Skip to main content

Advertisement

SpringerLink
Log in

Extraction of urinary cell-free DNA by using triamine-modified silica particles for liquid biopsy

  • Research Paper
  • Published:
Analytical and Bioanalytical Chemistry Aims and scope Submit manuscript

Abstract

The presence of approximately 200-bp cell-free DNA (cfDNA) in the urine has attracted attention as a biomarker for liquid biopsy. However, it is currently useful only for diagnoses of cancers in which a large amount of cfDNA is excreted in the urine. Therefore, the development of an efficient method for extracting cfDNA existing in small amounts in the urine is essential for diagnosing many other diseases. We examined the effect of particle size, small pore size (surface area), and surface modification of porous silica particles on the efficiency of DNA extraction. Our observations suggested that cfDNA could be captured by tertiary amine–modified particles and then removed from the particles by repeatedly washing with sodium bicarbonate (pH 11). Using this method with 30 mg of triamine-modified particles, we succeeded in extracting a few hundred nanograms of cfDNA from 15 mL urine. Furthermore, we could detect ~ 67 fg/mL caries DNA (211 bp) in 15 mL urine sample, suggesting that this method may be suitable for the extraction of genetic biomarkers for cfDNA-based liquid biopsy.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

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  CAS  Google Scholar 

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

    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, et al. Fecal microRNAs as novel biomarkers for colon cancer screening. Cancer Epidemiol Biomark Prev. 2010;19:1766–74.

    Article  CAS  Google Scholar 

  5. Su YH, Wang MJ, Brenner DE, Ng A, Melkonyan H, Umansky S, et al. 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 

  6. 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 

  7. Botezatu I, Serdyuk O, Potapova G, Shelepov V, Alechina R, Molyaka Y, et al. 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.

    Article  CAS  Google Scholar 

  8. Su YH, Wang MJ, Block TM, Landt O, Botezatu I, Serdyuk O, et al. Detection of mutated K-ras DNA in urine, plasma, and serum of patients with colorectal carcinoma or adenomatous polyps. Ann N Y Acad Sci. 2008;1137:197–206.

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  10. 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 

  11. 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 

  12. Bali LE, Diman A, Bernard A, Roosens NHC, De Keersmaecker SCJ. Comparative study of seven commercial kits for human DNA extraction from urine samples suitable for DNA biomarker-based public health studies. J Biomol Tech. 2014;25:96–110.

    PubMed  PubMed Central  Google Scholar 

  13. Lee EY, Lee E-J, Yoon H, Lee DH, Kim KH. Comparison of four commercial kits for isolation of urinary cell-free DNA and sample storage confitions. Diagnostics. 2020;10:234.

    Article  Google Scholar 

  14. Mohammed RH, Mesalhy O, Elsayed ML, Hou S, Su M, Chow LC. Physical properties and adsorption kinetics of silica-gel/water for adsorption chillers. Appl Therm Eng. 2018;137:368–76.

    Article  CAS  Google Scholar 

  15. Gong Y, Lei Y, Chen X, Song H, Liu R. A novel silica aerogel microspheres loaded with ammonium persulfate gel breaker for mid-deep reservoirs. J Sol-Gel Sci Technol. 2018;88:105–13.

    Article  CAS  Google Scholar 

  16. Jiang N, Shang R, Heijman SGJ, Rietveld LC. High-silica zeolites for adsorption of organic micro-pollutants in water treatment: a review. Water Res. 2018;144:145–61.

    Article  CAS  Google Scholar 

  17. Das RK, Pramanik A, Majhi M, Mohapatra S. Magnetic mesoporous silica gated with doped carbon dot for site-specific drug delivery, fluorescence, and MR imaging. Langmuir. 2018;34:5253–62.

    Article  CAS  Google Scholar 

  18. Takano S, Hu Q, Amamoto T, Refinetti P, Mimori K, Funatsu T, et al. Extraction of cell-free DNA from urine using polycationic polylysine-coated silica particles. Anal Bioanal Chem. 2017;409:4021–5.

    Article  CAS  Google Scholar 

  19. Karasawa K, Arakawa H, Igarashi T, Goto N, Maeda M. Detection of cariogenic bacterial genes by microchip electrophoresis. J Chromatogr B. 2004;810:41–7.

    Article  CAS  Google Scholar 

  20. Solberg SM, Landry CC. Adsorption of DNA into mesoporous silica. J Phys Chem B. 2006;110:15261–8.

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We thank the Microtrac BEL Corp. for the zeta-potential measurement using Stabino.

Funding

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.

Author information

Authors and Affiliations

  1. Division of Bioanalytical Chemistry, School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan

    Masaru Kato, Yumi Fujita, Takuya Iizuka, Kyohei Nozaki, Yoshihiro Sano, Shuhei Murayama & Koji Karasawa

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

    Sho Takano & Takashi Funatsu

Authors
  1. Masaru Kato
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yumi Fujita
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Takuya Iizuka
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Kyohei Nozaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Sho Takano
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Takashi Funatsu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yoshihiro Sano
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Shuhei Murayama
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Koji Karasawa
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Masaru Kato.

Ethics declarations

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

Conflict of interest

The authors declare that they have no conflicts of interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

ESM 1

(PDF 82 kb).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kato, M., Fujita, Y., Iizuka, T. et al. Extraction of urinary cell-free DNA by using triamine-modified silica particles for liquid biopsy. Anal Bioanal Chem 412, 5647–5652 (2020). https://doi.org/10.1007/s00216-020-02784-5

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00216-020-02784-5

Keywords

Search

Navigation