Spatial Transcriptomics of Micropapillary, Plasmacytoid, and Sarcomatoid Urothelial Carcinoma Reveals Distinct Molecular Landscapes.

Consensus molecular classes of urothelial carcinoma (UC) include basal/squamous (Ba/Sq), luminal papillary (LumP), luminal nonspecified (LumNS), luminal unstable (LumU), stroma-rich, and neuroendocrine (NE)-like. We aimed to determine the consensus molecular classifications of micropapillary (MP), plasmacytoid (PC), and sarcomatoid (SM) subtypes of bladder UC and characterize their spatial transcriptomic profiles. A tissue microarray of 17 FFPE cores (5 MP, 6 PC, 6 SM) was profiled for expression of 18,676 mRNAs using the Bruker GeoMx Digital Spatial Profiler. 38 areas of interest (AOIs) were selected based on H&E and fluorescence markers. Each AOI was assigned to a consensus molecular class using a published approach, and pathway analysis was performed using Reactome gene sets. Most MP and PC demonstrated luminal molecular classes, whereas SM was predominantly Ba/Sq. Adjacent mixed histological components within the same tumor frequently corresponded to distinct consensus molecular classes. Ba/Sq tumors upregulated invasion- and extracellular matrix (ECM) remodeling-associated genes, whereas luminal classes demonstrated distinct differentiation-associated signatures. MP demonstrated a predominantly luminal epithelial transcriptional program characterized by increased expression of luminal/urothelial differentiation markers (KRT20, UPK1A, PSCA, FOXA1), secretory-associated genes (LCN2, MUC1, MUC20, SPINK1), and relative ERBB2 enrichment, with suppression of basal/squamous-associated genes (KRT5, KRT6A, KRT14, TP63). In contrast, SM demonstrated a predominantly mesenchymal/stromal transcriptional program characterized by enrichment of mesenchymal/ECM-associated genes (FN1, VIM, COL6A1, TGFB1), and reduced expression of luminal/epithelial and adhesion-associated genes (TACSTD2, PSCA, NECTIN4, CDH1). PC appeared to demonstrate an intermediate phenotype between MP and SM, with partial preservation of epithelial differentiation and secretory programs, reduced adhesion programs, and moderate stromal-associated features. The therapeutic target NECTIN4 was relatively enriched in MP and PC compared with SM, whereas FGFR3 was relatively downregulated in MP and PC compared with CIUC. Pathway analysis demonstrated relative enrichment of IGF/IGFBP signaling across MP, PC, and SM, with MP enriched for protein secretory programs, PC for RTK/MAPK and WNT/β-catenin signaling, and SM for ECM remodeling. Adjacent histological components frequently corresponded to different consensus molecular classes in UC. MP, PC, and SM demonstrated distinct transcriptomic profiles, with PC exhibiting an intermediate phenotype between MP and SM.