GABAergic interneurons are key regulators of hippocampal circuits, but our understanding of the diversity and classification of these cells remains controversial. Here we analyze the organization of interneurons in the CA1 area, using the combinatorial patterns of gene expression revealed by single-cell mRNA sequencing (scRNA-seq). This analysis reveals a 5-level hierarchy of cell classes. Most of the predicted classes correspond closely to known interneuron types, allowing us to predict a large number of novel molecular markers of these classes. In addition we identified a major new interneuron population localized at the border of strata radiatum and lacunosum-moleculare that we term "R2C2 cells" after their characteristic combinatorial expression of Rgs12, Reln, Cxcl14, and Cpne5. Several predictions of this classification scheme were verified using in situ hybridization and immunohistochemistry, providing further confidence in the gene expression patterns and novel classes predicted by the single cell data.
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