Modular cell type organization of cortical areas revealed by in situ sequencing

Abstract

AbstractThe cortex is composed of neuronal types with diverse gene expression that are organized into specialized cortical areas. These areas, each with characteristic cytoarchitecture1–3, connectivity4,5, and neuronal activity6–10, are wired into modular networks4,5,11. However, it remains unclear whether cortical areas and their modular organization can be similarly defined by their transcriptomic signatures. Here we used BARseq, a high-throughput in situ sequencing technique, to interrogate the expression of 107 cell type marker genes in 1.2 million cells over a mouse forebrain hemisphere at cellular resolution.De novoclustering of gene expression in single neurons revealed transcriptomic types that were consistent with previous single-cell RNAseq studies12,13. Within medium-grained cell types that are shared across all cortical areas, gene expression and the distribution of fine-grained cell types vary along the contours of cortical areas. The compositions of transcriptomic types are highly predictive of cortical area identity. We grouped cortical areas into modules so that areas within a module, but not across modules, had similar compositions of transcriptomic types. Strikingly, these modules match cortical subnetworks that are highly interconnected4,5,11, suggesting that cortical areas that are similar in cell types are also wired together. This “wire-by-similarity” rule reflects a novel organizing principle for the connectivity of cortical areas. Our BARseq-based strategy is high-throughput and low-cost, and scaling up this approach to many animals can potentially reveal the brain-wide molecular architecture across individuals, developmental times, and disease models.