Genome Technology Center
Genome Technology Center
News Article | November 9, 2016
The most anticipated speaker late last month at an international conference devoted to the mysterious malady commonly known as chronic fatigue syndrome (CFS) was not a scientist with a hot new finding—although there was excitement about new research in the air. Rather, it was a National Institutes of Health (NIH) official bearing good news to a community that has long existed on the margins of the biomedical research establishment. Vicky Whittemore, the agency's CFS point person in Bethesda, Maryland, delivered on a promise that NIH Director Francis Collins made last year by announcing that NIH spending for research on the poorly understood disease should rise to roughly $15 million in 2017, doubling the estimated $7.6 million handed out in 2016. What's more, the NIH emissary said to those gathered here, the biomedical agency will in December solicit CFS proposals from outside scientists to establish several collaborative centers for basic and clinical research, and another center to manage their data on the illness. The calls for applications, which will come with dedicated funds from the planned budget increase, are the first of their kind for CFS from the United States's major medical research funder since 2005. "There is a shifting tide at NIH with regard to ME/CFS," Whittemore told the conference, incorporating the term that many with the multisystem illness prefer. (ME stands for "myalgic encephalomyelitis," and the meeting was convened by the International Association for CFS/ME.) Some scientists working on the disease agree. "The fact that there is a budget for it at all means that the agency is taking it seriously. And it's not coming only out of Francis Collins's discretionary fund, but from the individual NIH institutes," says Ian Lipkin, an immunologist at Columbia University, who serves on the Advisory Committee to the Director, Collins's key group of external advisers. Lipkin is also a principal investigator, with Columbia psychiatrist Mady Hornig, on a $766,000 grant from NIH's infectious diseases institute to collect samples from hundreds of patients and controls, looking for biomarkers that could be used to diagnose the disease and searching for clues to its causes. It has been nearly 3 decades since a group of researchers led by the U.S. Centers for Disease Control and Prevention (CDC) coined the term "chronic fatigue syndrome" after an investigation of two outbreaks in the United States. Typified by exhaustion that commonly worsens with physical, mental, or emotional exertion, the condition is also often characterized by short-term memory and concentration problems and profound fatigue that sleep does not relieve. Sufferers may experience widespread muscle and joint pain, immune system problems, headaches, and many other symptoms. The onset of the disease frequently follows an infectious illness. Ever since it was given a name, many researchers and physicians have viewed the malady, which has no Food and Drug Administration–approved treatment and no diagnostic test, as psychosomatic. Then, in 2015, the Institute of Medicine (IOM) dismissed the "misconception" of the disease as psychological in a report informed by a review of more than 9000 articles from 64 years of medical literature. "Remarkably little research funding has been made available to study the etiology, pathophysiology, and effective treatment of this disease, especially given the number of people affected," the authors noted. CDC estimates that ME/CFS affects more than 1 million Americans, a majority of them women. The IOM report "had an unbelievable effect," because it validated patients' experiences—"it told them that they weren't crazy," says geneticist Ronald Davis, who directs the Genome Technology Center at Stanford University in Palo Alto, California, and was one of the report's 15 authors. Davis became a passionate advocate for ME/CFS research and shifted his own studies to the topic after his now 33-year-old son fell ill with ME/CFS in 2008; he is now bedridden. "It also did a lot to NIH and the CDC, who had been ignoring this disease." Not long after the IOM report was published, NIH issued its own written assessment, concluding that research has neglected many of the biological factors behind ME/CFS and urging more basic science aimed at teasing out the mechanisms of the disease. Collins also announced a "strengthening" of the agency's ME/CFS effort. He moved oversight of the research out of the agency's small Office of Research on Women's Health and into the $1.7 billion National Institute of Neurological Disorders and Stroke (NINDS), and launched an intramural study that began enrolling people late last month. Forty patients who have developed the disease within the last 5 years, after an infection, will be run through a battery of exams at the Clinical Center, the NIH's research hospital. The assessments, from exercise stress tests to brain magnetic resonance imaging tests, will probe the biological and clinical characteristics of the disease—for which there is not even a broadly agreed-upon definition. For comparison, the study will also include healthy controls and people who have recovered from Lyme disease, which can cause similar symptoms. Some ME/CFS patients remain skeptical that the NIH moves reflect a genuine commitment to research on the disease. They have criticized what they call the narrow eligibility criteria being used for the Clinical Center study, and they complain that even $15 million scarcely begins to fund the research they say is needed. Critics such as Deborah Waroff, a retired Wall Street energy analyst who fell ill with ME/CFS in 1989, point, for instance, to multiple sclerosis, a similarly chronic, debilitating disease, which affects fewer than half as many Americans, according to one recent estimate. It received about 13 times as much NIH funding in 2016: $98 million. "ME still floats in space, belonging fully to no NIH institute and therefore having de jure claim to no budget," Waroff says. "The disease remains a beggar when it comes to budget." Any goodwill won by Whittemore's appearance in Florida may have evaporated after anger erupted last week when ME/CFS patients learned NIH had invited Edward Shorter, a medical historian at the University of Toronto in Canada, to give a 9 November talk at the agency. Shorter last year called the IOM report affirming the biological basis of ME/CFS "valueless; junk science at its worst." He traces the disease to a 1970s "brew of toxic beliefs about being tired all the time." Walter Koroshetz, the director of NINDS, defended the talk, writing in a letter to ME/CFS patients that "inclusion in the scientific conversation is not an endorsement." In an email to Science, he wrote that Shorter's talk was not "an official ME/CFS lecture. [An] announcement went out to the contrary. That was recalled. End of story." Tangible scientific progress on unraveling ME/CFS might be the best medicine to heal the current divisions. A study published in the Proceedings of the National Academy of Sciences in August found depressed blood levels of scores of metabolites in people with the disease compared with healthy controls, suggesting that the disease may push the body into a low-energy state some have compared with hibernation. Scientists and patients are eagerly waiting for the results of a similar study by Lipkin's team. If replicated, the tantalizing finding could fit with an emerging theory that subpar function by mitochondria, the organelles that provide energy for cells, drives the disease. Hints that the monoclonal antibody rituximab, a drug that destroys antibody-producing B cells, may help some people with ME/CFS have also sparked optimism. ME/CFS patients have a slightly elevated risk of developing B-cell lymphoma, and Norwegian researchers accidentally found that treating a woman who had both conditions with rituximab markedly improved her ME/CFS symptoms. The group went on to do a nonblinded study of the antibody in 29 ME/CFS patients, 18 of whom reported major or moderate improvements in their symptoms. The researchers are now running a larger, double-blind, randomized clinical trial of the drug in 152 patients, planning to evaluate its effectiveness next October. Øystein Fluge, one of the Norwegian trial's leaders and an oncologist at the University of Bergen's Haukeland University Hospital in Norway, remains cautious. "Many places on the internet say this is an autoimmune disease. We haven't said that. We think some features fit, probably, with some autoimmune mechanism. But that's a hypothesis. We aren't sure." Only one thing is sure: After decades of frustration, the mysterious disease remains maddeningly elusive.
News Article | November 14, 2016
In living beings, from roundworms to humans, some cells may ball up unwanted contents on their surfaces for other cells to "eat." This is the finding of a study led by researchers at NYU Langone Medical Center and published online November 14 in Nature Cell Biology. The results raise the possibility that cellular cannibalism may be more widespread than once thought, and may even shed light on certain brain disorders. The work was done in the worm species C. elegans, which is famous for its role in past discoveries of vital mechanisms also at work in human cells. Specifically, the study found that, as an embryo develops into a worm, cells that pass on genes to the next generation (primordial germ cells or PGCs) form outer lobes, or "balls," that are digested by nearby cells that form the worm's gut. By forming lobes destined to be clipped off and digested, germ cells may be discarding large amounts of material that would otherwise interfere with reproduction, say the study authors. "These findings define a new way in which cells dramatically change their contents via cannibalism, and, in doing so, may reveal a new set of genetic causes for diseases when this mechanism goes awry," says Jeremy Nance, PhD, associate professor in the Department of Cell Biology at NYU Langone. The study poses the question of whether this ability to quickly edit cell contents is vital to the function of many cell types in many organisms, including humans. A 2012 paper led by a separate research team, for instance, proposed that immune cells in the brain prune nerve connections by "eating" bulbs on nearby nerve cell extensions to edit brain circuitry. Some experts have asked whether some forms of autism may be caused by faulty cellular cannibalism. If these mechanisms exist, how widespread are they? In worms, as in humans, certain cells in a portion of the embryo, called the endoderm, migrate and become the cells that form the gut. In both species, cells that go on to form the sexual organs, and the cells that will become sperm and eggs, migrate alongside pre-gut cells to end up in their final location at the bottom of the gut. It was while studying this partnership between co-migrating cell types that the research team first observed one cell type eating part of another. Researchers also found that the lobes put forth for removal by PGCs contained large numbers of mitochondria, the cell powerhouses that convert blood sugar into molecules that serve as cellular energy currency. One theory for why this occurs is that mitochondria, as a side effect of making energy, also produce highly-reactive free radicals that can damage DNA in a process called oxidative stress. This is a problem for any cell, but more so for the gamete or germ cell, which carries the copy of genetic information that will serve as the template for the offspring. Any random change there could have devastating consequences, not just for one cell, but for future generations. The study results raise the question of whether germ cells trade lower energy production, by getting rid of mitochondria via cell cannibalism, for greater DNA protection. Researchers will also seek to determine if genetic risk for some forms of sterility proceeds from the failure of cannibalistic mechanisms to protect gametes from oxidative stress. Specifically, the research team found that lobe cannibalism is carefully choreographed by biochemical signals, with all lobes forming during the same developmental time window and bitten off in a set order. Furthermore, progenitor gamete cells in worms always form lobes full of mitochondria, but the lobes are only cut off if partnering endodermal cells are present. Moving forward, the research team will seek to identify the signals by which PGC lobes embed specifically into endodermal cells, and those that tell endodermal cells to eat lobes. The work may also help the field to determine whether similar cellular remodeling events shape brain circuitry, say the authors. Along with Nance, study authors were Yusuff Abdu and Chelsea Maniscalco in the Skirball Institute of Biomolecular Medicine, along with John Heddleston and Teng-Leong Chew from the Advanced Imaging Center at the Howard Hughes Medical Institute in Ashburn, Virginia. The study was funded by grants from the National Institutes of Health, and sequencing of genomic DNA samples was performed at the NYULMC Genome Technology Center, which is partially supported by a grant (P30CA016087) from the Perlmutter Cancer Center.
News Article | February 2, 2016
Researchers at the Stanford University School of Medicine have developed a fast, inexpensive and highly accurate test to screen newborns for cystic fibrosis. The new method detects virtually all mutations in the CF gene, preventing missed diagnoses that delay babies’ ability to begin receiving essential treatment. A paper describing the new test published online Feb. 1 in The Journal of Molecular Diagnostics. Cystic fibrosis, which causes mucus to build up in the lungs, pancreas and other organs, is the most common fatal genetic disease in the United States, affecting 30,000 people. To develop the disease, a child must inherit two mutated copies of the CF gene, one from each parent. Newborns in every U.S. state have been screened for CF since 2010, but the current tests have limitations. “The assays in use are time-consuming and don’t test the entire cystic fibrosis gene,” said the study’s senior author, Curt Scharfe, M.D., Ph.D.. “They don't tell the whole story.” Scharfe was a senior scientist at the Stanford Genome Technology Center when the study was conducted and is now associate professor of genetics at the Yale School of Medicine. “Cystic fibrosis newborn screening has shown us that early diagnosis really matters,” said Iris Schrijver, M.D., a co-author of the study and professor of pathology at Stanford. Schrijver directs the Stanford Molecular Pathology Laboratory, which has a contract with California for the state’s newborn CF testing. Prior studies have shown that newborn screening and prompt medical follow-up reduce symptoms of CF such as lung infections, airway inflammation, digestive problems and growth delays. “When the disease is caught early, physicians can prevent some of its complications, and keep the patients in better shape longer,” Schrijver said. Although classic CF still limits patients’ life spans, many of those who receive good medical care now live into or beyond their 40s. In the current test, babies’ blood is first screened for immunoreactive trypsinogen, an enzyme that is elevated in CF cases but also can be high for other reasons, such as in infants with one mutated copy and one normal copy of the CF gene. Since the majority of infants with high trypsinogen will not develop CF, most U.S. states follow up with genetic screening to detect mutations in the CF gene. California, which has the most comprehensive screening process, tests for 40 CF-causing mutations common in the state. (More than 2,000 mutations in the CF gene are known, though many are rare). If one of the common mutations is identified, the infant’s entire CF gene is sequenced to try to confirm whether the baby has a second, less common CF mutation. The process takes up to two weeks and can miss infants who carry two rare CF mutations, particularly in nonwhite populations about whose CF changes scientists have limited knowledge. The Stanford-developed method greatly improves the gene-sequencing portion of screening, comprehensively detecting CF-causing mutations in one step, at a lower cost and in about half the time now required. Stanford University is exploring the possibility of filing a patent for the technique. To enable these improvements, the team developed a new way to extract and make many copies of the CF gene from a tiny sample of DNA — about 1 nanogram — from the dried blood spots that are collected on cards from babies for newborn screening. “These samples are a very limited and precious resource,” Scharfe said. The entire CF gene then undergoes high-throughput sequencing. This is the first time scientists have found a way to reliably use dried blood spots for this type of sequencing for CF, which typically requires much more DNA. “In our new assay, we are reading every letter in the book of the CF gene,” Schrijver said. “Whatever mutations pop up, the technique should be able to identify. It’s a very flexible approach.” In order for the new test to be adopted, the molecular pathology lab needs to train its staff on the new procedure and run thorough validation studies as part of regulatory and quality requirements to show that the reliability of the test in a research setting will be maintained in the larger-scale clinical laboratory. California newborn screening officials will then have the opportunity to decide whether they want the new test to replace the current method. Schrijver expects the process will take less than a year. “Regardless of how the state decides, the new technique can be widely adopted in different settings,” she said, noting that the technique could also be used for carrier and diagnostic testing and to screen for other genetic diseases, not just CF. “Ultimately, we would like to develop a broader assay to include the most common and most troublesome newborn conditions, and be able to do the screening much faster, more comprehensively and much more cheaply,” Scharfe said. The work is an example of Stanford Medicine’s focus on precision health, the goal of which is to anticipate and prevent disease in the healthy and precisely diagnose and treat disease in the ill.
Schafer M.J.,New York University |
Schafer M.J.,Nathan Kline Institute |
Dolgalev I.,Genome Technology Center |
Alldred M.J.,Nathan Kline Institute |
And 5 more authors.
PLoS ONE | Year: 2015
Calorie restriction (CR) enhances longevity and mitigates aging phenotypes in numerous species. Physiological responses to CR are cell-type specific and variable throughout the lifespan. However, the mosaic of molecular changes responsible for CR benefits remains unclear, particularly in brain regions susceptible to deterioration during aging.We examined the influence of long-term CR on the CA1 hippocampal region, a key learning and memory brain area that is vulnerable to age-related pathologies, such as Alzheimer's disease (AD). Through mRNA sequencing and NanoString nCounter analysis, we demonstrate that one year of CR feeding suppresses age-dependent signatures of 882 genes functionally associated with synaptic transmission-related pathways, including calcium signaling, long-term potentiation (LTP), and Creb signaling in wild-type mice. By comparing the influence of CR on hippocampal CA1 region transcriptional profiles at younger-adult (5 months, 2.5 months of feeding) and older-adult (15 months, 12.5 months of feeding) timepoints, we identify conserved upregulation of proteome quality control and calcium buffering genes, including heat shock 70 kDa protein 1b (Hspa1b) and heat shock 70 kDa protein 5 (Hspa5), protein disulfide isomerase family A member 4 (Pdia4) and protein disulfide isomerase family A member 6 (Pdia6), and calreticulin (Calr). Expression levels of putative neuroprotective factors, klotho (Kl) and transthyretin (Ttr), are also elevated by CR in adulthood, although the global CR-specific expression profiles at younger and older timepoints are highly divergent. At a previously unachieved resolution, our results demonstrate conserved activation of neuroprotective gene signatures and broad CR-suppression of age-dependent hippocampal CA1 region expression changes, indicating that CR functionally maintains a more youthful transcriptional state within the hippocampal CA1 sector. © 2015 Schafer et al.
Maass K.,New York University |
Shekhar A.,New York University |
Lu J.,New York University |
Kang G.,New York University |
And 6 more authors.
Stem Cells | Year: 2015
The cardiac Purkinje fiber network is composed of highly specialized cardiomyocytes responsible for the synchronous excitation and contraction of the ventricles. Computational modeling, experimental animal studies, and intracardiac electrical recordings from patients with heritable and acquired forms of heart disease suggest that Purkinje cells (PCs) may also serve as critical triggers of life-threatening arrhythmias. Nonetheless, owing to the difficulty in isolating and studying this rare population of cells, the precise role of PC in arrhythmogenesis and the underlying molecular mechanisms responsible for their proarrhythmic behavior are not fully characterized. Conceptually, a stem cell-based model system might facilitate studies of PC-dependent arrhythmia mechanisms and serve as a platform to test novel therapeutics. Here, we describe the generation of murine embryonic stem cells (ESC) harboring pan-cardiomyocyte and PC-specific reporter genes. We demonstrate that the dual reporter gene strategy may be used to identify and isolate the rare ESC-derived PC (ESC-PC) from a mixed population of cardiogenic cells. ESC-PC display transcriptional signatures and functional properties, including action potentials, intracellular calcium cycling, and chronotropic behavior comparable to endogenous PC. Our results suggest that stem-cell derived PC are a feasible new platform for studies of developmental biology, disease pathogenesis, and screening for novel antiarrhythmic therapies. © 2015 Alpha Med Press.