Analysis of biased allelic enhancer activity of schizophrenia-linked common variants

Schizophrenia is a neuropsychiatric disorder with heritability estimates between 60% and 80%. Although genome-wide association studies have identified many genetic loci linked to the disorder, most of these are noncoding variants whose functional impacts are not well understood. To bridge this gap, we prioritized potential functional variants linked to schizophrenia by utilizing a human brain epigenomic roadmap. We assessed the regulatory activity of these variants using an adapted STARR-seq screening method across four cell lines: Neuro-2a, SH-SY5Y, HEK-293T, and PC-12. Furthermore, we pinpointed candidate target genes through functional characterization and investigated their roles using zebrafish models. Our study identified 351 candidate single nucleotide polymorphisms (SNPs). Among these, 46 SNPs exhibited biased allelic enhancer activity, termed baaSNPs, with notable cell-type specificity. Chromatin interaction profiling and expression quantitative trait loci analyses linked these baaSNPs to 217 candidate target genes, and pathway enrichment analysis indicated that these genes are involved in critical neurological processes such as synaptic transmission and GABAergic signaling. One baaSNP in particular, rs13072690, showed regulatory effects across all examined cell lines and was associated with reduced expression of the PCCB gene in multiple brain regions. Heterozygous pccb knockout zebrafish exhibited abnormal behaviors, including hyperactivity, increased anxiety-like responses, and social deficits. In conclusion, our study demonstrates a valuable strategy for functionally annotating putative risk variants, complementing epigenetic approaches by providing insights into the regulatory potential of noncoding variants associated with schizophrenia. These findings offer promising candidates for further research into the underlying mechanisms of the disorder.