Abstract A029: Transcriptome analysis of variant histology bladder cancer reveals drug target heterogeneity

Abstract Bladder cancers with predominant variant histologic subtypes were excluded from The Cancer Genome Atlas project and other large molecular studies of bladder cancer, limiting our understanding of the molecular biology of tumors with divergent differentiation. We therefore performed an analysis of transcriptomic data from a large cohort of bladder tumors displaying phenotypic plasticity. Tumors were reviewed by a board-certified genitourinary pathologist and the cohort was enriched for tumors displaying divergent differentiation as defined by the WHO classification of tumors. The specimens were microdissected to isolate areas of uniform histomorphology and subsequently underwent bulk whole transcriptome RNA sequencing. We identified 341 specimens from 254 patients; histologic subtypes represented included urothelial carcinoma, not otherwise specified (UC-NOS, N = 130), neuroendocrine (N = 50), squamous (N = 43), glandular (N = 36), sarcomatoid (n = 22), nested (N = 17), poorly differentiated (N = 16), plasmacytoid (N = 14), and micropapillary (N = 13). Application of the bladder cancer molecular consensus classification to each of the specimens revealed distinct variation in the distribution of molecular classes between each histologic subtype. Some subtypes were homogeneously composed of a single molecular class in 80% of cases—including sarcomatoid (81% basal/squamous), squamous (89% basal/squamous), neuroendocrine (84% neuroendocrine-like), and adenocarcinoma (100% stroma-rich) tumors—while the remaining tumor subtypes were highly heterogeneous. Evaluation of transcriptional patterns of markers of divergent differentiation also revealed significant heterogeneity. NOS, glandular, nested, plasmacytoid, and micropapillary tumors showed high levels of expression of luminal markers (GATA3, PPARG, FOXA1, UPK1A, UPK2). Basal markers (e. g. KRT5) were highly expressed in the squamous subtype with relatively low expression other variant subtypes and heterogeneous expression in NOS tumors. Neuroendocrine markers (CHGB, SYP, TUBB2B, NCAM1) were selectively expressed in neuroendocrine tumors, while markers of epithelial to mesenchymal transition (VIM, FOXC2) were more highly expressed in sarcomatoid tumors. There was significant heterogeneity in expression of antibody-drug conjugate targets between different histologic subtypes. NECTIN-4 and TACSTD2 expression was significantly downregulated among sarcomatoid, neuroendocrine, and adenocarcinoma tumors whereas other subtypes showed high expression. NECTIN-4 and TACSTD2 were both uniformly highly expressed in NOS tumors. ERBB2 had low expression levels in sarcomatoid, neuroendocrine, adenocarcinoma, squamous, and nested tumors, hetereogeneous expression among NOS, glandular, and plasmacytoid tumors, and high expression among micropapillary tumors. These data highlight the significant molecular heterogeneity found between different histologic subtypes of bladder cancer—a key challenge to precision oncology—and could be used as a guide for rational therapy selection and clinical trial design. Citation Format: Jacob E. Tallman, Fenshen Kuo, Syed M. Alam, Florestan Koll, Jianqian Luo, Sizhi Paul Gao, Eugene J. Pietzak, Gopa Iyer, David B. Solit, Hikmat Al-Ahmadie. Transcriptome analysis of variant histology bladder cancer reveals drug target heterogeneity abstract. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30 (10Suppl): Abstract nr A029.