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Wang L, Pu G, Liu T, Chen G, Li H, Amuda TO, Cao S, Yan H, Yin H, Fu B, Luo X. Parasite-derived microRNA let-7-5p detection for metacestodiasis based on rolling circular amplification-assisted CRISPR/Cas9. FASEB J 2024; 38:e23708. [PMID: 38805151 DOI: 10.1096/fj.202302449r] [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: 11/28/2023] [Revised: 04/23/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Metacestodiasis is an infectious disease caused by the larval stage of cestode parasites. This disease poses a serious health hazard to wildlife, livestock, and humans, and it incurs substantial economic losses by impacting the safety of the livestock industry, the quality of meat production, and public health security. Unfortunately, there is currently no available molecular diagnostic method capable of distinguishing cysticercus- and Echinococcus-derived microRNAs (miRNAs) from other helminthes and hosts in the plasma of metacestode-infected animals. This study aims to develop a specific, sensitive, and cost-efficient molecular diagnostic method for cysticercosis and echinococcosis, particularly for early detection. The study developed a rolling circular amplification (RCA)-assisted CRISPR/Cas9 detection method based on parasite-derived miRNA let-7-5p. Using a series of dilutions of the let-7 standard, the limit of detection (LOD) of the qPCR, RCA, and RCA-assisted CRISPR/Cas9 methods was compared. The specificity of qPCR and CRISPR/Cas9 was evaluated using four artificially synthesized let-7 standards from different species. A total of 151 plasma samples were used to evaluate the diagnostic performance. Additionally, the study also assessed the correlation between plasma levels of let-7-5p, the number of Taenia pisiformis cysticerci, and the weight of Echinococcus multilocularis cysts. The results demonstrated that the RCA-assisted CRISPR/Cas9 assay could significantly distinguish let-7 from cestodes and other species, achieving a LOD of 10 aM; the diagnostic sensitivity and specificity for rabbit cysticercosis and mouse E. multilocularis were 100% and 97.67%, and 100% and 100%, respectively. Notably, let-7-5p gradually increased in the plasma of T. pisiformis-infected rabbits from 15 days post infection (dpi), peaked at 60 dpi, and persisted until 120 dpi. In E. multilocularis-infected mice, let-7-5p gradually increased from 15 dpi and persisted until 90 dpi. Furthermore, the expression of let-7-5p positively correlated with the number of cysticerci and cyst weight. These results indicated that the let-7-5p-based RCA-assisted CRISPR/Cas9 assay is a sensitive and specific detection method that can be used as a universal diagnostic method for metacestodiasis, particularly for early diagnosis (15 dpi).
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Affiliation(s)
- Liqun Wang
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Guiting Pu
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Tingli Liu
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Guoliang Chen
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Hong Li
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Tharheer Oluwashola Amuda
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Shanling Cao
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Hongbin Yan
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Hong Yin
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Baoquan Fu
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xuenong Luo
- State Key Laboratory for Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu Province, National Para-reference Laboratory for Animal Echinococcosis, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, China
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Povedano E, Ruiz-Valdepeñas Montiel V, Sebuyoya R, Torrente-Rodríguez RM, Garranzo-Asensio M, Montero-Calle A, Pingarrón JM, Barderas R, Bartosik M, Campuzano S. Bringing to Light the Importance of the miRNA Methylome in Colorectal Cancer Prognosis Through Electrochemical Bioplatforms. Anal Chem 2024; 96:4580-4588. [PMID: 38348822 PMCID: PMC10955513 DOI: 10.1021/acs.analchem.3c05474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024]
Abstract
This work reports the first electrochemical bioplatforms developed for the determination of the total contents of either target miRNA or methylated target miRNA. The bioplatforms are based on the hybridization of the target miRNA with a synthetic biotinylated DNA probe, the capture of the formed DNA/miRNA heterohybrids on the surface of magnetic microcarriers, and their recognition with an antibody selective to these heterohybrids or to the N6-methyladenosine (m6A) epimark. The determination of the total or methylated target miRNA was accomplished by labeling such secondary antibodies with the horseradish peroxidase (HRP) enzyme. In both cases, amperometric transduction was performed on the surface of disposable electrodes after capturing the resulting HRP-tagged magnetic bioconjugates. Because of their increasing relevance in colorectal cancer (CRC) diagnosis and prognosis, miRNA let-7a and m6A methylation were selected. The proposed electrochemical bioplatforms showed attractive analytical and operational characteristics for the determination of the total and m6A-methylated target miRNA in less than 75 min. These bioplatforms, innovative in design and application, were applied to the analysis of total RNA samples extracted from cultured cancer cells with different metastatic profiles and from paired healthy and tumor tissues of patients diagnosed with CRC at different stages. The obtained results demonstrated, for the first time using electrochemical platforms, the potential of interrogating the target miRNA methylation level to discriminate the metastatic capacities of cancer cells and to identify tumor tissues and, in a pioneering way, the potential of the m6A methylation in miRNA let-7a to serve as a prognostic biomarker for CRC.
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Affiliation(s)
- Eloy Povedano
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, Madrid 28040, Spain
| | - Víctor Ruiz-Valdepeñas Montiel
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, Madrid 28040, Spain
| | - Ravery Sebuyoya
- Research
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Zluty kopec 7, Brno 656
53, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Rebeca M. Torrente-Rodríguez
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, Madrid 28040, Spain
| | - Maria Garranzo-Asensio
- Chronic
Disease Programme, UFIEC, Institute of Health
Carlos III, Majadahonda, Madrid 28220, Spain
| | - Ana Montero-Calle
- Chronic
Disease Programme, UFIEC, Institute of Health
Carlos III, Majadahonda, Madrid 28220, Spain
| | - José M. Pingarrón
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, Madrid 28040, Spain
| | - Rodrigo Barderas
- Chronic
Disease Programme, UFIEC, Institute of Health
Carlos III, Majadahonda, Madrid 28220, Spain
| | - Martin Bartosik
- Research
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Zluty kopec 7, Brno 656
53, Czech Republic
| | - Susana Campuzano
- Departamento
de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, Pza. de las Ciencias 2, Madrid 28040, Spain
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Rolling Circle and Loop Mediated Isothermal Amplification Strategy for Ultrasensitive miRNA Detection. SEPARATIONS 2021. [DOI: 10.3390/separations8100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Rolling circle amplification (RCA) and loop mediated isothermal amplification (LAMP) were combined to establish the rolling circle and loop mediated isothermal amplification (RC-LAMP) method for miRNA detection. With the participation of Bst 2.0 DNA Polymerase, the method enabled RCA and LAMP amplification to occur simultaneously without thermal cycling. The limit of detection of RC-LAMP was 500 amol/L, which is comparable to previously reported amplification strategies. Moreover, its upper limit of quantitation was higher and showed a stronger resistance to matrix interference. Therefore, it is possible to detect low concentrations of miRNA in samples by increasing the total RNA added. Owing to its facile detection mode and simple operation, this method has great potential in clinical sample detection.
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Xu M, Ye J, Yang D, Abdullah Al-Maskri AA, Hu H, Jung C, Cai S, Zeng S. Ultrasensitive detection of miRNA via one-step rolling circle-quantitative PCR (RC-qPCR). Anal Chim Acta 2019; 1077:208-215. [PMID: 31307711 DOI: 10.1016/j.aca.2019.05.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/21/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
A novel microRNA (miRNA) quantification method has been developed using one-step rolling circle-quantitative PCR (RC-qPCR) analysis. Vent (exo-) DNA polymerase is firstly utilized to combine a rolling circle amplification (RCA) and qPCR in one step with high sensitivity and specificity in our RC-qPCR assay. Before performing the RC-qPCR, a padlock probe is ligated only when it is perfectly hybridized with miRNA. This ligation-based miRNA assay is highly specific for mature miRNAs, discriminating among related miRNAs that differ by as little as one nucleotide. It exhibits a dynamic range of seven orders of magnitude with a detection limit of 500 aM, and could be also used for the quantification of other small RNA molecules such as short interfering RNAs (siRNAs).
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Affiliation(s)
- Mingcheng Xu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jiawei Ye
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Dan Yang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Abdu Ahmed Abdullah Al-Maskri
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Haihong Hu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Cheulhee Jung
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Hu B, Guo J, Xu Y, Wei H, Zhao G, Guan Y. A sensitive colorimetric assay system for nucleic acid detection based on isothermal signal amplification technology. Anal Bioanal Chem 2017; 409:4819-4825. [PMID: 28689323 DOI: 10.1007/s00216-017-0425-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/05/2017] [Accepted: 05/22/2017] [Indexed: 12/12/2022]
Abstract
Rapid and accurate detection of microRNAs in biological systems is of great importance. Here, we report the development of a visual colorimetric assay which possesses the high amplification capabilities and high selectivity of the rolling circle amplification (RCA) method and the simplicity and convenience of gold nanoparticles used as a signal indicator. The designed padlock probe recognizes the target miRNA and is circularized, and then acts as the template to extend the target miRNA into a long single-stranded nucleotide chain of many tandem repeats of nucleotide sequences. Next, the RCA product is hybridized with oligonucleotides tagged onto gold nanoparticles. This interaction leads to the aggregation of gold nanoparticles, and the color of the system changes from wine red to dark blue according to the abundance of miRNA. A linear correlation between fluorescence and target oligonucleotide content was obtained in the range 0.3-300 pM, along with a detection limit of 0.13 pM (n = 7) and a RSD of 3.9% (30 pM, n = 9). The present approach provides a simple, rapid, and accurate visual colorimetric assay that allows sensitive biodetection and bioanalysis of DNA and RNA nucleotides of interest in biologically important samples. Graphical abstract The colorimetric assay system for analyzing target oligonucleotides.
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Affiliation(s)
- Bo Hu
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Jing Guo
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Ying Xu
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Hua Wei
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Guojie Zhao
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China
| | - Yifu Guan
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, Liaoning, 110122, China.
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