pmc logo image
Logo of jnnpsycJournal of Neurology, Neurosurgery and PsychiatryCurrent TOCInstructions for authors

Formats:

J Neurol Neurosurg Psychiatry. 2004 April; 75(4): 529–538.
doi: 10.1136/jnnp.2003.026260.
PMCID: PMC1739030
Functional genomics and proteomics: application in neurosciences
K Wilson, M Ryan, J Prime, D Pashby, P Orange, G O'Beirne, J Whateley, S Bahn, and C Morris
MRC Building, Newcastle General Hospital, Westgate Road, Newcastle upon Tyne, UK.
Full Text
The Full Text of this article is available as a PDF (822K).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
  • Bahn S, Augood SJ, Ryan M, Standaert DG, Starkey M, Emson PC. Gene expression profiling in the post-mortem human brain--no cause for dismay. J Chem Neuroanat. 2001 Jul;22(1-2):79–94. [PubMed]
  • Castensson A, Emilsson L, Preece P, Jazin EE. High-resolution quantification of specific mRNA levels in human brain autopsies and biopsies. Genome Res. 2000 Aug;10(8):1219–1229. [PubMed]
  • Harrison PJ, Heath PR, Eastwood SL, Burnet PW, McDonald B, Pearson RC. The relative importance of premortem acidosis and postmortem interval for human brain gene expression studies: selective mRNA vulnerability and comparison with their encoded proteins. Neurosci Lett. 1995 Nov 24;200(3):151–154. [PubMed]
  • Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987 Apr;162(1):156–159. [PubMed]
  • Mikulowska-Mennis A, Taylor TB, Vishnu P, Michie SA, Raja R, Horner N, Kunitake ST. High-quality RNA from cells isolated by laser capture microdissection. Biotechniques. 2002 Jul;33(1):176–179. [PubMed]
  • Ellis Matthew, Davis Natalie, Coop Andrew, Liu Minetta, Schumaker Lisa, Lee Richard Y, Srikanchana Rujirutana, Russell Chris G, Singh Baljit, Miller William R, Stearns Vered, Pennanen Marie, Tsangaris Theodore, Gallagher Ann, Liu Aiyi, Zwart Alan, Hayes Daniel F, Lippman Marc E, Wang Yue, Clarke Robert. Development and validation of a method for using breast core needle biopsies for gene expression microarray analyses. Clin Cancer Res. 2002 May;8(5):1155–1166. [PubMed]
  • Rapley R. Enhancing PCR amplification and sequencing using DNA-binding proteins. Mol Biotechnol. 1994 Dec;2(3):295–298. [PubMed]
  • Hara E, Kato T, Nakada S, Sekiya S, Oda K. Subtractive cDNA cloning using oligo(dT)30-latex and PCR: isolation of cDNA clones specific to undifferentiated human embryonal carcinoma cells. Nucleic Acids Res. 1991 Dec;19(25):7097–7104. [PubMed]
  • Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science. 1995 Oct 20;270(5235):484–487. [PubMed]
  • Duguid JR, Dinauer MC. Library subtraction of in vitro cDNA libraries to identify differentially expressed genes in scrapie infection. Nucleic Acids Res. 1990 May 11;18(9):2789–2792. [PubMed]
  • Liang P, Pardee AB. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science. 1992 Aug 14;257(5072):967–971. [PubMed]
  • Mahadeva H, Starkey MP, Sheikh FN, Mundy CR, Samani NJ. A simple and efficient method for the isolation of differentially expressed genes. J Mol Biol. 1998 Dec 18;284(5):1391–1398. [PubMed]
  • Ryan M, Starkey M, Faull R, Emson P, Bahn S. Indexing-based differential display--studies on post-mortem Alzheimer's brains. Brain Res Mol Brain Res. 2001 Mar 31;88(1-2):199–202. [PubMed]
  • Bahn Sabine, Mimmack Michael, Ryan Margaret, Caldwell Maeve A, Jauniaux Eric, Starkey Michael, Svendsen Clive N, Emson Piers. Neuronal target genes of the neuron-restrictive silencer factor in neurospheres derived from fetuses with Down's syndrome: a gene expression study. Lancet. 2002 Jan 26;359(9303):310–315. [PubMed]
  • Kim Seong Hwan, Shim Ki Shuk, Lubec Gert. Human brain nascent polypeptide-associated complex alpha subunit is decreased in patients with Alzheimer' s disease and Down syndrome. J Investig Med. 2002 Jul;50(4):293–301. [PubMed]
  • Bustin SA. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J Mol Endocrinol. 2002 Aug;29(1):23–39. [PubMed]
  • Pasinetti GM. Use of cDNA microarray in the search for molecular markers involved in the onset of Alzheimer's disease dementia. J Neurosci Res. 2001 Sep 15;65(6):471–476. [PubMed]
  • Mandel Silvia, Weinreb Orly, Youdim Moussa B H. Using cDNA microarray to assess Parkinson's disease models and the effects of neuroprotective drugs. Trends Pharmacol Sci. 2003 Apr;24(4):184–191. [PubMed]
  • Pongrac Julie, Middleton Frank A, Lewis David A, Levitt Pat, Mirnics Károly. Gene expression profiling with DNA microarrays: advancing our understanding of psychiatric disorders. Neurochem Res. 2002 Oct;27(10):1049–1063. [PubMed]
  • Vawter Marquis P, Crook Jeremy M, Hyde Thomas M, Kleinman Joel E, Weinberger Daniel R, Becker Kevin G, Freed William J. Microarray analysis of gene expression in the prefrontal cortex in schizophrenia: a preliminary study. Schizophr Res. 2002 Nov 1;58(1):11–20. [PubMed]
  • Mimmack Michael L, Ryan Margaret, Baba Hajime, Navarro-Ruiz Juani, Iritani Shuji, Faull Richard L M, McKenna Peter J, Jones Peter B, Arai Heii, Starkey Michael, Emson Piers C, Bahn Sabine. Gene expression analysis in schizophrenia: reproducible up-regulation of several members of the apolipoprotein L family located in a high-susceptibility locus for schizophrenia on chromosome 22. Proc Natl Acad Sci U S A. 2002 Apr 2;99(7):4680–4685. [PubMed]
  • Watson A, Mazumder A, Stewart M, Balasubramanian S. Technology for microarray analysis of gene expression. Curr Opin Biotechnol. 1998 Dec;9(6):609–614. [PubMed]
  • Mirnics K, Middleton FA, Marquez A, Lewis DA, Levitt P. Molecular characterization of schizophrenia viewed by microarray analysis of gene expression in prefrontal cortex. Neuron. 2000 Oct;28(1):53–67. [PubMed]
  • Hakak Y, Walker JR, Li C, Wong WH, Davis KL, Buxbaum JD, Haroutunian V, Fienberg AA. Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia. Proc Natl Acad Sci U S A. 2001 Apr 10;98(8):4746–4751. [PubMed]
  • Colangelo Vittorio, Schurr Jill, Ball Melvyn J, Pelaez Ricardo Palacios, Bazan Nicolas G, Lukiw Walter J. Gene expression profiling of 12633 genes in Alzheimer hippocampal CA1: transcription and neurotrophic factor down-regulation and up-regulation of apoptotic and pro-inflammatory signaling. J Neurosci Res. 2002 Nov 1;70(3):462–473. [PubMed]
  • Napolitano Maddalena, Centonze Diego, Calce Angelica, Picconi Barbara, Spiezia Stefania, Gulino Alberto, Bernardi Giorgio, Calabresi Paolo. Experimental parkinsonism modulates multiple genes involved in the transduction of dopaminergic signals in the striatum. Neurobiol Dis. 2002 Aug;10(3):387–395. [PubMed]
  • Polacek Denise C, Passerini Anthony G, Shi Congzhu, Francesco Nadeene M, Manduchi Elisabetta, Grant Gregory R, Powell Steven, Bischof Helen, Winkler Hans, Stoeckert Christian J, Jr, Davies Peter F. Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA. Physiol Genomics. 2003 Apr 16;13(2):147–156. [PubMed]
  • Anderson L, Seilhamer J. A comparison of selected mRNA and protein abundances in human liver. Electrophoresis. 1997 Mar–Apr;18(3-4):533–537. [PubMed]
  • Weinreb Orly, Mandel Silvia, Youdim Moussa B H. cDNA gene expression profile homology of antioxidants and their antiapoptotic and proapoptotic activities in human neuroblastoma cells. FASEB J. 2003 May;17(8):935–937. [PubMed]
  • Bunney William E, Bunney Blynn G, Vawter Marquis P, Tomita Hiroaki, Li Jun, Evans Simon J, Choudary Prabhakara V, Myers Richard M, Jones Edward G, Watson Stanley J, Akil Huda. Microarray technology: a review of new strategies to discover candidate vulnerability genes in psychiatric disorders. Am J Psychiatry. 2003 Apr;160(4):657–666. [PubMed]
  • Higuchi R, Fockler C, Dollinger G, Watson R. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology (N Y). 1993 Sep;11(9):1026–1030. [PubMed]
  • Bustin Stephen A, Dorudi Sina. The value of microarray techniques for quantitative gene profiling in molecular diagnostics. Trends Mol Med. 2002 Jun;8(6):269–272. [PubMed]
  • Giulietti A, Overbergh L, Valckx D, Decallonne B, Bouillon R, Mathieu C. An overview of real-time quantitative PCR: applications to quantify cytokine gene expression. Methods. 2001 Dec;25(4):386–401. [PubMed]
  • Gibson UE, Heid CA, Williams PM. A novel method for real time quantitative RT-PCR. Genome Res. 1996 Oct;6(10):995–1001. [PubMed]
  • Heid CA, Stevens J, Livak KJ, Williams PM. Real time quantitative PCR. Genome Res. 1996 Oct;6(10):986–994. [PubMed]
  • Afonina I, Zivarts M, Kutyavin I, Lukhtanov E, Gamper H, Meyer RB. Efficient priming of PCR with short oligonucleotides conjugated to a minor groove binder. Nucleic Acids Res. 1997 Jul 1;25(13):2657–2660. [PubMed]
  • Aldape Kenneth, Ginzinger David G, Godfrey Tony E. Real-time quantitative polymerase chain reaction: a potential tool for genetic analysis in neuropathology. Brain Pathol. 2002 Jan;12(1):54–66. [PubMed]
  • Tkachev Dmitri, Mimmack Michael L, Ryan Margaret M, Wayland Matt, Freeman Tom, Jones Peter B, Starkey Michael, Webster Maree J, Yolken Robert H, Bahn Sabine. Oligodendrocyte dysfunction in schizophrenia and bipolar disorder. Lancet. 2003 Sep 6;362(9386):798–805. [PubMed]
  • O'Farrell PH. High resolution two-dimensional electrophoresis of proteins. J Biol Chem. 1975 May 25;250(10):4007–4021. [PubMed]
  • Klose J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik. 1975;26(3):231–243. [PubMed]
  • Klose J, Kobalz U. Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis. 1995 Jun;16(6):1034–1059. [PubMed]
  • Wildgruber R, Harder A, Obermaier C, Boguth G, Weiss W, Fey SJ, Larsen PM, Görg A. Towards higher resolution: two-dimensional electrophoresis of Saccharomyces cerevisiae proteins using overlapping narrow immobilized pH gradients. Electrophoresis. 2000 Jul;21(13):2610–2616. [PubMed]
  • Tsuji T, Shiozaki A, Kohno R, Yoshizato K, Shimohama S. Proteomic profiling and neurodegeneration in Alzheimer's disease. Neurochem Res. 2002 Oct;27(10):1245–1253. [PubMed]
  • Sickmann Albert, Dormeyer Wilma, Wortelkamp Stefanie, Woitalla Dirk, Kuhn Wilfried, Meyer Helmut E. Towards a high resolution separation of human cerebrospinal fluid. J Chromatogr B Analyt Technol Biomed Life Sci. 2002 May 5;771(1-2):167–196. [PubMed]
  • Davidsson P, Folkesson S, Christiansson M, Lindbjer M, Dellheden B, Blennow K, Westman-Brinkmalm A. 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. 2002;16(22):2083–2088. [PubMed]
  • Choe Leila H, Green Alison, Knight Richard S G, Thompson Edward J, Lee Kelvin H. Apolipoprotein E and other cerebrospinal fluid proteins differentiate ante mortem variant Creutzfeldt-Jakob disease from ante mortem sporadic Creutzfeldt-Jakob disease. Electrophoresis. 2002 Jul;23(14):2242–2246. [PubMed]
  • Johnson G, Brane D, Block W, van Kammen DP, Gurklis J, Peters JL, Wyatt RJ, Kirch DG, Ghanbari HA, Merril CR. Cerebrospinal fluid protein variations in common to Alzheimer's disease and schizophrenia. Appl Theor Electrophor. 1992;3(2):47–53. [PubMed]
  • Bergquist J, Gobom J, Blomberg A, Roepstorff P, Ekman R. Identification of nuclei associated proteins by 2D-gel electrophoresis and mass spectrometry. J Neurosci Methods. 2001 Aug 15;109(1):3–11. [PubMed]
  • Beranova-Giorgianni Sarka, Pabst Michael J, Russell Tara M, Giorgianni Francesco, Goldowitz Daniel, Desiderio Dominic M. Preliminary analysis of the mouse cerebellum proteome. Brain Res Mol Brain Res. 2002 Jan 31;98(1-2):135–140. [PubMed]
  • Leimgruber Richard M, Malone James P, Radabaugh Melissa R, LaPorte Michelle L, Violand Bernard N, Monahan Joseph B. Development of improved cell lysis, solubilization and imaging approaches for proteomic analyses. Proteomics. 2002 Feb;2(2):135–144. [PubMed]
  • Witzmann Frank A, Li Junyu. Cutting-edge technology. II. Proteomics: core technologies and applications in physiology. Am J Physiol Gastrointest Liver Physiol. 2002 May;282(5):G735–G741. [PubMed]
  • Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics. 2001 Mar;1(3):377–396. [PubMed]
  • Yan Jun X, Devenish Angelica T, Wait Robin, Stone Tim, Lewis Steve, Fowler Sue. Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics. 2002 Dec;2(12):1682–1698. [PubMed]
  • Aksenov MY, Aksenova MV, Butterfield DA, Geddes JW, Markesbery WR. Protein oxidation in the brain in Alzheimer's disease. Neuroscience. 2001;103(2):373–383. [PubMed]
  • Korolainen Minna A, Goldsteins Gundars, Alafuzoff Irina, Koistinaho Jari, Pirttilä Tuula. Proteomic analysis of protein oxidation in Alzheimer's disease brain. Electrophoresis. 2002 Sep;23(19):3428–3433. [PubMed]
  • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol. 1999 Oct;17(10):994–999. [PubMed]
  • Gygi SP, Aebersold R. Mass spectrometry and proteomics. Curr Opin Chem Biol. 2000 Oct;4(5):489–494. [PubMed]
  • Patton Wayne F. Detection technologies in proteome analysis. J Chromatogr B Analyt Technol Biomed Life Sci. 2002 May 5;771(1-2):3–31. [PubMed]
  • Moseley MA. Current trends in differential expression proteomics: isotopically coded tags. Trends Biotechnol. 2001 Oct;19(10 Suppl):S10–S16. [PubMed]
  • Sechi Salvatore, Oda Yoshiya. Quantitative proteomics using mass spectrometry. Curr Opin Chem Biol. 2003 Feb;7(1):70–77. [PubMed]
  • Yu Li-Rong, Johnson Mark D, Conrads Thomas P, Smith Richard D, Morrison Richard S, Veenstra Timothy D. Proteome analysis of camptothecin-treated cortical neurons using isotope-coded affinity tags. Electrophoresis. 2002 Jun;23(11):1591–1598. [PubMed]
  • Berggren KN, Chernokalskaya E, Lopez MF, Beechem JM, Patton WF. Comparison of three different fluorescent visualization strategies for detecting Escherichia coli ATP synthase subunits after sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Proteomics. 2001 Jan;1(1):54–65. [PubMed]
  • Smolka Marcus, Zhou Huilin, Aebersold Ruedi. Quantitative protein profiling using two-dimensional gel electrophoresis, isotope-coded affinity tag labeling, and mass spectrometry. Mol Cell Proteomics. 2002 Jan;1(1):19–29. [PubMed]
  • Haab BB, Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2001;2(2):RESEARCH0004. [PubMed]
  • Templin Markus F, Stoll Dieter, Schrenk Monika, Traub Petra C, Vöhringer Christian F, Joos Thomas O. Protein microarray technology. Drug Discov Today. 2002 Aug 1;7(15):815–822. [PubMed]
  • Lopez Mary F, Pluskal Malcolm G. Protein micro- and macroarrays: digitizing the proteome. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Apr 5;787(1):19–27. [PubMed]
  • MacBeath Gavin. Protein microarrays and proteomics. Nat Genet. 2002 Dec;32 Suppl:526–532. [PubMed]
  • Wingren Christer, Ingvarsson Johan, Lindstedt Malin, Borrebaeck Carl A K. Recombinant antibody microarrays--a viable option? Nat Biotechnol. 2003 Mar;21(3):223. [PubMed]
  • Madoz-Gúrpide J, Wang H, Misek DE, Brichory F, Hanash SM. Protein based microarrays: a tool for probing the proteome of cancer cells and tissues. Proteomics. 2001 Oct;1(10):1279–1287. [PubMed]
  • Lal Sean P, Christopherson Richard I, dos Remedios Cristobal G. Antibody arrays: an embryonic but rapidly growing technology. Drug Discov Today. 2002 Sep 15;7(18 Suppl):S143–S149. [PubMed]
  • Rowe CA, Scruggs SB, Feldstein MJ, Golden JP, Ligler FS. An array immunosensor for simultaneous detection of clinical analytes. Anal Chem. 1999 Jan 15;71(2):433–439. [PubMed]
  • Zhu H, Bilgin M, Bangham R, Hall D, Casamayor A, Bertone P, Lan N, Jansen R, Bidlingmaier S, Houfek T, Mitchell T, Miller P, Dean RA, Gerstein M, Snyder M. Global analysis of protein activities using proteome chips. Science. 2001 Sep 14;293(5537):2101–2105. [PubMed]
  • Miller Jeremy C, Zhou Heping, Kwekel Joshua, Cavallo Robert, Burke Jocelyn, Butler E Brian, Teh Bin S, Haab Brian B. Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics. 2003 Jan;3(1):56–63. [PubMed]
  • Knezevic V, Leethanakul C, Bichsel VE, Worth JM, Prabhu VV, Gutkind JS, Liotta LA, Munson PJ, Petricoin EF, 3rd, Krizman DB. Proteomic profiling of the cancer microenvironment by antibody arrays. Proteomics. 2001 Oct;1(10):1271–1278. [PubMed]
  • Dunn MJ. Studying heart disease using the proteomic approach. Drug Discov Today. 2000 Feb;5(2):76–84. [PubMed]
  • Jonsson AP. Mass spectrometry for protein and peptide characterisation. Cell Mol Life Sci. 2001 Jun;58(7):868–884. [PubMed]
  • Graves Paul R, Haystead Timothy A J. Molecular biologist's guide to proteomics. Microbiol Mol Biol Rev. 2002 Mar;66(1):39–contents. [PubMed]
  • Mo Wenjun, Karger Barry L. Analytical aspects of mass spectrometry and proteomics. Curr Opin Chem Biol. 2002 Oct;6(5):666–675. [PubMed]
  • Callea L, Arese M, Orlandini A, Bargnani C, Priori A, Bussolino F. Platelet activating factor is elevated in cerebral spinal fluid and plasma of patients with relapsing-remitting multiple sclerosis. J Neuroimmunol. 1999 Feb 1;94(1-2):212–221. [PubMed]
  • Ekman R, Juhasz P, Heilig M, Agren H, Costello CE. Novel neuropeptide Y processing in human cerebrospinal fluid from depressed patients. Peptides. 1996;17(7):1107–1111. [PubMed]
  • Nilsson CL, Karlsson G, Bergquist J, Westman A, Ekman R. Mass spectrometry of peptides in neuroscience. Peptides. 1998;19(4):781–789. [PubMed]
  • Merchant M, Weinberger SR. Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis. 2000 Apr;21(6):1164–1177. [PubMed]
  • Issaq Haleem J, Veenstra Timothy D, Conrads Thomas P, Felschow Donna. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochem Biophys Res Commun. 2002 Apr 5;292(3):587–592. [PubMed]
  • Mannes Andrew J, Martin Brian M, Yang Hsiu-Ying T, Keller Jason M, Lewin Stacy, Gaiser Robert R, Iadarola Michael J. Cystatin C as a cerebrospinal fluid biomarker for pain in humans. Pain. 2003 Apr;102(3):251–256. [PubMed]
  • Goldstein Lee E, Muffat Julien A, Cherny Robert A, Moir Robert D, Ericsson Maria H, Huang Xudong, Mavros Christine, Coccia Jennifer A, Faget Kyle Y, Fitch Karlotta A, Masters Colin L, Tanzi Rudolph E, Chylack Leo T, Jr, Bush Ashley I. Cytosolic beta-amyloid deposition and supranuclear cataracts in lenses from people with Alzheimer's disease. Lancet. 2003 Apr 12;361(9365):1258–1265. [PubMed]
  • Petricoin Emanuel F, Ardekani Ali M, Hitt Ben A, Levine Peter J, Fusaro Vincent A, Steinberg Seth M, Mills Gordon B, Simone Charles, Fishman David A, Kohn Elise C, Liotta Lance A. Use of proteomic patterns in serum to identify ovarian cancer. Lancet. 2002 Feb 16;359(9306):572–577. [PubMed]
  • Jr GL Wright, Cazares LH, Leung S-M, Nasim S, Adam B-L, Yip T-T, Schellhammer PF, Gong L, Vlahou A. Proteinchip(R) surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures. Prostate Cancer Prostatic Dis. 1999 Dec;2(5/6):264–276. [PubMed]
  • Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, Zhuang Z, Goldstein SR, Weiss RA, Liotta LA. Laser capture microdissection. Science. 1996 Nov 8;274(5289):998–1001. [PubMed]