Protein-protein interaction and pathway analyses of top schizophrenia genes reveal schizophrenia susceptibility

Schizophrenia Bulletin

Volumn 40, Issue 1, 2014, Pages 39-49

  Luo, Xiongjian ^a,b   Huang, Liang ^c,d,e   Jia, Peilin ^f   Li, Ming ^g   Su, Bing ^g   Zhao, Zhongming ^f   Gan, Lin ^a,b  

^a UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

^b HANGZHOU NORMAL UNIVERSITY   (China)

^c NANCHANG UNIVERSITY   (China)

^d Jiangxi Provincial People's Hospital   (China)

^e GANNAN MEDICAL UNIVERSITY   (China)

^f VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^g KUNMING INSTITUTE OF ZOOLOGY   (China)

Author keywords

common molecular networks; enrichment; genetic heterogeneity; genome wide association study; protein protein interaction; schizophrenia susceptibility genes

Indexed keywords

TRANSCRIPTOME;

ARTICLE; BRAIN TISSUE; CHROMATIN ASSEMBLY AND DISASSEMBLY; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; HUMAN; NONHUMAN; NUCLEOSOME; PREFRONTAL CORTEX; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SCHIZOPHRENIA; SINGLE NUCLEOTIDE POLYMORPHISM;

COMMON MOLECULAR NETWORKS; ENRICHMENT; GENETIC HETEROGENEITY; GENOME-WIDE ASSOCIATION STUDY; PROTEIN-PROTEIN INTERACTION; SCHIZOPHRENIA SUSCEPTIBILITY GENES;

CHROMATIN; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION STUDIES; GENETIC HETEROGENEITY; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; NEURAL PATHWAYS; NUCLEOSOMES; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; RANDOMIZED CONTROLLED TRIALS AS TOPIC; SCHIZOPHRENIA; SIGNAL TRANSDUCTION; TRANSCRIPTOME; VALIDATION STUDIES AS TOPIC;

EID: 84892654670     PISSN: 05867614     EISSN: 17451701     Source Type: Journal    
DOI: 10.1093/schbul/sbt066     Document Type: Article

References (39)

1. Jablensky A, Sartorius N, Korten A, et al. Incidence worldwide of schizophrenia. Br J Psychiatry. 1987;151:408-409.
2. Cardno AG, Gottesman II. Twin studies of schizophrenia: from bow-and-arrow concordances to star wars Mx and functional genomics. Am J Med Genet. 2000;97:12-17.
3. Sullivan PF, Kendler KS, Neale MC. Schizophrenia as a complex trait: evidence from a meta-analysis of twin studies. Arch Gen Psychiatry. 2003;60:1187-1192.
4. Pulver AE, Mulle J, Nestadt G, et al. Genetic heterogeneity in schizophrenia: stratification of genome scan data using co-segregating related phenotypes. Mol Psychiatry. 2000;5:650-653.
5. Beckmann H, Franzek E. The genetic heterogeneity of "schizophrenia. " World J Biol Psychiatry. 2000;1:35-41.
6. O'Donovan MC, Craddock N, Norton N, et al. Identification of loci associated with schizophrenia by genome-wide association and follow-up. Nat Genet. 2008;40:1053-1055.
7. Ripke S, Sanders AR, Kendler KS, et al. Genome-wide association study identifies five new schizophrenia loci. Nat Genet. 2011;43:969-976.
8. St Clair D. Copy number variation and schizophrenia. Schizophr Bull. 2009;35:9-12.
9. Levinson DF, Duan J, Oh S, et al. Copy number variants in schizophrenia: confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications. Am J Psychiatry. 2011;168:302-316.
10. Bassett AS, Scherer SW, Brzustowicz LM. Copy number variations in schizophrenia: critical review and new perspectives on concepts of genetics and disease. Am J Psychiatry. 2010;167:899-914.
11. Walsh T, McClellan JM, McCarthy SE, et al. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science. 2008;320:539-543.
12. Consortium IS. Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature. 2008;455:237-241.
13. Spencer CC, Su Z, Donnelly P, Marchini J. Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet. 2009;5:e1000477.
14. McCarthy MI, Abecasis GR, Cardon LR, et al. Genomewide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet. 2008;9:356-369.
15. Hamshere ML, Walters JT, Smith R, et al. Genome-wide significant associations in schizophrenia to ITIH3/4, CACNA1C and SDCCAG8, and extensive replication of associations reported by the Schizophrenia PGC. Mol Psychiatry. doi: 101038/mp201267.
16. Rossin EJ, Lage K, Raychaudhuri S, et al. Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet. 2011;7:e1001273.
17. Stefansson H, Ophoff RA, Steinberg S, et al. Common variants conferring risk of schizophrenia. Nature. 2009;460: 744-747.
18. Li J, Zhou G, Ji W, et al. Common variants in the BCL9 gene conferring risk of schizophrenia. Arch Gen Psychiatry. 2011;68:232-240.
19. Steinberg S, de Jong S, Andreassen OA, et al. Common variants at VRK2 and TCF4 conferring risk of schizophrenia. Hum Mol Genet. 2011;20:4076-4081.
20. Rietschel M, Mattheisen M, Degenhardt F, et al. Association between genetic variation in a region on chromosome 11 and schizophrenia in large samples from Europe. Mol Psychiatry. 2012;17:906-917.
21. Ikeda M, Aleksic B, Yamada K, et al. Genetic evidence for association between NOTCH4 and schizophrenia supported by a GWAS follow-up study in a Japanese population. Mol Psychiatry. 2012. doi: 2010.1038/mp.2012.2074.
22. Shi Y, Li Z, Xu Q, et al. Common variants on 8p12 and 1q24.2 confer risk of schizophrenia. Nat Genet. 2011;43:1224-1227.
23. Yue WH, Wang HF, Sun LD, et al. Genome-wide association study identifies a susceptibility locus for schizophrenia in Han Chinese at 11p11.2. Nat Genet. 2011;43:1228-1231.
24. Purcell SM, Wray NR, Stone JL, et al. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature. 2009;460:748-752.
25. Ayalew M, Le-Niculescu H, Levey DF, et al. Convergent functional genomics of schizophrenia: from comprehensive understanding to genetic risk prediction. Mol Psychiatry. 2012;17:887-905.
26. Fillman SG, Cloonan N, Catts VS, et al. Increased inflammatory markers identified in the dorsolateral prefrontal cortex of individuals with schizophrenia. Mol Psychiatry. 2012. doi: 10.1038/mp.2012.110.
27. Lage K, Karlberg EO, Størling ZM, et al. A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol. 2007;25:309-316.
28. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4:44-57.
29. Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37:1-13.
30. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27-30.
31. Xu J, Sun J, Chen J, et al. RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia. BMC Genomics. 2012;13(suppl 8):S2.
32. Warde-Farley D, Donaldson SL, Comes O, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 2010;38:W214-W220.
33. Shirts BH, Wood J, Yolken RH, Nimgaonkar VL. Association study of IL10, IL1beta, and IL1RN and schizophrenia using tag SNPs from a comprehensive database: suggestive association with rs16944 at IL1beta. Schizophr Res. 2006;88: 235-244.
34. Xu M, He L. Convergent evidence shows a positive association of interleukin-1 gene complex locus with susceptibility to schizophrenia in the Caucasian population. Schizophr Res. 2010;120:131-142.
35. Yoshida M, Shiroiwa K, Mouri K, et al. Haplotypes in the expression quantitative trait locus of interleukin-1? gene are associated with schizophrenia. Schizophr Res. 2012;140:185-191.
36. Gardiner EJ, Cairns MJ, Liu B, et al. Gene expression analysis reveals schizophrenia-associated dysregulation of immune pathways in peripheral blood mononuclear cells. J Psychiatr Res. 2013;47:425-437.
37. Michel M, Schmidt MJ, Mirnics K. Immune system gene dysregulation in autism and schizophrenia. Dev Neurobiol. 2012;72:1277-1287.
38. Fineberg AM, Ellman LM. Inflammatory cytokines and neurological and neurocognitive alterations in the course of schizophrenia [published online ahead of print]. Biol Psychiatry. 2013. doi: 10.1016/j.biopsych.2013.01.001.
39. Jia P, Zheng S, Long J, Zheng W, Zhao Z. dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics. 2011;27:95-102.