1
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Kawakatsu Y, Okada R, Hara M, Tsutsui H, Yanagisawa N, Higashiyama T, Arima A, Baba Y, Kurotani KI, Notaguchi M. Microfluidic Device for Simple Diagnosis of Plant Growth Condition by Detecting miRNAs from Filtered Plant Extracts. PLANT PHENOMICS (WASHINGTON, D.C.) 2024; 6:0162. [PMID: 38572468 PMCID: PMC10988387 DOI: 10.34133/plantphenomics.0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/03/2024] [Indexed: 04/05/2024]
Abstract
Plants are exposed to a variety of environmental stress, and starvation of inorganic phosphorus can be a major constraint in crop production. In plants, in response to phosphate deficiency in soil, miR399, a type of microRNA (miRNA), is up-regulated. By detecting miR399, the early diagnosis of phosphorus deficiency stress in plants can be accomplished. However, general miRNA detection methods require complicated experimental manipulations. Therefore, simple and rapid miRNA detection methods are required for early plant nutritional diagnosis. For the simple detection of miR399, microfluidic technology is suitable for point-of-care applications because of its ability to detect target molecules in small amounts in a short time and with simple manipulation. In this study, we developed a microfluidic device to detect miRNAs from filtered plant extracts for the easy diagnosis of plant growth conditions. To fabricate the microfluidic device, verification of the amine-terminated glass as the basis of the device and the DNA probe immobilization method on the glass was conducted. In this device, the target miRNAs were detected by fluorescence of sandwich hybridization in a microfluidic channel. For plant stress diagnostics using a microfluidic device, we developed a protocol for miRNA detection by validating the sample preparation buffer, filtering, and signal amplification. Using this system, endogenous sly-miR399 in tomatoes, which is expressed in response to phosphorus deficiency, was detected before the appearance of stress symptoms. This early diagnosis system of plant growth conditions has a potential to improve food production and sustainability through cultivation management.
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Affiliation(s)
- Yaichi Kawakatsu
- Bioscience and Biotechnology Center,
Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Ryo Okada
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Mitsuo Hara
- Department of Molecular and Macromolecular Chemistry,
Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Hiroki Tsutsui
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Naoki Yanagisawa
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute of Transformative Bio-Molecules,
Nagoya University, Nagoya 464-8601, Japan
| | - Tetsuya Higashiyama
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute of Transformative Bio-Molecules,
Nagoya University, Nagoya 464-8601, Japan
- Department of Biological Sciences,
Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akihide Arima
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Department of Biomolecular Engineering,
Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
- Institute of Quantum Life Science, National Institutes for Quantum Science and Technology (QST), Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
| | - Ken-ichi Kurotani
- Bioscience and Biotechnology Center,
Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Michitaka Notaguchi
- Bioscience and Biotechnology Center,
Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Botany,
Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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2
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Wu S, Abdullah Al-Maskri AA, Li Q, Liu J, Cai S. A Novel miRNA Detection Method Using Loop-Mediated Isothermal Amplification. Int J Anal Chem 2023; 2023:6624884. [PMID: 37732283 PMCID: PMC10508998 DOI: 10.1155/2023/6624884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 09/22/2023] Open
Abstract
A novel ligation-based loop-mediated isothermal amplification has been developed for miRNA detection. Two stem-loop structure DNA linker A/B probes which hybridized with miRNA were designed to establish a rapid and ultrasensitive miRNA-LAMP system for miRNA detection. Target miR-200a was used to template the ligation of Linker A/B probes with SplintR Ligase and used as a dumbbell-shaped amplicon. By adding BIP/FIP and Bst 2.0 DNA polymerase, the LAMP reaction was carried out, which brought greatly improved amplification efficiency. The double-stranded DNA fluorescent dye EvaGreen was added for the detection of amplification product to achieve the quantification of the target miRNA. This method can detect miRNA in a linear range of seven orders of magnitude, with a detection limit of 100 fM. Therefore, this ultrasensitive miRNA-LAMP assay provides a new path for the highly sensitive quantitative analysis of miRNA, thereby bringing convenience to clinical diagnosis and prognostic research.
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Affiliation(s)
- Saiwei Wu
- Department of Pharmacy, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Abdu Ahmed Abdullah Al-Maskri
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qun Li
- Department of Pharmacy, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Jiatong Liu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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3
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Ho V, Baker JR, Willison KR, Barnes PJ, Donnelly LE, Klug DR. Single cell quantification of microRNA from small numbers of non-invasively sampled primary human cells. Commun Biol 2023; 6:458. [PMID: 37100999 PMCID: PMC10133449 DOI: 10.1038/s42003-023-04845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Expression levels of microRNAs (miRNAs) in single cells are low and conventional miRNA detection methods require amplification that can be complex, time-consuming, costly and may bias results. Single cell microfluidic platforms have been developed; however, current approaches are unable to absolutely quantify single miRNA molecules expressed in single cells. Herein, we present an amplification-free sandwich hybridisation assay to detect single miRNA molecules in single cells using a microfluidic platform that optically traps and lyses individual cells. Absolute quantification of miR-21 and miR-34a molecules was achieved at a single cell level in human cell lines and validated using real-time qPCR. The sensitivity of the assay was demonstrated by quantifying single miRNA molecules in nasal epithelial cells and CD3+ T-cells, as well as nasal fluid collected non-invasively from healthy individuals. This platform requires ~50 cells or ~30 µL biofluid and can be extended for other miRNA targets therefore it could monitor miRNA levels in disease progression or clinical studies.
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Affiliation(s)
- Vanessa Ho
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Jonathan R Baker
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Keith R Willison
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
| | - Peter J Barnes
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Louise E Donnelly
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK.
| | - David R Klug
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
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4
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Bodulev OL, Sakharov IY. Modern Methods for Assessment of microRNAs. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:425-442. [PMID: 35790375 DOI: 10.1134/s0006297922050042] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
The review discusses modern methods for the quantitative and semi-quantitative analysis of miRNAs, which are small non-coding RNAs affecting numerous biological processes such as development, differentiation, metabolism, and immune response. miRNAs are considered as promising biomarkers in the diagnosis of various diseases.
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Affiliation(s)
- Oleg L Bodulev
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia
| | - Ivan Yu Sakharov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.
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5
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Ishihara R, Kitane R, Akiyama Y, Inomata S, Hosokawa K, Maeda M, Kikuchi A. Multiplex MicroRNA Detection on a Surface-Functionalized Power-Free Microfluidic Chip. ANAL SCI 2021; 37:747-751. [PMID: 33487598 DOI: 10.2116/analsci.20scp17] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Circulating microRNAs (miRNAs) have emerged as promising cancer biomarkers because their concentration profiles in body fluids are associated with the type and clinical stage of cancer. For multiplex miRNA detection, a novel surface-functionalized power-free microfluidic chip (SF-PF microchip) has been developed. The inner surface of the SF-PF microchip microchannels was functionalized via electron beam-induced graft polymerization and immobilization of capture probe DNAs. Simultaneous and specific duplex miRNA detection was achieved on the line-type SF-PF microchip with detection limits of 19.1 and 47.6 nmol L-1 for hsa-miR-16 and hsa-miR-500a-3p, respectively. Moreover, simultaneous and specific triplex miRNA detection was achieved on the stripe-type SF-PF microchip. The sample volume required for this microchip was 0.5 μL, and the time required for detection was 17 min. These results indicate that up to six types of miRNAs could be detected without compromising the advantages of the previous SF-PF microchips for cancer point-of-care testing.
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Affiliation(s)
| | - Ryoichi Kitane
- Department of Materials Science & Technology, Tokyo University of Science
| | | | - Shoko Inomata
- Department of Materials Science & Technology, Tokyo University of Science
| | - Kazuo Hosokawa
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Akihiko Kikuchi
- Department of Materials Science & Technology, Tokyo University of Science
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6
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Manicardi A, Cadoni E, Madder A. Visible-light triggered templated ligation on surface using furan-modified PNAs. Chem Sci 2020; 11:11729-11739. [PMID: 34094412 PMCID: PMC8162948 DOI: 10.1039/d0sc04875e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 12/25/2022] Open
Abstract
Oligonucleotide-templated reactions are frequently exploited for target detection in biosensors and for the construction of DNA-based materials and probes in nanotechnology. However, the translation of the specifically used template chemistry from solution to surfaces, with the final aim of achieving highly selective high-throughput systems, has been difficult to reach and therefore, poorly explored. Here, we show the first example of a visible light-triggered templated ligation on a surface, employing furan-modified peptide nucleic acids (PNAs). Tailored photo-oxidation of the pro-reactive furan moiety is ensured by the simultaneous introduction of a weak photosensitizer as well as a nucleophilic moiety in the reacting PNA strand. This allows one to ensure a localized production of singlet oxygen for furan activation, which is not affected by probe dilution or reducing conditions. Simple white light irradiation in combination with target-induced proximity between reactive functionalities upon recognition of a short 22mer DNA or RNA sequence that functions as a template, allows sensitive detection of nucleic acid targets in a 96 well plate format.
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Affiliation(s)
- Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
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7
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Xiang Y, Yan H, Zheng B, Faheem A, Hu Y. Microorganism@UiO-66-NH 2 Composites for the Detection of Multiple Colorectal Cancer-Related microRNAs with Flow Cytometry. Anal Chem 2020; 92:12338-12346. [PMID: 32657574 DOI: 10.1021/acs.analchem.0c02017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-throughput analyses of multitarget markers can facilitate rapid and accurate clinical diagnosis. Suspension array assays, a flow cytometry-based analysis technology, are among some of the most promising multicomponent analysis methods for clinical diagnostics and research purposes. These assays are appropriate for examining low-volume, complex samples having trace amounts of analytes due to superior elimination of background. Physical shape is an important and promising code system, which uses a set of visually distinct patterns to identify different assay particles. Here, we presented a morphology recognizable suspension arrays based on the microorganisms with different morphologies. In this study, UiO-66-NH2 (UiO stands for University of Oslo) metal-organic frameworks (MOFs), was wrapped on the microorganism surface to form an innovative class of microorganism@UiO-66-NH2 composites for suspension array assays. The use of microorganisms endowed composites barcoding ability with their different morphology and size. Meanwhile, the UiO-66-NH2 provided a stable rigid shell, large specific surface area, and metal(IV) ions with multiple binding sites, which could simplify the protein immobilization procedure and enhance detection sensitivity. With this method, simultaneous detection of three colorectal cancer-related microRNA (miRNA), including miRNA-21, miRNA-17, and miRNA-182, could be easily achieved with femtomolar sensitivity by using a commercial flow cytometer. The synergy between microorganisms and MOFs make the composites a prospective barcoding candidate with excellent characteristics for multicomponent analysis, offering great potential for the development of high throughput and accurate diagnostics.
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Affiliation(s)
- Yuqiang Xiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huaduo Yan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bingjie Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aroosha Faheem
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yonggang Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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8
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Zhu CS, Zhu L, Tan DA, Qiu XY, Liu CY, Xie SS, Zhu LY. Avenues Toward microRNA Detection In Vitro: A Review of Technical Advances and Challenges. Comput Struct Biotechnol J 2019; 17:904-916. [PMID: 31346383 PMCID: PMC6630062 DOI: 10.1016/j.csbj.2019.06.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/13/2019] [Accepted: 06/15/2019] [Indexed: 02/07/2023] Open
Abstract
Over the decades, the biological role of microRNAs (miRNAs) in the post-transcriptional regulation of gene expression has been discovered in many cancer types, thus initiating the tremendous expectation of their application as biomarkers in the diagnosis, prognosis, and treatment of cancer. Hence, the development of efficient miRNA detection methods in vitro is in high demand. Extensive efforts have been made based on the intrinsic properties of miRNAs, such as low expression levels, high sequence homology, and short length, to develop novel in vitro miRNA detection methods with high accuracy, low cost, practicality, and multiplexity at point-of-care settings. In this review, we mainly summarized the newly developed in vitro miRNA detection methods classified by three key elements, including biological recognition elements, additional micro-/nano-materials and signal transduction/readout elements, their current challenges and further applications are also discussed.
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Affiliation(s)
- Chu-shu Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, Hunan 410073, PR China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, Hunan 410073, PR China
- Corresponding authors.
| | - De-an Tan
- Department of Clinical Laboratory, Hospital of National University of Defense Technology, Changsha, Hunan 410073, PR China
| | - Xin-yuan Qiu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, Hunan 410073, PR China
| | - Chuan-yang Liu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, Hunan 410073, PR China
| | - Si-si Xie
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, Hunan 410073, PR China
| | - Lv-yun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, Hunan 410073, PR China
- Corresponding authors.
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9
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Miyagawa A, Harada M, Okada T. Multiple MicroRNA Quantification Based on Acoustic Levitation of Single Microspheres after One-Pot Sandwich Interparticle Hybridizations. Anal Chem 2018; 90:13729-13735. [DOI: 10.1021/acs.analchem.8b04143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Akihisa Miyagawa
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan
| | - Makoto Harada
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan
| | - Tetsuo Okada
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551, Japan
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10
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Sun L, Meckes DG. Methodological Approaches to Study Extracellular Vesicle miRNAs in Epstein⁻Barr Virus-Associated Cancers. Int J Mol Sci 2018; 19:ijms19092810. [PMID: 30231493 PMCID: PMC6164614 DOI: 10.3390/ijms19092810] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 02/07/2023] Open
Abstract
Epstein Barr-virus (EBV) was the first virus identified to be associated with human cancer in 1964 and is found ubiquitously throughout the world's population. It is now established that EBV contributes to the development and progression of multiple human cancers of both lymphoid and epithelial cell origins. EBV encoded miRNAs play an important role in tumor proliferation, angiogenesis, immune escape, tissue invasion, and metastasis. Recently, EBV miRNAs have been found to be released from infected cancer cells in extracellular vesicles (EVs) and regulate gene expression in neighboring uninfected cells present in the tumor microenvironment and possibly at distal sites. As EVs are abundant in many biological fluids, the viral and cellular miRNAs present within EBV-modified EVs may serve as noninvasion markers for cancer diagnosis and prognosis. In this review, we discuss recent advances in EV isolation and miRNA detection, and provide a complete workflow for EV purification from plasma and deep-sequencing for biomarker discovery.
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Affiliation(s)
- Li Sun
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA.
| | - David G Meckes
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA.
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11
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Hasegawa K, Negishi R, Matsumoto M, Yohda M, Hosokawa K, Maeda M. Specificity of MicroRNA Detection on a Power-free Microfluidic Chip with Laminar Flow-assisted Dendritic Amplification. ANAL SCI 2018; 33:171-177. [PMID: 28190836 DOI: 10.2116/analsci.33.171] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
MicroRNAs (miRNAs) are attracting considerable attention as potential biomarkers for the early diagnosis of cancer. We have been developing a detection method for miRNAs on a microfluidic chip with external-power-free fluid pumping and enzyme-free amplification. The assay is completed within 20 min. Here, we describe the specificity of this miRNA detection method. First, the specificity against mismatched sequences was investigated. The nonspecific detection of a 2-nucleotide mismatched sequence was negligible, while that of a 1-nucleotide mismatched sequence was observed to a reasonable extent. Next, the disturbance in mature miRNA detection by existence of its precursor miRNA was evaluated. One precursor miRNA out of four tested showed significant nonspecific responses at 1 nM or higher concentrations. However, those responses were much lower than that of the target mature miRNA at 0.1 nM. Finally, we tried to detect three endogenous miRNAs, which are known to be potential cancer biomarkers, in human leucocyte total RNA. The measured concentraions of these miRNAs agreed well with those obtained by quantitative reverse transcription polymerase chain reaction. These results indicate that the on-chip miRNA detection method has good specificity, which is promising for applications to real biological samples.
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12
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Ferhan AR, Jackman JA, Park JH, Cho NJ, Kim DH. Nanoplasmonic sensors for detecting circulating cancer biomarkers. Adv Drug Deliv Rev 2018; 125:48-77. [PMID: 29247763 DOI: 10.1016/j.addr.2017.12.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/29/2017] [Accepted: 12/08/2017] [Indexed: 12/20/2022]
Abstract
The detection of cancer biomarkers represents an important aspect of cancer diagnosis and prognosis. Recently, the concept of liquid biopsy has been introduced whereby diagnosis and prognosis are performed by means of analyzing biological fluids obtained from patients to detect and quantify circulating cancer biomarkers. Unlike conventional biopsy whereby primary tumor cells are analyzed, liquid biopsy enables the detection of a wide variety of circulating cancer biomarkers, including microRNA (miRNA), circulating tumor DNA (ctDNA), proteins, exosomes and circulating tumor cells (CTCs). Among the various techniques that have been developed to detect circulating cancer biomarkers, nanoplasmonic sensors represent a promising measurement approach due to high sensitivity and specificity as well as ease of instrumentation and operation. In this review, we discuss the relevance and applicability of three different categories of nanoplasmonic sensing techniques, namely surface plasmon resonance (SPR), localized surface plasmon resonance (LSPR) and surface-enhanced Raman scattering (SERS), for the detection of different classes of circulating cancer biomarkers.
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Affiliation(s)
- Abdul Rahim Ferhan
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Joshua A Jackman
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Jae Hyeon Park
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
| | - Dong-Hwan Kim
- School of Chemical Engineering, Sungkyunkwan University, 16419, Republic of Korea.
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13
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Wang Y, Wei CX, Shao LQ, Zhao M. MiRNA Signaling in Viral Myocarditis Novel and Unique Pathological Features. ACTA CARDIOLOGICA SINICA 2018; 34:77-86. [PMID: 29375227 DOI: 10.6515/acs.201801_34(1).20170901a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Background Micro-RNAs (miRNAs) are small non-coding RNAs that modulate many target genes. Viral myocarditis is common cardiomyopathy, however, there is an absence of effective therapeutic strategies for viral myocarditis (VMC). The purpose of this research was to characterize changes in miRNAs expression in VMC mice. Methods Atrial myocytes were infected coxsackievirus B3 and miRNAs microarray was performed. miRNAs target predicted and the bioinformatics analysis was carried out by gene ontology (GO) and KEGG pathway analysis. To validate the results, Difference miRNAs were identified in heart of mice by real-time polymerase chain reaction (PCR). Results We identified 94 miRNAs that were differentially expressed (27 were up-regulated and 67 were down-regulated by at least 2.0-fold). Real time PCR analysis has confirmed that the expression levels of 7 miRNAs up-regulated, 18 miRNAs down-regulated. They were mainly involved in protein binding, small GTPase mediated signal transduction, protein phosphorylation by GO. Pathway analysis showed that a significant enrichment in several pathways related to cAMP signaling pathway, AMPK signaling pathway, RAS signaling pathway, Rap1 signaling pathway, ErbB signaling pathway, Oxytocin signaling pathway. Conclusions Our results provide a better understanding of the mechanisms of viral myocarditis pathophysiology.
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Affiliation(s)
- Yu Wang
- Inner Mongolia University for the Nationalities.,Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System, Tongliao, Inner Mongolia, P.R. China
| | - Cheng-Xi Wei
- Inner Mongolia University for the Nationalities.,Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System, Tongliao, Inner Mongolia, P.R. China
| | - Li-Qun Shao
- First Clinical Medical of Inner Mongolia University for Nationalities
| | - Ming Zhao
- First Clinical Medical of Inner Mongolia University for Nationalities.,Inner Mongolia Key Laboratory of Mongolian Medicine Pharmacology for Cardio-Cerebral Vascular System, Tongliao, Inner Mongolia, P.R. China
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14
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Abstract
Recent advances in miRNA detection methods and new applications.
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Affiliation(s)
- Yongqiang Cheng
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Lijuan Dong
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Jiangyan Zhang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Yaqing Zhao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
| | - Zhengping Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis
- Ministry of Education
- Key Laboratory of Analytical Science and Technology of Hebei Province
- College of Chemistry and Environmental Science
- Hebei University
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15
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Zheng A, Zhang X, Huang Y, Cai Z, Liu X, Liu J. Polydopamine-assisted versatile modification of a nucleic acid probe for intracellular microRNA imaging and enhanced photothermal therapy. RSC Adv 2018; 8:6781-6788. [PMID: 35540353 PMCID: PMC9078363 DOI: 10.1039/c8ra00261d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 01/30/2018] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs play an important role in various biological processes, and their aberrant expression is closely associated with various human diseases, especially cancer. Real-time monitoring of microRNAs in living cells may help us to understand their role in cellular processes, which can further provide a basis for diagnosis and treatment. In this study, polydopamine was used to assist the versatile modification of a nucleic acid probe for intracellular microRNA imaging and enhanced photothermal therapy. Polydopamine can be covalently linked with a thiol-terminated nucleic acid probe through the Michael addition reaction under slightly alkaline conditions. This modification is mild and can be performed directly in an aqueous solution, which can better resist hydrolysis than the traditional modification processes, resulting in a nanoprobe with better stability and higher loading of nucleic acids. This prepared nanoprobe can easily enter cells without transfection agents and then realize the imaging of intracellular miRNA through fluorescence restoration. Moreover, the coating of PDA can enhance the photothermal conversion efficiency of the nanoprobe, making it suitable for photothermal therapy of cancer. It is expected that the PDA-based versatile modification can help to construct a promising platform for tumor imaging and treatment. Polydopamine can assist the versatile modification of a nucleic acid probe for intracellular miRNA responsed fluorescence imaging and enhanced photothermal therapy.![]()
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Affiliation(s)
- Aixian Zheng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
| | - Xiaolong Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
| | - Yanbing Huang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
| | - Jingfeng Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province
- Mengchao Hepatobiliary Hospital of Fujian Medical University
- Fuzhou 350025
- P. R. China
- The Liver Center of Fujian Province
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16
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Anazawa T, Yamazaki M. An ultra-small, multi-point, and multi-color photo-detection system with high sensitivity and high dynamic range. LAB ON A CHIP 2017; 17:4231-4242. [PMID: 29115316 DOI: 10.1039/c7lc01070b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Although multi-point, multi-color fluorescence-detection systems are widely used in various sciences, they would find wider applications if they are miniaturized. Accordingly, an ultra-small, four-emission-point and four-color fluorescence-detection system was developed. Its size (space between emission points and a detection plane) is 15 × 10 × 12 mm, which is three-orders-of-magnitude smaller than that of a conventional system. Fluorescence from four emission points with an interval of 1 mm on the same plane was respectively collimated by four lenses and split into four color fluxes by four dichroic mirrors. Then, a total of sixteen parallel color fluxes were directly input into an image sensor and simultaneously detected. The emission-point plane and the detection plane (the image-sensor surface) were parallel and separated by a distance of only 12 mm. The developed system was applied to four-capillary array electrophoresis and successfully achieved Sanger DNA sequencing. Moreover, compared with a conventional system, the developed system had equivalent high fluorescence-detection sensitivity (lower detection limit of 17 pM dROX) and 1.6-orders-of-magnitude higher dynamic range (4.3 orders of magnitude).
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17
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Amplification-free detection of microRNAs via a rapid microarray-based sandwich assay. Anal Bioanal Chem 2017; 409:3497-3505. [DOI: 10.1007/s00216-017-0298-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/27/2017] [Accepted: 03/06/2017] [Indexed: 12/16/2022]
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18
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Novel bead-based platform for direct detection of unlabelled nucleic acids through Single Nucleobase Labelling. Talanta 2016; 161:489-496. [PMID: 27769437 DOI: 10.1016/j.talanta.2016.08.072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/19/2016] [Accepted: 08/28/2016] [Indexed: 01/02/2023]
Abstract
Over the last decade, circulating microRNAs have received attention as diagnostic and prognostic biomarkers. In particular, microRNA122 has been demonstrated to be an early and more sensitive indicator of drug-induced liver injury than the widely used biomarkers such as alanine aminotransferase and aspartate aminotransferase. Recently, microRNA122 has been used in vitro to assess the cellular toxicity of new drugs and as a biomarker for the development of a rapid test for drug overdose/liver damage. In this proof-of-concept study, we report a PCR-free and label-free detection method that has a limit of detection (3 standard deviations) of 15 fmoles of microRNA122, by integrating a dynamic chemical approach for "Single Nucleobase Labelling" with a bead-based platform (Luminex®) thereby, in principle, demonstrating the exciting prospect of rapid and accurate profiling of any microRNAs related to diseases and toxicology.
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19
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Ishihara R, Hasegawa K, Hosokawa K, Maeda M. Multiplex MicroRNA Detection on a Power-free Microfluidic Chip with Laminar Flow-assisted Dendritic Amplification. ANAL SCI 2016; 31:573-6. [PMID: 26165275 DOI: 10.2116/analsci.31.573] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
MicroRNA (miRNA) profile-based point-of-care (POC) diagnostic methods have attracted considerable attention. In our laboratory, singleplex miRNA detection on a power-free poly(dimethylsiloxane) (PDMS) microfluidic chip with laminar flow-assisted dendritic amplification (LFDA) has been developed. In this study, to obtain the miRNA profile and to improve the reliability of the diagnosis, multiplex miRNA detection on the same system is demonstrated without compromising any advantages of the singleplex miRNA detection. The limit of detection (LOD) was at the femto- to picomolar level and the assay time was 20 min. The sensitivity, rapidity, and portability of the microfluidic chip are adequate for POC diagnosis.
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20
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Affiliation(s)
- Richard M. Graybill
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
| | - Ryan C. Bailey
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801
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21
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Iizuka R, Ueno T, Funatsu T. Detection and Quantification of MicroRNAs by Ligase-Assisted Sandwich Hybridization on a Microarray. Methods Mol Biol 2016; 1368:53-65. [PMID: 26614068 DOI: 10.1007/978-1-4939-3136-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Extracellular microRNAs (miRNAs) in body fluids have been identified as promising biomarkers for different human diseases. The high-throughput, multiplexed detection and quantification of these miRNAs are highly beneficial for the rapid and accurate diagnosis of diseases. Here, we developed a simple and convenient microarray-based technique, named ligase-assisted sandwich hybridization (LASH), for the detection and quantification of miRNAs. The LASH assay involves the hybridization of capture and detection probe pairs with the target miRNA to form a double-stranded structure which is then nick-sealed by T4 DNA ligase. Using this assay, we successfully demonstrated the multiplexed detection and quantification of different miRNAs in total RNA samples derived from blood obtained within 3 h. Here, we provide a detailed protocol for the LASH assay to detect a specific miRNA, as a model for the detection and quantification of extracellular miRNAs.
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Affiliation(s)
- Ryo Iizuka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Taro Ueno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo Bunkyo-ku, Tokyo, 113-0033, Japan.
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22
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Hunt EA, Broyles D, Head T, Deo SK. MicroRNA Detection: Current Technology and Research Strategies. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:217-37. [PMID: 25973944 DOI: 10.1146/annurev-anchem-071114-040343] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The relatively new field of microRNA (miR) has experienced rapid growth in methodology associated with its detection and bioanalysis as well as with its role in -omics research, clinical diagnostics, and new therapeutic strategies. The breadth of this area of research and the seemingly exponential increase in number of publications on the subject can present scientists new to the field with a daunting amount of information to evaluate. This review aims to provide a collective overview of miR detection methods by relating conventional, established techniques [such as quantitative reverse transcription polymerase chain reaction (RT-qPCR), microarray, and Northern blotting (NB)] and relatively recent advancements [such as next-generation sequencing (NGS), highly sensitive biosensors, and computational prediction of microRNA/targets] to common miR research strategies. This should guide interested readers toward a more focused study of miR research and the surrounding technology.
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Affiliation(s)
- Eric A Hunt
- Department of Biochemistry and Molecular Biology, University of Miami, Miami, Florida 33136;
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