Microarray technology: A review of new strategies to discover candidate vulnerability genes in psychiatric disorders

American Journal of Psychiatry

Volumn 160, Issue 4, 2003, Pages 657-666

  Bunney, William E ^a   Bunney, Blynn G ^b   Vawter, Marquis P ^b   Tomita, Hiroaki ^b   Li, Jun ^b   Evans, Simon J ^b   Choudary, Prabhakara V ^b   Myers, Richard M ^b   Jones, Edward G ^b   Watson, Stanley J ^b   Akil, Huda ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b NONE

Author keywords

[No Author keywords available]

Indexed keywords

PSYCHOTROPIC AGENT; RNA; MESSENGER RNA;

ANALYTIC METHOD; ANIMAL TISSUE; AUTOPSY; BRAIN TISSUE; CELLULAR DISTRIBUTION; CHROMOSOME; DNA MICROARRAY; DRUG TARGETING; GENE FUNCTION; GENE IDENTIFICATION; GENE STRUCTURE; GENE THERAPY; GENETIC LINKAGE; IN SITU HYBRIDIZATION; KNOCKOUT GENE; MEDICAL ASSESSMENT; MENTAL DISEASE; NONHUMAN; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVIEW; RNA EXTRACTION; TRANSGENIC ANIMAL; VALIDATION PROCESS; BRAIN LEVEL; GENE; GENETIC PREDISPOSITION; GENETICS; HUMAN; METHODOLOGY; PHYSIOLOGY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

BRAIN CHEMISTRY; GENE THERAPY; GENES; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MENTAL DISORDERS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER;

EID: 0038811923     PISSN: 0002953X     EISSN: None     Source Type: Journal    
DOI: 10.1176/appi.ajp.160.4.657     Document Type: Review

References (62)

1. Sawa A, Snyder SH: Schizophrenia: diverse approaches to a complex disease. Science 2002; 296:692-695
2. Mowry BJ, Nancarrow DJ: Molecular genetics of schizophrenia. Clin Exp Pharmacol Physiol 2001; 28:66-69
3. Nemeroff CB, Owens MJ: Treatment of mood disorders. Nat Neurosci 2002; 5(Nov suppl):1068-1070
4. Tandon R, Jibson MD: Efficacy of newer generation antipsychotics in the treatment of schizophrenia. Psychoneuroendocrinology 2003; 28(suppl 1):9-26
5. Kato C, Petronis A, Okazaki Y, Tochigi M, Umekage T, Sasaki T: Molecular genetic studies of schizophrenia: challenges and insights. Neurosci Res 2002; 43:295-304
6. Avissar S, Schreiber G: Toward molecular diagnostics of mood disorders in psychiatry. Trends Mol Med 2002; 8:294-300
7. Johnston-Wilson NL, Bouton CM, Pevsner J, Breen JJ, Torrey EF, Yolken RH: Emerging technologies for large-scale screening of human tissues and fluids in the study of severe psychiatric disease. Int J Neuropsychopharmacol 2001; 4:83-92
8. Shoemaker DD, Linsley PS: Recent developments in DNA microarrays. Curr Opin Microbiol 2002; 5:334-337
9. Novak G, Kim D, Seeman P, Tallerico T: Schizophrenia and Nogo: elevated mRNA in cortex, and high prevalence of a homozygous CAA insert. Brain Res Mol Brain Res 2002; 107:183-189
10. Mimmack ML, Ryan M, Baba H, Navarro-Ruiz J, Iritani S, Faull RL, McKenna PJ, Jones PB, Arai H, Starkey M, Emson PC, Bahn S: 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 USA 2002; 99:4680-4685
11. Middleton FA, Mirnics K, Pierri JN, Lewis DA, Levitt P: Gene expression profiling reveals alterations of specific metabolic pathways in schizophrenia. J Neurosci 2002; 22:2718-2729
12. Vawter MP, Barrett T, Cheadle C, Sokolov BP, Wood WH III, Donovan DM, Webster M, Freed WJ, Becker KG: Application of cDNA microarrays to examine gene expression differences in schizophrenia. Brain Res Bull 2001; 55:641-650
13. Mirnics K, Middleton FA, Lewis DA, Levitt P: Analysis of complex brain disorders with gene expression microarrays: schizophrenia as a disease of the synapse. Trends Neurosci 2001; 24:479-486
14. Mirnics K, Middleton FA, Stanwood GD, Lewis DA, Levitt P: Disease-specific changes in regulator of G-protein signaling 4 (RGS4) expression in schizophrenia. Mol Psychiatry 2001; 6: 293-301
15. Vawter MP, Crook JM, Hyde TM, Kleinman JE, Weinberger DR, Becker KG, Freed WJ: Microarray analysis of gene expression in the prefrontal cortex in schizophrenia: a preliminary study. Schizophr Res 2002; 58:11-20
16. 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 USA 2001; 98:4746-4751
17. Hof PR, Haroutunian V, Copland C, Davis KL, Buxbaum JD: Molecular and cellular evidence for an oligodendrocyte abnormality in schizophrenia. Neurochem Res 2002; 27:1193-1200
18. Wurmbach E, Gonzalez-Maeso J, Yuen T, Ebersole BJ, Mastaitis JW, Mobbs CV, Sealfon SC: Validated genomic approach to study differentially expressed genes in complex tissues. Neurochem Res 2002; 27:1027-1033
19. Bezchlibnyk YB, Wang JF, McQueen GM, Young LT: Gene expression differences in bipolar disorder revealed by cDNA array analysis of post-mortem frontal cortex. J Neurochem 2001; 79:826-834
20. 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; 28:53-67
21. Luo Z, Geschwind DH: Microarray applications in neuroscience. Neurobiol Dis 2001; 8:183-193
22. Lockhart DJ, Winzeler EA: Genomics, gene expression and DNA arrays. Nature 2000; 405:827-836
23. Watson SJ, Meng F, Thompson RC, Akil H: The "chip" as a specific genetic tool. Biol Psychiatry 2000; 48:1147-1156
24. Watson SJ, Akil H: Gene chips and arrays revealed: a primer on their power and their uses. Biol Psychiatry 1999; 45:533-543
25. Pongrac J, Middleton FA, Lewis DA, Levitt P, Mirnics K: Gene expression profiling with DNA microarrays: advancing our understanding of psychiatric disorders. Neurochem Res 2002; 27: 1049-1063
26. Cowan WM, Kopnisky KL, Hyman SE: The human genome project and its impact on psychiatry. Annu Rev Neurosci 2002; 25:1-50
27. Shilling PD, Kelsoe JR: Functional genomics approaches to understanding brain disorders. Pharmacogenomics 2002; 3:31-45
28. Akbarian S, Kim JJ, Potkin SG, Hetrick WP, Bunney WE Jr, Jones EG: Maldistribution of interstitial neurons in prefrontal white matter of the brains of schizophrenic patients. Arch Gen Psychiatry 1996; 53:425-436
29. Dunn RT, Kimbrell TA, Ketter TA, Frye MA, Willis MW, Luckenbaugh DA, Post RM: Principal components of the Beck Depression Inventory and regional cerebral metabolism in unipolar and bipolar depression. Biol Psychiatry 2002; 51:387-399
30. Bunney WE, Bunney BG: Evidence for a compromised dorsolateral prefrontal cortical parallel circuit in schizophrenia. Brain Res Brain Res Rev 2000; 31:138-146
31. Ketter TA, George MS, Kimbress TA, Willis MW, Benson BE, Post RM: Neuroanatomical models and brain imaging studies, in Bipolar Disorder: Biological Models and Their Clinical Applications. Edited by Young LT, Joffe RT. New York, Marcel Dekker, 1997, pp 179-217
32. Wu J, Buchsbaum MS, Gillin JC, Tang C, Cadwell S, Keator D, Fallon JH, Wiegand M, Najafi A, Klein E, Hazen K, Bunney WE Jr: Prediction of antidepressant effects of sleep deprivation by metabolic rates in the ventral anterior cingulate and medial prefrontal cortex. Am J Psychiatry 1999; 156:1149-1158; correction, 156:1666
33. Mayberg HS: Limbic-cortical dysregulation: a proposed model of depression. J Neuropsychiatry Clin Neurosci 1997; 9:471-481
34. Tamminga CA, Vogel M, Gao X, Lahti AC, Holcomb HH: The limbic cortex in schizophrenia: focus on the anterior cingulate. Brain Res Brain Res Rev 2000; 31:364-370
35. Jones EG, Hendry SH, Liu XB, Hodgins S, Potkin SG, Tourtellotte WW: A method for fixation of previously fresh-frozen human adult and fetal brains that preserves histological quality and immunoreactivity. J Neurosci Methods 1992; 44:133-144
36. Velculescu VE: Essay: Amersham Pharmacia Biotech and Science Prize: tantalizing transcriptomes - SAGE and its use in global gene expression analysis. Science 1999; 286:1491-1492
37. Sutcliffe JG, Foye PE, Erlander MG, Hilbush BS, Bodzin LJ, Durham JT, Hasel KW: TOGA: an automated parsing technology for analyzing expression of nearly all genes. Proc Natl Acad Sci USA 2000; 97:1976-1981
38. Brenner S, Johnson M, Bridgham J, Golda G, Lloyd DH, Johnson D, Luo S, McCurdy S, Foy M, Ewan M, Roth R, George D, Eletr S, Albrecht G, Vermaas E, Williams SR, Moon K, Burcham T, Pallas M, DuBridge RB, Kirchner J, Fearon K, Mao J, Corcoran K: Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat Biotechnol 2000; 18:630-634
39. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ: High-density synthetic oligonucleotide arrays. Nat Genet 1999; 21(1 suppl):20-24
40. Barrett T, Xie T, Piao Y, Dillon-Carter O, Kargul GJ, Lim MK, Chrest FJ, Wersto R, Rowley DL, Juhaszova M, Zhou L, Vawter MP, Becker KG, Cheadle C, Wood WH III, McCann UD, Freed WJ, Ko MS, Ricaurte GA, Donovan DM: A murine dopamine neuron-specific cDNA library and microarray: increased COX1 expression during methamphetamine neurotoxicity. Neurobiol Dis 2001; 8:822-833
41. Ramakrishnan R, Dorris D, Lublinsky A, Nguyen A, Domanus M, Prokhorova A, Gieser L, Touma E, Lockner R, Tata M, Zhu X, Patterson M, Shippy R, Sendera TJ, Mazumder A: An assessment of Motorola CodeLink microarray performance for gene expression profiling applications. Nucleic Acids Res 2002; 30(7):e30
42. Torres-Munoz J, Stockton P, Tacoronte N, Roberts B, Maronpot RR, Petito CK: Detection of HIV-1 gene sequences in hippocampal neurons isolated from postmortem AIDS brains by laser capture microdissection. J Neuropathol Exp Neurol 2001; 60:885-892
43. Kingsbury AE, Foster OJ, Nisbet AP, Cairns N, Bray L, Eve DJ, Lees AJ, Marsden CD: Tissue pH as an indicator of mRNA preservation in human post-mortem brain. Brain Res Mol Brain Res 1995; 28:311-318
44. Barton AJ, Pearson RC, Najlerahim A, Harrison PJ: Pre- and postmortem influences on brain RNA. J Neurochem 1993; 61:1-11
45. Akbarian S, Kim JJ, Potkin SG, Hagman JO, Tafazzoli A, Bunney WE Jr, Jones EG: Gene expression for glutamic acid decarboxylase is reduced without loss of neurons in prefrontal cortex of schizophrenics. Arch Gen Psychiatry 1995; 52:258-266
46. Akbarian S, Sucher NJ, Bradley D, Tafazzoli A, Trinh D, Hetrick WP, Potkin SG, Sandman CA, Bunney WE Jr, Jones EG: Selective alterations in gene expression for NMDA receptor subunits in prefrontal cortex of schizophrenics. J Neurosci 1996; 16:19-30
47. Evans SJ, Datson NA, Kabbaj M, Thompson RC, Vreugdenhil E, De Kloet ER, Watson SJ, Akil H: Evaluation of Affymetrix Gene Chip sensitivity in rat hippocampal tissue using SAGE (serial analysis of gene expression) analysis. Eur J Neurosci 2002; 16:409-413
48. Li C, Hung Wong W: Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2001; 2(8):RESEARCH0032
49. Irizarry RA, Hobbs B, Collins F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high-density oligonucleotide array probe level data. http://biosun01.biostat.jhsph.edu/ ~ririzarr/papers/affy1.pdf
50. Draghici S: Statistical intelligence: effective analysis of high-density microarray data. Drug Discov Today 2002; 7:S55-S63
51. Yang YH, Speed T: Design issues for cDNA microarray experiments. Nat Rev Genet 2002; 3:579-588
52. Nestler EJ, Gould E, Manji H, Buncan M, Duman RS, Greshenfeld HK, Hen R, Koester S, Lederhendler I, Meaney M, Robbins T, Winsky L, Zalcman S: Preclinical models: status of basic research in depression. Biol Psychiatry 2002; 52:503-528
53. Joo A, Shibata H, Ninomiya H, Kawasaki H, Tashiro N, Fukumaki Y: Structure and polymorphisms of the human metabotropic glutamate receptor type 2 gene (GRM2): analysis of association with schizophrenia. Mol Psychiatry 2001; 6:186-192
54. Niculescu AB III, Segal DS, Kuczenski R, Barrett T, Hauger RL, Kelsoe JR: Identifying a series of candidate genes for mania and psychosis: a convergent functional genomics approach. Pnysiol Genomics 2000; 4:83-91
55. Niculescu AB III, Kelsoe JR: The human genome: genetic testing and animal models (image, neuro). Am J Psychiatry 2001; 158:1587
56. Bosetti F, Seemann R, Bell JM, Zahorchak R, Friedman E, Rapoport SI, Manickam P: Analysis of gene expression with cDNA microarrays in rat brain after 7 and 42 days of oral lithium administration. Brain Res Bull 2002; 57:205-209
57. Yamada M, Yamazaki S, Takahashi K, Nara K, Ozawa H, Yamada S, Kiuchi Y, Oguchi K, Kamijima K, Higuchi T, Momose K: Induction of cysteine string protein after chronic antidepressant treatment in rat frontal cortex. Neurosci Lett 2001; 301:183-186
58. Manji HK, Chen G: PKC, MAP kinases and the bcl-2 family of proteins as long-term targets for mood stabilizers. Mol Psychiatry 2002; 7(suppl 1):S46-S56
59. Pennacchio LA, Olivier M, Hubacek JA, Cohen JC, Cox DR, Fruchart JC, Krauss RM, Rubin EM: An apolipoprotein influencing triglycerides in humans and mice revealed by comparative sequencing. Science 2001; 294:169-173
60. Tsien JZ, Chen DF, Gerber D, Tom C, Mercer EH, Anderson DJ, Mayford M, Kandel ER, Tonegawa S: Subregion- and cell type-restricted gene knockout in mouse brain. Cell 1996; 87:1317-1326
61. Mayford M, Bach ME, Huang YY, Wang L, Hawkins RD, Kandel ER: Control of memory formation through regulated expression of a CaMKII transgene. Science 1996; 274:1678-1683
62. DePrato Primeaux S, Holmes PV, Martin RJ, Dean RG, Edwards GL: Experimentally induced attenuation of neuropeptide-Y gene expression in transgenic mice increases mortality rate following seizures. Neurosci Lett 2000; 287:61-64