Llamas have become the surprising focal point of a new technology that is aimed at making “nanobodies” more accessible to the research community. Nanobodies, considered to be the “little cousins” of antibodies, are therapeutic proteins derived from their larger antibody cousins. Antibodies are proteins produced by the immune system and used to identify and neutralize foreign elements in the body. They are extremely valuable research tools that are used routinely in basic research, diagnostic testing and therapeutics. Nanobodies can perform the same functions as antibodies; however, their small size and extreme stability make them attractive replacements. Although the appeal of using nanobodies in research has been clear for some time, the difficulties of producing them in sufficient quantities have limited their usefulness.
A discovery in llamas has changed the trajectory of nanobody production. Although not the original developers of nanobodies, a research team headed by Michael Rout, an investigator funded by the National Center for Dynamic Interactome Research http://www.ncdir.org/, within the NIH Common Fund’s National Technology Centers for Networks and Pathways (TCNPs) http://commonfund.nih.gov/bbpn/overview#TCNPs initiative has developed a novel approach to increasing nanobody production. Dr. Rout and his colleagues have designed a faster more direct technique to generate nanobodies, making them more accessible to the scientific community. They chose the llama instead of more common laboratory animals as a model for this method because llamas were found to make a unique subset of antibodies that can easily be turned into nanobodies. Faster production of these highly versatile nanobodies has the potential to transform research and catalyze scientific advances in a timeframe of weeks to months, instead of years.
Fridy PC et. al. A robust pipeline for rapid production of versatile nanobody repertoires. Nat Methods. 2014 Dec;11(12):1253-60. doi: 10.1038/nmeth.3170.
More than 440 researchers in 32 labs around the world participating in the Common Fund’s Roadmap Epigenomics program have generated and analyzed 111 reference human epigenomes. This is the largest collection to date of reference human epigenomes from a broad range of representative primary cells and tissues. A genome is defined as the DNA sequences present in a cell, and an epigenome refers to the chemical modifications and non-sequence changes to DNA and DNA-associated proteins. Currently, researchers are beginning to understand the many consequences of these chemical modifications, and early insights from this new analysis reveal that different epigenomic states are associated with differences in age, sex, and tissue type. The many companion papers describing additional analyses demonstrate the broad applicability of the resource. These studies examine the biological importance of epigenetic changes in the context of stem cell differentiation, obesity, Alzheimer’s disease, cancer, and cardiac disease. This remarkable accomplishment will usher in new scientific understanding of the complexity of the human genome at a deeper level and spur new research advances in human health and disease.
Roadmap Epigenomics Consortium et al. Integrative analysis of 111 reference human epigenomes. Nature, Feb. 18, 2015; 518; 317-330.
Read the NIH press release here.
Read more about the Epigenomics program here.
See video on the Epigenome by Nature here.
Scientists have long known that the metabolism of tumor cells differs from normal, healthy cells. However, it has been challenging to study tumor metabolism in living tumor cells from a large number of cancer patients. Metabolomics, a technique that allows scientists to analyze the molecules involved in metabolism, may change that. Researchers at the Common Fund-supported Resource Center for Stable Isotope-Resolved Metabolomics (RC-SIRM) looked at how the molecule glucose is broken down as part of the metabolism of patients with non-small-cell lung cancer. Shortly before surgery for tumor removal, the researchers injected patients with a form of glucose that is non-radioactively labeled. Using metabolomic techniques, researchers can follow how the labeled glucose is broken down by both the tumor cells and healthy cells from the same patient. As the glucose is broken down into component molecules, the label will remain with one or more of the components. These labeled components are a clue to which metabolic processes are active in the tumor.
The RC-SIRM team found that tumor cells broke down the glucose using two processes, glycolysis and the tricarboxylic acid cycle (TCA cycle). They also found that an enzyme involved in the TCA cycle, called pyruvate carboxylase, was produced in greater quantities in tumors compared to healthy tissue. Reducing the level of this enzyme in lab-grown human lung cancer cells reduced cell growth and interfered with the ability of these cells to form tumors in mice. This study by the RC-SIRM team demonstrates the exciting potential for metabolomic approaches to reveal new pathways and players in cancer metabolism that may become novel targets for cancer therapy and diagnostics.
RC-SIRM at the University of Kentucky is a Regional Metabolomics Resource Core funded through the Common Fund Metabolomics program. Learn more about the Metabolomics program.
Read the press release and watch the video from the University of Kentucky on this discovery.
The original research article was published in the Journal of Clinical Investigation. Read the article abstract.
New research has demonstrated that a destructive biological process involved in Alzheimer’s disease may hold promise as a novel treatment strategy for cancer. Anomalies in protein folding can generate harmful protein deposits within cells, called amyloids. These amyloid deposits underlie several neurodegenerative disorders in humans, particularly Alzheimer's disease. While amyloids are widely recognized as killers of neurons, a new study from New Innovator Awardee Dr. Chengkai Dai at The Jackson Laboratory reveals that cancer cells are also vulnerable to these toxic proteins. Cancer cells manage to contain deleterious amyloids by hijacking a cellular stress response that has evolved to counter protein misfolding, thereby sustaining the cancer cells’ vicious survival and growth. But importantly, this study also points to a possible means of countering this effect. Surprisingly, the authors’ findings reveal that cancer cells, unlike normal cells, constantly suffer heightened intrinsic stress. As a result, cancer cells are therefore particularly susceptible to extrinsic insults, including the activity of therapeutic agents that either perturb protein folding or subdue the defensive stress response. These agents efficiently induce the generation of amyloids within cancer cells and thereby exert potent anti-cancer effects. Thus, this study highlights a potential therapeutic strategy that harnesses the culprit behind neurodegenerative diseases to combat malignancy.
Tang et al. MEK guards proteome stability and inhibits tumor-suppressive amyloidogenesis via HSF-1. Cell, 160, Feb 2015.
Pioneer awardee Dr. Joseph DeSimone has developed a device that uses electrical currents to drive chemotherapy drugs directly into tumors, potentially revolutionizing how doctors treat some of the most challenging types of cancer. Several types of cancer, notably pancreatic cancer, can be difficult to treat with surgery because the tumor can become enmeshed with healthy tissue and blood vessels. Intravenous chemotherapy treatment may also be ineffective, because these tumors often don’t have a good enough blood supply to deliver effective concentrations of the drug. To overcome these obstacles, Dr. DeSimone and colleagues at the University of North Carolina Chapel Hill, Duke University, and North Carolina State University designed a device that can be implanted directly on the tumor or applied to the skin to precisely deliver therapeutic doses chemotherapy drugs into the tumor, with minimal amounts of the drug spreading to other places in the body. In animal models of pancreatic and breast cancer, treatment with the device slowed tumor growth or even reduced tumor size. Treatment with the device was even more effective when combined with standard intravenous chemotherapy and radiation. These results suggest that the new approach pioneered by Dr. DeSimone may one day be added to the arsenal of weapons doctors use in the fight against cancer.
Byrne et al. Local ionophoretic administration of cytotoxic therapies to solid tumors. Science Translational Medicine, Feb 2015, 7(273).
Microscopes allow researchers to peer into tiny cells and tissues by making the objects appear larger. However, visualizing extremely tiny cellular structures requires specialized microscopes that are very expensive, and even the most advanced microscopes are limited in how much they can magnify objects. Using a paradigm-shifting technique called expansion microscopy (ExM), Pioneer and Transformative Research Awardee Dr. Edward Boyden is taking the novel approach of actually making the samples themselves larger. Using a material commonly found in baby diapers, Dr. Boyden and colleagues at the Massachusetts Institute of Technology (MIT) are able to expand tissues to about 4.5 times their normal size, enabling visualization of tiny cellular structures and proteins with ordinary microscopes. This material, called sodium acrylate, holds proteins in place while it swells in the presence of water, resulting in minimal distortion of the sample’s structure. Using ExM, researchers could image a 3-dimensional slice of brain tissue and could zoom in to see the tiny synapse where neurons communicate with each other. By eliminating the need for costly, specialized equipment, ExM has the potential to enable many more scientists to examine structures otherwise unobservable in the cell.
(Photo: Dr. Edward Boyden presenting ExM at the Common Fund's High Risk, High Reward Research Symposium in December 2014)
Listen to Dr. Boyden’s talk at the Common Fund’s High Risk, High Reward Research Symposium (starts at 1 hour, 33 minutes)
Read the press release from MIT
Read the NIH Press Release: Diaper compound may expand power of microscopes
Chen F, Tillberg PW, and Boyden ES. Expansion Microscopy. Science, Jan 2014, DOI: 10.1126/science.1260088.
Using a newly developed technology, a research team led by Dr. Kim Lewis of Northeastern University in Boston has discovered 25 new antibiotics, with one in particular very promising for potential future use to treat an array of difficult to treat human infections including MRSA (Methicillin-resistant Staphylococcus aureus), which in 2013 alone caused 480,000 infections. The Transformative Research Award was created specifically to support exceptionally innovative and/or unconventional research projects that have the potential to create or overturn fundamental paradigms. Although inherently risky, projects also have high potential to create breakthroughs that have the ability to change the landscape of a scientific area. (Photo: Slava Epstein/Northeastern University)
For more information please visit:
Researchers in the Common Fund’s Single Cell Analysis program have created a high-speed, large-scale 3D imaging system capable of visualizing the activity of individual neurons in a living animal. The technique created by Dr. Edward Boyden and colleagues at the Massachusetts Institute of Technology (MIT) and the University of Vienna can generate three-dimensional (3D) movies of entire brains at the millisecond timescale, the first time this has ever been accomplished. The new method optimizes a widely used technology known as light-field microscopy (LFM), which creates 3D images by measuring the angles of incoming rays of light. Boyden and colleagues sent the light emitted by the sample being imaged through an array of lenses, which refracted the light in different directions and generated about 400 different points of light. Using a computer algorithm, the points of light were recombined to generate the 3D structure of the sample. Using this new system they were able to simultaneously image the activity of every neuron in the worm Caenorhabditis elegans and the whole brain of a zebrafish larva expressing proteins that fluoresce when binding to calcium (a way to visualize neuron activation). The technique offers a more complete picture of nervous system activity than has previously been possible. Through monitoring and tracking neurons and neural pathways, scientists hope to discover how sensory input is processed and behavior generated.
Prevedel R, Yoon Y-G, Hoffmann M, Pak N, Wetzstein G, Kato S, Schrödel T, Raskar R, Zimmer M, Boyden ES, and Vaziri A. Simultaneous Whole-Animal 3D Imaging of Neuronal Activity Using Light-Field Microscopy. Nature Methods, July 2014. PMID: 24836920.
Research supported by the Common Fund’s Extracellular RNA Communication program is laying the foundation for using extracellular RNAs (exRNAs) in saliva to diagnose a variety of diseases, such as cancer, diabetes, autoimmune disorders, and potentially many more. Dr. David Wong and colleagues have conducted the most comprehensive analysis of human exRNAs in saliva to date, and have made several interesting discoveries. One surprising finding is the discovery of approximately 400 circular RNAs in saliva. Circular RNAs were only recently discovered to exist within cells and tissues, and this study marks the first discovery of circular RNAs in any body fluid. The researchers also discovered that saliva contains a significant number of piwi-interacting RNAs (piRNAs), whose functions are largely unknown. In contrast, blood and other body fluids contain very few piRNAs, suggesting that the salivary piRNAs did not originate from RNAs in the blood, and may have originated instead from skin or stem cells within the oral cavity. MicroRNAs (miRNAs), which play important roles in gene regulation, were also found in saliva, and show similar variability between individuals in the saliva samples compared to miRNAs from blood samples or within cells. This result suggests salivary miRNAs may have potential as stable biomarkers that can distinguish between individuals, with the advantage of being easily accessible compared to other body fluids. Together, this research is the first step for future studies on the biological functions of exRNAs in saliva, and opens the door to using salivary exRNAs as non-invasive biomarkers for a number of diseases.
Bahn JH, Zhang Q, Li F, Chan T-M, Lin X, Kim Y, Wong D, and Xiao X. The Landscape of MicroRNA, Piwi-Interacting RNA, and Circular RNA in Human Saliva. Clinical Chemistry, November 2014.
Molecular Libraries Discovery Leads to Phase 1 Clinical Trial for Multiple Myeloma
A compound originally identified with the support of the Molecular Libraries program has led to a drug candidate now entering a Phase 1 clinical trial in patients with multiple myeloma that has proved resistant to two or more established treatment options. The experimental compound, CB-5083, inhibits a protein called p97 that is critical to many cellular functions, including cell division. CB-5083 is derived from a compound called ML240 that was initially identified by Dr. Tsui-Fen Chou, working in the laboratory of Dr. Raymond Deshaies at Caltech. To identify ML240, Drs. Chou and Deshaies collaborated with members of the Molecular Libraries Probe Production Centers Network, including the Scripps Molecular Screening Center and the Specialized Chemistry Center at the University of Kansas. Ongoing research with CB-5083 has shown promise in treating other types of cancer in mice, and Phase 1 clinical trials for CB-5083 in the treatment of solid tumors are expected to start later this year.
Read the press release from Cleave Biosciences.
Read more about the Molecular Libraries contribution to CB-5083 in the Common Fund 10 Year Commemoration Book, under the “Molecular Libraries and Imaging” section.
LINCS Data Harnessed to Help Reveal How Cancer Cells Continuously Reproduce
Cancer, generally speaking, occurs due to unregulated cell reproduction. As cells grow and multiply unchecked they need to produce more proteins, ultimately leading to the formation of tumors. While it has long been known that cancer cells increase their production of proteins, the interface between production of proteins and gene expression in cells has remained unclear. In a 2013 study published in the journal Science, a research team used complex analyses to better understand these interactions. Through the use of Common Fund supported LINCS data, the researchers were able to show that HSF1, a critical cell regulator, was highly controlled by the production of proteins. The LINCS data used for these analyses are a large catalog of how human cells react at the genetic level to changes induced by a vast array of chemicals or interfering genetic molecules. The analyses of the data showed that the response of cells to an agent that blocks proteins from being made is similar to their response when a protein that controls genes is blocked, suggesting that this protein (HSF1) regulates the production of proteins in the cells. This is a key finding in better understanding why cancer cells continue to have energy, while ordinary cells would otherwise be worn out. HSF1 has long been known to be a critical regulator in cancer, playing a large role in maintaining uncontrolled growth. Therefore understanding how HSF1 is controlled is an important finding in the search for improved cancer treatments. In the study, the research team was able to use this information to reverse HSF1 activation and suppress tumor growth in a mouse model. In the model, human leukemia cells were grafted into the mice, showing that the effects have a potentially promising role in humans. These results are very encouraging for future studies that could impact a number of tumor-forming cancers affecting humans.
Santagata S, Mendillo ML, Tang YC, Subramanian A, Perley CC, Roche SP, Wong B, Narayan R, Kwon H, Koeva M, Amon A, Golub TR, Porco JA Jr, Whitesell L, Lindquist S. Tight coordination of protein translation and HSF1 activation supports the anabolic malignant state. Science, July 19, 2013; 341. PMID: 23869022.
REST: The Difference between Destruction and Protection of the Brain
The maintenance of cognitive ability during the aging process has become a significant medical challenge of our time. Alzheimer’s disease (AD), currently having no treatment, is one of the leading causes of death in the United States. A host of other neurodegenerative diseases cause a decline in mental ability that is capable of interfering with daily life. The reasons for the onset of these diseases are still being examined. Earlier studies suggest that neuronal loss was a normal consequence of brain aging; however, neuronal cells are preserved in the aging brain and decline only in the presence of neurodegenerative disease. Much of the research into the causes of diseases resulting in dementia has focused on the abnormal proteins that appear in the brains of people with neurodegenerative diseases; however some people with these abnormal protein clumps show little or no signs of cognitive decline. Why is it that some individuals, even those presenting dementia pathology, age with their cognitive function intact while others develop dementia?
A new study, led by Pioneer awardee, Dr. Bruce Yankner of Harvard Medical School, begins to answer this question. Dr. Yankner and colleagues have discovered a mechanism involving repressor element 1-silencing transcription factor (REST), a repressor of neuronal genes during embryonic development that is down regulated after this stage. The researchers show that REST returns later in life to protect aging neurons from various stresses and regulates a network of genes that mediate cell death, stress resistance and dementia pathology. In an example involving AD, in its early stages, REST disappears from the nucleus, causing the gene network to lose regulation. Further experiments in the study indicate that REST protects neurons from age-related toxic insults and that the elevated REST levels in aging humans are associated with the preservation of cognitive function as well as increased longevity. Additionally, the presence of REST increases the expression of other transcription factors and enzymes that act to resist oxidative stress. REST is also shown to protect against a model of a different dementia disease, Parkinson’s disease, indicating that it might be involved in a stress response that is protective of neurons in a range of dementia diseases. So, even when harboring the abnormal protein clumps associated with dementia diseases, when neuronal REST levels are high, these individuals do not proceed to dementia, suggesting that dementia protein presence may not be enough and that failure of the brain’s stress response system may also be necessary to present cognitive inability. This finding introduces new possibilities for therapeutic intervention.
To read more about this research, please see the publication in Nature.
Please also see the related press release from Dr. Yankner’s institution, Harvard Medical School.
Researchers in the Common Fund’s Extracellular RNA Communication program have discovered a potential treatment for multiple sclerosis (MS), a devastating neurological disorder characterized by muscle weakness, vision problems, difficulty with balance and coordination, and sometimes paralysis. Dr. Richard Kraig and colleagues from the University of Chicago are investigating the therapeutic potential of exosomes, small particles containing biologically active molecules such as RNA and proteins, which are released from cells to travel throughout the body and affect other cells at a distance. Dr. Kraig’s research shows immune cells can be stimulated to produce exosomes that promote formation of myelin to restore the protective insulation around nerve fibers that is damaged in MS. These exosomes contain small pieces of genetic material called microRNAs. Some microRNAs in the exosomes influence immature brain cells to develop into myelin-making cells called oligodendrocytes. Other microRNAs protect against inflammation, thought to contribute to myelin damage in MS. Treatment with exosomes containing these microRNAs increases myelin in both healthy rodent brains and in rat models of demyelination that mimic MS. Importantly, a nasal spray containing exosomes with microRNAs was found to increase myelin in rat brains, suggesting that this type of treatment may be easily administered. In related research, Dr. Kraig and colleagues found that microRNAs in exosomes from young animals and animals living in environmentally enriched conditions also promote myelination, suggesting multiple factors may influence production of microRNA-containing exosomes with therapeutic potential. Further studies will be needed to determine whether exosomal microRNAs can be used to treat patients with MS, but these early studies are a promising first step in developing microRNA-based therapeutics for MS and possibly many other neurological diseases and conditions.
Pusic AD, Pusic KM, Clayton BLL, and Kraig RP. IFNγ-stimulated dendritic cell exosomes as a potential therapeutic for remyelination. Journal of Immunology, Jan. 15, 2014; 266(1-2): 12-23. PMID: 24275061.
Pusic AD and Kraig RP. Youth and environmental enrichment generate serum exosomes containing miR-219 that promote CNS myelination. Glia, Feb. 2014; 62(2): 284-299. PMID: 24339157.
Read about this story in the news:
Naturally Occurring Packets Show Promise for Protecting Nerve Fibers in the Brain
Remyelination: Are Exosomes Containing microRNA the Answer?
Long chains of DNA make up our chromosomes and collectively contain the genetic information needed for our cells to function. However, we can synthesize DNA molecules in the laboratory and put them to use in other ways. Tiny chains of DNA that fold up into variety of 3-dimensional shapes that recognize and bind to a whole host of biological molecules are called aptamers. Because aptamers can target and bind to specific biological molecules within a complex mixture of molecules they are being developed as so-called “affinity reagents” that allow researchers to isolate and study targeted molecules. Large collections of aptamers are generated randomly and are screened for their interactions with target molecules. The aptamers that bind to the target molecule are selected for multiple rounds of testing until only the aptamers best able to recognize and bind to the target molecule survive the increasingly rigorous screening conditions. Dr. Soh, a Protein Capture Reagents Program grantee, and colleagues have developed a method called Quantitative Parallel Aptamer Selection System (QPASS) that enables them to test thousands of selected aptamers simultaneously. QPASS also reduces the number of rounds of screening necessary to find the aptamers that bind best. The increased efficiency in identifying aptamers that bind tightly to specific molecules could make aptamers a feasible and economical reagent for biomedical researchers who wish to isolate and study specific molecules in the future.
QPASS could also make aptamers a useful tool in creating new medical devices. Dr. Soh and his research team developed a sensor that uses aptamers to recognize specific drug molecules. The sensor continuously measures the amount of drug molecules in the bloodstream by recording an electrical signal when aptamers bind to drug molecules. Monitoring this signal over time informed the researchers how much drug was present at any time during of the course of the experiment.
The hope is that aptamers will be a less expensive and more efficient alternative to antibody molecules in research and medical practice. Antibodies are used every day in many diagnostic assays and as therapeutic agents when a certain target biological molecule needs to be recognized. However, antibodies are very complex molecules that are expensive to produce, and difficult to reproduce exactly from batch to batch. Aptamers are relatively straightforward to produce, and once an optimal aptamer has been found, it can be reproduced indefinitely with little or no variation from batch to batch.
Image information: Green drug molecules in the blood bind purple apatmers attached to the sensor. Image source: Ferguson et al. Sci Transl Med 5, 213ra165 (2013). Reprinted with permission from AAAS.
Science published a brief free-access article and video describing the sensor at:
Cho M, Soo Oh S, Nie J, Stewart R, Eisenstein M, Chambers J, Marth JD, Walker F, Thomson JA, Soh HT. Quantitative selection and parallel characterization of aptamers. PNAS, Nov 12, 2013; 110(46): 18460-5. PMID: 24167271.
Drug Sensor Reference:
Ferguson BS, Hoggarth DA, Maliniak D, Ploense K, White RJ, Woodward N, Hsieh K, Bonham AJ, Eisenstein M, Kippin TE, Plaxco KW, Soh HT. Real-time, aptamer-based tracking of circulating therapeutic agents in living animals. Science Translational Medicine. Nov 27, 2013; 5(213): 213ra165. PMID: 24285484.
Read more about the Protein Capture Reagents Program here.
Researchers in the Common Fund’s Epigenomics program have discovered a hidden layer of meaning contained within genes. Dr. John Stamatoyannopoulos at the University of Washington, along with his colleagues, have discovered some regions of DNA serve a double purpose. These regions contain instructions for how to make a protein, as well as information about when and how much of the protein should be made. Scientists previously thought that a particular stretch of DNA could be part of the genetic code, specifying the sequence of amino acid “building blocks” used to make a protein, or part of the regulatory code, containing elements that control expression of the protein. Dr. Stamatoyannopoulos and colleagues have identified “duons,” stretches of DNA within the genetic coding regions that also contain a regulatory sequence called a transcription factor binding site. The researchers created a map showing where transcription factors were bound within genetic coding regions. Looking across 81 diverse human cell types, they found that approximately 15 percent of DNA within genetic coding regions has this dual purpose. This study suggests that mutations within these duons could alter the protein sequence itself, the regulation of the protein, or possibly both simultaneously. These results have important implications for how researchers interpret genetic mutations to provide information about human health and disease.
Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM, Stamatoyannopoulos JA. Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution. Science, Dec. 13, 2013; 342; 1367-1372. PMID: 24337295.
Read the University of Washington press release here.
Read more about the Epigenomics program here.
DNA is perceived to be a stable “blueprint” molecule since it encodes the proteins that function within a cell and also passes genetic information through the generations. However, DNA is actually extremely dynamic in many ways. Just one example of how DNA can be altered in surprising ways is by transposable elements (TEs), also called “jumping genes.” TEs, which make up approximately half the human genome, are sequences of DNA that move from one location in the genome to another. Scientists previously thought that TEs were silenced in the human genome, tagged with epigenetic marks to ensure that TEs are locked in place and prevented from disrupting the normal functions of the genome. It has recently become appreciated that in some cases, TEs play important roles in regulating gene expression. However, it is not well understood how this occurs or how widespread this phenomenon is.
Drs. Ting Wang and Joseph Costello, supported by the Epigenomics program, along with their colleagues, identified epigenetic signatures marking regions of TEs that act as enhancers, regions of DNA that play a role in promoting gene expression. Intriguingly, the epigenetic signatures marking enhancer regions of TEs occur in a tissue-specific manner, and can be used to distinguish different tissues or possibly even cell types within tissues. The researchers also showed that these tissue-specific TE enhancer regions can influence expression of genes known to play important roles in the relevant tissue. For example, a TE region with an epigenomic signature for brain cells, but not immune cells, was found to influence expression of a gene involved in communication between brain cells, and did not influence expression of a gene involved in immune system responses. This research suggests that TEs may play a much more wide-spread role in tissue-specific gene regulation than was previously thought, and highlights the importance of including TEs in models of genetic and epigenetic regulation.
Read more about the Epigenomics program here.
This research also used data from the ENCODE (ENCyclopedia Of DNA Elements) project at the National Human Genome Research Institute (NHGRI). Read more about ENCODE here.
Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, Gascard P, Sigaroudinia M, Tlsty TD, Kadlecek T, Weiss A, O’Geen H, Farnham JP, Madden PA, Mungall AJ, Tam A, Kamoh B, Cho S, Moore R, Hirst M, Marra MA, Costello JF, Wang T. DNA hypomethylation within specific transposable elements families associates with tissue-specific enhancer landscape. Nature Genetics, 2013, Jul; 45(7): 836-41. PMID: 23708189.
More effective therapeutics are needed for numerous conditions affecting people, yet drug development remains inefficient. Investigators supported by the Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program have discovered new insights into the pharmacological properties of drugs that should help us design better therapeutics and more accurately predict their effects. While most studies of drug effects focus on measures of drug potency, e.g., by emphasizing the dose needed to experimentally reduce cell numbers in half, Fallahi-Sichani and colleagues at Harvard Medical School and the Oregon Health and Science University found that other measures of the response of cells to drugs can provide additional insights. They found that different measures are more informative at different doses of the drug response, e.g., some are more informative at higher doses and some at lower doses. They also found that the different measures do not always correlate with each other, e.g., when compared across different drugs or different cell types. Yet some measures correlate with cell type and others with drug class. In addition, the different measures each reveal unique information that contributes insights into the action of the drug. The findings indicate that it is worthwhile to compare multiple parameters when examining the variability of drug effects, and expand the way we should think about parameters of drug activity. In some cases the underlying explanation comes from how individual cells might behave differently from a population of cells.
Fallahi-Sichani M, Honarnejad S, Heiser LM, Gray JW, Sorger PK. Metrics other than potency reveal systematic variation in responses to cancer drugs. Nat Chem Biol. 2013 Sep 8. PMID 24013279.
Using PROMIS measures to evaluate patients’ recall of sexual function and activity reveals mood as a critical biasing factor
The NIH Common Fund Patient-Reported Outcome Measurement Information System® (PROMIS®) program aims to use patient-reported data to change the way clinical information is collected, utilized, and reported. For patients to be able to accurately report their symptoms and health-related quality of life to physicians and other care givers, measures must ask questions that are comprehensible and convey meaning to the patient while not burdening them with too many questions. If such patient reported measures are successfully developed and validated, they have the potential to improve clinical care. One important measure relates to overall sexual health and function, something that is hindered by numerous chronic diseases and conditions as well as their treatments. A new study led by PROMIS investigators at Duke University Medical Center has illustrated that people can remember their sexual function and activity over the previous month reasonably well, but their gender and the mood they feel at the time of reporting can influence what they report. They showed that while both genders overestimated interest in sexual function, males did so to a greater extent. The authors suggest that recall in this capacity could be affected by underlying gender stereotypes. Another major factor directly related to both over- and under-reporting was mood. If the patients were in a positive mood they tended to over-report and if they were in a negative mood they would generally under-report sexual interest. These findings indicate that physicians should consider the mood of their patients’ when administering the questionnaire. The findings from this study may lead to improved methods for accurately determining sexual health and activity, a critical factor in patients’ intimate relationships.
Read the Duke University Medical Center Press Release here
Weinfurt KP, Lin L, Dombeck CB, Broderick JE, Snyder DC, Williams MS, Fawzy MR, Flynn KE. Accuracy of 30-Day Recall for Components of Sexual Function and the Moderating Effects of Gender and Mood. J Sex Med. Jun 26, 2013. PMID: 23802907.
Most cells in the human body contain the same DNA, yet different types of cells have vastly different shapes, sizes, and functions. How do these differences arise? Chemical modifications to DNA and DNA-associated proteins, called epigenetic modifications, help instruct a cell to express only a sub-set of genes, giving rise to different characteristics for different cell types. Epigenetic regulation of gene expression changes during development, and can also change as a result of environmental exposures, pharmaceuticals, aging, and diet. Some epigenetic changes promote health and normal development, while others may contribute to a variety of diseases. Three recent publications in the journal Cell from the Epigenomics program’s Reference Epigenome Mapping Centers reveal important insights about epigenomic changes that take place during development, as non-specialized stem cells differentiate into specific cell types, such as heart, brain, skin, and many more.
Dr. Bing Ren at the San Diego Epigenome Center examined epigenetic events that occur during early embryonic development, as stem cells begin to differentiate into specific cell lineages. Dr. Ren’s work shows that distinct epigenetic mechanisms regulate early and late stages of stem cell differentiation. Interestingly, several gene families that are known to play important roles in development were notably lacking in one type of epigenetic mark, called DNA methylation, in early stages of development. Some of these same genes were found to have excess levels of DNA methylation in cancer, suggesting a possible role for epigenetic regulation of developmental genes in several types of cancer.
An additional study by Drs. Bradley Bernstein and Alexander Meissner, from the Reference Epigenome Mapping Center at the Broad Institute, examined epigenomic changes that occur as human embryonic stem cells differentiate into the three germ layers that develop in an embryo: ectoderm (which becomes epidermis, nervous system, eyes, and ears), mesoderm (which becomes muscle, bone, cartilage, the circulatory system, and the urogenital system), and endoderm (which becomes parts of the gastrointestinal tract, the liver, the pancreas, and the lungs). This study revealed several discrete events that occur during differentiation into each germ layer, providing new insight into how human germ layers are specified during development. Additionally, this information may prove useful to scientists who seek to differentiate induced pluripotent stem cells (iPSCs) for the purpose of repairing or replacing a wide range of tissues damaged by disease or injury.
In a separate study, Drs. Bernstein and Meissner, along with colleagues across the Epigenomics Mapping Consortium, systematically mapped global changes in chromatin, the physical structure of DNA and proteins inside a cell. The conformation of chromatin is regulated by epigenetic factors, leading to changes in gene expression (see “A Scientific Illustration of How Epigenetic Mechanisms Can Affect Health”). By generating over 300 chromatin state maps from diverse human tissues and stem cells, the researchers have discovered signature patterns of “active” chromatin, representing genes that are being expressed, versus “repressed” chromatin, representing genes that are not expressed. During development, chromatin changes from a largely accessible state to a more restrictive state. The chromatin state maps reveal that cells of different developmental stages, or exposed to different environmental conditions, can be distinguished by characteristic differences in chromatin state maps. Prior to this study, much of what scientists knew about chromatin states came from studying cell lines derived from various model organisms.
Collectively, these studies provide a wealth of information about epigenetic dynamics in human cells within different tissues, during various developmental stages, and under a variety of environmental conditions. The extensive data sets available in these publications will be a valuable resource for researchers in a wide range of biomedical fields.
Read more about the Epigenomics program here.
From Dr. Bing Ren:
Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, et al. Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells. Cell, 2013 May 7; http://dx.doi.org/10.1016/j.cell.2013.04.022 . PMID: 23664764.
From Drs. Bernstein and Meissner:
Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghev J, et al. Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells. Cell, 2013 May 7; http://dx.doi.org/10.1016/j.cell.2013.04.037 . PMID: 23664763.
Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, et al. Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues. Cell, 2013 Jan 31; 152(3): 1-13. PMID: 23333102.
Common Fund Supported Investigators Honored by Election to prestigious science academy
Each year, the National Academy of Sciences elects new members in recognition of their distinguished and continuing achievements in original research. Becoming elected as a member of the Academy is regarded as one of the highest honors that a scientist can receive for their academic accomplishments. In 2013, the academy elected a total of 84 new members in conjunction with its 150th annual meeting. Of this select cohort, eight have received funds from the NIH Common Fund to pursue highly innovative biomedical research. Each of these eight senior investigators contributed valuable research with potential for accelerating human health. The newly elected members to the academy who were supported in part through the Common Fund are:
- Barres, Ben A.; professor and chair, department of neurobiology, Stanford University School of Medicine, Stanford, Calif.
- Boeke, Jef D.; professor of molecular biology and genetics, department of molecular biology and genetics, Johns Hopkins University School of Medicine, Baltimore
- Quake, Stephen R.; investigator, Howard Hughes Medical Institute, professor, departments of bioengineering and of applied physics, Stanford University, Stanford, Calif.
- Breaker, Ronald R.; investigator, Howard Hughes Medical Institute, and Henry Ford II Professor, department of molecular, cellular, and developmental biology, Yale University, New Haven, Conn.
- Singer, Robert H.; co-director, Gruss Lipper Biophotonics Center, and professor and co-chair, department of anatomy and structural biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, N.Y.
- Turrigiano, Gina; professor, department of biology, Brandeis University, Waltham, Mass.
- Wagner, Gerhard; Elkan Rogers Blout Professor of Biological Chemistry and Molecular Pharmacology, department of biological chemistry and molecular pharmacology, Harvard Medical School, Boston
- Willard, Huntington F.; Nanaline H. Duke Professor of Genome Sciences and director, Institute for Genome Sciences and Policy, Duke University, Durham, N.C.
New Innovator Harald C. Ott and his colleagues at Massachusetts General Hospital (MGH) have developed a new method to bioengineer kidneys that could someday enable scientists to generate and transplant patient-specific bioengineered organs into patients. Kidneys play a critical role in the maintenance of homeostasis in the body by filtering waste and excess fluid from the blood. There are approximately one million patients in the U.S. with kidney failure, or end-stage renal disease (ESRD); the only possible cure is kidney transplantation. Currently, the waitlist for kidney transplants in the U.S. is more than three years long. Even with successful transplantation there is a high risk for transplant rejection or loss of transplant function over time.
The scientists from MGH were able to remove cells from cadaver kidneys, not normally suitable for transplantation, to create a cell-free kidney scaffold that maintained the protein structure and composition of normal functioning kidneys. Once the host cells were removed, the researchers used human umbilical vein cells and neonate mice kidney cells to repopulate the kidney. Following an incubation that mimics the human body environment, the researchers showed that the patient-specific kidneys had restored function and were able to reabsorb electrolytes and sugars, and produce urine both in the laboratory and in kidneys they transplanted into rats. These bioengineered kidneys could potentially address two major issues currently challenging kidney transplantations. First, they provide the initial steps towards developing kidneys in the lab that can be transplanted into patients, effectively reducing the wait time for critical ESRD patients. Second, developing the technology to repopulate bioengineered kidneys with patient-specific cells could result in a reduction in the risk of kidney rejection after transplantation. While these bioengineered kidneys still need to be developed further before they become a fully implantable treatment option in human patients, this new technology can be applied to other organs, and is leading the way toward organ bioengineering.
- Watch Dr. Ott describe this work on the NatureVideoChannel here
- Read the MGH News Release here
- Read more about the NIH Director’s New Innovator Award Program here.
Song JJ, Guyette JP, Gilpin SE, Gonzalez G, Vacanti JP, Ott HC. Regeneration and Experimental Ortotopic Transplantation of a Bioengineered Kidney. Nature Medicine, April 14, 2012. DOI: 10.1038/nm.3154.
A major challenge to researchers studying the brain has been the inability to study a fully intact brain, from both the global and microscopic perspectives. For example, researchers might want to examine the way a chemical interacts with brain cells, or neurons, both in the context individual neurons and of long neural circuits across the entire brain. Previously, researchers had to choose either to study a fully intact brain, which involves a lengthy sample preparation process and potential structural dissimilarities compared to the original organ, or to study small sections of the brain where one can examine fine molecular and cellular interactions without knowledge of the original complex structure of the neural circuit and structure of the intact brain. Dr. Karl Deisseroth, a 2012 Transformative Research Awardee from Stanford University and his colleagues, have combined tools from the fields of chemical engineering, computational optics, and molecular genetics to develop a new technology to solve this problem by transforming a fully intact mouse brain into a completely clear gel-based brain with all structural and molecular integrity intact. This new technology, named Clear Lipid-exchanged Anatomically Rigid Imaging/immunostaining-compatible Tissue hYdrogel (CLARITY) replaces lipids, or fats, which make the brain appear white outside of the body, and help form the structural basis for the brain, with a clear gel-like material that binds to cells, proteins, DNA, RNA, and other small molecules in the brain. The result is a completely clear brain with a gel-like consistency that maintains the same molecular and cellular relationships and structure as the original brain.
The new process, allows researchers to fluorescently tag small molecules and specific cell types to visualize individual molecular interactions as well as entire cellular networks in 3-D providing insight at both the molecular and whole system level which previously was not possible. CLARITY can be used by researchers to observe fine details of brains from animals and human patients with symptomatic neurological diseases without losing the larger-scale whole system perspective, potentially leading to new insights into diseases that affect the brain.
- Read more about this exciting new technology and watch videos of mouse brains transformed using CLARITY in the NIH Press Release here
- Read about this exciting new technology in the NIH Director’s Blog here
- Read the New York Times Article here
Chung K, Wallace J, Kim S-Y, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K. Structural and molecular interrogation of intact biological systems. Nature, April 10, 2012. DOI: 10.1038/Nature12107.
A team of scientists at the Oak Ridge National Laboratory (ORNL) funded by the NIH Common Fund Human Microbiome Project (HMP) have made new discoveries about a microbe that is important in human oral health. Using cutting-edge technology, the team was able to complete full sequencing of the genome from a single cell. The ability to isolate just a single bacterial cell and sequence the genome is an important component of examining the human microbiome because it allows for the study of species that cannot be cultured in the lab. The organism the examined is most closely related to sulfate reducers, which are normally found in salt marshes, sewer pipes, hot springs, and surprisingly the human mouth. Studies have shown that this type of bacteria is elevated in patients suffering from periodontitis, a disease marked by swelling and infection of areas that support our teeth. New findings presented in the current study show that this species uses a unique coding scheme that likely allows it to successfully compete in the complex oral microbial environment. The technology advancement and scientific findings reported in this study will increase our understanding of the role that our microbes play in oral health.
Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, Söll D, Podar M. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci USA 2013, Mar 18. PMID: 23509275.
More than 60,000 patients in the United States undergo general anesthesia for surgery every day. Currently, doctors use indirect measures of the brain state, such as heart rate and blood pressure, along with drug pharmacokinetics, pharmacodynamics and exhaled anesthetic gas typically are converted to a simple index score to indicate if a patient is adequately anesthetized during surgery. These indices are neither entirely reliable nor very informative. Inadequately administered anesthesia can result in intraoperative awareness and post-operative delirium. Drs. Emery N. Brown and Patrick L. Purdon, former NIH Director’s Pioneer Awardee and current NIH Director’s New Innovator Awardee, respectively, have studied brain activity during propofol-induced anesthesia using electroencephalogram (EEG) technology, which measures scalp electrical potentials, to better understand the mechanism of unconsciousness and to establish a direct method of tracking the transition between consciousness and unconsciousness during general anesthesia. In this study, the researchers gradually administered and reduced the anesthesia drug propofol in patients, while monitoring brain activity and behavioral loss of consciousness by asking patients to respond to auditory stimuli. This gradual induction and emergence from anesthesia allowed the researchers to precisely define an EEG brain signature, as well as behavioral markers that are associated with consciousness, unconsciousness, and the transition between these two states in patients undergoing propofol-induced general anesthesia. This research has provided a deeper understanding of the mechanism of propofol-induced loss of consciousness, and could be used to determine the EEG brain signatures of other anesthetics. Additionally, these results could be used to develop more direct and reliable methods for monitoring brain states of patients undergoing general anesthesia and could lead to new insights into the tailoring of drug dosage in real-time.
P. L. Purdon et al., Electroencephalogram signatures of loss and recovery of consciousness from propofol. Proceedings of the National Academy of Sciences, (March 4, 2013, 2013).
New approach to attacking viruses: Researchers discover effective inhibitor to control herpesvirus infection and reactivation
Members of the herpesvirus family establish life-long dormant infections in people that can reactivate at any time to cause disease. Presently, there has been a focus on treatments that target the late stages of infection in those with herpes, particularly simplex virus (HSV) types 1 and 2, which cause oral and genital herpes. Furthermore, serious illness occurs when immune-compromised patients previously infected with another type of herepesvirus, human cytomegalovirus (CMV) suffer a reactivation. To date, drugs have been developed to target late stages of infection, with some success. In a new study, a probe developed from the NIH Chemical Genomics Center (NCGC), which is funded by the NIH Common Fund Molecular Libraries program, has been shown to be effective during lab studies at repressing early expression genes and therefore preventing infections from establishing. This molecule works by targeting human proteins to fight infections. Their studies also demonstrate that reactivation can be inhibited by the probe compound. Overall, there are implications for the prevention of infections as well as long-term treatment in infected patient to prevent reactivation episodes. This new area of research is beginning to show results for a number of viral diseases.
Read more about this research advance here.
Liang Y, Vogel JL, Arbuckle JH, Rai G, Jadhav A, Simeonov A, Maloney DJ, Kristie TM. Targeting the JMJD2 Histone Demethylases to Epigenetically Control Herpesvirus Infection and Reactivation from Latency. Sci Transl Med. 2013 Jan 9. PMID: 23303604.
Three NIH Common Fund Awardees, Drs. Titia de Lange, Eric S. Lander, and Lewis C. Cantley, were selected as inaugural winners of the Breakthrough Prize administered by the Breakthrough Prize in Life Sciences Foundation. The Breakthrough Prize in Life Sciences Foundation is a non-profit corporation, founded by technology innovators, Sergey Brin and Anne Wojcicki, Mark Zuckerberg and Priscilla Chan, and Yuri Milner, developed with the goal of “advancing breakthrough research, celebrating scientists and generating excitement about the pursuit of science as a career.” Prizes are awarded based on past achievement, and in addition to the distinction of the being an awardee, winners receive three-million dollars to inspire more freedom and opportunity to pursue groundbreaking research.
Dr. Titia de Lange, a 2005 NIH Director’s Pioneer Award recipient, and Leon Hess Professor at the Rockefeller University, was selected for her trailblazing work on telomeres, illuminating how they protect chromosome ends and their role in genome instability in cancer. Drs. Lander and Cantley both received funds through the NIH Common Fund Molecular Libraries program. Dr. Lander, President and Founding Director of the Broad Institute of Harvard and MIT and Professor of Biology at MIT, was selected for the discovery of general principles for identifying human disease genes, and enabling their application to medicine. Dr. Cantley, Margaret and Herman Sokol Professor and Director of the Cancer Center at Weill Cornell Medical College and New York Presbyterian Hospital was awarded the prize for the discovery of PI 3-Kinase and its role in cancer metabolism.
Read more about NIH-funded scientists in the inaugural class of laureates on the NIH Director’s Blog here.
Read more about the Breakthrough Prize in Life Sciences Foundation, the Breakthrough Prize in Life Sciences Award, and the eleven inaugural awardees here.