biostudies-literatureMardamshina MEuropean Research Council10482https://www.ebi.ac.uk/biostudies/studies/S-EPMC12647654biostudies-literatureUnknown16(1)Tumor heterogeneity drives drug resistance and relapse, influencing immune evasion and tumor progression. While intratumor heterogeneity has been extensively studied at the genomic level, its functional outcomes and interactions with the tumor microenvironment remain underexplored. In contrast, the functional outcome of heterogeneity and the interplay with the tumor microenvironment have not been addressed. In this study, we integrate multi-region spatial MS-based proteomics of 280 tumor regions, exome sequencing, and imaging to investigate spatial proteomic heterogeneity in breast cancer. Our findings reveal increased proteomic heterogeneity with tumor progression, independent of genomic heterogeneity but closely associated with microenvironmental differences. Integration with immune and Nature communicationsIntegrated spatial proteomic analysis of breast cancer heterogeneity unravels cancer cell phenotypic plasticity.PMC12647654101044574639534Itzhacky NArad GFellus-Alyagor LGal-Yam ENecula DSharan RBarshack IShalmon BKaragach SMardamshina MShenoy AGeiger TMarin IPirak DMohan VAddadi YKrol KGolani OfalseIntegrated spatial proteomic analysis of breast cancer heterogeneity unravels cancer cell phenotypic plasticity.Tumor heterogeneity drives drug resistance and relapse, influencing immune evasion and tumor progression. While intratumor heterogeneity has been extensively studied at the genomic level, its functional outcomes and interactions with the tumor microenvironment remain underexplored. In contrast, the functional outcome of heterogeneity and the interplay with the tumor microenvironment have not been addressed. In this study, we integrate multi-region spatial MS-based proteomics of 280 tumor regions, exome sequencing, and imaging to investigate spatial proteomic heterogeneity in breast cancer. Our findings reveal increased proteomic heterogeneity with tumor progression, independent of genomic heterogeneity but closely associated with microenvironmental differences. Integration with immune and 2025-01-01T00:00:00Z2025 Nov2026-06-11T05:02:40.067Z2026-06-11T03:07:47.4ZS-EPMC126476544129066710.1038/s41467-025-65477-6