The incidence of melanoma continues to rise worldwide with an estimated 76,250 new cases in the US for 2012. Despite the advent of new therapies, melanoma remains an incurable malignancy and thus, represents a disease area of unmet medical need. Melanoma is notable for its association with early-in-life UV-light exposure, highest mutational rate (14-30 per Mb) among cancer genomes and ability to induce spontaneous T cell immunity. The most common (60%) somatic non-synonymous mutation in melanoma is BRAFV600E. Targeted therapies, such as vemurafenib, directed at inhibiting this driver mutation have resulted in high responses rates, albeit of limited duration due to acquisition of drug resistance. In contrast, immune-based therapies have yielded low response rates that are often durable. Emerging data suggest that BRAFV600E inhibition, through paradoxical increased MAPK signaling, potentiates anti-tumor T cell immunity. Altogether, these findings support testing vemurafenib in combination with immunotherapies to improved clinical outcomes. Among immunotherapies, investigational vaccines and adoptive T cell therapies (ACT) are beginning to show efficacy in early phase clinical trials. Our recent pilot phase 1 clinical trial using CD40L/IFN-? matured dendritic cells (DC) and melanocyte lineage-restricted gp100 antigen have revealed the therapeutic benefit of IL-12, produced by DC, in vaccination of patients with metastatic melanoma. However, a critical barrier to development of improved vaccines and ACT is the nature and paucity of validated melanoma antigens. To date, antigens targeted for immune intervention are predominantly derived from structurally unaltered germline/ lineage/differentiation proteins and have demonstrated limited clinical benefit. Novel strategies are needed to identify patient-specific/unique tumor antigens in order to develop the next generation of personalized cancer immunotherapies. Experimental evidence in pre-clinical models supports the thesis that these unique tumor antigens, primarily arising during neoplastic transformation, can elicit T cell immunity capable of protecting the host from cancer progression. The emergence of hybrid capture transcriptome sequencing (RNA-capture sequencing, RNA-cap seq) offers a sensitive method to interrogate cancer genomes for expressed somatic mutations and assess their level of expression. Our ongoing experiments studying the melanoma transcriptome, have found over 500 expressed somatic non-synonymous mutations per tumor. We propose to use RNA-cap seq along with in-silico HLA class I peptide binding prediction algorithms and in vitro T cell assays to test the hypothesis that somatic non- synonymous mutations give rise to unique melanoma antigens and that acquisition of resistance to BRAFV600E inhibition is accompanied by changes in the melanoma antigenic landscape. This hypothesis will be addressed in the experiments of the following Specific Aims: (1) Characterize the repertoire of melanoma expressed somatic mutations and evaluate their potential as unique antigens and (2) Evaluate the effect of targeted therapy (BRAFV600E, vemurafenib) on the repertoire of melanoma unique antigens. This exploratory study should provide insights into the validity and extent of somatic mutations as unique tumor antigens pave a new strategy to query genomic data for tumor antigen identification and potentially lead to improved patient-specific therapies in melanoma as well as other cancers.
This exploratory study is relevant to cancer immunotherapies for 2 reasons: First, it will systematically evaluate missense mutations as unique tumor antigens and inquire whether acquisition of resistance to targeted therapies affects the tumor antigen landscape. Findings from this study may pave a strategy for querying genomic data for tumor antigen identification leading to therapies tailored to each patient's tumor mutational landscape.