Background Family history is a risk factor of many diseases. Genome-wide sequencing efforts have identified naturally occurring genetic variations such as copy number variations (CNV) and single nucleotide polymorphisms (SNPs) across the human genome that could account for the risk associated with family history (1). In fact, genome-wide association studies (GWAS) have linked numerous SNPs with an increased risk of developing specific diseases, such as breast and prostate cancer (2-13). Interestingly, most risk-associated SNPs (raSNPs) map to non-coding genomic regions, which excludes their role in protein sequence/structure alterations (2-13). This has significantly complicated the understanding of how SNPs can contribute to cancer development and has hindered the development of therapeutic strategies based on SNP profiling. Genome-wide assays revealed the preferential recruitment of transcription factors to non-coding regions surrounding actively transcribed genes in breast and prostate cancer cells (14-17). In addition, changes to the genomic distribution of these transcription factors directly impacts transcriptional programs (18, 19). Hypothesis We hypothesize that raSNPs associate with cancer development by promoting transcriptional programs favorable to oncogenesis by altering transcription factor recruitment. Approach Combining multiple genomics datasets from different cancer types, we will determine the role of breast and prostate cancer raSNPs on transcription factor activity by 1) determining the cancer type- specificity of raSNPs and transcription factor recruitment, 2) defining the role of raSNPs on transcription factor recruitment and by 3) determining how raSNPs modulating transcription factor recruitment affects transcriptional programs. Relevance to the mission While breast and prostate cancer raSNPs serve important diagnostic and prognostic purposes, they lack therapeutic value. Defining the function of these raSNPs, as we currently propose, will reveal the therapeutic applicability of SNP profiling in breast and prostate cancer. Hence, our research will be of direct and rapid benefit to the clinic.
While single nucleotide polymorphism (SNP) profiling has identified specific genetic variations as risk factors for cancer development, the mechanisms responsible for the increased risk are ill defined. This hinders the therapeutic value of SNP profiling. Therefore, by defining the mechanism driving the risk associated with SNPs in breast and prostate cancer, as we currently propose, we will identify the therapeutic benefit of SNP profiling.
|Ahmed, Musaddeque; Sallari, Richard C; Guo, Haiyang et al. (2017) Variant Set Enrichment: an R package to identify disease-associated functional genomic regions. BioData Min 10:9|
|Zhou, Stanley; Treloar, Aislinn E; Lupien, Mathieu (2016) Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations. Cancer Discov 6:1215-1229|
|Bailey, Swneke D; Desai, Kinjal; Kron, Ken J et al. (2016) Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer. Nat Genet 48:1260-6|
|Bailey, Swneke D; Zhang, Xiaoyang; Desai, Kinjal et al. (2015) ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters. Nat Commun 2:6186|
|Bailey, Swneke D; Virtanen, Carl; Haibe-Kains, Benjamin et al. (2015) ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments. Bioinformatics 31:3057-9|
|Corradin, Olivia; Saiakhova, Alina; Akhtar-Zaidi, Batool et al. (2014) Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res 24:1-13|
|Zhang, Xiaoyang; Bailey, Swneke D; Lupien, Mathieu (2014) Laying a solid foundation for Manhattan--'setting the functional basis for the post-GWAS era'. Trends Genet 30:140-9|
|Chahar, Sanjay; Gandhi, Vishal; Yu, Shiyan et al. (2014) Chromatin profiling reveals regulatory network shifts and a protective role for hepatocyte nuclear factor 4? during colitis. Mol Cell Biol 34:3291-304|
|Ghoussaini, Maya; Edwards, Stacey L; Michailidou, Kyriaki et al. (2014) Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation. Nat Commun 4:4999|
|Magnani, Luca; Stoeck, Alexander; Zhang, Xiaoyang et al. (2013) Genome-wide reprogramming of the chromatin landscape underlies endocrine therapy resistance in breast cancer. Proc Natl Acad Sci U S A 110:E1490-9|
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