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. 2018 Mar 15;38(1):70–77. doi: 10.1007/s11596-018-1848-7

Bioinformatics Analysis of Genes and Pathways of CD11b+/Ly6Cintermediate Macrophages after Renal Ischemia-Reperfusion Injury

Dong Sun 1,#, Xin Wan 1,#, Bin-bin Pan 1, Qing Sun 2, Xiao-bing Ji 1, Feng Zhang 1, Hao Zhang 1, Chang-chun Cao 1,2,✉
PMCID: PMC7089064  PMID: 30074154

Abstract

Renal ischemia-reperfusion injury (IRI) is a major cause of acute kidney injury (AKI), which could induce the poor prognosis. The purpose of this study was to characterize the molecular mechanism of the functional changes of CDllb+/Ly6Cintermediate macrophages after renal IRI. The gene expression profiles of CDllb+/Ly6Cintermcdiate macrophages of the sham surgery mice, and the mice 4 h, 24 h and 9 days after renal IRI were downloaded from the Gene Expression Omnibus database. Analysis of mRNA expression profiles was conducted to identify differentially expressed genes (DEGs), biological processes and pathways by the series test of cluster. Protein-protein interaction network was constructed and analysed to discover the key genes. A total of 6738 DEGs were identified and assigned to 20 model profiles. DEGs in profile 13 were one of the predominant expression profiles, which are involved in immune cell chemotaxis and proliferation. Signet analysis showed that Atp5al, Atp5o, Cox4i, Cdc42, Rac2 and Nhp2 were the key genes involved in oxidation-reduction, apoptosis, migration, M1-M2 differentiation, and proliferation of macrophages. RPS18 may be an appreciate reference gene as it was stable in macrophages. The identified DEGs and their enriched pathways investigate factors that may participate in the functional changes of CD 1lb+Ly6Cintermediate macrophages after renal IRI. Moreover, the vital gene Nhp2 may involve the polarization of macrophages, which may be a new target to affect the process of AKI

Key words: renal ischemia-reperfiision injury, macrophage, differentially expressed genes, series test of cluster, functional enrichment analysis, protein-protein interaction

Footnotes

This work was supported by grants from the National Natural Science Foundation of China (No. 81670634), Graduate student scientific research innovation projects in Jiangsu province (No. KYLX15 0981), and Nanjing Medical University Science and Technology Development Fund (No. 2016NJMU065).

The authors contributed equally to this work.

Contributor Information

Dong Sun, Email: sundong@njmu.edu.cn.

Xin Wan, Email: wanxin@njmu.edu.cn.

Chang-chun Cao, Email: caochangchun@njmu.edu.cn.

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