Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry, and immunohistochemistry data.quanTIseq analysis of 8000 tumor samples revealed that cytotoxic T cell infiltration is more strongly associated with the activation of the CXCR3/CXCL9 axis than with mutational load and that deconvolution-based cell scores have prognostic value in several solid cancers. Finally, we used quanTIseq to show how kinase inhibitors modulate the immune contexture and to reveal immune-cell types that underlie differential patients' responses to checkpoint blockers.Availability: quanTIseq is available at http://icbi.at/quantiseq .

Abstract P1-08-02: Breast tumor-specific MHC-II expression drives a unique pattern of adaptive resistance to antitumor immunity through MHC-II receptor checkpoint engagement

Background: We have previously shown that some breast cancers express major histocompatibility complex II (MHC-II), correlating with enhanced immune infiltration. In other tumor types, we have shown that MHC-II expression on tumor cells predicts clinical response to checkpoint inhibition. We sought to determine the direct effects of MHC-II on anti-tumor immunity and characterize mechanisms of immune escape in this breast cancer subset.

Methods: To determine the functional effects of MHC-II on tumor cells, we generated isogenic mouse breast tumor cells with enforced MHC-II expression and determined their ability to generate tumors in syngeneic mice, the impact on immunity, and their response to checkpoint inhibition. In a series of molecularly-characterized HER2+ (n=8) and triple-negative breast cancers (TNBC; n=103), we performed immunohistochemistry (IHC) and quantitative immunofluorescence (QIF) for Lag-3, PD-L1, CD4, CD8, FCRL6, and granzyme B.

Results: Following injection in syngeneic immunocompetent mice, MHC-II+ mouse breast tumors were more frequently rejected (p=0.04) and recruited greater numbers of CD4+ TILs. When MHC-II+ tumors escaped rejection, they expressed higher degrees of PD-1 and Lag-3 in the tumor and in the draining lymph node. Since Lag-3 is a checkpoint that specifically targets MHC-II, we hypothesized that MHC-II+ breast cancers escape anti-tumor immunity through suppressing MHC-II-mediated antigen presentation. Combinations of anti-Lag-3 and anti-Pd-1 antibodies inhibited growth of MHC-II+ tumors. These findings led us to also explore Fc receptor-like 6 (FCRL6), a previously reported MHC-II receptor expressed on NK and cytotoxic T cells. Residual MHC-II+ TNBC post-neoadjuvant chemotherapy (NAC) recruited greater numbers of CD4+ and CD8+ TILs (p=0.0001 and p=0.0002), suggesting enhanced immune recognition. However, MHC-II+ TNBCs also demonstrated a greater frequency of Lag-3+ and FCRL6+ TILs (p<0.001 and p=0.01, respectively) which frequently co-occurred (p=0.003). Thus, our data suggest that MHC-II expression in breast tumors supports recruitment of MHC-II-specific checkpoint-positive TILs. In line with this concept, QIF analysis demonstrated that the presence of Lag3+ and/or FCRL6+ TILs was strongly associated with suppression of T cell cytotoxicity as assessed by granzyme-B+ CD8+ T cells (p=0.0001 and p=0.002, respectively). Functional analyses of FCRL6 on human NK cell lines and peripheral blood mononuclear cells (PBMCs) demonstrated that like Lag3, FCRL6 is a checkpoint which engages MHC-II and suppresses cytotoxic NK and T cell activity.

Conclusions: These data suggest that MHC-II+ breast tumors are immunologically active and circumvent anti-tumor immunity by targeting MHC-II antigen presentation through recruitment of Lag-3+ and FCRL6+ TILs. We describe herein FCRL6 as a novel bona fide immune checkpoint which targets MHC-II, which may impact a variety of cancers. MHC-II expression status may be a useful biomarker for patient stratification on anti-PD-1/anti-Lag-3 combination, and eventually, anti-PD-1/anti-FCRL6 combinations in patients with breast cancer.

Citation Format: Balko JM, Johnson DB, Ericsson-Gonzalez P, Nixon MJ, Salgado R, Sanchez V, Shreeder DM, Rimm DL, Loi S, Kim JY, Bordeaux J, Sanders ME, Davis RS. Breast tumor-specific MHC-II expression drives a unique pattern of adaptive resistance to antitumor immunity through MHC-II receptor checkpoint engagement [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-08-02.

MHC-II expression to drive a unique pattern of adaptive resistance to antitumor immunity through receptor checkpoint engagement

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Background: Anti-PD-1 therapy is effective in many cancers, but tumor-intrinsic factors governing response and resistance are largely unknown. MHC-II (HLA-DR) expression on tumor cells can predict response to anti-PD-1. Thus, we sought to determine the molecular features of MHC-II+ tumors in the evolution of anti-PD-1 response. Methods: We performed RNA-seq on 58 anti-PD-1 treated melanoma and lung tumors, including a subset of matched specimens prior to treatment and at acquired resistance. We performed immunohistochemistry (IHC) for immunologic markers, including HLA-DR on tumor cells. In triple-negative breast cancers (TNBC; n = 103), we performed IHC and/or quantitative immunofluorescence (QIF) for LAG3, PD-L1, CD4, CD8, Fc-receptor-like 6 (FCRL6), and granzyme B (GZMB). QIF images were assessed by Automated Quantitative Analysis (AQUA). To determine the functional effect of MHC-II on tumor cells, we generated isogenic MHC-II+ mouse tumors and assessed immune responsiveness and efficacy of checkpoint inhibition. Results: We identified unique inflammatory signatures in HLA-DR+ tumors, correlating with enhanced pre-treatment CD4+ and CD8+ tumor-infiltrating lymphocytes (TILs) and response to anti-PD-1. LAG3+ and FCRL6+ TILs were enriched in HLA-DR+ tumors. LAG3 and FCRL6, known inhibitory receptors which bind MHC-II, were elevated at anti-PD-1 resistance. Similarly, in > 100 TNBCs, HLA-DR+ tumor cells associated with increased CD4+ and CD8+ TILs and enhanced LAG3+ and FCRL6+ TILs. Further, presence of MHC-II-suppressing (LAG3+/FCRL6+) TILs associated with decreased GZMB+ CD8+ T cells, suggesting suppressed cytotoxicity. In mice, enforced expression of MHC-II on tumor cells enhanced CD4-enhanced anti-tumor immunity but was thwarted by LAG3+ TIL recruitment. Combined anti-LAG3 and anti-PD-1 therapy was selectively effective in MHC-II+ tumors. Conclusions: MHC-II+ tumors are immunologically active and may circumvent anti-tumor immunity by targeting MHC-II antigen presentation via recruitment of MHC-II-suppressing TILs. MHC-II expression may be useful to stratify patients to anti-PD-1/anti-LAG3 and eventually, anti-PD-1/anti-FCRL6 combinations.