Analyzing schizophrenia by DNA microarrays

Biological Psychiatry

Volumn 69, Issue 2, 2011, Pages 157-162

  Horvth, Szatmr ^a   Janka, Zoltn ^c   Mirnics, Kroly ^a,b  

^a VANDERBILT UNIVERSITY   (United States)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^c UNIVERSITY OF SZEGED   (Hungary)

Author keywords

DNA microarrays; gene expression; postmortem; RNA seq; schizophrenia; transcriptome

Indexed keywords

TRANSCRIPTOME;

AUTOPSY; BRAIN REGION; CELL TYPE; DNA MICROARRAY; ENERGY METABOLISM; GENE EXPRESSION; HUMAN; INTERNEURON; NERVE FIBER; NEUROTRANSMISSION; OLIGODENDROGLIA; PATHOPHYSIOLOGY; PRIORITY JOURNAL; REVIEW; SCHIZOPHRENIA; SYNAPTIC TRANSMISSION;

AUTOPSY; BRAIN; BRAIN CHEMISTRY; GENE EXPRESSION PROFILING; HUMANS; NERVE TISSUE PROTEINS; NEUROPSYCHIATRY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POSTMORTEM CHANGES; SCHIZOPHRENIA;

EID: 78650482936     PISSN: 00063223     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biopsych.2010.07.017     Document Type: Review

References (100)

1. K. Mirnics, P. Levitt, and D.A. Lewis Critical appraisal of DNA microarrays in psychiatric genomics Biol Psychiatry 60 2006 163 176
2. K. Mirnics, and J. Pevsner Progress in the use of microarray technology to study the neurobiology of disease Nat Neurosci 7 2004 434 439
3. K. Mirnics, P. Levitt, and D.A. Lewis DNA microarray analysis of postmortem brain tissue Int Rev Neurobiol 60 2004 153 181
4. J. Pongrac, F.A. Middleton, D.A. Lewis, P. Levitt, and K. Mirnics Gene expression profiling with DNA microarrays: Advancing our understanding of psychiatric disorders Neurochem Res 27 2002 1049 1063
5. H. Kretzschmar Brain banking: Opportunities, challenges and meaning for the future Nat Rev Neurosci 10 2009 70 78
6. W.T. Carpenter, and R.W. Buchanan Schizophrenia N Engl J Med 330 1994 681 690
7. P.J. Harrison, and D.R. Weinberger Schizophrenia genes, gene expression, and neuropathology: On the matter of their convergence Mol Psychiatry 10 2005 40 68 image 45
8. Y. Hakak, J.R. Walker, C. Li, W.H. Wong, K.L. Davis, and J.D. Buxbaum Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia Proc Natl Acad Sci U S A 98 2001 4746 4751
9. K. Mirnics, F.A. Middleton, A. Marquez, D.A. Lewis, and P. Levitt Molecular characterization of schizophrenia viewed by microarray analysis of gene expression in prefrontal cortex Neuron 28 2000 53 67
10. K. Mirnics, F.A. Middleton, G.D. Stanwood, D.A. Lewis, and P. Levitt Disease-specific changes in regulator of G-protein signaling 4 (RGS4) expression in schizophrenia Mol Psychiatry 6 2001 293 301
11. M.P. Vawter, J.M. Crook, T.M. Hyde, J.E. Kleinman, D.R. Weinberger, K.G. Becker, and W.J. Freed Microarray analysis of gene expression in the prefrontal cortex in schizophrenia: A preliminary study Schizophr Res 58 2002 11 20
12. D. Arion, T. Unger, D.A. Lewis, P. Levitt, and K. Mirnics Molecular evidence for increased expression of genes related to immune and chaperone function in the prefrontal cortex in schizophrenia Biol Psychiatry 62 2007 711 721
13. T. Hashimoto, D.W. Volk, S.M. Eggan, K. Mirnics, J.N. Pierri, and Z. Sun Gene expression deficits in a subclass of GABA neurons in the prefrontal cortex of subjects with schizophrenia J Neurosci 23 2003 6315 6326
14. F.A. Middleton, K. Mirnics, J.N. Pierri, D.A. Lewis, and P. Levitt Gene expression profiling reveals alterations of specific metabolic pathways in schizophrenia J Neurosci 22 2002 2718 2729
15. K. Iwamoto, M. Bundo, and T. Kato Altered expression of mitochondria-related genes in postmortem brains of patients with bipolar disorder or schizophrenia, as revealed by large-scale DNA microarray analysis Hum Mol Genet 14 2005 241 253
16. T. Sugai, M. Kawamura, S. Iritani, K. Araki, T. Makifuchi, and C. Imai Prefrontal abnormality of schizophrenia revealed by DNA microarray: Impact on glial and neurotrophic gene expression Ann N Y Acad Sci 1025 2004 84 91
17. C. Aston, L. Jiang, and B.P. Sokolov Microarray analysis of postmortem temporal cortex from patients with schizophrenia J Neurosci Res 77 2004 858 866
18. T. Hashimoto, D. Arion, T. Unger, J.G. Maldonado-Aviles, H.M. Morris, and D.W. Volk Alterations in GABA-related transcriptome in the dorsolateral prefrontal cortex of subjects with schizophrenia Mol Psychiatry 13 2008 147 161
19. N.A. Bowden, R.J. Scott, and P.A. Tooney Altered gene expression in the superior temporal gyrus in schizophrenia BMC Genomics 9 2008 199
20. T.T. Chu, Y. Liu, and E. Kemether Thalamic transcriptome screening in three psychiatric states J Hum Genet 54 2009 665 675
21. S.J. Glatt, I.P. Everall, W.S. Kremen, J. Corbeil, R. Sasik, and N. Khanlou Comparative gene expression analysis of blood and brain provides concurrent validation of SELENBP1 up-regulation in schizophrenia Proc Natl Acad Sci U S A 102 2005 15533 15538
22. J.L. Pongrac, F.A. Middleton, L. Peng, D.A. Lewis, P. Levitt, and K. Mirnics Heat shock protein 12A shows reduced expression in the prefrontal cortex of subjects with schizophrenia Biol Psychiatry 56 2004 943 950
23. V. Haroutunian, P. Katsel, S. Dracheva, D.G. Stewart, and K.L. Davis Variations in oligodendrocyte-related gene expression across multiple cortical regions: Implications for the pathophysiology of schizophrenia Int J Neuropsychopharmacol 10 2007 565 573
24. C.A. Altar, L.W. Jurata, V.L.A. Charles, P. Liu, Y. Bukhman, and Y. Bukhman Deficient hippocampal neuron expression of proteasome, ubiquitin, and mitochondrial genes in multiple schizophrenia cohorts Biol Psychiatry 58 2005 85 96
25. T. Hashimoto, H.H. Bazmi, K. Mirnics, Q. Wu, A.R. Sampson, and D.A. Lewis Conserved regional patterns of GABA-related transcript expression in the neocortex of subjects with schizophrenia Am J Psychiatry 165 2008 479 489
26. S. Marenco, and D.R. Weinberger The neurodevelopmental hypothesis of schizophrenia: Following a trail of evidence from cradle to grave Dev Psychopathol 12 2000 501 527
27. J.A. O'Connor, and S.E. Hemby Elevated GRIA1 mRNA expression in layer II/III and V pyramidal cells of the DLPFC in schizophrenia Schizophr Res 97 2007 277 288
28. D. Arion, S. Horvath, D.A. Lewis, and K. Mirnics Infragranular gene expression disturbances in the prefrontal cortex in schizophrenia: Signature of altered neural development? Neurobiol Dis 37 2009 738 746
29. W.B. Ruzicka, A. Zhubi, M. Veldic, D.R. Grayson, E. Costa, and A. Guidotti Selective epigenetic alteration of layer I GABAergic neurons isolated from prefrontal cortex of schizophrenia patients using laser-assisted microdissection Mol Psychiatry 12 2007 385 397
30. F.A. Middleton, L. Peng, D.A. Lewis, P. Levitt, and K. Mirnics Altered expression of 143-3 genes in the prefrontal cortex of subjects with schizophrenia Neuropsychopharmacology 30 2005 974 983
31. P. Saetre, L. Emilsson, E. Axelsson, J. Kreuger, E. Lindholm, and E. Jazin Inflammation-related genes up-regulated in schizophrenia brains BMC Psychiatry 7 2007 46
32. D. Martins-de-Souza, W.F. Gattaz, A. Schmitt, C. Rewerts, G. Maccarrone, E. Dias-Neto, and C.W. Turck Prefrontal cortex shotgun proteome analysis reveals altered calcium homeostasis and immune system imbalance in schizophrenia Eur Arch Psychiatry Clin Neurosci 259 2009 151 163
33. J.M. Williams, V.L. Thompson, S.E. Mason-Parker, W.C. Abraham, and W.P. Tate Synaptic activity-dependent modulation of mitochondrial gene expression in the rat hippocampus Brain Res Mol Brain Res 60 1998 50 56
34. N. Ishihara, M. Nomura, A. Jofuku, H. Kato, S.O. Suzuki, and K. Masuda Mitochondrial fission factor Drp1 is essential for embryonic development and synapse formation in mice Nat Cell Biol 11 2009 958 966
35. M.P. Mattson, M. Gleichmann, and A. Cheng Mitochondria in neuroplasticity and neurological disorders Neuron 60 2008 748 766
36. K. Mirnics, F.A. Middleton, D.A. Lewis, and P. Levitt Analysis of complex brain disorders with gene expression microarrays: Schizophrenia as a disease of the synapse Trends Neurosci 24 2001 479 486
37. B. Dean, S. Boer, A. Gibbons, T. Money, and E. Scarr Recent advances in postmortem pathology and neurochemistry in schizophrenia Curr Opin Psychiatry 22 2009 154 160
38. X. Chen, C. Dunham, S. Kendler, X. Wang, F.A. O'Neill, and D. Walsh Regulator of G-protein signaling 4 (RGS4) gene is associated with schizophrenia in Irish high density families Am J Med Genet B Neuropsychiatr Genet 129 2004 23 26
39. K.V. Chowdari, K. Mirnics, P. Semwal, J. Wood, E. Lawrence, and T. Bhatia Association and linkage analyses of RGS4 polymorphisms in schizophrenia Hum Mol Genet 11 2002 1373 1380
40. D.W. Morris, A. Rodgers, K.A. McGhee, S. Schwaiger, P. Scully, and J. Quinn Confirming RGS4 as a susceptibility gene for schizophrenia Am J Med Genet B Neuropsychiatr Genet 125 2004 50 53
41. N.M. Williams, A. Preece, G. Spurlock, N. Norton, H.J. Williams, and R.G. McCreadie Support for RGS4 as a susceptibility gene for schizophrenia Biol Psychiatry 55 2004 192 195
42. B.K. Lipska, T. Peters, T.M. Hyde, N. Halim, C. Horowitz, and S. Mitkus Expression of DISC1 binding partners is reduced in schizophrenia and associated with DISC1 SNPs Hum Mol Genet 15 2006 1245 1258
43. J.K. Millar, J.C. Wilson-Annan, S. Anderson, S. Christie, M.S. Taylor, and C.A. Semple Disruption of two novel genes by a translocation co-segregating with schizophrenia Hum Mol Genet 9 2000 1415 1423
44. A.M. Addington, M. Gornick, J. Duckworth, A. Sporn, N. Gogtay, and A. Bobb GAD1 (2q31.1), which encodes glutamic acid decarboxylase (GAD67), is associated with childhood-onset schizophrenia and cortical gray matter volume loss Mol Psychiatry 10 2005 581 588
45. R.E. Straub, Y. Jiang, C.J. MacLean, Y. Ma, B.T. Webb, and M.V. Myakishev Genetic variation in the 6p22.3 gene DTNBP1, the human ortholog of the mouse dysbindin gene, is associated with schizophrenia Am J Hum Genet 71 2002 337 348
46. C.S. Weickert, R.E. Straub, B.W. McClintock, M. Matsumoto, R. Hashimoto, and T.M. Hyde Human dysbindin (DTNBP1) gene expression in normal brain and in schizophrenic prefrontal cortex and midbrain Arch Gen Psychiatry 61 2004 544 555
47. P.J. Harrison, L. Lyon, L.J. Sartorius, P.W. Burnet, and T.A. Lane The group II metabotropic glutamate receptor 3 (mGluR3, mGlu3, GRM3): Expression, function and involvement in schizophrenia J Psychopharmacol 22 2008 308 322
48. T.L. Petryshen, F.A. Middleton, A. Kirby, K.A. Aldinger, S. Purcell, and A.R. Tahl Support for involvement of neuregulin 1 in schizophrenia pathophysiology Mol Psychiatry 10 2005 366 374 328
49. P.J. Harrison, and A.J. Law Neuregulin 1 and schizophrenia: Genetics, gene expression, and neurobiology Biol Psychiatry 60 2006 132 140
50. H. Stefansson, E. Sigurdsson, V. Steinthorsdottir, S. Bjornsdottir, T. Sigmundsson, and S. Ghosh Neuregulin 1 and susceptibility to schizophrenia Am J Hum Genet 71 2002 877 892
51. M. Ishikawa, K. Mizukami, M. Iwakiri, S. Hidaka, and T. Asada Immunohistochemical and immunoblot study of GABA(A) alpha1 and beta2/3 subunits in the prefrontal cortex of subjects with schizophrenia and bipolar disorder Neurosci Res 50 2004 77 84
52. W.S. Lo, C.F. Lau, Z. Xuan, C.F. Chan, G.Y. Feng, and L. He Association of SNPs and haplotypes in GABAA receptor beta2 gene with schizophrenia Mol Psychiatry 9 2004 603 608
53. M. Ikeda, T. Hikita, S. Taya, J. Uraguchi-Asaki, K. Toyooka, and A. Wynshaw-Boris Identification of YWHAE, a gene encoding 143-3epsilon, as a possible susceptibility gene for schizophrenia Hum Mol Genet 17 2008 3212 3222
54. A.H. Wong, O. Likhodi, J. Trakalo, M. Yusuf, A. Sinha, and C.N. Pato Genetic and post-mortem mRNA analysis of the 143-3 genes that encode phosphoserine/threonine-binding regulatory proteins in schizophrenia and bipolar disorder Schizophr Res 78 2005 137 146
55. Y. Jia, X. Yu, B. Zhang, Y. Yuan, Q. Xu, and Y. Shen An association study between polymorphisms in three genes of 143-3 (tyrosine 3-monooxygenase/ tryptophan 5-monooxygenase activation protein) family and paranoid schizophrenia in northern Chinese population Eur Psychiatry 19 2004 377 379
56. K. Toyooka, T. Muratake, T. Tanaka, S. Igarashi, H. Watanabe, and H. Takeuchi 14-3-3 protein eta chain gene (YWHAH) polymorphism and its genetic association with schizophrenia Am J Med Genet 88 1999 164 167
57. S. Guo, W. Tang, Y. Shi, K. Huang, Z. Xi, and Y. Xu RGS4 polymorphisms and risk of schizophrenia: An association study in Han Chinese plus meta-analysis Neurosci Lett 406 2006 122 127
58. H. Ishiguro, Y. Horiuchi, M. Koga, T. Inada, N. Iwata, and N. Ozaki RGS4 is not a susceptibility gene for schizophrenia in Japanese: Association study in a large case-control population Schizophr Res 89 2007 161 164
59. K.D. Winden, M.C. Oldham, K. Mirnics, P.J. Ebert, C.H. Swan, and P. Levitt The organization of the transcriptional network in specific neuronal classes Mol Syst Biol 5 2009 291
60. R. Edgar, M. Domrachev, and A.E. Lash Gene expression omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res 30 2002 207 210
61. H. Parkinson, M. Kapushesky, M. Shojatalab, N. Abeygunawardena, R. Coulson, and A. Farne ArrayExpressa public database of microarray experiments and gene expression profiles Nucleic Acids Res 35 2007 D747 D750
62. T. Barrett, and R. Edgar Gene expression omnibus: Microarray data storage, submission, retrieval, and analysis Methods Enzymol 411 2006 352 369
63. H. Parkinson, M. Kapushesky, N. Kolesnikov, G. Rustici, M. Shojatalab, and N. Abeygunawardena ArrayExpress updatefrom an archive of functional genomics experiments to the atlas of gene expression Nucleic Acids Res 37 2009 D868 D872
64. M. Lukk, M. Kapushesky, J. Nikkila, H. Parkinson, A. Goncalves, and W. Huber A global map of human gene expression Nat Biotechnol 28 2010 322 324
65. A. Brazma Minimum Information About a Microarray Experiment (MIAME)successes, failures, challenges ScientificWorldJournal 9 2009 420 423
66. A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, and C. Stoeckert Minimum information about a microarray experiment (MIAME)toward standards for microarray data Nat Genet 29 2001 365 371
67. T.F. Rayner, P. Rocca-Serra, P.T. Spellman, H.C. Causton, A. Farne, and E. Holloway A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB BMC Bioinformatics 7 2006 489
68. P.L. Whetzel, H. Parkinson, H.C. Causton, L. Fan, J. Fostel, and G. Fragoso The MGED Ontology: A resource for semantics-based description of microarray experiments Bioinformatics 22 2006 866 873
69. K. Mirnics Microarrays in brain research: The good, the bad and the ugly Nat Rev Neurosci 2 2001 444 447
70. M. Mistry, and P. Pavlidis A cross-laboratory comparison of expression profiling data from normal human postmortem brain Neuroscience 167 2010 384 395
71. D. Hollingshead, D.A. Lewis, and K. Mirnics Platform influence on DNA microarray data in postmortem brain research Neurobiol Dis 18 2005 649 655
72. K. Mirnics Microarrays in brain research: Data quality and limitations revisited Curr Genomics 7 2006 11 19
73. A.J. Matlin, F. Clark, and C.W. Smith Understanding alternative splicing: Towards a cellular code Nat Rev Mol Cell Biol 6 2005 386 398
74. D. Kampa, J. Cheng, P. Kapranov, M. Yamanaka, S. Brubaker, and S. Cawley Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22 Genome Res 14 2004 331 342
75. J. Ule, G. Stefani, A. Mele, M. Ruggiu, X. Wang, and B. Taneri An RNA map predicting Nova-dependent splicing regulation Nature 444 2006 580 586
76. A. Schmitt, E. Parlapani, O. Gruber, T. Wobrock, and P. Falkai Impact of neuregulin-1 on the pathophysiology of schizophrenia in human post-mortem studies Eur Arch Psychiatry Clin Neurosci 258 suppl 5 2008 35 39
77. A.J. Law, B.K. Lipska, C.S. Weickert, T.M. Hyde, R.E. Straub, and R. Hashimoto Neuregulin 1 transcripts are differentially expressed in schizophrenia and regulated by 5′ SNPs associated with the disease Proc Natl Acad Sci U S A 103 2006 6747 6752
78. K. Srinivasan, L. Shiue, J.D. Hayes, R. Centers, S. Fitzwater, and R. Loewen Detection and measurement of alternative splicing using splicing-sensitive microarrays Methods 37 2005 345 359
79. Z. Wang, M. Gerstein, and M. Snyder RNA-Seq: A revolutionary tool for transcriptomics Nat Rev Genet 10 2009 57 63
80. A. Mortazavi, B.A. Williams, K. McCue, L. Schaeffer, and B. Wold Mapping and quantifying mammalian transcriptomes by RNA-Seq Nat Methods 5 2008 621 628
81. V.E. Velculescu, L. Zhang, B. Vogelstein, and K.W. Kinzler Serial analysis of gene expression Science 270 1995 484 487
82. T. Shiraki, S. Kondo, S. Katayama, K. Waki, T. Kasukawa, and H. Kawaji Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage Proc Natl Acad Sci U S A 100 2003 15776 15781
83. S. Brenner, M. Johnson, J. Bridgham, G. Golda, D.H. Lloyd, and D. Johnson Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays Nat Biotechnol 18 2000 630 634
84. J. Shendure, and H. Ji Next-generation DNA sequencing Nat Biotechnol 26 2008 1135 1145
85. J. Shendure, R.D. Mitra, C. Varma, and G.M. Church Advanced sequencing technologies: Methods and goals Nat Rev Genet 5 2004 335 344
86. R.D. Mitra, and G.M. Church In situ localized amplification and contact replication of many individual DNA molecules Nucleic Acids Res 27 1999 e34
87. R.D. Mitra, J. Shendure, J. Olejnik, O. Edyta Krzymanska, and G.M. Church Fluorescent in situ sequencing on polymerase colonies Anal Biochem 320 2003 55 65
88. J.C. Marioni, C.E. Mason, S.M. Mane, M. Stephens, and Y. Gilad RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays Genome Res 18 2008 1509 1517
89. J. Shendure The beginning of the end for microarrays? Nat Methods 5 2008 585 587
90. S.D. Ginsberg, I. Elarova, M. Ruben, F. Tan, S.E. Counts, and J.H. Eberwine Single-cell gene expression analysis: Implications for neurodegenerative and neuropsychiatric disorders Neurochem Res 29 2004 1053 1064
91. K. Mirnics What is in the brain soup? Nat Neurosci 11 2008 1237 1238
92. M.C. Oldham, G. Konopka, K. Iwamoto, P. Langfelder, T. Kato, S. Horvath, and D.H. Geschwind Functional organization of the transcriptome in human brain Nat Neurosci 11 2008 1271 1282
93. L. Luo, R.C. Salunga, H. Guo, A. Bittner, K.C. Joy, and J.E. Galindo Gene expression profiles of laser-captured adjacent neuronal subtypes Nat Med 5 1999 117 122
94. D. Arion, T. Unger, D.A. Lewis, and K. Mirnics Molecular markers distinguishing supragranular and infragranular layers in the human prefrontal cortex Eur J Neurosci 25 2007 1843 1854
95. W. Byne, S. Dracheva, B. Chin, J.M. Schmeidler, K.L. Davis, and V. Haroutunian Schizophrenia and sex associated differences in the expression of neuronal and oligodendrocyte-specific genes in individual thalamic nuclei Schizophr Res 98 2008 118 128
96. L.W. Harris, M. Wayland, M. Lan, M. Ryan, T. Giger, and H. Lockstone The cerebral microvasculature in schizophrenia: A laser capture microdissection study PLoS ONE 3 2008 e3964
97. K.A. Garbett, S. Horvath, P.J. Ebert, M.J. Schmidt, K. Lwin, and A. Mitchell Novel animal models for studying complex brain disorders: BAC-driven miRNA-mediated in vivo silencing of gene expression [published online ahead of print February 2] Mol Psychiatry 2010 10.1038/mp.2010.1
98. S.J. Huffaker, J. Chen, K.K. Nicodemus, F. Sambataro, F. Yang, and V. Mattay A primate-specific, brain isoform of KCNH2 affects cortical physiology, cognition, neuronal repolarization and risk of schizophrenia Nat Med 15 2009 509 518
99. S. Horvath, and K. Mirnics Breaking the gene barrier in schizophrenia Nat Med 15 2009 488 490
100. S. Kim, and M.J. Webster The Stanley neuropathology consortium integrative database: A novel, web-based tool for exploring neuropathological markers in psychiatric disorders and the biological processes associated with abnormalities of those markers Neuropsychopharmacology 35 2010 473 482