Survey of the effect of genetic variations on gene expression in human prefrontal cortex and its application to genetics of psychiatric disorders

Neuroscience Research

Volumn 70, Issue 2, 2011, Pages 238-242

  Iwamoto, Kazuya ^a,b   Ueda, Junko ^a   Bundo, Miki ^a,b   Kojima, Toshio ^c,d   Kato, Tadafumi ^a  

^a RIKEN BRAIN SCIENCE INSTITUTE   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c RIKEN YOKOHAMA INSTITUTE   (Japan)

^d HAMAMATSU UNIVERSITY SCHOOL OF MEDICINE   (Japan)

Author keywords

Genetics; Microarray; Postmortem brain; Psychiatry

Indexed keywords

CIS ACTING ELEMENT;

ADULT; AKAP10 GENE; ARTICLE; BIPOLAR DISORDER; CONTROLLED STUDY; FEMALE; GENE; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN EXPERIMENT; HUMAN TISSUE; LYMPHOBLASTOID CELL; LYMPHOCYTE; MALE; MENTAL DISEASE; NORMAL HUMAN; PH; PREFRONTAL CORTEX; PRIORITY JOURNAL; PRKCI GENE; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION REGULATION;

ADULT; DELIRIUM, DEMENTIA, AMNESTIC, COGNITIVE DISORDERS; FEMALE; GENE EXPRESSION REGULATION; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENETIC VARIATION; GENETICS, BEHAVIORAL; HUMANS; MALE; MIDDLE AGED; PREFRONTAL CORTEX;

EID: 79955656595     PISSN: 01680102     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neures.2011.02.012     Document Type: Article

References (35)

1. Atz M., Walsh D., Cartagena P., Li J., Evans S., Choudary P., Overman K., Stein R., Tomita H., Potkin S., Myers R., Watson S.J., Jones E.G., Akil H., Bunney W.E., Vawter M.P. Methodological considerations for gene expression profiling of human brain. J. Neurosci. Methods 2007, 163:295-309.
2. Bahn S., Augood S.J., Ryan M., Standaert D.G., Starkey M., Emson P.C. Gene expression profiling in the post-mortem human brain - no cause for dismay. J. Chem. Neuroanat. 2001, 22:79-94.
3. Barton A.J., Pearson R.C., Najlerahim A., Harrison P.J. Pre- and postmortem influences on brain RNA. J. Neurochem. 1993, 61:1-11.
4. Burns-Hamuro L.L., Barraclough D.M., Taylor S.S. Identification and functional analysis of dual-specific A kinase-anchoring protein-2. Methods Enzymol. 2004, 390:354-374.
5. Chang A., Li P.P., Warsh J.J. Altered cAMP-dependent protein kinase subunit immunolabeling in post-mortem brain from patients with bipolar affective disorder. J. Neurochem. 2003, 84:781-791.
6. Cheung V.G., Spielman R.S., Ewens K.G., Weber T.M., Morley M., Burdick J.T. Mapping determinants of human gene expression by regional and genome-wide association. Nature 2005, 437:1365-1369.
7. Dennis G., Sherman B.T., Hosack D.A., Yang J., Gao W., Lane H.C., Lempicki R.A. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol. 2003, 4:P3.
8. Dixon A.L., Liang L., Moffatt M.F., Chen W., Heath S., Wong K.C., Taylor J., Burnett E., Gut I., Farrall M., Lathrop G.M., Abecasis G.R., Cookson W.O. A genome-wide association study of global gene expression. Nat. Genet. 2007, 39:1202-1207.
9. Goring H.H., Curran J.E., Johnson M.P., Dyer T.D., Charlesworth J., Cole S.A., Jowett J.B., Abraham L.J., Rainwater D.L., Comuzzie A.G., Mahaney M.C., Almasy L., MacCluer J.W., Kissebah A.H., Collier G.R., Moses E.K., Blangero J. Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat. Genet. 2007, 39:1208-1216.
10. Hahn C.G., Friedman E. Abnormalities in protein kinase C signaling and the pathophysiology of bipolar disorder. Bipolar Disord. 1999, 1:81-86.
11. Harrison P.J., Heath P.R., Eastwood S.L., Burnet P.W., McDonald B., Pearson R.C. 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, 200:151-154.
12. International Hapmap Consortium A haplotype map of the human genome. Nature 2005, 437:1299-1320.
13. Iwamoto K., Bundo M., Kato T. 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. 2005, 14:241-253.
14. Iwamoto K., Bundo M., Ueda J., Kato T. Expression of ribosomal subunit genes increased coordinately with postmortem interval in human brain. Mol. Psychiatry 2006, 11:1067-1069.
15. Iwamoto K., Kato T. Gene expression profiling in schizophrenia and related mental disorders. Neuroscientist 2006, 12:349-361.
16. Iwamoto K., Ueda J., Nakano Y., Bundo M., Ukai W., Hashimoto E., Saito T., Kato T. Evaluation of whole genome amplification methods using postmortem brain samples. J. Neurosci. Methods 2007, 165:104-110.
17. Kammerer S., Burns-Hamuro L.L., Ma Y., Hamon S.C., Canaves J.M., Shi M.M., Nelson M.R., Sing C.F., Cantor C.R., Taylor S.S., Braun A. Amino acid variant in the kinase binding domain of dual-specific A kinase-anchoring protein 2: a disease susceptibility polymorphism. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:4066-4071.
18. Kato T. Molecular neurobiology of bipolar disorder: a disease of 'mood-stabilizing neurons'?. Trends Neurosci. 2008, 31:495-503.
19. Kingsbury A.E., Foster O.J., Nisbet A.P., Cairns N., Bray L., Eve D.J., Lees A.J., Marsden C.D. Tissue pH as an indicator of mRNA preservation in human post-mortem brain. Brain Res. Mol. Brain Res. 1995, 28:311-318.
20. Li J.Z., Vawter M.P., Walsh D.M., Tomita H., Evans S.J., Choudary P.V., Lopez J.F., Avelar A., Shokoohi V., Chung T., Mesarwi O., Jones E.G., Watson S.J., Akil H., Bunney W.E., Myers R.M. Systematic changes in gene expression in postmortem human brains associated with tissue pH and terminal medical conditions. Hum. Mol. Genet. 2004, 13:609-616.
21. Liu C., Cheng L., Badner J.A., Zhang D., Craig D.W., Redman M., Gershon E.S. Whole-genome association mapping of gene expression in the human prefrontal cortex. Mol. Psychiatry 2010, 15:779-784.
22. Mirnics K., Levitt P., Lewis D.A. Critical appraisal of DNA microarrays in psychiatric genomics. Biol. Psychiatry 2006, 60:163-176.
23. Myers A.J., Gibbs J.R., Webster J.A., Rohrer K., Zhao A., Marlowe L., Kaleem M., Leung D., Bryden L., Nath P., Zismann V.L., Joshipura K., Huentelman M.J., Hu-Lince D., Coon K.D., Craig D.W., Pearson J.V., Holmans P., Heward C.B., Reiman E.M., Stephan D., Hardy J. A survey of genetic human cortical gene expression. Nat. Genet. 2007, 39:1494-1499.
24. Papapetropoulos S., Shehadeh L., McCorquodale D. Optimizing human post-mortem brain tissue gene expression profiling in Parkinson's disease and other neurodegenerative disorders: from target "fishing" to translational breakthroughs. J. Neurosci. Res. 2007, 85:3013-3024.
25. Ryan M.M., Huffaker S.J., Webster M.J., Wayland M., Freeman T., Bahn S. Application and optimization of microarray technologies for human postmortem brain studies. Biol. Psychiatry 2004, 55:329-336.
26. Shyamsundar R., Kim Y.H., Higgins J.P., Montgomery K., Jorden M., Sethuraman A., van de Rijn M., Botstein D., Brown P.O., Pollack J.R. A DNA microarray survey of gene expression in normal human tissues. Genome Biol. 2005, 6:R22.
27. Spielman R.S., Bastone L.A., Burdick J.T., Morley M., Ewens W.J., Cheung V.G. Common genetic variants account for differences in gene expression among ethnic groups. Nat. Genet. 2007, 39:226-231.
28. Storey J.D., Tibshirani R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:9440-9445.
29. Stranger B.E., Forrest M.S., Clark A.G., Minichiello M.J., Deutsch S., Lyle R., Hunt S., Kahl B., Antonarakis S.E., Tavare S., Deloukas P., Dermitzakis E.T. Genome-wide associations of gene expression variation in humans. PLoS Genet. 2005, 1:e78.
30. Stranger B.E., Forrest M.S., Dunning M., Ingle C.E., Beazley C., Thorne N., Redon R., Bird C.P., de Grassi A., Lee C., Tyler-Smith C., Carter N., Scherer S.W., Tavare S., Deloukas P., Hurles M.E., Dermitzakis E.T. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 2007, 315:848-853.
31. Stranger B.E., Nica A.C., Forrest M.S., Dimas A., Bird C.P., Beazley C., Ingle C.E., Dunning M., Flicek P., Koller D., Montgomery S., Tavare S., Deloukas P., Dermitzakis E.T. Population genomics of human gene expression. Nat. Genet. 2007, 39:1217-1224.
32. The Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls. Nature 2007, 447:661-678.
33. Tomita H., Vawter M.P., Walsh D.M., Evans S.J., Choudary P.V., Li J., Overman K.M., Atz M.E., Myers R.M., Jones E.G., Watson S.J., Akil H., Bunney W.E. Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain. Biol. Psychiatry 2004, 55:346-352.
34. Wang L., Sunahara R.K., Krumins A., Perkins G., Crochiere M.L., Mackey M., Bell S., Ellisman M.H., Taylor S.S. Cloning and mitochondrial localization of full-length D-AKAP2, a protein kinase A anchoring protein. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:3220-3225.
35. Weis S., Llenos I.C., Dulay J.R., Elashoff M., Martinez-Murillo F., Miller C.L. Quality control for microarray analysis of human brain samples: the impact of postmortem factors, RNA characteristics, and histopathology. J. Neurosci. Methods 2007, 165:198-209.