Spatiotemporal remodeling in habenula marks the onset of depression-related phenotypes.

Chronic stress has lasting adverse consequences that can lead, over time, to depression, yet the optimal timeframe for effective therapies remains unclear. The lateral habenula (LHb) has been implicated in stress-related behavioral repercussions, but the precise timing of its contribution is not understood. Here, using spatial transcriptomics, we generated a spatially resolved molecular atlas of the LHb of male mice, revealing a topographically organized and temporally defined remodeling of gene expression after chronic stress. Longitudinal in vivo two-photon calcium imaging of individual LHb neurons revealed progressively heightened excitatory responses to aversive stimuli. These neuronal adaptations mirrored both the progression of transcriptional changes and the emergence of depression-related behavioral phenotypes and were reversed by the antidepressant ketamine. Moreover, chemogenetically limiting LHb neuronal activity or administering ketamine at the onset of these changes exerted antidepressant effects. These findings link spatiotemporal signatures of LHb neuronal ensembles and genetic landscape with the onset of stress-induced depression-related states.