An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus

Cell types in the hippocampus with unique morphology, physiology and connectivity serve specialized functions associated with cognition and mood. These cell types are spatially organized, necessitating molecular profiling strategies that retain cytoarchitectural organization. Here we generated spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from anterior human hippocampus in ten adult neurotypical donors. Using non-negative matrix factorization (NMF) and label transfer, we integrated these data by defining gene expression patterns within the snRNA-seq data and then inferring expression in the SRT data. These patterns captured transcriptional variation across neuronal cell types and indicated spatial organization of excitatory and inhibitory postsynaptic specializations. Leveraging the NMF and label transfer approach with rodent datasets, we identified putative patterns of activity-dependent transcription and circuit connectivity in the human SRT dataset. Finally, we characterized the spatial organization of NMF patterns corresponding to pyramidal neurons and identified regionally-specific snRNA-seq clusters of the retrohippocampus, subiculum and presubiculum. To make this molecular atlas widely accessible, raw and processed data are freely available, including through interactive web applications. The topographical organization of cells in the hippocampus reflects its ability to regulate mood and cognition. Here the authors generate a spatially resolved gene expression map in the human hippocampus to enable cross-species and functional interpretation.