Identification of miRNA, lncRNA and mRNA-associated ceRNA networks and potential biomarker for MELAS with mitochondrial DNA A3243G mutation

Wei Wang,Yuying Zhao,Qianqian Zhuang,Bing Wen,Kunqian Ji,Wei Li,Chuanzhu Yan,Pengfei Lin

doi:10.1038/srep41639

Abstract

Researchers in the field of mitochondrial biology are increasingly unveiling of the complex mechanisms between mitochondrial dysfunction and noncoding RNAs (ncRNAs). However, roles of ncRNAs underlying mitochondrial myopathy remain unexplored. The aim of this study was to elucidate the regulating networks of dysregulated ncRNAs in Mitochondrial myopathy, Encephalopathy, Lactic Acidosis, and Stroke-like episodes (MELAS) with mitochondrial DNA (mtDNA) A3243G mutation, which might make contributions to the unveiling of the complex mechanisms underlying mitochondrial myopathy and, possibly, new tools applicable to clinical practice. Through high-throughput technology followed by quantitative real-time polymerase chain reaction (qRT-PCR) and bioinformatics analyses, for the first time, we found that the dysregulated muscle miRNAs and lncRNAs between 20 MELAS patients with mtDNA A3243G mutation and 20 controls formed complex regulation networks and participated in immune system, signal transduction, translation, muscle contraction and other pathways in discovery and training phase. Then, selected ncRNAs were validated in muscle and serum in independent validation cohorts by qRT-PCR. Finally, ROC curve analysis indicated reduced serum miR-27b-3p had the better diagnosis value than lactate and might serve as a novel, noninvasive biomarker for MELAS. Follow-up investigation is warranted to better understand roles of ncRNAs in mitochondrial myopathy pathogenesis.

Highlights

Understanding of mitochondrial epigenetics to mitochondrial dysfunction promises to deepen our understanding of mitochondrial disease pathogenesis, nominate new biomarkers, and motivate new therapeutic strategies
We hypothesized that ncRNAs driven by mitochondrial DNA (mtDNA) A3243G mutation could regulate the signaling pathways involved in mitochondrial myopathy and have firstly employed an integrated genomic approach to identify the dysregulated miRNAs and lncRNAs in muscle biopsies of a well characterized cohort of MELAS with mtDNA A3243G mutation, which allowed us to identify ncRNAs of interest that may underlie MELAS pathogenesis for further studies
The patients were only restricted to MELAS with mtDNA A3243G mutation to reduce the potential for confounding effects due to sample heterogeneity, which would be expected with the inclusion of other kinds of mitochondrial mutation

Summary

Introduction

Understanding of mitochondrial epigenetics to mitochondrial dysfunction promises to deepen our understanding of mitochondrial disease pathogenesis, nominate new biomarkers, and motivate new therapeutic strategies. We found that the deregulated ncRNAs caused by mtDNA A3243G mutation formed complex regulation networks and participated in immune system, signal transduction, translation, muscle contraction and other pathways Among these dysregulated ncRNAs, we found miR-27b-3p reduced in muscle and serum of MELAS patients with A3243G mutation or non-A3243G mutation, which was negatively associated with lactate, NMADS and the mutation load in muscle, had the better diagnosis value for MELAS than lactate. These results will enrich the genome-wide analysis of RNA molecules with potential cross-talk, provide the rationale for further confirmation studies in larger prospective cohorts and contribute to further systematic studies of mitochondrial disorders

Objectives

Methods

Results

Conclusion