Chengwen Gao, Qian Zhang, Chuanhong Wu, Lixia Peng, Mingxuan Wu et al.
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.
Chengwen Gao, Qian Zhang, Chuanhong Wu, Lixia Peng, Mingxuan Wu, Baokun Wang, Baiqiang Xue, Mingming Niu, Yajie Jiang, Wenli Yuan, Haiyan Song, Xiangyu Li, Xiangzhong Zhao, Yujuan Niu, Yuanchao Sun, Yonghe Ding, Zhiqiang Li. Analysis of biased allelic enhancer activity of schizophrenia-linked common variants. 2025-07-10. https://doi.org/10.1038/s42003-025-08456-3
The shared synthetic oligonucleotide library of schizophrenia-linked candidate variants was transfected into human SH-SY5Y neuroblastoma cells. Reference and alternative 200-bp allele fragments were tested in three SNP-centered contexts, with plasmid DNA input and RNA output quantified across three replicates.
The shared synthetic oligonucleotide library of schizophrenia-linked candidate variants was transfected into human HEK-293T cells. Reference and alternative 200-bp allele fragments were tested in three SNP-centered contexts, with plasmid DNA input and RNA output quantified across three replicates.
The shared synthetic oligonucleotide library of schizophrenia-linked candidate variants was transfected into rat PC-12 pheochromocytoma cells. Reference and alternative 200-bp allele fragments were tested in three SNP-centered contexts, with plasmid DNA input and RNA output quantified across the deposited replicates.
The shared synthetic oligonucleotide library of schizophrenia-linked candidate variants was transfected into mouse Neuro-2a cells. Reference and alternative 200-bp allele fragments were tested in three SNP-centered contexts, with plasmid DNA input and RNA output quantified across three replicates.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
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