Impact of cancer predisposition on oncogenic process, microenvironment, and treatment

癌症易感性对致癌过程、微环境和治疗的影响

基本信息

批准号：
10544995
负责人：
FENG CHEN
金额：
$ 46.89万
依托单位：
WASHINGTON UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-01-01 至 2026-12-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10544995
关键词：
ATAC-seq Address Biological Breast Cancer Cell Breast Cancer Model Cells Characteristics Clinical Clonality Computer Analysis Data Development Event Genes Genetic Counseling Genetic Models Genetic Models for Cancer Genetic Transcription Germ-Line Mutation Human Image Immune Incidence Malignant Neoplasms Modeling Molecular Mutation Nature Oncogene Activation Oncogenes Oncogenic Patient-derived xenograft models of breast cancer Patients Pattern Phenotype Predisposition Process Prognosis Proteins Proteomics Renal Cell Carcinoma Renal carcinoma Resolution Role Sampling Signal Transduction Somatic Mutation Susceptibility Gene Testing Tissue-Specific Gene Expression Tissues Transcend Tumor Suppressor Proteins Variant brca gene cancer cell cancer predisposition cancer type cell stroma differential expression experience human imaging improved mouse genetics mouse model multiple omics multiplexed imaging neoplastic cell patient derived xenograft model personalized cancer therapy pressure response single cell analysis single nucleus RNA-sequencing transcriptomics translational impact treatment choice treatment response tumor tumor initiation tumor microenvironment tumor progression tumorigenesis

项目摘要

Our previous study of more than 10 thousand tumors across 33 cancer types identified over 800 germline predisposition variants in both tumor suppressors and oncogenes. Although the impact of some of these variants on cancer onset, incidence rate, and clonality have been documented, the effects of these variants (especially when compared to somatic mutations) on molecular characteristics of cancer cells, contributions of non-cancer cells having germline variants, and treatment responses, are far less studied. Our recent single cell(sc) /single nucleus(sn) RNA-seq analyses of cancer samples provided comprehensive expression profiles at a single cell resolution and revealed the expression of key cancer predisposition genes, such as BRCA 112, VHL, BAP1, and c-MET in many non-cancer stromal and immune cells in the tumor microenvironment (TME). Our pilot analyses also revealed significant differential gene expression in cancer and non-cancer cells based on the nature of the driver event being germline or somatic. We hypothesize that tumors with certain germline predisposition variants in tumor suppressors and oncogenes may show differences in tumor progression and treatment responses from those tumors with somatic mutations in the same genes due to differential influence on mutational, transcriptomic, and proteomic profiles of the cancer cells and potentially distinctive contributions from non-cancer cells having those germline changes. To take advantage of the considerable progress over the last few years, namely newly accumulated cancer sequencing data, advances in single cell omics, patient-derived xenografts (PDX), and tumor genetic models, we propose to test these hypotheses by performing the following: compare germline predisposition variants and somatic mutations to dissect their differential biological impacts and interactions using computational analysis (Aim 1); perform single nucleus RNA-seq/ATAC-seq, spatial transcriptomics, and multiplex imaging analysis of human cancer samples to reveal the differential roles of germline predisposition variants and somatic mutations in tumor cells and the TME (Aim 2); use PDX and genetic cancer models to investigate potential functional differences between germline predisposition variants and somatic mutations in tumor cells, TME, and treatment responses (Aim 3). Results from this study will advance our understanding of the unique contributions of germline variants to cancer cells and TME alike, improve genetic counseling and prognosis, and provide guidance for differential treatment of tumors carrying germline variants vs somatic mutations in key cancer driver genes.

我们之前对 33 种癌症类型的 10,000 多个肿瘤进行的研究发现了 800 多个种系抑癌基因和癌基因的易感性变异。尽管其中一些影响变异对癌症发病、发病率和克隆性的影响已被记录，这些变异的影响（特别是与体细胞突变相比）对癌细胞分子特征的贡献，具有种系变异的非癌细胞和治疗反应的研究要少得多。我们最近的单曲癌症样本的细胞（sc）/单核（sn）RNA-seq分析提供了全面的表达谱以单细胞分辨率揭示了关键癌症易感基因的表达，例如 BRCA 112，肿瘤微环境 (TME) 中许多非癌基质细胞和免疫细胞中的 VHL、BAP1 和 c-MET。我们的初步分析还揭示了基于癌症和非癌细胞的显着差异基因表达关于驱动事件的性质是种系还是体细胞。我们假设具有某些种系的肿瘤抑癌基因和癌基因的易感性变异可能在肿瘤进展和预后方面表现出差异由于差异，相同基因中具有体细胞突变的肿瘤的治疗反应对癌细胞突变、转录组和蛋白质组谱的影响以及潜在的独特性来自具有这些种系变化的非癌细胞的贡献。为充分利用可观的过去几年的进展，即新积累的癌症测序数据、单细胞的进展组学、患者来源的异种移植物（PDX）和肿瘤遗传模型，我们建议通过以下方式检验这些假设：执行以下操作：比较种系易感性变异和体细胞突变以剖析它们使用计算分析来区分生物影响和相互作用（目标 1）；执行单人类癌症的核 RNA-seq/ATAC-seq、空间转录组学和多重成像分析样本揭示种系易感性变异和体细胞突变在肿瘤中的不同作用细胞和 TME（目标 2）；使用 PDX 和遗传癌症模型来研究潜在的功能肿瘤细胞、TME 和肿瘤细胞中种系易感性变异和体细胞突变之间的差异治疗反应（目标 3）。这项研究的结果将增进我们对独特的种系变异对癌细胞和 TME 等的贡献，改善遗传咨询和预后，并为携带种系变异与关键体细胞突变的肿瘤的差异化治疗提供指导癌症驱动基因。