Bioinformatics Analysis of Genes and Pathways of CD11b⁺/Ly6C^intermediate Macrophages after Renal Ischemia-Reperfusion Injury

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+/Ly6C^intermediate 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⁺Ly6C^intermediate 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

References

[1] Medicine (Baltimore), 2016, 95(19):

[2] XuG, PlayerP, ShepherdD, et al.. Identifying acute kidney injury in the community—a novel informatics approach. J Nephrol, 2016, 29(1): 93-98

[3] RanganathanPV, JayakumarC, MohamedR, et al.. Netrin-1 regulates the inflammatory response of neutrophils and macrophages, and suppresses ischemic acute kidney injury by inhibiting COX-2-mediated PGE2 production. Kidney Int, 2013, 83(6): 1087-1098

[4] PonceD, DiasDB, NascimentoGR, et al.. Long-term outcome of severe acute kidney injury survivors followed by nephrologists in a developing country. Nephrology (Carlton), 2016, 21(4): 327-334

[5] MehtaRL, BurdmannEA, CerdaJ, et al.. Recognition and management of acute kidney injury in the International Society of Nephrology 0by25 Global Snapshot: a multinational cross-sectional study. Lancet, 2016, 387(10032): 2017-2025

[6] HouL, ChenG, FengB, et al.. Small interfering RNA targeting TNF-alpha gene significantly attenuates renal ischemia-reperfusion injury in mice. J Huazhong Univ Sci Technolog Med Sci, 2016, 36(5): 634-638

[7] MartinaMN, NoelS, SaxenaA, et al.. Double-negative alphabeta T cells are early responders to AKI and are found in human kidney. J Am Soc Nephrol, 2016, 27(4): 1113-1123

[8] KarasawaK, AsanoK, MoriyamaS, et al.. Vascular-resident CD169-positive monocytes and macrophages control neutrophil accumulation in the kidney with ischemia-reperfusion injury. J Am Soc Nephrol, 2015, 26(4): 896-906

[9] LiangS, WangW, GouX. MicroRNA 26a modulates regulatory T cells expansion and attenuates renal ischemia-reperfusion injury. Mol Immunol, 2015, 65(2): 321-327

[10] HuenSC, HuynhL, MarlierA, et al.. GM-CSF promotes macrophage alternative activation after renal ischemia/reperfusion injury. J Am Soc Nephrol, 2015, 26(6): 1334-1345

[11] LeeS, HuenS, NishioH, et al.. Distinct macrophage phenotypes contribute to kidney injury and repair. J Am Soc Nephrol, 2011, 22(2): 317-326

[12] HuenSC, CantleyLG. Macrophage-mediated injury and repair after ischemic kidney injury. Pediatr Nephrol, 2015, 30(2): 199-209

[13] CaoQ, WangY, WangXM, et al.. Renal F4/80+ CDllc+ mononuclear phagocytes display phenotypic and functional characteristics of macrophages in health and in adriamycin nephropathy. J Am Soc Nephrol, 2015, 26(2): 349-363

[14] ClementsM, GershenovichM, ChaberC, et al.. Differential Ly6C expression after renal ischemia-reperfusion identifies unique macrophage populations. J Am Soc Nephrol, 2016, 27(1): 159-170

[15] DragomirAC, SunR, ChoiH, et al.. Role of galectin-3 in classical and alternative macrophage activation in the liver following acetaminophen intoxication. J Immunol, 2012, 189(12): 5934-5941

[16] RudnickPA, WangX, YanX, et al.. Improved normalization of systematic biases affecting ion current measurements in label-free proteomics data. Mol Cell Proteomics, 2014, 13(5): 1341-1351

[17] ZhaoYH, ZhangXF, ZhaoYQ, et al.. Time-series analysis in imatinib-resistant chronic myeloid leukemia K562-cells under different drug treatments. J Huazhong Univ Sci Technolog Med Sci, 2017, 37(4): 621-627

[18] Sci Total Environ, 2014, 472(872-879):

[19] PathanM, KeerthikumarS, AngCS, et al.. FunRich: An open access standalone functional enrichment and interaction network analysis tool. Proteomics, 2015, 15(15): 2597-2601

[20] WangZX, ZhouCX, ElsheikhaHM, et al.. Proteomic Differences between Developmental Stages of Toxoplasma gondii Revealed by iTRAQ-Based Quantitative Proteomics. Front Microbiol, 2017, 8(985): 1-15

[21] CongF, LiuX, HanZ, et al.. Transcriptome analysis of chicken kidney tissues following Coronavirus avian infectious bronchitis virus infection. BMC genomics, 2013, 14(743): 1-13

[22] ChinCH, ChenSH, WuHH, et al.. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol, 2014, 8: l-7

[23] ChenH, ChaiW, LiB, et al.. Effects of beta-catenin on differentially expressed genes in multiple myeloma. J Huazhong Univ Sei Technolog Med Sei, 2015, 35(4): 546-552

[24] DiCosmo-PonticelloCJ, HooverD, CoffinanFD, et al.. MIF inhibits monocytic movement through a non-canonical receptor and disruption of temporal Rho GTPase activities in U-937 cells. Cytokine, 2014, 69(1): 47-55

[25] PLoS One, 2014, 9(4):

[26] SablinaAA, HahnWC. SV40 small T antigen and PP2A phosphatase in cell transformation. Cancer Metastasis Rev, 2008, 27(2): 137-146

[27] PanX, ChenX, TongX, et al.. Ppp2ca knockout in mice spermatogenesis. Reproduction, 2015, 149(4): 385-391

[28] KatsiariCG, KyttarisVC, JuangYT, et al.. Protein phosphatase 2A is a negative regulator of IL-2 production in patients with systemic lupus erythematosus. J Clin Invest, 2005, 115(ll): 3193-3204

[29] BarronL, DoomsH, HoyerKK, et al.. Cutting edge: mechanisms of IL-2-dependent maintenance of functional regulatory T cells. J Immunol, 2010, 185(ll): 6426-6430

[30] OkamuraH, YangD, YoshidaK, et al.. Protein phosphatase 2A Calpha is involved in osteoclastogenesis by regulating RANKL and OPG expression in osteoblasts. FEBS Lett, 2013, 587(1): 48-53

[31] BhardwajA, SinghS, SrivastavaSK, et al.. Restoration of PPP2CA expression reverses epithelial-to-mesenchymal transition and suppresses prostate tumour growth and metastasis in an orthotopic mouse model. Br J Cancer, 2014, 110(8): 2000-2010

[32] TengT, MercerCA, HexleyP, et al.. Loss of tumor suppressor RPL5/RPL11 does not induce cell cycle arrest but impedes proliferation due to reduced ribosome content and translation capacity. Mol Cell Biol, 2013, 33(23): 4660-4671

[33] ZhouX, HaoQ, ZhangQ, et al.. Ribosomal proteins Lll and L5 activate TAp73 by overcoming MDM2 inhibition. Cell Death Differ, 2015, 22(5): 755-766

[34] FancelloL, KampenKR, HofmanIJ, et al.. The ribosomal protein gene RPL5 is a haploinsufficient tumor suppressor in multiple cancer types. Oncotarget, 2017, 8(9): 14462-14478

[35] WuH, FeigonJ. H7ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification. Proc Natl Acad Sci USA, 2007, 104(16): 6655-6660

[36] WatkinsNJ, GottschalkA, NeubauerG, et al.. Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Garlp in all H BOX/ACA-motif snoRNPs and constitute a common bipartite structure. RNA, 1998, 4(12): 1549-1568

[37] HenrasA, HenryY, Bousquet-AntonelliC, et al.. Nhp2p and Nop1 Op are essential for the function of H/ACA snoRNPs. EMBO J, 1998, 17(23): 7078-7090

[38] KangHS, JungHM, JunDY, et al.. Expression of the human homologue of the small nucleolar RNA-binding protein NHP2 gene during monocytic differentiation of U937 cells. Biochim Biophys Acta, 2002, 1575(1-3): 31-39

[39] LiS, DuanJ, LiD, et al.. Structure of the Shql-Cbf5-NoplO-Garl complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita. EMBO J, 2011, 30(24): 5010-5020

[40] ColginLM, ReddelRR. Telomere maintenance mechanisms and cellular immortalization. Curr Opin Genet Dev, 1999, 9(1): 97-103

[41] LiB, MatterEK, HoppertHT, et al.. Identification of optimal reference genes for RT-qPCR in the rat hypothalamus and intestine for the study of obesity. Int J Obes (Lond), 2014, 38(2): 192-197

[42] EissaN, KermarrecL, HusseinH, et al.. Appropriateness of reference genes for normalizing messenger RNA in mouse 2,4-dinitrobenzene sulfonic acid (DNBS)-induced colitis using quantitative real time PCR. Sci Rep, 2017, 7(42427): 1-13

[43] TanSC, IsmailMP, DuskiDR, et al.. Identification of optimal reference genes for normalization of RT-qPCR data in cancerous and non-cancerous tissues of human uterine cervix. Cancer Invest, 2017, 35(3): 163-173

RIGHTS & PERMISSIONS

Huazhong University of Science and Technology