Regulatory variants at 2q33.1 confer schizophrenia risk by modulating distal gene TYW5 expression

Abstract

Abstract Genome-wide association studies showed that genetic variants at 2q33.1 were strongly associated with schizophrenia. However, potential causal variants in this locus and their roles in schizophrenia remain unknown. Here we identified two functional variants (rs796364 and rs281759) that disrupt CTCF, RAD21 and FOXP2 binding at 2q33.1. We systematically investigated the regulatory mechanisms of these two variants with serial experiments, including reporter gene assays and electrophoretic mobility shift assay (EMSA). Intriguingly, these two SNPs physically interacted with TYW5 and showed the most significant associations with TYW5 expression in human brain. Consistently, CRISPR-Cas9-mediated genome editing also confirmed the regulatory effect of these two SNPs on TYW5 expression. Additionally, expression analysis indicated that TYW5 was significantly up-regulated in brains of schizophrenia cases compared with controls, suggesting that rs796364 and rs281759 might confer schizophrenia risk by modulating TYW5 expression. We over-expressed TYW5 in mouse neural stem cells (NSCs) and rat primary neurons to mimic its up-regulation in schizophrenia cases, and found significant alterations in proliferation and differentiation of NSCs, as well as dendritic spine density following TYW5 overexpression, indicating its important roles in neurodevelopment and spine morphogenesis. Furthermore, we independently confirmed the association between rs796364 and schizophrenia in a Chinese cohort of 8,202 subjects. Finally, transcriptome analysis revealed that TYW5 affected schizophrenia-associated pathways. These lines of evidence consistently revealed that rs796364 and rs281759 might contribute to schizophrenia risk through regulating expression of TYW5, a gene whose expression dysregulation affects two important schizophrenia pathophysiologic processes (i.e. neurodevelopment and dendritic spine formation).