Variant subtypes in bladder cancer and CA125-positive cancer cell state.

Abstract

694 Background: Variant subtypes in bladder cancer are clinically aggressive tumors associated with poor prognosis. The rarity of these tumors has made molecular characterization elusive. The aim of this study was to identify cell states unique to variant subtypes using single cell RNA sequencing. Methods: Fresh tissue was collected from bladder cancer patients undergoing surgery at our institution and sequenced using a bead-based single-cell RNA sequencing platform (SEQWELL). Tissue from histologic variants and high grade pure urothelial tumors were analyzed together for comparison. Pathologic diagnoses were independently confirmed. Analysis was performed using Seurat. Immunostaining validation was performed on a separately banked cohort. Bulk RNA sequencing data and clinical data were extracted and analyzed from The Cancer Genome Atlas (TCGA) database. Results: We generated a single cell RNA sequencing atlas of 9 variants (micropapillary, nested, squamous differentiation, pleomorphic giant-cell like, plasmacytoid, small cell) with 3 pure urothelial tumors for comparison. Our analyses reveal a tumor cell state shared among multiple variants that is characterized by highly specific expression of MUC16 (CA125) , KRT24, and WISP2 (Fig. 1). This cell state has transcriptional hallmarks of epithelial-mesenchymal transition and luminal-basal plasticity, and its signature is associated with poor survival and resistance to chemotherapy. Immunohistochemistry in a validation cohort demonstrates that CA125+ cells are found only in tumors with variant histology and not in conventional high-grade and low-grade urothelial carcinomas. Within variants tumors, CA125+ cells are more enriched in metastatic sites compared to the primary tumors, consistent with a more aggressive phenotype. Conclusions: A CA125+ cell state in variant subtypes in bladder cancer is associated with aggressive molecular features. Further investigation of this cell state is needed to define its role in the pathogenesis of variant tumors.