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A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder

Abstract

Epigenetic studies of DNA and histone modifications represent a new and important activity in molecular investigations of human disease. Our previous epigenome-wide scan identified numerous DNA methylation differences in post-mortem brain samples from individuals affected with major psychosis. In this article, we present the results of fine mapping DNA methylation differences at the human leukocyte antigen (HLA) complex group 9 gene (HCG9) in bipolar disorder (BPD). Sodium bisulfite conversion coupled with pyrosequencing was used to interrogate 28 CpGs spanning 700 bp region of HCG9 in 1402 DNA samples from post-mortem brains, peripheral blood cells and germline (sperm) of bipolar disease patients and controls. The analysis of nearly 40 000 CpGs revealed complex relationships between DNA methylation and age, medication as well as DNA sequence variation (rs1128306). Two brain tissue cohorts exhibited lower DNA methylation in bipolar disease patients compared with controls at an extended HCG9 region (P=0.026). Logistic regression modeling of BPD as a function of rs1128306 genotype, age and DNA methylation uncovered an independent effect of DNA methylation in white blood cells (odds ratio (OR)=1.08, P=0.0077) and the overall sample (OR=1.24, P=0.0011). Receiver operating characteristic curve A prime statistics estimated a 69–72% probability of correct BPD prediction from a case vs control pool. Finally, sperm DNA demonstrated a significant association (P=0.018) with BPD at one of the regions demonstrating epigenetic changes in the post-mortem brain and peripheral blood samples. The consistent multi-tissue epigenetic differences at HCG9 argue for a causal association with BPD.

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References

  1. Petronis A . Human morbid genetics revisited: relevance of epigenetics. Trends Genet 2001; 17: 142–146.

    CAS  Article  PubMed  Google Scholar 

  2. Robertson KD . DNA methylation and human disease. Nat Rev Genet 2005; 6: 597–610.

    CAS  Article  PubMed  Google Scholar 

  3. Feinberg AP . Phenotypic plasticity and the epigenetics of human disease. Nature 2007; 447: 433–440.

    CAS  Article  PubMed  Google Scholar 

  4. Petronis A . Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature 2010; 465: 721–727.

    CAS  Article  PubMed  Google Scholar 

  5. Yeivin A, Razin A . Gene methylation patterns and expression. In: Jost J, Saluz, H (eds). DNA Methylation: Molecular Biology and Biological Significance. Birkhauser Verlag: Basel, 1993 pp. 523–568.

    Chapter  Google Scholar 

  6. Holliday R, Ho T, Paulin R . Gene silencing in mammalian cells. In: VEA Russo RM, Riggs AD (eds). Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York, 1996, pp 47–59.

    Google Scholar 

  7. Riggs AD, Xiong Z, Wang L, Lebon JM . Methylation dynamics, epigenetic fidelity and X chromosome structure. Novartis Found Symp 1998; 214: 214–225; discussion 225–32.

    CAS  PubMed  Google Scholar 

  8. Ehrlich M, Ehrlich, K . Effect of DNA methylation and the binding of vertebrate and plant proteins to DNA. In: Jost J, Saluz P (eds). DNA Methylation: Molecular Biology and Biological Significance. Birkhauser Verlag: Basel, Switzerland, 1993, pp 145–168.

    Chapter  Google Scholar 

  9. Riggs A, Xiong Z, Wang L, Jm L . Methylation dynamics, epigenetic fidelity and X chromosome structure. In: Wolffe, A (ed). Epigenetics. John Wiley & Sons: Chistester, 1998, pp 214–227.

    Google Scholar 

  10. Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA 2005; 102: 10604–10609.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  11. Kaminsky ZA, Tang T, Wang SC, Ptak C, Oh GH, Wong AH et al. DNA methylation profiles in monozygotic and dizygotic twins. Nat Genet 2009; 41: 240–245.

    CAS  Article  PubMed  Google Scholar 

  12. Richards EJ . Inherited epigenetic variation—revisiting soft inheritance. Nat Rev Genet 2006; 7: 395–401.

    CAS  Article  PubMed  Google Scholar 

  13. Petronis A . Epigenetics and bipolar disorder: new opportunities and challenges. Am J Med Genet 2003; 123C: 65–75.

    Article  PubMed  Google Scholar 

  14. Petronis A . The genes for major psychosis: aberrant sequence or regulation? Neuropsychopharmacology 2000; 23: 1–12.

    CAS  Article  PubMed  Google Scholar 

  15. Kaminsky Z, Wang SC, Petronis A . Complex disease, gender and epigenetics. Ann Med 2006; 38: 530–544.

    CAS  Article  PubMed  Google Scholar 

  16. Hall JG . Genomic imprinting: review and relevance to human diseases. Am J Hum Genet 1990; 46: 857–873.

    CAS  PubMed Central  PubMed  Google Scholar 

  17. Barlow DP . Gametic imprinting in mammals. Science 1995; 270: 1610–1613.

    CAS  Article  PubMed  Google Scholar 

  18. Newberg AR, Catapano LA, Zarate CA, Manji HK . Neurobiology of bipolar disorder. Expert Rev Neurother 2008; 8: 93–110.

    CAS  Article  PubMed  Google Scholar 

  19. Guidotti A, Dong E, Kundakovic M, Satta R, Grayson DR, Costa E . Characterization of the action of antipsychotic subtypes on valproate-induced chromatin remodeling. Trends Pharmacol Sci 2009; 30: 55–60.

    CAS  Article  PubMed  Google Scholar 

  20. Dong E, Chen Y, Gavin DP, Grayson DR, Guidotti A . Valproate induces DNA demethylation in nuclear extracts from adult mouse brain. Epigenetics 2010; 5: 730–735.

    CAS  Article  PubMed  Google Scholar 

  21. Kwon B, Houpt TA . Phospho-acetylation of histone H3 in the amygdala after acute lithium chloride. Brain Res 2010; 1333: 36–47.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  22. Mccoll G, Killilea DW, Hubbard AE, Vantipalli MC, Melov S, Lithgow GJ . Pharmacogenetic analysis of lithium-induced delayed aging in Caenorhabditis elegans. J Biol Chem 2008; 283: 350–357.

    CAS  Article  PubMed  Google Scholar 

  23. Petronis A . The origin of schizophrenia: genetic thesis, epigenetic antithesis, and resolving synthesis. Biol Psychiatry 2004; 55: 965–970.

    CAS  Article  PubMed  Google Scholar 

  24. Schumacher A, Petronis A . Epigenetics of complex diseases: from general theory to laboratory experiments. Curr Top Microbiol Immunol 2006; 310: 81–115.

    CAS  PubMed  Google Scholar 

  25. Flanagan JM, Popendikyte V, Pozdniakovaite N, Sobolev M, Assadzadeh A, Schumacher A et al. Intra- and interindividual epigenetic variation in human germ cells. Am J Hum Genet 2006; 79: 67–84.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  26. Sutherland JE, Costa M . Epigenetics and the environment. Ann NY Acad Sci 2003; 983: 151–160.

    CAS  Article  PubMed  Google Scholar 

  27. Jaenisch, R, Bird, A . Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 2003; 33 (Suppl): 245–54.

    CAS  Article  Google Scholar 

  28. Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, Pe’er I et al. Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature 2009; 460: 753–757.

    CAS  PubMed Central  PubMed  Google Scholar 

  29. Purcell SM, Wray NR, Stone JL, Visscher PM, O’donovan MC, Sullivan PF et al. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 2009; 460: 748–752.

    CAS  PubMed  Google Scholar 

  30. Stefansson H, Ophoff RA, Steinberg S, Andreassen OA, Cichon S, Rujescu D et al. Common variants conferring risk of schizophrenia. Nature 2009; 460: 744–747.

    CAS  PubMed Central  PubMed  Google Scholar 

  31. Gaudieri, S, Longman-Jacobsen N, Tay GK, Dawkins RL . Sequence analysis of the MHC class I region reveals the basis of the genomic matching technique. Hum Immunol 2001; 62: 279–285.

    CAS  Article  Google Scholar 

  32. Seidl, C, Port M, Apostolidis C, Bruchertseifer F, Schwaiger M, Senekowitsch-Schmidtke R et al. Differential gene expression triggered by highly cytotoxic alpha-emitter-immunoconjugates in gastric cancer cells. Invest New Drugs 2010; 28: 49–60.

    CAS  Article  Google Scholar 

  33. Torrey EF, Webster M, Knable M, Johnston N, Yolken RH . The Stanley foundation brain collection and neuropathology consortium. Schizophr Res 2000; 44: 151–155.

    CAS  Article  PubMed  Google Scholar 

  34. Kaminsky Z, Petronis A . Methylation SNaPshot: a method for the quantification of site-specific DNA methylation levels. Methods Mol Biol 2009; 507: 241–255.

    CAS  Article  PubMed  Google Scholar 

  35. Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y et al The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 2009; 458: 362–366.

    CAS  Article  PubMed  Google Scholar 

  36. Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J et al. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 2008; 18: 1073–1083.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  37. Gabdank I, Barash D, Trifonov EN . FineStr: a web server for single-base-resolution nucleosome positioning. Bioinformatics 2010; 26: 845–846.

    CAS  Article  PubMed  Google Scholar 

  38. Surolia I, Pirnie SP, Chellappa V, Taylor KN, Cariappa A, Moya J et al. Functionally defective germline variants of sialic acid acetylesterase in autoimmunity. Nature 2010; 466: 243–247.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  39. Mill J, Tang T, Kaminsky Z, Khare T, Yazdanpanah S, Bouchard L et al. Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. Am J Hum Genet 2008; 82: 696–711.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  40. Fuke C, Shimabukuro M, Petronis A, Sugimoto J, Oda T, Miura K et al. Age related changes in 5-methylcytosine content in human peripheral leukocytes and placentas: an HPLC-based study. Ann Hum Genet 2004; 68 (Part 3): 196–204.

    CAS  Article  PubMed  Google Scholar 

  41. Rakyan VK, Down TA, Maslau S, Andrew T, Yang TP, Beyan H et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res 2010; 20: 434–439.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  42. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H et al. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res 2010; 20: 440–446.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  43. Depp CA, Jeste DV . Bipolar disorder in older adults: a critical review. Bipolar Disord 2004; 6: 343–367.

    Article  PubMed  Google Scholar 

  44. Frans EM, Sandin S, Reichenberg A, Lichtenstein P, Langstrom N, Hultman CM . Advancing paternal age and bipolar disorder. Arch Gen Psychiatry 2008; 65: 1034–1040.

    Article  PubMed  Google Scholar 

  45. Menezes PR, Lewis G, Rasmussen F, Zammit S, Sipos A, Harrison GL et al. Paternal and maternal ages at conception and risk of bipolar affective disorder in their offspring. Psychol Med 2010; 40: 477–485.

    CAS  Article  PubMed  Google Scholar 

  46. Crow TJ . Mutation and psychosis: a suggested explanation of seasonality of birth. Psychol Med 1987; 17: 821–828.

    CAS  Article  PubMed  Google Scholar 

  47. Kerkel K, Spadola A, Yuan E, Kosek J, Jiang L, Hod E et al. Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation. Nat Genet 2008; 40: 904–908.

    CAS  Article  PubMed  Google Scholar 

  48. Tycko, B . Allele-specific DNA methylation: beyond imprinting. Hum Mol Genet 2010; 19 (R2): R210–R220.

    CAS  Article  Google Scholar 

  49. Meaburn, EL, Schalkwyk LC, Mill J . Allele-specific methylation in the human genome Implications for genetic studies of complex disease. Epigenetics 2010; 5: 578–582.

    CAS  Article  Google Scholar 

  50. Cooper DN, Krawczak M . Cytosine methylation and the fate of CpG dinucleotides in vertebrate genomes. Hum Genet 1989; 83: 181–188.

    CAS  Article  PubMed  Google Scholar 

  51. Morgan HD, Sutherland HG, Martin DI, Whitelaw E . Epigenetic inheritance at the agouti locus in the mouse. Nat Genet 1999; 23: 314–318.

    CAS  Article  PubMed  Google Scholar 

  52. Oates NA, Van Vliet J, Duffy DL, Kroes HY, Martin NG, Boomsma DI et al. Increased DNA methylation at the AXIN1 gene in a monozygotic twin from a pair discordant for a caudal duplication anomaly. Am J Hum Genet 2006; 79: 155–162.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  53. Rakyan VK, Chong S, Champ ME, Cuthbert PC, Morgan HD, Luu KV et al. Transgenerational inheritance of epigenetic states at the murine Axin(Fu) allele occurs after maternal and paternal transmission. Proc Natl Acad Sci USA 2003; 100: 2538–2543.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  54. Dulac C . Brain function and chromatin plasticity. Nature 2010; 465: 728–735.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  55. Ehrlich M, Wang RY . 5-Methylcytosine in eukaryotic DNA. Science 1981; 212: 1350–1357.

    CAS  Article  PubMed  Google Scholar 

  56. Brown DD . Gene expression in eukaryotes. Science 1981; 211: 667–674.

    CAS  Article  PubMed  Google Scholar 

  57. Razin A, Riggs AD . DNA methylation and gene function. Science 1980; 210: 604–610.

    CAS  Article  PubMed  Google Scholar 

  58. Schwartz S, Ast G . Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing. EMBO J 2010; 5: 578–582.

    Google Scholar 

  59. Sims 3rd RJ, Millhouse S, Chen CF, Lewis BA, Erdjument-Bromage H, Tempst P et al. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Mol Cell 2007; 28: 665–676.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  60. Schor IE, Rascovan N, Pelisch F, Allo M, Kornblihtt AR . Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc Natl Acad Sci USA 2009; 106: 4325–4330.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  61. Hubbard RE, O’mahony MS, Calver BL, Woodhouse KW . Plasma esterases and inflammation in ageing and frailty. Eur J Clin Pharmacol 2008; 64: 895–900.

    CAS  Article  PubMed  Google Scholar 

  62. Matigian N, Windus L, Smith H, Filippich C, Pantelis C, Mcgrath J et al. Expression profiling in monozygotic twins discordant for bipolar disorder reveals dysregulation of the WNT signalling pathway. Mol Psychiatry 2007; 12: 815–825.

    CAS  Article  PubMed  Google Scholar 

  63. Kapczinski F, Dal-Pizzol F, Teixeira AL, Magalhaes PV, Kauer-Sant’anna M, Klamt F et al. Peripheral biomarkers and illness activity in bipolar disorder. J Psychiatr Res 2010; 45: 156–161.

    Article  PubMed  Google Scholar 

  64. Laan W, Grobbee DE, Selten JP, Heijnen CJ, Kahn RS, Burger H . Adjuvant aspirin therapy reduces symptoms of schizophrenia spectrum disorders: results from a randomized, double-blind, placebo-controlled trial. J Clin Psychiatry 2010; 71: 520–527.

    CAS  Article  PubMed  Google Scholar 

  65. Monji A, Kato T, Kanba S . Cytokines and schizophrenia: microglia hypothesis of schizophrenia. Psychiatry Clin Neurosci 2009; 63: 257–265.

    CAS  Article  PubMed  Google Scholar 

  66. Goldstein BI, Kemp DE, Soczynska JK, Mcintyre RS . Inflammation and the phenomenology, pathophysiology, comorbidity, and treatment of bipolar disorder: a systematic review of the literature. J Clin Psychiatry 2009; 70: 1078–1090.

    Article  PubMed  Google Scholar 

  67. Sugino H, Futamura T, Mitsumoto Y, Maeda K, Marunaka Y . Atypical antipsychotics suppress production of proinflammatory cytokines and up-regulate interleukin-10 in lipopolysaccharide-treated mice. Prog Neuropsychopharmacol Biol Psychiatry 2009; 33: 303–307.

    CAS  Article  PubMed  Google Scholar 

  68. Muller N . Inflammation and the glutamate system in schizophrenia: implications for therapeutic targets and drug development. Expert Opin Ther Targets 2008; 12: 1497–1507.

    Article  PubMed  Google Scholar 

  69. Chang H, Jeung HC, Jung JJ, Kim TS, Rha SY, Chung HC . Identification of genes associated with chemosensitivity to SAHA/taxane combination treatment in taxane-resistant breast cancer cells. Breast Cancer Res Treat 2011; 125: 55–63.

    CAS  Article  PubMed  Google Scholar 

  70. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009; 324: 930–935.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  71. Kriaucionis S, Heintz N . The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009; 324: 929–930.

    CAS  PubMed Central  PubMed  Google Scholar 

  72. Huang, Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A . The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 2010; 5: e8888.

    Article  Google Scholar 

  73. Zheng Y, Cohen-Karni D, Xu D, Chin HG, Wilson G, Pradhan S et al. A unique family of Mrr-like modification-dependent restriction endonucleases. Nucleic Acids Res 2010; 38: 5527–5534.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  74. Szwagierczak A, Bultmann S, Schmidt CS, Spada F, Leonhardt H . Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res 2010; 38: e181.

    Article  PubMed  PubMed Central  Google Scholar 

  75. Jin SG, Kadam S, Pfeifer GP . Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res 2010; 38: e125.

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We would like to thank the Stanley Medical Research Institute (SMRI) and Dr Francine Benes of the McLean Hospital Brain Bank for the provided brain tissues. ZK and JM were CIHR fellows. MT was supported by the Japan Society for the Promotion of Science Postdoctoral Fellowships for Research Abroad. AP is Senior Fellow, Ontario Mental Health Foundation, and Tapscott Chair in Schizophrenia Studies, University of Toronto. This work was supported by the Canadian Institutes for Health and Research (186007) and the National Institutes of Health (MH074127; MH088413) to AP.

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Correspondence to A Petronis.

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AceView, http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/

Clustal W2, http://www.ebi.ac.uk/Tools/clustalw2/index.html

FineStr, http://www.cs.bgu.ac.il/~nucleom/

Nucleosome Prediction Algorithm, http://genie.weizmann.ac.il/software/nucleo_prediction.html/

Online Mendelian Inheritance in Man (OMIM), http://www.ncbi.nlm.nih.gov/Omim/

Stanley Medical Research Institute Genomics Database, http://www.stanleygenomics.org/

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Kaminsky, Z., Tochigi, M., Jia, P. et al. A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder. Mol Psychiatry 17, 728–740 (2012). https://doi.org/10.1038/mp.2011.64

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Keywords

  • epigenetics
  • DNA methylation
  • pyrosequencing
  • bipolar disorder

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