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Yu Y, Fu W, Xie Y, Jiang X, Wang H, Yang X. A review on recent advances in assays for DNMT1: a promising diagnostic biomarker for multiple human cancers. Analyst 2024; 149:1002-1021. [PMID: 38204433 DOI: 10.1039/d3an01915b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
The abnormal expression of human DNA methyltransferases (DNMTs) is closely related with the occurrence and development of a wide range of human cancers. DNA (cytosine-5)-methyltransferase-1 (DNMT1) is the most abundant human DNA methyltransferase and is mainly responsible for genomic DNA methylation patterns. Abnormal expression of DNMT1 has been found in many kinds of tumors, and DNMT1 has become a valuable target for the diagnosis and drug therapy of diseases. Nowadays, DNMT1 has been found to be involved in multiple cancers such as pancreatic cancer, breast cancer, bladder cancer, lung cancer, gastric cancer and other cancers. In order to achieve early diagnosis and for scientific research, various analytical methods have been developed for qualitative or quantitative detection of low-abundance DNMT1 in biological samples and human tumor cells. Herein, we provide a brief explication of the research progress of DNMT1 involved in various cancer types. In addition, this review focuses on the types, principles, and applications of DNMT1 detection methods, and discusses the challenges and potential future directions of DNMT1 detection.
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Affiliation(s)
- Yang Yu
- Department of Laboratory Medicine, QianWei People's Hospital, Leshan 614400, China
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
| | - Wen Fu
- Department of Thoracic Surgery, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yaxing Xie
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
| | - Xue Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hong Wang
- Department of Laboratory Medicine, QianWei People's Hospital, Leshan 614400, China
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
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Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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Hu J, Yang Y, Lv X, Lao Z, Yu L. Dichlorodiphenyltrichloroethane metabolites inhibit DNMT1 activity which confers methylation-specific modulation of the sex determination pathway. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 279:116828. [PMID: 33765505 DOI: 10.1016/j.envpol.2021.116828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/11/2021] [Accepted: 02/21/2021] [Indexed: 06/12/2023]
Abstract
Dichlorodiphenyltrichloroethane (DDT) poses a significant health risk to humans which is associated with genomic DNA hypomethylation. However, the mechanism and biological consequences remain poorly understood. In vitro assays confirmed that the DDT metabolites 2,2-bis(p-chlorophenyl)-acetic acid (DDA) and 1-chloro-2,2-bis-(p-chlorophenyl)ethylene (DDMU), but not other DDT metabolites, significantly inhibited DNA methyltransferase 1 (DNMT1) activity, leading to genomic hypomethylation in cell culture assays. DNMT1 as a target for DNA hypomethylation induced by DDT metabolites was also confirmed using cell cultures in which DNMT1 was silenced or highly expressed. DDA and DDMU can modify methylation markers in the promoter regions of sexual development-related genes, and change the expression of Sox9 and Oct4 in embryonic stem cells. Molecular docking indicated that DDA and DDMU bound to DNMT1 with high binding affinity. Molecular dynamic simulation revealed that DDA and DDMU acted as allosteric modulators that reshaped the conformation of the catalytic domain of DNMT1. These findings provide a new insight into DDT-induced abnormalities in sexual development and demonstrate that selective binding to DNMT1 by DDA and DDMU can interfere with human DNMT1 activity and regulate the expression of the Sox9 and Oct4 genes.
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Affiliation(s)
- Junjie Hu
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Yan Yang
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, PR China; Synergy Innovation Institute of GDUT, Shantou, 515041, China
| | - Xiaomei Lv
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Zhilang Lao
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Lili Yu
- Translational Medicine Collaborative Innovation Center, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, 1017 Dongmen North Road, Luohu District, Shenzhen, 518020, Guangdong, China.
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Zhu L, Miao M, Shao X, Du Z, Huang K, Luo Y, Xu W. A Universal Electrochemical Biosensor Using Nick-HCR Nanostructure as Molecular Gate of Nanochannel for Detecting Chromium(III) Ions and MicroRNA. Anal Chem 2019; 91:14992-14999. [DOI: 10.1021/acs.analchem.9b03489] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Longjiao Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Miao Miao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Xiangli Shao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Zaihui Du
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Kunlun Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
| | - Yunbo Luo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture, Beijing 100083, P.R. China
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
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A simple and universal electrochemical assay for sensitive detection of DNA methylation, methyltransferase activity and screening of inhibitors. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.02.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Ying N, Ju C, Li Z, Liu W, Wan J. Visual detection of nucleic acids based on lateral flow biosensor and hybridization chain reaction amplification. Talanta 2017; 164:432-438. [DOI: 10.1016/j.talanta.2016.10.098] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/27/2016] [Accepted: 10/29/2016] [Indexed: 12/21/2022]
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Wang L, Yu F, Wang F, Chen Z. Electrochemical detection of DNA methylation using a glassy carbon electrode modified with a composite made from carbon nanotubes and β-cyclodextrin. J Solid State Electrochem 2016. [DOI: 10.1007/s10008-016-3122-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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Lemire M, Zaidi SHE, Zanke BW, Gallinger S, Hudson TJ, Cleary SP. The effect of 5-fluorouracil/leucovorin chemotherapy on CpG methylation, or the confounding role of leukocyte heterogeneity: An illustration. Genomics 2015; 106:340-7. [PMID: 26368860 DOI: 10.1016/j.ygeno.2015.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 12/31/2022]
Abstract
Blood-based epigenome-wide association studies that aim at comparing CpG methylation between colorectal cancer (CRC) patients and controls can lead to the discovery of diagnostic or prognostic biomarkers. Numerous confounders can lead to spurious associations. We aimed to see if 5-fluorouracil (5-FU)/leucovorin chemotherapy administered to cases prior to the collection of their blood has an effect on methylation. 304 patients who received treatment and 273 who did not were profiled on the HumanMethylation450 array. Association tests were adjusted for confounders, including proxies for leukocyte cell counts. There were substantial methylation differences between these two groups that vanished once the leukocyte heterogeneity was accounted for. We observed a significant decrease of T cells in the treatment group (CD4+: p=10(-6); CD8+: p=0.036) and significant increase of NK cells (p=0.05) and monocytes (p=0.0006). 5-FU/leucovorin has no effect on global and local blood-based methylation profiles, other than through differences in the leukocyte compositions that the treatment induced.
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Affiliation(s)
- Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.
| | - Syed H E Zaidi
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.
| | - Brent W Zanke
- Department of Medicine, University of Ottawa, Ottawa Hospital Research Institute, Ottawa, Ontario K1H 8L6, Canada.
| | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Division of General Surgery, Toronto General Hospital, Toronto, Ontario M5G 2C4, Canada.
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada.
| | - Sean P Cleary
- Department of Surgery, University Health Network, Toronto, Ontario M5G 2C4, Canada; Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario M5G 1X5, Canada.
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Liu P, Pang J, Yin H, Ai S. G-quadruplex functionalized nano mesoporous silica for assay of the DNA methyltransferase activity. Anal Chim Acta 2015; 879:34-40. [PMID: 26002474 DOI: 10.1016/j.aca.2015.04.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 11/25/2022]
Abstract
The abnormal level of DNA methyltransferase (MTase) may cause the aberrant DNA methylation, which has been found being associated with a growing number of human diseases, so it is necessary to create a sensitive and selective method to detect DNA MTase activity. In this paper, a new type of DNA functionalized nano mesoporous silica (MSNs) was creatively introduced to the detection of DNA MTase activity with G-quadruplex as a lock for signal molecule to release. The method was carried out by designing a particular DNA which could fold into G-quadruplex and complement with probe DNA. Next, MSNs was prepared before blocking methylene blue (MB) by G-quadruplex. Probe DNA was then fixed on gold nanoparticles modified glass carbon electrode, and the material was able to be transferred to the surface of electrode by DNA hybridization. After methylation of DNA MTase and the cutting of restriction endonuclease, the electrode was transferred to phosphate buffer solution (pH 9.0) for the releasing of MB. The response of differential pulse voltammetry was obtained from the release of MB. Consequently, the difference of signals with or without methylation could prove the assay of M. SssI MTase activity. The results showed that the responses from MB increased linearly with the increasing of the M. SssI MTase concentrations from 0.28 to 50UmL(-1). The limit of detection was 0.28UmL(-1). In addition, Zebularine, a nucleoside analog of cytidine, was utilized for studying the inhibition activity of M. SssI MTase.
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Affiliation(s)
- Pei Liu
- College of Chemistry and Material Science, Shandong Agricultural University, 271018 Taian, Shandong, PR China
| | - Junling Pang
- College of Chemistry and Material Science, Shandong Agricultural University, 271018 Taian, Shandong, PR China
| | - Huanshun Yin
- College of Chemistry and Material Science, Shandong Agricultural University, 271018 Taian, Shandong, PR China.
| | - Shiyun Ai
- College of Chemistry and Material Science, Shandong Agricultural University, 271018 Taian, Shandong, PR China.
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