期刊论文详细信息
BMC Medical Genomics
DNA methylation differences in monozygotic twin pairs discordant for schizophrenia identifies psychosis related genes and networks
Shiva M Singh1  Richard L O’Reilly1  Eric J Diehl2  Melkaye G Melka2  Benjamin I Laufer2  Christina A Castellani2 
[1] Department of Psychiatry, The University of Western Ontario, London, N6A 5B7, Ontario, Canada;Department of Biology, The University of Western Ontario, London, N6A 5B7, Ontario, Canada
关键词: Histone Clusters;    snoRNA;    Differentially Methylated Regions (DMRs);    Methylation Array;    MeDIP;    DNA Methylation;    Schizophrenia;    Monozygotic Twins;   
Others  :  1211007
DOI  :  10.1186/s12920-015-0093-1
 received in 2015-01-05, accepted in 2015-04-24,  发布年份 2015
PDF
【 摘 要 】

Background

Despite their singular origin, monozygotic twin pairs often display discordance for complex disorders including schizophrenia. It is a common (1%) and often familial disease with a discordance rate of ~50% in monozygotic twins. This high discordance is often explained by the role of yet unknown environmental, random, and epigenetic factors. The involvement of DNA methylation in this disease appears logical, but remains to be established.

Methods

We have used blood DNA from two pairs of monozygotic twins discordant for schizophrenia and their parents in order to assess genome-wide methylation using a NimbleGen Methylation Promoter Microarray.

Results

The genome-wide results show that differentially methylated regions (DMRs) exist between members representing discordant monozygotic twins. Some DMRs are shared with parent(s) and others appear to be de novo. We found twenty-seven genes affected by DMR changes that were shared in the affected member of two discordant monozygotic pairs from unrelated families. Interestingly, the genes affected by pair specific DMRs share specific networks. Specifically, this study has identified two networks; “cell death and survival” and a “cellular movement and immune cell trafficking”. These two networks and the genes affected have been previously implicated in the aetiology of schizophrenia.

Conclusions

The results are compatible with the suggestion that DNA methylation may contribute to the discordance of monozygotic twins for schizophrenia. Also, this may be accomplished by the direct effect of gene specific methylation changes on specific biological networks rather than individual genes. It supports the extensive genetic, epigenetic and phenotypic heterogeneity implicated in schizophrenia.

【 授权许可】

   
2015 Castellani et al.; licensee BioMed Central.

【 预 览 】
附件列表
Files Size Format View
20150609022218730.pdf 2267KB PDF download
Figure 5. 57KB Image download
20150216040454622.pdf 229KB PDF download
Figure 3. 37KB Image download
Figure 2. 73KB Image download
Figure 1. 17KB Image download
【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 5.

【 参考文献 】
  • [1]Boomsma D, Busjahn A, Peltonen L: Classical twin studies and beyond. Nat Rev Genet 2002, 3(11):872-82.
  • [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(1):12-7.
  • [3]Singh SM, Murphy B, O’Reilly R: Epigenetic contributors to the discordance of monozygotic twins. Clin Genet 2002, 62(2):97-103.
  • [4]Zwijnenburg PJ, Meijers-Heijboer H, Boomsma DI: Identical but not the same: the value of discordant monozygotic twins in genetic research. Am J Med Genet B Neuropsychiatr Genet 2010, 153B(6):1134-49.
  • [5]Bruder C, Piotrowski AEA: Phenotypically Concordant and Discordant Monozygotic Twins Display Different DNA Copy Number Variation Profiles. Am J Hum Genet 2008, 82(3):1-9.
  • [6]Maiti S, Kumar KH, Castellani CA, O’Reilly R, Singh SM: Ontogenetic de novo copy number variations (CNVs) as a source of genetic individuality: studies on two families with MZD twins for schizophrenia. PLoS One 2011, 6(3):e17125.
  • [7]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 U S A 2005, 102(30):10604-9.
  • [8]Ling C, Groop L: Epigenetics: a molecular link between environmental factors and type 2 diabetes. Diabetes 2009, 58(12):2718-25.
  • [9]Petronis A: Epigenetics as a unifying principle in the aetiology of complex traits and diseases. Nature 2010, 465(7299):721-7.
  • [10]Ollikainen M, Smith KR, Joo EJ, Ng HK, Andronikos R, Novakovic B, et al.: DNA methylation analysis of multiple tissues from newborn twins reveals both genetic and intrauterine components to variation in the human neonatal epigenome. Hum Mol Genet 2010, 19(21):4176-88.
  • [11]Levesque ML, Casey KF, Szyf M, Ismaylova E, Ly V, Verner MP, et al.: Genome-wide DNA methylation variability in adolescent monozygotic twins followed since birth. Epigenetics 2014, 9(10):1410-21.
  • [12]Dempster EL, Pidsley R, Schalkwyk LC, Owens S, Georgiades A, Kane F, et al.: Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder. Hum Mol Genet 2011, 20(24):4786-96.
  • [13]Bell JT, Spector TD: A twin approach to unraveling epigenetics. Trends Genet 2011, 27(3):116-25.
  • [14]Wong CC, Caspi A, Williams B, Craig IW, Houts R, Ambler A, et al.: A longitudinal study of epigenetic variation in twins. Epigenetics 2010, 5(6):516-26.
  • [15]Manikkam M, Guerrero-Bosagna C, Tracey R, Haque MM, Skinner MK: Transgenerational actions of environmental compounds on reproductive disease and identification of epigenetic biomarkers of ancestral exposures. PLoS One 2012, 7(2):e31901.
  • [16]Xu J, He G, Zhu J, Zhou X, St Clair D, Wang T, et al.: Prenatal nutritional deficiency reprogrammed postnatal gene expression in mammal brains: implications for schizophrenia. Int J Neuropsychopharmacol 2014, 18(4):10.
  • [17]Petronis A, Gottesman II, Kan P, Kennedy JL, Basile VS, Paterson AD, et al.: Monozygotic twins exhibit numerous epigenetic differences: clues to twin discordance? Schizophr Bull 2003, 29(1):169-78.
  • [18]Bonsch D, Wunschel M, Lenz B, Janssen G, Weisbrod M, Sauer H: Methylation matters? Decreased methylation status of genomic DNA in the blood of schizophrenic twins. Psychiatry Res 2012, 198(3):533-7.
  • [19]Kinoshita M, Numata S, Tajima A, Shimodera S, Ono S, Imamura A, et al.: DNA methylation signatures of peripheral leukocytes in schizophrenia. Neuromolecular Med 2013, 15(1):95-101.
  • [20]Abdolmaleky HM, Smith CL, Faraone SV, Shafa R, Stone W, Glatt SJ, et al.: Methylomics in psychiatry: Modulation of gene-environment interactions may be through DNA methylation. Am J Med Genet B Neuropsychiatr Genet 2004, 127B(1):51-9.
  • [21]Wockner LF, Noble EP, Lawford BR, Young RM, Morris CP, Whitehall VL, et al.: Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients. Transl Psychiatry 2014, 4:e339.
  • [22]Liao Q, Wang Y, Cheng J, Dai D, Zhou X, Zhang Y, et al.: DNA methylation patterns of protein coding genes and long noncoding RNAs in female schizophrenic patients. Eur J Med Genet 2015, 58(2):95-104.
  • [23]First MB, Spitzer RL, Gibbon M, Williams JBW: Clinical Interview for DSM-IV Axis I Disorders, Clinician Version (SCID-CV). American Psychiatric Press, Inc, Washington, D.C.; 1996.
  • [24]First MB, Gibbon M, Spitzer RL, Williams JBW, Benjamin L: Structured Clinical Interview for DSM-IV Axis II Personality Disorders, (SCID-II). American Psychiatric Press, Inc, Washington, D.C.; 1997.
  • [25]Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al.: Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 2013, 14:128-2105. BioMed Central Full Text
  • [26]Castellani CA, Melka MG, Diehl EJ, Laufer BI, O’Reilly RL, Singh SM: DNA methylation in psychosis: insights into etiology and treatment. Epigenomics 2015, 7(1):67-74.
  • [27]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(3):696-711.
  • [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(7256):753-7.
  • [29]Kano S, Colantuoni C, Han F, Zhou Z, Yuan Q, Wilson A, et al.: Genome-wide profiling of multiple histone methylations in olfactory cells: further implications for cellular susceptibility to oxidative stress in schizophrenia. Mol Psychiatry 2013, 18(7):740-2.
  • [30]Gavin DP, Sharma RP: Histone modifications, DNA methylation, and schizophrenia. Neurosci Biobehav Rev 2010, 34(6):882-8.
  • [31]Sharma RP, Grayson DR, Gavin DP: Histone deactylase 1 expression is increased in the prefrontal cortex of schizophrenia subjects: analysis of the National Brain Databank microarray collection. Schizophr Res 2008, 98(1–3):111-7.
  • [32]Runte M, Huttenhofer A, Gross S, Kiefmann M, Horsthemke B, Buiting K: The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Hum Mol Genet 2001, 10(23):2687-700.
  • [33]Gavin DP, Akbarian S: Epigenetic and post-transcriptional dysregulation of gene expression in schizophrenia and related disease. Neurobiol Dis 2012, 46(2):255-62.
  • [34]Leung KN, Vallero RO, DuBose AJ, Resnick JL, LaSalle JM: Imprinting regulates mammalian snoRNA-encoding chromatin decondensation and neuronal nucleolar size. Hum Mol Genet 2009, 18(22):4227-38.
  • [35]Kishore S, Khanna A, Zhang Z, Hui J, Balwierz PJ, Stefan M, et al.: The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Hum Mol Genet 2010, 19(7):1153-64.
  • [36]Bortolin-Cavaille ML, Cavaille J: The SNORD115 (H/MBII-52) and SNORD116 (H/MBII-85) gene clusters at the imprinted Prader-Willi locus generate canonical box C/D snoRNAs. Nucleic Acids Res 2012, 40(14):6800-7.
  • [37]Falaleeva M, Stamm S: Processing of snoRNAs as a new source of regulatory non-coding RNAs: snoRNA fragments form a new class of functional RNAs. Bioessays 2013, 35(1):46-54.
  • [38]Powell WT, Coulson RL, Crary FK, Wong SS, Ach RA, Tsang P, et al.: A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure. Hum Mol Genet 2013, 22(21):4318-28.
  • [39]Powell WT, Coulson RL, Gonzales ML, Crary FK, Wong SS, Adams S, et al.: R-loop formation at Snord116 mediates topotecan inhibition of Ube3a-antisense and allele-specific chromatin decondensation. Proc Natl Acad Sci U S A 2013, 110(34):13938-43.
  • [40]Stelzer Y, Sagi I, Yanuka O, Eiges R, Benvenisty N: The noncoding RNA IPW regulates the imprinted DLK1-DIO3 locus in an induced pluripotent stem cell model of Prader-Willi syndrome. Nat Genet 2014, 46(6):551-7.
  • [41]Murrell A: Cross-talk between imprinted loci in Prader-Willi syndrome. Nat Genet 2014, 46(6):528-30.
  • [42]Bieth E, Eddiry S, Gaston V, Lorenzini F, Buffet A, Conte Auriol F, et al.: Highly restricted deletion of the SNORD116 region is implicated in Prader-Willi Syndrome. Eur J Hum Genet 2014, 23(2):252-5.
  • [43]Lai JH, Zhu YS, Huo ZH, Sun RF, Yu B, Wang YP, et al.: Association study of polymorphisms in the promoter region of DRD4 with schizophrenia, depression, and heroin addiction. Brain Res 2010, 1359:227-32.
  • [44]Debnath M, Cannon DM, Venkatasubramanian G: Variation in the major histocompatibility complex [MHC] gene family in schizophrenia: associations and functional implications. Prog Neuropsychopharmacol Biol Psychiatry 2013, 42:49-62.
  • [45]Saetre P, Emilsson L, Axelsson E, Kreuger J, Lindholm E, Jazin E: Inflammation-related genes up-regulated in schizophrenia brains. BMC Psychiatry 2007, 7:46. BioMed Central Full Text
  • [46]Soderlund J, Schroder J, Nordin C, Samuelsson M, Walther-Jallow L, Karlsson H, et al.: Activation of brain interleukin-1beta in schizophrenia. Mol Psychiatry 2009, 14(12):1069-71.
  • [47]Schmitt A, Leonardi-Essmann F, Durrenberger PF, Parlapani E, Schneider-Axmann T, Spanagel R, et al.: Regulation of immune-modulatory genes in left superior temporal cortex of schizophrenia patients: a genome-wide microarray study. World J Biol Psychiatry 2011, 12(3):201-15.
  • [48]Boin F, Zanardini R, Pioli R, Altamura CA, Maes M, Gennarelli M: Association between -G308A tumor necrosis factor alpha gene polymorphism and schizophrenia. Mol Psychiatry 2001, 6(1):79-82.
  • [49]Paul-Samojedny M, Owczarek A, Suchanek R, Kowalczyk M, Fila-Danilow A, Borkowska P, et al.: Association study of interferon gamma (IFN-gamma) +874 T/A gene polymorphism in patients with paranoid schizophrenia. J Mol Neurosci 2011, 43(3):309-15.
  • [50]Benzel I, Bansal A, Browning BL, Galwey NW, Maycox PR, McGinnis R, et al.: Interactions among genes in the ErbB-Neuregulin signalling network are associated with increased susceptibility to schizophrenia. Behav Brain Funct 2007, 3:31. BioMed Central Full Text
  • [51]Hanninen K, Katila H, Saarela M, Rontu R, Mattila KM, Fan M, et al.: Interleukin-1 beta gene polymorphism and its interactions with neuregulin-1 gene polymorphism are associated with schizophrenia. Eur Arch Psychiatry Clin Neurosci 2008, 258(1):10-5.
  • [52]Ni X, Trakalo J, Valente J, Azevedo MH, Pato MT, Pato CN, et al.: Human p53 tumor suppressor gene (TP53) and schizophrenia: case–control and family studies. Neurosci Lett 2005, 388(3):173-8.
  • [53]Liu Y, Aryee MJ, Padyukov L, Fallin MD, Hesselberg E, Runarsson A, et al.: Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol 2013, 31(2):142-7.
  • [54]Melka MG, Laufer BI, McDonald P, Castellani CA, Rajakumar N, O’Reilly R, et al.: The effects of olanzapine on genome-wide DNA methylation in the hippocampus and cerebellum. Clin Epigenetics 2014, 6(1):1. BioMed Central Full Text
  文献评价指标  
  下载次数:47次 浏览次数:14次