Network analysis of human glaucomatous optic nerve head astrocytes

BMC Medical Genomics

Volumn 2, Issue , 2009, Pages

  Nikolskaya, Tatiana ^a   Nikolsky, Yuri ^b   Serebryiskaya, Tatiana ^a   Zvereva, Svetlana ^a   Sviridov, Eugene ^a   Dezso, Zoltan ^b   Rahkmatulin, Eugene ^b   Brennan, Richard J ^b   Yankovsky, Nick ^a   Bhattacharya, Sanjoy K ^c   Agapova, Olga ^d   Hernandez, M Rosario ^e   Shestopalov, Valery I ^c  

^a VAVILOV INSTITUTE OF GENERAL GENETICS   (Russian Federation)

^b GeneGo bioinformatics software Inc   (United States)

^c UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^d WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERIN; COMPLEMENT; CYTOKINE; EPHRIN; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AP 1; VITAMIN D RECEPTOR;

AGED; ARTICLE; ASTROCYTE; CADAVER; CELL ACTIVATION; CELL METABOLISM; CELL STIMULATION; CONTROLLED STUDY; FUNCTIONAL PROTEOMICS; GENE EXPRESSION; GENE FUNCTION; GENETIC ANALYSIS; GENETIC EPISTASIS; GLAUCOMA; HUMAN; HUMAN CELL; MOLECULAR INTERACTION; NEUROTOXICITY; OPTIC NERVE; PATHOLOGY; PRIORITY JOURNAL; REGULATORY DNA SEQUENCE; SIGNAL TRANSDUCTION;

EID: 68049149097     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-2-24     Document Type: Article

References (103)

1. The optic nerve head in glaucomatous optic neuropathy. MR Hernandez JD Pena, Arch Ophthalmol 1997 115 389 395 9076213
2. Astrocyte influences on ischemic neuronal death. RA Swanson W Ying TM Kauppinen, Curr Mol Med 2004 4 193 205 15032713
3. Astrocyte responses in human optic nerve head with primary open-angle glaucoma. HJ Varela MR Hernandez, J Glaucoma 1997 6 303 313 9327349
4. Reactive astrocytes in neural repair and protection. MV Sofroniew, Neuroscientist 2005 11 400 407 16151042
5. Long-term activation of c-Fos and c-Jun in optic nerve head astrocytes in experimental ocular hypertension in monkeys and after exposure to elevated pressure in vitro. K Hashimoto A Parker P Malone BT Gabelt C Rasmussen PS Kaufman MR Hernandez, Brain Res 2005 1054 103 115 16081055
6. Expression of nitric oxide synthase-2 (NOS-2) in reactive astrocytes of the human glaucomatous optic nerve head. B Liu AH Neufeld, Glia 2000 30 178 186 10719359
7. Neuronal death in glaucoma. HA Quigley, Prog Retin Eye Res 1999 18 39 57 9920498
8. Genetics, statistics and human disease: analytical retooling for complexity. TA Thornton-Wells JH Moore JL Haines, Trends Genet 2004 20 640 647 15522460
9. A literature network of human genes for high-throughput analysis of gene expression. TK Jenssen A Laegreid J Komorowski E Hovog, Nature Genetics 2001 28 21 28 11326270
10. Biological networks and analysis of experimental data in drug discovery. Y Nikolsky T Nikolskaya A Bugrim, Drug Discov Today 2005 10 653 662 15894230
11. Modeling cellular machinery through biological network comparison. R Sharan T Ideker, Nat Biotechnol 2006 24 427 433 16601728
12. Network biology: understanding the cell's functional organization. A-L Barabasi ZN Oltvai, Nature Reviews Genetics 2004 5 101 113 14735121
13. The large-scale organization of metabolic networks. H Jeong B Tombor R Albert ZN Oltvai AL Barabasi, Nature 2000 407 651 654 11034217
14. Hierarchical organization of modularity in metabolic networks. E Ravasz AL Somera DA Mongru ZN Oltvai AL Barabasi, Science 2002 297 1551 1555 12202830
15. Network motifs: simple building blocks of complex networks. R Milo S Shen-Orr S Itzkovitz N Kashtan D Chklovskii U Alon, Science 2002 298 824 827 12399590
16. Disease genes and intracellular protein networks. S Bortoluzzi C Romualdi A Bisognin GA Danieli, Physiol Genomics 2003 15 223 227 12966136
17. Computational systems biology. H Kitano, Nature 2002 420 206 210 12432404
18. Reverse engineering of biological complexity. ME Csete JC Doyle, Science 2002 295 1664 1669 11872830
19. Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms. S Ekins A Bugrim L Brovold E Kirillov Y Nikolsky E Rakhmatulin S Sorokina A Ryabov T Serebryiskaya A Melnikov, Xenobiotica 2006 36 877 901 17118913
20. A novel method for visualizing nuclear hormone receptor networks relevant to drug metabolism. S Ekins E Kirillov EA Rakhmatulin T Nikolskaya, Drug Metab Dispos 2005 33 474 481 15608136
21. Cytoscape: a software environment for integrated models of biomolecular interaction networks. P Shannon A Markiel O Ozier NS Baliga JT Wang D Ramage N Amin B Schwikowski T Ideker, Genome Res 2003 13 2498 2504 14597658
22. Differential gene expression in astrocytes from human normal and glaucomatous optic nerve head analyzed by cDNA microarray. MR Hernandez OA Agapova P Yang M Salvador-Silva CS Ricard S Aoi, Glia 2002 38 45 64 11921203
23. Expression of neural cell adhesion molecule (NCAM) characterizes a subpopulation of type 1 astrocytes in human optic nerve head. S Kobayashi I Vidal JD Pena MR Hernandez, Glia 1997 20 262 273 9215735
24. Gene expression profiling reveals the profound upregulation of hypoxia-responsive genes in primary human astrocytes. SM Mense A Sengupta M Zhou C Lan G Bentsman DJ Volsky L Zhang, Physiol Genomics 2006 25 435 449 16507782
25. Differential expression profile prioritization of positional candidate glaucoma genes: the GLC1C locus. FW Rozsa KM Scott H Pawar JR Samples MK Wirtz JE Richards, Arch Ophthalmol 2007 125 117 127 17210862
26. Glial responses, clusterin, and complement in permanent focal cerebral ischemia in the mouse. J Van Beek P Chan M Bernaudin E Petit ET MacKenzie M Fontaine, Glia 2000 31 39 50 10816605
27. Defined inflammatory states in astrocyte cultures: correlation with susceptibility towards CD95-driven apoptosis. J Falsig M Latta M Leist, J Neurochem 2004 88 181 193 14675162
28. Reactive astrocytes: cellular and molecular cues to biological function. JL Ridet SK Malhotra A Privat FH Gage, Trends Neurosci 1997 20 570 577 9416670
29. Astrocytes in injured adult rat spinal cord may acquire the potential of neural stem cells. B Lang HL Liu R Liu GD Feng XY Jiao G Ju, Neuroscience 2004 128 775 783 15464285
30. Axonal regeneration and lack of astrocytic gliosis in EphA4-deficient mice. Y Goldshmit MP Galea G Wise PF Bartlett AM Turnley, J Neurosci 2004 24 10064 10073 15537875
31. Ephrin A receptors and ligands in lesions and normal-appearing white matter in multiple sclerosis. RA Sobel, Brain Pathol 2005 15 35 45 15779235
32. Myelin-, reactive glia-, and scar-derived CNS axon growth inhibitors: expression, receptor signaling, and correlation with axon regeneration. A Sandvig M Berry LB Barrett A Butt A Logan, Glia 2004 46 225 251 15048847
33. Interleukin-6 protects retinal ganglion cells from pressure-induced death. RM Sappington M Chan DJ Calkins, Invest Ophthalmol Vis Sci 2006 47 2932 2942 16799036
34. Expression of ephrinB1 and its receptor in glaucomatous optic neuropathy. JF Schmidt OA Agapova P Yang PL Kaufman MR Hernandez, Br J Ophthalmol 2007 91 1219 1224 17301119
35. Cholesterol deficiency increases the vulnerability of hippocampal glia in primary culture to glutamate-induced excitotoxicity. YC Chou SB Lin LH Tsai HI Tsai CM Lin, Neurochem Int 2003 43 197 209 12689600
36. Global changes in optic nerve head gene expression after exposure to elevated intraocular pressure in a rat glaucoma model. EC Johnson L Jia WO Cepurna TA Doser JC Morrison, Invest Ophthalmol Vis Sci 2007 48 3161 3177 17591886
37. Factors contributing to neuronal degeneration in retinas of experimental glaucomatous rats. X Wang YK Ng SS Tay, J Neurosci Res 2005 82 674 689 16273539
38. The transcription factor c-jun is activated in retinal ganglion cells in experimental rat glaucoma. H Levkovitch-Verbin HA Quigley KR Martin N Harizman DF Valenta ME Pease S Melamed, Exp Eye Res 2005 80 663 670 15862173
39. Androgen receptor and NFkB expression in human normal and glaucomatous optic nerve head astrocytes in vitro and in experimental glaucoma. OA Agapova PL Kaufman MR Hernandez, Exp Eye Res 2006 82 1053 1059 16310187
40. Microarray analysis of changes in mRNA levels in the rat retina after experimental elevation of intraocular pressure. F Ahmed KM Brown DA Stephan JC Morrison EC Johnson SI Tomarev, Invest Ophthalmol Vis Sci 2004 45 1247 1258 15037594
41. Microarray analysis of retinal gene expression in the DBA/2J model of glaucoma. MR Steele DM Inman DJ Calkins PJ Horner ML Vetter, Invest Ophthalmol Vis Sci 2006 47 977 985 16505032
42. Retinal synthesis and deposition of complement components induced by ocular hypertension. MH Kuehn CY Kim J Ostojic M Bellin WL Alward EM Stone DS Sakaguchi SD Grozdanic YH Kwon, Exp Eye Res 2006 83 620 628 16677633
43. Altered expression of 3 alpha-hydroxysteroid dehydrogenases in human glaucomatous optic nerve head astrocytes. OA Agapova P Yang WH Wang DA Lane AF Clark BI Weinstein MR Hernandez, Neurobiol Dis 2003 14 63 73 13678667
44. Expression of EphrinB1 and its Receptor in Glaucomatous Optic Neuropathy. J Schmidt OA Agapova P Yang PL Kaufman MR Hernandez, Br J Ophthalmol 2007 91 9 1219 1224 17301119
45. The inflammatory transcriptome of reactive murine astrocytes and implications for their innate immune function. J Falsig P Porzgen S Lund A Schrattenholz M Leist, J Neurochem 2006 96 893 907 16405499
46. DNA microarray analysis of gene expression in human optic nerve head astrocytes in response to hydrostatic pressure. P Yang O Agapova A Parker W Shannon P Pecen J Duncan M Salvador-Silva MR Hernandez, Physiol Genomics 2004 17 157 169 14747662 (Pubitemid 38924162)
47. Epidermal growth factor receptor activation: an upstream signal for transition of quiescent astrocytes into reactive astrocytes after neural injury. B Liu H Chen TG Johns AH Neufeld, J Neurosci 2006 26 7532 7540 16837601
48. The optic nerve head in glaucoma: role of astrocytes in tissue remodeling. MR Hernandez, Prog Retin Eye Res 2000 19 297 321 10749379
49. Protein kinase C-zeta mediates retinal degeneration in response to TNF. H Liang C Baudouin F Behar-Cohen P Crisanti B Omri, J Neuroimmunol 2007 183 104 110 17207538
50. Transforming growth factor-beta-regulated gene transcription and protein expression in human GFAP-negative lamina cribrosa cells. RP Kirwan MO Leonard M Murphy AF Clark CJ O'Brien, Glia 2005 52 309 324 16078232
51. TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. H Yu X Zhu D Greenbaum J Karro M Gerstein, Nucleic Acids Res 2004 32 328 337 14724320
52. Topology of gene expression networks as revealed by data mining and modeling. AV Lukashin ME Lukashev R Fuchs, Bioinformatics 2003 19 1909 1916 14555623
53. MetaCore: An Integrated Software Platform and Statistical Evaluation Method for Network Analysis and Mapping of Human High Throughput Data. E Kirillov, Appl Bioinform 2006
54. Sp1 and NFkappaB pathways are regulated in brain in response to acute and chronic ethanol. SL Rulten TL Ripley CL Hunt DN Stephens LV Mayne, Genes Brain Behav 2006 5 257 273 16594979
55. New clues about vitamin D functions in the nervous system. E Garcion N Wion-Barbot CN Montero-Menei F Berger D Wion, Trends Endocrinol Metab 2002 13 100 105 11893522
56. Vitamin D receptor expression in human brain tumors. L Magrassi F Bono G Milanesi G Butti, J Neurosurg Sci 1992 36 27 30 1323646
57. Vitamin D is a membrane antioxidant. Ability to inhibit iron-dependent lipid peroxidation in liposomes compared to cholesterol, ergosterol and tamoxifen and relevance to anticancer action. H Wiseman, FEBS Lett 1993 326 285 288 8325381
58. AP-1 as a regulator of cell life and death. E Shaulian M Karin, Nat Cell Biol 2002 4 E131 136 11988758
59. Different Toll-like receptor agonists induce distinct macrophage responses. BW Jones TK Means KA Heldwein MA Keen PJ Hill JT Belisle MJ Fenton, J Leukoc Biol 2001 69 1036 1044 11404392
60. TLR signaling. T Kawai S Akira, Cell Death Differ 2006 13 816 825 16410796
61. Toll-like receptors; their physiological role and signal transduction system. O Takeuchi S Akira, Int Immunopharmacol 2001 1 625 635 11357875
62. The cytokine IL-1beta activates IFN response factor 3 in human fetal astrocytes in culture. MA Rivieccio GR John X Song HS Suh Y Zhao SC Lee CF Brosnan, J Immunol 2005 174 3719 3726 15749911
63. Astrocyte protection of neurons: role of transforming growth factor-beta signaling via a c-Jun-AP-1 protective pathway. KM Dhandapani M Hadman L De Sevilla MF Wade VB Mahesh DW Brann, J Biol Chem 2003 278 43329 43339 12888549
64. The genomic landscapes of human breast and colorectal cancers. LD Wood DW Parsons S Jones J Lin T Sjoblom RJ Leary D Shen SM Boca T Barber J Ptak, Science 2007 318 1108 1113 17932254
65. NF-kappaB and TNF-alpha stimulate androgen receptor expression in Sertoli cells. FJ Delfino JN Boustead C Fix WH Walker, Mol Cell Endocrinol 2003 201 1 12 12706288
66. Androgenic regulation of oxidative stress in the rat prostate: involvement of NAD(P)H oxidases and antioxidant defense machinery during prostatic involution and regrowth. NN Tam Y Gao YK Leung SM Ho, Am J Pathol 2003 163 2513 2522 14633623
67. Immunohistochemical study on superoxide dismutases in spinal cords from autopsied patients with amyotrophic lateral sclerosis. N Shibata K Asayama A Hirano M Kobayashi, Dev Neurosci 1996 18 492 498 8940623
68. A neuroactive steroid 5alpha-androstane-3alpha,17beta-diol regulates androgen receptor level in astrocytes. OA Agapova PE Malone MR Hernandez, J Neurochem 2006 98 355 363 16638015
69. 4-Hydroxynonenal, a product of oxidative stress, leads to an antioxidant response in optic nerve head astrocytes. PE Malone MR Hernandez, Exp Eye Res 2007 84 444 454 17173895
70. Parathyroid hormone-related protein (PTHrP) induction in reactive astrocytes following brain injury: a possible mediator of CNS inflammation. JL Funk CR Trout H Wei G Stafford S Reichlin, Brain Res 2001 915 195 209 11595209
71. Complement activation contributes to hypoxic-ischemic brain injury in neonatal rats. RM Cowell JM Plane FS Silverstein, J Neurosci 2003 23 9459 9468 14561876
72. Delayed, but prolonged increases in astrocytic clusterin (ApoJ) mRNA expression following acute cortical spreading depression in the rat: evidence for a role of clusterin in ischemic tolerance. AK Wiggins PJ Shen AL Gundlach, Brain Res Mol Brain Res 2003 114 20 30 12782389
73. Complement factor H polymorphism and age-related macular degeneration. AO Edwards R Ritter 3rd KJ Abel A Manning C Panhuysen LA Farrer, Science 2005 308 421 424 15761121
74. Complement and clusterin in the injured nervous system. E Tornqvist L Liu H Aldskogius HV Holst M Svensson, Neurobiol Aging 1996 17 695 705 8892342
75. Clusterin deficiency in eyes with pseudoexfoliation syndrome may be implicated in the aggregation and deposition of pseudoexfoliative material. M Zenkel FE Kruse AG Junemann GO Naumann U Schlotzer-Schrehardt, Invest Ophthalmol Vis Sci 2006 47 1982 1990 16639006
76. Apolipoprotein J (clusterin) activates rodent microglia in vivo and in vitro. Z Xie ME Harris-White PA Wals SA Frautschy CE Finch TE Morgan, J Neurochem 2005 93 1038 1046 15857407
77. Clusterin contributes to caspase-3-independent brain injury following neonatal hypoxia-ischemia. BH Han RB DeMattos LL Dugan JS Kim-Han RP Brendza JD Fryer M Kierson J Cirrito K Quick JA Harmony, Nat Med 2001 7 338 343 11231633
78. Role of STAT-1 and STAT-3 in ischaemia/reperfusion injury. A Stephanou, J Cell Mol Med 2004 8 519 525 15601580
79. STAT proteins: from normal control of cellular events to tumorigenesis. V Calo M Migliavacca V Bazan M Macaluso M Buscemi N Gebbia A Russo, J Cell Physiol 2003 197 157 168 14502555
80. Double-stranded RNA-activated protein kinase is required for the LPS-induced activation of STAT1 inflammatory signaling in rat brain glial cells. JH Lee EJ Park OS Kim HY Kim EH Joe I Jou, Glia 2005 50 66 79 15630703
81. Proteomics implicates peptidyl arginine deiminase 2 and optic nerve citrullination in glaucoma pathogenesis. SK Bhattacharya JS Crabb VL Bonilha X Gu H Takahara JW Crabb, Invest Ophthalmol Vis Sci 2006 47 2508 2514 16723463
82. Pathway mapping tools for analysis of high content data. SNY Ekins A Bugrim E Kirillov T Nikolskaya, High Content Screening Handbook Humana Press 2007 356 319 350 [Methods Mol. Biol.]
83. Complement component 1Q (C1Q) upregulation in retina of murine, primate, and human glaucomatous eyes. K Stasi D Nagel X Yang RF Wang L Ren SM Podos T Mittag J Danias, Invest Ophthalmol Vis Sci 2006 47 1024 1029 16505037
84. Proteomic identification of oxidatively modified retinal proteins in a chronic pressure-induced rat model of glaucoma. G Tezel X Yang J Cai, Invest Ophthalmol Vis Sci 2005 46 3177 3187 16123417
85. Expression and activities of aldo-keto oxidoreductases in Alzheimer disease. MJ Picklo SJ Olson WR Markesbery TJ Montine, J Neuropathol Exp Neurol 2001 60 686 695 11444797
86. Neuroprotective effects of lipoxygenase inhibitors against ischemic injury in rat hippocampal slice cultures. K Arai N Nishiyama N Matsuki Y Ikegaya, Brain Res 2001 904 167 172 11516426
87. Phospholipase A2 in astrocytes: responses to oxidative stress, inflammation, and G protein-coupled receptor agonists. GY Sun J Xu MD Jensen S Yu WG Wood FA Gonzalez A Simonyi AY Sun GA Weisman, Mol Neurobiol 2005 31 27 41 15953810
88. IKK mediates ischemia-induced neuronal death. O Herrmann B Baumann R de Lorenzi S Muhammad W Zhang J Kleesiek M Malfertheiner M Kohrmann I Potrovita I Maegele, Nat Med 2005 11 1322 1329 16286924
89. Nuclear factor-kappa B p65 in NMDA-induced retinal neurotoxicity. Y Kitaoka T Kumai Y Kitaoka TT Lam Y Munemasa K Isenoumi M Motoki K Kuribayashi J Kogo S Kobayashi S Ueno, Brain Res Mol Brain Res 2004 131 8 16 15530647
90. Inhibition of IkappaBalpha phosphorylation prevents glutamate-induced NF-kappaB activation and neuronal cell death. M Pizzi I Sarnico F Boroni A Benetti M Benarese PF Spano, Acta Neurochir Suppl 2005 93 59 63 15986728
91. NF-kappaB is activated and promotes cell death in focal cerebral ischemia. A Schneider A Martin-Villalba F Weih J Vogel T Wirth M Schwaninger, Nat Med 1999 5 554 559 10229233
92. Regulation of neuronal survival and death by extracellular signals during development. AM Davies, Embo J 2003 22 2537 2545 12773370
93. Complement factor B gene regulation: synergistic effects of TNF-alpha and IFN-gamma in macrophages. Y Huang PM Krein DA Muruve BW Winston, J Immunol 2002 169 2627 2635 12193734
94. Interleukin-4 and interleukin-10 modulate nuclear factor kappaB activity and nitric oxide synthase-2 expression in Theiler's virus-infected brain astrocytes. E Molina-Holgado A Arevalo-Martin A Castrillo L Bosca JM Vela C Guaza, J Neurochem 2002 81 1242 1252 12068072
95. Failure to activate NF-kappaB promotes apoptosis of retinal ganglion cells following optic nerve transection. JS Choi JA Kim DH Kim MH Chun BJ Gwag SK Yoon CK Joo, Brain Res 2000 883 60 68 11063988
96. Development of spontaneous optic neuropathy in NF-kappaBetap50-deficient mice: requirement for NF-kappaBetap50 in ganglion cell survival. Y Takahashi N Katai T Murata SI Taniguchi T Hayashi, Neuropathol Appl Neurobiol 2007 33 692 705 17931357
97. Modular epistasis in yeast metabolism. D Segre A Deluna GM Church R Kishony, Nat Genet 2005 37 77 83 15592468
98. Purification and characterization of astrocyte precursor cells in the developing rat optic nerve. H Mi BA Barres, J Neurosci 1999 19 1049 1061 9920668
99. Purification of astrocytes from adult human optic nerve heads by immunopanning. P Yang MR Hernandez, Brain Res Brain Res Protoc 2003 12 67 76 14613807
100. Elastosis of the lamina cribrosa in glaucomatous optic neuropathy. JD Pena PA Netland I Vidal DA Dorr A Rasky MR Hernandez, Exp Eye Res 1998 67 517 524 9878213
101. Histomorphometric analysis of optic nerve changes in experimental glaucoma. YH Yucel MW Kalichman AP Mizisin HC Powell RN Weinreb, J Glaucoma 1999 8 38 45 10084273
102. Techniques: application of systems biology to absorption, distribution, metabolism, excretion and toxicity. S Ekins Y Nikolsky T Nikolskaya, Trends Pharmacol Sci 2005 26 202 209 15808345
103. A novel method for generation of signature networks as biomarkers from complex high throughput data. Y Nikolsky S Ekins T Nikolskaya A Bugrim, Toxicol Lett 2005 158 20 29 15871913