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Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder

BACKGROUND: Major depressive disorder (MDD) is a common and serious mental illness. Many novel genes in MDD have been characterized by high-throughput methods such as microarrays or sequencing. Recently, noncoding RNAs (ncRNAs) were suggested to be involved in the complicated environmental-genetic r...

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Autores principales: Zou, Zhi-Li, Ye, Yu, Zhou, Bo, Zhang, Yuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Baishideng Publishing Group Inc 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10011943/
https://www.ncbi.nlm.nih.gov/pubmed/36925948
http://dx.doi.org/10.5498/wjp.v13.i2.36
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author Zou, Zhi-Li
Ye, Yu
Zhou, Bo
Zhang, Yuan
author_facet Zou, Zhi-Li
Ye, Yu
Zhou, Bo
Zhang, Yuan
author_sort Zou, Zhi-Li
collection PubMed
description BACKGROUND: Major depressive disorder (MDD) is a common and serious mental illness. Many novel genes in MDD have been characterized by high-throughput methods such as microarrays or sequencing. Recently, noncoding RNAs (ncRNAs) were suggested to be involved in the complicated environmental-genetic regulatory network of MDD occurrence; however, the interplay among RNA species, including protein-coding RNAs and ncRNAs, in MDD remains unclear. AIM: To investigate the RNA expression datasets downloaded from a public database and construct a network based on differentially expressed long noncoding RNA (lncRNAs), microRNAs (miRNAs), and mRNAs between MDD and controls. METHODS: Gene expression data were searched in NCBI Gene Expression Omnibus using the search term “major depressive disorder.” Six array datasets from humans were related to the search term: GSE19738, GSE32280, GSE38206, GSE52790, GSE76826, and GSE81152. These datasets were processed for initial assessment and subjected to quality control and differential expression analysis. Differentially expressed lncRNAs, miRNAs, and mRNAs were determined, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and protein-protein interaction network was generated. The results were analyzed for their association with MDD. RESULTS: After analysis, 3 miRNAs, 12 lncRNAs, and 33 mRNAs were identified in the competing endogenous RNA network. Two of these miRNAs were earlier shown to be involved in psychiatric disorders, and differentially expressed mRNAs were found to be highly enriched in pathways related to neurogenesis and neuroplasticity as per Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. The expression of hub gene fatty acid 2-hydroxylase was enriched, and the encoded protein was found to be involved in myelin formation, indicating that neurological development and signal transduction are involved in MDD pathogenesis. CONCLUSION: The present study presents candidate ncRNAs involved in the neurogenesis and neuroplasticity pathways related to MDD.
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spelling pubmed-100119432023-03-15 Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder Zou, Zhi-Li Ye, Yu Zhou, Bo Zhang, Yuan World J Psychiatry Basic Study BACKGROUND: Major depressive disorder (MDD) is a common and serious mental illness. Many novel genes in MDD have been characterized by high-throughput methods such as microarrays or sequencing. Recently, noncoding RNAs (ncRNAs) were suggested to be involved in the complicated environmental-genetic regulatory network of MDD occurrence; however, the interplay among RNA species, including protein-coding RNAs and ncRNAs, in MDD remains unclear. AIM: To investigate the RNA expression datasets downloaded from a public database and construct a network based on differentially expressed long noncoding RNA (lncRNAs), microRNAs (miRNAs), and mRNAs between MDD and controls. METHODS: Gene expression data were searched in NCBI Gene Expression Omnibus using the search term “major depressive disorder.” Six array datasets from humans were related to the search term: GSE19738, GSE32280, GSE38206, GSE52790, GSE76826, and GSE81152. These datasets were processed for initial assessment and subjected to quality control and differential expression analysis. Differentially expressed lncRNAs, miRNAs, and mRNAs were determined, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and protein-protein interaction network was generated. The results were analyzed for their association with MDD. RESULTS: After analysis, 3 miRNAs, 12 lncRNAs, and 33 mRNAs were identified in the competing endogenous RNA network. Two of these miRNAs were earlier shown to be involved in psychiatric disorders, and differentially expressed mRNAs were found to be highly enriched in pathways related to neurogenesis and neuroplasticity as per Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. The expression of hub gene fatty acid 2-hydroxylase was enriched, and the encoded protein was found to be involved in myelin formation, indicating that neurological development and signal transduction are involved in MDD pathogenesis. CONCLUSION: The present study presents candidate ncRNAs involved in the neurogenesis and neuroplasticity pathways related to MDD. Baishideng Publishing Group Inc 2023-02-19 /pmc/articles/PMC10011943/ /pubmed/36925948 http://dx.doi.org/10.5498/wjp.v13.i2.36 Text en ©The Author(s) 2023. Published by Baishideng Publishing Group Inc. All rights reserved. https://creativecommons.org/licenses/by-nc/4.0/This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial.
spellingShingle Basic Study
Zou, Zhi-Li
Ye, Yu
Zhou, Bo
Zhang, Yuan
Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder
title Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder
title_full Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder
title_fullStr Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder
title_full_unstemmed Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder
title_short Identification and characterization of noncoding RNAs-associated competing endogenous RNA networks in major depressive disorder
title_sort identification and characterization of noncoding rnas-associated competing endogenous rna networks in major depressive disorder
topic Basic Study
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10011943/
https://www.ncbi.nlm.nih.gov/pubmed/36925948
http://dx.doi.org/10.5498/wjp.v13.i2.36
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