Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice
ObjectiveIntracerebral hemorrhage (ICH) is a subtype of stroke with high mortality and morbidity rates. Our aim was to comprehensively analyze transcriptome and proteome in an experimental ICH model.MethodsAll mice were divided into ICH model (n = 3) and sham groups (n = 3). ICH was induced by colla...
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Frontiers Media S.A.
2020-12-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2020.551065/full |
| _version_ | 1818610223654371328 |
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| author | Fang Cao Yu Guo Qiang Zhang Yinchun Fan Qian Liu Jiancheng Song Hua Zhong Shengtao Yao |
| author_facet | Fang Cao Yu Guo Qiang Zhang Yinchun Fan Qian Liu Jiancheng Song Hua Zhong Shengtao Yao |
| author_sort | Fang Cao |
| collection | DOAJ |
| description | ObjectiveIntracerebral hemorrhage (ICH) is a subtype of stroke with high mortality and morbidity rates. Our aim was to comprehensively analyze transcriptome and proteome in an experimental ICH model.MethodsAll mice were divided into ICH model (n = 3) and sham groups (n = 3). ICH was induced by collagenase VII. The ipsilateral hemisphere was used for whole transcriptome and proteomics resequencing. After preprocessing, differentially expressed lncRNAs (DElncRNAs), mRNAs (DEmRNAs), miRNAs (DEmiRNAs), and DEproteins between ICH and sham groups were identified. Functional enrichment analysis was performed using the clusterProfiler package, followed by protein–protein interaction (PPI) analysis. After that, the Pearson correlation coefficient between DEmRNAs and DElncRNAs or between DEmRNAs and DEproteins was calculated. DElncRNAs with similar functions were analyzed by the GOSemSim package. After prediction of DEmiRNA–DEmRNA and DElncRNA–DEmiRNA relationships, a competing endogenous RNA (ceRNA) network was constructed. Several DEmRNAs and DElncRNAs were validated in ipsilateral hemisphere tissues of the ICH model and control groups using RT-qPCR and western blot.ResultsBetween the ICH and sham groups, 31 DElncRNAs, 367 DEmRNAs, 35 DEmiRNAs, and 96 DEproteins were identified. DEmRNAs were mainly enriched in inflammation, such as cytokine–cytokine receptor interaction, IL-17, and TNF signaling pathways. A PPI network of DEmRNAs was constructed and hub genes were identified, such as IL6 (degree = 59), TNF (degree = 44), and CXCR2 (degree = 39). 24 DElncRNAs with similar functions were identified, including 15 up- and 9 down-regulated lncRNAs. After integration of DEmiRNA–DEmRNA and DElncRNA–DEmiRNA relationships, we constructed a ceRNA network, composed of 71 DEmRNAs, 17 DEmiRNAs, and 12 DElncRNAs. RT-qPCR and western blot results confirmed that C3, Fga, and Slc4a1 proteins were more lowly expressed and Penk was more highly expressed in ICH than control groups, which could become potential markers for ICH.ConclusionOur findings identified ICH-related DE-RNAs and proteins and potential molecular mechanisms of ICH by transcriptome resequencing and quantitative proteomic analyses. |
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| spelling | doaj.art-d8a92d5a30fc445fa67f582f39e1a4972022-12-21T22:26:58ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-12-011110.3389/fgene.2020.551065551065Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in MiceFang Cao0Yu Guo1Qiang Zhang2Yinchun Fan3Qian Liu4Jiancheng Song5Hua Zhong6Shengtao Yao7Department of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, ChinaDepartment of Radiology, Daping Hospital, Army Medical University, Chongqing, ChinaDepartment of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, ChinaDepartment of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, ChinaDepartment of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, ChinaDepartment of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, ChinaCollege of Life Sciences, Wuhan University, Wuhan, ChinaDepartment of Cerebrovascular Disease, Affiliated Hospital of Zunyi Medical University, Zunyi, ChinaObjectiveIntracerebral hemorrhage (ICH) is a subtype of stroke with high mortality and morbidity rates. Our aim was to comprehensively analyze transcriptome and proteome in an experimental ICH model.MethodsAll mice were divided into ICH model (n = 3) and sham groups (n = 3). ICH was induced by collagenase VII. The ipsilateral hemisphere was used for whole transcriptome and proteomics resequencing. After preprocessing, differentially expressed lncRNAs (DElncRNAs), mRNAs (DEmRNAs), miRNAs (DEmiRNAs), and DEproteins between ICH and sham groups were identified. Functional enrichment analysis was performed using the clusterProfiler package, followed by protein–protein interaction (PPI) analysis. After that, the Pearson correlation coefficient between DEmRNAs and DElncRNAs or between DEmRNAs and DEproteins was calculated. DElncRNAs with similar functions were analyzed by the GOSemSim package. After prediction of DEmiRNA–DEmRNA and DElncRNA–DEmiRNA relationships, a competing endogenous RNA (ceRNA) network was constructed. Several DEmRNAs and DElncRNAs were validated in ipsilateral hemisphere tissues of the ICH model and control groups using RT-qPCR and western blot.ResultsBetween the ICH and sham groups, 31 DElncRNAs, 367 DEmRNAs, 35 DEmiRNAs, and 96 DEproteins were identified. DEmRNAs were mainly enriched in inflammation, such as cytokine–cytokine receptor interaction, IL-17, and TNF signaling pathways. A PPI network of DEmRNAs was constructed and hub genes were identified, such as IL6 (degree = 59), TNF (degree = 44), and CXCR2 (degree = 39). 24 DElncRNAs with similar functions were identified, including 15 up- and 9 down-regulated lncRNAs. After integration of DEmiRNA–DEmRNA and DElncRNA–DEmiRNA relationships, we constructed a ceRNA network, composed of 71 DEmRNAs, 17 DEmiRNAs, and 12 DElncRNAs. RT-qPCR and western blot results confirmed that C3, Fga, and Slc4a1 proteins were more lowly expressed and Penk was more highly expressed in ICH than control groups, which could become potential markers for ICH.ConclusionOur findings identified ICH-related DE-RNAs and proteins and potential molecular mechanisms of ICH by transcriptome resequencing and quantitative proteomic analyses.https://www.frontiersin.org/articles/10.3389/fgene.2020.551065/fullintracerebral hemorrhagetranscriptome resequencingproteomic analysesinflammationcompeting endogenous RNAprotein–protein interactions |
| spellingShingle | Fang Cao Yu Guo Qiang Zhang Yinchun Fan Qian Liu Jiancheng Song Hua Zhong Shengtao Yao Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice Frontiers in Genetics intracerebral hemorrhage transcriptome resequencing proteomic analyses inflammation competing endogenous RNA protein–protein interactions |
| title | Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice |
| title_full | Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice |
| title_fullStr | Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice |
| title_full_unstemmed | Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice |
| title_short | Integration of Transcriptome Resequencing and Quantitative Proteomics Analyses of Collagenase VII-Induced Intracerebral Hemorrhage in Mice |
| title_sort | integration of transcriptome resequencing and quantitative proteomics analyses of collagenase vii induced intracerebral hemorrhage in mice |
| topic | intracerebral hemorrhage transcriptome resequencing proteomic analyses inflammation competing endogenous RNA protein–protein interactions |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2020.551065/full |
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