48. INTEGRATIVE MULTI-OMICS ANALYSIS TO DISSECT THE CELL TYPE-SPECIFIC GENE REGULATORY ARCHITECTURE OF SCHIZOPHRENIA RISK DURING PRENATAL NEURODEVELOPMENT

Background Prenatal neurodevelopment is considered an important period of susceptibility where genetic and other risk factors can act to increase one’s likelihood of developing schizophrenia, a severe disorder that tends to onset in late adolescence/early adulthood. Genome-wide association studies (GWAS) have identified thousands of schizophrenia-associated single nucleotide polymorphisms (SNPs), many located in regulatory regions of the genome where they may perturb gene expression. To date, the specific SNPs driving schizophrenia risk and their gene regulatory effects, which may be restricted to specific brain cell types and developmental stages, remain unclear. Methods To pinpoint these SNPs and their context-specific regulatory effects, we utilized RegSCOUT (Regulatory Single-Cell Omics for Unraveling Trait-loci), a disease-agnostic computational pipeline developed in our lab, which integrates GWAS with various omics and complimentary datasets including: single-cell ATAC-sequencing (scATAC-seq), single-cell RNA-sequencing (scRNA-seq), Hi-C (a chromosome conformation capture-based technique), expression quantitative trait loci (eQTL), chromatin state annotation, and transcription factor (TF) binding motif data. We applied RegSCOUT to integrate 2 schizophrenia GWAS with 5 scATAC-seq datasets. This provided cell type-specificity across 3 mouse neurodevelopmental timepoints (embryonic days 13.5, 15.5 and 18.5), and the human brain in midgestation and adulthood, with a median of 10 cell types per timepoint. The mouse datasets provided additional granularity to pinpoint developmental day-specific regulatory networks associated with schizophrenia risk. Additionally, TF binding motifs from the JASPAR database were leveraged to identify SNPs that may impact TF binding. This analysis identified context-specific open chromatin regions, TFs, and SNPs relevant to schizophrenia pathogenesis. Subsequently, these results were coupled with 3 Hi-C and 2 eQTL datasets to elucidate context-specific, schizophrenia-associated genes. The expression of TFs in their associated cell types and developmental timepoints was investigated using 6 scRNA-seq datasets. EnrichR was used to conduct pathway enrichment analysis of prioritized genes. Results Overall, across the five prenatal timepoints, 393 SNPs colocalized with 563 context-specific open chromatin regions and impacted the binding of 415 TFs. Additionally, 146 protein coding genes, 122 lncRNAs, 6 miRNAs, and 28 biological pathways were prioritized. Notably, on average 12 schizophrenia risk-associated SNPs impacted the binding affinities of both DLX6 and NKX6-2, TFs important for GABAergic interneuron migration and differentiation. Furthermore, two genes which help specify the identities of excitatory neurons in the cortex, SATB2 and BCL11B, were associated with schizophrenia risk in neuronal progenitors at two prenatal timepoints. Discussion Our findings support the importance of SNP-mediated, context-specific gene regulation in the prenatal vulnerability window for schizophrenia. Neurodevelopmental perturbations during this period can increase an individual’s susceptibility to further insults during childhood and adolescence, which can lead to disorder onset. We substantiate existing hypotheses and generate novel mechanistic insights into the pathogenesis of schizophrenia, which can facilitate exploration of improved preventative/treatment approaches to tackling this severe disorder.