Decoding cardiac homeostasis and injury: the evolving landscape of spatial transcriptomics

The heart is a structurally complex organ where function is intimately tied to the precise spatial organization of diverse cell types. While single-cell RNA sequencing (scRNA-seq) has revolutionized cardiovascular research by providing a high-resolution "parts list" of the heart, the requisite tissue dissociation destroys the critical spatial context of intercellular communication and microenvironmental niches. Spatial transcriptomics (ST) has emerged as a transformative technology that bridges this gap, enabling the mapping of gene expression back to its histological coordinates. This review discusses the rapidly evolving landscape of spatial technologies, categorizing them into sequencing-based methods (e.g., Visium, Stereo-seq) which offer transcriptome-wide discovery, and imaging-based methods (e.g., MERFISH, Xenium, CosMx) which provide subcellular resolution with high sensitivity. We highlight recent applications of these tools in uncovering the spatial architecture of the heart at homeostasis and following injury. Furthermore, we explore the next frontier of spatial multi-omics, including simultaneous profiling of the proteome via sequential immunofluorescence (seq-IF) and expansion proteomics (iPEX), as well as chromatin accessibility. We conclude by discussing the computational challenges and future perspectives of integrating these multi-modal datasets to construct comprehensive atlases of the healthy and injured heart.