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Extraction of cell-free DNA from urine, using polylysine-coated silica particles

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Abstract

DNA analysis is used for a variety of purposes, including disease diagnosis and DNA profiling; this involves extracting DNA from living organisms. In this study, we prepared polycationic silica particles to extract DNA that has the negatively charged phosphate backbone from solution. The coated particles were prepared by mixing conventional silica gel particles and poly-Lys; these particles could efficiently extract 1.3 μg of cell-free DNA from 50 mL of (male) urine. It is expected that these easily prepared particles (just a mixture of two commercially available chemicals) can be used as a noninvasive diagnostic tool for genetic disorders such as cancer, diabetes, and hypertension.

Effective extraction method of cfDNA from urine was developed that used commercially available silica gel particles and poly-Lys.

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References

  1. Toyo'oka T. Diagnostic approach to disease using non-invasive samples based on derivatization and LC-ESI-MS/MS. Biol Pharm Bull. 2016;39:1397–411.

    Article  Google Scholar 

  2. Adamczyk B, Tharmalingam T, Rudd PM. Glycans as cancer biomarkers. Biochim Biophys Acta-General Subjects. 2012;1820:1347–53.

    Article  CAS  Google Scholar 

  3. Baranova A, Lal P, Birerdinc A, Younossi ZM. Non-invasive markers for hepatic fibrosis. BMC Gastroenterol. 2011;11:91.

    Article  Google Scholar 

  4. Link A, Balaguer F, Shen Y, Nagasaka T, Lozano JJ, Boland CR, Goel A. Fecal microRNAs as novel biomarkers for colon cancer screening. Cancer Epidemiol Biomark Prev. 2010;19:1766–74.

    Article  CAS  Google Scholar 

  5. Kim M, Long TI, Arakawa K, Wang RW, Yu MC, Laird PW. DNA methylation as a biomarker for cardiovascular disease risk. PLoS One. 2010;5:e9692.

    Article  Google Scholar 

  6. Breitbach S, Tug S, Helmig S, Zahn D, Kubiak T, Michal M, Gori T, Ehlert T, Beiter T, Simon P. Direct quantification of cell-free, circulating DNA from unpurified plasma. PLoS One. 2014;9:e87838.

    Article  Google Scholar 

  7. Zhang LH, Dang FQ, Kaji N, Baba Y. Fast extraction, amplification and analysis of genes from human blood. J Chromatogr A. 2006;1106(1–2):175–80.

    Article  CAS  Google Scholar 

  8. Russell E, Koren G, Rieder M, Van Uum S. Hair cortisol as a biological marker of chronic stress: current status, future directions and unanswered questions. Psychoneuroendocrinology. 2012;37:589–601.

    Article  CAS  Google Scholar 

  9. Tsutsui H, Maeda T, Min JZ, Inagaki S, Higashi T, Kagawa Y, Toyo'oka T. Biomarker discovery in biological specimens (plasma, hair, liver and kidney) of diabetic mice based upon metabolite profiling using ultra-performance liquid chromatography with electrospray ionization time-of-flight mass spectrometry. Clin Chim Acta. 2011;412:861–72.

    Article  CAS  Google Scholar 

  10. Decramer S, de Peredo AG, Breuil B, Mischak H, Monsarrat B, Bascands JL, Schanstra JP. Urine in clinical proteomics. Mol Cell Proteomics. 2008;7:1850–62.

    Article  CAS  Google Scholar 

  11. Wu LL, Chiou CC, Chang PY, Wu JT. Urinary 8-OHdG: a marker of oxidative stress to DNA and a risk factor for cancer, atherosclerosis and diabetics. Clin Chim Acta. 2004;339:1–9.

    Article  CAS  Google Scholar 

  12. Harpole M, Davis J, Espina V. Current state of the art for enhancing urine biomarker discovery. Expert Rev Proteomics. 2016;13:609–26.

    Article  CAS  Google Scholar 

  13. Su YH, Wang MJ, Brenner DE, Ng A, Melkonyan H, Umansky S, Syngal S, Block TM. Human urine contains small, 150 to 250 nucleotide-sized, soluble DNA derived from the circulation and may be useful in the detection of colorectal cancer. J Mol Diagn. 2004;6:101–7.

    Article  CAS  Google Scholar 

  14. Botezatu I, Serdyuk O, Potapova G, Shelepov V, Alechina R, Molyaka Y, Anan'ev V, Bazin I, Garin A, Narimanov M, Knysh V, Melkonyan H, Umansky S, Lichtenstein A. Genetic analysis of DNA excreted in urine: a new approach for detecting specific genomic DNA sequences from cells dying in an organism. Clin Chem. 2000;46:1078–84.

    CAS  Google Scholar 

  15. Su YH, Wang MJ, Block TM, Landt O, Botezatu I, Serdyuk O, Lichtenstein A, Melkonyan H, Tomei LD, Umansky S. Transrenal DNA as a diagnostic tool: important technical notes. Ann N Y Acad Sci. 2004;1022:81–9.

    Article  CAS  Google Scholar 

  16. Bergallo M, Costa C, Gribaudo G, Tarallo S, Baro S, Negro Ponzi A, Cavallo R. Evaluation of six methods for extraction and purification of viral DNA from urine and serum samples. New Microbiol. 2006;29:111–9.

    CAS  Google Scholar 

  17. Bryzgunova OE, Skvortsova TE, Kolesnikova EV, Starikov AV, Rykova EY, Vlassov VV, Laktionov PP. Isolation and comparative study of cell-free nucleic acids from human urine. Ann N Y Acad Sci. 2006;1075:334–40.

    Article  CAS  Google Scholar 

  18. van der Hel OL, van der Luijt RB, Bueno de Mesquita HB, van Noord PA, Slothouber B, Roest M, van der Schouw YT, Grobbee DE, Pearson PL, Peeters PH. Quality and quantity of DNA isolated from frozen urine in population-based research. Anal Biochem. 2002;304:206–11.

    Article  Google Scholar 

  19. Kaji N, Baba Y. Nanobiodevice-based single biomolecule analysis, single-cell analysis, and in vivo imaging for cancer diagnosis, cancer theranostics, and iPS cell-based regenerative medicine. Anal Sci. 2014;30(9):859–64.

    Article  CAS  Google Scholar 

  20. Benesova L, Belsanova B, Suchanek S, Kopeckova M, Minarikova P, Lipska L, Levy M, Visokai V, Zavoral M, Minarik M. Mutation-based detection and monitoring of cell-free tumor DNA in peripheral blood of cancer patients. Anal Biochem. 2013;433:227–34.

    Article  CAS  Google Scholar 

  21. Breadmore MC, Wolfe KA, Arcibal IG, Leung WK, Dickson D, Giordano BC, Power ME, Ferrance JP, Feldman SH, Norris PM, Landers JP. Microchip-based purification of DNA from biological samples. Anal Chem. 2003;75:1880–6.

    Article  CAS  Google Scholar 

  22. Boom R, Spl CJA, Salimans MMM, Jansen CL, Wertheimvandillen PME, Vandernoordaa J. Rapid and simple method for purification of nucleic acids. J Clin Microbiol. 1990;28:495–503.

    CAS  Google Scholar 

  23. Boom R, Sol C, Beld M, Weel J, Goudsmit J, Dillen Wertheim-van P. Improved silica-guanidiniumthiocyanate DNA isolation procedure based on selective binding of bovine alpha-casein to silica particles. J Clin Microbiol. 1999;37:615–9.

    CAS  Google Scholar 

  24. Prodelalova J, Rittich B, Spanova A, Petrova K, Benes MJ. Isolation of genomic DNA using magnetic cobalt ferrite and silica particles. J Chromatogr A. 2004;1056:43–8.

    Article  CAS  Google Scholar 

  25. Shan Z, Zhou Z, Chen H, Zhang Z, Zhou Y, Wen A, Oakes KD, Servos MR. PCR-ready human DNA extraction from urine samples using magnetic nanoparticles. J Chromatogr B. 2011;15(881–882):63–8.

    Google Scholar 

  26. Shima S, Sakai H. Polylysine produced by Streptomyces. Agric Biol Chem. 1977;41:1807–9.

    CAS  Google Scholar 

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Acknowledgements

We acknowledge Profs. T. Hashimoto and S. Ehata (University of Tokyo) for their kind advice on DNA analysis. P.R. expresses thanks for the support from the EPFL-U. Tokyo Scientific and Educational Exchange Program. This work was supported by grants (Kakenhi) from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan and JSPS Core-to-Core Program, A. Advanced Research Networks.

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Authors and Affiliations

  1. Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

    Sho Takano, Takaki Amamoto, Takashi Funatsu & Masaru Kato

  2. Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, 874-0838, Japan

    Qingjiang Hu & Koshi Mimori

  3. Institute of Bioengineering, EPFL School of Life Sciences and School of Engineering, Station 15, 1015, Lausanne, Switzerland

    Paulo Refinetti

Authors
  1. Sho Takano
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  2. Qingjiang Hu
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  3. Takaki Amamoto
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  4. Paulo Refinetti
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  5. Koshi Mimori
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  6. Takashi Funatsu
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  7. Masaru Kato
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Correspondence to Masaru Kato.

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All clinical studies involving human urine samples were conducted in adherence to the procedure approved by the Human Ethics Committee of the School of Pharmaceutical Sciences in University of Tokyo, and informed consent was received from the volunteers.

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The authors declare that they have no conflicts of interest.

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Takano, S., Hu, Q., Amamoto, T. et al. Extraction of cell-free DNA from urine, using polylysine-coated silica particles. Anal Bioanal Chem 409, 4021–4025 (2017). https://doi.org/10.1007/s00216-017-0345-3

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  • DOI: https://doi.org/10.1007/s00216-017-0345-3

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