Analyzing the Role of MicroRNAs in Schizophrenia in the Context of Common Genetic Risk Variants

Abstract

Importance: The recent implication of 108 genomic loci in schizophrenia marked a great advancement in our understanding of the disease. Against the background of its polygenic nature there is a necessity to identify how schizophrenia risk genes interplay. As regulators of gene expression, microRNAs (miRNAs) have repeatedly been implicated in schizophrenia etiology. It is therefore of interest to establish their role in the regulation of schizophrenia risk genes in disease-relevant biological processes.

Objective: To examine the role of miRNAs in schizophrenia in the context of disease-associated genetic variation.

Design, setting, and participants: The basis of this study was summary statistics from the largest schizophrenia genome-wide association study meta-analysis to date (83 550 individuals in a meta-analysis of 52 genome-wide association studies) completed in 2014 along with publicly available data for predicted miRNA targets. We examined whether schizophrenia risk genes were more likely to be regulated by miRNA. Further, we used gene set analyses to identify miRNAs that are regulators of schizophrenia risk genes.

Main outcomes and measures: Results from association tests for miRNA targetomes and related analyses.

Results: In line with previous studies, we found that similar to other complex traits, schizophrenia risk genes were more likely to be regulated by miRNAs (P < 2 × 10-16). Further, the gene set analyses revealed several miRNAs regulating schizophrenia risk genes, with the strongest enrichment for targets of miR-9-5p (P = .0056 for enrichment among the top 1% most-associated single-nucleotide polymorphisms, corrected for multiple testing). It is further of note that MIR9-2 is located in a genomic region showing strong evidence for association with schizophrenia (P = 7.1 × 10-8). The second and third strongest gene set signals were seen for the targets of miR-485-5p and miR-137, respectively.

Conclusions and relevance: This study provides evidence for a role of miR-9-5p in the etiology of schizophrenia. Its implication is of particular interest as the functions of this neurodevelopmental miRNA tie in with established disease biology: it has a regulatory loop with the fragile X mental retardation homologue FXR1 and regulates dopamine D2 receptor density.

Figure 1:. Illustrations of the analyses in this paper.

a) Flowchart of the linear model for assessing if schizophrenia risk genes are more likely to be targeted by miRNA. b) Flowchart for gene set analyses of all conserved miRNAs and the targeted gene set analyses. More information on the analytical strategies can be found in the main text.

Figure 2:. Visualizing the top-10 schizophrenia miRNA gene sets.

a) CIRCOS-plot of the top-10 scoring miRNA gene sets. The innermost 10 tracks illustrate the targets of each miRNA. The targets are color-coded based on their gene p-values. The miRNA were ordered by their correlational clustering. Peripherally to this, a Manhattan plot is shown (only SNPs with a p-value <0.02 located in protein coding genes are included). At the edge, the genome-wide significant genes targeted by the top-10 miRNA are shown. They are color-coded based on the number of miRNA in the top-10 list that target them. Note that for illustrative purposes the MHC-region is included here although it wasn't part of the gene set tests and that p-values from PGC2 are without replication. In eFigure 1, a zoomed in view of this region is presented. b) Legend for the figure and the clustering of miRNA based on the Jaccard distance between the targets of each miRNA. In eFigure 2 this clustering is repeated considering only the targets showing increasing degrees of association with schizophrenia. “Height” is the dissimilarity measure in the clustering. GW: Genome-wide.

Figure 2:. Visualizing the top-10 schizophrenia miRNA gene sets.

a) CIRCOS-plot of the top-10 scoring miRNA gene sets. The innermost 10 tracks illustrate the targets of each miRNA. The targets are color-coded based on their gene p-values. The miRNA were ordered by their correlational clustering. Peripherally to this, a Manhattan plot is shown (only SNPs with a p-value <0.02 located in protein coding genes are included). At the edge, the genome-wide significant genes targeted by the top-10 miRNA are shown. They are color-coded based on the number of miRNA in the top-10 list that target them. Note that for illustrative purposes the MHC-region is included here although it wasn't part of the gene set tests and that p-values from PGC2 are without replication. In eFigure 1, a zoomed in view of this region is presented. b) Legend for the figure and the clustering of miRNA based on the Jaccard distance between the targets of each miRNA. In eFigure 2 this clustering is repeated considering only the targets showing increasing degrees of association with schizophrenia. “Height” is the dissimilarity measure in the clustering. GW: Genome-wide.