Abstract
DNA methylation may predispose to multiple sclerosis (MS), as aberrant methylation in the promoter regions across the genome seems to underlie several processes of MS. We have currently determined the methylation status of eight genes in relapsing-remitting MS patients. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) was used to determine the status of 31 CpG islands, located across eight genes, in 33 healthy individuals and 66 MS patients (33 in relapse and 33 in remission). The methylation levels in the examined sites ranged from 0 to 31%. Methylation positivity for RUNX3 and CDKN2A differed significantly between MS patients and healthy controls. Maximum methylation in RUNX3, CDKN2A, SOCS1, and NEUROG1 genes was significantly different between patients and controls. Roc curves demonstrated that the appropriate cut-offs to distinguish patients from healthy controls were 2% for RUNX3 (OR 3.316, CI 1.207–9.107, p = 0.024) and 3% for CDKN2A (OR 3.077, CI 1.281–7.39, p = 0.018). No difference in methylation was observed between patients in relapse and patients in remission, in any of the genes examined. Methylation patterns of RUNX3 and CDKN2A may be able to distinguish between MS patients and healthy controls, but not between MS patients in relapse and in remission.
Similar content being viewed by others
References
Aggelakis K, Zacharaki F, Dardiotis E, Xiromerisiou G, Tsimourtou V, Ralli S, Gkaraveli M, Bourpoulas D, Rodopoulou P, Papadimitriou A, Hadjigeorgiou G (2010) Interleukin-1B and interleukin-1 receptor antagonist gene polymorphisms in Greek multiple sclerosis (MS) patients with bout-onset MS. Neurol Sci 31:253–257. https://doi.org/10.1007/s10072-009-0155-2
Baker BJ, Akhtar LN, Benveniste EN (2009) SOCS1 and SOCS3 in the control of CNS immunity. Trends Immunol 30:392–400. https://doi.org/10.1016/j.it.2009.07.001
Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, Miller NA, Zhang L, Farmer AD, Bell CJ, Kim RW, May GD, Woodward JE, Caillier SJ, McElroy JP, Gomez R, Pando MJ, Clendenen LE, Ganusova EE, Schilkey FD, Ramaraj T, Khan OA, Huntley JJ, Luo S, Kwok PY, Wu TD, Schroth GP, Oksenberg JR, Hauser SL, Kingsmore SF (2010) Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature 464:1351–1356. https://doi.org/10.1038/nature08990
Berg M, Hagland HR, Søreide K (2014) Comparison of CpG island methylator phenotype (CIMP) frequency in colon cancer using different probe- and gene-specific scoring alternatives on recommended multi-gene panels. PLoS One 9:e86657. https://doi.org/10.1371/journal.pone.0086657
Bos SD, Page CM, Andreassen BK, Elboudwarej E, Gustavsen MW, Briggs F, Quach H, Leikfoss IS, Bjølgerud A, Berge T, Harbo HF, Barcellos LF (2015) Genome-wide DNA methylation profiles indicate CD8+ T cell hypermethylation in multiple sclerosis. PLoS One 10:e0117403. https://doi.org/10.1371/journal.pone.0117403
Dardiotis E, Paterakis K, Siokas V, Tsivgoulis G, Dardioti M, Grigoriadis S, Simeonidou C, Komnos A, Kapsalaki E, Fountas K, Hadjigeorgiou GM (2015) Effect of angiotensin-converting enzyme tag single nucleotide polymorphisms on the outcome of patients with traumatic brain injury. Pharmacogenet Genomics 25:485–490. https://doi.org/10.1097/fpc.0000000000000161
Dardiotis E, Siokas V, Zafeiridis T, Paterakis K, Tsivgoulis G, Dardioti M, Grigoriadis S, Simeonidou C, Deretzi G, Zintzaras E, Jagiella J, Hadjigeorgiou GM (2016) Integrins AV and B8 gene polymorphisms and risk for intracerebral hemorrhage in Greek and Polish populations. NeuroMolecular Med 19:1–12. https://doi.org/10.1007/s12017-016-8429-3
Dardiotis E, Arseniou S, Sokratous M, Tsouris Z, Siokas V, Mentis AFA, Michalopoulou A, Andravizou A, Dastamani M, Paterakis K, Bogdanos D, Brotis A (2017a) Vitamin B12, folate, and homocysteine levels and multiple sclerosis: a meta-analysis. Mult Scler Relat Disord 17:190–197. https://doi.org/10.1016/j.msard.2017.08.004
Dardiotis E, Panayiotou E, Provatas A, Christodoulou K, Hadjisavvas A, Antoniades A, Lourbopoulos A, Pantzaris M, Grigoriadis N, Hadjigeorgiou GM, Kyriakides T (2017b) Gene variants of adhesion molecules act as modifiers of disease severity in MS. Neurol(R) Neuroimmunol Neuroinflammation 4:e350. https://doi.org/10.1212/nxi.0000000000000350
Dixit R, Wilkinson G, Cancino GI, Shaker T, Adnani L, Li S, Dennis D, Kurrasch D, Chan JA, Olson EC, Kaplan DR, Zimmer C, Schuurmans C (2014) Neurog1 and Neurog2 control two waves of neuronal differentiation in the piriform cortex. J Neurosci 34:539–553. https://doi.org/10.1523/jneurosci.0614-13.2014
Efthymiou G, Dardiotis E, Liaskos C, Marou E, Tsimourtou V, Rigopoulou EI, Scheper T, Daponte A, Meyer W, Sakkas LI, Hadjigeorgiou G, Bogdanos DP (2017) Immune responses against Helicobacter pylori-specific antigens differentiate relapsing remitting from secondary progressive multiple sclerosis. Sci Rep 7:7929. https://doi.org/10.1038/s41598-017-07801-9
Fagone P, Mangano K, di Marco R, Touil-Boukoffa C, Chikovan T, Signorelli S, Lombardo GAG, Patti F, Mammana S, Nicoletti F (2016) Expression of DNA methylation genes in secondary progressive multiple sclerosis. J Neuroimmunol 290:66–69. https://doi.org/10.1016/j.jneuroim.2015.11.018
Flagiello D, Apiou F, Gibaud A, Poupon MF, Dutrillaux B, Malfoy B (1997) Assignment of the genes for cellular retinoic acid binding protein 1 (CRABP1) and 2 (CRABP2) to human chromosome band 15q24 and 1q21.3, respectively, by in situ hybridization. Cytogenet Cell Genet 76:17–18
Gonzalo S (2010) Epigenetic alterations in aging. J Appl Physiol (1985) 109:586–597. https://doi.org/10.1152/japplphysiol.00238.2010
Hansen T, Skytthe A, Stenager E, Petersen HC, Bronnum-Hansen H, Kyvik KO (2005) Concordance for multiple sclerosis in Danish twins: an update of a nationwide study. Mult Scler (Houndmills, Basingstoke, England) 11:504–510. https://doi.org/10.1191/1352458505ms1220oa
Heyn H, Moran S, Hernando-Herraez I, Sayols S, Gomez A, Sandoval J, Monk D, Hata K, Marques-Bonet T, Wang L, Esteller M (2013) DNA methylation contributes to natural human variation. Genome Res 23:1363–1372. https://doi.org/10.1101/gr.154187.112
Hilven K, Goris A (2015) Genetic burden mirrors epidemiology of multiple sclerosis. Mult Scler (Houndmills, Basingstoke, England) 21:1353–1354. https://doi.org/10.1177/1352458515596603
Hirahara K, Poholek A, Vahedi G, Laurence A, Kanno Y, Milner JD, O'Shea JJ (2013) Mechanisms underlying helper T-cell plasticity: implications for immune-mediated disease. J Allergy Clin Immunol 131:1276–1287. https://doi.org/10.1016/j.jaci.2013.03.015
Huynh JL, Garg P, Thin TH, Yoo S, Dutta R, Trapp BD, Haroutunian V, Zhu J, Donovan MJ, Sharp AJ, Casaccia P (2014) Epigenome-wide differences in pathology-free regions of multiple sclerosis-affected brains. Nat Neurosci 17:121–130. https://doi.org/10.1038/nn.3588
Klose RJ, Bird AP (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci 31:89–97. https://doi.org/10.1016/j.tibs.2005.12.008
Krishnamurthy J, Torrice C, Ramsey MR, Kovalev GI, Al-Regaiey K, Su L, Sharpless NE (2004) Ink4a/Arf expression is a biomarker of aging. J Clin Investig 114:1299–1307. https://doi.org/10.1172/JCI200422475
Kulakova OG, Kabilov MR, Danilova LV, Popova EV, Baturina OA, Tsareva EY, Baulina NM, Kiselev IS, Boyko AN, Favorov AV, Favorova OO, Vlassov VV (2016) Whole-genome DNA methylation analysis of peripheral blood mononuclear cells in multiple sclerosis patients with different disease courses. Acta Nat 8:103–110
Levanon D, Negreanu V, Bernstein Y, Bar-Am I, Avivi L, Groner Y (1994) AML1, AML2, and AML3, the human members of the runt domain gene-family: cDNA structure, expression, and chromosomal localization. Genomics 23:425–432. https://doi.org/10.1006/geno.1994.1519
Levenson VV, Melnikov AA (2012) DNA methylation as clinically useful biomarkers—light at the end of the tunnel. Pharm (Basel) 5:94–113. https://doi.org/10.3390/ph5010094
Liggett T, Melnikov A, Tilwalli S, Yi Q, Chen H, Replogle C, Feng X, Reder A, Stefoski D, Balabanov R, Levenson V (2010) Methylation patterns of cell-free plasma DNA in relapsing-remitting multiple sclerosis. J Neurol Sci 290:16–21. https://doi.org/10.1016/j.jns.2009.12.018
Lill CM (2014) Recent advances and future challenges in the genetics of multiple sclerosis. Front Neurol 5:130. https://doi.org/10.3389/fneur.2014.00130
Lu F, Selak M, O'Connor J, Croul S, Lorenzana C, Butunoi C, Kalman B (2000) Oxidative damage to mitochondrial DNA and activity of mitochondrial enzymes in chronic active lesions of multiple sclerosis. J Neurol Sci 177:95–103
Maltby VE, Graves MC, Lea RA, Benton MC, Sanders KA, Tajouri L, Scott RJ, Lechner-Scott J (2015) Genome-wide DNA methylation profiling of CD8+ T cells shows a distinct epigenetic signature to CD4+ T cells in multiple sclerosis patients. Clin Epigenetics 7:118. https://doi.org/10.1186/s13148-015-0152-7
Mangano K, Fagone P, Bendtzen K, Meroni PL, Quattrocchi C, Mammana S, di Rosa M, Malaguarnera L, Coco M, Magro G, di Marco R, Nicoletti F (2014) Hypomethylating agent 5-aza-2′-deoxycytidine (DAC) ameliorates multiple sclerosis in mouse models. J Cell Physiol 229:1918–1925. https://doi.org/10.1002/jcp.24641
Mastronardi FG, Noor A, Wood DD, Paton T, Moscarello MA (2007) Peptidyl argininedeiminase 2 CpG island in multiple sclerosis white matter is hypomethylated. J Neurosci Res 85:2006–2016. https://doi.org/10.1002/jnr.21329
Mentis AA, Dardiotis E, Grigoriadis N, Petinaki E, Hadjigeorgiou GM (2017a) Viruses and endogenous retroviruses in multiple sclerosis: from correlation to causation. Acta Neurol Scand 136:606–616. https://doi.org/10.1111/ane.12775
Mentis AA, Dardiotis E, Grigoriadis N, Petinaki E, Hadjigeorgiou GM (2017b) Viruses and multiple sclerosis: from mechanisms and pathways to translational research opportunities. Mol Neurobiol 54:3911–3923. https://doi.org/10.1007/s12035-017-0530-6
Nobori T, Miura K, Wu DJ, Lois A, Takabayashi K, Carson DA (1994) Deletions of the cyclin-dependent kinase-4 inhibitor gene in multiple human cancers. Nature 368:753–756. https://doi.org/10.1038/368753a0
de Pagter-Holthuizen P, Jansen M, van der Kammen RA, van Schaik FM, Sussenbach JS (1988) Differential expression of the human insulin-like growth factor II gene. Characterization of the IGF-II mRNAs and an mRNA encoding a putative IGF-II-associated protein. Biochim Biophys Acta 950:282–295
Parnell GP, Gatt PN, Krupa M, Nickles D, McKay FC, Schibeci SD, Batten M, Baranzini S, Henderson A, Barnett M, Slee M, Vucic S, Stewart GJ, Booth DR (2014) The autoimmune disease-associated transcription factors EOMES and TBX21 are dysregulated in multiple sclerosis and define a molecular subtype of disease. Clin Immunol 151:16–24. https://doi.org/10.1016/j.clim.2014.01.003
Ramagopalan SV, Dobson R, Meier UC, Giovannoni G (2010) Multiple sclerosis: risk factors, prodromes, and potential causal pathways. Lancet Neurol 9:727–739. https://doi.org/10.1016/s1474-4422(10)70094-6
Renaudineau Y, Youinou P (2011) Epigenetics and autoimmunity, with special emphasis on methylation. Keio J Med 60:10–16
Sawcer S et al (2011) Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature 476:214–219. https://doi.org/10.1038/nature10251
Sawcer S, Franklin RJ, Ban M (2014) Multiple sclerosis genetics. Lancet Neurol 13:700–709. https://doi.org/10.1016/s1474-4422(14)70041-9
Shen S, Casaccia-Bonnefil P (2008) Post-translational modifications of nucleosomal histones in oligodendrocyte lineage cells in development and disease. J Mol Neurosci 35:13–22. https://doi.org/10.1007/s12031-007-9014-x
Sokratous M, Dardiotis E, Tsouris Z, Bellou E, Michalopoulou A, Siokas V, Arseniou S, Stamati T, Tsivgoulis G, Bogdanos D, Hadjigeorgiou GM (2016) Deciphering the role of DNA methylation in multiple sclerosis: emerging issues. Auto- Immun Highlights 7:12. https://doi.org/10.1007/s13317-016-0084-z
Vandenbroeck K, Alvarez J, Swaminathan B, Alloza I, Matesanz F, Urcelay E, Comabella M, Alcina A, Fedetz M, Ortiz MA, Izquierdo G, Fernandez O, Rodriguez-Ezpeleta N, Matute C, Caillier S, Arroyo R, Montalban X, Oksenberg JR, Antigüedad A, Aransay A (2012) A cytokine gene screen uncovers SOCS1 as genetic risk factor for multiple sclerosis. Genes Immun 13:21–28. https://doi.org/10.1038/gene.2011.44
Wang X, Wang J, Yu Y, Ma T, Chen P, Zhou B, Tao R (2017) Decitabine inhibits T cell proliferation via a novel TET2-dependent mechanism and exerts potent protective effect in mouse auto- and allo-immunity models. Oncotarget 8:56802–56815. https://doi.org/10.18632/oncotarget.18063
Weber M, Schubeler D (2007) Genomic patterns of DNA methylation: targets and function of an epigenetic mark. Curr Opin Cell Biol 19:273–280. https://doi.org/10.1016/j.ceb.2007.04.011
Wosik K, Antel J, Kuhlmann T, Bruck W, Massie B, Nalbantoglu J (2003) Oligodendrocyte injury in multiple sclerosis: a role for p53. J Neurochem 85:635–644
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
The study was approved by the University of Thessaly Ethics Committee and informed consent was provided by all participants.
Rights and permissions
About this article
Cite this article
Sokratous, M., Dardiotis, E., Bellou, E. et al. CpG Island Methylation Patterns in Relapsing-Remitting Multiple Sclerosis. J Mol Neurosci 64, 478–484 (2018). https://doi.org/10.1007/s12031-018-1046-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12031-018-1046-x