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Liu ZJ, Yang LY, Lu TC, Huang C, Liang YQ, Xu XW, Xu YF, Liu MM, Lin XH, Chen JY. Precise Differentiation of Wobble-Type Allele via Ratiometric Design of a Ligase Chain Reaction-Based Electrochemical Biosensor for CYP2C19*2 Genotyping of Clinical Samples. Anal Chem 2023; 95:14592-14599. [PMID: 37683102 DOI: 10.1021/acs.analchem.3c01907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
Due to the comparable stability between the perfect-base pair and the wobble-base pair, a precise differentiation of the wobble-type allele has remained a challenge, often leading to false results. Herein, we proposed a ligase chain reaction (LCR)-based ratiometric electrochemical DNA sensor, namely, R-eLCR, for a precise typing of the wobble-type allele, in which the traditionally recognized "negative" signal of wobble-base pair-mediated amplification was fully utilized as a "positive" one and a ratiometric readout mode was employed to ameliorated the underlying potential external influence and improved its detection accuracy in the typing of the wobble-type allele. The results showed that the ratio between current of methylene blue (IMB) and current of ferrocene (IFc) was partitioned in three regions and three types of wobble-type allele were thus precisely differentiated (AA homozygote: IMB/IFc > 2; GG homozygote: IMB/IFc < 1; GA heterozygote: 1 < IMB/IFc < 2); the proposed R-eLCR successfully discriminated the three types of CYP2C19*2 allele in nine cases of human whole blood samples, which was consistent with those of the sequencing method. These results evidence that the proposed R-eLCR can serve as an accurate and robust alternative for the identification of wobble-type allele, which lays a solid foundation and holds great potential for precision medicine.
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Affiliation(s)
- Zhou-Jie Liu
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Liang-Yong Yang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Tai-Cheng Lu
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Chen Huang
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Yu-Qi Liang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Xiong-Wei Xu
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Yan-Fang Xu
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - Meng-Meng Liu
- Department of Pharmacy, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Department of Pharmacy, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou 350212, China
| | - Xin-Hua Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Jin-Yuan Chen
- The Central Laboratory, Fujian Key Laboratory of Precision Medicine for Cancer, Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, the First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
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2
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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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3
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Huang B, Zhang B, Liang B, Fang L, Ye X. Ultra-low level detection of hepatocellular carcinoma global methylation using a AuNP modified carbon fiber microelectrode. RSC Adv 2020; 10:16277-16283. [PMID: 35498837 PMCID: PMC9052887 DOI: 10.1039/d0ra00905a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/30/2020] [Indexed: 01/31/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancerous diseases, with a low 5 year survival rate. Global hypomethylation drives genomic instability, which is regarded as one biomarker for early diagnosis. Long interspersed nucleotide element-1 (LINE-1) makes up around 17% of the genome, and could be regarded as a surrogate marker for global DNA methylation. In this work, a gold nanoparticle (AuNP) modified carbon fiber microelectrode (CFME) with a diameter of 7 μm was applied for the first time to detect the methylation level of LINE-1, by distinguishing adsorption affinities between different DNA bases and AuNPs. Several parameters, including AuNP electrodeposition time, sample adsorption time, and DNA concentration have been analyzed and optimized. The detection limit of our assay was 0.1 nM with only 2 μL sample solution. And the CFME had an excellent sensitivity of 10% methylation change and had the capacity to distinguish only one methylated CpG site. The global DNA methylation level of real samples including cell lines and clinical tissues was tested. Higher signals of HCC cell lines and cancer tissues were observed respectively, compared with normal hepatic cell lines and normal tissues. This work provides a promising approach for HCC early diagnosis and prognosis. Using a AuNP modified carbon fiber microelectrode to detect hepatocellular carcinoma global methylation with an ultra-low concentration of DNA samples.![]()
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Affiliation(s)
- Bobo Huang
- Biosensor National Special Laboratory
- Key Laboratory of Biomedical Engineering of Ministry of Education
- College of Biomedical Engineering and Instrument Science
- Innovation Center for Minimally Invasive Technique and Device
- Zhejiang University
| | - Bin Zhang
- Key Laboratory of Laparoscopic Technology of Zhejiang Province
- Department of General Surgery
- Sir Run-Run Shaw Hospital
- School of Medicine
- Zhejiang University
| | - Bo Liang
- Biosensor National Special Laboratory
- Key Laboratory of Biomedical Engineering of Ministry of Education
- College of Biomedical Engineering and Instrument Science
- Innovation Center for Minimally Invasive Technique and Device
- Zhejiang University
| | - Lu Fang
- College of Automation
- Hangzhou Dianzi University
- Hangzhou 310018
- PR China
| | - Xuesong Ye
- Biosensor National Special Laboratory
- Key Laboratory of Biomedical Engineering of Ministry of Education
- College of Biomedical Engineering and Instrument Science
- Innovation Center for Minimally Invasive Technique and Device
- Zhejiang University
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4
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Sina AAI, Carrascosa LG, Trau M. DNA Methylation-Based Point-of-Care Cancer Detection: Challenges and Possibilities. Trends Mol Med 2019; 25:955-966. [PMID: 31253589 DOI: 10.1016/j.molmed.2019.05.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/28/2019] [Accepted: 05/29/2019] [Indexed: 12/31/2022]
Abstract
Eukaryotic cell DNA conserves a distinct genomic methylation pattern, which acts as a molecular switch to control the transcriptional machinery of the cell. However, pathological processes can alter this methylation pattern, leading to the onset of diseases such as cancer. Recent advances in methylation analysis provide a more precise understanding of the consequence of DNA methylation changes towards cancer progression. Consequently, the discoveries of numerous methylation-based biomarkers have inspired the development of simple tests for cancer detection. In this opinion article, we systematically discuss the benefits and challenges associated with the promising methylation-based approaches and develop a point-of-care index to evaluate their potential in terms of point-of-care cancer diagnostics.
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Affiliation(s)
- Abu Ali Ibn Sina
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), Corner College and Cooper Roads (Bldg 75), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Laura G Carrascosa
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), Corner College and Cooper Roads (Bldg 75), The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), Corner College and Cooper Roads (Bldg 75), The University of Queensland, Brisbane, QLD 4072, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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Fu Y, Duan X, Huang J, Huang L, Zhang L, Cheng W, Ding S, Min X. Detection of KRAS mutation via ligation-initiated LAMP reaction. Sci Rep 2019; 9:5955. [PMID: 30976068 PMCID: PMC6459849 DOI: 10.1038/s41598-019-42542-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
KRAS mutations are abnormalities widely found in genomic DNA and circulating tumor DNA (ctDNA) of various types of cancers. Thus, highly sensitive detection of KRAS mutations in genomic DNA is of great significance in disease diagnosis and personalized medicine. Here, we developed a ligation-initiated loop-mediated isothermal amplification (LAMP) assaying method for ultrasensitive detection of KRAS mutation. In the presence of mutant KRAS DNA (mutDNA), the dumbbell-shaped structure (DSS) is formed by the specific ligation of two substrates (SLS1 and SLS2), which act as a template to initiate the following LAMP amplification. Making use of the outstanding specificity of ligation reaction and superior amplification of LAMP, 10 aM mutDNA can be accurately determined. In addition, as low as 0.1% mutDNA can be detected in the presence of a large excess of wild-type KRAS DNA (wtDNA), indicating the high sensitivity and specificity of the method. Furthermore, this strategy has been successfully applied for detection of a KRAS mutation from tissue samples of colorectal cancer patients. Thus, the developed ligation-initiated LAMP fluorescence assaying strategy presents a promising prospect for ultrasensitive detection of mutations.
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Affiliation(s)
- Yixin Fu
- Department of Laboratory Medicine, The Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, P.R. China.,School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China
| | - Xiaolei Duan
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China.,Key Laboratory of Clinical Laboratory Diagnostics (Ministry of education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Jian Huang
- Department of Laboratory Medicine, The Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, P.R. China.,School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China
| | - Lizhen Huang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Lutan Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Xun Min
- Department of Laboratory Medicine, The Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, P.R. China. .,School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China.
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6
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Čelešnik H, Potočnik U. Improved locus-specific unmethylated controls for MS-HRM analysis derived from 5-aza-2-deoxycytidine-treated DNA. Biotechniques 2019; 66:150-153. [DOI: 10.2144/btn-2018-0161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We report two restriction enzyme-based approaches for generating clean locus-specific unmethylated controls for methylation-sensitive high-resolution melting (MS-HRM) analyses. These unmethylated standards are derived from DNA treated with the demethylating agent 5-aza-2-deoxycytidine (5-Aza-dc). By using them, we overcome a limitation of 5-Aza-dc treatment – incomplete demethylation at various genomic regions. When 5-Aza-dc-treated DNA is used directly as unmethylated MS-HRM standard, partially demethylated DNA can give false methylation results. MS-HRM assay differentiates between methylated and unmethylated bisulfite-treated DNA based on the different melting profiles of PCR products amplified from them. To estimate test sample methylation levels, test sample melting profiles are compared to those of methylation standards. With our pure unmethylated controls, adequate standards of known methylation levels can be prepared for single-locus MS-HRM.
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Affiliation(s)
- Helena Čelešnik
- University of Maribor, Faculty of Chemistry & Chemical Engineering, Smetanova ulica 17, 2000 Maribor, Slovenia
- University of Maribor, Faculty of Medicine, Center for Human Molecular Genetics & Pharmacogenomics, Taborska ulica 8, 2000 Maribor, Slovenia
| | - Uroš Potočnik
- University of Maribor, Faculty of Chemistry & Chemical Engineering, Smetanova ulica 17, 2000 Maribor, Slovenia
- University of Maribor, Faculty of Medicine, Center for Human Molecular Genetics & Pharmacogenomics, Taborska ulica 8, 2000 Maribor, Slovenia
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7
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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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8
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Menschikowski M, Jandeck C, Friedemann M, Richter S, Thiem D, Lange BS, Suttorp M. Identification and Quantification of Heterogeneously-methylated DNA Fragments Using Epiallele-sensitive Droplet Digital Polymerase Chain Reaction (EAST-ddPCR). Cancer Genomics Proteomics 2018; 15:299-312. [PMID: 29976635 DOI: 10.21873/cgp.20088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/28/2018] [Accepted: 04/23/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND/AIM DNA methylation plays an important role in the initiation and propagation of carcinogenesis; however, the role of heterogeneously methylated epialleles is currently not well studied, also due to the lack of sensitive, unbiased and high throughput methods. Here, a newly developed droplet digital PCR (ddPCR)-based method was evaluated regarding its ability to quantify such heterogeneously methylated epialleles with sufficient analytical sensitivity and specificity. MATERIALS AND METHODS Genomic DNA from blood leukocytes and bone marrow aspirate of an 8-year old male with B-cell acute lymphoblastic leukemia (B-ALL) and from normal and malignant prostate cell lines were analysed using ddPCR. RESULTS By using these DNA samples, the specificity of an applied set of fluorescence-labeled probes was demonstrated as a proof of concept. CONCLUSION All individual heterogeneously-methylated epialleles were quantifiable by a set of fluorescence-labeled probes with complementary sequences to epialleles in a closed-tube and high-throughput manner. The new method named epiallele-sensitive droplet digital PCR (EAST-ddPCR) may give new insights in the generation and regulation of epialleles and may help in finding new biomarkers for the diagnosis of benign und malignant diseases.
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Affiliation(s)
- Mario Menschikowski
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Carsten Jandeck
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Markus Friedemann
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Susan Richter
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Dana Thiem
- Department of Pediatrics, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Björn Sönke Lange
- Department of Pediatrics, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
| | - Meinolf Suttorp
- Department of Pediatrics, University Hospital "Carl Gustav Carus", Technical University of Dresden, Dresden, Germany
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9
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Yuan Y, Hong T, Chen Y, Wang Y, Qiu X, Zheng F, Weng X, Zhou X. Luminescence Sensing for Qualitative and Quantitative Detection of 5-Methylcytosine. Anal Chem 2018; 90:10064-10068. [DOI: 10.1021/acs.analchem.8b02842] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yushu Yuan
- Key Laboratory
of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Tingting Hong
- Key Laboratory
of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Yi Chen
- Key Laboratory
of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Yafen Wang
- Key Laboratory
of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Xueping Qiu
- Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430071, People’s Republic of China
| | - Fang Zheng
- Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430071, People’s Republic of China
| | - Xiaocheng Weng
- Key Laboratory
of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Xiang Zhou
- Key Laboratory
of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
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10
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Haque MH, Gopalan V, Islam MN, Masud MK, Bhattacharjee R, Hossain MSA, Nguyen NT, Lam AK, Shiddiky MJA. Quantification of gene-specific DNA methylation in oesophageal cancer via electrochemistry. Anal Chim Acta 2017; 976:84-93. [PMID: 28576321 DOI: 10.1016/j.aca.2017.04.034] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/10/2017] [Accepted: 04/10/2017] [Indexed: 02/07/2023]
Abstract
Development of simple and inexpensive method for the analysis of gene-specific DNA methylation is important for the diagnosis and prognosis of patients with cancer. Herein, we report a relatively simple and inexpensive electrochemical method for the sensitive and selective detection of gene-specific DNA methylation in oesophageal cancer. The underlying principle of the method relies on the affinity interaction between DNA bases and unmodified gold electrode. Since the affinity trend of DNA bases towards the gold surface follows as adenine (A) > cytosine (C) > guanine (G)> thymine (T), a relatively larger amount of bisulfite-treated adenine-enriched unmethylated DNA adsorbs on the screen-printed gold electrodes (SPE-Au) in comparison to the guanine-enriched methylated sample. The methylation levels were (i.e., different level of surface attached DNA molecules due to the base dependent differential adsorption pattern) quantified by measuring saturated amount of charge-compensating [Ru(NH3)6]3+ molecules in the surface-attached DNAs by chronocoulometry as redox charge of the [Ru(NH3)6]3+ molecules quantitatively reflects the amount of the adsorbed DNA confined at the electrode surface. The assay could successfully distinguish methylated and unmethylated DNA sequences at single CpG resolution and as low as 10% differences in DNA methylation. In addition, the assay showed fairly good reproducibility (% RSD= <5%) with better sensitivity and specificity by analysing various levels of methylation in two cell lines and eight fresh tissues samples from patients with oesophageal squamous cell carcinoma. Finally, the method was validated with methylation specific-high resolution melting curve analysis and Sanger sequencing methods.
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Affiliation(s)
- Md Hakimul Haque
- Cancer Molecular Pathology Laboratory in Menzies Health Institute Queensland, Griffith University and School of Medicine, Gold Coast, QLD 4222, Australia; School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology Laboratory in Menzies Health Institute Queensland, Griffith University and School of Medicine, Gold Coast, QLD 4222, Australia.
| | - Md Nazmul Islam
- School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Mostafa Kamal Masud
- School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials, University of Wollongong, NSW 2519, Australia
| | - Ripon Bhattacharjee
- School of Natural Sciences, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia; Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Md Shahriar Al Hossain
- Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials, University of Wollongong, NSW 2519, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD 4111, Australia
| | - Alfred K Lam
- Cancer Molecular Pathology Laboratory in Menzies Health Institute Queensland, Griffith University and School of Medicine, Gold Coast, QLD 4222, Australia.
| | - Muhammad J A Shiddiky
- School of Natural Sciences, 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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11
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Hossain T, Mahmudunnabi G, Masud MK, Islam MN, Ooi L, Konstantinov K, Hossain MSA, Martinac B, Alici G, Nguyen NT, Shiddiky MJA. Electrochemical biosensing strategies for DNA methylation analysis. Biosens Bioelectron 2017; 94:63-73. [PMID: 28259051 DOI: 10.1016/j.bios.2017.02.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 12/31/2022]
Abstract
DNA methylation is one of the key epigenetic modifications of DNA that results from the enzymatic addition of a methyl group at the fifth carbon of the cytosine base. It plays a crucial role in cellular development, genomic stability and gene expression. Aberrant DNA methylation is responsible for the pathogenesis of many diseases including cancers. Over the past several decades, many methodologies have been developed to detect DNA methylation. These methodologies range from classical molecular biology and optical approaches, such as bisulfite sequencing, microarrays, quantitative real-time PCR, colorimetry, Raman spectroscopy to the more recent electrochemical approaches. Among these, electrochemical approaches offer sensitive, simple, specific, rapid, and cost-effective analysis of DNA methylation. Additionally, electrochemical methods are highly amenable to miniaturization and possess the potential to be multiplexed. In recent years, several reviews have provided information on the detection strategies of DNA methylation. However, to date, there is no comprehensive evaluation of electrochemical DNA methylation detection strategies. Herein, we address the recent developments of electrochemical DNA methylation detection approaches. Furthermore, we highlight the major technical and biological challenges involved in these strategies and provide suggestions for the future direction of this important field.
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Affiliation(s)
- Tanvir Hossain
- Department of Biochemistry & Molecular Biology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh
| | - Golam Mahmudunnabi
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh
| | - Mostafa Kamal Masud
- Department of Biochemistry & Molecular Biology, Shahjalal University of Science & Technology, Sylhet 3114, Bangladesh; Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia; Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia
| | - Md Nazmul Islam
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia; School of Natural Sciences, Griffith University (Nathan Campus), Nathan, QLD 4111, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, School of Biological Sciences, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Konstantin Konstantinov
- Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia
| | - Md Shahriar Al Hossain
- Institute for Superconducting and Electronic Materials, Australian Institute for Innovative Materials (AIIM), University of Wollongong, Squires Way, Innovation Campus, North Wollongong, NSW 2519, Australia
| | - Boris Martinac
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Gursel Alici
- ARC Centre of Excellence for Electromaterials Science, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan, QLD 4111, Australia; School of Natural Sciences, Griffith University (Nathan Campus), Nathan, QLD 4111, Australia.
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12
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Sina AAI, Foster MT, Korbie D, Carrascosa LG, Shiddiky MJA, Gao J, Dey S, Trau M. A multiplex microplatform for the detection of multiple DNA methylation events using gold–DNA affinity. Analyst 2017; 142:3573-3578. [DOI: 10.1039/c7an00611j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We report a new multiplexed strategy for the electrochemical detection of regional DNA methylation across multiple regions.
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Affiliation(s)
- Abu Ali Ibn Sina
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Matthew Thomas Foster
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Laura G. Carrascosa
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Muhammad J. A. Shiddiky
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Jing Gao
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Shuvashis Dey
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Matt Trau
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- School of Chemistry and Molecular Biosciences
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13
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Florio E, Keller S, Coretti L, Affinito O, Scala G, Errico F, Fico A, Boscia F, Sisalli MJ, Reccia MG, Miele G, Monticelli A, Scorziello A, Lembo F, Colucci-D'Amato L, Minchiotti G, Avvedimento VE, Usiello A, Cocozza S, Chiariotti L. Tracking the evolution of epialleles during neural differentiation and brain development: D-Aspartate oxidase as a model gene. Epigenetics 2016; 12:41-54. [PMID: 27858532 PMCID: PMC5270635 DOI: 10.1080/15592294.2016.1260211] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
We performed ultra-deep methylation analysis at single molecule level of the promoter region of developmentally regulated D-Aspartate oxidase (Ddo), as a model gene, during brain development and embryonic stem cell neural differentiation. Single molecule methylation analysis enabled us to establish the effective epiallele composition within mixed or pure brain cell populations. In this framework, an epiallele is defined as a specific combination of methylated CpG within Ddo locus and can represent the epigenetic haplotype revealing a cell-to-cell methylation heterogeneity. Using this approach, we found a high degree of polymorphism of methylated alleles (epipolymorphism) evolving in a remarkably conserved fashion during brain development. The different sets of epialleles mark stage, brain areas, and cell type and unravel the possible role of specific CpGs in favoring or inhibiting local methylation. Undifferentiated embryonic stem cells showed non-organized distribution of epialleles that apparently originated by stochastic methylation events on individual CpGs. Upon neural differentiation, despite detecting no changes in average methylation, we observed that the epiallele distribution was profoundly different, gradually shifting toward organized patterns specific to the glial or neuronal cell types. Our findings provide a deep view of gene methylation heterogeneity in brain cell populations promising to furnish innovative ways to unravel mechanisms underlying methylation patterns generation and alteration in brain diseases.
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Affiliation(s)
- Ermanno Florio
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.,b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy
| | - Simona Keller
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.,b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy
| | - Lorena Coretti
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.,b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy
| | - Ornella Affinito
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.,b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy
| | - Giovanni Scala
- c Dipartimento di Fisica , Università degli Studi di Napoli "Federico II" and Istituto Nazionale di Fisica Nucleare , Sezione di Napoli, Naples , Italy
| | - Francesco Errico
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.,d CEINGE Biotecnologie Avanzate , Naples , Italy
| | - Annalisa Fico
- e Institute of Genetics and Biophysics 'A. Buzzati-Traverso', Consiglio Nazionale delle Ricerche , Naples , Italy
| | - Francesca Boscia
- f Department of Neuroscience , Reproductive and Dentistry Sciences, Università degli Studi di Napoli 'Federico II' , Naples , Italy
| | - Maria Josè Sisalli
- f Department of Neuroscience , Reproductive and Dentistry Sciences, Università degli Studi di Napoli 'Federico II' , Naples , Italy
| | - Mafalda Giovanna Reccia
- g Department of Environmental , Biological and Pharmaceutical Science and Technologies, Second University of Naples , Caserta , Italy
| | - Gennaro Miele
- c Dipartimento di Fisica , Università degli Studi di Napoli "Federico II" and Istituto Nazionale di Fisica Nucleare , Sezione di Napoli, Naples , Italy
| | - Antonella Monticelli
- b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy
| | - Antonella Scorziello
- f Department of Neuroscience , Reproductive and Dentistry Sciences, Università degli Studi di Napoli 'Federico II' , Naples , Italy
| | - Francesca Lembo
- h Dipartimento di Farmacia , Università degli Studi di Napoli 'Federico II' , Naples , Italy
| | - Luca Colucci-D'Amato
- g Department of Environmental , Biological and Pharmaceutical Science and Technologies, Second University of Naples , Caserta , Italy
| | - Gabriella Minchiotti
- e Institute of Genetics and Biophysics 'A. Buzzati-Traverso', Consiglio Nazionale delle Ricerche , Naples , Italy
| | - Vittorio Enrico Avvedimento
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.,b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy
| | - Alessandro Usiello
- d CEINGE Biotecnologie Avanzate , Naples , Italy.,g Department of Environmental , Biological and Pharmaceutical Science and Technologies, Second University of Naples , Caserta , Italy
| | - Sergio Cocozza
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy
| | - Lorenzo Chiariotti
- a Dipartimento di Medicina Molecolare e Biotecnologie Mediche , Università degli Studi di Napoli 'Federico II' , Naples , Italy.,b Istituto di Endocrinologia ed Oncologia Sperimentale, IEOS, Consiglio Nazionale delle Ricerche , Naples , Italy
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14
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Haque MH, Gopalan V, Yadav S, Islam MN, Eftekhari E, Li Q, Carrascosa LG, Nguyen NT, Lam AK, Shiddiky MJA. Detection of regional DNA methylation using DNA-graphene affinity interactions. Biosens Bioelectron 2016; 87:615-621. [PMID: 27616287 DOI: 10.1016/j.bios.2016.09.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/29/2016] [Accepted: 09/04/2016] [Indexed: 12/26/2022]
Abstract
We report a new method for the detection of regional DNA methylation using base-dependent affinity interaction (i.e., adsorption) of DNA with graphene. Due to the strongest adsorption affinity of guanine bases towards graphene, bisulfite-treated guanine-enriched methylated DNA leads to a larger amount of the adsorbed DNA on the graphene-modified electrodes in comparison to the adenine-enriched unmethylated DNA. The level of the methylation is quantified by monitoring the differential pulse voltammetric current as a function of the adsorbed DNA. The assay is sensitive to distinguish methylated and unmethylated DNA sequences at single CpG resolution by differentiating changes in DNA methylation as low as 5%. Furthermore, this method has been used to detect methylation levels in a collection of DNA samples taken from oesophageal cancer tissues.
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Affiliation(s)
- Md Hakimul Haque
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Australia; School of Natural Sciences, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Vinod Gopalan
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Australia.
| | - Sharda Yadav
- School of Natural Sciences, Griffith University, Nathan Campus, QLD 4111, Australia; Queensland Micro and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Md Nazmul Islam
- School of Natural Sciences, Griffith University, Nathan Campus, QLD 4111, Australia; Queensland Micro and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Ehsan Eftekhari
- Queensland Micro and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia; School of Engineering, Griffith University, Nathan, QLD 4111, Australia
| | - Qin Li
- Queensland Micro and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia; School of Engineering, Griffith University, Nathan, QLD 4111, Australia
| | | | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Alfred K Lam
- Cancer Molecular Pathology Laboratory in School of Medicine, Menzies Health Institute Queensland, Griffith University, Gold Coast Campus, Australia.
| | - Muhammad J A Shiddiky
- School of Natural Sciences, Griffith University, Nathan Campus, QLD 4111, Australia; Queensland Micro and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia.
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15
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Wee EJH, Trau M. Simple Isothermal Strategy for Multiplexed, Rapid, Sensitive, and Accurate miRNA Detection. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00105] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Eugene J. H. Wee
- Center
for Personalized Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology and ‡School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Matt Trau
- Center
for Personalized Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology and ‡School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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16
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Wong NC, Pope BJ, Candiloro IL, Korbie D, Trau M, Wong SQ, Mikeska T, Zhang X, Pitman M, Eggers S, Doyle SR, Dobrovic A. MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing. BMC Bioinformatics 2016; 17:98. [PMID: 26911705 PMCID: PMC4765133 DOI: 10.1186/s12859-016-0950-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 02/15/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND DNA methylation at a gene promoter region has the potential to regulate gene transcription. Patterns of methylation over multiple CpG sites in a region are often complex and cell type specific, with the region showing multiple allelic patterns in a sample. This complexity is commonly obscured when DNA methylation data is summarised as an average percentage value for each CpG site (or aggregated across CpG sites). True representation of methylation patterns can only be fully characterised by clonal analysis. Deep sequencing provides the ability to investigate clonal DNA methylation patterns in unprecedented detail and scale, enabling the proper characterisation of the heterogeneity of methylation patterns. However, the sheer amount and complexity of sequencing data requires new synoptic approaches to visualise the distribution of allelic patterns. RESULTS We have developed a new analysis and visualisation software tool "Methpat", that extracts and displays clonal DNA methylation patterns from massively parallel sequencing data aligned using Bismark. Methpat was used to analyse multiplex bisulfite amplicon sequencing on a range of CpG island targets across a panel of human cell lines and primary tissues. Methpat was able to represent the clonal diversity of epialleles analysed at specific gene promoter regions. We also used Methpat to describe epiallelic DNA methylation within the mitochondrial genome. CONCLUSIONS Methpat can summarise and visualise epiallelic DNA methylation results from targeted amplicon, massively parallel sequencing of bisulfite converted DNA in a compact and interpretable format. Unlike currently available tools, Methpat can visualise the diversity of epiallelic DNA methylation patterns in a sample.
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Affiliation(s)
- Nicholas C Wong
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, 3084, Australia. .,Murdoch Childrens Research Institute, The Royal Children's Hospital, Parkville, Victoria, 3052, Australia. .,Department of Paediatrics, The University of Melbourne, Parkville, Victoria, 3052, Australia. .,Present Address: Pacific Edge Biotechnology Ltd, Dunedin, Otago, 9016, New Zealand.
| | - Bernard J Pope
- Victorian Life Sciences Computation Initiative (VLSCI), The University of Melbourne, Parkville, Victoria, 3052, Australia. .,Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria, 3052, Australia.
| | - Ida L Candiloro
- Department of Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Darren Korbie
- Centre for Personalised NanoMedicine, Australian Institute of Nanotechnology and Bioengineering, The University of Queensland, Brisbane, Queensland, 4072, Australia.
| | - Matt Trau
- Centre for Personalised NanoMedicine, Australian Institute of Nanotechnology and Bioengineering, The University of Queensland, Brisbane, Queensland, 4072, Australia. .,School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, 4072, Australia.
| | - Stephen Q Wong
- Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, Victoria, 3002, Australia. .,Present Address: Translational Research Laboratory, Division of Cancer Research, Peter MacCallum Cancer Centre, East Melbourne, Victoria, 3002, Australia.
| | - Thomas Mikeska
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, 3084, Australia. .,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, 3084, Australia.
| | | | - Mark Pitman
- BioResearch Software Consultants, Battle Ground, WA, USA.
| | - Stefanie Eggers
- Murdoch Childrens Research Institute, The Royal Children's Hospital, Parkville, Victoria, 3052, Australia.
| | - Stephen R Doyle
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, 3086, Australia.
| | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, 3084, Australia. .,Department of Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia. .,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, 3084, Australia.
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17
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Wee EJH, Ngo TH, Trau M. Colorimetric detection of both total genomic and loci-specific DNA methylation from limited DNA inputs. Clin Epigenetics 2015; 7:65. [PMID: 26167236 PMCID: PMC4498563 DOI: 10.1186/s13148-015-0100-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 06/25/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Aberrant DNA methylation marks are potential disease biomarkers, and detecting both total genomic and gene-specific DNA methylation can aid in clinical decisions. While a plethora of methods exist in research, simpler, more convenient alternatives are needed to enhance both routine diagnostics and research. RESULTS Herein, we describe colorimetric assays using methyl-binding domain (MBD) proteins for rapid and convenient evaluation of total genomic and gene-specific methylation from 50 ng or less DNA input in under 2 h. As little as 5 % methylation differences can be detected and are enhanced by a novel MBD protocol for improved specificity. Our assays could differentiate naïve from de-methylating drug-treated cells and detect the presence of a methylated prostate cancer biomarker in the urine. Finally, the assay was evolved onto disposable screen-printed electrodes for convenient detection of gene-specific methylation in urine. CONCLUSIONS Rapid MBD-based colorimetric and electrochemical approaches to detect DNA methylation from limited samples were successfully demonstrated and applied to clinical samples. We envision that the ease, low sample requirements and speed of these assays could have both clinical and research-wide applications.
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Affiliation(s)
- Eugene J H Wee
- Centre for Personalized NanoMedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland Australia
| | - Thu Ha Ngo
- Centre for Personalized NanoMedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland Australia ; School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland Australia ; Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Matt Trau
- Centre for Personalized NanoMedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland Australia ; School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland Australia
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18
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Wang Y, Wee EJH, Trau M. Highly sensitive DNA methylation analysis at CpG resolution by surface-enhanced Raman scattering via ligase chain reaction. Chem Commun (Camb) 2015; 51:10953-6. [DOI: 10.1039/c5cc03921e] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Highly sensitive DNA methylation analysis at CpG resolution is demonstrated by employing SERS nanotags via ligase chain reaction (LCR) and validated with sequencing.
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Affiliation(s)
- Yuling Wang
- Centre for Personalized NanoMedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- Corner College and Cooper Roads (Bldg 75)
- Australia
| | - Eugene J. H. Wee
- Centre for Personalized NanoMedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- Corner College and Cooper Roads (Bldg 75)
- Australia
| | - Matt Trau
- Centre for Personalized NanoMedicine
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- Corner College and Cooper Roads (Bldg 75)
- Australia
- School of Chemistry and Molecular Biosciences
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19
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Quantitative methodology is critical for assessing DNA methylation and impacts on correlation with patient outcome. Clin Epigenetics 2014; 6:22. [PMID: 25859283 PMCID: PMC4391486 DOI: 10.1186/1868-7083-6-22] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/17/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND DNA hypermethylation is reported as a frequent event and prognostic marker in head and neck squamous cell carcinomas (HNSCC). Methylation has been commonly assessed with non-quantitative methodologies, such as methylation-specific PCR (MSP). We investigated previously reported hypermethylated genes with quantitative methodology in oral tongue squamous cell carcinomas (OTSCC). RESULTS The methylation status of 12 genes in 115 OTSCC samples was assessed by one or more of three quantitative analyses: methylation sensitive high resolution melting (MS-HRM), sensitive-melting analysis after real time-methylation specific PCR (SMART-MSP), and bisulfite pyrosequencing. In contrast to much of the literature, either no or infrequent locus-specific methylation was identified by MS-HRM for DAPK1, RASSF1A, MGMT, MLH1, APC, CDH1, CDH13, BRCA1, ERCC1, and ATM. The most frequently methylated loci were RUNX3 (18/108 methylated) and ABO (22/107 methylated). Interrogation of the Cancer Genome Atlas (TCGA) HNSCC cohort confirmed the frequency of significant methylation for the loci investigated. Heterogeneous methylation of RUNX3 (18/108) and ABO (22/107) detected by MS-HRM, conferred significantly worse survival (P = 0.01, and P = 0.03). However, following quantification of methylation levels using pyrosequencing, only four tumors had significant quantities (>15%) of RUNX3 methylation which correlated with a worse patient outcome (P <0.001), while the prognostic significance of ABO hypermethylation was lost. RUNX3 methylation was not prognostic for the TCGA cohort (P = 0.76). CONCLUSIONS We demonstrated the critical need for quantification of methylation levels and its impact on correlative analyses. In OTSCC, we found little evidence of significant or frequent hypermethylation of many loci reported to be commonly methylated. It is likely that previous reports have overestimated the frequency of significant methylation events as a consequence of the use of non-quantitative methodology.
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