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

Selective serotonin reuptake inhibitors (SSRIs) are primary treatments for depression, yet their mechanism of action remains incompletely understood, particularly regarding the delayed therapeutic onset. This study aimed to map the molecular architecture of the dorsal raphe nucleus (DR)—the primary source of brain serotonin—and characterize how its distinct neuronal subpopulations respond to acute versus chronic fluoxetine treatment.

The researchers employed spatial transcriptomics on mouse brain sections to create a high-resolution molecular atlas of the DR. They identified six distinct serotonergic subpopulations based on unique gene expression signatures. To investigate the effects of SSRIs, they compared gene expression profiles in mice receiving acute (single dose) and chronic (22 days) fluoxetine against saline controls. Findings were validated using multiplexed fluorescent in situ hybridization (ISH) and integrated with existing single-cell RNA-seq data to map transcriptional changes to specific cell types.

The study identified extensive transcriptional remodeling in the DR following fluoxetine administration, with the most significant changes occurring between acute and chronic treatment conditions. Key pathways modulated by SSRIs include Ras, MAPK, cAMP signaling, and axonal guidance. A notable discovery is the biphasic, opposing regulation of two neuropeptides: Pdyn (prodynorphin) was upregulated after acute treatment but downregulated after chronic treatment, while Trh (thyrotropin-releasing hormone) showed the inverse pattern. These changes were spatially segregated, with Pdyn localized to the midline and Trh to the lateral DR. Furthermore, the study confirmed that while some transcriptional responses are shared across serotonergic subtypes, others—such as the upregulation of Bdnf—occur predominantly in non-serotonergic cells, suggesting that SSRIs engage a coordinated, multi-cell-type response within the DR.