BCG感染牛肺泡巨噬细胞的转录组测序和分析
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摘要
目的:通过卡介苗(BCG)感染牛肺泡巨噬细胞(BAM)的转录组测序及生物信息学分析,揭示差异表达的基因和长链非编码RNA (lncRNA),为巨噬细胞抗结核分枝杆菌感染的免疫调控机制研究提供理论依据。方法:采用肺脏灌洗离心法收集并培养BAM,分为感染组和未感染组,感染组经BCG感染后12h,利用转录组测序技术(RNA-Seq)检测感染组和未感染组BAM mRNA表达谱及lncRNA表达谱,并进行生物信息学相关分析。结果:与未感染组比较,感染组BAM差异表达的lncRNAs共有119个(P<0.05),差异表达的mRNA共有1 111个(P<0.05)。在差异表达基因的功能富集分析中,最显著富集项与免疫功能相关(GO:0006955,P<0.05),共有125个基因,其中有63个基因表达上调,62个基因表达下调,且白细胞介素6(IL-6)、白细胞介素17 (IL-17)和白细胞介素23A (IL-23A)等促炎因子表达上调。lncRNA靶基因预测,差异表达的lncRNA参与转化生长因子β(TGF-β)信号通路及ABC转运体信号通路的调控(P<0.05)。结论:BCG感染BAM后,激发宿主细胞产生强烈的免疫反应,引起lncRNA和mRNA表达谱的改变。
Objective:To reveal the differentially expressed genes and long non-coding RNAs(lncRNAs)by sequencing the transcriptome of bovine alveolar macrophages(BAM)infected with Bacillus Calmette-Guérin(BCG)and analyzing their bioinformations,and to provide theoretical foundation for the research on immune regulation mechanism of anti-infection of Mycobacteriumtuberculosisof macrophages.Methods:The BAM were collected by pulmonary lavage and centrifugation and cultured and divided into infected group and uninfected group.After infection for 12 hin infected group,the expression profiles of mRNA and lncRNA in infected group and uninfected group were detected by RNA-Seq,and bioinformatics analysis was carried out.Results:compared with uninfected group,there were 119 differentially expressed lncRNAs and 1111 differentially expressed mRNA in infected group(P<0.05).Gene Ontology functional enrichment analysis showed that the most significant enrichment was immune response(GO:0006955,P<0.05),including 125 genes,in which 63 were up-regulated and 62 were downregulated,and the expressions of proinflammatory factors interleukin-1(IL-6),interleukin-7(IL-7),and interleukin-23 A(IL-23 A)were up-regulated.Cis target gene prediction and KEGG pathway analysis showed that the differentially expressed lncRNAs were involved in the regulation of transforming growth factor-β(TGF-β)signaling pathway and ATP-binding cassette transporter(ABC transporter)signaling pathway(P <0.05).Conclusion:The host cells are stimulated to produce a strong immune response after the BAM are infected by BCG and results in the changes of lncRNA and mRNA expression profiles.
Objective:To reveal the differentially expressed genes and long non-coding RNAs(lncRNAs)by sequencing the transcriptome of bovine alveolar macrophages(BAM)infected with Bacillus Calmette-Guérin(BCG)and analyzing their bioinformations,and to provide theoretical foundation for the research on immune regulation mechanism of anti-infection of Mycobacteriumtuberculosisof macrophages.Methods:The BAM were collected by pulmonary lavage and centrifugation and cultured and divided into infected group and uninfected group.After infection for 12 hin infected group,the expression profiles of mRNA and lncRNA in infected group and uninfected group were detected by RNA-Seq,and bioinformatics analysis was carried out.Results:compared with uninfected group,there were 119 differentially expressed lncRNAs and 1111 differentially expressed mRNA in infected group(P<0.05).Gene Ontology functional enrichment analysis showed that the most significant enrichment was immune response(GO:0006955,P<0.05),including 125 genes,in which 63 were up-regulated and 62 were downregulated,and the expressions of proinflammatory factors interleukin-1(IL-6),interleukin-7(IL-7),and interleukin-23 A(IL-23 A)were up-regulated.Cis target gene prediction and KEGG pathway analysis showed that the differentially expressed lncRNAs were involved in the regulation of transforming growth factor-β(TGF-β)signaling pathway and ATP-binding cassette transporter(ABC transporter)signaling pathway(P <0.05).Conclusion:The host cells are stimulated to produce a strong immune response after the BAM are infected by BCG and results in the changes of lncRNA and mRNA expression profiles.
引文
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[20] WARSINSKE H C,PIENAAR E,LINDERMAN J J,et al.Deletion of TGF-beta1 increases bacterial clearance by cytotoxic T cells in a tuberculosis granuloma model[J].Front Immunol,2017,8:1843.
[2] WATERS W R,PALMER M V. Mycobacterium bovis infection of cattle and white-tailed deer:Translational research of relevance to human tuberculosis[J].Ilar J,2015,56(1):26-43.
[3] OUYANG J,HU J,CHEN J L.lncRNAs regulate the innate immune response to viral infection[J]. Wiley Interdiscip Rev RNA,2016,7(1):129-143.
[4] FU Y,XU X,XUE J,et al.Deregulated lncRNAs in B cells from patients with active tuberculosis[J].PLoS ONE,2017,12(1):1-14.
[5] YI Z,LI J,GAO K,et al.Identifcation of differentially expressed long non-coding RNAs in CD4+T cells response to latent tuberculosis infection[J].J Infect,2014,69(6):558-568.
[6] YANG X,YANG J,WANG J,et al.Microarray analysis of long noncoding RNA and mRNA expression profiles in human macrophages infected with ycobacterium tuberculosis[J].Sci Rep,2016,14(6):38963.
[7] MASTERS S L, MIELKE L A,CORNISH A L,et al.Regulation of interleukin-1beta by interferon-gamma is species specific,limited by suppressor of cytokine signalling 1and influences interleukin-17production[J].EMBO Rep,2010,11(8):640-646.
[8] MAGEE D A,CONLON K M,NALPAS N C,et al.Innate cytokine profiling of bovine alveolar macrophages reveals commonalitiesanddivergenceintheresponseto MycobacteriumbovisandMycobacteriumtuberculosis infection[J].Tuberculosis,2014,94(4):441-450.
[9] HMAMA Z, PENA-DIZAS, JOSEPHS, etal.Immunoevasion and immunosuppression of the macrophage by Mycobacterium tuberculosis[J].Immunol Rev, 2015,264(1):220-232.
[10] MORACO A H,KORNFELD H.Cell death and autophagy in tuberculosis[J].Semin Immunol,2014,26(6):497-511.
[11]VAN DER WEL N, DAVA D, HOUBEN D, et al.M.tuberculosis andM. leprae translocate fromthe phagolysosome to the cytosol in myeloid cells[J].Cell,2007,129(7):1287-1298.
[12]BACH H,PAPAVINASASUNDARAM K G, WONG D,et al.Mycobacterium tuberculosis virulence is mediated by PtpA dephosphorylation of human vacuolar protein sorting33B[J].Cell Host Microbe,2008,3(5):316-322.
[13] PAWAR K,HANISCH C,PALMA VERA S E,et al.Down regulated lncRNA MEG3 eliminates mycobacteria in macrophages via autophagy[J].Sci Rep,2016,14(6):19416.
[14]VAN DER DEEN M,DE VRIES E G,TIMENS W,et al.ATP-binding cassette(ABC)transporters in normal and pathological lung[J].Respir Res,2005.DOI:10.1186/1465-9921-6-59.
[15]YIN K,LIAO D F,TANG C K..ATP-binding membrane cassette transporter A1(ABCA1):A possible link between inflammation and reverse cholesterol transport[J].Mol Med,2010,16(9/10):438-449.
[16]CASTRILLO A,JOSEPH S B, VAIDYA S A,et al.Crosstalk between LXR and Toll-like receptor signaling mediates bacterial and viral antagonism of cholesterol metabolism[J].Mol Cell,2003,12(4):805-816.
[17] KHOVIDHUNKIT W,KIM M S,MEMON R A,et al.Effects of infection and inflammation on lipid and lipoprotein metabolism:mechanisms and consequences to the host[J].Lipid Res,2004,45(7):1169-1196.
[18]AZZAM K M,FESSLER M B.Crosstalk between reverse cholesterol transport and innate immunity[J]. Trends Endocrin Met,2012,23(4):169-178.
[19]刘萍,张丽,庞楠楠,等.血清IFN-γ、TGF-β1、IL-10检测对儿童潜伏性结核感染的诊断价值[J].中国病原生物学杂志,2011,6(9):650-652.
[20] WARSINSKE H C,PIENAAR E,LINDERMAN J J,et al.Deletion of TGF-beta1 increases bacterial clearance by cytotoxic T cells in a tuberculosis granuloma model[J].Front Immunol,2017,8:1843.
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