{"title":"Key immune regulators in retinal ischemia-reperfusion injury <i>via</i> RNA sequencing.","authors":"Shan He, Cui-Ying Liu, Chang-Hong Ren, Ting-Ting Meng, Heng Zhao, Xu-Xiang Zhang","doi":"10.18240/ijo.2025.07.06","DOIUrl":null,"url":null,"abstract":"<p><strong>Aim: </strong>To explore the immune cell infiltration and molecular mechanisms of retinal ischemia-reperfusion injury (RIRI) to identify potential therapeutic targets.</p><p><strong>Methods: </strong>In the bulk RNA-seq analysis, This study performed differential gene expression analysis, weighted gene co-expression network analysis, and protein-protein interaction network analysis to identify hub genes. QuanTIseq was used to determine the composition of infiltrating immune cells. Following the identification of hub genes, single-cell RNA-seq analysis was employed to pinpoint the specific immune cell types expressing these hub genes. Cell-cell communication analysis to explore signaling pathways and interactions between immune cells was further performed. Finally, the expression of these key immune regulators <i>in vivo</i> using quantitative real-time polymerase chain reaction (qRT-PCR) was validated.</p><p><strong>Results: </strong>Bulk RNA-seq analysis identified <i>Stat2</i>, <i>Irf7</i>, <i>Irgm1</i>, <i>Igtp</i>, <i>Parp</i>9, <i>Irgm2</i>, <i>Nlrc5</i>, and <i>Tap1</i> as hub genes, with strong correlations to immune cell infiltration. Single-cell RNA-seq analysis further revealed six immune cell clusters, showing <i>Irf7</i> predominantly in microglia and <i>Tap1</i> in dendritic cells (DCs). And cell-cell communication analysis showed that microglia and DCs play central roles in coordinating immune activity. qRT-PCR validated the upregulation of these genes.</p><p><strong>Conclusion: </strong>In the acute phase of RIRI, <i>Irf7</i> and <i>Tap1</i> may be the potential therapeutic targets to reduce inflammation and promote neurological function recovery.</p>","PeriodicalId":14312,"journal":{"name":"International journal of ophthalmology","volume":"18 7","pages":"1237-1251"},"PeriodicalIF":1.8000,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12207303/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"International journal of ophthalmology","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.18240/ijo.2025.07.06","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"OPHTHALMOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Aim: To explore the immune cell infiltration and molecular mechanisms of retinal ischemia-reperfusion injury (RIRI) to identify potential therapeutic targets.
Methods: In the bulk RNA-seq analysis, This study performed differential gene expression analysis, weighted gene co-expression network analysis, and protein-protein interaction network analysis to identify hub genes. QuanTIseq was used to determine the composition of infiltrating immune cells. Following the identification of hub genes, single-cell RNA-seq analysis was employed to pinpoint the specific immune cell types expressing these hub genes. Cell-cell communication analysis to explore signaling pathways and interactions between immune cells was further performed. Finally, the expression of these key immune regulators in vivo using quantitative real-time polymerase chain reaction (qRT-PCR) was validated.
Results: Bulk RNA-seq analysis identified Stat2, Irf7, Irgm1, Igtp, Parp9, Irgm2, Nlrc5, and Tap1 as hub genes, with strong correlations to immune cell infiltration. Single-cell RNA-seq analysis further revealed six immune cell clusters, showing Irf7 predominantly in microglia and Tap1 in dendritic cells (DCs). And cell-cell communication analysis showed that microglia and DCs play central roles in coordinating immune activity. qRT-PCR validated the upregulation of these genes.
Conclusion: In the acute phase of RIRI, Irf7 and Tap1 may be the potential therapeutic targets to reduce inflammation and promote neurological function recovery.
期刊介绍：
· International Journal of Ophthalmology-IJO (English edition) is a global ophthalmological scientific publication
and a peer-reviewed open access periodical (ISSN 2222-3959 print, ISSN 2227-4898 online).
This journal is sponsored by Chinese Medical Association Xi’an Branch and obtains guidance and support from
WHO and ICO (International Council of Ophthalmology). It has been indexed in SCIE, PubMed,
PubMed-Central, Chemical Abstracts, Scopus, EMBASE , and DOAJ. IJO JCR IF in 2017 is 1.166.
IJO was established in 2008, with editorial office in Xi’an, China. It is a monthly publication. General Scientific
Advisors include Prof. Hugh Taylor (President of ICO); Prof.Bruce Spivey (Immediate Past President of ICO);
Prof.Mark Tso (Ex-Vice President of ICO) and Prof.Daiming Fan (Academician and Vice President,
Chinese Academy of Engineering.
International Scientific Advisors include Prof. Serge Resnikoff (WHO Senior Speciatist for Prevention of
blindness), Prof. Chi-Chao Chan (National Eye Institute, USA) and Prof. Richard L Abbott (Ex-President of
AAO/PAAO) et al.
Honorary Editors-in-Chief: Prof. Li-Xin Xie(Academician of Chinese Academy of
Engineering/Honorary President of Chinese Ophthalmological Society); Prof. Dennis Lam (President of APAO) and
Prof. Xiao-Xin Li (Ex-President of Chinese Ophthalmological Society).
Chief Editor: Prof. Xiu-Wen Hu (President of IJO Press).
Editors-in-Chief: Prof. Yan-Nian Hui (Ex-Director, Eye Institute of Chinese PLA) and
Prof. George Chiou (Founding chief editor of Journal of Ocular Pharmacology & Therapeutics).
Associate Editors-in-Chief include:
Prof. Ning-Li Wang (President Elect of APAO);
Prof. Ke Yao (President of Chinese Ophthalmological Society) ;
Prof.William Smiddy (Bascom Palmer Eye instituteUSA) ;
Prof.Joel Schuman (President of Association of University Professors of Ophthalmology,USA);
Prof.Yizhi Liu (Vice President of Chinese Ophtlalmology Society);
Prof.Yu-Sheng Wang (Director of Eye Institute of Chinese PLA);
Prof.Ling-Yun Cheng (Director of Ocular Pharmacology, Shiley Eye Center, USA).
IJO accepts contributions in English from all over the world. It includes mainly original articles and review articles,
both basic and clinical papers.
Instruction is Welcome Contribution is Welcome Citation is Welcome
Cooperation organization
International Council of Ophthalmology(ICO), PubMed, PMC, American Academy of Ophthalmology, Asia-Pacific, Thomson Reuters, The Charlesworth Group, Crossref,Scopus,Publons, DOAJ etc.
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