A combined analysis of microarray gene expression studies of the human prefrontal cortex identifies genes implicated in schizophrenia

Journal of Psychiatric Research

Volumn 46, Issue 11, 2012, Pages 1464-1474

  Pérez Santiago, Josué ^a   Diez Alarcia, Rebeca ^b,c   Callado, Luis F ^b,c   Zhang, Jin X ^d   Chana, Gursharan ^e   White, Cory H ^a   Glatt, Stephen J ^f   Tsuang, Ming T ^d,g   Everall, Ian P ^e   Meana, J Javier ^b,c   Woelk, Christopher H ^a,d  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

^c CENTRO DE INVESTIGACIÓN BIOMÉDICA EN RED DE SALUD MENTAL CIBERSAM   (Spain)

^d VA SAN DIEGO HEALTHCARE SYSTEM   (United States)

^e UNIVERSITY OF MELBOURNE   (Australia)

^f State University of New York Upstate Medical University: College of Medicine   (United States)

^g UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Antipsychotic treatment; Brain; Gene expression; Microarray; Schizophrenia

Indexed keywords

BAG 3 PROTEIN; BREAST CANCER RESISTANCE PROTEIN; CALGRANULIN A; COMPLEMENT COMPONENT C4B; EARLY GROWTH RESPONSE FACTOR 1; METALLOTHIONEIN I; MITOGEN ACTIVATED PROTEIN KINASE; NEUROGENIC DIFFERENTIATION FACTOR; SOMATOSTATIN; STAT2 PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; AUTOPSY; BRAIN NERVE CELL; COHORT ANALYSIS; CONTROLLED STUDY; FETUS; GENE EXPRESSION; GENE IDENTIFICATION; HUMAN; HUMAN CELL; HUMAN TISSUE; INTRACELLULAR SIGNALING; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; PREFRONTAL CORTEX; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SCHIZOPHRENIA;

EID: 84866919007     PISSN: 00223956     EISSN: 18791379     Source Type: Journal    
DOI: 10.1016/j.jpsychires.2012.08.005     Document Type: Article

References (47)

1. Albus M., Hubmann W., Mohr F., Hecht S., Hinterberger-Weber P., Seitz N.N., et al. Neurocognitive functioning in patients with first-episode schizophrenia: results of a prospective 5-year follow-up study. European Archives of Psychiatry and Clinical Neuroscience 2006, 256:442-451.
2. Albus M., Hubmann W., Scherer J., Dreikorn B., Hecht S., Sobizack N., et al. A prospective 2-year follow-up study of neurocognitive functioning in patients with first-episode schizophrenia. European Archives of Psychiatry and Clinical Neuroscience 2002, 252:262-267.
3. Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological) 1995, 57:289-300.
4. Bolstad B.M., Collin F., Brettschneider J., Simpson K., Cope L., Irizarry R., et al. Quality assessment of Affymetrix GeneChip data. Bioinformatics and computational biology solutions using R and bioconductor 2005, 33-47. Springer, Heidelberg. R. Gentleman, V. Carey, W. Huber, R. Irizarry, S. Dutoit (Eds.).
5. Bousquet C., Guillermet J., Vernejoul F., Lahlou H., Buscail L., Susini C. Somatostatin receptors and regulation of cell proliferation. Digestive and Liver Disease 2004, 36(Suppl. 1):S2-S7.
6. Bray N.J. Gene expression in the etiology of schizophrenia. Schizophrenia Bulletin 2008, 34:412-418.
7. Chana G., Lucero G., Salaria S., Lozach J., Du P., Woelk C., et al. Upregulation of NRG-1 and VAMP-1 in human brain aggregates exposed to clozapine. Schizophrenia Research 2009, 113:273-276.
8. Choi K.H., Elashoff M., Higgs B.W., Song J., Kim S., Sabunciyan S., et al. Putative psychosis genes in the prefrontal cortex: combined analysis of gene expression microarrays. BMC Psychiatry 2008, 8:87.
9. Chu T.T., Liu Y. An integrated genomic analysis of gene-function correlation on schizophrenia susceptibility genes. Journal of Human Genetics 2010, 55:285-292.
10. Datson N.A., Speksnijder N., Mayer J.L., Steenbergen P.J., Korobko O., Goeman J., et al. The transcriptional response to chronic stress and glucocorticoid receptor blockade in the hippocampal dentate gyrus. Hippocampus 2010, 22:359-371.
11. English J.A., Pennington K., Dunn M.J., Cotter D.R. The neuroproteomics of schizophrenia. Biological Psychiatry 2011, 69:163-172.
12. Fatemi S.H., Reutiman T.J., Folsom T.D., Bell C., Nos L., Fried P., et al. Chronic olanzapine treatment causes differential expression of genes in frontal cortex of rats as revealed by DNA microarray technique. Neuropsychopharmacology 2006, 31:1888-1899.
13. Foster R., Kandanearatchi A., Beasley C., Williams B., Khan N., Fagerhol M.K., et al. Calprotectin in microglia from frontal cortex is up-regulated in schizophrenia: evidence for an inflammatory process?. European Journal of Neuroscience 2006, 24:3561-3566.
14. Frederiksen S.O., Ekman R., Gottfries C.G., Widerlov E., Jonsson S. Reduced concentrations of galanin, arginine vasopressin, neuropeptide Y and peptide YY in the temporal cortex but not in the hypothalamus of brains from schizophrenics. Acta Psychiatrica Scandinavica 1991, 83:273-277.
15. Gabriel S.M., Davidson M., Haroutunian V., Powchik P., Bierer L.M., Purohit D.P., et al. Neuropeptide deficits in schizophrenia vs. Alzheimer's disease cerebral cortex. Biological Psychiatry 1996, 39:82-91.
16. Garbett K., Gal-Chis R., Gaszner G., Lewis D.A., Mirnics K. Transcriptome alterations in the prefrontal cortex of subjects with schizophrenia who committed suicide. Neuropsychopharmacologia Hungarica 2008, 10:9-14.
17. Glatt S.J., Everall I.P., Kremen W.S., Corbeil J., Sasik R., Khanlou N., et al. Comparative gene expression analysis of blood and brain provides concurrent validation of SELENBP1 up-regulation in schizophrenia. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:15533-15538.
18. Gomez Ravetti M., Rosso O.A., Berretta R., Moscato P. Uncovering molecular biomarkers that correlate cognitive decline with the changes of hippocampus' gene expression profiles in Alzheimer's disease. PLoS One 2010, 5:e10153.
19. Hakak Y., Walker J.R., Li C., Wong W.H., Davis K.L., Buxbaum J.D., et al. Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia. Proceedings of the National Academy of Sciences of the United States of America 2001, 98:4746-4751.
20. Hashimoto T., Arion D., Unger T., Maldonado-Aviles J.G., Morris H.M., Volk D.W., et al. Alterations in GABA-related transcriptome in the dorsolateral prefrontal cortex of subjects with schizophrenia. Molecular Psychiatry 2008, 13:147-161.
21. Higgs B.W., Elashoff M., Richman S., Barci B. An online database for brain disease research. BMC Genomics 2006, 7:70.
22. Hoff A.L., Svetina C., Shields G., Stewart J., DeLisi L.E. Ten year longitudinal study of neuropsychological functioning subsequent to a first episode of schizophrenia. Schizophrenia Research 2005, 78:27-34.
23. Hollingshead D., Lewis D.A., Mirnics K. Platform influence on DNA microarray data in postmortem brain research. Neurobiology of Disease 2005, 18:649-655.
24. Iwamoto K., Kakiuchi C., Bundo M., Ikeda K., Kato T. Molecular characterization of bipolar disorder by comparing gene expression profiles of postmortem brains of major mental disorders. Molecular Psychiatry 2004, 9:406-416.
25. Johnson W.E., Li C., Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007, 8:118-127.
26. Kim S., Choi K.H., Baykiz A.F., Gershenfeld H.K. Suicide candidate genes associated with bipolar disorder and schizophrenia: an exploratory gene expression profiling analysis of post-mortem prefrontal cortex. BMC Genomics 2007, 8:413.
27. Maere S., Heymans K., Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21:3448-3449.
28. Maycox P.R., Kelly F., Taylor A., Bates S., Reid J., Logendra R., et al. Analysis of gene expression in two large schizophrenia cohorts identifies multiple changes associated with nerve terminal function. Molecular Psychiatry 2009, 14:1083-1094.
29. Maynard T.M., Sikich L., Lieberman J.A., LaMantia A.S. Neural development, cell-cell signaling, and the "two-hit" hypothesis of schizophrenia. Schizophrenia Bulletin 2001, 27:457-476.
30. Middleton F.A., Mirnics K., Pierri J.N., Lewis D.A., Levitt P. Gene expression profiling reveals alterations of specific metabolic pathways in schizophrenia. Journal of Neuroscience 2002, 22:2718-2729.
31. Mirnics K., Pevsner J. Progress in the use of microarray technology to study the neurobiology of disease. Nature Neuroscience 2004, 7:434-439.
32. Mistry M., Gillis J., Pavlidis P. Genome-wide expression profiling of schizophrenia using a large combined cohort. Molecular Psychiatry 2012.
33. Morris H.M., Hashimoto T., Lewis D.A. Alterations in somatostatin mRNA expression in the dorsolateral prefrontal cortex of subjects with schizophrenia or schizoaffective disorder. Cerebral Cortex 2008, 18:1575-1587.
34. Nacken W., Roth J., Sorg C., Kerkhoff C. S100A9/S100A8: myeloid representatives of the S100 protein family as prominent players in innate immunity. Microscopy Research and Technique 2003, 60:569-580.
35. Narayan S., Tang B., Head S.R., Gilmartin T.J., Sutcliffe J.G., Dean B., et al. Molecular profiles of schizophrenia in the CNS at different stages of illness. Brain Research 2008, 1239:235-248.
36. Prabakaran S., Swatton J.E., Ryan M.M., Huffaker S.J., Huang J.T., Griffin J.L., et al. Mitochondrial dysfunction in schizophrenia: evidence for compromised brain metabolism and oxidative stress. Molecular Psychiatry 2004, 9:684-697. 643.
37. Sequeira A., Morgan L., Walsh D.M., Cartagena P.M., Choudary P., Li J., et al. Gene expression changes in the prefrontal cortex, anterior cingulate cortex and nucleus accumbens of mood disorders subjects that committed suicide. PLoS One 2012, 7:e35367.
38. Simon R., The BRB-Array Tools Development Team, The EMMES Corporation BRB-array tools version 3.8 user's manual 2009, http://linus.nci.nih.gov/%7Ebrb/download_full_v3_8.html.
39. Struyf J., Dobrin S., Page D. Combining gene expression, demographic and clinical data in modeling disease: a case study of bipolar disorder and schizophrenia. BMC Genomics 2008, 9:531.
40. Torkamani A., Dean B., Schork N.J., Thomas E.A. Coexpression network analysis of neural tissue reveals perturbations in developmental processes in schizophrenia. Genome Research 2010, 20:403-412.
41. Trillo-Pazos G., Kandanearatchi A., Eyeson J., King D., Vyakarnam A., Everall I.P. Infection of stationary human brain aggregates with HIV-1 SF162 and IIIB results in transient neuronal damage and neurotoxicity. Neuropathology and Applied Neurobiology 2004, 30:136-147.
42. Uittenbogaard M., Martinka D.L., Johnson P.F., Vinson C., Chiaramello A. 5'UTR of the neurogenic bHLH Nex1/MATH-2/NeuroD6 gene is regulated by two distinct promoters through CRE and C/EBP binding sites. Journal of Neuroscience Research 2007, 85:1-18.
43. Woelk C.H., Singhania A., Perez-Santiago J., Glatt S.J., Tsuang M.T. The utility of gene expression in blood cells for diagnosing neuropsychiatric disorders. International Review of Neurobiology 2011, 101:41-63.
44. Wu Z., Irizarry R.A., Gentleman R., Martinez-Murillo F., Spencer F.A. Model-based background adjustment for oligonucleotide expression arrays. Journal of the American Statistical Association 2004, 99:909-917.
45. Xu E.Y., Perlina A., Vu H., Troth S.P., Brennan R.J., Aslamkhan A.G., et al. Integrated pathway analysis of rat urine metabolic profiles and kidney transcriptomic profiles to elucidate the systems toxicology of model nephrotoxicants. Chemical Research in Toxicology 2008, 21:1548-1561.
46. Yamada K., Gerber D.J., Iwayama Y., Ohnishi T., Ohba H., Toyota T., et al. Genetic analysis of the calcineurin pathway identifies members of the EGR gene family, specifically EGR3, as potential susceptibility candidates in schizophrenia. Proceedings of the National Academy of Sciences of the United States of America 2007, 104:2815-2820.
47. Zhu W., Smith J.W., Huang C.M. Mass spectrometry-based label-free quantitative proteomics. Journal of Biomedicine and Biotechnology 2010, 2010:840518.