Identification of Cooperative Genetic Alterations in the Pathogenesis of Oral Cancer

口腔癌发病机制中协同遗传改变的鉴定

• 批准号: 9084417
• 负责人: Olivier Gevaert
• 金额: $ 94.78万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-07-01 至 2019-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9084417
• 关键词: Adenocarcinoma; Advanced Development; Air; Algorithms; Architecture; Back; Bioinformatics; Biological Assay; Biological Models; Candidate Disease Gene; Carcinoma; Cell Survival; Cells; Chemosensitivity Assay; Clustered Regularly Interspaced Short Palindromic Repeats; Complementary DNA; Complex; Computer Analysis; Critical Pathways; DNA Methylation; DNA Sequence Alteration; Data; Data Set; Dependency; Development; Dysplasia; Gene Expression; Gene Mutation; Genes; Genetic; Genomic Instability; Genomics; Goals; Growth; Head and neck structure; Health; Human; Human Cell Line; In Vitro; Investigation; Label; Liquid substance; Malignant Neoplasms; Medicine; Methods; Methylation; Modeling; Molecular; Mus; Mutation; Nature; Neoplasm Metastasis; Normal tissue morphology; Oncogenes; Oncogenic; Operative Surgical Procedures; Oral mucous membrane structure; Organoids; Output; Pathogenesis; Pathway interactions; Patients; Pharmaceutical Preparations; Phenotype; Primary Neoplasm; Probability; Process; Protocols documentation; Regulator Genes; Sampling; Specimen; System; Testing; The Cancer Genome Atlas; Tissues; Transgenic Mice; Update; Validation; Viral; Xenograft Model; Xenograft procedure; actionable mutation; base; biobank; combinatorial; drug discovery; epigenomics; exome sequencing; experience; gastrointestinal; gene interaction; in vivo; in vivo Model; insight; malignant breast neoplasm; malignant mouth neoplasm; malignant phenotype; mouth squamous cell carcinoma; mutational status; neoplastic cell; next generation; novel; novel strategies; novel therapeutics; screening; single cell sequencing; small hairpin RNA; tissue culture; tumor; tumor microenvironment

 DESCRIPTION (provided by applicant): Recent in depth molecular analyses of human malignancies, through projects such as The Cancer Genome Atlas (TCGA), have revealed numerous frequently identified mutations; however, only a subset of these actually contribute to the development of particular cancers. The malignant phenotype is often the result of synthetic genetic interactions between multiple genomic and epigenomic aberrations. As such, subsets of tumors have specific co-occurring mutations or genomic alterations that cooperate in a co-dependent manner. The goal of this application is to identify the critical co-dependent molecular pathways that cooperate with known driver genomic alterations in oral squamous cell carcinoma (OSCC), one of the most frequent malignancies of the head and neck. The insight gained will, in turn, provide a platform for novel drug discovery and/or rationale for the investigation of novel combinations of existing drugs. Aim 1 will use sophisticated new bioinformatics algorithms developed by the Gevaert lab to integrate mutation and copy number alteration data with DNA methylation and gene expression data in OSCC TCGA data sets. These algorithms will be used to predict, with high probability, candidate genetic interactions among heterogeneous OSCC tumors and to identify master regulators of gene modules that are related to particular biologic processes, such as metastasis. In Aim 2, candidate gene interactions and master regulators will be validated by the Sunwoo lab using "next generation" in vivo synthetic lethality assays, using patient-derived xenografts to more closely reflect the primary tumor. Candidate master regulators of metastasis will also be evaluated using in vivo assays. In Aim 3, the Kuo lab has adapted their experience in culture and oncogenic transformation of gastrointestinal 3D air-liquid interface primary organoid cultures to OSCC. Accordingly, our validated wild-type oral mucosal organoid protocols will be used to introduce co-occurring mutations and gene alterations into wild-type human and mouse oral mucosa tissue to functionally validate the oncogenic activity and multigenic transforming synergy of putative OSCC genes from Aims 1 and 2. In Aim 3, the 3D organoid culture approach will also be used to grow primary human OSCC tumor organoids directly from surgical samples, for in vitro chemosensitivity testing, correlation against exome sequencing mutational status and shRNA/sgRNA-based gene validation. This bi-directional strategy of (1) targeting co-occurring mutations in patient-derived xenografts and primary tumors and (2) introducing co-occurring mutations into normal oral mucosa will provide important insight into our understanding of the synthetic genetic interactions in OSCC. Further, the functional and genetic data from Aims 2 and 3 will be channeled back to Aim 1 to continuously update the bioinformatics models.

 描述（由申请人提供）：最近通过癌症基因组图谱（TCGA）等项目对人类恶性肿瘤进行了深入的分子分析，揭示了许多常见的突变；然而，其中只有一部分实际上会导致特定癌症的发展。恶性表型通常是多个基因组和表观基因组畸变之间综合遗传相互作用的结果。因此，肿瘤的子集具有特定的共存突变或基因组改变，它们以相互依赖的方式合作。本申请的目标是确定与口腔鳞状细胞癌（OSCC）（头颈部最常见的恶性肿瘤之一）中已知的驱动基因组改变相配合的关键共同依赖分子途径。反过来，获得的见解将为新药发现和/或现有药物新组合研究的基本原理提供平台。目标 1 将使用 Gevaert 实验室开发的复杂的新型生物信息学算法，将突变和拷贝数改变数据与 OSCC TCGA 数据集中的 DNA 甲基化和基因表达数据整合起来。这些算法将用于以高概率预测异质 OSCC 肿瘤之间的候选遗传相互作用，并识别与特定生物过程（例如转移）相关的基因模块的主调控因子。在目标 2 中，Sunwoo 实验室将使用“下一代”体内合成致死性测定来验证候选基因相互作用和主调节因子，并使用患者来源的异种移植物来更密切地反映原发性肿瘤。还将使用体内测定来评估候选的转移主调节因子。在目标 3 中，Kuo 实验室将其在胃肠道 3D 气液界面原代类器官培养物的培养和致癌转化方面的经验应用于 OSCC。因此，我们经过验证的野生型口腔粘膜类器官方案将用于将共同发生的突变和基因改变引入野生型人类和小鼠口腔粘膜组织中，以功能验证来自目标 1 和 2 的假定 OSCC 基因的致癌活性和多基因转化协同作用。在目标 3 中，3D 类器官培养方法也将用于直接培养原代人 OSCC 肿瘤类器官 从手术样本中提取数据，用于体外化学敏感性测试、与外显子组测序突变状态的相关性以及基于 shRNA/sgRNA 的基因验证。这种双向策略（1）针对患者来源的异种移植物和原发性肿瘤中的共存突变以及（2）将共存突变引入正常口腔粘膜将为我们了解 OSCC 中的合成遗传相互作用提供重要的见解。此外，目标 2 和目标 3 的功能和遗传数据将被引导回目标 1，以不断更新生物信息学模型。