Abstract Introduction: Pleural mesothelioma (PM) is a rare and aggressive malignancy originating from the mesothelial cells of the pleural lining, with a well-established etiological association with asbestos exposure. Although immunochemotherapy is being applied as a first-line treatment, most patients fail to respond to the therapy. Previous single-cell RNA sequencing studies on PM have revealed cellular heterogeneity but lack spatial resolution and comparative analyses of immune checkpoint inhibitor (ICI) responses, limiting understanding of tumor microenvironment (TME)-mediated resistance mechanisms. This study aims to comprehensively identify the cellular composition and spatial architecture of the TME, as well as mechanisms responsible for ICI resistance in PM. Methods: Spatial transcriptomics analysis using the Xenium Prime 5K platform was conducted on baseline samples from 21 mesothelioma patients who received neoadjuvant immune checkpoint inhibitors (nivolumab/pembrolizumab), stratified as Responders (CR/PR, n=7) and Non-responders (PD/SD, n=14). Transcript-aware cell segmentation was performed with Proseg, followed by clustering and downstream analysis using Scanpy and Seurat. Copy number variations (CNV) were inferred with insituCNV, and pathway analysis was conducted via PROGENy and KEGG. Conserved spatial niches were identified using the BuildNicheAssay() function in Seurat v5. Results: Spatial transcriptomics identified distinct 36 cell clusters, including mesothelial, immune, stromal, and normal alveolar cells. Mesothelial cells exhibited chromosome 22 deletions, with CNV scores inversely correlating with treatment response. Mesothelial cells of non-responders displayed “Active Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6194.
Chun et al. (2026) studied this question.