Brain Spatial Genomics Atlases

Recent advances in single-cell RNA sequencing (scRNA-seq) have transformed neuroscience research by enabling the identification of genes, cell types, and molecular pathways involved in brain development and function. However, scRNA-seq lacks spatial information regarding the anatomic location of gene expression. Emerging spatial genomics technologies, including MERFISH, CosMx, Stereo-seq, and Visium Spatial Gene Expression overcome this limitation by enabling transcriptomic and epigenomic profiling within intact tissue architecture. Integration of spatial genomics with scRNA-seq has revolutionized genomics and biomedical research by allowing gene expression to be mapped in situ at cellular and even subcellular resolution. These advances have facilitated the construction of brain spatial genomics atlases in several species, including mouse, human, non-human primate, and zebrafish. Spatial genomics technologies are particularly valuable for defining cellular heterogeneity across brain regions and characterizing the spatial organization of neuronal circuits when integrated with single-cell sequencing approaches. These reference atlases provide powerful resources for investigating brain development, function and disease, and for identifying region-specific molecular signatures associated with neurological disorders. Here, we review currently available brain spatial genomics atlases and the spatial genomics technologies used to generate these reference resources.