Abstract 1613: A hypoxia-driven transcriptional program characterizes acquired resistance to immune checkpoint inhibitors in lung cancer
Authors: Robles-Oteiza Camila , Hastings Katherine , Kaech Susan M. , Politi Katerina 
Published: July 2021

Immune checkpoint inhibitors (ICIs) that block negative regulators of T cell function can generate lasting responses in lung cancer patients, yet only a minority of tumors respond to therapy and ~50% of patients whose tumors initially respond eventually develop acquired resistance. Mechanisms of acquired resistance to ICIs in lung cancer are not fully understood and strategies to overcome resistance are lacking. To address this challenge, we developed a new mouse model of acquired resistance to ICIs by knocking out the DNA mismatch repair gene Msh2 in Kras mutant mouse lung adenocarcinoma cells, leading to a higher mutation burden in these cells. Unlike Msh2 WT controls, Msh2 KO tumors transplanted into syngeneic mice are sensitive to ICIs. Importantly, chronic treatment with αPD-1 or αPD-1 + αCTLA-4 led to Msh2 KO tumors that initially responded to therapy but then developed acquired resistance. Tumors remained resistant to ICIs upon transplantation to new hosts, suggesting that tumor-intrinsic programs drive resistance. Gene set enrichment analysis (GSEA) of single cell RNA sequencing data revealed that tumors with acquired resistance to ICIs downregulated antigen processing and presentation gene signatures compared to tumors that were regressing on therapy. Specifically, tumor cells with acquired resistance downregulated expression of MHC class II, which was confirmed by flow cytometry, and this was accompanied by a decrease in expression of Stat1, Irf1, and Ciita, which drive MHC-II expression in response to IFNγ. Depletion of CD4+ T cells during αPD-1 + αCTLA-4 treatment abrogated the response to therapy, suggesting a functional role for tumor cell MHC-II expression. GSEA also revealed that tumors with acquired resistance to ICIs upregulated hypoxia and glycolysis gene signatures compared to tumors responding to therapy. Consistent with these results, resistant tumor cells had increased hypoxia, detected by pimonidazole staining, compared to tumor cells responding to therapy. Tumor infiltrating lymphocytes have been shown to be excluded from hypoxic tumor regions, suggesting that hypoxia in the tumor microenvironment may contribute to acquired resistance to ICIs by excluding T cells from these regions. Moreover, we found that Msh2 KO tumor cells upregulated MHC-II in response to IFNγ under normoxic in vitro conditions, but had lower MHC-II expression under hypoxia. Our data suggest that tumor hypoxia may contribute to both tumor-cell intrinsic transcriptional programs, such as alterations in antigen processing and presentation machinery, as well as tumor-cell extrinsic effects, such as exclusion of T cells from the tumor microenvironment, which together may impact the development of acquired resistance to immune checkpoint blockade. Our results can inform strategies to overcome acquired resistance, addressing a critical unmet need in cancer therapy.

Citation Format: Camila Robles-Oteiza, Katherine Hastings, Susan M. Kaech, Katerina Politi. A hypoxia-driven transcriptional program characterizes acquired resistance to immune checkpoint inhibitors in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1613.