Schizophrenia risk variants modulate transcription factor binding and gene expression in cortical cell types

Schizophrenia is a complex neuropsychiatric disorder with a strong genetic component. Genome-wide association studies (GWAS) have identified numerous risk variants, but their functional impact on gene regulation remains largely unknown. A major challenge lies in interpreting the function of non-coding variants, which comprise the majority of GWAS hits, making it difficult to determine their functional consequences, particularly in identifying the target genes and cell types involved. We investigated the disruption and enhancement of transcription factor (TF) binding motifs by schizophrenia-associated GWAS SNPs in 15 cortical cell types of the human brain. We integrated single-nucleus ATAC-seq and RNA-seq data from 71 donors (36 affected by schizophrenia) with GWAS summary statistics to identify TF motifs whose binding affinities are altered by schizophrenia-associated SNPs. We found that risk alleles of schizophrenia-associated SNPs disrupt and enhance TF binding. Furthermore, we demonstrated that disrupted TF motifs can lead to altered expression of target genes, including NAGA in excitatory neurons and SNX19 in protoplasmic astrocytes. These genes have been previously implicated in schizophrenia and our study provides a mechanism for their dysregulation through altered TF binding. Our findings highlight the importance of considering cell type-specific effects and provide a genome-wide map of TF motif disruptions in schizophrenia, offering insights into the regulatory mechanisms underlying disease risk. These findings may inform the development of novel therapeutic strategies targeting specific regulatory mechanisms.