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Volumn 111, Issue 49, 2014, Pages E5302-E5311

Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing

Author keywords

Autoimmune disease; Epigenetics; Genomic representation; Massively parallel sequencing; Size profiling

Indexed keywords

DNA; IMMUNOGLOBULIN G; PROTEIN G; BIOLOGICAL MARKER;

EID: 84917709441     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1421126111     Document Type: Article
Times cited : (113)

References (47)
  • 1
    • 34347376851 scopus 로고    scopus 로고
    • Prognosis, mortality and morbidity in systemic lupus erythematosus
    • eds Wallace DJ, Hahn BH (Lippincott Williams & Wilkins, Philadelphia), 7th Ed
    • Gladman DD, Urowitz MB (2007) Prognosis, mortality and morbidity in systemic lupus erythematosus. Dubois' Lupus Erythematosus, eds Wallace DJ, Hahn BH (Lippincott Williams & Wilkins, Philadelphia), 7th Ed, pp 1333-1353.
    • (2007) Dubois' Lupus Erythematosus , pp. 1333-1353
    • Gladman, D.D.1    Urowitz, M.B.2
  • 2
    • 82555196095 scopus 로고    scopus 로고
    • Systemic lupus erythematosus
    • Tsokos GC (2011) Systemic lupus erythematosus. N Engl J Med 365(22):2110-2121.
    • (2011) N Engl J Med , vol.365 , Issue.22 , pp. 2110-2121
    • Tsokos, G.C.1
  • 3
    • 0141891339 scopus 로고    scopus 로고
    • Morbidity and mortality in systemic lupus erythematosus during a 10-year period: A comparison of early and late manifestations in a cohort of 1, 000 patients
    • Cervera R, et al.; European Working Party on Systemic Lupus Erythematosus (2003) Morbidity and mortality in systemic lupus erythematosus during a 10-year period: A comparison of early and late manifestations in a cohort of 1, 000 patients. Medicine (Baltimore) 82(5):299-308.
    • (2003) Medicine (Baltimore) , vol.82 , Issue.5 , pp. 299-308
    • Cervera, R.1
  • 4
    • 84876282977 scopus 로고    scopus 로고
    • Recent insights into the genetic basis of systemic lupus er-ythematosus
    • Rullo OJ, Tsao BP (2013) Recent insights into the genetic basis of systemic lupus er-ythematosus. Ann Rheum Dis 72(Suppl 2):ii56-ii61.
    • (2013) Ann Rheum Dis , vol.72 , Issue.SUPPL. 2 , pp. ii56-ii61
    • Rullo, O.J.1    Tsao, B.P.2
  • 5
    • 8844271819 scopus 로고    scopus 로고
    • The immune response to cell death in SLE
    • Pisetsky DS (2004) The immune response to cell death in SLE. Autoimmun Rev 3(7-8): 500-504.
    • (2004) Autoimmun Rev , vol.3 , Issue.7-8 , pp. 500-504
    • Pisetsky, D.S.1
  • 6
    • 69149086135 scopus 로고    scopus 로고
    • The role of extracellular DNA in autoimmunity in SLE
    • Su KY, Pisetsky DS (2009) The role of extracellular DNA in autoimmunity in SLE. Scand J Immunol 70(3):175-183.
    • (2009) Scand J Immunol , vol.70 , Issue.3 , pp. 175-183
    • Su, K.Y.1    Pisetsky, D.S.2
  • 7
    • 0028330345 scopus 로고
    • Accelerated in vitro apoptosis of lymphocytes from patients with systemic lupus erythematosus
    • Emlen W, Niebur J, Kadera R (1994) Accelerated in vitro apoptosis of lymphocytes from patients with systemic lupus erythematosus. J Immunol 152(7):3685-3692.
    • (1994) J Immunol , vol.152 , Issue.7 , pp. 3685-3692
    • Emlen, W.1    Niebur, J.2    Kadera, R.3
  • 8
    • 24144501267 scopus 로고    scopus 로고
    • SLE-A disease of clearance deficiency?
    • Munoz LE, et al. (2005) SLE-A disease of clearance deficiency? Rheumatology (Oxford) 44(9):1101-1107.
    • (2005) Rheumatology (Oxford) , vol.44 , Issue.9 , pp. 1101-1107
    • Munoz, L.E.1
  • 9
    • 12544258204 scopus 로고    scopus 로고
    • Antinucleosome antibodies and decreased deoxyribonuclease activity in sera of patients with systemic lupus er-ythematosus
    • Sallai K, Nagy E, Derfalvy B, Müzes G, Gergely P (2005) Antinucleosome antibodies and decreased deoxyribonuclease activity in sera of patients with systemic lupus er-ythematosus. Clin Diagn Lab Immunol 12(1):56-59.
    • (2005) Clin Diagn Lab Immunol , vol.12 , Issue.1 , pp. 56-59
    • Sallai, K.1    Nagy, E.2    Derfalvy, B.3    Müzes, G.4    Gergely, P.5
  • 10
    • 42649095663 scopus 로고    scopus 로고
    • Epigenetics in human autoimmunity. Epigenetics in autoimmunity-DNA methylation in systemic lupus erythematosus and beyond
    • Strickland FM, Richardson BC (2008) Epigenetics in human autoimmunity. Epigenetics in autoimmunity-DNA methylation in systemic lupus erythematosus and beyond. Autoimmunity 41(4):278-286.
    • (2008) Autoimmunity , vol.41 , Issue.4 , pp. 278-286
    • Strickland, F.M.1    Richardson, B.C.2
  • 11
    • 0025666735 scopus 로고
    • Evidence for impaired T cell DNA methylation in systemic lupus erythematosus and rheumatoid arthritis
    • Richardson B, et al. (1990) Evidence for impaired T cell DNA methylation in systemic lupus erythematosus and rheumatoid arthritis. Arthritis Rheum 33(11): 1665-1673.
    • (1990) Arthritis Rheum , vol.33 , Issue.11 , pp. 1665-1673
    • Richardson, B.1
  • 12
    • 33744936286 scopus 로고    scopus 로고
    • The epigenetic face of systemic lupus erythematosus
    • Ballestar E, Esteller M, Richardson BC (2006) The epigenetic face of systemic lupus erythematosus. J Immunol 176(12):7143-7147.
    • (2006) J Immunol , vol.176 , Issue.12 , pp. 7143-7147
    • Ballestar, E.1    Esteller, M.2    Richardson, B.C.3
  • 13
    • 84872184582 scopus 로고    scopus 로고
    • Lupus autoimmunity altered by cellular methylation metabolism
    • Yang ML, et al. (2013) Lupus autoimmunity altered by cellular methylation metabolism. Autoimmunity 46(1):21-31.
    • (2013) Autoimmunity , vol.46 , Issue.1 , pp. 21-31
    • Yang, M.L.1
  • 14
    • 36448933805 scopus 로고    scopus 로고
    • DNA hypomethylation is crucial for apoptotic DNA to induce systemic lupus erythematosus-like autoimmune disease in SLE-non-susceptible mice
    • Wen ZK, et al. (2007) DNA hypomethylation is crucial for apoptotic DNA to induce systemic lupus erythematosus-like autoimmune disease in SLE-non-susceptible mice. Rheumatology (Oxford) 46(12):1796-1803.
    • (2007) Rheumatology (Oxford) , vol.46 , Issue.12 , pp. 1796-1803
    • Wen, Z.K.1
  • 15
    • 0013964845 scopus 로고
    • Deoxybonucleic acid (DNA) and antibodies to DNA in the serum of patients with systemic lupus erythematosus
    • Tan EM, Schur PH, Carr RI, Kunkel HG (1966) Deoxybonucleic acid (DNA) and antibodies to DNA in the serum of patients with systemic lupus erythematosus. J Clin Invest 45(11):1732-1740.
    • (1966) J Clin Invest , vol.45 , Issue.11 , pp. 1732-1740
    • Tan, E.M.1    Schur, P.H.2    Carr, R.I.3    Kunkel, H.G.4
  • 16
    • 0019201556 scopus 로고
    • Quantitation and characterization of plasma DNA in normals and patients with systemic lupus erythematosus
    • Raptis L, Menard HA (1980) Quantitation and characterization of plasma DNA in normals and patients with systemic lupus erythematosus. J Clin Invest 66(6):1391-1399.
    • (1980) J Clin Invest , vol.66 , Issue.6 , pp. 1391-1399
    • Raptis, L.1    Menard, H.A.2
  • 17
    • 34249795176 scopus 로고    scopus 로고
    • Sensitive detection of plasma/serum DNA in patients with systemic lupus erythematosus
    • Chen JA, et al. (2007) Sensitive detection of plasma/serum DNA in patients with systemic lupus erythematosus. Autoimmunity 40(4):307-310.
    • (2007) Autoimmunity , vol.40 , Issue.4 , pp. 307-310
    • Chen, J.A.1
  • 18
    • 0025284721 scopus 로고
    • Endogenous circulating DNA in systemic lupus er-ythematosus. Occurrence as multimeric complexes bound to histone
    • Rumore PM, Steinman CR (1990) Endogenous circulating DNA in systemic lupus er-ythematosus. Occurrence as multimeric complexes bound to histone. J Clin Invest 86(1):69-74.
    • (1990) J Clin Invest , vol.86 , Issue.1 , pp. 69-74
    • Rumore, P.M.1    Steinman, C.R.2
  • 19
    • 58149490683 scopus 로고    scopus 로고
    • Noninvasive prenatal diagnosis of fetal chromosomal aneu-ploidy by massively parallel genomic sequencing of DNA in maternal plasma
    • Chiu RWK, et al. (2008) Noninvasive prenatal diagnosis of fetal chromosomal aneu-ploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proc Natl Acad Sci USA 105(51):20458-20463.
    • (2008) Proc Natl Acad Sci USA , vol.105 , Issue.51 , pp. 20458-20463
    • Chiu, R.W.K.1
  • 20
    • 78650207098 scopus 로고    scopus 로고
    • Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus
    • Lo YMD, et al. (2010) Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med 2(61):61ra91.
    • (2010) Sci Transl Med , vol.2 , Issue.61 , pp. 61ra91
    • Lo, Y.M.D.1
  • 21
    • 80755172331 scopus 로고    scopus 로고
    • DNA sequencing of maternal plasma to detect Down syndrome: An international clinical validation study
    • Palomaki GE, et al. (2011) DNA sequencing of maternal plasma to detect Down syndrome: An international clinical validation study. Genet Med 13(11):913-920.
    • (2011) Genet Med , vol.13 , Issue.11 , pp. 913-920
    • Palomaki, G.E.1
  • 22
    • 77949740366 scopus 로고    scopus 로고
    • Next generation sequencing of serum circulating nucleic acids from patients with invasive ductal breast cancer reveals differences to healthy and nonmalignant controls
    • Beck J, Urnovitz HB, Mitchell WM, Schütz E (2010) Next generation sequencing of serum circulating nucleic acids from patients with invasive ductal breast cancer reveals differences to healthy and nonmalignant controls. Mol Cancer Res 8(3):335-342.
    • (2010) Mol Cancer Res , vol.8 , Issue.3 , pp. 335-342
    • Beck, J.1    Urnovitz, H.B.2    Mitchell, W.M.3    Schütz, E.4
  • 23
    • 84870312106 scopus 로고    scopus 로고
    • Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing
    • Leary RJ, et al. (2012) Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med 4(162):162ra154.
    • (2012) Sci Transl Med , vol.4 , Issue.162 , pp. 162ra154
    • Leary, R.J.1
  • 24
    • 84888119068 scopus 로고    scopus 로고
    • Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing
    • Chan KCA, et al. (2013) Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc Natl Acad Sci USA 110(47):18761-18768.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.47 , pp. 18761-18768
    • Chan, K.C.A.1
  • 25
    • 84872020299 scopus 로고    scopus 로고
    • Cancer genome scanning in plasma: Detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing
    • Chan KCA, et al. (2013) Cancer genome scanning in plasma: Detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clin Chem 59(1):211-224.
    • (2013) Clin Chem , vol.59 , Issue.1 , pp. 211-224
    • Chan, K.C.A.1
  • 26
    • 0026777352 scopus 로고
    • Derivation of the SLEDAI. A disease activity index for lupus patients
    • Bombardier C, Gladman DD, Urowitz MB, Caron D, Chang CH; The Committee on Prognosis Studies in SLE (1992) Derivation of the SLEDAI. A disease activity index for lupus patients. Arthritis Rheum 35(6):630-640.
    • (1992) Arthritis Rheum , vol.35 , Issue.6 , pp. 630-640
    • Bombardier, C.1    Gladman, D.D.2    Urowitz, M.B.3    Caron, D.4    Chang, C.H.5
  • 27
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative ge-nomics
    • Krzywinski M, et al. (2009) Circos: An information aesthetic for comparative ge-nomics. Genome Res 19(9):1639-1645.
    • (2009) Genome Res , vol.19 , Issue.9 , pp. 1639-1645
    • Krzywinski, M.1
  • 28
    • 84863230684 scopus 로고    scopus 로고
    • Nonhematopoietically derived DNA is shorter than hema-topoietically derived DNA in plasma: A transplantation model
    • Zheng YWL, et al. (2012) Nonhematopoietically derived DNA is shorter than hema-topoietically derived DNA in plasma: A transplantation model. Clin Chem 58(3):549-558.
    • (2012) Clin Chem , vol.58 , Issue.3 , pp. 549-558
    • Zheng, Y.W.L.1
  • 29
    • 84887080693 scopus 로고    scopus 로고
    • Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA
    • Lun FMF, et al. (2013) Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA. Clin Chem 59(11):1583-1594.
    • (2013) Clin Chem , vol.59 , Issue.11 , pp. 1583-1594
    • Lun, F.M.F.1
  • 30
    • 0142009533 scopus 로고    scopus 로고
    • Development of autoantibodies before the clinical onset of systemic lupus erythematosus
    • Arbuckle MR, et al. (2003) Development of autoantibodies before the clinical onset of systemic lupus erythematosus. N Engl J Med 349(16):1526-1533.
    • (2003) N Engl J Med , vol.349 , Issue.16 , pp. 1526-1533
    • Arbuckle, M.R.1
  • 31
    • 34447320202 scopus 로고    scopus 로고
    • Fifty years of anti-ds DNA antibodies: Are we approaching journey's end?
    • Isenberg DA, Manson JJ, Ehrenstein MR, Rahman A (2007) Fifty years of anti-ds DNA antibodies: Are we approaching journey's end? Rheumatology (Oxford) 46(7):1052-1056.
    • (2007) Rheumatology (Oxford) , vol.46 , Issue.7 , pp. 1052-1056
    • Isenberg, D.A.1    Manson, J.J.2    Ehrenstein, M.R.3    Rahman, A.4
  • 32
    • 0017337322 scopus 로고
    • Avidity of anti-DNA antibodies in serum and IgG glomerular eluates from patients with systemic lupus erythematosus. Association of high avidity antinative DNA antibody with glomerulonephritis
    • Winfield JB, Faiferman I, Koffler D (1977) Avidity of anti-DNA antibodies in serum and IgG glomerular eluates from patients with systemic lupus erythematosus. Association of high avidity antinative DNA antibody with glomerulonephritis. J Clin Invest 59(1): 90-96.
    • (1977) J Clin Invest , vol.59 , Issue.1 , pp. 90-96
    • Winfield, J.B.1    Faiferman, I.2    Koffler, D.3
  • 33
    • 0016210917 scopus 로고
    • Saturation of the reticuloendothelial system with soluble immune complexes
    • Haakenstad AO, Mannik M (1974) Saturation of the reticuloendothelial system with soluble immune complexes. J Immunol 112(5):1939-1948.
    • (1974) J Immunol , vol.112 , Issue.5 , pp. 1939-1948
    • Haakenstad, A.O.1    Mannik, M.2
  • 34
    • 0018776991 scopus 로고
    • Defective re-ticuloendothelial system Fc-receptor function in systemic lupus erythematosus
    • Frank MM, Hamburger MI, Lawley TJ, Kimberly RP, Plotz PH (1979) Defective re-ticuloendothelial system Fc-receptor function in systemic lupus erythematosus. N Engl J Med 300(10):518-523.
    • (1979) N Engl J Med , vol.300 , Issue.10 , pp. 518-523
    • Frank, M.M.1    Hamburger, M.I.2    Lawley, T.J.3    Kimberly, R.P.4    Plotz, P.H.5
  • 35
    • 0023794455 scopus 로고
    • C3b receptor (CR1) on phagocytic cells from SLE patients: Analysis of the defect and familial study
    • Mir A, Porteu F, Levy M, Lesavre P, Halbwachs-Mecarelli L (1988) C3b receptor (CR1) on phagocytic cells from SLE patients: Analysis of the defect and familial study. Clin Exp Immunol 73(3):461-466.
    • (1988) Clin Exp Immunol , vol.73 , Issue.3 , pp. 461-466
    • Mir, A.1    Porteu, F.2    Levy, M.3    Lesavre, P.4    Halbwachs-Mecarelli, L.5
  • 36
    • 58749093255 scopus 로고    scopus 로고
    • Autoreactive B cells discriminate CpG-rich and CpG-poor DNA and this response is modulated by IFN-alpha
    • Uccellini MB, et al. (2008) Autoreactive B cells discriminate CpG-rich and CpG-poor DNA and this response is modulated by IFN-alpha. J Immunol 181(9):5875-5884.
    • (2008) J Immunol , vol.181 , Issue.9 , pp. 5875-5884
    • Uccellini, M.B.1
  • 37
    • 84858859845 scopus 로고    scopus 로고
    • Selective binding of anti-DNA antibodies to native dsDNA fragments of differing sequence
    • Uccellini MB, Busto P, Debatis M, Marshak-Rothstein A, Viglianti GA (2012) Selective binding of anti-DNA antibodies to native dsDNA fragments of differing sequence. Immunol Lett 143(1):85-91.
    • (2012) Immunol Lett , vol.143 , Issue.1 , pp. 85-91
    • Uccellini, M.B.1    Busto, P.2    Debatis, M.3    Marshak-Rothstein, A.4    Viglianti, G.A.5
  • 38
    • 78751683468 scopus 로고    scopus 로고
    • Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: Large scale validity study
    • Chiu RWK, et al. (2011) Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: Large scale validity study. BMJ 342:c7401.
    • (2011) BMJ , vol.342 , pp. c7401
    • Chiu, R.W.K.1
  • 39
    • 84902193969 scopus 로고    scopus 로고
    • Size-based molecular diagnostics using plasma DNA for non-invasive prenatal testing
    • Yu SCY, et al. (2014) Size-based molecular diagnostics using plasma DNA for non-invasive prenatal testing. Proc Natl Acad Sci USA 111(23):8583-8588.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.23 , pp. 8583-8588
    • Yu, S.C.Y.1
  • 40
    • 84870552401 scopus 로고    scopus 로고
    • Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules
    • Kelly TK, et al. (2012) Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res 22(12):2497-2506.
    • (2012) Genome Res , vol.22 , Issue.12 , pp. 2497-2506
    • Kelly, T.K.1
  • 41
    • 0017082128 scopus 로고
    • Spontaneous extracellular synthesis of DNA released by human blood lymphocytes
    • Anker P, Stroun M, Maurice PA (1976) Spontaneous extracellular synthesis of DNA released by human blood lymphocytes. Cancer Res 36(8):2832-2839.
    • (1976) Cancer Res , vol.36 , Issue.8 , pp. 2832-2839
    • Anker, P.1    Stroun, M.2    Maurice, P.A.3
  • 42
    • 0015370111 scopus 로고
    • Excretion of deoxy-ribonucleic acid by lymphocytes stimulated with phytohemagglutinin or antigen
    • Rogers JC, Boldt D, Kornfeld S, Skinner A, Valeri CR (1972) Excretion of deoxy-ribonucleic acid by lymphocytes stimulated with phytohemagglutinin or antigen. Proc Natl Acad Sci USA 69(7):1685-1689.
    • (1972) Proc Natl Acad Sci USA , vol.69 , Issue.7 , pp. 1685-1689
    • Rogers, J.C.1    Boldt, D.2    Kornfeld, S.3    Skinner, A.4    Valeri, C.R.5
  • 43
    • 70350049103 scopus 로고    scopus 로고
    • Abnormal DNA methylation in CD4+ T cells from patients with systemic lupus erythematosus, systemic sclerosis, and dermatomyositis
    • Lei W, et al. (2009) Abnormal DNA methylation in CD4+ T cells from patients with systemic lupus erythematosus, systemic sclerosis, and dermatomyositis. Scand J Rheumatol 38(5):369-374.
    • (2009) Scand J Rheumatol , vol.38 , Issue.5 , pp. 369-374
    • Lei, W.1
  • 44
    • 84875961571 scopus 로고    scopus 로고
    • Impaired DNA methylation and its mechanisms in CD4(+)T cells of systemic lupus erythematosus
    • Zhang Y, Zhao M, Sawalha AH, Richardson B, Lu Q (2013) Impaired DNA methylation and its mechanisms in CD4(+)T cells of systemic lupus erythematosus. J Autoimmun 41:92-99.
    • (2013) J Autoimmun , vol.41 , pp. 92-99
    • Zhang, Y.1    Zhao, M.2    Sawalha, A.H.3    Richardson, B.4    Lu, Q.5
  • 45
    • 84868272966 scopus 로고    scopus 로고
    • High resolution size analysis of fetal DNA in the urine of pregnant women by paired-end massively parallel sequencing
    • Tsui NBY, et al. (2012) High resolution size analysis of fetal DNA in the urine of pregnant women by paired-end massively parallel sequencing. PLoS ONE 7(10):e48319.
    • (2012) PLoS ONE , vol.7 , Issue.10 , pp. e48319
    • Tsui, N.B.Y.1
  • 46
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: An improved ultrafast tool for short read alignment
    • Li R, et al. (2009) SOAP2: An improved ultrafast tool for short read alignment. Bio-informatics 25(15):1966-1967.
    • (2009) Bio-informatics , vol.25 , Issue.15 , pp. 1966-1967
    • Li, R.1
  • 47
    • 84903304809 scopus 로고    scopus 로고
    • Methy-Pipe: An integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis
    • Jiang P, et al. (2014) Methy-Pipe: An integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis. PLoS ONE 9(6):e100360.
    • (2014) PLoS ONE , vol.9 , Issue.6 , pp. e100360
    • Jiang, P.1


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