility to. 16q22.1
CENPACENTROMERIC PROTEIN A;  Centromeric proteins, see CENPB 2p23.3
CREB3L2cAMP RESPONSE ELEMENT-BINDING PROTEIN 3-LIKE 2; Member of the old astrocyte specifically induced substance (OASIS) DNA binding and basic leucine zipper dimerization (bzip) family of transcription factors, which includes CREB3 and CREB4. 7q33
Glaucoma 3A, primary open angle, congenital, juvenile,Or adult onset, Peters anomaly 231300
EGR; Discovered first as a putative G0/G1 switch regulatory gene in human blood lymphocyte cultures and named G0S30 (Forsdyke, 1985). Sequence analysis of the murine gene predicted a protein with 3 DNA-binding zinc fingers POSSIBLE TARGET
EGR1;EARLY GROWTH RESPONSE 1 Displays FOS-like induction kinetics in fibroblasts, epithelial cells, and lymphocyte. EGR1 is also known as KROX24. Or nerve growth factor-induced clone A (NGFIA). 5q31.2(Sukhatme et al., 1988).
EREG;EPIREGULIN Functions as a tumor growth-inhibitory factor inducing morphologic changes and exhibits low affinity for the EGF receptor. Found on hela,on human epidermoid carcinoma A431 cells. Toyoda et al. (1995), Toyoda et al. (1997)
GPR115; G PROTEIN-COUPLED RECEPTOR 115 Expression in pregnant uterus, breast, and genitourinary tract. 6p12.3fredriksson et al. (2002) POSSIBLE target
HK2; HEXOKINASE 2 Hexokinase (EC catalyzes the first step in glucose metabolism, using ATP for the phosphorylation of glucose to glucose-6-phosphate. Four different types of hexokinase, designated HK1, HK2, HK3, and HK4 (encoded by different genes, are present in mammalian tissues. 2p12
HTT; HUNTINGTON DISEASE  Huntington disease (HD) is caused by an expanded trinucleotide repeat (CAG)n, encoding glutamine, in the gene encoding Huntington. An autosomal dominant progressive neurodegenerative disorder with a distinct phenotype characterized by chorea, dystonia, incoordination, cognitive decline, and behavioral difficulties. 4p16.3
IGFBP4; INSULIN-LIKE GROWTH FACTOR-BINDING PROTEIN 4 Insulin-like growth factor binding proteins (igfbps), such as IGFBP4, are involved in the systemic and local regulation of IGF activity. Igfbps contain 3 structurally distinct domains each comprising approximately one-third of the molecule.). 17q21.2(Kiefer et al., 1992
IL1A; INTERLEUKIN 1-ALPHA IL1A is 1 of 2 structurally distinct forms of IL1, the other being IL1B (147720). The IL1A and IL1B proteins are synthesized by a variety of cell types, including activated macrophages, keratinocytes, stimulated B lymphocytes, and fibroblasts, and are potent mediators of inflammation and immunity 2q13(Lord et al., 1991).
IL1B; INTERLEUKIN 1-BETA {Gastric cancer risk after H. Pylori infection} 2q13
Crohn disease-associated growth, failure}, {Diabetes, susceptibility to}, {Kaposi sarcoma, susceptibility to}, {Intracranial hemorrhage in brain, Cerebrovascular malformations, susceptibility to}, {Rheumatoid arthritis, systemic juvenile}. 7p15.3 POSSIBLE COSTIMULATION TARGET
A member of the CXC chemokine family. These small basic heparin-binding proteins are proinflammatory and primarily mediate the activation and migration of neutrophils into tissue from peripheral blood. 4q13.3 (Hull et al., 2001). POSSIBLE  COSTIMULATION TARGET
Integrins are a family of cell surface adhesion molecules that play a major role in diverse cellular and developmental processes including morphogenesis, hemostasis, leukocyte activation, cellular adhesion, and homing.Immune responses at mucosal sites are mediated by lymphocytes associated with mammary glands and the gastrointestinal, genitourinary, and respiratory tracts. Cerf-Bensussan et al. (1987),Parker et al. (1992)
kiaa1644;TRIL;  TLR4 INTERACTOR WITH LEUCINE-RICH REPEATS TRIL is a component of the TLR4 complex and is induced in a number of cell types by lipopolysaccharide (LPS) 7p14.3(Carpenter et al., 2009).
LDO C1LLEUCINE ZIPPER, DOWNREGULATED IN CANCER 1; LDOC1 Contains a leucine zipper-like motif in its N-terminal region and a proline-rich region that shares marked similarity to an SH3-binding domain.  Northern blot analysis detected ubiquitous expression of LDOC1 in normal tissues, with high expression in brain and thyroid and low expression in placenta, liver, and leukocytes.  LDOC1 was expressed in 6 of 7 human breast cancer cell lines examined, but, with only 1 exception, was not expressed in any pancreatic or gastric cancer cell lines examined.  Fluorescence microscopy analysis demonstrated that the LDOC1 protein is located predominantly in the nucleus. Xq27.1 Nagasaki et al. (1999) COSTIMULATION TARGET
MID1; MIDLINE 1 Midline 1 ring finger gene
finger on x and y, mouse, homolog of; fxyOpitz gbbb syndrome, type I
mir-124; MICRO RNA 124-1 Lagos-Quintana et al. (2002) cloned mouse mir124a.Northern blot analysis showed that mir124a was highly expressed in mouse brain, but not in any other mouse tissues examined.Suh et al. (2004) cloned human mirna124a from embryonic stem cells. The mature mirna124a sequence is UUAAGGCACGCGGUGAAUGCCA.Sempere et al. (2004) found that mirna124 was preferentially expressed in brain. Chromosome 8
mir-290 Both of the major editing sites in pri-mir-376 rnas (+4 and +44) are located within the functionally critical 5-prime-proximal ‘seed’ sequences, critical for the hybridization of mirnas to targets, of mir-376, suggesting that edited mature mir-376 rnas may target genes different from those targeted by the unedited mir-376 rnas. Their results suggested that a single A-I base change is sufficient to redirect silencing mirnas to a new set of targets.Editing of mir-376 appears to be one of the mechanisms that ensure tight regulation of uric acid levels in select tissues such as the brain cortex. MICRO RNA 376-B; MIRN376B Kawahara et al. (2007)POSSIBLE COSTIMULATION TARGET
RB1;RB1 GENE Bladder cancer, somatic, Osteosarcoma, somatic, Retinoblastoma, Retinoblastoma, trilateral, Small cell cancer of the lung, somatic. 13q14.2Dryja et al. (1984)
GENE ENHANCER IN B CELLS 3Activated NFKB complex translocates into the nucleus and binds DNA at kappa-B-binding motifs such as 5-prime GGGRNNYYCC 3-prime or 5-prime HGGARNYYCC 3-prime (where H is A, C, or T; R is an A or G purine; and Y is a C or T pyrimidine). 
SERPINB2;SERPIN PEPTIDASE INHIBITOR,Clade B (Ovalbumin), Member 2Plasminogen Activator Inhibitor, Type 2; Pai2
Monocyte Arginine-Serpin
Monocyte-Derived Plasminogen Activator Inhibitor
Urokinase Inhibitor
The specific inhibitors of plasminogen activators have been classified into 4 immunologically distinct groups: PAI1 type PA inhibitor from endothelial cells; PAI2 type PA inhibitor from placenta, monocytes, and macrophages; urinary inhibitor; and protease-nexin-I.Plasminogen activator inhibitor-2 is also known as monocyte arg-serpin because it belongs to the superfamily of serine proteases in which the target specificity of each is determined by the amino acid residue located at its reactive center; i.e., met or val for elastase, leu for kinase, and arg for thrombin. 18q21.33
SH3RF1; SH3 DOMAIN-CONTAINING RING FINGER PROTEIN 2 Chen et al. (2010) cloned SH3RF2, which they called HEPP1. The deduced 186-amino acid protein contains a PP1-binding motif (KTVRFQ). Northern blot analysis detected 1.24- and 0.68-kb HEPP1 transcripts in heart and testis only. 5q32
STC2;STANNIOCALCIN-RELATED PROTEIN Northern blot analysis revealed that STC2 is expressed as multiple transcripts in several human tissues, with the strongest expression in skeletal muscle and heart. No entry??
TAF9; TAF9 RNA POLYMERASE II, TATA BOX-BINDING PROTEIN-ASSOCIATED FACTOR, 32-KD The tafs are required for activated rather than basal transcription and serve to mediate signals between various activators and the basal transcriptional machinery. 5q13.2
Camurati-Engelmann disease 131300
{Cystic fibrosis lung disease, modifier of}TGFB is a multifunctional peptide that controls proliferation, differentiation, and other functions in many cell types. TGFB acts synergistically with TGFA (190170) in inducing transformation. It also acts as a negative autocrine growth factor. Dysregulation of TGFB activation and signaling may result in apoptosis. Many cells synthesize TGFB and almost all of them have specific receptors for this peptide. TGFB1, TGFB2 (190220), and TGFB3 (190230) all function through the same receptor signaling systems.
  TIPARP; TCDD-INDUCIBLE POLY(ADP-RIBOSE) POLYMERASE Amplified and upregulated in head and neck squamous cell carcinoma (HNSCC). The N-terminal part of the TPH domain contains a CCCH-type zinc finger. 3q25.31Katoh and Katoh (2003)  Redon et al. (2001)
TOP2A DNA topoisomerase II, resistance to inhibition of, by amsacrine.  DNA topoisomerases (EC are enzymes that control and alter the topologic states of DNA in both prokaryotes and eukaryotes.There are about 100,000 molecules of topoisomerase II per hela cell nucleus, constituting about 0.1% of the nuclear extract. In a human leukemia cell line, HL-60/AMSA, Hinds et al. (1991) found that resistance to inhibition of topoisomerase II by amsacrine and other intercalating agents was dueTo a single base change, AGA (arginine) to AAA (lysine). 17q21.2
TP53; P53
TRP53Osteosarcoma, Choroid plexus papilloma, Breast cancer,Adrenal cortical carcinoma, Colorectal cancer, Hepatocellular carcinoma, Li-Fraumeni syndrome, Nasop haryngeal carcinoma, Pancreatic cancer, {Glioma susceptibility 1}, {Basal cell carcinoma 7} 
The transcription factor p53 responds to diverse cellular stresses to regulate target genes that induce cell cycle arrest, apoptosis, senescence, DNA repair, or changes in metabolism. In addition, p53 appears to induce apoptosis through nontranscriptional cytoplasmic processes.Activity of p53 is ubiquitously lost in human cancer either by mutation of the p53 gene itself or by loss of cell signaling upstream or downstream 17p13.1 POSSIBLE TARGET FOR CO-STIMULATION
TP73; p53-RELATED PROTEIN p73; p73
The p53 gene (TP53; 191170) is the most frequently mutated tumor suppressor in human cancers. The ability of p53 to inhibit cell growth is due, at least in part, to its ability to bind to specific DNA sequences and activate transcription of target genes, such as that encoding cell cycle inhibitor p21(Waf1/Cip1) 1p36.32
ZIC2; ZIC FAMILY MEMBER 2  Brown et al. (1998) reported that the human ZIC2 gene, a homolog of the Drosophila ‘odd-paired’ (opa) gene, maps to the region of chromosome 13 associated with holoprosencephaly (HPE5; 609637). Have zinc finger domain.Holoprosencephaly-5Holoprosencephaly is the most common structural anomaly of the human brain and is one of the anomalies seen in patients with deletions and duplications of chromosome 13 13q32.3

In T cells, tryptophan starvation induces Gcn2-dependent stress signaling pathway, which  initiates uncharged Trp-tRNA binding onto ribosomes. Elevated GCN2 expression stimulates elF2alfa phosphorylation to stop translation initiation (88). Therefore, most genes downregulated and LIP, an alternatively initiated isoform of the b/ZIP transcription factor NF-IL6/CEBP-beta (89).  This mechanism happens in tumor cells based on Prendergast group observations. As a result, not only IDO1 propagates itself while producing IFNalpha/IFNbeta, but also demonstrates homeostasis choosing between immunegenity by production of TH17or tolerance by Tregs. This mechanism acts like a see-saw. Yet, tolerance also can be broken by IL6 induction so reversal mechanism by SOC-3 dependent proteosomal degradation of the enzyme (90).  All proper responses require functional peripheral DCs to generate mature DCs for T cells to avoid autoimmunity (91)

Niacin (vitamin B3) is the final product of tryptophan catabolism and first molecule at Nicotinomic acid (NDA) Biosynthesis.  The function of IDO in tryptophan and NDA metabolism has a great importance to develop new clinical applications (40; 42; 41).  NAD+, biosynthesis and tryptophan metabolisms regulate several steps that can be utilize pharmacologically for reformation of healthy physiology (40).

IDO for protection in Microbial Infection with Toll-like Receptors

The mechanism of microbial response and infectious tolerance are complex and the origination of IDO based on duplication of microbial IDO (49).  During microbial responses, Toll-like receptors (TLRs) play a role to differentiate and determine the microbial structures as a ligand to initiate production of cytokines and pro-inflammatory agents to activate specific T helper cells (92; 93; 94; 95). Uniqueness of TLR comes from four major characteristics of each individual TLR by ligand specificity, signal transduction pathways, expression profiles and cellular localization (96). Thus, TLRs are important part of the immune response signaling mechanism to initiate and design adoptive responses from innate (naïve) immune system to defend the host.

TLRs are expressed cell type specific patterns and present themselves on APCs (DCs, MQs, monocytes) with a rich expression levels (96; 97; 98; 99; 93; 100; 101; 102; 87). Induction signals originate from microbial stimuli for the genesis of mature immune response cells.  Co-stimulation mechanisms stimulate immature DCs to travel from lymphoid organs to blood stream for proliferation of specific T cells (96).  After the induction of iDCs by microbial stimuli, they produce proinflammatory cytokines such as TNF and IL-12, which can activate differentiation of T cells into T helper cell, type one (Th1) cells. (103). Specific TLR stimulation links innate and acquired responses through simple recognition of pathogen-associated molecular patterns (PAMPs) or co-stimulation of PAMPs with other TLR or non-TLR receptors, or even better with proinflammatory cytokines.   Some examples of ligand- TLR specificity shown in Table1, which are bacterial lipopeptides, Pam3Cys through TLR2 (92; 104; 105), double stranded (ds) RNAs through TLR3 (106; 107), lipopolysaccharide (LPS) through TLR4, bacterial flagellin through TLR5 (108; 109), single stranded RNAs through TLR7/8 (97; 98), synthetic anti-viral compounds imiquinod through TLR 7 and resiquimod through TLR8, unmethylated CpG DNA motifs through TLR9 (Krieg, 2000).

The specificity is established by correct pairing of a TLR with its proinflammatory cytokine(s), so that these permutations influence creation and maintenance of cell differentiation. For example, leading the T cell response toward a preferred Th1 or Th2 response possible if the cytokines TLR-2 mediated signals induce a Th2 profile when combined with IL-2 but TLR4 mediated signals lean towards Th1 if it is combined with IL-10 or Il-12, (110; 111)  (112).

TLR ligand TLR Reference
Lipopolysaccharide, LPS TLR4 (96).  (112).
Lipopeptides, Pam3Cys TLR2 (92; 104; 105)
Double stranded (ds) RNAs TLR3 (106; 107)
Bacterial flagellin TLR5 (108; 109)
Single stranded RNAs TLR7/8 (97; 98)
Unmethylated CpG DNA motifs TLR9 (Krieg, 2000)
Synthetic anti-viral compounds imiquinod and resiquimod TLR7 and TLR8 (Lee J, 2003)

Furthermore, IL6 stimulated DCs relieve the suppression of effector T cells by regulatory T cells (113).  The modification of IDO+ monocytes towards specific subset of T cell activation with specific TLRs are significantly important (94).  The type of cell with correct TLR and stimuli improves or decreases the effectiveness of stimuli. Induction of IDO in monocytes by synthetic viral RNAs (isRNA) or CMV was possible but not in monocyte derived DCs or TLR2 ligand lipopeptide Pam3Cys.  Single- stranded RNA ligands target TLR7/8 in monocytes derive DCs only (Lee J, 2003).  These futures of TLRs important during design of experiments to target and improve the efficacy.

Double-Edged Sword of IDO: The Good and The Bad for Clinical intervention and Developments

High expression level of IDO has a positive impact during pregnancy (29; 28; 114), transplants (115; 116; 117; 118; 119), infectious diseases (96). On the other hand, high IDO expression leads the system to a tolerance state is negative during autoimmune-disorders (120; 121; 122), tumors of cancer (123; 124; 117; 121; 125; 126; 127) (127), and mood disorders (46).

Prevention of allogeneic fetal rejection is possible by tryptophan metabolism (26) by rejecting at lack of IDO but allocating with abundant IDO  (29; 28; 114). The plasticity of  mammary and uterus during reproduction may hold some more answers to prevent GVHD and tumors of cancer with good understanding of IDO and tryptophan mechanism (129; 130). These studies lead to find “the natural regulation mechanism” for protecting the transplants from graft versus host disease GVHD (128) and getting rid of tumors. After allogeneic bone marrow transplants the risk of solid tumor development increased about 80% among 19,229 patients,  even with a greater risk if patients are under 18 years old (117).  The adaptation of tolerance against host mechanism is connected to the IDO expression (131).   During implantation and early pregnancy IDO has a role by making CD4+CD25+Foxp3+ regulatory T cells (Tregs) and expressing in DCs and  MQs  (114; 132; 133).  Clonal deletion mechanism prevents mother to react with paternal products since female mice accepted the paternal MHC antigen-expressing tumor graft during pregnancy and rejected three weeks after delivery (134). CTLA-4Ig gene therapy alleviates abortion through regulation of apoptosis and inhibition of spleen lymphocytes (135).

AutoImmune Disorders:

The balance of IDO expression becomes necessary to prevent overactive immune response self-destruction, so modulation in tryptophan and NDA metabolisms maybe essential.  When splenic IDO-expressing CD11b (+) DCs from tolerized animals applied, they suppressed the development of arthritis, increased the Treg/Th17 cell ratio, and decreased the production of inflammatory cytokines in the spleen (136).   The role of Nicotinamide prevention on type 1 diabetes and ameliorates multiple sclerosis in animal model presented with activities of  NDAs stimulating GPCR109a to produce prostaglandins to induce IDO expression, then these PGEs and PGDs converted to the anti-inflammatory prostaglandin, 15d-PGJ(2) (137; 138; 139).  Thus, these events promote endogenous signaling mechanisms involving the GPCRs EP2, EP4, and DP1 along with PPARgamma. (137).

IDO (indoleamine 2,3-dioxygenase) and IDO2 control a tryptophan catabolism signaling pathway. (a) From tryptophan starvation to LIP activation. By catabolizing the essential amino acid tryptophan, IDO and IDO2 generate kynurenines and other reaction products that can modulate T-cell immunity as well as a local microenvironment that is starved for tryptophan. Little is known as yet of the precise mechanistic effects of the tryptophan catabolites generated. Elaboration of the starvation condition triggers a stress response in local T cells through Gcn2, which responds to amino-acid deprivation by phosphorylating the translation initiation factor eIF2alpha, leading to a blockade of most translation initiation with the exception of certain factors such as LIP involved in mediating responses to the stress. (b) LIP is a dominant negative isoform of the immune regulatory b/ZIP transcription factor NF-IL6, also known as CEBPbeta. LIP is an alternately translated isoform of the transcription factor NF-IL6/CEBPbeta implicated in regulating proliferation and immune response. Starvation responses switch NF-IL6/CEBPbeta expression from LAP isoforms to the LIP isoform through the use of a downstream translation start site in the mRNA. Encoding only a b/ZIP dimerization domain, LIP functions as a 'natural' dominant negative molecule that disrupts NF-IL6/CEBPbeta function by competing with LAP isoforms for binding to target gene promoters. Both IDO and IDO2 can switch on LIP, but subsequent restoration of tryptophan levels will only switch it off in the case of IDO, offering a possible mechanism for distal propagation of immune suppression away from the local tumor microenvironment (Figure 5). NF-IL6/CEBPbeta target genes with relevance to the function of IDO include the immune suppressive cytokines IL-6, IL-10 and TGF-beta, which may be upregulated as a result of LIP induction. (http://www.nature.com/onc/journal/v27/n28/fig_tab/onc200835f3.html)

IDO (indoleamine 2,3-dioxygenase) and IDO2 control a tryptophan catabolism signaling pathway. (a) From tryptophan starvation to LIP activation. By catabolizing the essential amino acid tryptophan, IDO and IDO2 generate kynurenines and other reaction products that can modulate T-cell immunity as well as a local microenvironment that is starved for tryptophan. Little is known as yet of the precise mechanistic effects of the tryptophan catabolites generated. Elaboration of the starvation condition triggers a stress response in local T cells through Gcn2, which responds to amino-acid deprivation by phosphorylating the translation initiation factor eIF2alpha, leading to a blockade of most translation initiation with the exception of certain factors such as LIP involved in mediating responses to the stress. (b) LIP is a dominant negative isoform of the immune regulatory b/ZIP transcription factor NF-IL6, also known as CEBPbeta. LIP is an alternately translated isoform of the transcription factor NF-IL6/CEBPbeta implicated in regulating proliferation and immune response. Starvation responses switch NF-IL6/CEBPbeta expression from LAP isoforms to the LIP isoform through the use of a downstream translation start site in the mRNA. Encoding only a b/ZIP dimerization domain, LIP functions as a ‘natural’ dominant negative molecule that disrupts NF-IL6/CEBPbeta function by competing with LAP isoforms for binding to target gene promoters. Both IDO and IDO2 can switch on LIP, but subsequent restoration of tryptophan levels will only switch it off in the case of IDO, offering a possible mechanism for distal propagation of immune suppression away from the local tumor microenvironment (Figure 5). NF-IL6/CEBPbeta target genes with relevance to the function of IDO include the immune suppressive cytokines IL-6, IL-10 and TGF-beta, which may be upregulated as a result of LIP induction. (http://www.nature.com/onc/journal/v27/n28/fig_tab/onc200835f3.html)

Modulating the immune response at non-canonical at canonocal pathway while keeping the non-canonical Nf-  KB intact may help to mend immune disorders. As a result, the targeted blocking in canonical at associated  kinase IKKβ and leaving non-canonocal Nf-kB pathway intact, DCs tips the balance towards immune supression.  Hence, noncanonical NF-κB pathway for regulatory functions in DCs required effective IDO induction, directly or  indirectly by endogenous ligand Kyn and negative regulation of proinflammatory cytokine production.

As a result, this may help to treat autoimmune diseases such as rheumatoid arthritis, type 1 diabetes,        inflammatory bowel disease, and multiple sclerosis, or allergy or transplant rejection. While the opposite action  needs to be taken during prevention of tumors, that is inhibition of non-canonical pathway.  Inflammation    induces not only relaxation of veins and lowering blood pressure but also stimulate coagulopathies that worsen  the microenvironment and decrease survival rate of patients after radio or chemotherapies .

Viable tumor environment. Tumor survival is dependent upon an exquisite interplay between the critical functions of stromal development and angiogenesis, local immune suppression and tumor tolerance, and paradoxical inflammation. TEMs: TIE-2 expressing monocytes; “M2” TAMs: tolerogenic tumor-associated macrophages; MDSCs: myeloid-derived suppressor cells; pDCs: plasmacytoid dendritic cells; co-stim.: co-stimulation; IDO: indoleamine 2,3-dioxygenase; VEGF: vascular endothelial growth factor; EGF: epidermal growth factor; MMP: matrix metaloprotease; IL: interleukin; TGF-β: transforming growth factor-beta; TLRs: toll-like receptors.  (reference: http://www.hindawi.com/journals/cdi/2012/937253/fig1/)

Viable tumor environment. Tumor survival is dependent upon an exquisite interplay between the critical functions of stromal development and angiogenesis, local immune suppression and tumor tolerance, and paradoxical inflammation. TEMs: TIE-2 expressing monocytes; “M2” TAMs: tolerogenic tumor-associated macrophages; MDSCs: myeloid-derived suppressor cells; pDCs: plasmacytoid dendritic cells; co-stim.: co-stimulation; IDO: indoleamine 2,3-dioxygenase; VEGF: vascular endothelial growth factor; EGF: epidermal growth factor; MMP: matrix metaloprotease; IL: interleukin; TGF-β: transforming growth factor-beta; TLRs: toll-like receptors. (reference: http://www.hindawi.com/journals/cdi/2012/937253/fig1/)


Generating tumor vaccines and using adjuvants underway (140).   Comparison of clinical correlation and genetic responses in several studies hopes to diagnose and target the system for cancer therapies (127; 141; 131).  The recent surveys on IDO expression and human cancers show that IDO targeting is a candidate for cancer therapy since IDO expression recruiting Tregs, downregulating MHC class I and creating negative immune microenvironment for protection of development of tumors (125; 27; 142).  Inhibition of IDO expression can make advances in immunotherapy and chemotherapy fields (143; 125; 131; 144).  IDO has a great importance on prevention of cancer development (126).    There are many approaches to create the homeostasis of immune response by Immunotherapy.  However, given the complexity of immune regulations, immunomodulation is a better approach to correct and relieve the system from the disease.  Some of the current IDO targeted immunotherapy or immmunomodulations are with RNA technology for cancer prevention (145; 146; 147; 148; 149; 150) or applied on human or animals  (75; 151; 12; 115; 152; 9; 125) or chemical, (153; 154) or  radiological (155).  The targeted cell type in immune system generally DCs, monocytes (94), T cells (110; 156) and neutrophils (146; 157). On this paper, we will concentrate on DCvax on cancer treatments.

IDO and the downstream enzymes in tryptophan pathway produce a series of immunosuppressive tryptophan     metabolites that may lead into Tregs proliferation or increase in T cell apoptosis (62; 16; 27; 158), and some can   affect NK cell function (159).  The interesting part of the mechanism is, even without presence of IDO itself,    downstream enzymes of IDO in the kynurenine tryptophan degradation still show immunosuppressive outcome   (160; 73) due to not only Kyn but also TGFbeta stimulated long term responses. DC vaccination with IDO is    plausible (161) due to its power in immune response changes and longevity in the bloodstream for reversing  the system for Th17 production (162).

Taking advantage of the DC’s central role and combining with enhancing molecules for induction of immunity may overcome tolerogenic DCs in tumors of cancers (163; 164). The first successful application of DC vaccine used against advanced melanoma after loading DCs with tumor peptides or autologous cell lysate in presence of adjuvants keyhole limpet hematocyanin (KLH) (165).  Previous animal and clinical studies show use of DCs against tumors created success (165; 166; 167) as well as some problems due to heterogeneity of DC populations in one study supporting tumor growth rather than diminishing (168).

DC vaccination applied onto over four thousand clinical trial but none of them used siRNA-IDO DC vaccination method. Clinical trials evaluating DCs, loaded ex vivo with purified TAAs as anticancer immunotherapeutic interventions, also did not include IDO (Table from (169). This data is coming from 30 clinical trials, 3 of which discontinued, evaluating DCs loaded ex vivo with TAAs as an anticancer immunotherapy for 12 types of cancer [(AML(1), Breast cancer (4), glioblastoma (1), glioma (2), hepatocellular carcinoma (1), hematological malignancies (1), melanoma (6), neuroblastoma sarcoma (2), NSCLC (1), ovarian cancer (3), pancreatic cancer (3), prostate cancer (10)] at phase I, II or I/II.

Tipping the balance between Treg and Th17 ratio has a therapeutic advantage for restoring the health.  This is shown in ovarian cancer by DC vaccination with adjuvants (161).  Rebalancing of the immune system towards immunogenicity may restore Treg/Th17 ratio (162; 170) but it is complicated. The stimulation of IL10 and IL12 induce Tregs produce less Th17 while inhibiting CTL activation and its function (76; 171; 172).  When animals were pre-treated with anti-TGFbeta before vaccination, elevation in the plasma levels of IL-15 for tumor specific T cell survival in (173; 174) ovarian cancer studies was observed.   After human papilloma virus infection, the system present an increase of IL12 (175).  Opposing signal mechanism downregulates the TGFbeta to activate CTL and Th1 population with IL12 and IL15 expression (162; 173).  The effects of IL17 on antitumor properties observed by unique subset of CD4+ T cells (176) called also CD8+ T cells secrete even more IL17 (177).

Use of cytokines as adjuvants during vaccination may improve the efficacy of vaccination, since cancer vaccines, unlike infections vaccines, applied after the infection or disease started against the established adoptive immune response.  It is an almost common practice to use adjuvants to improve efficacy in immunotherapy as a combination therapy (178). Enhancing cancer vaccine efficacy via modulation of the microenvironment is another solution, if only know who are the players.  For example, changing intercellular Ca signaling in T cells is necessary to convert them to Tregs.    Several molecules can be used to initiate and lengthen the activity of intervention to stimulate IDO expression without compromising the mechanism (179) because of the positive feedback loops.  The system is complicated so generally induction is completed ex-vivo stimulation of DCs in cell lysates, or in whole tumor lysates, to create the microenvironment and natural stimulatory agents. Introduction of molecules as an adjuvants on genetic regulation on modulation of DCs are critical, because order and time of the signals, specific location/ tissue, and heterogeneity of personal needs (174; 138; 180). These studies demonstrated that IL15 with low TGFb stimulates CTL and Th1, whereas elevated TGFb with IL10 increases Th17 and Tregs in cancer microenvironments.

For example Ret-peptide antitumor vaccine contains an extracellular fragment of Ret protein and Th1 polarized immunoregulator CpG oligonucleotide (1826), with 1MT, a potent inhibitor of IDO, brought a powerful as well as specific cellular and humoral immune responses in mice (152).  The main idea of choosing Ret is to produce vaccine in ret related carcinomas because ret fulfilled two requirements, first choosing patients self-antigens for cancer therapy with a non-mutated gene, and second, there is no evidence of genetic mutations in Ret amino acids 64-269.

Table 2- IDO Clinical Trials


Clinical Trials From Clinicaltrials.Gov

Title And Details Of The Study

NCT Number Recruitment Condition Primary Completion Date Sponsor/Collaborator Phase orObservation. Intervention Type
2 IDO Inhibitor Study For Relapsed Or Refractory Solid Tumors NCT00739609


Breast Cancer|Lung Cancer|Melanoma|Pancreatic Cancer|Solid Tumors October 2012 NewlLink enetics Corp. 1 CHEM
3  IDO2 Genetic Status Informs The Neoadjuvant Efficacy Of Chloroquine (CQ) In Brain Metastasis Radiotherapy NCT01727531


Brain Metastasis Dec. 2020 Main Line Health NA CHEM
4 Peptide Vaccine And Temozolomide For Metastatic Melanoma Patients NCT01543464


Malignant Melanoma September 2014 Newlink Genetics Corporation 2 CHEM
5 A Phase 1/2 Randomized, Blinded, Placebo Controlled Study Of Ipilimumab In Combination With INCB024360 Or Placebo In Subjects With Unresectable Or Metastatic Melanoma NCT01604889


Metastatic Melanoma August 2014 Incyte Corporation 1/2 BIOLINH+CHEM
6 A Phase 2 Study Of The IDO Inhibitor INCB024360 Versus Tamoxifen For Subjects With Biochemical-Recurrent-Only EOC, PPC Or FTC Following Complete Remission With First-Line Chemotherapy NCT01685255


April 2014 Incyte Corporation 2 CHEM
7   Different Injection Number Of The Same Dose Of Botulinum Toxin A On Overactive Bladder Syndrome NCT01657409


Overactive Bladder March 2014 Buddhist Tzu Chi General Hospital 2 CHEM
8  Study On The Effect Of Intravenous Ascorbic Acid On Intraoperative Blood Loss In Women With Uterine MyomaInterventions: Drug: Ascorbic Acid NCT01715597


Uterine Leiomyoma January 2014 Seoul National University Hospital 3 CHEM
9 1-Methyl-D-Tryptophan In Treating Patients With Metastatic Or Refractory Solid Tumors That Cannot Be Removed By Surgery NCT00567931


Unspecified Adult Solid Tumor, Protocol Specific September 2013 National Cancer Institute (NCI) 1 CHEM
10  Properties Of Mesenchymal Stem Cells In Lung Transplant NCT01668576


Lung Transplantation August 2013 Emory University OBS BIOL
11  The Effects Of Medical Clowns In Children Undergoing Blood Tests NCT01396876


Pain And Anxiety Reduction July 2012 Tel-Aviv Sourasky Medical Center NA BIOL
12   Saline Injection – Assisted Anesthesia In Eyelid Surgery NCT01239498


Blepharoptosis October 2011 Sheba Medical Center 4 CHEMBIOL
13   Effects Of The Consumption Of California Walnuts On Cardiovascular HealthInterventions:            Dietary Supplement: Walnuts NCT01235390


Cardiovascular Disease|Immune Health October 2011 University Of California, Davis|California Walnut Commission 1 FOODALERGY-WALNUT
14  Pomegranate To Reduce Maternal And Fetal Oxidative Stress And Improve Outcome In Pregnancies Complicated With Preterm Premature Rupture Of The Membranes NCT01584323


Preterm Premature Rupture Of Membranes|Pregnant State 2013 Rambam Health Care Campus NA FOODSUP
1 Phase II INCB024360 Study For Patients With Myelodysplastic Syndromes (MDS) NCT01822691

Not Yet Recruiting

Myelodysplastic Syndromes September 2015 H. Lee Moffitt Cancer Center And Research Institute|Incyte Corporation 2 CHEM-BIOL?
2   Title:  Schizophrenia Imaging NCT01655472

Not Yet Recruiting

Foetal Differences Between Healthy And Schizophernic Parents July 2014 Tel-Aviv Sourasky Medical Center IMAGEN
3  C11 AMT Positron Emission Tomography (PET) Imaging In Patients With Metastatic Invasive Breast Cancer NCT01302821

Not Yet Recruiting

Breast Cancer April 2014     H. Lee Moffitt Cancer Center And Research Institute|National Cancer Institute (NCI) NA BIOLDCAV-P53MTRADIA
4   Sonographic Evaluation Of Visceral Fat After Bariatric Surgery NCT01285791

Not Yet Recruiting

Morbid Obesity April 2012 Hadassah Medical Organization OBS BIOL CELL
5 How Our Immune System Can Help Fight Cancer NCT01042847

Not Yet Recruiting

Ovarian Cancer January 2011 Winthrop UniversityHospita EVALNA POLY.BIOL
6  Title: Study Of The Long-Term Effect Of Frequent Anti-VEGF Dosing On Retinal Function In Patients With Neovascular AMD NCT00533689

Not Yet Recruiting

Electrophysiology 2013 NA  Tel-Aviv Sourasky Medical Center NAEYE BIOL
7  Microbial Surveillance In Children Hospitalized For Cardiovascular Surgery NCT00426894

Not Yet Recruiting

Cardiac Surgery|Perioperative Prophylaxis 2013 NA Hadassah Medical Organization OBS
8 Study Of Chemotherapy In Combination With IDO Inhibitor In Metastatic Breast Cancer NCT01792050

Not Recruitinbut  Active  G

Metastatic Breast Cancer January 2015 Newlink Genetics Corporation 2 CHEM
9 A Dose-Escalation Study In Subjects With Advanced Malignancies NCT01195311

Not BUT  Active Recruiting

Advanced Malignancies November 2012 Incyte Corporation 1 CHEM DOSE
SP  Title:   Mesalamine To Reduce T Cell Activation In HIV Infection NCT01090102

Enrolling By Invitation

HIV Infections|Sexually Transmitted Diseases|Immune System Diseases|Lentivirus Infections|Acquired Immunodeficiency Syndrome January 2013 UC, San Francisco|California HIV/AIDS Research Program|Salix Pharmaceuticals 4 CHEM
1 Study Of Indoleamine 2,3-Dioxygenase Activity, Serum Levels Of Cytokines, BDNF, BH4 And NCT00919295


Fibromyalgia Syndrome October 2011 Mahidol University|University Of Texas|University Of Wuerzburg 2 CHEM.
2 Diagnosis Of Posttraumatic Stress Disorder Following Primary Rhegmatogenous Retinal Detachment NCT01233908


Stress Disorders, Post-Traumatic|Retinal Detachment September 2010 Sheba Medical Center OBSEYE BIOL
3 Comparison Of DCT, ORA And GAT In Eyes After Penetrating Keratoplasty NCT00834782


Corneal Transplantation December 2009 Sheba Medical Center 4
4 Disturbances Of Kynurenine Pathway Of Trytophan Metabolism In Schizophrenia: A Quantitative Reverse Transcription Polymerase Chain Reaction (RT-PCR) Study NCT00573300


Schizophrenia May 2009 North Suffolk Mental Health Association OBSV. BIOL
5 Effect Of Biological Therapy On Biomarkers In Patients With Untreated Hepatitis C, Metastatic Melanoma, Or Crohn Disease NCT00897312


Melanoma August 2008 Vanderbilt-Ingram Cancer Center|National Cancer Institute (NCI) OBSV.  BIOL-CHEM
6 A Prospective Comparative Study Of Induction Of Labor With A Cervical Ripening Double Balloon Vs Foley Catheter NCT00501033


Induction Of Labor|Cesarean|Endometritis February 2008 Western Galilee Hospital-Nahariya NA DEVICE
7 Tryptophan, Serotonin And Kynurenine In Septic Shock NCT00684736


Shock, Septic April 2007 Central Hospital, Versailles OBS KYN
8 Imatinib Mesylate In Treating Patients With Metastatic Breast Cancer NCT00045188


Male Breast Cancer|Recurrent Breast Cancer|Stage IV Breast Cancer July 2004 National Cancer Institute (NCI) 2 CHEM
9 IDO Peptid Vaccination For Stage III-IV Non Small-Cell Lung Cancer Patients. NCT01219348


NSCLC|Lung Cancer NA IDO Peptide Vaccinantio 1
10  Indoleamine 2,3-Dioxygenase (IDO) Activity In Patients With Chronic Lymphocytic Leukemia (CLL) NCT01397916


CLL NA Tampere University Hospital NA
11   Tryptophan Metabolism In Kidney Disease NCT00758537


Chronic Kidney Disease NA Charite University, Berlin, Germany OBS BIOLTRP LEVELS
12 Observational To Investigate The Efficacy Of CRESTOR 5mg In Reaching LDL-C Target Goals In Patients Who Are At High Risk For A Cardiovascular Event NCT00347217


HypercholesteremiaCardiovascular NA Astrazeneca 4 CHEM
13 The Association Between Delivery Method And Maternal Rehospitalization NCT00501501


Hospitalization NA Western Galilee Hospital-Nahariya OBS BIOL
14 Uterine Flora During Elective And Urgent Cesarean Sections NCT00500019


Endometritis NA Western Galilee Hospital-Nahariya OBS BIOL
15   Title: Pilot, Proof-Of-Concept Study Of Sublingual Tizanidine In Children With Chronic Traumatic Brain Injury (TBI) NCT00287157


 Traumatic Brain Injury NA Teva GTC 1B CHEM

Another example came from demonstration of proliferating hemangiomas, benign endothelial tumors and often referred as hemangiomas of infancy appearing at head or neck, expresses IDO and slowly regressed as a result of immune mediated process. Large scale of genomic analysis shows insulin like growth factor 2 as the key regulator of hematoma growth (Ritter et al. 2003).

We set out to develop new technology with our previous expertise in immunotherapy and immunomodulation (181; 182; 183; 184), correcting Th17/Th1 ratio (185), and siRNA technology (186; 187).  We developed siRNA-IDO-DCvax. Patented two technologies “Immunomodulation using Altered DCs (Patent No: US2006/0165665 A1) and Method of Cancer Treatments using siRNA Silencing (Patent No: US2009/0220582 A1). In melanoma cancer DCs were preconditioned with whole tumor lysate but in breast cancer model pretreatment completed with tumor cell lysate before siRNA-IDO-DCvax applied. Both of these studies presented a success without modifying the autanticity of DCs but decreasing the IDO expression to restore immunegenity by delaying tumor growth in breast cancer (147) and in melanoma (188).  Thus, our DCvax specifically interfere with IDO without disturbing natural structure and content of the DCs in vivo.  Thus, we showed that DCvax can carry on this technology to clinical applications.   Furthermore, our method of intervention is more sophisticated since it has a direct interaction mechanism with ex-vivo DC modulation without creating long term metabolism imbalance in Trp/Kyn metabolite mechanisms with corrective and non-invasive actioins.

There are several reasons for us to combine DCs with siRNA technology for making DCvax.  First, prevention of tumor development studies targeting non-enzymatic pathway initiated by pDCs conditioned with TGFbeta is specific to IDO1 (189). Second, IDO upregulation in antigen presenting cells allowing metastasis show that most human tumors express IDO at high levels (123; 124).  Third, tolerogenic DCs secretes several molecules some of them are transforming growth factor beta (TGFb), interleukin IL10), human leukocyte antigen G (HLA-G), and leukemia inhibitory factor (LIF), and non-secreted program cell death ligand 1 (PD-1 L) and IDO, indolamine 2.3-dioxygenase, which promote tumor tolerance. Thus, we took advantage of DCs properties and IDO specificity to prevent the tolerogenicity with siRNA-IDO DC vaccine in both melanoma and breast cancer.  Fourth, IDO expression in DCs makes them even more potent against tumor antigens and create more T cells against tumors. IDOs are expressed at different levels by both in broad range of tumor cells and many subtypes of DCs including monocyte-derived DCs (10), plasmacytoid DCs (142), CD8a+ DCs (190), IDO compotent DCs (17), IFNgamma-activated DCs used in DC vaccination.  These DCs suppress immune responses through several mechanisms for induction of apoptosis towards activated T cells (156) to mediate antigen-specific T cell anergy in vivo (142) and for enhancement of Treg cells production at sites of vaccination with IDO-positive DCs+ in human patients (142; 191; 192; 168; 193; 194).  If DCs are preconditioned with tumor lysate with 1MT vaccination they increase DCvax effectiveness unlike DCs originated from “normal”, healthy lysate with 1MT in pancreatic cancer (195).  As a result, we concluded that the immunesupressive effect of IDO can be reversed by siRNA because Treg cells enhance DC vaccine-mediated anti-tumor-immunity in cancer patients.

Gene silencing is a promising technology regardless of advantages simplicity for finding gene interaction mechanisms in vitro and disadvantages of the technology is utilizing the system with specificity in vivo yet improved(186; 196).  siRNA technology is one of the newest solution for the treatment of diseases as human genomics is only producing about 25,000 genes by representing 1% of its genome. Thus, utilizing RNA opens the doors for more comprehensive and less invasive effects on interventions. Thus this technology is still improving and using adjuvants.  Silencing of K-Ras inhibit the growth of tumors in human pancreatic cancers (197), silencing of beta-catenin in colon cancers causes tumor regression in mouse models (198), silencing of vascular endothelial growth factor (VGEF) decreased angiogenesis and inhibit tumor growth (199).   Combining siRNA IDO and DCvax from adult stem cell is a novel technology for regression of tumors in melanoma and breast cancers in vivo. Our data showed that IDO-siRNA reduced tumor derived T cell apoptosis and tumor derived inhibition of T cell proliferation.  In addition, silencing IDO made DCs more potent against tumors since treated or pretreated animals showed a delay or decreased the tumor growth (188; 147).

Clinical Trials:

First FDA approved DC-based cancer therapies for treatment of hormone-refractory prostate cancer as autologous cellular immunotherapy (163; 164).  However, there are many probabilities to iron out for a predictive outcome in patients.  Clinical trials report shows 38 total studies specifically IDO related function on cancer (16), eye (3), surgery (2), women health (4), obesity (1), Cardiovascular (2), brain (1), kidney (1), bladder (1), sepsis shock (1), transplant (1),  nervous system and behavioral studies (4), HIV (1).  Among these only 22 of which active, recruiting or not yet started to recruit, and 17 completed and one terminated. Most of these studies concentrated on cancer by the industry, Teva GTC ( Phase I traumatic brain injury), Astra Zeneca (Phase IV on efficacy of CRESTOR 5mg for cardiovascular health concern), Incyte corporation (Phase II ovarian cancer), NewLink Genetics Corporation (Phase I breast/lung/melanoma/pancreatic solid tumors that is terminated; Phase II malignant melanoma recruiting, Phase II active, not recruiting metastatic breast cancer, Phase I/II metastatic melanoma, Phase I advanced malignancies), and Salix Corp-UC, San Francisco and HIV/AIDS Research Programs (for HIV Phase IV enrolling by invitation).  Most of these studies based on chemotherapy but there are few that use biological methods completed study with  IDO vaccine peptide vaccination for Stage III-IV non-small-cell lung cancer patients (NCT01219348), observational study on effect of biological therapy on biomarkers in patients with untreated hepatitis C, metastasis melanoma, or Crohn disease by IFNalpha and chemical (ribavirin, ticilimumab (NCT00897312), polymorphisms of patients after 1MT drug application in treating patients with metastatic or unmovable refractory solid tumors by surgery (NCT00758537), IDO expression analysis on MSCs (NCT01668576), and not yet recruiting intervention with adenovirus-p53 transduced dendric cell vaccine , 1MT , radiation, Carbon C 11 aplha-methyltryptophan (NCT01302821).

Among the registered clinical trials some of them are not interventional but  observational and evaluation studies on Trp/Kyn ratio (NCT01042847), Kyn/Trp ratio (NCT01219348), Kyn levels (NCT00897312, NCT00573300),  RT-PCR analysis for Kyn metabolism (NCT00573300, NCT00684736, NCT00758537), and intrinsic IDO expression of mesenchymal stem cells in lung transplant with percent inhibition of CD4+ and CD8+ T cell proliferation toward donor cells (NCT01668576), determining polymorphisms (NCT00426894). These clinical trials/studies are immensely valuable to understand the mechanism and route of intervention development with the data collected from human populations.


Future Actions for Molecular Diagnosis and Targeted Therapies:

Current survival or response rate is around 40 to 50 % range.  By using specific cell type, selected inhibition/activation sequence based on patient’s genomic profile may improve the efficacy of clinical interventions on cancer treatments.

Targeted therapies for specific gene regulation through signal transduction are necessary but there are few studies with genomics based approach.  On the other hand, there are surveys, observational or evaluations (listed in clinical trials section) registered with www.clinicaltrials.gov that will provide a valuable short-list of molecules.  Preventing stimulation of Ido1 as well as Tgfb-1gene expression by modulating receptor mediated phosphorylation between TGFb/SMAD either at Mad-Homology 1 (MH1) or Mad-Homology 1 (MH2) domains is possible (79; 82; 80). Within Smads there is a conserved Mad-Homology 1 (MH1) domain, which is a DNA binding module contains tightly bound Zinc atom. So the zinc can be targeted with a small molecule adjuvant.  Smad MH2 domain is also well conserved as one the most diverse protein-signal interacting molecule during signal transduction due to two important Serine residues located extreme distal C-termini at Ser-Val-Ser in Smad 2 or at pSer-X-PSer in RSmads (80).  Kyn activated orphan G protein–coupled receptor, GPR35 with unknown function with a distinct expression pattern that collides with IDO sites since its expression at high levels of the immune system and the gut (63) (200; 63).


The first study to connect IDO with cancer shows that group (75) so direct targeting to regulate IDO expression is another method.  It is best to act through modulating ISREs in its promoter with RNA-peptide combination technology. Indirectly, IDO can be regulated through Bin1 gene expression control over IDO since Bin1 is a negative regulator of IDO and prevents IDO expression.  IDO is under negative genetic control of Bin1, BAR adapter–encoding gene Bin1 (also known as Amphiphysin2). Bin1 functions in cancer suppression, because attenuation of Bin1 observed in many human malignancies (141; 201; 202; 203; 204; 205; 206).  Absence of Bin1, null Bin1-/- mice studies, upregulates IDO through STAT1- and NF-kB-dependent in tumor cells to escape from T cell–dependent antitumor immunity.   Detailed molecular genetics studies showed that alternative spicing of Bin1 creates tumor suppressor affect.  Its activities also depends on these spliced outcome, such as Exon 10, in muscle. On the other hand, alternative spliced Exon12A contributes brain cell differentiation (209; 210).  In turn Exon 13 in mice has importance in role for regulating growth. When Bin1 is deleted or mutated C2C12 myoblasts interrupted due to its missing Myc, cyclinD1, or growth factor inhibiting genes like p21WAF1 (207; 208).  Thus, myc becomes a natural target and biomarker as well.

Myc is a target at the junction between IDO gene interaction and Trp metabolism.  Bin1 interacts with Myc either early-dependent on Myc or late-independent on Myc, meaning Myc is not present. This gene regulation also interfered by the long term signaling mechanism related to moonlighting pathway (73; 74).  Hence, Trp/Kyn, Kyn/Trp, Th1/Th17 ratios are important to be observed in patients peripheral blood. These direct and indirect gene interactions place Bin1 to function in cell differentiation (211; 212; 205).

Moonlighting maintains the tolerance. The key factor is in this pathway is Kyn so by reviewing one of the microarray analysis for Kyn affect is critical. This data showed that there are 25 genes affected by Kyn, two of which are upregulated and 23 of them downregulated (100). The list of genes and additional knowledge based on previous intervention methods are a good place to start creating a diagnostics panel as a biomarker to monitor outcomes of given immunotherapies. The short list of candidates are as an adjuvant or co-stimulation agents are myc, NfKB at IKKA, C2CD2, CREB3L2, GPR115, IL2, IL8, IL6, and IL1B, mir-376 RNA, NFKB3, TGFb, RelA, and SH3RF1. From the preivos studies we can also add LIP, Fox3P, CTLA-4, Bin1 and IMPACT to the list.  In addition, specific use of TLR, conserved sequences of IDO across its homologous structures and ISREs of IDO or glucorticoid response elements of TDO are great direct targets to modulate the mechanism. Furthermore, some of the signaling pathway molecules CCR6, CCR5, RORgammat, Jak, STAT, IRFs, MH1 and MH2 domains of Smads may add a value.

Endothelial cell coagulation activation mechanism and pDC maturation or immigration from lymph nodes to bloodstream should marry to control not only IDO expression but also genesis of preferred DC subsets. Stromal mesenchymal cells are activated by this modulation at vascular system and interferes with metastasis of cancer. First, thrombin (human factor II) is a well regulated protein in coagulation hemostasis has a role in cell differentiation and angiogenesis. Protein kinase activated receptors (PARs), type of GPCRs, moderate the actions. Second, during hematopoietic response endothelial cells produce hematopoietic growth factors (213; 214) to revise the vascular structure.  Third, components of bone marrow stroma cells include monocytes, adipocytes, and mesenchymal stem cells (215), which are addressing occurrence of coagulapathologies, DIC, bleeding, thrombosis, and penalizing patients response rate towards therapies and decreasing survival rates specially in breast, lung, prostate cancers.

Both silencing IDO in DCs and reinstallinig antitumor immunity by inhibiting tumor-derived immunosupressive molecule IDO through RNA inference combined with our specialization in stem cell technology created a novel method with a success in vivo.  This data suggests that IDO siRNA DCvax can provide a clinical intervention to increase survival rate and prevention of cancer.

Personal genomic profiles are powerful tool to improve efficacy in immunotherapies so considering the influence of age (young vs. adult) and state of immune system (innate vs. adopted or acquired immunity) are important as well.


IDO has a confined function in immune system through complex interactions to maintain hemostasis of immune responses. The genesis of IDO stem from duplication of bacterial IDO-like genes.  Inhibition of microbial infection and invasion by depleting tryptophan limits and kills the invader but during starvation of tryptophan the host may pass the twilight zone since tryptophan required by host’s T cells.  Thus, the host cells in these small pockets adapt to new microenvironment with depleted tryptophan and oxygen poor conditions. Hence, the cell metabolism differentiates to generate new cellular structures, like nodules and tumors under the protection of constitutively expressed IDO in tumors, DCs to inhibit T cell proliferation. On the other hand, having a dichotomy in IDO function can be a potential limiting factor that means is that IDO’s impact on biological system could be variable at many levels based on target cells, IDO’s capacity, pathologic state of the disease and conditions of the microenvironment.  This complexity requires a very close monitoring to analyze the outcome and to prevent conspiracies over the data since some previous studies generated paradoxical results.  Healthcare cost of current therapies through chemotherapies, radiotherapies is very high and provide low efficacy.  Clinical interventions of immunotherapies require control of more than one system, such as coagulation and vascular biology manipulations for a higher efficacy and survival rate in cancer patients. Our siRNA and DC technologies based on stem cell modulation will provide at least prevention of cancer development and hopefully prevention in cancer.


1. Biochemistry of tryptophan in health and disease. BenderDA. 1983, Mol Aspects Med , pp. 6:101–197.

2. Molecular insights into substrate recognition and catalysis by indolamine 2,3-dioxygenase. Forouhar, F., Anderson, R., Mowat, C.F, et al. 2006, PNAS, pp. vol. 104, no:2, 473-478.

3. Importance of the Two Interferon-stimulated Response Element. Konan KV, Taylor, MW. 1996, J. Biol. Chem.-, pp. 19140-5.

4. induction of indolamine 2,3 dioxygenase: A mechanism of the anti-tumor activity of interferon gamma. Ozaki, Y., Edelstein, M.P., Duch, D.S. 1998, PNAS USA., pp. vol:85, 1242-1246.

5. Localization of the human indoleamine 2,3-dioxygenase (IDO) gene to the pericentromeric region of human chromosome 8. . Burkin, D. J., Kimbro, K. S., Barr, B. L., Jones, C., Taylor, M. W., Gupta, S. L. 1993, Genomics , pp. 17: 262-263.

6. Localization of indoleamine 2,3-dioxygenase gene (INDO) to chromosome 8p12-p11 by fluorescent in situ hybridization. Najfeld, V., Menninger, J., Muhleman, D., Comings, D. E., Gupta, S. L. 1993, Cytogenet. Cell Genet. , pp. 64: 231-232.

7. Molecular cloning, sequencing and expression of human interferon-gamma-inducible indoleamine 2,3-dioxygenase cDNA. . Dai, W., Gupta, S. L. 1990, Biochem. Biophys. Res. Commun. , pp. 168: 1-8.

8. Gene structure of human indoleamine 2,3-dioxygenase. Kadoya, A., Tone, S., Maeda, H., Minatogawa, Y., Kido, R. 1992, Biochem. Biophys. Res. Commun. , pp. 189: 530-536.

9. A gene atlas of th emouse and human protein-encoding transcriptomes. Andrew I. Su, Tim Wiltshire, Serge Batalov , Hilmar Lapp , Keith A. Ching , David Block, Jie Zhang , Richard Soden , Mimi Hayakawa , Gabriel Kreiman , Michael P. Cooke , John R. Walker , and John B. Hogenesch. 2004, PNAS, pp. vol. 101, no. 166062-6067 (http://dx.doi.org:/10.1073/pnas.0400782101).

10. Indoleamine 2,3-dioxygenase production by human dendritic cells results in the inhibition of T cell proliferation. Hwu P, Du MX, Lapointe R, Do M, Taylor MW, Young HA. 2000, J. Immunol, pp. 164:3596–3599.

11. Inhibition of T cell proliferation by acrophage tryptophan catabolism. Munn, D.H. et al. 1999, J. Exp. Med., p. 189:1363.

12. HeLa cells cocultured with peripheral blood lymphocytes acquire an immuno-inhibitory phenotype through up-regulation of indoleamine 2,3-dioxygenase activity. Logan, G. J., Smyth, C. M. F., Earl, J. W., Zaikina, I., Rowe, P. B., Smythe, J. A., Alexander, I. E. 2002, Immunology, pp. 105:478-487.

13. Indoleamine 2,3-Dioxygenase – Is It an Immun Suppressor? Soliman H, Mediaville-Varela M, Antonia S. 2010, Cancer J. , pp. 16:354-359.

14. Targeting the immunoregulatory indoleamine 2,3-dioxygenase pathway in immunotherapy. Johnson BA, III, Baban B, Mellor AL. 2009, Immunotherapy. , pp. 645–661.

15. Indoleamine 2,3-dioxygenase and regulation of T cell immunity. AL., Mellor. 2005, Biochem Biophys Res Commun. , pp. 338(1):20–24.

16. Fallarino, F., Grohmann, U., Hwang, K. W., Orabona, C., Vacca, C., Bianchi, R., Belladonna, M. L., Fioretti, M. C.Modulation of tryptophan catabolism by regulatory T cells. Fallarino, F., Grohmann, U., Hwang, K. W., Orabona, C., Vacca, C., Bianchi, R., Belladonna, M. L., Fioretti, M. C., Alegre, M.-L., Puccetti, P. 2003, Nature Immun., pp. 4: 1206-1212.

17. CTLA-4-Ig regulates tryptophan catabolism in vivo. Grohmann, U., Orabona, C., Fallarino, F., Vacca, C., Calcinaro, F., Falorni, A., Candeloro, P., Belladonna, M. L., Bianchi, R., Fioretti, M. C., Puccetti, P. 2002, Nature Immun. , pp. 3: 1097-1101.

18. Reverse signaling through GITR ligand enables dexamethasone to activate IDO in allergy. Grohmann, U., Volpi, C., Fallarino, F., Bozza, S., Bianchi, R., Vacca, C., Orabona, C., Belladonna, M. L., Ayroldi, E., Nocentini, G., Boon, L., Bistoni, F., Fioretti, M. C., Romani, L., Riccardi, C., Puccetti, P. 2007, Nature Med., pp. 13:579-586.

19. Cells expressing indoleamine 2,3-dioxygenase inhibit T cell responses. Mellor, A. L., Keskin, D. B., Johnson, T., Chandler, P., Munn, D. H. 2002, J. Immun. , pp. 168: 3771-3776.

20. Chon, SY, Hassanain, HH, Piine, R., and Gupta, SL. 1995, J. Interferon Cytokine Res. , pp. 15, 517-526.

21. Levy, ED, KEsler, DS, Pine, R., Reich, N, and Darnell, JE.Jr et al. 1988, Genes Dev, pp. 2,383-393.

22. Benoist, C. and Manthis, D. 1990, Annu. Rev of Immunol., pp. 8, 681-715.

23. Dorn, A, Durand, B., Marling, C., Meur, M.L., Beoist, C., and Mathis, D. 1987, PNAS USA, pp. 34, 6249-6253.

24. Konan, K.V. Ph.D. Thesis. Transcriptional Regulation of the Indolamine 2,3-oxygenase Gene. s.l. : Indiana University, Bloominigton, 1995.

25. Tryptophan pyrrolase of rabbit intestine: D- and L–tryptophan cleaving enzyme or enzymes. Yamamoto, S., and Hayashi, O. 1967, J Biol Chem, pp. 242: 5260-5266.

26. Prevention of allogeneic fetal rejection by tryptophan catabolism. Munn, DH, Zhou M, Attwood JT, Bondarev I, Conway SJ, Marshall B, Brown C, Mellor AL. 1998, Science, pp. 281:1191–3.

27. Evidence for a tumoral immune resistance mechanismbased on tryptophan degradation by indoleamine 2,3-dioxygenase. Uyttenhove, C. et al. 2003, Nature Med. 9,, pp. 1269–1274 .

28. Pregnancy: success and failure within the Th1/Th2/Th3 paradigm. Raghupathy, R. 2001., Seminars in Immunology, pp. Volume 13, Issue 4, Pages 219–227.

29. Why is the fetal allograft not rejected? Davies, C. J. March 2007 , J ANIM SCI , pp. vol. 85 no. 13 suppl E32-E35 .

30. Exploring the mechanism of tryptoophan 2,3-dioxygenase. Thackray, S., Mowat, C.G., Chapman, K. 2008, Biochem. Society Transaction., pp. 36, 1120-1123.

31. The new life of a centenarian: signalling functions of NAD(P). Berger F, Ramírez-Hernández MH, Ziegler M. 2004, Trends Biochem Sci , pp. 29:111–118 .

32. Biochemistry of tryptophan in health and disease. DA, Bender. 1983, Mol Aspects Med, pp. 6:101–197.

33. Poliovirus induces indoleamine-2,3-dioxygenase and quinolinic acid synthesis in macaque brain. Heyes MP, Saito K, Jacobowitz D, Markey SP, Takikawa O, Vickers JH. 1992, FASEB J., pp. 6:2977–2989.

34. Sanni LA, Thomas SR, Tattam BN, Moore DE, Chaudhri G, Stocker R, Hunt NH 1998Dramatic changes in oxidative tryptophan metabolism along the kynurenine pathway in experimental cerebral and noncerebral malaria. . Sanni LA, Thomas SR, Tattam BN, Moore DE, Chaudhri G, Stocker R, Hunt NH. 1998, Am J Pathol, pp. 152:611–619.

35. Induction of pulmonary indoleamine 2,3-dioxygenase by intraperitoneal injection of bacterial lipopolysaccharide. . Yoshida R, Hayaishi O. 1978, Proc Natl Acad Sci USA , pp. 75:3998–4000.

36. Induction of indoleamine 2,3-dioxygenase in mouse lung during virus infection. . Yoshida R, Urade Y, Tokuda M, Hayaishi O. 1979, Proc Natl Acad Sci USA , pp. 76:4084–4086.

37. Induction of pulmonary indoleamine 2,3-dioxygenase by intraperitoneal injection of bacterial lipopolysaccharide. Yoshida R, Hayaishi. 1978, PNAS USA, pp. 3998-4000.

38. Sequence of human 2,3-dioxygenase (TDO2): presence of a glucorticoid response-like element composed of a GTT repeat and intronic CCCCT repeat. Comings DE, Muhleman D, Dietz G, Sherman M, Forest. 1995, Genomics, pp. 29:390-396165.

39. Studies on the biosynthesis of Nicotinamide adenine inucleotide. II.Arole of picolinic carboxylase in the Biosynthesisofnicotinamideadeninedinucleotidefromtryptophan in mammals. Ikeda M, Tsuji H, Nakamura S, Ichiyama A, Nishizuka Y, HayaishiO. 1965, J. Biol. Chem. , pp. 240: 1395-1401.

40. The Secret Life of NAD+: An Old Metabolite Controlling New Metabolic Signaling Pathways. Houtkooper R.H., Carles Cantó C. , Wanders, R.J. and Auwerx, J. 2010, Endocrine Reviews , pp. vol. 31 no. 2 194-223,  http://dx.doi.org:/10.1210/er.2009-0026.

41. Stimulation of Nicotinamide adenine dinucleotide biosynthetic pathways delays axonal degeneration after axotomy. Sasaki Y, Araki T, Milbrandt J. 2006, J Neurosci , pp. 26: 8484–8491.

42. European Nicotinamide Diabetes Intervention Trial (ENDIT): a randomised controlled trial of intervention before the onset of type 1 diabetes. Gale EA, Bingley PJ, Emmett CL, CollierT. 2004, Lancet., pp. 363:925–931.

43. Safety of high-dose nicotinamide: a review. Knip M, Douek IF, Moore WP, Gillmor HA, McLean AE, Bingley PJ, Gale EA. 2000, Diabetologia, pp. 43:1337–1345.

44. Large supplements of nicotinic acid and nicotinamide increase tissue NAD and poly(ADP-ribose) levels but do not affect diethylnitrosamine-induced altered hepatic foci in Fischer-344 rats. JacksonTM, Rawling JM, Roebuck BD, Kirkland JB. 1995, J Nutr , p. 125:1455.

45. Characterization and evolution of vertebrate indelamine 2,3-dihydrogenases IDOs from monotremes and marsupials. Yuasa, HJ, Ball, HJ, Ho, YF, Austin, CJ, et al. 2009, Comp. Biochem. Physiol. B. Biochem.. Mol. Biol., pp. 153 (2): 137-144.

46. Novel tryptophan catabolic enzyme IDO2 is the preferred biochemical target of the antitumor indolamine 2,3-dihydrogenase inhibitor compound D-1 methyl-tryptophan. Metz, R., Duhadaway, JB, Kamasani, U, Laury-Kleintop, L., Muller, AJ, Prendergast, GC. 2007, Cancer Res., pp. 67 (15): 7082-7087.

47. Total synthesis of exiguamines A and B inspired by catechollamine chemistry. Sofiyev, V, Lumb, JP, Volgraf, M., Trauner, D. 2012, Chemistry., pp. 18 (16): 4999-5005.

48. Molecular evolution of bacterial indolamine 2,3-dioxygenase. Yuasa, H J, Ushigoe, A, Ball, HJ. 2011, Gene., pp. 484 (1) : 22-31.

49. Infectious tolerance and the long-term acceptance of transplant tissue. Waldman, H., Adams, E., Fairchild, P., and Cobbold, S. 2006, J. Immunol., pp. 212:301-313.

50. Molecular evolution and characterizationof fungal indolamine 2,3-dioxygenases. Yuasa, HJ and Ball, HJ. 2012, J. Mol. Eval., pp. 72 (2): 160-168.

51. convergent evolution. The gene structure of Sulculus 41 kDa myoglobin is homologous with tht of human indolamine dioxygenase. Suzuki, T, Imai, K. 1996, Biochim. Biophys. Acta., pp. 1308(1):41-48.

52. Evolutionof myoglobin. Suzuki, T., Imai, K. 1998, Cell Mol Life Sci, pp. 54(9):979-1004.

53. A myoglobin evolved from indolamine 2,3-dioxygenase, trtptophan-degrading enzyme. Suzuki, T., Kawamichi, H., Imai, K. 1998, Comp Biochem Phisiol. Mol. Biol., pp. 121(2):117-128.

54. Do molluscs possess indolamine 2,3-dioxygenase? Yuasa, HJ and Suzuki, T. 2005, Comp. Biochem. Physiol. B. Biochem. Mol. Biol. , pp. (3) 445-454.

55. Comparison studies of the indolamine dioxygenase-like myoglobin from the abalone Sulculus diversicolor. Suzuki, T., Imai, K. 1997, Comp. Biohem. Phsiol B Biochem Mol Biol, pp. 117 (4)599-604.

56. Orchestration of the immune response by dendritic cells. Buckwalter MR, Albert ML. 2009, Curr Biol., pp. 19(9):355–361.

57. Dendritic cells and the control of immunity. Banchereau J, Steinman RM. 1998, Nature., pp. 245–52.

58. IDO expression by dendritic cells: tolerance and tryptophan catabolism. . Munn DH, Mellor AL. 2004, Nat Rev Immunol. , pp. 762–74.

59. Monocyte and Macrophage. Gordon, S. and Taylor, P.R. 2005, NATURE REVIEWS | IMMUNOLOGY , pp. vol:5, 953-964.

60. Blood monocytes consist of two principal subsets with distinct migratory properties. Geissmann F, Jung S, Littman DR. 2003, Immunity. , pp. 19:71–82.

61. Identification of a novel cell type in peripheral lymphoid organs of mice. I Morphology, quantitation, tissue distribution. . Steinman RM, Cohn ZA. 1973, J Exp Med., pp. 137(5):1142–1162.

62. T cell apoptosis by tryptophan catabolism. Fallarino F, Grohmann U, Vacca C, Bianchi R, Orabona C, Spreca A, Fioretti MC, Puccetti P. 2002, Cell Death Differ , pp. 9:1069–1077.

63. Kynurenine is a novel endothelium derived relaxing factor produced during inflammation. Wang, et al. 2010, Nat. Med., pp. 16(3): 279-285.

64. Activation of the noncanonical NF-kB pathway by HIV controls a Dendritic cell immunoregulatory phenotype. Manches, O. Fernandez, V.M.,, Plumas, J., Chaperot, L., and Bhardwaj, N. 2012, PNAS, pp. vol: 109, 14122-14127.

65. B cells inhibit induction of T cell-dependent tumor immunity. Qin, Z., Richter, G., Schuler, T., Ibe, S., Cao, X, Blakenstein, T. 1998, Nat. Med, p. 4:627.

66. Different partners, Opposite Outcmes: A new perspective of immunobiology of Indolamine 2,3 dioxygenase. Orabona, C., Pallotta, M.T., Grohman, U. 2012, Molecular Medicine., pp. 18:834-842.

67. Indolamine 2,3-dioxygenase: From catalyst to signaling function. Fallarino, F., Grohman, U., and Puccetti, P. 2012, Eurepean J. of Immunol. , pp. 42:1932-1937.

68. IDO: more than an enzyme. Chen, W. 2011, Nature Immonology, pp. 809-811.

69. Indolamine2,3-dehydrogenase in lung dendritic cells promotes Th2 responses and allergic inflammation. Xu, H., Oriss, T.B., Fei, M., Henry, A.C., Melgert, B.N., Chen, L., Mellor, A.L. 2008, PNAS USA, pp. 105: 6690-6695.

70. The immunoregulatory enzyme IDO paradoxically drives B-cellmediated autoimmunity. Scott, G.N., DuHadaway, J., Pigott, E., Ridge, N., Prendergast, G.C., Muller, A.J., Mandik-Nayak, L. 2009, J. Immunol., pp. 182:7509-7517.

71. Tryptophan deprivation sensitizes activated T cells to apoptosis prior to cell division. Lee GK, Park HJ, Macleod M, Chandler P, Munn DH, Mellor AL. 2002, Immunology , pp. 107:452–460.

72. Enzymology of NAD+ homeostasis in man. . Magni G, Amici A, Emanuelli M, Orsomando G, Raffaelli N, Ruggieri S. 2004, Cell Mol Life Sci , pp. 61:19–34.

73. Kynurenine pathway enzymes in dendritic cells initiate tolerogenesis in the absence of functional IDO. . Belladonna ML, Grohmann U, Guidetti P, Volpi C, Bianchi R, Fioretti MC, Schwarcz R, Fallarino F, Puccetti P. 2006, J Immunol. , pp. ;177:130–7.

74. An indogenous tumour promoting ligand of the human aryl hydrocarbon receptor. Opitz, et. al. 2011, pp.  http://dx.doi.org:/10.1038/nature10491,.

75. Inhibition of indoleamine 2,3-dioxygenase, animmunoregulatorytarget of the cancer suppression gene Bin1, potentiates cancer chemotherapy. Muller, A. J. et al. 2005, Nature Med. , pp. 11, 312–319 .

76. TGF-b; a master of all T cell trades. Li, M.O., Fravell, R.A. 2008, Cell. , pp. 134: 392-404.

77. Palotta, M.T. et al. 2011, Nat. Immunol., pp. 12:870-878.

78. Chen, W. et al. 2003, J. Exp. Immunol., p. 198: 1875.

79. Smads: transcriptional activators of TGF-beta responses. . Derynck R, Zhang Y, Feng XH. 1998, Cell , pp. 95 (6): 737–40.
http://dx.doi.org:/10.1016/S0092-8674(00)81696-7.PMID 9865691. .

80. Smad transcription factors. Massagué J, Seoane J, Wotton D. 2005, Genes Dev, pp. 19 (23): 2783–810.
http://dx.doi.org:/10.1101/gad.1350705. PMID .

81. A structural basis for mutational inactivation of the tumour suppressor Smad4. Shi Y, Hata A, Lo RS, Massagué J, Pavletich NP. 1997, Nature., pp. 388 (6637): 87–93.  http://dx.doi.org:/10.1038/40431. PMID 9214508.

82. Promoting bone morphogenetic protein signaling through negative regulation of inhibitory Smads. Itoh F, Asao H, Sugamura K, Heldin CH, ten Dijke P, Itoh S. 2001, EMBO J., pp. 20 (15): 4132–   http://dx.doi.org:/10.1093/emboj/20.15.4132. PMC 149146. PMID 11483516.

83. SMAD_Signaling_Network. http://www.sabiosciences.com. [Online] 2013. http://www.sabiosciences.com/pathway.php?sn=SMAD_Signaling_Network.

84. Immune inhibitory receptors. Revetch, J.V., and Lanier, L.L. 2000, Science., pp. 290:84-89.

85. Soc3 drives proteasomal degradation of indolamine 2,3-dioxygenase (IDO) and antagonizes IDO-dependent tolerogenesis. Orabona, C., Pallotta, M., Volpi, C., et al. 2008, PNAS USA, pp. 105: 20828-20833.

86. Cutting edge; silencing supressor of cytokine signaling3 expression in dendritic cells turns CD28-Ig from immune adjuvant to supressant. Orabona, C.,, Belladonna, M.L., et all. 2005, J. Immunol., pp. 174: 6582-6586.

87. Molecular signatures of T-cell inhibition in HIV-1 infection. Larsson, M., Shankar. E.M, Che, K.F., Ellegard, R., Barathan, M., Velu, V., and Kamarulzaman, A. 2013, Retrovirology, p. 10:31.

88. TGF-beta and CD4+CD25+ regulatory cells. Huber, S. and Schramn, C. 2006, Front. Bioscie., pp. 11:1014-1023.

89. Immune Escape as a fundemental trait of cancer; focus on IDO. Prendergast, G.C. 2008, Oncogene., pp. 27, 3889-3900.

90. Il-6 inhibits the tolerogenic functionof CD8+ dendritic cells expressing indolamine 2,3-dioxygenase. Grohman, U., Fallarino, F., et al. 2001, J. Immunol., pp. 167:708-714.

91. Avoiding horror autotoxicus: Th eimportance of dentritic cells in peripheral T cell tolerance. Steinman, R.M., and Nussenzweig, M.C. 2002, PNAS, pp. no:1, 351-358.

92. Dendritic-cell function in Toll-like receptor- and MyD88-knockout mice . Kaisho, T., Akira, S. 2001, Trends Immunol , pp. 22,78-83.

93. Innate sensing of self and non-self RNAs by Toll-like receptors. Sioud, M. 2006., Trends Mol Med., pp. 12:67–76.

94. Impaired expression of indoleamine 2, 3-dioxygenase in monocyte-derived dendritic cells in response to Toll-like receptor-7/8 ligands. Furset, G., Fløisand, Y. and Sioud, M. 2008, Immunology., pp. 123(2): 263–271, http://dx.doi.org:/10.1111/j.1365-2567.2007.02695.x.

95. Toll-;ike receptor 9 mediated induction of the immunorepressor pathway of tryptophan metabolism. Fallarino, F., and Puccetti, P. 2006, Eur. J. of Imm., pp. 36:8-11.

96. Toll-like receptors and host defense against microbial pathogens: bringing specificity to the innate immune system. . Netea MG, der Graaf C, Van der Meer JWM, Kullberg BJ. 2004, J Leukoc Biol. , pp. 75:749–55.

97. Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8. . Heil F, Hemmi H, Hochrein H, et al. 2004, Science. , pp. 303:1526–9.

98. Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA. . Diebold SS, Kaisho T, Hemmi H, Akira S, Reis e Sousa C. 2004., Science. , pp. 303:1529–31. .

99. The role of CpG motifs in innate immunity. Krieg, A.M. 2000., Curr Opin Immunol., pp. 12:35–43.

100. Anendogenous tumour-promoting ligand of the human aryl hydrocarbon receptor. Opitz, C.A., Litzenburger, U.M., Sahm, F., Ott,M., Tritschler, I., Trump, S. 2011, Nature, pp. vol 478; 197-203.

101. Impaired impression of Indolamine 2,3-deoxygenase in monocyte derived DCs in response to TLR-7/8. Furset, G., Floisand, Y., Sioud, M. 2007, Immunology, pp. 263-271.

102. Activationof the noncanonical NF-kB pathway by HIV controls a Dendritic cell immunoregulatory phenotype. Manches, O. Fernandez, V.M.,, Plumas, J., Chaperot, L., and Bhardwaj, N. 2012, PNAS, pp. vol: 109, 14122-14127.

103. Regulation of dendritic cell numbers and maturation by lipopolysaccharide in vivo . de Smedt, T., Pajak, B., Muraille, E., Lespagnard, L., Heinen, E., De Baetselier, P., Urbain, J., Leo, O., Moser, M. 1996, J. Exp. Med., pp. 184,1413-1424.

104. Subsets of dendritic cell precursors express different Toll-like receptors and respond to different microbial antigens . Kadowaki, N., Ho, S., Antonenko, S., de Waal Malefyt, R., Kastelein, R. A., Bazan, F., Liu, Y-J. 2001, J. Exp. Med., pp. 194,863-869 .

105. TRAF6 is a critical factor for dendritic cell maturation and development . Kobayashi, T., Walsh, P. T., Walsh, M. C., Speirs, K. M., Chiffoleau, E., King, C. G., Hancock, W. W., Caamano, J. H., Hunter, C. A., Scott, P., Turka, L. A., Choi, Y. 2003, Immunity , pp. 19,353-363 .

106. Activation of interferon regulatory factor-3 via toll-like receptor 3 and immunomodulatory functions detected in A549 lung epithelial cells exposed to misplaced U1-snRNA. Sadik CD, Bachmann M, Pfeilschifter J, Mühl H. 2009, Nucleic Acids Res. , pp. 37(15):5041-56. http://dx.doi.org:/10.1093/nar/gkp525. Epub 2009 Jun 18.

107. Triggering of the dsRNA sensors TLR3, MDA5, and RIG-I induces CD55 expression in synovial fibroblasts. Karpus ON, Heutinck KM, Wijnker PJ, Tak PP, Hamann J. 2012, PLoS One., p. 7(5):e35606.  http://dx.doi.org:/10.1371/journal.pone.0035606. Epub 2012 May 10.

108. The structure of the TLR5-flagellin complex: a new mode of pathogen detection, conserved receptor dimerization for signaling. Lu J, Sun PD. 2012, Sci Signal., p. 5(216):pe11.   http://dx.doi.org:/10.1126/scisignal.2002963. .

109. Flagellin/Toll-like receptor 5 response was specifically attenuated by keratan sulfate disaccharide via decreased EGFR phosphorylation in normal human bronchial epithelial cells. Shirato K, Gao C, Ota F, Angata T, Shogomori H, Ohtsubo K, Yoshida K, Lepenies B, Taniguchi N. 2013, Biochem Biophys Res Commun., pp. doi:pii:S0006-291X(13)00779-1. http://dx.doi.org:/10.1016/j.bbrc.2013.05.009. [Epub ahead of print].

110. Differential induction of interleukin-10 and interleukin-12 in dendritic cells by microbial Toll-like receptor activators and skewing of T-cell cytokine profiles Infect. Qi, H., Denning, T. L., Soong, L. 2003, Immun. , pp. 71,3337-3342 .

111. Thoma-Uszynski, S., Kiertscher, S. M., Ochoa, M. T., Bouis, D. A., Norgard, M. V., Miyake, K., Godowski, P. J., Roth, M. D.Activation of Toll-like receptor 2 on human dendritic cells triggers induction of IL-12, but not IL-10 . Thoma-Uszynski, S., Kiertscher, S. M., Ochoa, M. T., Bouis, D. A., Norgard, M. V., Miyake, K., Godowski, P. J., Roth, M. D., Modlin, R. L. 2000, J. Immunol. , pp. 165,3804-3810.

112. Toll-like receptor 2 (TLR2) and TLR4 differentially activate human dendritic cells . Re, F., Strominger, J. L. 2001, J. Biol. Chem. , pp. 276,37692-37699.

113. Pasare, C., Medzhitov, R. (2003) Toll pathway-dependent blockade of CD4+CD25+ T cell-mediated suppression by dendritic cells. Pasare, C., Medzhitov, R. 2003, Science , pp. 299,1033-1036 .

114. What is the role of regulatory T cells in the success of implantation and early pregnancy? Saito, S., Shima, T., Nakashima, A., Shiozaki, A., Ito, M., Sasaki, Y. 2007, J Assist Reprod Genet, pp. 24: 379-386.

115. Sleeping Beauty-based gene therapy with indoleamine 2,3-dioxygenase inhibits lung allograft fibrosis. . Liu H, Liu L, Fletcher BS, Visner GA. 2006, FASEB J, pp. 20:2384-2386. .

116. Indoleamine 2,3-dioxygenase expression in transplanted NOD Islets prolongs graft survival after adoptive transfer of diabetogenic splenocytes. Alexander AM, Crawford M, Bertera S, et al. 2002, Diabetes. , pp. 51(2):356–365.

117. Solid Cancers after Bone Marrow Transplantatioin. Curtis, R.E., Rowlings, P.A., Deeg, J., Schirer, D.A. et al. 1997, The New England Journal of Medicine., pp. 336, No: 13: 897-904.

118. More ADO about IDO; GVHD (commentary). Curti, A., Trabanelli, S., Lemoli, M. 2008, Blood, p. 2950.

119. Jasperson, et al, . 2008, Blood, p. 3257.

120. Tolerance, DCs and tryptophan: much ado about IDO. Grohmann U, Fallarino F, Puccetti P. 2003, Trends Immunol, pp. 24:242-248.

121. Evidence for a tumoral immune resistance mechanism based on tryptophan degradation by indoleamine 2,3-dioxygenase. Uyttenhove C, Pilotte L, Théate I, Stroobant V, Colau D, Parmentier N, et al. 2003, Nat Med , pp. 9:1269–74.

122. Indoleamine 2,3-dioxygenase is a critical regulator of acute graft-versus-host disease lethality. Lisa K. Jasperson, Christoph Bucher, Angela Panoskaltsis-Mortari, Patricia A. Taylor, Andrew L. Mellor, David H. Munn, and Bruce R. Blazar. 2008., Blood., pp. 111:3257-3265.

123. The metabolism of tryptophan. 2. The metabolism of tryptophan in patients suffering from cancer of the bladder. . Boyland, E. & Willliams, D.C. 1956, Biochem. J., pp. 64, 578−582 .

124. Tryptophan metabolism in carcinoma of the breast. . Rose, D. 1967, Lancet , pp. 1, 239−241 .

125. Inhibitors of indoleamine-2,3-dioxygenase for cancer therapy: can we see the wood for the trees? . Löb S, Königsrainer A, Rammensee HG, Opelz G, Terness P. 2009;, Nat Rev Cancer , pp. 9:445–52.  http://dx.doi.org:/10.1158/1078-0432.CCR-11-1331.

126. The hallmarks of cancer. . Hanahan, D. & Weinberg, R.A. 2000., Cell., pp. 100, 57−70.

127. Indoleamine 2,3-Dioxygenase Expression in Human Cancers: Clinical and Immunologic Perspectives. Godin-Ethier, J., Hanafi,L.A., Piccirillo,C.A. and Lapointe, R. 2011, Clin Cancer Res, pp. 17; 6985,  http://dx.doi.org:/10.1158/1078-0432.CCR-11-1331.

128. Dendritic cell modification as a route to inhibiting corneal graft rejection by the indirect pathway of allorecognition. Khan A, Fu H, Tan LA, Harper JE, Beutelspacher SC, Larkin DF, Lombardi G, McClure MO, George AJ. 2013, Eur J Immunol., pp. 43(3):734-46.  http://dx.doi.org:/10.1002/eji.201242914. Epub 2013 Jan 18.

129. Possible role of the ‘IDO-AhR axis’ in maternal-foetal tolerance. . Hao K, Zhou Q, Chen W, Jia W, Zheng J, Kang J, Wang K, Duan T. 2013, Cell Biol Int., pp. 37(2):105-8. doi: 10.1002/cbin.10023. Epub 2013 Jan 2.

130. Implication of indolamine 2,3 dioxygenase in the tolerance toward fetuses, tumors, and allografts. . Dürr S, Kindler V. 2013, J Leukoc Biol. , pp. 93(5):681-7. doi: 10.1189/jlb.0712347. Epub 2013 Jan 16.

131. Evidence for a tumoral immune resistance mechanism based on tryptophan degradation by indoleamine 2,3-dioxygenase. Uyttenhove C, Pilotte L, Théate I, Stroobant V, Colau D, Parmentier N, et al. 2003, Nat Med, pp. 9:1269–74.

132. NAturally arising CD4+ regulatory T cells for immunologic self-tolerance and negative control of immune responses. Sagaguchi, S. 2004, Annu. Rev. of Immunol., pp. 22: 531-562.

133. Regulatory T cells in transplantation tolerance. Wood, K.J., zZSakaguchi, S.,. 2003, Nat. Rev. Immunol., pp. 3; 199-210.

134. The cell awareness of paternal alloantigens during pregnancy. Tafuri, A., Alferink, J., Hammerling, G.J., Arnold, B. 1995, Science, pp. 270; 630-3.

135. Adenovirus mediated CTLA4Ig transgene therapy alleviates abortion by inhibiting spleen lymphocyte proliferation and regulating apoptosis in the feto-placental unit. Li W, Li B, Li S. 2013, J Reprod Immunol. , pp. 97(2):167-74.

136. A distinct tolerogenic subset of splenic IDO(+)CD11b(+) dendritic cells from orally tolerized mice is responsible for induction of systemic immune tolerance and suppression of collagen-induced arthritis. Park MJ, Park KS, Park HS, Cho ML, Hwang SY, Min SY, Park MK, Park SH, Kim HY. 2012, Cell Immunol. , pp. 278(1-2):45-54. http://dx.doi.org:/10.1016/j.cellimm.2012.06.009. Epub 2012 Jul 10.

137. Pharmacological targeting of IDO-mediated tolerance for treating autoimmune disease. Penberthy, W.T. 2007, Curr. Drug Metab., pp. 8:(3):245-266.

138. Indoleamine 2,3-dioxygenase expression in transplanted NOD Islets prolongs graft survival after adoptive transfer of diabetogenic splenocytes. Alexander AM, Crawford M, Bertera S, et al. 2002, Diabetes. , pp. 51(2):356–365.

139. Heme oxygenase-1 plays an important protective role in experimental autoimmune encephalomyelitis. . Liu Y, Zhu B, Luo L, Li P, Paty DW, Cynader MS. 2001., NeuroReport. , pp. 12(9):1841–1845. .

140. Tumor vaccines in 2010: need for integration. Koos, D., Josephs, SF, Alexandrescu, DT et al. 2010, Cell Immunol, pp. 263: 138-147.

141. BIN1 is a novel MYC-interacting protein with features of a tumor suppressor. . Sakamuro, D., Elliott, K., Wechsler-Reya, R. & Prendergast, G.C. 1996, Nat. Genet. , pp. 14, 69−77. .

142. Expression of Indolamine 2,3-dioxygenase by plasmacytoid dendritic cells in tumor draining nodes. Munn, S.H., Sharma, M.D., Hou, D., Baban, B. et al. 2004, J. Clin. Invest. , pp. 114: 280-290.

143. Indoleamine 2,3-Dioxygenase Expression in Human Cancers: Clinical and Immunologic Perspectives. Jessica Godin-Ethier, Laïla-Aïcha Hanafi, Ciriaco A. Piccirillo, and Réjean Lapointe. 2011 , Clin Cancer Res, pp. 17; 6985,   http://dx.doi.org:/10.1158/1078-0432.CCR-11-1331.

144. Potential regulatory function of human dendritic cells expressing indoleamine 2,3-dioxygenase. . Munn, D.H. et al. 2002, Science 297, 1867−1870, pp. 297, 1867−1870 .

145. An HDAC inhibitor enhances cancer therapeutic efficiency of RNA polymerase III promoter-driven IDO shRNA. Yen MC, Weng TY, Chen YL, Lin CC, Chen CY, Wang CY, Chao HL, Chen CS, Lai MD. 2013, Cancer Gene Ther. , p.  http://dx.doi.org:/10.1038/cgt.2013.27. [Epub ahead of print].

146. Systemic delivery of Salmonella typhimurium transformed with IDO shRNA enhances intratumoral vector colonization and suppresses tumor growth. Blache CA, Manuel ER, Kaltcheva TI, Wong AN, Ellenhorn JD, Blazar BR, Diamond DJ. 2012, Cancer Res. , pp. 72(24):6447-56.
http://dx.doi.org:/10.1158/0008-5472.CAN-12-0193. Epub 2012 Oct 22.

147. Silencing IDO in dendritic cells: a novel approach to enhance cancer immunotherapy in a murine breast cancer model. Zheng X, Koropatnick J, Chen D, Velenosi T, Ling H, Zhang X, Jiang N, Navarro B, Ichim TE, Urquhart B, Min W. 2013, Int J Cancer., pp. 132(4):967-77. http://dx.doi.org:/10.1002/ijc.27710. Epub 2012 Jul 20.

148. Immunosuppressive CD14+HLA-DRlow/neg IDO+ myeloid cells in patients following allogeneic hematopoietic stem cell transplantation. Mougiakakos D, Jitschin R, von Bahr L, Poschke I, Gary R, Sundberg B, Gerbitz A, Ljungman P, Le Blanc K. 2013, Leukemia. , pp. 27(2):377-88.
http://dx.doi.org:/10.1038/leu.2012.215. Epub 2012 Jul 25.

149. Upregulated expression of indoleamine 2, 3-dioxygenase in primary breast cancer correlates with increase of infiltrated regulatory T cells in situ and lymph node metastasis. Yu J, Sun J, Wang SE, Li H, Cao S, Cong Y, Liu J, Ren X. 2011, Clin Dev Immunol. , p. 11:469135.
http://dx.doi.org:/10.1155/2011/469135. Epub 2011 Oct 24.

150. Skin delivery of short hairpin RNA of indoleamine 2,3 dioxygenase induces antitumor immunity against orthotopic and metastatic liver cancer. Huang TT, Yen MC, Lin CC, Weng TY, Chen YL, Lin CM, Lai MD. 2011, Cancer Sci. , pp. 102(12):2214-20. http://dx.doi.org:/10.1111/j.1349-7006.2011.02094.x. .

151. Indoleamine 2,3-dioxygenase expression in transplanted NOD Islets prolongs graft survival after adoptive transfer of diabetogenic splenocytes. . Alexander AM, Crawford M, Bertera S, et al. 2002, Diabetes. , pp. 51(2):356–365.

152. Prevention of Spontaneous Tumor Development in a ret Transgenic Mouse Model by Ret Peptide Vaccination with Indoleamine 2,3-Dioxygenase Inhibitor 1-Methyl Tryptophan. Zeng, J., Cai, S., Yi, Y., et al. 2009, Cancer Res., pp. 69: 3963-3970, http://dx.doi.org:/10.1158/0008-5472.CAN-08-2476.

153. Medicinal electronomics bricolage design of hypoxia-targeting antineoplastic drugs and invention of boron tracedrugs as innovative future-architectural drugs. Hori H, Uto Y, Nakata E. 2010, Anticancer Res. , pp. 30(9):3233-42. .

154. Synthesis of 4-cyano and 4-nitrophenyl 1,6-dithio-D-manno-, L-ido- and D-glucoseptanosides possessing antithrombotic activity. Bozó E, Gáti T, Demeter A, Kuszmann J. 2002, Carbohydr Res. , pp. 3;337(15):1351-65.

155. Radiopharmaceuticals XXVII. 18F-labeled 2-deoxy-2-fluoro-d-glucose as a radiopharmaceutical for measuring regional myocardial glucose metabolism in vivo: tissue distribution and imaging studies in animals. Gallagher BM, Ansari A, Atkins H, Casella V, Christman DR, Fowler JS, Ido T, MacGregor RR, Som P, Wan CN, Wolf AP, Kuhl DE, Reivich M. 1977, J Nucl Med. , pp. 18(10):990-6.

156. Tryptophan deprivation sensitizes activated T cells to apoptosis prior to cell division. Lee GK, Park HJ, Macleod M, Chandler P, Munn DH, Mellor AL. 2002, Immunology, pp. 107:452–460.

157. Induction of indoleamine 2,3-dioxygenase by uropathogenic bacteria attenuates innate responses to epithelial infection. Loughman JA, Hunstad DA. 2012 , J Infect Dis. , pp. 205(12):1830-9. http://dx.doi.org:/10.1093/infdis/jis280.

158. Inhibition of allogeneic T cell proliferation by indoleamine 2,3-dioxygenase-expressing dendritic cells: mediation of suppression by tryptophan metabolites. . Terness, P., et al. 2002, J. Exp. Med.196:447–457., pp. 196:447–457.

159. The tryptophan catabolite L-kynurenine inhibits the surface expression of NKp46- and NKG2D-activating receptors and regulates NK-cell function. . Chiesa, M.D., et al. 2006, Blood. , pp. 108:4118–4125.38.

160. Differential effects of the tryptophan metabolite 3-hydroxyanthranilic acid on the proliferation of human CD8+ T cells induced by TCR triggering or homeostatic cytokines. Weber, W.P., et al. 2006, Eur. J. Immunol. , pp. 36:296-304.

161. Dendritic cell vaccination against ovarian cancer–tipping the Treg/TH17 balance to therapeutic advantage? Cannon MJ, Goyne H, Stone PJ, Chiriva-Internati M. 2011, Expert Opin Biol Ther. , pp. 11(4):441-5.  http://dx.doi.org:/10.1517/14712598.2011.554812. .

162. Phenotype, distribution, generation, and functional and clinical relevance of Th17 cells in the human tumor environments. . Kryczek I, Banerjee M, Cheng P, et al. 2009, Blood., pp. 114:1141–1149. .

163. The use of dendritic cells in cancer immunitherapy. Schuler, G., Schuker-Turner, B., Steinman, RM,. 2003, Curr. Opin. Immunol., pp. 15: 138-147.

164. Clinical applications of dentritic cell vaccines. Morse, MA, Lyerly, HK. 2000, Curr. Opin. Mol Ther., pp. 2:20-28.

165. Vaccination of melanoma patients with peptide or tumor lysate-pulsed dendritic cells. Nestle, FO, Alijagic, S., Gillet, M. et al. 1998, Nat. Med., pp. 4: 328-332.

166. Dentritic cell based tumor vaccination in prostate and renal cell cancer: a systamatic review. Draube, A., Klein-Gonzales, Matheus, S et al. 2011, Plos One, p. 6:e1881.

167. [Online] http://www.fda.gov/BiologicsBloodVaccines/CellularGeneTherapy-Products/ApprovedProducts/ucm210215.htm..

168. Dendritic cell based antitumor vaccination: impact of functional indolamine 2,3-dioxygenase expression. Wobster, m., Voigt, H., Houben, R. et al. 2007, Cancer Immunol Immunother, pp. 56:1017-1024.

169. [Online] oncoimmunology.2012 October1; 1(17):1111-1134, doi: 10.4161/onci.21494.

170. Interleukins 1beta and 6 but not transforming growth factor-beta are essential for the differentiation of interleukin 17-producing human T helper cells. Acosta-Rodriguez EV, Napolitani G, Lanzavecchia A, Sallusto F. 2007 , Nat Immunol. , pp. 8(9):942-9. .

171. IFNgamma promotes generationof Il-10 secreting CD4+ T cells that suppress generationof CD8responses in an antigen-experienced host. Liu, X.S., Leerberg, J., MacDonald, K., Leggatt, G.R., Frazer, I.H. 2009, J. Immunol., pp. 183: 51-58.

172. Antigen, in the presence of TGF-beta, induces up-regulationof FoxP3gfp+ in CD4+ TCR transgenic T cells that mediate linked supressionof CD8+ T cell responses. . Kapp, J.A., Honjo, K., Kapp, L.M., Goldsmith, K., Bucy, R.P. 2007, J. Immunol., pp. 179: 2105-2114.

173. Opposing effects of TGF-beta and IL-15 cytokines control the number of short lived effecctor CD8+ T cells. Sanjabi, S, Mosaheb, M.M., Flavell, R.A. 2009, Immunity., pp. 31; 131-144.

174. Synergestic enhancement of CD8+ T cell mediated tumor vaccines efficacy by an anti-tumor forming growth factor-beta monoclonal antibody. . Terabe, M., Ambrosino, E., Takaku, S. et al. 2009, Clin. Cancer Res., pp. 15; 6560-9.

175. IL-12 enhances CTL synapse formationand induces self-reactivity. Markinewicz, MA, Wise, EL, Buchwald, ZS et al. 2009, J. Immunol., pp. 182: 1351-1362.

176. Tumor specific Th17-polarized cells eradicate large established melanoma. Muranski, P., Boni, A., Antony, PA, et al. 2008, Blood, pp. 112; 362-373.

177. Type17 CD8+ T cells dispplay enhanced antitumor immunity. Hinrichs, C.S., Kaiser, A., Paulos, C.M., et al. 2008, Blood., pp. 112:362-373.

178. Marying Immunotherapy with Chemotherapy: Why Say IDO? Muller, AJ, and Prendergrast, GC. 2005, Cancer Research, pp. 65: 8065-8068.

179. Enhancing Cancer Vaccine efficacy via Modulationof the Tumor Environment. Disis, ML. 2009, Clin Cancer Res, pp. 15: 6476-6478.

180. Systemic inhibition of transforming growth factor beta 1 in glioma bearing mice improves the therapeutic efficacy of glioma-associated antigen peptide vaccines. Ueda, R., Fujita, M., Zhu, X., et al. 2009, Clin. Cancer res., pp. 15: 6551-9.

181. Immune modulation by silencing IL-12 productionin dendritic cells using smal interfering RNA. Hill, JA, Ichim, TE, Kusznieruk, KP, et al. 2003, J. Immunol, pp. 171:809-813.

182. Immune modulation and tolerance induction by RelB-silenced dentritic cells through RNA interference. Li, M. Zang, X, Zheng, X, et al. 2007, J. Immunol, pp. 178: 5480-7.

183. RNAi mediated CD40-CD54 interruption promotes tolerance in autoimmune arthritis. . Zheng, X., Suzuki, M., Zhang, X., et al. 2010, Arthritis Res. Ther., p. 12:R13.

184. Dendritic cells genetically engineered to express Fas ligand induce donor-specific hyporesponsiveness and prolong allograft survival. Min, WP. Gorczynki, R., huang, XY et al. 2000, J. Immunol., pp. 164:161-167.

185. LF15-0195 generates tolerogenic dendritic cells by supressionof NF-kappaB signaling through inhibitionof IKK activity. . Yang, J., Bernier, SM, Ichim, TE, et al. 2003, J Leukoc. Biol., pp. 74: 438-447.

186. RNA interfrence: A potent tool for gene specific therapeutics. . Ichim, TE, Li, M., Qian, H., Popov, HI, Rycerz, K., Zheng, X., White, D., Zhong, R., and Min, WP. 2004, Am. J. Transplant, pp. 4:1227-1236.

187. A novel in vivo siRNA delivery system specifically targeting dendritic cells and silencing CD40 genes for immunomodulation. Zheng, X., Vladau, C., Zhang, X. et al. 2009, Blood, pp. 113:2646-2654.

188. Reinstalling Antitumor Immunity by Inhibiting Tumor derived ImmunoSupressive Molecule IDO through RNA interference. Zheng, X et al. 2006, Int. Journal of Immunology., pp. 177:5639-5646.

189. Roles of TGFbeta in metastasis. Padua, D., Massague, J. 2009, Cell Res., pp. 19;89-102.

190. Functional expression of indolamine2,3-dioxygenase by murine CDalpha+dendritic cells. Fallarino, F., Vacca, C, Orabona, C et al. 2002, Int Immunol., pp. 14:65-8.

191. Indolamine2,3-dioxygenase controls conversion of Fox3+ Tregs to TH17-like cells in tumor draining lymph nodes. Sharma, MD, Hou, DY, Liu, Y et al. 2009, Blood, pp. 113: 6102-11.

192. IDO upregulates regulatory T cells via tryptoophan catabolite and supresses encephalitogenic T cell responses in experimental autoimmune encephalomyelitis. Yan, Y, Zhang, GX, Gran, B et al. 2010, J Immunol, pp. 185; 5953-61.

193. IDO activates regulatory T cells and blocks their conversion into Th-17-like T cells. Baban, B, Chandler, PR, Sharma, MD et al. 2009, J Immunol, pp. 183; 2475-83.

194. Enhancement of vaccine-mediated antitumor immunity in cancer patients after depletionof regulatory T cells. Dannull, J., Farrand, KJ, Mathews, SA, et al. 2005, J Clin Invest, pp. 115: 3623-33.

195. 1-MT enhances potency of tumor cell lysate pulled dentritic cells against pancreatic adenocarcinoma by downregulating percentage of Tregs. Li, Y, Xu, J, Zhou, H. et al. 2010, J Huazhong Univ Sci Technol Med Sci , pp. 30: 344-8.

196. siRNA mediated antitumorigenesis for drug target validation and therapeutics. Lu, PY, Xie, FY and Woodle, MC. 2003, Curr Opin Mol. Ther., pp. 5:225-234.

197. Stable supression of tumorigenicity by virus-mediated RNA interference. Brumellkamp, TR, Bernards, R, Agami, R. 2002, Cancer Cell, pp. 2; 243-247.

198. Small interferring RNAs directed against beta-catenin inhibit the in vitro and in vivo growth of colon cancer cells. Verma, UN, Surabhi, RM, Schmaltieg, A., Becerra, C., Gaynor, RB. 2003, Clin. Cancer. Res., pp. 9:1291-1300.

199. siRNA mediated inhibition of vascular endothelial growth factor severely limits tumor resistance to antiangiogeneic thromboposdin-1 and slows tumor vascularization and growth. Filleur, S., Courtin, A, Ait-Si-Ali, S., Guglielmi, J., Merel, C., Harel-Bellan, A., CLezardin, P., and Cabon, F. 2003, Cancer Res, pp. 63; 3919-3922.

200. Kynurenic acid as a ligand for orphan G protein-coupled receptor GPR35. . Wang, J., et al. 2006, J. Biol.Chem. , pp. 281:22021–22028.

201. Bin1 functionally interacts with Myc in cells and inhibits cell proliferation by multiple mechanisms. Elliott, K. et al. 1999, Oncogene , pp. 18, 3564−3573 .

202. Mechanism for elimination of a tumor suppressor: aberrant splicing of a brain-specific exon causes loss of function of Bin1 in melanoma. . Ge, K. et al. 1999, Proc. Natl. Acad. Sci. USA, pp. 96, 9689−9694. .

203. Losses of the tumor suppressor Bin1 in breast carcinoma are frequent and reflect deficits in a programmed cell death capacity. Ge, K. et al. 2000, Int. J. Cancer , pp. 85, 376−383.

204. Loss of heterozygosity and tumor suppressor activity of Bin1 in prostate carcinoma. Ge, K. et al. 2000, Int. J. Cancer , pp. 86, 155−161.

205. Expression of a MYCN-interacting isoform of the tumor suppressor BIN1 is reduced in neuroblastomas with unfavorable biological features. . Tajiri, T. et al. 2003, Clin. Cancer Res., pp. 9, 3345−3355.

206. Targeted deletion of the suppressor gene Bin1/Amphiphysin2 enhances the malignant character of transformed cells. Muller, A.J., DuHadaway, J.B., Donover, P.S., Sutanto-Ward, E. & Prendergast, G.C. 2004, Cancer Biol. Ther. , p. 3.

207. Interactions of myogenic factors and the retinoblastoma protein mediates muscle commitment and cell differentiation. Gu, WJ., Scheniider,W., Condrolli,G., Kaushal,, S, Mahdavi,V., Nadal-Gnard, B. 1993, Cell, pp. 72; 309-324.

208. Structural analysis of the human BIN1 gene: evidence of tissue-specific transcriptional regualtion and alternate splicing. Wechsler-Reya, R, Sakamuro, J., Zhang, J., DuHadaway, J., and Predengast. 1998, J of Biol Chem.

209. A role for th ePutative Tuimor Supressor Bin1 in Muscle Differentiation. Wechsler-Reya, R., Elliott, KJ, Prendergast, GC. 1998, Molecular and Cellular Biology, p. 18 (1) :566.

210. The putative tumor repressor BIN1 is a short lived nuclear phosphoprotein whose localization is altered in malignant cells. Wechsler-Reya, R., Elliot, K., Herlyn, M., Prendergast, GC. 1997, Cancer Res, pp. 57: 3258-3263.

211. Transformation selective apoptosis by farnesyltransferase inhibitors requires Bin1. DuHadaway, J.B. et al. 2003, Oncogene, pp. 22, 3578−3588 (2003).

212. The c-Myc-interacting adapter protein Bin1 activates a caspase-independent cell death program. Elliott, K., Ge, K., Du, W. & Prendergast, G.C. 2000., Oncogene , pp. 19, 4669−4684.

213. Growth stimulation of human bone marrow cells in agar culture by vascular cells. Knudtzon, S., and Mortensen, BT. 1975, Blood, pp. 46 (6) 937-943.

214. Exogenous endothelial cells as accelerators of hematopoietic reconstitution. Mizer, C., Ichim, TE, Alexandrescu, DT, DAsanu, CA, Ramos, F., Turner, A., Woods, EJ, Bogon, V., Murphy, MP, Koos, D., and Patel, A. 2013, J. Translational Medicine, p. 10: 231.

215. Dissecting the bone marrow microenvironment . Torok-Storb, B. et al. 1999, Annals of New York Academy of Science, pp. 872: 164-170.

217. Yuasa, XX and Ball YY. 2011.

218. Possible role of the ‘IDO-AhR axis’ in maternal-foetal tolerance. Hao K, Zhou Q, Chen W, Jia W, Zheng J, Kang J, Wang K, Duan T. 2013, Cell Biol Int. , pp. 37(2):105-8. doi: 10.1002/cbin.10023. .

219. Toll pathway-dependent blockade of CD4+CD25+ T cell-mediated suppression by dendritic cells. Pasare, C., Medzhitov, R. 2003, Science , pp. 299,1033-1036 .

220. Activation of Toll-like receptor 2 on human dendritic cells triggers induction of IL-12, but not IL-10. Thoma-Uszynski, S., Kiertscher, S. M., Ochoa, M. T., Bouis, D. A., Norgard, M. V., Miyake, K., Godowski, P. J., Roth, M. D., Modlin, R. L. 2000, J. Immunol. , pp. 165,3804-3810.

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Genome Jigsaws

Genome Jigsaws (Photo credit: dullhunk)

Sequencing became the household name.  In 2000s, it was thought to be the key of the Pandora’s box for cure.  Then, after completion of Human Genome Projects showed that there are less number of genes than expected.  This outcome induce to originate yet another set of sequencing programs and collaborations around the world, such as Human Protein Project, Human Microorganisms Projects, ENCODE, Transcriptome Sequencing and Consortiums etc.

It is in humankind to believe in magic and illusion.  The strength of biological diversity and complex mechanism of expression may chalanges the set up of a simple but informative specific essay.  Thus, there is a new developing field to mash rules of biology with mathematical formulas to develop the best bioinformatics or also called computational biology.  Predicting transcription start or termination sites, exon boundaries, possible binding sites of transcription regulators for chromatin modification activities, like histone acetylates and enhancer- and insulator-associated factors based on the human genome sequence.  Deep in mind, this assumption supports that the sequence contains signatures for chromatin modifications essential for gene regulation and development.

There are three primary colors, red, yellow and blue, however, an artist can create many shades. Recently, scientists combining and organizing more data to make sense of our blueprint of life to transfer info generation to generation with the hope to cure diseases of human kind.

Analyzing genome and transcriptome open the door.  These studies suggested that all eukaryotic cells has a rich portfolio of RNAs. Among these long non-coding RNAs has impact on protein coding gene expression, regulating multiple processes even including epigenetic gene expression.

Epigenetics, stemness and non-coding RNAs  play a great role to manipulate and correct the gene expression not only at a proper cell type but also location and time within genome without disturbing the host.

Main concern is differentiation of embryonic stem cells under these epigenetics and influencers.  The best known post-transcriptional modifications, which include methylation, acetylation, ubiquination, and SUMOylation of lysine residues, methylation of arginine residues, and phosphorylation of serines, occur on histone tails. “Epi” means “top” or
“above” so this mechanism give a new direction to the genetic pathways as long as the organism live sometime and may lead into evolutions.  It is critical to show the complexity of
mechanism and relativity of a gene role with a single example for each. 

For example,  DNA methylation occurs mostly on cytosine residues on the CpG islands usually located on promoter regions that are associated with tissue-specific gene expression.  However, there are many other forms of DNA methylations, such as  monoallelic methylation in gene imprinting and inactivation of the X chromosome,  in repetitive elements, like transposons.  There are two main mechanisms but this is not our main topic.  Yet, Myc and hypoxia-inducible factor-1α versus certain methyl-CpG-binding proteins, such as MBD1,MBD2, MBD4, MeCP2, and Kaiso works differently.

Stemness is an important factor for an intervention to correct a pathological condition. In terms of epigenetics, regulation and non-coding RNA Vascular endothelial growth factor A (VEGF-A) is an interesting example for differentiation of endothelial cells and morphogenesis of the vascular system during development with several reasons, epigenetics, gene interactions, time and space.  Everything has to be just right, because neither less nor too much can fulfill the destiny to become a complete adult cell or an organism.   For example, both having only one VEGF-A allele and having two-fold excess of VEGF-A results in death during early embryogenesis, since mice can’t develop proper vascular network.  However, explaining diverse mechanisms and functions of VEGF-A is require more information with specific details.  VEGF-A plays many roles in many pathological cases, such as cancer, inflammation, retinopathies, and arthritis because VEGF-A has also function in epigenetic reprogramming of the promoter regions of Rex1 and Oct4 genes, that are critical for a stem cell. Preferred mechanism is anti-angiogeneic state but tumor cells prefer hypermethylation to induce pro-angiogeneic state, thus VEGF-A stimulates PIGF in tumour cells among many other factors.

Now, let’s turn around to observe development of a cell with Polycomb repressive complexes (PRCs) because they are important chromatin regulators of embryonic stem (ES) cell function.  Originally, RYBP shown to function  as transcriptional repressor in reporter assays from both in tissue culture cells and in fruit fly (Drosophila melanogaster ) and as a direct interactor with Ring1A during embryogenesis through methylation. In addition, RYBP in epigenetic resetting during preimplantation development through repression of germ line genes and PcG targets before formation of pluripotent epiblast cells.  However, I do believe that the most important element is efficient repression of endogenous retroviruses (murine endogenous retrovirus called MuERV class),  preimplantation containing zygotic genome activation stage and germ line specific genes. The selective repressor activity of  RYBP  is in the ES cell state. When RYBP−/− ES cells were analyzed by measuring gene expression during differentiation as embryo bodies formed from mutant and wild-type cells, the result presented that  expression of pluripotency genes Oct4 and Nanog was usually downregulated. However, RYBP is able to bind genomic regions independently of H3K27me3 and there is no relation between altered RYBP binding in Dnmt1-mutant cells to DNA methylation status. In sum, RYBP has a large value in undifferentiated ES cells and may affect or even reset epigenetic landscape during early developmental stages. These are the gaps filled by long non coding RNAs.

We learn more compelling information by comparing and contrasting what is normal and what is abnormal. As a result, pathology is a key learning canvas for basic mechanisms in molecular genetics. Then peppered with functional genomics completes the story for an edible outcome.  We generally refer this as a Translational Research.  For example, recent foundlings suggest that H19 contributes to cancer, including hepatocellular carcinoma (HCC) after reviewing Oncomine resource.  According to these observations, in most HCC cases there is a lower expression of  H19 level is compared to the liver. Thus, in vitro and in vivo studies were undertaken with classical genetic analyzes based on loss- and gain-of-function on H19 to characterize two outcomes depend on H19, that are the effects on gene expression and on HCC metastasis. First, the expression of H19 showed gene expression variation since H19 expression was low in tumor cells than peripheral tumor cells.  Second, the metastasis of cancer based on alteration of miR-200 pathway contributing mesenchymal-to-epithelial transition by H19. Therefore, H19 and miR-200 are targets to be utilized during molecular diagnostics development and establishing targeted therapies in cancer.

Long story short, there is a circle of life where everything is connected even though they look different.  As a result, when we see a sunflower or a baby we remember to smile, because life is still an act to puzzle human.

References and Further Readings:


Non-coding RNAs as regulators of gene expression and epigenetics” Cardiovascular Res 1 June 2011: 430-440.

Epigenetic regulation of key vascular genes and growth factors” Cardiovasc Res 1 June 2011: 441-446.

Epigenetic Regulation by Long Noncoding RNAs” Science 14 December 2012: 1435-1439.

Epigenetic control of embryonic stem cell fate” JEM 25 October 2010: 2287-2295.

Transcribed dark matter: meaning or myth?” Hum Mol Genet 15 October 2010: R162-R168.

Epigenetic activation of the MiR-200 family contributes to H19-mediated metastasis suppression in hepatocellular carcinoma” Carcinogenesis 1 March 2013: 577-586.

Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA” Science 7 January 2011: 76-79.

Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context” Bioinformatics 1 May 2013: 1199-1205.


Further Readings specific to Embryonic Stem Cell Differentiation and Development :

“BMP Induces Cochlin Expression to Facilitate Self-renewal and Suppress Neural Differentiation of Mouse Embryonic Stem Cells” J. Biol. Chem. 2013 288:8053-8060


“Regulation of DNA Methylation in Rheumatoid Arthritis Synoviocytes”  J. Immunol. 2013 190:1297-1303


“DNA methylome signature in rheumatoid arthritis” Ann Rheum Dis 2013 72:110-117


“The histone demethylase Kdm3a is essential to progression through differentiation” Nucleic Acids Res 2012 40:7219-7232


“Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer” Nucleic Acids Res 2012 40:6725-6740


“Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells” Nucleic Acids Res 2012 40:3403-3418


“RYBP Represses Endogenous Retroviruses and Preimplantation- and Germ Line-Specific Genes in Mouse Embryonic Stem Cells” Mol. Cell. Biol. 2012 32:1139-1149


“Polycomb Repressor Complex-2 Is a Novel Target for Mesothelioma Therapy” Clin. Cancer Res. 2012 18:77-90


“OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes” Proc. Natl. Acad. Sci. USA 2011 108:14497-14502


“Genome-wide promoter DNA methylation dynamics of human hematopoietic progenitor cells during differentiation and aging” Blood 2011 117:e182-e189


“The CHD3 Chromatin Remodeler PICKLE and Polycomb Group Proteins Antagonistically Regulate Meristem Activity in the Arabidopsis” RootPlant Cell 2011 23:1047-1060


“Chromatin structure of pluripotent stem cells and induced pluripotent stem cells” Briefings in Functional Genomics 2011 10:37-49


Abbreviations used:

DNMT       DNA methyl transferase

ES             embryonic stem

JmjC         Jumonji C

lincRNA     long ncRNA

ncRNA       noncoding RNA

PcG          Polycomb group

PRC          Polycomb repressive complex

PRE          Polycomb repressive element

Previous Posts on Stem Cells:

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…  seen in hematologic malignancies such as cutaneous T-cell lymphoma and peripheral T-cell lymphoma and little or no positive outcome …  resistance to chemotherapeutics, and similarity to cancer stem cells(6-10). Figure 1. HDACis led to the induction of EMT phemotype. (A …

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