Spatial omics illuminates tumor heterogeneity

Intratumoral heterogeneity (ITH) is the coexistence of diverse cancer cell states, genotypes, and microenvironmental niches within a single tumor and is a major driver of therapeutic resistance and disease progression. While the clinical implications of ITH are well appreciated, conventional methods and models have been limited in resolving the spatial and functional complexity underlying ITH. Recent advances in single-cell and spatial omics, high-plex imaging, and in vivo CRISPR perturbation and lineage tracing now enable unprecedented, mechanistic dissection of tumor ecosystems. These technologies are beginning to reveal how cell-cell interactions, spatial organization, and clonal evolution collectively shape tumor behavior and treatment response. We review emerging methods for spatial proteomics and transcriptomics, functional genomics, and clonal tracing and highlight how their integration is redefining the study of ITH. We also discuss current challenges, including scalability, accessibility, and multimodal data integration, and opportunities as cancer biology enters the spatial era.