巨噬细胞极化相关差异基因的筛选及其在脓毒症中的潜在治疗价值
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摘要
目的运用生物信息学方法寻找巨噬细胞极化成M1、M2型的差异基因,为临床筛选脓毒症的免疫调节治疗靶点提供理论依据。方法从综合性基因表达(GEO)数据库下载2套基因芯片数据,以在γ-干扰素(IFN-γ)及脂多糖(LPS)作用下极化为M1型巨噬细胞,白细胞介素-4(IL-4)作用下极化为M2型巨噬细胞为条件筛选样本,并提交至GEO2R平台进行在线分析,将筛选出的差异基因取交集作为最终的差异基因。利用DAVID软件对差异基因进行GO富集分析及KEGG信号通路分析,同时在STRING数据库行蛋白质交互作用分析。结果共筛选出1 241个差异基因,其中在M1型巨噬细胞中表达上调而在M2型巨噬细胞中表达下调的基因有591个,在M1型巨噬细胞中表达下调而在M2型巨噬细胞中表达上调的基因有650个。功能富集分析结果显示,在M1型巨噬细胞中表达上调而在M2型巨噬细胞中表达下调的基因主要涉及炎症反应、细胞凋亡等功能,在M1型巨噬细胞中表达下调而在M2型巨噬细胞中表达上调的基因主要涉及能量代谢、氧化磷酸化等生物途径。STRING数据库分析结果显示,NDUFS3、ATP5D、ATP5I、NDUFB10等基因为相对核心的基因。结论本研究通过生物信息学筛选出的巨噬细胞极化核心差异基因,为脓毒症的免疫学治疗提供新的方向。
Objective To find the differentially expressed genes between M1 and M2 subtypes of macrophage by bioinformatics methods and to provide a theoretical basis for screening the target of immunomodulatory therapy for sepsis.Methods Two microarray data were downloaded from gene expression omnibus( GEO) database. The samples were screened under the conditions of the macrophages polarized to M1 type under the action of interferon-gamma( IFN-γ) and lipopolysaccharide( LPS),and the macrophages polarized to M2 type under the action of interleukin-4( IL-4). The samples were submitted to the GEO2 R platform for online analysis. The results of two gene expression profiles were cross-set to obtain the final differential expressed genes. The GO enrichment analysis and KEGG signaling pathway analysis of differentially expressed genes were performed by DAVID software and the protein-protein interaction was analysed by STRING database.Results A total of 1 241 differentially expressed genes were obtained. Among them,591 genes were up regulated in M1 macrophage while down regulated in M2 macrophage; and 650 were down regulated in M1 macrophage while up regulated in M2 macrophage. The function enrichment analysis suggested that the genes up regulated in M1 macrophage and down regulated in M2 macrophage were primarily involved in the inflammatory reaction and apoptosis,while the genes down regulated in M1 macrophage and up regulated in M2 macrophage were mainly involved in such biological processes as energy metabolism and oxidative phosphorylation. The STRING database analysis results showed that NDUFS3,CHCHD10,ATP5 D,ATP5 I,NDUFB10 and UQCR1 were relatively core genes. Conclusion The core differentially expressed genes of macrophage polarization which screened out by bioinformatics provide a new direction for the immunotherapy of sepsis.
Objective To find the differentially expressed genes between M1 and M2 subtypes of macrophage by bioinformatics methods and to provide a theoretical basis for screening the target of immunomodulatory therapy for sepsis.Methods Two microarray data were downloaded from gene expression omnibus( GEO) database. The samples were screened under the conditions of the macrophages polarized to M1 type under the action of interferon-gamma( IFN-γ) and lipopolysaccharide( LPS),and the macrophages polarized to M2 type under the action of interleukin-4( IL-4). The samples were submitted to the GEO2 R platform for online analysis. The results of two gene expression profiles were cross-set to obtain the final differential expressed genes. The GO enrichment analysis and KEGG signaling pathway analysis of differentially expressed genes were performed by DAVID software and the protein-protein interaction was analysed by STRING database.Results A total of 1 241 differentially expressed genes were obtained. Among them,591 genes were up regulated in M1 macrophage while down regulated in M2 macrophage; and 650 were down regulated in M1 macrophage while up regulated in M2 macrophage. The function enrichment analysis suggested that the genes up regulated in M1 macrophage and down regulated in M2 macrophage were primarily involved in the inflammatory reaction and apoptosis,while the genes down regulated in M1 macrophage and up regulated in M2 macrophage were mainly involved in such biological processes as energy metabolism and oxidative phosphorylation. The STRING database analysis results showed that NDUFS3,CHCHD10,ATP5 D,ATP5 I,NDUFB10 and UQCR1 were relatively core genes. Conclusion The core differentially expressed genes of macrophage polarization which screened out by bioinformatics provide a new direction for the immunotherapy of sepsis.
引文
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[2]罗淞元,李小霞,王喜梅.脉搏指示连续心排出量监测在脓毒症急性肾损伤治疗中的应用价值[J].新乡医学院学报,2018,35(3):231-234.
[3]孙杭,张宪伟,潘伟,等.补体消耗与脓毒症患儿病情严重程度的相关性[J].中华实用儿科临床杂志,2017,32(6):425-429.
[4] GOTTS J E,MATTHAY M A. Sepsis:pathophysiology and clinical management[J]. BMJ,2016,353:i1585.
[5]王昌理,薄禄龙,邓小明.单核/巨噬细胞代谢在脓毒症中的研究进展[J].中华危重病急救医学,2017,29(4):381-384.
[6]吴秀华,郑文洁.巨噬细胞极化[J].中华临床免疫和变态反应杂志,2017,11(2):161-165.
[7] GAIESKI D F,EDWARDS J M,KALLAN M J,et al. Benchmarking the incidence and mortality of severe sepsis in the United States[J]. Critical Care Medicine,2013,41(5):1167-1174.
[8] HALL M W,KNATZ N L,VETTERLY C,et al. Immunoparalysis and nosocomial infection in children with multiple organ dysfunction syndrome[J]. Intens Care Med,2011,37(3):525-532.
[9] WEBER G F,CHOUSTERMAN B G,HE S,et al. Interleukin-3amplifies acute inflammation and is a potential therapeutic target in sepsis[J]. Science,2015,347(6227):1260-1265.
[10] WYNN T A,CHAWLA A,POLLARD J W. Macrophage biology in development,homeostasis and disease[J]. Nature,2013,496(7446):445-455.
[11]许倩,李顺,陈善泽.巨噬细胞极化与炎症性疾病[J].国外医药(抗生素分册),2018,39(1):80-85.
[12] QIN S,WANG H,YUAN R,et al. Role of HMGB1 in apoptosismediated sepsis lethality[J]. Shock,2006,25(7):1637-1642.
[13] SRISKANDAN S,ALTMANN D M. The immunology of sepsis[J].J Pathol,2010,214(2):211-223.
[14]刘安雷,朱华栋,于学忠,等.脂多糖诱导脓毒症小鼠心功能障碍机制研究[J].中华急诊医学杂志,2015,24(8):825-829.
[15]王晶晶,杨敬平,齐明禄. TLR4介导的信号通路与脓毒症相关性研究[J].临床肺科杂志,2015,20(4):725-727.
[16] VAN ZOELEN M A D,ACHOUITI A,VAN D P T. The role of receptor for advanced glycation endproducts(RAGE)in infection[J]. Critical Care,2011,15(2):208.
[17] KAWAI T,AKIRA S. Toll-like receptor and RIG-I-like receptor signaling[J]. Ann N Y Acad Sci,2010,1143(1):1-20.
[18] OPITZ B,EITEL J,MEIXENBERGER K,et al. Role of Toll-like receptors,NOD-like receptors and RIG-I-like receptors in endothelial cells and systemic infections[J]. Thromb Haemost,2009,102(6):1103-1109.
[19] MARTINVALET D,DYKXHOORN D M,FERRINI R,et al.Granzyme A cleaves a mitochondrial complex I protein to initiate caspase-independent cell death[J]. Cell,2008,133(4):681-692.
[20] ELLIOTT T S,SWARTZ D A,PAISLEY E A,et al. F1Fo-ATPase subunit e gene isolated in a screen for diet regulated genes[J].Biochem Biophys Res Commun,1993,190(1):167-174.
[21] JORDAN E M,BREEN G A. Molecular cloning of an import precursor of the delta-subunit of the human mitochondrial ATP synthase complex[J]. Biochim Biophys Acta,1992,1130(1):123-126.
[22] TRIEPELS R,SMEITINK J,LOEFFEN J,et al. Characterization of the human complex I NDUFB7 and 17. 2-kDa c DNAs and mutational analysis of 19 genes of the HP fraction in complex Ideficient-patients[J]. Hum Genet,2000,106(4):385-391.