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A bioinformatics analysis of differentially expressed genes in Huh7 cells with low expression of Mindin
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摘要:
目的构建Mindin低表达的Huh7细胞并对其进行转录组学研究,以探索Mindin的生物学作用。方法设计并合成Mindin干扰序列,通过慢病毒载体GV248将其导入Huh7细胞,实时定量PCR检测对Mindin转录水平的抑制效果,获得Mindin低表达Huh7细胞并对该细胞及其对照细胞进行转录组学研究,生物信息学分析表达异常基因,Pathway分析Mindin可能参与的生物学功能。计量资料2组间比较采用t检验。结果与对照细胞相比,含干扰序列的慢病毒感染Huh7细胞后,其Mindin mRNA的敲减效率为63. 8%（P=0. 003）。Mindin稳定低表达的Huh7细胞迁移率明显高于对照细胞（3. 511±0. 538 vs 1. 701±0. 765,t=-3. 355,P=0. 03）。与对照细胞相比,Mindin低表达Huh7细胞有2888个上调基因,2516个下调基因。取满足∣log2FC∣> 2. 0且P<0. 05的895个差异表达基因进行GO分析和Pathway分析。Pathway分析排名前10位的Mindin参与的生物学功能依次为:肿瘤信号通路、趋化因子...
Abstract:Objective To perform a transcriptomic study of Huh7 cells with low expression of Mindin,and to investigate the biological effects of Mindin. Methods The Mindin interference sequence was designed,synthesized,and introduced into Huh7 cells via the lentiviral vector GV248. Real-time quantitative PCR was used to measure the inhibitory effect on Mindin transcription level. Huh7 cells with low expression of Mindin were obtained and a transcriptomic study was performed for such cells and their control cells. Bioinformatics was used to analyze abnormally expressed genes,and pathway analysis was used to investigate the possible biological functions involving Mindin. The t-test was used for comparison of continuous data between groups. Results Compared with the control cells,Huh7 cells transfected with the lentivirus containing interference sequence had a knockdown efficiency of Mindin mRNA of 63. 8%(P = 0. 003). Huh7 cells with stable low expression of Mindin had a significantly higher cell migration rate than the control cells(3. 511 ± 0. 538 vs 1. 701 ± 0. 765,t =-3. 355,P = 0. 03). Compared with the control cells,Huh7 cells with low expression of Mindin had 2888 upregulated genes and 2516 downregulated genes. Gene ontology analysis and pathway analysis were performed for 895 differentially expressed genes with | log2 FC | > 2. 0 and P<0. 05. The pathway analysis showed that the top 10 biological functions involving Mindin were tumor signaling pathway,chemokine signaling pathway,systemic lupus erythematosus,glycerophospholipid metabolism,neuroactive ligand-receptor interaction,hypertrophic cardiomyopathy,glycerolipid metabolism,MAPK signaling pathway,complement and coagulation cascades,and basal cell carcinoma. Conclusion Huh7 cells with low expression of Mindin are successfully constructed. Mindin has wide biological functions including tumors,chemokines,and lipid metabolism.
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Key words:
- Mindin /
- transcriptome /
- signal transduction /
- computational biology
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[1] FEINSTEIN Y,BORRELL V,GARCIA C,et al. F-spondin and mindin:Two structurally and functionally related genes expressed in the hippocampus that promote outgrowth of embryonic hippocampal neurons[J]. Development, 1999, 126(16):3637-3648. [2] JIA W,LI H,HE YW. The extracellular matrix protein mindin serves as an integrin ligand and is critical for inflammatory cell recruitment[J]. Blood,2005,106(12):3854-3859. [3] LIU YS,WANG LF,CHENG XS,et al. The pattern-recognition molecule mindin binds integrin Mac-1 to promote macrophage phagocytosis via Syk activation and NF-kappab p65translocation[J]. J Cell Mol Med,2019,23(5):3402-3416. [4] WANG LF,LIU YS,YANG B,et al. The extracellular matrix protein mindin attenuates colon cancer progression by blocking angiogenesis via Egr-1-mediated regulation[J]. Oncogene,2018,37(5):601-615. [5] GULENG B,LIAN YM,REN JL. Mindin is upregulated during colitis and may activate NF-kappaB in a TLR-9 mediated manner[J]. World J Gastroenterol,2010,16(9):1070-1075. [6] NAUDIN C,SMITH B,BOND DR,et al. Characterization of the early molecular changes in the glomeruli of Cd151(-/-)mice highlights induction of mindin and MMP-10[J]. Sci Rep,2017,7(1):15987. [7] DOGˇAN T,YETIM M,ELIK O,et al. Investigation of mindin levels in hypertensive patients with left ventricular hypertrophy and QRS fragmentation on electrocardiography[J]. Acta Cardiol,2018,73(6):544-549. [8] MACRITCHIE N,MAFFIA P.'Blow my mind(in)'-mindin neutralization for the prevention of atherosclerosis?[J]. Clin Sci(Lond),2018,132(14):1509-1512. [9] WANG L,LU Y,ZHANG X,et al. Mindin is a critical mediator of ischemic brain injury in an experimental stroke model[J].Exp Neurol,2013,247:506-516. [10] JIA W,LI H,HE YW. Pattern recognition molecule mindin promotes intranasal clearance of influenza viruses[J]. J Immunol,2008,180(9):6255-6261. [11] HE YW,LI H,ZHANG J,et al. The extracellular matrix protein mindin is a pattern-recognition molecule for microbial pathogens[J]. Nat Immunol,2004,5(1):88-97. [12] LI H,OLIVER T,JIA W,et al. Efficient dendritic cell priming of T lymphocytes depends on the extracellular matrix protein mindin[J]. EMBO J,2006,25(17):4097-4107. [13] LIAO CH,YEH SC,HUANG YH,et al. Positive regulation of spondin 2 by thyroid hormone is associated with cell migration and invasion[J]. Endocr Relat Cancer,2010,17(1):99-111. [14] LUO JH,REN B,KERYANOV S,et al. Transcriptomic and genomic analysis of human hepatocellular carcinomas and hepatoblastomas[J]. Hepatology,2006,44(4):1012-1024. [15] ZHANG YL,LI Q,YANG XM,et al. SPON2 promotes M1-like macrophage recruitment and inhibits hepatocellular carcinoma metastasis by distinct integrin-Rho GTPase-hippo pathways[J]. Cancer Res,2018,78(9):2305-2317. [16] RAJKUMAR T,VIJAYALAKSHMI N,GOPAL G,et al. Identification and validation of genes involved in gastric tumorigenesis[J]. Cancer Cell Int,2010,10:45. [17] JIN C,LIN JR,MA L,et al. Elevated spondin-2 expression correlates with progression and prognosis in gastric cancer[J]. Oncotarget,2017,8(6):10416-10424. [18] CHANDRASINGHE P,STEBBING J,WARUSAVITARNE J. The MACC1-SPON2 axis:A new biomarker and therapeutic target in colorectal cancer[J]. Oncogene,2017,36(11):1474-1475. [19] SCHMID F,WANG Q,HUSKA MR,et al. Spon2,a newly identified target gene of macc1,drives colorectal cancer metastasis in mice and is prognostic for colorectal cancer patient survival[J]. Oncogene,2016,35(46):5942-5952. [20] ZHANG Q,WANG XQ,WANG J,et al. Upregulation of spondin-2 predicts poor survival of colorectal carcinoma patients[J].Oncotarget,2015,6(17):15095-15110. [21] SIMON I,LIU Y,KRALL KL,et al. Evaluation of the novel serum markers B7-H4,spondin 2,and DcR3 for diagnosis and early detection of ovarian cancer[J]. Gynecol Oncol,2007,106(1):112-118. [22] QIAN X,LI C,PANG B,et al. Spondin-2(SPON2),a more prostate-cancer-specific diagnostic biomarker[J]. PLo S One,2012,7(5):e37225. [23] LUCARELLI G,RUTIGLIANO M,BETTOCCHI C,et al. Spondin-2,a secreted extracellular matrix protein,is a novel diagnostic biomarker for prostate cancer[J]. J Urol,2013,190(6):2271-2277. [24] YUAN X,BIAN T,LIU J,et al. Spondin2 is a new prognostic biomarker for lung adenocarcinoma[J]. Oncotarget,2017,8(35):59324-59332. [25] HERS I,VINCENT EE,TAVARJM. Akt signalling in health and disease[J]. Cell Signal,2011,23(10):1515-1527. [26] SUN P,ZHANG P,WANG PX,et al. Mindin deficiency protects the liver against ischemia/reperfusion injury[J]. J Hepatol,2015,63(5):1198-1211. [27] ZHANG X,WANG W,ZHAI S,et al. Down-regulated expression of pattern recognition molecule mindinmindin in acute hepatic injury induced by CCl4in mice[J]. J Clin Hepatol,2019,35(2):368-371.(in Chinese)张欣,王文俊,翟嵩,等.模式识别分子Mindin蛋白在CCl4诱导急性肝损伤小鼠模型中的表达[J].临床肝胆病杂志,2019,35(2):368-371. [28] ZHU LH,WANG A,LUO P,et al. Mindin/spondin 2 inhibits hepatic steatosis,insulin resistance,and obesity via interaction with peroxisome proliferator-activated receptor alpha in mice[J]. J Hepatol,2014,60(5):1046-1054. [29] FENG Y,HU Y,MAO Q,et al. Upregulation of spondin-2protein expression correlates with poor prognosis in hepatocellular carcinoma[J]. J Int Med Res,2019,47(2):569-579. [30] HAO PQ,ZHANG XY,GUO H,et al. Research progress on pathophysiological function of SOS1 protein[J]. Acta Physiologica Sinica,2018,70(5):107-112.(in Chinese)郝佩琪,张新宇,郭慧,等. SOS1蛋白病理生理功能研究进展[J].生理学报,2018,70(5):107-112. [31] YU Y,WU TT,JIANG CL,et al. Effects of hepatitis B virus X protein on cell proliferation and GSK3βexpression of human liver cell line L02[J]. Cancer,2011,31(5):406-411.(in Chinese)喻垚,吴婷婷,蒋崇亮,等.乙型肝炎病毒X蛋白对肝细胞L02增殖及GSK3β表达的影响[J].肿瘤,2011,31(5):406-411. 期刊类型引用(25)
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