Differentially expressed gene profiles and associated ceRNA network in ATG7-Deficient lens epithelial cells under oxidative stress
Oxidation is an essential factor during cataract development. Autophagy, usually a cytoprotective process, is always found elevated in lens epithelial cells under oxidation, yet its roles and associated molecular mechanisms under such circumstances are rarely elucidated. Herein, we extracted and re-...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2022.1088943/full |
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| author | Hongyu Li Hongyu Li Lixiong Gao Jinlin Du Tianju Ma Zi Ye Zhaohui Li Zhaohui Li |
| author_facet | Hongyu Li Hongyu Li Lixiong Gao Jinlin Du Tianju Ma Zi Ye Zhaohui Li Zhaohui Li |
| author_sort | Hongyu Li |
| collection | DOAJ |
| description | Oxidation is an essential factor during cataract development. Autophagy, usually a cytoprotective process, is always found elevated in lens epithelial cells under oxidation, yet its roles and associated molecular mechanisms under such circumstances are rarely elucidated. Herein, we extracted and re-analyzed the RNA sequencing data of the GSE161701 dataset from the Gene Expression Omnibus database to identify the differentially expressed mRNAs and lncRNAs by using the R package “DESeq2”. Further analyses of gene ontology and KEGG enrichment were implemented via the packages “clusterProfiler” and “enrichplot”. We found that after the knockout of ATG7, differentially expressed genes were more associated with hemopoiesis, vasculature development, axonogenesis, and hypoxia regulation. When stimulated with H2O2, LECs displayed a gene expression profile correlating with apoptotic and proliferative pathways, such as the MAPK signaling pathway and FoxO signaling pathway. The differentially expressed gene profiles of the two types of LECs (wild type and ATG7 deficient) under oxidation were distinct to a large extent. Furthermore, 1,341 up-regulated and 1912 down-regulated differential mRNAs and 263 up-regulated and 336 down-regulated differential lncRNAs between these two types of LECs subjected to H2O2 were detected, among which 292 mRNAs and 24 lncRNAs possibly interacted with ten cataract-related miRNAs. A competing endogenous lncRNA-miRNA-mRNA network based on such interactions was finally constructed. |
| first_indexed | 2024-04-11T13:28:56Z |
| format | Article |
| id | doaj.art-71391956c4ce4bd3ac3f47869bb4220a |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-11T13:28:56Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-71391956c4ce4bd3ac3f47869bb4220a2022-12-22T04:21:54ZengFrontiers Media S.A.Frontiers in Genetics1664-80212022-12-011310.3389/fgene.2022.10889431088943Differentially expressed gene profiles and associated ceRNA network in ATG7-Deficient lens epithelial cells under oxidative stressHongyu Li0Hongyu Li1Lixiong Gao2Jinlin Du3Tianju Ma4Zi Ye5Zhaohui Li6Zhaohui Li7Medical School of Chinese PLA, Beijing, ChinaSenior Department of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, ChinaSenior Department of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, ChinaSenior Department of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, ChinaSenior Department of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, ChinaSenior Department of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, ChinaMedical School of Chinese PLA, Beijing, ChinaSenior Department of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing, ChinaOxidation is an essential factor during cataract development. Autophagy, usually a cytoprotective process, is always found elevated in lens epithelial cells under oxidation, yet its roles and associated molecular mechanisms under such circumstances are rarely elucidated. Herein, we extracted and re-analyzed the RNA sequencing data of the GSE161701 dataset from the Gene Expression Omnibus database to identify the differentially expressed mRNAs and lncRNAs by using the R package “DESeq2”. Further analyses of gene ontology and KEGG enrichment were implemented via the packages “clusterProfiler” and “enrichplot”. We found that after the knockout of ATG7, differentially expressed genes were more associated with hemopoiesis, vasculature development, axonogenesis, and hypoxia regulation. When stimulated with H2O2, LECs displayed a gene expression profile correlating with apoptotic and proliferative pathways, such as the MAPK signaling pathway and FoxO signaling pathway. The differentially expressed gene profiles of the two types of LECs (wild type and ATG7 deficient) under oxidation were distinct to a large extent. Furthermore, 1,341 up-regulated and 1912 down-regulated differential mRNAs and 263 up-regulated and 336 down-regulated differential lncRNAs between these two types of LECs subjected to H2O2 were detected, among which 292 mRNAs and 24 lncRNAs possibly interacted with ten cataract-related miRNAs. A competing endogenous lncRNA-miRNA-mRNA network based on such interactions was finally constructed.https://www.frontiersin.org/articles/10.3389/fgene.2022.1088943/fullcataractoxidative stressautophagylens epithelial cellsdifferentially expressed genes (DEG)competing endogenous RNAs (ceRNA) |
| spellingShingle | Hongyu Li Hongyu Li Lixiong Gao Jinlin Du Tianju Ma Zi Ye Zhaohui Li Zhaohui Li Differentially expressed gene profiles and associated ceRNA network in ATG7-Deficient lens epithelial cells under oxidative stress Frontiers in Genetics cataract oxidative stress autophagy lens epithelial cells differentially expressed genes (DEG) competing endogenous RNAs (ceRNA) |
| title | Differentially expressed gene profiles and associated ceRNA network in ATG7-Deficient lens epithelial cells under oxidative stress |
| title_full | Differentially expressed gene profiles and associated ceRNA network in ATG7-Deficient lens epithelial cells under oxidative stress |
| title_fullStr | Differentially expressed gene profiles and associated ceRNA network in ATG7-Deficient lens epithelial cells under oxidative stress |
| title_full_unstemmed | Differentially expressed gene profiles and associated ceRNA network in ATG7-Deficient lens epithelial cells under oxidative stress |
| title_short | Differentially expressed gene profiles and associated ceRNA network in ATG7-Deficient lens epithelial cells under oxidative stress |
| title_sort | differentially expressed gene profiles and associated cerna network in atg7 deficient lens epithelial cells under oxidative stress |
| topic | cataract oxidative stress autophagy lens epithelial cells differentially expressed genes (DEG) competing endogenous RNAs (ceRNA) |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2022.1088943/full |
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