Epi/Genomic characterization and molecular mechanisms of immunotherapy resistance in Hgf-Cdk4^R24Cpreclinical model of human melanoma

Abstract

Molecular studies empowered novel therapeutic strategies against melanoma in recent years, however, therapy resistance lowers the efficacy of targeted therapies and immunotherapies and remained a complex obstacle. Dedifferentiation in melanoma indicates phenotypic plasticity and imposes resistance to immunotherapy and targeted therapy. Murine preclinical models provide vital tools for comparative onco-genomics to study molecular mechanisms underlying tumor phenotypes and to improve therapeutic strategies in human patients. Hgf-Cdk4^R24C mouse preclinical model demonstrated invasive melanoma with proinflammatory induced dedifferentiation and resistance to T-cell mediated immunotherapy. Therefore, it serves as an informative and helpful model to study molecular mechanisms of adaptive therapy resistance in melanoma. <br /> I performed the first integrative analysis of genome-wide mutations, methylation, and expression profiles of primary and relapsed melanoma cells of Hgf-Cdk4^R24C mouse preclinical model of human melanoma under adoptive T cell transfer (ACT) immunotherapy. I analyzed somatic mutations, differentially methylated genes, and differentially expressed genes and featured the corresponding biological pathways and functions. My analyses revealed significant DNA methylation alterations in developmental and differentiation genes notably hypermethylation and downregulation of MITF in melanoma cells with dedifferentiated phenotype, loss of melanocyte-specific antigens, and resistance to ACT immunotherapy. <br /> My findings consistent with my hypothesis indicated that reversible epigenetic alterations regulate melanocytic dedifferentiation and phenotype plasticity beyond genetic mutations. Using differential expression analysis and comparative exome data analysis I found an identical mutation in the AXL gene with upregulated expression in all ACT therapy-resistant melanoma cells. Delineation of the functional relevance of AXL mutation with melanoma cell plasticity and therapy resistance would bring more insights to therapeutic strategies. I provided significant evidence indicating the importance of epigenetic regulation specifically DNA methylation in dedifferentiation-mediated therapy resistance in melanoma. Therefore, I suggest DNA methylation marks of the master regulator of melanocytic differentiation – MITF – as highly potential targets to restore melanoma cell differentiation and response to the therapy.