HLA Class II Loss and JAK1/2 Deficiency Coevolve in Melanoma Leading to CD4 T-cell and IFNg Cross-Resistance

Purpose: Recent studies have demonstrated HLA class II (HLA-II)-dependent killing of melanoma cells by cytotoxic CD4 T cells. We investigated evolution of HLA-II-loss tumors that escape cytotoxic CD4 T-cell activity and contribute to immunotherapy resistance. Experimental Design: Melanoma cells from longitudinal metas-tases were studied for constitutive and IFN-inducible HLA-II expression, sensitivity towards autologous CD4 T cells, and immune evasion by HLA-II loss. Clinical significance of HLA-II-low tumors was determined by analysis of transcriptomic data sets from patients with immune checkpoint blockade (ICB). Results: Analysis of longitudinal samples revealed strong inter-metastatic heterogeneity in melanoma cell-intrinsic HLA-II expres-sion and subclonal HLA-II loss. Tumor cells from early lesions either constitutively expressed HLA-II, sensitizing to cytotoxic CD4 T cells, or induced HLA-II and gained CD4 T-cell sensitivity in the presence of IFNg. In contrast, late outgrowing subclones displayed a stable CD4 T-cell-resistant HLA-II-loss phenotype. These cells lacked not only constitutive but also IFNg-inducible HLA-II due to JAK1/2-STAT1 pathway inactivation. Coevolution of JAK1/2 defi- ciency and HLA-II loss established melanoma cross-resistance to IFNg and CD4 T cells, as detected in distinct stage IV metastases. In line with their immune-evasive phenotype, HLA-II-low melano-mas showed reduced CD4 T-cell infiltrates and correlated with disease progression under ICB. Conclusions: Our study links melanoma resistance to CD4 T cells, IFNg, and ICB at the level of HLA-II, highlighting the significance of tumor cell-intrinsic HLA-II antigen presentation in disease control and calling for strategies to overcome its down-regulation for improvement of patient outcome.