Zebrafish screen of schizophrenia risk genes reveals convergent dysregulation of cholesterol metabolism

Rare coding variants provide a tractable entry point for understanding the molecular mechanisms underlying schizophrenia risk. Here, we generated and characterized zebrafish lines with mutations in the orthologs of >20 human schizophrenia-associated genes, including eight of the top ten SCHEMA genes, genes disrupted in childhood-onset schizophrenia (COS), and genes located within recurrent copy number variants. Whole-brain phospho-Erk activity mapping and behavioral profiling identified phenotypes in multiple mutant lines. We prioritized a protein-truncating mutation in <i>sp4</i>, which encodes an activity-dependent transcription factor, and a COS-associated missense mutation in <i>atp1a3a</i>, which encodes a Na+/K+ ATPase pump, for additional characterization. Both knockout and point mutations in <i>atp1a3a</i> disrupted brain activity and behavior in larvae and impaired navigation of a Y-maze in juveniles. Bulk RNA sequencing data from adult <i>sp4</i> and <i>atp1a3a</i> brains highlighted convergent upregulation of sterol biosynthesis pathways, including increased expression of <i>srebf2</i> and <i>msmo1.</i> Analysis of previously published telencephalon single-cell data demonstrated that cholesterol synthesis genes are enriched in astrocyte-like cells and increase in expression during post-larval development. Consistent with transcriptomic findings, filipin staining indicated increased free cholesterol in juvenile <i>sp4</i> and <i>atp1a3a</i> mutant brains. Our findings identify dysregulation of glial and sterol-associated programs as a shared molecular consequence of two distinct schizophrenia risk mutations. Although whether sterol pathway dysregulation represents a primary pathogenic mechanism or a secondary response to changes in neuronal activity requires further investigation, the convergence observed between genetic models and developmental stages suggests that disruptions to lipid homeostasis could represent a shared feature of schizophrenia disease biology.