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Archive for the ‘Gene Regulation and Evolution’ Category

Cold Spring Harbor Conference Meetings

Larry H. Bernstein, MD, FCAP, Curator

LPBI

Cold Spring Harbor Meetings

  1. “MicroRNAs in aging” from the Molecular Basis of Aging and Disease meeting CSHL ASIA 9/17/2015

CSHL Keynote; Dr. Frank Slack, Harvard Medical School

by CSHL Leading Strand

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  1. Dorcus Cummings Lecture “The Genetic Legacy of Neanderthals” from the 80th Symposium: 21st Century Genetics – Genes at Work 5/30/15

CSHL Keynote, Dr Svante Paabo, Max-Planck-Institute

by CSHL Leading Strand

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  1. “Neuron-glia metabolic coupling—Relevance for neuronal plasticity and functional brain imaging” from the New Insights into Glia Function and Dysfunction meeting, Suzhou China

CSHL Keynote Series; Dr. Pierre J Magistretti, University of Lausanne

by CSHL Leading Strand

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  1. 2015 Cold Spring Harbor Symposium
    21st Century Genetics:

CSHL 2015 Symposium Interview Series with Emmanuelle Charpentier

by CSHL Leading Strand

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  1. 2015 Cold Spring Harbor Symposium
    21st Century Genetics:

 13:33

CSHL 2015 Symposium Interview Series with Joanna Wysocka

by CSHL Leading Strand

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  1. 2015 Cold Spring Harbor Symposium
    21st Century Genetics:

CSHL 2015 Symposium Interview Series wth Wolf Reik

by CSHL Leading Strand

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  1. 2015 Cold Spring Harbor Symposium
    21st Century Genetics:

CSHL 2015 Symposium Interview Series with Susan Lindquist

by CSHL Leading Strand
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  1. 2015 Cold Spring Harbor Symposium
    21st Century Genetics:

CSHL 2015 Symposium Interview Series with Richard Young

by CSHL Leading Strand

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  1. 2015 Cold Spring Harbor Symposium
    21st Century Genetics:

CSHL 2015 Symposium Interviews with Svante Pääbo

by CSHL Leading Strand

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  1. 2015 Cold Spring Harbor Symposium
    21st Century Genetics:

CSHL 2015 Interview Series with Anne Ferguson-Smith

by CSHL Leading Strand

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  1. 2015 Cold Spring Harbor Symposium
    21st Century Genetics:

CSHL 2015 Symposium Interview Series with Jennifer Doundna

by CSHL Leading Strand

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  1. 2015 Cold Spring Harbor Symposium
    21st Century Genetics:

CSHL 2015 Symposium Interview Series with Job Dekker

by CSHL Leading Strand

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  1. 2015 Cold Spring Harbor Symposium
    21st Century Genetics:

CSHL 2015 Symposium Interview Series with Julius Brennecke

by CSHL Leading Strand

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  1. “Mendelian randomization: Harnessing genocopy/phenocopy to identify modifiable causes of disease” from the Biology of Genomes meeting 5/8/2015

CSHL Keynote; Dr George Davey Smith, University of Bristol

by CSHL Leading Strand

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  1. 2015 Cold Spring Harbor Symposium
    21st Century Genetics:

CSHL 2015 Symposium Interview Series with Titia de Lange

by CSHL Leading Strand

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  1. “Ubiquitin and Autophagy Networks” from the The Ubiquitin Family meeting April 24, 2015

CSHL Keynote; Dr Ivan Dikic, Goethe University Medical School

by CSHL Leading Strand

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  1. “How biology optimizes both specificity and efficiency—Single molecule studies of ubiquitylation” from the Cellular Dynamics & Models meeting 3/4/2015

CSHL Keynote; Dr. Marc Kirschner, Harvard Medical School

by CSHL Leading Strand

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  1. The Glymphatic System” from the Blood Brain Barrier meeting 12/12/2014

CSHL Keynote, Dr. Maiken Nedergaard, University of Rochester Medical Center

by CSHL Leading Strand

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  1. Pushing the scale of genetic engineering” from the Synthetic Biology meeting in Suzhou China, CSHL-Asia 12/2/2014

CSHL Keynote Series, Dr. Christopher Voight, Massachusetts Institute of Technology

by CSHL Leading Strand

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Quantitative Biology

2012 Cold Spring Harbor Asia Conference on Synthetic Biology

Hongyu Zhao*

http://dx.doi.org/10.1007/s40484-013-0010-6

Keynote speeches

In the first keynote speech, Birger Lindberg Møller presented a lecture on “Plant power: the ultimate way to go green”. Plant can produce bioactive defense compounds when attacked by insects and microbes. Several of these compounds are used in the treatment of human diseases including cancer. They use the “share-your-parts” principle of synthetic biology to

promote the production of bioactive compounds that are difficult or impossible to synthesize using chemical methods. The second keynote speaker, Lars K. Nielsen presented “Metabolic and regulatory models for synthetic biology design”. He reviewed the status of rational in-silico strain design, providing a cost effective way of constructing metabolic pathways for making biocompounds. The last keynote speaker Sven Panke provided promises and ambition on technical advances as well as on a conceptual rethinking of how we design biocatalysts. He illustrated principles of designing biocatalysts with examples from his own work on nanoand pico-liter reactor design for screening purposes, on real-time mass spectrometry for pathway analysis and optimization, and protein switching for orthogonal in vitro pathways.

Prokaryotic genome engineering

Yu-Sin Jang (KAIST, Korea) reported that the direct butanol-forming pathway is a better channel for optimization of butanol production. An interesting topic was shared by Akio Kawahara-Kobayash (Tokyo Institute of Technology, Japan). At earlier stages in the evolution of the universal genetic code, fewer than 20 amino acids were considered for use. They made artificial genetic codes involving a reduced alphabet to provide not only new insights into primordial genetic codes, but also an essential protein engineering tool for the assessment of the early stages of protein evolution and for the improvement of pharmaceuticals. To meet the demands of industrial production, microbes should maintain a maximized and fixed carbon flux towards target metabolites regardless of fluctuations in intracellular or extracellular environments.

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Behavior

Curator: Larry H Bernstein, MD, FCAP

 

Behavior Brief

The Scientist

http://www.the-scientist.com//?articles.view/articleNo/43904/title/Behavior-Brief/

Wasp-directed webs make better cocoons?

Scientists have uncovered more detail about the unique relationship between the parasitic ichneumon wasp (Reclinervellus nielseni) and its arachnid host, the orb-weaving spider (Cyclosa argenteoalba). While the spider carries the wasp’s egg—and later, hatched larva—within its abdomen, the arachnid spins an atypical web, according to a study published last month (August 5) in The Journal of Experimental Biology. When the larva emerges, killing the spider host, the wasp uses the modified webbing to build a cocoon.

“This discovery—of enhanced behavior as opposed to merely switched behavior—is completely new, impressively demonstrated, and rather unexpected I think,” Mark Shaw an entomologist at the National Museum of Scotland, who was not involved in the study, told Newsweek.

According to The Vergescientists from Kobe University in Japan along with their collaborators determined that the modified web is similar to the orb-weaving spider’s resting web that it uses when it molts—only it is 40 times stronger. This may help the wasp larva build a more durable cocoon. Ecologist Sophie Labaude of the University of Burgundy in France, who was not involved in the work told The Verge that the altered web composition may be a coincidental side effect of chemicals thought to be introduced into the spider during the course of the parasitic infection.

Catharus ustulatus with a tracker on its back J. CRAVES

Some songbirds don’t set cruising altitude

A study published last month (August 12) in The Auk: Ornithological Advances reported the first complete flight-altitude data for a songbird, revealing that one species, the Swainson’s thrush (Catharus ustulatus), changes its altitude intermittently throughout its migration.

“I really thought that the birds would mostly behave like commercial aircraft, ascending to a particular altitude, leveling off and cruising near that altitude, and then coming down just before they landed,” study coauthor Melissa Bowlin of the University of Michigan-Dearborn said in a statement. “I was shocked when I made the first graph for the first bird, and thought it was an anomaly. The more data we obtained, however, the more often we saw the up-and-down pattern to the birds’ flight.”

Bowlin and her colleagues attached radio transmitters to nine Swainson’s thrushes captured from a forest in Illinois during the birds’ spring migration seasons between 2011 and 2013. Once the birds took off, the researchers followed them in a car, keeping track of the birds’ altitudes as they flew through different landscapes. The researchers found that the birds often altered their altitudes by more than 100 meters during their migration. While the authors noted that the precise locations at which the birds ascended and descended cannot be determined until more data are analyzed, they speculated that the birds’ decisions to change altitude may be related to atmospheric changes.

“Dr. Bowlin and her colleagues’ unique yet perplexing records of migrant altitudes raise a number of thought-provoking questions that have implications for species conservation,” Robert Diehl of the US Geological Survey’s Northern Rocky Mountain Science Center said in a statement.

FLICKR, LAGGEDONUSER

Bonobos reuse “peeps”

Humans may not be the only species that can disassociate their communication from their environment. Bonobos (Pan paniscus) also seem to produce the same high-pitched “peep” noises to express psychological states regardless of their context or circumstances, according to study published last month (August 4) in PeerJ. This ability, called functional flexibility, is analogous to the cries or laughter of a human infant, the study’s authors wrote.

“When I studied the bonobos in their native setting in the Congo, I was struck by how frequent their peeps were, and how many different contexts they produce them in,” study coauthor Zanna Clay, a psychologist at the University of Birmingham, told The Guardian. “It became apparent we couldn’t always differentiate between peeps. We needed to understand the context to get to the root of their communication.”

Clay and her colleagues recorded bonobo peeps made during a range of situations, including feeding, sleeping, and traveling. The researchers found that peeps produced during positive situations, such as feeding were indistinguishable from those made within neutral contexts such as resting. However, in negative circumstances such as a state of alarm, the bonobos’ peeps were acoustically different.

“We interpret this evidence as an example of an evolutionary early transition away from fixed vocal signaling towards functional flexibility,” Clay told The Guardian.

An ant (Pristomyrmex punctatus) stands guard over a Japanese oakblue caterpillar (Narathura japonica).WIKIMEDIA, L. SHYAMAL

Manipulation or mutalism?

A new study suggests that a species of Japanese ant (Pristomyrmex punctatus) that imbibes the sweet nectar secreted by Japanese oakblue butterfly (Narathura japonica) caterpillars must pay a price. According to a study published this summer (July 28) in Current Biology, chemicals in the nectar can effectively brainwash the ants, turning them into loyal bodyguards for the caterpillars.

An international group of researchers led by investigators at Kobe University found that ants who fed upon N. japonica’s sweet secretion displayed more aggressive behavior and had lower levels of dopamine in their brains than ants found near caterpillars that didn’t consume the nectar, according toScience.

The results suggest that the relationship between the ants and caterpillar may not be mutualistic, as previously thought, but may have an aspect of parasitism.

“It’s possible that these common food-for-defense interactions, which are typically assumed to be mutualistic, may in fact be maintained primarily through parasitic manipulation of ant behavior,” the authors wrote in their report.

NATURE COMMUNICATIONS, J. COSTELLO ET AL.

Young siphonophores take the lead

For physonect siphonophores (Nanomia bijuga), jellyfish-like marine creatures that travel together as a single unit, the youngest colony members alwaysride shotgun, according to a study published yesterday (September 1) in Nature Communications.

To cover distances of up to 200 meters a day to find food, N. bijuga colony members have to work together. “The younger swimming bells at the tip of the colony are responsible for turning. They generate a lot of torque,” study coauthor Kelly Sutherland, an oceanographer at the University of Oregon, said in a statement. “The older swimming bells toward the base of the colony are responsible for thrust.”

Sutherland and her colleagues recorded swimming colonies from Friday Harbor, Washington, and tracked how the organism displaced particles around it to discern the contribution each unit makes to the movement. They found that even small amounts of water displacement exerted by the youngest members at the tip of the colony had big impacts on which direction the unit travelled.

“They are like the handle of a door,” study coauthor John Costello, a biologist at the Marine Biological Laboratory in Woods Hole, Massachusetts, said in a statement. “If you push on a door near its hinges—its axis of rotation—the door is hard to open. But if you push on the door handle, which is far from the axis of rotation, the door opens easily. A little force placed with a big lever arm has a big effect on turning.”

The authors suggested that the siphonophore’s strategy involving multiple propulsion “engines” and efficient directional control could inspire improved designs for underwater vehicles.

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songbirdplanktonparasitismparasitic wasporb web spidernon-human primatesmigration

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The structure of our visual and auditory system

Larry H. Bernstein, MD, FCAP, Curator

Leaders in Pharmaceutical Intelligence

Series E. 2; 5.8

Revised 9/30/2015

Torsten N. Wiesel (1921— )
President Emeritus
Vincent and Brooke Astor Professor Emeritus – Rockefeller Univerity
1981 Nobel Prize in Physiology or Medicine

Torsten N. Wiesel

The structure of our visual system, beginning at the eyes and ending at the primary visual cortex at the back of the brain, is a little like a maze, intricately constructed to send visual signals through myriad portals and passageways to reach just the right neurons at the end of the path. In the 1950s, H. Keffer Hartline, a member of The Rockefeller Institute for Medical Research, charted the first avenues of that maze when he revealed how the visual stimulus received by the retina is divided, altered and sharpened by the optic nerve network in order to send a more useful picture to the brain. Former Rockefeller president Torsten N. Wiesel, along with his colleague David H. Hubel, continued Dr. Hartline’s exploration at their Harvard Medical School laboratory by delving further back, into the brain, and described for the first time how the system develops innately, how experience shapes it further and how it analyzes visual signals. For this work, Drs. Wiesel and Hubel shared the 1981 Nobel Prize in Physiology or Medicine.

The complex array of stimuli in our visual field passes first through several distinct layers of cells known collectively as the retina. Next they are analyzed by the optic nerve and make their way to the lateral geniculate nucleus (LGN), the first visual processing center in the brain, located in the thalamus of each brain hemisphere. From the LGN, the signals are sent to the primary visual cortex, also known as the striate cortex. Working with cats and rhesus macaque monkeys, Drs. Wiesel and Hubel recorded the electrical impulses of cortical cells in response to various patterns flashed before the eyes. They coined the terms “simple” and “complex” for cells that respond to only one type of stimulus and those that respond to multiple and opposite stimuli.

To understand the differentiation, the scientists conducted a series of experiments to observe the brain’s response when one eye is kept closed for different periods of time. They discovered that animals with one eye closed for the first three months of life become blind in that eye. Examinations revealed no change in the eye itself or in the retina; the LGN cells devoted to that eye had shrunken but still responded to stimulation of the deprived eye as efficiently as those for the normal eye. The difference, they concluded, must therefore be in the striate cortex.

Awards: Nobel Prize in Physiology or Medicine, Louisa Gross Horwitz Prize, National Medal of Science for Biological Sciences

Swedish-born American neurobiologist Torsten N. Wiesel was raised at Beckomberga Hospital, the mental institute where his father was chief psychiatrist. He described himself as a lazy student until his late teens, before embarking on a career of research into the physiology of vision. Wiesel was awarded the Nobel Prize for Medicine in 1981, along with his long-time collaborator David H. Hubel, for mapping the visual or striate cortex, the posterior section of the cerebral cortex. Roger W. Sperry shared that year’s Nobel honors, for work conducted at CalTech. Wiesel also demonstrated the importance of early diagnosis of childhood visual problems.

When a reporter informed him he had won the Nobel Prize, Wiesel’s first response was, “Oh, no, I was afraid of that”, explaining that he feared the hubbub might prove a distraction from his work. In the 1990s he was President of Rockefeller University, and since 2000, he has been Secretary-General of the Human Frontier Science Program, a group which supports collaboration across different scientific fields. He also served more than a decade as Chair of the Human Rights Committee for the National Academy of Sciences.

In 2001, he was named to a high-level post at the National Institutes of Health, but his nomination was scuttled by then-Secretary of Health and Human Services Tommy Thompson, with the official explanation that he had “signed too many full-page letters in the New York Times critical of President Bush.” Wiesel responded, “I have not signed a statement against Bush, but nonetheless for some reason I am on the administration’s blacklist. Perhaps [it is because of] my human rights activities and being contrary in general.”

Structure and evolution of hearing

9.2015 The Scientist

Inner Ear Cartography

Scientists map the position of cells within the organ of Corti.  by Ruth Williams

Age-related hearing loss caused by damage to the sensory hair cells within the cochlea is extremely common, but studying the inner ear is tough. “It’s in the densest bone in the body, so you don’t have access,” says John Brigande of Oregon Health and Science University in Portland. Even if you can extract cells, he says, “there are so darn few of them.” Despite these technical difficulties, researchers have gleaned gene-expression information about different cell types within the organ of Corti—home to the sensory cells within the cochlea. But “it’s not only important to know what a cell expresses,” says Robert Durruthy-Durruthy, a postdoc in the Stanford University lab of Stefan Heller. “It’s also important to know where it can be found within a tissue.” To this end, Durruthy-Durruthy, Heller, and postdoc Jörg Waldhaus have derived a 2-D map of organ of Corti cells from neonatal mice. First, the team sorted all cell types across the medial-to-lateral axis (or width) of the organ based on marker gene expression. The approximately 900 sorted cells, representing nine cell types, were then each quantitatively analyzed for the expression of 192 selected genes. Computational analysis of these expression data then enabled reconstruction of the cells’ positions along the organ’s apical-to-basal (length) and medial-to-lateral axes. In principle, the technique, which harnesses gene-expression information to determine cells’ spatial organization, could be applied to generate 2-D maps of any complex tissue, says Durruthy-Durruthy. Within the mammalian cochlea, apical cells retain regenerative capacity for a few weeks after birth, but basal cells do not. “Spatial mapping allows us to get at the differences [between these cells],” says Brigande, and that could ultimately highlight possible ways to reinstate regeneration in the adult ear. (Cell Reports, 11:1385-99, 2015) To build a map of cells within the organ of Corti—where sound is translated to neural activity— scientists divide the cochlea in two. Each half of the organ of Corti is then broken up into its constituent cells, which comprise nine cell types (represented by the nine colors) spanning the organ’s medial-to-lateral axis.

FROM CELLS TO GENE-EXPRESSION: Each cell is analyzed for the expression of 192 selected genes. Based on the pattern of expression, a cell is given a position within the organ of Corti along both the basal-apical and the medial-lateral axes. Each column represents one of the nine cell types.

Human Hearing: A Primer

Semicircular canals of the vestibular system OSSICLES Ear canal Tympanic membrane (eardrum) When sound enters the ear canal, it vibrates the tympanic membrane, or eardrum. These vibrations are passed through the inner ear via three small bones called ossicles: the malleus, the incus, and the stapes. Finally, vibrations of the stapes stimulate the movement of a fluid called perilymph within the bony labyrinth of the inner ear.

Cochlea – How the human ear translates sound waves into nervous impulses.

Perilymph fills the both the vestibular and tympanic ducts of the cochlea. Between these two channels lies the cochlear duct, which is home to the organ of Corti. There, the soundinduced movement of perilymph in the cochlea is translated to an electrical signal that is sent to the brain for processing.

The organ of Corti sits on the basilar membrane, which separates the cochlear duct from the tympanic duct. As the basilar membrane vibrates in response to fluid movement, it pushes the organ along the tectorial membrane, which shifts laterally over the hair cells. This shift bends projections at the tips of the cells, called stereocilia, resulting in the generation of electrical signals.

The bending of the stereocilia results in the depolarization of the inner hair cell and initiates a nerve impulse through the spinal ganglion neuron at the base of the cell. A series of outer hair cells serves to mechanically amplify the vibrations that trigger the inner hair cells to fire. High-frequency sounds stimulate hair cells at the base of the cochlea, while low-frequency sounds stimulate hair cells at the apex.

Aural History -The form and function of the ears of modern land vertebrates cannot be understood without knowing how they evolved.

by Geoffrey A. Manley

Unlike eyes, which are generally instantly recognizable, ears differ greatly in their appearance throughout the animal kingdom. Some hearing structures may not be visible at all. For example, camouflaged in the barn owl’s facial ruff—a rim of short, brown feathers surrounding the bird’s white face—are clusters of stiff feathers that act as external ears on either side of its head. These feather structures funnel sound collected by two concave facial disks to the ear canal openings, increasing the bird’s hearing sensitivity by 20 decibels—approximately the difference between normal conversation and shouting.

Similar increases in sensitivity result from the large and often mobile external structures, or pinnae, of many mammals, such as cats and bats. Internally, the differences among hearing organs are even more dramatic.

Although fish can hear, only amphibians and true land vertebrates—including the aquatic species that descended from them, such as whales and pinnipeds—have dedicated hearing organs. In land vertebrates belonging to the group Amniota, including lizards, birds, and mammals, sound usually enters through an external canal and impinges on an eardrum that is connected through middle-ear bones to the inner ear. There, hundreds or thousands of sensory hair cells are spread along an elongated membrane that acts as a spectral analyzer, with the result that each local group of hair cells responds best to a certain range of pitches, or sound frequencies. The hair cells then feed this information into afferent nerve fibers that carry the information to the brain. (See “Hearing Primer” on page 34.)

Together, these hair cells and nerve fibers encode a wide range of sounds that enter the ear on that side of the head. Two ears complete the picture, allowing animals’ brains to localize the source of the sounds they hear by comparing the two inputs. Although it seems obvious that the ability to process nearby sounds would be enormously useful, modern amniote ears in fact arose quite late in evolutionary history, and to a large extent independently in different lineages. As a result, external, middle, and inner ears of various amniotes are characteristically different.1

Moreover, the early evolution of these dedicated auditoryorgans in land vertebrates led to the loss of the heavy otolithic membrane that overlies the hair-cell bundles of vestibular organs and is responsible for their slow responses. What remains is the watery macromolecular gel known as the tectorial membrane, which assures that local groups of hair cells move synchronously, resulting in greater sensitivity.

Good high-frequency hearing did not exist from the start, however. For a period of at least 50 million years after amniotes arose, the three main lineages were most likely quite hard of hearing. They had not yet evolved any mechanism for absorbing sound energy from air; they lacked the middle ear and eardrum that are vital for the function of modern hearing organs. As such, ancestral amniotes most likely perceived only sounds of relatively low frequency and high amplitude that reached the inner ear via the limbs or, if the skull were rested on the ground, through the tissues of the head. It is unclear what kind of stimuli could have existed that would have led to the retention of such hearing organs for such a long time.

The magnificent middle ear

During the Triassic period, some 250 to 200 million years ago, a truly remarkable thing happened. Independently, but within just 20 million to 30 million years of one another, all three amniote lineages evolved a tympanic middle ear from parts of the skull and the jaws.2 The tympanic middle ear is the assemblage of tiny bones that connects at one end to an eardrum and at the other end to the oval window, an aperture in the bone of the inner ear. Despite the temporal coincidence in the evolution of these structures in the three amniote lineages and the functional similarities of the adaptations, the groups were by this time so far separated that the middle ears evolved from different structures into two different configurations. The single middle-ear bone, the columella, of archosaurs and lepidosaurs derived from the hyomandibular, a bone that earlier had formed a large strut connecting the braincase to the outer skull.

Research on hearing organs have revealed the remarkable history of this unexpected diversity of ears. Divergence from a common origin Amniote vertebrates comprise three lineages of extant groups that diverged roughly 300 million years ago: the lepidosaurs, which include lizards and snakes; the archosaurs, which include crocodilians and birds; and mammals, which include egg-laying, pouched, and placental mammals. By comparing the skulls of the extinct common ancestors of these three lineages, as well as the ears of the most basal modern amniotes, researchers have concluded that ancestral amniotes had a small (perhaps less than 1 millimeter in length) but dedicated hearing organ: a sensory epithelium called a basilar papilla, with perhaps a few hundred sensory hair cells supported by a thin basilar membrane that is freely suspended in fluid. These rudimentary structures evolved from the hair cells of vestibular organs, which help organisms maintain their balance by responding to physical input, such as head rotation or gravity. Initially, the hearing organ only responded to low-frequency sounds. On their apical surface, all hair cells have tight tufts or bundles of large, hairlike villi known as stereovilli (or, more commonly stereocilia, even though they are not true cilia), which give hair cells their name. Between these stereovilli are proteinaceous links, most of which are closely coupled to sensory transduction channels that respond to a tilting of the stereovilli bundles caused by sound waves.

The amniote hearing organ evolved as a separate group of hair cells that lay between two existing vestibular epithelia. Low-frequency vestibular hair cells became specialized to transduce higher frequencies, requiring much faster response rates. This change is attributable in part to modifications in the ion channels of the cell membrane, such that each cell is “electrically tuned” to a particular frequency, a phenomenon still observed in some modern amniote ears.

MODERN INNER EARS

Arose starting about 200 million years ago In all three lineages, hair cells are arranged along the auditory papilla from low- to high-frequency sensitivity, called a tonotopic organization. In both archosaurs and mammals, one type of hair cell serves to amplify the sound signal received by the other type. In lepidosaurs, the auditory papilla ranges from a few hundred micrometers to 2 millimeters in length and contains two types of hair cells: one with taller bundles and fewer stereovilli that responds to sounds below 1 kHz and another with shorter, thicker bundles that responds to higher-frequency pitches.

The archosaur papilla, which reaches lengths of up to 10 millimeters in some owls, contains many thousands of hair cells of types: tall hair cells, which serve to detect sound, and short hair cells, which amplify the signal. In most mammals, the auditory papilla, called the organ of Corti, evolved to be so long that it began to coil on top of itself. The papilla ranges from 1.5 to 4 coils and 7 millimeters (mouse) to 75 millimeters (blue whale) in length. Mammals have two types of hair cells: covering the oval window, which detect sound, and outer hair cells, which inner hair cells amplify it.

Tectorial membrane

Tall hair cell

Short hair cell

Basilar membrane

Inner

hair cell

Outer

hair cell

In modern representatives, the columella is long and thin, with several, usually cartilaginous extensions known as the extracolumella. One of these, the “inferior process,” connects the inner surface of the eardrum and the columella, which then connects to the footplate that covers the oval window of the inner ear. This two-part system forms a lever that, together with the pressure increase incurred by transmitting from the much larger eardrum to the footplate, greatly magnifies sound entering the inner ear.

In the mammals of the Triassic, the equivalent events were more complex, but the functional result was remarkably similar. Mammal ancestors reduced the number of bones in the lower jaw from seven to one and, in the process, formed a new jaw joint. Initially, the old and new jaw structures existed in parallel, but over time the old joint moved towards the rear of the head. This event, which at any other time would likely have led to the complete loss of the old joint bones, occurred simultaneously with the origin of the mammalian tympanic middle ear. Older paleontological and newer developmental evidence from Shigeru Kuratani’s lab at RIKEN in Japan indicate that the mammalian eardrum evolved at a lower position on the skull relative to that of the other amniotes, a position outside the old jaw joint.3 In time, the bones of this old joint, together with the hyomandibula, became the three bony ossicles (malleus, incus, and stapes) of the new middle ear. Like the middle ear of archosaurs and lepidosaurs, these ossicles form a lever system that, along with the large area difference between eardrum and footplate, greatly magnifies sound input. Thus, remarkably, these complex events led independently to all modern amniotes possessing a middle ear that, at frequencies below 10 kHz, works equally effectively despite the diverse structures and origins. There is also evidence that the three-ossicle mammalian middle ear itself evolved at least twice—in egg-laying mammals such as the platypus, and in therians, which include marsupials and placentals—with similar outcomes.

More…

Aural History

The form and function of the ears of modern land vertebrates cannot be understood without knowing how they evolved.

http://www.the-scientist.com//?articles.view/articleNo/43806/title/Aural-History/

By Geoffrey A. Manley | September 1, 2015

PHOTO CREDITS SEE END OF ARTICLE
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Unlike eyes, which are generally instantly recognizable, ears differ greatly in their appearance throughout the animal kingdom. Some hearing structures may not be visible at all. For example, camouflaged in the barn owl’s facial ruff—a rim of short, brown feathers surrounding the bird’s white face—are clusters of stiff feathers that act as external ears on either side of its head. These feather structures funnel sound collected by two concave facial disks to the ear canal openings, increasing the bird’s hearing sensitivity by 20 decibels—approximately the difference between normal conversation and shouting. Similar increases in sensitivity result from the large and often mobile external structures, or pinnae, of many mammals, such as cats and bats. Internally, the differences among hearing organs are even more dramatic.

Although fish can hear, only amphibians and true land vertebrates—including the aquatic species that descended from them, such as whales and pinnipeds—have dedicated hearing organs. In land vertebrates belonging to the group Amniota, including lizards, birds, and mammals, sound usually enters through an external canal and impinges on an eardrum that is connected through middle-ear bones to the inner ear. There, hundreds or thousands of sensory hair cells are spread along an elongated membrane that acts as a spectral analyzer, with the result that each local group of hair cells responds best to a certain range of pitches, or sound frequencies. The hair cells then feed this information into afferent nerve fibers that carry the information to the brain. (See “Human Hearing: A Primer.”)

For a period of at least 50 million years after amniotes arose, the three main lineages were most likely quite hard of hearing.

Together, these hair cells and nerve fibers encode a wide range of sounds that enter the ear on that side of the head. Two ears complete the picture, allowing animals’ brains to localize the source of the sounds they hear by comparing the two inputs. Although it seems obvious that the ability to process nearby sounds would be enormously useful, modern amniote ears in fact arose quite late in evolutionary history, and to a large extent independently in different lineages. As a result, external, middle, and inner ears of various amniotes are characteristically different.1 New paleontological studies and comparative research on hearing organs have revealed the remarkable history of this unexpected diversity of ears.

Divergence from a common origin

Amniote vertebrates comprise three lineages of extant groups that diverged roughly 300 million years ago: the lepidosaurs, which include lizards and snakes; the archosaurs, which include crocodilians and birds; and mammals, which include egg-laying, pouched, and placental mammals. By comparing the skulls of the extinct common ancestors of these three lineages, as well as the ears of the most basal modern amniotes, researchers have concluded that ancestral amniotes had a small (perhaps less than 1 millimeter in length) but dedicated hearing organ: a sensory epithelium called a basilar papilla, with perhaps a few hundred sensory hair cells supported by a thin basilar membrane that is freely suspended in fluid. These rudimentary structures evolved from the hair cells of vestibular organs, which help organisms maintain their balance by responding to physical input, such as head rotation or gravity. Initially, the hearing organ only responded to low-frequency sounds. On their apical surface, all hair cells have tight tufts or bundles of large, hairlike villi known as stereovilli (or, more commonly stereocilia, even though they are not true cilia), which give hair cells their name. Between these stereovilli are proteinaceous links, most of which are closely coupled to sensory transduction channels that respond to a tilting of the stereovilli bundles caused by sound waves.

The amniote hearing organ evolved as a separate group of hair cells that lay between two existing vestibular epithelia. Low-frequency vestibular hair cells became specialized to transduce higher frequencies, requiring much faster response rates. This change is attributable in part to modifications in the ion channels of the cell membrane, such that each cell is “electrically tuned” to a particular frequency, a phenomenon still observed in some modern amniote ears. Moreover, the early evolution of these dedicated auditory organs in land vertebrates led to the loss of the heavy otolithic membrane that overlies the hair-cell bundles of vestibular organs and is responsible for their slow responses. What remains is the watery macromolecular gel known as the tectorial membrane, which assures that local groups of hair cells move synchronously, resulting in greater sensitivity.

Good high-frequency hearing did not exist from the start, however. For a period of at least 50 million years after amniotes arose, the three main lineages were most likely quite hard of hearing. They had not yet evolved any mechanism for absorbing sound energy from air; they lacked the middle ear and eardrum that are vital for the function of modern hearing organs. As such, ancestral amniotes most likely perceived only sounds of relatively low frequency and high amplitude that reached the inner ear via the limbs or, if the skull were rested on the ground, through the tissues of the head. It is unclear what kind of stimuli could have existed that would have led to the retention of such hearing organs for such a long time.

The magnificent middle ear

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CONVERGING ON THE EAR: Starting around 250 million years ago, the three amniote lineages—lepidosaurs (lizards and snakes), archosaurs (crocodilians and birds), and mammals—separately evolved a tympanic middle ear, followed by evolution of the inner ear, both of which served to increase hearing sensitivity. Despite the independent origin of hearing structures in the three lineages, the outcomes were functionally quite similar, serving as a remarkable example of convergent evolution.
See full infographic: JPG

ILLUSTRATIONS: PHEBE LI FOR THE SCIENTIST. ICONS: ISTOCK.COMDuring the Triassic period, some 250 to 200 million years ago, a truly remarkable thing happened. Independently, but within just 20 million to 30 million years of one another, all three amniote lineages evolved a tympanic middle ear from parts of the skull and the jaws.2

The tympanic middle ear is the assemblage of tiny bones that connects at one end to an eardrum and at the other end to the oval window, an aperture in the bone of the inner ear. Despite the temporal coincidence in the evolution of these structures in the three amniote lineages and the functional similarities of the adaptations, the groups were by this time so far separated that the middle ears evolved from different structures into two different configurations. The single middle-ear bone, the columella, of archosaurs and lepidosaurs derived from the hyomandibular, a bone that earlier had formed a large strut connecting the braincase to the outer skull. In modern representatives, the columella is long and thin, with several, usually cartilaginous extensions known as the extracolumella. One of these, the “inferior process,” connects the inner surface of the eardrum and the columella, which then connects to the footplate that covers the oval window of the inner ear. This two-part system forms a lever that, together with the pressure increase incurred by transmitting from the much larger eardrum to the footplate, greatly magnifies sound entering the inner ear.

In the mammals of the Triassic, the equivalent events were more complex, but the functional result was remarkably similar. Mammal ancestors reduced the number of bones in the lower jaw from seven to one and, in the process, formed a new jaw joint. Initially, the old and new jaw structures existed in parallel, but over time the old joint moved towards the rear of the head. This event, which at any other time would likely have led to the complete loss of the old joint bones, occurred simultaneously with the origin of the mammalian tympanic middle ear. Older paleontological and newer developmental evidence from Shigeru Kuratani’s lab at RIKEN in Japan indicate that the mammalian eardrum evolved at a lower position on the skull relative to that of the other amniotes, a position outside the old jaw joint.3 In time, the bones of this old joint, together with the hyomandibula, became the three bony ossicles (malleus, incus, and stapes) of the new middle ear. Like the middle ear of archosaurs and lepidosaurs, these ossicles form a lever system that, along with the large area difference between eardrum and footplate, greatly magnifies sound input.

Thus, remarkably, these complex events led independently to all modern amniotes possessing a middle ear that, at frequencies below 10 kHz, works equally effectively despite the diverse structures and origins. There is also evidence that the three-ossicle mammalian middle ear itself evolved at least twice—in egg-laying mammals such as the platypus, and in therians, which include marsupials and placentals—with similar outcomes.

Inner-ear evolution

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PITCH PERFECT: The hearing organs of amniotes are organized tonotopically, with hair cells sensitive to high frequencies at the basal end of the papilla, grading into low-frequency hair cells at the apical end.BASED ON MED-EL WWW.MEDEL.COMThe evolution of tympanic middle ears kick-started the evolution of modern inner ears, where sound waves are converted into the electrical signals that are sent to the brain. The inner ear is least developed in the lepidosaurs, most of which retained a relatively small auditory papilla, in some just a few hundred micrometers long. Many lepidosaurs, predominantly diurnal species, also lost their eardrum. Snakes reduced their middle ear, limiting their hearing to frequencies less than 1 kHz, about two octaves above middle C. (For comparison, humans can hear sounds up to about 15 or 16 kHz.) Clearly, hearing was not under strong selective pressure in this group. There are a few exceptions, however. In geckos, for example, which are largely nocturnal, the papillar structure shows unique specializations, accompanied by high sensitivity and strong frequency selectivity. Indeed, the frequency selectivity of gecko auditory nerve fibers exceeds that of many mammals.

One part of the inner ear that did improve in lizards (but not in snakes) is the hair cells, with the papillae developing different areas occupied by two structural types of these sound-responsive cells. One of these hair cell groups responds to sounds below 1 kHz and perhaps corresponds to the ancestral version. The higher-frequency hair cells have a more specialized structure, particularly with regard to the size and height of the stereovilli, with bundle heights and stereovillus numbers varying consistently along the papilla’s length. Taller bundles with fewer stereovilli, which are much less stiff and therefore respond best to low frequencies, are found at one end of the membrane, while shorter, thicker bundles with more stereovilli that respond best to higher frequencies are found at the other end—a frequency distribution known as a tonotopic organization. Still, with the exception of one group of geckos, lizard hearing is limited to below 5 to 8 kHz.

In contrast to the relatively rudimentary lepidosaur inner ear, the auditory papilla of archosaurs (birds, crocodiles, and their relatives) evolved much greater length. Owls, highly proficient nocturnal hunters, boast the longest archosaur papilla, measuring more than 10 millimeters and containing many thousands of hair cells. As in lizards, archosaur hair cells show strong tonotopic organization, with a gradual change in the diameter and height of the stereovillar bundles contributing to the gradually changing frequency sensitivity along the papilla. In addition, the hair cells are divided along and across the basilar membrane, with tall hair cells (THCs) resting on the inner side and the apical end, most distant from the middle ear, grading into short hair cells (SHCs) on the outer side and at the basal end. Interestingly, many SHCs completely lack afferent innervation, which is the only known case of sensory cells lacking a connection to the brain. Instead of transmitting sensory information to the brain, these hair cells likely amplify the signal received by the inner ear. Despite the more complex anatomy, however, bird hearing is also generally limited to between 5 and 8 kHz, with the exception of some owls, which can hear up to 12 kHz.

The mammalian papilla, called the organ of Corti, also evolved to be larger—generally, but not always, longer than those of birds—but the extension in length varies in different lineages.4 Mammalian papillae also have a unique cellular arrangement. The papillae of modern egg-laying monotremes, which likely resemble those of the earliest mammals, include two groups of hair cells separated by numerous supporting pillar cells that form the tunnel of Corti. In any given cross section, there are approximately five inner hair cells (IHCs) on the inner side of the pillar cells, closer to the auditory nerve, and eight outer hair cells (OHCs) on the outer side. In therian mammals (marsupials and placentals), the numbers of each cell group have been much reduced, with only two pillar cells forming the tunnel in any given cross-section, and generally just a single IHC and three or four OHCs, though the functional consequences of this reduction remain unclear. About 90 percent of afferent fibers innervate IHCs, while only 10 percent or fewer innervate OHCs, despite the fact that OHCs account for some 80 percent of all hair cells. As with bird SHCs that lack afferent innervation, there are indications that the main function of OHCs is to amplify the physical sound signal at very low sound-pressure levels.

Therian mammals also evolved another key hearing adaptation: the cochlea. Shortly before marsupial and placental lineages diverged, the elongating hearing organ, which had always been curved, reached full circle. The only way to further increase its length was to form more than one full coil, a state that was reached roughly 120 million years ago. The result is hearing organs with 1.5 to 4 coils and lengths from 7 millimeters (mouse) to 75 millimeters (blue whale). Hearing ranges also diverged, partly depending on the size of the animal (larger mammals tend to have lower upper-frequency limits), but with a number of remarkable specializations, as expected in a lineage that radiated greatly during several evolutionary episodes.

As a result of these adaptations, most mammals have an upper frequency-response limit that well exceeds those of lepidosaurs and archosaurs. Human hearing extends to frequencies of about 15 kHz; a guinea pig can hear sounds up to about 45 kHz; and in the extreme cases of many bats and toothed whales, hearing extends into ultrasonic frequencies, sometimes as high as 180 kHz, allowing these animals to echolocate in air and water. This impressive increase in frequency limits is due to an extremely stiff middle ear, as well as a stiff cochlea. During early therian evolution, the bone of the canal surrounding the soft tissues invaded the supporting ridges of the basilar membrane, creating stiff laminae. Such bony ridges were retained in species perceiving ultrasonic frequencies, but tended to be reduced and replaced by softer connective-tissue supports in those with lower-frequency limits, such as humans.

Amplification within the ear

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HAIRS OF THE EAR: Rows of inner-ear hair cells have villous bundles (blue) on their apical surface that convert sound waves to nervous signals sent to the brain.© STEVE GSCHMEISSNER/SCIENCE SOURCEIn addition to the specialized structures of the middle and inner ears of amniotes that served to greatly increase hearing sensitivity, the hair cells themselves can produce active movements that further amplify sound stimuli. The evolutionarily oldest such active mechanism was discovered in the late 1980s by Jim Hudspeth’s group, then at the University of California, San Francisco, School of Medicine, working with frogs,5 and Andrew Crawford and Robert Fettiplace, then at the University of Cambridge, working with turtles.6 The amplification mechanism, called the active bundle mechanism, probably evolved in the ancestors of vertebrates and helped overcome the viscous forces of the surrounding fluids, which resist movement. When sound stimuli move the hair-cell bundle and thus open transduction channels to admit potassium ions, some calcium ions also enter the cell. These calcium ions bind to and influence the open transduction channels, increasing the speed with which these channels close. Such closing forces are exerted in phase with the incoming sound waves, increasing the distance that the hair cells move in response, and thereby increasing their sensitivity. It is likely that this mechanism operates in all vertebrate hair cells.5 In lizards, my group provided evidence that this bundle mechanism really does operate in the living animal.7

In 1986, a second mechanism of hair cell–driven sound amplification was discovered in mammalian OHCs by Bill Brownell’s group, then at the University of Florida School of Medicine. Brownell and his colleagues showed that mammalian OHCs, but not IHCs, changed their length very rapidly in phase with the signal if exposed to an alternating electrical field.8 Such fields occur when hair cells respond to sound. Subsequent experiments showed that the change in cell length is due to changes in the molecular configuration of a protein, later named prestin, which occurs in high density along the lateral cell membrane of OHCs. In mammals, the force produced by the OHCs is so strong that the entire organ of Corti, which includes all cell types that surround the hair cells and the basilar membrane itself, is driven in an up-and-down motion. This movement can amplify sounds by at least 40dB, allowing very quiet noises to be detected. There is evidence for the independent evolution of specific molecular configurations of prestins that allow for the amplification of very high ultrasonic frequencies in bats and whales.9

Bird ears also appear to produce active forces that amplify sound. The SHCs have bundles comprising up to 300 stereovilli (about three times as many as the bundles of mammalian OHCs),10 and the movement of these bundles probably drives the movement of THCs indirectly via the tectorial membrane. Also, very recent data from the lab of Fettiplace, now at the University of Wisconsin–Madison, suggests that in birds, prestin (albeit in a different molecular form) may work in the plane across the hearing organ (i.e., not up and down as in mammals), perhaps reinforcing the influence of the bundle active mechanism on the THCs via the tectorial membrane.11

Three hundred million years of evolution have resulted in a fascinating variety of ear configurations that, despite their struc­tural diversity, show remarkably similar physiological responses.

In addition to amplifying hair-cell activity, these active mechanisms manifest as spontaneous movements of the hearing organ, oscillating even in the absence of sound stimuli. Such spontaneous movements actually produce sound that is emitted through the middle ear to the outside world and can be measured in the ear canal. These spontaneous otoacoustic emissions (SOAEs) enable remote sensing of what is going on within the inner ear and have permitted increasingly important research on inner-ear mechanisms and new clinical diagnostic methods to monitor the health of the ear’s sensory epithelium. We recently showed that spectral patterns of SOAEs in lizards, birds, and mammals are remarkably similar, despite up to 70-fold differences in the size of the hearing organs, suggesting that there are profound commonalities among the inner ears of amniotes that we still do not really understand.12

Remarkable convergence

Three hundred million years of evolution have resulted in a fascinating variety of ear configurations that, despite their structural diversity, show remarkably similar physiological responses. There are hardly any differences in sensitivity between the hearing of endothermal birds and mammals, and the frequency selectivity of responses is essentially the same in most lizards, birds, and mammals. The combined research efforts of paleontologists, anatomists, physiologists, and developmental biologists over several decades have clarified the major evolutionary steps in all lineages that modified the malleable middle and inner ears into their present-day kaleidoscopic variety of form, yet a surprising consensus in their function.

Geoffrey A. Manley is a retired professor from the Institute of Zoology at the Technical University in Munich, Germany. He is currently a guest scientist in the laboratory of his wife, Christine Köppl, at Oldenburg University in Germany.

References

  1. G.A. Manley, C. Köppl, “Phylogenetic development of the cochlea and its innervation,” Curr Opin Neurobiol, 8:468-74, 1998.
  2. J.A. Clack, “Patterns and processes in the early evolution of the tetrapod ear,” J Neurobiol, 53:251-64, 2002.
  3. T. Kitazawa et al., “Developmental genetic bases behind the independent origin of the tympanic membrane in mammals and diapsids,” Nat Commun, 6:6853, 2015.
  4. G.A. Manley, “Evolutionary paths to mammalian cochleae,” JARO, 13:733-43, 2012.
  5. A.J. Hudspeth, “How the ear’s works work: Mechanoelectrical transduction and amplification by hair cells,” C R Biol, 328:155-62, 2005.
  6. A.C. Crawford, R. Fettiplace, “The mechanical properties of ciliary bundles of turtle cochlear hair cells,” J Physiol, 364:359-79, 1985.
  7. G.A. Manley et al., “In vivo evidence for a cochlear amplifier in the hair-cell bundle of lizards,” PNAS, 98:2826-31, 2001.
  8. B. Kachar et al., “Electrokinetic shape changes of cochlear outer hair cells,” Nature, 322:365-68, 1986.
  9. Y. Liu et al., “Convergent sequence evolution between echolocating bats and dolphins,” Curr Biol, 20:R53-R54, 2010.
  10. C. Köppl et al., “Big and powerful: A model of the contribution of bundle motility to mechanical amplification in hair cells of the bird basilar papilla,” in Concepts and Challenges in the Biophysics of Hearing, ed. N.P. Cooper, D.T. Kemp (Singapore: World Scientific, 2009), 444-50.
  11. M. Beurg et al., “A prestin motor in chicken auditory hair cells: Active force generation in a nonmammalian species,” Neuron, 79:69-81, 2013.
  12. C. Bergevin et al., “Salient features of otoacoustic emissions are common across tetrapod groups and suggest shared properties of generation mechanisms,” PNAS, 112:3362-67, 2015.

Sea Lion: © iStock/LFStewart; Squirrel: © Erik Mandre/Shutterstock; Frog: ©Frank B. Yuwono/Shutterstock; Owl: ©XNature.Photography/Shutterstock; Lizard: ©Andrew Wijesuriya/Shutterstock; Bat: © iStock/GlobalP; Ostrich: © Jamen Percy/Shutterstock; Dog: ©Annette Shaff/Shutterstock; Lynx: © Dmitri Gomon/Shutterstock

Correction (September 15, 2015): Citation #8 of this story has been updated to accurately reflect the research referenced in the text. The Scientist regrets the error.

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vertebratessensory biologyhearingevolutionary biologyevolution and amniotes

Early Hominin Hearing

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Based on the structure of fossilized skulls and ear bones, researchers learn that early hominins heard sounds best between the frequencies that humans and chimpanzees do.

By Karen Zusi | September 29, 2015

africanus skullWIKIMEDIA, JOSÉ BRAGA

http://www.the-scientist.com/images/Nutshell/Sept2015/hominin310.jpg

Early hominin species Australopithecus africanus andParanthropus robustus, which lived around 2 million years ago, possessed hearing capabilities largely similar to modern-day chimpanzees but with a few differences that made their sense more akin to that of humans, according to a recent study. The results were reported last week (September 25) in Science Advances.

“We know that the hearing patterns, or audiograms, in chimpanzees and humans are distinct because their hearing abilities have been measured in the laboratory in living subjects,” study coauthor Rolf Quam of Binghamton University in New York said in a press release. “So we were interested in finding out when this human-like hearing pattern first emerged during our evolutionary history.”

Quam and an international team of researchers studied the anatomy of the ear in three complete fossilized specimens, as well as several partial specimens, from South Africa. The team reconstructed the size and relative proportions of up to six different structures—such as the stapes, a middle ear bone—using 3-D CT scans. The researchers then used a published model to predict how the early hominins may have heard, based on these measurements.

Both species of early hominin evolved an anatomy that allowed them to hear sounds at slightly higher frequencies than chimpanzees, best in the 1.0 kHz to 3.5 kHz range. In comparison, chimpanzees can hear sounds best between 1.0 kHz and 3.0 kHz. Humans can typically hear sounds best between 1.0 kHz and 4.5 kHz; this range encompasses most sounds formed in spoken language.

“[The early hominins] didn’t hear as well as humans, and they are more like chimps,” Quam told The New York Times. But the researchers speculated that the changes in hearing anatomy over time were driven by a lifestyle spent on the open savanna, where short-range communication would have been favored.

“Hearing abilities are closely tied with verbal communication,” Quam wrote at The Conversation. “By figuring out when certain hearing capacities emerged during our evolutionary history, we might be able to shed some light on when spoken language started to evolve.”

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paleontologyhuman evolutionhomininhearingfossilsCT scan and chimpanzee

Hearing Explained

Observe the ins and outs of how our ears perceive sound.

By The Scientist Staff | September 1, 2015

http://www.the-scientist.com//?articles.view/articleNo/43884/title/Hearing-Explained/

Human Hearing: A Primer

How the human ear translates sound waves into nervous impulses

By The Scientist Staff | September 1, 2015

https://youtu.be/46aNGGNPm7s

When sound enters the ear canal, it vibrates the tympanic membrane, or eardrum. These vibrations are passed through the inner ear via three small bones called ossicles: the malleus, the incus, and the stapes. Finally, vibrations of the stapes stimulate the movement of a fluid called perilymph within the bony labyrinth of the inner ear.

See labeled infographic: JPG© CATHERINE DELPHIA

hearing

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Perilymph fills the both the vestibular and tympanic ducts of the cochlea. Between these two channels lies the cochlear duct, which is home to the organ of Corti. There, the sound induced movement of perilymph in the cochlea is translated to an electrical signal that is sent to the brain for processing.

An electrical signal is generated by inner hair cells that sit above the basilar membrane, which separates the cochlear duct from the tympanic duct. As the basilar membrane vibrates in response to fluid movement, it pushes the hair cells along another membrane, known as the tectorial membrane, which shifts laterally to bend projections at the tips of the cells, called stereocilia.

The bending of the stereocilia results in the depolarization of the inner hair cell and initiates a nerve impulse through the spiral ganglion neuron at the base of the cell. A series of outer hair cells serves to mechanically amplify the vibrations that trigger the inner hair cells to fire. High-frequency sounds stimulate hair cells at the base of the cochlea, while low-frequency sounds stimulate hair cells at the apex.

See labeled infographic: JPG© CATHERINE DELPHIA

HAIRS OF THE EAR ear_hair

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spiral ganglion neuronssensory biologyneuroscienceneuronsmechanotransductionmechanoreception and hearing

Author of books:
Brain Mechanisms of Vision (1991, with David H. Hubel)
Colloquium on Vision: From Photon to Perception (200, with John Dowling and Lubert Stryer)
Brain and Visual Perception: The Story of a 25-Year Collaboration (2005, with David H. Hubel)

Professor: Physiology, Harvard University (1964-74)
Professor: Neurobiology, Harvard University (1974-84)
Professor: Neurobiology, Rockefeller University (1984-98)
Administrator: President, Rockefeller University (1991-98)

The interplay of light and life

Lubert Stryer (born March 2, 1938, in Tianjin, China) is the Mrs. George A. Winzer Professor of Cell Biology, Emeritus, at the Stanford University School of Medicine.[1][2] His research over more than four decades has been centered on the interplay of light and life. In 2007 he received the National Medal of Science for elucidating the biochemical basis of signal amplification in vision, pioneering the development of high density micro-arrays for genetic analysis, and authoring the biochemistry textbook.[3]

Stryer received his B.S. degree from the University of Chicago in 1957 and his M.D. degree from Harvard Medical School. He was a Helen Hay Whitney Research Fellow[4] in the Department of Physics at Harvard and then at the MRC Laboratory of Molecular Biology[5] in Cambridge, England, before joining the faculty of the Department of Biochemistry at Stanford in 1963. In 1969 he moved to Yale to become Professor of Molecular Biophysics and Biochemistry, and in 1976, he returned to Stanford to head a new Department of Structural Biology.[6]

Stryer and coworkers pioneered the use of fluorescence spectroscopy, particularly Förster resonance energy transfer (FRET), to monitor the structure and dynamics of biological macromolecules.[7][8] In 1967, Stryer and Haugland showed that the efficiency of energy transfer depends on the inverse sixth power of the distance between the donor and acceptor,[9][10] as predicted by Förster’s theory. They proposed that energy transfer can serve as a spectroscopic ruler to reveal proximity relationships in biological macromolecules.

A second contribution was Stryer’s discovery of the primary stage of amplification in visual excitation.[11][12] Stryer, together with Fung and Hurley, showed that a single photoexcited rhodopsin molecule activates many molecules of transducin, which in turn activate many molecules of a cyclic GMP phosphodiesterase. Stryer’s laboratory has also contributed to our understanding of the role of calcium in visual recovery and adaptation.[13][14][15]

Stryer participated in developing light-directed, spatially addressable parallel chemical synthesis for the synthesis of peptides and polynucleotides.[16][17][18] Light-directed combinatorial synthesis has been used by Stephen Fodor and coworkers at Affymetrix to make DNA arrays containing millions of different sequences for genetic analyses.

Download Biochemistry Jeremy M Berg John L Tymoczko …

Dec 13, 2014 – Uploaded by Marquita Iraely

Download Biochemistry Jeremy M Berg John L Tymoczko Lubert Stryer PDF. Marquita Iraely …

Macmillan Higher Education: Biochemistry Seventh Edition …

http://www.macmillanhighered.com/Catalog/…/biochemistry-seventhedition-be…

Jeremy M. Berg , John L. Tymoczko (Carleton College) , Lubert Stryer (Stanford … this extraordinary textbook has helped shape the way biochemistry is taught, …

Loose-leaf Version for Biochemistry Seventh Edition Edition

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Stress-response gene networks

Larry H Bernstein, MD, FCAP, Curator

Leaders in Pharmaceutical Intelligence

Series E. 2; 3.6

Nina V. Fedoroff
Evan Pugh Professor of Biology, Willaman Professor of Life Science
Ph.D., The Rockefeller University, Molecular Biology , 1972

 

After graduating from Rockefeller University she joined the faculty of the University of California, Los Angeles, where she did research into nuclear RNA.[10] She then worked on developmental biology at the Department of Embryology at the Carnegie Institution for Science in Baltimore, Maryland, USA, where she pioneered DNA sequencing and worked out the nucleotide sequence of the first complete gene.[10] In 1978, she became a staff member at the Carnegie Institute and joined the faculty of Johns Hopkins University Biology Department, where she did groundbreaking work on the molecular characterization of maizetransposable elements or jumping genes (for which Barbara McClintock had been awarded a Nobel Prize in 1983).[10]

Fedoroff has been honored with the Howard Taylor Ricketts Award from University of Chicago in 1990,[4] and in 1992 she received the New York Academy of Sciences Outstanding Contemporary Women Scientist Award.[4] In 1997, Fedoroff received the John P. McGovern Science and Society Medal from Sigma Xi.[9] She was awarded in 2003 Syracuse University‘s George Arents Pioneer medal.[9]

President Bill Clinton appointed Fedoroff to the National Science Board, which oversees the National Science Foundation, in 2001.[4] The foundation administers the science awards, established by the United States Congress in 1959. Fedoroff was Science and Technology Adviser to U.S. Secretaries of State, Condoleezza Rice and Hillary Clinton[13] and to the administrator Rajiv Shah for the United States Agency for International Development from 2007 to 2010.[14]

A major project in the laboratory is investigating the responses of plants to biotic (pathogens) and abiotic (ozone, temperature, chemicals) stresses using DNA microarray gene expression profiling and reverse genetics. We have identified more than 1,200 stress-modulated Arabidopsis genes, and we are studying their expression under various conditions. Among the genes induced by various stresses are signaling genes, transcription factors, and effector genes that include enzymes that alter the cells structure and properties in response to stress. The signaling molecules include MAP kinases and receptor-like kinases. We are suppressing and overexpressing potential regulatory genes to identify the genes under their control. We want to understand the structure of the stress-response gene networks and to explore molecular-genetic approaches to modifying the stress response (see Holter et al., 2000, 2001).

Hormone Responses

The hyl1 Arabidopsis mutant has a transposon insertion mutation in a gene that is involved in several hormonal signaling pathways, including those for abscisic acid, auxin, and cytokinin. The mutant is affected in many growth parameters, including graviperception. It is not as sensitive to exogenous auxins and cytokinins as the wildtype, but it is hypersensitive to abscisic acid. The HYL1 protein binds to double-stranded RNA and localizes to the nucleus. The mutant is described in Lu and Fedoroff (2000). We are investigating how this protein affects hormone signaling.

Transposable Elements

Transposable elements or transposons were discovered in corn (maize) plants by the famous geneticist Barbara McClintock through classical genetic analysis of unstable mutations (for a brief history, see http://www.ergito.com or Fedoroff 2001). Maize transposons were cloned in our laboratory almost 20 years ago and are now widely used for insertional mutagenesis. We have created a database of several hundred Arabidopsis transposon insertion lines using a transposon tagging system developed in the laboratory (Smith et al., 1996; Raina et al., 2001).

Epigenetic Mechanisms

The maize Suppressor-mutator (Spm) transposon is epigenetically inactivated by methylation and encodes a protein, TnpA, which is capable of reversing the inactivation (Schläppi et al., 1994; Fedoroff et al., 1995). Using an inducible promoter to express TnpA, current experiments seek to understand how TnpA demethylates the Spm promoter. Some ideas about plant transposon evolution are explored in Fedoroff (2000).

 

The World Food Prize laureates for 2013 were announced in June. They are Marc van Montagu, Mary-Dell Chilton and Rob Fraley. These scientists played seminal roles, together with the late Jeff Schell, in developing modern plant molecular modification techniques. Fraley is chief technology officer of Monsanto. Chilton is a Distinguished Science Fellow at Syngenta. Montagu founded Plant Genetic Systems (now part of Bayer CropScience) and CropDesign (today owned by BASF).

Van Montagu and Chilton independently developed the technology in the 1980s to stably transfer foreign genes into plants, a discovery that set up a race to develop tools to genetically engineer plants. It allowed other scientists to incorporate genetic traits in plants to better withstand drought, extreme heat and to fight off pests and disease. Fraley was the first to successfully transfer immunity to specific bacteria into a plant.

Fraley genetically engineered the first herbicide-resistant soybean in 1996.

The three laureates (and their colleagues) developed molecular techniques for plant genetic modification. We can now use these methods to make precise improvements by adding just a gene (or two or a few) that codes for proteins whose function we know with precision. Yet plants modified by these techniques, the best and safest we’ve ever invented, are the only ones we now call GM. Almost everyone believes we’ve never fiddled with plant genes before, as if beefsteak tomatoes, elephant garlic and corn were somehow products of unfettered nature.

If the popular mythology about farmer suicides, tumors and toxicity had an ounce of truth to it, these companies would long since have gone out of business. Instead, they’re taking more market share every year. There’s a mismatch between mythology and reality. Maybe it’s worth remembering that technology vilification is about as old as technology itself. What’s new is electronic gossip and the proliferation of organizations that peddle such gossip for a living.

Author: Nina Fedoroff is distinguished professor of biosciences at the King Abdullah University of Science and Technology in Saudi Arabia and Evan Pugh professor at Penn State University. She has no material interest in Monsanto or its products.

Nina Fedoroff did her undergraduate work at Syracuse University, graduating summa cum laude with a dual major in biology and chemistry. She attended the Rockefeller University, where she earned her Ph.D. in Molecular Biology in 1972. Both her undergraduate research at Syracuse University and her graduate research on RNA bacteriophage at The Rockefeller University were supported by grants and fellowships from the National Science Foundation. Following graduation from The Rockefeller University, she joined the faculty at the University of California, Los Angeles (UCLA), and carried out research on nuclear RNA. In 1974 Fedoroff received fellowships from the Damon Runyan-Walter Winchell Cancer Research Fund and the National Institutes of Health (NIH) for postdoctoral work, first at UCLA and then in the Department of Embryology of the Carnegie Institution of Washington in Baltimore. Working in the laboratory of Donald Brown, Fedoroff pioneered in DNA sequencing, determining the nucleotide sequence of the first complete gene. In 1978, Fedoroff became a staff member of the Carnegie Institution of Washington and a faculty member in the Biology Department at Johns Hopkins University. Her research focus changed to the molecular characterization of maize transposable elements. The isolation of the maize transposons, discovered genetically by Barbara McClintock in the 1940s, was achieved in the early 1980s. In subsequent years, Fedoroff’s lab showed that the maize transposons were active in a variety of other plants, developed transposon tagging systems, and studied the epigenetic regulation of transposon activity. In 1995 Fedoroff joined the faculty of the Pennsylvania State University as Willaman Professor of Life Sciences.

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CRISPR/Cas9 Finds Its Way As an Important Tool For Drug Discovery & Development

  UPDATED 6/11/2021

CRISPR Diagnostics: CRISPR-dx Comes of Age: Tool in Drug Development

The past five years has seen a rapid expansion of the ability of CRISPR based tools toward diagnostic testing. Recently, CRISPR has been used to detect SARS-CoV-2 in patients. An article in the journal Science describes the different classes of CRISPR diagnostics in use today .

Update near end of post

UPDATED 8/08/2020

Association to Causation: Using GWAS to Identify Druggable Targets

A Gen Webinar Thursday, August 6, 2020; 11:00am – 12:30pm EST

See at end of post

Curator: Stephen J. Williams, Ph.D.

 

2.1.2.1

CRISPR/Cas9 Finds Its Way As an Important Tool For Drug Discovery & Development, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 2: CRISPR for Gene Editing and DNA Repair

The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA.

CRISPR/Cas systems are part of the adaptive immune system of bacteria and archaea, protecting them against invading nucleic acids such as viruses by cleaving the foreign DNA in a sequence-dependent manner. Although CRISPR arrays were first identified in the Escherichia coli genome in 1987 (Ishino et al., 1987), their biological function was not understood until 2005, when it was shown that the spacers were homologous to viral and plasmid sequences suggesting a role in adaptive immunity (Bolotin et al., 2005; Mojica et al., 2005; Pourcel et al., 2005). Two years later, CRISPR arrays were confirmed to provide protection against invading viruses when combined with Cas genes (Barrangou et al., 2007). The mechanism of this immune system based on RNA-mediated DNA targeting was demonstrated shortly thereafter (Brouns et al., 2008; Deltcheva et al., 2011; Garneau et al., 2010; Marraffini and Sontheimer, 2008).

Jennifer Doudna, PhD Professor of Molecular and Cell Biology and Chemistry, University of California, Berkeley Investigator, Howard Hughes Medical Institute has recently received numerous awards and accolades for the discovery of CRISPR/Cas9 as a tool for mammalian genetic manipulation as well as her primary intended research target to understand bacterial resistance to viral infection.

A good post on the matter and Dr. Doudna can be seen below:

http://pharmaceuticalintelligence.com/2014/06/13/215-245-6132014-jennifer-doudna-the-biology-of-crisprs-from-genome-defense-to-genetic-engineering/

In Delineating a Role for CRISPR-Cas9 in Pharmaceutical Targeting inheritable metabolic disorders in which may benefit from a CRISPR-Cas9 mediated therapy is discussed. However this curation is meant to focus on CRISPR/CAS9 AS A TOOL IN PRECLINICAL DRUG DEVELOPMENT.

 

Three Areas of Importance of CRISPR/Cas9 as a TOOL in Preclinical Drug Discovery Include:

  1. Gene-Function Studies: CRISPR/CAS9 ability to DEFINE GENETIC LESION and INSERTION SITE
  2. CRISPR/CAS9 Use in Developing Models of Disease
  3. CRISPR/CAS9 Use as a Diagnostic Tool
  • Using CRISPR/Cas9 in PRECLINICAL TOXICOLOGY STUDIES

I.     Gene-Function Studies: CRISPR/CAS9 ability to DEFINE GENETIC LESION and INSERTION SITE

The advent of the first tools for manipulating genetic material (cloning, PCR, transgenic technology, and before microarray and other’omic methods) allowed scientists to probe novel, individual gene functions as well as their variants and mutants in a “one-gene-at-a time” process. In essence, a gene (or mutant gene) was sequenced, cloned into expression vectors and transfected into recipient cells where function was evaluated.

However, some of the experimental issues with this methodology involved

  • Most transfections experiments result in NON ISOGENIC cell lines – by definition the insertion of a transgene alters the genetic makeup of a cell line. Simple transfection experiments with one transgene compared to a “null” transfectant compares non-isogenic lines, possibly confusing the interpretation of gene-function studies. Therefore a common technique is to develop cell lines with inducible gene expression, thereby allowing the investigator to compare a gene’s effect in ISOGENIC cell lines.
  1. Use of CRSPR in Highthrough-put Screening of Genetic Function

A very nice presentation and summary of CRSPR’s use in determining gene function in a high-throughput manner can be found below

www.rna.uzh.ch/events/journalclub/20140429JCCaihong.pdf

  1. Determining Off-target Effects of Gene Therapy Simplified with CRSPR

In GUIDE-seq: First genome-wide method of detecting off-target DNA breaks induced by CRISPR-Cas nucleases (from This Journal’s series on Live Meeting Coverage) at a 2014 Koch lecture

Shengdar Q Tsai and J Keith Joung describe

an approach for global detection of DNA double-stranded breaks (DSBs) introduced by RGNs and potentially other nucleases. This method, called genome-wide, unbiased identification of DSBs enabled by sequencing (GUIDE-seq), relies on capture of double-stranded oligodeoxynucleotides into DSBs. Application of GUIDE-seq to 13 RGNs in two human cell lines revealed wide variability in RGN off-target activities and unappreciated characteristics of off-target sequences. The majority of identified sites were not detected by existing computational methods or chromatin immunoprecipitation sequencing (ChIP-seq). GUIDE-seq also identified RGN-independent genomic breakpoint ‘hotspots’.

SOURCE http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3117.html

II. CRISPR/Cas9 Use in Developing Models of Disease

 

  1. Developing Animal Tumor Models

In a post this year I discussed a talk at the recent 2015 AACR National Meeting on a laboratories ability to use CRISPR gene editing in-vivo to produce a hepatocarcinoma using viral delivery. The post can be seen here: Notes from Opening Plenary Session – The Genome and Beyond from the 2015 AACR Meeting in Philadelphia PA; Sunday April 19, 2015

1) In this talk Dr. Tyler Jacks discussed his use of CRSPR to generate a mouse model of liver tumor in an immunocompetent mouse. Some notes from this talk are given below

  1. B) Engineering Cancer Genomes: Tyler Jacks, Ph.D.; Director, Koch Institute for Integrative Cancer Research
  • Cancer GEM’s (genetically engineered mouse models of cancer) had moved from transgenics to defined oncogenes
  • Observation that p53 -/- mice develop spontaneous tumors (lymphomas)
  • then GEMs moved to Cre/Lox systems to generate mice with deletions however these tumor models require lots of animals, much time to create, expensive to keep;
  • figured can use CRSPR/Cas9 as rapid, inexpensive way to generate engineered mice and tumor models
  • he used CRSPR/Cas9 vectors targeting PTEN to introduce PTEN mutations in-vivo to hepatocytes; when they also introduced p53 mutations produced hemangiosarcomas; took ONLY THREE months to produce detectable tumors
  • also produced liver tumors by using CRSPR/Cas9 to introduce gain of function mutation in β-catenin

See an article describing this study by MIT News “A New Way To Model Cancer: New gene-editing technique allows scientists to more rapidly study the role of mutations in tumor development.”

The original research article can be found in the August 6, 2014 issue of Nature[1]

And see also on the Jacks Lab site under Research

2)     In the Upcoming Meeting New Frontiers in Gene Editing multiple uses of CRISPR technology is discussed in relation to gene knockout/function studies, tumor model development and

New Frontiers in Gene Editing

Session Spotlight:
BUILDING IN VIVO MODELS FOR DRUG DISCOVERY

Genome Editing Animal Models in Drug Discovery
Myung Shin, Ph.D., Senior Principal Scientist, Biology-Discovery, Genetics and Pharmacogenomics, Merck Research Laboratories

Recent advances in genome editing have greatly accelerated and expanded the ability to generate animal models. These tools allow generating mouse models in condensed timeline compared to that of conventional gene-targeting knock-out/knock-in strategies. Moreover, the genome editing methods have expanded the ability to generate animal models beyond mice. In this talk, we will discuss the application of ZFN and CRISPR to generate various animal models for drug discovery programs.

In vivo Cancer Modeling and Genetic Screening Using CRISPR/Cas9
Sidi Chen, Ph.D., Postdoctoral Fellow, Laboratories of Dr. Phillip A. Sharp and Dr. Feng Zhang, Koch Institute for Integrative Cancer Research at MIT and Broad Institute of Harvard and MIT

Here we describe a genome-wide CRISPR-Cas9-mediated loss-of-function screen in tumor growth and metastasis. We mutagenized a non-metastatic mouse cancer cell line using a genome-scale library. The mutant cell pool rapidly generates metastases when transplanted into immunocompromised mice. Enriched sgRNAs in lung metastases and late stage primary tumors were found to target a small set of genes, suggesting specific loss-of-function mutations drive tumor growth and metastasis.

FEATURED PRESENTATION: In vivo Chromosome Engineering Using CRISPR-Cas9
Andrea Ventura, M.D., Ph.D., Assistant Member, Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center

We will discuss our experience using somatic genome editing to engineer oncogenic chromosomal rearrangements in vivo. More specifically, we will present the results of our ongoing efforts aimed at modeling cancers driven by chromosomal rearrangements using viral mediated delivery of Crispr-Cas9 to adult animals.

RNAi and CRISPR/Cas9-Based in vivo Models for Drug Discovery
Christof Fellmann, Ph.D., Postdoctoral Fellow, Laboratory of Dr. Jennifer Doudna, Department of Molecular and Cell Biology, The University of California, Berkeley

Genetically engineered mouse models (GEMMs) are a powerful tool to study disease initiation, treatment response and relapse. By combining CRISPR/Cas9 and “Sensor” validated, tetracycline-regulated “miR-E” shRNA technology, we have developed a fast and scalable platform to generate RNAi GEMMs with reversible gene silencing capability. The synergy of CRISPR/Cas9 and RNAi enabled us to not only model disease pathogenesis, but also mimic drug therapy in mice, providing us capability to perform preclinical studies in vivo.

In vivo Genome Editing Using Staphylococcus aureus Cas9
Fei Ann Ran, Ph.D., Post-doctoral Fellow, Laboratory of Dr. Feng Zhang, Broad Institute and Junior Fellow, Harvard Society of Fellows

The RNA-guided Cas9 nuclease from the bacterial CRISPR/Cas system has been adapted as a powerful tool for facilitating targeted genome editing in eukaryotes. Recently, we have identified an additional small Cas9 nuclease from Staphylococcus aureus that can be packaged with its guide RNA into a single adeno-associated virus (AAV) vector for in vivo applications. We demonstrate the use of this system for effective gene modification in adult animals and further expand the Cas9 toolbox for in vivo genome editing.

OriGene, Making the Right Tools for CRISPR Research
Xuan Liu, Ph.D., Senior Director, Marketing, OriGene

CRISPR technology has quickly revolutionized the scientific community. Its simplicity has democratized the genome editing technology and enabled every lab to consider its utility in gene function research. As the largest tool box for gene functional research, OriGene created a large collection of CRISPR-related tools, including various all-in-one vectors for gRNA cloning, donor vector backbones, genome-wide knockout kits, AAVS1 insertion vectors, etc. OriGene’s high quality products will accelerate CRISPR research.

  1. Transgenic Animals : Custom Mouse and Rat Model Generation Service Using CRISPR/Cas9 by AppliedStem Cell Inc. (http://www.appliedstemcell.com/)

A critical component of producing transgenic animals is the ability of each successive generations to pass on the transgene. In her post on this site, A NEW ERA OF GENETIC MANIPULATION  Dr. Demet Sag discusses the molecular biology of Cas9 systems and their efficiency to cause point mutations which can be passed on to subsequent generations

This group developed a new technology for editing genes that can be transferable change to the next generation by combining microbial immune defense mechanism, CRISPR/Cas9 that is the latest ground breaking technology for translational genomics with gene therapy-like approach.

  • In short, this so-called “mutagenic chain reaction” (MCR) introduces a recessive mutation defined by CRISPR/Cas9 that lead into a high rate of transferable information to the next generation. They reported that when they crossed the female MCR offspring to wild type flies, the yellow phenotype observed more than 95 percent efficiency.

The advantage of CRISPR/Cas9 over ZFNs or TALENs is its scalability and multiplexibility in that multiple sites within the mammalian genome can be simultaneously modified, providing a robust, high-throughput approach for gene editing in mammalian cells.

Applied StemCell, Inc. offers various services related to animal models including conventional transgenic rats, and phenotype analysis using knock-in, knock-out strategies.

Further explanation of their use of CRSPR can be found at the site below:

http://pharmaceuticalintelligence.com/2014/10/29/gene-editing-at-crispr-speed-services-and-tools/

In addition, ReproCELL Inc., a Tokyo based stem cell company, uses CRSPR to develop

· Tailored disease model cells (hiPSC-Disease Model Cells)

  • 2 types of services
  • ReproUNUS™-g:human iPS cell derived functional cells involving gene editing by CRISPR/Cas9 system
  • eproUNUS™-p:patient derived iPS cell derived functional cells

III. Using CRISPR/Cas9 in PRECLINICAL TOXICOLOGY STUDIES

As of now it is unclear as to the strategy of pharma in how to use this technology for toxicology testing however a few companies have licensed the technology to use across their R&D platforms including

A recent paper used a sister technique TALEN to generate knock-in pigs which suggest that it would be possible to generate pigs with human transgenes, especially in human liver isozymes in orer to study hepatotoxicity of drugs.

Efficient bi-allelic gene knockout and site-specific knock-in mediated by TALENs in pigs

Jing Yao, Jiaojiao Huang, Tang Hai, Xianlong Wang, Guosong Qin, Hongyong Zhang, Rong Wu, Chunwei Cao, Jianzhong Jeff Xi, Zengqiang Yuan, Jianguo Zhao

Sci Rep. 2014; 4: 6926. Published online 2014 November 5. doi: 10.1038/srep06926

UPDATED 8/08/2020

Association to Causation: Using GWAS to Identify Druggable Targets

A Gen Webinar Thursday, August 611:00am – 12:30pm

This webinar is available at https://www.genengnews.com/resources/webinars/association-to-causation-using-gwas-to-identify-druggable-target/

Speakers:

Martin Kampmann, PhD

matinkampmann ucsf

Associate Professor
UCSF
Investigator
Chan Zuckerberg Biohub

Kevin Holden, PhD

kevinholdn sythego

Head of Science
Synthego

Abhi Saharia, PhD

abhisharia sythego

VP, Commercial Development
Synthego

Human genetics provides perhaps the single best opportunity to innovate and improve clinical success rates, through the identification of novel drug targets for complex disease. Even as correlation identifies multiple genetic variants associated with disease, it is challenging to conduct requisite functional studies to identify the causal variants, especially since most association signals map to non-coding regions of the genome.

Genetic editing technologies, such as CRISPR, have enabled the modeling of associated variants at their native loci, including non-coding loci, empowering the identification of underlying biological mechanisms of disease with potential causal genes. However, genome editing is largely manual today severely limiting scale, and forcing the use of rational filters to prioritize which variants to investigate functionally.

In this GEN webinar, we will discuss several strategies enabling large-scale functional investigation of disease-associated variants in a cost- and time-effective manner, including different types of pooled CRISPR-based screens and the development of a fully automated genome engineering platform. We will also review how optimization of genome engineering on this platform enables the engineering of disease-associated variants at scale in pluripotent cells.

  • They will be presenting on use of wide scale CRSPR screens to validate druggable targets
  • The presenters will also discuss new platforms for these wide scale screens

Martin Kampmann, PhD UCSF

  • Multiple genetic variants associated with disease
  • Big gap between accumulation of genetic variant information and functions of these variants
  • CRSPRi or CRSPa (siRNA coupled or enhancer coupled CRSPR guides)
  • Arrayed screens: multiplate guide RNAs and phenotype measured (phenotype can be morphology, complex biological systems like organoids or non autonomous functions
  • Using pooled screens and use of suitable cell model critical for this strategy
  • For example in iPSC vs. neurons has different expression patterns upon same CRSPR of UBA1
  • Advantage is using CRSPR to take iPSC from diseased variant patient to make a corrected isogenic control then introduce gRNAs and use modifier screens to determine phenotypes
  • Generated a platform called CRISPRbrain.org to do bioinformatics on various experiments with different guide RNAs (CRSPRs)

Abhi Saharia, PhD Syntheco

  • Target identification with CSRSPR at Scale
  • Nature medicine paper did GWAS and found 27 SNV associated with high risk disease and a rational filter focused on 1 SNV in noncoding region but why study a single variant and if studied all 27 would they have been able to identify a more representative druggable set?
  • Goal is to reduce or eliminate these rational filters
  • HALO (scalable RNA guide), ECLIPSE platform (automated generation of modified cell lines, BIOINFORMATIC platform (integrated informatics)
  • Syntheco uses an electroporation with ribonucleic proteins (RNP) to give highest efficiency and minimizes off target as complex is only in cells for a short period of time
  • They confirm they are doing single cell cloning by using automated microscopy to confirm single cell growth in each cloning well

Kevin Holden, Head of Science at Syntheco

  • Engineering iPSc genetically modified cells at scale
  • The closer you get to your target site the more efficient your CRSPR so a big factor when making guides, especially for knock-in CRSPR
  • Adding a small molecule non homologous end joining inhibitor increases efficiency to 95%
  • Cold shocking the cells also assists in homologous repair
  • Use cleavage resistant templates

III. CRISPR/CAS9 AS A DIAGNOSTIC TOOL

     In the journal Science, Omar Abudayyeh and Jonathan Gootenberg discuss how CRISPR-based diagnostic (CRISPR-dx) tools offer a solution, and multiple CRISPR-dx products for detection of the SARS-CoV-2 RNA genome have been authorized by the US Food and Drug Administration (FDA).  In addition they discuss the work by Jiao et al. in combining this technique to develop a rapid and sensitive SARS-CoV2 diagnostic test.

Omar O. AbudayyehJonathan S. Gootenberg. Science  28 May 2021: CRISPR Diagnostics
Vol. 372, Issue 6545, pp. 914-915; DOI: 10.1126/science.abi9335

Summary

Although clinical diagnostics take many forms, nucleic acid–based testing has become the gold standard for sensitive detection of many diseases, including pathogenic infections. Quantitative polymerase chain reaction (qPCR) has been widely adopted for its ability to detect only a few DNA or RNA molecules that can unambiguously specify a particular disease. However, the complexity of this technique restricts application to laboratory settings. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has underscored the need for the development and deployment of nucleic acid tests that are economical, easily scaled, and capable of being run in low-resource settings, without sacrifices in speed, sensitivity or specificity. CRISPR-based diagnostic (CRISPR-dx) tools offer a solution, and multiple CRISPR-dx products for detection of the SARS-CoV-2 RNA genome have been authorized by the US Food and Drug Administration (FDA). On page 941 of this issue, Jiao et al. (1) describe a new CRISPR-based tool to distinguish several SARS-CoV-2 variants in a single reaction.

Although clinical diagnostics take many forms, nucleic acid–based testing has become the gold standard for sensitive detection of many diseases, including pathogenic infections. Quantitative polymerase chain reaction (qPCR) has been widely adopted for its ability to detect only a few DNA or RNA molecules that can unambiguously specify a particular disease. However, the complexity of this technique restricts application to laboratory settings. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has underscored the need for the development and deployment of nucleic acid tests that are economical, easily scaled, and capable of being run in low-resource settings, without sacrifices in speed, sensitivity or specificity. CRISPR-based diagnostic (CRISPR-dx) tools offer a solution, and multiple CRISPR-dx products for detection of the SARS-CoV-2 RNA genome have been authorized by the US Food and Drug Administration (FDA). On page 941 of this issue, Jiao et al. (1) describe a new CRISPR-based tool to distinguish several SARS-CoV-2 variants in a single reaction.

There are multiple types of CRISPR systems comprising basic components of a single protein or protein complex, which cuts a specific DNA or RNA target programmed by a complementary guide sequence in a CRISPR-associated RNA (crRNA). The type V and VI systems and the CRISPR-associated endonucleases Cas12 (23) and Cas13 (45) bind and cut DNA or RNA, respectively. Furthermore, upon recognizing a target DNA or RNA sequence, Cas12 and Cas13 proteins exhibit “collateral activity” whereby any DNA or RNA, respectively, in the sample is cleaved regardless of its nucleic acid sequence (46). Thus, reporter DNAs or RNAs, which allow for visual or fluorescent detection upon cleavage, can be added to a sample to infer the presence or absence of specific DNA or RNA species (48).

Initial versions of CRISPR-dx utilizing Cas13 alone were sensitive to the low picomolar range, corresponding to a limit of detection of millions of molecules in a microliter sample. To improve sensitivity, preamplification methods, such as recombinase polymerase amplification (RPA), PCR, loop-mediated isothermal amplification (LAMP), or nucleic acid sequence–based amplification (NASBA), can be used with Cas12 or Cas13 to enable a limit of detection down to a single molecule (8). This preamplification approach, applicable to both Cas12 and Cas13 (67), enabled a suite of detection methods and multiplexing up to four orthogonal targets (7). Additional developments expanded CRISPR-dx readouts beyond fluorescence, including lateral flow (7), colorimetric (9), and electronic or material responsive readouts (10), allowing for instrument-free approaches. In addition, post–collateral-cleavage amplification methods, such as the use of the CRISPR-associated enzyme Csm6, have been combined with Cas13 to further increase the speed of CRISPR-dx tests (7). As an alternative to collateral-cleavage–based detection, type III CRISPR systems, which involve large multiprotein complexes capable of targeting both DNA and RNA, have been used for SARS-CoV-2 detection through production of colorimetric or fluorometric readouts (11).

FDA-authorized CRISPR-dx tests are currently only for use in centralized labs, because the most common CRISPR detection protocols require fluid handling steps and two different incubations, precluding their immediate use at the point of care. Single-step formulations have been developed to overcome this limitation, and these “one-pot” versions of CRISPR-dx are simple to run, operate at a single temperature, and run without complex equipment, producing either fluorescence or lateral flow readouts. The programmability of CRISPR makes new diagnostic tests easier to develop, and within months of the release of the SARS-CoV-2 genome, many COVID-19–specific CRISPR tests were reported and distributed around the world.

The broader capability for Cas enzyme–enhanced nucleic acid binding or cleavage has led to several other detection modalities. Cas9-based methods for cleaving nucleic acids in solution for diagnostic purposes have been combined with other detection platforms, such as destruction of undesired amplicons for preparation of next-generation sequencing libraries (12), or selective removal of alleles for nucleotide-specific detection (13). Alternatively, the programmable cleavage event from the Cas nuclease can be used to initiate an amplification reaction (14). Cas9-based DNA targeting has also been used for nucleotide detection in combination with solid-state electronics, promising an amplification-free platform for detection. In this platform, called CRISPR-Chip, the Cas9 protein binds nucleotide targets of interest (often in the context of the native genome) to graphene transistors, where the presence of these targets alters either current or voltage (15). By utilizing additional Cas9 orthologs and specific guide designs, CRISPR-Chip approaches have been tuned for single–base-pair sensitivity (15). Because they are integrated with electronic readers, CRISPR-Chip platforms may allow facile point-of-care detection with handheld devices.

 

Different classes of CRISPR diagnostics. GRAPHIC: ERIN DANIEL


Jiao et al. use a distinct characteristic of type II CRISPR systems, which involve Cas9, to develop a new type of noncollateral based CRISPR detection. Unlike Cas12s and Cas13, Cas9-crRNA complex formation requires an additional RNA known as the trans-activating CRISPR RNA (tracrRNA). By sequencing RNAs bound to Cas9 from Campylobacter jejuni in its natural host, the authors identified unexpected crRNAs, called noncanonical crRNA (ncrRNA), that corresponded to endogenous transcripts. Upon investigation of this surprising observation, it became clear that the tracrRNA was capable of hybridizing to semi-complementary sequences from a variety of RNA sources, leading to biogenesis of ncrRNAs of various sizes. Recognizing that they could program tracrRNAs to target a transcript of interest, the authors generated a reprogrammed tracrRNA (Rptr) that could bind and cleave a desired transcript, converting a piece of that transcript into a functional guide RNA. By then creating fluorescent DNA sensors that would be cleaved by the Rptr and ncrRNAs, the sensing of RNA by Cas9 could be linked to a detectable readout. This platform, called LEOPARD (leveraging engineered tracrRNAs and on-target DNAs for parallel RNA detection), can be combined with gel-based readouts and enables multiplexed detection of several different sequences in a single reaction (see the figure).

Jiao et al. also combined LEOPARD with PCR in a multistep workflow to detect SARS-CoV-2 genomes from patients with COVID-19. Although more work is needed to integrate this Cas9-based detection modality into a single step with RPA or LAMP to create a portable and sensitive isothermal test, an advantage of this approach is the higher-order multiplexing that can be achieved, allowing multiple pathogens, diseases, or variants to be detected simultaneously. More work is also needed to combine this technology with extraction-free methods for better ease of use; alternative readouts to gel-based readouts, such as lateral flow and colorimetric readouts, would be beneficial for point-of-care detection.

In just 5 years, the CRISPR-dx field has rapidly expanded, growing from a set of peculiar molecular biology discoveries to multiple FDA-authorized COVID-19 tests and spanning four of the six major subtypes of CRISPR systems. Despite the tremendous promise of CRISPR-dx, substantial challenges remain to adapting these technologies for point-of-care and at-home settings. Simplification of the chemistries to operate as a single reaction in a matter of minutes would be revolutionary, especially if the reaction could be run at room temperature without any complex or expensive equipment. These improvements to CRISPR-dx assays can be achieved by identification or engineering of additional Cas enzymes with lower-temperature requirements, higher sensitivity, or faster kinetics, enabling rapid and simple amplification-free detection with single-molecule sensitivity.

Often overlooked is the necessity for a sample DNA or RNA preparation step that is simple enough to be added directly to the CRISPR reaction to maintain a simple workflow for point-of-care testing. In addition, higher-order multiplexing developments would allow for expansive testing menus and approach the possibility of testing for all known diseases. As these advancements are realized, innovative uses of CRISPR-dx will continue in areas such as surveillance, integration with biomaterials, and environmental monitoring. In future years, CRISPR-dx assays may become universal in the clinic and at home, reshaping how diseases are diagnosed.

References and Notes

Other related articles on CRISPR/Cas9 were published in this Open Access Online Scientific Journal, include the following:

Search Results for ‘CRISPR’

Where is the most promising avenue to success in Pharmaceuticals with CRISPR-Cas9?

CRISPR/Cas9 genome editing tool for Staphylococcus aureus Cas9 complex (SaCas9) @ MIT’s Broad Institute

Delineating a Role for CRISPR-Cas9 in Pharmaceutical Targeting

Using CRISPR to investigate pancreatic cancer

Simple technology makes CRISPR gene editing cheaper

RNAi, CRISPR, and Gene Editing: Discussions on How To’s and Best Practices @14th Annual World Preclinical Congress June 10-12, 2015 | Westin Boston Waterfront | Boston, MA

CRISPR/Cas9: Contributions on Endoribonuclease Structure and Function, Role in Immunity and Applications in Genome Engineering

CRISPR-CAS editing brings cloning of woolly mammoth one step closer to reality

GUIDE-seq: First genome-wide method of detecting off-target DNA breaks induced by CRISPR-Cas nucleases

The Patents for CRISPR, the DNA editing technology as the Biggest Biotech Discovery of the Century

CRISPR: Applications for Autoimmune Diseases @UCSF

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Metabolic Genomics and Pharmaceutics, Vol. 1 of BioMed Series D available on Amazon Kindle

Metabolic Genomics and Pharmaceutics, Vol. 1 of BioMed Series D available on Amazon Kindle

Reporter: Stephen S Williams, PhD

Article ID #180: Metabolic Genomics and Pharmaceutics, Vol. 1 of BioMed Series D available on Amazon Kindle. Published on 8/15/2015

WordCloud Image Produced by Adam Tubman

Leaders in Pharmaceutical Business Intelligence would like to announce the First volume of their BioMedical E-Book Series D:

Metabolic Genomics & Pharmaceutics, Vol. I

SACHS FLYER 2014 Metabolomics SeriesDindividualred-page2

which is now available on Amazon Kindle at

http://www.amazon.com/dp/B012BB0ZF0.

This e-Book is a comprehensive review of recent Original Research on  METABOLOMICS and related opportunities for Targeted Therapy written by Experts, Authors, Writers. This is the first volume of the Series D: e-Books on BioMedicine – Metabolomics, Immunology, Infectious Diseases.  It is written for comprehension at the third year medical student level, or as a reference for licensing board exams, but it is also written for the education of a first time baccalaureate degree reader in the biological sciences.  Hopefully, it can be read with great interest by the undergraduate student who is undecided in the choice of a career. The results of Original Research are gaining value added for the e-Reader by the Methodology of Curation. The e-Book’s articles have been published on the Open Access Online Scientific Journal, since April 2012.  All new articles on this subject, will continue to be incorporated, as published with periodical updates.

We invite e-Readers to write an Article Reviews on Amazon for this e-Book on Amazon.

All forthcoming BioMed e-Book Titles can be viewed at:

http://pharmaceuticalintelligence.com/biomed-e-books/

Leaders in Pharmaceutical Business Intelligence, launched in April 2012 an Open Access Online Scientific Journal is a scientific, medical and business multi expert authoring environment in several domains of  life sciences, pharmaceutical, healthcare & medicine industries. The venture operates as an online scientific intellectual exchange at their website http://pharmaceuticalintelligence.com and for curation and reporting on frontiers in biomedical, biological sciences, healthcare economics, pharmacology, pharmaceuticals & medicine. In addition the venture publishes a Medical E-book Series available on Amazon’s Kindle platform.

Analyzing and sharing the vast and rapidly expanding volume of scientific knowledge has never been so crucial to innovation in the medical field. WE are addressing need of overcoming this scientific information overload by:

  • delivering curation and summary interpretations of latest findings and innovations on an open-access, Web 2.0 platform with future goals of providing primarily concept-driven search in the near future
  • providing a social platform for scientists and clinicians to enter into discussion using social media
  • compiling recent discoveries and issues in yearly-updated Medical E-book Series on Amazon’s mobile Kindle platform

This curation offers better organization and visibility to the critical information useful for the next innovations in academic, clinical, and industrial research by providing these hybrid networks.

Table of Contents for Metabolic Genomics & Pharmaceutics, Vol. I

Chapter 1: Metabolic Pathways

Chapter 2: Lipid Metabolism

Chapter 3: Cell Signaling

Chapter 4: Protein Synthesis and Degradation

Chapter 5: Sub-cellular Structure

Chapter 6: Proteomics

Chapter 7: Metabolomics

Chapter 8:  Impairments in Pathological States: Endocrine Disorders; Stress

                   Hypermetabolism and Cancer

Chapter 9: Genomic Expression in Health and Disease 

 

Summary 

Epilogue

 

 

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 Sequencing yourself! and Learn more on Genome Sequencing on Tuesday, November 17, 2015 from 8am-5pm in the Joseph B. Martin Conference Center of the Harvard New Research Building at Harvard Medical School, Volume 2 (Volume Two: Latest in Genomics Methodologies for Therapeutics: Gene Editing, NGS and BioInformatics, Simulations and the Genome Ontology), Part 1: Next Generation Sequencing (NGS)

Sequencing yourself! and Learn more on Genome Sequencing on Tuesday, November 17, 2015 from 8am-5pm in the Joseph B. Martin Conference Center of the Harvard New Research Building at Harvard Medical School

Reporter: Aviva Lev-Ari, PhD, RN

Become one of the first humans to have your entire genome sequenced, while participating in an interactive set of presentations and debates about the promise and limitations of genome sequencing from some of the world’s leading genomic scientists.

The UYG Boston is an invitation-only, interactive symposium in which approximately 60 leaders from the Boston business and academic communities will have the opportunity to undergo whole genome sequencing, and to explore their own genome as part of an all-day educational conference with exciting presentations, debates and comments from some of the most thought-provoking leaders in the field of sequencing, informatics and genomic medicine.

Co-sponsors:

  • Brigham Genome Medicine, Brigham and Women’s Hospital
  • Partners Personalized Medicine and Laboratory for Molecular Medicine
  • Precision Medicine Program at Brigham and Women’s Hospital
  • Department of Pathology at Brigham and Women’s Hospital
  • Analytic and Translational Genetics Unit, Massachusetts General Hospital
  • The Broad Institute of Harvard and MIT
  • Department of Pathology at Massachusetts General Hospital
  • Division of Genetics, Department of Medicine, Brigham and Women’s Hospital

http://uygboston.uygsymposium.com/

 

Draft Agenda for UYG Agenda, November 17, 2015, NRB Rotunda Room

Registration is still open at this link: http://uygboston.uygsymposium.com

Breakfast and Registration

7:30-8:30

Module 1: Understanding the Basics of Genetics and Genomics

 

Moderator: __________________________________

8:30 am -9:55 am

(10) Robert Green: Welcome and Introductory Remarks

(20) Stacey Gabriel: Technical Overview of Sequencing, Alignment and Variant Calling

(20) Heidi Rehm: Variant Classification and Lab Reporting: the Good, the Bad and the VUS

(20) Daniel MacArthur: Using Large Datasets to Explore Penetrance

(15) Questions and Discussion

Coffee Break

9:55 am – 10:10 am

Module 2: Sequencing and Informatics in Clinical Care

 

Moderator: __________________________________

10:10 am-11:30 noon

(20) Dick Maas: Sequencing in Undiagnosed Cases

(20) Kricket Seidman: Sequencing in the Care of Specific Diseases (Cardiomyopathy)

(20) Zak Kohane: Sequencing and Informatics

(20) Discussion

Luncheon: Understand Your Genome®

11:30 noon – 1:00 pm

Pechet Room

Lunch for those who have been sequenced or wish to learn to use the MyGenome web portal with the demo genome (seating is limited to 40 WGS attendees + 10 additional attendees):

(30) Erica Ramos: Clinical Whole Genome Sequencing in a Healthy Population

(30) Erica Ramos: MyGenome Web Portal Revealed

(30) Erica Ramos and Genetic Counselors: Holding and Exploring Your Own Genome

Lunch served separately for those who do not wish to explore MyGenome Web App

Module 3: Sequencing in Research: from Discovery to Patient Care

 

Moderator: __________________________________

1:00 pm – 2:40 pm

(10) Jeff Flier: Afternoon welcome and remarks

(20) Sek Kathiresan: Developing Medicines that Mimic Natural Genomic Successes

(20) Calum MacRae: Global Phenotyping and the Clinic of the Future

(10) Heidi Rehm: ClinGen and Matchmaker Exchange

(20) Robert Green: Clinical Outcomes Research in Sequencing

(20) Discussion

Module 4: Academic Medical Centers and Personalized/Precision Medicine

 

Moderator: __________________________________

2:40- 3:35

(15) Betsy Nabel: Direct-to Consumer Sequencing and the Academic Medical Center

(20) Jeff Golden: Precision Medicine, Regulation and Reimbursement

(20) Discussion

Afternoon Break

3:35-3:50

Module 5: Debate on the Benefits, Harms and Costs of Sequencing Health Individuals by Individual Speakers with the Entire Panel of Speakers and the Attendees

3:50-4:55

Five Minute Pro or Con by Each Speaker and Select Audience Members, Followed by Debate

 

“DNA Team” Captains: “There is Benefit” Jeff Golden/Jeff Flier

“RNA Team” Captains: “There is No Benefit” Sek Kathiresan/Betsy Nabel

Closing Remarks

4:55 – 5:00

(5) Robert Green

Wine and Cheese Reception for Speakers and Attendees

5:00-6:00


Registration

– See more at: http://personalizedmedicine.partners.org/education/personalized-medicine-conference/program.aspx#sthash.cnydkNG1.dpuf

Fee:

Register by July 15th to attend for $3,100!
After July 15th registration will be $3,500.

Pricing includes:

$2,900 TruGenome™ Predisposition Screen plus a conference registration fee

When:

November 17, 2015
General Session: 8am – 5pm
Reception: 5pm – 7pm

Where:

The Joseph B. Martin Conference Center
Harvard Medical School
77 Avenue Louis Pasteur
Boston, MA 02115

Confirmed Speakers

  • George Church, PhD,
    Harvard Medical School
  • Stacey Gabriel, PhD
    The Broad Institute
  • Jeff Golden, MD
    Brigham and Women’s Hospital
  • Robert Green, MD, MPH
    Brigham and Women’s Hospital
  • Sek Kathiresan, MD
    Massachusetts General Hospital
  • Zak Kohane, MD, PhD
    Harvard Medical School
  • Richard Maas, MD, PhD
    Brigham and Women’s Hospital
  • Daniel MacArthur, PhD
    Massachusetts General Hospital
  • Calum MacRae, MD
    Brigham and Women’s Hospital
  • Betsy Nabel, MD
    Brigham and Women’s Hospital
  • Heidi Rehm, PhD
    Laboratory of Molecular Medicine
  • Christine Seidman, MD
    Brigham and Women’s Hospital

SOURCE

From: Robert Green <rcgreen@genetics.med.harvard.edu>

Date: Tuesday, July 7, 2015 at 1:46 PM

Subject: Learn about genome sequencing by sequencing yourself!

Robert C. Green, MD, MPH

Director, G2P Research Program

Associate Director for Research, Partners Center for Personalized Genetic Medicine

Division of Genetics, Department of Medicine

Brigham and Women’s Hospital and Harvard Medical School

EC Alumnae Building, Suite 301, 41 Avenue Louis Pasteur, Boston, MA 02115                                    

(office) 617-264-5834, (fax) 617-264-3018, (cell) 617-966-3216

(email) rcgreen@genetics.med.harvard.edu 

(web) www.genomes2people.org

Dear Colleagues:

We are inviting you, as one of a small group of forward looking thought leaders, to attend an exciting educational and experiential event: the Boston “Understand your Genome” conference. This conference will take place the day before this year’s Partners Personalized Medicine Conference at Harvard Medical School and will have two components.

First, a panel of world-renowned speakers will discuss the current progress and promise of genomic medicine, and debate the controversial issues surrounding the sequencing of healthy individuals for prediction and prevention.

Second, the conference will provide you with the option to become one of the first people on the planet to have your whole genome sequenced at a CLIA facility where a report will be generated by a board certified molecular geneticist on 1,691 genes with well-established associations to 1,232 Mendelian conditions, and 11 genes associated with responses to 16 different medications.

This conference is a non-profit educational event that is sponsored by the Division of Genetics, in the Department of Medicine at Brigham and Women’s Hospital with co-sponsorship by Partners Personalized Medicine and the Laboratory for Molecular Medicine, the Precision Medicine Program at Brigham and Women’s Hospital, the Department of Pathology at Brigham and Women’s Hospital, the Analytic and Translational Genetics Unit at Massachusetts General Hospital, the Department of Pathology at Massachusetts General Hospital and the Broad Institute. Together, we have assembled a remarkable panel of speakers for the first component of the program.

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Therapeutic Implications for Targeted Therapy from the Resurgence of Warburg ‘Hypothesis’

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

(Note that each portion of the discussion is followed by a reference)

It is now a time to pause after almost a century of a biological scientific discoveries that have transformed the practice of medicine and impacted the lives of several generations of young minds determined to probe the limits of our knowledge.  In the century that we have entered into the scientific framework of medicine has brought together a difficult to grasp evolution of the emergence of human existence from wars, famine, droughts, storms, infectious diseases, and insect born pestilence with betterment of human lives, only unevenly divided among societal classes that have existed since time immemorial. In this short time span there have emerged several generations of physicians who have benefited from a far better medical education that their forebears could have known. In this expansive volume on cancer, we follow an incomplete and continuing challenge to understand cancer, a disease that has become associated with longer life spans in developed nations.

While there are significant improvements in the diagnosis and treatment of cancers, there is still a personal as well as locality factor in the occurrence of this group of diseases, which has been viewed incorrectly as a “dedifferentiation” of mature tissue types and the emergence of a cell phenotype that is dependent on glucose, reverts to a cancer “stem cell type” (loss of stemness), loses cell to cell adhesion, loses orderly maturation, and metastasizes to distant sites. At the same time, physician and nurses are stressed in the care of patients by balancing their daily lives and maintaining a perspective.

The conceptual challenge of cancer diagnosis and management has seemed insurmountable, but owes much to the post World War I activities of Otto Heinrich Warburg. It was Warburg who made the observation that cancer cells metabolize glucose by fermentation in much the way Pasteur 60 years earlier observed fermentation of yeast cells. This metabolic phenomenon occurs even in the presence of an oxygen supply, which would provide a huge deficit in ATP production compared with respiration. The cancer cell is “addicted to glucose” and produced lactic acid. Warburg was awarded the Nobel Prize in Medicine for this work in 1931.

In the last 15 years there has been a resurgence of work on the Warburg effect that sheds much new light on the process that was not previously possible, with significant therapeutic implications.  In the first place, the metabolic mechanism for the Warburg effect was incomplete even at the beginning of the 21st century.  This has been partly rectified with the enlightening elucidation of genome modifications, cellular metabolic regulation, and signaling pathways.

The following developments have become central to furthering our understanding of malignant transformation.

  1. There is usually an identifiable risk factor, such as, H. pylori, or of a chronic inflammatory state, as in the case of Barrett’s esophagus.
  2. There are certain changes in glucose metabolism that have been unquestionably been found in the evolution of this disease. The changes are associated with major changes in metabolic pathways, miRN signaling, and the metabolism geared to synthesis of cells with an impairment of the cell death cycle. In these changes, mitochondrial function is central to both the impaired respiration and the autophagy geared to the synthesis of cancer cells.

The emergence of this cell prototype is characterized by the following, again related to the Warburg effect:

  1. Cancer cells oxidize a decreased fraction of the pyruvate generated from glycolysis
  2. The mitochondrial pyruvate carrier (MPC), composed of the products of the MPC1 and MPC2 genes, modulates fractional pyruvate oxidation. MPC1 is deleted or underexpressed in multiple cancers and correlates with poor prognosis.
  3. Cancer cells tend to express a partially inhibited splice variant of pyruvate kinase (PK-M2), leading to decreased pyruvate production.
  4. The two proteins that mediate pyruvate conversion to lactate and its export, M-type lactate dehydrogenase and the monocarboxylate transporter MCT-4, are commonly upregulated in cancer cells leading to decreased pyruvate oxidation.
  5. The enzymatic step following mitochondrial entry is the conversion of pyruvate to acetyl-CoA by the pyruvate dehydrogenase (PDH) complex. Cancer cells frequently exhibit increased expression of the PDH kinase PDK1, which phosphorylates and inactivates PDH. This PDH regulatory mechanism is required for oncogene induced transformation and reversed in oncogene-induced senescence.
  6. The PDK inhibitor dichloroacetate has shown some clinical efficacy, which correlates with increased pyruvate oxidation. One of the simplest mechanisms to explain decreased mitochondrial pyruvate oxidation in cancer cells, a loss of mitochondrial pyruvate import, has been observed repeatedly over the past 40 years. This process has been impossible to study at a molecular level until recently, however, as the identities of the protein(s) that mediate mitochondrial pyruvate uptake were unknown.
  7. The mitochondrial pyruvate carrier (MPC) as a multimeric complex that is necessary for efficient mitochondrial pyruvate uptake. The MPC contains two distinct proteins, MPC1 and MPC2; the absence of either leads to a loss of mitochondrial pyruvate uptake and utilization in yeast, flies, and mammalian cells.

A Role for the Mitochondrial Pyruvate Carrier as a Repressor of the Warburg Effect and Colon Cancer Cell Growth

John C. Schell, Kristofor A. Olson, Lei Jiang, Amy J. Hawkins, et al.
Molecular Cell Nov 6, 2014; 56: 400–413.
http://dx.doi.org/10.1016/j.molcel.2014.09.026

In addition to the above, the following study has therapeutic importance:

Glycolysis has become a target of anticancer strategies. Glucose deprivation is sufficient to induce growth inhibition and cell death in cancer cells. The increased glucose transport in cancer cells has been attributed primarily to the upregulation of glucose transporter 1 (Glut1),  1 of the more than 10 glucose transporters that are responsible for basal glucose transport in almost all cell types. Glut1 has not been targeted until very recently due to the lack of potent and selective inhibitors.

First, Glut1 antibodies were shown to inhibit cancer cell growth. Other Glut1 inhibitors and glucose transport inhibitors, such as fasentin and phloretin, were also shown to be effective in reducing cancer cell growth. A group of inhibitors of glucose transporters has been recently identified with IC50 values lower than 20mmol/L for inhibiting cancer cell growth. However, no animal or detailed mechanism studies have been reported with these inhibitors.

Recently, a small molecule named STF-31 was identified that selectively targets the von Hippel-Lindau (VHL) deficient kidney cancer cells. STF-31 inhibits VHL deficient cancer cells by inhibiting Glut1. It was further shown that daily intraperitoneal injection of a soluble analogue of STF-31 effectively reduced the growth of tumors of VHL-deficient cancer cells grafted on nude mice. On the other hand, STF-31 appears to be an inhibitor with a narrow cell target spectrum.

These investigators recently reported the identification of a group of novel small compounds that inhibit basal glucose transport and reduce cancer cell growth by a glucose deprivation–like mechanism. These compounds target Glut1 and are efficacious in vivo as anticancer agents. A novel representative compound WZB117 not only inhibited cell growth in cancer cell lines but also inhibited cancer growth in a nude mouse model. Daily intraperitoneal injection of WZB117 resulted in a more than 70% reduction in the size of human lung cancer of A549 cell origin. Mechanism studies showed that WZB117 inhibited glucose transport in human red blood cells (RBC), which express Glut1 as their sole glucose transporter. Cancer cell treatment with WZB117 led to decreases in levels of Glut1 protein, intracellular ATP, and glycolytic enzymes. All these changes were followed by increase in ATP sensing enzyme AMP-activated protein kinase (AMPK) and declines in cyclin E2 as well as phosphorylated retinoblastoma, resulting in cell-cycle arrest, senescence, and necrosis. Addition of extracellular ATP rescued compound-treated cancer cells, suggesting that the reduction of intracellular ATP plays an important role in the anticancer mechanism of the molecule.

A Small-Molecule Inhibitor of Glucose Transporter 1 Downregulates Glycolysis, Induces Cell-Cycle Arrest, and Inhibits Cancer Cell Growth In Vitro and In Vivo

Yi Liu, Yanyan Cao, Weihe Zhang, Stephen Bergmeier, et al.
Mol Cancer Ther Aug 2012; 11(8): 1672–82
http://dx.doi.org://10.1158/1535-7163.MCT-12-0131

Alterations in cellular metabolism are among the most consistent hallmarks of cancer. These investigators have studied the relationship between increased aerobic lactate production and mitochondrial physiology in tumor cells. To diminish the ability of malignant cells to metabolize pyruvate to lactate, M-type lactate dehydrogenase levels were knocked down by means of LDH-A short hairpin RNAs. Reduction in LDH-A activity resulted in stimulation of mitochondrial respiration and decrease of mitochondrial membrane potential. It also compromised the ability of these tumor cells to proliferate under hypoxia. The tumorigenicity of the LDH-A-deficient cells was severely diminished, and this phenotype was reversed by complementation with the human ortholog LDH-A protein. These results demonstrate that LDH-A plays a key role in tumor maintenance.

The results are consistent with a functional connection between alterations in glucose metabolism and mitochondrial physiology in cancer. The data also reflect that the dependency of tumor cells on glucose metabolism is a liability for these cells under limited-oxygen conditions. Interfering with LDH-A activity as a means of blocking pyruvate to lactate conversion could be exploited therapeutically. Because individuals with complete deficiency of LDH-A do not show any symptoms under ordinary circumstances, the genetic data suggest that inhibition of LDH-A activity may represent a relatively nontoxic approach to interfere with tumor growth.

Attenuation of LDH-A expression uncovers a link between glycolysis, mitochondrial physiology, and tumor maintenance

Valeria R. Fantin Julie St-Pierre and Philip Leder
Cancer Cell Jun 2006; 9: 425–434.
http://dx.doi.org:/10.1016/j.ccr.2006.04.02

The widespread clinical use of positron-emission tomography (PET) for the detection of aerobic glycolysis in tumors and recent findings have rekindled interest in Warburg’s theory. Studies on the physiological changes in malignant conversion provided a metabolic signature for the different stages of tumorigenesis; during tumorigenesis, an increase in glucose uptake and lactate production have been detected. The fully transformed state is most dependent on aerobic glycolysis and least dependent on the mitochondrial machinery for ATP synthesis.

Tumors ferment glucose to lactate even in the presence of oxygen (aerobic glycolysis; Warburg effect). The pentose phosphate pathway (PPP) allows glucose conversion to ribose for nucleic acid synthesis and glucose degradation to lactate. The nonoxidative part of the PPP is controlled by transketolase enzyme reactions. We have detected upregulation of a mutated transketolase transcript (TKTL1) in human malignancies, whereas transketolase (TKT) and transketolase-like-2 (TKTL2) transcripts were not upregulated. Strong TKTL1 protein expression was correlated to invasive colon and urothelial tumors and to poor patients outcome. TKTL1 encodes a transketolase with unusual enzymatic properties, which are likely to be caused by the internal deletion of conserved residues. We propose that TKTL1 upregulation in tumors leads to enhanced, oxygen-independent glucose usage and a lactate based matrix degradation. As inhibition of transketolase enzyme reactions suppresses tumor growth and metastasis, TKTL1 could be the relevant target for novel anti-transketolase cancer therapies. We suggest an individualized cancer therapy based on the determination of metabolic changes in tumors that might enable the targeted inhibition of invasion and metastasis.

Other important links between cancer-causing genes and glucose metabolism have been already identified. Activation of the oncogenic kinase Akt has been shown to stimulate glucose uptake and metabolism in cancer cells and renders these cells susceptible to death in response to glucose withdrawal. Such tumor cells have been shown to be dependent on glucose because the ability to induce fatty acid oxidation in response to glucose deprivation is impaired by activated Akt. In addition, AMP-activated protein kinase (AMPK) has been identified as a link between glucose metabolism and the cell cycle, thereby implicating p53 as an essential component of metabolic cell-cycle control.

Expression of transketolase TKTL1 predicts colon and urothelial cancer patient survival: Warburg effect reinterpreted

S Langbein, M Zerilli, A zur Hausen, W Staiger, et al.
British Journal of Cancer (2006) 94, 578–585.
http://dx.doi.org:/10.1038/sj.bjc.6602962

The unique metabolic profile of cancer (aerobic glycolysis) might confer apoptosis resistance and be therapeutically targeted. Compared to normal cells, several human cancers have high mitochondrial membrane potential (DJm) and low expression of the K+ channel Kv1.5, both contributing toapoptosis resistance. Dichloroacetate (DCA) inhibits mitochondrial pyruvate dehydrogenase kinase (PDK), shifts metabolism from glycolysis to glucose oxidation, decreases DJm, increases mitochondrial H2O2, and activates Kv channels in all cancer, but not normal, cells; DCA upregulates Kv1.5 by an NFAT1-dependent mechanism. DCA induces apoptosis, decreases proliferation, and inhibits tumor growth, without apparent toxicity. Molecular inhibition of PDK2 by siRNA mimics DCA. The mitochondria-NFAT-Kv axis and PDK are important therapeutic targets in cancer; the orally available DCA is a promising selective anticancer agent.

Cancer progression and its resistance to treatment depend, at least in part, on suppression of apoptosis. Although mitochondria are recognized as regulators of apoptosis, their importance as targets for cancer therapy has not been adequately explored or clinically exploited. In 1930, Warburg suggested that mitochondrial dysfunction in cancer results in a characteristic metabolic phenotype, that is, aerobic glycolysis (Warburg, 1930). Positron emission tomography (PET) imaging has now confirmed that most malignant tumors have increased glucose uptake and metabolism. This bioenergetic feature is a good marker of cancer but has not been therapeutically pursued..

The small molecule DCA is a metabolic modulator that has been used in humans for decades in the treatment of lactic acidosis and inherited mitochondrial diseases. Without affecting normal cells, DCA reverses the metabolic electrical remodeling that we describe in several cancer lines (hyperpolarized mitochondria, activated NFAT1, downregulated Kv1.5), inducing apoptosis and decreasing tumor growth. DCA in the drinking water at clinically relevant doses for up to 3 months prevents and reverses tumor growth in vivo, without apparent toxicity and without affecting hemoglobin, transaminases, or creatinine levels. The ease of delivery, selectivity, and effectiveness  make DCA an attractive candidate for proapoptotic cancer therapy which can be rapidly translated into phase II–III clinical trials.

A Mitochondria-K+ Channel Axis Is Suppressed in Cancer and Its Normalization Promotes Apoptosis and Inhibits Cancer Growth

Sebastien Bonnet, Stephen L. Archer, Joan Allalunis-Turner, et al.

Cancer Cell Jan 2007; 11: 37–51.
http://dx.doi.org:/10.1016/j.ccr.2006.10.020

Tumor cells, just as other living cells, possess the potential for proliferation, differentiation, cell cycle arrest, and apoptosis. There is a specific metabolic phenotype associated with each of these conditions, characterized by the production of both energy and special substrates necessary for the cells to function in that particular state. Unlike that of normal living cells, the metabolic phenotype of tumor cells supports the proliferative state. Aim: To present the metabolic hypothesis that (1) cell transformation and tumor growth are associated with the activation of metabolic enzymes that increase glucose carbon utilization for nucleic acid synthesis, while enzymes of the lipid and amino acid synthesis pathways are activated in tumor growth inhibition, and (2) phosphorylation and allosteric and transcriptional regulation of intermediary metabolic enzymes and their substrate availability together mediate and sustain cell transformation from one condition to another. Conclusion: Evidence is presented that demonstrates opposite changes in metabolic phenotypes induced by TGF-β, a cell transforming agent, and tumor growth-inhibiting phytochemicals such as genistein and Avemar, or novel synthetic antileukemic drugs such as STI571 (Gleevec).  Intermediary metabolic enzymes that mediate the growth signaling pathways and promote malignant cell transformation may serve as high efficacy nongenetic novel targets for cancer therapies.

A Metabolic Hypothesis of Cell Growth and Death in Pancreatic Cancer

Laszlo G. Boros, Wai-Nang Paul Lee, and Vay Liang W. Go
Pancreas 2002; 24(1):26–33

Clear cell renal cell carcinoma (ccRCC) is the most common pathological subtype of kidney cancer. Here, we integrated an unbiased genome-wide RNA interference screen for ccRCC survival regulators with an analysis of recurrently overexpressed genes in ccRCC to identify new therapeutic targets in this disease. One of the most potent survival regulators, the monocarboxylate transporter MCT4 (SLC16A3), impaired ccRCC viability in all eight ccRCC lines tested and was the seventh most overexpressed gene in a meta-analysis of five ccRCC expression datasets.

MCT4 silencing impaired secretion of lactate generated through glycolysis and induced cell cycle arrest and apoptosis. Silencing MCT4 resulted in intracellular acidosis, and reduction in intracellular ATP production together with partial reversion of the Warburg effect in ccRCC cell lines. Intra-tumoral heterogeneity in the intensity of MCT4 protein expression was observed in primary ccRCCs.

MCT4 protein expression analysis based on the highest intensity of expression in primary ccRCCs was associated with poorer relapse-free survival, whereas modal intensity correlated with Fuhrman nuclear grade. Consistent with the potential selection of subclones enriched for MCT4 expression during disease progression, MCT4 expression was greater at sites of metastatic disease. These data suggest that MCT4 may serve as a novel metabolic target to reverse the Warburg effect and limit disease progression in ccRCC.

Clear cell carcinoma (ccRCC) is the commonest subtype of renal cell carcinoma, accounting for 80% of cases. These tumors are highly resistant to cytotoxic chemotherapy and until recently, systemic treatment options for advanced ccRCC were limited to cytokine based therapies, such as interleukin-2 and interferon-α. Recently, anti-angiogenic drugs and mTOR inhibitors, all targeting the HIF–VEGF axis which is activated in up to 91% of ccRCCs through loss of the VHL tumor suppressor gene [1], have been shown to be effective in metastatic ccRCC [2–5]. Although these drugs increase overall survival to more than 2 years [6], resistance invariably occurs, making the identification of new molecular targets a major clinical need to improve outcomes in patients with metastatic ccRCC.

Genome-wide RNA interference analysis of renal carcinoma survival regulators identifies MCT4 as a Warburg effect metabolic target

Marco Gerlinger, Claudio R Santos, Bradley Spencer-Dene, et al.
J Pathol 2012; 227: 146–156
http://dx.doi.org:/10.1002/path.4006

Hypoxia-inducible factor 1 (HIF-1) plays a key role in the reprogramming of cancer metabolism by activating transcription of genes encoding glucose transporters and glycolytic enzymes, which take up glucose and convert it to lactate; pyruvate dehydrogenase kinase 1, which shunts pyruvate away from the mitochondria; and BNIP3, which triggers selective mitochondrial autophagy. The shift from oxidative to glycolytic metabolism allows maintenance of redox homeostasis and cell survival under conditions of prolonged hypoxia. Many metabolic abnormalities in cancer cells increase HIF-1 activity. As a result, a feed-forward mechanism can be activated that drives HIF-1 activation and may promote tumor progression.

Metastatic cancer is characterized by reprogramming of cellular metabolism leading to increased uptake of glucose for use as both an anabolic and a catabolic substrate. Increased glucose uptake is such a reliable feature that it is utilized clinically to detect metastases by positron emission tomography using 18F-fluorodeoxyglucose (FDG-PET) with a sensitivity of >90% [1]. As with all aspects of cancer biology, the details of metabolic reprogramming differ widely among individual tumors. However, the role of specific signaling pathways and transcription factors in this process is now understood in considerable detail. This review will focus on the involvement of hypoxia-inducible factor 1 (HIF-1) in both mediating metabolic reprogramming and responding to metabolic alterations. The placement of HIF-1 both upstream and downstream of cancer metabolism results in a feed-forward mechanism that may play a major role in the development of the invasive, metastatic, and lethal cancer phenotype.

O2 concentrations are significantly reduced in many human cancers compared with the surrounding normal tissue. The median PO2 in breast cancers is 10 mmHg, as compared with65 mmHg in normal breast tissue. Reduced O2 availability induces HIF-1, which regulates the transcription of hundreds of genes that encode proteins involved in every aspect of cancer biology, including: cell immortalization and stem cell maintenance; genetic instability; glucose and energy metabolism; vascularization; autocrine growth factor signaling; invasion and metastasis; immune evasion; and resistance to chemotherapy and radiation therapy.

HIF-1 is a transcription factor that consists of an O2 regulated HIF-1a and a constitutively expressed HIF-1b subunit. In well-oxygenated cells, HIF-1a is hydroxylated on proline residue 402 (Pro-402) and/or Pro-564 by prolyl hydroxylase domain protein 2 (PHD2), which uses O2 and a-ketoglutarate as substrates in a reaction that generates CO2 and succinate as byproducts. Prolylhydroxylated HIF-1a is bound by the von Hippel–Lindau tumor suppressor protein (VHL), which recruits an E3-ubiquitin ligase that targets HIF-1a for proteasomal degradation (Figure 1a). Asparagine 803 in the transactivation domain is hydroxylated in well-oxygenated cells by factor inhibiting HIF-1 (FIH-1), which blocks the binding of the coactivators p300 and CBP. Under hypoxic conditions, the prolyl and asparaginyl hydroxylation reactions are inhibited by substrate (O2) deprivation and/or the mitochondrial generation of reactive oxygen species (ROS), which may oxidize Fe(II) present in the catalytic center of the hydroxylases.

The finding that acute changes in PO2 increase mitochondrial ROS production suggests that cellular respiration is optimized at physiological PO2 to limit ROS generation and that any deviation in PO2 – up or down – results in increased ROS generation. If hypoxia persists, induction of HIF-1 leads to adaptive mechanisms to reduce ROS and re-establish homeostasis, as described below. Prolyl and asparaginyl hydroxylation provide a molecular mechanism by which changes in cellular oxygenation can be transduced to the nucleus as changes in HIF-1 activity.

HIF-1: upstream and downstream of cancer metabolism

Gregg L Semenza
Current Opinion in Genetics & Development 2010, 20:51–56

This review comes from a themed issue on Genetic and cellular mechanisms of oncogenesis Edited by Tony Hunter and Richard Marais

http://dx.doi.org:/10.1016/j.gde.2009.10.009

Hypoxia-inducible factor 1 (HIF-1) regulates the transcription of many genes involved in key aspects of cancer biology, including immortalization, maintenance of stem cell pools, cellular dedifferentiation, genetic instability, vascularization, metabolic reprogramming, autocrine growth factor signaling, invasion/metastasis, and treatment failure. In animal models, HIF-1 overexpression is associated with increased tumor growth, vascularization, and metastasis, whereas HIF-1 loss-of-function has the opposite effect, thus validating HIF-1 as a target. In further support of this conclusion, immunohistochemical detection of HIF-1a overexpression in biopsy sections is a prognostic factor in many cancers. A growing number of novel anticancer agents have been shown to inhibit HIF-1 through a  variety of molecular mechanisms. Determining which combination of drugs to administer to any given patient remains a major obstacle to improving cancer treatment outcomes.

Intratumoral hypoxia The majority of locally advanced solid tumors contain regions of reduced oxygen availability. Intratumoral hypoxia results when cells are located too far from a functional blood vessel for diffusion of adequate amounts of O2 as a result of rapid cancer cell proliferation and the formation of blood vessels that are structurally and functionally abnormal. In the most extreme case, O2 concentrations are below those required for survival, resulting in cell death and establishing a selection for cancer cells in which apoptotic pathways are inactivated, anti-apoptotic pathways are activated, or invasion/metastasis pathways that promote escape from the hypoxic microenvironment are activated. This hypoxic adaptation may arise by alterations in gene expression or by mutations in the genome or both and is associated with reduced patient survival.

Hypoxia-inducible factor 1 (HIF-1) The expression of hundreds of genes is altered in each cell exposed to hypoxia. Many of these genes are regulated by HIF-1. HIF-1 is a heterodimer formed by the association of an O2-regulated HIF1a subunit with a constitutively expressed HIF-1b subunit. The structurally and functionally related HIF-2a protein also dimerizes with HIF-1b and regulates an overlapping battery of target genes. Under nonhypoxic conditions, HIF-1a (as well as HIF-2a) is subject to O2-dependent prolyl hydroxylation and this modification is required for binding of the von Hippel–Lindau tumor suppressor protein (VHL), which also binds to Elongin C and thereby recruits a ubiquitin ligase complex that targets HIF-1a for ubiquitination and proteasomal degradation. Under hypoxic conditions, the rate of hydroxylation and ubiquitination declines, resulting in accumulation of HIF-1a. Immunohistochemical analysis of tumor biopsies has revealed high levels of HIF-1a in hypoxic but viable tumor cells surrounding areas of necrosis.

Genetic alterations in cancer cells increase HIF-1 activity In the majority of clear-cell renal carcinomas, VHL function is lost, resulting in constitutive activation of HIF-1. After re-introduction of functional VHL, renal carcinoma cell lines are no longer tumorigenic, but can be made tumorigenic by expression of HIF2a in which the prolyl residues that are subject to hydroxylation have been mutated. In addition to VHL loss-of-function, many other genetic alterations that inactivate tumor suppressors

Evaluation of HIF-1 inhibitors as anticancer agents

Gregg L. Semenza
Drug Discovery Today Oct 2007; 12(19/20).
http://dx.doi.org:/10.1016/j.drudis.2007.08.006

Hypoxia-inducible factor-1 (HIF-1), which is present at high levels in human tumors, plays crucial roles in tumor promotion by upregulating its target genes, which are involved in anaerobic energy metabolism, angiogenesis, cell survival, cell invasion, and drug resistance. Therefore, it is apparent that the inhibition of HIF-1 activity may be a strategy for treating cancer. Recently, many efforts to develop new HIF-1-targeting agents have been made by both academic and pharmaceutical industry laboratories. The future success of these efforts will be a new class of HIF-1-targeting anticancer agents, which would improve the prognoses of many cancer patients. This review focuses on the potential of HIF-1 as a target molecule for anticancer therapy, and on possible strategies to inhibit HIF-1 activity. In addition, we introduce YC-1 as a new anti-HIF-1, anticancer agent. Although YC-1 was originally developed as a potential therapeutic agent for thrombosis and hypertension, recent studies demonstrated that YC-1 suppressed HIF-1 activity and vascular endothelial growth factor expression in cancer cells. Moreover, it halted tumor growth in immunodeficient mice without serious toxicity during the treatment period. Thus, we propose that YC-1 is a good lead compound for the development of new anti-HIF-1, anticancer agents.

Although many anticancer regimens have been introduced to date, their survival benefits are negligible, which is the reason that a more innovative treatment is required. Basically, the identification of the specific molecular features of tumor promotion has allowed for rational drug discovery in cancer treatment, and drugs have been screened based upon the modulation of specific molecular targets in tumor cells. Target-based drugs should satisfy the following two conditions.

First, they must act by a described mechanism.

Second, they must reduce tumor growth in vivo, associated with this mechanism.

Many key factors have been found to be involved in the multiple steps of cell growth signal-transduction pathways. Targeting these factors offers a strategy for preventing tumor growth; for example, competitors or antibodies blocking ligand–receptor interaction, and receptor tyrosine kinase inhibitors, downstream pathway inhibitors (i.e., RAS farnesyl transferase inhibitors, mitogen-activated protein kinase and mTOR inhibitors), and cell-cycle arresters (i.e., cyclin-dependent kinase inhibitors) could all be used to inhibit tumor growth.

In addition to the intracellular events, tumor environmental factors should be considered to treat solid tumors. Of these, hypoxia is an important cancer-aggravating factor because it contributes to the progression of a more malignant phenotype, and to the acquisition of resistance to radiotherapy and chemotherapy. Thus, transcription factors that regulate these hypoxic events are good targets for anticancer therapy and in particular HIF-1 is one of most compelling targets. In this paper, we introduce the roles of HIF-1 in tumor promotion and provide a summary of new anticancer strategies designed to inhibit HIF-1 activity.

New anticancer strategies targeting HIF-1

Eun-Jin Yeo, Yang-Sook Chun, Jong-Wan Park
Biochemical Pharmacology 68 (2004) 1061–1069
http://dx.doi.org:/10.1016/j.bcp.2004.02.040

Classical work in tumor cell metabolism focused on bioenergetics, particularly enhanced glycolysis and suppressed oxidative phosphorylation (the ‘Warburg effect’). But the biosynthetic activities required to create daughter cells are equally important for tumor growth, and recent studies are now bringing these pathways into focus. In this review, we discuss how tumor cells achieve high rates of nucleotide and fatty acid synthesis, how oncogenes and tumor suppressors influence these activities, and how glutamine metabolism enables macromolecular synthesis in proliferating cells.

Otto Warburg’s demonstration that tumor cells rapidly use glucose and convert the majority of it to lactate is still the most fundamental and enduring observation in tumor metabolism. His work, which ushered in an era of study on tumor metabolism focused on the relationship between glycolysis and cellular bioenergetics, has been revisited and expanded by generations of tumor biologists. It is now accepted that a high rate of glucose metabolism, exploited clinically by 18FDGPET scanning, is a metabolic hallmark of rapidly dividing cells, correlates closely with transformation, and accounts for a significant percentage of ATP generated during cell proliferation. A ‘metabolic transformation’ is required for tumorigenesis. Research over the past few years has reinforced this idea, revealing the conservation of metabolic activities among diverse tumor types, and proving that oncogenic mutations can promote metabolic autonomy by driving nutrient uptake to levels that often exceed those required for cell growth and proliferation.

In order to engage in replicative division, a cell must duplicate its genome, proteins, and lipids and assemble the components into daughter cells; in short, it must become a factory for macromolecular biosynthesis. These activities require that cells take up extracellular nutrients like glucose and glutamine and allocate them into metabolic pathways that convert them into biosynthetic precursors (Figure 1). Tumor cells can achieve this phenotype through changes in the expression of enzymes that determine metabolic flux rates, including nutrient transporters and enzymes [8– 10]. Current studies in tumor metabolism are revealing novel mechanisms for metabolic control, establishing which enzyme isoforms facilitate the tumor metabolic phenotype, and suggesting new targets for cancer therapy.

The ongoing challenge in tumor cell metabolism is to understand how individual pathways fit together into the global metabolic phenotype of cell growth. Here we discuss two biosynthetic activities required by proliferating tumor cells: production of ribose-5 phosphate for nucleotide biosynthesis and production of fatty acids for lipid biosynthesis. Nucleotide and lipid biosynthesis share three important characteristics.

  • First, both use glucose as a carbon source.
  • Second, both consume TCA cycle intermediates, imposing the need for a mechanism to replenish the cycle.
  • Third, both require reductive power in the form of NADPH.

In this Essay, we discuss the possible drivers, advantages, and potential liabilities of the altered metabolism of cancer cells (Figure 1, not shown). Although our emphasis on the Warburg effect reflects the focus of the field, we would also like to encourage a broader approach to the study of cancer metabolism that takes into account the contributions of all interconnected small molecule pathways of the cell.

The Tumor Microenvironment Selects for Altered Metabolism One compelling idea to explain the Warburg effect is that the altered metabolism of cancer cells confers a selective advantage for survival and proliferation in the unique tumor microenvironment. As the early tumor expands, it outgrows the diffusion limits of its local blood supply, leading to hypoxia and stabilization of the hypoxia-inducible transcription factor, HIF. HIF initiates a transcriptional program that provides multiple solutions to hypoxic stress (reviewed in Kaelin and Ratcliffe, 2008). Because a decreased dependence on aerobic respiration becomes advantageous, cell metabolism is shifted toward glycolysis by the increased expression of glycolytic enzymes, glucose transporters, and inhibitors of mitochondrial metabolism. In addition, HIF stimulates angiogenesis (the formation of new blood vessels) by upregulating several factors, including most prominently vascular endothelial growth factor (VEGF).

Blood vessels recruited to the tumor microenvironment, however, are disorganized, may not deliver blood effectively, and therefore do not completely alleviate hypoxia (reviewed in Gatenby and Gillies, 2004). The oxygen levels within a tumor vary both spatially and temporally, and the resulting rounds of fluctuating oxygen levels potentially select for tumors that constitutively upregulate glycolysis. Interestingly, with the possible exception of tumors that have lost the von Hippel-Lindau protein (VHL), which normally mediates degradation of HIF, HIF is still coupled to oxygen levels, as evident from the heterogeneity of HIF expression within the tumor microenvironment. Therefore, the Warburg effect—that is, an uncoupling of glycolysis from oxygen levels—cannot be explained solely by upregulation of HIF. Other molecular mechanisms are likely to be important, such as the metabolic changes induced by oncogene activation and tumor suppressor loss.

Oncogene Activation Drives Changes in Metabolism Not only may the tumor microenvironment select for a deranged metabolism, but oncogene status can also drive metabolic changes. Since Warburg’s time, the biochemical study of cancer metabolism has been overshadowed by efforts to identify the mutations that contribute to cancer initiation and progression. Recent work, however, has demonstrated that the key components of the Warburg effect—

  • increased glucose consumption,
  • decreased oxidative phosphorylation, and
  • accompanying lactate production—
  • are also distinguishing features of oncogene activation.

The signaling molecule Ras, a powerful oncogene when mutated, promotes glycolysis (reviewed in Dang and Semenza, 1999; Ramanathan et al., 2005). Akt kinase, a well-characterized downstream effector of insulin signaling, reprises its role in glucose uptake and utilization in the cancer setting (reviewed in Manning and Cantley, 2007), whereas the Myc transcription factor upregulates the expression of various metabolic genes (reviewed in Gordan et al., 2007). The most parsimonious route to tumorigenesis may be activation of key oncogenic nodes that execute a proliferative program, of which metabolism may be one important arm. Moreover, regulation of metabolism is not exclusive to oncogenes.

Cancer Cell Metabolism: Warburg & Beyond

Hsu PP & Sabatini DM
Cell  Sep 5, 2008; 134, 703-705
http://dx.doi.org:/10.1016/j.cell.2008.08.021

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 de novo 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.

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

László G. Boros, Daniel J. Brackett and George G. Harrigan
Current Cancer Drug Targets, 2003, 3, 447-455 447

Pyruvate constitutes a critical branch point in cellular carbon metabolism. We have identified two proteins, Mpc1 and Mpc2, as essential for mitochondrial pyruvate transport in yeast, Drosophila, and humans. Mpc1 and Mpc2 associate to form an ~150 kilodalton complex in the inner mitochondrial membrane. Yeast and Drosophila mutants lacking MPC1 display impaired pyruvate metabolism, with an accumulation of upstream metabolites and a depletion of tricarboxylic acid cycle intermediates. Loss of yeast Mpc1 results in defective mitochondrial pyruvate uptake, while silencing of MPC1 or MPC2 in mammalian cells impairs pyruvate oxidation. A point mutation in MPC1 provides resistance to a known inhibitor of the mitochondrial pyruvate carrier. Human genetic studies of three families with children suffering from lactic acidosis and hyperpyruvatemia revealed a causal locus that mapped to MPC1, changing single amino acids that are conserved throughout eukaryotes. These data demonstrate that Mpc1 and Mpc2 form an essential part of the mitochondrial pyruvate carrier.

A Mitochondrial Pyruvate Carrier Required for Pyruvate Uptake in Yeast, Drosophila , and Humans

Daniel K. Bricker, Eric B. Taylor, John C. Schell, Thomas Orsak, et al.
Science Express 24 May 2012
http://dx.doi.org:/10.1126/science.1218099

Adenosine deaminase acting on RNA (ADAR) enzymes convert adenosine (A) to inosine (I) in double-stranded (ds) RNAs. Since Inosine is read as Guanosine, the biological consequence of ADAR enzyme activity is an A/G conversion within RNA molecules. A-to-I editing events can occur on both coding and non-coding RNAs, including microRNAs (miRNAs), which are small regulatory RNAs of ~20–23 nucleotides that regulate several cell processes by annealing to target mRNAs and inhibiting their translation. Both miRNA precursors and mature miRNAs undergo A-to-I RNA editing, affecting the miRNA maturation process and activity. ADARs can also edit 3′ UTR of mRNAs, further increasing the interplay between mRNA targets and miRNAs. In this review, we provide a general overview of the ADAR enzymes and their mechanisms of action as well as miRNA processing and function. We then review the more recent findings about the impact of ADAR-mediated activity on the miRNA pathway in terms of biogenesis, target recognition, and gene expression regulation.

Review ADAR Enzyme and miRNA Story: A Nucleotide that Can Make the Difference 

Sara Tomaselli, Barbara Bonamassa, Anna Alisi, Valerio Nobili, Franco Locatelli and Angela Gallo
Int. J. Mol. Sci. 19 Nov 2013; 14, 22796-22816 http://dx.doi.org:/10.3390/ijms141122796

The fermented wheat germ extract (FWGE) nutraceutical (Avemar™), manufactured under “good manufacturing practice” conditions and, fulfilling the self-affirmed “generally recognized as safe” status in the United States, has been approved as a “dietary food for special medical purposes for cancer patients” in Europe. In this paper, we report the adjuvant use of this nutraceutical in the treatment of high-risk skin melanoma patients. Methods: In a randomized, pilot, phase II clinical trial, the efficacy of dacarbazine (DTIC)-based adjuvant chemotherapy on survival parameters of melanoma patients was compared to that of the same treatment supplemented with a 1-year long administration of FWGE. Results: At the end of an additional 7-year-long follow-up period, log-rank analyses (Kaplan-Meier estimates) showed significant differences in both progression-free (PFS) and overall survival (OS) in favor of the FWGE group. Mean PFS: 55.8 months (FWGE group) versus 29.9 months (control group), p  0.0137. Mean OS: 66.2 months (FWGE group) versus 44.7 months (control group), p < 0.0298. Conclusions: The inclusion of Avemar into the adjuvant protocols of high-risk skin melanoma patients is highly recommended.

Adjuvant Fermented Wheat Germ Extract (Avemar™) Nutraceutical Improves Survival of High-Risk Skin Melanoma Patients: A Randomized, Pilot, Phase II Clinical Study with a 7-Year Follow-Up

LV Demidov, LV Manziuk, GY Kharkevitch, NA Pirogova, and EV Artamonova
Cancer Biotherapy & Radiopharmaceuticals 2008; 23(4)
http://dx.doi.org:/10.1089/cbr.2008.0486

Cancer cells possess unique metabolic signatures compared to normal cells, including shifts in aerobic glycolysis, glutaminolysis, and de novo biosynthesis of macromolecules. Targeting these changes with agents (drugs and dietary components) has been employed as strategies to reduce the complications associated with tumorigenesis. This paper highlights the ability of several food components to suppress tumor-specific metabolic pathways, including increased expression of glucose transporters, oncogenic tyrosine kinase, tumor-specific M2-type pyruvate kinase, and fatty acid synthase, and the detection of such effects using various metabonomic technologies, including liquid chromatography/mass spectrometry (LC/MS) and stable isotope-labeled MS. Stable isotope-mediated tracing technologies offer exciting opportunities for defining specific target(s) for food components. Exposures, especially during the early transition phase from normal to cancer, are critical for the translation of knowledge about food components into effective prevention strategies. Although appropriate dietary exposures needed to alter cellular metabolism remain inconsistent and/or ill-defined, validated metabonomic biomarkers for dietary components hold promise for establishing effective strategies for cancer prevention.

Bioactive Food Components and Cancer-Specific Metabonomic Profiles

Young S. Kim and John A. Milner
Journal of Biomedicine and Biotechnology 2011, Art ID 721213, 9 pages
http://dx.doi.org:/10.1155/2011/721213

This reviewer poses the following observation.  The importance of the pyridine nucleotide reduced/oxidized ratio has not been alluded to here, but the importance cannot be understated. It has relevance to the metabolic functions of anabolism and catabolism of the visceral organs.  The importance of this has ties to the pentose monophosphate pathway. The importance of the pyridine nucleotide transhydrogenase reaction remains largely unexplored.  In reference to the NAD-redox state, the observation was made by Nathan O. Kaplan that the organs may be viewed with respect to their primary functions in anabolic or high energy catabolic activities. Thus we find that the endocrine organs are largely tied to anabolic functioning, and to NADP, whereas cardiac and skeletal muscle are highly dependent on NAD. The consequence of this observed phenomenon appears to be related to a difference in the susceptibility to malignant transformation.  In the case of the gastrointestinal tract, the rate of turnover of the epithelium is very high. However, with the exception of the liver, there is no major activity other than cell turnover. In the case of the liver, there is a major commitment to synthesis of lipids, storage of fuel, and synthesis of proteins, which is largely anabolic, but there is also a major activity in detoxification, which is not.  In addition, the liver has a double circulation. As a result, a Zahn infarct is uncommon.  Now we might also consider the heart.  The heart is a muscle syncytium with a high need for oxygen.  Cutting of the oxygen supply makes the myocytes vulnerable to ischemic insult and abberant rhythm abnormalities.  In addition, the cardiomyocyte can take up lactic acid from the circulation for fuel, which is tied to the utilization of lactate from vigorous skeletal muscle activity.  The skeletal muscle is tied to glycolysis in normal function, which has a poor generation of ATP, so that the recycling of excess lactic acid is required by cardiac muscle and hepatocytes.  This has not been a part of the discussion, but this reviewer considers it important to remember in considering the organ-specific tendencies to malignant transformation.

Comment (Aurelian Udristioiu):

Otto Warburg observed that many cancers lose their capacity for mitochondrial respiration, limiting ATP production to anaerobic glycolytic pathways. The phenomenon is particularly prevalent in aggressive malignancies, most of which are also hypoxic [1].
Hypoxia induces a stochastic imbalance between the numbers of reduced mitochondrial species vs. available oxygen, resulting in increased reactive oxygen species (ROS) whose toxicity can lead to apoptotic cell death.
Mechanism involves inhibition of glycolytic ATP production via a Randle-like cycle while increased uncoupling renders cancers unable to produce compensatory ATP from respiration-.generation in the presence of intact tricarboxylic acid (TCA) enzyme.
One mitochondrial adaptation to increased ROS is over-expression of the uncoupling protein 2 (UCP2) that has been reported in multiple human cancer cell lines [2-3]. Increased UCP2 expression was also associated with reduced ATP production in malignant oxyphilic mouse leukemia and human lymphoma cell lines [4].
Hypoxia reduces the ability of cells to maintain their energy levels, because less ATP is obtained from glycolysis than from oxidative phosphorylation. Cells adapt to hypoxia by activating the expression of mutant genes in glycolysis.
-Severe hypoxia causes a high mutation rate, resulting in point mutations that may be explained by reduced DNA mismatch repairing activity.
The most direct induction of apoptosis caused by hypoxia is determined by the inhibition of the electron carrier chain from the inner membrane of the mitochondria. The lack of oxygen inhibits the transport of protons and thereby causes a decrease in membrane potential. Cell survival under conditions of mild hypoxia is mediated by phosphoinositide-3 kinase (PIK3) using severe hypoxia or anoxia, and then cells initiate a cascade of events that lead to apoptosis [5].
After DNA damage, a very important regulator of apoptosis is the p53 protein. This tumor suppressor gene has mutations in over 60% of human tumors and acts as a suppressor of cell division. The growth-suppressive effects of p53 are considered to be mediated through the transcriptional trans-activation activity of the protein. In addition to the maturational state of the clonal tumor, the prognosis of patients with CLL is dependent of genetic changes within the neoplastic cell population.

1.Warburg O. On the origin of cancer cells. Science 1956; 123 (3191):309-314
PubMed Abstract ; Publisher Full Text

2.Giardina TM, Steer JH, Lo SZ, Joyce DA. Uncoupling protein-2 accumulates rapidly in the inner mitochondrial membrane during mitochondrial reactive oxygen stress in macrophages. Biochim Biophys Acta 2008, 1777(2):118-129. PubMed Abstract | Publisher Full Text

3. Horimoto M, Resnick MB, Konkin TA, Routhier J, Wands JR, Baffy G. Expression of uncoupling protein-2 in human colon cancer. Clin Cancer Res 2004; 10 (18 Pt1):6203-6207. PubMed Abstract | Publisher Full Text

4. Randle PJ, England PJ, Denton RM. Control of the tricarboxylate cycle and it interactions with glycolysis during acetate utilization in rat heart. Biochem J 1970; 117(4):677-695. PubMed Abstract | PubMed Central Full Text

5. Gillies RJ, Robey I, Gatenby RA. Causes and consequences of increased glucose metabolism of cancers. J Nucl Med 2008; 49(Suppl 2):24S-42S. PubMed Abstract | Publisher Full Text

Shortened version of Comment –

Hypoxia induces a stochastic imbalance between the numbers of reduced mitochondrial species vs. available oxygen, resulting in increased reactive oxygen species (ROS) whose toxicity can lead to apoptotic cell death.
Mechanism involves inhibition of glycolytic ATP production via a Randle-like cycle while increased uncoupling renders cancers unable to produce compensatory ATP from respiration-.generation in the presence of intact tricarboxylic acid (TCA) enzyme.
One mitochondrial adaptation to increased ROS is over-expression of the uncoupling protein 2 (UCP2) that has been reported in multiple human cancer cell lines. Increased UCP2 expression was also associated with reduced ATP production in malignant oxyphilic mouse leukemia and human lymphoma cell lines.
Severe hypoxia causes a high mutation rate, resulting in point mutations that may be explained by reduced DNA mismatch repairing activity.

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Endometrial Cancer: Mutations, Molecular Types and Immune Responses Evoked by Mutation-prone Endometrial, Ovarian Cancer Subtypes

Curator: Aviva Lev-Ari, PhD, RN

 

This Open Access Online Scientific Journal represents a repository of curated scientific literature on the following types of cancer of relevance to the subject matter of this article. See below the FRONTIER of Research on:

Breast Cancer

http://pharmaceuticalintelligence.com/?s=Breast+Cancer

Ovarian Cancer

http://pharmaceuticalintelligence.com/?s=Ovarian+Cancer

Genomics of Endometriosis

http://pharmaceuticalintelligence.com/?s=Endometriosis+

Reproductive Genomics

http://pharmaceuticalintelligence.com/?s=Reproductive+Genomics

Genomic Endocrinology

http://pharmaceuticalintelligence.com/?s=Endocrinology+Genomic

 

Endometrial Cancer: Mutations, Molecular Types and Immune Responses Evoked by Mutation-prone Endometrial, Ovarian Cancer Subtypes – New Findings

 

CONCLUSIONS

  • the team saw an apparent jump in PD-1 representation in the lymphocytes that were infiltrating neighboring tumors in the BRCA1/2-mutated tumors relative to the other ovarian cancers, though staining for the immune checkpoint contributors within tumors themselves appeared similar regardless of the subtype considered.
  • Strickland and his colleagues reasoned that such a feature may partly explain the relatively high progression-free survival and overall survival rates reported in BRCA1/2-mutated ovarian cancers, though they are continuing to study the relationship between BRCA mutations and tumor features.
  • Memorial Sloan Kettering medical oncologist Alexandra Snyder Charen discussed potential implications of the endometrial and ovarian cancer studies, noting that distinct mutation signatures in different tumor types could also affect immune response.
  • While she expressed enthusiasm about potential treatment clues provided by more-or-less mutated endometrial and ovarian cancers, Snyder Charen noted that additional research is needed on additional forms of the disease, since the work described was done using primary tumors.

 

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

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

Testing for Multiple Genetic Mutations via NGS for Patients: Very Strong Family History of Breast & Ovarian Cancer, Diagnosed at Young Ages, & Negative on BRCA Test

http://pharmaceuticalintelligence.com/2013/05/20/testing-for-multiple-genetic-mutations-via-ngs-for-patients-very-strong-family-history-of-breast-ovarian-cancer-diagnosed-at-young-ages-negative-on-brca-test/

TCGA Analysis Uncovers Four Molecular Subtypes for Endometrial Cancer

For tumors from the high-risk serous subtype, meanwhile, they saw genetic and genomic features that resemble those found in serous ovarian cancer and basal-like breast cancer, albeit with more frequent mutations to genes such as PIK3CA, FBXW7, PPP2R1A, and ARID1A.

These and other molecular features identified in the current study could have prognostic and treatment implications, they noted. For instance, survival patterns in the POLE subtype seem to be favorable, despite the rampant mutations present in the genomes of those tumors.

In contrast, individuals with serous or serous-like tumors appear to do much worse, Levine noted.

That, in turn, suggests that there could be a benefit to offering more aggressive treatment to individuals with endometrioid cases falling in the new serous-like category, which is characterized by a higher-than-usual burden of copy number changes coupled with frequent mutations in the TP53 gene, a common cancer culprit.

“Clinicians should carefully consider treating copy-number-altered endometrioid patients with chemotherapy rather than adjuvant radiation,” Levine and his co-authors wrote, “and formally test such hypotheses in prospective clinical trials.”

For their part, researchers involved in the current study recently completed the accrual process for a clinical trial that will involve a little more than 300 endometrial cancer patients being treated with various chemotherapy regimens.

By prospectively collecting and tumors and determining their molecular subtypes, Levine said, it should be possible to track outcomes in relation to the four subtypes identified in the current study and, eventually, to get a better sense of treatment response and survival patterns in each group.

https://www.genomeweb.com/clinical-genomics/tcga-analysis-uncovers-four-molecular-subtypes-endometrial-cancer

 

Immune Responses Evoked by Mutation-prone Endometrial, Ovarian Cancer Subtypes

researchers from Brigham and Women’s Hospital, Harvard Medical School, and the Dana-Farber Cancer Institute characterized tumor-infiltrating immune cell activity and immune checkpoint contributor expression in dozens of archival endometrial tumors samples from mutation-heavy polymerase epsilon (POLE) mutations and microsatellite instability subtypes, comparing them with patterns in more mutation-light microsatellite stable tumors.

The results suggest endometrial cancers from subtypes prone to more widespread mutation also trigger stronger immune responses that might be further enhanced by drugs that inhibit cancer cells’ immune checkpoints, explained Brooke Howitt, a pathologist at the Brigham and Women’s Hospital, who presented the research at ASCO.

Howitt and her colleagues used immunohistochemistry to profile tumor infiltrating lymphocyte and expression of the immune checkpoint players PD-1 and PD-L1 in four POLE-mutated endometrial cancers, 28 endometrial cancers with microsatellite instability, and 32 microsatellite stable endometrial cancers.

Indeed, their results pointed to more pronounced tumor infiltration by CD3+ , CD4+, and CD8+ lymphocytes in the group of POLE-mutated and microsatellite unstable tumors than in the microsatellite stable subtype, consistent with T-cell activity against the mutation-rich tumors.

When they compared the more mutated endometrial cancer subtypes to the microsatellite stable group, the researchers saw signs of enhanced PD-L1 and PD-1 expression in both infiltrating lymphocytes and in the tumors themselves, hinting that the oft-mutated subtypes may respond to immune-targeting PD-1 inhibitor drugs.

Dana-Farber Cancer Institute researcher Kyle Strickland provided evidence for a similar pattern of bolstered immune activity against extensively mutated tumors.

For their part, though, Strickland and his team focused on BRCA1- and/or BRCA2-mutated, high-grade serous ovarian cancers, using immunohistochemistry to see if the high mutational load found in tumors with hampered BRCA-mediated DNA repair activity might also be a flag for the immune system.

There, researchers compared tumor infiltrating lymphocyte patterns in 37 BRCA1/2-mutated tumor samples and in samples from 16 tumors lacking germline or somatic mutations in BRCA1, BRCA2, or related mutations or expression changes — features verified by high-throughput sequencing.

Results from that comparison suggested that all of the ovarian cancers had comparable levels of certain tumor infiltrating lymphocytes, such as the CD3+ or CD20+ lymphocytes.

But compared with the “homologous recombination intact” tumors, the BRCA1/2-mutated ovarian cancers appeared to be marked by higher CD8+ tumor infiltrating lymphocytes and lower CD4+ tumor infiltrating lymphocytes, Strickland explained.

https://www.genomeweb.com/cancer/asco-session-explores-immune-responses-evoked-mutation-prone-endometrial-ovarian-cancer

 

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Goes to Clinic @MGH: Clinically validated versions of Exome Sequencing and Analysis using Broad-developed methods like Hybrid Capture, the Genome Analysis Toolkit (GATK), and MuTect

Reporter: Aviva Lev-Ari, PhD, RN

Better data for the bedside: Broad sequencing gets closer to the clinic

By Leah Eisenstadt, Broad Communications, May 1st, 2015
  • The Broad’s Clinical Research Sequencing Platform provides high-quality
    validated genetic sequencing for clinical researchers
    Image courtesy of iStockphoto and Broad Communications

http://www.broadinstitute.org/news/6785

The Broad Institute aims to transform biomedicine using systematic approaches in the biological sciences to dramatically accelerate the understanding and treatment of disease. This goal cannot be accomplished purely in the laboratory, but must include efforts to bridge findings to the clinic.

In 2013, the Broad launched the institute’s Clinical Research Sequencing Platform (CRSP) to provide high-quality, validated genetic sequencing for clinical researchers in academic, medical, biotechnology, and pharmaceutical organizations, and to bolster the utility of genomic information in medicine. CRSP was developed and is operated by the Genomics Platform under the leadership of Stacey Gabriel, the platform’s director, and Niall Lennon, who directs the platform’s clinical development. Since its launch CRSP has created clinically validated versions of exome sequencing and analysis using Broad-developed methods like hybrid capture, the Genome Analysis Toolkit (GATK), and MuTect. These methods have already been applied to numerous clinical research projects involving more than 1,000 individual samples.

The platform is now expanding its clinical diagnostic expertise by bringing on institute member Heidi Rehm, Ph.D., FACMG, as clinical director. Rehm will continue to serve as the director of the Laboratory for Molecular Medicine (LMM), the CLIA-certified molecular diagnostic laboratory she founded in 2001 at Partners Healthcare Personalized Medicine, and she will build on this experience to lead CRSP on a part-time basis along with assistant director Ozge Ceyhan-Birsoy, Ph.D., a recent graduate of Rehm’s Clinical Molecular Genetics training program at Harvard Medical School. Together with Genomics Platform leadership, they will help guide the development of CRSP services so that they best serve the end users: clinicians and clinical researchers. “The Genomics Platform is thrilled to have Heidi and Ozge join us to help us refine our offerings and outline a strategic vision for the platform’s coming years” said Gabriel.


Incoming clinical director, Heidi Rehm
Photo courtesy of Brigham and Women’s Hospital

CRSP is accredited by the College of American Pathologists (CAP), licensed by the State of Massachusetts, and registered with the Centers for Medicare and Medicaid Services to provide testing under the Clinical Laboratory Improvement Amendments (CLIA) regulations. These certifications ensure that the data generated in the platform is “validated” and can be used by physicians to make clinical decisions about diagnosis and treatment of patients or incorporated into clinical trials.

Services offered by CRSP currently include sequencing of the whole exome (all the protein-coding parts of the genome) for germline DNA (typically used to identify mutations underlying Mendelian, or single gene, diseases) and somatic DNA (primarily tumor and normal tissue samples from cancer patients). These validated exomes are produced on the Illumina sequencing platform, using a method that members of the Broad Genomics Platform co-designed with Illumina. Scientists in the Genomics Platform have used Illumina exome sequencing extensively for research applications, but with recent CLIA validation of the process, it can now be used by CRSP in a clinical context.

CRSP currently supports several clinical research projects, including: BabySeq, an NHGRI-funded initiative to explore the return of genomic data to newborns led by Broad associate member Robert Green and Alan Beggs; sequencing of brain cancer samples for the Accelerating Brain Cancer Cure (ABC2) research project; a Dana-Farber Cancer Institute endeavor to facilitate trials of personalized vaccines for cancer patients; and CanSeq, an effort to use whole-exome sequencing to guide the care of cancer patients, co-led by Levi Garraway, institute member of the Broad. The CRSP team also recently completed targeted sequencing on more than 1,000 samples for a large clinical trial in partnership with a biotechnology company.

The platform welcomes its new clinical director Heidi Rehm to help forge even closer connections to the clinic. In particular, one new avenue will be a close collaboration with the LMM. Scientists in CRSP have already begun collaborating more closely with the LMM’s clinical geneticists and scientists to help refine the content of exomes produced at the Broad so that they are the highest value to users of the data, for example, prioritizing disease-relevant regions of the genome in sequencing data.

“The Broad offers innovation and expertise in sequencing and information technology, and the LMM is great at curating and interpreting content in a clinical context,” said Rehm. “The two together are a perfect marriage, but we’ll need to work more closely to get a truly integrated approach and develop compatible solutions. By having people who are using these products on the Broad’s clinical development team, we can ensure that the technology we develop is actually what’s needed by the clinical labs.”

Rehm explained that she plans for the partnership with LMM to serve as a template for developing closer ties with other clinical partners in the Boston and Cambridge area. To start, she is teaming up LMM members with CRSP scientists on task groups to define new services and products that the joint activity would support.

One challenge in this endeavor is that the Broad offers what is known as a “technical exome” — a data file that contains either the raw sequence data or a list of genetic variants that deviate from the human reference genome. It doesn’t tell the physician what the results mean or what is clinically actionable. The end user of the data may be a geneticist or molecular pathologist who needs some assistance in interpreting the data, perhaps annotation on what is known about individual variants and their association with human disease or biology. Rehm would like to see more flexibility with how groups are able to interact with CRSP, so they can use it with customized levels of support that best fit their needs ranging from raw data files to fully annotated exomes.

In CRSP’s coming years, Rehm hopes to see more overlap in the platform’s clinical and research activities. In her own experience leading the LMM for twelve years, she saw it grow from serving as a purely clinical lab that provided tests for use in the clinic, to one that supported research studies with its clinical services and even made its own discoveries through original research.

“There is an increased blurring of the lines between research and clinical services as medicine recognizes the need to support a continuous learning system,” said Rehm. “Allowing Broad CRSP to play a larger role in diagnostic services by supporting physicians and clinical researchers in a more integrated fashion will advance research and medicine.”

With CRSP’s growing capabilities, new collaborative efforts with clinical researchers, and closer partnerships with diagnostic labs, the platform is positioned to help realize the promise of clinical sequencing, by bringing high-quality, expertly curated sequencing data to the bedside.

SOURCE

http://www.broadinstitute.org/news/6785

Other related article on this topic was published in this Open Access Online Scientific Journal, including the following:

Personalized Cardiovascular Genetic Medicine at Partners HealthCare and Harvard Medical School

Center for Personalized Genetic Medicine, Partners HealthCare and Harvard Medical School

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