Construction of competitive endogenous RNA network mediated by lung ischemia-reperfusion core genes
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摘要:
目的 分析肺缺血-再灌注损伤发生的核心基因并构建竞争性内源性RNA（ceRNA）网络。 方法 从基因表达综合（GEO）数据库下载GSE145989的原始数据当作训练集，GSE172222和GSE9634数据集作为验证集，并鉴定差异表达基因（DEG）。进行基因本体（GO）、京都基因与基因组百科全书（KEGG）富集分析。构建蛋白质-蛋白质相互作用（PPI）网络，筛选核心基因并分析核心基因的诊断价值、免疫细胞的免疫浸润水平。构建并验证ceRNA网络。分析基于ceRNA网络的靶向药物。 结果 共检测到179个DEG，其中61个下调基因，118个上调基因。GO分析结果显示，DEG与细胞迁移、分化和调节等生物学过程有关；与内吞囊泡膜、浆膜和膜筏等细胞成分有关；与趋化因子受体、G蛋白偶联受体、免疫受体活性和抗原结合等分子功能有关。KEGG分析显示DEG参与肿瘤坏死因子（TNF）、Wnt、白细胞介素（IL）-17和核因子（NF）-κB等信号通路。PPI网络提示CD8A、IL2RG、STAT1、CD3G和SYK是肺缺血-再灌注损伤的核心基因。ceRNA网络提示miR-146a-3p、miR-28-5p和miR-593-3p与CD3G的表达相关；miR-149-3p、miR-342-5p、miR-873-5p和miR-491-5p与IL2RG表达相关；miR-194-3p、miR-512-3p、miR-377-3p和miR-590-3p与SYK表达相关；miR-590-3p和miR-875-3p与CD8A表达相关；miR-143-5p、miR-1231、miR-590-3p、miR-875-3p与STAT1表达相关。CD3G有13种靶向药物，IL2RG有4种靶向药物，SYK有28种靶向药物，lncRNA MUC2有3种靶向药物，未发现CD8A、STAT1和其他ceRNA网络基因的靶向药物。 结论 CD8A、IL2RG、STAT1、CD3G和SYK是肺缺血-再灌注损伤的核心基因，对核心基因进行研究分析可能有助于肺缺血-再灌注损伤的诊断，并提供新的研究思路和治疗靶点。 Abstract:Objective To analyze the core genes of lung ischemia-reperfusion injury and construct a competitive endogenous RNA (ceRNA) network. Methods Original data of GSE145989 were downloaded from the Gene Expression Omnibus (GEO) database as the training set, and the GSE172222 and GSE9634 datasets were used as the validation sets, and the differentially-expressed genes (DEG) were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. Protein-protein interaction (PPI) network was constructed, and the core genes were screened, and the diagnostic values of these core genes and the immune infiltration levels of immune cells were evaluated. The ceRNA network was constructed and validated. The targeted drugs based on ceRNA network were assessed. Results A total of 179 DEG were identified, including 61 down-regulated and 118 up-regulated genes. GO analysis showed that DEGs were associated with multiple biological processes, such as cell migration, differentiation and regulation, etc. They were correlated with cell components, such as vesicle membrane, serosa and membrane raft, etc. They were also associated with multiple molecular functions, such as chemokine receptor, G protein-coupled receptor, immune receptor activity and antigen binding, etc. KEGG pathway enrichment analysis revealed that DEG were involved in tumor necrosis factor (TNF), Wnt, interleukin (IL)-17 and nuclear factor (NF)-κB signaling pathways, etc. PPI network suggested that CD8A, IL2RG, STAT1, CD3G and SYK were the core genes of lung ischemia-reperfusion injury. The ceRNA network prompted that miR-146a-3p, miR-28-5p and miR-593-3p were related to the expression level of CD3G. The miR-149-3p, miR-342-5p, miR-873-5p and miR-491-5p were correlated with the expression level of IL-2RG. The miR-194-3p, miR-512-3p, miR-377-3p and miR-590-3p were associated with the expression level of SYK. The miR-590-3p and miR-875-3p were related to the expression level of CD8A. The miR-143-5p, miR-1231, miR-590-3p and miR-875-3p were associated with the expression level of STAT1. There were 13 targeted drugs for CD3G, 4 targeted drugs for IL-2RG, 28 targeted drugs for SYK and 3 targeted drugs for lncRNA MUC2. No targeted drugs were identified for CD8A, STAT1 and other ceRNA network genes. Conclusions CD8A, IL2RG, STAT1, CD3G and SYK are the core genes of lung ischemia-reperfusion injury. The research and analysis of these core genes probably contribute to the diagnosis of lung ischemia-reperfusion injury and providing novel research ideas and therapeutic targets. -
图 1 DEG的GO、KEGG和免疫细胞浸润分析
注：A图为前100个DEG；B图和C图为GO分析；D图为KEGG分析；E图为免疫细胞浸润分析。
Figure 1. GO, KEGG and immune cell infiltration analysis of DEG
图 2 核心基因的筛选
注：A图为DEG的PPI网络，绿色为下调基因，红色为上调基因；B图为基因打分，红色为得分；C图为核心基因；D图为核心基因的相关性分析。
Figure 2. Screening of the core genes
图 3 核心基因的验证
注：A图为GSE145989数据集核心基因的表达；B图为GSE172222数据集核心基因的表达；C图为GSE9634数据集核心基因的表达；D图为核心基因在GSE172222数据集中的诊断效力；E图为核心基因在GSE9634数据集中的诊断效力。
Figure 3. Validation of core genes
图 5 ceRNA网络构建与表达验证
注：A图为基于核心基因mRNA-miRNA-lncRNA的ceRNA网络；B图为ceRNA网络成员表达情况。
Figure 5. ceRNA network construction and expression validation
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[1] AFONSO JÚNIOR JE, WEREBE EDE C, CARRARO RM, et al. Lung transplantation[J]. Einstein (Sao Paulo), 2015, 13(2): 297-304. DOI: 10.1590/S1679-45082015RW3156. [2] GLORION M, POLARD V, FAVEREAU F, et al. Prevention of ischemia-reperfusion lung injury during static cold preservation by supplementation of standard preservation solution with HEMO2life® in pig lung transplantation model[J]. Artif Cells Nanomed Biotechnol, 2018, 46(8): 1773-1780. DOI: 10.1080/21691401.2017.1392315. [3] CHAN JCY, CHABAN R, CHANG SH, et al. Future of lung transplantation: xenotransplantation and bioengineering lungs[J]. Clin Chest Med, 2023, 44(1): 201-214. DOI: 10.1016/j.ccm.2022.11.003. [4] JIANG T, YANG W, ZHANG H, et al. Hydrogen sulfide ameliorates lung ischemia-reperfusion injury through SIRT1 signaling pathway in type 2 diabetic rats[J]. Front Physiol, 2020, 11: 596. DOI: 10.3389/fphys.2020.00596. [5] CAPUZZIMATI M, HOUGH O, LIU M. Cell death and ischemia-reperfusion injury in lung transplantation[J]. J Heart Lung Transplant, 2022, 41(8): 1003-1013. DOI: 10.1016/j.healun.2022.05.013. [6] ALMEIDA FM, BATTOCHIO AS, NAPOLI JP, et al. Creatine supply attenuates ischemia-reperfusion injury in lung transplantation in rats[J]. Nutrients, 2020, 12(9): 2765. DOI: 10.3390/nu12092765. [7] TEIJEIRO-PARADIS R, CYPEL M, DEL SORBO L. Protective mechanical ventilation in organ donors: a lifesaving maneuver[J]. Am J Respir Crit Care Med, 2020, 202(2): 167-169. DOI: 10.1164/rccm.202005-1559ED. [8] STARKE H, VON DOSSOW V, KARSTEN J. Intraoperative circulatory support in lung transplantation: current trend and its evidence[J]. Life (Basel), 2022, 12(7): 1005. DOI: 10.3390/life12071005. [9] VLASTOS D, ZEINAH M, NINKOVIC-HALL G, et al. The effects of ischaemic conditioning on lung ischaemia-reperfusion injury[J]. Respir Res, 2022, 23(1): 351. DOI: 10.1186/s12931-022-02288-z. [10] AVTAAR SINGH SS, DAS DE S, AL-ADHAMI A, et al. Primary graft dysfunction following lung transplantation: from pathogenesis to future frontiers[J]. World J Transplant, 2023, 13(3): 58-85. DOI: 10.5500/wjt.v13.i3.58. [11] ZOGG H, SINGH R, RO S. Current advances in RNA therapeutics for human diseases[J]. Int J Mol Sci, 2022, 23(5): 2736. DOI: 10.3390/ijms23052736. [12] ALA U. Competing endogenous RNAs, non-coding RNAs and diseases: an intertwined story[J]. Cells, 2020, 9(7): 1574. DOI: 10.3390/cells9071574. [13] LIU X, ZHANG Y, ZHOU S, et al. Circular RNA: an emerging frontier in RNA therapeutic targets, RNA therapeutics, and mRNA vaccines[J]. J Control Release, 2022, 348: 84-94. DOI: 10.1016/j.jconrel.2022.05.043. [14] CHEN L, WANG C, SUN H, et al. The bioinformatics toolbox for circRNA discovery and analysis[J]. Brief Bioinform, 2021, 22(2): 1706-1728. DOI: 10.1093/bib/bbaa001. [15] ZHAO M, FENG J, TANG L. Competing endogenous RNAs in lung cancer[J]. Cancer Biol Med, 2021, 18(1): 1-20. DOI: 10.20892/j.issn.2095-3941.2020.0203. [16] JANG J, HWANG I, JUNG I. TimesVector-Web: a web service for analysing time course transcriptome data with multiple conditions[J]. Genes (Basel), 2021, 13(1): 73. DOI: 10.3390/genes13010073. [17] HUANG DW, SHERMAN BT, TAN Q, et al. The DAVID gene functional classification tool: a novel biological module-centric algorithm to functionally analyze large gene lists[J]. Genome Biol, 2007, 8(9): R183. DOI: 10.1186/gb-2007-8-9-r183. [18] SZKLARCZYK D, GABLE AL, NASTOU KC, et al. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets[J]. Nucleic Acids Res, 2021, 49(D1): D605-D612. DOI: 10.1093/nar/gkaa1074. [19] LIU X, HONG Z, LIU J, et al. Computational methods for identifying the critical nodes in biological networks[J]. Brief Bioinform, 2020, 21(2): 486-497. DOI: 10.1093/bib/bbz011. [20] ROBIN X, TURCK N, HAINARD A, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves[J]. BMC Bioinformatics, 2011, 12: 77. DOI: 10.1186/1471-2105-12-77. [21] 焦国慧, 王梓涛, 陈静瑜. 肺移植全球发展概况与展望[J]. 器官移植, 2022, 13(4): 417-424. DOI: 10.3969/j.issn.1674-7445.2022.04.002.JIAO GH, WANG ZT, CHEN JY. Current status and prospect of global development of lung transplantation[J]. Organ Transplant, 2022, 13(4): 417-424. DOI: 10.3969/j.issn.1674-7445.2022.04.002. [22] CHEN-YOSHIKAWA TF. Ischemia-reperfusion injury in lung transplantation[J]. Cells, 2021, 10(6): 1333. DOI: 10.3390/cells10061333. [23] 王净, 胡春兰, 于慧智, 等. 肺移植期间肺缺血再灌注损伤及药物治疗的研究进展[J]. 东南大学学报(医学版), 2022, 41(4): 578-582. DOI: 10.3969/j.issn.1671-6264.2022.04.021.WANG J, HU CL, YU HZ, et al. Research progress on pulmonary ischemia-reperfusion injury and drug therapy during lung transplantation[J]. J Southeast Univ (Med Sci Edit), 2022, 41(4): 578-582. DOI: 10.3969/j.issn.1671-6264.2022.04.021. [24] AKBARPOUR M, LECUONA E, CHIU SF, et al. Residual endotoxin induces primary graft dysfunction through ischemia/reperfusion-primed alveolar macrophages[J]. J Clin Invest, 2020, 130(8): 4456-4469. DOI: 10.1172/JCI135838. [25] GAO W, JIANG T, LIU YH, et al. Endothelial progenitor cells attenuate the lung ischemia/reperfusion injury following lung transplantation via the endothelial nitric oxide synthase pathway[J]. J Thorac Cardiovasc Surg, 2019, 157(2): 803-814. DOI: 10.1016/j.jtcvs.2018.08.092. [26] 祝卿, 周文琴, 万里, 等. 1-磷酸鞘氨醇及受体1在小鼠肺缺血再灌注损伤中的表达变化和意义[J]. 四川大学学报(医学版), 2018, 49(6): 891-894.ZHU Q, ZHOU WQ, WAN L, et al. The expression of sphingosine-1-phosphate and sphingosine-1-phosphate receptor 1 in mouse model of pulmonary ischemia-reperfusion injury[J]. J Sichuan Univ (Med Sci), 2018, 49(6): 891-894. [27] XING D, HAGE FG, FENG W, et al. Endothelial cells overexpressing CXCR1/2 are renoprotective in rats with acute kidney injury[J]. Am J Physiol Renal Physiol, 2023, 324(4): F374-F386. DOI: 10.1152/ajprenal.00238.2022. [28] HSIAO HM, FERNANDEZ R, TANAKA S, et al. Spleen-derived classical monocytes mediate lung ischemia-reperfusion injury through IL-1β[J]. J Clin Invest, 2018, 128(7): 2833-2847. DOI: 10.1172/JCI98436. [29] WANG F, WANG F, LI F, et al. Methane attenuates lung ischemia-reperfusion injury via regulating PI3K-Akt-NFκB signaling pathway[J]. J Recept Signal Transduct Res, 2020, 40(3): 209-217. DOI: 10.1080/10799893.2020.1727925. [30] GENDY AM, AMIN MM, AL-MOKADDEM AK, et al. Cilostazol mitigates mesenteric ischemia/reperfusion-induced lung lesion: contribution of PPAR-γ, NF-κB, and STAT3 crosstalk[J]. Life Sci, 2021, 266: 118882. DOI: 10.1016/j.lfs.2020.118882. [31] DAI SH, CHEN LJ, QI WH, et al. microRNA-145 inhibition upregulates SIRT1 and attenuates autophagy in a mouse model of lung ischemia/reperfusion injury via NF-κB-dependent Beclin 1[J]. Transplantation, 2021, 105(3): 529-539. DOI: 10.1097/TP.0000000000003435. [32] WATANABE T, MARTINU T, CHRUSCINSKI A, et al. A B cell-dependent pathway drives chronic lung allograft rejection after ischemia-reperfusion injury in mice[J]. Am J Transplant, 2019, 19(12): 3377-3389. DOI: 10.1111/ajt.15550. [33] CHEN D, CHEN C, XIAO X, et al. TNF-α induces neutrophil apoptosis delay and promotes intestinal ischemia-reperfusion-induced lung injury through activating JNK/FoxO3a pathway[J]. Oxid Med Cell Longev, 2021: 8302831. DOI: 10.1155/2021/8302831. [34] LU Y, WANG YL, LIU Q, et al. MiRNA-122 promotes ischemia-reperfusion injury after lung transplantation via the toll-like receptor signaling pathway[J]. Curr Med Sci, 2021, 41(6): 1231-1238. DOI: 10.1007/s11596-021-2487-y. [35] JIN H, ZHANG C, SUN C, et al. OX40 expression in neutrophils promotes hepatic ischemia/reperfusion injury[J]. JCI Insight, 2019, 4(21): e129736. DOI: 10.1172/jci.insight.129736. [36] ZHOU H, SHI C, HU S, et al. BI1 is associated with microvascular protection in cardiac ischemia reperfusion injury via repressing Syk-Nox2-Drp1-mitochondrial fission pathways[J]. Angiogenesis, 2018, 21(3): 599-615. DOI: 10.1007/s10456-018-9611-z. [37] YANG CC, SUNG PH, CHEN CH, et al. Additional benefit of induced pluripotent stem cell-derived mesenchymal stem cell therapy on sepsis syndrome-associated acute kidney injury in rat treated with antibiotic[J]. Stem Cell Res Ther, 2021, 12(1): 526. DOI: 10.1186/s13287-021-02582-5. [38] MARTÍNEZ-LÓPEZ M, IBORRA S, CONDE-GARROSA R, et al. Microbiota sensing by Mincle-Syk axis in dendritic cells regulates interleukin-17 and -22 production and promotes intestinal barrier integrity[J]. Immunity, 2019, 50(2): 446-461. DOI: 10.1016/j.immuni.2018.12.020. [39] LI C, XUE VW, WANG QM, et al. The Mincle/Syk/NF-κB signaling circuit is essential for maintaining the protumoral activities of tumor-associated macrophages[J]. Cancer Immunol Res, 2020, 8(8): 1004-1017. DOI: 10.1158/2326-6066.CIR-19-0782. [40] SADRAS T, MARTIN M, KUME K, et al. Developmental partitioning of SYK and ZAP70 prevents autoimmunity and cancer[J]. Mol Cell, 2021, 81(10): 2094-2111. DOI: 10.1016/j.molcel.2021.03.043. [41] HUFFAKER TB, EKIZ HA, BARBA C, et al. A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages[J]. Nat Commun, 2021, 12(1): 2620. DOI: 10.1038/s41467-021-22923-5. [42] YANG L, CHEN S, ZHAO Q, et al. Histone deacetylase 3 contributes to the antiviral innate immunity of macrophages by interacting with FOXK1 to regulate STAT1/2 transcription[J]. Cell Rep, 2022, 38(4): 110302. DOI: 10.1016/j.celrep.2022.110302. [43] UZHACHENKO RV, SHANKER A. CD8+T lymphocyte and NK cell network: circuitry in the cytotoxic domain of immunity[J]. Front Immunol, 2019, 10: 1906. DOI: 10.3389/fimmu.2019.01906. [44] NIEDERLOVA V, TSYKLAURI O, CHADIMOVA T, et al. CD8+Tregs revisited: a heterogeneous population with different phenotypes and properties[J]. Eur J Immunol, 2021, 51(3): 512-530. DOI: 10.1002/eji.202048614. [45] MA K, QIAO Y, WANG H, et al. Comparative expression analysis of PD-1, PD-L1, and CD8A in lung adenocarcinoma[J]. Ann Transl Med, 2020, 8(22): 1478. DOI: 10.21037/atm-20-6486. [46] HE L, WANG Z, ZHOU R, et al. Dexmedetomidine exerts cardioprotective effect through miR-146a-3p targeting IRAK1 and TRAF6 via inhibition of the NF-κB pathway[J]. Biomed Pharmacother, 2021, 133: 110993. DOI: 10.1016/j.biopha.2020.110993. [47] HE X, ZHENG Y, LIU S, et al. MiR-146a protects small intestine against ischemia/reperfusion injury by down-regulating TLR4/TRAF6/NF-κB pathway[J]. J Cell Physiol, 2018, 233(3): 2476-2488. DOI: 10.1002/jcp.26124. [48] YANG Y, LI L. Depleting microRNA-146a-3p attenuates lipopolysaccharide-induced acute lung injury via up-regulating SIRT1 and mediating NF-κB pathway[J]. J Drug Target, 2021, 29(4): 420-429. DOI: 10.1080/1061186X.2020.1850738. [49] NONG Y, GUO Y, GUMPERT A, et al. Single dose of synthetic microRNA-199a or microRNA-149 mimic does not improve cardiac function in a murine model of myocardial infarction[J]. Mol Cell Biochem, 2021, 476(11): 4093-4106. DOI: 10.1007/s11010-021-04227-w. [50] CHEN F, HAN J, WANG D. Identification of key microRNAs and the underlying molecular mechanism in spinal cord ischemia-reperfusion injury in rats[J]. PeerJ, 2021, 9: e11454. DOI: 10.7717/peerj.11454. [51] XU N, HE D, SHAO Y, et al. Lung-derived exosomes in phosgene-induced acute lung injury regulate the functions of mesenchymal stem cells partially via miR-28-5p[J]. Biomed Pharmacother, 2020, 121: 109603. DOI: 10.1016/j.biopha.2019.109603. [52] YU Z, ZHU M, SHU D, et al. LncRNA PEG11as aggravates cerebral ischemia/reperfusion injury after ischemic stroke through miR-342-5p/PFN1 axis[J]. Life Sci, 2023, 313: 121276. DOI: 10.1016/j.lfs.2022.121276. [53] CHEN W, LI S, LIU Q, et al. MicroRNA-342-5p protects against myocardial ischemia-reperfusion injury by targeting the GPRC5A pathway[J]. Pharmazie, 2020, 75(6): 271-274. DOI: 10.1691/ph.2020.0383. [54] LIU W, HU C, ZHANG B, et al. Exosomal microRNA-342-5p secreted from adipose-derived mesenchymal stem cells mitigates acute kidney injury in sepsis mice by inhibiting TLR9[J]. Biol Proced Online, 2023, 25(1): 10. DOI: 10.1186/s12575-023-00198-y. [55] MA J, LI YT, ZHANG SX, et al. MiR-590-3p attenuates acute kidney injury by inhibiting tumor necrosis factor receptor-associated factor 6 in septic mice[J]. Inflammation, 2019, 42(2): 637-649. DOI: 10.1007/s10753-018-0921-5. [56] WEI X, YI X, LV H, et al. MicroRNA-377-3p released by mesenchymal stem cell exosomes ameliorates lipopolysaccharide-induced acute lung injury by targeting RPTOR to induce autophagy[J]. Cell Death Dis, 2020, 1(8): 657. DOI: 10.1038/s41419-020-02857-4. [57] HUANG T, GAO Y, CAO Y, et al. Downregulation of mmu_circ_0000943 ameliorates renal ischemia reperfusion-triggered inflammation and oxidative stress via regulating mmu-miR-377-3p/Egr2 axis[J]. Int Immunopharmacol, 2022, 106: 108614. DOI: 10.1016/j.intimp.2022.108614. [58] WANG Y, JIN F, HUANG L, et al. MiR-590-3p protects against ischaemia/reperfusion injury in an oxygen-glucose deprivation and reoxygenation cellular model by regulating HMGB1/TLR4/MyD88/NF-κB signaling[J]. Histol Histopathol, 2023, 38(8): 941-951. DOI: 10.14670/HH-18-562. [59] LEON-CORIA A, KUMAR M, WORKENTINE M, et al. Muc2 mucin and nonmucin microbiota confer distinct innate host defense in disease susceptibility and colonic injury[J]. Cell Mol Gastroenterol Hepatol, 2021, 11(1): 77-98. DOI: 10.1016/j.jcmgh.2020.07.003. [60] WANG P, BAO W, LIU X, et al. LncRNA miR143HG inhibits the proliferation of glioblastoma cells by sponging miR-504[J]. Int J Neurosci, 2022, 132(11): 1137-1142. DOI: 10.1080/00207454.2020.1865950. -
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