Archive for the ‘Biological Engineering’ Category

Mimicking vaginal cells and microbiome interactions on chip microfluidic culture

Posted in Automated Cell Processing, Bio Instrumentation in Experimental Life Sciences Research, Biological Engineering, Biological Networks, Biotechnology, Cell Level, Clinical & Translational, Clinical Diagnostics, Diagnostics and Lab Tests, Medical Device Therapies for Altzheimer’s Disease, Microbiology, MicroEngineering Cell-Tissue & Systems, Microfuidics, Mobile Healthcare, Organ-on-a-Chip, Patient-centered Medicine, Personal Health Applications: Tech Innovations serves HealhCare, Personalized and Precision Medicine & Genomic Research, Population Health Management, Population Health Management, Genetics & Pharmaceutical, Reproductive Andrology, Embryology, Genomic Endocrinology, Preimplantation Genetic Diagnosis and Reproductive Genomics, Reproductive Biology & Bio Instrumentation, Signaling, Tissue Engineering, Women Health, tagged artificial vagina, reproduction, reproductive health, reproductive medicine, reproductive research, reproductive toxicology on February 14, 2023| Leave a Comment »

Mimicking vaginal cells and microbiome interactions on chip microfluidic culture

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

Scientists at Harvard University’s Wyss Institute for Biologically Inspired Engineering have developed the world’s first “vagina-on-a-chip,” which uses living cells and bacteria to mimic the microbial environment of the human vagina. It could help to test drugs against bacterial vaginosis, a common microbial imbalance that makes millions of people more susceptible to sexually transmitted diseases and puts them at risk of preterm delivery when pregnant. Vaginal health is difficult to study in a laboratory setting partly because laboratory animals have “totally different microbiomes” than humans. To address this, scientists have created an unique chip, which is an inch-long, rectangular polymer case containing live human vaginal tissue from a donor and a flow of estrogen-carrying material to simulate vaginal mucus.

The organs-on-a-chip mimic real bodily function, making it easier to study diseases and test drugs. Previous examples include models of the lungs and the intestines. In this case, the tissue acts like that of a real vagina in some important ways. It even responds to changes in estrogen by adjusting the expression of certain genes. And it can grow a humanlike microbiome dominated by “good” or “bad” bacteria. The researchers have demonstrated that Lactobacilli growing on the chip’s tissue help to maintain a low pH by producing lactic acid. Conversely, if the researchers introduce Gardnerella, the chip develops a higher pH, cell damage and increased inflammation: classic bacterial vaginosis signs. So, the chip can demonstrate how a healthy / unhealthy microbiome affects the vagina.

The next step is personalization or subject specific culture from individuals. The chip is a real leap forward, it has the prospect of testing how typical antibiotic treatments against bacterial vaginosis affect the different bacterial strains. Critics of organ-on-a-chip technology often raise the point that it models organs in isolation from the rest of the body. There are limitations such as many researchers are interested in vaginal microbiome changes that occur during pregnancy because of the link between bacterial vaginosis and labor complications. Although the chip’s tissue responds to estrogen, but it does not fully mimic pregnancy without feedback loops from other organs. The researchers are already working on connecting the vagina chip to a cervix chip, which could better represent the larger reproductive system.

All these information indicate that the human vagina chip offers a new model to study host-vaginal microbiome interactions in both optimal and non-optimal states, as well as providing a human relevant preclinical model for development and testing of reproductive therapeutics, including live bio-therapeutics products for bacterial vaginosis. This microfluidic human vagina chip that enables flow through an open epithelial lumen also offers a unique advantage for studies on the effect of cervicovaginal mucus on vaginal health as clinical mucus samples or commercially available mucins can be flowed through this channel. The role of resident and circulating immune cells in host-microbiome interactions also can be explored by incorporating these cells into the vagina chip in the future, as this has been successfully done in various other organ chip models.

References:

https://www.scientificamerican.com/article/first-vagina-on-a-chip-will-help-researchers-test-drugs/

https://www.webmd.com/infertility-and-reproduction/news/20230209/scientists-create-vagina-on-chip-what-to-know

https://www.livescience.com/vagina-on-a-chip

https://link.springer.com/article/10.1186/s40168-022-01400-1

https://www.nature.com/articles/s41585-022-00717-8

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Genomic data can predict miscarriage and IVF failure

Posted in Advanced Computing Platform, Artificial Intelligence - Breakthroughs in Theories and Technologies, Artificial Intelligence - General, Artificial Intelligence Applications in Health Care, Artificial Intelligence in Health Care - Tools & Innovations, Artificial Intelligence in Medicine - Application for Diagnosis, Artificial Intelligence in Medicine - Applications in Therapeutics, BioIT: BioInformatics, BioIT: BioInformatics, NGS, Clinical & Translational, Pharmaceutical R&D Informatics, Clinical Genomics, Cancer Informatics, Biological Engineering, Biological Networks, Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, Cell Level, Computational Biology/Systems and Bioinformatics, Computational Histopathology, Deep Learning in Pathology, Developmental biology, Diagnostics and Lab Tests, Digital HealthCare – biotech & internet joint ventures, Disease Biology, Genomic Testing: Methodology for Diagnosis, Genomics Pharmacy, HealthCare IT, Healthcare Reform, Machine Learning, MicroEngineering Cell-Tissue & Systems, Placenta, Preimplantation Genetic Diagnosis and Reproductive Genomics, Reproductive Andrology, Embryology, Genomic Endocrinology, Preimplantation Genetic Diagnosis and Reproductive Genomics, Reproductive Biology & Bio Instrumentation, therapeutics, Tissue Engineering, Translational Research, Women Health, tagged aneuploidy, Diagnosis, Genomic data, IVF, Miscarriage, treatment on June 15, 2022| 1 Comment »

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

Infertility is a major reproductive health issue that affects about 12% of women of reproductive age in the United States. Aneuploidy in eggs accounts for a significant proportion of early miscarriage and in vitro fertilization failure. Recent studies have shown that genetic variants in several genes affect chromosome segregation fidelity and predispose women to a higher incidence of egg aneuploidy. However, the exact genetic causes of aneuploid egg production remain unclear, making it difficult to diagnose infertility based on individual genetic variants in mother’s genome. Although, age is a predictive factor for aneuploidy, it is not a highly accurate gauge because aneuploidy rates within individuals of the same age can vary dramatically.

Researchers described a technique combining genomic sequencing with machine-learning methods to predict the possibility a woman will undergo a miscarriage because of egg aneuploidy—a term describing a human egg with an abnormal number of chromosomes. The scientists were able to examine genetic samples of patients using a technique called “whole exome sequencing,” which allowed researchers to home in on the protein coding sections of the vast human genome. Then they created software using machine learning, an aspect of artificial intelligence in which programs can learn and make predictions without following specific instructions. To do so, the researchers developed algorithms and statistical models that analyzed and drew inferences from patterns in the genetic data.

As a result, the scientists were able to create a specific risk score based on a woman’s genome. The scientists also identified three genes—MCM5, FGGY and DDX60L—that when mutated and are highly associated with a risk of producing eggs with aneuploidy. So, the report demonstrated that sequencing data can be mined to predict patients’ aneuploidy risk thus improving clinical diagnosis. The candidate genes and pathways that were identified in the present study are promising targets for future aneuploidy studies. Identifying genetic variations with more predictive power will serve women and their treating clinicians with better information.

References:

https://medicalxpress-com.cdn.ampproject.org/c/s/medicalxpress.com/news/2022-06-miscarriage-failure-vitro-fertilization-genomic.amp

https://pubmed.ncbi.nlm.nih.gov/35347416/

https://pubmed.ncbi.nlm.nih.gov/31552087/

https://pubmed.ncbi.nlm.nih.gov/33193747/

https://pubmed.ncbi.nlm.nih.gov/33197264/

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Sperm epigenetic clock and pregnancy outcomes

Posted in Biological Engineering, Biological Networks, Gene Regulation and Evolution, Biomarkers & Medical Diagnostics, Biomedical Measurement Science, Cell Biology, Cell Biology, Signaling & Cell Circuits, Cell Processing System in Cell Therapy Process Development, Epigenetics and Environmental Factors, Genomic Endocrinology, Human aging, Methylation, MicroEngineering Cell-Tissue & Systems, Molecular Genetics & Pharmaceutical, Population Health Management, Genetics & Pharmaceutical, Preimplantation Genetic Diagnosis and Reproductive Genomics, Reproductive Andrology, Embryology, Genomic Endocrinology, Preimplantation Genetic Diagnosis and Reproductive Genomics, Reproductive Biology & Bio Instrumentation, tagged DNA methylation, Epigenetics, infertility, pregnancy, sperm on May 14, 2022| 1 Comment »

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

Infertility has been primarily treated as a female predicament but around one-half of infertility cases can be tracked to male factors. Clinically, male infertility is typically determined using measures of semen quality recommended by World Health Organization (WHO). A major limitation, however, is that standard semen analyses are relatively poor predictors of reproductive capacity and success. Despite major advances in understanding the molecular and cellular functions in sperm over the last several decades, semen analyses remain the primary method to assess male fecundity and fertility.

Chronological age is a significant determinant of human fecundity and fertility. The disease burden of infertility is likely to continue to rise as parental age at the time of conception has been steadily increasing. While the emphasis has been on the effects of advanced maternal age on adverse reproductive and offspring health, new evidence suggests that, irrespective of maternal age, higher male age contributes to longer time-to-conception, poor pregnancy outcomes and adverse health of the offspring in later life. The effect of chronological age on the genomic landscape of DNA methylation is profound and likely occurs through the accumulation of maintenance errors of DNA methylation over the lifespan, which have been originally described as epigenetic drift.

In recent years, the strong relation between age and DNA methylation profiles has enabled the development of statistical models to estimate biological age in most somatic tissue via different epigenetic ‘clock’ metrics, such as DNA methylation age and epigenetic age acceleration, which describe the degree to which predicted biological age deviates from chronological age. In turn, these epigenetic clock metrics have emerged as novel biomarkers of a host of phenotypes such as allergy and asthma in children, early menopause, increased incidence of cancer types and cardiovascular-related diseases, frailty and cognitive decline in adults. They also display good predictive ability for cancer, cardiovascular and all-cause mortality.

Epigenetic clock metrics are powerful tools to better understand the aging process in somatic tissue as well as their associations with adverse disease outcomes and mortality. Only a few studies have constructed epigenetic clocks specific to male germ cells and only one study reported that smokers trended toward an increased epigenetic age compared to non-smokers. These results indicate that sperm epigenetic clocks hold promise as a novel biomarker for reproductive health and/or environmental exposures. However, the relation between sperm epigenetic clocks and reproductive outcomes has not been examined.

There is a critical need for new measures of male fecundity for assessing overall reproductive success among couples in the general population. Data shows that sperm epigenetic clocks may fulfill this need as a novel biomarker that predicts pregnancy success among couples not seeking fertility treatment. Such a summary measure of sperm biological age is of clinical importance as it allows couples in the general population to realize their probability of achieving pregnancy during natural intercourse, thereby informing and expediting potential infertility treatment decisions. With the ability to customize high throughput DNA methylation arrays and capture sequencing approaches, the integration of the epigenetic clocks as part of standard clinical care can enhance our understanding of idiopathic infertility and the paternal contribution to reproductive success and offspring health.

References:

https://academic.oup.com/humrep/advance-article/doi/10.1093/humrep/deac084/6583111?login=false

https://pubmed.ncbi.nlm.nih.gov/33317634/

https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-019-0656-7

https://pubmed.ncbi.nlm.nih.gov/19319879/

https://pubmed.ncbi.nlm.nih.gov/31901222/

https://pubmed.ncbi.nlm.nih.gov/25928123/

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Embryogenesis in Mechanical Womb

Posted in Bio Instrumentation in Experimental Life Sciences Research, Biochemical pathways, Biological Engineering, Biological Networks, Biological Networks, Gene Regulation and Evolution, Cell Biology, Cell Biology, Signaling & Cell Circuits, Developmental biology, Embryology, Fetal Ultrasound, Gene Therapy & Gene Editing Development, Genome Biology, Medical Devices R&D and Inventions, Methods, Placenta, Pre-Clinical Animal Model Development, Preimplantation Genetic Diagnosis and Reproductive Genomics, Reproductive Andrology, Embryology, Genomic Endocrinology, Preimplantation Genetic Diagnosis and Reproductive Genomics, Reproductive Biology & Bio Instrumentation, Signaling & Cell Circuits, tagged development, embryo, gastrulation, mechanical womb, uterus on April 8, 2021| Leave a Comment »

Embryogenesis in Mechanical Womb

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

A highly effective platforms for the ex utero culture of post-implantation mouse embryos have been developed in the present study by scientists of the Weizmann Institute of Science in Israel. The study was published in the journal Nature. They have grown more than 1,000 embryos in this way. This study enables the appropriate development of embryos from before gastrulation (embryonic day (E) 5.5) until the hindlimb formation stage (E11). Late gastrulating embryos (E7.5) are grown in three-dimensional rotating bottles, whereas extended culture from pre-gastrulation stages (E5.5 or E6.5) requires a combination of static and rotating bottle culture platforms.

At Day 11 of development more than halfway through a mouse pregnancy the researchers compared them to those developing in the uteruses of living mice and were found to be identical. Histological, molecular and single-cell RNA sequencing analyses confirm that the ex utero cultured embryos recapitulate in utero development precisely. The mouse embryos looked perfectly normal. All their organs developed as expected, along with their limbs and circulatory and nervous systems. Their tiny hearts were beating at a normal 170 beats per minute. But, the lab-grown embryos becomes too large to survive without a blood supply. They had a placenta and a yolk sack, but the nutrient solution that fed them through diffusion was no longer sufficient. So, a suitable mechanism for blood supply is required to be developed.

Till date the only way to study the development of tissues and organs is to turn to species like worms, frogs and flies that do not need a uterus, or to remove embryos from the uteruses of experimental animals at varying times, providing glimpses of development more like in snapshots than in live videos. This research will help scientists understand how mammals develop and how gene mutations, nutrients and environmental conditions may affect the fetus. This will allow researchers to mechanistically interrogate post-implantation morphogenesis and artificial embryogenesis in mammals. In the future it may be possible to develop a human embryo from fertilization to birth entirely outside the uterus. But the work may one day raise profound questions about whether other animals, even humans, should or could be cultured outside a living womb.

References:

https://www.nature.com/articles/s41586-021-03416-3

https://www.sciencedirect.com/science/article/pii/S0092867414000750?via%3Dihub

https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-185X.1978.tb00993.x

https://www.nature.com/articles/199297a0

https://rep.bioscientifica.com/view/journals/rep/35/1/jrf_35_1_018.xml

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National Resilience, Inc. is a first-of-its-kind manufacturing and technology company dedicated to broadening access to complex medicines and protecting biopharmaceutical supply chains against disruption – the Acquisition of Two Premier Biologics Manufacturing Facilities: Boston and in Ontario, Canada

Posted in Advanced Drug Manufacturing Technology, Automated Cell Processing, Bio Instrumentation in Experimental Life Sciences Research, Biological Engineering, Biological Networks, Biological Networks, Gene Regulation and Evolution, Biomedical Measurement Science, BioTechnology - Venture Creation, Venture Capital, Seeking Talent, Virology on March 4, 2021| Leave a Comment »

National Resilience, Inc. is a first-of-its-kind manufacturing and technology company dedicated to broadening access to complex medicines and protecting biopharmaceutical supply chains against disruption – the Acquisition of Two Premier Biologics Manufacturing Facilities: Boston and in Ontario, Canada

Reporter: Aviva Lev-Ari, PhD, RN

Resilience’s new facility, located at 500 Soldiers Field Rd., Boston, MA. (Photo: Business Wire) – The Genzyme-Sanofi Building

March 02, 2021 08:01 AM Eastern Standard Time

SAN DIEGO & BOSTON–(BUSINESS WIRE)–Resilience (National Resilience, Inc.), a new company building the world’s most advanced biopharmaceutical manufacturing ecosystem, announced it has acquired two premier commercial manufacturing facilities in North America, joining other facilities already in Resilience’s network to boost total capacity under management to more than 750,000 square feet.

“These locations will serve as hubs for the future of biopharma manufacturing, leading the way and shaping the future of Resilience.”

The acquired facilities include a 310,000-square-foot plant in Boston, MA, purchased from Sanofi; and in a separate transaction,
a 136,000-square-foot plant in Mississauga, Ontario, Canada.

Both facilities, which currently produce commercial, marketed products, will see significant investments as Resilience adds capacity and capabilities to produce new therapies at these locations. In addition, the company has offered employment to the existing plant staff and intends to add more jobs at each facility.

“We have big plans for these facilities including investing in new capacity, applying new manufacturing technologies, creating jobs and bringing in new customers,” said Rahul Singhvi, Sc.D, Chief Executive Officer of Resilience. “These locations will serve as hubs for the future of biopharma manufacturing, leading the way and shaping the future of Resilience.”

As part of its agreement with Sanofi, Resilience will continue to manufacture a marketed product at the Boston location. The facility plan includes a build out to facilitate multi-modality manufacturing and state-of-the-art quality laboratories to ensure safe, reliable supply to patients. The facility itself is certified ISO 14001 (Environmental management system), OSHAS 18001 (Health & safety management system) and ISO 50001 (Energy management system).

This is currently the largest of several facilities in Resilience’s growing biologics and advanced therapeutics manufacturing network, with plans to acquire and develop other sites in the U.S. this year. The facility offers 24/7/365 production, multiple 2000L bioreactors capacity and multiple downstream processing trains, with investment in additional capabilities to come.

Our state-of-the-art flexible facility in Mississauga, Ontario, provides upstream, downstream and aseptic fill finish, and is designed to comply with cGMP. The plant has been inspected and approved by multiple regulatory bodies, and handles development and commercialized products.

About Resilience

Resilience (National Resilience, Inc.) is a first-of-its-kind manufacturing and technology company dedicated to broadening access to complex medicines and protecting biopharmaceutical supply chains against disruption. Founded in 2020, the company is building a sustainable network of high-tech, end-to-end manufacturing solutions to ensure the medicines of today and tomorrow can be made quickly, safely, and at scale. Resilience offers the highest quality and regulatory capabilities, and flexible and adaptive facilities to serve partners of all sizes. By continuously advancing the science of biopharmaceutical manufacturing and development, Resilience frees partners to focus on the discoveries that improve patients’ lives.

For more information, visit www.Resilience.com.

Contacts

Ryan Flinn
Head of Communications
Ryan.flinn@Resilience.com
510-207-7616

SOURCE

https://www.businesswire.com/news/home/20210302005391/en/Resilience-Expands-North-American-Capacity-with-the-Acquisition-of-Two-Premier-Biologics-Manufacturing-Facilities

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Joe Biden Announced Science Team Nominations for the New Administration

Posted in and Bioethics, Biological Engineering, Evidence-based decision-making, Foundations for supporting Science and Education, Funding Opportunities for Cancer Research, Health Law & Patient Safety, Health Law Policy, HealthCare IT, Interviews with Key Opinion Leaders (KOLs), Leadership, Power, Social Interlocking Connections, National Academy of Sciences AWARDS, Nobel Prize WInners, Personalized and Precision Medicine & Genomic Research, Precision Cancer Medicine, Women in Life Sciences, women in science, tagged aerospace, bioengineering, Broad Institute, Eric Lander, genomics, global warming, Human Genome Project, Joe Biden, MIT, nobel leureates, precision medicine, Princeton University, Science Advisory Panel, science policy, US science on January 17, 2021| Leave a Comment »

Reporter: Stephen J. Williams, PhD

In an announcement televised on C-Span, President Elect Joseph Biden announced his new Science Team to advise on science policy matters, as part of the White House Advisory Committee on Science and Technology. Below is a video clip and the transcript, also available at

https://www.c-span.org/video/?508044-1/president-elect-biden-introduces-white-house-science-team

COMING UP TONIGHT ON C-SPAN, NEXT, PRESIDENT-ELECT JOE BIDEN AND VICE PRESIDENT-ELECT KAMALA HARRIS ANNOUNCE SEVERAL MEMBERS OF THEIR WHITE HOUSE SCIENCE TEAM. AND THEN SENATE MINORITY LEADER CHUCK SCHUMER TALKS ABOUT THE IMPEACHMENT OF PRESIDENT TRUMP IN THE WEEKLY DEMOCRATIC ADDRESS. AND AFTER THAT, TODAY’S SPEECH BY VICE PRESIDENT MIKE PENCE TO SAILORS AT NAVAL AIR STATION LAMORE IN CALIFORNIA. NEXT, PRESIDENT-ELECT JOE BIDEN AND VICE PRESIDENT-ELECT KAMALA HARRIS ANNOUNCE SEVERAL MEMBERS OF THEIR WHITE HOUSE SCIENCE TEAM. FROM WILMINGTON, DELAWARE, THIS IS ABOUT 40 MINUTES. PRESIDENT-ELECT BIDEN: GOOD AFTERNOON, FOLKS. I WAS TELLING THESE FOUR BRILLIANT SCIENTISTS AS I STOOD IN THE BACK, IN A WAY, THEY — THIS IS THE MOST EXCITING ANNOUNCEMENT THAT I’VE GOTTEN TO MAKE IN THE ENTIRE CABINET RAISED TO A CABINET LEVEL POSITION IN ONE CASE. THESE ARE AMONG THE BRIGHTEST MOST DEDICATED PEOPLE NOT ONLY IN THE COUNTRY BUT THE WORLD. THEY’RE COMPOSED OF SOME OF THE MOST SCIENTIFIC BRILLIANT MINDS IN THE WORLD. WHEN I WAS VICE PRESIDENT AS — I I HAD INTENSE INTEREST IN EVERYTHING THEY WERE DOING AND I PAID ENORMOUS ATTENTION. AND I WOULD — LIKE A KID GOING BACK TO SCHOOL. SIT DOWN AND CAN YOU EXPLAIN TO ME AND THEY WERE — VERY PATIENT WITH ME. AND — BUT AS PRESIDENT, I WANTED YOU TO KNOW I’M GOING TO PAY A GREAT DEAL OF ATTENTION. WHEN I TRAVEL THE WORLD AS VICE PRESIDENT, I WAS OFTEN ASKED TO EXPLAIN TO WORLD LEADERS, THEY ASKED ME THINGS LIKE DEFINE AMERICA. TELL ME HOW CAN YOU DEFINE AMERICA? WHAT’S AMERICA? AND I WAS ON A TIBETAN PLATEAU WITH AT THE TIME WITH XI ZIN PING AND WE HAD AN INTERPRETER CAN I DEFINE AMERICA FOR HIM? I SAID YES, I CAN. IN ONE WORD. POSSIBILITIES. POSSIBILITIES. I THINK IT’S ONE OF THE REASONS WHY WE’VE OCCASIONALLY BEEN REFERRED TO AS UGLY AMERICANS. WE THINK ANYTHING’S POSSIBLE GIVEN THE CHANCE, WE CAN DO ANYTHING. AND THAT’S PART OF I THINK THE AMERICAN SPIRIT. AND WHAT THE PEOPLE ON THIS STAGE AND THE DEPARTMENTS THEY WILL LEAD REPRESENT ENORMOUS POSSIBILITIES. THEY’RE THE ONES ASKING THE MOST AMERICAN OF QUESTIONS, WHAT NEXT? WHAT NEXT? NEVER SATISFIED, WHAT’S NEXT? AND WHAT’S NEXT IS BIG AND BREATHTAKING. HOW CAN — HOW CAN WE MAKE THE IMPOSSIBLE POSSIBLE? AND THEY WERE JUST ASKING QUESTIONS FOR THE SAKE OF QUESTIONS, THEY’RE ASKING THESE QUESTIONS AS CALL TO ACTION. , TO INSPIRE, TO HELP US IMAGINE THE FUTURE AND FIGURE OUT HOW TO MAKE IT REAL AND IMPROVE THE LIVES OF THE AMERICAN PEOPLE AND PEOPLE AROUND THE WORLD. THIS IS A TEAM THAT ASKED US TO IMAGINE EVERY HOME IN AMERICA BEING POWERED BY RENEWABLE ENERGY WITHIN THE NEXT 10 YEARS. OR 3-D IMAGE PRINTERS RESTORING TISSUE AFTER TRAUMATIC INJURIES AND HOSPITALS PRINTING ORGANS FOR ORGAN TRANSPLANTS. IMAGINE, IMAGINE. AND THEY REALLY — AND, YOU KNOW, THEN RALLY, THE SCIENTIFIC COMMUNITY TO GO ABOUT DOING WHAT WE’RE IMAGINING. YOU NEED SCIENCE, DATA AND DISCOVERY WAS A GOVERNING PHILOSOPHY IN THE OBAMA-BIDEN ADMINISTRATION. AND EVERYTHING FROM THE ECONOMY TO THE ENVIRONMENT TO CRIMINAL JUSTICE REFORM AND TO NATIONAL SECURITY. AND ON HEALTH CARE. FOR EXAMPLE, A BELIEF IN SCIENCE LED OUR EFFORTS TO MAP THE HUMAN BRAIN AND TO DEVELOP MORE PRECISE INDIVIDUALIZED MEDICINES. IT LED TO OUR ONGOING MISSION TO END CANCER AS WE KNOW IT, SOMETHING THAT IS DEEPLY PERSONAL TO BOTH MY FAMILY AND KAMALA’S FAMILY AND COUNTLESS FAMILIES IN AMERICA. WHEN PRESIDENT OBAMA ASKED ME TO LEAD THE CANCER MOON SHOT, I KNEW WE HAD TO INJECT A SENSE OF URGENCY INTO THE FIGHT. WE BELIEVED WE COULD DOUBLE THE RATE OF PROGRESS AND DO IN FIVE YEARS WHAT OTHERWISE WOULD TAKE 10. MY WIFE, JILL, AND I TRAVELED AROUND THE COUNTRY AND THE WORLD MEETING WITH THOUSANDS OF CANCER PATIENTS AND THEIR FAMILIES, PHYSICIANS, RESEARCHERS, PHILANTHROPISTS, TECHNOLOGY LEADERS AND HEADS OF STATE. WE SOUGHT TO BETTER UNDERSTAND AND BREAK DOWN THE SILOS AND STOVE PIPES THAT PREVENT THE SHARING OF INFORMATION AND IMPEDE ADVANCES IN CANCER RESEARCH AND TREATMENT WHILE BUILDING A FOCUSED AND COORDINATED EFFORT HERE AT HOME AND ABROAD. WE MADE PROGRESS. BUT THERE’S SO MUCH MORE THAT WE CAN DO. WHEN I ANNOUNCED THAT I WOULD NOT RUN IN 2015 AT THE TIME, I SAID I ONLY HAD ONE REGRET IN THE ROSE GARDEN AND IF I HAD ANY REGRETS THAT I HAD WON, THAT I WOULDN’T GET TO BE THE PRESIDENT TO PRESIDE OVER CANCER AS WE KNOW IT. WELL, AS GOD WILLING, AND ON THE 20TH OF THIS MONTH IN A COUPLE OF DAYS AS PRESIDENT I’M GOING TO DO EVERYTHING I CAN TO GET THAT DONE. I’M GOING TO — GOING TO BE A PRIORITY FOR ME AND FOR KAMALA AND IT’S A SIGNATURE ISSUE FOR JILL AS FIRST LADY. WE KNOW THE SCIENCE IS DISCOVERY AND NOT FICTION. AND IT’S ALSO ABOUT HOPE. AND THAT’S AMERICA. IT’S IN THE D.N.A. OF THIS COUNTRY, HOPE. WE’RE ON THE CUSP OF SOME OF THE MOST REMARKABLE BREAKTHROUGHS THAT WILL FUNDAMENTALLY CHANGE THE WAY OF LIFE FOR ALL LIFE ON THIS PLANET. WE CAN MAKE MORE PROGRESS IN THE NEXT 10 YEARS, I PREDICT, THAN WE’VE MADE IN THE LAST 50 YEARS. AND EXPONENTIAL MOVEMENT. WE CAN ALSO FACE SOME OF THE MOST DIRE CRISES IN A GENERATION WHERE SCIENCE IS CRITICAL TO WHETHER OR NOT WE MEET THE MOMENT OF PERIL AND PROMISE THAT WE KNOW IS WITHIN OUR REACH. IN 1944, FRANKLIN ROOSEVELT ASKED HIS SCIENCE ADVISOR HOW COULD THE UNITED STATES FURTHER ADVANCE SCIENTIFIC RESEARCH IN THE CRITICAL YEARS FOLLOWING THE SECOND WORLD WAR? THE RESPONSE LED TO SOME OF THE MOST GROUND BREAKING DISCOVERIES IN THE LAST 75 YEARS. AND WE CAN DO THAT AGAIN. AND WE CAN DO MORE. SO TODAY, I’M PROUD TO ANNOUNCE A TEAM OF SOME OF THE COUNTRY’S MOST BRILLIANT AND ACCOMPLISHED SCIENTISTS TO LEAD THE WAY. AND I’M ASKING THEM TO FOCUS ON FIVE KEY AREAS. FIRST THE PANDEMIC AND WHAT WE CAN LEARN ABOUT WHAT IS POSSIBLE OR WHAT SHOULD BE POSSIBLE TO ADDRESS THE WIDEST RANGE OF PUBLIC HEALTH NEEDS. SECONDLY, THE ECONOMY, HOW CAN WE BUILD BACK BETTER TO ENSURE PROSPERITY IS FULLY SHARED ALL ACROSS AMERICA? AMONG ALL AMERICANS? AND THIRDLY, HOW SCIENCE HELPS US CONFRONT THIS CLIMATE CRISIS WE FACE IN AMERICA AND THE WORLD BUT IN AMERICA HOW IT HELPS US CONFRONT THE CLIMATE CRISIS WITH AMERICAN JOBS AND INGENUITY. AND FOURTH, HOW CAN WE ENSURE THE UNITED STATES LEADS THE WORLD IN TECHNOLOGIES AND THE INDUSTRIES THAT THE FUTURE THAT WILL BE CRITICAL FOR OUR ECONOMIC PROSPERITY AND NATIONAL SECURITY? ESPECIALLY WITH THE INTENSE INCREASED COMPETITION AROUND THE WORLD FROM CHINA ON? AND FIFTH, HOW CAN WE ASSURE THE LONG-TERM HEALTH AND TRUST IN SCIENCE AND TECHNOLOGY IN OUR NATION? YOU KNOW, THESE ARE EACH QUESTIONS THAT CALL FOR ACTION. AND I’M HONORED TO ANNOUNCE A TEAM THAT IS ANSWERING THE CALL TO SERVE. AS THE PRESIDENTIAL SCIENCE ADVISOR AND DIRECTOR OF THE OFFICE OF SCIENCE AND TECHNOLOGY POLICY, I NOMINATE ONE OF THE MOST BRILLIANT GUYS I KNOW, PERSONS I KNOW, DR. ERIC LANDER. AND THANK YOU, DOC, FOR COMING BACK. THE PIONEER — HE’S A PIONEER IN THE STIFFING COMMUNITY. PRINCIPAL LEADER IN THE HUMAN GENOME PROJECT. AND NOT HYPERBOLE TO SUGGEST THAT DR. LANDER’S WORK HAS CHANGED THE COURSE OF HUMAN HISTORY. HIS ROLE IN HELPING US MAP THE GENOME PULLED BACK THE CURTAIN ON HUMAN DISEASE, ALLOWING SCIENTISTS, EVER SINCE, AND FOR GENERATIONS TO COME TO EXPLORE THE MOLECULAR BASIS FOR SOME OF THE MOST DEVASTATING ILLNESSES AFFECTING OUR WORLD. AND THE APPLICATION OF HIS PIONEERING WORK AS — ARE POISED TO LEAD TO INCREDIBLE CURES AND BREAKTHROUGHS IN THE YEARS TO COME. DR. LANDER NOW SERVES AS THE PRESIDENT AND FOUNDING DIRECTOR OF THE BRODE INSTITUTE AT M.I.T. AND HARVARD, THE WORLD’S FOREMOST NONPROFIT GENETIC RESEARCH ORGANIZATION. AND I CAME TO APPRECIATE DR. LANDER’S EXTRAORDINARY MIND WHEN HE SERVED AS THE CO-CHAIR OF THE PRESIDENT’S COUNCIL ON ADVISORS AND SCIENCE AND TECHNOLOGY DURING THE OBAMA-BIDEN ADMINISTRATION. AND I’M GRATEFUL, I’M GRATEFUL THAT WE CAN WORK TOGETHER AGAIN. I’VE ALWAYS SAID THAT BIDEN-HARRIS ADMINISTRATION WILL ALSO LEAD AND WE’RE GOING TO LEAD WITH SCIENCE AND TRUTH. WE BELIEVE IN BOTH. [LAUGHTER] GOD WILLING OVERCOME THE PANDEMIC AND BUILD OUR COUNTRY BETTER THAN IT WAS BEFORE. AND THAT’S WHY FOR THE FIRST TIME IN HISTORY, I’M GOING TO BE ELEVATING THE PRESIDENTIAL SCIENCE ADVISOR TO A CABINET RANK BECAUSE WE THINK IT’S THAT IMPORTANT. AS DEPUTY DIRECTOR OF THE OFFICE OF SCIENCE AND TECHNOLOGY POLICY AND SCIENCE AND — SCIENCE AND SOCIETY, I APPOINT DR. NELSON. SHE’S A PROFESSOR AT THE INSTITUTE OF ADVANCED STUDIES AT PRINCETON UNIVERSITY. THE PRESIDENT OF THE SOCIAL SCIENCE RESEARCH COUNCIL. AND ONE OF AMERICA’S LEADING SCHOLARS IN THE — AN AWARD-WINNING AUTHOR AND RESEARCHER AND EXPLORING THE CONNECTIONS BETWEEN SCIENCE AND OUR SOCIETY. THE DAUGHTER OF A MILITARY FAMILY, HER DAD SERVED IN THE UNITED STATES NAVY AND HER MOM WAS AN ARMY CRIPPING TO RAFFER. DR. NELSON DEVELOPED A LOVE OF TECHNOLOGY AT A VERY YOUNG AGE PARTICULARLY WITH THE EARLY COMPUTER PRODUCTS. COMPUTING PRODUCTS AND CODE-BREAKING EQUIPMENT THAT EVERY KID HAS AROUND THEIR HOUSE. AND SHE GREW UP WITHIN HER HOME. WHEN I WROTE THAT DOWN, I THOUGHT TO MYSELF, I MEAN, HOW MANY KIDS — ANY WAY, THAT PASSION WAS A PASSION FORGED A LIFELONG CURIOSITY ABOUT THE INEQUITIES AND THE POWER DIAMONDICS THAT SIT BENEATH THE SURFACE OF SCIENTIFIC RESEARCH AND THE TECHNOLOGY WE BUILD. DR. NELSON IS FOCUSED ON THOSE INSIGHTS. AND THE SCIENCE, TECHNOLOGY AND SOCIETY, LIKE FEW BEFORE HER EVER HAVE IN AMERICAN HISTORY. BREAKING NEW GROUND ON OUR UNDERSTANDING OF THE ROLE SCIENCE PLAYS IN AMERICAN LIFE AND OPENING THE DOOR TO — TO A FUTURE WHICH SCIENCE BETTER SERVES ALL PEOPLE. AS CO-CHAIR OF THE PRESIDENT’S COUNCIL ON ADVISORS OF SCIENCE AND TECHNOLOGY, I APPOINT DR. FRANCIS ARNOLD, DIRECTOR OF THE ROSE BIOENGINEERING CENTER AT CALTECH AND ONE OF THE WORLD’S LEADING EXPERTS IN PROTEIN ENGINEERING, A LIFE-LONG CHAMPION OF RENEWABLE ENERGY SOLUTIONS WHO HAS BEEN INDUCTED INTO THE NATIONAL INVENTORS’ HALL OF FAME. THAT AIN’T A BAD PLACE TO BE. NOT ONLY IS SHE THE FIRST WOMAN TO BE ELECTED TO ALL THREE NATIONAL ACADEMIES OF SCIENCE, MEDICINE AND ENGINEERING AND ALSO THE FIRST WOMAN, AMERICAN WOMAN, TO WIN A NOBEL PRIZE IN CHEMISTRY. A VERY SLOW LEARNER, SLOW STARTER, THE DAUGHTER OF PITTSBURGH, SHE WORKED AS A CAB DRIVER, A JAZZ CLUB SERVER, BEFORE MAKING HER WAY TO BERKELEY AND A CAREER ON THE LEADING EDGE OF HUMAN DISCOVERY. AND I WANT TO MAKE THAT POINT AGAIN. I WANT — IF ANY OF YOUR CHILDREN ARE WATCHING, LET THEM KNOW YOU CAN DO ANYTHING. THIS COUNTRY CAN DO ANYTHING. ANYTHING AT ALL. AND SO SHE SURVIVED BREAST CANCER, OVERCAME A TRAGIC LOSS IN HER FAMILY WHILE RISING TO THE TOP OF HER FIELD, STILL OVERWHELMINGLY DOMINATED BY MEN. HER PASSION HAS BEEN A STEADFAST COMMITMENT TO RENEWABLE ENERGY FOR THE BETTERMENT OF OUR PLANET AND HUMANKIND. SHE IS AN INSPIRING FIGURE TO SCIENTISTS ACROSS THE FIELD AND ACROSS NATIONS. AND I WANT TO THANK DR. ARNOLD FOR AGREEING TO CO-CHAIR A FIRST ALL WOMAN TEAM TO LEAD THE PRESIDENT’S COUNCIL OF ADVISORS ON SCIENCE AND TECHNOLOGY WHICH LEADS ME TO THE NEXT MEMBER OF THE TEAM. AS CO-CHAIR, THE PRESIDENT’S COUNCIL OF ADVISORS ON SCIENCE AND TECHNOLOGY, I APPOINT DR. MARIE ZUBER. A TRAIL BLAZER BRAISING GEO PHYSICIST AND PLANETARY SCIENTIST A. FORMER CHAIR OF THE NATIONAL SCIENCE BOARD. FIRST WOMAN TO LEAD THE SCIENCE DEPARTMENT AT M.I.T. AND THE FIRST WOMAN TO LEAD NASA’S ROBOTIC PLANETARY MISSION. GROWING UP IN COLE COUNTRY NOT FAR FROM HEAVEN, SCRANTON, PENNSYLVANIA, IN CARBON COUNTY, PENNSYLVANIA, ABOUT 50 MILES SOUTH OF WHERE I WAS A KID, SHE DREAMED OF EXPLORING OUTER SPACE. COULD HAVE TOLD HER SHE WOULD JUST GO TO GREEN REACH IN SCRANTON AND FIND WHERE IT WAS. AND I SHOULDN’T BE SO FLIPPANT. BUT I’M SO EXCITED ABOUT THESE FOLKS. YOU KNOW, READING EVERY BOOK SHE COULD FIND AND LISTENING TO HER MOM’S STORIES ABOUT WATCHING THE EARLIEST ROCKET LAUNCH ON TELEVISION, MARIE BECAME THE FIRST PERSON IN HER FAMILY TO GO TO COLLEGE AND NEVER LET GO OF HER DREAM. TODAY SHE OVERSEES THE LINCOLN LABORATORY AT M.I.T. AND LEADS THE INSTITUTION’S CLIMATE ACTION PLAN. GROWING UP IN COLD COUNTRY, NOT AND FINALLY, COULD NOT BE HERE TODAY, BUT I’M PLEASED TO ANNOUNCE THAT I’VE HAD A LONG CONVERSATION WITH DR. FRANCIS COLLINS AND COULD NOT BE HERE TODAY. AND I’VE ASKED THEM TO STAY ON AS DIRECTOR OF THE INSTITUTE OF HEALTH AND — AT THIS CRITICAL MOMENT. I’VE KNOWN DR. COLLINS FOR MANY YEARS. I WORKED WITH HIM CLOSELY. HE’S BRILLIANT. A PIONEER. A TRUE LEADER. AND ABOVE ALL, HE’S A MODEL OF PUBLIC SERVICE AND I’M HONORED TO BE WORKING WITH HIM AGAIN. AND IT IS — IN HIS ABSENCE I WANT TO THANK HIM AGAIN FOR BEING WILLING TO STAY ON. I KNOW THAT WASN’T HIS ORIGINAL PLAN. BUT WE WORKED AN AWFUL LOT ON THE MOON SHOT AND DEALING WITH CANCER AND I JUST WANT TO THANK HIM AGAIN. AND TO EACH OF YOU AND YOUR FAMILIES, AND I SAY YOUR FAMILIES, THANK YOU FOR THE WILLINGNESS TO SERVE. AND NOT THAT YOU HAVEN’T BEEN SERVING ALREADY BUT TO SERVE IN THE ADMINISTRATION. AND THE AMERICAN PEOPLE, TO ALL THE AMERICAN PEOPLE, THIS IS A TEAM THAT’S GOING TO HELP RESTORE YOUR FAITH IN AMERICA’S PLACE IN THE FRONTIER OF SCIENCE AND DISCOVER AND HOPE. I’M NOW GOING TO TURN THIS OVER STARTING WITH DR. LANDER, TO EACH OF OUR NOMINEES AND THEN WITH — HEAR FROM THE VICE PRESIDENT. BUT AGAIN, JUST CAN’T THANK YOU ENOUGH AND I REALLY MEAN IT. THANK YOU, THANK YOU, THANK YOU FOR WILLING TO DO THIS. DOCTOR, IT’S ALL YOURS. I BETTER PUT MY MASK ON OR I’M GOING TO GET IN TROUBLE.

Director’s Page

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Biomolecular Condensates: A new approach to biology originated @MIT – Drug Discovery at DewPoint Therapeutics, Cambridge, MA gets new leaders, Ameet Nathwani, MD (ex-Sanofi, ex-Novartis) as CEO and Arie Belldegrun, PhD on R&D

Posted in Bio Instrumentation in Experimental Life Sciences Research, Biological Engineering, Biological Networks, Gene Regulation and Evolution, Biomedical Measurement Science, BioTechnology - Venture Creation, BioTechnology - Venture Creation, Venture Capital, Gene Regulation, Genetics & Innovations in Treatment, Genetics & Pharmaceutical, Genome Biology, Genomics Pharmacy on October 15, 2020| Leave a Comment »

Biomolecular Condensates: A new approach to biology originated @MIT – Drug Discovery at DewPoint Therapeutics, Cambridge, MA gets new leaders, Ameet Nathwani, MD (ex-Sanofi, ex-Novartis) as Chief Executive Officer and Arie Belldegrun, PhD (ex-Kite Therapeutics) on R&D

Curator & Reporter: Aviva Lev-Ari, PhD, RN

Hooked by the science, Arie Belldegrun joins a group of influentials who believe Dewpoint may have the key to the next big thing in biotech

A new approach to biology

“The real voyage of discovery consists, not in seeking new landscapes, but in having new eyes.” Marcel Proust

Starting with the study of P granules in C.elegans embryos in 2009, Tony Hyman, working with his collaborators like Frank Julicher, Cliff Brangwynne, Simon Alberti, Mike Rosen, and Rohit Pappu, began to unravel the mysteries of biomolecular condensates. These scientists realized that P granules behave like liquid droplets that form by phase separation (think of oil droplets in salad dressing) and called them condensates.

In subsequent studies, they found to their surprise that many compartments inside cells had the behavior of condensates: they are liquid-like and form by phase separation.

Inspired by the work of Tony and his colleagues, Richard Young, Phillip Sharp, and Arup Chakraborty at MIT applied these approaches to the study of gene expression, similarly shedding light on many important questions in gene control.

Rick Young on condensates and gene control.

Tony Hyman on how cells form compartments. (From LatestThinking.org via CC BY 4.0; trimmed for length.)

Foundational Papers in Biomolecular Condensates

Germline P granules are liquid droplets that localize by controlled dissolution/condensation (Science, June 2009)

Liquid-Liquid Phase Separation in Biology (Annual Review of Cell & Developmental Biology, Oct 2014)

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation (Cell, Aug 2015)

Biomolecular condensates: organizers of cellular biochemistry (Nature Review Cell Biology, Feb 2017)

A Phase Separation Model for Transcriptional Control. (Cell, March 2017)

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains (Cell, Nov 2018)

SOURCE

https://dewpointx.com/

Press releases and Dewpoint in the news

Dewpoint Therapeutics Appoints Ameet Nathwani as Chief Executive Officer

October 13, 2020

Dewpoint

New York Times interviews Rick Young and Amy Gladfelter on the role of condensate “droplets” in COVID-19

October 9, 2020

New York Times

Dewpoint Therapeutics raises $77 million to go after ‘undruggable’ diseases

September 29, 2020

Boston Globe

Hooked by the science, Arie Belldegrun joins a group of influentials who believe Dewpoint may have the key to the next big thing in biotech

September 29, 2020

Endpoint News

Dewpoint Therapeutics to put ‘pedal to the metal’ with $77M round

September 29, 2020

FierceBiotech

Dewpoint Therapeutics Raises $77M Series B Financing to Advance the Development of Drugs That Target Biomolecular Condensates

September 29, 2020

Dewpoint

21 biotech startups that are set to take off, according to top VCs

August 13, 2020

Business Insider

Proteins — and labs — coming together to prevent Rett Syndrome

July 22, 2020

Whitehead Institute

Dewpoint Therapeutics Collaborates with Merck to Evaluate Novel Approach for the Treatment of HIV

July 13, 2020

Dewpoint

Discovery of how cancer drugs find their targets could lead to a new toolset for drug development

June 18, 2020

Whitehead Institute

SOURCE

https://dewpointx.com/news/

UC Berkeley accelerates bio-preservation research as part NSF center

Posted in Biological Engineering, tagged biological cells, biological tissues, Organ transplantation, preservation, viabilitiy on August 25, 2020| Leave a Comment »

UC Berkeley accelerates bio-preservation research as part NSF center

Reporter: Irina Robu, PhD

National Science Foundation funded a new research center which focuses on advancing methods for storing and preserving biological cells and tissues. The new center will be directed by John Bischof at the University of Minnesota and co-directed by Mehmet Toner at Massachusetts General Hospital in collaboration with researchers from UC Berkeley and UC Riverside. It is known that the inability to extend shelf life of biological tissues means that patients in Florida can’t receive a heart or lung from California. And when thawing any cell culture, the survival rate of the cells are about 60 percent, which is considered normal .

NSF Engineering Research Centers were founded to bring together academic and industry partners in interdisciplinary collaborations to tackle complex, long-range engineering challenges. The anticipation is that the centers will brood whole new industries with new systems-level technologies. In 2025, the award for ATP-Bio may be renewed for an additional five years.

SOURCE

https://engineering.berkeley.edu/news/2020/08/uc-berkeley-part-of-26m-nsf-center-to-accelerate-research-in-bio-preservation/

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Live Notes, Real Time Conference Coverage @AACR #AACR20: Tuesday June 23, 2020 3:00 PM-5:30 PM Educational Sessions

Posted in Artificial Intelligence - Breakthroughs in Theories and Technologies, Artificial Intelligence - General, Artificial Intelligence Applications in Health Care, Artificial Intelligence in CANCER, Artificial Intelligence in Health Care - Tools & Innovations, Artificial Intelligence in Medicine - Application for Diagnosis, Artificial Intelligence in Medicine - Applications in Therapeutics, Big Data, BioIT: BioInformatics, Biological Engineering, Biological Networks, Biological Networks, Gene Regulation and Evolution, Breast Cancer - impalpable breast lesions, CANCER BIOLOGY & Innovations in Cancer Therapy, Cancer Genomics, cancer metabolism, Deep Learning in Pathology, Genomic Expression, Glioblastoma, Inflammasome, Intelligent Information Systems, Personalized and Precision Medicine & Genomic Research, Prostate Cancer: Monitoring vs Treatment, REAL TIME Conference Coverage Twitter's Hashtags and Handles per Presentation/session, Single Cell Genomics, Single-cell sequencing, tumor microenvironment, tagged #AACR20, AACR, Artificial intelligence, Cancer Genomics, functional proteomics, Machine Learning, mass spectrometry, natural language processing, Proteomics, tumor microenvironment on June 24, 2020| Leave a Comment »

Live Notes, Real Time Conference Coverage AACR 2020: Tuesday June 23, 2020 3:00 PM-5:30 PM Educational Sessions

Reporter: Stephen J. Williams, PhD

Follow Live in Real Time using

#AACR20

@pharma_BI

@AACR

Register for FREE at https://www.aacr.org/

uesday, June 23

3:00 PM – 5:00 PM EDT

Virtual Educational Session

Tumor Biology, Bioinformatics and Systems Biology

The Clinical Proteomic Tumor Analysis Consortium: Resources and Data Dissemination

This session will provide information regarding methodologic and computational aspects of proteogenomic analysis of tumor samples, particularly in the context of clinical trials. Availability of comprehensive proteomic and matching genomic data for tumor samples characterized by the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) and The Cancer Genome Atlas (TCGA) program will be described, including data access procedures and informatic tools under development. Recent advances on mass spectrometry-based targeted assays for inclusion in clinical trials will also be discussed.

Amanda G Paulovich, Shankha Satpathy, Meenakshi Anurag, Bing Zhang, Steven A Carr

Methods and tools for comprehensive proteogenomic characterization of bulk tumor to needle core biopsies

Shankha Satpathy

TCGA has 11,000 cancers with >20,000 somatic alterations but only 128 proteins as proteomics was still young field
CPTAC is NCI proteomic effort
Chemical labeling approach now method of choice for quantitative proteomics
Looked at ovarian and breast cancers: to measure PTM like phosphorylated the sample preparation is critical

Data access and informatics tools for proteogenomics analysis

Bing Zhang

Raw and processed data (raw MS data) with linked clinical data can be extracted in CPTAC
Python scripts are available for bioinformatic programming

Pathways to clinical translation of mass spectrometry-based assays

Meenakshi Anurag

· Using kinase inhibitor pulldown (KIP) assay to identify unique kinome profiles

· Found single strand break repair defects in endometrial luminal cases, especially with immune checkpoint prognostic tumors

· Paper: JNCI 2019 analyzed 20,000 genes correlated with ET resistant in luminal B cases (selected for a list of 30 genes)

· Validated in METABRIC dataset

· KIP assay uses magnetic beads to pull out kinases to determine druggable kinases

· Looked in xenografts and was able to pull out differential kinomes

· Matched with PDX data so good clinical correlation

· Were able to detect ESR1 fusion correlated with ER+ tumors

Tuesday, June 23

3:00 PM – 5:00 PM EDT

Virtual Educational Session

Survivorship

Artificial Intelligence and Machine Learning from Research to the Cancer Clinic

The adoption of omic technologies in the cancer clinic is giving rise to an increasing number of large-scale high-dimensional datasets recording multiple aspects of the disease. This creates the need for frameworks for translatable discovery and learning from such data. Like artificial intelligence (AI) and machine learning (ML) for the cancer lab, methods for the clinic need to (i) compare and integrate different data types; (ii) scale with data sizes; (iii) prove interpretable in terms of the known biology and batch effects underlying the data; and (iv) predict previously unknown experimentally verifiable mechanisms. Methods for the clinic, beyond the lab, also need to (v) produce accurate actionable recommendations; (vi) prove relevant to patient populations based upon small cohorts; and (vii) be validated in clinical trials. In this educational session we will present recent studies that demonstrate AI and ML translated to the cancer clinic, from prognosis and diagnosis to therapy.
NOTE: Dr. Fish’s talk is not eligible for CME credit to permit the free flow of information of the commercial interest employee participating.

Ron C. Anafi, Rick L. Stevens, Orly Alter, Guy Fish

Overview of AI approaches in cancer research and patient care

Rick L. Stevens

Deep learning is less likely to saturate as data increases
Deep learning attempts to learn multiple layers of information
The ultimate goal is prediction but this will be the greatest challenge for ML
ML models can integrate data validation and cross database validation
What limits the performance of cross validation is the internal noise of data (reproducibility)
Learning curves: not the more data but more reproducible data is important
Neural networks can outperform classical methods
Important to measure validation accuracy in training set. Class weighting can assist in development of data set for training set especially for unbalanced data sets

Discovering genome-scale predictors of survival and response to treatment with multi-tensor decompositions

Orly Alter

Finding patterns using SVD component analysis. Gene and SVD patterns match 1:1
Comparative spectral decompositions can be used for global datasets
Validation of CNV data using this strategy
Found Ras, Shh and Notch pathways with altered CNV in glioblastoma which correlated with prognosis
These predictors was significantly better than independent prognostic indicator like age of diagnosis

Identifying targets for cancer chronotherapy with unsupervised machine learning

Ron C. Anafi

Many clinicians have noticed that some patients do better when chemo is given at certain times of the day and felt there may be a circadian rhythm or chronotherapeutic effect with respect to side effects or with outcomes
ML used to determine if there is indeed this chronotherapy effect or can we use unstructured data to determine molecular rhythms?
Found a circadian transcription in human lung
Most dataset in cancer from one clinical trial so there might need to be more trials conducted to take into consideration circadian rhythms

Stratifying patients by live-cell biomarkers with random-forest decision trees

Guy Fish CEO Cellanyx Diagnostics

Some clinicians feel we may be overdiagnosing and overtreating certain cancers, especially the indolent disease
Platform published in 2018 paper (Clinical Proof-of-concept of a Novel Platform Utilizing Biopsy-derived Live Single Cells, Phenotypic Biomarkers, and Machine Learning Toward a Precision Risk Stratification Test for Prostate Cancer Grade Groups 1 and 2 (Gleason 3 + 3 and 3 + 4)
Problem: their information knowledgebase based on cultured cells
Their platform first used to stratify prostate cancer

Tuesday, June 23

3:00 PM – 5:00 PM EDT

Virtual Educational Session

Tumor Biology, Molecular and Cellular Biology/Genetics, Bioinformatics and Systems Biology, Prevention Research

The Wound Healing that Never Heals: The Tumor Microenvironment (TME) in Cancer Progression

This educational session focuses on the chronic wound healing, fibrosis, and cancer “triad.” It emphasizes the similarities and differences seen in these conditions and attempts to clarify why sustained fibrosis commonly supports tumorigenesis. Importance will be placed on cancer-associated fibroblasts (CAFs), vascularity, extracellular matrix (ECM), and chronic conditions like aging. Dr. Dvorak will provide an historical insight into the triad field focusing on the importance of vascular permeability. Dr. Stewart will explain how chronic inflammatory conditions, such as the aging tumor microenvironment (TME), drive cancer progression. The session will close with a review by Dr. Cukierman of the roles that CAFs and self-produced ECMs play in enabling the signaling reciprocity observed between fibrosis and cancer in solid epithelial cancers, such as pancreatic ductal adenocarcinoma.

Harold F Dvorak, Sheila A Stewart, Edna Cukierman

The importance of vascular permeability in tumor stroma generation and wound healing

Harold F Dvorak

Aging in the driver’s seat: Tumor progression and beyond

Sheila A Stewart

Why won’t CAFs stay normal?

Edna Cukierman

Tuesday, June 23

3:00 PM – 5:00 PM EDT

The Relevance of Glycans in the Viral Pathology of COVID-19

Posted in Biological Engineering, Glycobiology: Biopharmaceutical Production, Microbiology, Virology, tagged #COVID-19, blood_types on March 23, 2020| Leave a Comment »

The Relevance of Glycans in the Viral Pathology of COVID-19

Reporter: Ofer Markman, PhD

While we are constantly cautioning people from putting too high validity to the results seen in the bellow mentioned Study,

The ABO blood groups are a result of various and different glycans on the surfaces of red blood cells and their definition is related to Blood Immunology and Blood Typing classification used for Blood Donations. It was the hallmark of the 1930 Nobel prize of medicine.

In the article, ABO blood group glycans modulate sialic acid recognition on erythrocytes the authors claim that the ABH(O) glycan can modulate the surface of cells and their interactions to pathogens, in this case the Malaria pathogen.

Glycans are involved in the interaction of the flu virus to the host cell and the antiviral drug Tamiflu (Oseltamivir ) is based on the inhibition of that sort of interaction/modulation.

The Relevance of Glycans in the Viral Pathology of COVID-19

Even if true, the numbers in this paper show statistical significant difference but mildly significant difference in the risk profile suggesting we are to pay too much attention to the phenomena or worry, regardless of the fact these result have no significance on behavioral instructions nor would call for testing one’s blood type in regards to a viral infection. I would neither totally ignore the finding as it may shed light on viral pathology and infection mechanisms and understanding of the later may lead us to treatment or effective vaccines. But we are still early on this path.

SOURCE

https://www.medrxiv.org/content/10.1101/2020.03.11.20031096v1

Original Reference

Jiao Zhao, Yan Yang, Han-Ping Huang, Dong Li, Dong-Feng Gu, Xiang-Feng Lu, Zheng Zhang, Lei Liu, Ting Liu, Yu-Kun Liu, Yun-Jiao He, Bin Sun, Mei-Lan Wei, Guang-Yu Yang, View ORCID Profile Xinghuan Wang, Li Zhang, Xiao-Yang Zhou, Ming-Zhao Xing, View ORCID Profile Peng George Wang

doi: https://doi.org/10.1101/2020.03.11.20031096

yet a more relevant understanding of glycans in the biology of the virus:-

this week NEJM interview shed some more light on the issue in their 2nd part of the talk when they discussed again blood group risk factors in the covid-19 context.

https://www.nejm.org/doi/full/10.1056/NEJMe2023276?query=TOC