1,467
Views
0
CrossRef citations to date
0
Altmetric
Research Paper

Association of DNA methylation signatures with premature ageing and cardiovascular death in patients with end-stage kidney disease: a pilot epigenome-wide association study

, , , , &
Article: 2214394 | Received 29 Dec 2022, Accepted 09 May 2023, Published online: 19 May 2023

References

  • Go AS, Chertow GM, Fan D, et al. Chronic kidney disease and the risks of death, cardiovascular events, and hospitalization. N Engl J Med. 2004;351(13):1296–11.
  • Franceschi C, Bonafe M, Valensin S, et al. Inflamm-aging. An evolutionary perspective on immunosenescence. Ann N Y Acad Sci. 2000;908:244–254.
  • Ferrucci L, Fabbri E. Inflammageing: chronic inflammation in ageing, cardiovascular disease, and frailty. Nat Rev Cardiol. 2018;15(9):505–522.
  • Kooman JP, Kotanko P, Schols AM, et al. Chronic kidney disease and premature ageing. Nat Rev Nephrol. 2014;10(12):732–742.
  • Stenvinkel P, Larsson TE. Chronic kidney disease: a clinical model of premature aging. Am J Kidney Dis. 2013;62(2):339–351.
  • Chambers JC, Loh M, Lehne B, et al. Epigenome-wide association of DNA methylation markers in peripheral blood from Indian Asians and Europeans with incident type 2 diabetes: a nested case-control study. Lancet Diabetes Endocrinol. 2015;3(7):526–534. DOI:10.1016/S2213-8587(15)00127-8
  • Reddy MA, Natarajan R. Epigenetics in diabetic kidney disease. J Am Soc Nephrol. 2011;22(12):2182–2185.
  • Zhang Y, Schottker B, Florath I, et al. Smoking-associated DNA methylation biomarkers and their predictive value for all-cause and cardiovascular mortality. Environ Health Perspect. 2016;124(1):67–74. DOI:10.1289/ehp.1409020
  • Hannum G, Guinney J, Zhao L, et al. Genome-wide methylation profiles reveal quantitative views of human aging rates. Mol Cell. 2013;49(2):359–367. DOI:10.1016/j.molcel.2012.10.016
  • Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013;14(10):R115.
  • Marioni RE, Shah S, McRae AF, et al. DNA methylation age of blood predicts all-cause mortality in later life. Genome Biol. 2015;16:25.
  • Breitling LP, Saum KU, Perna L, et al. Frailty is associated with the epigenetic clock but not with telomere length in a German cohort. Clin Epigenetics. 2016;8:21.
  • Christiansen L, Lenart A, Tan Q, et al. DNA methylation age is associated with mortality in a longitudinal Danish twin study. Aging Cell. 2016;15(1):149–154. DOI:10.1111/acel.12421
  • Marioni RE, Harris SE, Shah S, et al. The epigenetic clock and telomere length are independently associated with chronological age and mortality. Int J Epidemiol. 2018;45(2):424–432. DOI:10.1093/ije/dyw041
  • Lin Q, Weidner CI, Costa IG, et al. DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy. Aging. 2016;8(2):394–401. DOI:10.18632/aging.100908
  • Bell JT, Tsai PC, Yang TP, et al. Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet. 2012;8(4):e1002629. DOI:10.1371/journal.pgen.1002629
  • Marttila S, Kananen L, Hayrynen S, et al. Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression. BMC Genomics. 2015;16:179.
  • Jung M, Pfeifer GP. Aging and DNA methylation. BMC Biol. 2015;13:7.
  • Perna L, Zhang Y, Mons U, et al. Epigenetic age acceleration predicts cancer, cardiovascular, and all-cause mortality in a German case cohort. Clin Epigenetics. 2016;8:64.
  • Bell CG, Lowe R, Adams PD, et al. DNA methylation aging clocks: challenges and recommendations. Genome Biol. 2019;20(1):249. DOI:10.1186/s13059-019-1824-y
  • Han Z, Xiao Z, Kalantar-Zadeh K, et al. Validation of a novel modified aptamer-based array proteomic platform in patients with end-stage renal disease. Diagnostics (Basel). 2018;8(4):71. DOI:10.3390/diagnostics8040071
  • Sumida K, Han Z, Dashputre AA, et al. Association between Nrf2 and CDKN2A expression in patients with end-stage renal disease: a pilot study. Aging. 2020;12(16):16357–16367.
  • Sumida K, Pierre JF, Han Z, et al. Circulating microbial signatures and cardiovascular death in patients with ESRD. Kidney Int Rep. 2021;6(10):2617–2628. DOI:10.1016/j.ekir.2021.07.023
  • Aryee MJ, Jaffe AE, Corrada-Bravo H, et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014;30(10):1363–1369. DOI:10.1093/bioinformatics/btu049
  • Sandoval-Sierra JV, Salgado Garcia FI, Brooks JH, et al. Effect of short-term prescription opioids on DNA methylation of the OPRM1 promoter. Clin Epigenetics. 2020;12(1):76.
  • Bartlett AH, Liang JW, Sandoval-Sierra JV, et al. Longitudinal study of leukocyte DNA methylation and biomarkers for cancer risk in older adults. Biomark Res. 2019;7:10.
  • Reinius LE, Acevedo N, Joerink M, et al. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PLoS ONE. 2012;7(7):e41361. DOI:10.1371/journal.pone.0041361
  • Koestler DC, Christensen B, Karagas MR, et al. Blood-based profiles of DNA methylation predict the underlying distribution of cell types: a validation analysis. Epigenetics. 2013;8(8):816–826. DOI:10.4161/epi.25430
  • Houseman EA, Accomando WP, Koestler DC, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinf. 2012;13:86.
  • Levine ME, Lu AT, Quach A, et al. An epigenetic biomarker of aging for lifespan and healthspan. Aging. 2018;10(4):573–591. DOI:10.18632/aging.101414
  • Lu AT, Quach A, Wilson JG, et al. DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging. 2019;11(2):303–327. DOI:10.18632/aging.101684
  • Kresovich JK, Martinez Lopez AM, Garval EL, et al. Alcohol consumption and methylation-based measures of biological age. J Gerontol A Biol Sci Med Sci. 2021;76(12):2107–2111. DOI:10.1093/gerona/glab149
  • Liang X, Sinha R, Justice AC, et al. A new monocyte epigenetic clock reveals nonlinear effects of alcohol consumption on biological aging in three independent cohorts (N = 2242). Alcohol Clin Exp Res. 2022;46:736–748.
  • Chen BH, Marioni RE, Colicino E, et al. DNA methylation-based measures of biological age: meta-analysis predicting time to death. Aging. 2016;8(9):1844–1865. DOI:10.18632/aging.101020
  • Horvath S, Gurven M, Levine ME, et al. An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. Genome Biol. 2016;17(1):171. DOI:10.1186/s13059-016-1030-0
  • Mansell G, Gorrie-Stone TJ, Bao Y, et al. Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array. BMC Genomics. 2019;20(1):366. DOI:10.1186/s12864-019-5761-7
  • Turner SD. Qqman: an R package for visualizing GWAS results using Q-Q and Manhattan plots. J Open Source Softw. 2018;3(25):731.
  • Zhao J, Wei J, Mialki RK, et al. F-box protein FBXL19-mediated ubiquitination and degradation of the receptor for IL-33 limits pulmonary inflammation. Nat Immunol. 2012;13(7):651–658. DOI:10.1038/ni.2341
  • Zhao J, Mialki RK, Wei J, et al. SCF E3 ligase F-box protein complex SCF(FBXL19) regulates cell migration by mediating Rac1 ubiquitination and degradation. FASEB J. 2013;27(7):2611–2619. DOI:10.1096/fj.12-223099
  • Dong S, Zhao J, Wei J, et al. F-box protein complex FBXL19 regulates TGFbeta1-induced E-cadherin down-regulation by mediating Rac3 ubiquitination and degradation. Mol Cancer. 2014;13:76.
  • Derwish R, Paterno GD, Gillespie LL. Differential HDAC1 and 2 recruitment by members of the MIER family. PLoS ONE. 2017;12(1):e0169338.
  • Stenvinkel P, Luttropp K, McGuinness D, et al. CDKN2A/P16ink4(a) expression is associated with vascular progeria in chronic kidney disease. Aging. 2017;9(2):494–507. DOI:10.18632/aging.101173
  • Sanchis P, Ho CY, Liu Y, et al. Arterial “inflammaging” drives vascular calcification in children on dialysis. Kidney Int. 2019;95(4):958–972. DOI:10.1016/j.kint.2018.12.014
  • Jaenisch R, Bird A Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet. 2003;33 Suppl:245–254.
  • Stenvinkel P, Karimi M, Johansson S, et al. Impact of inflammation on epigenetic DNA methylation - a novel risk factor for cardiovascular disease? J Intern Med. 2007;261(5):488–499. DOI:10.1111/j.1365-2796.2007.01777.x
  • Zawada AM, Rogacev KS, Hummel B, et al. SuperTAG methylation-specific digital karyotyping reveals uremia-induced epigenetic dysregulation of atherosclerosis-related genes. Circ Cardiovasc Genet. 2012;5(6):611–620. DOI:10.1161/CIRCGENETICS.112.963207
  • Witasp A, Luttropp K, Qureshi AR, et al. Longitudinal genome-wide DNA methylation changes in response to kidney failure replacement therapy. Sci Rep. 2022;12(1):470. DOI:10.1038/s41598-021-04321-5
  • Karimi M, Johansson S, Ekstrom TJ. Using LUMA: a Luminometric-based assay for global DNA-methylation. Epigenetics. 2006;1(1):45–48.
  • McEwen LM, Jones MJ, Lin DTS, et al. Systematic evaluation of DNA methylation age estimation with common preprocessing methods and the Infinium MethylationEPIC BeadChip array. Clin Epigenetics. 2018;10(1):123. DOI:10.1186/s13148-018-0556-2
  • Yusipov I, Kondakova E, Kalyakulina A, et al. Accelerated epigenetic aging and inflammatory/immunological profile (ipAGE) in patients with chronic kidney disease. Geroscience. 2022;44(2):817–834. DOI:10.1007/s11357-022-00540-4
  • Acharya A, Berry DC, Zhang H, et al. MiR-26 suppresses adipocyte progenitor differentiation and fat production by targeting Fbxl19. Genes Dev. 2019;33(19–20):1367–1380. DOI:10.1101/gad.328955.119
  • Bagchi RA, Weeks KL. Histone deacetylases in cardiovascular and metabolic diseases. J Mol Cell Cardiol. 2019;130:151–159.
  • Smeir E, Kintscher U, Foryst-Ludwig A. Adipose tissue-heart crosstalk as a novel target for treatment of cardiometabolic diseases. Curr Opin Pharmacol. 2021;60:249–254.