A microarray data analysis investigating the pathogenesis and potential biomarkers of autophagy and ferroptosis in intervertebral disc degeneration
Background: Intervertebral disc degeneration (IDD) entails complex pathological changes and causes lower back pain (LBP). However, there is still a lack of understanding of the mechanisms involved in IDD, particularly regarding the roles of autophagy and ferroptosis. The current study used microarra...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-01-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.1090467/full |
| _version_ | 1797667916584321024 |
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| author | Wenhao Kuang Cong Jiang Cheng Yu Jinwei Hu Yang Duan Zhong Chen |
| author_facet | Wenhao Kuang Cong Jiang Cheng Yu Jinwei Hu Yang Duan Zhong Chen |
| author_sort | Wenhao Kuang |
| collection | DOAJ |
| description | Background: Intervertebral disc degeneration (IDD) entails complex pathological changes and causes lower back pain (LBP). However, there is still a lack of understanding of the mechanisms involved in IDD, particularly regarding the roles of autophagy and ferroptosis. The current study used microarray data to investigate the pathogenesis of IDD and potential biomarkers related to autophagy and ferroptosis in IDD.Methods: Differentially expressed genes (DEGs) were identified by analyzing the mRNA and miRNA expression profiles of IDD patients from the Gene Expression Omnibus (GEO). The protein-protein interaction network, Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and gene set enrichment analysis (GSEA) were utilized. The Human Autophagy Database (HADb) and Ferroptosis Database were used in conjunction with hub genes to identify autophagy- and ferroptosis-related genes. The Transcription Factor -hub gene-miRNA network was constructed. Lastly, the expression of DEGs in normal and degenerated nucleus pulposus cells (NPCs) was investigated via the quantitative reverse transcription polymerase chain reaction (qRT-PCR).Results: A total of 362 DEGs associated with IDD were identified. GO and KEGG analyses indicated that oxidative stress, extracellular matrix, PI3K-AKT signaling pathway, and ferroptosis were key factors in IDD occurrence. GSEA indicated that IDD was associated with changes in autophagy, iron ion homeostasis, extracellular matrix, and oxidative stress. Eighty-nine hub genes were obtained, including five that were autophagy-related and three that were ferroptosis-related. Of these, TP53 and SESN2 were the intersections of autophagy- and ferroptosis-related genes. In qRT-PCR analysis, CANX, SLC38A1, and TP53 were downregulated in degenerative NPCs, whereas GNAI3, SESN2, and VAMP3 were upregulated.Conclusion: The current study revealed aspects of autophagy- and ferroptosis-related genes involved in IDD pathogenesis, warranting further investigation. |
| first_indexed | 2024-03-11T20:20:33Z |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-11T20:20:33Z |
| publishDate | 2023-01-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-88af09593ac84b169edd34ffc5d84caa2023-10-03T04:41:38ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-01-011310.3389/fgene.2022.10904671090467A microarray data analysis investigating the pathogenesis and potential biomarkers of autophagy and ferroptosis in intervertebral disc degenerationWenhao KuangCong JiangCheng YuJinwei HuYang DuanZhong ChenBackground: Intervertebral disc degeneration (IDD) entails complex pathological changes and causes lower back pain (LBP). However, there is still a lack of understanding of the mechanisms involved in IDD, particularly regarding the roles of autophagy and ferroptosis. The current study used microarray data to investigate the pathogenesis of IDD and potential biomarkers related to autophagy and ferroptosis in IDD.Methods: Differentially expressed genes (DEGs) were identified by analyzing the mRNA and miRNA expression profiles of IDD patients from the Gene Expression Omnibus (GEO). The protein-protein interaction network, Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and gene set enrichment analysis (GSEA) were utilized. The Human Autophagy Database (HADb) and Ferroptosis Database were used in conjunction with hub genes to identify autophagy- and ferroptosis-related genes. The Transcription Factor -hub gene-miRNA network was constructed. Lastly, the expression of DEGs in normal and degenerated nucleus pulposus cells (NPCs) was investigated via the quantitative reverse transcription polymerase chain reaction (qRT-PCR).Results: A total of 362 DEGs associated with IDD were identified. GO and KEGG analyses indicated that oxidative stress, extracellular matrix, PI3K-AKT signaling pathway, and ferroptosis were key factors in IDD occurrence. GSEA indicated that IDD was associated with changes in autophagy, iron ion homeostasis, extracellular matrix, and oxidative stress. Eighty-nine hub genes were obtained, including five that were autophagy-related and three that were ferroptosis-related. Of these, TP53 and SESN2 were the intersections of autophagy- and ferroptosis-related genes. In qRT-PCR analysis, CANX, SLC38A1, and TP53 were downregulated in degenerative NPCs, whereas GNAI3, SESN2, and VAMP3 were upregulated.Conclusion: The current study revealed aspects of autophagy- and ferroptosis-related genes involved in IDD pathogenesis, warranting further investigation.https://www.frontiersin.org/articles/10.3389/fgene.2022.1090467/fullautophagyDEGsferroptosishub genesintegrated bioinformaticsintervertebral disc degeneration |
| spellingShingle | Wenhao Kuang Cong Jiang Cheng Yu Jinwei Hu Yang Duan Zhong Chen A microarray data analysis investigating the pathogenesis and potential biomarkers of autophagy and ferroptosis in intervertebral disc degeneration Frontiers in Genetics autophagy DEGs ferroptosis hub genes integrated bioinformatics intervertebral disc degeneration |
| title | A microarray data analysis investigating the pathogenesis and potential biomarkers of autophagy and ferroptosis in intervertebral disc degeneration |
| title_full | A microarray data analysis investigating the pathogenesis and potential biomarkers of autophagy and ferroptosis in intervertebral disc degeneration |
| title_fullStr | A microarray data analysis investigating the pathogenesis and potential biomarkers of autophagy and ferroptosis in intervertebral disc degeneration |
| title_full_unstemmed | A microarray data analysis investigating the pathogenesis and potential biomarkers of autophagy and ferroptosis in intervertebral disc degeneration |
| title_short | A microarray data analysis investigating the pathogenesis and potential biomarkers of autophagy and ferroptosis in intervertebral disc degeneration |
| title_sort | microarray data analysis investigating the pathogenesis and potential biomarkers of autophagy and ferroptosis in intervertebral disc degeneration |
| topic | autophagy DEGs ferroptosis hub genes integrated bioinformatics intervertebral disc degeneration |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.1090467/full |
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