Mendelian randomization facilitates identification of schizophrenia risk enhancer RNAs

TL;DR

This study uses genetic data to identify enhancer RNAs linked to schizophrenia risk and shows how they influence disease risk through gene regulation.

Contribution

The study introduces a novel approach using SMR analysis to identify schizophrenia-risk enhancer RNAs and validates their regulatory role experimentally.

Findings

61 schizophrenia-risk TNEs were identified using SMR analysis, with 19 overlapping with differential expression results.

Reduced levels of ZNF135 in schizophrenia were linked to derepression of motif-matched TNEs.

The enhancer RNA RGS6e was experimentally validated to regulate nervous system genes and reduce schizophrenia risk.

Abstract

The transcription of enhancer RNA (eRNA) marks enhancer activity and may confer context-dependent regulatory functions, yet its underlying mechanism remains elusive. Leveraging BrainSeq data, we constructed ancestry-stratified expression quantitative trait locus (eQTL) maps for 71,022 transcriptional non-coding enhancer (TNE) RNAs. By integrating the latest Psychiatric Genomics Consortium (PGC3) schizophrenia GWAS with European-ancestry population-based eQTLs via Summary-data-based Mendelian Randomization (SMR), we identified 61 schizophrenia-risk TNEs, 19 of which overlapped with those from differential expression (DE) analysis. Intriguingly, for 19 overlapping TNEs, effects from DE analysis were inversely correlated with SMR effects (r = −0.57, P = 0.01), attributable to the opposing contributions of phenotype and genotype to TNE expression (r = −0.78, P = 2.96E−3). We further linked this discrepancy to reduced levels of the repressor ZNF135 in schizophrenia, which derepressed motif-matched TNEs. Finally, we identified and experimentally validated that an enhancer RNA within the intronic region of RGS6, termed RGS6e, regulates the expression of genes associated with the nervous system through trans-acting mechanisms, promoting neuronal differentiation and thereby reducing the risk of schizophrenia, consistent with the SMR results. This study underscores the significance of eQTL-based SMR analysis in elucidating the role of enhancers and their transcriptional products in schizophrenia risk. The eQTL map of TNEs developed in our study holds considerable potential for application in enhancer research related to other mental diseases or neurodegenerative diseases, thereby enhancing our understanding of how enhancers contribute to disease pathogenesis and progression.

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