National Institutes of Health to expand ENCODE project

The National Institutes of Health plans to expand its Encyclopedia of DNA Elements (ENCODE) Project, a genomics resource used by many scientists to study human health and disease. Funded by the National Human Genome Research Institute (NHGRI), part of NIH, the ENCODE Project is generating a catalog of all the genes and regulatory elements the parts of the genome that control whether genes are active or not in humans and select model organisms. With four years of additional support, NHGRI builds on a long-standing commitment to developing freely available genomics resources for use by the scientific community.

The genome in three dimensions folds up, forming loops and other shapes, to fit inside the nucleus.
Credit: Ernesto Del Aguila, NHGRI

“ENCODE has created high-quality and easily accessible sets of data, tools and analyses that are being used extensively in studies to interpret genome sequences and to understand the consequence of genomic variation,” said Elise Feingold, Ph.D., a program director in the Division of Genome Sciences at NHGRI. “These awards provide the opportunity to strengthen this foundation by expanding the breadth and depth of the resource.”

Since launching in 2003, ENCODE has funded a network of researchers to develop and apply methods for mapping candidate functional elements in the genome, and to analyze the enormous database of generated genomic information. The data and tools generated by ENCODE are organized by two groups: a data coordinating center, which houses the data and provides access to the resource through an open-access portal, and a data analysis center, which synthesizes the data into an encyclopedia for use by the research community.

Pending the availability of funds, NHGRI plans to commit up to $31.5 million in the fiscal year 2017 for these awards. With this funding, ENCODE will expand the scope of these efforts to include characterization centers, which will study the biological role that candidate functional elements may play and develop methods to determine how they contribute to gene regulation in a variety of cell types and model systems. Additionally, the project will enhance the ENCODE catalog by developing a way to incorporate data provided by the research community, and will use biological samples from research participants who have explicitly consented for unrestricted sharing of their genomic data.

More information about ENCODE project.
Adapted from press release by National Human Genome Research Institute.

Role of protein TRAP1 in Prostate cancer

Scientists at The Wistar Institute have demonstrated how a protein called TRAP1 – an important regulator of energy production in healthy and cancerous cells – is an important driver of prostate cancer and appears to be a valuable therapeutic target for the disease. The findings were published in the Journal of Biological Chemistry.

TRAP1 is a chaperone protein that is structurally similar to heat shock protein 90 (HSP90), which is found in larger amounts in the mitochondria of cancer cells. In a prior study, Dario C. Altieri, M.D., president and CEO of The Wistar Institute, director of The Wistar Institute Cancer Center, the Robert & Penny Fox Distinguished Professor, and colleagues bred mice with the TRAP1 protein “knocked out” to determine what impact it may have on disease. These special mice lived longer and experienced fewer age-related illnesses, suggesting that the protein played an important role in disease.

In this study, instead of removing the TRAP1 protein, the Altieri laboratory generated mice with the TRAP1 protein overexpressed. Additionally, the mice were bred to lose one copy of the PTEN gene, which is an important tumor suppressor gene. At least one copy of PTEN is deleted in about 40 percent of cases of prostate cancer and is often found in more aggressive tumors, so mice without this gene more accurately simulate the behavior of the disease.

The combination of increased TRAP1 coupled with the loss of PTEN resulted in aggressive, early-onset invasive prostate cancer, according to the study. Altieri and colleagues found increased tumor cell proliferation, inhibition of apoptosis (a form of programmed cell death that is thought to halt the progression of tumor cells), and increased epithelial cell invasion. These findings suggest that TRAP1 has a role in promoting the mitochondrial “fitness” of a prostate tumor, making it more aggressive and less responsive to treatment.

“What is exciting about these findings is the fact that we believe TRAP1 is a druggable target,” Altieri said. “We are continuing to advance our promising research and development program aimed at targeting the mitochondria in tumors.”

Citation: Lisanti, Sofia, David S. Garlick, Kelly G. Bryant, Michele Tavecchio, Gordon B. Mills, Yiling Lu, Andrew V. Kossenkov, Louise C. Showe, Lucia R. Languino, and Dario C. Altieri. “Transgenic Expression of Mitochondrial Chaperone TRAP1 Accelerates Prostate Cancer Development.” Journal of Biological Chemistry (2016): jbc-M116.
Research funding: NIH/National Cancer Institute, Office of the Assistant Secretary of Defense for Health Affairs through the Prostate Cancer Research Program, Prostate Cancer Foundation.
Adapted from press release by The Wistar Institute 

Genetic signature for Rhabdoid meningioma discovered

Meningiomas are the most common primary brain tumors, but the term encompasses over a dozen subtypes that range from benign to highly aggressive. Rhabdoid meningiomas are classified as highly aggressive due to their high rates of recurrence and mortality, but the experience and outcomes for patients with this rare form of brain tumor vary widely. Researchers from Brigham and Women’s Hospital, in collaboration with colleagues at Massachusetts General Hospital, have identified genetic mutations in this form of brain cancer that can distinguish aggressive rhabdoid meningiomas from more benign forms using routine laboratory tests. The work is published in the journal Neuro-Oncology.

BAP1 immunohistochemistry of a rhabdoid meningioma
sample from a patient that carries a BAP1 mutation. The
protein is completely lost in the tumor cells but is still fully
maintained in normal blood vessel cells and in infiltrating
fibroblasts and immune cells.
Credit: Sandro Santagata, Brigham and Women’s Hospital

Usually, rhabdoid meningiomas are classified based on physical appearance and characteristics, but these enigmatic tumors can be difficult for pathologists to accurately classify. To find a molecular fingerprint that could help identify rhabdoid meningioma, Santagata and his colleagues sequenced 560 cancer-related genes from 14 meningiomas. In one sample, the team detected a mutation in the BAP1 gene along with telltale physical features (such as the shape of the tumor cells) of rhabdoid meningioma. Previous studies had found that people with inherited mutations in the BAP1 gene that cause a loss of BAP1 protein are prone to a tumor predisposition syndrome – a condition that puts them at a very high risk of developing several kinds of tumors including tumors in the eye, lung, kidney and elsewhere. But primary brain tumors had not been associated with the syndrome before.

The team went on to analyze samples from 47 patients with rhabdoid meningiomas as well as 265 additional meningiomas of diverse subtypes and grades. None of the non-rhabdoid meningiomas had a loss of BAP1. However, five of the 47 patients with rhabdoid meningiomas did have mutations or deletions affecting BAP1. These patients had poor clinical outcomes: two died of the disease and two had multiple cases of recurrence; clinical follow-up information was not available for the fifth. For those patients with intact BAP1, average time of disease progression was 116 months; for the patients with BAP1 mutations, it was only 26 months.

The presence or absence of BAP1 can be monitored with a simple and inexpensive test known as immunohistochemistry – in which a tissue sample is collected and stained for a particular protein. This approach is currently in routine use for characterizing samples of an eye cancer known as uveal melanoma and a tumor that arises from the linings of the chest and abdomen known as mesothelioma – forms of cancer tied to the tumor predisposition syndrome.

The number of cases of rhabdoid meningioma studied in this work was small; larger studies will be needed to determine the prevalence of BAP1 mutations in rhabdoid meningiomas and to assess the impact of their detection on clinical care. However, the new work strongly suggests that a careful assessment of family history is a critical for patients who develop rhabdoid meningiomas and that patients with BAP1 negative tumors may warrant more careful observation and focused care.

“Testing for BAP1 in rhabdoid meningiomas could be performed routinely and at a low cost, with the potential to change the course of clinical care and avoid overtreatment or to identify those who may need more aggressive therapy,” said Santagata. “We hope that this new work will offer insights for clinicians and patients alike as they seek more information on these tumors.”

Citation:Germline and somatic BAP1 mutations in high-grade rhabdoid meningiomas”.
Ganesh M. Shankar, Malak Abedalthagafi, Rachael A. Vaubel, Parker H. Merrill, Naema Nayyar, Corey M. Gill, Ryan Brewster, Wenya Linda Bi, Pankaj K. Agarwalla, Aaron R. Thorner, David A. Reardon, Ossama Al-Mefty, Patrick Y. Wen, Brian M. Alexander, Paul van Hummelen, Tracy T. Batchelor, Keith L. Ligon, Azra H. Ligon, Matthew Meyerson, Ian F. Dunn, Rameen Beroukhim, David N. Louis, Arie Perry, Scott L. Carter, Caterina Giannini, William T. Curry Jr, Daniel P. Cahill, Frederick G. Barker II, Priscilla K. Brastianos and Sandro Santagata. Neuro-Oncology. 2016 pp: now235
Research funding: Brain Science Foundation, Jared Branfman Sunflowers for Life Fund for Pediatric Brain and Spinal Cancer Research, King Abdulaziz City for Science and Technology Saudi Arabia, Ludwig Center at Harvard, National Institutes of Health, Susan G. Komen
Adapted from press release by Brigham and Women’s Hospital.

Signaling pathway that controls blood vessel development in brain has ability stop medulloblastoma, a cerebellar tumor.

A research team at the Krembil Research Institute has discovered that a signaling pathway which controls blood vessel development in the brain has the ability to stop brain tumor formation in animal models of medulloblastoma, the most common malignant brain tumor diagnosed in children.

The findings, published in the journal eLife, are the first to show that blocking a signaling pathway called Norrin/Frizzled4 (Fzd4) drives changes in the support structures that surround pre-cancer cells and promotes medulloblastoma development in subjects that are genetically susceptible to the disease. Researchers found that blocking the Norrin/Fzd4 signal created more opportunities to form pre-cancerous growths and speed up tumour initiation. This work also suggests that an activated pathway may therefore block tumour formation.

“Our study brings a new dimension to our understanding of Medulloblastoma,” says Dr. Valerie Wallace, principal investigator of the study, Norrin/Frizzled4 Signaling in the Preneoplastic Niche Blocks Medulloblastoma Initiation, and Co-Director of the Donald K. Johnson Eye Institute.

The research, which was carried out in large part by Dr. Erin Bassett and Mr. Nicholas Tokarew, was initiated at the Ottawa Hospital Research Institute and continued at the Krembil Research Institute after Dr. Wallace relocated to Toronto. The discovery came from replication of a human condition called Gorlin Syndrome in lab experiments. People with Gorlin Syndrome have one copy of a tumour-suppressing gene instead of two, which makes them susceptible to medulloblastoma.

The team’s next step will be to investigate how the blood vessels impacted by Norrin/Fzd4 signaling communicate with pre-cancerous cells to make them more likely to become malignant.

Citation: Bassett, Erin A., Nicholas Tokarew, Ema A. Allemano, Chantal Mazerolle, Katy Morin, Alan J. Mears, Brian McNeill et al. “Norrin/Frizzled4 signalling in the preneoplastic niche blocks medulloblastoma initiation.” eLife 5 (2016): e16764.
Research funding: Canadian Cancer Society, Cancer Research Society
Adapted from press release by University Health Network Ca

Research finds role of Messenger RNA in Huntington’s disease patholgy

A research effort at the Centre for Genomic Regulation in Barcelona, Spain, reveals new molecular mechanisms of Huntington’s disease. The results, published in The Journal of Clinical Investigation, question the approaches used up to now for treatment of the disease. They also point to messenger RNA as a key pathogenic component that will make it possible to define new therapeutic strategies.

Fluorescent detection of foci in red fibroblasts of patients with
Huntington’s disease. Up: cells showing mutated RNA foci.
Down: Cells with blocked RNA do not show foci.
Credit: Centre for Genoic Regulation

Huntington’s disease is a neurodegenerative disease that is presently incurable. Scientists around the world are researching its causes and molecular processes in the attempt to find a treatment. Huntington’s disease is caused by the excessive repetition of a nucleotide triplet (CAG) in the Huntingtin gene. The number of CAG repetitions varies from person to person. Healthy individuals can have up to 36 repetitions. Nevertheless, as of 36 repetitions, Huntington’s disease develops. The direct consequence of this excess of repetitions is the synthesis of a mutated protein–different from what would be obtained without the additional CAG repetitions–which has been considered the main cause of the disease for the past 20 years.

The research by a group of scientists from the Centre for Genomic Regulation (CRG) led by Eulàlia Martí, in cooperation with researchers from the University of Barcelona (UB) and August Pi i Sunyer Biomedical Research Institute (IDIBAPS), has brought to light new information on the molecular mechanisms that cause Huntington’s disease, and defines new pathways to therapy discovery.

What we have observed in our study is that the mutated fragment acting as a conveyor–the so-called messenger RNA–is key in the pathogenesis,” says Dr. Eulàlia Martí, lead author of the research project, together with Xavier Estivill, and acting group leader of the Genes and Disease laboratory at the Centre for Genomic Regulation. “The research on this disease being done by most groups around the world seeking new therapeutic strategies focuses on trying to prevent expression of the mutated protein. Our work suggests that blocking the activity of messenger RNA (the “conveyor”), would be enough to revert the alterations associated with Huntington’s disease. We hope this will contribute to improving the strategies in place to find a cure,” states the researcher.

Going deeper in molecular mechanisms enables progress to future applications. This work underscores the importance of rethinking the mechanisms behind illnesses in order to find new treatments. The work of scientists at the CRG has helped explore the molecular mechanisms that cause the disease. Now, their results will contribute to better delimit research efforts towards a cure.

As opposed to most other research groups, Eulàlia Martí’s team has sought to identify whether the problem resided in the messenger RNA – which would be the copy responsible for manufacturing the protein – or in the resulting protein. Prior work indicated that mRNA produced, in addition to defective protein, other damages. This previous work was the starting point for Martí and her fellow researchers, who have finally demonstrated that mRNA has a key role in the pathogenesis of Huntington’s chorea. “The research we have just published points to RNA’s clear role in Huntington’s disease. This information is very important in translational research to take on new treatments,” says the researcher.

More in-depth studies on these mechanisms are yet to be done. For example, research must explore whether it will be possible to revert the effects of Huntington’s disease in patients, just as researchers have demonstrated in mouse models. It also remains to be seen whether the proposal of the CRG researchers can be used in a preventive way, as the disease does not generally appear until after 40 years of age (in humans). Despite the remaining gaps, the published work makes for a key step in knowledge of the mechanisms of this neurodegenerative disease that, as of today, remains incurable.

Citation: Rué, Laura, Mónica Bañez-Coronel, Jordi Creus-Muncunill, Albert Giralt, Rafael Alcalá-Vida, Gartze Mentxaka, Birgit Kagerbauer et al. “Targeting CAG repeat RNAs reduces Huntington’s disease phenotype independently of huntingtin levels.” The Journal of Clinical Investigation 126, no. 11 (2016).
Adapted from press release by Centre for Genomic Regulation

New approach to treating cancer with therapeutic short interfering RNA (siRNA) delivered by nanohydrogel nanoparticles

A novel targeted therapy using nanoparticles has enabled researchers at the Georgia Institute of Technology to purge ovarian tumors in limited, in vivo tests in mice. “The dramatic effect we see is the massive reduction or complete eradication of the tumor, when the ‘nanohydrogel’ treatment is given in combination with existing chemotherapy,” said chief researcher John McDonald.

That nanohydrogel is a minute gel pellet that honed in on malignant cells with a payload of an RNA strand. The RNA entered the cell, where it knocked down a protein gone awry that is involved in many forms of cancer.

In trials on mice, it put the brakes on ovarian cancer growth and broke down resistance to chemotherapy. That allowed a common chemotherapy drug, cisplatin, to drastically reduce or eliminate large carcinomas with very similar speed and manner. The successful results in treatment of four mice with the combination of siRNA and cisplatin showed little variance.

The therapeutic short interfering RNA (siRNA) developed by McDonald and Georgia Tech researchers Minati Satpathy and Roman Mezencev, thwarted cancer-causing overproduction of cell structures called epidermal growth factor receptors (EGFRs), which extend out of the wall of certain cell types. EGFR overproduction is associated with aggressive cancers. The nanohydrogel that delivers the siRNA to the cancer cells is a colloid ball of a common, compact organic molecule and about 98 percent water. Another molecule is added to the surface of the nanohydrogel as a guide. In the in vivo trials, the siRNA, which contained a fluorescent tag, allowed researchers to observe nanoparticles successfully honing in on the cancer cells.

The researchers from Georgia Tech’s School of Biological Sciences published their results on Monday, November 7, 2016, in the journal Scientific Reports.

The new treatment has not been tested on humans, and research would be required by science and by law to demonstrate consistent results – efficacy – among other things, before preliminary human trials could become possible.

Citation: Minati Satpathy, Roman Mezencev, Lijuan Wang & John F. McDonald. “Targeted in vivo delivery of EGFR siRNA inhibits ovarian cancer growth and enhances drug sensitivity”
Scientific Reports 6, Article number: 36518 (2016)
Research funding: National Institutes of Health’s IMAT Program, Ovarian Cancer Institute, Deborah Nash Endowment Fund, Curci Foundation and Markel Foundation.
Adapted from press release by Georgia Institute of Technology

Researchers map short RNA molecules in single cell

Researchers at Karolinska Institutet have measured the absolute numbers of short, non-coding, RNA sequences in individual embryonic stem cells. The new method could improve the understanding of how our genes are regulated and different cell types develop.

When information in our genes is used, for example to build a protein, it is first translated to messenger-RNA which functions as a blueprint for the protein. Our cells also contain non-coding, short, RNA sequences that do not contribute to the formation of proteins and whose functions are partly unknown. The best known of these is micro RNA (miRNAs), which can interact with the messenger RNA, and thereby regulate genes and cell function.

Researchers at Karolinska Institutet have now mapped the presence of short RNA-sequences in an individual cell. Previous research on short RNA molecules is based on analysis of many cells simultaneously, making it difficult to study the precise function.

“Our knowledge of the function of short RNA molecules is quite general. We have a picture of the general mechanisms, but it is less clear what specific role these molecules play in different types of cells or diseases,” says Rickard Sandberg, professor at the Department of Cell and Molecular Biology, who is also affiliated to the Stockholm center of Ludwig Cancer Research.

The analysis was done using single-cell transcriptomics, a technique which makes it possible to measure the absolute numbers of short RNA molecules in a cell. Two types of embryonic stem cells were used, intended to mimic the early embryo, before and after it has attached to the uterine lining.

The researchers could detect large numbers of small RNAs in both cell states, including miRNA as well as shorter RNA fragments (tRNA and snoRNA) whose function is largely unknown. The researchers also found that large numbers of miRNAs are expressed differently in the two cell states.

“This is basic research and a demonstration that the method works, giving suggestions for further research. To map the levels of short RNA molecules in a cell is a first step in identifying the specific function of these molecules,” says Omid Faridani, one of the lead authors of the study. In the long run, Rickard Sandberg can imagine clinical applications of the method.

Citation: Faridani, Omid R., Ilgar Abdullayev, Michael Hagemann-Jensen, John P. Schell, Fredrik Lanner, and Rickard Sandberg. “Single-cell sequencing of the small-RNA transcriptome.” Nature Biotechnology (2016).
Adapted from press release by Karolinska Institutet

Study finds that hybrid structures composed of DNA and RNA and enzyme RNase H play important role in DNA repair

Scientists at The Australian National University (ANU) and Heidelberg University in Germany have found an essential component in the DNA repair process which could open the door to the development of new cancer drugs.

Lead researcher Associate Professor Tamás Fischer from ANU said the research found hybrid structures composed of DNA and RNA play an important role in restoring the genetic information after the DNA is damaged. RNAs are short-lived copies of the genetic information stored in DNA. The study also discovered that RNase H enzymes that target these hybrid structures are also essential for the efficient and precise repair of damaged DNA.

“This discovery opens the possibility for the development of new drugs that can target these enzymes, modulate their activity and block or enhance the efficiency of this important DNA repair pathway,” Dr Fischer said.  He said the accumulation of mutations in the human genome was the main driving force behind ageing-related diseases and cancer development.

“RNase H enzymes have been studied and used in molecular biology for many years but their biological function was not entirely clear until now.  

Dr Fischer said one of the most surprising findings was that RNA – DNA hybrids, which were previously thought to only negatively affect the integrity of the human genome – are actually also involved in protecting the DNA.

Citation: Ohle, Corina, Rafael Tesorero, Géza Schermann, Nikolay Dobrev, Irmgard Sinning, and Tamás Fischer. “Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair.” Cell (2016).
Adapted from press release by The Australian National University and Heidelberg University