Single cell view of tumor microenvironment gradients in pleural mesothelioma

Abstract

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.

Comprehensive multi-site profiling of the malignant pleural mesothelioma micro-environment identifies candidate molecular determinants of histopathologic type

“…While previous studies in bulk RNA identified a continuous EM gradient across samples (Alcala et al, 2019; Blum et al, 2019), these analyses were unable to identify which cell components were driving this phenotype. The concordance between bulk and malignant cell-specific EM signatures demonstrated in the present study suggests that previous findings in bulk tissue were largely representative of malignant cell variation and is consistent with another recent PM scRNA-seq study (Giotti et al, 2024). Furthermore, we describe a new malignant cell state, termed uncommitted, in PM most frequently isolated in biphasic tumor samples.…”

“…While mutations remove the checkpoint on proliferation, it may be that non-malignant cells provide the fuel for proliferation, where mesenchymal cells tend to be driven by GAS6-AXL and epithelioid tumors by HBEGF-EGFR signaling. Notably, GAS6-AXL signaling has been previously identified as a an important EMT gene in PM (Engelsen et al, 2022; Ou et al, 2011)and AXL was recently described as associated with sarcomatoid malignant cell module gene expression in another PM scRNA-seq study(Giotti et al, 2024). We also identify inhibition of WNT as a potential mechanism for maintaining an uncommitted cell state, given the identification of SFRP2, HHIP , DKK1 , DKK2 , and DKK3 as either signature biomarkers or significantly differentially expressed in in uncommitted cells.…”