ИЮЛЬ-АВГУСТ 2017 / 04

Следующая статья

DOI: 10.24075/brsmu.2017-04-01

ОБЗОР

Диагностический потенциал внеклеточной ДНК в качестве жидкостной биопсии

М. Л. Филипенко1,2
Информация об авторах

1 Лаборатория фармакогеномики,
Институт химической биологии и фундаментальной медицины СО РАН, Новосибирск

2 Новосибирский государственный университет, Новосибирск

Для корреспонденции: Филипенко Максим Леонидович
Пр-т Ак. Лаврентьева, д. 8, г. Новосибирск, 630090; ur.csn.hcobin@xam

Информация о статье

Финансирование: статья подготовлена в рамках базового проекта Программы фундаментальных научных исследований государственных академий наук на 2017–2020 гг. Тема № VI.62.2.2 «Развитие методов персонализированной медицины» (0309-2016-0007).

Статья получена: 25.08.2017 Статья принята к печати: 30.08.2017
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  1. Mandel P, Metais P. Les acides nucléiques du plasma sanguin chez l'homme. C R Seances Soc Biol Fil. 1948 Feb; 142 (3–4): 241–3.
  2. Koffler D, Agnello V, Winchester R, Kunkel HG. The occurrence of single-stranded DNA in the serum of patients with systemic lupus erythematosus and other diseases. J Clin Invest. 1973 Jan; 52 (1): 198–204.
  3. Leon SA, Ehrlich GE, Shapiro B, Labbate VA. Free DNA in the serum of rheumatoid arthritis patients. J Rheumatol. 1977 Summer; 4 (2): 139–43.
  4. Tan EM, Schur PH, Carr RI, Kunkel HG. Deoxybonucleic acid (DNA) and antibodies to DNA in the serum of patients with systemic lupus erythematosus. J Clin Invest. 1966 Nov; 45 (11): 1732–40.
  5. Stroun M, Anker P, Maurice P, Gahan PB. Circulating nucleic acids in higher organisms. Int Rev Cytol. 1977; 51: 1–48.
  6. Leon SA, Shapiro B, Sklaroff DM, Yaros MJ. Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res. 1977 Mar; 37 (3): 646–50.
  7. Sorenson GD, Pribish DM, Valone FH, Memoli VA, Bzik DJ, Yao SL. Soluble normal and mutated DNA sequences from single-copy genes in human blood. Cancer Epidemiol Biomarkers Prev. 1994 Jan–Feb; 3 (1): 67–71.
  8. Shaw JA, Smith BM, Walsh T, Johnson S, Primrose L, Slade MJ et al. Microsatellite alterations plasma DNA of primary breast cancer patients. Clin Cancer Res. 2000 Mar; 6 (3): 1119–24.
  9. Fujiwara K, Fujimoto N, Tabata M, Nishii K, Matsuo K, Hotta K et al. Identification of epigenetic aberrant promoter methylation in serum DNA is useful for early detection of lung cancer. Clin Cancer Res. 2005 Feb 1; 11 (3): 1219–25.
  10. Lo YM, Leung TN, Tein MS, Sargent IL, Zhang J, Lau TK et al. Quantitative abnormalities of fetal DNA in maternal serum in preeclampsia. Clin Chem. 1999 Feb; 45 (2): 184–8.
  11. Zhong XY, Bürk MR, Troeger C, Kang A, Holzgreve W, Hahn S. Fluctuation of maternal and fetal free extracellular circulatory DNA in maternal plasma. Obstet Gynecol. 2000 Dec; 96 (6): 991–6.
  12. Wang BG, Huang HY, Chen YC, Bristow RE, Kassauei K, Cheng CC et al. Increased plasma DNA integrity in cancer patients. Cancer Res. 2003 Jul 15; 63 (14): 3966–8.
  13. Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR. Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proc Natl Acad Sci U S A. 2008 Oct 21; 105 (42): 16266–71.
  14. Chu T, Bunce K, Hogge WA, Peters DG. Statistical model for whole genome sequencing and its application to minimally invasive diagnosis of fetal genetic disease. Bioinformatics. 2009 May 15; 25 (10): 1244–50.
  15. Stroun M, Anker P, Maurice P, Lyautey J, Lederrey C, Beljanski M. Neoplastic characteristics of the DNA found in the plasma of cancer patients. Oncology. 1989; 46 (5): 318–22.
  16. Vasioukhin V, Anker P, Maurice P, Lyautey J, Lederrey C, Stroun M. Point mutations of the N-ras gene in the blood plasma DNA of patients with myelodysplastic syndrome or acute myelogenous leukaemia. Br J Haematol. 1994 Apr; 86 (4): 774–9.
  17. Lo YM, Zhang J, Leung TN, Lau TK, Chang AM, Hjelm NM. Rapid clearance of fetal DNA from maternal plasma. Am J Hum Genet. 1999 Jan; 64 (1): 218–24.
  18. Tsumita T, Iwanaga M. Fate of injected deoxyribonucleic acid in mice. Nature. 1963 Jun 15; 198: 1088–9.
  19. Jahr S, Hentze H, Englisch S, Hardt D, Fackelmayer FO, Hesch RD et al. DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res. 2001 Feb 15; 61 (4): 1659–65.
  20. Diehl F, Li M, Dressman D, He Y, Shen D, Szabo S et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci U S A. 2005 Nov 8; 102 (45): 16368–73.
  21. Fairbairn DW, O'Neill KL. Necrotic DNA degradation mimics apoptotic nucleosomal fragmentation comet tail length. In Vitro Cell Dev Biol Anim. 1995 Mar; 31 (3): 171–3.
  22. Tran TT, Groben P, Pisetsky DS. The release of DNA into the plasma of mice following hepatic cell death by apoptosis and necrosis. Biomarkers. 2008 Mar; 13 (2): 184–200.
  23. van Nieuwenhuijze AE, van Lopik T, Smeenk RJ, Aarden LA. Time between onset of apoptosis and release of nucleosomes from apoptotic cells: putative implications for systemic lupus erythematosus. Ann Rheum Dis. 2003 Jan; 62 (1): 10–4.
  24. Brinkmann V, Reichard U, Goosmann C, Fauler B, Uhlemann Y, Weiss DS et al. Neutrophil extracellular traps kill bacteria. Science. 2004 Mar 5; 303 (5663): 1532–5.
  25. Gupta AK, Hasler P, Holzgreve W, Gebhardt S, Hahn S. Induction of neutrophil extracellular DNA lattices by placental microparticles and IL-8 and their presence in preeclampsia. Hum Immunol 2005 Nov; 66 (11): 1146–54.
  26. Gupta AK, Joshi MB, Philippova M, Erne P, Hasler P, Hahn S et al. Activated endothelial cells induce neutrophil extracellular traps and are susceptible to NETosis-mediated cell death. FEBS Lett. 2010 Jul 16; 584 (14): 3193–7.
  27. Demers M, Krause DS, Schatzberg D, Martinod K, Voorhees JR, Fuchs TA et al. Cancers predispose neutrophils to release extracellular DNA traps that contribute to cancer-associated thrombosis. Proc Natl Acad Sci U S A. 2012 Aug 7; 109 (32): 13076–81.
  28. Erpenbeck L, Schön MP. Neutrophil extracellular traps: protagonists of cancer progression? Oncogene. 2017 May 4; 36 (18): 2483–90.
  29. Peters DL, Pretorius PJ. Origin, translocation and destination of extracellular occurring DNA — A new paradigm in genetic behaviour. Clin Chim Acta. 2011 May 12; 412 (11–12): 806–11.
  30. Reclusa P, Sirera R, Araujo A, Giallombardo M, Valentino A, Sorber L et al. Exosomes genetic cargo in lung cancer: a truly Pandora's box. Transl Lung Cancer Res. 2016 Oct; 5 (5): 483–91.
  31. van der Vaart M, Pretorius PJ. The origin of circulating free DNA. Clin Chem. 2007 Dec; 53 (12): 2215.
  32. Gahan PB, Anker P, Stroun M. Metabolic DNA as the origin of spontaneously released DNA? Ann N Y Acad Sci. 2008 Aug; 1137: 7–17.
  33. Aucamp J, Bronkhorst AJ, Peters DL, Van Dyk HC, Van der Westhuizen FH, Pretorius PJ. Kinetic analysis, size profiling, and bioenergetic association of DNA released by selected cell lines in vitro. Cell Mol Life Sci. 2017 Jul; 74 (14): 2689–707.
  34. Lo YM, Corbetta N, Chamberlain PF, Rai V, Sargent IL, Redman CW et al. Presence of fetal DNA in maternal plasma and serum. Lancet. 1997 Aug 16; 350 (9076): 485–7.
  35. Rink BD, Norton ME. Screening for fetal aneuploidy. Semin Perinatol. 2016 Feb; 40 (1): 35–43.
  36. Twiss P, Hill M, Daley R, Chitty LS. Non-invasive prenatal testing for Down syndrome. Semin Fetal Neonatal Med. 2014 Feb; 19 (1): 9–14.
  37. Guissart C, Dubucs C, Raynal C, Girardet A, Tran Mau Them F et al. Non-invasive prenatal diagnosis (NIPD) of cystic fibrosis: an optimized protocol using MEMO fluorescent PCR to detect the p.Phe508del mutation. J Cyst Fibros. 2017 Mar; 16 (2): 198–206.
  38. De Franco E, Caswell R, Houghton JA, Iotova V, Hattersley AT, Ellard S. Analysis of cell-free fetal DNA for non-invasive prenatal diagnosis in a family with neonatal diabetes. Diabet Med. 2017 Apr; 34 (4): 582–5.
  39. Scalici E, Traver S, Molinari N, Mullet T, Monforte M, Vintejoux E et al. Cell-free DNA in human follicular fluid as a biomarker of embryo quality. Hum Reprod. 2014 Dec; 29 (12): 2661–9.
  40. Shamonki MI, Jin H, Haimowitz Z, Liu L. Proof of concept: preimplantation genetic screening without embryo biopsy through analysis of cell-free DNA in spent embryo culture media. Fertil Steril. 2016 Nov; 106 (6): 1312–8.
  41. De Vlaminck I, Martin L, Kertesz M, Patel K, Kowarsky M, Strehl C et al. Noninvasive monitoring of infection and rejection after lung transplantation. Proc Natl Acad Sci U S A. 2015 Oct 27; 112 (43): 13336–41.
  42. Bloom RD, Bromberg JS, Poggio ED, Bunnapradist S, Langone AJ, Sood P et al. Cell-Free DNA and Active Rejection in Kidney Allografts. J Am Soc Nephrol. 2017 Jul; 28 (7): 2221–32.
  43. Margraf S, Lögters T, Reipen J, Altrichter J, Scholz M, Windolf J. Neutrophil-derived circulating free DNA (cf-DNA/NETs): a potential prognostic marker for posttraumatic development of inflammatory second hit and sepsis. Shock. 2008 Oct; 30 (4): 352–8.
  44. Hamaguchi S, Akeda Y, Yamamoto N, Seki M, Yamamoto K, Oishi K et al. Origin of Circulating Free DNA in Sepsis: Analysis of the CLP Mouse Model. Mediators Inflamm. 2015; 2015: 614518.
  45. Jung K, Fleischhacker M, Rabien A. Cell-free DNA in the blood as a solid tumor biomarker — a critical appraisal of the literature. Clin Chim Acta. 2010 Nov 11; 411 (21–22): 1611–24.
  46. Crowley E, Di Nicolantonio F, Loupakis F, Bardelli A. Liquid biopsy: monitoring cancer-genetics in the blood. Nat Rev Clin Oncol. 2013 Aug; 10 (8): 472–84.
  47. Wan JC, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C et al. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer. 2017 Apr; 17 (4): 223–38.
  48. Bidart J-M, Thuillier F, Augereau C, Chalas J, Daver A, Jacob N et al. Kinetics of serum tumor marker concentrations and usefulness in clinical monitoring. Clin Chem. 1999 Oct; 45 (10): 1695–707.
  49. Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M et al. Circulating mutant DNA to assess tumor dynamics. Nat Med. 2008 Sep; 14 (9): 985–90.
  50. Thierry AR, Mouliere F, Gongora C, Ollier J, Robert B, Ychou M et al. Origin and quantification of circulating DNA in mice with human colorectal cancer xenografts. Nucleic Acids Res. 2010 Oct; 38 (18): 6159–75.
  51. Zhou J, Chang L, Guan Y, Yang L, Xia X, Cui L et al. Application of Circulating Tumor DNA as a Non-Invasive Tool for Monitoring the Progression of Colorectal Cancer. PLoS One. 2016 Jul 26; 11 (7): e0159708.
  52. Takahashi H, Kagara N, Tanei T, Naoi Y, Shimoda M, Shimomura A et al. Correlation of Methylated Circulating Tumor DNA with Response to Neoadjuvant Chemotherapy in Breast Cancer Patients. Clin Breast Cancer. 2017 Feb; 17 (1): 61–69.
  53. Visvanathan K, Fackler MS, Zhang Z, Lopez-Bujanda ZA, Jeter SC, Sokoll LJ et al. Monitoring of Serum DNA Methylation as an Early Independent Marker of Response and Survival in Metastatic Breast Cancer: TBCRC 005 Prospective Biomarker Study. J Clin Oncol. 2017 Mar; 35 (7): 751–8.
  54. Tie J, Wang Y, Tomasetti C, Li L, Springer S, Kinde I et al. Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer. Sci Transl Med. 2016 Jul 6; 8 (346): 346ra92.
  55. Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014 Feb 19; 6 (224): 224ra24.
  56. Margolin G, Petrykowska HM, Jameel N, Bell DW, Young AC, Elnitski L. Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development. J Mol Diagn. 2016 Mar; 18 (2): 283–98.
  57. Lehmann-Werman R, Neiman D, Zemmour H, Moss J, Magenheim J, Vaknin-Dembinsky A et al. Identification of tissue-specific cell death using methylation patterns of circulating DNA. Proc Natl Acad Sci U S A. 2016 Mar 29; 113 (13): E1826–34.
  58. Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. Cell. 2016 Jan 14; 164 (1–2): 57–68.
  59. Smith J, Kean V, Bianchi DW, Feldman G, Petrucelli N, Simon M et al. Cell-free DNA results lead to unexpected diagnosis. Clin Case Rep. 2017 Jul 3; 5 (8): 1323–6.
  60. Raptis L, Menard HA. Quantitation and characterization of plasma DNA in normals and patients with systemic lupus erythematosus. J Clin Invest. 1980 Dec; 66 (6): 1391–9.
  61. Truszewska A, Foroncewicz B, Pączek L. The role and diagnostic value of cell-free DNA in systemic lupus erythematosus. Clin Exp Rheumatol. 2017 Mar–Apr; 35 (2): 330–6.
  62. Ershova ES, Jestkova EM, Chestkov IV, Porokhovnik LN, Izevskaya VL, Kutsev SI et al. Quantification of cell-free DNA in blood plasma and DNA damage degree in lymphocytes to evaluate dysregulation of apoptosis in schizophrenia patients. J Psychiatr Res. 2017 Apr; 87: 15–22.
  63. Breitbach S, Tug S, Simon P. Circulating cell-free DNA: an up-coming molecular marker in exercise physiology. Sports Med. 2012 Jul; 42 (7): 565–86.
  64. Marcos V, Zhou-Suckow Z, Önder Yildirim A, Bohla A, Hector A, Vitkov L et al. Free DNA in cystic fibrosis airway fluids correlates with airflow obstruction. Mediators Inflamm. 2015; 2015: 408935.
  65. Hardy T, Zeybel M, Day CP, Dipper C, Masson S, McPherson S et al. Plasma DNA methylation: a potential biomarker for stratification of liver fibrosis in non-alcoholic fatty liver disease. Gut. 2017 Jul; 66 (7): 1321–8.