Spatial biology in cancer epigenetics

Cancer develops inside organized tissue environments wherein cellular behavior is heavily influenced by local interactions and spatially restricted regulatory programs. While bulk and single-cell sequencing technologies have fundamentally revolutionized our understanding of tumor biology, these techniques often disrupt tissue architecture and therefore fail to capture the spatial context in which molecular processes occur. Spatial transcriptomics has provided important insights into tumor heterogeneity, microenvironmental organization, and cell-to-cell communication. However, gene expression alone offers only an indirect view of the regulatory mechanisms governing cellular states. The emergence of spatial epigenomic technologies now enables the investigation of chromatin accessibility, histone modifications, and DNA methylation while preserving tissue structure. Here, we discuss the current landscape of spatial epigenomics, including spatial ATAC-seq, spatial CUT&Tag, emerging spatial CUT&RUN approaches, spatial DNA methylation profiling, and multimodal strategies integrating epigenetic, transcriptional, and proteomic information within the same tissue context. Despite remaining technical and computational challenges, continued advances are expected to establish spatial epigenomics as a powerful tool for studying cancer pathways and their regulation within intact tissues.