Dissecting Co-Dependent Pathways in Oral Cancers

 描述（由申请人提供）：在主要三级中心就诊的晚期口腔鳞状细胞癌（OSCC）患者中，超过50%的患者在一线治疗复发后5年内死亡。我们相信，通过改善我们正在进行的精准医学试验，可以提高总生存率，在这些试验中，在正确的时间给予正确的治疗，但这需要全面了解疾病的分子亚群。尽管已经从公开的OSCC测序数据中获得了知识，并且由于驱动因子和丢失的抑制因子的多样性，但测序的病例太少，无法在整合的基因组和转录组水平上对疾病进行分子分层。重要的是，针对常见的分子改变，包括EGFR、FGFR 1/3、PIK 3CA、NOTCH等，已经有了几种靶向治疗;然而，由于先天遗传或补偿性抗性，这些药物作为单一疗法通常表现不佳，从而强烈需要合理的联合疗法。事实上，NOTCH通路的各种成员在约50%的OSCC中发生突变，虽然我们和其他人最近将WNT通路抑制剂推进到该分子亚群的临床试验中，但NOTCH缺陷型肿瘤经常具有额外的病变，这些病变可能会混淆靶向单一疗法的治疗益处。我们收集了一组独特的手术治疗的反应性和复发性口腔鳞癌肿瘤，我们建议使用整合遗传和转录组测序研究共同改变病变的频率。通过对基因定义的OSCC细胞系模型进行初步合并的CRISPR和小分子筛选，我们将验证一种定义联合治疗靶点的策略。此外，我们显示了初步的结果，使用手术切除，离体口腔鳞癌组织作为模型系统，以评估新的组合疗法。利用这些工具和技术，我们将测试我们的中心假设，即驱动对靶向单一疗法的耐药性的先天或代偿途径可以通过我们的综合方法进行识别，并用于开发克服耐药性的有效组合方案。我们将通过以下目的来解决这一假设：1）通过手术无应答的OSCC中的整合下一代测序来鉴定用于组合疗法的共依赖分子靶标，2）使用慢病毒CRISPR和小分子文库来定义OSCC细胞系中细胞增殖的关键基因和途径的组合，3）使用体内模型来开发用于遗传上定义的OSCC的组合治疗策略。我们的主要目标是开发新的联合策略，通过识别共同依赖的治疗靶点来提高OSCC患者的生存率。

 DESCRIPTION (provided by applicant): Over 50% of patients with advanced Oral cavity Squamous Cell Carcinomas (OSCCs) seen at major tertiary centers die within five years of diagnosis following relapse from frontline therapy. We believe that improvements to overall survival will be made by improving our ongoing precision medicine trials, in which the right therapies are given at the right time, but this requires a comprehensive understanding of molecular subsets of the disease. Despite the knowledge that has been gained from publicly available OSCC sequencing data and because of the diversity of drivers and lost suppressors, too few cases have been sequenced to molecularly stratify the disease on an integrated genomic and transcriptomic level. Importantly, several targeted therapies have been advanced for common molecular alterations including EGFR, FGFR1/3, PIK3CA, NOTCH, etc.; however, these often perform poorly as monotherapies due to innate genetic or compensatory resistance creating a strong need for rational combination therapy. In fact, various members of the NOTCH pathway are mutated in ~50% of all OSCCs, and while we and others have recently advanced WNT pathway inhibitors to clinical trials for this molecular subset, NOTCH-deficient tumors frequently harbor additional lesions that can confound the therapeutic benefits of targeted monotherapy. We have collected a unique set of surgically treated responsive and relapsed OSCC tumors, which we propose to study for the frequency of co-altered lesions using integrative genetic and transcriptomic sequencing. Through preliminary pooled CRISPR and small molecule screening of genetically defined OSCC cell line models, we will validate a strategy that defines targets for combination therapy. Further, we show preliminary results using surgically excised, ex vivo OSCC tissue as a model system to evaluate novel combination therapies. Leveraging these tools and techniques, we will test our central hypothesis that innate or compensatory pathways, which drive resistance to targeted monotherapies, can be identified through our integrative approach and exploited to develop effective combination protocols that overcome resistance. We will address this hypothesis with the following Aims: 1) Identify co-dependent molecular targets for combination therapy through integrative next generation sequencing in surgically non-responsive OSCC, 2) Define the combinations of genes and pathways pivotal for cell proliferation in OSCC cell lines using lentiviral CRISPR and small molecule libraries, 3) Develop combination treatment strategies for genetically defined OSCC using in vivo models. Our primary goal is to develop novel combination strategies to improve the survival of patients with OSCC through identification of co-dependent therapeutic targets.