Uncovering colorectal cancer etiology and biology by integrating proteomics with other omics data

通过将蛋白质组学与其他组学数据相结合，揭示结直肠癌的病因学和生物学

基本信息

批准号：
10585424
负责人：
Xingyi Guo
金额：
$ 76万
依托单位：
VANDERBILT UNIVERSITY MEDICAL CENTER
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-04-11 至 2028-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10585424
关键词：
Acceleration Affect African ancestry Asia Asian Asian ancestry Asian population Association of Community Cancer Centers Biological Biological Assay Biological Process Biology Black Populations Blood Proteins Blood specimen CRISPR interference Cancer Biology Cancer Etiology Cancer Patient Cancer-Predisposing Gene Carcinoma Cell physiology Cells Co-Immunoprecipitations Cohort Studies Collaborations Colon Colon Carcinoma Colorectal Cancer Colorectal Neoplasms Communities Complex Data Development Diagnostic Epidemiology Etiology European European ancestry Freezing Gene Expression Genes Genetic Genetic Models Genetic Predisposition to Disease Immunofluorescence Immunologic In Vitro Incidence Individual Length MAP Kinase Gene Malignant Neoplasms Measures Messenger RNA Methodology Methods Modeling Nested Case-Control Study PIK3CG gene Pathogenesis Pathway interactions Patient Care Patients Phosphorylation Pilot Projects Play Predisposition Prevention Prospective, cohort study Protein Biosynthesis Protein Kinase Proteins Proteome Proteomics Regulatory Pathway Research Design Resources Risk Assessment Role Sampling Signal Transduction Susceptibility Gene TP53 gene Technology Tissues Transforming Growth Factor beta Translating Translational Regulation Translations United States Western Blotting Women&apos s Health adenoma biomarker identification causal variant colon cancer cell line colon tumorigenesis colorectal cancer prevention colorectal cancer risk common treatment density disorder prevention disorder risk experimental study gene product genome wide association study genomic data improved in vitro Assay insight male health novel protein biomarkers protein expression therapeutic development therapeutic target transcriptome transcriptome sequencing translational genetics tumor progression

项目摘要

PROJECT SUMMARY Genetic factors play a significant role in the etiology of colorectal cancer (CRC). To date, approximately 180 genetic susceptibility loci have been identified for CRC through genome-wide association studies (GWAS). However, causal genes for the large majority of these loci remain unknown, hindering the translation of GWAS findings into disease prevention and treatment. Recently, we and others have identified many putative CRC susceptibility genes using transcriptome-wide association studies (TWAS) that focus exclusively on mRNAs. However, it is the proteins not mRNAs that primarily perform cellular functions. Furthermore, cellular proteins are only moderately correlated with their corresponding mRNAs, and for many proteins, correlation is poor as many factors affect protein synthesis and post-translation stability. Herein, we propose a well-powered proteome-wide association study (PWAS) to systematically search the proteome to identify proteins associated with CRC risk and further characterize their roles in colorectal tumor progression and cellular functions. Specifically, we propose the following aims. Aim 1: To conduct a well-powered PWAS to identify proteins for CRC risk. We will generate proteomics (~10,000 proteins) and genomics data in normal colon tissues from 300 subjects to build genetic models to predict protein expression across the proteome. These models will be applied to the GWAS data of 125,487 individuals (58,131 cases) of European descent to evaluate associations of genetically predicted proteins with CRC risk. We will integrate PWAS findings, along with results from GWAS/TWAS to assess inter-relationships of genes, mRNAs and proteins in the pathogenesis of CRC. Aim 2: To investigate potential roles of PWAS-identified proteins in the adenoma-carcinoma sequence. We will analyze spatial expression of 30 selected PWAS-identified proteins in FFPE samples from 150 early-, late- stage adenoma, and invasive carcinoma from white patients (N= 50 for each group) to investigate if these proteins affect the adenoma-carcinoma sequence. Aim 3: To conduct a nested case-control study to evaluate associations of CRC risk with promising blood proteins uncovered in Aims 1/2: We will analyze circulating levels of 21 proteins selected from Aims 1 and 2 in pre-diagnostic blood samples collected from 1,000 and their matched 1,200 controls of Asian, African and European ancestry. Aim 4: To investigate effects of up to 10 selected PWAS-identified proteins on cellular functions using CRISPRi/a perturbation experiments in multiple normal colon epithelial, and CRC cell lines. We will also assess their potential roles in regulating known CRC signaling, and newly identified CRC pathways uncovered from our study by performing RNA-sequencing and further in vitro verification in both treated and vehicle cells. Given the rigorous study design, the unique resources, and the methodological strengths, we expect that this proposed study will greatly advance our understanding of CRC biology to accelerate the translation of genetic findings in CRC prevention and the development of therapeutic targets.

项目概要遗传因素在结直肠癌（CRC）的病因学中起着重要作用。迄今为止，大约有 180 通过全基因组关联研究 (GWAS) 已确定了 CRC 的遗传易感位点。然而，这些基因座中的大多数的因果基因仍然未知，阻碍了 GWAS 的翻译疾病预防和治疗的研究成果。最近，我们和其他人发现了许多假定的 CRC 使用专门关注 mRNA 的全转录组关联研究 (TWAS) 来确定易感基因。然而，主要执行细胞功能的是蛋白质而不是 mRNA。此外，细胞蛋白与其相应的 mRNA 仅中度相关，并且对于许多蛋白质来说，相关性很差，因为许多因素影响蛋白质合成和翻译后稳定性。在此，我们提出了一种功能强大的全蛋白质组关联研究（PWAS）系统性地搜索蛋白质组以识别相关蛋白质结直肠癌风险，并进一步表征它们在结直肠肿瘤进展和细胞功能中的作用。具体来说，我们提出以下目标。目标 1：进行功能强大的 PWAS 来识别蛋白质结直肠癌风险。我们将在 300 个正常结肠组织中生成蛋白质组学（约 10,000 种蛋白质）和基因组学数据受试者建立遗传模型来预测整个蛋白质组的蛋白质表达。这些模型将应用到 125,487 名欧洲血统个体（58,131 例）的 GWAS 数据来评估关联性具有 CRC 风险的基因预测蛋白质。我们将整合 PWAS 的发现以及来自 GWAS/TWAS 用于评估 CRC 发病机制中基因、mRNA 和蛋白质的相互关系。目标 2：研究 PWAS 鉴定的蛋白质在腺瘤-癌序列中的潜在作用。我们将分析来自 150 个早期、晚期的 FFPE 样品中 30 个选定的 PWAS 鉴定蛋白质的空间表达阶段腺瘤和来自白人患者的浸润性癌（每组 N = 50），以调查这些是否蛋白质影响腺瘤-癌的顺序。目标 3：进行巢式病例对照研究以评估 CRC 风险与目标 1/2 中发现的有希望的血液蛋白的关联：我们将分析循环从 1,000 名患者采集的诊断前血液样本及其样本中选出的目标 1 和 2 中的 21 种蛋白质的水平匹配了 1,200 个具有亚洲、非洲和欧洲血统的对照。目标 4：研究最多 10 个因素的影响使用 CRISPRi/a 微扰实验在多个细胞功能中选择 PWAS 鉴定的蛋白质正常结肠上皮细胞和结直肠癌细胞系。我们还将评估它们在监管已知 CRC 方面的潜在作用信号传导，以及我们通过进行 RNA 测序和研究发现的新发现的 CRC 通路在处理细胞和载体细胞中进行进一步的体外验证。鉴于严格的研究设计，独特的资源和方法论优势，我们期望这项拟议的研究将极大地推进我们的研究了解结直肠癌生物学，加速结直肠癌预防和治疗中遗传学发现的转化治疗靶点的开发。