Muscle-invasive bladder cancer (MIBC) is clinically heterogeneous, and current molecular subtyping does not capture the spatial organization of tumor states and microenvironmental context. Here, we construct a spatial atlas of MIBC by integrating spatial transcriptomics from 22 tumors with matched bulk RNA and whole-exome sequencing data. We identify a continuous, spatially organized luminal-to-basal axis within individual tumors that is associated with greater chromosomal instability and transcriptional plasticity. Luminal tumor cores are enriched for FGFR3 and NECTIN4, whereas basal-like states localize toward invasive margins and are associated with elevated EGFR signaling, epithelial-mesenchymal transition, genomic instability, immune infiltration, and greater chemotherapy sensitivity. Spatial analyses further reveal lineage- and location-associated differences in tertiary lymphoid structure states. Pan-cohort analyses across over 3,000 tumors confirm conserved FGFR3-EGFR lineage exclusivity and associated immune programs. Together, these findings define a spatial framework for understanding lineage states, immune architecture, and therapeutic vulnerabilities in MIBC.
Cancer discovery. 2026 May 13 [Epub ahead of print]
Kai Yu, Jianfeng Chen, Yu-Yi Chu, Sajith Nair, Emanuele Crupi, Elshad Hasanov, Ying Mei, Xueshuai Han, Yang Liu, Yunhe Liu, Guangsheng Pei, Fuduan Peng, Jianlong Liao, Enyu Dai, Tian Chu, Kyung Serk Cho, Jiahui Jiang, Xinmiao Yan, Yibo Dai, Jun Wang, Baifeng Zhang, Giannicola Genovese, Nagireddy Putluri, Livia Eberlin, Liuqing Yang, Chunru Lin, Lawrence N Kwong, Diana Shamsutdinova, Khalida M Wani, Bogdan A Czerniak, Wendong Yu, Jianping Zhao, Charles C Guo, Donna Hansel, Curtis Pettaway, Louis Pisters, Kelly Bree, Neema Navai, Byron H Lee, Ashish M Kamat, Padmanee Sharma, Paul Corn, Cindy Y Jiang, Amishi Y Shah, Omar Alhalabi, Pavlos Msaouel, Arlene O Siefker-Radtke, Christopher J Logothetis, Matthew T Campbell, Alexander J Lazar, Jianjun Gao, Linghua Wang
The University of Texas MD Anderson Cancer Center Houston, Texas United States., The University of Texas MD Anderson Cancer Center Houston United States., The University of Texas MD Anderson Cancer Center Houston, TX United States., James Cancer Hospital Columbus, OH United States., University of Texas MD Anderson Cancer Center Houston, TX United States., Baylor College of Medicine HOUSTON, TEXAS United States., Baylor College of Medicine United States., The University of Texas MD Anderson Cancer Center Houston, TEXAS United States., BostonGene Waltham, MA United States., The University of Texas MD Anderson Cancer Center Houston, Tx United States., MD Anderson Houston, Tx United States.