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Comprehensive analysis of molecular pathways and key genes involved in lumbar disc herniation
Based on the Thompson classification of intervertebral discs (IVDs), we systematically analyzed gene expression differences between severely degenerated and mildly degenerated IVDs and explored the underlying molecular mechanisms using bioinformatics methods and multichip integration. We used multio...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Lippincott Williams & Wilkins
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9282072/ https://www.ncbi.nlm.nih.gov/pubmed/33761671 http://dx.doi.org/10.1097/MD.0000000000025093 |
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author | Liu, Quanxiang Chen, Qian Zhuang, Xinming Qi, Mingyu Guo, Jianping Li, Zengxin Dai, Qizhi Cheng, Wei |
author_facet | Liu, Quanxiang Chen, Qian Zhuang, Xinming Qi, Mingyu Guo, Jianping Li, Zengxin Dai, Qizhi Cheng, Wei |
author_sort | Liu, Quanxiang |
collection | PubMed |
description | Based on the Thompson classification of intervertebral discs (IVDs), we systematically analyzed gene expression differences between severely degenerated and mildly degenerated IVDs and explored the underlying molecular mechanisms using bioinformatics methods and multichip integration. We used multiomics analysis, includes mRNA microarray and methylation chips, to explore the genetic network and mechanisms of lumbar disc herniation (LDH). Subsequently, the Combat function of the R language SVA package was applied to eliminate heterogeneity between the gene expression data. And the protein–protein interaction (PPI) network, gene ontology (GO), and molecular pathways were used to constructs the mechanisms network. Consequently, we obtained 149 differentially expressed genes. Related molecular pathways are the following: ribosome activity, oxidative phosphorylation, extracellular matrix response. Besides, through PPI network analysis, genes with higher connectivity such as UBA52, RPLP0, RPL3, RPLP2, and RPL27 were also identified, suggesting that they play important regulatory roles in the complex network associated with LDH. Additionally, cg12556991 (RPL27) and cg06852319 (RPLP0) were found to be LDH-related candidate DNA methylation modification sites in the IVDs tissue of LDH patients. In conclusions, ribosome activity, oxidative phosphorylation, and extracellular matrix response may be potential molecular mechanisms underlying LDH, while hub genes involved in UBA52, RPLP0, RPL3, RPLP2, and RPL27, and candidate DNA methylation modification sites of cg12556991and cg06852319 are likely key regulators in the development of LDH. |
format | Online Article Text |
id | pubmed-9282072 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Lippincott Williams & Wilkins |
record_format | MEDLINE/PubMed |
spelling | pubmed-92820722022-08-02 Comprehensive analysis of molecular pathways and key genes involved in lumbar disc herniation Liu, Quanxiang Chen, Qian Zhuang, Xinming Qi, Mingyu Guo, Jianping Li, Zengxin Dai, Qizhi Cheng, Wei Medicine (Baltimore) 3200 Based on the Thompson classification of intervertebral discs (IVDs), we systematically analyzed gene expression differences between severely degenerated and mildly degenerated IVDs and explored the underlying molecular mechanisms using bioinformatics methods and multichip integration. We used multiomics analysis, includes mRNA microarray and methylation chips, to explore the genetic network and mechanisms of lumbar disc herniation (LDH). Subsequently, the Combat function of the R language SVA package was applied to eliminate heterogeneity between the gene expression data. And the protein–protein interaction (PPI) network, gene ontology (GO), and molecular pathways were used to constructs the mechanisms network. Consequently, we obtained 149 differentially expressed genes. Related molecular pathways are the following: ribosome activity, oxidative phosphorylation, extracellular matrix response. Besides, through PPI network analysis, genes with higher connectivity such as UBA52, RPLP0, RPL3, RPLP2, and RPL27 were also identified, suggesting that they play important regulatory roles in the complex network associated with LDH. Additionally, cg12556991 (RPL27) and cg06852319 (RPLP0) were found to be LDH-related candidate DNA methylation modification sites in the IVDs tissue of LDH patients. In conclusions, ribosome activity, oxidative phosphorylation, and extracellular matrix response may be potential molecular mechanisms underlying LDH, while hub genes involved in UBA52, RPLP0, RPL3, RPLP2, and RPL27, and candidate DNA methylation modification sites of cg12556991and cg06852319 are likely key regulators in the development of LDH. Lippincott Williams & Wilkins 2021-03-26 /pmc/articles/PMC9282072/ /pubmed/33761671 http://dx.doi.org/10.1097/MD.0000000000025093 Text en Copyright © 2021 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), 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. http://creativecommons.org/licenses/by-nc/4.0 (https://creativecommons.org/licenses/by-nc/4.0/) |
spellingShingle | 3200 Liu, Quanxiang Chen, Qian Zhuang, Xinming Qi, Mingyu Guo, Jianping Li, Zengxin Dai, Qizhi Cheng, Wei Comprehensive analysis of molecular pathways and key genes involved in lumbar disc herniation |
title | Comprehensive analysis of molecular pathways and key genes involved in lumbar disc herniation |
title_full | Comprehensive analysis of molecular pathways and key genes involved in lumbar disc herniation |
title_fullStr | Comprehensive analysis of molecular pathways and key genes involved in lumbar disc herniation |
title_full_unstemmed | Comprehensive analysis of molecular pathways and key genes involved in lumbar disc herniation |
title_short | Comprehensive analysis of molecular pathways and key genes involved in lumbar disc herniation |
title_sort | comprehensive analysis of molecular pathways and key genes involved in lumbar disc herniation |
topic | 3200 |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9282072/ https://www.ncbi.nlm.nih.gov/pubmed/33761671 http://dx.doi.org/10.1097/MD.0000000000025093 |
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