Time-dependent variation of pathways and networks in a 24-hour window after cerebral ischemia-reperfusion injury

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• 作者：Li-Ying Wang (1)
  Jun Liu (1)
  Yuan Li (2)
  Bing Li (3)
  Ying-Ying Zhang (1)
  Zhi-Wei Jing (5)
  Ya-Nan Yu (1)
  Hai-Xia Li (4)
  Shan-Shan Guo (6)
  Yi-Jun Zhao (5)
  Zhong Wang (1)
  Yong-Yan Wang (1)
  
  1. Institute of Basic Research in Clinical Medicine ; China Academy of Chinese Medical Sciences ; Dongzhimennei Nanxiaojie 16# ; Beijing ; 100700 ; China
  2. Beijing University of Chinese Medicine ; No. 11 East Road ; North of 3rd Ring Road ; Beijing ; 100029 ; China
  3. Institute of Information on Traditional Chinese Medicine ; China Academy of Chinese Medical Sciences ; Dongzhimennei Nanxiaojie 16# ; Beijing ; 100700 ; China
  5. China Academy of Chinese Medical Sciences ; Dongzhimennei Nanxiaojie 16# ; Beijing ; 100700 ; China
  4. Guang鈥檃nmen Hospital ; China Academy of China Medical Sciences ; No.5 Beixiange ; Beijing ; 100053 ; China
  6. Institute of Chinese Materia Medica ; China Academy of Chinese Medical Sciences ; Dongzhimennei Nanxiaojie 16# ; Beijing ; 100700 ; China
  
• 关键词：Ischemia ; reperfusion injury ; Dynamic variation ; Pathway ; Process network
• 刊名：BMC Systems Biology
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：9
• 期：1
• 全文大小：1,637 KB
• 参考文献：1. Liu, B, Zhang, Q, Zhang, Y, Zhang, JX (2007) Study on the changes of pathology and cell apoptosis in different time point following cerebral ischemic reperfusion in rat. Shanxi Med J 36: pp. 395-7
  2. Nakase, T, Yoshioka, S, Suzuki, A (2011) Free radical scavenger, edaravone, reduces the lesion size of lacunar infarction in human brain ischemic stroke. BMC Neurol 11: pp. 39 CrossRef
  3. Neumann-Haefelin, T, Kastrup, A, Crespigny, A, Yenari, MA, Ringer, T, Sun, GH (2000) Serial MRI after transient focal cerebral ischemia in rats: dynamics of tissue injury, blood鈥揵rain barrier damage, and edema formation. Stroke 31: pp. 1965-72 CrossRef
  4. Reischl, S, Li, L, Walkinshaw, G, Flippin, LA, Marti, HH, Kunze, R (2014) Inhibition of HIF prolyl-4-hydroxylases by FG-4497 reduces brain tissue injury and edema formation during ischemic stroke. PLoS One 9: pp. e84767 CrossRef
  5. Dohmen, C, Kumura, E, Rosner, G, Heiss, WD, Graf, R (2005) Extracellular correlates of glutamate toxicity in short-term cerebral ischemia and reperfusion: a direct in vivo comparison between white and gray matter. Brain Res 1037: pp. 43-51 CrossRef
  6. Harari, OA, Liao, JK (2010) NF-魏B and innate immunity in ischemic stroke. Ann N Y Acad Sci 1207: pp. 32-40 CrossRef
  7. Guo, ZH, Li, F, Wang, WZ (2009) The mechanisms of brain ischemic insult and potential protective interventions. Neurosci Bull 25: pp. 139-52 CrossRef
  8. Vay, L, Hern谩ndez-Sanmiguel, E, Santo-Domingo, J, Lobat贸n, CD, Moreno, A, Montero, M (2007) Modulation of Ca2+ release and Ca2+ oscillations in HeLa cells and fibroblasts by mitochondrial Ca2鈥?鈥塽niporter stimulation. J Physiol 580: pp. 39-49 CrossRef
  9. Lee JC, Kim IH, Cho GS. Ischemic preconditioning-induced neuroprotection against transient cerebral ischemic damage via attenuating ubiquitin aggregation. J Neurol Sci. 2013. doi: 10.1016/j.jns.2013.10.010.
  10. Bao, SY, Shi, XQ, Zhang, ZL (2014) Changes in expression level of aquaporin-4 during cerebral ischemia-reperfusion injury in rats. Cerebrovasc Dis Foreign Med Sci 12: pp. 122-6
  11. Tang, X, Zhong, W, Tu, Q, Ding, B (2014) NADPH oxidase mediates the expression of MMP-9 in cerebral tissue after ischemia reperfusion damage. Neurol Res 36: pp. 118-25 CrossRef
  12. Park, JH, Lee, CH, Kim, IH, Ahn, JH, Cho, JH, Yan, BC (2013) Time-course Changes in Immunoreactivities of Glucokinase and Glucokinase Regulatory Protein in the Gerbil Hippocampus Following Transient Cerebral Ischemia. Neurochem Res 38: pp. 2640-9 CrossRef
  13. Stavchanski沫, VV, Tvorogova, TV, Botsina, AI, Limborskaia, SA, Skvortsova, VI, Miasoedov, NF (2013) The effect of semax and its C-end peptide PGP on Vegfa gene expression in the rat brain during incomplete global ischemia. Mol Biol (Mosk) 47: pp. 461-6 CrossRef
  14. Wang, L, Zhou, C, Wang, Z, Liu, J, Jing, Z, Zhang, Z (2011) Dynamic variation of genes profiles and pathways in the hippocampus of ischemic mice: a genomic study. Brain Res 1372: pp. 13-21 CrossRef
  15. GeneGo MetaCoreTM software. Online References: http://www.genego.com and http://www.genego.com/metacore.php.
  16. Baitaluk, M, Sedova, M, Ray, A, Gupta, A (2006) Biological Networks: visualization and analysis tool for systems biology. Nucleic Acids Res 34(Web Server issue): pp. W466-71 CrossRef
  17. Leeuwen, DM, Pedersen, M, Knudsen, LE, Bonassi, S, Fenech, M, Kleinjans, JC (2011) Transcriptomic network analysis of micronuclei-related genes: a case study. Mutagenesis 26: pp. 27-32 CrossRef
  18. Hara, H, Huang, PL, Panahian, N, Fishman, MC, Moskowitz, MA (1996) Reduced brain edema and infarction volume in mice lacking the neuronal isoform of nitric oxide synthase after transient MCA occlusion. J Cereb Blood Flow Metab 16: pp. 605-11 CrossRef
  19. Chen, YH, Chen, CJ, Yeh, S, Lin, YN, Wu, YC, Hsieh, WT (2014) Urethral Dysfunction in Female Mice with Estrogen Receptor 尾 Deficiency. PLoS One 9: pp. e109058 CrossRef
  20. Liu, Y, Zhang, GY, Hou, XY, Xu, TL (2003) Two types of calcium channels regulating activation of proline-rich tyrosine kinase 2 induced by transient brain ischemia in rat hippocampus. Neurosci Lett 348: pp. 127-30 CrossRef
  21. Tang H, Pan CS, Mao XW, Liu YY, Yan L, Zhou CM, et al. Role of NADPH Oxidase in Total Salvianolic Acid Injection Attenuating Ischemia-Reperfusion Impaired Cerebral Microcirculation and Neurons: Implication of AMPK/Akt/PKC. Microcirculation. 2014. doi: 10.1111/micc.12140. [Epub ahead of print].
  22. MacManus, JP, Koch, CJ, Jian, M, Walker, T, Zurakowski, B (1999) Decreased brain infarct following focal ischemia in mice lacking the transcription factor E2F1. Neuroreport 10: pp. 2711-4 CrossRef
  23. Medvedeva, EV, Dmitrieva, VG, Povarova, OV, Limborska, SA, Skvortsova, VI, Myasoedov, NF (2013) Effect of semax and its C-terminal fragment Pro-Gly-Pro on the expression of VEGF family genes and their receptors in experimental focal ischemia of the rat brain. J Mol Neurosci 49: pp. 328-33 CrossRef
  24. Zhang, Q, Chen, C, L眉, J, Xie, M, Pan, D, Luo, X (2009) Cell cycle inhibition attenuates microglial proliferation and production of IL-1beta, MIP-1alpha, and NO after focal cerebral ischemia in the rat. Glia 57: pp. 908-20 CrossRef
  25. Zhu, Y, Jin, K, Mao, XO, Greenberg, DA (2003) Vascular endothelial growth factor promotes proliferation of cortical neuron precursors by regulating E2F expression. FASEB J 17: pp. 186-93 CrossRef
  26. Jiang, SX, Slinn, J, Aylsworth, A, Hou, ST (2012) Vimentin participates in microglia activation and neurotoxicity in cerebral ischemia. J Neurochem 122: pp. 764-74 CrossRef
  27. Boyce, RL, Ellison, PC (2001) Choosing the best similarity index when performing fuzzy set ordination on binary data. J Veg Sci 12: pp. 711-20 CrossRef
  28. Deng, C, Luan, F, Cruz-Monteagudo, M, Borges, F, Cordeiro, MN (2013) Recent advances on QSAR-based profiling of agonist and antagonist A3 adenosine receptor ligands. Curr Top Med Chem 13: pp. 1048-68 CrossRef
  29. Pham N, Dhar A, Khalaj S, Desai K, Taghibiglou C. Down regulation of brain cellular prion protein in an animal model of insulin resistance: Possible implication in increased prevalence of stroke in pre-diabetics/diabetics. Biochem Biophys Res Commun. 2014. [Epub ahead of print].
  30. Hu, H, Li, Z, Zhu, X, Lin, R, Peng, J, Tao, J (2013) GuaLou GuiZhi decoction inhibits LPS-induced microglial cell motility through the MAPK signaling pathway. Int J Mol Med 32: pp. 1281-6
  31. Wang, J, Li, PT, Du, H, Hou, JC, Li, WH, Pan, YS (2011) Impact of paracrine signals from brain microvascular endothelial cells on microglial proliferation and migration. Brain Res Bull 86: pp. 53-9 CrossRef
  32. Henshall, DC, Engel, T (2013) Contribution of apoptosis-associated signaling pathways to epileptogenesis: lessons from Bcl-2 family knockouts. Front Cell Neurosci 7: pp. 110
  33. Yin, XH, Yan, JZ, Hou, XY, Wu, SL, Zhang, GY (2013) Neuroprotection of S-nitrosoglutathione against ischemic injury by down-regulating Fas S-nitrosylation and downstream signaling. Neuroscience 248C: pp. 290-8 CrossRef
  34. Zhang, Y, Li, YW, Wang, YX, Zhang, HT, Zhang, XM, Liang, Y (2013) Remifentanil preconditioning alleviating brain damage of cerebral ischemia reperfusion rats by regulating the JNK signal pathway and TNF-伪/TNFR1 signal pathway. Mol Biol Rep 40: pp. 6997-7006 CrossRef
  35. Choi, IY, Ju, C, Anthony Jalin, AM, Lee, I, Prather, PL, Kim, WK (2013) Activation of cannabinoid CB2 receptor-mediated AMPK/CREB pathway reduces cerebral ischemic injury. Am J Pathol 182: pp. 928-39 CrossRef
  36. Chu, LF, Wang, WT, Ghanta, VK, Lin, CH, Chiang, YY, Hsueh, CM (2008) Ischemic brain cell-derived conditioned medium protects astrocytes against ischemia through GDNF/ERK/NF-kB signaling pathway. Brain Res 1239: pp. 24-35 CrossRef
  37. Pyne-Geithman, GJ, Nair, SG, Stamper, DN, Clark, JF (2013) Role of bilirubin oxidation products in the pathophysiology of DIND following SAH. Acta Neurochir Suppl 115: pp. 267-73
  38. Kim, YR, Kim, HN, Ahn, SM, Choi, YH, Shin, HK, Choi, BT (2014) Electroacupuncture promotes post-stroke functional recovery via enhancing endogenous neurogenesis in mouse focal cerebral ischemia. PLoS One 9: pp. e90000 CrossRef
  39. White, BC, Sullivan, JM, DeGracia, DJ, O鈥橬eil, BJ, Neumar, RW, Grossman, LI (2000) Brain ischemia and reperfusion: molecular mechanisms of neuronal injury. J Neurol Sci 179: pp. 1-33 CrossRef
  40. Chen, C, Wang, W, Xie, MJ, Zhu, Z, Liu, JY, Yu, YF (2005) Effect of cell cycle regulation on delayed neuronal death in rat hippocampus after global ischemia. J Histochem Cytochem 14: pp. 1-6
  41. Chen, ZB, Zou, F, Yuan, F (2005) Alterations in Protein expression of NMDA receptor subunits NRZA and NRZB during reperfusion after ischemia in the rat brain. J Apoplexy Nervous Dis 22: pp. 326-8
  42. Deng, X, Zhong, Y, Gu, L, Shen, W, Guo, J (2013) MiR-21 involve in ERK-mediated upregulation of MMP9 in the rat hippocampus following cerebral ischemia. Brain Res Bull 94: pp. 56-62 CrossRef
  43. Hasan, R, Chauhan, SS, Sharma, R, Ralhan, R (2012) siRNA-mediated downregulation of TC21 sensitizes esophageal cancer cells to cisplatin. World J Gastroenterol 18: pp. 4127-35 CrossRef
  44. Chen, HZ, Chen, WM (2007) Expression of genes Bim and JNK signaling transduction pathway in rat brain following cerebral ischemia. China J Mod Med 17: pp. 809-12
  45. Hu, JP, Li, J, Gao, L (2004) Effect of Qi-invigorating and blood-activating therapy on Fas and FasL protein expression in rats with Qi-deficiency and blood stasis syndrome following local cerebral ischemia reperfusion injury. J Anhui TCM Coll 23: pp. 35-7
  46. Wu, XW, Yang, H, Wu, L, Xue, RL (2010) Study on relationship between expression of ERK and cell apoptosis. Nei Mongol J Tradition Chinese Med 15: pp. 103-4
  47. Zhang, YL, Liu, C, Liu, XM, Zheng, H, Tao, Y, Huang, QF (2010) Effect on expression of VEGF and VEGFR2 mRNA of Xinnaoshutong Capsule in rat following focal cerebral ischemia reperfusion. Chin J Pathophysiol 26: pp. 587-9
  48. Wang, YQ, Li, J, Cao, H, Li, GM, Zeng, YM (2006) The expression and role of ERK and JNK in cerebral ischemic preconditioning in gerbil. Chinese Pharmacol Bull 22: pp. 337-40
  49. Wang, N, Wu, L, Cao, Y, Wang, Y, Zhang, Y (2013) The protective activity of imperatorin in cultured neural cells exposed to hypoxia re-oxygenation injury via anti-apoptosis. Fitoterapia 90: pp. 38-43 CrossRef
  50. Santana-Codina, N, Carretero, R, Sanz-Pamplona, R, Cabrera, T, Guney, E, Oliva, B (2013) A transcriptome-proteome integrated network identifies endoplasmic reticulum thiol oxidoreductase (ERp57) as a hub that mediates bone metastasis. Mol Cell Proteomics 12: pp. 2111-25 CrossRef
  51. Luo, T, Wu, S, Shen, X, Li, L (2013) Network cluster analysis of protein-protein interaction network identified biomarker for early onset colorectal cancer. Mol Biol Rep 40: pp. 6561-8 CrossRef
  52. Zhou, Y, Xu, J, Liu, Y, Li, J, Chang, C, Xu, C (2014) Rat hepatocytes weighted gene co-expression network analysis identifies specific modules and hub genes related to liver regeneration after partial hepatectomy. PLoS One 9: pp. e94868 CrossRef
  53. Wasserman, S, Faust, K (1994) Social networks analysis:methods and applications[M]. Cambridge University Press, Cambridge CrossRef
  54. Freeman, LC (1979) Centrality in social networks:L Conceptual clarifieation[J]. Soc Networks 1: pp. 215-39 CrossRef
  55. Yang, K, Lei, G, Jackson, MF, Macdonald, JF (2010) The involvement of PACAP/VIP system in the synaptic transmission in the hippocampus. J Mol Neurosci 42: pp. 319-26 CrossRef
  56. Liu, X, Hunter, C, Chi, OZ (2010) Effects of blockade of ionotropic glutamate receptors on blood brain barrier disruption in focal cerebral ischemia. Neurol Sci 31: pp. 699 CrossRef
  57. Honda, H, Inaba, T, Suzuki, T, Oda, H, Ebihara, Y, Tsuiji, K (1999) Expression of E2A-HLF chimeric protein induced T-cell apoptosis, B-cell maturation arrest, and development of acute lymphoblastic leukemia. Blood 93: pp. 2780-90
  58. Alpern, D, Langer, D, Ballester, B, Gras, S, Romier, C, Mengus, G (2014) TAF4, a subunit of transcription factor II D, directs promoter occupancy of nuclear receptor HNF4A during post-natal hepatocyte differentiation. Elife 10: pp. 3
  59. Sun, L, Chen, C, Jiang, B, Li, Y, Deng, Q, Sun, M (2014) Grb2-associated binder 1 is essential for cardioprotection against ischemia/reperfusion injury. Basic Res Cardiol 109: pp. 420 CrossRef
  
• 刊物主题：Bioinformatics; Systems Biology; Simulation and Modeling; Computational Biology/Bioinformatics; Physiological, Cellular and Medical Topics; Algorithms;
• 出版者：BioMed Central
• ISSN：1752-0509

文摘

Background Cerebral ischemia-reperfusion injury may simultaneously result in functional variation of multiple genes/pathways. However, most prior time-sequence studies on its pathomechanism only focused on a single gene or pathway. Our study aimed to systematically analyze the time-dependent variation in the expression of multiple pathways and networks within 24 h after cerebral ischemia-reperfusion injury. Results By uploading 374 ischemia-related genes into the MetaCore software, the variation in the expression of multiple pathways and networks in 3 h, 12 h, and 24 h after cerebral ischemia-reperfusion injury had been analyzed. The conserved TNFR1-signaling pathway, among the top 10 pathways, was consistently enriched in 3 h, 12 h, and 24 h groups. Three overlapping pathways were found between 3 h and 12 h groups; 2 between 12 h and 24 h groups; and 1 between 3 h and 24 h groups. Five, 4, and 6 non-overlapping pathways were observed in 3 h, 12 h, and 24 h groups, respectively. Apart from pathways reported by earlier studies, we identified a novel pathway related to the time-dependent development of cerebral ischemia pathogenesis. The process of apoptosis stimulation by external signals, among the top 10 processes, was consistently enriched in 3 h, 12 h, and 24 h groups; 2, 1, and 2 processes overlapped between 3 h and 12 h groups, 12 h and 24 h groups, and 3 h and 24 h groups, respectively. Four, 5, and 5 non-overlapping processes were found in 3 h, 12 h and 24 h groups, respectively. The presence of apoptotic processes was observed in all the 3 groups; while anti-apoptotic processes only existed in 3 h and 12 h groups. Additionally, according to node degree, network comparison identified 1, 8,and 5 important genes or proteins (e.g. Pyk2, PKC, E2F1, and VEGF-A) in 3 h, 12 h, and 24 h groups, respectively. The Jaccard similarity index revealed a higher level of similarity between 12 h and 24 h groups than that between 3 h and 12 h groups. Conclusion Time-dependent treatment can be utilized to reduce apoptosis, which may activate anti-apoptotic pathways within 12 h after cerebral ischemia-reperfusion injury. Pathway and network analyses may help identify novel pathways and genes implicated in disease pathogenesis.