Transcriptome-wide association study to identify susceptibility genes for colorectal cancer

项目摘要 遗传因素在结直肠癌（CRC）的病因学中起重要作用。截至目前，约50 已经通过全基因组关联研究（GWAS）鉴定了CRC的遗传基因座。但这些 基因座只能解释遗传力的一小部分。此外，靶基因和潜在的机制，为大多数 这些风险位点仍不清楚。绝大多数是非编码变体，其中许多已被证明是 调节基因表达。最近的研究表明，约80%的疾病遗传率可以解释为 调节变体。然而，这些变异每一个都只与疾病风险的一个小的变化有关; 因此难以使用GWAS来识别它们。最近，一种新的方法，转录组范围的关联， 第三世界科学院（TWAS）的研究是为了系统地研究转录组与疾病风险的关系。 在TWAS中，使用参考转录组构建模型以预测具有顺式SNP的基因表达，然后 应用于GWAS数据，以评估其与疾病风险的相关性。在这里，我们建议使用这种创新的 一种扫描整个转录组的方法，以发现新的CRC易感基因， 在先前的GWAS中发现的基因座中的致病基因。在目标1中，我们将在欧洲后裔中进行TWAS。 我们将建立数百个结直肠癌组织中编码基因和非编码RNA的表达预测模型， 组织、其他多种组织和交叉组织，使用来自 基因型组织表达（GTEx）项目中的欧洲血统个体。这些模型将用于 使用来自大约27，911例CRC病例和23，059例CRC病例的GWAS数据预测基因表达水平， 结肠直肠跨学科研究（CORECT）中包括的对照和 结直肠癌（GECCO）财团，然后评估其与CRC风险的关联。在目标2中，我们将 在东亚后裔中进行TWAS。我们将生成转录组数据和高密度基因分型 来自亚洲结直肠癌联盟（ACCC）的400名亚洲血统的CRC患者的数据。我们将 利用这些数据建立编码基因和非编码RNA的表达预测模型， 来自ACCC的大约18，999例CRC病例和31，269例对照的TWAS。在第三阶段，我们将... 在心理上评估目标1和2中确定的前30个基因的生物学功能。基于关联 在它们的表达水平和CRC风险之间的方向，我们将使用CRISPRi抑制表达， 使用CRISPRa在多种正常结肠上皮和CRC细胞系中促进它。我们将在试管中 分析和分析生物信息学证据，以检查这些选定基因的生物功能， 评估它们在调节已知癌症相关途径中的潜在作用。我们提出的研究非常 具有成本效益，因为欧洲后裔的转录组数据集（GTEx）和GWAS数据都是 已经提供给我们。这项拟议的研究将提供强有力的证据，查明CRC的易感性 基因，从而促进我们的研究成果转化为癌症预防和病人护理。

PROJECT SUMMARY Genetic factors play an important role in the etiology of colorectal cancer (CRC). To date, approximately 50 genetic loci have been identified for CRC through genome-wide association studies (GWAS). However, these loci explain only a small fraction of heritability. Moreover, target genes and underlying mechanisms for most of these risk loci remain unclear. The large majority are noncoding variants, many of which have been shown to regulate gene expression. Recent studies suggest that ~80% of disease heritability can be explained by regulatory variants. However, these variants are each associated with only a small alteration in disease risk; thus they are difficult to identify using GWAS. Recently, a novel approach, the transcriptome-wide association study (TWAS), was developed to systematically investigate the transcriptome's association with disease risk. In TWAS, models are built to predict gene expression with cis-SNPs using a reference transcriptome, and then applied to GWAS data to evaluate their associations with disease risk. Here, we propose to use this innovative approach to scan the whole transcriptome to discover novel CRC susceptibility genes and uncover likely causal genes in loci revealed in previous GWAS. In Aim 1, we will conduct a TWAS in European descendants. We will build expression prediction models for coding genes and non-coding RNAs in hundreds of colorectal tissues, other multiple tissues, and cross tissues using transcriptome and high-density genotyping data from individuals of European ancestry in the Genotype-Tissue Expression (GTEx) project. The models will be used to predict gene expression levels using GWAS data from approximately 27,911 CRC cases and 23,059 controls included in the ColoRectal Transdisciplinary Study (CORECT) and the Genetics and Epidemiology of Colorectal Cancer (GECCO) consortia, and then to evaluate their associations with CRC risk. In Aim 2, we will conduct a TWAS in East-Asian descendants. We will generate transcriptome data and high-density genotyping data from 400 CRC patients of Asian ancestry from the Asia Colorectal Cancer Consortium (ACCC). We will use these data to build expression prediction models for coding genes and non-coding RNAs and perform a TWAS in approximately 18,999 CRC cases and 31,269 controls from the ACCC. In Aim 3, we will experi- mentally evaluate biological function of the top 30 genes identified in Aims 1 and 2. Based on the association direction between their expression levels and CRC risk, we will either suppress expression using CRISPRi or promote it using CRISPRa in multiple normal colon epithelial and CRC cell lines. We will then perform in vitro assays and analyze bioinformatics evidence to examine the biological functions of these selected genes and to assess their potential roles in regulating known cancer-related pathways. Our proposed study is extremely cost-efficient, as both the transcriptome dataset (GTEx) for European descendants and the GWAS data are already available to us. This proposed study will provide strong evidence for pinpointing CRC susceptibility genes, thereby facilitating the translation of our findings to cancer prevention and patient care.