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Research Paper

Assessment of aberrant DNA methylation two years after paediatric critical illness: a pre-planned secondary analysis of the international PEPaNIC trial

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Article: 2146966 | Received 10 Jun 2022, Accepted 07 Nov 2022, Published online: 16 Nov 2022

References

  • Mesotten D, Gielen M, Sterken C, et al. Neurocognitive development of children 4 years after critical illness and treatment with tight glucose control: a randomized controlled trial. JAMA. 2012;308(16):1641–12.
  • Mammen C, Al Abbas A, Skippen P, et al. Long-term risk of CKD in children surviving episodes of acute kidney injury in the intensive care unit: a prospective cohort study. Am J Kidney Dis. 2012;59:523–530.
  • Banwell BL, Mildner RJ, Hassall AC, et al. Muscle weakness in critically ill children. Neurology. 2003;61:1779–1782.
  • Verstraete S, Verbruggen SC, Hordijk JA, et al. Long-term developmental effects of withholding parenteral nutrition for 1 week in the paediatric intensive care unit: a 2-year follow-up of the PEPaNIC international, randomised, controlled trial. Lancet Respir Med. 2019;7:141–153.
  • Lee JH, Choong K. Time to focus on paediatric critical care survivorship. Lancet Respir Med. 2019;7:103–105.
  • Jacobs A, Dulfer K, Eveleens RD, et al. Long-term developmental effect of withholding parenteral nutrition in paediatric intensive care units: a 4-year follow-up of the PEPaNIC randomised controlled trial. Lancet Child Adolesc Health. 2020;4:503–514.
  • Fivez T, Kerklaan D, Mesotten D, et al. Early versus Late parenteral nutrition in critically ill children. N Engl J Med. 2016;374:1111–1122.
  • Guiza F, Vanhorebeek I, Verstraete S, et al. Effect of early parenteral nutrition during paediatric critical illness on DNA methylation as a potential mediator of impaired neurocognitive development: a pre-planned secondary analysis of the PEPaNIC international randomised controlled trial. Lancet Respir Med. 2020;8:288–303.
  • Vandiver AR, Idrizi A, Rizzardi L, et al. DNA methylation is stable during replication and cell cycle arrest. Sci Rep. 2015;5:17911.
  • Wilson AS, Power BE, Molloy PL. DNA hypomethylation and human diseases. Biochim Biophys Acta. 2007;1775(1):138–162.
  • Petryk N, Bultmann S, Bartke T, et al. Staying true to yourself: mechanisms of DNA methylation maintenance in mammals. Nucleic Acids Res. 2021;49:3020–3032.
  • Team RC. R: a language and environment for statistical computing R foundation for statistical computing. 2019; Accessed 13 09, 2022. https://www.r-project.org
  • LICMEpigenetics Package GitHub. 2022 Accessed 06 04, 2022. https://github.com/LICMLeuven/LICMEpigenetics
  • PEPanic 2Y Epigenetic analysis GitHub. 2022; Accessed 13 09, 2022. https://github.com/LICMLeuven/PEPaNIC_2Y_Epigenetics
  • Wu MC, Kuan P-F. A Guide to Illumina BeadChip Data Analysis. In: Tost J, editor. DNA Methylation Protocols. New York: Springer New York; 2018. p. 303–330.
  • Fortin JP, Triche TJ, Hansen KD. Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. Bioinformatics. 2017;33:558–560.
  • Hansen KD IlluminaHumanMethylationEPICanno.ilm10b4.hg19: annotation for Illumina’s EPIC methylation arrays 2017; Accessed 06 04, 2022. https://bitbucket.com/kasperdanielhansen/Illumina_EPIC
  • Teschendorff A. Computational and Statistical Epigenomics. Computational Statistical Epigenomics. 2015;7:1–217.
  • Lehne B, Drong AW, Loh M, et al. A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. Genome Biol. 2015;16:12.
  • Reiner A, Yekutieli D, Benjamini Y. Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics. 2003;19:368–375.
  • Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47.
  • Peters TJ, Buckley MJ, Statham AL, et al. De novo identification of differentially methylated regions in the human genome. Epigenetics Chromatin. 2015;8:16.
  • Kanehisa M, Furumichi M, Sato Y, et al. KEGG: integrating viruses and cellular organisms. Nucleic Acids Res. 2021;49:D545–D51.
  • Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.
  • Bostock M, Ogievetsky V, Heer J. D3: data-Driven Documents. IEEE Trans Vis Comput Graph. 2011;17:2301–2309.
  • Coppens G PEPaNIC 2Y Epigenetics interactive visualisation tool. 2022; Accessed 03 03, 2022. https://www.pepanic.com/2Y_epigenetics
  • Merrill SM, Moore SR, Gladish N, et al. Paternal adverse childhood experiences: associations with infant DNA methylation. Dev Psychobiol. 2021;63:e22174.
  • Rzehak P, Saffery R, Reischl E, et al. Maternal smoking during pregnancy and DNA-Methylation in children at age 5.5 years: epigenome-wide-analysis in the European childhood obesity project (CHOP)-Study. PLoS One. 2016;11:e0155554.
  • Xu R, Hong X, Zhang B, et al. DNA methylation mediates the effect of maternal smoking on offspring birthweight: a birth cohort study of multi-ethnic US mother-newborn pairs. Clin Epigenetics. 2021;13:47.
  • van Dijk SJ, Tellam RL, Morrison JL, et al. Recent developments on the role of epigenetics in obesity and metabolic disease. Clin Epigenetics. 2015;7:66.
  • Nikpay M, Ravati S, Dent R, et al. Epigenome-wide study identified methylation sites associated with the risk of obesity. Nutrients. 2021;13: 1984.
  • Meijer M, Klein M, Hannon E, et al. Genome-Wide DNA Methylation Patterns in Persistent Attention-Deficit/Hyperactivity Disorder and in Association With Impulsive and Callous Traits. Front Genet. 2020;11:16.
  • Walton E, Relton CL, Caramaschi D. Using openly accessible resources to strengthen causal inference in epigenetic epidemiology of neurodevelopment and mental health. Genes (Basel). 2019;10:193.
  • Hoffmann A, Sportelli V, Ziller M, et al. Epigenomics of major depressive disorders and schizophrenia: early life decides. Int J Mol Sci. 2017;18:1711.
  • Chuang YH, Lu AT, Paul KC, et al. Longitudinal Epigenome-Wide Methylation Study of Cognitive Decline and Motor Progression in Parkinson’s Disease. J Parkinsons Dis. 2019;9:389–400.
  • Moore K, McKnight AJ, Craig D, et al. Epigenome-wide association study for Parkinson’s disease. Neuromolecular Med. 2014;16:845–855.
  • Li QS, Vasanthakumar A, Davis JW, et al. Association of peripheral blood DNA methylation level with Alzheimer’s disease progression. Clin Epigenetics. 2021;13:191.
  • Chuang YH, Paul KC, Bronstein JM, et al. Parkinson’s disease is associated with DNA methylation levels in human blood and saliva. Genome Med. 2017;9:76.
  • Manotas MC, González DM, Céspedes C, et al. Genetic and Epigenetic Control of Puberty. Sex Dev. 2022;16:1–10.
  • Bouwland-Both MI, van Mil NH, Stolk L, et al. DNA methylation of IGF2DMR and H19 is associated with fetal and infant growth: the generation R study. PLoS One. 2013;8:e81731.
  • Fasolino M, Zhou Z. The Crucial Role of DNA Methylation and MeCP2 in Neuronal Function. Genes (Basel). 2017;8:141.
  • Mattonet K, Nowack-Weyers N, Vogel V, et al. Prenatal exposure to endocrine disrupting chemicals is associated with altered DNA methylation in cord blood. Epigenetics. 2022;17:935–952.
  • Leroy JL, Frongillo EA, Dewan P, et al. Can children catch up from the consequences of undernourishment? evidence from child linear growth, developmental epigenetics, and brain and neurocognitive development. Adv Nutr. 2020;11:1032–1041.
  • Qureshi IA, Mehler MF. Understanding neurological disease mechanisms in the era of epigenetics. JAMA Neurol. 2013;70:703–710.
  • Jakovcevski M, Akbarian S. Epigenetic mechanisms in neurological disease. Nat Med. 2012;18:1194–1204.