Summary: Researchers created a high-resolution spatial map of molecular changes that selective serotonin reuptake inhibitors (SSRIs) produce within the brain’s primary serotonin hub. Using spatial transcriptomics, the team traced gene-expression shifts in the dorsal raphe nucleus after both short-term and long-term fluoxetine treatment.
These results challenge the traditional idea that the serotonin system is uniform. Instead, the study shows two distinct serotonin neuron populations respond in opposite directions to the same drug, a divergence that mirrors the clinical timeline of SSRI therapy: transient early side effects often give way to delayed therapeutic relief.
Key Facts
- The Serotonin Homogeneity Fallacy: Antidepressants are widely prescribed—over 10% of people in some countries use them—yet how SSRIs change gene expression within serotonin neurons has been incompletely understood.
- High-Resolution Spatial Mapping: The study examined fluoxetine’s molecular footprint inside the dorsal raphe nucleus, the brain’s main serotonin-producing region. Spatial transcriptomics enabled researchers to read gene activity at near single-cell resolution without mixing distinct neuron types.
- The Transient Phase (Group 1): Short-term fluoxetine exposure produced a rapid, temporary increase in the neuropeptide prodynorphin (Pdyn) in one serotonin neuron subpopulation. Pdyn has been associated with stress-linked depressive behaviors, offering a molecular explanation for the increased anxiety or worse mood some patients experience when first starting an SSRI.
- The Delayed Therapeutic Phase (Group 2): A different serotonin neuron subpopulation showed increased expression of thyrotropin-releasing hormone (TRH) only after chronic treatment. TRH signaling has been associated with antidepressant-like effects in other contexts, matching the multi-week delay before clinical symptom improvement typically appears.
- Next-Generation Drug Discovery: According to lead investigator Dr. Iskra Pollak Dorocic, isolating these opposite molecular pathways provides a blueprint for engineering targeted antidepressants that preserve beneficial TRH-driven effects while avoiding the early Pdyn-related stress response.
Source: Stockholm University
Antidepressants are among the most widely prescribed medications worldwide. In Sweden, more than one in ten people use an antidepressant, and SSRIs are the most common class.
“We still understand surprisingly little about what these drugs actually do in the brain. Our study set out to map the gene-expression changes SSRIs induce in their primary target, the brain’s serotonin neurons,” says Iskra Pollak Dorocic, Assistant Professor at the Department of Biochemistry and Biophysics, Stockholm University.
Mapping changes
Focusing on fluoxetine, the team analyzed the dorsal raphe nucleus using spatial transcriptomics, a spatially resolved RNA-sequencing method applied to intact brain tissue. This approach preserves spatial relationships between cells while profiling their gene-expression signatures, enabling identification of distinct neuronal subtypes within the same anatomical region.
“Instead of treating the serotonin system as a single uniform population, we used spatial transcriptomics to map gene activity at high resolution and distinguish different serotonin neuron types in the same area. That revealed far greater diversity and showed that neurons do not all respond to the drug in the same way,” Dorocic explains.
Two different paths
The analysis revealed widespread, treatment-dependent shifts in gene expression and identified six distinct serotonergic subpopulations with specific molecular signatures and spatial locations. Among the most striking findings were opposing responses in neuropeptide expression within different subpopulations:
- One subgroup exhibited a marked increase in prodynorphin (Pdyn) expression after short-term fluoxetine exposure. Pdyn signaling has been linked to stress-related depressive symptoms elsewhere in the brain. This transient elevation declined with prolonged exposure, suggesting a molecular basis for the early adverse effects some patients report when beginning SSRI therapy.
- A second subgroup showed a delayed rise in thyrotropin-releasing hormone (TRH) expression that emerged only after chronic treatment. TRH has been associated with antidepressant-like effects in prior studies, and its late-onset activation here aligns with the weeks-long delay before SSRIs produce therapeutic benefit for many patients.
Good and bad effects
The study highlights the cellular complexity of the serotonin system and suggests different serotonin neuron types contribute to distinct phases of the antidepressant response. One population appears to drive an early, transient stress-linked response, while another engages a slower, therapeutic pathway.
“We found two distinct serotonin neuron populations pushed in opposite directions by the same drug: one rapidly and transiently, the other slowly over weeks. That mirrors the clinical picture—unpleasant effects often come first and relief comes later—and it gives us concrete molecular candidates to investigate further,” says Dorocic.
The genes, pathways and cell types identified provide valuable leads for research into depression’s biological mechanisms and could guide development of more targeted antidepressant treatments with fewer side effects and improved efficacy.
Key Questions Answered:
A: The study suggests a temporary chemical spike in a specific group of serotonin neurons. Short-term SSRI exposure forces one neuron population to rapidly produce prodynorphin (Pdyn), a stress-linked neuropeptide. This reaction diminishes with continued treatment.
A: Therapeutic pathways activate on a slower timetable. A separate serotonin neuron population increases production of thyrotropin-releasing hormone (TRH) only after prolonged exposure, which aligns with the delayed clinical improvement.
A: By revealing that “serotonin neurons” are heterogeneous. Spatial transcriptomics maps different cell types within the same region, enabling drug development aimed at activating beneficial TRH-expressing cells while avoiding the Pdyn-expressing cells that drive early adverse effects.
Editorial Notes:
- This article was edited by a Neuroscience News editor.
- The journal paper was reviewed in full.
- Additional context was added by editorial staff.
About this neuroscience and SSRI research news
Author: Press Office
Source: Stockholm University
Contact: Press Office – Stockholm University
Image: The image is credited to Neuroscience News
Original Research: Open access. “Effects of SSRIs on the spatial transcriptome of dorsal raphe serotonin neurons” by Charlotta Henningson, Jakub Mlost & Iskra Pollak Dorocic. Molecular Psychiatry. DOI: 10.1038/s41380-026-03644-x
Abstract
Effects of SSRIs on the spatial transcriptome of dorsal raphe serotonin neurons
The serotonin system is the primary target of selective serotonin reuptake inhibitors (SSRIs) used to treat depression, yet SSRI mechanisms remain incompletely understood. To investigate molecular and transcriptional effects on serotonin neurons, the researchers applied spatial transcriptomics, a spatially resolved RNA-sequencing method, to intact mouse brain tissue containing the dorsal raphe nucleus and adjacent midbrain structures.
Analysis revealed six distinct serotonergic subpopulations with unique molecular signatures and spatial distributions. Both acute and chronic fluoxetine treatment induced numerous gene-expression changes in the dorsal raphe nucleus.
Notably, Htr1a expression increased after acute treatment but decreased following chronic administration, supporting prior observations about 5-HT1A autoreceptor regulation by serotonin transporter blockade. Gene-enrichment and network analyses highlighted Ras, MAPK and cAMP signaling pathways and pathways involved in axonal guidance as being modulated by SSRI administration.
The study also found opposing, treatment-dependent transcriptional changes in neuropeptides—particularly Thyrotropin-releasing hormone (Trh) and Prodynorphin (Pdyn)—with distinct spatial localization within the dorsal raphe nucleus.
Together, the transcriptomic and in situ hybridization results reveal spatial and cell-type-specific heterogeneity in SSRI action within the dorsal raphe nucleus, offering new molecular insights into how SSRIs affect the brain and potential leads for more targeted antidepressant strategies.