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深静脉血栓关键基因 AP2B1 和 miRNAs 及其相关通路的筛选

Screening of key gene AP2B1, miRNAs and related pathways in deep venous thrombosis

作者: 祁莎莎  曹鑫  徐宁宁  陈静 
单位:青岛市第八人民医院手术室(山东青岛 266041),<br />山东第一医科大学基础医学院(济南 250000),<br />通信作者:陈静。E-mail:chenjing@sdfmu.edu.cn
关键词: 深静脉血栓;生物信息学;关键基因;AP2B1;miRNAs 
分类号:R318 &nbsp;
出版年·卷·期(页码):2022·41·4(344-351)
摘要:

目的 通过生物信息学方法预测深静脉血栓的关键基因和miRNAs,并对其相关通路进行研究,为深静脉血栓的诊断及治疗提供新的思路。方法 通过分析GEO在线数据库中人类深静脉血栓(deep vein thrombosis, DVT)GSE17078数据集,其中包含正常对照27例和DVT 3例,筛选其中表达差异最显著的基因作为DVT的关键基因;利用Networkanalyst网站对关键基因进行器官富集分析,查看关键基因在器官内的富集情况;应用TargetScan、miRDB及mirTARBASE在线数据库预测关键基因相关的miRNAs,并利用Venn图对预测得到的miRNAs取交集,得到最相关的miRNAs,通过mirTARBASE在线数据库对miRNAs进行基因本体论GO(gene ontology)分析和信号通路富集KEGG(Kyoto Encyclopedia of Genes and Genome)分析;通过STRING网站对关键基因进行进行PPI(protein-protein interaction)网络构建及蛋白互作网络基因的GO分析和KEGG分析。最后通过动物实验,对关键基因及相关的miRNAs进行定量分析。结果 通过差异基因分析得出DVT关键基因是AP2B1(P=2.99e-09),在人脑中表达量最高,且在海马体中AP2B1与之相互作用的基因最多;经在线数据库预测得出关键基因AP2B1的miRNAs,再通过Venn图取交集后得出概率最大的miRNAs是hsa-miRNA4780、hsa-miRNA-106b-5p及hsa-miRNA-16-5p(P<0.05);通过mirTARBASE数据库对hsa-miRNA-4780、hsa-miRNA-106b-5p及hsa-miRNA-16-5p进行通路富集分析,得出其显著富集于TGF-β信号通路、细胞周期及脂肪酸生物合成等16个信号通路中(P<0.05);通过STRING网站对关键基因AP2B1进行PPI构建图分析出AP2B1编码的蛋白质与AP1M1等10种蛋白质相互作用复杂;并对蛋白互作网络基因进行GO分析及KEGG分析,发现其在病毒防御、受体代谢等功能富集,在内吞作用、内分泌相关的钙离子重吸收等KEGG通路富集;动物实验结果证实,DVT组AP2B1基因表达量低于对照组,而hsa-miRNA-4780、hsa-miRNA-106b-5p及hsa-miRNA-16-5p的表达量高于对照组(P<0.05)。结论 通过预测得出hsa-miRNA-106b-5p及hsa-miRNA-16-5p可能通过TGF-β等信号通路调控关键基因AP2B1的表达,参与深静脉血栓形成发展的病理生理过程,可作为新型生物诊断标志物,为深静脉血栓的临床诊断及治疗提供新的思路。

Objective The key gene and miRNAs in DVT were predicted by bioinformatics methods, and their related pathways were studied to provide new ideas for the diagnosis and treatment of DVT. Methods By analyzing the DATA set GSE17078 of human deep vein thrombosis (DVT) in GEO online database, including 27 normal control cases and 3 DVT cases, the genes with the most significant expression difference were screened as the key gene of DVT. Networkanalyst website was used to perform organ enrichment analysis to check the enrichment of key gene in organs; TargetScan, miRDB and mirTARBASE online databases were used to predict the related miRNAs of key gene, and Venn graph was used to take the intersection of the predicted miRNAs, and the miRNAs with higher correlation were obtained. GO (Gene Ontology) analysis and KEGG (Kyoto Encyclopedia of Genes and Genome) analysis of miRNAs were conducted by mirTARBASE online database. By STRING website, protein-protein Interaction (PPI) network was constructed and GO analysis and KEGG analysis were conducted for the genes of PPI. Finally, through animal experiments, the key gene AP2B1 and its related hsa-miRNA-4780、hsa-miRNA-106b-5p and hsa-miRNA-16-5p were quantitatively analyzed. Results Through differential gene analysis, the key differential gene of DVT was AP2B1 (P = 2.99e-09), which had the highest expression level in human brain. In addition,AP2B1 interacted with other genes mostly in hippocampus. The miRNAs of gene AP2B1 were predicted by online databases, and the most probable miRNAs were hsa-miRNA-4780, hsa-miRNA-106b-5p and hsa-miRNA-16-5p(P<0.05) by Venn diagram. The results showed that hsa-miRNA-4780, hsa-miRNA-106b-5p and hsa-miRNA-16-5p were significantly enriched in 16 signaling pathways, including TGF - β signaling pathway, cell cycle and fatty acid biosynthesis (P < 0.05). Through the PPI construction map of the key gene AP2B1 on the STRING website, it was analyzed that the protein encoded by AP2B1 had complex interactions with 10 proteins such as AP1M1. GO analysis and KEGG analysis illustrated that the protein interaction network genes were enriched in viral defense, receptor metabolism and other functions, and enriched in KEGG pathways such as endocytosis and endocrine related calcium reabsorption. The results of animal experiments confirmed that the expression level of AP2B1 in DVT group was lower than that in control group, while the expression levels of hsa-miRNA-4780, hsa-miRNA-106b-5p and hsa-miRNA-16-5p were higher than that in control group, and the differences were statistically significant. Conclusions By bioinformatics prediction, it is concluded that hsa-miRNA-106b-5p and hsa-miRNA-16-5p might regulate the expression of target gene AP2B1 through TGF-β and other signaling pathways, and participate in the pathophysiological process of DVT, which can be used as new biological diagnostic markers to provide a new idea for the clinical diagnosis and treatment of DVT .

参考文献:

[1] Morelli VM, Br?kkan S, Hansen JB. Role of microRNAs in venous thromboembolism[J]. International Journal of Molecular Sciences, 2020, 21(7): 2602.
[2]蒋知云,马俊芬,明亮. microRNA 在深静脉血栓形成中的作用及临床价值研究进展[J]. 医学研究生学报, 2017, 30(8): 893-896.
Jiang ZY, Ma JF, Ming L. Advances in the study of microRNA in deep vein thrombosis[J]. Journal of Medical Postgraduates, 2017, 30(8): 893-896.
[3] 褚楚,刘文,郭红,等. miR-664b-3p调控Caspase-1介导细胞焦亡在深静脉血栓形成中的作用[J].山东医药,2021,61(8):20-23.
Zhu C, Liu W, Guo H, et al. Regulatory role of miR-664b-3p in caspase-1-mediated pyroptosis in patients with deep vein thrombosis[J].Shandong Medical Journal,2021,61(8):20-23.
[4] 冯涛,李晶,潘金强,等. miR-5189-3p在下腔深静脉血栓形成的调控机制的研究[J].临床外科杂志,2021,29(5):478-481.
Feng T, Li J, Pan JQ, et al. Study on the regulatory mechanism of miR-5189-3p in deep venous thrombosis of lower extremities
[J]. Journal of Clinical Surgery, 2021, 29(5): 478-481.
[5]霍艳兵,彭琪,彭星华,等. MicroRNA-374a-5p水平与混合型深静脉血栓形成患者临床特征的关系及在预后判断中的价值[J].中国现代医学杂志, 2020, 30(19): 23-28.
Huo YB, Peng Q, Peng XH, et al. Clinical characters and prognostic values of microRNA-374a-5p in patients with mixed deep vein thrombosis[J].China Journal of Modern Medicine, 2020, 30(19): 23-28.
[6]Aigner A. MicroRNAs (miRNAs) in cancer invasion and metastasis: therapeutic approaches based on metastasis-related miRNAs[J]. Journal of Molecular Medicine, 2011, 89(5): 445-457.
[7]Hembrom AA, Srivastava S, Garg I, et al. MicroRNAs in venous thrombo-embolism[J]. Clinica Chimica Acta, 2020, 504: 66–72.?
[8] Jiang Z, Ma J, Wang Q, et al. Circulating microRNA expression and their target genes in deep vein thrombosis: a systematic review and bioinformatics analysis[J]. Medicine (Baltimore), 2017, 96(50): e9330.
[9] Bijak M, Dzieciol M, Rywaniak J, et al. Platelets miRNA as a prediction marker of thrombotic episodes[J]. Disease Markers, 2016, 2016: 2872507.?
[10] Sahu A, Jha PK, Prabhakar A, et al. MicroRNA-145 impedes thrombus formation via targeting tissue factor in venous thrombosis[J]. EBioMedicine, 2017, 26: 175-186.
[11]Jiang Z, Ma J, Wang Q, et al. Combination of circulating miRNA-320a/b and D-dimer improves diagnostic accuracy in deep vein thrombosis patients[J]. Medical Science Monitor, 2018, 24: 2031–2037.
[12] Du X, Hong L, Sun L, et al. miR-21 induces endothelial progenitor cells proliferation and angiogenesis via targeting FASLG and is a potential prognostic marker in deep venous thrombosis[J]. Journal of Translational Medicine, 2019, 17(1): 270.
[13] Thibord F, Munsch G, Perret C, et al. Bayesian network analysis of plasma microRNA sequencing data in patients with venous thrombosis[J]. European Heart Journal Supplements, 2020, 22(Suppl C): C34-C45.
[14]高浩然,王岩,段雨晴,等.神经重症患者静脉血栓栓塞的发生率、危险因素及住院结局分析[J].中国卒中杂志,2021,16(7):694-698.
Gao HR, Wang Y, Duan YQ, et al. Incidence, risk factors and in-hospital outcome of venous thromboembolism in neurocritical patients[J]. Chinese Journal of Stroke, 2021, 16(7): 694-698.
[15] Koscielny A, Malik AR, Liszewska E, et al. Adaptor complex 2 controls dendrite morphology via mTOR-dependent expression of GluA2[J]. Molecular Neurobiology, 2018, 55(2): 1590-1606.
[16] Suzuki HI. MicroRNA control of TGF-β signaling[J]. International Journal of Molecular Sciences,2018, 19(7):1901.
[17]Janakiraman H, House RP, Gangaraju VK, et al. The long (lncRNA) and short (miRNA) of it: TGFβ-mediated control of RNA-binding proteins and noncoding RNAs[J]. Molecular Cancer Research,2018,16(4): 567–579.
[18] Sj?din S, Brinkmalm G, ?hrfelt A, et al. Endo-lysosomal proteins and ubiquitin CSF concentrations in Alzheimer's and Parkinson's disease[J]. Alzheimer's Research?& Therapy, 2019, 11(1): 82.

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