Psychiatric research: Psychoproteomics, degradomics and systems biology

Expert Review of Proteomics

Volumn 5, Issue 2, 2008, Pages 293-314

  Kobeissy, Firas H ^a   Sadasivan, Shankar ^c   Liu, Jing ^c   Gold, Mark S ^c   Wang, Kevin K W ^a,b  

^a UNIVERSITY OF FLORIDA HEALTH   (United States)

^b BANYAN BIOMARKERS INC   (United States)

^c UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

Biomarkers; Degradomics; Drug of abuse; Proteomics; Psychiatry; Systems biology

Indexed keywords

3,4 DIHYDROXYPHENYLACETIC ACID; 3,4 METHYLENEDIOXYMETHAMPHETAMINE; 4 AMINOBUTYRIC ACID; 5 HYDROXYINDOLEACETIC ACID; ALBUMIN; ALCOHOL; BETA ENDORPHIN; BIOLOGICAL MARKER; COLLAPSIN RESPONSE MEDIATOR PROTEIN 2; CONNECTIVE TISSUE GROWTH FACTOR; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN BINDING PROTEIN; DEATH RECEPTOR 6; DIAZEPAM BINDING INHIBITOR; DNA; DOPAMINE; FK 506 BINDING PROTEIN; GALECTIN 1; GELSOLIN; GLUCOCORTICOID; GUANINE NUCLEOTIDE BINDING PROTEIN; INTERLEUKIN 6; MATRIX METALLOPROTEINASE; MESSENGER RNA; METHAMPHETAMINE; N METHYL DEXTRO ASPARTIC ACID RECEPTOR; NICOTINE; OPIATE; PROTEINASE INHIBITOR; SEROTONIN; UNINDEXED DRUG;

BLOOD CHEMISTRY; BRAIN DISEASE; BRAIN FUNCTION; CEREBROSPINAL FLUID ANALYSIS; CLINICAL RESEARCH; DEGRADATION KINETICS; DNA FRAGMENTATION; DRUG ABUSE; GABAERGIC TRANSMISSION; GENETIC SUSCEPTIBILITY; HUMAN; KIDNEY FAILURE; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MENTAL DISEASE; MOLECULAR BIOLOGY; NEUROCHEMISTRY; NEUROSCIENCE; NEUROTOXICITY; NONHUMAN; OXIDATIVE STRESS; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN BLOOD LEVEL; PROTEOMICS; PSYCHOBIOLOGY; PSYCHOPROTEOMICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SCHIZOPHRENIA; SUBSTANCE ABUSE; SYSTEMS BIOLOGY; TRANSCRIPTOMICS;

BIOLOGICAL MARKERS; HUMANS; MENTAL DISORDERS; PROTEOMICS; PSYCHIATRY; RESEARCH; SYSTEMS BIOLOGY;

EID: 43449117811     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.5.2.293     Document Type: Review

References (202)

1. Drabik A, Bierczynska-Krzysik A, Bodzon-Kulakowska A, Suder P, Kotlinska J, Silberring J. Proteomics in neurosciences. Mass Spectrom. Rev. 26(3), 432-450 (2007).
2. Kobeissy FH, Warren M, Ottens AK et al. Psychoproteomic analysis of rat cortex following acute methamphetamine exposure. J. Proteome Res. (2008) (In Press).
3. Nestler EJ. Psychogenomics: opportunities for understanding addiction. J. Neurosci. 21(21), 8324-8327 (2001).
4. Choudhary J, Grant SG. Proteomics in postgenomic neuroscience: the end of the beginning. Nat. Neurosci. 7(5), 440-445 (2004).
5. Kim SI, Voshol H, van Oostrum J, Hastings TG, Cascio M, Glucksman MJ. Neuroproteomics: expression profiling of the brain's proteomes in health and disease. Neurochem. Res. 29(6), 1317-1331 (2004).
6. Williams K, Wu T, Colangelo C, Nairn AC. Recent advances in neuroproteomics and potential application to studies of drug addiction. Neuropharmacology 47(Suppl. 1), 148-166 (2004).
7. Wang KK, Ottens AK, Liu MC et al. Proteomic identification of biomarkers of traumatic brain injury. Expert Rev. Proteomics 2(4), 603-614 (2005).
8. Morrison RS, Kinoshita Y, Johnson MD et al. Proteomic analysis in the neurosciences. Mol. Cell Proteomics 1(8), 553-560 (2002).
9. Wang KK, Ottens A, Haskins W et al. Proteomics studies of traumatic brain injury. Int. Rev. Neurobiol. 61, 215-240 (2004).
10. Freeman WM, Brebner K, Amara SG, Reed MS, Pohl J, Phillips AG. Distinct proteomic profiles of amphetamine self-administration transitional states. Pharmacogenomics J. 5(3), 203-214 (2005).
11. Denslow N, Michel ME, Temple MD, Hsu CY, Saatman K, Hayes RL. Application of proteomics technology to the field of neurotrauma. J. Neurotrauma 20(5), 401-407 (2003).
12. Missler M, Sudhof TC. Neurexins: three genes and 1001 products. Trends Genet. 14(1), 20-26 (1998).
13. Hunnerkopf R, Grassl J, Thome J. Proteomics: biomarker research in psychiatry. Fortschr. Neurol. Psychiatr. 75(10), 579-586 (2007).
14. Wu Q, Maniatis T. A striking organization of a large family of human neural cadherin-like cell adhesion genes. Cell 97(6), 779-790 (1999).
15. Patton WF. Detection technologies in proteome analysis. J. Chromatogr. 771(1-2), 3-31 (2002).
16. Hortin GL, Jortani SA, Ritchie JC Jr, Valdes R Jr, Chan DW. Proteomics: a new diagnostic frontier. Clin. Chem. 52(7), 1218-1222 (2006).
17. Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics 1(11), 845-867 (2002).
18. Omenn GS, States DJ, Adamski M et al. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 5(13), 3226-3245 (2005).
19. Schmidt O, Schulenborg T, Meyer HE, Marcus K, Hamacher M. How proteomics reveals potential biomarkers in brain diseases. Expert Rev. Proteomics 2(6), 901-913 (2005).
20. Grant SG, Blackstock WP. Proteomics in neuroscience: from protein to network. J. Neurosci. 21(21), 8315-8318 (2001).
21. Vercauteren FG, Bergeron JJ, Vandesande F, Arckens L, Quirion R. Proteomic approaches in brain research and neuropharmacology. Eur. J. Clin. Pharmacol. 500(1-3), 385-398 (2004).
22. Taylor CM, Pfeiffer SE. Enhanced resolution of glycosylphosphatidylinositol-anchored and transmembrane proteins from the lipid-rich myelin membrane by two-dimensional gel electrophoresis. Proteomics 3(7), 1303-1312 (2003).
23. Dackis CA, O'Brien CP. Cocaine dependence: a disease of the brain's reward centers. J. Subst. Abuse Treat. 21(3), 111-117 (2001).
24. Dackis C, O'Brien C. Neurobiology of addiction: treatment and public policy ramifications. Nat. Neurosci. 8(11), 1431-1436 (2005).
25. Volkow N, Li TK. The neuroscience of addiction. Nat. Neurosci. 8(11), 1429-1430 (2005).
26. Volkow ND, Fowler JS, Wang GJ, Swanson JM. Dopamine in drug abuse and addiction: results from imaging studies and treatment implications. Mol. Psychiatry 9(6), 557-569 (2004).
27. Volkow N. Drug dependence and addiction, III: expectation and brain function in drug abuse. Am. J. Psychiatry 161(4), 621 (2004).
28. Uhl GR. Molecular genetics of addiction vulnerability. NeuroRx 3(3), 295-301 (2006).
29. Liu QR, Drgon T, Johnson C, Walther D, Hess J, Uhl GR. Addiction molecular genetics: 639,401 SNP whole genome association identifies many "cell adhesion" genes. Am. J. Med. Genet. B Neuropsychiatr. Genet. 141(8), 918-925 (2006).
30. Perrotti LI, Bolanos CA, Choi KH et al. DeltaFosB accumulates in a GABAergic cell population in the posterior tail of the ventral tegmental area after psychostimulant treatment. Eur. J. Neurosci. 21(10), 2817-2824 (2005).
31. Bibb JA, Chen J, Taylor JR et al. Effects of chronic exposure to cocaine are regulated by the neuronal protein Cdk5. Nature 410(6826), 376-380 (2001).
32. Carlezon WA Jr, Nestler EJ. Elevated levels of GluR1 in the midbrain: a trigger for sensitization to drugs of abuse? Trends Neurosci. 25(12), 610-615 (2002).
33. Roche KW. The expanding role of PSD-95: a new link to addiction. Trends Neurosci. 27(12), 699-700 (2004).
34. Nestler EJ. Under siege: the brain on opiates. Neuron 16(5), 897-900 (1996).
35. Blackstock WP, Weir MP. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol. 17(3), 121-127 (1999).
36. Nestler EJ. Molecular mechanisms of opiate and cocaine addiction. Curr. Opin. Neurobiol. 7(5), 713-719 (1997).
37. Tso PH, Wong YH. Molecular basis of opioid dependence: role of signal regulation by G-proteins. Clin. Exp. Pharmacol. Physiol. 30(5-6), 307-316 (2003).
38. Bailey CP, Connor M. Opioids: cellular mechanisms of tolerance and physical dependence. Curr. Opin. Pharmacol. 5(1), 60-68 (2005).
39. Ueda H, Inoue M, Mizuno K. New approaches to study the development of morphine tolerance and dependence. Life Sci. 74(2-3), 313-320 (2003).
40. Granados-Soto V, Kalcheva I, Hua X, Newton A, Yaksh TL. Spinal PKC activity and expression: role in tolerance produced by continuous spinal morphine infusion. Pain 85(3), 395-404 (2000).
41. 3H]MK-801 binding affinity and constitutive neuronal nitric oxide synthase expression in rat spinal cord. Br. J. Anaesth. 85(4), 587-591 (2000).
42. Shui HA, Ho ST, Wang JJ et al. Proteomic analysis of spinal protein expression in rats exposed to repeated intrathecal morphine injection. Proteomics 7(5), 796-803 (2007).
43. Neasta J, Uttenweiler-Joseph S, Chaoui K, Monsarrat B, Meunier JC, Mouledous L. Effect of long-term exposure of SH-SY5Y cells to morphine: a whole cell proteomic analysis. Proteome Sci. 4, 23 (2006).
44. Yang L, Sun ZS, Zhu YP. Proteomic analysis of rat prefrontal cortex in three phases of morphine-induced conditioned place preference. J. Proteome Res. 6(6), 2239-2247 (2007).
45. Bodzon-Kulakowska A, Bierczynska-Krzysik A, Drabik A et al. Morphinome - proteome of the nervous system after morphine treatment. Amino acids 28(1), 13-19 (2005).
46. Bierczynska-Krzysik A, Bonar E, Drabik A et al. Rat brain proteome in morphine dependence. Neurochem. Int. 49(4), 401-406 (2006).
47. Li KW, Jimenez CR, van der Schors RC, Hornshaw MP, Schoffelmeer AN, Smit AB. Intermittent administration of morphine alters protein expression in rat nucleus accumbens. Proteomics 6(6), 2003-2008 (2006).
48. Moron JA, Abul-Husn NS, Rozenfeld R, Dolios G, Wang R, Devi LA. Morphine administration alters the profile of hippocampal postsynaptic density-associated proteins: a proteomics study focusing on endocytic proteins. Mol. Cell. Proteomics 6(1), 29-42 (2007).
49. Li KW. Proteomics of synapse. Anal. Bioanal. Chem. 387(1), 25-28 (2007).
50. Prokai L, Zharikova AD, Stevens SM Jr. Effect of chronic morphine exposure on the synaptic plasma-membrane subproteome of rats: a quantitative protein profiling study based on isotope-coded affinity tags and liquid chromatography/mass spectrometry. J. Mass Spectrom. 40(2), 169-175 (2005).
51. Warren MW, Kobeissy FH, Liu MC, Hayes RL, Gold MS, Wang KK. Concurrent calpain and caspase-3 mediated proteolysis of ? II-spectrin and tau in rat brain after methamphetamine exposure: a similar profile to traumatic brain injury. Life Sci. 78(3), 301-309 (2005).
52. Warren MW, Kobeissy FH, Liu MC, Hayes RL, Gold MS, Wang KK. Ecstasy toxicity: a comparison to methamphetamine and traumatic brain injury. J. Addict. Dis. 25(4), 115-123 (2006).
53. Warren MW, Larner SF, Kobeissy FH et al. Calpain and caspase proteolytic markers co-localize with rat cortical neurons after exposure to methamphetamine and MDMA. Acta Neuropathol. 114(3), 277-286 (2007).
54. Warren MW, Zheng W, Kobeissy FH et al. Calpain- and caspase-mediated ?II-spectrin and tau proteolysis in rat cerebrocortical neuronal cultures after ecstasy or methamphetamine exposure. Int. J. Neuropsychopharmacol. 10(4), 479-489 (2007).
55. Kim SY, Chudapongse N, Lee SM et al. Proteomic analysis of phosphotyrosyl proteins in morphine-dependent rat brains. Brain Res. Mol. Brain Res. 133(1), 58-70 (2005).
56. Kumar A, Choi KH, Renthal W et al. Chromatin remodeling is a key mechanism underlying cocaine-induced plasticity in striatum. Neuron 48(2), 303-314 (2005).
57. Levine AA, Guan Z, Barco A, Xu S, Kandel ER, Schwartz JH. CREB-binding protein controls response to cocaine by acetylating histones at the fosB promoter in the mouse striatum. Proc. Natl Acad. Sci. USA 102(52), 19186-19191 (2005).
58. Marcus K, Schmidt O, Schaefer H, Hamacher M, van Hall A, Meyer HE. Proteomics - application to the brain. Int. Rev. Neurobiol. 61, 285-311 (2004).
59. Iwazaki T, McGregor IS, Matsumoto I. Protein expression profile in the striatum of acute methamphetamine-treated rats. Brain Res. 1097(1), 19-25 (2006).
60. Iwazaki T, McGregor IS, Matsumoto I. Protein expression profile in the striatum of rats with methamphetamine-induced behavioral sensitization. Proteomics 7(7), 1131-1139 (2007).
61. Sokolov BP, Cadet JL. Methamphetamine causes alterations in the MAP kinaserelated pathways in the brains of mice that display increased aggressiveness. Neuropsychopharmacology 31(5), 956-966 (2006).
62. Ottens AK, Kobeissy FH, Wolper RA et al. A multidimensional differential proteomic platform using dual-phase ion-exchange chromatography-polyacrylamide gel electrophoresis/reversed-phase liquid chromatography tandem mass spectrometry. Anal. Chem. 77(15), 4836-4845 (2005).
63. Svetlov SI, Xiang Y, Oli MW et al. Identification and preliminary validation of novel biomarkers of acute hepatic ischaemia/reperfusion injury using dual-platform proteomic/degradomic approaches. Biomarkers 11(4), 355-369 (2006).
64. Kobeissy FH, Ottens AK, Zhang Z et al. Novel differential neuroproteomics analysis of traumatic brain injury in rats. Mol. Cell. Proteomics 5(10), 1887-1898 (2006).
65. Lewohl JM, van Dyk DD, Craft GE et al. The application of proteomics to the human alcoholic brain. Ann. NY Acad. Sci. 1025, 14-26 (2004).
66. Kashem MA, James G, Harper C, Wilce P, Matsumoto I. Differential protein expression in the corpus callosum (splenium) of human alcoholics: a proteomics study. Neurochem. Int. 50(2), 450-459 (2007).
67. Pfefferbaum A, Sullivan EV, Mathalon DH, Lim KO. Frontal lobe volume loss observed with magnetic resonance imaging in older chronic alcoholics. Alcohol. Clin. Exp. Res. 21(3), 521-529 (1997).
68. Alexander-Kaufman K, Dedova I, Harper C, Matsumoto I. Proteome analysis of the dorsolateral prefrontal region from healthy individuals. Neurochem. Int. 51(6-7), 433-439 (2007).
69. Alexander-Kaufman K, Harper C, Wilce P, Matsumoto I. Cerebellar vermis proteome of chronic alcoholic individuals. Alcohol. Clin. Exp. Res. 31(8), 1286-1296 (2007).
70. Alexander-Kaufman K, James G, Sheedy D, Harper C, Matsumoto I. Differential protein expression in the prefrontal white matter of human alcoholics: a proteomics study. Mol. Psychiatry 11(1), 56-65 (2006).
71. Matsuda-Matsumoto H, Iwazaki T, Kashem MA, Harper C, Matsumoto I. Differential protein expression profiles in the hippocampus of human alcoholics. Neurochem. Int. 51(6-7), 370-376 (2007).
72. Matsumoto I, Alexander-Kaufman K, Iwazaki T, Kashem MA, Matsuda-Matsumoto H. CNS proteomes in alcohol and drug abuse and dependence. Expert Rev. Proteomics 4(4), 539-552 (2007).
73. Quinn HR, Matsumoto I, Callaghan PD et al. Adolescent rats find repeated ?(9)-THC less aversive than adult rats but display greater residual cognitive deficits and changes in hippocampal protein expression following exposure. Neuropsychopharmacology 33(5), 1113-1126 (2008).
74. Johnston-Wilson NL, Sims CD, Hofmann JP et al. Disease-specific alterations in frontal cortex brain proteins in schizophrenia, bipolar disorder, and major depressive disorder. The Stanley Neuropathology Consortium. Mol. Psychiatry 5(2), 142-149 (2000).
75. Susser E, Wanderling J. Epidemiology of nonaffective acute remitting psychosis vs schizophrenia. Sex and sociocultural setting. Arch. Gen. Psychiatry 51(4), 294-301 (1994).
76. Lakhan SE. Schizophrenia proteomics: biomarkers on the path to laboratory medicine? Diagn. Pathol. 1, 11 (2006).
77. Sawa A, Snyder SH. Schizophrenia: diverse approaches to a complex disease. Science 296(5568), 692-695 (2002).
78. Frankle WG, Lerma J, Laruelle M. The synaptic hypothesis of schizophrenia. Neuron 39(2), 205-216 (2003).
79. Benes FM. Emerging principles of altered neural circuitry in schizophrenia. Brain Res. 31(2-3), 251-269 (2000).
80. Cotter D, Landau S, Beasley C et al. The density and spatial distribution of GABAergic neurons, labelled using calcium binding proteins, in the anterior cingulate cortex in major depressive disorder, bipolar disorder, and schizophrenia. Biol. Psychiatry 51(5), 377-386 (2002).
81. Gallinat J, Obermayer K, Heinz A. Systems neurobiology of the dysfunctional brain: schizophrenia. Pharmacopsychiatry 40(Suppl. 1), S40-S44 (2007).
82. Iritani S. Neuropathology of schizophrenia: a mini review. Neuropathology 27(6), 604-608 (2007).
83. Tan HY, Callicott JH, Weinberger DR. Dysfunctional and compensatory prefrontal cortical systems, genes and the pathogenesis of schizophrenia. Cereb. Cortex 17(Suppl. 1), i171-i181 (2007).
84. Waddington JL. Neuroimaging and other neurobiological indices in schizophrenia: relationship to measurement of functional outcome. Br. J. Psychiatry Suppl. 50, S52-S57 (2007).
85. Waddington JL, Corvin AP, Donohoe G, O'Tuathaigh CM, Mitchell KJ, Gill M. Functional genomics and schizophrenia: endophenotypes and mutant models. Psychiatr. Clin. North Am. 30(3), 365-399 (2007).
86. Clark WG. Schizophrenia and genomics: linking research to practice. J. Psychosoc. Nurs. Ment. Health Serv. 45(6), 24-28 (2007).
87. McClellan JM, Susser E, King MC. Schizophrenia: a common disease caused by multiple rare alleles. Br. J. Psychiatry 190, 194-199 (2007).
88. Vazza G, Bertolin C, Scudellaro E et al. Genome-wide scan supports the existence of a susceptibility locus for schizophrenia and bipolar disorder on chromosome 15q26. Mol. Psychiatry 12(1), 87-93 (2007).
89. Owen MJ. Genomic approaches to schizophrenia. Clin. Ther. 27(Suppl. A), S2-S7 (2005).
90. Hallmayer JF, Kalaydjieva L, Badcock J et al. Genetic evidence for a distinct subtype of schizophrenia characterized by pervasive cognitive deficit. Am. J. Hum. Genet. 77(3), 468-476 (2005).
91. Porteous DJ, Evans KL, Millar JK et al. Genetics of schizophrenia and bipolar affective disorder: strategies to identify candidate genes. Cold Spring Harb. Symp. Quant. Biol. 68, 383-394 (2003).
92. Prabakaran S, Swatton JE, Ryan MM et al. Mitochondrial dysfunction in schizophrenia: evidence for compromised brain metabolism and oxidative stress. Mol. Psychiatry 9(7), 684-697, 643 (2004).
93. Edgar PF, Schonberger SJ, Dean B, Faull RL, Kydd R, Cooper GJ. A comparative proteome analysis of hippocampal tissue from schizophrenic and Alzheimer's disease individuals. Mol. Psychiatry 4(2), 173-178 (1999).
94. van Kammen DP, Guidotti A, Kelley ME et al. CSF diazepam binding inhibitor and schizophrenia: clinical and biochemical relationships. Biol. Psychiatry 34(8), 515-522 (1993).
95. Jiang L, Lindpaintner K, Li HF et al. Proteomic analysis of the cerebrospinal fluid of patients with schizophrenia. Amino Acids 25(1), 49-57 (2003).
96. Huang JT, McKenna T, Hughes C, Leweke FM, Schwarz E, Bahn S. CSF biomarker discovery using label-free nano-LC-MS based proteomic profiling: technical aspects. J. Sep. Sci. 30(2), 214-225 (2007).
97. Clark D, Dedova I, Cordwell S, Matsumoto I. A proteome analysis of the anterior cingulate cortex gray matter in schizophrenia. Mol. Psychiatry 11(5), 459-470, 423 (2006).
98. Clark D, Dedova I, Cordwell S, Matsumoto I. Altered proteins of the anterior cingulate cortex white matter proteome in schizophrenia. Proteomics Clin. Appl. 1(2), 157-166 (2007).
99. Hempel A, Hempel E, Schonknecht P, Stippich C, Schroder J. Impairment in basal limbic function in schizophrenia during affect recognition. Psychiatr. Res. Neuroim. 122(2), 115-124 (2003).
100. Carter CS, Barch DB, McDonald A et al. Anterior cingulate cortex and cognitive disability in schizophrenia. Biol. Psychiatry 45(8S), S60-S60 (1999).
101. Ross LL, Barch DB, Cohen JD et al. Anterior cingulate cortex dysfunction and cognitive disability in schizophrenia. J. Cogn. Neurosci. 62-63 (1999).
102. Salgado-Pineda P, Baeza I, Perez-Gomez M et al. Sustained attention impairment correlates to gray matter decreases in first episode neuroleptic-naive schizophrenic patients. Neuroimage 19(2), 365-375 (2003).
103. Fujiwara H, Hirao K, Namiki C et al. Anterior cingulate pathology and social cognition in schizophrenia: a study of gray matter, white matter and sulcal morphometry. Neuroimage 36(4), 1236-1245 (2007).
104. Zetzsche T, Preuss U, Frodl T et al. In-vivo topography of structural alterations of the anterior cingulate in patients with schizophrenia: new findings and comparison with the literature. Schizophr. Res. 96(1-3), 34-45 (2007).
105. Mitelman SA, Brickman AM, Shihabuddin L et al. A comprehensive assessment of gray and white matter volumes and their relationship to outcome and severity in schizophrenia. Neuroimage 37(2), 449-462 (2007).
106. Sivagnanasundaram S, Crossett B, Dedova I, Cordwell S, Matsumoto I. Abnormal pathways in the genu of the corpus callosum in schizophrenia pathogenesis: a proteome study. Proteomics Clin. Appl. 1(10), 1291-1305 (2007).
107. Mu J, Xie P, Yang ZS et al. Neurogenesis and major depression: implications from proteomic analyses of hippocampal proteins in a rat depression model. Neurosci. Lett. 416(3), 252-256 (2007).
108. Belmaker RH, Agam G. Major depressive disorder. N. Engl. J. Med. 358(1), 55-68 (2008).
109. Swaab DF, Bao AM, Lucassen PJ. The stress system in the human brain in depression and neurodegeneration. Ageing Res. Rev. 4(2), 141-194 (2005).
110. Merali Z, Du L, Hrdina P et al. Dysregulation in the suicide brain: mRNA expression of corticotropin-releasing hormone receptors and GABAA receptor subunits in frontal cortical brain region. J. Neurosci. 24(6), 1478-1485 (2004).
111. Naismith SL, Hickie IB, Turner K et al. Neuropsychological performance in patients with depression is associated with clinical, etiological and genetic risk factors. J. Clin. Exp. Neuropsychol. 25(6), 866-877 (2003).
112. Campbell S, Macqueen G. The role of the hippocampus in the pathophysiology of major depression. J. Psychiatry Neurosci. 29(6), 417-426 (2004).
113. 2 and concomitant changes in mitochondrial redox state. J. Neurosci. 28(5), 1153-1162 (2008).
114. Zhao Y, Ma R, Shen J, Su H, Xing D, Du L. A mouse model of depression induced by repeated corticosterone injections. Eur. J. Clin. Pharmacol. 581(1,2), 113-120 (2007).
115. Bergstrom A, Jayatissa MN, Mork A, Wiborg O. Stress sensitivity and resilience in the chronic mild stress rat model of depression; an in situ hybridization study. Brain Res. 1196, 41-52 (2007).
116. Santarelli L, Saxe M, Gross C et al. Requirement of hippocampal neurogenesis for the behavioral effects of antidepressants. Science 301(5634), 805-809 (2003).
117. Duman RS, Malberg J, Nakagawa S, D'Sa C. Neuronal plasticity and survival in mood disorders. Biol. Psychiatry 48(8), 732-739 (2000).
118. Khawaja X, Xu J, Liang JJ, Barrett JE. Proteomic analysis of protein changes developing in rat hippocampus after chronic antidepressant treatment: Implications for depressive disorders and future therapies. J. Neurosci. Res. 75(4), 451-460 (2004).
119. Ali SF, Chang LW, Slikker W Jr. Biogenic amines as biomarkers for neurotoxicity. Biomed. Environ. Sci. 4(1-2), 207-216 (1991).
120. Ishigami A, Tokunaga I, Gotohda T, Kubo S. Immunohistochemical study of myoglobin and oxidative injury-related markers in the kidney of methamphetamine abusers. Leg. Med. (Tokyo) 5(1), 42-48 (2003).
121. Yuan X, Desiderio DM. Human cerebrospinal fluid peptidomics. J. Mass Spectrom. 40(2), 176-181 (2005).
122. Yuan X, Desiderio DM. Proteomics analysis of human cerebrospinal fluid. J. Chromatogr. 815(1-2), 179-189 (2005).
123. Yuan X, Desiderio DM. Proteomics analysis of prefractionated human lumbar cerebrospinal fluid. Proteomics 5(2), 541-550 (2005).
124. Davidsson P, Sjogren M. The use of proteomics in biomarker discovery in neurodegenerative diseases. Dis. Markers 21(2), 81-92 (2005).
125. Huang JT, Leweke FM, Tsang TM et al. CSF metabolic and proteomic profiles in patients prodromal for psychosis. PLoS ONE 2(1), E756 (2007).
126. Bendikov I, Nadri C, Amar S et al. A CSF and postmortem brain study of D-serine metabolic parameters in schizophrenia. Schizophr. Res. 90(1-3), 41-51 (2007).
127. Chua SE, Cheung C, Cheung V et al. Cerebral grey, white matter and CSF in never-medicated, first-episode schizophrenia. Schizophr. Res. 89(1-3), 12-21 (2007).
128. Muller N, Schwarz M. Schizophrenia as an inflammation-mediated dysbalance of glutamatergic neurotransmission. Neurotox. Res. 10(2), 131-148 (2006).
129. Raedler TJ, Wiedemann K. CSF-studies in neuropsychiatric disorders. Neuro Endocrinol. Lett. 27(3), 297-305 (2006).
130. Frye MA, Tsai GE, Huggins T, Coyle JT, Post RM. Low cerebrospinal fluid glutamate and glycine in refractory affective disorder. Biol. Psychiatry 61(2), 162-166 (2007).
131. Haskins WE, Kobeissy FH, Wolper RA et al. Rapid discovery of putative protein biomarkers of traumatic brain injury by SDS-PAGE-capillary liquid chromatography-tandem mass spectrometry. J. Neurotrauma 22(6), 629-644 (2005).
132. Motoyama A, Xu T, Ruse CI, Wohlschlegel JA, Yates JR III. Anion and cation mixed-bed ion exchange for enhanced multidimensional separations of peptides and phosphopeptides. Anal. Chem. 79(10), 3623-3634 (2007).
133. Delahunty CM, Yates JR III. MudPIT: multidimensional protein identification technology. BioTechniques 43(5), 563, 565, 567 passim (2007).
134. Abdi F, Quinn JF, Jankovic J et al. Detection of biomarkers with a multiplex quantitative proteomic platform in cerebrospinal fluid of patients with neurodegenerative disorders. J. Alzheimers Dis. 9(3), 293-348 (2006).
135. Melanson JE, Avery SL, Pinto DM. High-coverage quantitative proteomics using amine-specific isotopic labeling. Proteomics 6(16), 4466-4474 (2006).
136. Sato T, Ishihama Y, Oda Y. Quantitative proteomics of mouse brain and specific protein-interaction studies using stable isotope labeling. Methods Mol. Biol. 359, 53-70 (2007).
137. Nilsson CL, Larsson T, Gustafsson E, Karlsson KA, Davidsson P. Identification of protein vaccine candidates from Helicobacter pylori using a preparative two-dimensional electrophoretic procedure and mass spectrometry. Anal. Chem. 72(9), 2148-2153 (2000).
138. Davidsson P, Folkesson S, Christiansson M et al. Identification of proteins in human cerebrospinal fluid using liquid-phase isoelectric focusing as a prefractionation step followed by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionisation mass spectrometry. Rapid Commun. Mass Spectrom. 16(22), 2083-2088 (2002).
139. Zhan X, Desiderio DM. Nitroproteins from a human pituitary adenoma tissue discovered with a nitrotyrosine affinity column and tandem mass spectrometry. Anal. Biochem. 354(2), 279-289 (2006).
140. Gokulrangan G, Zaidi A, Michaelis ML, Schoneich C. Proteomic analysis of protein nitration in rat cerebellum: effect of biological aging. J. Neurochem. 100(6), 1494-1504 (2007).
141. Vaishnav RA, Getchell ML, Poon HF et al. Oxidative stress in the aging murine olfactory bulb: redox proteomics and cellular localization. J. Neurosci. Res. 85(2), 373-385 (2007).
142. Sultana R, Perluigi M, Butterfield DA. Protein oxidation and lipid peroxidation in brain of subjects with Alzheimer's disease: insights into mechanism of neurodegeneration from redox proteomics. Antioxid. Redox Signal. 8(11-12), 2021-2037 (2006).
143. Butterfield DA, Perluigi M, Sultana R. Oxidative stress in Alzheimer's disease brain: new insights from redox proteomics. Eur. J. Clin. Pharmacol. 545(1), 39-50 (2006).
144. Poon HF, Shepherd HM, Reed TT et al. Proteomics analysis provides insight into caloric restriction mediated oxidation and expression of brain proteins associated with age-related impaired cellular processes: mitochondrial dysfunction, glutamate dysregulation and impaired protein synthesis. Neurobiol. Aging 27(7), 1020-1034 (2006).
145. Castegna A, Thongboonkerd V, Klein JB, Lynn B, Markesbery WR, Butterfield DA. Proteomic identification of nitrated proteins in Alzheimer's disease brain. J. Neurochem. 85(6), 1394-1401 (2003).
146. Do KQ, Trabesinger AH, Kirsten-Kruger M et al. Schizophrenia: glutathione deficit in cerebrospinal fluid and prefrontal cortex in vivo. Eur. J. Neurosci. 12(10), 3721-3728 (2000).
147. Taneli F, Pirildar S, Akdeniz F, Uyanik BS, Ari Z. Serum nitric oxide metabolite levels and the effect of antipsychotic therapy in schizophrenia. Arch. Med. Res. 35(5), 401-405 (2004).
148. Ramirez J, Garnica R, Boll MC, Montes S, Rios C. Low concentration of nitrite and nitrate in the cerebrospinal fluid from schizophrenic patients: a pilot study. Schizophr. Res. 68(2-3), 357-361 (2004).
149. Ng F, Berk M, Dean O, Bush AI. Oxidative stress in psychiatric disorders: evidence base and therapeutic implications. Int. J. Neuropsychopharmacol. 1-26 PMID: 18205981 (2008) (Epub ahead of print).
150. McQuibban GA, Gong JH, Tam EM, McCulloch CA, Clark-Lewis I, Overall CM. Inflammation dampened by gelatinase A cleavage of monocyte chemoattractant protein-3. Science 289(5482), 1202-1206 (2000).
151. Lopez-Otin C, Overall CM. Protease degradomics: a new challenge for proteomics. Nat. Rev. Mol. Cell Biol. 3(7), 509-519 (2002).
152. auf dem Keller U, Doucet A, Overall CM. Protease research in the era of systems biology. Biol. Chem. 388(11), 1159-1162 (2007).
153. Warren MW, Zheng W, Kobeissy FH et al. Calpain- and caspase-mediated ?II-spectrin and tau proteolysis in rat cerebrocortical neuronal cultures after ecstasy or methamphetamine exposure. Int. J. Neuropsychopharmacol. 10(4), 479-489 (2007).
154. Bernath E, Kupina N, Liu MC, Hayes RL, Meegan C, Wang KK. Elevation of cytoskeletal protein breakdown in aged Wistar rat brain. Neurobiol. Aging 27(4), 624-632 (2006).
155. Lee AY, Park BC, Jang M et al. Identification of caspase-3 degradome by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionizationtime of flight analysis. Proteomics 4(11), 3429-3436 (2004).
156. Overall CM, Dean RA. Degradomics: systems biology of the protease web. Pleiotropic roles of MMPs in cancer. Cancer Metastasis Rev. 25(1), 69-75 (2006).
157. Liu MC, Akle V, Zheng W et al. Comparing calpain- and caspase-3-mediated degradation patterns in traumatic brain injury by differential proteome analysis. Biochem. J. 394(Pt 3), 715-725 (2006).
158. Dunckley T, Coon KD, Stephan DA. Discovery and development of biomarkers of neurological disease. Drug Discov. Today 10(5), 326-334 (2005).
159. Hollywood K, Brison DR, Goodacre R. Metabolomics: current technologies and future trends. Proteomics 6(17), 4716-4723 (2006).
160. Ohdoi C, Nyhan WL, Kuhara T. Chemical diagnosis of Lesch-Nyhan syndrome using gas chromatography-mass spectrometry detection. J. Chromatogr. B 792(1), 123-130 (2003).
161. Kell DB. Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol. 7(3), 296-307 (2004).
162. Westerhoff HV, Palsson BO. The evolution of molecular biology into systems biology. Nat. Biotechnol. 22(10), 1249-1252 (2004).
163. Noble F, Roques BP. Protection of endogenous enkephalin catabolism as natural approach to novel analgesic and antidepressant drugs. Expert Opin. Ther. Targets 11(2), 145-159 (2007).
164. Terenius L, Sandin J, Sakurada T. Nociceptin/orphanin FQ metabolism and bioactive metabolites. Peptides 21(7), 919-922 (2000).
165. Chen H, Noble F, Coric P, Fournie-Zaluski MC, Roques BP. Aminophosphinic inhibitors as transition state analogues of enkephalin-degrading enzymes: a class of central analgesics. Proc. Natl Acad. Sci. USA 95(20), 12028-12033 (1998).
166. Chen H, Noble F, Mothe A et al. Phosphinic derivatives as new dual enkephalin-degrading enzyme inhibitors: synthesis, biological properties, and antinociceptive activities. J. Med. Chem. 43(7), 1398-1408 (2000).
167. Warren M, Larner S, Jeung J et al. Calpain and caspase proteolytic markers co-localize with rat cortical neurons after meth and MDMA use. J. Neurochem. 114(3), 277-286 (2007).
168. Wallace TL, Vorhees CV, Zemlan FP, Gudelsky GA. Methamphetamine enhances the cleavage of the cytoskeletal protein tau in the rat brain. Neuroscience 116(4), 1063-1068 (2003).
169. Skynner HA, Amos DP, Murray F et al. Proteomic analysis identifies alterations in cellular morphology and cell death pathways in mouse brain after chronic corticosterone treatment. Brain Res. 1102(1), 12-26 (2006).
170. Kitano H. Computational systems biology. Nature 420(6912), 206-210 (2002).
171. Kitano H. Systems biology: a brief overview. Science 295(5560), 1662-1664 (2002).
172. Barabasi AL, Albert R. Emergence of scaling in random networks. Science 286(5439), 509-512 (1999).
173. Grant SG. Systems biology in neuroscience: bridging genes to cognition. Curr. Opin. Neurobiol. 13(5), 577-582 (2003).
174. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 422(6928), 198-207 (2003).
175. Dujon B, Albermann K, Aldea M et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome XV. Nature 387(6632 Suppl.), 98-102 (1997).
176. Johnston M, Hillier L, Riles L et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome XII. Nature 387(6632 Suppl.), 87-90 (1997).
177. Bussey H, Storms RK, Ahmed A et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Nature 387(6632 Suppl.), 103-105 (1997).
178. Ideker T, Thorsson V, Ranish JA et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292(5518), 929-934 (2001).
179. van der Greef J, Stroobant P, van der Heijden R. The role of analytical sciences in medical systems biology. Curr. Opin. Chem. Biol. 8(5), 559-565 (2004).
180. van der Greef J. Systems biology, connectivity and the future of medicine. Syst. Biol. (Stevenage) 152(4), 174-178 (2005).
181. Jordan BA, Ziff EB. Getting to synaptic complexes through systems biology. Genome Biol. 7(4), 214 (2006).
182. Fitzgerald JB, Schoeberl B, Nielsen UB, Sorger PK. Systems biology and combination therapy in the quest for clinical efficacy. Nat. Chem. Biol. 2(9), 458-466 (2006).
183. Ikonomidou C, Mosinger JL, Salles KS, Labruyere J, Olney JW. Sensitivity of the developing rat brain to hypobaric/ischemic damage parallels sensitivity to N-methyl-aspartate neurotoxicity. J. Neurosci. 9(8), 2809-2818 (1989).
184. Wang C, Showalter VM, Hillman GR, Johnson KM. Chronic phencyclidine increases NMDA receptor NR1 subunit mRNA in rat forebrain. J. Neurosci. Res. 55(6), 762-769 (1999).
185. Ikonomidou C, Bosch F, Miksa M et al. Blockade of NMDA receptors and apoptotic neurodegeneration in the developing brain. Science 283(5398), 70-74 (1999).
186. Abi-Saab WM, D'Souza DC, Moghaddam B, Krystal JH. The NMDA antagonist model for schizophrenia: promise and pitfalls. Pharmacopsychiatry 31(Suppl. 2), 104-109 (1998).
187. Carter AJ. Antagonists of the NMDA receptor-channel complex and motor coordination. Life Sci. 57(10), 917-929 (1995).
188. Catts SV, Ward PB, Lloyd A et al. Molecular biological investigations into the role of the NMDA receptor in the pathophysiology of schizophrenia. Aust. NZ J. Psychiatry 31(1), 17-26 (1997).
189. Benes FM, McSparren J, Bird ED, SanGiovanni JP, Vincent SL. Deficits in small interneurons in prefrontal and cingulate cortices of schizophrenic and schizoaffective patients. Arch. Gen. Psychiatry 48(11), 996-1001 (1991).
190. Slikker W Jr, Paule MG, Wright LK, Patterson TA, Wang C. Systems biology approaches for toxicology. J. Appl. Toxicol. 27(3), 201-217 (2007).
191. Carlsson A, Lindqvist M. Effect of chlorpromazine or haloperidol on formation of 3-methoxytyramine and normetanephrine in mouse brain. Acta Pharmacol. Toxicol. (Copenh.) 20, 140-144 (1963).
192. Grace AA. Phasic versus tonic dopamine release and the modulation of dopamine system responsivity: a hypothesis for the etiology of schizophrenia. Neuroscience 41(1), 1-24 (1991).
193. Abi-Dargham A, Rodenhiser J, Printz D et al. Increased baseline occupancy of D2 receptors by dopamine in schizophrenia. Proc. Natl Acad. Sci. USA 97(14), 8104-8109 (2000).
194. Juckel G, Schlagenhauf F, Koslowski M et al. Dysfunction of ventral striatal reward prediction in schizophrenia. Neuroimage 29(2), 409-416 (2006).
195. Laruelle M, Abi-Dargham A, Gil R, Kegeles L, Innis R. Increased dopamine transmission in schizophrenia: relationship to illness phases. Biol. Psychiatry 46(1), 56-72 (1999).
196. Krystal JH, Perry EB Jr, Gueorguieva R et al. Comparative and interactive human psychopharmacologic effects of ketamine and amphetamine: implications for glutamatergic and dopaminergic model psychoses and cognitive function. Arch. Gen. Psychiatry 62(9), 985-994 (2005).
197. Jentsch JD, Taylor JR, Roth RH. Subchronic phencyclidine administration increases mesolimbic dopaminergic system responsivity and augments stress- and psychostimulant-induced hyperlocomotion. Neuropsychopharmacology 19(2), 105-113 (1998).
198. Carlsson A. The neurochemical circuitry of schizophrenia. Pharmacopsychiatry 39(Suppl. 1), S10-S14 (2006).
199. Carlsson A, Carlsson ML. A dopaminergic deficit hypothesis of schizophrenia: the path to discovery. Dialogues Clin. Neurosci. 8(1), 137-142 (2006).
200. Sesack SR, Carr DB, Omelchenko N, Pinto A. Anatomical substrates for glutamate-dopamine interactions: evidence for specificity of connections and extrasynaptic actions. Ann. NY Acad. Sci. 1003, 36-52 (2003).
201. Mann M. Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol. 7(12), 952-958 (2006).
202. Stratagene. An agilant technologies company www.stratagene.com