Effects of SSRIs on the spatial transcriptome of dorsal raphe serotonin neurons

The serotonin system is the main therapeutic target for antidepressant drugs, most notably the selective serotonin reuptake inhibitors (SSRIs). SSRIs such as fluoxetine are routinely prescribed as a first-line treatment for depression, as well as for a range of comorbid conditions, however the drugs’ mechanism is not well understood. In order to study the molecular and transcriptional effects of SSRI administration on their primary target serotonin neurons we performed spatial transcriptomics, a spatially resolved RNA-sequencing method in intact brain tissue. Mouse brain sections containing the dorsal raphe nucleus and surrounding midbrain structures were sequenced using Visium spatial gene expression platform (10X Genomics). We characterized six molecularly and spatially distinct serotonin subpopulations. Both acute and chronic fluoxetine treatment induces a large number of changes in gene expression in the dorsal raphe nucleus. The Htr1a gene is upregulated after acute, and downregulated after chronic treatment, consistent with previous studies showing that blocking of the serotonin transporter SERT has downstream effects on 5HT _1a autoreceptors. Gene enrichment and network analysis identified key pathways modulated by SSRI administration, including Ras, MAPK and cAMP signalling pathways as well as pathways involved in axonal guidance. We also describe opposing treatment-dependent transcriptional changes of neuropeptides thyrotropin-releasing hormone ( Trh ) and Prodynorphin ( Pdyn ) with specific spatial localization within the dorsal raphe nucleus, among others. Overall, our transcriptomic and in-situ hybridization analysis reveals spatial and cell-type specific heterogeneity in SSRI action within the dorsal raphe nucleus.