Overdispersed gene expression characterizes schizophrenic brains

Abstract

Schizophrenia (SCZ) is a severe, highly heterogeneous psychiatric disorder with varied clinical presentations. The polygenic genetic architecture of SCZ makes identification of causal variants daunting. Gene expression analyses have shown that SCZ may result in part from transcriptional dysregulation of a number of genes. However, most of these studies took the commonly used approach--differential gene expression analysis, assuming people with SCZ are a homogenous group, all with similar expression levels for any given gene. Here we show that the overall gene expression variability in SCZ is higher than that in an unaffected control (CTL) group. Specifically, we applied the test for equality of variances to the normalized expression data generated by the CommonMind Consortium (CMC) and identified 87 genes with significantly higher expression variances in the SCZ group than the CTL group. One of the genes with differential variability, VEGFA, encodes a vascular endothelial growth factor, supporting a vascular-ischemic etiology of SCZ. We also applied a Mahalanobis distance-based test for multivariate homogeneity of group dispersions to gene sets and identified 19 functional gene sets with higher expression variability in the SCZ group than the CTL group. Several of these gene sets are involved in brain development (e.g., development of cerebellar cortex, cerebellar Purkinje cell layer and neuromuscular junction), supporting that structural and functional changes in the cortex cause SCZ. Finally, using expression variability QTL (evQTL) analysis, we show that common genetic variants contribute to the increased expression variability in SCZ. Our results reveal that SCZ brains are characterized by overdispersed gene expression, resulting from dysregulated expression of functional gene sets pertaining to brain development, necrotic cell death, folic acid metabolism, and several other biological processes. Using SCZ as a model of complex genetic disorders with a heterogeneous etiology, our study provides a new conceptual framework for variability-centric analyses. Such a framework is likely to be important in the era of personalized medicine. (313 words)