45. A “PERTURB-SEQ” STUDY OF SCHIZOPHRENIA

Background Schizophrenia affects approximately 1% of the population worldwide and is among the most heritable psychiatric disorders. Decades of genomic discovery have identified hundreds of risk loci via genome-wide association studies (GWAS), whole-exome sequencing (WES), copy number variant (CNV), and single-gene disorders with psychosis. Despite genomic progress, the mechanisms connecting genetic risk to disease remain poorly understood. Methods To address this, we conducted a large-scale Perturb-seq screen in which ∼2,000 schizophrenia candidate genes (from all four genomic discovery approaches) were individually silenced in single excitatory neurons using CRISPR inhibition (CRISPRi, human WTC11 iPSC-derived excitatory neurons). Single-cell RNA sequencing captured the transcriptional consequences of each perturbation across ∼14,000 genes, yielding a comprehensive map of how schizophrenia risk gene knockdown reshapes the neuronal transcriptome. Results Approximately 1,600 perturbations were validated as successful, with a median knockdown to ⅓ of baseline gene expression. For each perturbation, we identified differentially expressed secondary genes, revealing perturbation footprints ranging from 0 to 1000s of transcriptional changes. Strikingly, despite originating from distinct modes of genetic discovery, genes implicated through GWAS, WES, CNVs, and single-gene disorders converged on shared transcriptional signatures. This suggests common downstream biological pathways regardless of the nature of the upstream genetic risk. Discussion These findings provide a rich resource for schizophrenia biology, nominating high-confidence transcriptional effectors, biological modules, and potential therapeutic targets. This work represents one of the largest functional genomic screens in a human neuronal model to date and demonstrates the power of Perturb-seq for translating psychiatric genetic findings into mechanistic insight. Updated results will be shown.