Defining Mechanisms of Tumor Immunity

Abstract

Tumor immunotherapy, including immune checkpoint blockade (ICB), has led to dramatic clinical benefit in a variety of cancers. Yet many patients do not respond to ICB or do not have durable benefit. There is an urgent need to identify combination partners for ICB. To discover new immunotherapy targets we created CHIME: CHimeric IMmune Editing, a CRISPR-Cas9 bone marrow delivery system to rapidly evaluate gene function in innate and adaptive immune cells in vivo without ex vivo manipulation of mature lineages. We used this system to perform an in vivo pooled genetic screen and identified Ptpn2 as a negative regulator of CD8+ T cell-mediated responses to LCMV Clone 13 viral infection. We found that Ptpn2 acted as a novel regulator of the differentiation of the Tim-3+ exhausted subpopulation through its role in attenuating type 1 interferon (IFN-I) signaling. Consistent with this, Ptpn2-deletion in CD8+ T cells enhanced Tim-3+ anti-tumor responses and improved tumor control. Deletion of Ptpn2 throughout the immune system resulted in complete clearance of immunogenic MC38 tumors and improved PD-1 ICB responses to less immunogenic B16 tumors. These findings demonstrate that increasing the Tim-3+ exhausted subpopulation can improve tumor control and highlight Ptpn2 as an immunotherapy target. Additionally, we investigated an orthologous mechanism of resistance: priming of T cell responses to tumors. Endogenous retrovirus (ERV) expression and production of IFN-I are known to inflame poorly infiltrated tumors. Through an in vitro screen in cancer cells for chemical compounds that induced expression of ERVs and IFN-I, LSD1 was identified as a negative regulator of IFN-I expression through its role in demethylation of ERV loci and the RISC complex. Knockout of LSD1 increased dsRNA stress and subsequent production of IFN-I, through enhanced production and decreased degradation of ERVs. This led to increased T cell infiltration in poorly immunogenic tumor models, decreased tumor growth, and synergistic effects with PD-1 ICB. Our studies enable future discovery of immunotherapy targets using the CHIME system and delineate two new mechanisms of resistance to tumor immunity. Together they suggest that cell- intrinsic screens can uncover novel mechanisms of resistance and approaches to overcome resistance to improve tumor immunity.