Clear cell renal cell carcinoma, the most common subtype of kidney cancer, is characterized by mutations in genes encoding chromatin modifiers. One of these genes, SETD2, encodes the only methyltransferase capable of trimethylation of histone H3 lysine 36 (H3K36me3). In patients, mutation of SETD2 has been associated with decreased overall survival and time to recurrence. Previous work has shown that mutation of SETD2 in human tumors is associated with altered chromatin accessibility and wide-spread RNA processing defects. Common mutations in SETD2 include early frameshift/nonsense mutations, mutations in the catalytic SET domain and mutations in the SRI domain, which mediates the interaction between SETD2 and RNA polymerase. The central hypothesis of this proposal is that SETD2 acts as a tumor suppressor by regulating chromatin during transcription, and that disruption of this process promotes cancer through both transcriptional processing defects and widespread reorganization of chromatin packaging.
Aim 1 will identify the effect of specific SETD2 mutations in the SET and SRI domains on cellular transformation and RNA processing. Cell lines have been engineered for SETD2 inactivation and expression of tumor-associated SETD2 mutants in the SET domain and SRI domain. These cells will be used to study proliferation, anchorage independent growth, and cell migration. These cells will also be examined for altered RNA processing, including aberrant splicing, altered exon utilization, and alternate transcription start/termination sites, using RNA-seq data and published and custom generated computational algorithms.
Aim 2 will examine the effect of SETD2 mutation on H3K36me3 placement as well as overall chromatin organization. H3K36me3 localization will be examined by ChIP-seq in cell harboring SRI domain mutants. Cells will be tested for changes in chromatin organization by FAIRE-seq and MNAse-seq. RNA, ChIP, chromatin accessibility and nucleosome positioning data will then be integrated to explore the role of SETD2 and its effect on chromatin organization. Results from this study will further our understanding of the ability of SETD2 to suppress tumor development by maintaining epigenomic organization and transcriptomic fidelity.

Public Health Relevance

SETD2 is a commonly mutated gene in kidney cancer, and patients with mutation in this gene have worse outcomes. It is not understood how specific mutations in this gene alter its function. This work will study particular mutations in SETD2 in order to understand how these mutations alter SETD2 function, and further our understanding of the role of SETD2 in kidney cancer development.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Individual Predoctoral NRSA for M.D./Ph.D. Fellowships (ADAMHA) (F30)
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Special Emphasis Panel (ZRG1)
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Damico, Mark W
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University of North Carolina Chapel Hill
Schools of Public Health
Chapel Hill
United States
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Fahey, Catherine C; Davis, Ian J (2017) SETting the Stage for Cancer Development: SETD2 and the Consequences of Lost Methylation. Cold Spring Harb Perspect Med 7:
Hacker, Kathryn E; Fahey, Catherine C; Shinsky, Stephen A et al. (2016) Structure/Function Analysis of Recurrent Mutations in SETD2 Protein Reveals a Critical and Conserved Role for a SET Domain Residue in Maintaining Protein Stability and Histone H3 Lys-36 Trimethylation. J Biol Chem 291:21283-21295
Park, In Young; Powell, Reid T; Tripathi, Durga Nand et al. (2016) Dual Chromatin and Cytoskeletal Remodeling by SETD2. Cell 166:950-962
Fahey, Catherine C; Rathmell, W Kimryn (2015) A tale of two cancers: Complete genetic analysis of chromophobe renal cell carcinoma contrasts with clear cell renal cell carcinoma. Mol Cell Oncol 2:e979686