Exploring metabolic pathway disruption in the subchronic phencyclidine model of schizophrenia with the Generalized Singular Value Decomposition

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Xiao, Xiaolin ^a   Dawson, Neil ^a,b   MacIntyre, Lynsey ^a   Morris, Brian J ^b,c   Pratt, Judith A ^a,b   Watson, David G ^a   Higham, Desmond J ^a  

^a UNIVERSITY OF STRATHCLYDE   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c UNIVERSITY OF GLASGOW   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; RATTUS;

GLUTAMIC ACID; LIGAND; PHENCYCLIDINE;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; CLUSTER ANALYSIS; COGNITION; COMPUTER PROGRAM; DISEASE MODEL; GENE EXPRESSION REGULATION; GENOME; HUMAN; METABOLISM; METHODOLOGY; PRINCIPAL COMPONENT ANALYSIS; RAT; SCHIZOPHRENIA; STATISTICAL MODEL; SYSTEMS BIOLOGY;

ALGORITHMS; ANIMALS; CLUSTER ANALYSIS; COGNITION; DISEASE MODELS, ANIMAL; GENE EXPRESSION REGULATION; GENOME; GLUTAMIC ACID; HUMANS; LIGANDS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; PHENCYCLIDINE; PRINCIPAL COMPONENT ANALYSIS; RATS; SCHIZOPHRENIA; SOFTWARE; SYSTEMS BIOLOGY;

EID: 79955916792     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-72     Document Type: Article

References (75)

1. Davidson LL, Heinrichs RW. Quantification of frontal and temporal lobe brain-imaging findings in schizophrenia: a meta-analysis. Psychiatry Research: Neuroimaging 2003, 122:69-87. 10.1016/S0925-4927(02)00118-X, 12714172.
2. Hill K, Mann L, Laws KR, Stephenson CME, Nimmo-Smith I, McKenna PJ. Hypofrontality in schizophrenia: a meta-analysis of functional imaging studies. Acta Psychiatrica Scandinavica 2004, 110:243-256. 10.1111/j.1600-0447.2004.00376.x, 15352925.
3. Cochran SM, Kennedy M, McKerchar CE, Steward LJ, Pratt JA, Morris BJ. Induction of Metabolic Hypofunction and Neurochemical Deficits after Chronic Intermittent Exposure to Phencyclidine: Differential Modulation by Antipsychotic Drugs. Neuropsychopharmacology 2003, 28:265-275. 10.1038/sj.npp.1300031, 12589379.
4. Dawson N, Thompson RJ, McVie A, Thomson DM, Morris BJ, Pratt JA. Modafinil reverses phencyclidine (PCP)-induced deficits in cognitive flexibility, cerebral metabolism and functional brain connectivity. Schizophrenia Bulletin
5. Egerton A, Reid L, McGregor S, Cochran SM, Morris BJ, Pratt JA. Subchronic and chronic PCP treatment produces temporally distinct deficits in attentional set shifting and prepulse inhibition in rats. Psychopharmacology 2008, 198:37-49. 10.1007/s00213-008-1071-5, 18427784.
6. Egerton A, Reid L, McKerchar CE, Morris BJ, Pratt JA. Impairment in perceptual attentional set-shifting following PCP administration: a rodent model of set-shifting deficits in schizophrenia. Psychopharmacology 2005, 179:77-84. 10.1007/s00213-004-2109-y, 15682304.
7. Steward LJ, Kennedy MD, Morris BJ, Pratt JA. The atypical antipsychotic drug clozapine enhances chronic PCP-induced regulation of prefrontal cortex 5-HT2A receptors. Neuropharmacology 2004, 47:527-537. 10.1016/j.neuropharm.2004.04.020, 15380371.
8. Fiehn O. Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comparative and Functional Genomics 2001, 2:155-168. 10.1002/cfg.82, 2447208, 18628911.
9. Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB. Metabolomics by numbers: acquiring and understanding global metabolite data. Trends in Biotechnology 2004, 22:245-252. 10.1016/j.tibtech.2004.03.007, 15109811.
10. Goodacre R, York EV, Heald JK, Scott IM. Chemometric discrimination of unfractionated plant extracts analyzed by electrospray mass spectrometry. Phytochemistry 2003, 62:859-863. 10.1016/S0031-9422(02)00718-5, 12590113.
11. Oliver SG, Winson MK, Kell DB, Baganz F. Systematic functional analysis of the yeast genome. Trends in Biotechnology 1998, 16:373-378. 10.1016/S0167-7799(98)01214-1, 9744112.
12. Kaddurah-Daouk R, Krishnan KRR. Metabolomics: A Global Biochemical Approach to the Study of Central Nervous System Diseases. Neuropsychopharmacology 2009, 34:173-186. 10.1038/npp.2008.174, 18843269.
13. Quinones MP, Kaddurah-Daouk R. Metabolomics tools for identifying biomarkers for neuropsychiatric diseases. Neurobiology of Disease 2009, 35:165-176. 10.1016/j.nbd.2009.02.019, 19303440.
14. Greenberg N, Grassano A, Thambisetty M, Lovestone S, Legido-Quigley C. A proposed metabolic strategy for monitoring disease progression in Alzheimer's disease. Electrophoresis 2009, 30:1235-1239. 10.1002/elps.200800589, 19288586.
15. Chen C, Gonzalez FJ, Idle JR. LC-MS-based metabolomics in drug metabolism. Drug Metab Rev 2007, 39:581-597. 10.1080/03602530701497804, 2140249, 17786640.
16. Lindon JC, Holmes E, Nicholson JK. Metabonomics in pharmaceutical research and development. FEBS Journal 2007, 274:1140-1151. 10.1111/j.1742-4658.2007.05673.x, 17298438.
17. Robertson DG. Metabonomics in Toxicology: A Review. Toxicological Sciences 2005, 85:809-822. 10.1093/toxsci/kfi102, 15689416.
18. Cheng KK, Benson GM, Grimsditch DC, Reid DG, Connor SC, Griffin JL. Metabolomic study of the LDL receptor null mouse fed a high-fat diet reveals profound perturbations in choline metabolism that are shared with ApoE null mice. Physiological Genomics 2010, 41:224-231.
19. Dettmer K, Aronov PA, Hammock BD. Mass spectrometry-based metabolomics. Mass Spectrometry Reviews 2007, 26:51-78. 10.1002/mas.20108, 1904337, 16921475.
20. Lu W, Bennett BD, Rabinowitz JD. Analytical strategies for LC-MS-based targeted metabolomics. Journal of Chromatography B 2008, 871:236-242.
21. Wilson ID, Plumb R, Granger J, Major H, Williams R, Lenz EM. HPLC-MS-based methods for the study of metabonomics. Journal of Chromatography B 2005, 817:67-76.
22. Ohta D, Kanaya S, Suzuki H. Application of Fourier-transform ion cyclotron resonance mass spectrometry to metabolic profiling and metabolite identification. Current Opinion in Biotechnology 2010, 21:35-44. 10.1016/j.copbio.2010.01.012, 20171870.
23. Hu Q, Noll RJ, Li H, Makarov A, Hardman M, Graham Cooks R. The Orbitrap: a new mass spectrometer. Journal of Mass Spectrometry 2005, 40:430-443. 10.1002/jms.856, 15838939.
24. Calvano CD, Zambonin CG, Jensen ON. Assessment of lectin and HILIC based enrichment protocols for characterization of serum glycoproteins by mass spectrometry. Journal of Proteomics 2008, 71:304-317. 10.1016/j.jprot.2008.06.013, 18638581.
25. Cubbon S, Bradbury T, Wilson J, Thomas-Oates J. Hydrophilic Interaction Chromatography for Mass Spectrometric Metabonomic Studies of Urine. Analytical Chemistry 2007, 79:8911-8918. 10.1021/ac071008v, 17973349.
26. Gika HG, Theodoridis GA, Wilson ID. Hydrophilic interaction and reversed-phase ultra-performance liquid chromatography TOF-MS for metabonomic analysis of Zucker rat urine. Journal of Separation Science 2008, 31(9):1598-1608. 10.1002/jssc.200700644, 18461568.
27. Idborg H, Zamani L, Edlund PO, Schuppe-Koistinen I, Jacobsson SP. Metabolic fingerprinting of rat urine by LC/MS: Part 1. Analysis by hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry. Journal of Chromatography B 2005, 828:9-13.
28. Kind T, Tolstikov V, Fiehn O, Weiss RH. A comprehensive urinary metabolomic approach for identifying kidney cancer. Analytical Biochemistry 2007, 363:185-195. 10.1016/j.ab.2007.01.028, 17316536.
29. Nordstrom A, Want E, Northen T, Lehtio J, Siuzdak G. Multiple Ionization Mass Spectrometry Strategy Used To Reveal the Complexity of Metabolomics. Analytical Chemistry 2008, 80:421-429. 10.1021/ac701982e, 18085752.
30. Paek IB, Moon Y, Ji HY, Kim HH, Lee HW, Lee YB, Lee HS. Hydrophilic interaction liquid chromatography-tandem mass spectrometry for the determination of levosulpiride in human plasma. Journal of Chromatography B 2004, 809:345-350.
31. Zhang X, Rauch A, Lee H, Xiao H, Rainer G, Logothetis NK. Capillary hydrophilic interaction chromatography/mass spectrometry for simultaneous determination of multiple neurotransmitters in primate cerebral cortex. Rapid Communications in Mass Spectrometry 2007, 21:3621-3628. 10.1002/rcm.3251, 17939159.
32. Dunn WB, Bailey NJC, Johnson HE. Measuring the metabolome: current analytical technologies. The Analyst 2005, 130:606-625. 10.1039/b418288j, 15852128.
33. Spagou K, Tsoukali H, Raikos N, Gika H, Wilson ID, Theodoridis G. Hydrophilic interaction chromatography coupled to MS for metabonomic/metabolomic studies. Journal of Separation Science 2010, 33:716-727. 10.1002/jssc.200900803, 20187037.
34. Albert R, Barabási AL. Statistical mechanics of complex networks. Reviews of Modern Physics 2002, 74:47-97.
35. Newman MEJ. The structure and function of complex networks. SIAM Review 2003, 45:167-256.
36. Strogatz SH. Exploring complex networks. Nature 2001, 410:268-276. 10.1038/35065725, 11258382.
37. Shi J, Malik J. Normalized Cuts and Image Segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence 2000, 22:888-905.
38. Higham DJ. Spectral reordering of a range-dependent weighted random graph. IMA J. Numer. Anal 2005, 25:443-457.
39. Estrada E. Protein bipartivity and essentiality in the yeast protein-protein interaction network. J. Proteome Res 2006, 5:2177-2184. 10.1021/pr060106e, 16944929.
40. Estrada E, Higham DJ, Hatano N. Communicability and multipartite structures in complex networks at negative absolute temperatures. Phys. Rev. E 2008, 77:026102.
41. Morrison JL, Breitling R, Higham DJ, Gilbert DR. A Lock-and-Key Model for Protein-Protein Interactions. Bioinformatics 2006, 2:2012-2019.
42. Thomas A, Cannings R, Monk NAM, Cannings C. On the structure of protein-protein interaction networks. Biochemical Soc. Trans 2003, 31:1491-1496.
43. Alter O, Brown PO, Botstein D. Generalized Singular Value Decomposition for Comparative Analysis of Genome-Scale Expression Datasets of Two Different Organisms. Proceedings of the National Academy of Sciences 2003, 100:3351-3356.
44. Schreiber A, Shirley NJ, Burton RA, Fincher GB. Combining transcriptional datasets using the generalized singular value decomposition. BMC Bioinformatics 2008, 9:335. 10.1186/1471-2105-9-335, 2562393, 18687147.
45. Higham DJ, Kalna G, Kibble M. Spectral clustering and its use in bioinformatics. J. Computational and Applied Math 2007, 204:25-37.
46. Fiedler M. A property of eigenvectors of nonnegative symmetric matrices and its application to graph theory. Czechoslovak Mathematical Journal 1975, 25:619-633.
47. Atkins JE, Boman EG, Hendrickson B. A spectral algorithm for seriation and the consecutive ones problem. SIAM Journal on Computing 1998, 28:297-310.
48. Robles-Kelly A, Hancock ER. Graph Edit Distance from Spectral Seriation. IEEE Transactions on Pattern Analysis and Machine Intelligence 2005, 27:365-378.
49. Golub GH, Van Loan CF. Matrix Computations 1996, Baltimore: Johns Hopkins University Press.
50. Strang G. Computational Science and Engineering 2008, Wellesley-Cambridge Press.
51. Estrada E. Topological structural classes of complex networks. Physical Review E 2007, 75:016103.
52. Xiao X. Complex Networks and the Generalized Singular Value Decomposition. PhD thesis 2010, University of Strathclyde, Department of Mathematics and Statistics, .
53. Murai R, Noda Y, Matsui K, Kamei H, Mouri A, Matsuba K, Nitta A, Furukawa H, Nabeshima T. Hypofunctional glutamatergic neurotransmission in the prefrontal cortex is involved in the emotional deficit induced by repeated treatment with phencyclidine in mice: Implications for abnormalities of glutamate release and NMDA-CaMKII signaling. Behavioural Brain Research 2007, 180:152-160. 10.1016/j.bbr.2007.03.003, 17451820.
54. Hahn CG, Wang HY, Cho DS, Talbot K, Gur RE, Berrettini WH, Bakshi K, Kamins J, Borgmann-Winter KE, Siegel SJ, Gallop RJ, Arnold SE. Altered neuregulin 1-erbB4 signaling contributes to NMDA receptor hypofunction in schizophrenia. Nature Medicine 2006, 12:824-828. 10.1038/nm1418, 16767099.
55. Lewis DA, Moghaddam B. Cognitive Dysfunction in Schizophrenia: Convergence of gamma-Aminobutyric Acid and Glutamate Alterations. Arch Neurol 2006, 63:1372-1376. 10.1001/archneur.63.10.1372, 17030651.
56. Javitt DC, Balla A, Burch S, Suckow R, Xie S, Sershen H. Reversal of Phencyclidine-Induced Dopaminergic Dysregulation by N-Methyl-D-Aspartate Receptor//Glycine-site Agonists. Neuropsychopharmacology 2003, 29:300-307.
57. Sershen H, Balla A, Aspromonte JM, Xie S, Cooper TB, Javitt DC. Characterization of interactions between phencyclidine and amphetamine in rodent prefrontal cortex and striatum: Implications in NMDA/glycine-site-mediated dopaminergic dysregulation and dopamine transporter function. Neurochemistry International 2008, 52:119-129. 10.1016/j.neuint.2007.07.011, 17716783.
58. Yang CR, Svensson KA. Allosteric modulation of NMDA receptor via elevation of brain glycine and d-serine: The therapeutic potentials for schizophrenia. Pharmacology & Therapeutics 2008, 120:317-332. 10.1016/j.pharmthera.2008.08.004, 21647947.
59. Magistretti PJ. Role of glutamate in neuron-glia metabolic coupling. Am J Clin Nutr 2009, 90:875S-880S. 10.3945/ajcn.2009.27462CC, 19571222.
60. Patel AB, de Graaf RA, Mason GF, Rothman DL, Shulman RG, Behar KL. The contribution of GABA to glutamate/glutamine cycling and energy metabolism in the rat cortex in vivo. Proceedings of the National Academy of Sciences 2005, 102:5588-5593.
61. Rameau GA, Tukey DS, Garcin-Hosfield ED, Titcombe RF, Misra C, Khatri L, Getzoff ED, Ziff EB. Biphasic Coupling of Neuronal Nitric Oxide Synthase Phosphorylation to the NMDA Receptor Regulates AMPA Receptor Trafficking and Neuronal Cell Death. The Journal of Neuroscience 2007, 27:3445-3455. 10.1523/JNEUROSCI.4799-06.2007, 17392461.
62. Fejgin K, Palsson E, Wass C, Svensson L, Klamer D. Nitric Oxide Signaling in the Medial Prefrontal Cortex is Involved in the Biochemical and Behavioral Effects of Phencyclidine. Neuropsychopharmacology 2008, 33:1874-1833. 10.1038/sj.npp.1301587, 17895915.
63. Wass C, Svensson L, Fejgin K, Pålsson E, Archer T, Engel JA, Klamer D. Nitric oxide synthase inhibition attenuates phencyclidine-induced disruption of cognitive flexibility. Pharmacology Biochemistry and Behavior 2008, 89:352-359.
64. Xing G, Chavko M, Zhang LX, Yang S, Post RM. Decreased calcium-dependent constitutive nitric oxide synthase (cNOS) activity in prefrontal cortex in schizophrenia and depression. Schizophrenia Research 2002, 58:21-30. 10.1016/S0920-9964(01)00388-7, 12363386.
65. Tsuang MT, Nossova N, Yager T, Tsuang MM, Guo SC, Shyu KG, Glatt SJ, Liew C. Assessing the validity of blood-based gene expression profiles for the classification of schizophrenia and bipolar disorder: A preliminary report. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 2005, 133B:1-5.
66. Zhang F, Xu Y, Liu P, Fan H, Huang X, Sun G, Song Y, Sham P. Association analyses of the interaction between the ADSS and ATM genes with schizophrenia in a Chinese population. BMC Medical Genetics 2008, 9:119-125. 10.1186/1471-2350-9-119, 2654671, 19115993.
67. Spiegel EK, Colman RF, Patterson D. Adenylosuccinate lyase deficiency. Molecular Genetics and Metabolism 2006, 89(1-2):19-31. 10.1016/j.ymgme.2006.04.018, 16839792.
68. Stone RL, Aimi J, Barshop BA, Jaeken J, Van den Berghe G, Zalkin H, Dixon JE. A mutation in adenylosuccinate lyase associated with mental retardation and autistic features. Nature Genetics 1992, 1:59-63. 10.1038/ng0492-59, 1302001.
69. Fon E, Demczuk S, Delattre O, Thomas G, Rouleau G. Mapping of the human adenylosuccinate lyase (ADSL) gene to chromosome 22q13.1→q13.2. Cytogenetics and Cell Genetics 1993, 64:201-203. 10.1159/000133575, 8404037.
70. Jorgensen T, Børglum A, Mors O, Wang A, Pinaud M, Flint T, Dahl H, Vang M, Kruse T, Ewald H. Search for common haplotypes on chromosome 22q in patients with schizophrenia or bipolar disorder from the Faroe Islands. American Journal of Medical Genetics 2002, 114:245-252. 10.1002/ajmg.10191, 11857589.
71. Pulver AE, Karayiorgou M, Wolyniec PS, Lasseter VK, Kasch L, Nestadt G, Antonarakis S, Housman D, Kazazian HH, Meyers D, Ott J, Lamacz M, Liang KY, Hanfelt J, Ullrich G, DeMarchi N, Ramu E, McHugh PR, Adler L, Thomas M, Carpenter WT, Manschreck T, Gordon CT, Kimberland M, Babb R, Puck J, Childs B. Sequential strategy to identify a susceptibility gene for schizophrenia: Report of potential linkage on chromosome 22q12-q13.1: Part 1. American Journal of Medical Genetics 1994, 54:36-43. 10.1002/ajmg.1320540108, 8178837.
72. Saleem Q, Dash D, Gandhi C, Kishore A, Benegal V, Sherrin T, Mukherjee O, Jain S, Brahmachari SK. Association of CAG repeat loci on chromosome 22 with schizophrenia and bipolar disorder. Molecular Psychiatry 2001, 6:694-700. 10.1038/sj.mp.4000924, 11673798.
73. De Volder AG, Jaeken J, Den Berghe GV, Bol A, Michel C, Cogneau M, Goffinet AM. Regional Brain Glucose Utilization in Adenylosuccinase-Deficient Patients Measured by Positron Emission Tomography. Pediatric Research 1998, 24:238-242.
74. Paxinos G, Watson C. The Rat Brain in Stereotaxic Coordinates 1998, Academic Press.
75. Wu H, Southam AD, Hines A, Viant MR. High-throughput tissue extraction protocol for NMR- and MS-based metabolomics. Analytical Biochemistry 2008, 372:204-212. 10.1016/j.ab.2007.10.002, 17963684.