Journal of Orthopaedic Surgery and Research | |
Microarray analysis for differentially expressed genes of patients undergoing total knee arthroplasty with ischemia preconditioning | |
Junjian Liu1  Zhengdong Cai1  Jianguang Wang2  | |
[1] Department of Orthopedics, Shanghai First People’s Hospital, No.100 Haining Road, Hongkou District, Shanghai 200080, China;Department of Orthopedics, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai 200072, China | |
关键词: Protein-protein interaction network; Transcriptional factor; microRNA; Ischemia preconditioning; | |
Others : 1138829 DOI : 10.1186/s13018-014-0133-0 |
|
received in 2014-09-19, accepted in 2014-11-27, 发布年份 2014 | |
【 摘 要 】
Background
Ischemia preconditioning (IPC) has been proved as a powerful method of protecting tissues against ischemia reperfusion insults. We aimed to elucidate the mechanism of IPC in ischemia reperfused tissues.
Methods
GSE21164 containing 16 muscle biopsies taken from the operative knee of four IPC-treated patients and four control at the onset of surgery (T = 0) and 1 h into surgery (T = 1) undergoing primary total knee arthroplasty was downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between IPC group and control were screened with Limma package in R language. KEGG pathway enrichment analysis was performed by the DAVID online tool. Meanwhile, potential regulatory microRNAs (miRNAs) for downregulated DEGs and targets of transcription factors for upregulated DEGs were screened out. Based on the above DEGs, protein-protein interaction (PPI) networks were constructed by the STRING software.
Results
Significantly upregulated DEGs at T1 were mainly enriched in asthma and p53 signaling pathway. Meanwhile, significantly enriched transcriptional factor NOTCH1 at T1 and GABP at T0 were obtained. Moreover, miRNA analysis showed that targets of miR141/200a were enriched in downregulated DEGs both at T0 and T1. Mostly, RPA1 and JAK2 in PPI network at T1 were with higher degree.
Conclusions
In our study, obtained DEGs, regulatory transcriptional factors, and miRNA might play a vital role in the protection of ischemia reperfusion injury. This finding will provide a deeper understanding to the mechanism of IPC.
【 授权许可】
2014 Wang et al.; licensee BioMed Central.
【 预 览 】
Files | Size | Format | View |
---|---|---|---|
20150320112659124.pdf | 875KB | download | |
Figure 2. | 44KB | Image | download |
Figure 1. | 40KB | Image | download |
【 图 表 】
Figure 1.
Figure 2.
【 参考文献 】
- [1]Beyersdorf F, Unger A, Wildhirt A, Kretzer U, Deutschlander N, Kruger S, Matheis G, Hanselmann A, Zimmer G, Satter P: Studies of reperfusion injury in skeletal muscle: preserved cellular viability after extended periods of warm ischemia. J Cardiovasc Surg (Torino) 1991, 32:664-676.
- [2]Murry CE, Jennings RB, Reimer KA: Preconditioning with ischemia: a delay of lethal cell injury in ischemic myocardium. Circulation 1986, 74:1124-1136.
- [3]Hausenloy DJ, Yellon DM: Remote ischaemic preconditioning: underlying mechanisms and clinical application. Cardiovasc Res 2008, 79:377-386.
- [4]Deutsch E, Berger M, Kussmaul WG, Hirshfeld JW Jr, Herrmann HC, Laskey WK: Adaptation to ischemia during percutaneous transluminal coronary angioplasty. Clinical, hemodynamic, and metabolic features. Circulation 1990, 82:2044-2051.
- [5]Jenkins DP, Pugsley WB, Alkhulaifi AM, Kemp M, Hooper J, Yellon DM: Ischaemic preconditioning reduces troponin T release in patients undergoing coronary artery bypass surgery. Heart 1997, 77:314-318.
- [6]Clavien PA, Selzner M, Rudiger HA, Graf R, Kadry Z, Rousson V, Jochum W: A prospective randomized study in 100 consecutive patients undergoing major liver resection with versus without ischemic preconditioning. Ann Surg 2003, 238:843-850. discussion 851–842
- [7]Chen S, Li G, Long L: Clinical research of ischemic preconditioning on lung protection. Hunan Yi Ke Da Xue Xue Bao 1999, 24:357-359.
- [8]Stokman G, Stroo I, Claessen N, Teske GJ, Florquin S, Leemans JC: SDF-1 provides morphological and functional protection against renal ischaemia/reperfusion injury. Nephrol Dial Transplant 2010, 25:3852-3859.
- [9]Sola A, Hotter G, Prats N, Xaus C, Gelpi E, Rosello-Catafau J: Modification of oxidative stress in response to intestinal preconditioning. Transplantation 2000, 69:767-772.
- [10]Saita Y, Yokoyama K, Nakamura K, Itoman M: Protective effect of ischaemic preconditioning against ischaemia-induced reperfusion injury of skeletal muscle: how many preconditioning cycles are appropriate? Br J Plast Surg 2002, 55:241-245.
- [11]Grace PA: Ischaemia-reperfusion injury. Br J Surg 1994, 81:637-647.
- [12]Cinel I, Avlan D, Cinel L, Polat G, Atici S, Mavioglu I, Serinol H, Aksoyek S, Oral U: Ischemic preconditioning reduces intestinal epithelial apoptosis in rats. Shock 2003, 19:588-592.
- [13]Cohen MV, Baines CP, Downey JM: Ischemic preconditioning: from adenosine receptor to KATP channel. Annu Rev Physiol 2000, 62:79-109.
- [14]Liu GS, Thornton J, Van Winkle DM, Stanley AW, Olsson RA, Downey JM: Protection against infarction afforded by preconditioning is mediated by A1 adenosine receptors in rabbit heart. Circulation 1991, 84:350-356.
- [15]Goto M, Liu Y, Yang XM, Ardell JL, Cohen MV, Downey JM: Role of bradykinin in protection of ischemic preconditioning in rabbit hearts. Circ Res 1995, 77:611-621.
- [16]Baines CP, Goto M, Downey JM: Oxygen radicals released during ischemic preconditioning contribute to cardioprotection in the rabbit myocardium. J Mol Cell Cardiol 1997, 29:207-216.
- [17]Ytrehus K, Liu Y, Downey JM: Preconditioning protects ischemic rabbit heart by protein kinase C activation. Am J Physiol 1994, 266:H1145-H1152.
- [18]Tong H, Chen W, Steenbergen C, Murphy E: Ischemic preconditioning activates phosphatidylinositol-3-kinase upstream of protein kinase C. Circ Res 2000, 87:309-315.
- [19]Tong H, Imahashi K, Steenbergen C, Murphy E: Phosphorylation of glycogen synthase kinase-3beta during preconditioning through a phosphatidylinositol-3-kinase–dependent pathway is cardioprotective. Circ Res 2002, 90:377-379.
- [20]Weinbrenner C, Liu GS, Cohen MV, Downey JM: Phosphorylation of tyrosine 182 of p38 mitogen-activated protein kinase correlates with the protection of preconditioning in the rabbit heart. J Mol Cell Cardiol 1997, 29:2383-2391.
- [21]Hecker JG, Mcgarvey M: Heat shock proteins as biomarkers for the rapid detection of brain and spinal cord ischemia: a review and comparison to other methods of detection in thoracic aneurysm repair. Cell Stress Chaperones 2011, 16:119-131.
- [22]Murphy T, Walsh PM, Doran PP, Mulhall KJ: Transcriptional responses in the adaptation to ischaemia-reperfusion injury: a study of the effect of ischaemic preconditioning in total knee arthroplasty patients. J Transl Med 2010, 8:46. BioMed Central Full Text
- [23]Sha Y, Xu YQ, Zhao WQ, Tang H, Li FB, Li X, Li CX: Protective effect of ischaemic preconditioning in total knee arthroplasty. Eur Rev Med Pharmacol Sci 2014, 18:1559-1566.
- [24]Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264.
- [25]Smyth GK: Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Edited by Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S. Springer, New York; 2005:397-420.
- [26]Da Huang W, Sherman BT, Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4:44-57.
- [27]Lachmann A, Xu H, Krishnan J, Berger SI, Mazloom AR, Ma’ayan A: ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 2010, 26:2438-2444.
- [28]Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB: Prediction of mammalian microRNA targets. Cell 2003, 115:787-798.
- [29]Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, Von Mering C: STRING v9. 1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res 2013, 41:D808-D815.
- [30]Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011, 27:431-432.
- [31]Otani H: Ischemic preconditioning: from molecular mechanisms to therapeutic opportunities. Antioxid Redox Signal 2008, 10:207-247.
- [32]Kamphuis W, Dijk F, Bergen AA: Ischemic preconditioning alters the pattern of gene expression changes in response to full retinal ischemia. Mol Vis 2007, 13:1892-1901.
- [33]Hoshi M, Sato M, Kondo S, Takashima A, Noguchi K, Takahashi M, Ishiguro K, Imahori K: Different localization of tau protein kinase I/glycogen synthase kinase-3 beta from glycogen synthase kinase-3 alpha in cerebellum mitochondria. J Biochem 1995, 118:683-685.
- [34]Rudiger HA, Clavien PA: Tumor necrosis factor alpha, but not Fas, mediates hepatocellular apoptosis in the murine ischemic liver. Gastroenterology 2002, 122:202-210.
- [35]Cohen O, Inbal B, Kissil JL, Raveh T, Berissi H, Spivak-Kroizaman T, Feinstein E, Kimchi A: DAP-kinase participates in TNF-alpha- and Fas-induced apoptosis and its function requires the death domain. J Cell Biol 1999, 146:141-148.
- [36]Yadav SS, Sindram D, Perry DK, Clavien PA: Ischemic preconditioning protects the mouse liver by inhibition of apoptosis through a caspase-dependent pathway. Hepatology 1999, 30:1223-1231.
- [37]Nian-Kang S, Shang-Lang H, Kun-Yi C, Chuck C-KC: Golgi-SNARE GS28 potentiates cisplatin-induced apoptosis by forming GS28-MDM2-p53 complexes and by preventing the ubiquitination and degradation of p53. Biochem J 2012, 444:303-314.
- [38]Arumugam TV, Chan SL, Jo DG, Yilmaz G, Tang SC, Cheng A, Gleichmann M, Okun E, Dixit VD, Chigurupati S, Mughal MR, Ouyang X, Miele L, Magnus T, Poosala S, Granger DN, Mattson MP: Gamma secretase-mediated Notch signaling worsens brain damage and functional outcome in ischemic stroke. Nat Med 2006, 12:621-623.
- [39]Yang Q, Yan W, Li X, Hou L, Dong H, Wang Q, Wang S, Zhang X, Xiong L: Activation of canonical notch signaling pathway is involved in the ischemic tolerance induced by sevoflurane preconditioning in mice. Anesthesiology 2012, 117:996-1005.
- [40]Takeshita K, Satoh M, Ii M, Silver M, Limbourg FP, Mukai Y, Rikitake Y, Radtke F, Gridley T, Losordo DW, Liao JK: Critical role of endothelial Notch1 signaling in postnatal angiogenesis. Circ Res 2007, 100:70-78.
- [41]Pei H, Yu Q, Xue Q, Guo Y, Sun L, Hong Z, Han H, Gao E, Qu Y, Tao L: Notch1 cardioprotection in myocardial ischemia/reperfusion involves reduction of oxidative/nitrative stress. Basic Res Cardiol 2013, 108:373.
- [42]Gregory PA, Bert AG, Paterson EL, Barry SC, Tsykin A, Farshid G, Vadas MA, Khew-Goodall Y, Goodall GJ: The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1. Nat Cell Biol 2008, 10:593-601.
- [43]Choi PS, Zakhary L, Choi WY, Caron S, Alvarez-Saavedra E, Miska EA, Mcmanus M, Harfe B, Giraldez AJ, Horvitz HR, Schier AF, Dulac C: Members of the miRNA-200 family regulate olfactory neurogenesis. Neuron 2008, 57:41-55.
- [44]Lee ST, Chu K, Jung KH, Yoon HJ, Jeon D, Kang KM, Park KH, Bae EK, Kim M, Lee SK, Roh JK: MicroRNAs induced during ischemic preconditioning. Stroke 2010, 41:1646-1651.
- [45]Li JS, Yao ZX: MicroRNAs: novel regulators of oligodendrocyte differentiation and potential therapeutic targets in demyelination-related diseases. Mol Neurobiol 2012, 45:200-212.
- [46]Taira N, Nihira K, Yamaguchi T, Miki Y, Yoshida K: DYRK2 is targeted to the nucleus and controls p53 via Ser46 phosphorylation in the apoptotic response to DNA damage. Mol Cell 2007, 25:725-738.
- [47]Hattori R, Maulik N, Otani H, Zhu L, Cordis G, Engelman RM, Siddiqui MA, Das DK: Role of STAT3 in ischemic preconditioning. J Mol Cell Cardiol 2001, 33:1929-1936.
- [48]Bolli R, Dawn B, Xuan YT: Role of the JAK-STAT pathway in protection against myocardial ischemia/reperfusion injury. Trends Cardiovasc Med 2003, 13:72-79.
- [49]Dawn B, Xuan YT, Guo Y, Rezazadeh A, Stein AB, Hunt G, Wu WJ, Tan W, Bolli R: IL-6 plays an obligatory role in late preconditioning via JAK-STAT signaling and upregulation of iNOS and COX-2. Cardiovasc Res 2004, 64:61-71.