Identification and Characterization of Gene Fusions in Lung Adenocarcinoma

描述(申请人提供)：肺癌是世界范围内癌症死亡的主要原因，肺腺癌是发病率增加的亚型。识别特定的改变，如EGFR突变和最近的ALK激酶基因融合，已经导致了对其肺腺癌包含这些改变的患者的更有效的治疗。我们利用了一种新的策略来鉴定肺癌中的基因融合(Wang等人，自然生物技术)，揭示了肺腺癌中的R3HDM2-NFE2和最近的HSPA1A-NFKBIL1基因融合，并提名了许多其他潜在的基因融合候选者。我们推测，在肺腺癌中识别新的基因融合可能为这种癌症的高选择性治疗提供新的途径，以及为癌症检测或治疗监测提供特异的标志物。提出了三个具体目标。目的一是在含有这些改变的肺癌细胞系中利用siRNA敲除R3HDM2-NFE2基因融合的新的功能特征，并使用经工程改造的高表达NFE2的肺癌细胞系。对肿瘤细胞增殖、侵袭和特定转录程序的影响将确定R3HDM2-NFE2致癌活性的机制。目的二是用组织芯片荧光原位杂交技术确定HSPA1A-NFKBIL1融合基因在肺癌中的发生频率，并与目的一中的R3HDM2-NFE2基因融合基因的致癌活性进行功能分析。目的三将利用发现R3HDM2-NFE2和HSPA1A-NFKBIL1融合的成功方法，识别、验证和功能表征其他涉及肺癌重要细胞过程的新融合。优先考虑的将是靶向治疗的候选基因融合，或者涉及可能开发治疗的基因和关键细胞靶点的基因融合。此外，还将更加重视出现频率较高或可识别的肿瘤亚群内的候选病例。这些研究有可能确定治疗癌症死亡的主要原因的新方法。 公共卫生相关性：肺癌是所有癌症中死亡率最高的，如果及早发现或直接针对癌症特有的改变进行治疗，则是最好的治疗方法。基因融合代表了肺癌中一种新的基因改变，可以证明这种癌症特异性，并可能对新的治疗方法产生反应。这项研究计划将利用新开发的生物信息学方法结合下一代测序数据来识别肺癌中的新基因融合。有很大的潜力可以确定新的治疗靶点以及早期发现的直接影响特定肺癌患者生存的标志物。

DESCRIPTION (provided by applicant): Lung cancer is the leading cause of cancer mortality worldwide with lung adenocarcinomas representing the subtype that is increasing in incidence. Identification of specific alterations such as EGFR mutations and more recently, ALK kinase gene fusions, have lead to the more efficacious treatment of patients whose lung adenocarcinomas contain these alterations. We have utilized a novel strategy for the identification of gene fusions in lung cancer (Wang et al, Nature Biotechnology) revealing the R3HDM2-NFE2 and more recently the HSPA1A-NFKBIL1 gene fusions in lung adenocarcinomas, as well as nominating many additional potential gene-fusion candidates. We hypothesize that identification of novel gene fusions in lung adenocarcinoma may provide new avenues for highly selective treatments of this cancer as well as specific markers for cancer detection or therapeutic monitoring. Three specific aims are proposed. Aim one is to functionally characterize the novel R3HDM2-NFE2 gene fusion utilizing siRNA knockdown in lung cancer lines containing these alterations as well as using lung cell lines engineered to overexpress NFE2. Effects on tumor cell proliferation, invasion and specific transcriptional programs will define the mechanisms underlying R3HDM2-NFE2 oncogenic activity. Aim two is to define the frequency of occurrence of the novel HSPA1A-NFKBIL1 gene fusion in primary lung cancers using fluorescence in situ hybridization with tissue microarrays, followed by functional analyses of the oncogenic activity of the fusion gene as those utilized for the R3HDM2-NFE2 in Aim one. Aim three will employ the successful methodologies used for the discovery of the R3HDM2-NFE2 and HSPA1A- NFKBIL1 fusions, to identify, validate and functionally characterize additional novel fusions involving functionally important cellular processes in lung cancer. Priority will be gene fusions that are candidates for targeted therapeutics or that involve genes and critical cellular targets for which therapies may be potentially developed. Higher emphasis will also be placed on candidates occurring at high frequency or within identifiable tumor subgroups. These studies have potential to identify new approaches to treat the leading cause of cancer death. PUBLIC HEALTH RELEVANCE: Lung cancer has the highest mortality of all cancers and best treated when detected early or with therapies directly against cancer-specific alterations. Gene fusions represent a new category of genetic alterations in lung cancer that can demonstrate this cancer-specificity and may be responsive to new therapies. This research proposal will identify new gene-fusions in lung cancer utilizing a newly developed bioinformatics approach combined with next-generation sequencing data. There is great potential that new therapeutic targets may be identified as well as markers for early detection that would directly impact survival of specific patients with lung cancer.