Methyl-binding domain protein-based DNA isolation from human blood serum combines DNA analyses and serum-autoantibody testing

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• 作者：Matthias Wielscher (1)
  Walter Pulverer (1)
  Johannes Peham (1)
  Manuela Hofner (1)
  Christine F Rappaport (2)
  Christian Singer (2)
  Christof Jungbauer (3)
  Christa N?hammer (1)
  Andreas Weinh?usel (1)
  
• 刊名：BMC Clinical Pathology
• 出版年：2011
• 出版时间：December 2011
• 年：2011
• 卷：11
• 期：1
• 全文大小：276KB
• 参考文献：1. Lo YM, Chiu RW: Next-generation sequencing of plasma/serum DNA: an emerging research and molecular diagnostic tool. / Clin Chem 2009, 55:607-08. CrossRef
  2. Dobrzycka B, Terlikowski SJ, Mazurek A, Kowalczuk O, Niklinska W, Chyczewski L, Kulikowski M: Circulating free DNA, p53 antibody and mutations of KRAS gene in endometrial cancer. / Int J Cancer 2009.
  3. Fleischhacker M, Schmidt B: Circulating nucleic acids (CNAs) and cancer--a survey. / Biochim Biophys Acta 2007, 1775:181-32.
  4. Anker P, Mulcahy H, Chen XQ, Stroun M: Detection of circulating tumour DNA in the blood (plasma/serum) of cancer patients. / Cancer Metastasis Rev 1999, 18:65-3. CrossRef
  5. Wang BG, Huang HY, Chen YC, Bristow RE, Kassauei K, Cheng CC, Roden R, Sokoll LJ, Chan DW, Shih I: Increased plasma DNA integrity in cancer patients. / Cancer Res 2003, 63:3966-968.
  6. Elrick MM, Walgren JL, Mitchell MD, Thompson DC: Proteomics: recent applications and new technologies. / Basic Clin Pharmacol Toxicol 2006, 98:432-41. CrossRef
  7. Anker P, Mulcahy H, Stroun M: Circulating nucleic acids in plasma and serum as a noninvasive investigation for cancer: time for large-scale clinical studies? / Int J Cancer 2003, 103:149-52. CrossRef
  8. Schaub NP, Jones KJ, Nyalwidhe JO, Cazares LH, Karbassi ID, Semmes OJ, Feliberti EC, Perry RR, Drake RR: Serum proteomic biomarker discovery reflective of stage and obesity in breast cancer patients. / J Am Coll Surg 2009, 208:970-78. CrossRef
  9. Kijanka G, Murphy D: Protein arrays as tools for serum autoantibody marker discovery in cancer. / J Proteomics 2009, 72:936-44. CrossRef
  10. Anderson KS, Wong J, Vitonis A, Crum CP, Sluss PM, Labaer J, Cramer D: p53 autoantibodies as potential detection and prognostic biomarkers in serous ovarian cancer. / Cancer Epidemiol Biomarkers Prev 2010, 19:859-68. CrossRef
  11. Wu TL, Zhang D, Chia JH, Tsao KH, Sun CF, Wu JT: Cell-free DNA: measurement in various carcinomas and establishment of normal reference range. / Clin Chim Acta 2002, 321:77-7. CrossRef
  12. Seefeld M, El TS, Fan AX, Hahn S, Holzgreve W, Zhong XY: Parallel assessment of circulatory cell-free DNA by PCR and nucleosomes by ELISA in breast tumors. / Int J Biol Markers 2008, 23:69-3.
  13. Lewis JD, Meehan RR, Henzel WJ, Maurer-Fogy I, Jeppesen P, Klein F, Bird A: Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. / Cell 1992, 69:905-14. CrossRef
  14. Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP: Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. / Nat Genet 1998, 19:187-91. CrossRef
  15. Weitzel JM, Buhrmester H, Stratling WH: Chicken MAR-binding protein ARBP is homologous to rat methyl-CpG-binding protein MeCP2. / Mol Cell Biol 1997, 17:5656-666.
  16. Klose RJ, Sarraf SA, Schmiedeberg L, McDermott SM, Stancheva I, Bird AP: DNA binding selectivity of MeCP2 due to a requirement for A/T sequences adjacent to methyl-CpG. / Mol Cell 2005, 19:667-78. CrossRef
  17. Cross SH, Charlton JA, Nan X, Bird AP: Purification of CpG islands using a methylated DNA binding column. / Nat Genet 1994, 6:236-44. CrossRef
  18. Shiraishi M, Chuu YH, Sekiya T: Isolation of DNA fragments associated with methylated CpG islands in human adenocarcinomas of the lung using a methylated DNA binding column and denaturing gradient gel electrophoresis. / Proc Natl Acad Sci USA 1999, 96:2913-918. CrossRef
  19. Serre D, Lee BH, Ting AH: MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. / Nucleic Acids Res 2010, 38:391-99. CrossRef
  20. Zou H, Harrington J, Rego RL, Ahlquist DA: A novel method to capture methylated human DNA from stool: implications for colorectal cancer screening. / Clin Chem 2007, 53:1646-651. CrossRef
  21. Yu Y, Blair S, Gillespie D, Jensen R, Myszka D, Badran AH, Ghosh I, Chagovetz A: Direct DNA methylation profiling using methyl binding domain proteins. / Anal Chem 2010, 82:5012-019. CrossRef
  22. Yegnasubramanian S, Lin X, Haffner MC, DeMarzo AM, Nelson WG: Combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes (COMPARE-MS) for the rapid, sensitive and quantitative detection of DNA methylation. / Nucleic Acids Res 2006, 34:e19. CrossRef
  23. Zanetti-Dallenbach R, Wight E, Fan AX, Lapaire O, Hahn S, Holzgreve W, Zhong XY: Positive correlation of cell-free DNA in plasma/serum in patients with malignant and benign breast disease. / Anticancer Res 2008, 28:921-25.
  24. Cross SH, Charlton JA, Nan X, Bird AP: Purification of CpG islands using a methylated DNA binding column. / Nat Genet 1994, 6:236-44. CrossRef
  25. Muller HM, Widschwendter A, Fiegl H, Ivarsson L, Goebel G, Perkmann E, Marth C, Widschwendter M: DNA methylation in serum of breast cancer patients: an independent prognostic marker. / Cancer Res 2003, 63:7641-645.
  26. Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y: Analysis of Gene Expression Data Using BRB-Array Tools. / Cancer Inform 2007, 3:11-7.
  27. Weinhaeusel A, Thiele S, Hofner M, Hiort O, Noehammer C: PCR-based analysis of differentially methylated regions of GNAS enables convenient diagnostic testing of pseudohypoparathyroidism type Ib. / Clin Chem 2008, 54:1537-545. CrossRef
  28. Zhong XY, Hahn S, Kiefer V, Holzgreve W: Is the quantity of circulatory cell-free DNA in human plasma and serum samples associated with gender, age and frequency of blood donations? / Ann Hematol 2007, 86:139-43. CrossRef
  29. Gahan PB, Swaminathan R: Circulating nucleic acids in plasma and serum. Recent developments. / Ann N Y Acad Sci 2008, 1137:1-. CrossRef
  30. Nygaard V, Hovig E: Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling. / Nucleic Acids Res 2006, 34:996-014. CrossRef
  31. Ho KL, McNae IW, Schmiedeberg L, Klose RJ, Bird AP, Walkinshaw MD: MeCP2 binding to DNA depends upon hydration at methyl-CpG. / Mol Cell 2008, 29:525-31. CrossRef
  32. Jang JS, Lee SJ, Choi JE, Cha SI, Lee EB, Park TI, Kim CH, Lee WK, Kam S, Choi JY, Kang YM, Park RW, Kim IS, Cho YL, Jung TH, Han SB, Park JY: Methyl-CpG binding domain 1 gene polymorphisms and risk of primary lung cancer. / Cancer Epidemiol Biomarkers Prev 2005, 14:2474-480. CrossRef
  33. Holdenrieder S, Stieber P, Chan LY, Geiger S, Kremer A, Nagel D, Lo YM: Cell-free DNA in serum and plasma: comparison of ELISA and quantitative PCR. / Clin Chem 2005, 51:1544-546. CrossRef
  34. Andriani F, Conte D, Mastrangelo T, Leon M, Ratcliffe C, Roz L, Pelosi G, Goldstraw P, Sozzi G, Pastorino U: Detecting lung cancer in plasma with the use of multiple genetic markers. / Int J Cancer 2004, 108:91-6. CrossRef
  35. Kohler C, Radpour R, Barekati Z, Asadollahi R, Bitzer J, Wight E, Burki N, Diesch C, Holzgreve W, Zhong XY: Levels of plasma circulating cell free nuclear and mitochondrial DNA as potential biomarkers for breast tumors. / Mol Cancer 2009, 8:105. CrossRef
  36. Van dA, Elst HJ, Van Laere SJ, Maes H, Huget P, van DP, Van Marck EA, Vermeulen PB, Dirix LY: The presence of circulating total DNA and methylated genes is associated with circulating tumour cells in blood from breast cancer patients. / Br J Cancer 2009, 100:1277-286. CrossRef
  37. Tokuhisa Y, Iizuka N, Sakaida I, Moribe T, Fujita N, Miura T, Tamatsukuri S, Ishitsuka H, Uchida K, Terai S, Sakamoto K, Tamesa T, Oka M: Circulating cell-free DNA as a predictive marker for distant metastasis of hepatitis C virus-related hepatocellular carcinoma. / Br J Cancer 2007, 97:1399-403. CrossRef
  38. Ionov Y: A high throughput method for identifying personalized tumor-associated antigens. / Oncotarget 2010, 1:148-55.
  39. Ludwig N, Keller A, Comtesse N, Rheinheimer S, Pallasch C, Fischer U, Fassbender K, Steudel WI, Lenhof HP, Meese E: Pattern of serum autoantibodies allows accurate distinction between a tumor and pathologies of the same organ. / Clin Cancer Res 2008, 14:4767-774. CrossRef
  40. The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1472-6890/11/11/prepub
  
• 作者单位：Matthias Wielscher (1)
  Walter Pulverer (1)
  Johannes Peham (1)
  Manuela Hofner (1)
  Christine F Rappaport (2)
  Christian Singer (2)
  Christof Jungbauer (3)
  Christa N?hammer (1)
  Andreas Weinh?usel (1)
  
  1. Molecular Medicine, Austrian Institute of Technology, Muthgasse 11, 1190, Vienna, Austria
  2. Department of Obstetrics and Gynecology, Medical University of Vienna, W?hringer Grütel 18 - 20, 1090, Vienna, Austria
  3. Blood Donation Center for Vienna, Lower Austria and Burgenland, Austrian Red Cross, Wiedner Hauptstra?e 32, 1040, Vienna, Austria
  

文摘

Background Circulating cell free DNA in serum as well as serum-autoantibodies and the serum proteome have great potential to contribute to early cancer diagnostics via non invasive blood tests. However, most DNA preparation protocols destroy the protein fraction and therefore do not allow subsequent protein analyses. In this study a novel approach based on methyl binding domain protein (MBD) is described to overcome the technical difficulties of combining DNA and protein analysis out of one single serum sample. Methods Serum or plasma samples from 98 control individuals and 54 breast cancer patients were evaluated upon silica membrane- or MBD affinity-based DNA isolation via qPCR targeting potential DNA methylation markers as well as by protein-microarrays for tumor-autoantibody testing. Results In control individuals, an average DNA level of 22.8 ± 25.7 ng/ml was detected applying the silica membrane based protocol and 8.5 ± 7.5 ng/ml using the MBD-approach, both values strongly dependent on the serum sample preparation methods used. In contrast to malignant and benign tumor serum samples, cell free DNA concentrations were significantly elevated in sera of metastasizing breast cancer patients. Technical evaluation revealed that serum upon MBD-based DNA isolation is suitable for protein-array analyses when data are consistent to untreated serum samples. Conclusion MBD affinity purification allows DNA isolations under native conditions retaining the protein function, thus for example enabling combined analyses of DNA methylation and autoantigene-profiles from the same serum sample and thereby improving minimal invasive diagnostics.