Deep in the brain's dorsal raphe nucleus, fluoxetine molecules are orchestrating a molecular symphony with an unexpected rhythm—and now scientists have finally mapped how it plays out. A team at Stockholm University used cutting-edge spatial transcriptomics to reveal that when SSRIs reshape the serotonin system, they don't do it uniformly. Instead, two distinct populations of serotonin neurons respond in nearly opposite directions, explaining something that has puzzled patients and doctors for decades: why antidepressants often feel worse before they feel better.
This matters because SSRIs are among the most widely prescribed medications in the world. In Sweden alone, more than 1 in 10 people currently take an antidepressant, yet researchers have understood surprisingly little about what these drugs actually do at the cellular level. "Rather than treating the serotonin system as a single uniform population, we used spatial transcriptomics to read out gene activity at high resolution and map different types of serotonin neurons in the same brain area," explains Iskra Pollak Dorocic, assistant professor at Stockholm University's Department of Biochemistry and Biophysics. "That allowed us to see that these neurons are far more diverse than a single label suggests, and importantly, that they do not all respond to the drug in the same way."
Published in Molecular Psychiatry, the study focused on fluoxetine, one of the most widely prescribed SSRIs, examining how it changes gene expression in the dorsal raphe nucleus—the brain's main serotonin-producing region—after both short-term and long-term treatment. The results revealed two strikingly different molecular pathways.
One serotonin neuron population showed increased expression of the neuropeptide prodynorphin (Pdyn) after short-term SSRI treatment. Prodynorphin signaling has been linked to stress-induced depressive symptoms in other brain regions, and this early surge appears to explain the unpleasant effects many patients experience when first starting medication—increased anxiety, mood worsening, or emotional numbness. But this effect diminished with longer exposure to the drug, suggesting it is temporary and eventually gives way to improvement.
Meanwhile, a second serotonin neuron population responded in the opposite direction. These cells increased their expression of thyrotropin-releasing hormone (TRH) only after prolonged treatment, weeks into the course. TRH signaling has previously been associated with antidepressive functions, suggesting that this slower, delayed response may underlie the therapeutic benefits that typically emerge after several weeks of SSRI use.
"We found that two distinct serotonin neuron populations are pushed in opposite directions by the same drug, one early and transiently, and one slowly over weeks," Pollak Dorocic says. "That mirrors the clinical picture, where unpleasant effects often come first and relief comes later, and it gives us concrete molecular candidates to interrogate next."
The discovery transforms how researchers understand antidepressant response. Rather than a single mechanism unfolding over time, SSRI treatment involves competing molecular forces—one that briefly amplifies stress signals, another that gradually strengthens antidepressive pathways. The specific genes, pathways, and cell types identified in this study now provide concrete leads for developing more targeted treatments with fewer side effects and better efficacy. For the millions of people navigating the difficult early weeks of antidepressant treatment, this molecular map offers hope that future medications might tip the scales toward relief without the initial struggle.