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Archive - 2018

October 19th

“We Are All Africans”--Presidential Symposium on Origin of Human Species Electrifies Record 9,000 Attendees at ASHG Annual Meeting

(BY MICHAEL A. GOLDMAN, PhD, Professor, Former Chairman of Biology, San Francisco State University). The American Society of Human Genetics (ASHG) Presidential Symposium, titled “Origins of Our Species: Advances in Our Understanding of Ancient Humans in Africa,” began in late afternoon Thursday October 18, and was open to all of the meeting’s ~9,000 attendees (an ASHG meeting attendance record). This symposium featured stimulating presentations by three prominent evolutionary geneticists, followed by a brief panel discussion amongst the three speakers, which was moderated by Dr. Charles N. Rotimi, of the National Human Genome Research Institute (NHGRI) in Bethesda, Maryland, and Dr. Sarah Tishkoff, of the University of Pennsylvania in Philadelphia, Pennsylvania. Dr. Rotimi is a Senior Investigator at NIH, and Dr. Tishkoff is David and Lyn Silfen University Professor, Departments of Genetics and Biology, Perelman School of Medicine and School of Arts and Sciences, University of Pennsylvania. The essence of being human, according to first presenter paleoanthropologist Dr. John D. Hawks of the University of Wisconsin-Madison, is a process, rather than a specific thing. We share a common heritage, and we will make a common future, he said. We are all part of that process whether we share particular traits that are thought to be characteristic of humans, such as speech and walking upright, or not. This simple observation belies the extraordinarily complex and controversial story of human origins featured in the President's Symposium. In a field where each new fossil discovery seems to add yet another gap to the record, Dr. Hawks admits that we still have much to learn, and that we will be continuously surprised, as now is as exciting as any time in the study of human evolution. Dr.

October 18th

Environmental Associations with Genes May Yield Opportunities for Precision Medicine; Findings Reported at ASHG 2018 Annual Meeting

A new approach to genetic analysis finds associations between environmental factors and pharmacogenes – genes associated with a person’s response to drugs – sparking ideas for new research at the interface of population genetics and medicine. Findings were presented Thursday, October 18, at the American Society of Human Genetics (ASHG) 2018 Annual Meeting in San Diego, California (October 16-20). “Humans have developed and used pharmaceutical drugs for a few centuries, but their genes have been functioning on their own and interacting with other environmental factors for long before that,” explained presenting author Chris Gignoux (photo), PhD, of the University of Colorado Anschutz Medical Campus. Like changes in the physical environment, drugs affect the micro- environment within the body, which alters the way its cells and genes function. This suggests that genes with pharmacogenomic relevance may also be useful in studying broader correlations between genetics and environment. To explore a variety of environmental factors, Dr. Gignoux collaborated with Elena Sorokin, PhD, of Stanford University, who created a geocoded resource of over 20 climate, geographic, and ecological variables, using data from NASA, the World Wildlife Fund, and other sources. With collaborators from across the United States, they examined samples from the Population Architecture using Genomics and Epidemiology (PAGE) Study, a large initiative to highlight the utility of studying clinically and epidemiologically relevant variation in 51,698 individuals from 99 global populations. In a new type of analysis they termed an Enviro-WAS (environment-wide association study), the researchers examined 19,690 pharmacogenomically-relevant variants to identify associations between genotypes and the 20 environmental variables.

Docs May Be Overly Conservative in Use of New Drug Combinations for Cancer, UCSD Speaker Suggests; Over 4 Million Three-Drug Combinations of Existing Drugs Possible, Too Many for Clinical Trials; Biomarker Use to Target Treatment Is Recommended

(BY MICHAEL A. GOLDMAN, PhD, Professor, Former Chairman of Biology, San Francisco State University). Speaking at this week's 2018 annual meeting of the American Society for Human Genetics (ASHG) in San Diego (October 16-20), Razelle Kurzrock (photo),MD, Director of the UC San Diego (UCSD) Center for Personalized Cancer Therapy, told a very large audience that oncologists have been conservative about using new drug combination therapies. Yet, with nearly 300 drugs on the market, there are more than 4 million 3-drug combinations, far too many to test in controlled trials. She uses a patient-centric, rather than a drug-centric, treatment plan, employing a consistent strategy, but with different drugs or, when appropriate, immunotherapy. Addressing more than 600 scientists and clinicians in a two-day symposium sponsored by the Pharmacogenomics Research Network (PGRN), Dr. Kurzrock said cancers are like malignant snowflakes, each different and magnificently complex. Profiling more than 12,000 tumors using genomic markers, her group uses biomarkers to target treatment in a "tissue-agnostic" manner. For example, PIK3CA mutations are found in 10% of patients with advanced cancers, and can be seen in a subset of most cancer types. Elevated HER2 expression occurs across a wide variety of tumors, and the same HER2 antagonists seem to work. Dr. Kurzrock calls her approach PREDICT (Profile-Related Evidence Determining Individual Cancer Therapy), which reflects a family of master protocols at UCSD. These protocols for trial combinations of drugs have limited exclusion criteria; almost every patient in need is eligible. Dr. Kurzrock stressed the need for genomics education for medical professionals, which she finds to be inadequate today. "In five years," she says, "it will be routine practice to do these [genomic] tests."

EXOSOME NEWS: Fat Cells & Extracellular Vesicles (EVs) They Release May Hold Solutions for Diabetes; “Findings Represent a New Way of Thinking for Researchers Who Study Diabetes, Obesity, and Metabolism”

Researchers have long known that cells in the human body communicate with one another. Now a team of scientists at the University of Texas (UT) Southwestern Medical Center is hacking into this communication network to learn how fat cells talk with other cells and tissues in the body. Dr. Philipp Scherer, a metabolism expert and Director of the Touchstone Center for Diabetes Research at UT Southwestern, is excited about the new findings because they will allow researchers to test new ideas and re-examine old ones. The study, published online on October 4, 2018 in Cell, shows that fat cells communicate with endothelial cells of the blood vessels that course through fat tissue, and potentially with other organs, by secreted packages of information (extracellular vesicles or EVs, often called exosomes). This communication between cells was demonstrated in a number of new mouse models that researchers created. The title of the new article is “An Endothelial-to-Adipocyte Extracellular Vesicle Axis Governed by Metabolic State.” These findings represent a new way of thinking for researchers who study diabetes, obesity, and metabolism. They open an entirely new door to our understanding of how tissues communicate,” said Dr. Clair Crewe, a postdoctoral researcher in the Touchstone Diabetes Center and first author of the study. “Once we understand the communication process, we can potentially shape it to either enhance or reduce the signaling effect.” The study identified a type of vesicle, a membrane-enclosed sphere, released by fat and other cells. Dr. Scherer compares them to the chocolate surrounding a bonbon. The “filling” includes lipids, signaling molecules, and proteins. The timing of their release is regulated by cycles of fasting and feeding. These vesicles travel throughout the body.

Ancient Andean Genomes Show Distinct Adaptations to Farming and Altitude; Findings Presented at ASHG 2018 Annual Meeting

Ancient populations in the Andes mountains of Peru adapted to their high-altitude environment and the introduction of agriculture in ways distinct from other global populations that faced similar circumstances, according to findings presented on October 17 at the American Society of Human Genetics (ASHG) 2018 Annual Meeting in San Diego, California (October 16-20). The ASHG has reported a record attendance of 8,500 at this year’s meeting. John Lindo, PhD, JD, Assistant Professor of Anthropology at Emory University, and a group of international collaborators headed by Anna Di Rienzo, PhD, at the University of Chicago and Mark Aldenderfer, PhD, at the University of California, Merced, set out to use newly available samples of 7,000-year-old DNA from seven whole genomes to study how ancient people in the Andes adapted to their environment. The scientists compared these genomes with 64 modern-day genomes from both highland Andean populations and lowland populations in Chile, in order to identify the genetic adaptations that took place before the arrival of Europeans in the 1500’s. “Contact with Europeans had a devastating impact on South American populations, such as the introduction of disease, war, and social disruption,” explained Dr. Lindo. “By focusing on the period before that, we were able to distinguish environmental adaptations from adaptations that stemmed from historical events.” The scientists found that Andean populations’ genomes adapted to the introduction of agriculture and resulting increase in starch consumption differently from other populations. For example, the genomes of European farming populations show an increased number of copies of the gene coding for amylase, an enzyme in saliva that helps break down starch.

October 17th

Genome Sequencing Found Feasible & Informative for Pediatric Cancer Treatment; Recommendations Reported at ASHG 2018 Annual Meeting; Work Is Part of St. Jude’s “Genomes for Kids” Study

Comprehensive genetic testing of tumors and non-cancerous tissue from pediatric cancer patients is a feasible and clinically useful approach that can guide patient care, according to findings presented on October 17 at the American Society of Human Genetics (ASHG) 2018 Annual Meeting in San Diego, California (October 16-20). The ASHG reports a record attendance of 8,500 for this year's meeting. Presenting author Scott Newman, PhD; Jinghui Zhang, PhD; and Kim Nichols (photo), MD, along with an interdisciplinary team at St. Jude Children’s Research Hospital, studied 253 pediatric oncology patients with a variety of cancers. In 79 percent of cases, there was at least one finding that could help guide care by providing a diagnosis, revealing patient-specific risks, or identifying drug targets. The researchers conducted whole genome sequencing (WGS), whole exome sequencing (WES), and RNA sequencing of the patients’ tumors, as well as WGS and WES of non-cancerous tissue from the same patient. WGS involves sequencing the patient’s complete genome, while WES involves sequencing those portions that are transcribed into mRNA, most of which codes for proteins. This work was part of the “Genomes for Kids” study (G4K), a large effort to understand how best to use genetic data for pediatric cancer diagnosis and treatment. Differing from other studies that require a specific diagnosis to participate, this study had no prerequisite beyond the presence of adequate tumor tissue for testing. “To my knowledge, this is the first study to offer comprehensive sequencing prospectively for all new patients with adequate samples," said Dr. Nichols. She also noted that the diversity of cancers that were tested helped to verify the relationships between genetic variants and disease. Dr.

October 14th

RNA Key (Non-Coding 886) That Unlocks Innate Immunity

RNA has long been the neglected middle child of biomolecules, the go-between from DNA, which encodes the cell's instructions, to proteins, which carry them out. Increasingly, though, researchers are recognizing RNA as a versatile molecule with, possibly, as many functions as proteins have. New research from Emory University, published in the October 12, 2018 issue of the Journal of Biological Chemistry, shows that one such versatile RNA molecule may be a key player in human cells' frontline defenses against viruses. The title of the article is “A Human Cellular Noncoding RNA Activates the Antiviral Protein 2′–5′-Oligoadenylate Synthetase 1,” Dr. Graeme Conn, the biochemistry professor who oversaw the work, studies how RNA is involved in the body's responses to infections. When a human cell senses a virus, it activates a signaling pathway: a protein called OAS (oligoadenylate synthetase) gets turned on and produces a signaling molecule, which in turn activates another protein that both directly defends against the virus as well as activating other parts of the cell's innate immune system. As it turns out, human RNA might play an important role in this pathway, specifically a human RNA molecule called nc886. The "nc" stands for "noncoding," which means this RNA molecule is not carrying instructions for building a protein. It's doing something all on its own. What it's doing, the new JBC paper shows, is turning on OAS, thus setting off the chain of events that destroys viruses. "We saw that (nc886) wasn't just an activator of this pathway, but a very potent activator," said Brenda Calderon, who carried out the research as a graduate student in Dr. Conn's lab. The nc886 molecule can adopt two different shapes, and one of them is much better at activating OAS than the other.

October 10th

NanoView Completes $10 Million Series B Financing Funding to Support Commercialization of ExoView™ System, NanoView’s Complete Exosome Detection and Characterization Platform; Financing Led by Northpond Ventures

On October 10, 2018, NanoView Biosciences, an emerging leader in the field of exosome detection and characterization, announced the closing of a $10 million Series B financing led by Northpond Ventures. Existing investors, including Sands Capital Ventures and PBM Capital Group, participated in the financing round. Proceeds will be used to complete development of the ExoView system, NanoView’s complete exosome detection and characterization platform, and to prepare the product for commercial launch. “Northpond Ventures really understands the need for more accurate, efficient approaches to characterizing exosomes and we are excited to have them join our current investors,” said Jerry Williamson, Chief Executive Officer of NanoView. “With these funds we are well positioned to complete the development of the first applications of our ExoView system. We plan to launch this platform for research markets in early 2019 and then expand into developing tools for clinical markets in the future.” Exosomes are nanoscale extracellular vesicles secreted by most cell types; they represent a communication system between cells. A growing body of research supports the potential of exosomes to diagnose, monitor, and even treat a broad range of diseases. Most currently available methods for analyzing exosomes are cumbersome, expensive, and require large sample volumes that are not readily available. According to NanoView, the ExoView system is an innovative instrument and consumables platform that efficiently and accurately enables complete detection and characterization of extracellular vesicles, including exosomes.

October 10th

Anti-Psychotic Drug May Be Effective Against Triple-Negative Breast Cancer

A commonly used anti-psychotic drug could also be effective against triple-negative breast cancer, the form of the disease that is most difficult to treat, new research has found. The study, led by the University of Bradford in the UK, also showed that the drug, pimozide, has the potential to treat the most common type of lung cancer. Anti-psychotic drugs are known to have anti-cancer properties, with some studies, albeit inconclusive, showing a reduced incidence of cancer amongst people with schizophrenia. The new research, published online on October 9, 2018 in Oncotarget, is the first to identify how one of these drugs acts against triple-negative breast cancer, with the potential to be the first targeted treatment for the disease. Lead researcher, Professor Mohamed El-Tanani (photo) from the University of Bradford, said: "Triple-negative breast cancer has lower survival rates and increased risk of recurrence. It is the only type of breast cancer for which only limited targeted treatments are available. Our research has shown that pimozide could potentially fill this gap. And because this drug is already in clinical use, it could move quickly into clinical trials." The researchers, from the University of Bradford, Queen's University Belfast (Northern Ireland), and the University of Salamanca (Spain), tested pimozide in the laboratory on triple-negative breast cancer cells, non-small cell lung cancer cells, and normal breast cells. They found that, at the highest dosage used, up to 90 per cent of the cancer cells died following treatment with the drug, compared with only 5 per cent of the normal cells. The researchers then tested the drug on mice implanted with triple-negative breast cancer.

Specific Gene Types Driving Higher Frequency of Myeloma Diagnosis in African-Americans Identified By Mayo Clinic Researchers; DNA Sequencing Used to More Accurately Determine Racial Ancestry; Findings May Aid Insight into Best Forms of Therapy

Researchers at the Mayo Clinic in Rochester, Minnesota, have identified three specific gene types that account for a known two-to-three-fold increase in myeloma diagnoses among African-Americans. Researchers also demonstrated the ability to study race and racial admixture more accurately using DNA analysis. The findings were published online on October 10, 2018 in Blood Cancer Journal. The open-access article is titled “Differences in Genomic Abnormalities Among African Individuals with Monoclonal Gammopathies Using Calculated Ancestry.” "Myeloma is a serious blood cancer that occurs two to three times more often in African-Americans than Caucasians," says Vincent Rajkumar(photo), MD. a hematologist at the Mayo Clinic and senior author of the study. "We sought to identifying the mechanisms of this health disparity to help us better understand why myeloma occurs in the first place and provide insight into the best forms of therapy." Dr. Rajkumar and his colleagues studied 881 patients of various racial groups. Researchers found that the higher risk of myeloma known to occur in African-Americans was driven by three specific subtypes of the cancer characterized by the presence of genetic translocations in cancer cells. Translocations are genetic abnormalities in cancer cells caused by the rearrangement of parts between nonhomologous chromosomes. The translocation researchers identified were t(11;14), t(14;16), and (t14;20). "Previous efforts to understand this disparity have relied on self-reported race rather than on genetic ancestry, which may have resulted in bias," explains Dr. Rajkumar. "A major new aspect of this study is that we identified the ancestry of each patient through DNA sequencing, which allowed us to determine ancestry more accurately." Dr.