Supplementary Figures S1-S15 from A Spatial Atlas of Muscle-Invasive Bladder Cancer Reveals Lineage-Specific Vulnerabilities and Immune Architecture

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Abstract
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.