Grant Details
Grant Number: |
5R01CA204279-06 Interpret this number |
Primary Investigator: |
Casey, Graham |
Organization: |
University Of Virginia |
Project Title: |
Biology of Colorectal Cancer Risk Enhancers |
Fiscal Year: |
2020 |
Abstract
DESCRIPTION (provided by applicant): 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.
Publications
Ethanol exposure drives colon location specific cell composition changes in a normal colon crypt 3D organoid model.
Authors: Devall M.
, Plummer S.J.
, Bryant J.
, Jennelle L.T.
, Eaton S.
, Dampier C.H.
, Huyghe J.R.
, Peters U.
, Powell S.M.
, Casey G.
.
Source: Scientific reports, 2021-01-11; 11(1), p. 432.
EPub date: 2021-01-11.
PMID: 33432071
Related Citations
Robust Hi-C Maps of Enhancer-Promoter Interactions Reveal the Function of Non-coding Genome in Neural Development and Diseases.
Authors: Lu L.
, Liu X.
, Huang W.K.
, Giusti-Rodríguez P.
, Cui J.
, Zhang S.
, Xu W.
, Wen Z.
, Ma S.
, Rosen J.D.
, et al.
.
Source: Molecular cell, 2020-08-06; 79(3), p. 521-534.e15.
EPub date: 2020-06-26.
PMID: 32592681
Related Citations
Functional Enhancers Shape Extrachromosomal Oncogene Amplifications.
Authors: Morton A.R.
, Dogan-Artun N.
, Faber Z.J.
, MacLeod G.
, Bartels C.F.
, Piazza M.S.
, Allan K.C.
, Mack S.C.
, Wang X.
, Gimple R.C.
, et al.
.
Source: Cell, 2019-11-27; 179(6), p. 1330-1341.e13.
EPub date: 2019-11-21.
PMID: 31761532
Related Citations
Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer.
Authors: Bien S.A.
, Su Y.R.
, Conti D.V.
, Harrison T.A.
, Qu C.
, Guo X.
, Lu Y.
, Albanes D.
, Auer P.L.
, Banbury B.L.
, et al.
.
Source: Human genetics, 2019 Apr; 138(4), p. 307-326.
EPub date: 2019-02-28.
PMID: 30820706
Related Citations
Mismatch repair-signature mutations activate gene enhancers across human colorectal cancer epigenomes.
Authors: Hung S.
, Saiakhova A.
, Faber Z.J.
, Bartels C.F.
, Neu D.
, Bayles I.
, Ojo E.
, Hong E.S.
, Pontius W.D.
, Morton A.R.
, et al.
.
Source: eLife, 2019-02-13; 8, .
EPub date: 2019-02-13.
PMID: 30759065
Related Citations
Discovery of common and rare genetic risk variants for colorectal cancer.
Authors: Huyghe J.R.
, Bien S.A.
, Harrison T.A.
, Kang H.M.
, Chen S.
, Schmit S.L.
, Conti D.V.
, Qu C.
, Jeon J.
, Edlund C.K.
, et al.
.
Source: Nature genetics, 2019 01; 51(1), p. 76-87.
EPub date: 2018-12-03.
PMID: 30510241
Related Citations
Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer.
Authors: Patten D.K.
, Corleone G.
, Győrffy B.
, Perone Y.
, Slaven N.
, Barozzi I.
, Erdős E.
, Saiakhova A.
, Goddard K.
, Vingiani A.
, et al.
.
Source: Nature medicine, 2018 09; 24(9), p. 1469-1480.
EPub date: 2018-07-23.
PMID: 30038216
Related Citations
Enhancers: bridging the gap between gene control and human disease.
Authors: Karnuta J.M.
, Scacheri P.C.
.
Source: Human molecular genetics, 2018-08-01; 27(R2), p. R219-R227.
PMID: 29726898
Related Citations
Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis.
Authors: Forrest M.E.
, Saiakhova A.
, Beard L.
, Buchner D.A.
, Scacheri P.C.
, LaFramboise T.
, Markowitz S.
, Khalil A.M.
.
Source: Scientific reports, 2018-05-09; 8(1), p. 7324.
EPub date: 2018-05-09.
PMID: 29743621
Related Citations
Targeting Epigenetics to Prevent Obesity Promoted Cancers.
Authors: Berger N.A.
, Scacheri P.C.
.
Source: Cancer prevention research (Philadelphia, Pa.), 2018 03; 11(3), p. 125-128.
EPub date: 2018-02-23.
PMID: 29476043
Related Citations
CHD7 represses the retinoic acid synthesis enzyme ALDH1A3 during inner ear development.
Authors: Yao H.
, Hill S.F.
, Skidmore J.M.
, Sperry E.D.
, Swiderski D.L.
, Sanchez G.J.
, Bartels C.F.
, Raphael Y.
, Scacheri P.C.
, Iwase S.
, et al.
.
Source: JCI insight, 2018-02-22; 3(4), .
EPub date: 2018-02-22.
PMID: 29467333
Related Citations
Positively selected enhancer elements endow osteosarcoma cells with metastatic competence.
Authors: Morrow J.J.
, Bayles I.
, Funnell A.P.W.
, Miller T.E.
, Saiakhova A.
, Lizardo M.M.
, Bartels C.F.
, Kapteijn M.Y.
, Hung S.
, Mendoza A.
, et al.
.
Source: Nature medicine, 2018 02; 24(2), p. 176-185.
EPub date: 2018-01-15.
PMID: 29334376
Related Citations
Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling.
Authors: Mack S.C.
, Pajtler K.W.
, Chavez L.
, Okonechnikov K.
, Bertrand K.C.
, Wang X.
, Erkek S.
, Federation A.
, Song A.
, Lee C.
, et al.
.
Source: Nature, 2018-01-04; 553(7686), p. 101-105.
EPub date: 2017-12-20.
PMID: 29258295
Related Citations
Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome.
Authors: Cohen A.J.
, Saiakhova A.
, Corradin O.
, Luppino J.M.
, Lovrenert K.
, Bartels C.F.
, Morrow J.J.
, Mack S.C.
, Dhillon G.
, Beard L.
, et al.
.
Source: Nature communications, 2017-02-07; 8, p. 14400.
EPub date: 2017-02-07.
PMID: 28169291
Related Citations
Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry.
Authors: Corradin O.
, Cohen A.J.
, Luppino J.M.
, Bayles I.M.
, Schumacher F.R.
, Scacheri P.C.
.
Source: Nature genetics, 2016 11; 48(11), p. 1313-1320.
EPub date: 2016-09-19.
PMID: 27643537
Related Citations