EpiGenie is stoked to bring you coverage of the first World Epigenetics Summit. After getting the details from the Broad Institute’s Manching Ku, we’re sure there will be many more to come. Check out Manching’s report below to see for yourself:
The first inaugural World Epigenetics Summit took place on 26-28, July 2011 at the John Hynes Convention Centre at downtown Boston, MA in the US. Around 100 attendees from industry and academia listened to seminars by 21 speakers, 2 pre-conference technical workshops and 2 panel discussions on the future of epigenetic drug development. The conference location is focused and intimate, but the organizers were still able to invite many world-renowned epigenetics leaders from the pharmaceutical industry and academia to discuss research on biomarkers, therapeutic targets, and diagnostic tools. A novel and exciting speed networking session broke the ice between attendees and encouraged a great interaction among us.
Unlocking the Potential of Epigenetic Drug Products
Robert Gould, Epizyme
Dr. Gould’s talk was separated into 3 areas, 1) the definition of epigenetics, 2) histone methyl transferases and 3) DOT1L MLL leukemia. He gave a thorough definition on the definition of Epigenetics, that it serves as a bridge from genotype (DNA sequences) to phenotype (presentation). He’s determined that epigenetic therapies can also serve as a bridge from disease states to healthy states. He’s given 2 historical examples; the Sweden Överkalix study and the Dutch Famine in 1944 to illustrate that the heredity and profound effect of epigenetics are cross-generational.
He then went on to introduce how histone methyl transferases can confer different states depending on the lysine or arginine methylation. To date, there are 52 lysine methyl transferases, 44 arginine methyl transferases and 25 lysine demethylases, which are potentially important epigenetic therapeutic targets. One of the enzymes that Epizyme has focused on was MLL (mixed-lineage leukemia).
MLL is a histone 3 lysine 4 methyl transferase, however it was often translocated in leukemia, where the enzymatic SET domain was deleted and fused with other proteins, e.g. DOT1L. DOT1L in turn is a methyl transferase for H3K79, thus one of the phenotypes of MLL-DOT1L fusion is the increase of K79 methylation and decrease of K4 methylation. Epizyme has developed a specific inhibitor to abolish deleterious defects caused by MLL-DOT1L fusion proteins. This demonstrates the reversibility of modulation histone methyl transferases by chemical inhibitors to yield desired effects.
Epigenomics and Cellular States
Alexander Meissner, Harvard Stem Cell Institute
Among the many epigenetic biomarkers developed to date, CpG methylation is one of the most studied. Dr. Meissner’s talk focused on illustrating RRBS (reduced representation bisulfite sequencing), a technology developed by him, for interrogating DNA methylation genomewide at single base pair resolution. RRBS relies on the fact that MspI digestion can enrich genomic DNA that is rich in CG, and then bisulfite treated and coupled with next-generation high-throughput sequencing. His lab was able to sequence about 10% of the genome using only 50 cells. With the limitation of pluripotency tests for human embryonic and pluripotent cell lines, he has applied this technology to compare the DNA methylation profiles of 20 different human pluripotent cell lines.
He has found many interesting CpG methylation constant regions, as well as highly variable ones. Non CpG methylation is more prominent in pluripotent cells, and decrease in differentiated cell types. He was also able to apply the same technology to distinguish lineage potentials between myeloid and lymphoid in the hematopoietic cells by studying DNA methylation status of GATA1.
Chemical Inhibition of Bromodomains
James Bradner, Dana-Farber Cancer Institute
Several different protein complexes can modulate gene expression. Dr. Bradner introduced complexes that can influence gene expression, include transcription factors, epigenetic enzymes and histone binding proteins. Solving crystal structures of proteins can lead to discovery and optimization of chemical inhibitors. He focuses his efforts of BRD4, a bromodomain-containing protein that recognizes acetyl-histone. BRD4 was also discovered to reside on chromosome 19, which was commonly amplified in multiple myeloma.
BRD4 expression also increased during progression of multiple myeloma. His lab has developed an inhibitor JQ1 that attenuated MYC and E2F target genes’ expression. During JQ1 treatment, MYC was shown to be released from chromatin and cells that are at S phase were decreased by 50%. JQ1 was also effective in MLL, by decreasing proliferation, increase differentiation and decrease the expression of MYC and its targets.
Open Access Research Tools to Promote Target Discovery
Aled Edwards, Structural Genomics Consortium
The SGC has been focused on systematically solving 3D structure of proteins, synthesizing chemical probes and generate antibodies by phage display. Dr. Edwards introduced the open access nature of the consortium and urged scientists from both academia and pharmaceutical industries to share their findings to speed up the process of basic science research, as well as drug discovery processes. He stated that the current funding systems do not encourage innovation because of the lack of scientific basis, availability of reagents on novel, under-studied targets, but with potentials from previous screens. The SGC has focused their efforts on many popular epigenetic targets such as methyl transferases and bromodomain proteins.
Histone Methyl Transferase (HMT) Inhibitors as Oncology Treatments
Peter Tummino, GlaxoSmithKline
Important chromatin regulators can be altered in tumors in several ways including over expression, translocation, gene amplification and active mutations. The mechanism in cancer cells involves changing transcription status and modifying other protein targets. EZH2 is a popular therapeutic target because its increased expression suggests poor prognosis in solid tumors such as prostate, breast and small cell lung cancers. EZH2 causes increased Histone 3 K27 methylation at tumor suppressor genes.
Other relevant potential cancer biomarkers include UTX (the demethylase for H3K27), HOTAIR (EZH2-associating lincRNA) and activating mutations in EZH2. The residue Y641 of EZH2 was found to be mutated to amino acids F,C,H or S in lymphomas. Using a peptide library of canonical histones with various modifications, Dr. Tummino’s group was able to determine that mutant EZH2 prefers H3K27me2 as a substrate, while wild type (WT) EZH2 prefers non-methylated H3K27. Thus cancer cells show a higher level of H3K27me3 than H3K27me2, shown by both western blot and ELISA assays, suggesting stronger repression during carcinogenesis. They then screened for chemical inhibitors using in vitro reconstitution of polycomb repressive complexes 2 and H3K27me3 peptides.
The compound GSK-2 from their chemical library was found to be specific inhibitor for EZH2 and not for EZH1 or other methyl transferases. When breast cancer cells were treated with GSK-2, H3K27me3 level was decreased dramatically and EZH2 target gene expression was derepressed. GSK-2 was also shown to have anti-proliferative effects in cancer cells. Dr. Tummino’s group is working on treating mice with GSK-2 to study any anti-cancer effects in vivo.
**EpiGenie would like to give a huge ‘Thank you’ for providing this coverage to Manching Ku, PhD., who is a Postdoctoral fellow at Broad Institute.