Arlene O. Siefker-Radtke

Supplementary Methods file contains extended methods, including the processing and analysis of multiple sequencing datasets.

Supplementary Tables file contains key information and supporting datasets. Table S1 | Clinicopathological features of the 22 MIBC patients. Table S2 | The top 50 most significantly differentially expressed genes between the 15 single cell clusters. Table S3 | GSEA pathway enrichment results for 4 spatial clusters. Table S4 | Clinical characteristics and spatial tumor state composition across samples. Table S5 | Bootstrap-based robustness analysis of spatial tumor state proportions. Table S6 | The top 50 most significantly differentially expressed genes between the 4 spatial clusters.

Supplementary Figures file contains Supplementary Figures S1–S15. Figure S1 | Pathology-guided spatial annotation across 22 MIBC tumors. Figure S2 | Validation of spatial deconvolution accuracy and cell-type compartmentalization. Figure S3 | Additional tumors demonstrating spatial CNV-based subclones and transcriptional divergence. Figure S4 | Cross-platform concordance of CNV profiles inferred from spatial transcriptomics and WES. Figure S5 | Transcriptional and functional features across the luminal-to-basal differentiation continuum. Figure S6 | Single-cell analysis recapitulates the spatial luminal-to-basal differentiation continuum. Figure S7 | Spatial validation of lineage-associated EGFR and FGFR3 expression patterns. Figure S8 | Lineage-associated expression of FGFR3–EGFR signaling and transcriptional regulators across normal tissue, tumor states, and independent cohorts. Figure S9 | Pathology-guided spatial annotation across all MIBC tumors. Figure S10 | Spatial tumor states associate with chemotherapy response and stress-related gene expression. Figure S11 | NECTIN4 expression is enriched in luminal tumors and declines at the tumor-normal boundary. Figure S12 | Subtype-associated genomic alterations and their relationship with basal program activity. Figure S13 | Associations between basal signature scores and clinical or molecular features across MIBC cohorts. Figure S14 | Pathologist-guided TLS annotation confirms spatial transcriptomic predictions. Figure S15 | Lineage-associated chemokine programs and tumor–TLS interactions.

Overall survival from treatment initiation with ixazomib plus gemcitabine plus doxorubicin.

Single-cell landscape of TME and epithelial cells from longitudinally collected tumor samples at baseline and during trial therapy.

Cell–cell communication between malignant and TME populations through BMP and WNT signaling.

Probability density functions for the two co-primary endpoints in trial and historical control cohorts.

Treatment emergent adverse events at least possibly related to study therapy.

Treatment emergent adverse events regardless of attribution.