Research Article
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Circulating tumor DNA (ctDNA) Detection via electrochemical Biosensing Tools

Year 2024, , 104 - 115, 21.06.2024

Sonya Sahin , Nimet Yıldırım Tirgil

https://doi.org/10.51354/mjen.1375211

Abstract

Cancer is characterized by the presence of mutated alleles in DNA, leading to the formation of tumors. A delayed diagnosis of this condition can result in fatal outcomes, making it a significant global cause of mortality. WHO has emphasized that early detection could significantly increase the chances of successful treatment and recovery. Traditional cancer diagnosis relies on invasive tissue biopsies, which pose risks to both patient’s and healthcare professionals due to the use of formaldehyde, a known carcinogenic agent, for specimen preservation. In recent times, liquid biopsies have emerged as a promising alternative, particularly for the analysis of circulating tumor DNA (ctDNA), a fraction of which originates from tumor cells and circulates in the bloodstream. However, conventional molecular genetic tests for ctDNA analysis are often costly and time-consuming. Advancements in technology and the field of nanoscience offer the potential to develop cost-effective, rapid, highly sensitive, and selective diagnostic tools. Among these, biosensors stand out as a promising option. In this article, we delve into the quantification of ctDNA in plasma, discuss amplification techniques for ctDNA, and explore the development of electrochemical-based biosensors tailored for ctDNA detection. Finally, we highlight recent studies and innovations in the field of ctDNA detection.

Keywords

Liquid biopsies Circulating tumor DNA ctDNA Amplification techniques Biosensors Electrochemical detection

References

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  • [8]. A. Kustanovich, R. Schwartz, T. Peretz, and A. Grinshpun, “Life and death of circulating cell-free DNA,” Cancer Biology and Therapy, vol. 20, no. 8. Taylor and Francis Inc., pp. 1057–1067, Aug. 03, 2019. doi: 10.1080/15384047.2019.1598759.
  • [9]. Z. Qin, V. A. Ljubimov, C. Zhou, Y. Tong, and J. Liang, “Cell-free circulating tumor DNA in cancer,” Chinese Journal of Cancer, vol. 35, no. 5. Landes Bioscience, May 01, 2016. doi: 10.1186/s40880-016-0092-4.
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  • [13]. L. S. Pessoa, M. Heringer, and V. P. Ferrer, “ctDNA as a cancer biomarker: A broad overview,” Critical Reviews in Oncology/Hematology, vol. 155. Elsevier Ireland Ltd, Nov. 01, 2020. doi: 10.1016/j.critrevonc.2020.103109.
  • [14]. K. Wang, Z. Peng, X. Lin, W. Nian, X. Zheng, and J. Wu, “Electrochemical Biosensors for Circulating Tumor DNA Detection,” Biosensors (Basel), vol. 12, no. 8, Aug. 2022, doi: 10.3390/bios12080649.
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  • [16]. C. Alix-Panabières, H. Schwarzenbach, and K. Pantel, “Circulating tumor cells and circulating tumor DNA,” Annual Review of Medicine, vol. 63. pp. 199–215, 2012. doi: 10.1146/annurev-med-062310-094219.
  • [17]. S. Campuzano, P. Yáñez-Sedeño, and J. M. Pingarrón, “Electrochemical genosensing of circulating biomarkers,” Sensors (Switzerland), vol. 17, no. 4, Apr. 2017, doi: 10.3390/s17040866.
  • [18]. D. Saerens, L. Huang, K. Bonroy, and S. Muyldermans, “Antibody fragments as probe in biosensor development,” Sensors, vol. 8, no. 8. pp. 4669–4686, Aug. 2008. doi: 10.3390/s8084669.
  • [19]. K. Wang, Z. Peng, X. Lin, W. Nian, X. Zheng, and J. Wu, “Electrochemical Biosensors for Circulating Tumor DNA Detection,” Biosensors (Basel), vol. 12, no. 8, Aug. 2022, doi: 10.3390/bios12080649.
  • [20]. C. Whalley et al., “Ultra-low DNA input into whole genome methylation assays and detection of oncogenic methylation and copy number variants in circulating tumour DNA,” Epigenomes, vol. 5, no. 1, p. 6, 2021.
  • [21]. F. Khatami et al., “Circulating ctDNA methylation quantification of two DNA methyl transferases in papillary thyroid carcinoma,” J Cell Biochem, vol. 120, no. 10, pp. 17422–17437, 2019.
  • [22]. E. J. H. Wee, M. J. A. Shiddiky, M. A. Brown, and M. Trau, “eLCR: Electrochemical detection of single DNA base changes viaLigase Chain Reaction,” Chemical Communications, vol. 48, no. 98, pp. 12014–12016, Nov. 2012, doi: 10.1039/c2cc35841g.
  • [23]. K. Wang, Z. Peng, X. Lin, W. Nian, X. Zheng, and J. Wu, “Electrochemical Biosensors for Circulating Tumor DNA Detection,” Biosensors (Basel), vol. 12, no. 8, Aug. 2022, doi: 10.3390/bios12080649.
  • [24]. V. Manohar Raju et al., “A novel disposable electrochemical DNA biosensor for the rapid detection of Bacillus thuringiensis,” Microchemical Journal, vol. 159, Dec. 2020, doi: 10.1016/j.microc.2020.105434.
  • [25]. M. N. Islam and R. B. Channon, “Electrochemical sensors,” in Bioengineering Innovative Solutions for Cancer, Elsevier, 2019, pp. 47–71. doi: 10.1016/B978-0-12-813886-1.00004-8.
  • [26]. E. Cano, D. Lafuente, and D. M. Bastidas, “Use of EIS for the evaluation of the protective properties of coatings for metallic cultural heritage: A review,” Journal of Solid State Electrochemistry, vol. 14, no. 3. pp. 381– 391, 2010. doi: 10.1007/s10008-009-0902-6.
  • [27]. Q. Gong, H. Yang, Y. Dong, and W. Zhang, “A sensitive impedimetric DNA biosensor for the determination of the HIV gene based on electrochemically reduced graphene oxide,” Analytical Methods, vol. 7, no. 6, pp. 2554–2562, Mar. 2015, doi: 10.1039/c5ay00111k.
  • [28]. Z. O. Uygun, L. Yeniay, and F. Gı̇rgı̇n Sağın, “CRISPR-dCas9 powered impedimetric biosensor for label- free detection of circulating tumor DNAs,” Anal Chim Acta, vol. 1121, pp. 35–41, Jul. 2020, doi: 10.1016/j.aca.2020.04.009.
  • [29]. K. Chen, H. Zhao, Z. Wang, and M. Lan, “A novel signal amplification label based on AuPt alloy nanoparticles supported by high-active carbon for the electrochemical detection of circulating tumor DNA,” Anal Chim Acta, vol. 1169, Jul. 2021, doi: 10.1016/j.aca.2021.338628.
  • [30]. Y. F. Huang et al., “A novel nest hybridization chain reaction based electrochemical assay for sensitive detection of circulating tumor DNA,” Anal Chim Acta, vol. 1107, pp. 40–47, Apr. 2020, doi: 10.1016/j.aca.2020.02.006.
  • [31]. H. F. Wang et al., “A versatile label-free electrochemical biosensor for circulating tumor DNA based on dual enzyme assisted multiple amplification strategy,” Biosens Bioelectron, vol. 122, pp. 224–230, Dec. 2018, doi: 10.1016/j.bios.2018.09.028.
  • [32]. H. F. Wang et al., “A versatile label-free electrochemical biosensor for circulating tumor DNA based on dual enzyme assisted multiple amplification strategy,” Biosens Bioelectron, vol. 122, pp. 224–230, Dec. 2018, doi: 10.1016/j.bios.2018.09.028.
  • [33]. D. Chen, Y. Wu, S. Hoque, R. D. Tilley, and J. J. Gooding, “Rapid and ultrasensitive electrochemical
  • detection of circulating tumor DNA by hybridization on the network of gold-coated magnetic nanoparticles,” Chem Sci, vol. 12, no. 14, pp. 5196–5201, Apr. 2021, doi: 10.1039/d1sc01044a.
  • [34]. R. Sebuyoya et al., “Electrochemical DNA biosensor coupled to LAMP reaction for early diagnostics of cervical precancerous lesions,” Biosens Bioelectron X, vol. 12, Dec. 2022, doi: 10.1016/j.biosx.2022.100224.
  • [35]. H. Zhao et al., “A novel sandwich-type electrochemical biosensor enabling sensitive detection of circulating tumor DNA,” Microchemical Journal, vol. 171, Dec. 2021, doi: 10.1016/j.microc.2021.106783.

Year 2024, , 104 - 115, 21.06.2024

Sonya Sahin , Nimet Yıldırım Tirgil

https://doi.org/10.51354/mjen.1375211

Abstract

References

  • [1]. M. N. Islam and R. B. Channon, “Electrochemical sensors,” in Bioengineering Innovative Solutions for Cancer, Elsevier, 2019, pp. 47–71. doi: 10.1016/B978-0-12-813886-1.00004-8.
  • [2]. J. Ferlay et al., “Cancer statistics for the year 2020: An overview,” Int J Cancer, vol. 149, no. 4, pp. 778–789, Aug. 2021, doi: 10.1002/ijc.33588.
  • [3]. F. Diehl et al., “Circulating mutant DNA to assess tumor dynamics,” Nat Med, vol. 14, no. 9, pp. 985–990, Sep. 2008, doi: 10.1038/nm.1789.
  • [4]. X. Li et al., “Liquid biopsy of circulating tumor DNA and biosensor applications,” Biosensors and Bioelectronics, vol. 126. Elsevier Ltd, pp. 596–607, Feb. 01, 2019. doi: 10.1016/j.bios.2018.11.037.
  • [5]. D. W. Cescon, S. V. Bratman, S. M. Chan, and L. L. Siu, “Circulating tumor DNA and liquid biopsy in oncology,” Nature cancer, vol. 1, no. 3. NLM (Medline), pp. 276–290, Mar. 01, 2020. doi: 10.1038/s43018-020- 0043-5.
  • [6]. J. Das and S. O. Kelley, “High-Performance Nucleic Acid Sensors for Liquid Biopsy Applications,” Angewandte Chemie - International Edition, vol. 59, no. 7. Wiley-VCH Verlag, pp. 2554–2564, Feb. 10, 2020. doi: 10.1002/anie.201905005.
  • [7]. H. Schwarzenbach, D. S. B. Hoon, and K. Pantel, “Cell-free nucleic acids as biomarkers in cancer patients,” Nature Reviews Cancer, vol. 11, no. 6. pp. 426–437, Jun. 2011. doi: 10.1038/nrc3066.
  • [8]. A. Kustanovich, R. Schwartz, T. Peretz, and A. Grinshpun, “Life and death of circulating cell-free DNA,” Cancer Biology and Therapy, vol. 20, no. 8. Taylor and Francis Inc., pp. 1057–1067, Aug. 03, 2019. doi: 10.1080/15384047.2019.1598759.
  • [9]. Z. Qin, V. A. Ljubimov, C. Zhou, Y. Tong, and J. Liang, “Cell-free circulating tumor DNA in cancer,” Chinese Journal of Cancer, vol. 35, no. 5. Landes Bioscience, May 01, 2016. doi: 10.1186/s40880-016-0092-4.
  • [10]. X. Wen, H. Pu, Q. Liu, Z. Guo, and D. Luo, “Circulating Tumor DNA—A Novel Biomarker of Tumor Progression and Its Favorable Detection Techniques,” Cancers, vol. 14, no. 24. MDPI, Dec. 01, 2022. doi: 10.3390/cancers14246025.
  • [11]. R. I. Chin et al., “Detection of Solid Tumor Molecular Residual Disease (MRD) Using Circulating Tumor DNA (ctDNA),” Molecular Diagnosis and Therapy. Springer International Publishing, 2019. doi: 10.1007/s40291-019- 00390-5.
  • [12]. M. A. Morales and J. M. Halpern, “Guide to Selecting a Biorecognition Element for Biosensors,” Bioconjug Chem, vol. 29, no. 10, pp. 3231–3239, Oct. 2018, doi: 10.1021/acs.bioconjchem.8b00592.
  • [13]. L. S. Pessoa, M. Heringer, and V. P. Ferrer, “ctDNA as a cancer biomarker: A broad overview,” Critical Reviews in Oncology/Hematology, vol. 155. Elsevier Ireland Ltd, Nov. 01, 2020. doi: 10.1016/j.critrevonc.2020.103109.
  • [14]. K. Wang, Z. Peng, X. Lin, W. Nian, X. Zheng, and J. Wu, “Electrochemical Biosensors for Circulating Tumor DNA Detection,” Biosensors (Basel), vol. 12, no. 8, Aug. 2022, doi: 10.3390/bios12080649.
  • [15]. Y. Krishnan and M. Bathe, “Designer nucleic acids to probe and program the cell,” Trends in Cell Biology, vol. 22, no. 12. pp. 624–633, Dec. 2012. doi: 10.1016/j.tcb.2012.10.001.
  • [16]. C. Alix-Panabières, H. Schwarzenbach, and K. Pantel, “Circulating tumor cells and circulating tumor DNA,” Annual Review of Medicine, vol. 63. pp. 199–215, 2012. doi: 10.1146/annurev-med-062310-094219.
  • [17]. S. Campuzano, P. Yáñez-Sedeño, and J. M. Pingarrón, “Electrochemical genosensing of circulating biomarkers,” Sensors (Switzerland), vol. 17, no. 4, Apr. 2017, doi: 10.3390/s17040866.
  • [18]. D. Saerens, L. Huang, K. Bonroy, and S. Muyldermans, “Antibody fragments as probe in biosensor development,” Sensors, vol. 8, no. 8. pp. 4669–4686, Aug. 2008. doi: 10.3390/s8084669.
  • [19]. K. Wang, Z. Peng, X. Lin, W. Nian, X. Zheng, and J. Wu, “Electrochemical Biosensors for Circulating Tumor DNA Detection,” Biosensors (Basel), vol. 12, no. 8, Aug. 2022, doi: 10.3390/bios12080649.
  • [20]. C. Whalley et al., “Ultra-low DNA input into whole genome methylation assays and detection of oncogenic methylation and copy number variants in circulating tumour DNA,” Epigenomes, vol. 5, no. 1, p. 6, 2021.
  • [21]. F. Khatami et al., “Circulating ctDNA methylation quantification of two DNA methyl transferases in papillary thyroid carcinoma,” J Cell Biochem, vol. 120, no. 10, pp. 17422–17437, 2019.
  • [22]. E. J. H. Wee, M. J. A. Shiddiky, M. A. Brown, and M. Trau, “eLCR: Electrochemical detection of single DNA base changes viaLigase Chain Reaction,” Chemical Communications, vol. 48, no. 98, pp. 12014–12016, Nov. 2012, doi: 10.1039/c2cc35841g.
  • [23]. K. Wang, Z. Peng, X. Lin, W. Nian, X. Zheng, and J. Wu, “Electrochemical Biosensors for Circulating Tumor DNA Detection,” Biosensors (Basel), vol. 12, no. 8, Aug. 2022, doi: 10.3390/bios12080649.
  • [24]. V. Manohar Raju et al., “A novel disposable electrochemical DNA biosensor for the rapid detection of Bacillus thuringiensis,” Microchemical Journal, vol. 159, Dec. 2020, doi: 10.1016/j.microc.2020.105434.
  • [25]. M. N. Islam and R. B. Channon, “Electrochemical sensors,” in Bioengineering Innovative Solutions for Cancer, Elsevier, 2019, pp. 47–71. doi: 10.1016/B978-0-12-813886-1.00004-8.
  • [26]. E. Cano, D. Lafuente, and D. M. Bastidas, “Use of EIS for the evaluation of the protective properties of coatings for metallic cultural heritage: A review,” Journal of Solid State Electrochemistry, vol. 14, no. 3. pp. 381– 391, 2010. doi: 10.1007/s10008-009-0902-6.
  • [27]. Q. Gong, H. Yang, Y. Dong, and W. Zhang, “A sensitive impedimetric DNA biosensor for the determination of the HIV gene based on electrochemically reduced graphene oxide,” Analytical Methods, vol. 7, no. 6, pp. 2554–2562, Mar. 2015, doi: 10.1039/c5ay00111k.
  • [28]. Z. O. Uygun, L. Yeniay, and F. Gı̇rgı̇n Sağın, “CRISPR-dCas9 powered impedimetric biosensor for label- free detection of circulating tumor DNAs,” Anal Chim Acta, vol. 1121, pp. 35–41, Jul. 2020, doi: 10.1016/j.aca.2020.04.009.
  • [29]. K. Chen, H. Zhao, Z. Wang, and M. Lan, “A novel signal amplification label based on AuPt alloy nanoparticles supported by high-active carbon for the electrochemical detection of circulating tumor DNA,” Anal Chim Acta, vol. 1169, Jul. 2021, doi: 10.1016/j.aca.2021.338628.
  • [30]. Y. F. Huang et al., “A novel nest hybridization chain reaction based electrochemical assay for sensitive detection of circulating tumor DNA,” Anal Chim Acta, vol. 1107, pp. 40–47, Apr. 2020, doi: 10.1016/j.aca.2020.02.006.
  • [31]. H. F. Wang et al., “A versatile label-free electrochemical biosensor for circulating tumor DNA based on dual enzyme assisted multiple amplification strategy,” Biosens Bioelectron, vol. 122, pp. 224–230, Dec. 2018, doi: 10.1016/j.bios.2018.09.028.
  • [32]. H. F. Wang et al., “A versatile label-free electrochemical biosensor for circulating tumor DNA based on dual enzyme assisted multiple amplification strategy,” Biosens Bioelectron, vol. 122, pp. 224–230, Dec. 2018, doi: 10.1016/j.bios.2018.09.028.
  • [33]. D. Chen, Y. Wu, S. Hoque, R. D. Tilley, and J. J. Gooding, “Rapid and ultrasensitive electrochemical
  • detection of circulating tumor DNA by hybridization on the network of gold-coated magnetic nanoparticles,” Chem Sci, vol. 12, no. 14, pp. 5196–5201, Apr. 2021, doi: 10.1039/d1sc01044a.
  • [34]. R. Sebuyoya et al., “Electrochemical DNA biosensor coupled to LAMP reaction for early diagnostics of cervical precancerous lesions,” Biosens Bioelectron X, vol. 12, Dec. 2022, doi: 10.1016/j.biosx.2022.100224.
  • [35]. H. Zhao et al., “A novel sandwich-type electrochemical biosensor enabling sensitive detection of circulating tumor DNA,” Microchemical Journal, vol. 171, Dec. 2021, doi: 10.1016/j.microc.2021.106783.
There are 36 citations in total.

Details

Primary Language English
Subjects Biomedical Engineering (Other), Bioengineering (Other)
Journal Section Research Article
Authors

Sonya Sahin 0009-0002-7722-3520

Nimet Yıldırım Tirgil 0000-0002-5973-8830

Publication Date June 21, 2024
Submission Date October 16, 2023
Acceptance Date January 8, 2024
Published in Issue Year 2024

Cite

APA Sahin, S., & Yıldırım Tirgil, N. (2024). Circulating tumor DNA (ctDNA) Detection via electrochemical Biosensing Tools. MANAS Journal of Engineering, 12(1), 104-115. https://doi.org/10.51354/mjen.1375211
AMA Sahin S, Yıldırım Tirgil N. Circulating tumor DNA (ctDNA) Detection via electrochemical Biosensing Tools. MJEN. June 2024;12(1):104-115. doi:10.51354/mjen.1375211
Chicago Sahin, Sonya, and Nimet Yıldırım Tirgil. “Circulating Tumor DNA (ctDNA) Detection via Electrochemical Biosensing Tools”. MANAS Journal of Engineering 12, no. 1 (June 2024): 104-15. https://doi.org/10.51354/mjen.1375211.
EndNote Sahin S, Yıldırım Tirgil N (June 1, 2024) Circulating tumor DNA (ctDNA) Detection via electrochemical Biosensing Tools. MANAS Journal of Engineering 12 1 104–115.
IEEE S. Sahin and N. Yıldırım Tirgil, “Circulating tumor DNA (ctDNA) Detection via electrochemical Biosensing Tools”, MJEN, vol. 12, no. 1, pp. 104–115, 2024, doi: 10.51354/mjen.1375211.
ISNAD Sahin, Sonya - Yıldırım Tirgil, Nimet. “Circulating Tumor DNA (ctDNA) Detection via Electrochemical Biosensing Tools”. MANAS Journal of Engineering 12/1 (June 2024), 104-115. https://doi.org/10.51354/mjen.1375211.
JAMA Sahin S, Yıldırım Tirgil N. Circulating tumor DNA (ctDNA) Detection via electrochemical Biosensing Tools. MJEN. 2024;12:104–115.
MLA Sahin, Sonya and Nimet Yıldırım Tirgil. “Circulating Tumor DNA (ctDNA) Detection via Electrochemical Biosensing Tools”. MANAS Journal of Engineering, vol. 12, no. 1, 2024, pp. 104-15, doi:10.51354/mjen.1375211.
Vancouver Sahin S, Yıldırım Tirgil N. Circulating tumor DNA (ctDNA) Detection via electrochemical Biosensing Tools. MJEN. 2024;12(1):104-15.

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