The goal of the proposed study is to discern the functional and biological relevance of colorectal cancer (CRC) risk variants identified through genome wide association studies (GWAS). During the first funding period we established a functional characterization pipeline to investigate the mechanistic basis underlying CRC risk. Using this pipeline we identified functional regulatory elements/enhancers/promoters for 8 GWAS regions and target genes for 8 GWAS regions by eQTL analysis. To keep pace with the rate of discovery of novel GWAS risk variants and to further interrogate the mechanistic and biological relevance of GWAS risk variants we now propose the following Specific Aims.
Aim 1 : We will build upon the successful molecular characterization pipeline we have developed and identify additional novel functional regulatory regions/enhancers/promoters and target genes from GWAS risk regions through incorporation of fine mapping data from the OncoArray study, genome wide chromatin immunoprecipitation and sequencing (ChIPseq) data from normal colon crypts from 10 healthy subjects, and apply genome wide eQTL analyses using RNA-seq data from >1100 normal colon epithelial biopsies.
Aim 2 : Using data from Aim 1 we will knock down or over-express candidate risk target genes in normal human 3D colon epithelial organoid cultures using lentiviral systems and examine the effect on morphology, proliferation, apoptosis and common signaling pathways followed by validation in normal tissues by immunohistochemical/fluorescence approaches. We will confirm the correlation between active regulatory elements and target genes following knock out of regulatory elements by CRISPR-Cas9 methods in CRC cell lines followed by RT-qPCR validation. Where no target genes of active regulatory regions have been identified we will identify candidate target genes following knock out of regulatory elements by CRISPR-Cas9 methods in CRC cell lines followed by RNA-Seq eQTL analysis. Finally, in Aim 3: We will test the hypothesis that CRC risk variants lead to a premature aging phenotype in colon crypts. We will determine the correlation between risk variant burden and accumulated DNA mutations in colon crypts. DNA damage will be assessed by measuring histone H2AX phosphorylation, whole genome sequencing and telomere length measured by quantitative PCR. This study will provide insight into the role of genetic risk variants on normal biology of the colon crypt and CRC etiology.

Public Health Relevance

The goal of our proposal is to determine the mechanistic and functional consequences of inherited risk variants identified through CRC genome wide association studies. Our work is motivated by our success in identifying functional consequences of a growing number of risk variants. An improved understanding of the biological relevance of risk variants identified through GWAS should substantially aid in our understanding of early carcinogenic events, which can be translated to improvements in current guidelines for surveillance, intervention and potentially treatment of CRC.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
2R01CA143237-06A1
Application #
9026600
Study Section
Special Emphasis Panel (ZRG1-PSE-K (90))
Program Officer
Johnson, Ronald L
Project Start
2010-02-01
Project End
2021-01-31
Budget Start
2016-03-11
Budget End
2017-01-31
Support Year
6
Fiscal Year
2016
Total Cost
$835,117
Indirect Cost
$301,939
Name
University of Southern California
Department
Public Health & Prev Medicine
Type
Schools of Medicine
DUNS #
072933393
City
Los Angeles
State
CA
Country
United States
Zip Code
90032
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Lindström, Sara; Finucane, Hilary; Bulik-Sullivan, Brendan et al. (2017) Quantifying the Genetic Correlation between Multiple Cancer Types. Cancer Epidemiol Biomarkers Prev 26:1427-1435
Cohen, Andrea J; Saiakhova, Alina; Corradin, Olivia et al. (2017) Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome. Nat Commun 8:14400
Rodriguez-Broadbent, Henry; Law, Philip J; Sud, Amit et al. (2017) Mendelian randomisation implicates hyperlipidaemia as a risk factor for colorectal cancer. Int J Cancer 140:2701-2708
Orlando, Giulia; Law, Philip J; Palin, Kimmo et al. (2016) Variation at 2q35 (PNKD and TMBIM1) influences colorectal cancer risk and identifies a pleiotropic effect with inflammatory bowel disease. Hum Mol Genet 25:2349-2359
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Ananthakrishnan, Ashwin N; Du, Mengmeng; Berndt, Sonja I et al. (2015) Red meat intake, NAT2, and risk of colorectal cancer: a pooled analysis of 11 studies. Cancer Epidemiol Biomarkers Prev 24:198-205

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