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Yang Y, Sun L, Zhao J, Jiao Y, Han T, Zhou X. Improving trans-cleavage activity of CRISPR-Cas13a using engineered crRNA with a uridinylate-rich 5'-overhang. Biosens Bioelectron 2024; 255:116239. [PMID: 38552526 DOI: 10.1016/j.bios.2024.116239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/28/2024] [Accepted: 03/21/2024] [Indexed: 04/15/2024]
Abstract
The engieering of Cas13a crRNA to enhance its binding affinity with the Cas enzyme or target is a promising method of improving the collateral cleavage efficiency of CRISPR-Cas13a systems, thereby amplifying the sensitivity of nucleic acid detection. An examination of the top-performing engineered crRNA (24 nt 5'7U LbuCas13a crRNA, where the 5'-end was extended using 7-mer uridinylates) and optimized conditions revealed an increased rate of LbuCas13a-mediated collateral cleavage activity that was up to seven-fold higher than that of the original crRNA. Particularly, the 7-mer uridinylates extension to crRNA was determined to be spacer-independent for enhancing the LbuCas13a-mediacted collateral cleavage activity, and also benefited the LwaCas13a system. The improved trans-cleavage activity was explained by the interactions between crRNA and LbuCas13a at the molecular level, i.e. the 5'-overhangs were anchored in the cleft formed between the Helical-1 and HEPN2 domains with the consequence of more stable complex, and experimentally verified. Consequently, the improved CRISPR-Cas13a system detected the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA with a sensitivity of 2.36 fM that was 160-times higher than that of the original system. Using isothermal amplification via reverse transcription-recombinase polymerase amplification (RT-RPA), the system was capable to detect SARS-CoV-2 with attomolar sensitivity and accurately identified the SARS-CoV-2 Omicron variant (20/21 agreement) in clinical samples within 40 min.
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Affiliation(s)
- Yihan Yang
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Lingli Sun
- Beijing Chaoyang Center for Disease Control and Prevention, Beijing, 100021, PR China
| | - Jianhong Zhao
- Beijing Chaoyang Center for Disease Control and Prevention, Beijing, 100021, PR China
| | - Yang Jiao
- Beijing Chaoyang Center for Disease Control and Prevention, Beijing, 100021, PR China
| | - Taoli Han
- Beijing Chaoyang Center for Disease Control and Prevention, Beijing, 100021, PR China
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing, 100084, PR China.
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2
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Yu J, Zhang J, Li M, You Y, Zhang C. CRISPR/Cas13a-triggered entropy-driven amplification for colorimetric and fluorescent dual-mode detection of microRNA. Anal Biochem 2024; 689:115499. [PMID: 38431141 DOI: 10.1016/j.ab.2024.115499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
MicroRNAs (miRNAs) are crucial biomarkers for the early detection and monitoring of disease progression of chronic obstructive pulmonary disease (COPD). Herein, we have devised a method for detecting miRNA using a combination of colorimetric and graphene oxide-based fluorescent techniques. The target miRNA in our design could precisely activate the trans-cleavage activity of the CRISPR-Cas13a system. The activated Cas13a enzyme cuts the "rUrU" section in the P1 probe, generating a nicking site to induce entropy-driven amplification (EDA). One of the available EDA products has the capability to unfold the hairpin probe, thereby initiating the catalytic hairpin assembly, exposing the G-quadruplex structure, facilitating the subsequent color response. The fuel strand labeled with Cy3 successfully established a double-stranded DNA structure with DNA3, and consequently the Cy3 would not be quenched by graphene oxide (GO). The implementation of the dual-mode technique in this method yields greater benefits in terms of improving the precision and consistency of the miRNA measurements. The developed method has the capability to fluorescently measure miRNA-21 levels down to a concentration of 5.8 fM. In addition, the analysis of miRNA targets from clinical samples using this method demonstrates its promising utility in the fields of biomedical research of COPD.
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Affiliation(s)
- Juanchun Yu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Army Medical University, Chongqing, 400037, China
| | - Junhong Zhang
- Department of Geriatrics and Special Service Medicine, The First Affiliated Hospital of Army Medical University, Chongqing, 400038, China
| | - Meng Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Army Medical University, Chongqing, 400037, China
| | - Yiqin You
- Department of Clinical Laboratory, The Second Affiliated Hospital of Army Medical University, Chongqing, 400037, China
| | - Chenchen Zhang
- Department of Geriatrics and Special Service Medicine, The First Affiliated Hospital of Army Medical University, Chongqing, 400038, China.
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3
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Li M, He Q, Li T, Wan W, Zhou H. Development and evaluation of a CRISPR-Cas13a system-based diagnostic for hepatitis E virus. Clin Chem Lab Med 2024; 62:1237-1247. [PMID: 38153113 DOI: 10.1515/cclm-2023-1007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/14/2023] [Indexed: 12/29/2023]
Abstract
OBJECTIVES Hepatitis E virus (HEV) is the leading cause of acute viral hepatitis worldwide. HEV RNA detection is the gold standard for HEV infection diagnosis and PCR methods are commonly used but are usually time-consuming and expensive, resulting in low detection efficiency and coverage, especially in low-income areas. Here, we developed a simpler and more accessible HEV RNA detection method based on CRISPR-Cas13a system. METHODS A total of 265 samples of different types and sources, including 89 positive samples and 176 negative samples, were enrolled for evaluations. The sensitivity and specificity of the Cas13a-crRNA detection system were evaluated. The World Health Organization reference panel for HEV genotypes was used to evaluate the capability for detecting different HEV genotypes. The validity of the assay was compared with RT-qPCR. RESULTS The 95 % limits of detection (LOD) of Cas13a-crRNA-based fluorescence assay and strip assay were 12.5 and 200 IU/mL, respectively. They did not show cross-reactivity with samples positive for hepatitis A virus, hepatitis B virus, hepatitis C virus, coxsackievirus A16, rotavirus, enterovirus 71, norovirus or enteropathic Escherichia coli. Different HEV genotypes (HEV1-4) can be detected by the assay. Compared to RT-qPCR, the positive predictive agreements of Cas13a-crRNA-based fluorescence and strip assay were 98.9 % (95 % CI: 93.9-99.8 %) and 91.0 % (95 % CI: 83.3-95.4 %), respectively. The negative predictive agreements were both 100 % (95 % CI: 97.8-100 %). CONCLUSIONS In conclusion, we established a rapid and convenient HEV RNA detection method with good sensitivity and specificity based on CRISPR-Cas13a system, providing a new option for HEV infection diagnosis.
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Affiliation(s)
- Manyu Li
- Division I of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, P.R. China
| | - Qiyu He
- Department of Microbiology and Infection Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P.R. China
| | - Tingting Li
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, P.R. China
| | - Wenjun Wan
- Division I of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, P.R. China
| | - Haiwei Zhou
- Division I of In Vitro Diagnostics for Infectious Diseases, Institute for In Vitro Diagnostics Control, National Institutes for Food and Drug Control, Beijing, P.R. China
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Zhang H, Zhang M, Zhou Y, Qiao Z, Gao L, Cao L, Yin H, Wang M. Organic photoelectrochemical transistor aptasensor for dual-mode detection of DEHP with CRISPR-Cas13a assisted signal amplification. J Hazard Mater 2024; 470:134175. [PMID: 38574662 DOI: 10.1016/j.jhazmat.2024.134175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/25/2024] [Accepted: 03/29/2024] [Indexed: 04/06/2024]
Abstract
Emerging organic photoelectrochemical transistors (OPECTs) with inherent amplification capabilities, good biocompatibility and even self-powered operation have emerged as a promising detection tool, however, they are still not widely studied for pollutant detection. In this paper, a novel OPECT dual-mode aptasensor was constructed for the ultrasensitive detection of di(2-ethylhexyl) phthalate (DEHP). MXene/In2S3/In2O3 Z-scheme heterojunction was used as a light fuel for ion modulation in sensitive gated OPECT biosensing. A transistor system based on poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) converted biological events associated with photosensitive gate achieving nearly a thousand-fold higher current gain at zero bias voltage. This work quantified the target DEHP by aptamer-specific induction of CRISPR-Cas13a trans-cutting activity with target-dependent rolling circle amplification as the signal amplification unit, and incorporated the signal changes strategy of biocatalytic precipitation and TMB color development. Combining OPECT with the auxiliary validation of colorimetry (CM), high sensitivity and accurate detection of DEHP were achieved with a linear range of 0.1 pM to 200 pM and a minimum detection limit of 0.02 pM. This study not only provides a new method for the detection of DEHP, but also offers a promising prospect for the gating and application of the unique OPECT.
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Affiliation(s)
- Haowei Zhang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Miao Zhang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Zhen Qiao
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Lanlan Gao
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Lulu Cao
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Huanshun Yin
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Minghui Wang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Science, Nanjing Forestry University, Nanjing 210037, PR China
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Xiao X, Lin X, Ting CL, Huang X, Zeng B, Liu T, Zeng T. Extraction-free, immuno-RPA-CRISPR/Cas13a-based one-pot detection of glypican-3 directly from extracellular vesicles. Anal Chim Acta 2024; 1297:342385. [PMID: 38438232 DOI: 10.1016/j.aca.2024.342385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Glypican-3 (GPC3) is a heparan sulfate proteoglycan (HSPG) that binds to the cell membrane via glycosylphosphatidylinositol (GPI). It is not found in healthy adult liver but is overexpressed in human hepatocellular carcinoma (HCC). The protein marker GPC3 on extracellular vesicles (GPC3+ EVs) is also useful for HCC detection. Nevertheless, the absence of practical and dependable quantitative techniques to evaluate EVs proteins prevents their clinical implementation. RESULTS Here, using an immuno-recombinase polymerase amplification (immuno-RPA) process and dual amplification of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13a, we firstly create an extraction-free one-pot immuno-RPA-CRISPR (opiCRISPR) for the direct and extremely sensitive detection of EVs proteins. The EVs protein-targeted detection probe is amplified by RPA to generate a long repetitive sequence containing multiple CRISPR RNA (crRNA) targeting barcodes, and the signal is further amplified by the CRISPR-Cas13a side-chain cleavage activity to generate a fluorescent signal. The results show that circulating extracellular vesicle GPC3 (eGPC3) levels are a reliable marker for GPC3 expression in tumor, opening up new avenues for tumor diagnosis. SIGNIFICANCE AND NOVELTY We created an eGPC3 assay based on the CRISPR-Cas13a system, and successfully study the significance of extracellular vesicle GPC3 markers in hepatocellular carcinoma.
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Affiliation(s)
- Xiangyan Xiao
- Laboratory Medicine Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, PR China; Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, PR China
| | - Xiaocong Lin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guang Dong Medical University, 524023, Zhanjiang, PR China
| | - Chu Lok Ting
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guang Dong Medical University, 524023, Zhanjiang, PR China
| | - Xueran Huang
- Laboratory Medicine Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, PR China
| | - Biyun Zeng
- School of Medical Technology, Guangdong Medical University, Dongguan, Guangdong, PR China
| | - Tiancai Liu
- Key Laboratory of Antibody Engineering of Guangdong Higher Education Institutes, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, PR China.
| | - Tao Zeng
- Laboratory Medicine Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, PR China.
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Feng W, Peng H, Zhang H, Weinfeld M, Le XC. A Sensitive Technique Unravels the Kinetics of Activation and Trans-Cleavage of CRISPR-Cas Systems. Angew Chem Int Ed Engl 2024:e202404069. [PMID: 38526321 DOI: 10.1002/anie.202404069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 03/26/2024]
Abstract
Activation of the CRISPR-Cas13a system requires the formation of a crRNA-Cas13a ribonucleoprotein (RNP) complex and the binding of an RNA activator to the RNP. These two binding processes play a crucial role in the performance of the CRISPR-Cas13a system. However, the binding kinetics remain poorly understood, and a main challenge is the lack of a sensitive method for real-time measurements of the dynamically formed active CRISPR-Cas13a enzyme. We describe here a new method to study the binding kinetics and report the rate constants (kon and koff) and dissociation constant (Kd) for the binding between Cas13a and its activator. The method is able to unravel and quantify the kinetics of binding and cleavage separately, on the basis of measuring the real-time trans-cleavage rates of the CRISPR-Cas system and obtaining the real-time concentrations of the active CRISPR-Cas ternary complex. We further discovered that once activated, the Cas13a system operates at a wide range of temperatures (7-37 °C) with fast trans-cleavage kinetics. The new method and findings are important for diverse applications of the Cas13a system, such as the demonstrated quantification of microRNA at ambient temperatures (e.g., 25 °C).
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Affiliation(s)
- Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Michael Weinfeld
- Cross Cancer Institute and Department of Oncology, University of Alberta, Edmonton, Alberta, T6G 1Z2, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
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7
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Erratum: Advances in application of CRISPR-Cas13a system. Front Cell Infect Microbiol 2024; 14:1393044. [PMID: 38524180 PMCID: PMC10958657 DOI: 10.3389/fcimb.2024.1393044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/26/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fcimb.2024.1291557.].
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Zhang Y, Li S, Li R, Qiu X, Fan T, Wang B, Zhang B, Zhang L. Advances in application of CRISPR-Cas13a system. Front Cell Infect Microbiol 2024; 14:1291557. [PMID: 38524179 PMCID: PMC10958658 DOI: 10.3389/fcimb.2024.1291557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/26/2024] [Indexed: 03/26/2024] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and CRISPR-associated (Cas) proteins serve as an adaptive immune system that safeguards prokaryotes and some of the viruses that infect prokaryotes from foreign nucleic acids (such as viruses and plasmids). The genomes of the majority of archaea and about half of all bacteria contain various CRISPR-Cas systems. CRISPR-Cas systems depend on CRISPR RNAs (crRNAs). They act as a navigation system to specifically cut and destroy foreign nucleic acids by recognizing invading foreign nucleic acids and binding Cas proteins. In this review, we provide a brief overview of the evolution and classification of the CRISPR-Cas system, focusing on the functions and applications of the CRISPR-Cas13a system. We describe the CRISPR-Cas13a system and discuss its RNA-directed ribonuclease function. Meanwhile, we briefly introduce the mechanism of action of the CRISPR-Cas13a system and summarize the applications of the CRISPR-Cas13a system in pathogen detection, eukaryotes, agriculture, biosensors, and human gene therapy. We are right understanding of CRISPR-Cas13a has been broadened, and the CRISPR-Cas13a system will be useful for developing new RNA targeting tools. Therefore, understanding the basic details of the structure, function, and biological characterization of CRISPR-Cas13a effector proteins is critical for optimizing RNA targeting tools.
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Affiliation(s)
- Yue Zhang
- The Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Shengjun Li
- The Department of Clinical Laboratory, Qingdao Women and Children’s Hospital, Qingdao, Shandong, China
| | - Rongrong Li
- The Department of Medical Imaging, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xu Qiu
- The Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Tianyu Fan
- The Department of Hematology, Taian City Central Hospital, Taian, Shandong, China
| | - Bin Wang
- The Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Bei Zhang
- The Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Li Zhang
- The Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
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Yang Y, Wang F, Xue B, Zhou X. Field-deployable assay based on CRISPR-Cas13a coupled with RT-RPA in one tube for the detection of SARS-CoV-2 in wastewater. J Hazard Mater 2023; 459:132077. [PMID: 37473568 DOI: 10.1016/j.jhazmat.2023.132077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/22/2023]
Abstract
CRISPR-based nucleic acid detection is easy to implement, field deployable, and always coupled with isothermal amplification to improve the sensitivity. However, the conventional detection requires two separate steps, which can cause long-lasting amplicon aerosol contaminants, hence leading to false-positive results. To address this problem, we proposed a one-tube assay based on CRISPR-Cas13a coupled with reverse transcription-recombinase polymerase amplification to avoid aerosol pollution. The one-tube assay could be completed within 40 min with a sensitivity of up to 180 copies of RNA per reaction, and exhibited no cross reactivity with two related coronaviruses. Our technology showed reproducibility with relative standard deviation of 4.6% responding to 1 fM nucleic acid for three times. It could be used to detect SARS-CoV-2 nucleic acids in raw wastewater with a limit of detection of 103 copies/mL. We also validated the practicability of this technique for viral detection in environmental water samples by detecting SARS-CoV-2 in wastewater, which were not detectable by RT-qPCR technology, showing resistance of this technology to wastewater matrix. It is anticipated that the robustness and high sensitivity will significantly promote the development of a point-of-care method in environmental virus monitoring.
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Affiliation(s)
- Yihan Yang
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing 100084, China
| | - Fan Wang
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing 100084, China
| | - Boyuan Xue
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing 100084, China.
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Yu Z, Pan L, Ma X, Li T, Wang F, Yang D, Li M, Wang P. Detection of SARS-CoV-2 RNA with a plasmonic chiral biosensor. Biosens Bioelectron 2023; 237:115526. [PMID: 37453279 DOI: 10.1016/j.bios.2023.115526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
The detection of SARS-CoV-2 infection is crucial for effective prevention and surveillance of COVID-19. In this study, we report the development of a novel detection assay named CENSOR that enables sensitive and specific detection of SARS-CoV-2 RNA using a plasmonic chiral biosensor in combination with CRISPR-Cas13a. The chiral biosensor was designed by assembling gold nanorods (AuNR) into three-dimensional plasmonic architectures of controllable chirality on a DNA origami template. This modular assembly mode enhances the flexibility and adaptability of the sensor, thereby improving its universality as a sensing platform. In the presence of SARS-CoV-2 RNA, the CRISPR-Cas13a enzyme triggers collateral cleavage of RNA molecules, resulting in a differential chiral signal readout by the biosensor compared to when there are no RNA targets present. Notably, even subtle variations in the concentration of SARS-CoV-2 RNA can provoke significant changes in chiral signals after preamplification of RNA targets (calculated LOD: 0.133 aM), which establishes the foundation for quantitative detection. Furthermore, CENSOR demonstrated high sensitivity and accuracy in detecting SARS-CoV-2 RNA from clinical samples, suggesting its potential application in clinical settings for viral detection beyond SARS-CoV-2.
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Affiliation(s)
- Zhicai Yu
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Li Pan
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiaowei Ma
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Tianming Li
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fukai Wang
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Donglei Yang
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Min Li
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Pengfei Wang
- Department of Laboratory Medicine, Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Center for DNA Information Storage, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
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11
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Li X, Su B, Yang L, Kou Z, Wu H, Zhang T, Liu L, Han Y, Niu M, Sun Y, Li H, Jiang T. Highly sensitive and rapid point-of-care testing for HIV-1 infection based on CRISPR-Cas13a system. BMC Infect Dis 2023; 23:627. [PMID: 37749486 PMCID: PMC10518925 DOI: 10.1186/s12879-023-08492-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 07/28/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Human immunodeficiency virus type one (HIV-1) is the leading cause of acquired immunodeficiency syndrome (AIDS). AIDS remains a global public health concern but can be effectively suppressed by life-long administration of combination antiretroviral therapy. Early detection and diagnosis are two key strategies for the prevention and control of HIV/AIDS. Rapid and accurate point-of-care testing (POCT) provides critical tools for managing HIV-1 epidemic in high-risk areas and populations. METHODS In this study, a POCT for HIV-1 RNA was developed by CRISPR-Cas13a lateral flow strip combined with reverse transcriptase recombinase-aided amplification (RT-RAA) technology, the results can be directly observed by naked eyes. RESULTS Moreover, with the degenerate base-binding CRISPR-Cas13a system was introduced into the RT-RAA primer designing, the technology developed in this study can be used to test majority of HIV-1 RNA with limit of detection (LOD) 1 copy/μL, while no obvious cross-reaction with other pathogens. We evaluated this method for detecting HIV-1 RNA of clinical samples, the results showed that the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy were 91.81% (85.03- 96.19%), 100% (92.60-100%), 100% (96.41-100%), 39.14% (25.59-54.60%) and 92.22% (86.89-95.88%), respectively. The lowest viral load detectable by this method was 112copies/mL. CONCLUSION Above all, this method provides a point-of-care detection of HIV-1 RNA, which is stable, simple and with good sensitivity and specificity. This method has potential to be developed for promoting early diagnosis and treatment effect monitoring of HIV patients in clinical.
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Affiliation(s)
- Xiaohui Li
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
- State Key Laboratory of Pathogens and Biosafety, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Lan Yang
- State Key Laboratory of Pathogens and Biosafety, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Zhihua Kou
- State Key Laboratory of Pathogens and Biosafety, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Hao Wu
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Tong Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Lifeng Liu
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China
| | - Yao Han
- State Key Laboratory of Pathogens and Biosafety, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Mengwei Niu
- State Key Laboratory of Pathogens and Biosafety, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yansong Sun
- State Key Laboratory of Pathogens and Biosafety, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Hao Li
- State Key Laboratory of Pathogens and Biosafety, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
| | - Taiyi Jiang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
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12
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Wang F, Zhang C, Xu H, Zeng W, Ma L, Li Z. Structural Basis for the Ribonuclease Activity of a Thermostable CRISPR-Cas13a from Thermoclostridium caenicola. J Mol Biol 2023; 435:168197. [PMID: 37442412 DOI: 10.1016/j.jmb.2023.168197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 06/11/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023]
Abstract
The RNA-targeting type VI CRISPR-Cas effector complexes are widely used in biotechnology applications such as gene knockdown, RNA editing, and molecular diagnostics. Compared with Cas13a from mesophilic organisms, a newly discovered Cas13a from thermophilic bacteria Thermoclostridium caenicola (TccCas13a) shows low sequence similarity, high thermostability, and lacks pre-crRNA processing activity. The thermostability of TccCas13a has been harnessed to make a sensitive and robust tool for nucleic acid detection. Here we present the structures of TccCas13a-crRNA binary complex at 2.8 Å, and TccCas13a at 3.5 Å. Although TccCas13a shares a similarly bilobed architecture with other mesophilic organism-derived Cas13a proteins, TccCas13a displayed distinct structure features. Specifically, it holds a long crRNA 5'-flank, forming extensive polar contacts with Helical-1 and HEPN2 domains. The detailed analysis of the interaction between crRNA 5'-flank and TccCas13a suggested lack of suitable nucleophile to attack the 2'-OH of crRNA 5'-flank may explain why TccCas13a fails to cleave pre-crRNA. The stem-loop segment of crRNA spacer toggles between double-stranded and single-stranded conformational states, suggesting a potential safeguard mechanism for target recognition. Superimposition of the structures of TccCas13a and TccCas13a-crRNA revealed several conformational changes required for crRNA loading, including dramatic movement of Helical-2 domain. Collectively, these structural insights expand our understanding into type VI CRISPR-Cas effectors, and would facilitate the development of TccCas13a-based applications.
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Affiliation(s)
- Feng Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Chendi Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Haijiang Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Wanting Zeng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Zhuang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
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13
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Ortiz-Cartagena C, Pablo-Marcos D, Fernández-García L, Blasco L, Pacios O, Bleriot I, Siller M, López M, Fernández J, Aracil B, Fraile-Ribot PA, García-Fernández S, Fernández-Cuenca F, Hernández-García M, Cantón R, Calvo-Montes J, Tomás M. CRISPR-Cas13a-Based Assay for Accurate Detection of OXA-48 and GES Carbapenemases. Microbiol Spectr 2023; 11:e0132923. [PMID: 37466441 PMCID: PMC10434040 DOI: 10.1128/spectrum.01329-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/22/2023] [Indexed: 07/20/2023] Open
Abstract
Carbapenem-resistant pathogens have been recognized as a health concern as they are both difficult to treat and detect in clinical microbiology laboratories. Researchers are making great efforts to develop highly specific, sensitive, accurate, and rapid diagnostic techniques, required to prevent the spread of these microorganisms and improve the prognosis of patients. In this context, CRISPR-Cas systems are proposed as promising tools for the development of diagnostic methods due to their high specificity; the Cas13a endonuclease can discriminate single nucleotide changes and displays collateral cleavage activity against single-stranded RNA molecules when activated. This technology is usually combined with isothermal pre-amplification reactions in order to increase its sensitivity. We have developed a new LAMP-CRISPR-Cas13a-based assay for the detection of OXA-48 and GES carbapenemases in clinical samples without the need for nucleic acid purification and concentration. To evaluate the assay, we used 68 OXA-48-like-producing Klebsiella pneumoniae clinical isolates as well as 64 Enterobacter cloacae complex GES-6, 14 Pseudomonas aeruginosa GES-5, 9 Serratia marcescens GES-6, 5 P. aeruginosa GES-6, and 3 P. aeruginosa (GES-15, GES-27, and GES-40) and 1 K. pneumoniae GES-2 isolates. The assay, which takes less than 2 h and costs approximately 10 € per reaction, exhibited 100% specificity and sensitivity (99% confidence interval [CI]) for both OXA-48 and all GES carbapenemases. IMPORTANCE Carbapenems are one of the last-resort antibiotics for defense against multidrug-resistant pathogens. Multiple nucleic acid amplification methods, including multiplex PCR, multiplex loop-mediated isothermal amplification (LAMP) and multiplex RPAs, can achieve rapid, accurate, and simultaneous detection of several resistance genes to carbapenems in a single reaction. However, these assays need thermal cycling steps and specialized instruments, giving them limited application in the field. In this work, we adapted with high specificity and sensitivity values, a new LAMP CRISPR-Cas13a-based assay for the detection of OXA-48 and GES carbapenemases in clinical samples without the need for RNA extraction.
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Affiliation(s)
- Concha Ortiz-Cartagena
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Daniel Pablo-Marcos
- Microbiology Service, University Hospital Marqués de Valdecilla – IDIVAL, Santander, Spain
| | - Laura Fernández-García
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Lucía Blasco
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Olga Pacios
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Inés Bleriot
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - María Siller
- Microbiology Service, University Hospital Marqués de Valdecilla – IDIVAL, Santander, Spain
| | - María López
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
| | - Javier Fernández
- Microbiology Service, University Hospital Central de Asturias. Translational Microbiology Group, ISPA, Oviedo, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Belén Aracil
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Pablo Arturo Fraile-Ribot
- Microbiology Service, University Hospital Son Espases and Health Research Institute Illes Balears (IdISBa), Palma de Mallorca, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Felipe Fernández-Cuenca
- Clinical Unit of Infectious Diseases and Microbiology, University Hospital Virgen Macarena, Institute of Biomedicine of Sevilla (University Hospital Virgen Macarena/CSIC/University of Sevilla), Sevilla, Spain
| | - Marta Hernández-García
- Microbiology Service, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Cantón
- Microbiology Service, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Calvo-Montes
- Microbiology Service, University Hospital Marqués de Valdecilla – IDIVAL, Santander, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - María Tomás
- Multidisciplinary and Translational Microbiology Group (MicroTM), Biomedical Research Institute of A Coruña (INIBIC), Microbiology Service, University Hospital of A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) on behalf of the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid, Spain
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14
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Iida T, Shinoda H, Watanabe R. SATORI: Amplification-free digital RNA detection method for the diagnosis of viral infections. Biophys Physicobiol 2023; 20:e200031. [PMID: 38124795 PMCID: PMC10728625 DOI: 10.2142/biophysico.bppb-v20.0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/10/2023] [Indexed: 12/23/2023] Open
Abstract
With the recent global outbreak of COVID-19, there is an urgent need to establish a versatile diagnostic method for viral infections. Gene amplification test or antigen test are widely used to diagnose viral infections; however, these methods generally have technical drawbacks either in terms of sensitivity, accuracy, or throughput. To address this issue, we recently developed an amplification-free digital RNA detection method (SATORI), which can identify and detect viral genes at the single-molecule level in approximately 9 min, satisfying almost all detection performance requirements for the diagnosis of viral infections. In addition, we also developed practical platforms for SATORI, such as an automated platform (opn-SATORI) and a low-cost compact fluorescence imaging system (COWFISH), with the aim of application in clinical settings. Our latest technologies can be inherently applied to diagnose a variety of RNA viral infections, such as COVID-19 and Influenza A/B, and therefore, we expect that SATORI will be established as a versatile platform for point-of-care testing of a wide range of infectious diseases, thus contributing to the prevention of future epidemics. This article is an extended version of the Japanese article published in the SEIBUTSU BUTSURI Vol. 63, p. 115-118 (2023).
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Affiliation(s)
- Tatsuya Iida
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan
| | - Hajime Shinoda
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan
| | - Rikiya Watanabe
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan
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15
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Liu X, Yang S, Wang L, Wu X, Wang X, Ou C, Yang J, Song L, Zhou S, Wu Q, Gong C. Hierarchically tumor-activated nano CRISPR-Cas13a facilitates efficient microRNA disruption for multi-pathway-mediated tumor suppression. Theranostics 2023; 13:2774-2786. [PMID: 37284454 PMCID: PMC10240819 DOI: 10.7150/thno.81776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/06/2023] [Indexed: 06/08/2023] Open
Abstract
Rationale: CRISPR-Cas13a is an efficient tool for robust RNA knockdown with lower off-target effect, which may be a potentially powerful and safe tool for cancer gene therapy. However, therapeutic effect of current cancer gene therapy that targeting monogene was compromised by the multi-mutational signal pathway alterations of tumorigenesis. Methods: Here, hierarchically tumor-activated nanoCRISPR-Cas13a (CHAIN) is fabricated for multi-pathway-mediated tumor suppression by efficient microRNA disruption in vivo. A fluorinated polyetherimide (PEI; Mw=1.8KD) with graft rate of 33% (PF33) was utilized to compact the CRISPR-Cas13a megaplasmid targeting microRNA-21 (miR-21) (pCas13a-crRNA) via self-assemble to constitute a nanoscale 'core' (PF33/pCas13a-crRNA), which was further wrapped by modified hyaluronan (HA) derivatives (galactopyranoside-PEG2000-HA, GPH) to form CHAIN. Results: The dual-tumor-targeting and tumor-activated CHAIN not only manifested long-term circulation, but augmented tumor cellular uptake and endo/lysosomal escape, thus achieving efficient transfection of CRISPR-Cas13a megaplasmid (~ 13 kb) in tumor cells with minimal toxity. Efficient knockdown of miR-21 by CHAIN restored programmed cell death protein 4 (PDCD4) and reversion-inducing-cysteine-rich protein with Kazal motifs (RECK) and further crippled downstream matrix metalloproteinases-2 (MMP-2), which undermined cancer proliferation, migration and invasion. Meanwhile, the miR-21-PDCD4-AP-1 positive feedback loop further functioned as an enhanced force for anti-tumor activity. Conclusion: Treatment with CHAIN in hepatocellular carcinoma mouse model achieved significant inhibition of miR-21 expression and rescued multi-pathway, which triggered substantial tumor growth suppression. By efficient CRISPR-Cas13a induced interference of one oncogenic microRNA, the CHAIN platform exerted promising capabilities in cancer treatment.
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Affiliation(s)
- Xiaowei Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Suleixin Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Li Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Xinyue Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Xinxin Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Chunqing Ou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Jin Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Linjiang Song
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, P. R. China
| | - Shiyao Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Qinjie Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Changyang Gong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
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16
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Zhao D, Tang J, Tan Q, Xie X, Zhao X, Xing D. CRISPR/Cas13a-triggered Cas12a biosensing method for ultrasensitive and specific miRNA detection. Talanta 2023; 260:124582. [PMID: 37116358 DOI: 10.1016/j.talanta.2023.124582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/17/2023] [Accepted: 04/20/2023] [Indexed: 04/30/2023]
Abstract
Constructing an ultrasensitive CRISPR/Cas-based biosensing strategy is highly significant for the detection of trace targets. Here we presented a dual-amplified biosensing method based on CRISPR/Cas13a-triggered Cas12a, namely, Cas13a-12a amplification. As proof-of-principle, the developed strategy was used for miRNA-155 detection. The target bound to the Cas13a-crRNA complex and activated the cleavage activity of Cas13a for cleaving uracil ribonucleotides (rU) in the bulge structure of blocker strand (BS), resulting in the release of primer strand (PS) from the BS modified on magnetic beads. Then, the released PS activated the cleavage activity of Cas12a to cleave single-strand DNA reporter probes, producing a significantly increased fluorescent signal. The detection limit of the Cas13a-12a amplification using synthetic miRNA-155 was as low as 0.35 fM, which was much lower than that of the only Cas13a-based assay. The applied performance of this amplification strategy was verified by accurately quantifying miRNA-155 expression levels in different cancer patients. Therefore, the developed strategy offers a supersensitive and highly specific miRNAs sensing platform for clinical application.
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Affiliation(s)
- Dan Zhao
- Department of Clinical Laboratory, Chongqing University Three Gorges Hospital, Chongqing, 404000, China
| | - Jiutang Tang
- Center for Neuroscience Research, Chongqing Medical University, 400010, Chongqing, China
| | - Qin Tan
- Department of Clinical Laboratory, Chongqing Wanzhou Shanghai Hospital, Chongqing, 404000, China
| | - Xiaohong Xie
- Department of Clinical Laboratory, Chongqing University Three Gorges Hospital, Chongqing, 404000, China
| | - Xin Zhao
- Department of Clinical Laboratory, Chongqing University Three Gorges Hospital, Chongqing, 404000, China
| | - Dingpei Xing
- Department of Pediatric Surgery, Chongqing University Three Gorges Hospital, Chongqing, 404000, China.
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17
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Waitkus J, Chang Y, Liu L, Puttaswamy SV, Chung T, Vargas AMM, Dollery SJ, O'Connell MR, Cai H, Tobin GJ, Bhalla N, Du K. Gold Nanoparticle Enabled Localized Surface Plasmon Resonance on Unique Gold Nanomushroom Structures for On-Chip CRISPR-Cas13a Sensing. Adv Mater Interfaces 2023; 10:2201261. [PMID: 37091050 PMCID: PMC10121183 DOI: 10.1002/admi.202201261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Indexed: 05/03/2023]
Abstract
A novel localized surface plasmon resonance (LSPR) system based on the coupling of gold nanomushrooms (AuNMs) and gold nanoparticles (AuNPs) is developed to enable a significant plasmonic resonant shift. The AuNP size, surface chemistry, and concentration are characterized to maximize the LSPR effect. A 31 nm redshift is achieved when the AuNMs are saturated by the AuNPs. This giant redshift also increases the full width of the spectrum and is explained by the 3D finite-difference time-domain (FDTD) calculation. In addition, this LSPR substrate is packaged in a microfluidic cell and integrated with a CRISPR-Cas13a RNA detection assay for the detection of the SARS-CoV-2 RNA targets. Once activated by the target, the AuNPs are cleaved from linker probes and randomly deposited on the AuNM substrate, demonstrating a large redshift. The novel LSPR chip using AuNP as an indicator is simple, specific, isothermal, and label-free; and thus, provides a new opportunity to achieve the next generation multiplexing and sensitive molecular diagnostic system.
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Affiliation(s)
- Jacob Waitkus
- University of California, Riverside, Riverside, CA, USA
| | - Yu Chang
- University of California, Riverside, Riverside, CA, USA
| | - Li Liu
- University of California, Riverside, Riverside, CA, USA
| | - Srinivasu Valagerahally Puttaswamy
- NIBEC School of Engineering, Ulster University, Belfast, UK
- Healthcare Technology Hub, School of Engineering, Ulster University, Belfast, UK
| | - Taerin Chung
- Tech4Health Institute and Department of Radiology, New York University Langone Health New York, USA
| | | | | | | | - Haogang Cai
- Tech4Health Institute and Department of Radiology, New York University Langone Health New York, USA
| | | | - Nikhil Bhalla
- NIBEC School of Engineering, Ulster University, Belfast, UK
- Healthcare Technology Hub, School of Engineering, Ulster University, Belfast, UK
| | - Ke Du
- University of California, Riverside, Riverside, CA, USA
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18
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Wang Y, Liu L, Liu X, Wu K, Zhu X, Ma L, Su J. An Ultrasensitive PCR-Based CRISPR-Cas13a Method for the Detection of Helicobacter pylori. J Pers Med 2022; 12:jpm12122082. [PMID: 36556302 PMCID: PMC9784247 DOI: 10.3390/jpm12122082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/17/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
The rapid and simple detection of Helicobacter pylori (H. pylori) is essential for its clinical eradication. Although various methods for detecting H. pylori have been well established, such as endoscopy in combination with histology or culture, rapid urease test (RUT) and molecular tests using clinical specimens, it is of great importance to develop an ultrasensitive and accurate nucleic acid detection platform and apply it to identify H. pylori. To meet these demands, a novel method based on PCR and CRISPR-Cas13a, called PCR-Cas13a, was developed and validated using the DNA of 84 clinical strains and 71 clinical specimens. PCR primers for the pre-amplification of conservative sequence and CRISPR RNA (crRNA) for the detection of specific sequence were designed according to the principle. The designed primers and crRNA were specific to H. pylori, and the assay showed a high degree of specificity compared with other common pathogens. Our detection system can screen H. pylori with a limit of 2.2 copies/μL within 30 mins after PCR amplification. Using a coincidence analysis with traditional methods, our method exhibited 100% accuracy for the detection of H. pylori. Furthermore, its diagnostic performance was compared, in parallel with a q-PCR. The PCR-Cas13a demonstrates 98% sensitivity and 100% specificity. Moreover, our approach had a lower limit of detection (LOD) than q-PCR. Herein, we present a diagnostic system for the highly sensitive screening of H. pylori and distinguish it from other pathogens. All the results demonstrated that this PCR-based CRISPR assay has wide application prospects for the detection of H. pylori and other slow-growth pathogens.
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Affiliation(s)
- Yaxuan Wang
- Department of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Liyang Liu
- Department of Gastroenterology, Jingdong Medical Area, General Hospital of Chinese PLA, Beijing 101149, China
| | - Xiaochuan Liu
- Department of Gastroenterology, Emergency General Hospital, Beijing 100028, China
| | - Kai Wu
- Department of Gastroenterology, The Eighth Medical Center of PLA General Hospital, Beijing 100091, China
| | - Xiaoyan Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Liyan Ma
- Department of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Jianrong Su
- Department of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
- Correspondence:
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19
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Song Z, Yu Y, Bai X, Jia Y, Tian J, Gu K, Zhao M, Zhou C, Zhang X, Wang H, Tang Y. Pathogen-Specific Bactericidal Method Mediated by Conjugative Delivery of CRISPR-Cas13a Targeting Bacterial Endogenous Transcripts. Microbiol Spectr 2022;:e0130022. [PMID: 35950861 DOI: 10.1128/spectrum.01300-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The emergence of antibiotic-resistant bacteria threatens public health, and the use of broad-spectrum antibiotics often leads to unintended consequences, including disturbing the beneficial gut microbiota and resulting in secondary diseases. Therefore, developing a novel strategy that specifically kills pathogens without affecting the residential microbiota is desirable and urgently needed. Here, we report the development of a precise bactericidal system by taking advantage of CRISPR-Cas13a targeting endogenous transcripts of Salmonella enterica serovar Typhimurium delivered through a conjugative vehicle. In vitro, the CRISPR-Cas13a system exhibited specific killing, growth inhibition, and clearance of S. Typhimurium in mixed microbial flora. In a mouse infection model, the CRISPR-Cas13a system, when delivered by a donor Escherichia coli strain, significantly reduced S. Typhimurium colonization in the intestinal tract. Overall, the results demonstrate the feasibility and efficacy of the designed CRISPR-Cas13a system in selective killing of pathogens and broaden the utility of conjugation-based delivery of bactericidal approaches. IMPORTANCE Antibiotics with broad-spectrum activities are known to disturb both pathogens and beneficial gut microbiota and cause many undesired side effects, prompting increased interest in developing therapies that specifically eliminate pathogenic bacteria without damaging gut resident flora. To achieve this goal, we developed a strategy utilizing bacterial conjugation to deliver CRISPR-Cas13a programmed to specifically kill S. Typhimurium. This system produced pathogen-specific killing based on CRISPR RNA (crRNAs) targeting endogenous transcripts in pathogens and was shown to be effective in both in vitro and in vivo experiments. Additionally, the system can be readily delivered by conjugation and is adaptable for targeting different pathogens. With further optimization and improvement, the system has the potential to be used for biotherapy and microbial community modification.
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20
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Song G, Li X, Wang Z, Dong C, Xie X, Yan X. Structure of AcrVIA2 and its binding mechanism to CRISPR-Cas13a. Biochem Biophys Res Commun 2022; 612:84-90. [PMID: 35512461 DOI: 10.1016/j.bbrc.2022.04.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 04/20/2022] [Indexed: 11/26/2022]
Abstract
Phages and non-phage derived bacteria have evolved many anti-CRISPR proteins (Acrs) to escape the adaptive immune system of prokaryotes. Thus Acrs can be applied as a regulatory tool for gene edition by CRISPR system. Recently, a non-phage derived AcrVIA2 has been identified as an inhibitor that blocks the editing activity of Cas13a in vitro by binding to Cas13a. Here, we solved the crystal structure of AcrVIA2 at a resolution of 2.59 Å and confirmed that AcrVIA2 can bind to Helical-I domain in LshCas13a. Structural analysis show that the V-shaped acidic groove formed by β3-β3 hairpin of AcrVIA2 dimer is the key region that mediates the interaction between AcrVIA2 and Helical-I domain. In addition, we also reveal that Asp37 of AcrVIA2 plays an essential role in the functioning of the V-shaped acidic groove, and the functional dimer conformation of AcrVIA2 is stabilized by hydrogen bonds formed between Tyr41 of one monomer with Glu35 and Asp37 of the other monomer. These data expand the current understanding of the diverse interaction mechanisms between Acrs and Cas proteins, and also provide new ideas for the development of CRISPR-Cas13a regulatory tool.
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Affiliation(s)
- Guangyong Song
- Department of Biochemistry and Molecular Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xuzichao Li
- Department of Biochemistry and Molecular Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Zhangzhao Wang
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, 300134, China
| | - Cheng Dong
- Department of Biochemistry and Molecular Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xiangyang Xie
- NHC Key Laboratory of Hormones and Development, Tianjin Key Laboratory of Metabolic Diseases, Chu Hsien-I Memorial Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, 300134, China.
| | - Xiaojie Yan
- Department of Biochemistry and Molecular Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
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21
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Zhang J, Luo J, Zhao Y, Huang Y, Chen J, Hao W. [Advances of using CRISPR-Cas13a system for tumor diagnosis and treatment]. Sheng Wu Gong Cheng Xue Bao 2022; 38:2079-2086. [PMID: 35786463 DOI: 10.13345/j.cjb.210814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
CRISPR-Cas systems are well known gene editing tools, among which CRISPR-Cas9 system targeting DNA is the most well developed. Compared with CRISPR-Cas9 system, CRISPR-C2c2/ Cas13a system derived from TYPE VI of CRISPR family that can target RNA has attracted increasingly intense investigations in recent years. The CRISPR-Cas13a system is featured by specific recognition and binding of single stranded RNA sequences, thus playing a role in non-specific cleavage of RNA. This feature could be potentially applied to detect free nucleic acid in tumors or peripheral blood as a diagnostic approach. Since Cas13a specifically targets RNA, it can directly edit mRNA transcripts of genomic DNA to achieve the downregulation of target proteins without involving DNA editing. Therefore, Cas13a system could be used in tumor treatment. This review summarized the advances of using CRISPR-Cas13a for RNA targeting in tumor diagnosis and treatment, and prospected future applications.
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Affiliation(s)
- Jing Zhang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Jiahao Luo
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Yijun Zhao
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Ying'er Huang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Jialing Chen
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
| | - Wenbo Hao
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou 510515, Guangdong, China
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22
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Zhao J, Li Y, Xue Q, Zhu Z, Zou M, Fang F. A novel rapid visual detection assay for Toxoplasma gondii combining recombinase-aided amplification and lateral flow dipstick coupled with CRISPR-Cas13a fluorescence (RAA-Cas13a-LFD). Parasite 2022; 29:21. [PMID: 35420541 PMCID: PMC9009239 DOI: 10.1051/parasite/2022021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
Toxoplasmosis, a parasitic disease resulting from Toxoplasma gondii infection, remains prevalent worldwide, and causes great harm to immunodepressed patients, pregnant women and newborns. Although various molecular approaches to detect T. gondii infection are available, they are either costly or technically complex. This study aimed at developing a rapid visual detection assay using recombinase-aided amplification (RAA) and lateral flow dipstick (LFD) coupled with CRISPR-Cas13a fluorescence (RAA-Cas13a-LFD) to detect T. gondii. The RAA-Cas13a-LFD assay was performed in an incubator block at 37 °C within 2 h, and the amplification results were visualized and determined through LFD by the naked eye. The detection limit was 1 × 10-6 ng/μL by our developed RAA-Cas13a-LFD protocol, 100-fold higher than that by qPCR assay (1 × 10-8 ng/μL). No cross-reaction occurred either with the DNA of human blood or Ascaris lumbricoides, Digramma interrupta, Entamoeba coli, Fasciola gigantica, Plasmodium vivax, Schistosoma japonicum, Taenia solium, and Trichinella spiralis, and the positive rate by RAA-Cas13a-LFD assay was identical to that by qPCR assay (1.50% vs. 1.50%) in detecting T. gondii infection in the unknown blood samples obtained from clinical settings. Our findings demonstrate that this RAA-Cas13a-LFD assay is not only rapid, sensitive, and specific and allows direct visualization by the naked eye, but also eliminates sophisticated and costly equipment. More importantly, this technique can be applied to on-site surveillance of T. gondii.
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Affiliation(s)
- Jinhong Zhao
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China - Provincial Key Laboratory of Active Biological Macro-Molecules, Wuhu 241002, Anhui, China
| | - Yuanyuan Li
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Qiqi Xue
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Zhiwei Zhu
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Minghui Zou
- Department of Medical Parasitology, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Fang Fang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College, Wuhu 241001, Anhui, China
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23
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Liu L, Xu Z, Awayda K, Dollery SJ, Bao M, Fan J, Cormier D, O'Connell M, Tobin GJ, Du K. Gold Nanoparticle-Labeled CRISPR-Cas13a Assay for the Sensitive Solid-State Nanopore Molecular Counting. Adv Mater Technol 2022; 7:2101550. [PMID: 36338309 PMCID: PMC9632472 DOI: 10.1002/admt.202101550] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A gold nanoparticle (AuNP) labeled CRISPR-Cas13a nucleic acid assay has been developed for sensitive solid-state nanopore sensing. Instead of directly detecting the translocation of RNA through a nanopore, our system utilizes non-covalent conjugates of AuNPs and RNA targets. Upon CRISPR activation, the AuNPs are liberated from the RNA, isolated, and passed through a nanopore sensor. Detection of the AuNPs can be observed as increasing ionic current in the chip. Each AuNP that is detected is enumerated as an event, leading to quantitative of molecular targets. Leveraging the high signal-to-noise ratio enabled by the AuNPs, a detection limit of 50 fM before front-end target amplification is achieved using SARS-CoV-2 RNA segments as a Cas13 target. Furthermore, a dynamic range of six orders of magnitude is demonstrated for quantitative RNA sensing. This simplified AuNP-based CRISPR assay is performed at the physiological temperature without relying on thermal cyclers. In addition, the nanopore reader is similar in size to a smartphone, making the assay system suitable for rapid and portable nucleic acid biomarker detection in either low-resource settings or hospitals.
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Affiliation(s)
- Li Liu
- Department of Microsystems Engineering, Rochester Institute of Technology, Rochester, NY 14623, USA
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Zhiheng Xu
- Department of Industrial & Systems Engineering, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Kamel Awayda
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | | | - Mengdi Bao
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Jianlin Fan
- Institute of Semiconductors, Guangdong Academy of Sciences, Guangzhou, 510651, China
| | - Denis Cormier
- Department of Industrial & Systems Engineering, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Mitchell O'Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Gregory J. Tobin
- Biological Mimetics, Inc., 124 Byte Drive, Frederick, MD 21702, USA
| | - Ke Du
- Department of Microsystems Engineering, Rochester Institute of Technology, Rochester, NY 14623, USA
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, NY 14623, USA
- College of Health Sciences and Technology, Rochester Institute of Technology, Rochester, NY 14623, USA
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY 14623, USA
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24
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Xue T, Lu Y, Yang H, Hu X, Zhang K, Ren Y, Wu C, Xia X, Deng R, Wang Y. Isothermal RNA Amplification for the Detection of Viable Pathogenic Bacteria to Estimate the Salmonella Virulence for Causing Enteritis. J Agric Food Chem 2022; 70:1670-1678. [PMID: 35099949 DOI: 10.1021/acs.jafc.1c07182] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Viable foodborne pathogens can cause intestinal infection and food poisoning. Herein, we reported an RNA assay allowing for sensitive (close to 1 CFU and 1% viable bacteria detectable) and rapid (within 2.5 h) detection of viable pathogenic bacteria by coupling isothermal RNA amplification (nucleic acid sequence-based amplification, NASBA) with a CRISPR/Cas13a system. NASBA allowed direct amplification of 16S rRNA extracted from viable S. enterica (RNAs degrade rapidly in dead bacteria), and the specificity of amplification was ensured using Cas13a/crRNA to recognize the amplicons. We used the CRISPR/Cas13-based NASBA assay (termed cNASBA assay) to investigate the in vivo colonization and intestinal infection of S. enterica in mice. We found that S. enterica was mainly colonized at the cecum, colon, and rectum, and the severity of enteritis caused by S. enterica was determined by the number of viable S. enterica rather than the total count of S. enterica. The cNASBA assay can quantify viable S. enterica and thus can improve the accuracy of virulence estimation compared to qPCR. It shows promise as a reliable tool for monitoring pathogen contamination and biosafety control.
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Affiliation(s)
- Ting Xue
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ying Lu
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hao Yang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Xinyue Hu
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, China
| | - Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Chengyong Wu
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, China
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25
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An B, Zhang H, Su X, Guo Y, Wu T, Ge Y, Zhu F, Cui L. Rapid and Sensitive Detection of Salmonella spp. Using CRISPR-Cas13a Combined With Recombinase Polymerase Amplification. Front Microbiol 2021; 12:732426. [PMID: 34733250 PMCID: PMC8558462 DOI: 10.3389/fmicb.2021.732426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/14/2021] [Indexed: 11/23/2022] Open
Abstract
Salmonella spp. is one of the most common foodborne disease-causing pathogens that can cause severe diseases in very low infectious doses. Rapid and sensitive detecting Salmonella spp. is advantageous to the control of its spread. In this study, a conserved short fragment of the Salmonella invA gene was selected and used to design primers and specific crRNA (CRISPR RNA) for establishing a one-tube and two-step reaction system for Salmonella spp. detection, by combining recombinase polymerase amplification (RPA) with CRISPR-Cas13a (Clustered Regularly Interspaced Short Palindromic Repeats associated protein 13a) cleavage. The established one-tube RPA-Cas13a method can complete the detection within 20 min and the two-step RPA-Cas13a method detection time within 45 min. The designed primers were highly specific to Salmonella spp. and had no cross-reaction with the other nine diarrheal bacteria. The one-tube RPA-Cas13a could detect the Salmonella genome with the limit of 102 copies, which was the same as real-time polymerase chain reaction (PCR), but less sensitive than two-step RPA-Cas13a (100 copies). The detection results of one-tube or two-step RPA-Cas13a and real-time PCR were highly consistent in clinical samples. One-tube RPA-Cas13a developed in this study provides a simple, rapid, and specific detection method for Salmonella spp. While two-step assay was more sensitive and suitable for samples at low abundance.
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Affiliation(s)
- Bailin An
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,College of Pharmacy, Nankai University, Tianjin, China
| | - Hongbin Zhang
- Jiangyin City Center for Disease Control and Prevention, Wuxi, China
| | - Xuan Su
- College of Pharmacy, Nankai University, Tianjin, China
| | - Yue Guo
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tao Wu
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yiyue Ge
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Fengcai Zhu
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Lunbiao Cui
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China.,School of Public Health, Nanjing Medical University, Nanjing, China
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26
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Liu L, Wang Z, Wang Y, Luan J, Morrissey JJ, Naik RR, Singamaneni S. Plasmonically Enhanced CRISPR/Cas13a-Based Bioassay for Amplification-Free Detection of Cancer-Associated RNA. Adv Healthc Mater 2021; 10:e2100956. [PMID: 34369102 PMCID: PMC8542602 DOI: 10.1002/adhm.202100956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/25/2021] [Indexed: 12/15/2022]
Abstract
Novel methods that enable sensitive, accurate and rapid detection of RNA would not only benefit fundamental biological studies but also serve as diagnostic tools for various pathological conditions, including bacterial and viral infections and cancer. Although highly sensitive, existing methods for RNA detection involve long turn-around time and extensive capital equipment. Here, an ultrasensitive and amplification-free RNA quantification method is demonstrated by integrating CRISPR-Cas13a system with an ultrabright fluorescent nanolabel, plasmonic fluor. This plasmonically enhanced CRISPR-powered assay exhibits nearly 1000-fold lower limit-of-detection compared to conventional assay relying on enzymatic reporters. Using a xenograft tumor mouse model, it is demonstrated that this novel bioassay can be used for ultrasensitive and quantitative monitoring of cancer biomarker (lncRNA H19). The novel biodetection approach described here provides a rapid, ultrasensitive, and amplification-free strategy that can be broadly employed for detection of various RNA biomarkers, even in resource-limited settings.
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Affiliation(s)
- Lin Liu
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Zheyu Wang
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Yixuan Wang
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Jingyi Luan
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
| | - Jeremiah J. Morrissey
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rajesh R. Naik
- 711 Human Performance Wing, Air Force Research Laboratory, Wright Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Srikanth Singamaneni
- Department of Mechanical Engineering and Materials Science, Institute of Materials Science and Engineering, Washington University in St. Louis, St Louis, MO, 63130, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
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27
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Yao R, Xu Y, Wang L, Wang D, Ren L, Ren C, Li C, Li X, Ni W, He Y, Hu R, Guo T, Li Y, Li L, Wang X, Hu S. CRISPR-Cas13a-Based Detection for Bovine Viral Diarrhea Virus. Front Vet Sci 2021; 8:603919. [PMID: 34179152 PMCID: PMC8219879 DOI: 10.3389/fvets.2021.603919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 04/21/2021] [Indexed: 12/26/2022] Open
Abstract
Bovine Viral Diarrhea Virus (BVDV) is the main pathogen of bovine viral diarrhea disease (BVD), which leads to enormous economic losses in the cattle industry. A sensitive and specific detection for BVDV is advantageous to the control of BVDV. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have been used for detecting virus RNA. In this study, the expression and purification of LwCas13a protein was optimized and the RNase activity of LwCas13a in vitro was verified. CRISPR-LwCas13a system could detect BVDV virus and BVDV RNA with high specificity and simplicity. The detection limit of the LwCas13a system was 103 pM, and there were no cross-reactions with HEK293T and MDBK. In summary, a sensitive, specific, and simple nucleic acid detection method based on CRISPR-Cas13a was developed for BVDV. This method provides a new detection strategy for early diagnosis of BVDV.
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Affiliation(s)
- Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Lang Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Dawei Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Linchang Ren
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Changling Ren
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Cunyuan Li
- College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yanhua He
- College of Animal Science and Technology, Shihezi University, Shihezi, China.,State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Ruirui Hu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Tao Guo
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yaxin Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Lei Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Xiaokui Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, China
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28
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Yang Y, Liu J, Zhou X. A CRISPR-based and post-amplification coupled SARS-CoV-2 detection with a portable evanescent wave biosensor. Biosens Bioelectron 2021; 190:113418. [PMID: 34119838 PMCID: PMC8182983 DOI: 10.1016/j.bios.2021.113418] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/23/2021] [Accepted: 06/04/2021] [Indexed: 12/13/2022]
Abstract
The continuing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which causes coronavirus disease 2019 (COVID-19), has spread globally and its reliable diagnosis is one of the foremost priorities for protecting public health. Herein a rapid (<1 h), easy-to-implement, and accurate CRISPR-based evanescent wave fluorescence biosensing platform for detection of SARS-CoV-2 is reported. The collateral effect of Cas13a is combined with a universal autonomous enzyme-free hybridization chain reaction (HCR) by designing a cleavage hairpin reporter, which is cleaved upon target recognition, and hence releasing the initiator sequence to trigger the downstream HCR circuits. Detection of HCR assemblies is accomplished by first adsorbing to the desthiobiotin-modified optical fiber, followed by fluorescence emission induced by an evanescent field. Three Cas13a crRNAs targeting the genes of S, N and Orf1ab of SARS-CoV-2 are programmed to specifically target SARS-CoV-2 or broadly detect related coronavirus strains, such as MERS-CoV and SARS-CoV. The HCR amplification coupled Cas13a-based biosensing platform is capable of rapid detection of SARS-CoV-2 with attomolar sensitivity. This method is further validated by adding target RNA of SARS-CoV-2 in negative oropharyngeal swabs. The good discrimination capability of this technique demonstrates its promising potential for point-of-care diagnosis of COVID-19.
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Affiliation(s)
- Yihan Yang
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jinchuan Liu
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPC, Center for Sensor Technology of Environment and Health, School of Environment, Tsinghua University, Beijing, 100084, China.
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29
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Huang K, Yu H, Chen Z, Lin G, Zhang Z, Zhang X, Dong Y, Chen H, Zhang Z, Ma W, Wu Y, Liu T. CRISPR-Cas13a-based diagnostic method for Chlamydia trachomatis from nongonococcal urethritis. Bioanalysis 2021; 13:901-12. [PMID: 33961493 DOI: 10.4155/bio-2021-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Development of a routine screening technique for Chlamydia trachomatis infection. The proposed approach involves the CRISPR RNA (crRNA). In the presence of the target sequence, the RNase activity of the Cas13a protein is activated, and it cleaves RNA fluorescent probe so that fluorescence will be emitted. Results: The sensitivity of the detection based on CRISPR-Cas13a was 10 fM. The results obtained by CRISPR-Cas13a and quantitative polymerase chain reaction were closely correlated: χ2 = 81.798 (p < 0.001). Conclusion: The method can be carried out at room temperature and yields results within 2 h. The developed technique does not require expensive instruments and, thus, can meet the needs of community hospitals and other institutions for screening.
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30
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Gao S, Liu J, Li Z, Ma Y, Wang J. Sensitive detection of foodborne pathogens based on CRISPR-Cas13a. J Food Sci 2021; 86:2615-2625. [PMID: 33931854 DOI: 10.1111/1750-3841.15745] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 12/12/2022]
Abstract
Salmonella, being one of the most widespread foodborne pathogens, is a compulsory test item required by national food safety standard of China and many other countries. More sensitive and specific Salmonella detection method is still needed since traditional methods are time consuming and highly dependent on enormous manpower and material resources. In this research, a bacteria detection method based on CRISPR-Cas13a system (where CRISPR is Clustered Regularly Interspaced Short Palindromic Repeats) was proposed. The target DNA was amplified by PCR and transcribed into RNA by T7 transcriptase, which can activate the RNase activity of the Cas13a protein. The self-folding quenched fluorescent probe can be cleaved by the activated Cas13a protein to generate fluorescent signal. We named this method as PCF detection (PCR-CRISPR-Fluorescence based nucleic acid detection). In this study, PCF detection showed excellent sensitivity, which can detect Salmonella genomic DNA with a minimum of 101 aM or 10° CFU/ml Salmonella bacteria in 2 hr. It also showed good specificity with no cross-reaction with other common foodborne bacteria. PRACTICAL APPLICATION: The PCF detection method proposed in this article can detect Salmonella sensitively and specifically, providing a novel strategy for the detection of foodborne pathogens in food and has great application potential in other microbial detection fields.
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Affiliation(s)
- Song Gao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jingwen Liu
- Guangzhou Customs Technology Centre, Guangzhou, China
| | - Zhiyong Li
- Guangzhou Customs Technology Centre, Guangzhou, China
| | - Yi Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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Tian T, Shu B, Jiang Y, Ye M, Liu L, Guo Z, Han Z, Wang Z, Zhou X. An Ultralocalized Cas13a Assay Enables Universal and Nucleic Acid Amplification-Free Single-Molecule RNA Diagnostics. ACS Nano 2021; 15:1167-1178. [PMID: 33498106 DOI: 10.1021/acsnano.0c08165] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Existing methods for RNA diagnostics, such as reverse transcription PCR (RT-PCR), mainly rely on nucleic acid amplification (NAA) and RT processes, which are known to introduce substantial issues, including amplification bias, cross-contamination, and sample loss. To address these problems, we introduce a confinement effect-inspired Cas13a assay for single-molecule RNA diagnostics, eliminating the need for NAA and RT. This assay involves confining the RNA-triggered Cas13a catalysis system in cell-like-sized reactors to enhance local concentrations of target and reporter simultaneously, via droplet microfluidics. It achieves >10 000-fold enhancement in sensitivity when compared to the bulk Cas13a assay and enables absolute digital single-molecule RNA quantitation. We experimentally demonstrate its broad applicability for precisely counting microRNAs, 16S rRNAs, and SARS-CoV-2 RNA from synthetic sequences to clinical samples with excellent accuracy. Notably, this direct RNA diagnostic technology enables detecting a wide range of RNA molecules at the single-molecule level. Moreover, its simplicity, universality, and excellent quantification capability might render it to be a dominant rival to RT-qPCR.
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Affiliation(s)
- Tian Tian
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Bowen Shu
- Department of Laboratory Medicine, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
- Clinical Molecular Medicine and Molecular Diagnosis Key Laboratory of Guangdong Province, Guangzhou 510180, China
| | - Yongzhong Jiang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Miaomiao Ye
- Hubei Provincial Center for Disease Control and Prevention, Wuhan 430079, China
| | - Lei Liu
- Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, Center for Studies of Psychological Application, South China Normal University, Guangzhou 510631, China
| | - Zhonghui Guo
- Department of Clinical Laboratory Medicine, Central Hospital of Panyu District, Guangzhou 511400, China
| | - Zeping Han
- Department of Clinical Laboratory Medicine, Central Hospital of Panyu District, Guangzhou 511400, China
| | - Zhang Wang
- Institute of Ecological Science, School of Life Sciences, South China Normal University, Guangzhou 510180, China
| | - Xiaoming Zhou
- School of Life Sciences, South China Normal University, Guangzhou 510631, China
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Wang L, Zhou J, Wang Q, Wang Y, Kang C. Rapid design and development of CRISPR-Cas13a targeting SARS-CoV-2 spike protein. Theranostics 2021; 11:649-664. [PMID: 33391497 PMCID: PMC7738867 DOI: 10.7150/thno.51479] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/05/2020] [Indexed: 12/20/2022] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide epidemic of the lethal respiratory coronavirus disease (COVID-19), necessitating urgent development of specific and effective therapeutic tools. Among several therapeutic targets of coronaviruses, the spike protein is of great significance due to its key role in host invasion. Here, we report a potential anti-SARS-CoV-2 strategy based on the CRISPR-Cas13a system. Methods: A comprehensive set of bioinformatics methods, including sequence alignment, structural comparison, and molecular docking, was utilized to identify a SARS-CoV-2-spike(S)-specific segment. A tiling crRNA library targeting this specific RNA segment was designed, and optimal crRNA candidates were selected using in-silico methods. The efficiencies of the crRNA candidates were tested in human HepG2 and AT2 cells. Results: The most effective crRNA sequence inducing a robust cleavage effect on S and a potent collateral cleavage effect were identified. Conclusions: This study provides a rapid design pipeline for a CRISPR-Cas13a-based antiviral tool against SARS-CoV-2. Moreover, it offers a novel approach for anti-virus study even if the precise structures of viral proteins are indeterminate.
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Affiliation(s)
- Lin Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China
- Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin 300052, China
| | - Junhu Zhou
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China
- Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin 300052, China
| | - Qixue Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China
- Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin 300052, China
| | - Yunfei Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China
- Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin 300052, China
| | - Chunsheng Kang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China
- Tianjin Neurological Institute, Key Laboratory of Post-neurotrauma Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin 300052, China
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Zhang N, Bewick B, Xia G, Furling D, Ashizawa T. A CRISPR-Cas13a Based Strategy That Tracks and Degrades Toxic RNA in Myotonic Dystrophy Type 1. Front Genet 2020; 11:594576. [PMID: 33362853 PMCID: PMC7758406 DOI: 10.3389/fgene.2020.594576] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/23/2020] [Indexed: 12/18/2022] Open
Abstract
Cas13a, an effector of type VI CRISPR-Cas systems, is an RNA guided RNase with multiplexing and therapeutic potential. This study employs the Leptotrichia shahii (Lsh) Cas13a and a repeat-based CRISPR RNA (crRNA) to track and eliminate toxic RNA aggregates in myotonic dystrophy type 1 (DM1) – a neuromuscular disease caused by CTG expansion in the DMPK gene. We demonstrate that LshCas13a cleaves CUG repeat RNA in biochemical assays and reduces toxic RNA load in patient-derived myoblasts. As a result, LshCas13a reverses the characteristic adult-to-embryonic missplicing events in several key genes that contribute to DM1 phenotype. The deactivated LshCas13a can further be repurposed to track RNA-rich organelles within cells. Our data highlights the reprogrammability of LshCas13a and the possible use of Cas13a to target expanded repeat sequences in microsatellite expansion diseases.
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Affiliation(s)
- Nan Zhang
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, United States
| | - Brittani Bewick
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, United States
| | - Guangbin Xia
- Indiana University School of Medicine, Fort Wayne, IN, United States
| | - Denis Furling
- Institut National de la Sante et de la Recherche Medicale (INSERM), Centre de Recherche en Myologie (CRM), Association Institut de Myologie, Sorbonne Université, Paris, France
| | - Tetsuo Ashizawa
- Department of Neurology, Houston Methodist Research Institute, Houston, TX, United States
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Saifullah, Sakari M, Suzuki T, Yano S, Tsukahara T. Effective RNA Knockdown Using CRISPR-Cas13a and Molecular Targeting of the EML4-ALK Transcript in H3122 Lung Cancer Cells. Int J Mol Sci 2020; 21:E8904. [PMID: 33255340 DOI: 10.3390/ijms21238904] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
RNAi technology has significant potential as a future therapeutic and could theoretically be used to knock down disease-specific RNAs. However, due to frequent off-target effects, low efficiency, and limited accessibility of nuclear transcripts, the clinical application of the technology remains challenging. In this study, we first assessed the stability of Cas13a mRNA and guide RNA. Next, we titrated Cas13a and guide RNA vectors to achieve effective knockdown of firefly luciferase (FLuc) RNA, used as a target transcript. The interference specificity of Cas13a on guide RNA design was next explored. Subsequently, we targeted the EML4-ALK v1 transcript in H3122 lung cancer cells. As determined by FLuc assay, Cas13a exhibited activity only toward the orientation of the crRNA–guide RNA complex residing at the 5′ of the crRNA. The activity of Cas13a was maximal for guide RNAs 24–30 bp in length, with relatively low mismatch tolerance. After knockdown of the EML4-ALK transcript, cell viability was decreased up to 50%. Cas13a could effectively knock down FLuc luminescence (70–76%), mCherry fluorescence (72%), and EML4-ALK at the protein (>80%) and transcript levels (26%). Thus, Cas13a has strong potential for use in RNA regulation and therapeutics, and could contribute to the development of personalized medicine.
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35
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Che W, Ye S, Cai A, Cui X, Sun Y. CRISPR-Cas13a Targeting the Enhancer RNA-SMAD7e Inhibits Bladder Cancer Development Both in vitro and in vivo. Front Mol Biosci 2020; 7:607740. [PMID: 33282916 PMCID: PMC7705062 DOI: 10.3389/fmolb.2020.607740] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/22/2020] [Indexed: 12/26/2022] Open
Abstract
Enhancers are cis-acting elements that can promote the expression of target genes and respond to estrogen to induce the transcription of eRNAs, which are closely associated with cancer development. Further study on eRNAs may lead to a better understanding of the significance of transcriptional regulation and the progression of malignant tumors. SMAD7 enhancer RNA (SMAD7e) is an estrogen-responsive eRNA. However, the relationship between SMAD7e and bladder cancer remains unclear. SMAD7e was significantly upregulated in bladder cancer tissues and estrogen-stimulated cells. Knockdown of SMAD7e by CRISPR-Cas13a suppressed cell proliferation and migration, and induced cell apoptosis and inhibited cell invasion. Estrogen caused overexpression of SMAD7e and played a facilitating role in bladder cancer cells. Furthermore, knockdown of SMAD7e by CRISPR-Cas13a prevented the cancer-promoting effects of estrogen on bladder cancer both in vitro and in vivo. The present study suggested the crucial role of SMAD7e in bladder cancer. Estrogen might promote the development of bladder cancer by inducing SMAD7e production. These findings may provide a potential target for CRISPR-mediated gene therapy for bladder cancer in the future.
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Affiliation(s)
- Wenan Che
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, China
| | - Shanting Ye
- Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Aoxiang Cai
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, China
| | - Xiaojuan Cui
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, China
| | - Yuandong Sun
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Sciences, Hunan University of Science and Technology, Xiangtan, China
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Gao J, Luo T, Lin N, Zhang S, Wang J. A New Tool for CRISPR-Cas13a-Based Cancer Gene Therapy. Mol Ther Oncolytics 2020; 19:79-92. [PMID: 33102691 PMCID: PMC7554321 DOI: 10.1016/j.omto.2020.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 09/13/2020] [Indexed: 02/07/2023]
Abstract
Cas13a has already been successfully applied to virus detection. However, as a new gene interference tool, its potential in cancer treatment was not fully explored until now. This study constructed a new Cas13a expression vector, decoy minimal promoter-Cas13a-U6-guide RNA (DMP-Cas13a-U6-gRNA [DCUg]), by controlling the Cas13a and gRNA expression with a nuclear factor κB (NF-κB)-specific promoter and U6 promoter, respectively. DCUg could specifically and effectively knock down the expression of reporter genes in the 293T and HepG2 cells. DCUg could also similarly knock down the expression of endogenous oncogenes (TERT, EZH2, and RelA) at both mRNA and protein levels in a human hepatoma cell HepG2, which led to significant apoptosis and growth inhibition. In contrast, the same transfection did not affect the target gene expression, cell apoptosis, and growth of a human normal liver cell HL7702. Finally, DCUg targeting these oncogenes was packaged into adeno-associated virus (AAV) and treated four cells (HepG2, HL7702, WEHI-3, and Hepa1-6) and tumor-bearing mice. As results, the recombinant AAV significantly inhibited the growth of three cancer cells (HepG2, Hepa1-6, and WEHI-3) in vitro and the xenografted Hepa1-6 and WEHI-3 tumors in mice. This study therefore developed a new tool for the CRISPR-Cas13a-based cancer gene therapy.
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Affiliation(s)
- Jinliang Gao
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, P.R. China
| | - Tao Luo
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, P.R. China
| | - Na Lin
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, P.R. China
| | - Shuyan Zhang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, P.R. China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, P.R. China
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37
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Wang S, Li H, Kou Z, Ren F, Jin Y, Yang L, Dong X, Yang M, Zhao J, Liu H, Dong N, Jia L, Chen X, Zhou Y, Qiu S, Hao R, Song H. Highly sensitive and specific detection of hepatitis B virus DNA and drug resistance mutations utilizing the PCR-based CRISPR-Cas13a system. Clin Microbiol Infect 2020; 27:443-450. [PMID: 32360447 DOI: 10.1016/j.cmi.2020.04.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Undetectable or low-level hepatitis B virus (HBV) DNA and drug resistance mutations in patients may increase the risk of HBV transmission or cause active viral replication and other clinical problems. Here, we established a highly sensitive and practical method for HBV and drug resistance detection using a polymerase chain reaction (PCR) -based CRISPR-Cas13a detection system (referred to as PCR-CRISPR) and evaluated its detection capability using clinical samples. METHODS Specific CRISPR RNAs (crRNAs) are designed for HBV DNA detection and YMDD (tyrosine-methionine-aspartate-aspartate) variant identification. The HBV DNA was detected in 312 serum samples for HBV diagnosis using quantification PCR (qPCR) and PCR-CRISPR. Additionally, 424 serum samples for YMDD testing were detected by qPCR, direct sequencing, and our assay. RESULTS Using PCR-CRISPR, one copy per test of HBV DNA was detected with HBV-1 crRNA in 15 min after PCR amplification. Consistent results with qPCR were observed for 302 samples, while the remaining 10 samples with low-level HBV DNA were detectable by PCR-CRISPR and droplet digital PCR but not by qPCR. PCR-CRISPR diagnosed all 412 drug-resistant samples detected by the YMDD detection qPCR kit and direct sequencing, as well as the other 12 drug-resistant samples with low-level HBV DNA undetectable by qPCR and direct sequencing. CONCLUSIONS We developed a novel PCR-CRISPR method for highly sensitive and specific detection of HBV DNA and drug resistance mutations. One copy per test for HBV DNA and YMDD drug resistance mutations could be detected. This method has wide application prospects for the early detection of HBV infection, drug resistance monitoring and treatment guidance.
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Affiliation(s)
- S Wang
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - H Li
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Z Kou
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - F Ren
- Beijing Artificial Liver Treatment and Training Centre, Beijing You An Hospital, Affiliated Hospital of Capital Medical University, Beijing, China
| | - Y Jin
- Beijing Artificial Liver Treatment and Training Centre, Beijing You An Hospital, Affiliated Hospital of Capital Medical University, Beijing, China
| | - L Yang
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - X Dong
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - M Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - J Zhao
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - H Liu
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - N Dong
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - L Jia
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - X Chen
- Beijing Artificial Liver Treatment and Training Centre, Beijing You An Hospital, Affiliated Hospital of Capital Medical University, Beijing, China
| | - Y Zhou
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - S Qiu
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China.
| | - R Hao
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China.
| | - H Song
- Graduate School of the Academy of Military Medical Sciences, Academy of Military Sciences, Beijing, China; Chinese PLA Center for Disease Control and Prevention, Beijing, China.
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Li C, Guo L, Liu G, Guo M, Wei H, Yang Q, Wang J, Chen H. Reprogrammed CRISPR-Cas13a targeting the HPV16/18 E6 gene inhibits proliferation and induces apoptosis in E6-transformed keratinocytes. Exp Ther Med 2020; 19:3856-3860. [PMID: 32346451 DOI: 10.3892/etm.2020.8631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/04/2020] [Indexed: 12/26/2022] Open
Abstract
The long-lasting infection of high-risk type (type 16 or type 18) human papillomavirus (HPV) is the main cause of gynecological and urinary malignancies. Given the high mortality rate after surgery, the development of a new molecular therapy would be of value to clinicians. The aim of the present study was to achieve targeted inactivation of the viral E6 gene in keratinocytes using the reprogrammed CRISPR-Cas13a system. To accomplish this, a reprogrammed CRISPR-Cas13a system, targeting both the HPV16/18 E6 genes was constructed using a guide RNA expressing vector. The expression levels of E6 protein were measured using western blot analysis after transfection of the vector into E6-transformed keratin oocytes. Cell proliferation was analyzed using CCK-8 assays and cell apoptosis was evaluated using Hoechst 33258 staining and ELISAs examining caspase-3 levels. The results indicated that both the HPV16/18 E6 genes can be inactivated using the CRISPR-Cas13a system. Furthermore, silencing E6 inhibited cell proliferation (14±1.8% on average) and induced apoptosis (80.2±3.2% on average) in E6-transformed keratinocytes but not in normal keratinocytes. In conclusion, results of the present study demonstrate that the reprogrammed CRISPR-Cas13a system has the potential for inactivating HPV E6 gene functions.
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Affiliation(s)
- Chunjing Li
- Department of Urology, Foshan Maternal and Child Health Hospital, Southern Medical University, Foshan, Guangdong 528000, P.R. China
| | - Liwen Guo
- Department of Gynecology, Ningde Municipal Hospital, Fujian Medical University, Ningde, Fujian 352100, P.R. China
| | - Guoqing Liu
- Department of Urology, Foshan Maternal and Child Health Hospital, Southern Medical University, Foshan, Guangdong 528000, P.R. China
| | - Mingjuan Guo
- Department of Urology, Foshan Maternal and Child Health Hospital, Southern Medical University, Foshan, Guangdong 528000, P.R. China
| | - Huiling Wei
- Department of Urology, Foshan Maternal and Child Health Hospital, Southern Medical University, Foshan, Guangdong 528000, P.R. China
| | - Qiqiong Yang
- Department of Urology, Foshan Maternal and Child Health Hospital, Southern Medical University, Foshan, Guangdong 528000, P.R. China
| | - Jianfeng Wang
- Department of Urology, Foshan Maternal and Child Health Hospital, Southern Medical University, Foshan, Guangdong 528000, P.R. China
| | - Huihua Chen
- Department of Gynecology, Ningde Municipal Hospital, Fujian Medical University, Ningde, Fujian 352100, P.R. China
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Kulkarni A, Yu W, Moon AS, Pandey A, Hanley KA, Xu J. Programmable CRISPR interference for gene silencing using Cas13a in mosquitoes. J Genomics 2020; 8:30-36. [PMID: 32190127 PMCID: PMC7064736 DOI: 10.7150/jgen.43928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023] Open
Abstract
In the CRISPR-Cas systems, Cas13a is an RNA-guided RNA nuclease specifically targeting single strand RNA. We developed a Cas13a mediated CRISPR interference tool to target mRNA for gene silencing in mosquitoes. A Cas13a expressing plasmid was delivered to mosquitoes by intrathoracic injection, and Cas13a transcripts were detectable at least 10 days post-delivery. The target specific crRNA was synthesized in vitro using T7 RNA polymerase. The Cas13a plasmid and target crRNA can be delivered by intrathoracic injection together, or the Cas13a construct can be provided first, and then target crRNA can be given later when appropriate. The machinery was tested in two mosquito species. In Anopheles gambiae, vitellogenin gene was silenced by Cas13a/Vg-crRNA, which was accompanied by a significant reduction in egg production. In Aedes aegypti, the α- and δ-subunits of COPI genes were silenced by Cas13a/crRNA, which resulted in mortality and fragile midguts, reproducing a phenotype reported previously. Co-silencing genes simultaneously is achievable when a cocktail of target crRNAs is given. No detectable collateral cleavages of non-target transcripts were observed in the study. In addition to dsRNA or siRNA mediated RNA interference, the programmable CRISPR interference method offers an alternative to knock down genes in mosquitoes.
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Affiliation(s)
- Aditi Kulkarni
- Department of Biology, New Mexico State University, PO Box 30001 MSC 3AF, Las Cruces NM, 88003, USA
| | - Wanqin Yu
- Department of Biology, New Mexico State University, PO Box 30001 MSC 3AF, Las Cruces NM, 88003, USA
| | - Alex S Moon
- Department of Biology, New Mexico State University, PO Box 30001 MSC 3AF, Las Cruces NM, 88003, USA
| | - Ashmita Pandey
- Department of Biology, New Mexico State University, PO Box 30001 MSC 3AF, Las Cruces NM, 88003, USA
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, PO Box 30001 MSC 3AF, Las Cruces NM, 88003, USA
| | - Jiannong Xu
- Department of Biology, New Mexico State University, PO Box 30001 MSC 3AF, Las Cruces NM, 88003, USA
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Fan J, Liu Y, Liu L, Huang Y, Li X, Huang W. A Multifunction Lipid-Based CRISPR-Cas13a Genetic Circuit Delivery System for Bladder Cancer Gene Therapy. ACS Synth Biol 2020; 9:343-355. [PMID: 31891494 DOI: 10.1021/acssynbio.9b00349] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The treatment of bladder cancer has recently shown minimal progress. Gene therapy mediated by CRISPR provides a new option for bladder cancer treatment. In this study, we developed a versatile liposome system to deliver the CRISPR-Cas13a gene circuits into bladder cancer cells. After in vitro studies and intravesical perfusion studies in mice, this system showed five advantages: (1) CRISPR-Cas13a, a transcriptional targeting and cleavage tool for gene expression editing, did not affect the stability of the cell genome; (2) the prepared liposome systems were targeted to hVEGFR2, which is always highly expressed in bladder cancer cells; (3) the CRISPR-Cas13a sequence was driven by an artificial tumor specific promoter to achieve further targeting; (4) a near-infrared photosensitizer released using near-infrared light was introduced to control the delivery system; and (5) the plasmids were constructed with three crRNA tandem sequences to achieve multiple targeting and wider therapeutic results. This tumor cell targeting lipid delivery system with near-infrared laser-controlled ability provided a versatile strategy for CRISPR-Cas13a based gene therapy of bladder cancer.
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Affiliation(s)
- Jing Fan
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China
- Reproductive Medicine Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen 518028, China
- The State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China
| | - Yuchen Liu
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China
| | - Lisa Liu
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China
| | - Yikun Huang
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China
| | - Xuemei Li
- Reproductive Medicine Center, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen 518028, China
| | - Weiren Huang
- Department of Urology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518039, China
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Watanabe S, Cui B, Kiga K, Aiba Y, Tan XE, Sato'o Y, Kawauchi M, Boonsiri T, Thitiananpakorn K, Taki Y, Li FY, Azam AH, Nakada Y, Sasahara T, Cui L. Corrigendum: Composition and Diversity of CRISPR-Cas13a Systems in the Genus Leptotrichia. Front Microbiol 2020; 11:179. [PMID: 32117179 PMCID: PMC7029190 DOI: 10.3389/fmicb.2020.00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 01/24/2020] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2019.02838.].
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Affiliation(s)
- Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Bintao Cui
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Kotaro Kiga
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yoshifumi Aiba
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yusuke Sato'o
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Moriyuki Kawauchi
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Tanit Boonsiri
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Kanate Thitiananpakorn
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yusuke Taki
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Fen-Yu Li
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Aa Haeruman Azam
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yumi Nakada
- Division of Clinical Laboratory, Tottori University Hospital, Tottori, Japan
| | - Teppei Sasahara
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
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42
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Watanabe S, Cui B, Kiga K, Aiba Y, Tan XE, Sato'o Y, Kawauchi M, Boonsiri T, Thitiananpakorn K, Taki Y, Li FY, Azam AH, Nakada Y, Sasahara T, Cui L. Composition and Diversity of CRISPR-Cas13a Systems in the Genus Leptotrichia. Front Microbiol 2019; 10:2838. [PMID: 31921024 PMCID: PMC6914741 DOI: 10.3389/fmicb.2019.02838] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13a, previously known as CRISPR-C2c2, is the most recently identified RNA-guided RNA-targeting CRISPR-Cas system that has the unique characteristics of both targeted and collateral single-stranded RNA (ssRNA) cleavage activities. This system was first identified in Leptotrichia shahii. Here, the complete whole genome sequences of 11 Leptotrichia strains were determined and compared with 18 publicly available Leptotrichia genomes in regard to the composition, occurrence and diversity of the CRISPR-Cas13a, and other CRISPR-Cas systems. Various types of CRISPR-Cas systems were found to be unevenly distributed among the Leptotrichia genomes, including types I-B (10/29, 34.4%), II-C (1/29, 2.6%), III-A (6/29, 15.4%), III-D (6/29, 15.4%), III-like (3/29, 7.7%), and VI-A (11/29, 37.9%), while 8 strains (20.5%) had no CRISPR-Cas system at all. The Cas13a effectors were found to be highly divergent with amino acid sequence similarities ranging from 61% to 90% to that of L. shahii, but their collateral ssRNA cleavage activities leading to impediment of bacterial growth were conserved. CRISPR-Cas spacers represent a sequential achievement of former intruder encounters, and the retained spacers reflect the evolutionary phylogeny or relatedness of strains. Analysis of spacer contents and numbers among Leptotrichia species showed considerable diversity with only 4.4% of spacers (40/889) were shared by two strains. The organization and distribution of CRISPR-Cas systems (type I-VI) encoded by all registered Leptotrichia species revealed that effector or spacer sequences of the CRISPR-Cas systems were very divergent, and the prevalence of types I, III, and VI was almost equal. There was only one strain carrying type II, while none carried type IV or V. These results provide new insights into the characteristics and divergences of CRISPR-Cas systems among Leptotrichia species.
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Affiliation(s)
- Shinya Watanabe
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Bintao Cui
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Kotaro Kiga
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yoshifumi Aiba
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Xin-Ee Tan
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yusuke Sato'o
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Moriyuki Kawauchi
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Tanit Boonsiri
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Kanate Thitiananpakorn
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yusuke Taki
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Fen-Yu Li
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Aa Haeruman Azam
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Yumi Nakada
- Division of Clinical Laboratory, Tottori University Hospital, Tottori, Japan
| | - Teppei Sasahara
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
| | - Longzhu Cui
- Division of Bacteriology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Tochigi, Japan
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Khan H, Khan A, Liu Y, Wang S, Bibi S, Xu H, Liu Y, Durrani S, Jin L, He N, Xiong T. CRISPR-Cas13a mediated nanosystem for attomolar detection of canine parvovirus type 2. CHINESE CHEM LETT 2019; 30:2201-2204. [PMID: 32288403 PMCID: PMC7129497 DOI: 10.1016/j.cclet.2019.10.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 12/15/2022]
Abstract
Canine parvovirus type 2 (CPV-2) infection is the most lethal disease of dogs with higher mortality in puppies worldwide. In today’s world, dogs are an integral part of our communities as well as dogs breeding and rearing has become a lucrative business. Therefore, a fast, accurate, portable, and cost-effective CPV-2 detection method with the ability for on-site detection is highly desired. In this study, we for the first time proposed a nanosystem for CPV-2 DNA detection with RNA-guided RNA endonuclease Cas13a, which upon activation results in collateral RNA degradation. We expressed LwCas13a in prokaryotic expression system and purified it through nickel column. Activity of Cas13a was verified by RNA-bound fluorescent group while using a quenched fluorescent probe as signals. Further Cas13a was combined with Recombinase polymerase amplification (RPA) and T7 transcription to establish molecular detection system termed specific high-sensitivity enzymatic reporter un-locking (SHERLOCK) for sensitive detection of CPV-2 DNA. This nanosystem can detect 100 amol/L CPV-2 DNA within 30 min. The proposed nanosystem exhibited high specificity when tested for CPV-2 and other dog viruses. This CRISPR-Cas13a mediated sensitive detection approach can be of formidable advantage during CPV-2 outbreaks because it is time-efficient, less laborious and does not involve the use of sophisticated instruments.
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Affiliation(s)
- Haroon Khan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Adeel Khan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yufeng Liu
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China.,College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Su Wang
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China.,College of Life Science, Yangtze University, Jingzhou 434025, China
| | - Sumaira Bibi
- Bio Resources Conservation Institute, National Agriculture Research Centre, Islamabad 350000, Pakistan
| | - Hongpan Xu
- Department of Clinical Laboratory, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Yuan Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Samran Durrani
- Laboratory of Biointerface & Biomaterials, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Lian Jin
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.,Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China.,National Center for International Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Theranostics, Guangxi Medical University, Nanning 530021, China
| | - Tao Xiong
- College of Life Science, Yangtze University, Jingzhou 434025, China
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44
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Chang Y, Deng Y, Li T, Wang J, Wang T, Tan F, Li X, Tian K. Visual detection of porcine reproductive and respiratory syndrome virus using CRISPR-Cas13a. Transbound Emerg Dis 2019; 67:564-571. [PMID: 31541593 DOI: 10.1111/tbed.13368] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/11/2019] [Accepted: 09/15/2019] [Indexed: 12/26/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) has varied constantly and circulated in the pig industry worldwide. The prevention and control of porcine reproductive and respiratory syndrome (PRRS) is complicated. A visual, sensitive and specific diagnostic method is advantageous to the control of PRRS. The collateral cleavage activity of LwCas13a is activated to degrade non-targeted RNA, when crRNA of LwCas13a bond to target RNA. The enhanced Cas13a detection is the combination of collateral cleavage activity of LwCas13a and recombinase polymerase amplification (RPA). In this study, the enhanced Cas13a detection for PRRSV was established. The novel method was an isothermal detection at 37°C, and the detection can be used for real-time analysis or visual readout. The detection limit of the enhanced Cas13a detection was 172 copies/μl, and there were no cross-reactions with porcine circovirus 2, porcine parvovirus, classical swine fever virus and pseudorabies virus. The enhanced Cas13a detection can work well in clinical samples. In summary, a visual, sensitive and specific nucleic acid detection method based on CRISPR-Cas13a was developed for PRRSV.
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Affiliation(s)
- Yafei Chang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yue Deng
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Tianyu Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Juan Wang
- National Research Center for Veterinary Medicine, Luoyang, China
| | - Tongyan Wang
- National Research Center for Veterinary Medicine, Luoyang, China
| | - Feifei Tan
- National Research Center for Veterinary Medicine, Luoyang, China
| | - Xiangdong Li
- National Research Center for Veterinary Medicine, Luoyang, China
| | - Kegong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,National Research Center for Veterinary Medicine, Luoyang, China.,OIE Reference Laboratory for PRRS in China, Beijing, China
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45
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Ding M, Zhan H, Liao X, Li A, Zhong Y, Gao Q, Liu Y, Huang W, Cai Z. Enhancer RNA - P2RY2e induced by estrogen promotes malignant behaviors of bladder cancer. Int J Biol Sci 2018; 14:1268-1276. [PMID: 30123075 PMCID: PMC6097482 DOI: 10.7150/ijbs.27151] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 06/23/2018] [Indexed: 12/26/2022] Open
Abstract
Enhancers are transcriptional regulatory elements that increase target gene expression. It has reported that enhancers could universally transcribe into enhancer RNAs (eRNAs) with stimulation. Increasing evidence showed eRNAs participated in various disease processes including malignant tumors. P2RY2 enhancer RNA (P2RY2e) is an estrogen-responsive eRNA and involved in the development of breast cancer. However, the relationship between P2RY2e and bladder cancer (BCa) is unclear. In the study, we discovered that P2RY2e was upregulated in BCa tissues and estrogen-treated cells. Estrogen promoted the malignant abilities of BCa cells. P2RY2e knockdown by CRISPR-Cas13a inhibit the cell multiplication, invasion and migration. Additionally, the cell apoptosis was facilitated. What's more, downregulation of P2RY2e could weaken the cancer-promoting effects of estrogen on BCa. Our study revealed that P2RY2e played a carcinogenic role in BCa and estrogen might promote the initiation of BCa by inducing P2RY2e. We provide a potential therapeutic target for BCa and a new perspective for the tumorigenesis of bladder cancer.
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Affiliation(s)
- Mengting Ding
- Clinical Medicine College of Anhui Medical University, Department of Urology, Shenzhen Second People's Hospital, Shenzhen 518000, Guangdong, China.,Anhui Medical University, Hefei 230032, Anhui Province, China
| | - Hengji Zhan
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Xinhui Liao
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Aolin Li
- Clinical Medicine College of Anhui Medical University, Department of Urology, Shenzhen Second People's Hospital, Shenzhen 518000, Guangdong, China
| | - Yucheng Zhong
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Qunjun Gao
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Yuchen Liu
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Weiren Huang
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
| | - Zhiming Cai
- Department of Urology, Shenzhen Second People's Hospital, the First Affiliated Hospital of Shenzhen University, Shenzhen 518000, China
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