Transcriptomic analysis of the human habenula in schizophrenia.

IMPORTANCE: Habenula (Hb) pathophysiology is involved in many neuropsychiatric disorders, including schizophrenia. Deep brain stimulation and pharmacological targeting of the Hb are emerging as promising therapeutic treatments. However, little is known about the cell type-specific transcriptomic organization of the human Hb or how it is altered in schizophrenia.

OBJECTIVE: To define the molecular neuroanatomy of the human habenula and identify transcriptomic changes in individuals with schizophrenia compared to neurotypical controls.

DESIGN SETTING AND PARTICIPANTS: This study utilized Hb-enriched postmortem human brain tissue. Single nucleus RNA-sequencing (snRNA-seq) and single molecule fluorescent in situ hybridization (smFISH) experiments were conducted to identify molecularly defined Hb cell types and map their spatial location (n=3-7 donors). Bulk RNA-sequencing and cell type deconvolution were used to investigate transcriptomic changes in Hb-enriched tissue from 35 individuals with schizophrenia and 33 neurotypical controls. Gene expression changes associated with schizophrenia in the Hb were compared to those previously identified in the dorsolateral prefrontal cortex (DLPFC), hippocampus, and caudate.

MAIN OUTCOMES AND MEASURES: Semi-supervised snRNA-seq cell type clustering. Transcript visualization and quantification of smFISH probes. Bulk RNA-seq cell type deconvolution using reference snRNA-seq data. Schizophrenia-associated gene differential expression analysis adjusting for Hb and thalamus fractions, RNA degradation-associated quality surrogate variables, and other covariates. Cross-brain region schizophrenia-associated gene expression comparison.

RESULTS: snRNA-seq identified 17 cell type clusters across 16,437 nuclei, including 3 medial and 7 lateral Hb populations. Cell types were conserved with those identified in a rodent model. smFISH for cell type marker genes validated snRNA-seq Hb cell types and depicted the spatial organization of subpopulations. Bulk RNA-seq analyses yielded 45 schizophrenia-associated differentially expressed genes (FDR < 0.05), with 32 (71%) unique to Hb-enriched tissue.

CONCLUSIONS: These results identify topographically organized cell types with distinct molecular signatures in the human Hb. They further demonstrate unique transcriptomic changes in the epithalamus associated with schizophrenia, thereby providing molecular insights into the role of Hb in neuropsychiatric disorders.

KEY POINTS: Question: What is the molecular and cellular organization of the human habenula and how is it uniquely disrupted in schizophrenia? Findings: In this single cell and spatial transcriptomic study of postmortem human habenula, we identified 10 molecularly defined medial and lateral habenula cell types. Several of these subpopulations were topographically organized and conserved across species. Bulk RNA-sequencing and cell type deconvolution of habenula-enriched tissue samples from 35 subjects with schizophrenia and 33 neurotypical controls revealed both shared and unique transcriptomic changes associated with schizophrenia compared to other brain regions. Meaning: The results of this study identify molecular changes in the human epithalamus associated with schizophrenia, further justifying the habenula as a relevant therapeutic target for neuropsychiatric disorders.