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Identification of key genes and potential mechanisms based on the autophagy regulatory network in intervertebral disc degeneration

Intervertebral disc degeneration (IDD) is a common musculoskeletal disease that develops with increasing age. However, the exact occurrence and progression of IDD remains unclear. Gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) repository. The NCBI GEO2R analysis tool...

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Autores principales: Lv, Chang, Chen, Kai, Zhu, Lixin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Lippincott Williams & Wilkins 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10082314/
https://www.ncbi.nlm.nih.gov/pubmed/37026912
http://dx.doi.org/10.1097/MD.0000000000033482
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author Lv, Chang
Chen, Kai
Zhu, Lixin
author_facet Lv, Chang
Chen, Kai
Zhu, Lixin
author_sort Lv, Chang
collection PubMed
description Intervertebral disc degeneration (IDD) is a common musculoskeletal disease that develops with increasing age. However, the exact occurrence and progression of IDD remains unclear. Gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) repository. The NCBI GEO2R analysis tool was used to identify differentially expressed genes. The protein-protein interaction (PPI) network was predicted using the STRING website and visualized using the Cytoscape software. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to enrich GO terms and signaling pathways using the Metascape database. To identify potential upstream miRNA targets of these differentially expressed genes, the mRNA-miRNA interaction networks were predicted by Network Analyst database. To identify the 2 key genes with significant differences among the 10 hub genes, the GraphPad Prism Tool and GeneCards database were used for analysis. 22 genes were identified. A PPI network was constructed and the other 30 related genes were deduced. GO and Kyoto Encyclopedia of Genes and Genomes enrichment networks indicated extracellular matrix organization, collagen-containing extracellular matrix and extracellular matrix structural constituent in extracellular matrix (ECM) regulation in IDD. The mRNA-miRNA interaction networks suggested that many miRNAs could regulate autophagy-related genes individually and collectively. The GraphPad Prism Tool and GeneCards database analysis results suggested that 2 hub genes were involved in IDD. Our results revealed that the role of ECM could be a regulatory mechanism in IDD and that these ECM-related genes might be targets for the intervention of IDD.
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spelling pubmed-100823142023-04-09 Identification of key genes and potential mechanisms based on the autophagy regulatory network in intervertebral disc degeneration Lv, Chang Chen, Kai Zhu, Lixin Medicine (Baltimore) 3500 Intervertebral disc degeneration (IDD) is a common musculoskeletal disease that develops with increasing age. However, the exact occurrence and progression of IDD remains unclear. Gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) repository. The NCBI GEO2R analysis tool was used to identify differentially expressed genes. The protein-protein interaction (PPI) network was predicted using the STRING website and visualized using the Cytoscape software. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to enrich GO terms and signaling pathways using the Metascape database. To identify potential upstream miRNA targets of these differentially expressed genes, the mRNA-miRNA interaction networks were predicted by Network Analyst database. To identify the 2 key genes with significant differences among the 10 hub genes, the GraphPad Prism Tool and GeneCards database were used for analysis. 22 genes were identified. A PPI network was constructed and the other 30 related genes were deduced. GO and Kyoto Encyclopedia of Genes and Genomes enrichment networks indicated extracellular matrix organization, collagen-containing extracellular matrix and extracellular matrix structural constituent in extracellular matrix (ECM) regulation in IDD. The mRNA-miRNA interaction networks suggested that many miRNAs could regulate autophagy-related genes individually and collectively. The GraphPad Prism Tool and GeneCards database analysis results suggested that 2 hub genes were involved in IDD. Our results revealed that the role of ECM could be a regulatory mechanism in IDD and that these ECM-related genes might be targets for the intervention of IDD. Lippincott Williams & Wilkins 2022-04-07 /pmc/articles/PMC10082314/ /pubmed/37026912 http://dx.doi.org/10.1097/MD.0000000000033482 Text en Copyright © 2023 the Author(s). Published by Wolters Kluwer Health, Inc. https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial License 4.0 (CCBY-NC) (https://creativecommons.org/licenses/by-nc/4.0/) , where it is permissible to download, share, remix, transform, and buildup the work provided it is properly cited. The work cannot be used commercially without permission from the journal.
spellingShingle 3500
Lv, Chang
Chen, Kai
Zhu, Lixin
Identification of key genes and potential mechanisms based on the autophagy regulatory network in intervertebral disc degeneration
title Identification of key genes and potential mechanisms based on the autophagy regulatory network in intervertebral disc degeneration
title_full Identification of key genes and potential mechanisms based on the autophagy regulatory network in intervertebral disc degeneration
title_fullStr Identification of key genes and potential mechanisms based on the autophagy regulatory network in intervertebral disc degeneration
title_full_unstemmed Identification of key genes and potential mechanisms based on the autophagy regulatory network in intervertebral disc degeneration
title_short Identification of key genes and potential mechanisms based on the autophagy regulatory network in intervertebral disc degeneration
title_sort identification of key genes and potential mechanisms based on the autophagy regulatory network in intervertebral disc degeneration
topic 3500
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10082314/
https://www.ncbi.nlm.nih.gov/pubmed/37026912
http://dx.doi.org/10.1097/MD.0000000000033482
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