Identification of Synthetic Lethal Partners of Cancer Germline Mutations using PanCancer Human Primary Tumor Data

项目总结 我们提出了一种新的计算方法来确定生殖系突变癌症的治疗靶点 应用泛癌原发肿瘤胚系突变和体细胞改变的综合分析 数据。这种方法将用于在乳腺癌中寻找新的治疗靶点，以寻找胚系突变。 BRCA1、BRCA2和PALB2。胚系突变导致癌症风险增加的基因被称为 癌症易感基因(CPGs)。许多Cpg已经为人所知，DNA的最新进展 测序预示着有更多的CPG发现。鉴于生殖系携带者患癌症的风险增加 CpG突变，迫切需要确定新的治疗和化学预防策略 这些突变。这些突变大多是功能丧失的改变，不能直接下药。合成的 致命性为确定这些突变的新治疗靶点提供了基础。目前， 合成致死(SL)伙伴是使用大型功能筛查来识别的，这些筛查会受到负面影响 由于细胞培养条件的人为和具有特定突变的细胞系的有限的可用性 正确的癌症背景。我们建议挖掘患者肿瘤数据库来识别生殖系的SL伙伴 突变。我们的假设是，生殖系突变的SL伴侣将被选择性扩增或永远不会被删除 并且在含有突变的原发肿瘤样本中也过度表达。此前，我们开发了一部小说 分析原发肿瘤数据以确定SL合作伙伴的计算方法(挖掘合成致死，MISL) 特定肿瘤类型的体细胞突变。我们建议开发一个基于MISL的计算流水线来 确定与生殖系突变的遗传交互作用。在目标1中，我们将开发一个基于MISL的计算程序 鉴定癌症胚系突变的SL配对的方法。这一方法将应用于基因组和 来自多个大规模癌症基因组测序项目和基因表达数据的转录数据集 从GTEx(基因-组织表达)的正常组织中鉴定SL配对的胚系突变 三个著名的乳腺癌CPG，BRCA1，BRCA2和PALB2。在目标2中，我们将通过实验验证 SL在两个步骤中为目标1中确定的每个生殖系突变配对。首先，在目标2a中，我们将验证 SL通过在同基因乳房中利用可诱导的shRNA基因敲除SL伴侣来应对每个突变 体外培养的癌细胞株(+/-突变)。接下来，在Aim 2b中，我们将验证前三个突变-SL合作伙伴 利用遗传学和药理学基因敲除技术在小鼠人乳腺癌细胞系异种移植中的组合。 我们期望这项拟议的研究将为乳房的治疗和化学预防确定新的可用药靶点。 癌症。长期目标是开发一种新的系统方法来确定潜在的目标 癌症生殖系突变患者的治疗和化学预防方法。建议进行的研究 对PQ3做出反应，并将阐明具有生殖系突变的肿瘤对基于以下因素的靶向治疗的反应 种系突变和体细胞变化之间的遗传SL交互作用。

PROJECT SUMMARY We propose a novel computational approach to identify therapeutic targets for cancers with germline mutations using integrative analysis of germline mutations and somatic alterations from pan-cancer primary human tumor data. This method will be used to identify new therapeutic targets in breast cancer for germline mutations in BRCA1, BRCA2, and PALB2. Genes in which germline mutations confer increased risks of cancer are called cancer predisposition genes (CPGs). Numerous CPGs are already known, and recent advances in DNA sequencing hold the promise of more CPG discoveries. Given the increased cancer risk in people with germline CPG mutations, there is an urgent need to identify new therapeutic and chemopreventive strategies specific to these mutations. Most of these mutations are loss-of-function alterations and not directly druggable. Synthetic lethality provides the basis for an approach to identify new therapeutic targets for these mutations. Currently, synthetic lethal (SL) partners are identified using large-scale functional screens, which are negatively impacted by the artificiality of the cell culture conditions and limited availability of cell lines with the specific mutations in the right cancer context. We propose to mine patient tumor databases to identify SL partners of germline mutations. Our hypothesis is that SL partners of a germline mutation will be selectively amplified or never deleted and also over-expressed in primary tumor samples harboring the mutation. Previously, we developed a novel computational method (Mining Synthetic Lethals, MiSL) that analyzes primary tumor data to identify SL partners of somatic mutations in specific tumor types. We propose to develop a computational pipeline based on MiSL to identify genetic interactions with germline mutations. In Aim 1, we will develop a MiSL-based computational method to identify SL partners of germline mutations in cancer. This method will be applied to genomic and transcriptomic datasets from multiple large-scale cancer genome sequencing projects and gene expression data for normal tissues from GTEx (Genotype-Tissue Expression) to identify SL partners of germline mutations in three well-known breast cancer CPGs, BRCA1, BRCA2, and PALB2. In Aim 2, we will experimentally validate the SL partners for each germline mutation identified in Aim 1 in two steps. First, in Aim 2a, we will validate the SL partners for each mutation using genetic knockdown of the SL partner with inducible shRNA in isogenic breast cancer cell lines (+/-mutation) in vitro. Next, in Aim 2b, we will validate the top three mutation-SL partner combinations in human breast cancer cell line xenografts in mice using genetic and pharmacologic knockdown. We expect the proposed study will identify novel druggable targets for treatment and chemoprevention in breast cancer. The long-term objective is to develop a new systematic methodology to identify potential targeted therapies for treatment and chemoprevention of patients with germline mutations in cancer. The proposed study responds to PQ3 and will elucidate how tumors with germline mutations respond to targeted therapies based on genetic SL interactions between germline mutations and somatic alterations.