Genomic Analysis of Tumor Context Vulnerabilities in Human Metastatic Melanoma

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DESCRIPTION (provided by applicant): Despite decades of research, metastatic malignant melanoma remains an incurable disease. Only a minority of patients diagnosed with metastatic melanoma show a clinical response to chemotherapy, while still fewer are cured; the 5-year survival rate for patients with disseminated disease ranges from 5-18%. The focus and underlying goal of this project is to identify specific genetic changes in melanoma, confirmed through both functional genomic screening and in vivo validation, which provide a context of genetic vulnerability that can be exploited in advanced stage melanoma. Specifically, we are proposing to undertake a high-throughput functional RNA interference (RNAi) screen to systematically identify genes that mediate melanoma cell sensitivity (Specific Aim 1). We will subsequently validate the role of these genes (Specific Aim 2) by confirming siRNA-mediated gene knockdown in vitro, characterizing protein expression in human melanomas using tissue microarrays (TMAs), performing high-content mechanistic assays to elucidate the mechanism by which these genes mediate melanoma cell sensitivity in vitro, and evaluating the effectiveness of inhibiting these genes in vitro in combination with the selecting agent. Lastly, we will evaluate whether our validated genetic targets can add to molecularly-informed combination therapies in vivo against xenograft models of melanoma (Specific Aim 3). We hypothesize that this functional-based genomic approach will identify the context of genetic perturbations associated with tumor progression that are critical to rendering melanoma cells more resistant to chemotherapy. We speculate that these validated genes could facilitate the combined targeting of these tumor-context vulnerabilities and could be of direct relevance to clinical exploitation. Relevance: The long-term prognosis for patients diagnosed with advanced stage melanoma is dismal, with a five-year survival rate ranging from 5-18%. The proposed research aims to identify genetic vulnerabilities acquired by metastatic melanoma cells that may be exploited to improve the effectiveness of clinical intervention in this disease.