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Luo B, Zhou J, Zhan X, Ying B, Lan F, Wu Y. Visual and colorimetric detection of microRNA in clinical samples based on strand displacement amplification and nanozyme-mediated CRISPR-Cas12a system. Talanta 2024; 277:126310. [PMID: 38815319 DOI: 10.1016/j.talanta.2024.126310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024]
Abstract
The sensitive and accurate detection of target microRNA is especially important for the diagnosis, staging, and treatment of hepatocellular carcinoma (HCC). Herein, we report a simple strand displacement and CRISPR-Cas12a amplification strategy with nanozymes as a signal reporter for the binary visual and colorimetric detection of the HCC related microRNA. Pt@Au nanozymes with excellent peroxidase enzyme activity were prepared and linked to magnetic beads via a single-stranded DNA (ssDNA) linker. The target microRNA was designed to trigger strand displacement amplification and release a DNA promoter to activate the CRISPR-Cas12a system. The activated CRISPR-Cas12a system efficiently cleaved the linker ssDNA and released Pt@Au nanozymes from magnetic beads to induce the colorimetric reaction of 3,3',5,5'-tetramethylbenzidine. The strand displacement amplification converted the single microRNA input into abundant DNA promoter output, which improved the detection sensitivity by over two orders of magnitude. Through integration of strand displacement amplification and the nanozyme-mediated CRISPR-Cas12a system, limits of detection of 0.5 pM and 10 pM for miRNA-21 were achieved with colorimetric and visual readouts, respectively. The proposed strategy can achieve accurate quantitative detection of miRNA-21 in the range from 1 pM to 500 pM. The detection results for miRNA-21 using both colorimetric and visual readouts were validated in 40 clinical serum samples. Significantly, the proposed strategy achieved visual HCC diagnosis with the naked eye and could distinguish distinct Barcelona clinical HCC stages by colorimetric detection, showing good application prospects for sensitive and facile point-of-care testing for HCC.
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Affiliation(s)
- Bin Luo
- Analytical and Testing Center, Sichuan University, Chengdu, 610064, PR China
| | - Juan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Xiaohui Zhan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, PR China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, PR China
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, PR China.
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Luo B, Zhou J, Zhan X, Ying B, Lan F, Wu Y. Smartphone-Based Free-to-Total Prostate Specific Antigen Ratio Detection System Using a Colorimetric Reaction Integrated with Proximity-Induced Bio-Barcode and CRISPR/Cas12a Assay. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310212. [PMID: 38342699 DOI: 10.1002/smll.202310212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/24/2024] [Indexed: 02/13/2024]
Abstract
The free-to-total prostate-specific antigen (f/t-PSA) ratio is of great significance in the accurate diagnosis of prostate cancer. Herein, a smartphone-based detection system is reported using a colorimetric reaction integrated with proximity-induced bio-barcode and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a assay for f/t-PSA ratio detection. DNA/antibody recognition probes are designed to bind f-PSA or t-PSA and induce the release of the DNA bio-barcode. The CRISPR/Cas12a system is activated by the DNA bio-barcode to release Ag+ from the C-Ag+-C structure of the hairpin DNA. The released Ag+ is used to affect the tetramethylbenzidine (TMB)-H2O2-based colorimetric reaction catalyzed by Pt nanoparticles (NPs), as the peroxidase-like activity of the Pt NPs can be efficiently inhibited by Ag+. A smartphone with a self-developed app is used as an image reader and analyzer to analyze the colorimetric reaction and provide the results. A limit of detection of 0.06 and 0.04 ng mL-1 is achieved for t-PSA and f-PSA, respectively. The smartphone-based method showed a linear response between 0.1 and 100 ng mL-1 of t-PSA or f-PSA. In tests with clinical samples, the smartphone-based method successfully diagnosed prostate cancer patients from benign prostatic hyperplasia patients and healthy cases with high sensitivity and specificity.
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Affiliation(s)
- Bin Luo
- Analytical and Testing Center, Sichuan University, Chengdu, 610064, P. R. China
| | - Juan Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Xiaohui Zhan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, P. R. China
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
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Cai J, Zhu Q. New advances in signal amplification strategies for DNA methylation detection in vitro. Talanta 2024; 273:125895. [PMID: 38508130 DOI: 10.1016/j.talanta.2024.125895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
5-methylcytosine (5 mC) DNA methylation is a prominent epigenetic modification ubiquitous in the genome. It plays a critical role in the regulation of gene expression, maintenance of genome stability, and disease control. The potential of 5 mC DNA methylation for disease detection, prognostic information, and prediction of response to therapy is enormous. However, the quantification of DNA methylation from clinical samples remains a considerable challenge due to its low abundance (only 1% of total bases). To overcome this challenge, scientists have recently developed various signal amplification strategies to enhance the sensitivity of DNA methylation biosensors. These strategies include isothermal nucleic acid amplification and enzyme-assisted target cycling amplification, among others. This review summarizes the applications, advantages, and limitations of these signal amplification strategies over the past six years (2018-2023). Our goal is to provide new insights into the selection and establishment of DNA methylation analysis. We hope that this review will offer valuable insights to researchers in the field and facilitate further advancements in this area.
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Affiliation(s)
- Jiajing Cai
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China
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Liu Y, Liu S, Zhen D, Huang J, He F. Ultrasensitive Detection of Tumor Suppressor Gene Methylation by Piezoelectric Sensing Based on Enrichment of Transcription Activator-Like Effectors. Anal Chem 2024; 96:8534-8542. [PMID: 38743638 DOI: 10.1021/acs.analchem.4c00484] [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: 05/16/2024]
Abstract
The detection of DNA methylation at cytosine/guanine dinucleotide (CpG) islands in promoter regions of tumor suppressor genes has great potential for early cancer screening, diagnosis, and prognosis monitoring. Nevertheless, achieving accurate, sensitive, cost-effective, and quantitative detection of target methylated DNA remains challenging. Herein, we propose a novel piezoelectric sensor (series piezoelectric quartz crystal (SPQC)) based on transcription activator-like effectors (TALEs) for detecting DNA methylation of Ras association domain family 1 isoform A (RASSF1A) tumor suppressor genes (R-5mC). The sensor employs TALEs-Ni magnetic beads to specifically recognize and separate the R-5mC, thereby improving the detection selectivity. The TALEs-Ni magnetic beads-R-5mC complex is sheared by a nucleic acid enzyme (DNAzyme) to release the single-stranded DNA (ST). ST initiates a catalyzed hairpin assembly (CHA) reaction on the surface of the electrode, which in turn triggers the hybridization chain reaction (HCR) and silver staining for enhanced detection sensitivity. The strategy exhibits a linear response in the detection of R-5mC in the range of 1 fM to 1 nM with a detection limit of 0.79 fM. R-5mC as low as 0.01% can be detected, even in the presence of large numbers of unmethylated DNA. The detection of R-5mC in circulating cell-free DNA (cfDNA) derived from clinical plasma specimens of lung cancer patients yielded satisfactory results.
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Affiliation(s)
- Yu Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Shuyi Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Deshuai Zhen
- Hunan Key Laboratory of Typical Environment Pollution and Health Hazards, College of Public Health, University of South China, Hengyang 421001, PR China
| | - Ji Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Fengjiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
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Shavali M, Moradi A, Tahmaseb M, Mohammadian K, Ganji SM. Circulating-tumour DNA methylation of HAND1 gene: a promising biomarker in early detection of colorectal cancer. BMC Med Genomics 2024; 17:117. [PMID: 38689296 PMCID: PMC11061902 DOI: 10.1186/s12920-024-01893-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the significant global health concerns with an increase in cases. Regular screening tests are crucial for early detection as it is often asymptomatic in the initial stages. Liquid biopsies, a non-invasive approach that examines biomarkers in biofluids, offer a promising future in diagnosing and screening cancer. Circulating-tumour DNA (ctDNA) is the genetic material in biofluids released into the circulatory system by cells. ctDNA is a promising marker for monitoring patients since cancer cells display distinct DNA methylation patterns compared to normal cells. The potential of our research to contribute to early detection and improved patient outcomes is significant. AIMS The primary objective of this research project was to explore the HAND1 methylation levels in plasma ctDNA as a potential biomarker for diagnosing CRC and evaluate the methylation level of the well-established gene SPET9 to compare it with the methylation level of HAND1. MATERIALS AND METHODS Plasma samples were collected from 30 CRC patients and 15 healthy individuals, with CRC samples obtained pre-treatment. ctDNA was extracted and treated with bisulfite for methylation status assessment. Quantitative methylation-specific PCR (qMS-PCR) was performed for HAND1 and SEPT9, using β-actin (ACTB gene) as a reference. The study aims to evaluate the potential of these genes as diagnostic biomarkers for CRC, contributing to early detection and improved patient outcomes. RESULTS Our study yielded significant results: 90% of CRC patients (27 out of 30) had hypermethylation in the SEPT9 gene, and 83% (25 out of 30) exhibited hypermethylation in the HAND1 gene. The methylation levels of both genes were significantly higher in CRC patients than in healthy donors. These findings underscore the potential of SEPT9 and HAND1 methylation as promising biomarkers for diagnosing CRC, potentially leading to early detection and improved patient outcomes. CONCLUSION These findings highlight the potential of SEPT9 and HAND1 methylation as promising biomarkers for diagnosing CRC. However, further research and validation studies are needed to confirm these findings and to explore their clinical utility in CRC diagnosis and management.
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Affiliation(s)
- Mehrdad Shavali
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | - Arash Moradi
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, P.O. Box 14965/161, Tehran, Tehran - Karaj Highway, Iran
| | - Mohammad Tahmaseb
- Department of Cell and Molecular Biology, Faculty of Biological Science, Kharazmi University, Tehran, Iran
| | - Kamal Mohammadian
- Department of Radiation Oncology, Hamadan University of Medical Sciences, Hamadan, Iran
- Cancer Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shahla Mohammad Ganji
- Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, P.O. Box 14965/161, Tehran, Tehran - Karaj Highway, Iran.
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Ding L, Cao S, Qu C, Wu Y, Yu S. Ratiometric CRISPR/Cas12a-Triggered CHA System Coupling with the MSRE to Detect Site-Specific DNA Methylation. ACS Sens 2024; 9:1877-1885. [PMID: 38573977 DOI: 10.1021/acssensors.3c02571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
The precise determination of DNA methylation at specific sites is critical for the timely detection of cancer, as DNA methylation is closely associated with the initiation and progression of cancer. Herein, a novel ratiometric fluorescence method based on the methylation-sensitive restriction enzyme (MSRE), CRISPR/Cas12a, and catalytic hairpin assembly (CHA) amplification were developed to detect site-specific methylation with high sensitivity and specificity. In detail, AciI, one of the commonly used MSREs, was employed to distinguish the methylated target from nonmethylated targets. The CRISPR/Cas12a system was utilized to recognize the site-specific target. In this process, the protospacer adjacent motif and crRNA-dependent identification, the single-base resolution of Cas12a, can effectively ensure detection specificity. The trans-cleavage ability of Cas12a can convert one target into abundant activators and can then trigger the CHA reaction, leading to the accomplishment of cascaded signal amplification. Moreover, with the structural change of the hairpin probe during CHA, two labeled dyes can be spatially separated, generating a change of the Förster resonance energy transfer signal. In general, the proposed strategy of tandem CHA after the CRISPR/Cas12a reaction not only avoids the generation of false-positive signals caused by the target-similar nucleic acid but can also improve the sensitivity. The use of ratiometric fluorescence can eradicate environmental effects by self-calibration. Consequently, the proposed approach had a detection limit of 2.02 fM. This approach could distinguish between colorectal cancer and precancerous tissue, as well as between colorectal patients and healthy people. Therefore, the developed method can serve as an excellent site-specific methylation detection tool, which is promising for biological and disease studies.
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Affiliation(s)
- Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shengnan Cao
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Chenling Qu
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
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Zhang H, Wu S, Xiao HJ, Wang HB, Fang L, Cao JT. Chemical-chemical redox cycling for improving the sensitivity of the fluorescent assay: A proof-of-concept towards DNA methylation detection. Talanta 2024; 268:125363. [PMID: 37906997 DOI: 10.1016/j.talanta.2023.125363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023]
Abstract
Ultrasensitive analytical methods are still urgent for the discovery of trace level biomarkers and the early clinical diagnosis of disease. In this work, an ultrasensitive universal sensing platform was constructed by integrating fluorescent assay with chemical-chemical redox cycling signal amplification strategy. Using Ru@SiO2 nanoparticles wrapped by MnO2 nanosheets (Ru@SiO2@MnO2) as fluorescent probe, the chemical-chemical redox cycling system was conducted upon ascorbic acid (AA) and tris(2-carboxyethyl)phosphine (TCEP) as reductants and MnO2 nanosheets as oxidant. The MnO2 nanosheets not only could quench the fluorescence of Ru@SiO2 nanoparticles to reduce the background, but also could serve as oxidants to react with AA, generating dehydroascorbic acid (DHA). The DHA was reduced by TCEP in turn to form AA that participated in the next cycling of chemical-chemical redox reaction. Thus, the constantly released AA from the chemical-chemical redox cycling system could massively etch MnO2 nanosheets on Ru@SiO2 surface, making the fluorescence of Ru@SiO2 nanoparticles greatly recovered. It was shown that the sensitivity of the fluorescent assay was improved almost 52 times by utilizing the chemical-chemical redox cycling signal amplification strategy. This strategy was further employed to detect DNA methylation with the aid of AA-encapsulated liposomes that were modified with 5 mC antibodies to bind with the methylated DNA captured in 96-well plate. A detection of limit down to 16.2 fM was achieved for the detection of methylated DNA. It's believed that the incorporation of chemical-chemical redox cycling signal amplification strategy into fluorescent sensing paves a new way for ultrasensitive detection of biomarkers.
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Affiliation(s)
- Hongding Zhang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang, 464000, PR China.
| | - Sifei Wu
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang, 464000, PR China
| | - Hui-Jin Xiao
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang, 464000, PR China
| | - Hai-Bo Wang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang, 464000, PR China
| | - Linxia Fang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang, 464000, PR China
| | - Jun-Tao Cao
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang, 464000, PR China.
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Zhang H, Wu S, Xing Z, Wang HB. ALP-assisted chemical redox cycling signal amplification for ultrasensitive fluorescence detection of DNA methylation. Analyst 2023; 148:5753-5761. [PMID: 37842979 DOI: 10.1039/d3an01383a] [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: 10/17/2023]
Abstract
Affinity assays allow direct detection of DNA methylation events without requiring a special sequence. However, the signal amplification of these methods heavily depends on nanocatalysts and bioenzymes, making them suffer from low sensitivity. In this work, alkaline phosphatase (ALP)-assisted chemical redox cycling was employed to amplify the sensitivity of fluorescence affinity assays for DNA methylation detection using Ru@SiO2@MnO2 nanocomposites as fluorescent probes. In the ALP-assisted chemical redox cycling reaction system, ALP hydrolyzed 2-phosphate-L-ascorbic acid trisodium salt (AAP) to produce AA, which could reduce MnO2 nanosheets to form Mn2+, making the fluorescence recovery of Ru@SiO2 nanoparticles possible. Meanwhile, AA was oxidized to dehydroascorbic acid (DHA), which was re-reduced by tris(2-carboxyethyl) phosphine (TCEP) to trigger a redox cycling reaction. The constantly generated AA could etch large amounts of MnO2 nanosheets and greatly recover Ru@SiO2 fluorescence, amplifying the signal of the fluorescence assay. Employing the proposed ALP-assisted chemical redox cycling signal amplification strategy, a sensitive affinity assay for DNA methylation detection was achieved using ALP encapsulated liposomes that were linked with the 5mC antibody (Ab) to bind with methylated sites. A detection limit down to 2.9 fM was obtained for DNA methylation detection and a DNA methylation level as low as 0.1% could be distinguished, which was superior to conventional affinity assays. Moreover, the affinity assays could detect DNA methylation more specifically and directly, implying their great potential for the analysis of tumor-specific genes in liquid biopsy.
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Affiliation(s)
- Hongding Zhang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Sifei Wu
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
| | - Zhenhua Xing
- Xinyang Branch, Henan Boiler and Pressure Vessel Inspection Technology Research Institute, Xinyang 464000, PR China
| | - Hai-Bo Wang
- College of Chemistry and Chemical Engineering, Xinyang Key Laboratory of Functional Nanomaterials for Bioanalysis, Xinyang Normal University, Xinyang 464000, PR China.
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Dou B, Zhou H, Han X, Wang P. Wedged DNA Walker Coupled with a Bimetallic Metal-Organic Framework Electrocatalyst for Rapid and Sensitive Monitoring of DNA Methylation. Anal Chem 2023; 95:994-1001. [PMID: 36601781 DOI: 10.1021/acs.analchem.2c03669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The dissociation of the walking strand from the track gives rise to decreased efficiency and long reaction time of DNA walkers. In this work, we constructed a DNA walker combining the introduction of a wedge segment with a bimetallic metal-organic framework (MOF) electrocatalyst to solve this problem. The target methylated DNA acted as a single-legged walker, and the immobilization probe assembled on the track contained a wedge segment that was complementary to the target methylated DNA persistently, inhibiting its dissociation from the track. The fuel strand modified with a bimetallic MOF would drive the target strand to conduct branch migration and move processively along the track. The stepwise movement of the target strand resulted in the loading of numerous bimetallic MOF catalysts to reduce H2O2 at the electrode interface, thereby a significantly increased current response would be obtained for the detection of methylated DNA. This DNA walker achieved a detection limit of 200 aM within 20 min and effectively distinguished DNA with different methylation statuses, which would pave a way for rapid and sensitive monitoring of DNA methylation.
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Affiliation(s)
- Baoting Dou
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Hui Zhou
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Xiguang Han
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Po Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
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Koowattanasuchat S, Ngernpimai S, Matulakul P, Thonghlueng J, Phanchai W, Chompoosor A, Panitanarak U, Wanna Y, Intharah T, Chootawiriyasakul K, Anata P, Chaimnee P, Thanan R, Sakonsinsiri C, Puangmali T. Rapid detection of cancer DNA in human blood using cysteamine-capped AuNPs and a machine learning-enabled smartphone. RSC Adv 2023; 13:1301-1311. [PMID: 36686949 PMCID: PMC9814906 DOI: 10.1039/d2ra05725e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
DNA methylation occurs when a methyl group is added to a cytosine (C) residue's fifth carbon atom, forming 5-methylcytosine (5-mC). Cancer genomes have a distinct methylation landscape (Methylscape), which could be used as a universal cancer biomarker. This study developed a simple, low-cost, and straightforward Methylscape sensing platform using cysteamine-decorated gold nanoparticles (Cyst/AuNPs), in which the sensing principle is based on methylation-dependent DNA solvation. Normal and cancer DNAs have distinct methylation profiles; thus, they can be distinguished by observing the dispersion of Cyst/AuNPs adsorbed on these DNA aggregates in MgCl2 solution. After optimising the MgCl2, Cyst/AuNPs, DNA concentration, and incubation time, the optimised conditions were used for leukemia screening, by comparing the relative absorbance (ΔA 650/525). Following the DNA extraction from actual blood samples, this sensor demonstrated effective leukemia screening in 15 minutes with high sensitivity, achieving 95.3% accuracy based on the measurement by an optical spectrophotometer. To further develop for practical realisation, a smartphone assisted by machine learning was used to screen cancer patients, achieving 90.0% accuracy in leukemia screening. This sensing platform can be applied not only for leukemia screening but also for other cancers associated with epigenetic modification.
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Affiliation(s)
| | - Sawinee Ngernpimai
- Department of Physics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Piyaporn Matulakul
- Department of Physics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Janpen Thonghlueng
- Department of Physics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Witthawat Phanchai
- Department of Physics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Apiwat Chompoosor
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University Bangkok 10240 Thailand
| | - Uthumporn Panitanarak
- Department of Biostatistics, Faculty of Public Health, Mahidol University Bangkok 10400 Thailand
| | - Yupaporn Wanna
- Department of Statistics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Thanapong Intharah
- Department of Statistics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | | | - Pimjai Anata
- Molecular Diagnosis Unit, Central Laboratory, Srinagarind Hospital, Khon Kaen University Khon Kaen 40002 Thailand
| | - Prajuab Chaimnee
- Molecular Diagnosis Unit, Central Laboratory, Srinagarind Hospital, Khon Kaen University Khon Kaen 40002 Thailand
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University Khon Kaen 40002 Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University Khon Kaen 40002 Thailand
| | - Theerapong Puangmali
- Department of Physics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
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