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Review

Psychiatric research: psychoproteomics, degradomics and systems biology

, , , &
Pages 293-314 | Published online: 09 Jan 2014

References

  • 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).
  • Kobeissy FH, Warren M, Ottens AK et al. Psychoproteomic analysis of rat cortex following acute methamphetamine exposure. J. Proteome Res. (2008) (In Press).
  • Nestler EJ. Psychogenomics: opportunities for understanding addiction. J. Neurosci.21(21), 8324–8327 (2001).
  • Choudhary J, Grant SG. Proteomics in postgenomic neuroscience: the end of the beginning. Nat. Neurosci.7(5), 440–445 (2004).
  • 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).
  • Williams K, Wu T, Colangelo C, Nairn AC. Recent advances in neuroproteomics and potential application to studies of drug addiction. Neuropharmacology47(Suppl. 1), 148–166 (2004).
  • Wang KK, Ottens AK, Liu MC et al. Proteomic identification of biomarkers of traumatic brain injury. Expert Rev. Proteomics2(4), 603–614 (2005).
  • Morrison RS, Kinoshita Y, Johnson MD et al. Proteomic analysis in the neurosciences. Mol. Cell Proteomics1(8), 553–560 (2002).
  • Wang KK, Ottens A, Haskins W et al. Proteomics studies of traumatic brain injury. Int. Rev. Neurobiol.61, 215–240 (2004).
  • 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).
  • Denslow N, Michel ME, Temple MD, Hsu CY, Saatman K, Hayes RL. Application of proteomics technology to the field of neurotrauma. J. Neurotrauma20(5), 401–407 (2003).
  • Missler M, Sudhof TC. Neurexins: three genes and 1001 products. Trends Genet.14(1), 20–26 (1998).
  • Hunnerkopf R, Grassl J, Thome J. Proteomics: biomarker research in psychiatry. Fortschr. Neurol. Psychiatr.75(10), 579–586 (2007).
  • Wu Q, Maniatis T. A striking organization of a large family of human neural cadherin-like cell adhesion genes. Cell97(6), 779–790 (1999).
  • Patton WF. Detection technologies in proteome analysis. J. Chromatogr.771(1–2), 3–31 (2002).
  • Hortin GL, Jortani SA, Ritchie JC Jr, Valdes R Jr, Chan DW. Proteomics: a new diagnostic frontier. Clin. Chem.52(7), 1218–1222 (2006).
  • Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics1(11), 845–867 (2002).
  • 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. Proteomics5(13), 3226–3245 (2005).
  • Schmidt O, Schulenborg T, Meyer HE, Marcus K, Hamacher M. How proteomics reveals potential biomarkers in brain diseases. Expert Rev. Proteomics2(6), 901–913 (2005).
  • Grant SG, Blackstock WP. Proteomics in neuroscience: from protein to network. J. Neurosci.21(21), 8315–8318 (2001).
  • 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).
  • Taylor CM, Pfeiffer SE. Enhanced resolution of glycosylphosphatidylinositol-anchored and transmembrane proteins from the lipid-rich myelin membrane by two-dimensional gel electrophoresis. Proteomics3(7), 1303–1312 (2003).
  • Dackis CA, O’Brien CP. Cocaine dependence: a disease of the brain’s reward centers. J. Subst. Abuse Treat.21(3), 111–117 (2001).
  • Dackis C, O’Brien C. Neurobiology of addiction: treatment and public policy ramifications. Nat. Neurosci.8(11), 1431–1436 (2005).
  • Volkow N, Li TK. The neuroscience of addiction. Nat. Neurosci.8(11), 1429–1430 (2005).
  • Volkow ND, Fowler JS, Wang GJ, Swanson JM. Dopamine in drug abuse and addiction: results from imaging studies and treatment implications. Mol. Psychiatry9(6), 557–569 (2004).
  • Volkow N. Drug dependence and addiction, III: expectation and brain function in drug abuse. Am. J. Psychiatry161(4), 621 (2004).
  • Uhl GR. Molecular genetics of addiction vulnerability. NeuroRx3(3), 295–301 (2006).
  • 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).
  • 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).
  • Bibb JA, Chen J, Taylor JR et al. Effects of chronic exposure to cocaine are regulated by the neuronal protein Cdk5. Nature410(6826), 376–380 (2001).
  • 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).
  • Roche KW. The expanding role of PSD-95: a new link to addiction. Trends Neurosci.27(12), 699–700 (2004).
  • Nestler EJ. Under siege: the brain on opiates. Neuron16(5), 897–900 (1996).
  • Blackstock WP, Weir MP. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol.17(3), 121–127 (1999).
  • Nestler EJ. Molecular mechanisms of opiate and cocaine addiction. Curr. Opin. Neurobiol.7(5), 713–719 (1997).
  • 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).
  • Bailey CP, Connor M. Opioids: cellular mechanisms of tolerance and physical dependence. Curr. Opin. Pharmacol.5(1), 60–68 (2005).
  • 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).
  • 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. Pain85(3), 395–404 (2000).
  • Wong CS, Hsu MM, Chou YY, Tao PL, Tung CS. Morphine tolerance increases [3H]MK-801 binding affinity and constitutive neuronal nitric oxide synthase expression in rat spinal cord. Br. J. Anaesth.85(4), 587–591 (2000).
  • Shui HA, Ho ST, Wang JJ et al. Proteomic analysis of spinal protein expression in rats exposed to repeated intrathecal morphine injection. Proteomics7(5), 796–803 (2007).
  • 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).
  • 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).
  • Bodzon-Kulakowska A, Bierczynska-Krzysik A, Drabik A et al. Morphinome – proteome of the nervous system after morphine treatment. Amino acids28(1), 13–19 (2005).
  • Bierczynska-Krzysik A, Bonar E, Drabik A et al. Rat brain proteome in morphine dependence. Neurochem. Int.49(4), 401–406 (2006).
  • 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. Proteomics6(6), 2003–2008 (2006).
  • 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. Proteomics6(1), 29–42 (2007).
  • Li KW. Proteomics of synapse. Anal. Bioanal. Chem.387(1), 25–28 (2007).
  • 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).
  • Warren MW, Kobeissy FH, Liu MC, Hayes RL, Gold MS, Wang KK. Concurrent calpain and caspase-3 mediated proteolysis of a II-spectrin and tau in rat brain after methamphetamine exposure: a similar profile to traumatic brain injury. Life Sci.78(3), 301–309 (2005).
  • 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).
  • 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).
  • Warren MW, Zheng W, Kobeissy FH et al. Calpain- and caspase-mediated αII-spectrin and tau proteolysis in rat cerebrocortical neuronal cultures after ecstasy or methamphetamine exposure. Int. J. Neuropsychopharmacol.10(4), 479–489 (2007).
  • 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).
  • Kumar A, Choi KH, Renthal W et al. Chromatin remodeling is a key mechanism underlying cocaine-induced plasticity in striatum. Neuron48(2), 303–314 (2005).
  • 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. USA102(52), 19186–19191 (2005).
  • 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).
  • Iwazaki T, McGregor IS, Matsumoto I. Protein expression profile in the striatum of acute methamphetamine-treated rats. Brain Res.1097(1), 19–25 (2006).
  • Iwazaki T, McGregor IS, Matsumoto I. Protein expression profile in the striatum of rats with methamphetamine-induced behavioral sensitization. Proteomics7(7), 1131–1139 (2007).
  • Sokolov BP, Cadet JL. Methamphetamine causes alterations in the MAP kinase-related pathways in the brains of mice that display increased aggressiveness. Neuropsychopharmacology31(5), 956–966 (2006).
  • 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).
  • 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. Biomarkers11(4), 355–369 (2006).
  • Kobeissy FH, Ottens AK, Zhang Z et al. Novel differential neuroproteomics analysis of traumatic brain injury in rats. Mol. Cell. Proteomics5(10), 1887–1898 (2006).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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. Psychiatry11(1), 56–65 (2006).
  • 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).
  • Matsumoto I, Alexander-Kaufman K, Iwazaki T, Kashem MA, Matsuda-Matsumoto H. CNS proteomes in alcohol and drug abuse and dependence. Expert Rev. Proteomics4(4), 539–552 (2007).
  • Quinn HR, Matsumoto I, Callaghan PD et al. Adolescent rats find repeated δ(9)-THC less aversive than adult rats but display greater residual cognitive deficits and changes in hippocampal protein expression following exposure. Neuropsychopharmacology33(5), 1113–1126 (2008).
  • 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. Psychiatry5(2), 142–149 (2000).
  • Susser E, Wanderling J. Epidemiology of nonaffective acute remitting psychosis vs schizophrenia. Sex and sociocultural setting. Arch. Gen. Psychiatry51(4), 294–301 (1994).
  • Lakhan SE. Schizophrenia proteomics: biomarkers on the path to laboratory medicine? Diagn. Pathol.1, 11 (2006).
  • Sawa A, Snyder SH. Schizophrenia: diverse approaches to a complex disease. Science296(5568), 692–695 (2002).
  • Frankle WG, Lerma J, Laruelle M. The synaptic hypothesis of schizophrenia. Neuron39(2), 205–216 (2003).
  • Benes FM. Emerging principles of altered neural circuitry in schizophrenia. Brain Res.31(2–3), 251–269 (2000).
  • 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. Psychiatry51(5), 377–386 (2002).
  • Gallinat J, Obermayer K, Heinz A. Systems neurobiology of the dysfunctional brain: schizophrenia. Pharmacopsychiatry40(Suppl. 1), S40–S44 (2007).
  • Iritani S. Neuropathology of schizophrenia: a mini review. Neuropathology27(6), 604–608 (2007).
  • Tan HY, Callicott JH, Weinberger DR. Dysfunctional and compensatory prefrontal cortical systems, genes and the pathogenesis of schizophrenia. Cereb. Cortex17(Suppl. 1), i171–i181 (2007).
  • Waddington JL. Neuroimaging and other neurobiological indices in schizophrenia: relationship to measurement of functional outcome. Br. J. Psychiatry Suppl.50, S52–S57 (2007).
  • 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).
  • Clark WG. Schizophrenia and genomics: linking research to practice. J. Psychosoc. Nurs. Ment. Health Serv.45(6), 24–28 (2007).
  • McClellan JM, Susser E, King MC. Schizophrenia: a common disease caused by multiple rare alleles. Br. J. Psychiatry190, 194–199 (2007).
  • 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. Psychiatry12(1), 87–93 (2007).
  • Owen MJ. Genomic approaches to schizophrenia. Clin. Ther.27(Suppl. A), S2–S7 (2005).
  • 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).
  • 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).
  • Prabakaran S, Swatton JE, Ryan MM et al. Mitochondrial dysfunction in schizophrenia: evidence for compromised brain metabolism and oxidative stress. Mol. Psychiatry9(7), 684–697, 643 (2004).
  • 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. Psychiatry4(2), 173–178 (1999).
  • van Kammen DP, Guidotti A, Kelley ME et al. CSF diazepam binding inhibitor and schizophrenia: clinical and biochemical relationships. Biol. Psychiatry34(8), 515–522 (1993).
  • Jiang L, Lindpaintner K, Li HF et al. Proteomic analysis of the cerebrospinal fluid of patients with schizophrenia. Amino Acids25(1), 49–57 (2003).
  • 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).
  • Clark D, Dedova I, Cordwell S, Matsumoto I. A proteome analysis of the anterior cingulate cortex gray matter in schizophrenia. Mol. Psychiatry11(5), 459–470, 423 (2006).
  • 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).
  • 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).
  • Carter CS, Barch DB, McDonald A et al. Anterior cingulate cortex and cognitive disability in schizophrenia. Biol. Psychiatry45(8S), S60–S60 (1999).
  • Ross LL, Barch DB, Cohen JD et al. Anterior cingulate cortex dysfunction and cognitive disability in schizophrenia.J. Cogn. Neurosci.62–63 (1999).
  • 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. Neuroimage19(2), 365–375 (2003).
  • 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. Neuroimage36(4), 1236–1245 (2007).
  • 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).
  • 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. Neuroimage37(2), 449–462 (2007).
  • 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).
  • 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).
  • Belmaker RH, Agam G. Major depressive disorder. N. Engl. J. Med.358(1), 55–68 (2008).
  • 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).
  • 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).
  • 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).
  • Campbell S, Macqueen G. The role of the hippocampus in the pathophysiology of major depression. J. Psychiatry Neurosci.29(6), 417–426 (2004).
  • Huchzermeyer C, Albus K, Gabriel HJ et al. g oscillations and spontaneous network activity in the hippocampus are highly sensitive to decreases in pO2 and concomitant changes in mitochondrial redox state. J. Neurosci.28(5), 1153–1162 (2008).
  • 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).
  • 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).
  • Santarelli L, Saxe M, Gross C et al. Requirement of hippocampal neurogenesis for the behavioral effects of antidepressants. Science301(5634), 805–809 (2003).
  • Duman RS, Malberg J, Nakagawa S, D’Sa C. Neuronal plasticity and survival in mood disorders. Biol. Psychiatry48(8), 732–739 (2000).
  • 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).
  • Ali SF, Chang LW, Slikker W Jr. Biogenic amines as biomarkers for neurotoxicity. Biomed. Environ. Sci.4(1–2), 207–216 (1991).
  • 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).
  • Yuan X, Desiderio DM. Human cerebrospinal fluid peptidomics. J. Mass Spectrom.40(2), 176–181 (2005).
  • Yuan X, Desiderio DM. Proteomics analysis of human cerebrospinal fluid. J. Chromatogr.815(1–2), 179–189 (2005).
  • Yuan X, Desiderio DM. Proteomics analysis of prefractionated human lumbar cerebrospinal fluid. Proteomics5(2), 541–550 (2005).
  • Davidsson P, Sjogren M. The use of proteomics in biomarker discovery in neurodegenerative diseases. Dis. Markers21(2), 81–92 (2005).
  • Huang JT, Leweke FM, Tsang TM et al. CSF metabolic and proteomic profiles in patients prodromal for psychosis. PLoS ONE2(1), E756 (2007).
  • 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).
  • 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).
  • Muller N, Schwarz M. Schizophrenia as an inflammation-mediated dysbalance of glutamatergic neurotransmission. Neurotox. Res.10(2), 131–148 (2006).
  • Raedler TJ, Wiedemann K. CSF-studies in neuropsychiatric disorders. Neuro Endocrinol. Lett.27(3), 297–305 (2006).
  • Frye MA, Tsai GE, Huggins T, Coyle JT, Post RM. Low cerebrospinal fluid glutamate and glycine in refractory affective disorder. Biol. Psychiatry61(2), 162–166 (2007).
  • 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. Neurotrauma22(6), 629–644 (2005).
  • 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).
  • Delahunty CM, Yates JR III. MudPIT: multidimensional protein identification technology. BioTechniques43(5), 563, 565, 567 passim (2007).
  • 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).
  • Melanson JE, Avery SL, Pinto DM. High-coverage quantitative proteomics using amine-specific isotopic labeling. Proteomics6(16), 4466–4474 (2006).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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. Aging27(7), 1020–1034 (2006).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • McQuibban GA, Gong JH, Tam EM, McCulloch CA, Clark-Lewis I, Overall CM. Inflammation dampened by gelatinase A cleavage of monocyte chemoattractant protein-3. Science289(5482), 1202–1206 (2000).
  • Lopez-Otin C, Overall CM. Protease degradomics: a new challenge for proteomics. Nat. Rev. Mol. Cell Biol.3(7), 509–519 (2002).
  • auf dem Keller U, Doucet A, Overall CM. Protease research in the era of systems biology. Biol. Chem.388(11), 1159–1162 (2007).
  • Warren MW, Zheng W, Kobeissy FH et al. Calpain- and caspase-mediated αII-spectrin and tau proteolysis in rat cerebrocortical neuronal cultures after ecstasy or methamphetamine exposure. Int. J. Neuropsychopharmacol.10(4), 479–489 (2007).
  • Bernath E, Kupina N, Liu MC, Hayes RL, Meegan C, Wang KK. Elevation of cytoskeletal protein breakdown in aged Wistar rat brain. Neurobiol. Aging27(4), 624–632 (2006).
  • Lee AY, Park BC, Jang M et al. Identification of caspase-3 degradome by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization-time of flight analysis. Proteomics4(11), 3429–3436 (2004).
  • 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).
  • 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).
  • Dunckley T, Coon KD, Stephan DA. Discovery and development of biomarkers of neurological disease. Drug Discov. Today10(5), 326–334 (2005).
  • Hollywood K, Brison DR, Goodacre R. Metabolomics: current technologies and future trends. Proteomics6(17), 4716–4723 (2006).
  • Ohdoi C, Nyhan WL, Kuhara T. Chemical diagnosis of Lesch–Nyhan syndrome using gas chromatography-mass spectrometry detection. J. Chromatogr. B792(1), 123–130 (2003).
  • Kell DB. Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol.7(3), 296–307 (2004).
  • Westerhoff HV, Palsson BO. The evolution of molecular biology into systems biology. Nat. Biotechnol.22(10), 1249–1252 (2004).
  • Noble F, Roques BP. Protection of endogenous enkephalin catabolism as natural approach to novel analgesic and antidepressant drugs. Expert Opin. Ther. Targets11(2), 145–159 (2007).
  • Terenius L, Sandin J, Sakurada T. Nociceptin/orphanin FQ metabolism and bioactive metabolites. Peptides21(7), 919–922 (2000).
  • 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. USA95(20), 12028–12033 (1998).
  • 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).
  • 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).
  • Wallace TL, Vorhees CV, Zemlan FP, Gudelsky GA. Methamphetamine enhances the cleavage of the cytoskeletal protein tau in the rat brain. Neuroscience116(4), 1063–1068 (2003).
  • 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).
  • Kitano H. Computational systems biology. Nature420(6912), 206–210 (2002).
  • Kitano H. Systems biology: a brief overview. Science295(5560), 1662–1664 (2002).
  • Barabasi AL, Albert R. Emergence of scaling in random networks. Science286(5439), 509–512 (1999).
  • Grant SG. Systems biology in neuroscience: bridging genes to cognition. Curr. Opin. Neurobiol.13(5), 577–582 (2003).
  • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature422(6928), 198–207 (2003).
  • Dujon B, Albermann K, Aldea M et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome XV. Nature387(6632 Suppl.), 98–102 (1997).
  • Johnston M, Hillier L, Riles L et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome XII. Nature387(6632 Suppl.), 87–90 (1997).
  • Bussey H, Storms RK, Ahmed A et al. The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI. Nature387(6632 Suppl.), 103–105 (1997).
  • Ideker T, Thorsson V, Ranish JA et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science292(5518), 929–934 (2001).
  • 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).
  • van der Greef J. Systems biology, connectivity and the future of medicine. Syst. Biol. (Stevenage)152(4), 174–178 (2005).
  • Jordan BA, Ziff EB. Getting to synaptic complexes through systems biology. Genome Biol.7(4), 214 (2006).
  • 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).
  • 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).
  • 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).
  • Ikonomidou C, Bosch F, Miksa M et al. Blockade of NMDA receptors and apoptotic neurodegeneration in the developing brain. Science283(5398), 70–74 (1999).
  • Abi-Saab WM, D’Souza DC, Moghaddam B, Krystal JH. The NMDA antagonist model for schizophrenia: promise and pitfalls. Pharmacopsychiatry31(Suppl. 2), 104–109 (1998).
  • Carter AJ. Antagonists of the NMDA receptor-channel complex and motor coordination. Life Sci.57(10), 917–929 (1995).
  • 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. Psychiatry31(1), 17–26 (1997).
  • 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. Psychiatry48(11), 996–1001 (1991).
  • Slikker W Jr, Paule MG, Wright LK, Patterson TA, Wang C. Systems biology approaches for toxicology. J. Appl. Toxicol.27(3), 201–217 (2007).
  • 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).
  • Grace AA. Phasic versus tonic dopamine release and the modulation of dopamine system responsivity: a hypothesis for the etiology of schizophrenia. Neuroscience41(1), 1–24 (1991).
  • Abi-Dargham A, Rodenhiser J, Printz D et al. Increased baseline occupancy of D2 receptors by dopamine in schizophrenia. Proc. Natl Acad. Sci. USA97(14), 8104–8109 (2000).
  • Juckel G, Schlagenhauf F, Koslowski M et al. Dysfunction of ventral striatal reward prediction in schizophrenia. Neuroimage29(2), 409–416 (2006).
  • Laruelle M, Abi-Dargham A, Gil R, Kegeles L, Innis R. Increased dopamine transmission in schizophrenia: relationship to illness phases. Biol. Psychiatry46(1), 56–72 (1999).
  • 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. Psychiatry62(9), 985–994 (2005).
  • Jentsch JD, Taylor JR, Roth RH. Subchronic phencyclidine administration increases mesolimbic dopaminergic system responsivity and augments stress- and psychostimulant-induced hyperlocomotion. Neuropsychopharmacology19(2), 105–113 (1998).
  • Carlsson A. The neurochemical circuitry of schizophrenia. Pharmacopsychiatry39(Suppl. 1), S10–S14 (2006).
  • Carlsson A, Carlsson ML. A dopaminergic deficit hypothesis of schizophrenia: the path to discovery. Dialogues Clin. Neurosci.8(1), 137–142 (2006).
  • 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).
  • Mann M. Functional and quantitative proteomics using SILAC. Nat. Rev. Mol. Cell Biol.7(12), 952–958 (2006).

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