Integrative multiomics profiling of cortical brain organoids reveals a druggable alternative splicing program in schizophrenia

Abstract

Clozapine (CLZ) is the only available pharmacological option for treatment resistant schizophrenia (TRS), but its use is limited due to adverse drug reactions and potential cytotoxicity. Despite decades of research, the precise mechanisms of action of CLZ in the human brain remain poorly understood. To address this, we derived cortical brain organoids from a large cohort of schizophrenia (SCZ) patients and healthy controls and employed a comprehensive multiomics strategy to dissect the cellular mechanisms of long-term CLZ exposure of up to 24 weeks. We uncovered a SCZ-specific and metabolism-independent alternative splicing program that was amenable to non-toxic CLZ treatment. In-depth analysis revealed a key role of exon skipping and intron retention in glutamatergic neurons. This program was further found to recapitulate disease mechanisms in primary human brain tissue and capture splicing-mediated genetic signals of SCZ risk. These findings highlight alternative splicing as a promising avenue for therapeutic developments in TRS.