Discovery of Homologous Recombination DNA Repair Deficiency in Lung Tumor

描述（由申请人提供）：范可尼贫血（FA）途径是响应遗传毒性损伤的同源重组DNA修复的主要机制。FA缺乏的细胞对DNA损伤剂如顺铂和丝裂霉素C（MMC）高度敏感。BRCA基因与相同修复途径（FA途径）中的其他基因协作，在DNA损伤诱导后或在细胞周期的S期在染色质上形成DNA修复灶。鉴于这一通路中涉及大量基因，我们假设相当大比例的肺癌患者具有体细胞遗传或表观遗传改变，导致FA同源重组修复缺陷。这些患者更有可能从链间DNA交联剂中获益。有必要进行一项测试，以检查整个通路的功能，并实际应用于大规模筛查，以确定这些患者。我们最近报道了一种FA三重染色免疫荧光（FATSI）测试，以评估FANCD 2病灶的存在或不存在，并生成了包括肺癌在内的几个器官部位的患者肿瘤中该途径体细胞缺陷的初步数据。然而，在这些散发性肿瘤中导致FA通路失活的特定遗传和表观遗传改变仍然未知。为了提供足够的分子证据来支持临床治疗的这种选择，并了解导致肺癌中FA通路缺陷的遗传和表观遗传变化，我们建议实现以下目标：（1）通过分析100个人肺肿瘤和100个匹配的非肿瘤样品来鉴定肺癌患者中的FANCD 2病灶缺陷肿瘤，和（2）通过使用下一代测序（RNAseq）分析肿瘤和邻近非肿瘤组织中与FA途径相关的RNA转录组，对目的1中鉴定的FANCD 2病灶缺陷性肿瘤进行功能基因组学分析，以及（3）研究目的1中鉴定的FANCD 2灶缺陷肿瘤中FA基因启动子甲基化。预计从该项目获得的信息将有助于 验证基于免疫荧光的三重染色试验，其可用于证明肺癌患者的后续临床治疗。

DESCRIPTION (provided by applicant): The Fanconi Anemia (FA) pathway is a major mechanism of homologous recombination DNA repair in response to genotoxic insults. Cells with FA deficiency are hypersensitive to DNA damage agents such as cisplatin and mitomycin C (MMC). BRCA genes collaborate with other genes in the same repair pathway, the FA pathway, to form foci of DNA repair on chromatin following DNA damage induction, or during the S phase of cell cycle. Given the large number of genes involved in this pathway, we hypothesize that a substantial proportion of patients with lung cancer harbor somatic genetic or epigenetic alterations resulting in defective FA homologous recombination repair. These patients are more likely to derive benefit from interstrand DNA crosslink agents. A test that could examine the functionality of this pathway as a whole and that could be practically applied for large-scale screening would be necessary to identify these patients. We have recently reported a FA triple-staining immunofluorescence (FATSI) test to evaluate the presence or absence of FANCD2 foci, and have generated preliminary data for somatic deficiency of this pathway in patients' tumors across several organ sites that include lung cancers. However, the specific genetic and epigenetic alterations that lead to inactivation of FA pathway in these sporadic tumors are still unknown. In order to provide sufficient molecular evidence to support such selection for clinical treatment and to understand the genetic and epigenetic changes that lead to FA pathway deficiency in lung cancers, we propose to accomplish following aims: (1) to identify FANCD2 foci defective tumor in lung cancer patients by analyzing 100 human lung tumor and 100 matching non-tumor samples, and (2) to perform a functional genomics analysis of FANCD2 foci defective tumors identified in aim 1 through analysis of the RNA transcriptome associated with the FA pathway in the tumor and adjacent non-tumor tissues, using next generation sequencing (RNAseq), and (3) to investigate promoter methylation of FA genes in FANCD2 foci defective tumors identified in aim 1. The information obtained from this project is expected to be useful for validating the immunofluorescence based triple staining test which can be used for justifying subsequent clinical therapeutic treatment for the patient with lung cancer.