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

 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.




Transcriptome-wide In Vitro Effects of Aspirin on Patient-derived Normal Colon Organoids.
Authors: Devall M.A.M. , Drew D.A. , Dampier C.H. , Plummer S.J. , Eaton S. , Bryant J. , Díez-Obrero V. , Mo J. , Kedrin D. , Zerjav D.C. , et al. .
Source: Cancer prevention research (Philadelphia, Pa.), 2021-08-13; , .
EPub date: 2021-08-13.
PMID: 34389629
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SNPs associated with colorectal cancer at 15q13.3 affect risk enhancers that modulate GREM1 gene expression.
Authors: Fortini B.K. , Tring S. , Devall M.A. , Ali M.W. , Plummer S.J. , Casey G. .
Source: Human mutation, 2021 Mar; 42(3), p. 237-245.
EPub date: 2021-02-02.
PMID: 33476087
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Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects.
Authors: Guo X. , Lin W. , Wen W. , Huyghe J. , Bien S. , Cai Q. , Harrison T. , Chen Z. , Qu C. , Bao J. , et al. .
Source: Gastroenterology, 2021 03; 160(4), p. 1164-1178.e6.
EPub date: 2020-10-12.
PMID: 33058866
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A functional variant on 20q13.33 related to glioma risk alters enhancer activity and modulates expression of multiple genes.
Authors: Ali M.W. , Patro C.P.K. , Zhu J.J. , Dampier C.H. , Plummer S.J. , Kuscu C. , Adli M. , Lau C. , Lai R.K. , Casey G. .
Source: Human mutation, 2021 Jan; 42(1), p. 77-88.
EPub date: 2020-11-22.
PMID: 33169458
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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