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Research Paper

Cell lineage-specific genome-wide DNA methylation analysis of patients with paediatric-onset systemic lupus erythematosus

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Pages 341-351 | Received 12 Oct 2018, Accepted 12 Feb 2019, Published online: 16 Mar 2019

References

  • Wakeland EK, Liu K, Graham RR, et al. Delineating the genetic basis of systemic lupus erythematosus. Immunity. 2001 Sep;15(3):397–408.
  • Domenech I, Aydintug O, Cervera R, et al. Systemic lupus erythematosus in 50 year olds. Postgrad Med J. 1992 Jun;68(800):440–444.
  • Ward MM, Polisson RP. A meta-analysis of the clinical manifestations of older-onset systemic lupus erythematosus. Arthritis Rheum. 1989 Oct;32(10):1226–1232.
  • Stichweh D, Arce E, Pascual V. Update on pediatric systemic lupus erythematosus. Curr Opin Rheumatol. 2004 Sep;16(5):577–587.
  • Kamphuis S, Silverman ED. Prevalence and burden of pediatric-onset systemic lupus erythematosus. Nat Rev Rheumatol. 2010 Sep;6(9):538–546.
  • Hiraki LT, Benseler SM, Tyrrell PN, et al. Clinical and laboratory characteristics and long-term outcome of pediatric systemic lupus erythematosus: a longitudinal study. J Pediatr. 2008 Apr;152(4):550–556.
  • Pluchinotta FR, Schiavo B, Vittadello F, et al. Distinctive clinical features of pediatric systemic lupus erythematosus in three different age classes. Lupus. 2007;16(8):550–555.
  • Levy DM, Kamphuis S. Systemic lupus erythematosus in children and adolescents. Pediatr Clin North Am. 2012 Apr;59(2):345–364.
  • Joo YB, Park SY, Won S, et al. Differences in clinical features and mortality between childhood-onset and adult-onset systemic lupus erythematosus: a prospective single-center study. J Rheumatol. 2016 Aug;43(8):1490–1497.
  • Tucker LB. Making the diagnosis of systemic lupus erythematosus in children and adolescents. Lupus. 2007;16(8):546–549.
  • Absher DM, Li X, Waite LL, et al. Genome-wide DNA methylation analysis of systemic lupus erythematosus reveals persistent hypomethylation of interferon genes and compositional changes to CD4+ T-cell populations. PLoS Genet. 2013;9(8):e1003678.
  • Coit P, Yalavarthi S, Ognenovski M, et al. Epigenome profiling reveals significant DNA demethylation of interferon signature genes in lupus neutrophils. J Autoimmun. 2015 Apr;58:59–66.
  • Coit P, Jeffries M, Altorok N, et al. Genome-wide DNA methylation study suggests epigenetic accessibility and transcriptional poising of interferon-regulated genes in naive CD4+ T cells from lupus patients. J Autoimmun. 2013 Jun;43:78–84.
  • Yeung KS, Chung BH, Choufani S, et al. Genome-wide DNA methylation analysis of chinese patients with systemic lupus erythematosus identified hypomethylation in genes related to the type I interferon pathway. PLoS One. 2017;12(1):e0169553.
  • Ulff-Moller CJ, Asmar F, Liu Y, et al. Twin DNA methylation profiling reveals flare-dependent interferon signature and B cell promoter hypermethylation in systemic lupus erythematosus. Arthritis Rheumatol. 2018 Jun;70(6):878–890.
  • Imgenberg-Kreuz J, Carlsson Almlof J, Leonard D, et al. DNA methylation mapping identifies gene regulatory effects in patients with systemic lupus erythematosus. Ann Rheum Dis. 2018 May;77(5):736–743.
  • Joseph S, George NI, Green-Knox B, et al. Epigenome-wide association study of peripheral blood mononuclear cells in systemic lupus erythematosus: identifying DNA methylation signatures associated with interferon-related genes based on ethnicity and SLEDAI. J Autoimmun. 2018 Oct 6. DOI:10.1016/j.jaut.2018.09.007
  • Coit P, Renauer P, Jeffries MA, et al. Renal involvement in lupus is characterized by unique DNA methylation changes in naive CD4+ T cells. J Autoimmun. 2015 Jul;61:29–35.
  • Mok A, Solomon O, Nayak RR, et al. Genome-wide profiling identifies associations between lupus nephritis and differential methylation of genes regulating tissue hypoxia and type 1 interferon responses. Lupus Sci Med. 2016;3(1):e000183.
  • Zhu H, Mi W, Luo H, et al. Whole-genome transcription and DNA methylation analysis of peripheral blood mononuclear cells identified aberrant gene regulation pathways in systemic lupus erythematosus. Arthritis Res Ther. 2016;18:162.
  • Chung SA, Nititham J, Elboudwarej E, et al. Genome-wide assessment of differential DNA methylation associated with autoantibody production in systemic lupus erythematosus. PLoS One. 2015;10(7):e0129813.
  • Coit P, Dozmorov MG, Merrill JT, et al. Epigenetic reprogramming in naive CD4+ T cells favoring T cell activation and Non-Th1 effector T cell immune response as an early event in lupus flares. Arthritis Rheumatol. 2016 Sep;68(9):2200–2209.
  • Ji H, Ehrlich LI, Seita J, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010 Sep 16;467(7313):338–342.
  • Accomando WP, Wiencke JK, Houseman EA, et al. Quantitative reconstruction of leukocyte subsets using DNA methylation. Genome Biol. 2014 Mar 05;15(3):R50.
  • Houseman EA, Accomando WP, Koestler DC, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics. 2012;13:86.
  • 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.
  • Yano S, Ghosh P, Kusaba H, et al. Effect of promoter methylation on the regulation of IFN-gamma gene during in vitro differentiation of human peripheral blood T cells into a Th2 population. J Immunol. 2003 Sep 01;171(5):2510–2516.
  • McGregor K, Bernatsky S, Colmegna I, et al. An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies. Genome Biol. 2016;17:84.
  • Teschendorff AE, Breeze CE, Zheng SC, et al. A comparison of reference-based algorithms for correcting cell-type heterogeneity in epigenome-wide association studies. BMC Bioinformatics. 2017 Feb 13;18(1):105.
  • Jury EC, Kabouridis PS, Abba A, et al. Increased ubiquitination and reduced expression of LCK in T lymphocytes from patients with systemic lupus erythematosus. Arthritis Rheumatism. 2003 May;48(5):1343–1354.
  • Jury EC, Kabouridis PS, Flores-Borja F, et al. Altered lipid raft-associated signaling and ganglioside expression in T lymphocytes from patients with systemic lupus erythematosus. J Clin Invest. 2004 Apr;113(8):1176–1187.
  • Crow MK, Kirou KA, Wohlgemuth J. Microarray analysis of interferon-regulated genes in SLE. Autoimmunity. 2003 Dec;36(8):481–490.
  • Bruyns E, Marie-Cardine A, Kirchgessner H, et al. T cell receptor (TCR) interacting molecule (TRIM), a novel disulfide-linked dimer associated with the TCR-CD3-zeta complex, recruits intracellular signaling proteins to the plasma membrane. J Exp Med. 1998 Aug 03;188(3):561–575.
  • Zhao M, Zhou Y, Zhu B, et al. IFI44L promoter methylation as a blood biomarker for systemic lupus erythematosus. Ann Rheum Dis. 2016 Nov;75(11):1998–2006.
  • Liu YJ. IPC: professional type 1 interferon-producing cells and plasmacytoid dendritic cell precursors. Annu Rev Immunol. 2005;23:275–306.
  • Maqbool M, Vidyadaran S, George E, et al. Optimisation of laboratory procedures for isolating human peripheral blood derived neutrophils. Med J Malaysia. 2011 Oct;66(4):296–299.
  • Buhule OD, Minster RL, Hawley NL, et al. Stratified randomization controls better for batch effects in 450K methylation analysis: a cautionary tale. Front Genet. 2014;5:354.
  • 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 May 15;30(10):1363–1369.
  • Chen YA, Lemire M, Choufani S, et al. Discovery of cross-reactive probes and polymorphic CpGs in the illumina infinium HumanMethylation450 microarray. Epigenetics. 2013 Feb;8(2):203–209.
  • McCartney DL, Walker RM, Morris SW, et al. Identification of polymorphic and off-target probe binding sites on the illumina infinium MethylationEPIC BeadChip. Genom Data. 2016 Sep;9:22–24.
  • Warde-Farley D, Donaldson SL, Comes O, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W214–W220.

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