Identifying therapeutic vulnerabilities in RAS pathway–driven melanoma

Abstract

Cutaneous melanoma is a malignancy that arises from melanocytes within the skin. Over 100,000 new diagnoses of melanoma are predicted within the United States in 2024, and incidence rates of melanoma have continued to increase, despite public health efforts to enhance melanoma prevention and management. While immune checkpoint blockade has revolutionized the standard of care and clinical outcome for advanced melanoma, many tumors are intrinsically resistant or often become resistant to immunotherapy over time, highlighting the urgent need to identify and develop novel therapeutic strategies to provide clinical benefit for patients with melanoma. The majority of melanomas are characterized by oncogenic driver mutations in genes within the RAS–MAPK signaling pathway, including BRAF, NRAS, and NF1, and may respond to targeted inhibition of this pathway. Indeed, combined inhibition of BRAF and MEK has been approved for the treatment of BRAFV600-mutant melanoma, although disease progression is common. Moreover, MEK inhibitors are not effective as single agents in NRAS-mutant melanoma and no other targeted therapies have been approved for these malignancies. To this end, this dissertation describes a genome-scale investigation of genetic pathways that sensitize RAS pathway–mutant melanoma to RAS pathway inhibition, leading to the development of two distinct approaches to induce melanoma cell death. Through the analysis of a genome-scale CRISPR–Cas9 knockout screen in NRAS-mutant melanoma cells, we identified the deubiquitinating enzyme USP7 as a target that elicits potent antitumor effects in vitro and in vivo when co-suppressed along with MEK inhibition. Integration of functional genetic approaches with epigenetic and transcriptomic analyses revealed that inhibition of USP7 in the context of RAS pathway inhibition influenced melanoma cell state in some settings and led to the upregulation of multiple transcriptional programs that contributed to melanoma cell death in NRAS-mutant as well as BRAF-mutant melanomas. This dissertation also describes the identification of the E3 ubiquitin ligase MARCH5 as a distinct vulnerability in NRAS-mutant melanoma that may be targeted in combination with MEK inhibition to promote melanoma cell death, likely by converging on a process of mitochondrial morphology and homeostasis. This dissertation concludes with a comprehensive overview of preclinical and clinical literature and categorizes combinatorial strategies that may be effective in RAS pathway–driven tumors of other tissues of origin. In summary, we have identified two distinct therapeutic vulnerabilities in RAS pathway–mutant melanoma and have provided a conceptual framework for future development of combination therapies in the treatment of melanoma and other RAS pathway–driven tumors.