Động học DNA methylation theo thời gian như một chỉ số thực tiễn trong di truyền học biểu sinh lâm sàng

Berdasco M, Esteller M. Clinical epigenetics: seizing opportunities for translation. Nat Rev Genet. 2019;20:109–27. https://doi.org/10.1038/s41576-018-0074-2. Li M, Zou D, Li Z, Gao R, Sang J, Zhang Y, et al. EWAS Atlas: a curated knowledgebase of epigenome-wide association studies. Nucleic Acids Res. 2019;47:D983–8. Horvath S, Raj K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat Rev Genet. 2018;19:371–84. https://doi.org/10.1038/s41576-018-0004-3. Fahy GM, Brooke RT, Watson JP, Good Z, Vasanawala SS, Maecker H, et al. Reversal of epigenetic aging and immunosenescent trends in humans. Aging Cell. 2019;18: e13028. https://doi.org/10.1111/acel.13028. Zaimi I, Pei D, Koestler DC, Marsit CJ, De Vivo I, Tworoger SS, et al. Variation in DNA methylation of human blood over a 1-year period using the Illumina MethylationEPIC array. Epigenetics. 2018;13:1056–71. https://doi.org/10.1080/15592294.2018.1530008. Talens RP, Boomsma DI, Tobi EW, Kremer D, Jukema JW, Willemsen G, et al. Variation, patterns, and temporal stability of DNA methylation: considerations for epigenetic epidemiology. FASEB J. 2010;24:3135–44. Byun HM, Nordio F, Coull BA, Tarantini L, Hou L, Bonzini M, et al. Temporal stability of epigenetic markers: sequence characteristics and predictors of short-term DNA methylation variations. PLoS ONE. 2012;7:1–9. Shvetsov YB, Song MA, Cai Q, Tiirikainen M, Xiang YB, Shu XO, et al. Intraindividual variation and short-term temporal trend in DNA methylation of human blood. Cancer Epidemiol Biomarkers Prev. 2015;24:490–7. Furukawa R, Hachiya T, Ohmomo H, Shiwa Y, Ono K, Suzuki S, et al. Intraindividual dynamics of transcriptome and genome-wide stability of DNA methylation. Sci Rep. 2016;6:26424. Pidsley R, Wong CC, Volta M, Lunnon K, Mill J, Schalkwyk LC. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genom. 2013;14:293. https://doi.org/10.1186/1471-2164-14-293. Tadaka S, Hishinuma E, Komaki S, Motoike IN, Kawashima J, Saigusa D, et al. jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population. Nucleic Acids Res. 2020;2018:1–9. Dor Y, Cedar H. Principles of DNA methylation and their implications for biology and medicine. Lancet. 2018;392:777–86. https://doi.org/10.1016/S0140-6736(18)31268-6. Hachiya T, Furukawa R, Shiwa Y, Ohmomo H, Ono K, Katsuoka F, et al. Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies. npj Genom Med. 2017;2:11. Flanagan JM, Brook MN, Orr N, Tomczyk K, Coulson P, Fletcher O, et al. Temporal stability and determinants of white blood cell DNA methylation in the breakthrough generations study. Cancer Epidemiol Biomarkers Prev. 2015;24:221–9. Komaki S, Shiwa Y, Furukawa R, Hachiya T, Ohmomo H, Otomo R, et al. iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation. Hum Genome Var. 2018;5:18008. Cavalcante RG, Sartor MA. Annotatr: genomic regions in context. Bioinformatics. 2017;33:2381–3. Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484–92. The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9. The Gene Ontology Consortium. The gene ontology resource: enriching a gold mine. Nucleic Acids Res. 2021;49:D325–34. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30. https://doi.org/10.1093/nar/28.1.27. Phipson B, Maksimovic J, Oshlack A. MissMethyl: an R package for analyzing data from Illumina’s HumanMethylation450 platform. Bioinformatics. 2016;32:286–8. Viechtbauer W. Conducting meta-analyses in R with the metafor. J Stat Softw. 2010;36:1–48. Morató X, Luján R, López-Cano M, Gandiá J, Stagljar I, Watanabe M, et al. The Parkinson’s disease-associated GPR37 receptor interacts with striatal adenosine A2A receptor controlling its cell surface expression and function in vivo. Sci Rep. 2017;7:1–13. Fujita-Jimbo E, Yu ZL, Li H, Yamagata T, Mori M, Momoi T, et al. Mutation in Parkinson disease-associated, G-protein-coupled receptor 37 (GPR37/PaelR) is related to autism spectrum disorder. PLoS ONE. 2012;7:3–8. Tanabe Y, Fujita-Jimbo E, Momoi MY, Momoi T. CASPR2 forms a complex with GPR37 via MUPP1 but not with GPR37(R558Q), an autism spectrum disorder-related mutation. J Neurochem. 2015;134:783–93. Shi Y, Zhao T, Yang X, Sun B, Li Y, Duan J, et al. PM2.5-induced alteration of DNA methylation and RNA-transcription are associated with inflammatory response and lung injury. Sci Total Environ. 2019;650:908–21. https://doi.org/10.1016/j.scitotenv.2018.09.085. Ling SH, van Eeden SF. Particulate matter air pollution exposure: role in the development and exacerbation of chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis. 2009;4:233–43. Camprubí C, Salas-Huetos A, Aiese-Cigliano R, Godo A, Pons MC, Castellano G, et al. Spermatozoa from infertile patients exhibit differences of DNA methylation associated with spermatogenesis-related processes: an array-based analysis. Reprod Biomed. 2016;33:709–19. https://doi.org/10.1016/j.rbmo.2016.09.001. Urdinguio RG, Bayón GF, Dmitrijeva M, Toraño EG, Bravo C, Fraga MF, et al. Aberrant DNA methylation patterns of spermatozoa in men with unexplained infertility. Hum Reprod. 2015;30:1014–28. Xue J, Gharaibeh RZ, Pietryk EW, Brouwer C, Tarantino LM, Valdar W, et al. Impact of vitamin D depletion during development on mouse sperm DNA methylation. Epigenetics. 2018;13:959–74. https://doi.org/10.1080/15592294.2018.1526027. Sujit KM, Sarkar S, Singh V, Pandey R, Agrawal NK, Trivedi S, et al. Genome-wide differential methylation analyses identifies methylation signatures of male infertility. Hum Reprod. 2018;33:2256–67. Denham J, O’Brien BJ, Marques FZ, Charchar FJ. Changes in the leukocyte methylome and its effect on cardiovascular-related genes after exercise. J Appl Physiol. 2015;118:475–88. https://doi.org/10.1152/japplphysiol.00878.2014. Sobreira N, Brucato M, Zhang L, Ladd-Acosta C, Ongaco C, Romm J, et al. Patients with a Kabuki syndrome phenotype demonstrate DNA methylation abnormalities. Eur J Hum Genet. 2017;25:1335–44. https://doi.org/10.1038/s41431-017-0023-0. Heindel JJ, Blumberg B, Cave M, Machtinger R, Mantovani A, Mendez MA, et al. Metabolism disrupting chemicals and metabolic disorders. Reprod Toxicol. 2017;68:3–33. https://doi.org/10.1016/j.reprotox.2016.10.001. Dedeurwaerder S, Defrance M, Bizet M, Calonne E, Bontempi G, Fuks F. A comprehensive overview of Infinium Human Methylation450 data processing. Brief Bioinform. 2013;15:929–41. Everson-Rose SA, Meyer PM, Powell LH, Pandey D, Torréns JI, Kravitz HM, et al. Depressive symptoms, insulin resistance, and risk of diabetes in women at midlife. Diabetes Care. 2004;27:2856–62. Pan A, Keum N, Okereke OI, Sun Q, Kivimaki M, Rubin RR, et al. Bidirectional association between depression and metabolic syndrome: a systematic review and meta-analysis of epidemiological studies. Diabetes Care. 2012;35:1171–80. Penninx BWJH, Lange SMM. Metabolic syndrome in psychiatric patients: overview, mechanisms, and implications. Dialogues Clin Neurosci. 2018;20:63–73. Chokka P, Tancer M, Yeragani VK. Metabolic syndrome: relevance to antidepressant treatment. J Psychiatry Neurosci. 2006;31:414. Hagenaars SP, Coleman JRI, Choi SW, Gaspar H, Adams MJ, Howard DM, et al. Genetic comorbidity between major depression and cardio-metabolic traits, stratified by age at onset of major depression. Am J Med Genet Part B Neuropsychiatr Genet. 2020;183:309–30. Amare AT, Schubert KO, Klingler-Hoffmann M, Cohen-Woods S, Baune BT. The genetic overlap between mood disorders and cardiometabolic diseases: a systematic review of genome wide and candidate gene studies. Transl Psychiatry. 2017;7:e1007. Grundy SM, Cleeman JI, Daniels SR, Donato KA, Eckel RH, Franklin BA, et al. Diagnosis and management of the metabolic syndrome. Circulation. 2005;112:2735–52. https://doi.org/10.1161/CIRCULATIONAHA.105.169404. Rochlani Y, Pothineni NV, Kovelamudi S, Mehta JL. Metabolic syndrome: pathophysiology, management, and modulation by natural compounds. Ther Adv Cardiovasc Dis. 2017;11:215–25. https://doi.org/10.1177/1753944717711379. Lusis AJ, Attie AD, Reue K. Metabolic syndrome: from epidemiology to systems biology. Nat Rev Genet. 2008;9:819–30. https://doi.org/10.2337/diacare.27.12.2856. Wang M, Aaron CP, Madrigano J, Hoffman EA, Angelini E, Yang J, et al. Association between long-term exposure to ambient air pollution and change in quantitatively assessed emphysema and lung function. JAMA J Am Med Assoc. 2019;322:546–56. Chen J, Wu J, Hao S, Yang M, Lu X, Chen X, et al. Long term outcomes in survivors of epidemic Influenza A (H7N9) virus infection. Sci Rep. 2017;7:1–8. https://doi.org/10.1038/s41598-017-17497-6. Chuang KJ, Chan CC, Su TC, Te LC, Tang CS. The effect of urban air pollution on inflammation, oxidative stress, coagulation, and autonomic dysfunction in young adults. Am J Respir Crit Care Med. 2007;176:370–6. Finzel S, Schaffer S, Rizzi M, Voll RE. Pathogenesis of systemic lupus erythematosus. Z Rheumatol. 2018;77:789–98. Petersen AMW, Pedersen BK. The anti-inflammatory effect of exercise. J Appl Physiol. 2005;98:1154–62. McInnes IB, Schett G. The pathogenesis of rheumatoid arthritis. N Engl J Med. 2011;365:2205–19. https://doi.org/10.1056/NEJMra1004965. Lindholm ME, Marabita F, Gomez-Cabrero D, Rundqvist H, Ekström TJ, Tegnér J, et al. An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training. Epigenetics. 2014;9:1557–69. https://doi.org/10.4161/15592294.2014.982445. Denham J, Marques FZ, Bruns EL, O’Brien BJ, Charchar FJ. Epigenetic changes in leukocytes after 8 weeks of resistance exercise training. Eur J Appl Physiol. 2016;116:1245–53. Schenk A, Koliamitra C, Bauer CJ, Schier R, Schweiger MR, Bloch W, et al. Impact of acute aerobic exercise on genome-wide DNA-methylation in natural killer cells—a pilot study. Genes (Basel). 2019;10:380. Mostafavi N, Vermeulen R, Ghantous A, Hoek G, Probst-Hensch N, Herceg Z, et al. Acute changes in DNA methylation in relation to 24 h personal air pollution exposure measurements: a panel study in four European countries. Environ Int. 2018;120:11–21. Carmeliet P. Angiogenesis in health and disease. Nat Med. 2003;9:653–60. Hanahan D, Folkman J. Patterns and emerging mechanisms of the angiogenic switch during tumorigenesis. Cell. 1996;86:353–64. Kholodnyuk I, Kadisa A, Svirskis S, Gravelsina S, Studers P, Spaka I, et al. Proportion of the CD19-positive and CD19-negative lymphocytes and monocytes within the peripheral blood mononuclear cell set is characteristic for rheumatoid arthritis. Med. 2019;55:1–14.