Screening of core DEL.
<div><p>Long non-coding RNAs (lncRNAs) are among the most abundant types of non-coding RNAs in the genome and exhibit particularly high expression levels in the brain, where they play crucial roles in various neurophysiological and neuropathological processes. Although ischemic stroke is...
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| المؤلف الرئيسي: | |
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| مؤلفون آخرون: | , , , , , , |
| منشور في: |
2025
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| الموضوعات: | |
| الوسوم: |
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| _version_ | 1852023324514713600 |
|---|---|
| author | Meimei Xu (744867) |
| author2 | Shan Yuan (7870886) Xing Luo (5449928) Mengsi Xu (636298) Guangze Hu (20606198) Zhe He (508742) Xinyuan Yang (12170651) Rui Gao (247606) |
| author2_role | author author author author author author author |
| author_facet | Meimei Xu (744867) Shan Yuan (7870886) Xing Luo (5449928) Mengsi Xu (636298) Guangze Hu (20606198) Zhe He (508742) Xinyuan Yang (12170651) Rui Gao (247606) |
| author_role | author |
| dc.creator.none.fl_str_mv | Meimei Xu (744867) Shan Yuan (7870886) Xing Luo (5449928) Mengsi Xu (636298) Guangze Hu (20606198) Zhe He (508742) Xinyuan Yang (12170651) Rui Gao (247606) |
| dc.date.none.fl_str_mv | 2025-01-23T18:31:28Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pone.0317710.s007 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Screening_of_core_DEL_/28265456 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biochemistry Medicine Cell Biology Genetics Molecular Biology Neuroscience Physiology Biological Sciences not elsewhere classified providing novel insights play crucial roles pathway analyses revealed competing endogenous rna 191 target mrnas interaction network based complex multifactorial disease 16 sponge mirnas 183 lncrnas detected rat cerebral cortex differentially expressed mrnas although ischemic stroke mediated cerna network inflammatory regulatory mechanisms cortical lncrnas post complex network differentially expressed ipsilateral cortex inflammatory responses four mirnas cerebral ischemia derived lncrnas various neurophysiological transcriptional regulation throughput sequencing targeting relationships stroke processes stroke mechanisms significantly enriched related pathways pathophysiological processes participate extensively operated groups neuropathological processes microglial activation male sprague level regulators kyoto encyclopedia integrated analysis including angiogenesis gene ontology findings highlight dawley rats coding rnas axonal regeneration 05 ). |
| dc.title.none.fl_str_mv | Screening of core DEL. |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | <div><p>Long non-coding RNAs (lncRNAs) are among the most abundant types of non-coding RNAs in the genome and exhibit particularly high expression levels in the brain, where they play crucial roles in various neurophysiological and neuropathological processes. Although ischemic stroke is a complex multifactorial disease, the involvement of brain-derived lncRNAs in its intricate regulatory networks remains inadequately understood. In this study, we established a cerebral ischemia-reperfusion injury model using middle cerebral artery occlusion (MCAO) in male Sprague-Dawley rats. High-throughput sequencing was performed to profile the expression of cortical lncRNAs post-stroke, with subsequent validation using RT-PCR and qRT-PCR. Among the 31,183 lncRNAs detected in the rat cerebral cortex, 551 were differentially expressed between the MCAO and sham-operated groups in the ipsilateral cortex (fold change ≥2.0, P < 0.05). An integrated analysis of the 20 most abundant and significantly differentially expressed lncRNAs (DELs) identified 25 core cytoplasmic DELs, which were used to construct an interaction network based on their targeting relationships. This led to the establishment of a comprehensive lncRNA-miRNA-mRNA regulatory network comprising 12 lncRNAs, 16 sponge miRNAs, and 191 target mRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that differentially expressed mRNAs (DEmRNAs) were significantly enriched in stroke-related pathways. Our analysis predicted four key lncRNAs, four miRNAs, and eleven crucial mRNAs involved in post-transcriptional regulation through competing endogenous RNA (ceRNA) mechanisms. These molecules were shown to participate extensively in post-stroke processes, including angiogenesis, axonal regeneration, inflammatory responses, microglial activation, blood-brain barrier (BBB) disruption, apoptosis, autophagy, ferroptosis, and thrombocytopenia. These findings highlight the role of lncRNAs as multi-level regulators in the complex network of post-stroke mechanisms, providing novel insights into the pathophysiological processes of stroke.</p></div> |
| eu_rights_str_mv | openAccess |
| id | Manara_41d94bc02376535fc76ff119261cc533 |
| identifier_str_mv | 10.1371/journal.pone.0317710.s007 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/28265456 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Screening of core DEL.Meimei Xu (744867)Shan Yuan (7870886)Xing Luo (5449928)Mengsi Xu (636298)Guangze Hu (20606198)Zhe He (508742)Xinyuan Yang (12170651)Rui Gao (247606)BiochemistryMedicineCell BiologyGeneticsMolecular BiologyNeurosciencePhysiologyBiological Sciences not elsewhere classifiedproviding novel insightsplay crucial rolespathway analyses revealedcompeting endogenous rna191 target mrnasinteraction network basedcomplex multifactorial disease16 sponge mirnas183 lncrnas detectedrat cerebral cortexdifferentially expressed mrnasalthough ischemic strokemediated cerna networkinflammatory regulatory mechanismscortical lncrnas postcomplex networkdifferentially expressedipsilateral cortexinflammatory responsesfour mirnascerebral ischemiaderived lncrnasvarious neurophysiologicaltranscriptional regulationthroughput sequencingtargeting relationshipsstroke processesstroke mechanismssignificantly enrichedrelated pathwayspathophysiological processesparticipate extensivelyoperated groupsneuropathological processesmicroglial activationmale spraguelevel regulatorskyoto encyclopediaintegrated analysisincluding angiogenesisgene ontologyfindings highlightdawley ratscoding rnasaxonal regeneration05 ).<div><p>Long non-coding RNAs (lncRNAs) are among the most abundant types of non-coding RNAs in the genome and exhibit particularly high expression levels in the brain, where they play crucial roles in various neurophysiological and neuropathological processes. Although ischemic stroke is a complex multifactorial disease, the involvement of brain-derived lncRNAs in its intricate regulatory networks remains inadequately understood. In this study, we established a cerebral ischemia-reperfusion injury model using middle cerebral artery occlusion (MCAO) in male Sprague-Dawley rats. High-throughput sequencing was performed to profile the expression of cortical lncRNAs post-stroke, with subsequent validation using RT-PCR and qRT-PCR. Among the 31,183 lncRNAs detected in the rat cerebral cortex, 551 were differentially expressed between the MCAO and sham-operated groups in the ipsilateral cortex (fold change ≥2.0, P < 0.05). An integrated analysis of the 20 most abundant and significantly differentially expressed lncRNAs (DELs) identified 25 core cytoplasmic DELs, which were used to construct an interaction network based on their targeting relationships. This led to the establishment of a comprehensive lncRNA-miRNA-mRNA regulatory network comprising 12 lncRNAs, 16 sponge miRNAs, and 191 target mRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that differentially expressed mRNAs (DEmRNAs) were significantly enriched in stroke-related pathways. Our analysis predicted four key lncRNAs, four miRNAs, and eleven crucial mRNAs involved in post-transcriptional regulation through competing endogenous RNA (ceRNA) mechanisms. These molecules were shown to participate extensively in post-stroke processes, including angiogenesis, axonal regeneration, inflammatory responses, microglial activation, blood-brain barrier (BBB) disruption, apoptosis, autophagy, ferroptosis, and thrombocytopenia. These findings highlight the role of lncRNAs as multi-level regulators in the complex network of post-stroke mechanisms, providing novel insights into the pathophysiological processes of stroke.</p></div>2025-01-23T18:31:28ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.1371/journal.pone.0317710.s007https://figshare.com/articles/dataset/Screening_of_core_DEL_/28265456CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/282654562025-01-23T18:31:28Z |
| spellingShingle | Screening of core DEL. Meimei Xu (744867) Biochemistry Medicine Cell Biology Genetics Molecular Biology Neuroscience Physiology Biological Sciences not elsewhere classified providing novel insights play crucial roles pathway analyses revealed competing endogenous rna 191 target mrnas interaction network based complex multifactorial disease 16 sponge mirnas 183 lncrnas detected rat cerebral cortex differentially expressed mrnas although ischemic stroke mediated cerna network inflammatory regulatory mechanisms cortical lncrnas post complex network differentially expressed ipsilateral cortex inflammatory responses four mirnas cerebral ischemia derived lncrnas various neurophysiological transcriptional regulation throughput sequencing targeting relationships stroke processes stroke mechanisms significantly enriched related pathways pathophysiological processes participate extensively operated groups neuropathological processes microglial activation male sprague level regulators kyoto encyclopedia integrated analysis including angiogenesis gene ontology findings highlight dawley rats coding rnas axonal regeneration 05 ). |
| status_str | publishedVersion |
| title | Screening of core DEL. |
| title_full | Screening of core DEL. |
| title_fullStr | Screening of core DEL. |
| title_full_unstemmed | Screening of core DEL. |
| title_short | Screening of core DEL. |
| title_sort | Screening of core DEL. |
| topic | Biochemistry Medicine Cell Biology Genetics Molecular Biology Neuroscience Physiology Biological Sciences not elsewhere classified providing novel insights play crucial roles pathway analyses revealed competing endogenous rna 191 target mrnas interaction network based complex multifactorial disease 16 sponge mirnas 183 lncrnas detected rat cerebral cortex differentially expressed mrnas although ischemic stroke mediated cerna network inflammatory regulatory mechanisms cortical lncrnas post complex network differentially expressed ipsilateral cortex inflammatory responses four mirnas cerebral ischemia derived lncrnas various neurophysiological transcriptional regulation throughput sequencing targeting relationships stroke processes stroke mechanisms significantly enriched related pathways pathophysiological processes participate extensively operated groups neuropathological processes microglial activation male sprague level regulators kyoto encyclopedia integrated analysis including angiogenesis gene ontology findings highlight dawley rats coding rnas axonal regeneration 05 ). |