Integrated bioinformatics analysis of retinal ischemia/reperfusion injury in rats with potential key genes
Abstract The tissue damage caused by transient ischemic injury is an essential component of the pathogenesis of retinal ischemia, which mainly hinges on the degree and duration of interruption of the blood supply and the subsequent damage caused by tissue reperfusion. Some research indicated that th...
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| Format: | Article |
| Language: | English |
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BMC
2024-04-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-024-10288-0 |
| _version_ | 1797199610020626432 |
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| author | Kai-Xiong Qing Amy C. Y. Lo Siduo Lu You Zhou Dan Yang Di Yang |
| author_facet | Kai-Xiong Qing Amy C. Y. Lo Siduo Lu You Zhou Dan Yang Di Yang |
| author_sort | Kai-Xiong Qing |
| collection | DOAJ |
| description | Abstract The tissue damage caused by transient ischemic injury is an essential component of the pathogenesis of retinal ischemia, which mainly hinges on the degree and duration of interruption of the blood supply and the subsequent damage caused by tissue reperfusion. Some research indicated that the retinal injury induced by ischemia-reperfusion (I/R) was related to reperfusion time. In this study, we screened the differentially expressed circRNAs, lncRNAs, and mRNAs between the control and model group and at different reperfusion time (24h, 72h, and 7d) with the aid of whole transcriptome sequencing technology, and the trend changes in time-varying mRNA, lncRNA, circRNA were obtained by chronological analysis. Then, candidate circRNAs, lncRNAs, and mRNAs were obtained as the intersection of differentially expression genes and trend change genes. Importance scores of the genes selected the key genes whose expression changed with the increase of reperfusion time. Also, the characteristic differentially expressed genes specific to the reperfusion time were analyzed, key genes specific to reperfusion time were selected to show the change in biological process with the increase of reperfusion time. As a result, 316 candidate mRNAs, 137 candidate lncRNAs, and 31 candidate circRNAs were obtained by the intersection of differentially expressed mRNAs, lncRNAs, and circRNAs with trend mRNAs, trend lncRNAs and trend circRNAs, 5 key genes (Cd74, RT1-Da, RT1-CE5, RT1-Bb, RT1-DOa) were selected by importance scores of the genes. The result of GSEA showed that key genes were found to play vital roles in antigen processing and presentation, regulation of the actin cytoskeleton, and the ribosome. A network included 4 key genes (Cd74, RT1-Da, RT1-Bb, RT1-DOa), 34 miRNAs and 48 lncRNAs, and 81 regulatory relationship axes, and a network included 4 key genes (Cd74, RT1-Da, RT1-Bb, RT1-DOa), 9 miRNAs and 3 circRNAs (circRNA_10572, circRNA_03219, circRNA_11359) and 12 regulatory relationship axes were constructed, the subcellular location, transcription factors, signaling network, targeted drugs and relationship to eye diseases of key genes were predicted. 1370 characteristic differentially expressed mRNAs (spec_24h mRNA), 558 characteristic differentially expressed mRNAs (spec_72h mRNA), and 92 characteristic differentially expressed mRNAs (spec_7d mRNA) were found, and their key genes and regulation networks were analyzed. In summary, we screened the differentially expressed circRNAs, lncRNAs, and mRNAs between the control and model groups and at different reperfusion time (24h, 72h, and 7d). 5 key genes, Cd74, RT1-Da, RT1-CE5, RT1-Bb, RT1-DOa, were selected. Key genes specific to reperfusion time were selected to show the change in biological process with the increased reperfusion time. These results provided theoretical support and a reference basis for the clinical treatment. |
| first_indexed | 2024-04-24T07:18:29Z |
| format | Article |
| id | doaj.art-695c67db23ba42bba0cd13481f370c7f |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-24T07:18:29Z |
| publishDate | 2024-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-695c67db23ba42bba0cd13481f370c7f2024-04-21T11:10:10ZengBMCBMC Genomics1471-21642024-04-0125112410.1186/s12864-024-10288-0Integrated bioinformatics analysis of retinal ischemia/reperfusion injury in rats with potential key genesKai-Xiong Qing0Amy C. Y. Lo1Siduo Lu2You Zhou3Dan Yang4Di Yang5Department of Cardiac & Vascular Surgery, First Affiliated Hospital of Kunming Medical University, Kunming Medical UniversityDepartment of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong KongDepartment of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical UniversityDepartment of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical UniversityDepartment of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical UniversityDepartment of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical UniversityAbstract The tissue damage caused by transient ischemic injury is an essential component of the pathogenesis of retinal ischemia, which mainly hinges on the degree and duration of interruption of the blood supply and the subsequent damage caused by tissue reperfusion. Some research indicated that the retinal injury induced by ischemia-reperfusion (I/R) was related to reperfusion time. In this study, we screened the differentially expressed circRNAs, lncRNAs, and mRNAs between the control and model group and at different reperfusion time (24h, 72h, and 7d) with the aid of whole transcriptome sequencing technology, and the trend changes in time-varying mRNA, lncRNA, circRNA were obtained by chronological analysis. Then, candidate circRNAs, lncRNAs, and mRNAs were obtained as the intersection of differentially expression genes and trend change genes. Importance scores of the genes selected the key genes whose expression changed with the increase of reperfusion time. Also, the characteristic differentially expressed genes specific to the reperfusion time were analyzed, key genes specific to reperfusion time were selected to show the change in biological process with the increase of reperfusion time. As a result, 316 candidate mRNAs, 137 candidate lncRNAs, and 31 candidate circRNAs were obtained by the intersection of differentially expressed mRNAs, lncRNAs, and circRNAs with trend mRNAs, trend lncRNAs and trend circRNAs, 5 key genes (Cd74, RT1-Da, RT1-CE5, RT1-Bb, RT1-DOa) were selected by importance scores of the genes. The result of GSEA showed that key genes were found to play vital roles in antigen processing and presentation, regulation of the actin cytoskeleton, and the ribosome. A network included 4 key genes (Cd74, RT1-Da, RT1-Bb, RT1-DOa), 34 miRNAs and 48 lncRNAs, and 81 regulatory relationship axes, and a network included 4 key genes (Cd74, RT1-Da, RT1-Bb, RT1-DOa), 9 miRNAs and 3 circRNAs (circRNA_10572, circRNA_03219, circRNA_11359) and 12 regulatory relationship axes were constructed, the subcellular location, transcription factors, signaling network, targeted drugs and relationship to eye diseases of key genes were predicted. 1370 characteristic differentially expressed mRNAs (spec_24h mRNA), 558 characteristic differentially expressed mRNAs (spec_72h mRNA), and 92 characteristic differentially expressed mRNAs (spec_7d mRNA) were found, and their key genes and regulation networks were analyzed. In summary, we screened the differentially expressed circRNAs, lncRNAs, and mRNAs between the control and model groups and at different reperfusion time (24h, 72h, and 7d). 5 key genes, Cd74, RT1-Da, RT1-CE5, RT1-Bb, RT1-DOa, were selected. Key genes specific to reperfusion time were selected to show the change in biological process with the increased reperfusion time. These results provided theoretical support and a reference basis for the clinical treatment.https://doi.org/10.1186/s12864-024-10288-0Retinal ischemia/reperfusion (RIR)ncRNAsWhole transcriptome sequencing |
| spellingShingle | Kai-Xiong Qing Amy C. Y. Lo Siduo Lu You Zhou Dan Yang Di Yang Integrated bioinformatics analysis of retinal ischemia/reperfusion injury in rats with potential key genes BMC Genomics Retinal ischemia/reperfusion (RIR) ncRNAs Whole transcriptome sequencing |
| title | Integrated bioinformatics analysis of retinal ischemia/reperfusion injury in rats with potential key genes |
| title_full | Integrated bioinformatics analysis of retinal ischemia/reperfusion injury in rats with potential key genes |
| title_fullStr | Integrated bioinformatics analysis of retinal ischemia/reperfusion injury in rats with potential key genes |
| title_full_unstemmed | Integrated bioinformatics analysis of retinal ischemia/reperfusion injury in rats with potential key genes |
| title_short | Integrated bioinformatics analysis of retinal ischemia/reperfusion injury in rats with potential key genes |
| title_sort | integrated bioinformatics analysis of retinal ischemia reperfusion injury in rats with potential key genes |
| topic | Retinal ischemia/reperfusion (RIR) ncRNAs Whole transcriptome sequencing |
| url | https://doi.org/10.1186/s12864-024-10288-0 |
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