{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T17:21:21Z","timestamp":1789924881759,"version":"4.0.1"},"reference-count":38,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2016,12,16]],"date-time":"2016-12-16T00:00:00Z","timestamp":1481846400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Thymomas are uncommon neoplasms that arise from epithelial cells of the thymus and are often associated with myasthenia gravis (MG), an autoimmune disease characterized by autoantibodies directed to different targets at the neuromuscular junction. Little is known, however, concerning epigenetic changes occurring in thymomas from MG individuals. To further address this issue, we analyzed DNA methylation levels of genes involved in one-carbon metabolism (MTHFR) and DNA methylation (DNMT1, DNMT3A, and DNMT3B) in blood, tumor tissue, and healthy thymic epithelial cells from MG patients that underwent a surgical resection of a thymic neoplasm. For the analyses we applied the methylation-sensitive high-resolution melting technique. Both MTHFR and DNMT3A promoters showed significantly higher methylation in tumor tissue with respect to blood, and MTHFR also showed significantly higher methylation levels in tumor tissue respect to healthy adjacent thymic epithelial cells. Both DNMT1 and DNMT3B promoter regions were mostly hypomethylated in all the investigated tissues. The present study suggests that MTHFR methylation is increased in thymomas obtained from MG patients; furthermore, some degrees of methylation of the DNMT3A gene were observed in thymic tissue with respect to blood.<\/jats:p>","DOI":"10.3390\/ijms17122121","type":"journal-article","created":{"date-parts":[[2016,12,16]],"date-time":"2016-12-16T10:55:28Z","timestamp":1481885728000},"page":"2121","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":19,"title":["Gene-Specific Methylation Analysis in Thymomas of Patients with Myasthenia Gravis"],"prefix":"10.3390","volume":"17","author":[{"given":"Angela","family":"Lopomo","sequence":"first","affiliation":[{"name":"Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy"},{"name":"Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roberta","family":"Ricciardi","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy"},{"name":"Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michelangelo","family":"Maestri","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"De Rosa","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, Neurology Unit, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franca","family":"Melfi","sequence":"additional","affiliation":[{"name":"Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Lucchi","sequence":"additional","affiliation":[{"name":"Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfredo","family":"Mussi","sequence":"additional","affiliation":[{"name":"Division of Thoracic Surgery, Cardiothoracic and Vascular Surgery Department, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabio","family":"Copped\u00e8","sequence":"additional","affiliation":[{"name":"Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucia","family":"Migliore","sequence":"additional","affiliation":[{"name":"Department of Translational Research and New Technologies in Medicine and Surgery, Division of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2016,12,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"596","DOI":"10.1097\/JTO.0000000000000154","article-title":"ITMIG consensus statement on the use of the WHO histological classification of thymoma and thymic carcinoma: Refined definitions, histological criteria, and reporting","volume":"9","author":"Marx","year":"2014","journal-title":"J. Thorac. Oncol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1093\/ejcts\/ezv426","article-title":"State of the art: Diagnostic tools and innovative therapies for treatment of advanced thymoma and thymic carcinoma","volume":"49","author":"Ried","year":"2016","journal-title":"Eur. J. Cardiothorac. Surg."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1007\/s00415-016-8045-z","article-title":"Clinical features, pathogenesis, and treatment of myasthenia gravis: A supplement to the guidelines of the German neurological society","volume":"263","author":"Melzer","year":"2016","journal-title":"J. Neurol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.expneurol.2015.02.010","article-title":"Thymoma related myasthenia gravis in humans and potential animal models","volume":"270","author":"Marx","year":"2015","journal-title":"Exp. Neurol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"S131","DOI":"10.1097\/JTO.0000000000000298","article-title":"State of the art of genetic alterations in thymic epithelial tumors","volume":"9","author":"Rajan","year":"2014","journal-title":"J. Thorac. Oncol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1038\/nrg3230","article-title":"Functions of DNA methylation: Islands, start sites, gene bodies and beyond","volume":"13","author":"Jones","year":"2012","journal-title":"Nat. Rev. Genet."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1016\/j.tips.2014.05.004","article-title":"Epigenetic mechanisms of importance for drug treatment","volume":"35","author":"Ivanov","year":"2014","journal-title":"Trends Pharmacol. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.canlet.2010.10.017","article-title":"DNA methylation in thoracic neoplasms","volume":"301","author":"Chen","year":"2011","journal-title":"Cancer Lett."},{"key":"ref_9","first-page":"1621","article-title":"Aberrant methylation: Common in thymic carcinomas, rare in thymomas","volume":"14","author":"Suzuki","year":"2005","journal-title":"Oncol. Rep."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1002\/(SICI)1097-0215(19971127)73:5<639::AID-IJC5>3.0.CO;2-Y","article-title":"p16INK4, pRB, p53 and cyclin D1 expression and hypermethylation of CDKN2 gene in thymoma and thymic carcinoma","volume":"73","author":"Hirabayashi","year":"1997","journal-title":"Int. J. Cancer"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/j.lungcan.2013.12.004","article-title":"Methylation and expression profiles of MGMT gene in thymic epithelial tumors","volume":"83","author":"Mokhtar","year":"2014","journal-title":"Lung Cancer"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/j.canlet.2011.12.030","article-title":"Epigenetic biomarkers of colorectal cancer: Focus on DNA methylation","volume":"342","year":"2014","journal-title":"Cancer Lett."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.gene.2013.09.063","article-title":"Folate: Metabolism, genes, polymorphisms and the associated diseases","volume":"533","author":"Nazki","year":"2014","journal-title":"Gene"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1080\/07357900802620869","article-title":"Aberrant DNA Methylation in Thymic Epithelial Tumors","volume":"27","author":"Chen","year":"2009","journal-title":"Cancer Investig."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1158\/0008-5472.CAN-08-2489","article-title":"Quantitative analysis of DNA methylation profiles in lung cancer identifies aberrant DNA methylation of specific genes and its association with gender and cancer risk factors","volume":"69","author":"Hung","year":"2009","journal-title":"Cancer Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1038\/leu.2013.362","article-title":"Epimutations mimic genomic mutations of DNMT3A in acute myeloid leukemia","volume":"28","author":"Jost","year":"2014","journal-title":"Leukemia"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1002\/jcb.25003","article-title":"Epigenetic modifications, chromatin distribution and TP53 transcription in a model of breast cancer progression","volume":"116","author":"Santos","year":"2015","journal-title":"J. Cell. Biochem."},{"key":"ref_18","first-page":"167976","article-title":"A potential epigenetic marker mediating serum folate and vitamin B12 levels contributes to the risk of ischemic stroke","volume":"2015","author":"Wei","year":"2015","journal-title":"BioMed Res. Int."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1007\/s11033-013-2906-7","article-title":"DNA methylation status of the methylenetetrahydrofolate reductase gene promoter in peripheral blood of end-stage renal disease patients","volume":"41","author":"Ghattas","year":"2014","journal-title":"Mol. Biol. Rep."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.1093\/humrep\/dep194","article-title":"MTHFR promoter hypermethylation in testicular biopsies of patients with non-obstructive azoospermia: The role of epigenetics in male infertility","volume":"24","author":"Khazamipour","year":"2009","journal-title":"Hum. Reprod."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Wu, W., Shen, O., Qin, Y., Niu, X., Lu, C., Xia, Y., Song, L., Wang, S., and Wang, X. (2010). Idiopathic male infertility is strongly associated with aberrant promoter methylation of methylenetetrahydrofolate reductase (MTHFR). PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0013884"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3632","DOI":"10.1093\/humrep\/des319","article-title":"Methylenetetrahydrofolate reductase gene promoter hypermethylation in semen samples of infertile couples correlates with recurrent spontaneous abortion","volume":"27","author":"Rotondo","year":"2012","journal-title":"Hum. Reprod."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"8021","DOI":"10.4238\/2015.July.17.10","article-title":"Correlation between MTHFR gene methylation and pre-eclampsia, and its clinical significance","volume":"14","author":"Ge","year":"2015","journal-title":"Genet. Mol. Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1111\/jcmm.12032","article-title":"Methylenetetrahydrofolate reductase (MTHFR) polymorphisms and promoter methylation in cervicaloncogenic lesions and cancer","volume":"17","author":"Botezatu","year":"2013","journal-title":"J. Cell. Mol. Med."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"270","DOI":"10.4161\/epi.7.3.19306","article-title":"DNA methylation changes associated with risk factors in tumors of the upper aerodigestive tract","volume":"7","author":"Mani","year":"2012","journal-title":"Epigenetics"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.neulet.2015.06.009","article-title":"Methylation analysis of multiple genes in blood DNA of Alzheimer\u2019s disease and healthy individuals","volume":"600","author":"Tannorella","year":"2015","journal-title":"Neurosci. Lett."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.mrfmmm.2016.02.008","article-title":"Increased MTHFR promoter methylation in mothers of Down syndrome individuals","volume":"787","author":"Denaro","year":"2016","journal-title":"Mutat. Res."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1158\/1940-6207.CAPR-10-0212","article-title":"Constitutional methylation of the BRCA1 promoter is specifically associated with BRCA1 mutation-associated pathology in early-onset breast cancer","volume":"4","author":"Wong","year":"2011","journal-title":"Cancer Prev. Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1802","DOI":"10.1038\/bjc.2014.463","article-title":"Methylated Glutathione S-transferase 1 (mGSTP1) is a potential plasma free DNA epigenetic marker of prognosis and response to chemotherapy in castrate-resistant prostate cancer","volume":"111","author":"Mahon","year":"2014","journal-title":"Br. J. Cancer"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.3233\/JAD-160210","article-title":"Artificial neural networks link one-carbon metabolism to gene-promoter methylation in Alzheimer\u2019s disease","volume":"53","author":"Grossi","year":"2016","journal-title":"J. Alzheimers Dis."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1016\/j.molimm.2011.09.022","article-title":"DNA methylation signatures of the AIRE promoter in thymic epithelial cells, thymomas and normal tissues","volume":"49","author":"Kont","year":"2011","journal-title":"Mol. Immunol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"474","DOI":"10.1016\/j.tig.2012.05.006","article-title":"De novo DNA methyltransferases: Oncogenes, tumor suppressors, or both?","volume":"28","author":"Fernandez","year":"2012","journal-title":"Trends Genet."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1182\/blood-2014-08-594648","article-title":"Dnmt3a loss predisposes murine hematopoietic stem cells to malignant transformation","volume":"125","author":"Mayle","year":"2015","journal-title":"Blood"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"7336","DOI":"10.1038\/srep07336","article-title":"Mutations of epigenetic regulatory genes are common in thymic carcinomas","volume":"4","author":"Wang","year":"2014","journal-title":"Sci. Rep."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"e111","DOI":"10.1038\/oncsis.2014.25","article-title":"ASXL1 and DNMT3A mutation in a cytogenetically normal B3 thymoma","volume":"3","author":"Belani","year":"2014","journal-title":"Oncogenesis"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Copped\u00e8, F., Ricciardi, R., Denaro, M., de Rosa, A., Provenzano, C., Bartoccioni, E., Baggiani, A., Lucchi, M., Mussi, A., and Migliore, L. (2013). Association of the DNMT3B \u2212579G>T polymorphism with risk of thymomas in patients with myasthenia gravis. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0080846"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Migheli, F., Stoccoro, A., Copped\u00e8, F., Omar, W.A., Failli, A., Consolini, R., Seccia, M., Spisni, R., Miccoli, P., and Mathers, J.C. (2013). Comparison study of MS-HRM and pyrosequencing techniques for quantification of APC and CDKN2A gene methylation. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0052501"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"621","DOI":"10.4161\/epi.27956","article-title":"Gene promoter methylation in colorectal cancer and healthy adjacent mucosa specimens: Correlation with physiological and pathological characteristics, and with biomarkers of one-carbon metabolism","volume":"9","author":"Migheli","year":"2014","journal-title":"Epigenetics"}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/17\/12\/2121\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T19:28:43Z","timestamp":1760210923000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/17\/12\/2121"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,12,16]]},"references-count":38,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["ijms17122121"],"URL":"https:\/\/doi.org\/10.3390\/ijms17122121","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,12,16]]}}}