The overarching goal of the Cancer Genomics and Epigenomics (CGE) Program is to define the mechanisms, both genetic and epigenetic, that preserve genome integrity in normal cells and elicit genome instability in cancer cells. The CGE Program is led by Jean Gautier, PhD and Raul Rabadan, PhD who have complementary expertise in experimental and computational cancer biology. The CGE Program, which was founded in 2008, has 41 Members representing 13 departments across three different schools at Columbia University. The scientific goals of the CGE Program are achieved through three interrelated Specific Aims: (1) Genome Plasticity: To evaluate how normal and pathological pathways of DNA repair contribute to the genomic instability associated with cancer; (2) Epigenetics: To determine how changes in chromatin modification and organization promote tumor development; and 3. Computational Genomics and Genetics: To develop and implement multiscale, genome-wide strategies to identify the genomic aberrations that drive cancer development. In particular, CGE Members continue to provide pivotal insights into how DNA repair, a critical tumor suppression mechanism, is essential for maintenance of genome stability. Furthermore, following major strategic investments in cancer genomics and epigenomics, CGE Members work at the forefront of research in several tumor types, including ALL, PTCL, DLBCL and glioblastoma, with strong computational biology collaborations. The CGE Program addresses research relevant to the HICCC Catchment Area by focusing on triple-negative breast cancer and peripheral T cell lymphoma. In turn, the HICCC facilitates CGE research and development by supporting internal pilot studies, multi-investigator grants proposals, strategic faculty recruitments, and use of Shared Resources. Consequently, the CGE Program maintains a strong portfolio of intra- and inter- programmatic multi-investigator grants, which includes existing NCI-funded programs that anchor both Aim 1 (P01-CA174653; DNA double-strand break repair, chromosomes translocations and cancer) and Aim 3 (U54- CA193313, Topology of cancer evolution and heterogeneity), as well as a developing epigenetics program project aligned with Aim 2. The CGE Members contribute to the daily operation of multiple HICCC Shared Resources and participate actively in cancer training at all levels. Finally, the computational/mathematical genomics research of CGE Members continues to have a growing impact across all HICCC activities, encompassing the full spectrum of basic, translational, clinical and population research. In 2018, 41 program members had a total of $16M in cancer-focused, peer-reviewed funding (direct costs), of which $9.2M (57%) was from NCI, $4.8M (30%) from other NIH sources, and $1.9M (12%) from other peer- review agencies. During the current project period, CGE Members authored a total of 959 cancer-relevant publications, of which 112 (12%) were intra-programmatic and 202 (21%) inter-programmatic. Notably, 29% of these CGE publications appeared in journals with impact factors >10.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Center Core Grants (P30)
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Subcommittee I - Transistion to Independence (NCI)
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Columbia University (N.Y.)
New York
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DiCarlo, James E; Mahajan, Vinit B; Tsang, Stephen H (2018) Gene therapy and genome surgery in the retina. J Clin Invest 128:2177-2188
Wert, Katherine J; Velez, Gabriel; Cross, Madeline R et al. (2018) Extracellular superoxide dismutase (SOD3) regulates oxidative stress at the vitreoretinal interface. Free Radic Biol Med 124:408-419
Lee, Andreia; CingĂ–z, Oya; Sabo, Yosef et al. (2018) Characterization of interaction between Trim28 and YY1 in silencing proviral DNA of Moloney murine leukemia virus. Virology 516:165-175
Schrank, Benjamin R; Aparicio, Tomas; Li, Yinyin et al. (2018) Nuclear ARP2/3 drives DNA break clustering for homology-directed repair. Nature 559:61-66
Proto, Jonathan D; Doran, Amanda C; Gusarova, Galina et al. (2018) Regulatory T Cells Promote Macrophage Efferocytosis during Inflammation Resolution. Immunity 49:666-677.e6
Hernandez, Celine; Huebener, Peter; Pradere, Jean-Philippe et al. (2018) HMGB1 links chronic liver injury to progenitor responses and hepatocarcinogenesis. J Clin Invest 128:2436-2451
Lee, Younghyun; Pujol Canadell, Monica; Shuryak, Igor et al. (2018) Candidate protein markers for radiation biodosimetry in the hematopoietically humanized mouse model. Sci Rep 8:13557
Kraakman, Michael J; Liu, Qiongming; Postigo-Fernandez, Jorge et al. (2018) PPAR? deacetylation dissociates thiazolidinedione's metabolic benefits from its adverse effects. J Clin Invest 128:2600-2612
Cui, Xuan; Jauregui, Ruben; Park, Karen Sophia et al. (2018) Multimodal characterization of a novel mutation causing vitamin B6-responsive gyrate atrophy. Ophthalmic Genet 39:512-516
Evans, Lucy P; Newell, Elizabeth A; Mahajan, MaryAnn et al. (2018) Acute vitreoretinal trauma and inflammation after traumatic brain injury in mice. Ann Clin Transl Neurol 5:240-251

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