The full potential of genome wide association studies (GWAS) will only be realized once we fully understand the biological consequences of genetic risk associations. The goal of the proposed study is to identify gene targets of validated colorectal cancer (CRC) GWAS risk enhancers using a series of complementary approaches and to begin to establish the biological role of risk enhancers in normal crypt development and CRC etiology using a novel in vivo murine-based method. This study builds upon our previous successes in identifying CRC risk enhancers within GWAS loci on chromosomes 1q41, 3p14.1, 8q24.21, 11q23.1, 15q13.3 (3 risk enhancers), 18q21.1, 19q13.11, 19q21 and 20p12.3.
In Aim 1 we will identify novel target genes of these CRC risk enhancers by conducting genome wide eQTL analyses using RNA-Seq data from >1000 normal colon epithelial biopsies and by CRISPR/Cas9-mediated knock out of the risk enhancers in CRC cell lines followed by RNA-Seq eQTL analysis.
In Aim 2 we will identify and validate risk enhancer-target gene(s) interactions using chromosome conformation capture methods. We will identify and validate the physical interaction between risk enhancers and target genes using the circularized chromosome conformation capture (4C) method using HCT116 and SW480 CRC cell lines. Specific enhancer-target gene interactions will be further validated using chromatin conformation capture (3C) and fluorescence in situ hybridization (FISH).
In Aim 3 we will test the biological effect of CRC risk enhancers using a novel mouse model system. Mice will be developed that harbor selected human BACs corresponding to 3 risk enhancer GWAS regions (including the multiple enhancer region on 15q13.3) with known local target genes (8q24.21/cMYC/ CCAT2, 11q23.1/C11orf53/ C11orf92/ C11orf93 and 15q13.3/GREM1/ FMN1/ ax747968). BACs will be inserted into mouse ES cells and CRISPR/Cas9 technology will be used to introduce either risk or non-risk variants within risk enhancers. The modified ES cells will be combined with wild type tetraploid embryos to generate chimeric mice in which the entire embryo-proper was derived from the modified ES cells. The effects of the risk and non-risk SNPs on target gene transcript levels using transcriptome profiling (RNA-Seq) will be determined in these mice in intestinal crypts and non-colon cells (e.g. liver, spleen). Histological studies will be conducted to examine the effects of risk enhancer SNPs on normal crypt and intestine polyp/tumor development. These experiments will be carried out in transgenic mice that are wild-type for Apc, as well as mice that carry a heterozygous-null mutation in the Apc gene. The proposed research will provide insight into the biological role of risk enhancers in the intestinal crypt and CRC etiology and the discovery of risk enhancer target genes will provide tools for future early surveillance and prevention studies of CRC.

Public Health Relevance

The goal of our proposal is to determine the functional consequences of colorectal cancer (CRC) risk enhancers identified through genome wide association studies (GWAS). Our work is motivated by our success in identifying CRC risk enhancers for a growing number of CRC GWAS regions. 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 #
1R01CA204279-01
Application #
9081353
Study Section
Special Emphasis Panel (ZRG1-PSE-K (90)S)
Program Officer
Nelson, Stefanie A
Project Start
2016-07-01
Project End
2021-06-30
Budget Start
2016-07-01
Budget End
2017-06-30
Support Year
1
Fiscal Year
2016
Total Cost
$676,516
Indirect Cost
$201,035
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
Berger, Nathan A; Scacheri, Peter C (2018) Targeting Epigenetics to Prevent Obesity Promoted Cancers. Cancer Prev Res (Phila) 11:125-128
Mack, Stephen C; Pajtler, Kristian W; Chavez, Lukas et al. (2018) Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling. Nature 553:101-105
Karnuta, Jaret M; Scacheri, Peter C (2018) Enhancers: bridging the gap between gene control and human disease. Hum Mol Genet 27:R219-R227
Morrow, James J; Bayles, Ian; Funnell, Alister P W et al. (2018) Positively selected enhancer elements endow osteosarcoma cells with metastatic competence. Nat Med 24:176-185
Patten, Darren K; Corleone, Giacomo; Gy?rffy, Balázs et al. (2018) Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer. Nat Med 24:1469-1480
Forrest, Megan E; Saiakhova, Alina; Beard, Lydia et al. (2018) Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis. Sci Rep 8:7324
Yao, Hui; Hill, Sophie F; Skidmore, Jennifer M et al. (2018) CHD7 represses the retinoic acid synthesis enzyme ALDH1A3 during inner ear development. JCI Insight 3:
Cohen, Andrea J; Saiakhova, Alina; Corradin, Olivia et al. (2017) Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome. Nat Commun 8:14400
Corradin, Olivia; Cohen, Andrea J; Luppino, Jennifer M et al. (2016) Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry. Nat Genet 48:1313-1320