Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy

Cell-free DNA (cfDNA) and extracellular vesicles (EVs) are molecular biomarkers in liquid biopsies that can be applied for cancer detection, which are known to carry information on the necessary conditions for oncogenesis and cancer cell-specific activities after oncogenesis, respectively. Analyses...

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Main Authors: Takahashi, Hiromi, Yasui, Takao, Hirano, Masaki, Shinjo, Keiko, Miyazaki, Yusuke, Shinoda, Wataru, Hasegawa, Takeshi, Natsume, Atsushi, Kitano, Yotaro, Ida, Mikiko, Zhang, Min, Shimada, Taisuke, Paisrisarn, Piyawan, Zhu, Zetao, Ohka, Fumiharu, Aoki, Kosuke, Rahong, Sakon, Nagashima, Kazuki, Yanagida, Takeshi, Baba, Yoshinobu
Other Authors: School of Mechanical and Aerospace Engineering
Format: Article
Language:English
Published: 2024
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Online Access:https://hdl.handle.net/10356/174543
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Institution: Nanyang Technological University
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spelling sg-ntu-dr.10356-1745432024-04-06T16:48:44Z Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy Takahashi, Hiromi Yasui, Takao Hirano, Masaki Shinjo, Keiko Miyazaki, Yusuke Shinoda, Wataru Hasegawa, Takeshi Natsume, Atsushi Kitano, Yotaro Ida, Mikiko Zhang, Min Shimada, Taisuke Paisrisarn, Piyawan Zhu, Zetao Ohka, Fumiharu Aoki, Kosuke Rahong, Sakon Nagashima, Kazuki Yanagida, Takeshi Baba, Yoshinobu School of Mechanical and Aerospace Engineering Engineering Cell-free DNA Extracellular vesicles Cell-free DNA (cfDNA) and extracellular vesicles (EVs) are molecular biomarkers in liquid biopsies that can be applied for cancer detection, which are known to carry information on the necessary conditions for oncogenesis and cancer cell-specific activities after oncogenesis, respectively. Analyses for both cfDNA and EVs from the same body fluid can provide insights into screening and identifying the molecular subtypes of cancer; however, a major bottleneck is the lack of efficient and standardized techniques for the isolation of cfDNA and EVs from clinical specimens. Here, we achieved catch-and-release isolation by hydrogen bond-mediated binding of cfDNA in urine to zinc oxide (ZnO) nanowires, which also capture EVs by surface charge, and subsequently we identified genetic mutations in urinary cfDNA. The binding strength of hydrogen bonds between single-crystal ZnO nanowires and DNA was found to be equal to or larger than that of conventional hydrophobic interactions, suggesting the possibility of isolating trace amounts of cfDNA. Our results demonstrated that nanowire-based cancer screening assay can screen cancer and can identify the molecular subtypes of cancer in urine from brain tumor patients through EV analysis and cfDNA mutation analysis. We anticipate our method to be a starting point for more sophisticated diagnostic models of cancer screening and identification. Published version This research was supported by the Japan Science and Technology Agency (JST) PRESTO (JPMJPR19H9), JST SICORP (JPMJSC19E3), the New Energy and Industrial Technology Development Organization (NEDO) JPNP20004, the JSPS Grant-in-Aid for Scientific Research (S) 18H05243, the JSPS Grant-in-Aid for Scientific Research (B) 21H01960, the JSPS Grant-in-Aid for Transformative Research Area (A) 21H05778, a Medical Research and Development Program (AMED Grant Nos. JP21he2302007 and JP21zf0127004 ) the e-ASIA Joint Research Program (e-ASIA JRP) JRA-CO-2563-11330-TH and research grants from each of the following: Advanced Technology Institute Research Grants 2019, the Nanotechnology Platform Program (Molecule and Material Synthesis) of the Ministry of Education, Culture, Sports, Science and Technology (MEXT), the Cooperative Research Program of the “Network Joint Research Center for Materials and Devices”, and Nagoya University Research Fund. H.T. gratefully acknowledges the support from the Yoshida Scholarship Foundation. 2024-04-02T01:43:11Z 2024-04-02T01:43:11Z 2023 Journal Article Takahashi, H., Yasui, T., Hirano, M., Shinjo, K., Miyazaki, Y., Shinoda, W., Hasegawa, T., Natsume, A., Kitano, Y., Ida, M., Zhang, M., Shimada, T., Paisrisarn, P., Zhu, Z., Ohka, F., Aoki, K., Rahong, S., Nagashima, K., Yanagida, T. & Baba, Y. (2023). Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy. Biosensors and Bioelectronics, 234, 115318-. https://dx.doi.org/10.1016/j.bios.2023.115318 0956-5663 https://hdl.handle.net/10356/174543 10.1016/j.bios.2023.115318 37172361 2-s2.0-85157976918 234 115318 en Biosensors and Bioelectronics © 2023 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/bync-nd/4.0/). application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic Engineering
Cell-free DNA
Extracellular vesicles
spellingShingle Engineering
Cell-free DNA
Extracellular vesicles
Takahashi, Hiromi
Yasui, Takao
Hirano, Masaki
Shinjo, Keiko
Miyazaki, Yusuke
Shinoda, Wataru
Hasegawa, Takeshi
Natsume, Atsushi
Kitano, Yotaro
Ida, Mikiko
Zhang, Min
Shimada, Taisuke
Paisrisarn, Piyawan
Zhu, Zetao
Ohka, Fumiharu
Aoki, Kosuke
Rahong, Sakon
Nagashima, Kazuki
Yanagida, Takeshi
Baba, Yoshinobu
Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy
description Cell-free DNA (cfDNA) and extracellular vesicles (EVs) are molecular biomarkers in liquid biopsies that can be applied for cancer detection, which are known to carry information on the necessary conditions for oncogenesis and cancer cell-specific activities after oncogenesis, respectively. Analyses for both cfDNA and EVs from the same body fluid can provide insights into screening and identifying the molecular subtypes of cancer; however, a major bottleneck is the lack of efficient and standardized techniques for the isolation of cfDNA and EVs from clinical specimens. Here, we achieved catch-and-release isolation by hydrogen bond-mediated binding of cfDNA in urine to zinc oxide (ZnO) nanowires, which also capture EVs by surface charge, and subsequently we identified genetic mutations in urinary cfDNA. The binding strength of hydrogen bonds between single-crystal ZnO nanowires and DNA was found to be equal to or larger than that of conventional hydrophobic interactions, suggesting the possibility of isolating trace amounts of cfDNA. Our results demonstrated that nanowire-based cancer screening assay can screen cancer and can identify the molecular subtypes of cancer in urine from brain tumor patients through EV analysis and cfDNA mutation analysis. We anticipate our method to be a starting point for more sophisticated diagnostic models of cancer screening and identification.
author2 School of Mechanical and Aerospace Engineering
author_facet School of Mechanical and Aerospace Engineering
Takahashi, Hiromi
Yasui, Takao
Hirano, Masaki
Shinjo, Keiko
Miyazaki, Yusuke
Shinoda, Wataru
Hasegawa, Takeshi
Natsume, Atsushi
Kitano, Yotaro
Ida, Mikiko
Zhang, Min
Shimada, Taisuke
Paisrisarn, Piyawan
Zhu, Zetao
Ohka, Fumiharu
Aoki, Kosuke
Rahong, Sakon
Nagashima, Kazuki
Yanagida, Takeshi
Baba, Yoshinobu
format Article
author Takahashi, Hiromi
Yasui, Takao
Hirano, Masaki
Shinjo, Keiko
Miyazaki, Yusuke
Shinoda, Wataru
Hasegawa, Takeshi
Natsume, Atsushi
Kitano, Yotaro
Ida, Mikiko
Zhang, Min
Shimada, Taisuke
Paisrisarn, Piyawan
Zhu, Zetao
Ohka, Fumiharu
Aoki, Kosuke
Rahong, Sakon
Nagashima, Kazuki
Yanagida, Takeshi
Baba, Yoshinobu
author_sort Takahashi, Hiromi
title Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy
title_short Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy
title_full Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy
title_fullStr Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy
title_full_unstemmed Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy
title_sort mutation detection of urinary cell-free dna via catch-and-release isolation on nanowires for liquid biopsy
publishDate 2024
url https://hdl.handle.net/10356/174543
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