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Mishra M, Ahmed R, Das DK, Pramanik DD, Dash SK, Pramanik A. Recent Advancements in the Application of Circulating Tumor DNA as Biomarkers for Early Detection of Cancers. ACS Biomater Sci Eng 2024. [PMID: 38950521 DOI: 10.1021/acsbiomaterials.4c00606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Early detection of cancer is vital for increasing patient survivability chances. The three major techniques used to diagnose cancers are instrumental examination, tissue biopsy, and tumor biomarker detection. Circulating tumor DNA (ctDNA) has gained much attention in recent years due to advantages over traditional technology, such as high sensitivity, high specificity, and noninvasive nature. Through the mechanism of apoptosis, necrosis, and circulating exosome release in tumor cells, ctDNA can spread throughout the circulatory system and carry modifications such as methylations, mutations, gene rearrangements, and microsatellite instability. Traditional gene-detection technology struggles to achieve real-time, low-cost, and portable ctDNA measurement, whereas electrochemical biosensors offer low cost, high specificity alongside sensitivity, and portability for the detection of ctDNA. Therefore, this review focuses on describing the recent advancements in ctDNA biomarkers for various cancer types and biosensor developments for real-time, noninvasive, and rapid ctDNA detection. Further in the review, ctDNA sensors are also discussed in regards to their selections of probes for receptors based on the electrode surface recognition elements.
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Affiliation(s)
- Mahima Mishra
- Amity Institute of Biotechnology, Amity University, Noida 201301, India
| | - Rubai Ahmed
- Department of Physiology, University of Gour Banga, Malda-732103, West Bengal, India
| | - Deepak Kumar Das
- Department of Chemistry and Nanoscience, GLA University, Mathura, 281406 Uttar Pradesh, India
| | | | - Sandeep Kumar Dash
- Department of Physiology, University of Gour Banga, Malda-732103, West Bengal, India
| | - Arindam Pramanik
- Amity Institute of Biotechnology, Amity University, Noida 201301, India
- School of Medicine, University of Leeds, Leeds LS53RL, United Kingdom
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Djermane R, Nieto C, Vega MA, Del Valle EMM. Antibody-Loaded Nanoplatforms for Colorectal Cancer Diagnosis and Treatment: An Update. Pharmaceutics 2023; 15:pharmaceutics15051514. [PMID: 37242756 DOI: 10.3390/pharmaceutics15051514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
At present, colorectal cancer (CRC) is the second deadliest type of cancer, partly because a high percentage of cases are diagnosed at advanced stages when tumors have already metastasized. Thus, there is an urgent need to develop novel diagnostic systems that allow early detection as well as new therapeutic systems that are more specific than those currently available. In this context, nanotechnology plays a very important role in the development of targeted platforms. In recent decades, many types of nanomaterials with advantageous properties have been used for nano-oncology applications and have been loaded with different types of targeted agents, capable of recognizing tumor cells or biomarkers. Indeed, among the different types of targeted agents, the most widely used are monoclonal antibodies, as the administration of many of them is already approved by the main drug regulatory agencies for the treatment of several types of cancer, including CRC. In this way, this review comprehensively discusses the main drawbacks of the conventional screening technologies and treatment for CRC, and it presents recent advances in the application of antibody-loaded nanoplatforms for CRC detection, therapy or theranostics applications.
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Affiliation(s)
- Rania Djermane
- Chemical Engineering Department, University of Salamanca, Plaza de los Caídos s/n, 37008 Salamanca, Spain
| | - Celia Nieto
- Chemical Engineering Department, University of Salamanca, Plaza de los Caídos s/n, 37008 Salamanca, Spain
- Biomedical Research Institute of Salamanca (IBSAL), University Care Complex of Salamanca, Paseo de San Vicente 58, 37007 Salamanca, Spain
| | - Milena A Vega
- Chemical Engineering Department, University of Salamanca, Plaza de los Caídos s/n, 37008 Salamanca, Spain
- Biomedical Research Institute of Salamanca (IBSAL), University Care Complex of Salamanca, Paseo de San Vicente 58, 37007 Salamanca, Spain
| | - Eva M Martín Del Valle
- Chemical Engineering Department, University of Salamanca, Plaza de los Caídos s/n, 37008 Salamanca, Spain
- Biomedical Research Institute of Salamanca (IBSAL), University Care Complex of Salamanca, Paseo de San Vicente 58, 37007 Salamanca, Spain
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Bao J, Ding K, Zhu Y. An electrochemical biosensor for detecting DNA methylation based on AuNPs/rGO/g-C 3N 4 nanocomposite. Anal Biochem 2023; 673:115180. [PMID: 37146956 DOI: 10.1016/j.ab.2023.115180] [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: 02/25/2023] [Revised: 04/20/2023] [Accepted: 05/02/2023] [Indexed: 05/07/2023]
Abstract
DNA methylation as a ubiquitously regulation is closely associated with cell proliferation and differentiation. Growing data shows that aberrant methylation contributes to disease incidence, especially in tumorigenesis. The approach for identifying DNA methylation usually depends on treatment of sodium bisulfite, which is time-consuming and conversion-insufficient. Here, with a special biosensor, we establish an alternative approach for detecting DNA methylation. The biosensor is consisted of two parts, which are gold electrode and nanocomposite (AuNPs/rGO/g-C3N4). Nanocomposite was fabricated by three components, which are gold nanoparticles (AuNPs), reduced graphene oxide (rGO) and graphite carbon nitride (g-C3N4). For methylated DNA detection, the target DNA was captured by probe DNA immobilized on the gold electrode surface through thiolating process and subjected to hybrid with anti-methylated cytosine conjugated to nanocomposite. When the methylated cytosines in target DNA were recognized by anti-methylated cytosine, a change of electrochemical signals will be observed. With different size of target DNAs, the concentration and methylation level were tested. It is shown that in short size methylated DNA fragment, the linear range and LOD of concentration is 10-7M-10-15M and 0.74 fM respectively; in longer size methylated DNA, the linear range of methylation proportion and LOD of copy number is 3%-84% and 103 respectively. Also, this approach has a high sensitivity and specificity as well as anti-disturbing ability.
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Affiliation(s)
- Junming Bao
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, PR China
| | - Kejian Ding
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, PR China.
| | - Yunfeng Zhu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, PR China.
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4
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Goto A, Yoshida W. Hybridization-based CpG methylation level detection using methyl-CpG-binding domain-fused luciferase. Anal Bioanal Chem 2023; 415:2329-2337. [PMID: 36961575 DOI: 10.1007/s00216-023-04657-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/02/2023] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
Hypermethylation of tumor-suppressor genes and global hypomethylation, which is related to methylation level at the retroelement, have been recognized as features of the cancer genome. In this study, we developed a hybridization-based CpG methylation level detection method using methyl-CpG-binding domain-fused firefly luciferase (MBD-Fluc). In this method, methylated probe oligonucleotides were used to capture target oligonucleotides. Fully methylated and hemimethylated double-stranded DNA (dsDNA) was formed by hybridization of the methylated captured oligonucleotides with methylated or unmethylated target oligonucleotides, respectively. MBD-Fluc specifically binds to fully methylated dsDNA but not to hemimethylated dsDNA; therefore, methylated target oligonucleotides can be detected by measuring the luciferase activity of the bound MBD-Fluc. Using the corresponding methylated probe oligonucleotides, the CpG methylation levels of SEPT9, BRCA1, and long interspersed nuclear element-1 (LINE-1) oligonucleotides were quantified. Moreover, we demonstrated that the emission detection signal was not affected by the methylation state of the overhang region of the target oligonucleotide, which was not hybridized to the probe oligonucleotide, indicating that methylated CpG of the target region could be accurately detected. Unmethylated-CpG-binding domain-fused luciferases and 5-hydroxymethyl-CpG-binding domain-fused luciferases have been constructed, suggesting that other modified bases can be detected by the same platform.
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Affiliation(s)
- Ayano Goto
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan
| | - Wataru Yoshida
- Graduate School of Bionics, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
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Nam NN, Do HDK, Trinh KTL, Lee NY. Recent Progress in Nanotechnology-Based Approaches for Food Monitoring. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:nano12234116. [PMID: 36500739 PMCID: PMC9740597 DOI: 10.3390/nano12234116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 05/10/2023]
Abstract
Throughout the food supply chain, including production, storage, and distribution, food can be contaminated by harmful chemicals and microorganisms, resulting in a severe threat to human health. In recent years, the rapid advancement and development of nanotechnology proposed revolutionary solutions to solve several problems in scientific and industrial areas, including food monitoring. Nanotechnology can be incorporated into chemical and biological sensors to improve analytical performance, such as response time, sensitivity, selectivity, reliability, and accuracy. Based on the characteristics of the contaminants and the detection methods, nanotechnology can be applied in different ways in order to improve conventional techniques. Nanomaterials such as nanoparticles, nanorods, nanosheets, nanocomposites, nanotubes, and nanowires provide various functions for the immobilization and labeling of contaminants in electrochemical and optical detection. This review summarizes the recent advances in nanotechnology for detecting chemical and biological contaminations in the food supply chain.
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Affiliation(s)
- Nguyen Nhat Nam
- Biotechnology Center, School of Agriculture and Aquaculture, Tra Vinh University, Tra Vinh City 87000, Vietnam
| | - Hoang Dang Khoa Do
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ward 13, District 04, Ho Chi Minh City 70000, Vietnam
| | - Kieu The Loan Trinh
- Department of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
- Correspondence: (K.T.L.T.); (N.Y.L.)
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si 13120, Gyeonggi-do, Republic of Korea
- Correspondence: (K.T.L.T.); (N.Y.L.)
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Electrochemical Biosensors for Circulating Tumor DNA Detection. BIOSENSORS 2022; 12:bios12080649. [PMID: 36005048 PMCID: PMC9406149 DOI: 10.3390/bios12080649] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/24/2022]
Abstract
Early diagnosis and treatment have always been highly desired in the fight against cancer, and detection of circulating tumor DNA (ctDNA) has recently been touted as highly promising for early cancer-screening. Consequently, the detection of ctDNA in liquid biopsy is gaining much attention in the field of tumor diagnosis and treatment, which has also attracted research interest from industry. However, it is difficult to achieve low-cost, real-time, and portable measurement of ctDNA in traditional gene-detection technology. Electrochemical biosensors have become a highly promising solution to ctDNA detection due to their unique advantages such as high sensitivity, high specificity, low cost, and good portability. Therefore, this review aims to discuss the latest developments in biosensors for minimally invasive, rapid, and real-time ctDNA detection. Various ctDNA sensors are reviewed with respect to their choices of receptor probes, designs of electrodes, detection strategies, preparation of samples, and figures of merit, sorted by type of electrode surface recognition elements. The development of biosensors for the Internet of Things, point-of-care testing, big data, and big health is analyzed, with a focus on their portable, real-time, and non-destructive characteristics.
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Ye Q, Zhang Z, Liu J, Wang X. Screen-printed electrode-based biosensors modified with functional nucleic acid probes and their applications in this pandemic age: a review. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2961-2975. [PMID: 35913361 DOI: 10.1039/d2ay00666a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Electrochemical methodology has probably been the most used sensing platform in the past few years as they provide superior advantages. In particular, screen-printed electrode (SPE)-based sensing applications stand out as they provide extraordinary miniaturized but robust and user-friendly detection system. In this context, we are focusing on the modification of SPE with functional nucleic acid probes and nanostructures to improve the electrochemical detection performance in versatile sensing applications, particularly in the fight against the COVID-19 pandemic. Aptamers are immobilized on the electrode surface to detect non-nucleic acid targets and complementary probes to recognize and capture nucleic acid targets. In a step further, SPE-based biosensors with the modification of self-assembled DNA nanostructures are emphasized as they offer great potential for the interface engineering of the electrode surface and promote the excellent performance of various interface reactions. By equipping with a portable potentiostat and a smartphone monitoring device, the realization of this SPE-based miniaturized diagnostic system for the further requirement of fast and POC detection is revealed. Finally, more novel and excellent works are previewed and future perspectives in this field are mentioned.
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Affiliation(s)
- Qingqing Ye
- Precision Medicine Center, Beilun People's Hospital, Zhejiang University School of Medicine First Affiliated Hospital Beilun Branch, Ningbo, Zhejiang, 315806, P. R. China.
| | - Zhenqi Zhang
- Precision Medicine Center, Beilun People's Hospital, Zhejiang University School of Medicine First Affiliated Hospital Beilun Branch, Ningbo, Zhejiang, 315806, P. R. China.
| | - Jian Liu
- Precision Medicine Center, Beilun People's Hospital, Zhejiang University School of Medicine First Affiliated Hospital Beilun Branch, Ningbo, Zhejiang, 315806, P. R. China.
| | - Xuyao Wang
- Precision Medicine Center, Beilun People's Hospital, Zhejiang University School of Medicine First Affiliated Hospital Beilun Branch, Ningbo, Zhejiang, 315806, P. R. China.
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Liang Y, Zhang B, Xue Z, Ye X, Liang B. Magnetic Immunosensor Coupled to Enzymatic Signal for Determination of Genomic DNA Methylation. BIOSENSORS 2022; 12:bios12030162. [PMID: 35323432 PMCID: PMC8946087 DOI: 10.3390/bios12030162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 12/18/2022]
Abstract
Aberrations of genomic DNA methylation have been confirmed to be involved in the evolution of human cancer and have thus gained the potential to be depicted as biomarkers for cancer diagnostics and prognostic predictions, which implicates an urgent need for detection of total genomic DNA methylation. In this work, we suggested an assay for the quantification of global DNA methylation, utilizing methylation specific antibody (5mC) modified magnetic beads (MBs) for immunorecognition and affinity enrichment. Subsequently, the captured DNA on the surface of MBs interacted with the glucose oxidase-conjugated DNA antibody whose catalytic reaction product was engaged in electrochemical detection of the overall level of DNA methylation on a PB-doped screen-printed electrode. With 15 pg of input DNA, which, to our best knowledge, is the lowest required amount of DNA without sodium bisulfite treatment or amplification, this test strategy was able to perceive as low as 5% methylation level within 70 min including the preparation of anti-5mC-MBs. We believe this detection technique offers a promising option to detect global DNA methylation in both academic and clinical scenarios.
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Affiliation(s)
- Yitao Liang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China; (Y.L.); (Z.X.); (X.Y.)
| | - Bin Zhang
- Sir Run-Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China;
| | - Zexin Xue
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China; (Y.L.); (Z.X.); (X.Y.)
| | - Xuesong Ye
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China; (Y.L.); (Z.X.); (X.Y.)
| | - Bo Liang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China; (Y.L.); (Z.X.); (X.Y.)
- Correspondence:
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Tiwari A, Chaskar J, Ali A, Arivarasan VK, Chaskar AC. Role of Sensor Technology in Detection of the Breast Cancer. BIONANOSCIENCE 2022. [DOI: 10.1007/s12668-021-00921-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Moteshareie H, Hassen WM, Vermette J, Dubowski JJ, Tayabali AF. Strategies for capturing Bacillus thuringiensis spores on surfaces of (001) GaAs-based biosensors. Talanta 2022; 236:122813. [PMID: 34635209 DOI: 10.1016/j.talanta.2021.122813] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/18/2021] [Accepted: 08/16/2021] [Indexed: 12/17/2022]
Abstract
Bacillus thuringiensis (Bt) is used as a bioinsecticide since it effectively kills insect larvae. Bt is also genetically similar to Bacillus cereus (Bc), a well recognized foodborne human pathogen; they are both members of the Bacillus cereus group (BC group). Although approved Bt bioinsecticide products have been confirmed to be non-pathogenic to humans, close monitoring of Bt during dissemination is important for cost considerations and to limit impact on biodiversity towards nontarget organisms. As such, developing rapid, sensitive, and specific tools for quantitative detection of Bt spores during and following spray operations is highly desirable. The goals of this study were to investigate commercially available detection reagents for sensitivity and selectivity in detecting Bt spores, and then functionalize a surface of (001) GaAs used in photonic biosensing. To achieve these goals, we (1) screened commercial antibodies for their capacity to bind recombinant proteins from Bt spores, (2) screened antibodies and aptamers for their sensitivity and selectivity against Bt spores, and (3) tested the efficiency of selected antibodies and aptamers in capturing Bt spores on the surface of functionalized GaAs biochips. Seven genes encoding Bt spore proteins were cloned and expressed in Escherichia coli. The binding of each purified spore antigen was tested by commercially available polyclonal and monoclonal antibodies claimed to exclusively target spores. Of the seven targets, Bacillus collagen-like protein A, was the most abundant protein on Bt spores and demonstrated the strongest binding affinity to all test antibodies. The commercial antibodies (Abs) were also tested for specificity to BC Group versus non-BC Group spores. Three of six commercial antibodies showed selectivity to Bt spores, with recombinant Abs providing the most robust lower range of detection (102 to 6 × 103 spores/mL). The sensitivity and selectivity of three published DNA aptamer sequences demonstrated a wide range of detection sensitivity for Bt spores. Two of the three test aptamers also showed reasonable selectivity towards Bt spores while the third demonstrated reactivity to non-BC Group B. megaterium and B. subtilis. Of the reagents tested, a thiolated aptamer and llama recombinant Ab showed highest Bt spore capture efficiency as measured by spore coverage of the GaAs surface. These results confirm that the selected aptamer and llama rAb can be considered strong candidates for the development of GaAs-based biosensing devices.
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Affiliation(s)
- Houman Moteshareie
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada; Interdisciplinary Institute for Technological Innovation (3IT), CNRS UMI-3463, Laboratory for Quantum Semiconductors and Photon-based BioNanotechnology, Department of Electrical and Computer Engineering, Sherbrooke, Québec, Canada.
| | - Walid M Hassen
- Interdisciplinary Institute for Technological Innovation (3IT), CNRS UMI-3463, Laboratory for Quantum Semiconductors and Photon-based BioNanotechnology, Department of Electrical and Computer Engineering, Sherbrooke, Québec, Canada
| | - Jonathan Vermette
- Interdisciplinary Institute for Technological Innovation (3IT), CNRS UMI-3463, Laboratory for Quantum Semiconductors and Photon-based BioNanotechnology, Department of Electrical and Computer Engineering, Sherbrooke, Québec, Canada
| | - Jan J Dubowski
- Interdisciplinary Institute for Technological Innovation (3IT), CNRS UMI-3463, Laboratory for Quantum Semiconductors and Photon-based BioNanotechnology, Department of Electrical and Computer Engineering, Sherbrooke, Québec, Canada.
| | - Azam F Tayabali
- Biotechnology Laboratory, Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario, Canada; Interdisciplinary Institute for Technological Innovation (3IT), CNRS UMI-3463, Laboratory for Quantum Semiconductors and Photon-based BioNanotechnology, Department of Electrical and Computer Engineering, Sherbrooke, Québec, Canada.
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Mc Auley MT. DNA methylation in genes associated with the evolution of ageing and disease: A critical review. Ageing Res Rev 2021; 72:101488. [PMID: 34662746 DOI: 10.1016/j.arr.2021.101488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/30/2021] [Accepted: 10/12/2021] [Indexed: 12/28/2022]
Abstract
Ageing is characterised by a physical decline in biological functioning which results in a progressive risk of mortality with time. As a biological phenomenon, it is underpinned by the dysregulation of a myriad of complex processes. Recently, however, ever-increasing evidence has associated epigenetic mechanisms, such as DNA methylation (DNAm) with age-onset pathologies, including cancer, cardiovascular disease, and Alzheimer's disease. These diseases compromise healthspan. Consequently, there is a medical imperative to understand the link between epigenetic ageing, and healthspan. Evolutionary theory provides a unique way to gain new insights into epigenetic ageing and health. This review will: (1) provide a brief overview of the main evolutionary theories of ageing; (2) discuss recent genetic evidence which has revealed alleles that have pleiotropic effects on fitness at different ages in humans; (3) consider the effects of DNAm on pleiotropic alleles, which are associated with age related disease; (4) discuss how age related DNAm changes resonate with the mutation accumulation, disposable soma and programmed theories of ageing; (5) discuss how DNAm changes associated with caloric restriction intersect with the evolution of ageing; and (6) conclude by discussing how evolutionary theory can be used to inform investigations which quantify age-related DNAm changes which are linked to age onset pathology.
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Affiliation(s)
- Mark Tomás Mc Auley
- Faculty of Science and Engineering, University of Chester, Exton Park, Chester CH1 4BJ, UK.
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Lu Y, Zhou Q, Xu L. Non-Invasive Electrochemical Biosensors for TNF-α Cytokines Detection in Body Fluids. Front Bioeng Biotechnol 2021; 9:701045. [PMID: 34621727 PMCID: PMC8490748 DOI: 10.3389/fbioe.2021.701045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/10/2021] [Indexed: 01/13/2023] Open
Abstract
The measurement of pro-inflammatory cytokine tumour necrosis factor-alpha (TNF-α), which is an important indicator of the inflammatory process, has received increasing attention recently because it is easy to extract from body fluid and serves as an early sign of a serious systemic inflammatory disease. Developing fast and simple detection methods to quantify the concentration of TNF-α is essential. Saliva, tears, and urine, which can easily be sampled in a non-invasive way, are considered to be important matrices for monitoring and assessing the physiological status of humans; importantly, they also provide an ideal window for monitoring the concentration of TNF-α. As a fast, accurate, inexpensive, portable, and scalable method, electrochemical biosensors are very promising for biomarker detection in matrices obtained in a non-invasive manner. This review summarises and compares the electrochemical biosensors for the detection of TNF-α in a non-invasive manner and highlights recent advances and future prospects in developing high-performance electrochemical platforms for noninvasive measurement of TNF-α.
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Affiliation(s)
- Yang Lu
- Department of Cardiovascular, The Second Hospital of Jilin University, Jilin University, Changchun, China
| | - Qingqing Zhou
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
| | - Lin Xu
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun, China
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13
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Shen D, Hu W, He Q, Yang H, Cui X, Zhao S. A highly sensitive electrochemical biosensor for microRNA122 detection based on a target-induced DNA nanostructure. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:2823-2829. [PMID: 34075941 DOI: 10.1039/d1ay00390a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Specific and sensitive biomarker detection is significant for the early diagnosis of cancers. Herein, a highly sensitive electrochemical biosensor employing a tetrahedral DNA nanostructure (TDN) probe and multiple signal amplification strategies has been constructed, and successfully applied to microRNA-122 (miR-122) detection. The platform consisted of a TDN probe anchoring on a gold nanoparticle-coated gold electrode and multiple signal amplification procedures combining the electrodeposition of gold nanoparticles, hybridization chain reaction (HCR), and horseradish peroxidase enzymatic catalysis (HPEC). In the presence of the target, the hairpin structure of the helper probe could be opened and trigger the HCR through the hybridization of H1 and H2 probes, and then avidin-HRP was attached on the surface of the gold electrode that can produce an electro-catalytic signal. We used TDN probe as the scaffold to increase the reactivity and multiple signal amplification greatly improve the sensitivity of this biosensor. This biosensor offers an excellent sensitivity (a limit of detection of 0.74 aM) and differentiation ability for single and multiple mismatches. This multiplexing biosensor for trace microRNA detection shows promising applications in the early diagnosis of cancer.
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Affiliation(s)
- Ding Shen
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
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14
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Balderston S, Taulbee JJ, Celaya E, Fung K, Jiao A, Smith K, Hajian R, Gasiunas G, Kutanovas S, Kim D, Parkinson J, Dickerson K, Ripoll JJ, Peytavi R, Lu HW, Barron F, Goldsmith BR, Collins PG, Conboy IM, Siksnys V, Aran K. Discrimination of single-point mutations in unamplified genomic DNA via Cas9 immobilized on a graphene field-effect transistor. Nat Biomed Eng 2021; 5:713-725. [PMID: 33820980 DOI: 10.1038/s41551-021-00706-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 02/23/2021] [Indexed: 02/02/2023]
Abstract
Simple and fast methods for the detection of target genes with single-nucleotide specificity could open up genetic research and diagnostics beyond laboratory settings. We recently reported a biosensor for the electronic detection of unamplified target genes using liquid-gated graphene field-effect transistors employing an RNA-guided catalytically deactivated CRISPR-associated protein 9 (Cas9) anchored to a graphene monolayer. Here, using unamplified genomic samples from patients and by measuring multiple types of electrical response, we show that the biosensors can discriminate within one hour between wild-type and homozygous mutant alleles differing by a single nucleotide. We also show that biosensors using a guide RNA-Cas9 orthologue complex targeting genes within the protospacer-adjacent motif discriminated between homozygous and heterozygous DNA samples from patients with sickle cell disease, and that the biosensors can also be used to rapidly screen for guide RNA-Cas9 complexes that maximize gene-targeting efficiency.
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Affiliation(s)
- Sarah Balderston
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
- Cardea, San Diego, CA, USA
| | | | | | - Kandace Fung
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | | | - Kasey Smith
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Reza Hajian
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
- Cardea, San Diego, CA, USA
| | - Giedrius Gasiunas
- CasZyme, Vilnius, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Daehwan Kim
- University of California, Berkeley, Berkeley, CA, USA
| | | | | | | | | | - Hsiang-Wei Lu
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
- Cardea, San Diego, CA, USA
| | | | | | | | | | - Virginijus Siksnys
- CasZyme, Vilnius, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA.
- Cardea, San Diego, CA, USA.
- University of California, Berkeley, Berkeley, CA, USA.
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15
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Ranjan P, Thomas V, Kumar P. 2D materials as a diagnostic platform for the detection and sensing of the SARS-CoV-2 virus: a bird's-eye view. J Mater Chem B 2021; 9:4608-4619. [PMID: 34013310 PMCID: PMC8559401 DOI: 10.1039/d1tb00071c] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Worldwide infections and fatalities caused by the SARS-CoV-2 virus and its variants responsible for COVID-19 have significantly impeded the economic growth of many nations. People in many nations have lost their livelihoods, it has severely impacted international relations and, most importantly, health infrastructures across the world have been tormented. This pandemic has already left footprints on human psychology, traits, and priorities and is certainly going to lead towards a new world order in the future. As always, science and technology have come to the rescue of the human race. The prevention of infection by instant and repeated cleaning of surfaces that are most likely to be touched in daily life and sanitization drives using medically prescribed sanitizers and UV irradiation of textiles are the first steps to breaking the chain of transmission. However, the real challenge is to develop and uplift medical infrastructure, such as diagnostic tools capable of prompt diagnosis and instant and economic medical treatment that is available to the masses. Two-dimensional (2D) materials, such as graphene, are atomic sheets that have been in the news for quite some time due to their unprecedented electronic mobilities, high thermal conductivity, appreciable thermal stability, excellent anchoring capabilities, optical transparency, mechanical flexibility, and a unique capability to integrate with arbitrary surfaces. These attributes of 2D materials make them lucrative for use as an active material platform for authentic and prompt (within minutes) disease diagnosis via electrical or optical diagnostic tools or via electrochemical diagnosis. We present the opportunities provided by 2D materials as a platform for SARS-CoV-2 diagnosis.
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Affiliation(s)
- Pranay Ranjan
- Department of Physics, UAE University, Al-Ain, Abu Dhabi 15551, United Arab Emirates
| | - Vinoy Thomas
- Department of Materials Science and Engineering, University of Alabama at Birmingham, USA.
| | - Prashant Kumar
- Department of Physics, Indian Institute of Technology Patna, India.
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16
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Kim S, Yoo H. Self-Assembled Monolayers: Versatile Uses in Electronic Devices from Gate Dielectrics, Dopants, and Biosensing Linkers. MICROMACHINES 2021; 12:mi12050565. [PMID: 34067620 PMCID: PMC8155888 DOI: 10.3390/mi12050565] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 11/19/2022]
Abstract
Self-assembled monolayers (SAMs), molecular structures consisting of assemblies formed in an ordered monolayer domain, are revisited to introduce their various functions in electronic devices. SAMs have been used as ultrathin gate dielectric layers in low-voltage transistors owing to their molecularly thin nature. In addition to the contribution of SAMs as gate dielectric layers, SAMs contribute to the transistor as a semiconducting active layer. Beyond the transistor components, SAMs have recently been applied in other electronic applications, including as remote doping materials and molecular linkers to anchor target biomarkers. This review comprehensively covers SAM-based electronic devices, focusing on the various applications that utilize the physical and chemical properties of SAMs.
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17
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A polyaniline/platinum coated fiber optic surface plasmon resonance sensor for picomolar detection of 4-nitrophenol. Sci Rep 2021; 11:10086. [PMID: 33980883 PMCID: PMC8115283 DOI: 10.1038/s41598-021-89396-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/26/2021] [Indexed: 12/19/2022] Open
Abstract
The paper reports for the first time an innovative polyaniline (PANI)/platinum (Pt)-coated fiber optic-surface plasmon resonance (FO-SPR) sensor used for highly-sensitive 4-nitrophenol (4-NP) pollutant detection. The Pt thin film was coated over an unclad core of an optical fiber (FO) using a DC magnetron sputtering technique, while the 4-NP responsive PANI layer was synthetized using a cost-effective electroless polymerization method. The presence of the electrolessly-grown PANI on the Pt-coated FO was observed by field-emission scanning electron microscopy and subsequently evidenced by energy dispersive X-ray analysis. These FO-SPR sensors with a demonstrated bulk sensitivity of 1515 nm/RIU were then employed for 4-NP sensing, exhibiting an excellent limit-of-detection (LOD) in the low picomolar range (0.34 pM). The proposed sensor’s configuration has many other advantages, such as low-cost production, small size, immunity to electromagnetic interferences, remote sensing capability, and moreover, can be operated as a “stand-alone device”, making it thus well-suited for applications such as “on-site” screening of extremely low-level trace pollutants.
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18
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Farhana FZ, Umer M, Saeed A, Pannu AS, Husaini S, Sonar P, Firoz SH, Shiddiky MJA. e-MagnetoMethyl IP: a magnetic nanoparticle-mediated immunoprecipitation and electrochemical detection method for global DNA methylation. Analyst 2021; 146:3654-3665. [PMID: 33949437 DOI: 10.1039/d1an00345c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The quantification of global 5-methylcytosine (5mC) content has emerged as a promising approach for the diagnosis and prognosis of cancers. However, conventional methods for the global 5mC analysis require large quantities of DNA and may not be useful for liquid biopsy applications, where the amount of DNA available is limited. Herein, we report magnetic nanoparticles-assisted methylated DNA immunoprecipitation (e-MagnetoMethyl IP) coupled with electrochemical quantification of global DNA methylation. Carboxyl (-COOH) group-functionalized iron oxide nanoparticles (C-IONPs) synthesized by a novel starch-assisted gel formation method were conjugated with anti-5mC antibodies through EDC/NHS coupling (anti-5mC/C-IONPs). Anti-5mC/C-IONPs were subsequently mixed with DNA samples, in which they acted as dispersible capture agents to selectively bind 5mC residues and capture the methylated fraction of genomic DNA. The target-bound Anti-5mC/C-IONPs were magnetically separated and directly adsorbed onto the gold electrode surface using gold-DNA affinity interaction. The amount of DNA adsorbed on the electrode surface, which corresponds to the DNA methylation level in the sample, was electrochemically estimated by differential pulse voltammetric (DPV) study of an electroactive indicator [Ru(NH3)6]3+ bound to the surface-adsorbed DNA. Using a 200 ng DNA sample, the assay could successfully detect differences as low as 5% in global DNA methylation levels with high reproducibility (relative standard deviation (% RSD) = <5% for n = 3). The method could also reproducibly analyze various levels of global DNA methylation in synthetic samples as well as in cell lines. The method avoids bisulfite treatment, does not rely on enzymes for signal generation, and can detect global DNA methylation using clinically relevant quantities of sample DNA without PCR amplification. We believe that this proof-of-concept method could potentially find applications for liquid biopsy-based global DNA methylation analysis in point-of-care settings.
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Affiliation(s)
- Fatema Zerin Farhana
- Department of Chemistry, Bangladesh University of Engineering and Technology (BUET), Dhaka 1000, Bangladesh.
| | - Muhammad Umer
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia.
| | - Ayad Saeed
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia.
| | - Amandeep Singh Pannu
- School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane 4000, Australia and Centre for Material Science, Queensland University of Technology (QUT), Brisbane 4000, Australia
| | - Sediqa Husaini
- School of Environment and Science (ESC), Griffith University, Nathan Campus, QLD 4111, Australia
| | - Prashant Sonar
- School of Chemistry and Physics, Queensland University of Technology (QUT), Brisbane 4000, Australia and Centre for Material Science, Queensland University of Technology (QUT), Brisbane 4000, Australia
| | - Shakhawat H Firoz
- Department of Chemistry, Bangladesh University of Engineering and Technology (BUET), Dhaka 1000, Bangladesh.
| | - Muhammad J A Shiddiky
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, QLD 4111, Australia. and School of Environment and Science (ESC), Griffith University, Nathan Campus, QLD 4111, Australia
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19
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Martisova A, Holcakova J, Izadi N, Sebuyoya R, Hrstka R, Bartosik M. DNA Methylation in Solid Tumors: Functions and Methods of Detection. Int J Mol Sci 2021; 22:ijms22084247. [PMID: 33921911 PMCID: PMC8073724 DOI: 10.3390/ijms22084247] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i) sodium bisulfite conversion, (ii) methylation-sensitive restriction enzymes, and (iii) interactions of 5-methylcytosine (5mC) with methyl-binding proteins or antibodies against 5mC. In addition to standard methods, we describe recent advances in next generation sequencing technologies applied to DNA methylation analysis, as well as in development of biosensors that represent their cheaper and faster alternatives. Most importantly, we highlight not only advantages, but also disadvantages and challenges of each method.
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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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Electrochemically detecting DNA methylation in the EN1 gene promoter: implications for understanding ageing and disease. Biosci Rep 2021; 40:226876. [PMID: 33135722 PMCID: PMC7670582 DOI: 10.1042/bsr20202571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/29/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
There is a growing need for biomarkers which predict age-onset pathology. Although this is challenging, the methylome offers significant potential. Cancer is associated with the hypermethylation of many gene promoters, among which are developmental genes. Evolutionary theory suggests developmental genes arbitrate early-late life trade-offs, causing epimutations that increase disease vulnerability. Such genes could predict age-related disease. The aim of this work was to optimise an electrochemical procedure for the future investigation of a broad range of ageing-related pathologies. An electrochemical approach, which adopted three analytical techniques, was used to investigate DNA methylation in the engrailed-1 (EN1) gene promoter. Using synthetic single-stranded DNA, one technique was able to detect DNA at concentrations as low as 10 nM, with methylation status distinguishable at concentrations >25 nM. A negative correlation could be observed between % methylation of a heterogeneous solution and the key electrochemical parameter, charge transfer resistance (Rct; r = -0.982, P<0.01). The technique was applied to the breast cancer cell line Michigan Cancer Foundation-7 (MCF-7), where a similar correlation was observed (r = -0.965, P<0.01). These results suggest electrochemistry can effectively measure DNA methylation at low concentrations of DNA. This has implications for the future detection of age-related disease.
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22
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Wang YH, Song Z, Hu XY, Wang HS. Circulating tumor DNA analysis for tumor diagnosis. Talanta 2021; 228:122220. [PMID: 33773726 DOI: 10.1016/j.talanta.2021.122220] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/05/2021] [Accepted: 02/13/2021] [Indexed: 01/10/2023]
Abstract
Tumor is a kind of abnormal organism generated by the proliferation and differentiation of cells in the body under the action of various initiating and promoting factors, which seriously threatens human life and health. Tumorigenesis is a gradual process that involves multistage reactions and the accumulation of mutations. Gene mutation usually occurs during tumorigenesis, and can be used for tumor diagnosis. Early diagnosis is the most effective way to improve the cure rate and reduce the mortality rate. Among the peripheral blood circulating tumor DNA (ctDNA), gene mutation in keeping with tumor cells can be detected, which can potentially replace tumor tissue section for early diagnosis. It has been considered as a liquid biopsy marker with good clinical application prospect. However, the high fragmentation and low concentration of ctDNA in blood result in the difficulty of tumor stage determination. Therefore, high sensitive and specific mutation detection methods have been developed to detect trace mutant ctDNA. At present, the approaches include digital PCR (dPCR), Bead, Emulsion, Amplification and Magnetic (BEAMing), Next Generation Sequencing (NGS), Amplification Refractory Mutation System (ARMS), etc. In this paper, the principle, characteristics, latest progress and application prospects of these methods are reviewed, which will facilitate researchers to choose appropriate ctDNA detection approaches.
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Affiliation(s)
- Yi-Hui Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing, 210009, China; Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhen Song
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing, 210009, China; Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, 210009, China
| | - Xin-Yuan Hu
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing, 210009, China; Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, 210009, China
| | - Huai-Song Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (Ministry of Education), China Pharmaceutical University, Nanjing, 210009, China; Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, 210009, China.
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23
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Ahmadi M, Ghoorchian A, Dashtian K, Kamalabadi M, Madrakian T, Afkhami A. Application of magnetic nanomaterials in electroanalytical methods: A review. Talanta 2020; 225:121974. [PMID: 33592722 DOI: 10.1016/j.talanta.2020.121974] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/07/2020] [Accepted: 12/03/2020] [Indexed: 02/08/2023]
Abstract
Magnetic nanomaterials (MNMs) have gained high attention in different fields of studies due to their ferromagnetic/superparamagnetic properties and their low toxicity and high biocompatibility. MNMs contain magnetic elements such as iron and nickel in metallic, bimetallic, metal oxide, and mixed metal oxide. In electroanalytical methods, MNMs have been applied as sorbents for sample preparation before the electrochemical detection (sorbent role), as the electrode modifier (catalytic role), and the integration of the above two roles (as both sorbent and catalytic agent). In this paper, the application of MNMs in electroanalytical methods have been classified based on the main role of the nanomaterial and discussed separately. Furthermore, catalytic activities of MNMs in electroanalytical methods such as redox electrocatalytic, nanozymes catalytic (peroxidase, catalase activity, oxidase activity, superoxide dismutase activity), catalyst gate, and nanocontainer have been discussed.
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Affiliation(s)
- Mazaher Ahmadi
- Faculty of Chemistry, Bu-Ali Sina University, Hamedan, Iran.
| | | | | | | | | | - Abbas Afkhami
- Faculty of Chemistry, Bu-Ali Sina University, Hamedan, Iran.
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24
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Zhang S, Huang J, Lu J, Liu M, Chen X, Su S, Mo F, Zheng J. Electrochemical and Optical Biosensing Strategies for DNA Methylation Analysis. Curr Med Chem 2020; 27:6159-6187. [DOI: 10.2174/0929867326666190903161750] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/24/2019] [Accepted: 08/07/2019] [Indexed: 12/14/2022]
Abstract
DNA methylation is considered as a crucial part of epigenetic modifications and a popular
research topic in recent decades. It usually occurs with a methyl group adding to the fifth carbon
atom of cytosine while the base sequence of DNA remains unchanged. DNA methylation has significant
influences on maintaining cell functions, genetic imprinting, embryonic development and
tumorigenesis procedures and hence the analysis of DNA methylation is of great medical significance.
With the development of analytical techniques and further research on DNA methylation,
numerous DNA methylation detection strategies based on biosensing technology have been developed
to fulfill various study requirements. This article reviewed the development of electrochemistry
and optical biosensing analysis of DNA methylation in recent years; in addition, we also reviewed
some recent advances in the detection of DNA methylation using new techniques, such as
nanopore biosensors, and highlighted the key technical and biological challenges involved in these
methods. We hope this paper will provide useful information for the selection and establishment of
analysis of DNA methylation.
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Affiliation(s)
- Shu Zhang
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, 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
| | - Jingrun Lu
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Min Liu
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Xi Chen
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Shasha Su
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Fei Mo
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, 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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25
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Dong D, Zhang J, Zhang R, Li F, Li Y, Jia Y. Multiprobe Assay for Clinical SEPT9 Methylation Based on the Carbon Dot-Modified Liquid-Exfoliated Graphene Field Effect Transistor with a Potential to Present a Methylation Panorama. ACS OMEGA 2020; 5:16228-16237. [PMID: 32656445 PMCID: PMC7346271 DOI: 10.1021/acsomega.0c02022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/11/2020] [Indexed: 05/11/2023]
Abstract
The hypermethylation in the promoter region of the SEPT9 gene is associated with the development of colorectal cancer (CRC). Although its clinical significance for early diagnosis and screening of CRC has been demonstrated, the tedious operations in the conventional DNA methylation (DNAm) detection hinder its wide application. Herein, an electronic method for determining SEPT9 methylation in CRC patients is proposed by using the carbon dot-modified liquid exfoliated graphene field effect transistor (CDs-LEG-FET) as the DNAm sensor, the specifically designed probes to capture the SEPT9 gene and the immunologic recognition to recognize 5-methylcytosine (5mC) positions on the anchored sequences. The identification and nanomorphology of the as-prepared materials and devices are executed first by the characterizations of UV-vis, Raman, atomic force microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and electronic measurements. Then, the role of CDs in enhancing DNAm sensitivity of CD-LEG-FET is manifested by comparing it with that of CD-free LEG-FET. Third, the captured SEPT9 genes on CD-LEG-FETs by different probes are evaluated, and the optimized temperature for hybridizing the target ssDNA sequences is determined to be 48 °C. Furthermore, the detection sensitivity for the low-quantity of DNA samples is demonstrated to be as low as 2 ng. Finally, the methylation degree of the tumor and corresponding noncancerous tissue DNA samples were examined by the proposed electric method and methylight assay in parallel. The diagnostic value of the electrical assay is confirmed by using the receiver operating characteristic curves; meanwhile, the superiority of the CD-LEG-FET platform is found to present a methylation panorama of the target gene.
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Affiliation(s)
- Dong Dong
- Department
of Laboratory, Tianjin’s Clinical Research Center for Cancer,
Key Laboratory of Cancer Prevention and Therapy, National Clinical
Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin 300060, China
| | - Jizhao Zhang
- College
of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071, China
| | - Runshi Zhang
- Department
of Laboratory, Tianjin’s Clinical Research Center for Cancer,
Key Laboratory of Cancer Prevention and Therapy, National Clinical
Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin 300060, China
| | - Fang Li
- College
of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071, China
| | - Yueguo Li
- Department
of Laboratory, Tianjin’s Clinical Research Center for Cancer,
Key Laboratory of Cancer Prevention and Therapy, National Clinical
Research Center for Cancer, Tianjin Medical
University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yunfang Jia
- College
of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071, China
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26
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Tang C, He Z, Liu H, Xu Y, Huang H, Yang G, Xiao Z, Li S, Liu H, Deng Y, Chen Z, Chen H, He N. Application of magnetic nanoparticles in nucleic acid detection. J Nanobiotechnology 2020; 18:62. [PMID: 32316985 PMCID: PMC7171821 DOI: 10.1186/s12951-020-00613-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 12/16/2022] Open
Abstract
Nucleic acid is the main material for storing, copying, and transmitting genetic information. Gene sequencing is of great significance in DNA damage research, gene therapy, mutation analysis, bacterial infection, drug development, and clinical diagnosis. Gene detection has a wide range of applications, such as environmental, biomedical, pharmaceutical, agriculture and forensic medicine to name a few. Compared with Sanger sequencing, high-throughput sequencing technology has the advantages of larger output, high resolution, and low cost which greatly promotes the application of sequencing technology in life science research. Magnetic nanoparticles, as an important part of nanomaterials, have been widely used in various applications because of their good dispersion, high surface area, low cost, easy separation in buffer systems and signal detection. Based on the above, the application of magnetic nanoparticles in nucleic acid detection was reviewed.
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Affiliation(s)
- Congli Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziyu He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yuyue Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hao Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Gaojian Yang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Ziqi Xiao
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096 China
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Chen X, Wang L, Lou J. Nanotechnology Strategies for the Analysis of Circulating Tumor DNA: A Review. Med Sci Monit 2020; 26:e921040. [PMID: 32200389 PMCID: PMC7111132 DOI: 10.12659/msm.921040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Circulating tumor DNA (ctDNA) describes the fragmented DNA released from tumor cells into the blood. The ctDNA may have the same genetic changes as the primary tumor. Currently, ctDNA has become a popular biomarker for diagnosis, treatment, real-time clinical response monitoring, and prognosis, for solid tumors. Detection of ctDNA is minimally invasive, and repeat sampling can easily be performed. However, due to its low quality and short DNA fragment length, ctDNA detection still faces challenges and requires highly sensitive analytical techniques. Recently, liquid biopsies for the analysis of circulating tumor cells (CTCs) and circulating tumor-derived exosomes have been studied, and nanotechnology techniques have rapidly developed. Compared to traditional analytical methods, these nanotechnology-based platforms have the advantages of sensitivity, multiplex detection, simplicity, miniaturization, and automation, which support their potential use in clinical practice. This review aims to discuss the recent nanotechnological strategies for ctDNA analysis and the design of reliable techniques for ctDNA detection and to identify the potential clinical applications.
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Affiliation(s)
- Xiaomin Chen
- Nano Biomedical Research Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China (mainland).,Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China (mainland)
| | - Lin Wang
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China (mainland)
| | - Jiatao Lou
- Department of Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China (mainland)
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Povedano E, Ruiz-Valdepeñas Montiel V, Gamella M, Pedrero M, Barderas R, Peláez-García A, Mendiola M, Hardisson D, Feliú J, Yáñez-Sedeño P, Campuzano S, Pingarrón JM. Amperometric Bioplatforms To Detect Regional DNA Methylation with Single-Base Sensitivity. Anal Chem 2020; 92:5604-5612. [PMID: 32073832 DOI: 10.1021/acs.analchem.0c00628] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This work reports the first bioplatform able to determine electrochemically 5-hydroxymethylcytosine (5-hmC) methylation events at localized sites and single-base sensitivity. The described bioplatform relies on a specific antibody (anti-5-hmC), further conjugated with commercial bioreagents loaded with multiple horseradish peroxidase (HRP) molecules, recognizing the epimark in a target DNA, captured through hybridization onto streptavidin-magnetic microbeads (Strep-MBs) modified with a complementary DNA capture probe. The electrochemical detection is performed by amperometry (-0.20 V vs Ag pseudoreference electrode) at disposable screen-printed carbon electrodes (SPCEs) in the presence of H2O2/hydroquinone (HQ) upon magnetic capture of the modified MBs onto the SPCE. The use of the commercial bioreagents ProtA-polyHRP80 and Histostar, very scarcely explored so far in electrochemical biosensors, provides high sensitivities for a synthetic target DNA sequence with a unique 5-hmC in the promoter region of MGMT tumor suppressor gene. Amplification factors of 43.6 and 55.2 were achieved using ProtA-polyHRP80 or Histostar, respectively, compared to the conventional secondary antibody labeling. This amplification was crucial to detect methylation events at single-nucleotide resolution achieving limits of detection (LODs) of 23.0 and 13.2 pM, respectively, without any target DNA amplification. The ProtA-polyHRP80-based bioplatform, selected as a compromise between sensitivity and cost per determination, exhibited full discrimination toward the target 5-hmC against the closely related 5-mC. In addition, the bioplatform detected 5-hmC at the regional level (MGMT promoter region) in just 10 ng of genomic DNA (gDNA, ∼2700 genomes) extracted from cancer cells and tissues from colorectal cancer (CRC) patients within 60 min.
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Affiliation(s)
- Eloy Povedano
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | - Maria Gamella
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - María Pedrero
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Rodrigo Barderas
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Alberto Peláez-García
- Molecular Pathology and Therapeutic Targets Group, IdiPAZ, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group, IdiPAZ, Hospital Universitario La Paz, 28046 Madrid, Spain.,Translational Oncology Group, IdiPAZ, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - David Hardisson
- Molecular Pathology and Therapeutic Targets Group, IdiPAZ, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Jaime Feliú
- Center for Biomedical Research in the Cancer Network, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Paloma Yáñez-Sedeño
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Susana Campuzano
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - José M Pingarrón
- Departamento de Quı́mica Analı́tica, Facultad de CC. Quı́micas, Universidad Complutense de Madrid, 28040 Madrid, Spain
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29
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Bahri M, Baraket A, Zine N, Ben Ali M, Bausells J, Errachid A. Capacitance electrochemical biosensor based on silicon nitride transducer for TNF-α cytokine detection in artificial human saliva: Heart failure (HF). Talanta 2020; 209:120501. [DOI: 10.1016/j.talanta.2019.120501] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 02/03/2023]
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30
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Campuzano S, Barderas R, Pedrero M, Yáñez-Sedeño P, Pingarrón JM. Electrochemical biosensing to move forward in cancer epigenetics and metastasis: A review. Anal Chim Acta 2020; 1109:169-190. [PMID: 32252900 DOI: 10.1016/j.aca.2020.01.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/13/2022]
Abstract
Early detection and effective treatment are crucial to reduce the physical, emotional, and financial pressure exerted by growing cancer burden on individuals, families, communities, and health systems. Currently, it is clear that the accurate analysis of emerging cancer epigenetic and metastatic-related biomarkers at different molecular levels is envisaged as an exceptional solution for early and reliable diagnosis and the improvement of therapy efficiency through personalized treatments. Within this field, electrochemical biosensing has demonstrated to be competitive over other emerging and currently used methodologies for the determination of these biomarkers accomplishing the premises of user-friendly, multiplexing ability, simplicity, reduced costs and decentralized analysis, demanded by clinical oncology, thus priming electrochemical biosensors to spark a diagnostic revolution for cancer prediction and eradication. This review article critically discusses the main characteristics, opportunities and versatility exhibited by electrochemical biosensing, through highlighting representative examples published during the last two years, for the reliable determination of these emerging biomarkers, with great diagnostic, predictive and prognostic potential. Special attention is paid on electrochemical affinity biosensors developed for the single or multiplexed determination of methylation events, non-coding RNAs, ctDNA features and metastasis-related protein biomarkers both in liquid and solid biopsies of cancer patients. The main challenges to which further work must be addressed and the impact of these advances should have in the clinical acceptance of these emerging biomarkers are also discussed which decisively will contribute to understand the molecular basis involved in the epigenetics and metastasis of cancer and to apply more efficient personalized therapies.
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Affiliation(s)
- S Campuzano
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain.
| | - R Barderas
- Chronic Disease Programme, UFIEC, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain
| | - M Pedrero
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - P Yáñez-Sedeño
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - J M Pingarrón
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain.
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31
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Carr O, Raymundo-Pereira PA, Shimizu FM, Sorroche BP, Melendez ME, de Oliveira Pedro R, Miranda PB, Carvalho AL, Reis RM, Arantes LMRB, Oliveira ON. Genosensor made with a self-assembled monolayer matrix to detect MGMT gene methylation in head and neck cancer cell lines. Talanta 2019; 210:120609. [PMID: 31987176 DOI: 10.1016/j.talanta.2019.120609] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 12/24/2022]
Abstract
DNA methylation is involved in the oncogenesis of head and neck squamous cell carcinoma and could be used for early detection of cancer to increase the chances of cure, but unfortunately diagnosis is usually made at late stages of the disease. In this work we developed genosensors to detect DNA methylation of the MGMT gene in head and neck cancer cell lines. The probe for MGMT promoter methylation was immobilized on gold electrodes modified with 11-mercaptoundecanoic acid (11-MUA) self-assembled monolayers (SAM). Detection was performed with electrochemical impedance spectroscopy, with clear distinction between methylated and non-methylated DNA from head and neck cell lines. The genosensor is sensitive with a low detection limit of 0.24 × 10-12 mol L-1. In addition, the cell lines FaDu, JHU28 and SCC25 for the MGMT gene, could be distinguished from the HN13 cell line which has a high degree of MGMT methylation (97%), thus confirming the selectivity. Samples with different percentages of MGMT DNA methylation could be separated in multidimensional projections using the visualization technique interactive document mapping (IDMAP). The genosensor matrix and the immobilization procedures are generic, and can be extended to other DNA methylation biomarkers.
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Affiliation(s)
- Olivia Carr
- São Carlos Institute of Physics, University of São Paulo, 13566-590, São Carlos, Brazil
| | | | - Flávio M Shimizu
- São Carlos Institute of Physics, University of São Paulo, 13566-590, São Carlos, Brazil
| | - Bruna Pereira Sorroche
- Molecular Oncology Research Center, Barretos Cancer Hospital, 14784-400, Barretos, Brazil
| | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, 14784-400, Barretos, Brazil
| | | | - Paulo B Miranda
- São Carlos Institute of Physics, University of São Paulo, 13566-590, São Carlos, Brazil
| | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, 14784-400, Barretos, Brazil
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, 14784-400, Barretos, Brazil; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Lídia M R B Arantes
- Molecular Oncology Research Center, Barretos Cancer Hospital, 14784-400, Barretos, Brazil
| | - Osvaldo N Oliveira
- São Carlos Institute of Physics, University of São Paulo, 13566-590, São Carlos, Brazil.
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32
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Mohajeri N, Imani M, Akbarzadeh A, Sadighi A, Zarghami N. An update on advances in new developing DNA conjugation diagnostics and ultra-resolution imaging technologies: Possible applications in medical and biotechnological utilities. Biosens Bioelectron 2019; 144:111633. [DOI: 10.1016/j.bios.2019.111633] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
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33
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Sadighbayan D, Sadighbayan K, Khosroushahi AY, Hasanzadeh M. Recent advances on the DNA-based electrochemical biosensing of cancer biomarkers: Analytical approach. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.07.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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34
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Nanomaterials as efficient platforms for sensing DNA. Biomaterials 2019; 214:119215. [DOI: 10.1016/j.biomaterials.2019.05.026] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/13/2019] [Accepted: 05/16/2019] [Indexed: 02/07/2023]
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35
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Opportunities, Challenges, and Prospects in Electrochemical Biosensing of Circulating Tumor DNA and its Specific Features. SENSORS 2019; 19:s19173762. [PMID: 31480367 PMCID: PMC6749466 DOI: 10.3390/s19173762] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/24/2019] [Accepted: 08/25/2019] [Indexed: 12/19/2022]
Abstract
Nowadays, analyzing circulating tumor DNA (ctDNA), a very small part of circulating free DNA (cfDNA) carried by blood, is considered to be an interesting alternative to conventional single-site tumor tissue biopsies, both to assess tumor burden and provide a more comprehensive snapshot of the time-related and spatial heterogeneity of cancer genetic/epigenetic scenery. The determination of ctDNA and/or mapping its characteristic features, including tumor-specific mutations, chromosomal aberrations, microsatellite alterations, and epigenetic changes, are minimally invasive, powerful and credible biomarkers for early diagnosis, follow-up, prediction of therapy response/resistance, relapse monitoring, and tracking the rise of new mutant subclones, leading to improved cancer outcomes This review provides an outline of advances published in the last five years in electrochemical biosensing of ctDNA and surrogate markers. It emphasizes those strategies that have been successfully applied to real clinical samples. It highlights the unique opportunities they offer to shift the focus of cancer patient management methods from actual decision making, based on clinic-pathological features, to biomarker-driven treatment strategies, based on genotypes and customized targeted therapies. Also highlighted are the unmet hurdles and future key points to guide these devices in the development of liquid biopsy cornerstone tools in routine clinical practice for the diagnosis, prognosis, and therapy response monitoring in cancer patients.
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36
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Huang B, Ji L, Liang B, Cao Q, Tu T, Ye X. A simple and low-cost screen printed electrode for hepatocellular carcinoma methylation detection. Analyst 2019; 144:3282-3288. [PMID: 30942220 DOI: 10.1039/c9an00191c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There is a great demand for robust diagnostic and prognostic approaches for Hepatocellular Carcinoma (HCC). DNA methylation, a common epigenetic modification, has been found in many promoter regions of tumor suppressor genes. Hypermethylation of these gene promoters will repress the gene transcription and lead to the occurrence of cancers. The abnormal methyation level of the p16 gene promoter could be a promising marker for the detection of HCC. The adsorption affinities between different DNA bases and AuNPs are not the same. After bisulfite treatment and asymmetric PCR, methylation and unmethylation sequences can be changed into guanine-enriched and adenine-enriched sequences, respectively. A home-made gold nanoparticle modified screen printed carbon electrode (AuNP-SPCE) was employed to distinguish the adsorption affinities between guanine-enriched and adenine-enriched sequences, which could be used to analyze the level of DNA methylation. Several key experimental factors were investigated and optimized. The results had shown that the optimal AuNP electrodeposition time was 100 s and 15 min of adsorption could distinguish guanine-enriched and adenine-enriched sequences with a concentration of 100 nM at 25 °C. The detection limit of our AuNP-SPCE was 1.1 ng, and the assay had a good sensitivity of 10% methylation change and was able to distinguish only one methylated CpG site. What's more, the RSD over three assays with a disposable AuNP-SPCE was ≤7.2%. The assay was applied to real samples including cell lines and clinical tissues. Compared with normal hepatic cell lines and normal tissues, lower signals of HCC cell lines and cancer tissues were observed, respectively. It had shown a good discrimination of the abnormal methylation level of the p16 gene promoter.
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Affiliation(s)
- Bobo Huang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, PR China.
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37
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Wang Z, Hu S, Li F, Fan Q, Jia Y. Study of porphyrin-modified liquid exfoliated graphene field-effect transistors for evaluating DNA methylation degree. Analyst 2019; 144:4787-4794. [PMID: 31305809 DOI: 10.1039/c9an00993k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The applications of graphene field-effect transistors (FETs) for monitoring DNA hybridization have been widely accepted; however, for evaluating DNA methylation degree, an emerging requirement of epigenetic research, no work has been found due to the difficulties in detecting 5-methylcytosine (5mC) sites along the genomic sequence as well as counting their amount (NmC). Herein, to achieve this, a strategy for exploiting a liquid exfoliated graphene (LEG)-based FET (LEG-FET) as a sensing platform was proposed. First, LEG-FETs were prepared and activated by tetra-4-aminophenyl-porphyrin (TAPP) for anchoring single-strand DNAs (ssDNAs). Second, the 5mC sites in ssDNA were recognized by the specifically absorbed 5mC antibody (5mCab) and transduced to the changed currents (ΔIDS) by LEG-FET according to the integration of the methylation-immuno sensing principle and FET's working mechanism. Briefly, more 5mCab molecules could be captured by more 5mC sites, resulting in larger ΔIDS. The TAPP effects on LEG-FET were analyzed by SEM, Raman, AFM, and XPS characterizations as well as electronic measurements. The validity of this LEG-FET sensing platform for evaluating DNA methylation degree was proven step by step; this included the examinations of the synthesized ssDNAs with the known NmC and real ssDNA samples, whose methylation degrees were pre-determined by the gold-standard method, which is based on tedious bisulphite sequence operations and expensive mass spectrometry technology. Moreover, theoretical explanations were also provided for the sensing mechanism in the proposed DNA methylation analytical components. In conclusion, the positive and linear relations of IDS changing ratio vs. NmC as well as the detection limit of one 5mC site indicate that TAPP-modified LEG-FET can provide an alternative analytical tool to realize fast and economical DNA methylation evaluation.
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Affiliation(s)
- Zhongrong Wang
- College of Electronic Information and Optical Engineering, Nankai University, Tianjin, China.
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38
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Rafique S, Khan S, Bashir S, Nasir R. Facile development of highly sensitive femtomolar electrochemical DNA biosensor using gold nanoneedle-modified electrode. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00874-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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39
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Sato S, Nishi Y, Takenaka S. Electrochemical Aberrant Methylation Detection Based on Ferrocenyl Naphthalene Diimide Carrying β‐Cyclodextrin, FNC. ELECTROANAL 2019. [DOI: 10.1002/elan.201900282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Shinobu Sato
- Department of Applied ChemistryKyushu Institute of Technology Fukuoka 804-8550 Japan
- Research Center for Bio-microsensing TechnologyKyushu Institute of Technology Fukuoka 804-8550 Japan
| | - Yukiko Nishi
- Department of Applied ChemistryKyushu Institute of Technology Fukuoka 804-8550 Japan
| | - Shigeori Takenaka
- Department of Applied ChemistryKyushu Institute of Technology Fukuoka 804-8550 Japan
- Research Center for Bio-microsensing TechnologyKyushu Institute of Technology Fukuoka 804-8550 Japan
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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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41
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Yáñez-Sedeño P, Campuzano S, Pingarrón JM. Pushing the limits of electrochemistry toward challenging applications in clinical diagnosis, prognosis, and therapeutic action. Chem Commun (Camb) 2019; 55:2563-2592. [PMID: 30688320 DOI: 10.1039/c8cc08815b] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Constant progress in the identification of biomarkers at different molecular levels in samples of different natures, and the need to conduct routine analyses, even in limited-resource settings involving simple and short protocols, are examples of the growing current clinical demands not satisfied by conventional available techniques. In this context, the unique features offered by electrochemical biosensors, including affordability, real-time and reagentless monitoring, simple handling and portability, and versatility, make them especially interesting for adaptation to the increasingly challenging requirements of current clinical and point-of-care (POC) diagnostics. This has allowed the continuous development of strategies with improved performance in the clinical field that were unthinkable just a few years ago. After a brief introduction to the types and characteristics of clinically relevant biomarkers/samples, requirements for their analysis, and currently available methodologies, this review article provides a critical discussion of the most important developments and relevant applications involving electrochemical biosensors reported in the last five years in response to the demands of current diagnostic, prognostic, and therapeutic actions related to high prevalence and high mortality diseases and disorders. Special attention is paid to the rational design of surface chemistry and the use/modification of state-of-the-art nanomaterials to construct electrochemical bioscaffolds with antifouling properties that can be applied to the single or multiplex determination of biomarkers of accepted or emerging clinical relevance in particularly complex clinical samples, such as undiluted liquid biopsies, whole cells, and paraffin-embedded tissues, which have scarcely been explored using conventional techniques or electrochemical biosensing. Key points guiding future development, challenges to be addressed to further push the limits of electrochemical biosensors towards new challenging applications, and their introduction to the market are also discussed.
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Affiliation(s)
- P Yáñez-Sedeño
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
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42
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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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Povedano E, Montiel VRV, Valverde A, Navarro-Villoslada F, Yáñez-Sedeño P, Pedrero M, Montero-Calle A, Barderas R, Peláez-García A, Mendiola M, Hardisson D, Feliú J, Camps J, Rodríguez-Tomàs E, Joven J, Arenas M, Campuzano S, Pingarrón JM. Versatile Electroanalytical Bioplatforms for Simultaneous Determination of Cancer-Related DNA 5-Methyl- and 5-Hydroxymethyl-Cytosines at Global and Gene-Specific Levels in Human Serum and Tissues. ACS Sens 2019; 4:227-234. [PMID: 30499292 DOI: 10.1021/acssensors.8b01339] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This paper reports the preparation of versatile electrochemical biosensing platforms for the simple, rapid, and PCR-independent detection of the most frequent DNA methylation marks (5-methylcytosine, 5-mC, and/or 5-hydroxymethylcytosine, 5-hmC) both at global and gene-specific levels. The implemented strategies, relying on the smart coupling of immuno-magnetic beads (MBs), specific DNA probes and amperometric detection at screen-printed carbon electrodes (SPCEs), provided sensitive and selective determination of the target methylated DNAs in less than 90 min with a great reproducibility and demonstrated feasibility for the simultaneous detection of the same or different cytosine epimarks both at global level and in different loci of the same gene or in different genes. The bioplatforms were applied to determine global methylation events in paraffin-embedded colorectal tissues and specific methylation at promoters of tumor suppressor genes in genomic DNA extracted from cancer cells and paraffin-embedded colorectal tissues, and in serum without previous DNA extraction from cancer patients.
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Affiliation(s)
- Eloy Povedano
- Departamento de
Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | | | - Alejandro Valverde
- Departamento de
Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Fernando Navarro-Villoslada
- Departamento de
Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Paloma Yáñez-Sedeño
- Departamento de
Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - María Pedrero
- Departamento de
Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Ana Montero-Calle
- Departamento de
Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Rodrigo Barderas
- UFIEC, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain
| | - Alberto Peláez-García
- Molecular Pathology and Therapeutic Targets Group Hospital Universitario La Paz IdiPAZ, 28046 Madrid, Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group Hospital Universitario La Paz IdiPAZ, 28046 Madrid, Spain
- Center for Biomedical Research in the Cancer Network (Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - David Hardisson
- Molecular Pathology and Therapeutic Targets Group Hospital Universitario La Paz IdiPAZ, 28046 Madrid, Spain
| | - Jaime Feliú
- Center for Biomedical Research in the Cancer Network (Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Translational Oncology Group Hospital Universitario La Paz IdiPAZ, 28046 Madrid, Spain
| | - Jordi Camps
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d́Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, E-43204 Reus, Spain
| | - Elisabet Rodríguez-Tomàs
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d́Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, E-43204 Reus, Spain
- Department of Radiation Oncology, Hospital Universitari Sant Joan, Institut d́Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, E-43204 Reus, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d́Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, E-43204 Reus, Spain
| | - Meritxell Arenas
- Unitat de Recerca Biomèdica, Hospital Universitari Sant Joan, Institut d́Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, E-43204 Reus, Spain
| | - Susana Campuzano
- Departamento de
Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - José M. Pingarrón
- Departamento de
Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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Bhattacharjee R, Moriam S, Umer M, Nguyen NT, Shiddiky MJA. DNA methylation detection: recent developments in bisulfite free electrochemical and optical approaches. Analyst 2018; 143:4802-4818. [PMID: 30226502 DOI: 10.1039/c8an01348a] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is one of the significant epigenetic modifications involved in mammalian development as well as in the initiation and progression of various diseases like cancer. Over the past few decades, an enormous amount of research has been carried out for the quantification of DNA methylation in the mammalian genome. Earlier, most of these methodologies used bisulfite treatment. However, the low conversion, false reading, longer assay time and complex chemical reaction are the common limitations of this method that hinder their application in routine clinical screening. Thus, as an alternative to bisulfite conversion-based DNA methylation detection, numerous bisulfite-free methods have been proposed. In this regard, electrochemical biosensors have gained much attention in recent years for being highly sensitive yet cost-effective, portable, and simple to operate. On the other hand, biosensors with optical readouts enable direct real time detection of biological molecules and are easily adaptable to multiplexing. Incorporation of electrochemical and optical readouts into bisulfite free DNA methylation analysis is paving the way for the translation of this important biomarker into standard patient care. In this review, we provide a critical overview of recent advances in the development of electrochemical and optical readout based bisulfite free DNA methylation assays.
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Affiliation(s)
- Ripon Bhattacharjee
- School of Environment and Science, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia.
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45
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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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46
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Povedano E, Valverde A, Montiel VR, Pedrero M, Yáñez‐Sedeño P, Barderas R, San Segundo‐Acosta P, Peláez‐García A, Mendiola M, Hardisson D, Campuzano S, Pingarrón JM. Rapid Electrochemical Assessment of Tumor Suppressor Gene Methylations in Raw Human Serum and Tumor Cells and Tissues Using Immunomagnetic Beads and Selective DNA Hybridization. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Eloy Povedano
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Alejandro Valverde
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Víctor Ruiz‐Valdepeñas Montiel
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - María Pedrero
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Paloma Yáñez‐Sedeño
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Rodrigo Barderas
- CROSADISInstituto de Salud Carlos III 28220 Majadahonda Madrid Spain
| | | | - Alberto Peláez‐García
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - David Hardisson
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - Susana Campuzano
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - José M. Pingarrón
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
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Povedano E, Valverde A, Montiel VR, Pedrero M, Yáñez‐Sedeño P, Barderas R, San Segundo‐Acosta P, Peláez‐García A, Mendiola M, Hardisson D, Campuzano S, Pingarrón JM. Rapid Electrochemical Assessment of Tumor Suppressor Gene Methylations in Raw Human Serum and Tumor Cells and Tissues Using Immunomagnetic Beads and Selective DNA Hybridization. Angew Chem Int Ed Engl 2018; 57:8194-8198. [DOI: 10.1002/anie.201804339] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/05/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Eloy Povedano
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Alejandro Valverde
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Víctor Ruiz‐Valdepeñas Montiel
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - María Pedrero
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Paloma Yáñez‐Sedeño
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - Rodrigo Barderas
- CROSADISInstituto de Salud Carlos III 28220 Majadahonda Madrid Spain
| | | | - Alberto Peláez‐García
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - David Hardisson
- Molecular Pathology and Therapeutic Targets GroupHospital Universitario La Paz IdiPAZ Madrid Spain
| | - Susana Campuzano
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
| | - José M. Pingarrón
- Departamento de Química AnalíticaFacultad de Ciencias QuímicasUniversidad Complutense de Madrid Av. Complutense s/n 28040 Madrid Spain
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