A conserved BDNF, glutamate- and GABA-enriched gene module related to human depression identified by coexpression meta-analysis and DNA variant genome-wide association studies

PLoS ONE

Volumn 9, Issue 3, 2014, Pages

  Chang, Lun Ching ^a   Jamain, Stephane ^b,c,d   Lin, Chien Wei ^a   Rujescu, Dan ^e   Tseng, George C ^a,f   Sibille, Etienne ^g  

^a UNIVERSITY OF PITTSBURGH GRADUATE SCHOOL OF PUBLIC HEALTH   (United States)

^b INSERM   (France)

^c UNIVERSITÉ PARIS EST CRÉTEIL   (France)

^d FONDATION FONDAMENTAL   (France)

^e MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^f UNIVERSITY OF PITTSBURGH   (United States)

^g UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

4 AMINOBUTYRIC ACID; 4 AMINOBUTYRIC ACID A RECEPTOR ALPHA2; 4 AMINOBUTYRIC ACID A RECEPTOR ALPHA4; BRAIN DERIVED NEUROTROPHIC FACTOR; EPHRIN RECEPTOR A3; EPHRIN RECEPTOR A5; GLUTAMIC ACID; METABOTROPIC RECEPTOR 1; METABOTROPIC RECEPTOR 7; REELIN; TRANSCRIPTOME; 4 AMINOBUTYRIC ACID RECEPTOR; BRAIN-DERIVED NEUROTROPHIC FACTOR, HUMAN; EPHRIN RECEPTOR; METABOTROPIC RECEPTOR; NERVE CELL ADHESION MOLECULE; NERVE PROTEIN; REELIN PROTEIN; SCLEROPROTEIN; SERINE PROTEINASE;

ARTICLE; AUTOPSY; BRAIN FUNCTION; BRAIN TISSUE; CONTROLLED STUDY; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ASSOCIATION; GENETIC VARIABILITY; HIGH RISK POPULATION; HUMAN; HUMAN TISSUE; MAJOR DEPRESSION; MENTAL DISEASE; NONHUMAN; SINGLE NUCLEOTIDE POLYMORPHISM; AGED; BRAIN; CASE CONTROL STUDY; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC PREDISPOSITION; GENETICS; HUMAN GENOME; MALE; METABOLISM; MIDDLE AGED; MULTIGENE FAMILY; PATHOPHYSIOLOGY;

AGED; BRAIN; BRAIN-DERIVED NEUROTROPHIC FACTOR; CASE-CONTROL STUDIES; CELL ADHESION MOLECULES, NEURONAL; DEPRESSIVE DISORDER, MAJOR; EXTRACELLULAR MATRIX PROTEINS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; METABOLIC NETWORKS AND PATHWAYS; MIDDLE AGED; MULTIGENE FAMILY; NERVE TISSUE PROTEINS; RECEPTORS, EPH FAMILY; RECEPTORS, GABA; RECEPTORS, METABOTROPIC GLUTAMATE; SERINE ENDOPEPTIDASES; TRANSCRIPTOME;

EID: 84897414615     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0090980     Document Type: Article

References (48)

1. Hasin DS, Goodwin RD, Stinson FS, Grant BF (2005) Epidemiology of major depressive disorder: results from the National Epidemiologic Survey on Alcoholism and Related Conditions. Archives of general psychiatry 62: 1097-1106. (Pubitemid 41396935)
2. Mueller TI, Leon AC, Keller MB, Solomon DA, Endicott J, et al. (1999) Recurrence after recovery from major depressive disorder during 15 years of observational follow-up. The American journal of psychiatry 156: 1000-1006. (Pubitemid 29302790)
3. Weissman MM, Bland R, Joyce PR, Newman S, Wells JE, et al. (1993) Sex differences in rates of depression: cross-national perspectives. Journal of affective disorders 29: 77-84. (Pubitemid 23334115)
4. Sullivan PF, Neale MC, Kendler KS (2000) Genetic epidemiology of major depression: review and meta-analysis. The American journal of psychiatry 157: 1552-1562.
5. Gaiteri C, Ding Y, Tseng GC, Sibille E (2013) Beyond Modules & Hubs: Investigating pathogenic molecular mechanisms of brain disorders through gene coexpression networks. Submitted.
6. Rietschel M, Mattheisen M, Frank J, Treutlein J, Degenhardt F, et al. (2010) Genome-wide association-, replication-, and neuroimaging study implicates HOMER1 in the etiology of major depression. Biological psychiatry 68: 578-585.
7. Shi J, Potash JB, Knowles JA, Weissman MM, Coryell W, et al. (2011) Genome-wide association study of recurrent early-onset major depressive disorder. Molecular psychiatry 16: 193-201.
8. Muglia P, Tozzi F, Galwey NW, Francks C, Upmanyu R, et al. (2010) Genome-wide association study of recurrent major depressive disorder in two European case-control cohorts. Molecular psychiatry 15: 589-601.
9. Lewis CM, Ng MY, Butler AW, Cohen-Woods S, Uher R, et al. (2010) Genome-wide association study of major recurrent depression in the U.K. population. The American journal of psychiatry 167: 949-957.
10. Shyn SI, Shi J, Kraft JB, Potash JB, Knowles JA, et al. (2011) Novel loci for major depression identified by genome-wide association study of Sequenced Treatment Alternatives to Relieve Depression and meta-analysis of three studies. Molecular psychiatry 16: 202-215.
11. MDD GWAS consortium (2012) A mega-analysis of genome-wide association studies for major depressive disorder. Mol Psychiatry.
12. Hek K, Demirkan A, Lahti J, Terracciano A, Teumer A, et al. (2013) A Genome-Wide Association Study of Depressive Symptoms. Biol Psychiatry.
13. Kupfer DJ, Angst J, Berk M, Dickerson F, Frangou S, et al. (2011) Advances in bipolar disorder: selected sessions from the 2011 International Conference on Bipolar Disorder. Ann N Y Acad Sci 1242: 1-25.
14. Cristino AS, Williams SM, Hawi Z, An JY, Bellgrove MA, et al. (2013) Neurodevelopmental and neuropsychiatric disorders represent an interconnected molecular system. Mol Psychiatry.
15. Niculescu AB (2013) Convergent functional genomics of psychiatric disorders. Am J Med Genet B Neuropsychiatr Genet.
16. Le-Niculescu H, Kurian SM, Yehyawi N, Dike C, Patel SD, et al. (2009) Identifying blood biomarkers for mood disorders using convergent functional genomics. Mol Psychiatry 14: 156-174.
17. Le-Niculescu H, Balaraman Y, Patel SD, Ayalew M, Gupta J, et al. (2011) Convergent functional genomics of anxiety disorders: translational identification of genes, biomarkers, pathways and mechanisms. Transl Psychiatry 1: e9.
18. Tripp A, Oh H, Guilloux JP, Martinowich K, Lewis DA, et al. (2012) Brain-derived neurotrophic factor signaling and subgenual anterior cingulate cortex dysfunction in major depressive disorder. Am J Psychiatry 169: 1194-1202.
19. Klempan TA, Sequeira A, Canetti L, Lalovic A, Ernst C, et al. (2009) Altered expression of genes involved in ATP biosynthesis and GABAergic neurotransmission in the ventral prefrontal cortex of suicides with and without major depression. MolPsychiatry 14: 175-189.
20. Sequeira A, Mamdani F, Ernst C, Vawter MP, Bunney WE, et al. (2009) Global brain gene expression analysis links glutamatergic and GABAergic alterations to suicide and major depression. PLoS One 4: e6585.
21. Choudary PV, Molnar M, Evans SJ, Tomita H, Li JZ, et al. (2005) Altered cortical glutamatergic and GABAergic signal transmission with glial involvement in depression. ProcNatlAcadSci USA 102: 15653-15658. (Pubitemid 41528111)
22. Guilloux JP, Douillard-Guilloux G, Kota R, Wang X, Gardier AM, et al. (2012) Molecular evidence for BDNF- and GABA-related dysfunctions in the amygdala of female subjects with major depression. Mol Psychiatry 17: 1130-1142.
23. Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P (2004) Coexpression analysis of human genes across many microarray data sets. Genome research 14: 1085-1094. (Pubitemid 38811545)
24. Gaiteri C, Guilloux JP, Lewis DA, Sibille E (2010) Altered gene synchrony suggests a combined hormone-mediated dysregulated state in major depression. PloS one 5: e9970.
25. Dobrin R, Zhu J, Molony C, Argman C, Parrish ML, et al. (2009) Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease. Genome biology 10: R55.
26. Elo LL, Jarvenpaa H, Oresic M, Lahesmaa R, Aittokallio T (2007) Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process. Bioinformatics 23: 2096-2103. (Pubitemid 47394109)
27. Sibille E, French B (2013) Biological substrates underpinning diagnosis of major depression. Int J Neuropsychopharmacol 16: 1893-1909.
28. Pan A, Keum N, Okereke OI, Sun Q, Kivimaki M, et al. (2012) Bidirectional association between depression and metabolic syndrome: a systematic review and meta-analysis of epidemiological studies. Diabetes Care 35: 1171-1180.
29. Musselman DL, Evans DL, Nemeroff CB (1998) The relationship of depression to cardiovascular disease: epidemiology, biology, and treatment. ArchGenPsychiatry 55: 580-592. (Pubitemid 28340345)
30. Wang X, Lin Y, Song C, Sibille E, Tseng GC (2012) Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: with application to major depressive disorder. BMC Bioinformatics 13: 52.
31. Sibille E, Arango V, Galfalvy HC, Pavlidis P, Erraji-BenChekroun L, et al. (2004) Gene expression profiling of depression and suicide in human prefrontal cortex. Neuropsychopharmacology 29: 351-361. (Pubitemid 38175153)
32. Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S (2005) Bioinformatics and computational biology solutions using R and Bioconductor: Springer New York.
33. Tseng GC (2007) Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data. Bioinformatics 23: 2247-2255.
34. Thalamuthu A, Mukhopadhyay I, Zheng X, Tseng GC (2006) Evaluation and comparison of gene clustering methods in microarray analysis. Bioinformatics 22: 2405-2412. (Pubitemid 44566970)
35. Hubert L, Arabie P (1985) Comparing Partitions. Journal of the Classification 2: 193-218.
36. Efron B (1979) Bootstrap Methods: Another Look at the Jackknife. The annals of statistics 7: 1-26.
37. van den Oord EJ, Kuo PH, Hartmann AM, Webb BT, Moller HJ, et al. (2008) Genomewide association analysis followed by a replication study implicates a novel candidate gene for neuroticism. Archives of general psychiatry 65: 1062-1071.
38. Wray NR, Pergadia ML, Blackwood DH, Penninx BW, Gordon SD, et al. (2012) Genome-wide association study of major depressive disorder: new results, meta-analysis, and lessons learned. Molecular psychiatry 17: 36-48.
39. Psychiatric GWAS Consortium Bipolar Disorder Working Group (2011) Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. Nat Genet 43: 977-983.
40. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences of the United States of America 106: 9362-9367.
41. Stouffer SA (1949) A study of attitudes. Scientific American 180: 11-15.
42. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I (2001) Controlling the false discovery rate in behavior genetics research. Behavioural brain research 125: 279-284. (Pubitemid 33000466)
43. Ripke S, O'Dushlaine C, Chambert K, Moran JL, Kahler AK, et al. (2013) Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nature genetics 45: 1150-1159.
44. Luscher B, Shen Q, Sahir N (2011) The GABAergic deficit hypothesis of major depressive disorder. Mol Psychiatry 16: 383-406.
45. Belmaker RH, Agam G (2008) Major depressive disorder. NEnglJ Med 358: 55-68.
46. Nestler EJ, Barrot M, DiLeone RJ, Eisch AJ, Gold SJ, et al. (2002) Neurobiology of depression. Neuron 34: 13-25. (Pubitemid 34270695)
47. Duman RS, Monteggia LM (2006) A neurotrophic model for stress-related mood disorders. Biol Psychiatry 59: 1116-1127.
48. Rajkowska G, O'Dwyer G, Teleki Z, Stockmeier CA, Miguel-Hidalgo JJ (2007) GABAergic neurons immunoreactive for calcium binding proteins are reduced in the prefrontal cortex in major depression. Neuropsychopharmacology 32: 471-482. (Pubitemid 46106953)