Temporal genomic analysis of melanoma rejection identifies regulators of tumor immune evasion

Abstract

Decreased intra-tumor heterogeneity (ITH) correlates with increased patient survival and immunotherapy response. However, even highly homogenous tumors may display variability in their aggressiveness, and how immunologic-factors impinge on their aggressiveness remains understudied. Here we studied the mechanisms responsible for the immune-escape of murine tumors with low ITH. We compared the temporal growth of homogeneous, genetically-similar single-cell clones that are rejected vs. those that are not- rejected after transplantationin-vivousing single-cell RNA sequencing and immunophenotyping. Non- rejected clones showed high infiltration of tumor-associated-macrophages (TAMs), lower T-cell infiltration, and increased T-cell exhaustion compared to rejected clones. Comparative analysis of rejection- associated gene expression programs, combined within-vivoCRISPR knockout screens of candidate mediators, identifiedMif(macrophage migration inhibitory factor) as a regulator of immune rejection.Mifknockout led to smaller tumors and reversed non-rejection-associated immune composition, particularly, leading to the reduction of immunosuppressive macrophage infiltration. Finally, we validated these results in melanoma patient data.Statement of significanceHere, we uncover the association ofMifexpression with tumor growth and aggressiveness, specifically in low ITH tumors. These findings could facilitate the development of new strategies to treat patients with homogeneous, high-MIFexpressing tumors that are unresponsive to immune checkpoint therapy.

MIF and CD74 as Emerging Biomarkers for Immune Checkpoint Blockade Therapy

“…Potentially using combination therapy with both anti-CTLA-4 and a MIF inhibitor could increase immune cell infiltration in the tumor and reduce the expression of PD-L1 in melanoma cells [12]. TAM infiltration is associated with poor prognosis and tumor progression in several cancers, including melanoma and pancreatic, breast, and bladder cancers, and single-cell RNA sequencing has revealed that high TAM infiltration is associated with an increase in CD8+ T cell exhaustion and the number of Tregs [85].…”