Cellular Diversity in Human Subgenual Anterior Cingulate and Dorsolateral Prefrontal Cortex by Single-Nucleus RNA-sequencing.

Regional cellular heterogeneity is a fundamental feature of the human neocortex; however, details of this heterogeneity are still undefined. We utilized single-nucleus RNA-sequencing (snRNA-seq) to examine cell-specific transcriptional features in the dorsolateral prefrontal cortex (DLPFC) and the subgenual anterior cingulate cortex (sgACC)-regions implicated in major psychiatric disorders. Droplet-based nuclei-capture and library preparation were performed on replicate samples from eight male donors without history of psychiatric or neurological disorder. Unsupervised clustering identified major neural cell classes. Subsequent iterative clustering of neurons further revealed 20 excitatory and 22 inhibitory subclasses. Inhibitory cells were consistently more abundant in the sgACC and excitatory neuron subclusters exhibited considerable variability across brain regions. Excitatory cell subclasses also exhibited greater within-class transcriptional differences between the two regions. We utilized these molecular definitions to determine which cell classes might be enriched in loci carrying a genetic signal in genome-wide association studies (GWAS) or for differentially expressed genes (DEGs) in mental illness. We found that the heritable signals of psychiatric disorders were enriched in neurons and that while the gene expression changes detected in bulk-RNA-sequencing studies was dominated by glial cells, some alterations could be identified in specific classes of excitatory and inhibitory neurons. Intriguingly, only two excitatory cell classes exhibited concomitant region-specific enrichment for both GWAS loci and transcriptional dysregulation. In sum, by detailing the molecular and cellular diversity of the DLPFC and sgACC, we were able generate hypotheses on regional and cell-specific dysfunctions that may contribute to the development of mental illness. SIGNIFICANCE STATEMENT: Dysfunction of the subgenual anterior cingulate cortex (sgACC) has been implicated in mood disorders, particularly major depressive disorder, and the dorsolateral prefrontal cortex (DLPFC)-a subsection of the Prefrontal cortex involved in executive functioning-has been implicated in schizophrenia. Understanding the cellular composition of these regions is critical to elucidating the neurobiology underlying psychiatric and neurological disorders. We studied cell type diversity of the sgACC and DLPFC of humans with no neuropsychiatric illness utilizing a clustering analysis of single-nuclei RNA-sequencing (snRNA-seq) data. Defining the transcriptomic profile of cellular subpopulations in these cortical regions is a first step to demystifying the cellular and molecular pathways involved in psychiatric disorders.