IL-4 mediated TAP2 downregulation is a dominant and reversible mechanism of immune evasion and immunotherapy resistance in non-small cell lung cancer

Abstract

BACKGROUND: Resistance to both naturally occurring anti-cancer immunity and to immunotherapy is common in patients with aggressive non-small cell lung cancer (NSCLC). Recent studies indicate a role of loss of the HLA class-I antigen presentation machinery (APM) protein β-2-microglobulin in acquired resistance to immune checkpoint blockers. However, the mechanisms, functional consequences and therapeutic potential of APM defects in NSCLC remain poorly understood. METHODS: effector Tumor-Infiltrating Lymphocytes (TILs) and the APM components TAP1 and TAP2 in 819 baseline/pre-treatment NSCLCs from patients treated with and without PD-1 axis blockers in 4 independent cohorts. The impact of TAP1/2 silencing in lung cancer cells using siRNAs and CRISPR/Cas9 was studied using transcriptomic analysis, phosphoprotein arrays, ATAC-sequencing, measurement of surface HLA-peptide complexes and in vitro tumor-antigen specific T-cell killing. We established autologous co-cultures of tumor and immune cells from primary human NSCLCs to study the functional impact of IL4Rα and/or PD-1 blockade using monoclonal antibodies. A high-throughput drug screen supported the identification of compounds able to increase TAP2 expression in NSCLC cells. RESULTS: We identified cancer cell selective TAP2 protein downregulation in 42.4% of treatment naïve NSCLCs associated with reduced sensitivity to immune checkpoint blockers. TAP1 downregulation occurred in 24.4% of lung tumors without survival impact. Silencing of TAP2 in lung cancer cells altered key intracellular immunomodulatory pathways, limited sensitivity to proinflammatory cytokines, reduced the levels of surface peptide-HLA complexes and protected malignant cells from tumor antigen-specific T-cell killing via SOCS1 upregulation. TAP2 loss in human NSCLCs was associated with reduced TAP2 promoter chromatin accessibility and elevated IL-4 IL-4 expression. Treatment with IL-4 reduced TAP2 levels and the chromatin accessibility of the TAP2 gene promoter in NSCLC cells and reproduced all the functional consequences of TAP2 loss. In intact human NSCLC, IL-4 IL-4 transcripts were detected in intratumoral myeloid cells and IL-4Rα blockade increased human NSCLC cell killing by autologous TILs. Epigenetic modulators and other drugs with known anti-cancer activity increased TAP2 expression and its function in lung cancer cells. CONCLUSIONS: Our study reveals previously unrecognized functions of TAP2 beyond antigen presentation and establishes a reversible multi-cellular axis mediating adaptive immune evasion and immunotherapy resistance with clinical potential.

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