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。在合成中 致命的相互作用，一个基因的改变会导致对另一个基因的依赖。这两种变化本身都不是 是生存所必需的，但这些改变共同导致癌细胞死亡。目前，合成致死(SL) 使用大型功能屏幕确定合作伙伴，这会受到人为因素的负面影响 在正确的癌症背景下，具有特定突变的细胞系的细胞培养条件和可获得性有限。 我们建议挖掘患者肿瘤数据库以确定胚系突变的SL伙伴。我们的假设是 生殖系突变的SL配对将被选择性地扩增或永远不会被删除，并且在 含有突变的原发肿瘤样本。提出了两个具体目标：在目标1中，我们将开发一种 一种基于挖掘大规模基因组和转录数据集识别SL伙伴的计算方法 癌症中的生殖系突变。该方法将应用于来自 癌症基因组图谱(TCGA)和GTEx正常组织的基因表达数据(基因类型-组织 表达)以确定三个众所周知的乳腺癌CPGs、BRCA1、 BRCA2和PALB2。在目标2中，我们将对每个生殖系突变的SL伙伴进行实验验证 在目标1中用两个步骤确定。首先，在目标2a中，我们将使用基因验证SL合作伙伴的每个突变 SL配对与可诱导的shRNA在体外等基因乳腺癌细胞系(+/-突变)中的击倒。下一首, 在Aim 2b中，我们将验证人类乳腺癌细胞系中前三个突变-SL配对组合 用遗传学和药理学方法敲除小鼠的异种移植。我们预计拟议的研究将确定 乳腺癌治疗和化学预防的新药物靶点。长期目标是 开发一种新的系统方法，以确定潜在的治疗和靶向治疗 癌症生殖系突变患者的化学预防。拟议的研究对PQ3做出了回应，并将 阐明具有生殖系突变的肿瘤对基于遗传SL相互作用的靶向治疗的反应 胚系突变和体细胞变化之间的关系。

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. In synthetic lethal interactions, an alteration in one gene leads to dependency on a second gene. Neither alteration by itself is essential for survival, but together these alterations lead to cancer cell death. 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. Two specific aims are proposed: In Aim 1, we will develop a computational method based on mining large-scale genomic and transcriptomic datasets to identify SL partners of germline mutations in cancer. This method will be applied to genomic and transcriptomic datasets from The Cancer Genome Atlas (TCGA), 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.