The objectives of this grant, which has been funded for almost 35 years, have been to understand the mechanisms for the establishment and alteration of the human epigenome in cancer by focusing on DNA methylation patterns. We also strive to understand how drugs such as 5-aza-2'-deoxycytidine (5-aza-CdR) interfere with cytosine methylation and reactivate silenced genes. This research has led to the approval by the FDA of two DNA demethylating agents (5-aza-CR and 5-aza-CdR) for the treatment of myelodysplastic syndrome (MDS) and we have been successful over the last five years in the preclinical development of the first next-generation nucleoside inhibitor of DNA methylation called SGI110. This drug has been undergoing Phase I/II testing and shows great promise. In the next five year period of the project, we hope to take advantage of an innovative new technique we have developed called NOMe-seq which allows us to simultaneously map nucleosomes and DNA methylation patterns either at the level of individual DNA molecules (i.e., replicas of individual transcription start sites, etc.), or genome-wide. By coupling this technique with ChIP-seq and RNA expression analysis and next-generation sequencing, we gain a holistic view of the human epigenome and how it is altered in cancer for the first time.
In Specific Aim 1, we will use this approach to define how DNA methylation acts genome-wide to position nucleosomes at regulatory regions and throughout the genome. We will then explore the mechanisms by which chromatin remodelers and histone methyltransferases alter the epigenome. This is crucial because a large number of mutations in chromatin modifiers have been discovered over the past five years, but we know little about the potential effects of these mutations on the epigenome.
In Specific Aim 2, we investigate how perturbing DNA methylation with 5-aza- CdR alters the entire epigenome and the expression of subsets of genes. We are particularly interested in exploring the time course by which different sets of genes become activated and then become resilenced as a function of time after treatment. A novel part of this Aim will be to investigate the effect of gene body methylation on transcriptional elongation which may, unexpectedly, play a role in the patient's response to these drugs.
In Specific Aim 3, we plan a first epigenome-wide analysis of uncultured human tumors by focusing on colon tumors and adjacent tissue. The completion of these Specific Aims will give us a better understanding of why and how the epigenome is altered in cancer, how it responds to drugs and hopefully will result in better treatments for patients.
This grant will show, in a holistic way, how the epigenome is modified in cancer, help explain how mutations alter the structure of the epigenome, measure the response of the epigenome to demethylation inhibitors and provide the first comprehensive integrated view of chromatin in uncultured human cancers. It has profound implications for the future development of epigenetic therapies.
|Taberlay, Phillippa C; Statham, Aaron L; Kelly, Theresa K et al. (2014) Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res 24:1421-32|
|Yang, Xiaojing; Han, Han; De Carvalho, Daniel D et al. (2014) Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell 26:577-90|
|Yang, Xiaojing; Noushmehr, Houtan; Han, Han et al. (2012) Gene reactivation by 5-aza-2'-deoxycytidine-induced demethylation requires SRCAP-mediated H2A.Z insertion to establish nucleosome depleted regions. PLoS Genet 8:e1002604|
|Chuang, Jody C; Warner, Steven L; Vollmer, David et al. (2010) S110, a 5-Aza-2'-deoxycytidine-containing dinucleotide, is an effective DNA methylation inhibitor in vivo and can reduce tumor growth. Mol Cancer Ther 9:1443-50|
|Sharma, Shikhar; Kelly, Theresa K; Jones, Peter A (2010) Epigenetics in cancer. Carcinogenesis 31:27-36|
|Jeong, Shinwu; Liang, Gangning; Sharma, Shikhar et al. (2009) Selective anchoring of DNA methyltransferases 3A and 3B to nucleosomes containing methylated DNA. Mol Cell Biol 29:5366-76|
|Saito, Yoshimasa; Friedman, Jeffrey M; Chihara, Yoshitomo et al. (2009) Epigenetic therapy upregulates the tumor suppressor microRNA-126 and its host gene EGFL7 in human cancer cells. Biochem Biophys Res Commun 379:726-31|
|Bouazoune, Karim; Miranda, Tina B; Jones, Peter A et al. (2009) Analysis of individual remodeled nucleosomes reveals decreased histone-DNA contacts created by hSWI/SNF. Nucleic Acids Res 37:5279-94|
|van Rietschoten, J G I; Gal-Yam, E N; Jeong, S et al. (2008) Epigenetic regulation and nucleosome positioning in the human TATA-less IL-1 alpha promoter. Genes Immun 9:582-90|
|Gal-Yam, Einav Nili; Egger, Gerda; Iniguez, Leo et al. (2008) Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line. Proc Natl Acad Sci U S A 105:12979-84|
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