Single cell view of tumor microenvironment gradients in pleural mesothelioma

Immunotherapies have shown great promise in pleural mesothelioma (PM), yet most patients still do not achieve significant clinical response, highlighting the importance of improving understanding of the tumor microenvironment (TME). Here, we utilized high-throughput, single-cell RNA-sequencing to de novo identify 54 expression programs and construct a comprehensive cellular catalogue of the PM TME. We found four cancer- intrinsic programs associated with poor disease outcome and a novel fetal-like, endothelial cell population that likely responds to VEGF signaling and promotes angiogenesis. Throughout cellular compartments, we observe substantial difference in the TME associated with a cancer-intrinsic sarcomatoid signature, including enrichment in fetal-like endothelial cells, CXCL9+ macrophages, cytotoxic, exhausted, and regulatory T cells, which we validated using imaging and bulk deconvolution analyses on two independent cohorts. Finally, we show, both computationally and experimentally, that NKG2A-HLA-E interaction between NK and tumor cells represents an important new therapeutic axis in PM, especially for epithelioid cases. Patient-matching primary tumor resections and blood samples were collected from 13 MPM patients. Dissociated single cells from the tumor samples were profiled using the Chromium platform (10x Genomics, Pleasanton, CA) with the 3′ gene expression (3′ GEX) V3 kit or 5' gene expression (5' GEX) kits according to manufacturer instructions. Cells from the blood samples were profiled with the 10x Chromium Next GEM Chip K Kit and TCR CDR3 sequences were enriched using the human V(D)J T cell enrichment.