DNA modification study of major depressive disorder: Beyond locus-by-locus comparisons

Biological Psychiatry

Volumn 77, Issue 3, 2015, Pages 246-255

  Oh, Gabriel ^a   Wang, Sun Chong ^a,b   Pal, Mrinal ^a   Chen, Zheng Fei ^c   Khare, Tarang ^a   Tochigi, Mamoru ^a,d   Ng, Catherine ^a   Yang, Yeqing A ^a,e   Kwan, Andrew ^a   Kaminsky, Zachary A ^a,f   Mill, Jonathan ^g,q   Gunasinghe, Cerisse ^g,p   Tackett, Jennifer L ^h   Gottesman, Irving I ⁱ   Willemsen, Gonneke ^j   De Geus, Eco J C ^j   Vink, Jacqueline M ^j   Slagboom, P Eline ^k   Wray, Naomi R ^l   Heath, Andrew C ^m   Montgomery, Grant W ^l   Turecki, Gustavo ^n,o   Martin, Nicholas G ^l   Boomsma, Dorret I ^j   McGuffin, Peter ^g,p   Kustra, Rafal ^c   Petronis, Art ^a   more..

^a CENTRE FOR ADDICTION AND MENTAL HEALTH   (Canada)

^b NATIONAL CENTRAL UNIVERSITY   (Taiwan)

^c UNIVERSITY OF TORONTO   (Canada)

^d UNIVERSITY OF TOKYO   (Japan)

^e NORTHWESTERN UNIVERSITY   (United States)

^f JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^g KING'S COLLEGE LONDON   (United Kingdom)

^h UNIVERSITY OF HOUSTON   (United States)

ⁱ UNIVERSITY OF MINNESOTA   (United States)

^j VU UNIVERSITY AMSTERDAM   (Netherlands)

^k LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^l UNIVERSITY OF QUEENSLAND   (Australia)

^m WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁿ MCGILL UNIVERSITY   (Canada)

^o MCGILL UNIVERSITY   (Canada)

^p SOUTH LONDON AND MAUDSLEY NHS FOUNDATION TRUST   (United Kingdom)

^q UNIVERSITY OF EXETER MEDICAL SCHOOL   (United Kingdom)

more..

Author keywords

DNA modification; Epigenetic outliers; Epigenetics; Heteroscedasticity; Major depressive disorder; Molecular networks

Indexed keywords

AGE; ALGORITHM; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DISCRIMINANT ANALYSIS; DISEASE SEVERITY; DNA MODIFICATION; EPIGENETICS; GENE LOCUS; GENE MAPPING; GERM LINE; HUMAN; HUMAN CELL; LEUKOCYTE; MACHINE LEARNING; MAJOR CLINICAL STUDY; MAJOR DEPRESSION; MALE; MICROARRAY ANALYSIS; MONOZYGOTIC TWINS; PHENOTYPE; PREFRONTAL CORTEX; PRIORITY JOURNAL; PYROSEQUENCING; TWIN DISCORDANCE; ADOLESCENT; ADULT; AGED; FEMALE; GENETIC EPIGENESIS; GENETICS; MIDDLE AGED; SPERMATOZOON; TWINS; YOUNG ADULT;

ADOLESCENT; ADULT; AGED; CPG ISLANDS; DEPRESSIVE DISORDER, MAJOR; EPIGENESIS, GENETIC; FEMALE; HUMANS; LEUKOCYTES; MALE; MICROARRAY ANALYSIS; MIDDLE AGED; PREFRONTAL CORTEX; SPERMATOZOA; TWINS, MONOZYGOTIC; YOUNG ADULT;

EID: 84928210305     PISSN: 00063223     EISSN: 18732402     Source Type: Journal    
DOI: 10.1016/j.biopsych.2014.06.016     Document Type: Article

References (62)

1. American Psychiatric Association (2013): Diagnostic and Statistical Manual of Mental Disorders, 5th ed. Arlington, VA: American Psychiatric Publishing.
2. Kessler RC, Berglund P, Demler O, Jin R, Koretz D, Merikangas KR, et al. (2003): The epidemiology of major depressive disorder: Results from the National Comorbidity Survey Replication (NCS-R). JAMA 289:3095-3105.
3. World Health Organization (2002): Global Burden of Disease. Geneva: World Health Organization.
4. Sullivan PF, Neale MC, Kendler KS (2000): Genetic epidemiology of major depression: Review and meta-analysis. Am J Psychiatry 157:1552-1562.
5. Kendler KS, Gatz M, Gardner CO, Pedersen NL (2006): A Swedish national twin study of lifetime major depression. Am J Psychiatry 163:109-114.
6. Major Depressive Disorder Working Group of the Psychiatric Gwas Consortium, Ripke S, Wray NR, Lewis CM, Hamilton SP, Weissman MM, et al. (2013): A mega-analysis of genome-wide association studies for major depressive disorder. Mol Psychiatry 18:497-511.
7. Mill J, Petronis A (2007): Molecular studies of major depressive disorder: The epigenetic perspective. Mol Psychiatry 12:799-814.
8. Piccinelli M, Wilkinson G (2000): Gender differences in depression. Critical review. Br J Psychiatry 177:486-492.
9. Jansson M, Gatz M, Berg S, Johansson B, Malmberg B, McClearn GE, et al. (2004): Gender differences in heritability of depressive symptoms in the elderly. Psychol Med 34:471-479.
10. Deecher D, Andree TH, Sloan D, Schechter LE (2008): From menarche to menopause: Exploring the underlying biology of depression in women experiencing hormonal changes. Psychoneuroendocrinology 33:3-17.
11. Richards D (2011): Prevalence and clinical course of depression: A review. Clin Psychol Rev 31:1117-1125.
12. Henikoff S, Matzke MA (1997): Exploring and explaining epigenetic effects. Trends Genet 13:293-295.
13. Feil R, Fraga MF (2011): Epigenetics and the environment: Emerging patterns and implications. Nat Rev Genet 13:97-109.
14. Jirtle RL, Skinner MK (2007): Environmental epigenomics and disease susceptibility. Nat Rev Genet 8:253-262.
15. Wong AH, Gottesman II, Petronis A (2005): Phenotypic differences in genetically identical organisms: The epigenetic perspective. Hum Mol Genet 14:R11-R18.
16. Richards EJ (2006): Inherited epigenetic variation-revisiting soft inheritance. Nat Rev Genet 7:395-401.
17. Kaminsky ZA, Tang T, Wang S-C, Ptak C, Oh GHT, Wong AH, et al. (2009): DNA methylation profiles in monozygotic and dizygotic twins. Nat Genet 41:240-245.
18. Benazzi F (2007): Is there a continuity between bipolar and depressive disorders? Psychother Psychosom 76:70-76.
19. McGuffin P, Rijsdijk F, Andrew M, Sham P, Katz R, Cardno A (2003): The heritability of bipolar affective disorder and the genetic relationship to unipolar depression. Arch Gen Psychiatry 60:497-502.
20. Nestor C, Ruzov A, Meehan R, Dunican D (2010): Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA. Biotechniques 48:317-319.
21. Schumacher A, Kapranov P, Kaminsky Z, Flanagan J, Assadzadeh A, Yau P, et al. (2006): Microarray-based DNA methylation profiling: Technology and applications. Nucleic Acids Res 34:528-542.
22. Cross SH, Charlton JA, Nan X, Bird AP (1994): Purification of CpG islands using a methylated DNA binding column. Nat Genet 6:236-244.
23. Heisler LE, Torti D, Boutros PC, Watson J, Chan C, Winegarden N, et al. (2005): CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome. Nucleic Acids Res 33:2952-2961.
24. Kaminsky Z, Petronis A (2009): Methylation SNaPshot: A method for the quantification of site-specific DNA methylation levels. Methods Mol Biol 507:241-255.
25. Li LC, Dahiya R (2002): MethPrimer: Designing primers for methylation PCRs. Bioinformatics 18:1427-1431.
26. Kang HJ, Adams DH, Simen A, Simen BB, Rajkowska G, Stockmeier CA, et al. (2007): Gene expression profiling in postmortem prefrontal cortex of major depressive disorder. J Neurosci 27:13329-13340.
27. Liang MH, Wendland JR, Chuang DM (2008): Lithium inhibits Smad3/4 transactivation via increased CREB activity induced by enhanced PKA and AKT signaling. Mol Cell Neurosci 37:440-453.
28. Sabunciyan S, Aryee MJ, Irizarry RA, Rongione M, Webster MJ, Kaufman WE, et al. (2012): Genome-wide DNA methylation scan in major depressive disorder. PLoS One 7:e34451.
29. Bao L, Zhou M, Cui Y (2008): CTCFBSDB: A CTCF-binding site database for characterization of vertebrate genomic insulators. Nucleic Acids Res 36:D83-D87.
30. Yang AS, Estecio MR, Doshi K, Kondo Y, Tajara EH, Issa JP (2004): A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 32:e38.
31. Burghardt KJ, Pilsner JR, Bly MJ, Ellingrod VL (2012): DNA methylation in schizophrenia subjects: Gender and MTHFR 677C/T genotype differences. Epigenomics 4:261-268.
32. Dempster EL, Pidsley R, Schalkwyk LC, Owens S, Georgiades A, Kane F, et al. (2011): Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder. Hum Mol Genet 20:4786-4796.
33. Christensen MV, Kyvik KO, Kessing LV (2007): Subclinical psychopathology and socio-economic status in unaffected twins discordant for affective disorder. J Psychiatr Res 41:229-238.
34. Vinberg M, Mortensen EL, Kyvik KO, Kessing LV (2007): Personality traits in unaffected twins discordant for affective disorder. Acta Psychiatr Scand 115:442-450.
35. Kirk KM, Birley AJ, Statham DJ, Haddon B, Lake RI, Andrews JG, Martin NG (2000): Anxiety and depression in twin and sib pairs extremely discordant and concordant for neuroticism: Prodromus to a linkage study. Twin Res 3:299-309.
36. Lewis CM, Ng MY, Butler AW, Cohen-Woods S, Uher R, Pirlo K, et al. (2010): Genome-wide association study of major recurrent depression in the U.K. population. Am J Psychiatry 167:949-957.
37. Kendler KS, Gatz M, Gardner CO, Pedersen NL (2006): Personality and major depression: A Swedish longitudinal, population-based twin study. Arch Gen Psychiatry 63:1113-1120.
38. Sjoholm L, Lavebratt C, Forsell Y (2009): A multifactorial developmental model for the etiology of major depression in a population-based sample. J Affect Disord 113:66-76.
39. Ranjith G, Farmer A, McGuffin P, Cleare AJ (2005): Personality as a determinant of social functioning in depression. J Affect Disord 84:73-76.
40. Langfelder P, Horvath S (2008): WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics 9:559.
41. Plaisier CL, Horvath S, Huertas-Vazquez A, Cruz-Bautista I, Herrera MF, Tusie-Luna T, et al. (2009): A systems genetics approach implicates USF1, FADS3, and other causal candidate genes for familial combined hyperlipidemia. PLoS Genet 5:e1000642.
42. Voineagu I, Wang X, Johnston P, Lowe JK, Tian Y, Horvath S, et al. (2011): Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 474:380-384.
43. Opgen-Rhein R, Strimmer K (2007): From correlation to causation networks: A simple approximate learning algorithm and its application to high-dimensional plant gene expression data. BMC Syst Biol 1:37.
44. Becker KG, Barnes KC, Bright TJ, Wang SA (2004): The genetic association database. Nat Genet 36:431-432.
45. Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L, et al. (2008): Epigenomic pro filing reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 82:696-711.
46. Byrne EM, Carrillo-Roa T, Henders AK, Bowdler L, McRae AF, Heath AC, et al. (2013): Monozygotic twins affected with major depressive disorder have greater variance in methylation than their unaffected co-twin. Transl Psychiatry 3:e269.
47. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, et al. (2011): Increased methylation variation in epigenetic domains across cancer types. Nat Genet 43:768-775.
48. Jylha P, Isometsa E (2006): The relationship of neuroticism and extraversion to symptoms of anxiety and depression in the general population. Depress Anxiety 23:281-289.
49. Fanous A, Gardner CO, Prescott CA, Cancro R, Kendler KS (2002): Neuroticism, major depression and gender: A population-based twin study. Psychol Med 32:719-728.
50. Mitchell ND, Baker GB (2010): An update on the role of glutamate in the pathophysiology of depression. Acta Psychiatr Scand 122:192-210.
51. de Wit L, Luppino F, van Straten A, Penninx B, Zitman F, Cuijpers P (2010): Depression and obesity: A meta-analysis of community-based studies. Psychiatry Res 178:230-235.
52. Williams AL, Girard C, Jui D, Sabina A, Katz DL (2005): S-adenosylmethionine (SAMe) as treatment for depression: A systematic review. Clin Invest Med 28:132-139.
53. Fiori LM, Zouk H, Himmelman C, Turecki G (2011): X chromosome and suicide. Mol Psychiatry 16:216-226.
54. Hashimoto R, Okada T, Kato T, Kosuga A, Tatsumi M, Kamijima K, Kunugi H (2005): The breakpoint cluster region gene on chromosome 22q11 is associated with bipolar disorder. Biol Psychiatry 57:1097-1102.
55. Tadokoro K, Hashimoto R, Tatsumi M, Kosuga A, Kamijima K, Kunugi H (2005): The Gem interacting protein (GMIP) gene is associated with major depressive disorder. Neurogenetics 6:127-133.
56. Whitfield JB, Zhu G, Heath AC, Martin NG (2005): Choice of residential location: Chance, family influences, or genes? Twin Res Hum Genet 8:22-26.
57. Willemsen G, Posthuma D, Boomsma DI (2005): Environmental factors determine where the Dutch live: Results from the Netherlands twin register. Twin Res Hum Genet 8:312-317.
58. Palmer C, Diehn M, Alizadeh AA, Brown PO (2006): Cell-type specific gene expression profiles of leukocytes in human peripheral blood. BMC Genomics 7:115.
59. Lopez JP, Mamdani F, Labonte B, Beaulieu MM, Yang JP, Berlim MT, et al. (2013): Epigenetic regulation of BDNF expression according to antidepressant response. Mol Psychiatry 18:398-399.
60. Yamawaki Y, Fuchikami M, Morinobu S, Segawa M, Matsumoto T, Yamawaki S (2012): Antidepressant-like effect of sodium butyrate (HDAC inhibitor) and its molecular mechanism of action in the rat hippocampus. World J Biol Psychiatry 13:458-467.
61. Tsankova NM, Berton O, Renthal W, Kumar A, Neve RL, Nestler EJ (2006): Sustained hippocampal chromatin regulation in a mouse model of depression and antidepressant action. Nat Neurosci 9:519-525.
62. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. (2009): Circos: An information aesthetic for comparative genomics. Genome Res 19:1639-1645.