Inherited colorectal cancer risk variants: from association to biology

遗传性结直肠癌风险变异：从关联到生物学

基本信息

批准号：
9922218
负责人：
GRAHAM CASEY
金额：
$ 77.11万
依托单位：
UNIVERSITY OF VIRGINIA
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-02-01 至 2022-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9922218
关键词：
11q23 12q13 19q13 1q41 20p12 3-Dimensional 8q24 Aging Alleles Apoptosis Biological Biological Assay Biology Biopsy CRISPR/Cas technology Cancer Etiology Candidate Disease Gene ChIP-seq Chromosome Mapping Colon Colorectal Cancer DNA Damage DNA Sequence Alteration Data Data Set Development Enhancers Epithelial Epithelium Event Fluorescence Funding Future Gene Expression Gene Targeting Genes Genetic Enhancer Element Genetic Risk Genome Stability Genotype Goals Grant Guidelines H2AFX gene Human Immunofluorescence Immunologic Immunohistochemistry In Vitro Incidence Individual Inherited Intervention Knock-out Lead Length MADH7 gene Measures Methods Molecular Morphology Normal tissue morphology Nucleic Acid Regulatory Sequences Organoids Pathway interactions Patients Phase Phenotype Phosphorylation Play Population Premature aging syndrome Proteins Regulatory Element Risk Risk Factors Role Sampling Signal Pathway Signal Transduction System TCF7L2 gene Technology Testing Transforming Growth Factor beta Translating Ulcerative Colitis Validation Variant Work Xp22 carcinogenicity colon cancer cell line colorectal cancer prevention colorectal cancer risk colorectal cancer treatment crypt cell genome sequencing genome wide association study genome-wide improved insight knock-down lifetime risk novel overexpression premature promoter public health relevance risk variant success telomere tool transcriptome sequencing tumor whole genome

项目摘要

DESCRIPTION (provided by applicant): 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.

描述（由申请人提供）：拟议研究的目标是辨别通过全基因组关联研究（GWAS）确定的结直肠癌（CRC）风险变异的功能和生物学相关性。在第一个资助期间，我们建立了功能表征管道。为了研究 CRC 风险的机制基础，我们通过 eQTL 分析确定了 8 个 GWAS 区域的功能调控元件/增强子/启动子和目标基因。为了发现新的 GWAS 风险变异，并进一步探讨 GWAS 风险变异的机制和生物学相关性，我们现在提出以下具体目标 1：我们将在我们开发的成功分子表征管道的基础上，确定其他新的功能调控区域。通过结合来自 OncoArray 研究的精细图谱数据、来自正常结肠的全基因组染色质免疫沉淀和测序 (ChIPseq) 数据，来自 GWAS 风险区域的/增强子/启动子和靶基因目标 2：使用目标 1 的数据，我们将在正常人 3D 结肠中敲低或过度表达候选风险目标基因。使用慢病毒系统进行上皮类器官培养，并检查对形态、增殖、凋亡和常见信号通路的影响，然后通过免疫组织化学/荧光方法在正常组织中进行验证。通过 CRC 细胞系中的 CRISPR-Cas9 方法敲除调节元件，然后进行 RT-qPCR 验证，在未鉴定出活性调节区域的靶基因的情况下，我们将鉴定敲除后的候选靶基因。最后，在目标 3 中，我们将检验 CRC 风险变异导致结肠隐窝过早衰老表型的假设。之间本研究将通过测量组蛋白 H2AX 磷酸化、全基因组测序和定量 PCR 测量端粒长度来评估变异风险负担和结肠隐窝中累积的 DNA 突变。结肠隐窝和结直肠癌病因学。

项目成果

期刊论文数量（11）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

A Race-Specific, DNA Methylation Analysis of Aging in Normal Rectum: Implications for the Biology of Aging and Its Relationship to Rectal Cancer.

DOI：
10.3390/cancers15010045
发表时间：
2022-12-22
期刊：
Cancers
影响因子：
5.2
作者：
通讯作者：

Multi-omic analysis in normal colon organoids highlights MSH4 as a novel marker of defective mismatch repair in Lynch syndrome and microsatellite instability.

DOI：
10.1002/cam4.6048
发表时间：
2023-06
期刊：
Cancer medicine
影响因子：
4
作者：
通讯作者：

Controlling for cellular heterogeneity using single-cell deconvolution of gene expression reveals novel markers of colorectal tumors exhibiting microsatellite instability.

DOI：
10.18632/oncotarget.27935
发表时间：
2021-04-13
期刊：
Oncotarget
影响因子：
0
作者：
Devall MAM;Casey G
通讯作者：
Casey G

Erratum: A new GWAS and meta-analysis with 1000Genomes imputation identifies novel risk variants for colorectal cancer.

DOI：
10.1038/srep12372
发表时间：
2015-08-03
期刊：
Scientific reports
影响因子：
4.6
作者：
Al-Tassan NA;Whiffin N;Hosking FJ;Palles C;Farrington SM;Dobbins SE;Harris R;Gorman M;Tenesa A;Meyer BF;Wakil SM;Kinnersley B;Campbell H;Martin L;Smith CG;Idziaszczyk S;Barclay E;Maughan TS;Kaplan R;Kerr R;Kerr D;Buchanan DD;Win AK;Hopper J;Jenkins M;Lindor NM;Newcomb PA;Gallinger S;Conti D;Schumacher F;Casey G;Dunlop MG;Tomlinson IP;Cheadle JP;Houlston RS
通讯作者：
Houlston RS

Multiple functional risk variants in a SMAD7 enhancer implicate a colorectal cancer risk haplotype.

DOI：
10.1371/journal.pone.0111914
发表时间：
2014
期刊：
PloS one
影响因子：
3.7
作者：
Fortini BK;Tring S;Plummer SJ;Edlund CK;Moreno V;Bresalier RS;Barry EL;Church TR;Figueiredo JC;Casey G
通讯作者：
Casey G