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Ye C, Zhao Z, Lai P, Chen C, Jian F, Liang H, Guo Q. Strategies for the detection of site-specific DNA methylation and its application, opportunities and challenges in the field of electrochemical biosensors. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5496-5508. [PMID: 39051422 DOI: 10.1039/d4ay00779d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in various biological processes. Aberrant DNA methylation is closely associated with the onset of diseases, and the specific localization of methylation sites in the genome offers further insight into the connection between methylation and diseases. Currently, there are numerous methods available for site-specific methylation detection. Electrochemical biosensors have garnered significant attention due to their distinct advantages, such as rapidity, simplicity, high sensitivity, low cost, and the potential for miniaturization. In this paper, we present a systematic review of the primary sensing strategies utilized in the past decade for analyzing site-specific methylation and their applications in electrochemical sensors, from a novel perspective focusing on the localization analysis of site-specific methylation. These strategies include bisulfite treatment, restriction endonuclease treatment, other sensing strategies, and deamination without direct bisulfite treatment. We hope that this paper can offer ideas and references for establishing site-specific methylation electrochemical analysis in clinical practice.
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Affiliation(s)
- Chenliu Ye
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Zhibin Zhao
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Penghui Lai
- The Second Hospital of Longyan, Longyan 364000, China
| | - Chunmei Chen
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Fumei Jian
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Haiying Liang
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Qiongying Guo
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
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2
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Cai J, Zhu Q. New advances in signal amplification strategies for DNA methylation detection in vitro. Talanta 2024; 273:125895. [PMID: 38508130 DOI: 10.1016/j.talanta.2024.125895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
5-methylcytosine (5 mC) DNA methylation is a prominent epigenetic modification ubiquitous in the genome. It plays a critical role in the regulation of gene expression, maintenance of genome stability, and disease control. The potential of 5 mC DNA methylation for disease detection, prognostic information, and prediction of response to therapy is enormous. However, the quantification of DNA methylation from clinical samples remains a considerable challenge due to its low abundance (only 1% of total bases). To overcome this challenge, scientists have recently developed various signal amplification strategies to enhance the sensitivity of DNA methylation biosensors. These strategies include isothermal nucleic acid amplification and enzyme-assisted target cycling amplification, among others. This review summarizes the applications, advantages, and limitations of these signal amplification strategies over the past six years (2018-2023). Our goal is to provide new insights into the selection and establishment of DNA methylation analysis. We hope that this review will offer valuable insights to researchers in the field and facilitate further advancements in this area.
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Affiliation(s)
- Jiajing Cai
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China
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3
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Zhang H, Su Y, Zhao J, Song H, Zhou X. A ratiometric fluorescence assay for the detection of DNA methylation based on an alkaline phosphatase triggered in situ fluorogenic reaction. Analyst 2024; 149:507-514. [PMID: 38073500 DOI: 10.1039/d3an01854g] [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: 01/16/2024]
Abstract
The accurate and sensitive quantification of DNA methylation is significant for the early diagnosis of cancer. In this work, an alkaline phosphatase (ALP) triggered in situ fluorogenic reaction between ascorbic acid (AA) and 2,3-DAN was employed as a ratiometric fluorescent probe for the accurate and sensitive detection of DNA methylation with the assistance of ALP encapsulated liposomes. The quinoxaline derivative with a yellow fluorescence emission (I525) was generated from the reaction between AA and 2,3-DAN. Meanwhile, the consumption of 2,3-DAN declined its fluorescence intensity (I386). A ratiometric fluorescent probe (I525/I386) constructed by the above in situ fluorogenic reaction was applied for the accurate detection of DNA methylation. The methylated DNA was first captured by its complementary DNA in 96-well plates. Then, 5mC antibody (Ab) linked liposomes that were encapsulated with ALP recognized and combined with the methylation sites of the target DNA. After the liposomes were lysed by Triton X-100, the released ALP triggered the hydrolysis of ascorbic acid diphosphate (AAP) to form AA, participating in the fluorogenic reaction with 2,3-DAN to produce a quinoxaline derivative. Thus, the ratiometric fluorescence detection of DNA methylation was achieved using I525/I386 values. Using the ALP-enzyme catalyzed reaction and liposomes as signal amplifiers, a low detection limit of 82 fM was obtained for DNA methylation detection. Moreover, the accuracy of the assay could be improved using ratiometric fluorescent probes. We hope that the proposed assay will pave a new way for the accurate determination of low-abundance biomarkers.
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Affiliation(s)
- Hongding Zhang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Yinhui Su
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Jiamiao Zhao
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Huixi Song
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Xiaohong Zhou
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
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4
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Liu Y, Wang X, Li Y, Wu H. An all-in-one strategy for bisulfite-free DNA methylation detection by temperature-programmed enzymatic reactions. Anal Chim Acta 2023; 1251:341001. [PMID: 36925290 DOI: 10.1016/j.aca.2023.341001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/08/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
The fragmentation and low concentration of cell-free DNA (cfDNA) pose higher challenges for the cfDNA methylation detection technologies. Conventional bisulfite conversion-based methods are inadequate for cfDNA methylation analysis due to cumbersome operation and exacerbating cfDNA degradation. Herein, we proposed temperature-programmed enzymatic reactions for cfDNA methylation analysis in a single tube. Endonuclease was used to mildly recognize DNA methylation to avoid the degradation of cfDNA. And two stages of amplification reactions significantly improved the detection sensitivity for GC-rich sequence. With vimentin as the target, the detection sensitivity was 10 copies of methylated DNA. Meanwhile, the proposed method can accurately quantify the methylation level of target sequence from 1000-fold of unmethylated DNA background. Further, the methylated vimentin gene in 20 clinical plasma samples was successfully detected. The results shown significant differences in methylation levels of the vimentin gene between healthy volunteers and colorectal cancer patients. These results lead us to believe that the proposed method has great application potential for DNA methylation analysis as a complement to bisulfite conversion-based methods.
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Affiliation(s)
- Yunlong Liu
- State Key Laboratory of Natural Medicines, Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, 211198, PR China.
| | - Xiaoming Wang
- Department of Clinical Laboratory, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, 210009, PR China
| | - Yujiao Li
- Department of Pharmacology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, PR China
| | - Haiping Wu
- Department of Pharmacology, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, PR China; School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, PR China.
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5
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Ratiometric Electrochemical Biosensing of Methyltransferase Activity. Catalysts 2022. [DOI: 10.3390/catal12111362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this work, a novel ratiometric electrochemical readout platform was proposed and developed for the fast and flexible analysis of M.SssI methyltransferase (MTase) activity. In this platform, two hairpin DNAs (H1 and H2) were designed. H1 contains the palindromic sequence of 5′-CCGG-3′ in its stem which could be methylated and hybridize with H2 labeled by methylene blue (MB) as one of the signal reporters on a gold electrode (GE) in the presence of M.SssI MTase. Additionally, a specific immunoreaction was introduced by conjugating an anti-5-methylcytosine antibody, a DNA CpG methylation recognition unit, with 1,3-ferrocenedicarboxylic acid (Fc) as the second signal reporter. The results showed that when the Fc tag approaches, the MB tag was far from the gold electrode surface, resulting in a decrease in the oxidation peak current of MB (IMB) and an increase in the oxidation peak current of Fc (IFc). The ratiometric electrochemical method above shows the linear range of detection was 0 U/mL 40 U/mL with a detection limit of 0.083 U/mL (the mean signal of blank measures þ3s).
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Chemi F, Pearce SP, Clipson A, Hill SM, Conway AM, Richardson SA, Kamieniecka K, Caeser R, White DJ, Mohan S, Foy V, Simpson KL, Galvin M, Frese KK, Priest L, Egger J, Kerr A, Massion PP, Poirier JT, Brady G, Blackhall F, Rothwell DG, Rudin CM, Dive C. cfDNA methylome profiling for detection and subtyping of small cell lung cancers. NATURE CANCER 2022; 3:1260-1270. [PMID: 35941262 PMCID: PMC9586870 DOI: 10.1038/s43018-022-00415-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/28/2022] [Indexed: 12/03/2022]
Abstract
Small cell lung cancer (SCLC) is characterized by morphologic, epigenetic and transcriptomic heterogeneity. Subtypes based upon predominant transcription factor expression have been defined that, in mouse models and cell lines, exhibit potential differential therapeutic vulnerabilities, with epigenetically distinct SCLC subtypes also described. The clinical relevance of these subtypes is unclear, due in part to challenges in obtaining tumor biopsies for reliable profiling. Here we describe a robust workflow for genome-wide DNA methylation profiling applied to both patient-derived models and to patients' circulating cell-free DNA (cfDNA). Tumor-specific methylation patterns were readily detected in cfDNA samples from patients with SCLC and were correlated with survival outcomes. cfDNA methylation also discriminated between the transcription factor SCLC subtypes, a precedent for a liquid biopsy cfDNA-methylation approach to molecularly subtype SCLC. Our data reveal the potential clinical utility of cfDNA methylation profiling as a universally applicable liquid biopsy approach for the sensitive detection, monitoring and molecular subtyping of patients with SCLC.
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Affiliation(s)
- Francesca Chemi
- Nucleic Acid Biomarker Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Simon P Pearce
- Bioinformatics and Biostatistics Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Alexandra Clipson
- Nucleic Acid Biomarker Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Steven M Hill
- Bioinformatics and Biostatistics Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Alicia-Marie Conway
- Nucleic Acid Biomarker Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Sophie A Richardson
- Nucleic Acid Biomarker Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Katarzyna Kamieniecka
- Bioinformatics and Biostatistics Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Rebecca Caeser
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel J White
- Nucleic Acid Biomarker Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Sumitra Mohan
- Nucleic Acid Biomarker Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Victoria Foy
- Nucleic Acid Biomarker Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Kathryn L Simpson
- Preclinical and Pharmacology Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Melanie Galvin
- Preclinical and Pharmacology Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Kristopher K Frese
- Preclinical and Pharmacology Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Lynsey Priest
- Division of Cancer Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Jacklynn Egger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alastair Kerr
- Bioinformatics and Biostatistics Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Pierre P Massion
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John T Poirier
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Gerard Brady
- Nucleic Acid Biomarker Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK
| | - Fiona Blackhall
- The Christie NHS Foundation Trust, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Dominic G Rothwell
- Nucleic Acid Biomarker Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK.
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Caroline Dive
- Nucleic Acid Biomarker Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK.
- Bioinformatics and Biostatistics Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK.
- Preclinical and Pharmacology Team, Cancer Biomarker Centre, Cancer Research UK Manchester Institute, University of Manchester, Alderley Edge, UK.
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7
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Kolkman R, Michel-Souzy S, Wasserberg D, Segerink LI, Huskens J. Density Control over MBD2 Receptor-Coated Surfaces Provides Superselective Binding of Hypermethylated DNA. ACS APPLIED MATERIALS & INTERFACES 2022; 14:40579-40589. [PMID: 36052432 PMCID: PMC9478954 DOI: 10.1021/acsami.2c09641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Using the biomarker hypermethylated DNA (hmDNA) for cancer detection requires a pretreatment to isolate or concentrate hmDNA from nonmethylated DNA. Affinity chromatography using a methyl binding domain-2 (MBD2) protein can be used, but the relatively low enrichment selectivity of MBD2 limits its clinical applicability. Here, we developed a superselective, multivalent, MBD2-coated platform to improve the selectivity of hmDNA enrichment. The multivalent platform employs control over the MBD2 surface receptor density, which is shown to strongly affect the binding of DNA with varying degrees of methylation, improving both the selectivity and the affinity of DNAs with higher numbers of methylation sites. Histidine-10-tagged MBD2 was immobilized on gold surfaces with receptor density control by tuning the amount of nickel nitrilotriacetic acid (NiNTA)-functionalized thiols in a thiol-based self-assembled monolayer. The required MBD2 surface receptor densities for DNA surface binding decreases for DNA with higher degrees of methylation. Both higher degrees of superselectivity and surface coverages were observed upon DNA binding at increasing methylation levels. Adopting the findings of this study into hmDNA enrichment of clinical samples has the potential to become more selective and sensitive than current MBD2-based methods and, therefore, to improve cancer diagnostics.
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Affiliation(s)
- Ruben
W. Kolkman
- Molecular
Nanofabrication Group, Department for Molecules & Materials, MESA+
Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
- BIOS
Lab on a Chip Group, MESA+ Institute and TechMed Centre, Max Planck
Institute for Complex Fluid Dynamics, Faculty of Electrical Engineering,
Mathematics and Computer Science, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Sandra Michel-Souzy
- Biomolecular
Nanotechnology Group, Department for Molecules & Materials, MESA+
Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Dorothee Wasserberg
- BIOS
Lab on a Chip Group, MESA+ Institute and TechMed Centre, Max Planck
Institute for Complex Fluid Dynamics, Faculty of Electrical Engineering,
Mathematics and Computer Science, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Loes I. Segerink
- BIOS
Lab on a Chip Group, MESA+ Institute and TechMed Centre, Max Planck
Institute for Complex Fluid Dynamics, Faculty of Electrical Engineering,
Mathematics and Computer Science, University
of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Jurriaan Huskens
- Molecular
Nanofabrication Group, Department for Molecules & Materials, MESA+
Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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8
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Sensitive GlaI digestion and terminal transferase PCR for DNA methylation detection. Talanta 2022; 247:123616. [DOI: 10.1016/j.talanta.2022.123616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 11/30/2022]
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9
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Safarzadeh M, Pan G. Detection of a Double-Stranded MGMT Gene Using Electrochemically Reduced Graphene Oxide (ErGO) Electrodes Decorated with AuNPs and Peptide Nucleic Acids (PNA). BIOSENSORS 2022; 12:bios12020098. [PMID: 35200358 PMCID: PMC8869880 DOI: 10.3390/bios12020098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 11/16/2022]
Abstract
The ability to detect double-stranded DNA (dsDNA) as a biomarker without denaturing it to single-stranded DNA (ss-DNA) continues to be a major challenge. In this work, we report a sandwich biosensor for the detection of the ds-methylated MGMT gene, a potential biomarker for brain tumors and breast cancer. The purpose of this biosensor is to achieve simultaneous recognition of the gene sequence, as well as the presence of methylation. The biosensor is based on reduced graphene oxide (rGO) electrodes decorated with gold nanoparticles (AuNPs) and uses Peptide Nucleic Acid (PNA) that binds to the ds-MGMT gene. The reduction of GO was performed in two ways: electrochemically (ErGO) and thermally (TrGO). XPS and Raman spectroscopy, as well as voltammetry techniques, showed that the ErGO was more efficiently reduced, had a higher C/O ratio, showed a smaller crystallite size of the sp2 lattice, and was more stable during measurement. It was also revealed that the electro-deposition of the AuNPs was more successful on the ErGO surface due to the higher At% of Au on the ErGO electrode. Therefore, the ErGO/AuNPs electrode was used to develop biosensors to detect the ds-MGMT gene. PNA, which acts as a bio-recognition element, was used to form a self-assembled monolayer (SAM) on the ErGO/AuNPs surface via the amine-AuNPs interaction, recognizing the ds-MGMT gene sequence by its invasion of the double-stranded DNA and the formation of a triple helix. The methylation was then detected using biotinylated-anti-5mC, which was then measured using the amperometric technique. The selectivity study showed that the proposed biosensor was able to distinguish between blank, non-methylated, non-complementary, and target dsDNA spiked in mouse plasma. The LOD was calculated to be 0.86 pM with a wide linear range of 1 pM to 50 µM. To the best of our knowledge, this is the first report on using PNA to detect ds-methylated DNA. This sandwich design can be modified to detect other methylated genes, making it a promising platform to detect ds-methylated biomarkers.
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Stefancu A, Moisoiu V, Desmirean M, Iancu SD, Tigu AB, Petrushev B, Jurj A, Cozan RG, Budisan L, Fetica B, Roman A, Dobie G, Turcas C, Zdrenghea M, Teodorescu P, Pasca S, Piciu D, Dima D, Bálint Z, Leopold N, Tomuleasa C. SERS-based DNA methylation profiling allows the differential diagnosis of malignant lymphadenopathy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120216. [PMID: 34364036 DOI: 10.1016/j.saa.2021.120216] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/12/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
This study highlights the potential of surface-enhanced Raman scattering (SERS) to differentiate between B-cell lymphoma (BCL), T-cell lymphoma (TCL), lymph node metastasis of melanoma (Met) and control (Ctr) samples based on the specific SERS signal of DNA extracted from lymph node tissue biopsy. Differences in the methylation profiles as well as the specific interaction of malignant and non-malignant DNA with the metal nanostructure are captured in specific variations of the band at 1005 cm-1, attributed to 5-methylcytosine and the band at 730 cm-1, attributed to adenine. Thus, using the area ratio of these two SERS marker bands as input for univariate classification, an area under the curve (AUC) of 0.70 was achieved in differentiating between malignant and non-malignant DNA. In addition, DNA from the BCL and TCL groups exhibited differences in the area of the SERS band at 730 cm-1, yielding an AUC of 0.84 in differentiating between these two lymphadenopathies. Lastly, using multivariate data analysis techniques, an overall accuracy of 94.7% was achieved in the differential diagnosis between the BCL, TCL, Met and Ctr groups. These results pave the way towards the implementation of SERS as a novel tool in the clinical setting for improving the diagnosis of malignant lymphadenopathy.
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Affiliation(s)
- Andrei Stefancu
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Vlad Moisoiu
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Minodora Desmirean
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Pathology, Constantin Papilian Military Hospital, Cluj-Napoca, Romania
| | - Stefania D Iancu
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Adrian B Tigu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Bobe Petrushev
- Department of Pathology, Octavian Fodor Gastroenterology Institute, Cluj-Napoca, Romania
| | - Ancuta Jurj
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ramona G Cozan
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Liviuta Budisan
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Bogdan Fetica
- Department of Pathology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Andrei Roman
- Department of Radiology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Radiology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Gina Dobie
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Turcas
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihnea Zdrenghea
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Hematology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Patric Teodorescu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Hematology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Sergiu Pasca
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Hematology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Doina Piciu
- Department of Nuclear Medicine, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Delia Dima
- Department of Hematology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Zoltán Bálint
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Nicolae Leopold
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania; Biomed Data Analytics SRL, Cluj-Napoca, Romania.
| | - Ciprian Tomuleasa
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Hematology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
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11
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Bu L, Luo T, Yan J, Li G, Huang J. Single-molecule analysis of genome-wide DNA methylation by fiber FISH coupled with atomic force microscopy. Analyst 2022; 147:1559-1566. [DOI: 10.1039/d2an00216g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A straightforward single-molecule approach was developed for identifying whole-genome DNA methylation through fiber-FISH coupled with AFM. This method has advantages of low DNA input, reproduction, long reads and low cost.
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Affiliation(s)
- Lingli Bu
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Tao Luo
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Jiangyu Yan
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Guorui Li
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
| | - Jing Huang
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, China
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12
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Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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13
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Lin Q, Fang X, Chen H, Weng W, Liu B, Kong J. Dual-modality loop-mediated isothermal amplification for pretreatment-free detection of Septin9 methylated DNA in colorectal cancer. Mikrochim Acta 2021; 188:307. [PMID: 34453211 PMCID: PMC8396143 DOI: 10.1007/s00604-021-04979-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/07/2021] [Indexed: 12/25/2022]
Abstract
Currently, the determination of DNA methylation is still a challenge due to the limited efficiency of enrichment, bisulfite modification, and detection. In this study, a dual-modality loop-mediated isothermal amplification integrated with magnetic bead isolation is proposed for the determination of methylated Septin9 gene in colorectal cancer. Magnetic beads modified with anti-methyl cytosine antibody were prepared for fast enrichment of methylated DNA through specific immunoaffinity (30 min). One-pot real-time fluorescence and colorimetric loop-mediated isothermal amplification were simultaneously developed for detecting methylated Septin9 gene (60 min). The real-time fluorescence generating by SYTO-9 dye (excitation: 470 nm and emission: 525 nm) and pH indicator (neutral red) was used for quantitative and visualized detection of methylated DNA. This method was demonstrated to detect methylated DNA from HCT 116 cells ranging from 2 to 0.02 ng/μL with a limit of detection of 0.02 ± 0.002 ng/μL (RSD: 9.75%). This method also could discriminate methylated Septin9 in 0.1% HCT 116 cells (RSD: 6.60%), suggesting its high specificity and sensitivity. The feasibility of this assay was further evaluated by clinical plasma samples from 20 colorectal cancer patients and 20 healthy controls, which shows the potential application in simple, low cost, quantitative, and visualized detection of methylated nucleic acids.
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Affiliation(s)
- Qiuyuan Lin
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
| | - Xueen Fang
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hui Chen
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Wenhao Weng
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai, 200090, China.
| | - Baohong Liu
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
- Shanghai Stomatological Hospital, Shanghai, 200438, People's Republic of China
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China.
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Cai Y, Zhang Y, Wang H, Lin X, Yu K, Li C, Jie G. Cyclometalated Iridium(III) Complex-Sensitized NiO-Based-Cathodic Photoelectrochemical Platform for DNA Methyltransferase Assay. ACS APPLIED BIO MATERIALS 2021; 4:6103-6111. [PMID: 35006914 DOI: 10.1021/acsabm.1c00445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This work reports an efficient [(C6)2Ir(dppz)]+PF6- (C6 = coumarin 6 and dppz = dipyridophenazine)-sensitized NiO photocathode and its application in photoelectrochemical (PEC) bioanalysis field for the first time. This dye-sensitized NiO photocathode was found to exhibit a markedly enhanced cathodic photocurrent. A sensitive cathodic PEC platform was proposed integrating the as-prepared photocathode with enzyme-free cascaded amplification strategies of the catalytic hairpin assembly (CHA) and the hybridization chain reaction (HCR) for DNA methyltransferase (MTase) assay. A hairpin DNA(HDam) with specific recognition site of Dam MTase in its stem was designed. The site of HDam was methylated in the presence of Dam MTase and then cut by endonuclease DpnI. The released loop fragment, as an initiator, triggered the CHA circuit and the follow-up HCR circuit, resulting in long dsDNA concatemers on the ITO electrode. Numerous [(C6)2Ir(dppz)]+PF6- were intercalated into dsDNA, and highly efficient signal amplification was realized. Benefiting from the superior iridium(III) complex-sensitized NiO photocathode and effective amplification strategy, a detection limit of 0.0028 U/mL for the determination of Dam MTase was achieved. Moreover, this work further demonstrated that these proposed tactics could be applied to screen Dam MTase activity inhibitors.
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Affiliation(s)
- Yueyuan Cai
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Yingtao Zhang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Huan Wang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Xiaojia Lin
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Kunpeng Yu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Chunxiang Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Guifen Jie
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
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15
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Soda N, Gonzaga ZJ, Pannu AS, Kashaninejad N, Kline R, Salomon C, Nguyen NT, Sonar P, Rehm BHA, Shiddiky MJA. Electrochemical Detection of Global DNA Methylation Using Biologically Assembled Polymer Beads. Cancers (Basel) 2021; 13:3787. [PMID: 34359688 PMCID: PMC8345084 DOI: 10.3390/cancers13153787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022] Open
Abstract
DNA methylation is a cell-type-specific epigenetic marker that is essential for transcriptional regulation, silencing of repetitive DNA and genomic imprinting. It is also responsible for the pathogenesis of many diseases, including cancers. Herein, we present a simple approach for quantifying global DNA methylation in ovarian cancer patient plasma samples based on a new class of biopolymer nanobeads. Our approach utilises the immune capture of target DNA and electrochemical quantification of global DNA methylation level within the targets in a three-step strategy that involves (i) initial preparation of target single-stranded DNA (ss-DNA) from the plasma of the patients' samples, (ii) direct adsorption of polymer nanobeads on the surface of a bare screen-printed gold electrode (SPE-Au) followed by the immobilisation of 5-methylcytosine (5mC)-horseradish peroxidase (HRP) antibody, and (iii) immune capture of target ss-DNA onto the electrode-bound PHB/5mC-HRP antibody conjugates and their subsequent qualification using the hydrogen peroxide/horseradish peroxidase/hydroquinone (H2O2/HRP/HQ) redox cycling system. In the presence of methylated DNA, the enzymatically produced (in situ) metabolites, i.e., benzoquinone (BQ), binds irreversibly to cellular DNA resulting in the unstable formation of DNA adducts and induced oxidative DNA strand breakage. These events reduce the available BQ in the system to support the redox cycling process and sequel DNA saturation on the platform, subsequently causing high Coulombic repulsion between BQ and negatively charged nucleotide strands. Thus, the increase in methylation levels on the electrode surface is inversely proportional to the current response. The method could successfully detect as low as 5% methylation level. In addition, the assay showed good reproducibility (% RSD ≤ 5%) and specificity by analysing various levels of methylation in cell lines and plasma DNA samples from patients with ovarian cancer. We envision that our bioengineered polymer nanobeads with high surface modification versatility could be a useful alternative platform for the electrochemical detection of varying molecular biomarkers.
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Affiliation(s)
- Narshone Soda
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia;
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; (N.K.); (N.-T.N.)
| | - Zennia Jean Gonzaga
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, QLD 4111, Australia;
| | - Amandeep Singh Pannu
- Centre for Material Science, School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD 4001, Australia; (A.S.P.); (P.S.)
- Centre for Biomedical Technologies, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD 4001, Australia
| | - Navid Kashaninejad
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; (N.K.); (N.-T.N.)
| | - Richard Kline
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Ochsner Clinic Foundation, New Orleans, LA 70121, USA;
| | - Carlos Salomon
- Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Ochsner Clinic Foundation, New Orleans, LA 70121, USA;
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women’s Hospital, The University of Queensland, Brisbane, QLD 4029, Australia
- Departamento de Investigación, Postgrado y Educación Continua (DIPEC), Facultad de Ciencias de la Salud, Universidad Pedro de Valdivia, Santiago 8320000, Chile
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; (N.K.); (N.-T.N.)
| | - Prashant Sonar
- Centre for Material Science, School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD 4001, Australia; (A.S.P.); (P.S.)
- Centre for Biomedical Technologies, School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane, QLD 4001, Australia
| | - Bernd H. A. Rehm
- Centre for Cell Factories and Biopolymers (CCFB), Griffith Institute for Drug Discovery (GRIDD), Griffith University, Nathan, QLD 4111, Australia;
- Menzies Health Institute Queensland (MHIQ), Griffith University, Gold Coast Campus, Gold Coast, QLD 4222, Australia
| | - Muhammad J. A. Shiddiky
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia;
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; (N.K.); (N.-T.N.)
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16
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End-labeling-based electrochemical strategy for detection of adenine methylation in nucleic acid by differential pulse voltammetry. Mikrochim Acta 2021; 188:250. [PMID: 34254196 DOI: 10.1007/s00604-021-04898-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/13/2021] [Indexed: 10/20/2022]
Abstract
A promising electrochemical strategy for assay of N6-methyladenosine (m6A)/N6-methyladenine (6mA) in RNA/DNA is proposed. The key of this strategy is the end-labeling of nucleic acid, which makes it possible to detect methylation level in unknown sequence. Firstly, the end of m6A-RNA or 6mA-DNA was labeled with sulfhydryl group through T4 polynucleotide kinase (T4 PNK) and then directly assembled on a gold nanoparticle-modified glassy carbon electrode (AuNPs/GCE). Secondly, methylation sites in RNA/DNA were specifically recognized by anti-m6A-antibody, and then, horseradish peroxidase-labeled goat anti-rabbit IgG (HRP-IgG) was further conjugated on the antibody. Thirdly, HRP-IgG catalyzed the hydroquinone oxidation reaction to generate amplified current signal which correlates with the amount of m6A/6mA in nucleic acid. This method showed a wide linear range from 0.0001 to 10 nM for m6A-RNA, 0.001 to 100 nM for 6mA-dsDNA, and 0.0001 to 10 nM for 6mA-ssDNA. The method was successfully applied to detection of m6A/6mA in RNA/DNA from HeLa cells and E. coli cells and validation of the decrease of m6A-RNA in HeLa cells after treatment with FTO protein.
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17
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Liebold I, Grützkau A, Göckeritz A, Gerl V, Lindquist R, Feist E, Zänker M, Häupl T, Poddubnyy D, Zernicke J, Smiljanovic B, Alexander T, Burmester GR, Gay S, Stuhlmüller B. Peripheral blood mononuclear cells are hypomethylated in active rheumatoid arthritis and methylation correlates with disease activity. Rheumatology (Oxford) 2021; 60:1984-1995. [PMID: 33200208 DOI: 10.1093/rheumatology/keaa649] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/31/2020] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE Epigenetic modifications are dynamic and influence cellular disease activity. The aim of this study was to investigate global DNA methylation in peripheral blood mononuclear cells (PBMCs) of RA patients to clarify whether global DNA methylation pattern testing might be useful in monitoring disease activity as well as the response to therapeutics. METHODS Flow cytometric measurement of 5-methyl-cytosine (5'-mC) was established using the cell line U937. In the subsequent prospective study, 62 blood samples were investigated, including 17 healthy donors and 45 RA patients at baseline and after 3 months of treatment with methotrexate, the IL-6 receptor inhibitor sarilumab, and Janus kinase inhibitors. Methylation status was assessed with an anti-5'-mC antibody and analysed in PBMCs and CD4+, CD8+, CD14+ and CD19+ subsets. Signal intensities of 5'-mC were correlated with 28-joint DASs with ESR and CRP (DAS28-ESR and DAS28-CRP). RESULTS Compared with healthy individuals, PBMCs of RA patients showed a significant global DNA hypomethylation. Signal intensities of 5'-mC correlated with transcription levels of DNMT1, DNMT3B and MTR genes involved in methylation processes. Using flow cytometry, significant good correlations and linear regression values were achieved in RA patients between global methylation levels and DAS28-ESR values for PBMCs (r = -0.55, P = 0.002), lymphocytes (r = -0.57, P = 0.001), CD4+ (r = -0.57, P = 0.001), CD8+ (r = -0.54, P = 0.001), CD14+ (r = -0.49, P = 0.008) and CD19+ (r = -0.52, P = 0.004) cells. CONCLUSIONS The degree of global DNA methylation was found to be associated with disease activity. Based on this novel approach, the degree of global methylation is a promising biomarker for therapy monitoring and the prediction of therapy outcome in inflammatory diseases.
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Affiliation(s)
- Ilka Liebold
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Andreas Grützkau
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz-Institute, Berlin, Germany
| | - Anika Göckeritz
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Velia Gerl
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Randall Lindquist
- Deutsches Rheuma-Forschungszentrum Berlin (DRFZ), a Leibniz-Institute, Berlin, Germany
| | - Eugen Feist
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany.,Department of Rheumatology, Helios Fachklinik, Vogelsang-Gommern, Germany
| | - Michael Zänker
- Immanuel Klinikum Bernau Herzzentrum Brandenburg, Medizinische Hochschule Brandenburg, Bernau, Germany
| | - Thomas Häupl
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Denis Poddubnyy
- Division of Gastroenterology, Infectious Diseases and Rheumatology, Charité - Universitätsmedizin Berlin, Corporate Member of Berlin Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Jan Zernicke
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Biljana Smiljanovic
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Tobias Alexander
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Gerd R Burmester
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
| | - Steffen Gay
- Center of Experimental Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Bruno Stuhlmüller
- Division of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Institute of Health, Freie Universität and Humboldt-Universität, Berlin, Germany
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18
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DNA-functionalized biosensor for amplifying signal detection of DNA methyltransferase activity. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Park HJ, Kim Y, Yoo TH. One-pot colorimetric detection of molecules based on proximity proteolysis reaction. Biosens Bioelectron 2021; 188:113349. [PMID: 34030090 DOI: 10.1016/j.bios.2021.113349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 01/06/2023]
Abstract
Various types of molecules serve as biomarkers of diseases, and numerous methods have been reported to detect and quantify them. Recently, research efforts have been made to develop point-of-care (POC) tests, which contribute to early diagnoses of diseases, particularly in resource-limited settings. An assay performed in a homogeneous phase is an obvious route to develop these methods. Here, simple homogeneous methods based on proximity proteolysis reactions (PPR) are reported to detect biological molecules. A typical PPR system has been designed such that the proteolysis reaction between protease and zymogen is enhanced in the presence of a target analyte. The activated zymogen generates a color signal by hydrolyzing a chromophore. A protease and zymogen are linked to target binders using specific hybridization between complementary single-stranded DNAs, and several molecules, including proteins, antibodies, aptamers, and small molecules, are used as target binders. The developed assay methods successfully detected several kinds of analytes at subnanomolar concentrations with the one-step procedure and color signal. The modular design of the PPR-based assay will enable the development of simple POC diagnostics for various biomarkers.
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Affiliation(s)
- Hyeon Ji Park
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Yuseon Kim
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea; Department of Applied Chemistry and Biological Engineering, Ajou University, 206 World Cup-ro, Yengtong-gu, Suwon, 16499, South Korea.
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20
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Safarzadeh M, Suhail A, Sethi J, Sattar A, Jenkins D, Pan G. A Label-Free DNA-Immunosensor Based on Aminated rGO Electrode for the Quantification of DNA Methylation. NANOMATERIALS 2021; 11:nano11040985. [PMID: 33921234 PMCID: PMC8070590 DOI: 10.3390/nano11040985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023]
Abstract
In this work, we developed a sandwich DNA-immunosensor for quantification of the methylated tumour suppressor gene O-6-methylguanine-DNA methyltransferase (MGMT), which is a potential biomarker for brain tumours and breast cancer. The biosensor is based on aminated reduced graphene oxide electrode, which is achieved by ammonium hydroxide chemisorption and anti-5-methylcytosine (anti-5mC) as a methylation bioreceptor. The target single-strand (ss) MGMT oligonucleotide is first recognised by its hybridisation with complementary DNA to form double-stranded (ds) MGMT, which is then captured by anti-5mC on the electrode surface due to the presence of methylation. Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and Scanning electron microscopy (SEM) techniques were used to characterise the electrode surface. Cyclic voltammetry (CV) and differential pulse voltammetry (DPV) techniques were used for electrochemical measurements. Under optimised conditions, the proposed biosensor is able to quantify a linear range of concentrations of the MGMT gene from 50 fM to 100 pM with a limit of detection (LOD) of 12 fM. The sandwich design facilitates the simultaneous recognition and quantification of DNA methylation, and the amination significantly improves the sensitivity of the biosensor. This biosensor is label-, bisulfite- and PCR-free and has a simple design for cost-efficient production. It can also be tailor-made to detect other methylated genes, which makes it a promising detection platform for DNA methylation-related disease diagnosis and prognosis.
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Affiliation(s)
- Mina Safarzadeh
- Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Devon PL4 8AA, UK; (A.S.); (J.S.); (D.J.); (G.P.)
- Correspondence:
| | - Ahmed Suhail
- Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Devon PL4 8AA, UK; (A.S.); (J.S.); (D.J.); (G.P.)
| | - Jagriti Sethi
- Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Devon PL4 8AA, UK; (A.S.); (J.S.); (D.J.); (G.P.)
| | - Anas Sattar
- School of Biomedical and Healthcare Sciences, Peninsula Schools of Medicine and Dentistry, University of Plymouth, Devon PL4 8AA, UK;
| | - David Jenkins
- Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Devon PL4 8AA, UK; (A.S.); (J.S.); (D.J.); (G.P.)
| | - Genhua Pan
- Wolfson Nanomaterials and Devices Laboratory, School of Engineering, Computing and Mathematics, Faculty of Science and Engineering, University of Plymouth, Devon PL4 8AA, UK; (A.S.); (J.S.); (D.J.); (G.P.)
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21
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Current Advances in DNA Methylation Analysis Methods. BIOMED RESEARCH INTERNATIONAL 2021; 2021:8827516. [PMID: 33824878 PMCID: PMC8007345 DOI: 10.1155/2021/8827516] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/04/2021] [Accepted: 03/01/2021] [Indexed: 12/18/2022]
Abstract
DNA methylation is one of the epigenetic changes, which plays a major role in regulating gene expression and, thus, many biological processes and diseases. There are several methods for determining the methylation of DNA samples. However, selecting the most appropriate method for answering biological questions appears to be a challenging task. The primary methods in DNA methylation focused on identifying the state of methylation of the examined genes and determining the total amount of 5-methyl cytosine. The study of DNA methylation at a large scale of genomic levels became possible following the use of microarray hybridization technology. The new generation of sequencing platforms now allows the preparation of genomic maps of DNA methylation at the single-open level. This review includes the majority of methods available to date, introducing the most widely used methods, the bisulfite treatment, biological identification, and chemical cutting along with their advantages and disadvantages. The techniques are then scrutinized according to their robustness, high throughput capabilities, and cost.
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Ultra performance liquid chromatography-tandem mass spectrometry assay for the quantification of RNA and DNA methylation. J Pharm Biomed Anal 2021; 197:113969. [PMID: 33636646 DOI: 10.1016/j.jpba.2021.113969] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/17/2021] [Accepted: 02/09/2021] [Indexed: 02/08/2023]
Abstract
Previous studies have reported that nucleic acid methylation is a critical element in cardiovascular disease, and most studies mainly focused on sequencing and biochemical research. Here we developed an Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/ MS) method for the quantification analysis of the dissociative epigenetic modified nucleosides (5mdC, 5mrC, m6A) in Myocardial Infarction (MI) SD rats from different periods (1 week, 4 weeks, 8 weeks) after the surgery. The samples for analysis were obtained from heart tissue and blood of the rats. All the quantification results are compared with the sham-operated group. Total RNA and DNA were isolated by enzymatic hydrolytic methods before the UPLC-MS/MS analysis. The statistical analysis demonstrates the dynamic changes of modified nucleosides in MI rats, and it showed good specificity, accuracy, stability and less samples were needed in the method. In this paper, we discovered that the concentration of 5mdC, 5mrC, m6A from heart tissue significantly increased at 8 weeks after the surgery. Furthermore, UPLC-MS/MS helps us observe the similar change of the concentration of those 3 methylated biomarkers in peripheral blood after 8 weeks. The result shows that the dynamic process of those 3 methylated biomarkers in peripheral blood is related to the content of methylated biomarkers from the heart tissue. Based on the scientific evidence available, we proved that the methylation of genetic materials in peripheral blood is similar to myocardial infarction tissue. The relation between them indicates that peripheral blood could be a promising alternative to the heart tissue which monitor the level of methylation and MI diagnosis-aided.
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Yan XL, Xue XX, Deng XM, Jian YT, Luo J, Jiang MM, Zheng XJ. Chemiluminescence strategy induced by HRP-sandwich structure based on strand displacement for sensitive detection of DNA methyltransferase. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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He X, Xu W, Ding F, Xu C, Li Y, Chen H, Shen J. Reaction-Based Ratiometric and Colorimetric Chemosensor for Bioimaging of Biosulfite in Live Cells, Zebrafish, and Food Samples. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11774-11781. [PMID: 32886514 DOI: 10.1021/acs.jafc.0c03983] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this work, a reaction-based ratiometric and colorimetric sensor was designed and synthesized for probing bisulfite (HSO3-) by coupling coumarin (CM) with barbituric (BA) moiety. Further tests have shown that CM-BA has high selectivity and sensitivity for the recognition of HSO3-, which can be applied for the detection of HSO3- in environmental and biological systems very effectively. The fluorescence intensity ratios (F462/F568) exhibited an outstanding HSO3--dependent response with ultrafast response time (within 20 s) and a lower detection limit (105 nM). Meanwhile, the color of the CM-BA solution changed from green to colorless during the recognition process, and its fluorescence changed from green to blue. The mechanism of response is confirmed by the density functional theory (DFT) model. In summary, CM-BA has demonstrated low toxicity and good permeability, which can be applied for imaging HSO3- in cells and zebrafish safely and effectively. Besides, this novel sensor CM-BA successfully realized the quantification of the concentration of HSO3- in paper strips and food samples.
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Affiliation(s)
- Xiaojun He
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Wei Xu
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Feng Ding
- Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Chuchu Xu
- School of Stomatology, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yahui Li
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Hong Chen
- Luoyang Key Laboratory of Organic Functional Molecules, College of Food and Drug, Luoyang Normal University, Luoyang, Henan 471934, China
| | - Jianliang Shen
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
- Engineering Research Center of Clinical Functional Materials and Diagnosis & Treatment Devices of Zhejiang Province, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
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25
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Li ZM, Pi T, Yan XL, Tang XM, Deng RH, Zheng XJ. Label-free and enzyme-free one-step rapid colorimetric detection of DNA methylation based on unmodified gold nanoparticles. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 238:118375. [PMID: 32438293 DOI: 10.1016/j.saa.2020.118375] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/22/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation has been identified as one of the important causes of tumorigenesis, so it is important to develop some advanced methods for detecting and quantifying DNA methylation. In this study, a label-free and enzyme-free one-step rapid colorimetric detection of DNA methylation based on unmodified Au nanoparticles(Au NPs)has been proposed. This method can quickly, efficiently, economically and easily colorimetric detect methylated DNA only by the color change of unmodified Au NPs solution without the covalent modification of Au NPs in advance or complicated instruments for implementation with practical limitations or expensive biological enzymes or traditional organic dyes during the reaction. The strategy employed the difference in electrostatic attraction of single-stranded DNA and double-stranded DNA against salt-induced aggregation of Au NPs. The method has a DNA methylated detection limit of 8.47 nM and it is distinctly visible to detect methylated DNA with the naked eye as low as 20 nM. Furthermore, the strategy has an ability to detect methylated DNA in the presence of abundant unmethylated DNA with the detection limit of 0.13% and as low as 1% methylated DNA can be distinguished in heterogeneous samples with the naked eye. Also, the stratagem provides a convenient and rapid platform for methylated DNA detection of human serum samples in one step, which displays a huge potential for clinical diagnosis and treatment of oncological diseases.
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Affiliation(s)
- Zhi-Mei Li
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Ting Pi
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Xi-Luan Yan
- College of resources, environment and chemical engineering, Nanchang university, Nanchang 330031, PR China
| | - Xiao-Meng Tang
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Rui-Hong Deng
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China
| | - Xiang-Juan Zheng
- Department of Chemistry, Nanchang University, Nanchang 330031, PR China.
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26
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Kilgour E, Rothwell DG, Brady G, Dive C. Liquid Biopsy-Based Biomarkers of Treatment Response and Resistance. Cancer Cell 2020; 37:485-495. [PMID: 32289272 DOI: 10.1016/j.ccell.2020.03.012] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/06/2020] [Accepted: 03/16/2020] [Indexed: 02/07/2023]
Abstract
Predictive biomarkers aid selection of personalized therapy targeted to molecular alterations within an individual's tumor. Patients' responses to targeted therapies are commonly followed by treatment resistance. Here, we survey liquid biopsies as alternatives to tumor biopsies to assess predictive and therapy response biomarkers. We examine the potential of liquid biopsies to meet the challenges of minimal residual disease monitoring after curative intent treatment for earlier detection of disease recurrence. We focus on blood, the most commonly collected minimally invasive clinical sample, and on the two most widely studied assays, circulating tumor DNA and circulating tumor cells.
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Affiliation(s)
- Elaine Kilgour
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, University of Manchester, Alderley Park, Macclesfield SK10 4TG, UK; Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Dominic G Rothwell
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, University of Manchester, Alderley Park, Macclesfield SK10 4TG, UK; Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Ged Brady
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, University of Manchester, Alderley Park, Macclesfield SK10 4TG, UK; Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Caroline Dive
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, University of Manchester, Alderley Park, Macclesfield SK10 4TG, UK; Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Oxford Road, Manchester M13 9PL, UK.
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27
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Ulukan B, Sila Ozkaya Y, Zeybel M. Advances in the epigenetics of fibroblast biology and fibrotic diseases. Curr Opin Pharmacol 2019; 49:102-109. [DOI: 10.1016/j.coph.2019.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 10/10/2019] [Indexed: 02/09/2023]
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Total DNA Methylation Changes Reflect Random Oxidative DNA Damage in Gliomas. Cells 2019; 8:cells8091065. [PMID: 31514401 PMCID: PMC6770701 DOI: 10.3390/cells8091065] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/02/2019] [Accepted: 09/09/2019] [Indexed: 01/12/2023] Open
Abstract
DNA modifications can be used to monitor pathological processes. We have previously shown that estimating the amount of the main DNA epigenetic mark, 5-methylcytosine (m5C), is an efficient and reliable way to diagnose brain tumors, hypertension, and other diseases. Abnormal increases of reactive oxygen species (ROS) are a driving factor for mutations that lead to changes in m5C levels and cancer evolution. 8-oxo-deoxyguanosine (8-oxo-dG) is a specific marker of ROS-driven DNA-damage, and its accumulation makes m5C a hotspot for mutations. It is unknown how m5C and 8-oxo-dG correlate with the malignancy of gliomas. We analyzed the total contents of m5C and 8-oxo-dG in DNA from tumor tissue and peripheral blood samples from brain glioma patients. We found an opposite relationship in the amounts of m5C and 8-oxo-dG, which correlated with glioma grade in the way that low level of m5C and high level of 8-oxo-dG indicated increased glioma malignancy grade. Our results could be directly applied to patient monitoring and treatment protocols for gliomas, as well as bolster previous findings, suggesting that spontaneously generated ROS react with m5C. Because of the similar mechanisms of m5C and guanosine oxidation, we concluded that 8-oxo-dG could also predict glioma malignancy grade and global DNA demethylation in cancer cells.
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29
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Meronard K, Josowicz M, Saheb A. Voltammetric Label‐free Detection of DNA Hypermethylation Using Polypyrrole‐modified Microelectrode Array. ELECTROANAL 2019. [DOI: 10.1002/elan.201900278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Kenton Meronard
- Department of Chemistry and Forensic ScienceAlbany State University Albany, GA USA
| | - Mira Josowicz
- School of Chemistry and BiochemistryGeorgia Institute of Technology Atlanta, GA USA
| | - Amir Saheb
- Department of Chemistry and Forensic ScienceAlbany State University Albany, GA USA
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30
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Ferrari L, Pavanello S, Bollati V. Molecular and epigenetic markers as promising tools to quantify the effect of occupational exposures and the risk of developing non-communicable diseases. LA MEDICINA DEL LAVORO 2019; 110:168-190. [PMID: 31268425 PMCID: PMC7812541 DOI: 10.23749/mdl.v110i3.8538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 06/06/2019] [Indexed: 12/18/2022]
Abstract
Non-communicable diseases (NCDs) are chronic diseases that are by far the leading cause of death in the world. Many occupational hazards, together with social, economic and demographic factors, have been associated to NCDs development. Genetic susceptibility or environmental exposures alone are not usually sufficient to explain the pathogenesis of NCDs, but can be integrated in a more complex scenario that can result in pathological phenotypes. Epigenetics is a crucial component of this scenario, as its changes are related to specific exposures, therefore potentially able to display the effects of environment on the genome, filling the gap between genetic asset and environment in explaining disease development. To date, the most promising biomarkers have been assessed in occupational cohorts as well as in case/control studies and include DNA methylation, histone modifications, microRNA expression, extracellular vesicles, telomere length, and mitochondrial alterations.
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Affiliation(s)
- Luca Ferrari
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, via San Barnaba 8, 20122 Milan, Italy..
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31
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Campuzano S, Pedrero M, Yánez‐Sedeño P, Pingarrón JM. Advances in Electrochemical (Bio)Sensing Targeting Epigenetic Modifications of Nucleic Acids. ELECTROANAL 2019. [DOI: 10.1002/elan.201900180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Susana Campuzano
- Departamento de Química Analítica Facultad de CC. QuímicasUniversidad Complutense de Madrid E-28040 Madrid Spain
| | - María Pedrero
- Departamento de Química Analítica Facultad de CC. QuímicasUniversidad Complutense de Madrid E-28040 Madrid Spain
| | - Paloma Yánez‐Sedeño
- Departamento de Química Analítica Facultad de CC. QuímicasUniversidad Complutense de Madrid E-28040 Madrid Spain
| | - José M. Pingarrón
- Departamento de Química Analítica Facultad de CC. QuímicasUniversidad Complutense de Madrid E-28040 Madrid Spain
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32
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Dovrolis N, Filidou E, Kolios G. Systems biology in inflammatory bowel diseases: on the way to precision medicine. Ann Gastroenterol 2019; 32:233-246. [PMID: 31040620 PMCID: PMC6479645 DOI: 10.20524/aog.2019.0373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic and recurrent inflammatory disorders of the gastrointestinal tract. The elucidation of their etiopathology requires complex and multiple approaches. Systems biology has come to fulfill this need in approaching the pathogenetic mechanisms of IBD and its etiopathology, in a comprehensive way, by combining data from different scientific sources. In combination with bioinformatics and network medicine, it uses principles from computer science, mathematics, physics, chemistry, biology, medicine and computational tools to achieve its purposes. Systems biology utilizes scientific sources that provide data from omics studies (e.g., genomics, transcriptomics, etc.) and clinical observations, whose combined analysis leads to network formation and ultimately to a more integrative image of disease etiopathogenesis. In this review, we analyze the current literature on the methods and the tools utilized by systems biology in order to cover an innovative and exciting field: IBD-omics.
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Affiliation(s)
- Nikolas Dovrolis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eirini Filidou
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Correspondence to: Prof. George Kolios, MD PhD, Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Dragana, Alexandroupolis, 68100, Greece, e-mail:
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33
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Chen X, Huang J, Zhang S, Mo F, Su S, Li Y, Fang L, Deng J, Huang H, Luo Z, Zheng J. Electrochemical Biosensor for DNA Methylation Detection through Hybridization Chain-Amplified Reaction Coupled with a Tetrahedral DNA Nanostructure. ACS APPLIED MATERIALS & INTERFACES 2019; 11:3745-3752. [PMID: 30624036 DOI: 10.1021/acsami.8b20144] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA methylation is a key factor in the pathogenesis of gene expression diseases or malignancies. Thus, it has become a significant biomarker for the diagnosis and prognosis of these diseases. In this paper, we designed an ultrasensitive and specific electrochemical biosensor for DNA methylation detection. The platform consisted of stem-loop-tetrahedron composite DNA probes anchoring at a Au nanoparticle-coated gold electrode, a restriction enzyme digestion of HpaII, and signal amplification procedures including electrodeposition of Au nanoparticles, hybridization chain reaction, and horseradish peroxidase enzymatic catalysis. Under optimal conditions, the design showed a broad dynamic range from 1 aM to 1 pM and a detection limit of about 0.93 aM. The approach also showed ideal specificity, repeatability, and stability. The recovery test demonstrated that the design is a promising platform for DNA methylation detection under clinical circumstances and could meet the need for cancer diagnosis.
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Affiliation(s)
- Xi Chen
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Jian Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Shu Zhang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | | | | | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Jun Deng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | - Hui Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
| | | | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science , Army Medical University , 30 Gaotanyan Street , Shapingba District, Chongqing 400038 , China
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Bhattacharjee R, Moriam S, Nguyen NT, Shiddiky MJA. A bisulfite treatment and PCR-free global DNA methylation detection method using electrochemical enzymatic signal engagement. Biosens Bioelectron 2018; 126:102-107. [PMID: 30396016 DOI: 10.1016/j.bios.2018.10.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 02/09/2023]
Abstract
In this paper we report on a bisulfite treatment and PCR amplification-free method for sensitive and selective quantifying of global DNA methylation. Our method utilizes a three-step strategy that involves (i) initial isolation and denaturation of global DNA using the standard isolation protocol and direct adsorption onto a bare gold electrode via gold-DNA affinity interaction, (ii) selective interrogation of methylation sites in adsorbed DNA via methylation-specific 5mC antibody, and (iii) subsequent signal enhancement using an electrochemical-enzymatic redox cycling reaction. In the redox cycling reaction, glucose oxidase (GOx) is used as an enzyme label, glucose as a substrate and ruthenium complex as a redox mediator. We initially investigated the enzymatic properties of GOx by varying glucose and ruthenium concentration to delineate the redox cyclic mechanism of our assay. Because of the fast electron transfer by ruthenium (Ru) complex and intrinsic signal amplification from GOx label, this method could detect as low as 5% methylation level in 50 ng of total DNA input. Moreover, the use of methylation-specific 5mC antibody conjugated GOx makes this assay relatively highly selective for DNA methylation analysis. The data obtained from the electrochemical response for different levels of methylation showed excellent interassay reproducibility of RSD (relative standard deviation) < 5% for n = 3. We believe that this inexpensive, rapid, and sensitive assay will find high relevance as an alternative method for DNA methylation analysis both in research and clinical platforms.
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Affiliation(s)
- Ripon Bhattacharjee
- School of Environment and Science, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro, and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Sofia Moriam
- School of Environment and Science, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro, and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro, and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro, and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia.
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