Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis

Abstract

Genome-wide association studies have identified 108 schizophrenia risk loci, but biological mechanisms for individual loci are largely unknown. Using developmental, genetic and illness-based RNA sequencing expression analysis in human brain, we characterized the human brain transcriptome around these loci and found enrichment for developmentally regulated genes with novel examples of shifting isoform usage across pre- and postnatal life. We found widespread expression quantitative trait loci (eQTLs), including many with transcript specificity and previously unannotated sequence that were independently replicated. We leveraged this general eQTL database to show that 48.1% of risk variants for schizophrenia associate with nearby expression. We lastly found 237 genes significantly differentially expressed between patients and controls, which replicated in an independent dataset, implicated synaptic processes, and were strongly regulated in early development. These findings together offer genetics- and diagnosis-related targets for better modeling of schizophrenia risk. This resource is publicly available at http://eqtl.brainseq.org/phase1 .

Figure 1:

Developmental regulation of expression. (A) Principal component #1 of the gene-level expression data versus age (N=320 independent samples/subjects); PCW: post-conception weeks, remaining ages are in years. (B) Expression features fall into two main development regulation signatures, increasing in expression from fetal to postnatal life (orange) or decreasing from fetal to postnatal life (blue). Y-axis is Z-scaled expression (to standard normal), dark lines represent median expression levels, and confidence bands represent 25^th-75^th percentiles of expression levels for each class of features. (C) KEGG pathways enriched for genes with isoform shifts, stratified by which feature type identified the gene as having a switch. Coloring/scaling represents -log10(FDR) for gene set enrichment. Analogous data for GO gene sets (biological processes, BP, and molecular function, MF) are available in Table S6. DER: differentially expressed region. Enrichment analyses for isoform shift genes among PGC2 schizophrenia GWAS risk loci with exon and junction counts using both (D) parametric p-values) and (E) permutation-based p-values. OR: odds ratio.

Figure 2:

Clinical enrichment of schizophrenia risk using representative eQTLs. (A) Association between rs1233578 and intergenic sequence downstream (B) of ZSCAN23. (B) Association between rs3849046 and a splice junction (C) of a particular longer isoform (D) of CNNTA1. (E) Association between rs9841616 and very proximal extended UTR (F) of SOX2-OT. Associations between risk SNPs and annotated sequences are shown for (G) CD46, (H) SRR and (I) GPM6A. In panels B, D, and F: thicker/dark blue: exon, thinner/light blue: intron; coordinates relative to hg19; N=412 independent samples for all panels; box plots show median and interquartile range (IQR), with whiskers representing 2.5*IQR.

Figure 3:

Differential expression comparing patients with schizophrenia to controls. (A) Histogram of fold changes of the diagnosis effect of those features that were significant and independently replicated, colored by feature type. (B) Gene set analyses of genes with decreased expression in patients compared to controls by feature type. Coloring/scaling represents -log10(FDR) for gene set enrichment. Significant directional effects of developmental regulation among diagnosis-associated genes for those that (C) increased and (D) decreased across development. P-values (two-sided) were calculated using linear regression Wald tests for those genes developmentally regulated among case-control differences to those not developmentally regulated across the 24,122 expressed genes.