New targeted epigenetic therapy for lymphoma shows promise

New compounds targeting epigenetics have shown promise in treating patients with lymphoma, according to data presented at the Targeted Anticancer Therapies International Congress 2018 in Paris, France. ESMO’s phase-I oncology meeting featured early clinical studies with BET inhibitors and EZH2 inhibitors.

Dr. Anastasios Stathis, head of the New Drugs Development Unit of the Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland, was one of the first oncologists to research this field. He said BET inhibitors had shown some activity in leukemia, lymphoma and also a rare and aggressive solid tumor driven by a translocation involving BET genes called NUT carcinoma. His previous phase I research on the first-in-class BET inhibitor birabresib (OTX015/MK-8628) showed some activity in diffuse large B-cell lymphoma, providing proof-of-concept for this approach. (1)

Subsequently, birabresib was used on a single-patient compassionate basis in four patients with NUT carcinoma. Stathis said: “This was the first evidence that preclinical findings with BET inhibitors in models of NUT carcinoma could be translated into activity in patients.” (2)

Multiple BET inhibitors have been studied in clinical trials, and preliminary results have confirmed that they may be effective in patients with diffuse large B-cell lymphoma and NUT carcinoma. (3) Some of the significant side effects include Thrombocytopaenia which appears to be dose-limiting and is reversible and not accompanied by major bleeding events, fatigue and gastrointestinal symptoms.

Regarding activity, patients do eventually progress on treatment, and the duration of response is unknown. Stathis said: “It’s not clear what the real clinical impact of BET inhibitors could be. Compounds approved for lymphoma in the last five years had single-agent phase-I response rates above 30%, but activity with BET inhibitors is less than 30%. The hope is to identify the patients that would benefit most and test BET inhibitors in combination with other compounds. Also, there are new classes of BET inhibitors in preclinical studies, and we need to wait to see if they have better activity.”

Another area where clinical data is emerging is related to EZH2 inhibitors for which data will be presented at Targeted Anticancer Therapies International Congress 2018. EZH2 is a protein that exhibits relatively frequent mutations in lymphoma. Results will be presented from a study in patients with B-cell lymphoma showing evidence of antitumor activity with an EZH2 inhibitor, which was well tolerated and had manageable toxicities. (4) Study author Dr. Adrian Senderowicz of Constellation Pharmaceuticals, Cambridge, US, said: “If approved by health authorities, EZH2 inhibition may become a new treatment paradigm in relapse or refractory EZH2 mutant follicular lymphoma patients.”

A previous study showed that another EZH2 inhibitor, tazemetostat, induced objective response rates of 92% in patients with EZH2 mutant follicular lymphoma and 26% in those with the wild-type. (5) Stathis said: “The question is whether it makes sense to treat patients without the mutation since the response is so much lower. However, these patients do show some response and researchers want to know why.”

Stathis said: “We do have proof, and we will see further evidence at TAT 2018, that epigenetics are a promising target in lymphomas.”

Citations:

1 Amorim S, Stathis A, Gleeson M, et al. Bromodomain inhibitor OTX015 in patients with lymphoma or multiple myeloma: a dose-escalation, open-label, pharmacokinetic, phase 1 study. Lancet Haematol. 2016;3(4):e196-204. doi: 10.1016/S2352-3026(16)00021-1.

2 Stathis A, Zucca E, Bekradda M, et al. Clinical Response of Carcinomas Harboring the BRD4-NUT Oncoprotein to the Targeted Bromodomain Inhibitor OTX015/MK-8628. Cancer Discov. 2016;6(5):492-500. doi: 10.1158/2159-8290.CD-15-1335.

3 Stathis A, Bertoni F. BET Proteins as Targets for Anticancer Treatment. Cancer Discov. 2018;8(1):24-36. doi: 10.1158/2159-8290.CD-17-0605.

4 Abstract 42O ‘A Phase 1 Study of CPI-1205, a Small Molecule Inhibitor of EZH2, Preliminary Safety in Patients with B-Cell Lymphomas’: presented by Adrian Senderowicz during Proffered Paper Session 2 on Tuesday, 6 March, 11:00 to 12:30 (CET) in Room Scene AB.

5 Morschhauser F, Salles G, McKay P, et al. Interim report from a phase 2 multicenter study of tazemetostat, an EZH2 inhibitor, in patients with relapsed or refractory B-cell non-Hodgkin lymphomas. Hematol Oncol. 2017;35(S2):24-25. https://doi.org/10.1002/hon.2437_3

Adapted from press release by European Society of Medical Oncology.

The role of PRC2 in controlling gene activity in human stem cells.

Researchers at the Babraham Institute have revealed a new understanding of the molecular switches that control gene activity in human embryonic stem cells.

In the developing embryo and during the specialisation of stem cells, the activity of genes must be tightly controlled so that the correct genes are switched on and off at the right time and in the right cells. One of the main ways that this process is regulated is by a protein complex called Polycomb Repressive Complex 2 (PRC2), which keeps genes switched off until they are needed. Earlier research showed that PRC2 is necessary for controlling gene activity during the development of the fruit fly and the mouse. Current research study focusses PRC2’s role in human embryonic stem cells.

As described in the journal Cell Reports, the researchers used the CRISPR gene editing technique to delete PRC2 from human embryonic stem cells. Loss of PRC2 caused the cells to switch on many genes that are not normally active in these cells. These changes led to the inability of embryonic stem cells lacking PRC2 to specialize correctly into mature cell types.

Dr Peter Rugg-Gunn, senior author on the research paper and research group leader at the Babraham Institute explained: “This work is exciting because it reveals that gene activity is controlled by similar molecular switches in human development as in other species such as the fly and mouse. We have also uncovered human-specific differences in the way that embryonic stem cells respond to genes being misregulated. These findings provide new insights into the development of our own species, and might enable new ways to turn embryonic stem cells into useful cell types, such as heart and pancreas, which can be used for cell-replacement therapies.”

References: Collinson, Adam, Amanda J. Collier, Natasha P. Morgan, Arnold R. Sienerth, Tamir Chandra, Simon Andrews, and Peter J. Rugg-Gunn. “Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells.” Cell Reports 17, no. 10 (2016): 2700-714.
doi:10.1016/j.celrep.2016.11.032.
Research funding: The Wellcome Trust, Medical Research Council, Biotechnology and Biological Sciences Research Council.
Adapted from press release by Babraham Institute.

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.

Obesity related Epigenetic changes in DNA

Obesity has been linked to “letter” changes at many different sites in the genome, yet these differences do not fully explain the variation in people’s body mass index (BMI) or why some overweight people develop health complications while others don’t. A large study from Boston Children’s Hospital, the University of Edinburgh, the Harvard School of Public Health, the Framingham Heart Study and the National Heart, Lung, and Blood Institute (NHLBI) provides more insight, linking obesity with epigenetic modifications to DNA that in turn are tied to an increased risk of weight-related health problems such as coronary artery disease.

The study is one of the largest to date to examine the link between BMI, obesity-related disease and DNA methylation  a type of epigenetic modification that influences whether genes are turned on or off. Findings were published in PLoS Medicine.

“Even though we’ve genetically sequenced more and more people at greater and greater breadth and depth, we haven’t completely explained who develops obesity and why,” says Michael Mendelson, MD, ScM, a pediatric cardiologist with the Preventive Cardiology Program at Boston Children’s Hospital, who shared first authorship on the paper with Riccardo Marioni of the University of Edinburgh. “We found that obesity is related to widespread changes in DNA methylation. Unlike your DNA sequence, these regulatory modifications change over time and can influence your risk of disease in later life.”

The researchers studied blood samples from 7,800 adults from the Framingham Heart Study, the Lothian Birth Cohort and three other population studies. They systematically looked for markers of DNA methylation at more than 400,000 sites in the genome. They then looked to see if these markers differed according to BMI in a predictable pattern.

Their analysis identified strong associations between BMI and DNA methylation at 83 locations in 62 different genes. Methylation at these sites was, in turn, associated with differences in the expression of genes involved in energy balance and lipid metabolism.

When Mendelson and colleagues scored people in the study for how many methylation changes they had, they found that the more changes, the greater their BMI. The methylation score captured 18 percent of the variation in BMI when tested in a separate population. For each standard deviation increase in the score, the odds ratio for obesity was 2.8 times higher.

The researchers then applied a statistical technique called Mendelian randomization, which provides supportive evidence that a detected association is causal. They concluded that 16 of the 83 identified sites in the genome were differently methylated as a result of obesity, a finding that held true across people of different ethnicities.

Difference in methylation at one gene, SREBF1, appeared to be causative of obesity and was clearly linked with unhealthy blood lipid profiles, glycemic traits (a risk factor for diabetes) and coronary artery disease. It encodes a known regulator of lipid metabolism and could be a target for a drug treatment, the researchers say.

“Taken together, these results suggest that epigenetic modifications may help identify therapeutic targets to prevent or treat obesity-related disease in the population,” says Mendelson, who is also a research fellow in the Population Sciences Branch of the NHLBI. “The next step is to understand how we can modify epigenetic modifications to prevent the development of cardiometabolic disease.”
Since the study was done in blood cells, it also suggests that with further study, methylation markers could be easily accessible biomarkers to guide therapy bringing a “precision medicine” approach to preventive cardiology, says Mendelson.

“We’ve known for a long time that people who are overweight or obese are more likely to develop metabolic risk factors like diabetes, lipid abnormalities and hypertension,” adds study coauthor Daniel Levy, MD. He is director of the Framingham Heart Study, which is supported by the NHLBI. “This study may help us understand the molecular mechanism linking obesity to metabolic risk, and that knowledge may pave the way for new approaches to prevent even more dire complications such as cardiovascular disease.”

Citation: Michael M. Mendelson, Riccardo E. Marioni, Roby Joehanes, Chunyu Liu, Åsa K. Hedman, Stella Aslibekyan, Ellen W. Demerath, Weihua Guan, Degui Zhi, Chen Yao, Tianxiao Huan, Christine Willinger, Brian Chen, Paul Courchesne, Michael Multhaup, Marguerite R. Irvin, Ariella Cohain, Eric E. Schadt, Megan L. Grove, Jan Bressler, Kari North, Johan Sundström, Stefan Gustafsson, Sonia Shah, Allan F. McRae, Sarah E. Harris, Jude Gibson, Paul Redmond, Janie Corley, Lee Murphy, John M. Starr, Erica Kleinbrink, Leonard Lipovich, Peter M. Visscher, Naomi R. Wray, Ronald M. Krauss, Daniele Fallin, Andrew Feinberg, Devin M. Absher, Myriam Fornage, James S. Pankow, Lars Lind, Caroline Fox, Erik Ingelsson, Donna K. Arnett, Eric Boerwinkle, Liming Liang, Daniel Levy and Ian J. Deary. “Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardio metabolic Disease: A Mendelian Randomization Approach.”
DOI: 10.1371/journal.pmed.1002215

Research funding: National Heart, Lung, and Blood Institute of the NIH, Tommy Kaplan Fund (Department of Cardiology, Boston Children’s Hospital), UK Biotechnology and Biological Sciences Research Council, UK Royal Society, Chief Scientist Office of the Scottish Government, Age UK, Wellcome Trust Institutional Strategic Support Fund, UK Economic and Social Research Council, UK Medical Research Council, Australian National Health and Medical Research Council.

Adapted from press release by Boston Children’s Hospital.

Similar epigenetic mark found in brain cells of different types of autism disorder

UCLA scientists and their colleagues have found evidence that an abnormal pattern of brain cells is common in people with different types of autism disorders. The abnormal pattern discovered in the study, reported in journal Cell, concerns a certain type of “epigenetic mark,” a chemical modification that occurs frequently on chromosomes and helps regulate the activity of nearby genes.

The findings suggest that although autism disorders have multiple causes, they mostly involve problems in a common set of biological pathways, which are actions among certain molecules within a cell that lead to specific changes such as turning genes on or off or assembling new molecules. The findings may lead to a better understanding of how autism disorders arise, and perhaps one day to the development of drugs that target some of these aberrant pathways. Researchers evaluated brain tissue of 45 people who had autism spectrum disorders and 49 who did not. The team mapped one specific type of epigenetic mark called “histone acetylation.”

In the study, mapping of histone acetylation marks revealed the same broad pattern or “signature” of abnormality in more than 80 percent of the samples from the cerebral cortexes of the autism cases, compared to the non-autism cases. The cortex, the most advanced brain region, is the one that appears to be most affected in autism disorders. The abnormal pattern, which did not appear in samples from other parts of the brain, involved changes at more than 5,000 locations on the human genome.

Scientists have only recently begun to conduct systematic investigations of epigenetic abnormalities in people, but they have already found that these abnormal chemical modifications contribute to cancers and other important diseases. This study was the first to map this type of epigenetic mark across the genome in a human disease.

“Thus, in addition to its value to autism research, this work paves the way for similar studies aimed at understanding other diseases,” Geschwind, study co-senior author and the Gordon and Virginia MacDonald Distinguished Chair in Human Genetics at the David Geffen School of Medicine at UCLA.

The team now hopes to determine which of the many epigenetic abnormalities uncovered in the study are true causes of autism behaviors — and could thus be potential targets for future autism drugs. Drugs that affect histone acetylation have already been developed as potential cancer treatments, and some older psychiatric drugs also influence histone acetylation.

Citation: Sun, Wenjie, Jeremie Poschmann, Ricardo Cruz-Herrera del Rosario, Neelroop N. Parikshak, Hajira Shreen Hajan, Vibhor Kumar, Ramalakshmi Ramasamy, T. Grant Belgard, Bavani Elanggovan, Chloe Chung Yi Wong, Jonathan Mill, Daniel H. Geschwind and Shyam Prabhakar. “Histone Acetylome-wide Association Study of Autism Spectrum Disorder.” Cell 167, no. 5 (2016): 1385-1397.
DOI: 10.1016/j.cell.2016.10.031
Research funding: National Institutes of Health, Singapore’s Agency for Science Technology and Research.
Adapted from press release by UCLA.
Different types of autism disorders share abnormal pattern of brain cells

Vitamins A and Vitamin C help erase epigenetic memory held by cells

Vitamins A and C aren’t just good for your health, they affect your DNA too. Researchers at the Babraham Institute and their international collaborators have discovered how vitamins A and C act to modify the epigenetic ‘memory’ held by cells; insight which is significant for regenerative medicine and our ability to reprogramme cells from one identity to another. The research is published in Proceedings of the National Academy of Science (PNAS).

For regenerative medicine, the holy grail is to be able to generate a cell that can be directed to become any other cell, such as brain cells, heart cells and lung cells. Cells with this ability are present in the early embryo (embryonic stem cells, ESC) and give rise to the many different cell types in the body. For the purposes of regenerative medicine, we need to be able to force adult cells from a patient to regress back to possessing embryonic-like capabilities and to ‘forget’ their previous identity.

A cell’s identity is established at the DNA level by epigenetic changes to the DNA. These changes don’t alter the order of the DNA letters but control which parts of the genome can be read and accessed. Consequently, every different cell type has a unique epigenetic fingerprint, enforcing and maintaining specific patterns of gene expression appropriate to the cell type. To reverse cells back to the naïve pluripotent state this epigenetic layer of information has to be lost to open up the full genome again.

Researchers from the Babraham Institute, UK, University of Stuttgart, Germany and University of Otago, New Zealand worked together to uncover how vitamins A and C affect the erasure of epigenetic marks from the genome. They looked in particular at the epigenetic modification where a methyl chemical tag is added to the C letters in the DNA sequence. Embryonic stem cells show low levels of this C tagging, called cytosine methylation, but in established cell types much more of the genome is marked by this modification. Removing the methyl tags from the DNA, called demethylation, is a central part of achieving pluripotency and wiping epigenetic memory.

The family of enzymes responsible for active removal of the methyl tags are called TET. The researchers looked at the molecular signals that control TET activity to understand more about how the activity of the TET enzymes can be manipulated during cellular programming to achieve pluripotency.

They found that vitamin A enhances epigenetic memory erasure in naïve ESC by increasing the amount of TET enzymes in the cell, meaning greater removal of methyl tags from the C letters of the DNA sequence. In contrast, they found that vitamin C boosted the activity of the TET enzymes by regenerating a co-factor required for effective action.

Dr Ferdinand von Meyenn, postdoctoral researcher at the Babraham Institute and co-first author on the paper, explained: “Both vitamins A and C act individually to promote demethylation, enhancing the erasure of epigenetic memory required for cell reprogramming.” Dr Tim Hore, previously a Human Frontier Long Term Research Fellow at the Babraham Institute, now Lecturer at the University of Otago, New Zealand and co-first author on the paper, continued: “We found out that the mechanisms of how vitamins A and C enhance demethylation are different, yet synergistic.”

The improved understanding of the effect of vitamin A on the TET2 enzyme also potentially explains why a proportion of patients with acute promyelocytic leukaemia (once considered the deadliest form of acute leukaemia) are resistant to effective combination treatment with vitamin A. By providing a possible explanation for this insensitivity for further investigation, this work could point the way to better management of the vitamin A resistant cases.

Professor Wolf Reik, Head of the Epigenetics Programme at the Babraham Institute, said: “This research provides an important understanding in order to progress the development of cell treatments for regenerative medicine. It also enhances our understanding of how intrinsic and extrinsic signals shape the epigenome; knowledge that could provide valuable insight into human disease, such as acute promyelocytic leukaemia and other cancers. Putting the full picture together will allow us to understand the full complexity of the epigenetic control of the genome.”

This work was funded by The Wellcome Trust, the Biotechnology and Biological Sciences Research Council, the Medical Research Council, the European Union EpiGeneSys Network of Excellence, the European Union BLUEPRINT Consortium, the Human Frontier Science Program, the Swiss National Science Foundation/Novartis and the German Research Foundation. The Babraham Institute is strategically supported by the Biotechnology and Biological Sciences Research Council.

Publication: Retinol and ascorbate drive erasure of epigenetic memory and enhance reprogramming to naïve pluripotency by complementary mechanisms.
DOI: http://dx.doi.org/1073/pnas.1608679113                       
Journal: Proceedings of the National Academy of Sciences of the United States of Americanews.
Adapted from press release by Babraham Institute.