Next Generation Cancer Immunotherapies to Defeat Melanoma

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PROJECT SUMMARY / ABSTRACT This is a Type 2 renewal application aimed at building on the progress over the initial funding period to develop new therapies for patients with melanoma and studying the mechanistic basis of response and resistance to melanoma immunotherapies. We made significant progress in the three scientific areas of the initial funding period. We defined genetic mechanisms of primary and acquired to immune checkpoint blockade (ICB) through loss of function mutations in the antigen presenting machinery and the interferon-gamma (IFN-g) signaling pathway, which led us to successfully test combination therapies in mouse models and bring them back to patients in ongoing clinical trials. In the scientific area of combinatorial approaches of immunotherapy and targeted therapy, our mouse model data provided the justification for three triple therapy (BRAF plus MEK inhibitors and anti-PD-1 or -PD-L1) clinical programs, one of them resulting in an FDA approval. In the scientific theme of advancing gene engineered adoptive cell transfer (ACT) therapies, we have conducted three clinical trials, developed optimized means to isolate T cell receptors (TCRs), helped develop an approach for non-viral T cell gene editing, and develop approaches to provide superior cytokine support for in vivo T cell expansion. The new R35 proposal has three themes. Theme 1 is centered on how cancer cells are recognized or escape T cells, focusing on the antigen presentation machinery. It will use a repository of 1,031 already collected biopsies that will be analyze using newly developed methods of isolation, sequencing and bioinformatics analyses. Theme 2 is based on the key role of IFN-g in shaping an antitumor immune response; the realization that this cytokine turns the cancer cells into enablers of the antitumor immune response provides opportunities for exploiting the knowledge to improve immunotherapies. This will be achieved using CRISPR and drug screens in a panel of melanoma cell lines, followed by pathway analyses and mechanistic studies hopefully leading to new pharmacological targets to improve IFN-g antitumor activity. Theme 3 is focused on the T cell function and target recognition, and in particular in avoiding T cell dysfunction upon repeated antigen exposure, which is a major limitation to long term antitumor responses. This project will use CRISPR screens in T cells undergoing repeated antigen exposure to find genes that, when knocked-out, result in superior ability of T cells to maintain their functionality upon repeated TCR engagement. Furthermore, we will analyze the transcription factors that guide a superior in vivo expansion and antitumor activity of adoptively transferred T cells. In conclusion, the new R35 proposal builds on the science from the current OIA. We propose to use state-of- the-art approaches to analyze large numbers of patient biopsies, use CRISPR screens for mechanistic analyses and use model systems to improve responses and treat resistance to cancer immunotherapies. 1