Alterations in esophageal microRNAs expression in primary esophageal achalasia by next-generation sequencing

Abstract

Background The molecular knowledge of primary esophageal achalasia is essential for the early diagnosis and treatment of this neurodegenerative motility disorder. So it is substantial to find the main microRNAs (miRNAs), which are related to mechanisms of achalasia. Methods This study aimed to determine some patterns of deregulated miRNAs in achalasia. This case-control study was performed on 52 achalasia patients and 50 non-achalasia controls. The miRNA expression profiling was conducted on esophageal tissue samples from achalasia and non-achalasia patients, via next-generation sequencing (NGS). Differential expression of miRNAs was analyzed by edgeR software. The selected dysregulated miRNAs were additionally confirmed using RT-qPCR. Potential target genes of the down-regulated and up-regulated miRNAs were also predicted to understand the putative role of the miRNAs in achalasia. Results We identified 15 miRNAs that were significantly altered in the achalasia tissues compared to controls. Among these miRNAs, three; miR-133a-5p, miR-143-3p and miR-6507-5p were up-regulated. Also we found six miRNAs; miR-215-5p, miR-216a-5p, miR-216b-5p, miR-217, miR-7641 and miR-194-5p were down-regulated significantly. The predicted targets for the dysregulated miRNAs showed significant disease-associated pathways like neuron cell apoptosis, neuromuscular balance, neuron growth factor signaling and immune response regulation. Gene expression analysis confirmed significant downregulation of hsa-miR-217 (p-value =0.004) in LES of achalasia patients with significant enrichment in myelination process ontology. This study provides the first integrated miRNA expression profile using NGS in achalasia. Our findings introduced 15 candidate microRNAs as achalasia associated non-coding RNAs genes showing confirmed downregulation of the hsa-miR-217 in Achalasia disease. Conclusions Our results may serve as a basis for more future functional studies to discover the role of candidate miRNAs in the etiology of achalasia and their application in diagnosis and probably treatment.