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Gu X, Tang Q, Zhu Y, Sun C, Wu L, Ji H, Wang Q, Wu L, Qin Y. Advancements of CRISPR technology in public health-related analysis. Biosens Bioelectron 2024; 261:116449. [PMID: 38850734 DOI: 10.1016/j.bios.2024.116449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024]
Abstract
Pathogens and contaminants in food and the environment present significant challenges to human health, necessitating highly sensitive and specific diagnostic methods. Traditional approaches often struggle to meet these requirements. However, the emergence of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system has revolutionized nucleic acid diagnostics. The present review provides a comprehensive overview of the biological sensing technology based on the CRISPR/Cas system and its potential applications in public health-related analysis. Additionally, it explores the enzymatic cleavage capabilities mediated by Cas proteins, highlighting the promising prospects of CRISPR technology in addressing bioanalysis challenges. We discuss commonly used CRISPR-Cas proteins and elaborate on their application in detecting foodborne bacteria, viruses, toxins, other chemical pollution, and drug-resistant bacteria. Furthermore, we highlight the advantages of CRISPR-based sensors in the field of public health-related analysis and propose that integrating CRISPR-Cas biosensing technology with other technologies could facilitate the development of more diverse detection platforms, thereby indicating promising prospects in this field.
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Affiliation(s)
- Xijuan Gu
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China; Xinglin College, Nantong University, Qidong, Jiangsu, 226236, PR China
| | - Qu Tang
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Yidan Zhu
- Medical School, Nantong University, Nantong, Jiangsu, 226001, PR China
| | - Chenling Sun
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Lingwei Wu
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Haiwei Ji
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Qi Wang
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Li Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Life Sciences, Nantong University, Nantong, Jiangsu, 226019, PR China; School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Yuling Qin
- School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
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Jaybhaye SG, Chavhan RL, Hinge VR, Deshmukh AS, Kadam US. CRISPR-Cas assisted diagnostics of plant viruses and challenges. Virology 2024; 597:110160. [PMID: 38955083 DOI: 10.1016/j.virol.2024.110160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 06/04/2024] [Accepted: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Plant viruses threaten global food security by infecting commercial crops, highlighting the critical need for efficient virus detection to enable timely preventive measures. Current techniques rely on polymerase chain reaction (PCR) for viral genome amplification and require laboratory conditions. This review explores the applications of CRISPR-Cas assisted diagnostic tools, specifically CRISPR-Cas12a and CRISPR-Cas13a/d systems for plant virus detection and analysis. The CRISPR-Cas12a system can detect viral DNA/RNA amplicons and can be coupled with PCR or isothermal amplification, allowing multiplexed detection in plants with mixed infections. Recent studies have eliminated the need for expensive RNA purification, streamlining the process by providing a visible readout through lateral flow strips. The CRISPR-Cas13a/d system can directly detect viral RNA with minimal preamplification, offering a proportional readout to the viral load. These approaches enable rapid viral diagnostics within 30 min of leaf harvest, making them valuable for onsite field applications. Timely identification of diseases associated with pathogens is crucial for effective treatment; yet developing rapid, specific, sensitive, and cost-effective diagnostic technologies remains challenging. The current gold standard, PCR technology, has drawbacks such as lengthy operational cycles, high costs, and demanding requirements. Here we update the technical advancements of CRISPR-Cas in viral detection, providing insights into future developments, versatile applications, and potential clinical translation. There is a need for approaches enabling field plant viral nucleic acid detection with high sensitivity, specificity, affordability, and portability. Despite challenges, CRISPR-Cas-mediated pathogen diagnostic solutions hold robust capabilities, paving the way for ideal diagnostic tools. Alternative applications in virus research are also explored, acknowledging the technology's limitations and challenges.
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Affiliation(s)
- Siddhant G Jaybhaye
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Rahul L Chavhan
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Vidya R Hinge
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Abhijit S Deshmukh
- Vilasrao Deshmukh College of Agricultural Biotechnology, Nanded Road, Latur, Vasantrao Naik Marathwada Krishi Vidyapeeth, Maharashtra, India
| | - Ulhas S Kadam
- Plant Molecular Biology and Biotechnology Research Centre (PMBBRC), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Gyeongsangnam-do, South Korea.
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Zeng Q, Zhou M, Deng W, Gao Q, Li Z, Wu L, Liang D. Sensitive and visual detection of SARS-CoV-2 using RPA-Cas12a one-step assay with ssDNA-modified crRNA. Anal Chim Acta 2024; 1309:342693. [PMID: 38772660 DOI: 10.1016/j.aca.2024.342693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND CRISPR-Cas12a based one-step assays are widely used for nucleic acid detection, particularly for pathogen detection. However, the detection capability of the one-step assay is reduced because the Cas12a protein competes with the isothermal amplification enzymes for the target DNA and cleaves it. Therefore, the key to improving the sensitivity of the one-step assay is to address the imbalance between isothermal amplification and CRISPR detection. In previous study, we developed a Cas12a one-step assay using single-stranded DNA (ssDNA)-modified crRNA (mD-crRNA) and applied this method for the detection of pathogenic DNA. RESULTS Here, we utilized mD-crRNA to establish a sensitive one-step assay that enables the visual detection of SARS-CoV-2 under ultraviolet light, achieving a detection limit of 5 aM without cross-reactivity. The sensitivity of mD-crRNA in the one-step assay was 100-fold higher than that of wild-type crRNA. Mechanistic studies revealed that the addition of ssDNA at the 3' end of mD-crRNA attenuates the binding affinity between the Cas12a-mD-crRNA complex and the target DNA. Consequently, this reduction in binding affinity decreases the cis-cleavage activity of Cas12a, mitigating its cleavage of the target DNA in the one-step assay. As a result, there is an augmentation in the amplification and accumulation of target DNA, thereby enhancing detection sensitivity. In the clinical testing of 40 SARS-CoV-2 RNA samples, the concordance between the results of the one-step assay and known qPCR results was 97.5 %. SIGNIFICANCE The one-step assay using mD-crRNA proves to be highly sensitive and specificity and visually effective for the detection of SARS-CoV-2. Our study delves into the application of the mD-crRNA-mediated one-step assay in nucleic acid detection and its associated reaction mechanism. This holds great significance in addressing the inherent incompatibility issues between isothermal amplification and CRISPR detection.
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Affiliation(s)
- Qinlong Zeng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Miaojin Zhou
- MOE Key Lab of Rare Pediatric Diseases, Department of Cell Biology and Genetics, School of Basic Medical Sciences, University of South China, Hengyang, 421200, China
| | - Weiheng Deng
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Qian Gao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410078, China
| | - Zhuo Li
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China.
| | - Lingqian Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China.
| | - Desheng Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078, China.
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Lee JC, Ryu SM, Lee Y, Jang H, Song J, Kang T, Lee KH, Park S. CRISPR/Cas12a antifouling nanocomposite electrochemical biosensors enable amplification-free detection of Monkeypox virus in complex biological fluids. NANOSCALE 2024; 16:11318-11326. [PMID: 38804270 DOI: 10.1039/d4nr01618a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The escalating global threat of infectious diseases, including monkeypox virus (MPXV), necessitates advancements in point-of-care diagnostics, moving beyond the constraints of conventional methods tethered to centralized laboratories. Here, we introduce multiple CRISPR RNA (crRNA)-based biosensors that can directly detect MPXV within 35 minutes without pre-amplification, leveraging the enhanced sensitivity and antifouling attributes of the BSA-based nanocomposite. Multiple crRNAs, strategically targeting diverse regions of the F3L gene of MPXV, are designed and combined to amplify Cas12a activation and its collateral cleavage of reporter probes. Notably, our electrochemical sensors exhibit the detection limit of 669 fM F3L gene without amplification, which is approximately a 15-fold improvement compared to fluorescence detection. This sensor also shows negligible changes in peak current after exposure to complex biological fluids, such as whole blood and serum, maintaining its sensitivity at 682 fM. This sensitivity is nearly identical to the conditions when only the F3L gene was present in PBS. In summary, our CRISPR-based electrochemical biosensors can be utilized as a high-performance diagnostic tool in resource-limited settings, representing a transformative leap forward in point-of-care testing. Beyond infectious diseases, the implications of this technology extend to various molecular diagnostics, establishing itself as a rapid, accurate, and versatile platform for detection of target analytes.
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Affiliation(s)
- Jeong-Chan Lee
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seuk-Min Ryu
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - YongJin Lee
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Forensic Sciences, Sungkyunkwan University (SKKU), Suwon-si, Gyeongi-do 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon-si, Gyeongi-do 16419, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon-si, Gyeongi-do 16419, Republic of Korea
| | - Kwan Hyi Lee
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Steve Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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Mohammad N, Talton L, Dalgan S, Hetzler Z, Steksova A, Wei Q. Ratiometric nonfluorescent CRISPR assay utilizing Cas12a-induced plasmid supercoil relaxation. Commun Chem 2024; 7:130. [PMID: 38851849 PMCID: PMC11162422 DOI: 10.1038/s42004-024-01214-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/30/2024] [Indexed: 06/10/2024] Open
Abstract
Most CRISPR-based biosensors rely on labeled reporter molecules and expensive equipment for signal readout. A recent approach quantifies analyte concentration by sizing λ DNA reporters via gel electrophoresis, providing a simple solution for label-free detection. Here, we report an alternative strategy for label-free CRISPR-Cas12a, which relies on Cas12a trans-nicking induced supercoil relaxation of dsDNA plasmid reporters to generate a robust and ratiometric readout. The ratiometric CRISPR (rCRISPR) measures the relative percentage of supercoiled plasmid DNA to the relaxed circular DNA by gel electrophoresis for more accurate target concentration quantification. This simple method is two orders of magnitude more sensitive than the typical fluorescent reporter. This self-referenced strategy solves the potential application limitations of previously demonstrated DNA sizing-based CRISPR-Dx without compromising the sensitivity. Finally, we demonstrated the applicability of rCRISPR for detecting various model DNA targets such as HPV 16 and real AAV samples, highlighting its feasibility for point-of-care CRISPR-Dx applications.
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Affiliation(s)
- Noor Mohammad
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka, 1000, Bangladesh
| | - Logan Talton
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Selen Dalgan
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Zach Hetzler
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Anastasiia Steksova
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA.
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Bisht D, Salave S, Desai N, Gogoi P, Rana D, Biswal P, Sarma G, Benival D, Kommineni N, Desai D. Genome editing and its role in vaccine, diagnosis, and therapeutic advancement. Int J Biol Macromol 2024; 269:131802. [PMID: 38670178 DOI: 10.1016/j.ijbiomac.2024.131802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/25/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024]
Abstract
Genome editing involves precise modification of specific nucleotides in the genome using nucleases like CRISPR/Cas, ZFN, or TALEN, leading to increased efficiency of homologous recombination (HR) for gene editing, and it can result in gene disruption events via non-homologous end joining (NHEJ) or homology-driven repair (HDR). Genome editing, particularly CRISPR-Cas9, revolutionizes vaccine development by enabling precise modifications of pathogen genomes, leading to enhanced vaccine efficacy and safety. It allows for tailored antigen optimization, improved vector design, and deeper insights into host genes' impact on vaccine responses, ultimately enhancing vaccine development and manufacturing processes. This review highlights different types of genome editing methods, their associated risks, approaches to overcome the shortcomings, and the diverse roles of genome editing.
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Affiliation(s)
- Deepanker Bisht
- ICAR- Indian Veterinary Research Institute, Izatnagar 243122, Bareilly, India
| | - Sagar Salave
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Nimeet Desai
- Indian Institute of Technology Hyderabad, Kandi 502285, Telangana, India
| | - Purnima Gogoi
- School of Medicine and Public Health, University of Wisconsin and Madison, Madison, WI 53726, USA
| | - Dhwani Rana
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India
| | - Prachurya Biswal
- College of Veterinary and Animal Sciences, Bihar Animal Sciences University, Kishanganj 855115, Bihar, India
| | - Gautami Sarma
- College of Veterinary & Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, U.S. Nagar, Uttarakhand, India
| | - Derajram Benival
- National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad 382355, Gujarat, India.
| | | | - Dhruv Desai
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Xue L, Bu S, Xu M, Wei J, Zhou H, Xu Y, Hao Z, Li Z, Wan J. A sensitive fluorescence biosensor based on ligation-transcription and CRISPR/Cas13a-assisted cascade amplification strategies to detect the H1N1 virus. Anal Bioanal Chem 2024; 416:3195-3203. [PMID: 38613682 DOI: 10.1007/s00216-024-05269-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/13/2024] [Accepted: 03/21/2024] [Indexed: 04/15/2024]
Abstract
We propose a sensitive H1N1 virus fluorescence biosensor based on ligation-transcription and CRISPR/Cas13a-assisted cascade amplification strategies. Products are generated via the hybridization of single-stranded DNA (ssDNA) probes containing T7 promoter and crRNA templates to a target RNA sequence using SplintR ligase. This generates large crRNA quantities in the presence of T7 RNA polymerase. At such crRNA quantities, ternary Cas13a, crRNA, and activator complexes are successfully constructed and activate Cas13a to enhance fluorescence signal outputs. The biosensor sensitively and specifically monitored H1N1 viral RNA levels down to 3.23 pM and showed good linearity when H1N1 RNA concentrations were 100 pM-1 µM. Biosensor specificity was also excellent. Importantly, our biosensor may be used to detect other viral RNAs by altering the sequences of the two probe junctions, with potential applications for the clinical diagnosis of viruses and other biomedical studies.
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Affiliation(s)
- Lulu Xue
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China
| | - Shengjun Bu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
- School of Life Science and Technology, Changchun University of Science and Technology, Changchun, 130022, China
| | - Mengyao Xu
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China
| | - Jiaqi Wei
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Hongyu Zhou
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Yao Xu
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China
| | - Zhuo Hao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China
| | - Zehong Li
- College of Life Science, Jilin Agricultural University, Changchun, 130118, China.
| | - Jiayu Wan
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China.
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8
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Zhou P, Pan Y, Liu B, Pan W, Li N, Tang B. Thermophoretic Aggregation Imaging of Tumor-Derived Exosomes by CRISPR-Cas13a-Based Nanoprobes. Anal Chem 2024; 96:4791-4799. [PMID: 38470324 DOI: 10.1021/acs.analchem.3c04646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
The inherent heterogeneity of tumor-derived exosomes holds great promise for enhancing the precision of cancer diagnostics. MicroRNAs (miRNAs) encapsulated in tumor-associated exosomes have emerged as valuable biomarkers for the early detection of cancers. Nevertheless, the flexible structure and inherent instability of RNA limit its application in biological diagnostics. The CRISPR-Cas13a system, distinguished by its target-responsive "collateral effect", represents a powerful tool for advancing cancer diagnostics. In this study, we harness the CRISPR-Cas13a system as an innovative signal amplification tool to image cancer-related exosomal miRNA in situ. Furthermore, we capitalize on the thermophoretic aggregation effect exhibited by gold nanoparticles (Au NPs) to consolidate the fluorescent signals generated by the CRISPR-Cas13a system. Subsequently, the developed nanoprobe is applied to detect lung cancer-related exosomal miRNA from human serum, enabling the aggregated visualization of low-abundance cancer exosomes in individuals with lung cancer compared with healthy individuals. This sensitive thermophoretic aggregation assay provides a diagnostic tool for lung cancer in the clinic.
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Affiliation(s)
- Ping Zhou
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Yingbo Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Bo Liu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Wei Pan
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Institute of Molecular and Nano Science, Shandong Normal University, Jinan 250014, P. R. China
- Laoshan Laboratory, Qingdao 266237, P. R. China
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9
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Zhu XX, Wang YS, Li SJ, Peng RQ, Wen X, Peng H, Shi QS, Zhou G, Xie XB, Wang J. Rapid detection of mexX in Pseudomonas aeruginosa based on CRISPR-Cas13a coupled with recombinase polymerase amplification. Front Microbiol 2024; 15:1341179. [PMID: 38357344 PMCID: PMC10864651 DOI: 10.3389/fmicb.2024.1341179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
The principal pathogen responsible for chronic urinary tract infections, immunocompromised hosts, and cystic fibrosis patients is Pseudomonas aeruginosa, which is difficult to eradicate. Due to the extensive use of antibiotics, multidrug-resistant P. aeruginosa has evolved, complicating clinical therapy. Therefore, a rapid and efficient approach for detecting P. aeruginosa strains and their resistance genes is necessary for early clinical diagnosis and appropriate treatment. This study combines recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats-association protein 13a (CRISPR-Cas13a) to establish a one-tube and two-step reaction systems for detecting the mexX gene in P. aeruginosa. The test times for one-tube and two-step RPA-Cas13a methods were 5 and 40 min (including a 30 min RPA amplification reaction), respectively. Both methods outperform Quantitative Real-time Polymerase Chain Reactions (qRT-PCR) and traditional PCR. The limit of detection (LoD) of P. aeruginosa genome in one-tube and two-step RPA-Cas13a is 10 aM and 1 aM, respectively. Meanwhile, the designed primers have a high specificity for P. aeruginosa mexX gene. These two methods were also verified with actual samples isolated from industrial settings and demonstrated great accuracy. Furthermore, the results of the two-step RPA-Cas13a assay could also be visualized using a commercial lateral flow dipstick with a LoD of 10 fM, which is a useful adjunt to the gold-standard qRT-PCR assay in field detection. Taken together, the procedure developed in this study using RPA and CRISPR-Cas13a provides a simple and fast way for detecting resistance genes.
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Affiliation(s)
- Xiao-Xuan Zhu
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Ying-Si Wang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Su-Juan Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Ru-Qun Peng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Xia Wen
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Hong Peng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Qing-Shan Shi
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Gang Zhou
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Xiao-Bao Xie
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong, China
| | - Jie Wang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, Guangdong, China
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Ma Z, Guo J, Jiang L, Zhao S. Lateral flow immunoassay (LFIA) for dengue diagnosis: Recent progress and prospect. Talanta 2024; 267:125268. [PMID: 37813013 DOI: 10.1016/j.talanta.2023.125268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/22/2023] [Accepted: 10/01/2023] [Indexed: 10/11/2023]
Abstract
Dengue is one of the most widespread and fatal arboviral infections in the world. Early detection of dengue virus (DENV) is essential to prevent the spread of the disease and provide an immediate response. The lateral flow immunoassay (LFIA) systems are low-cost, rapid, sensitive, targeted, and straightforward detection, which is an ideal early detection candidate for point-of-care testing (POCT) in dengue-affected areas. However, current commercial LFIA kits cannot fully satisfy the sensitivity, specificity, serotype differentiation, and multiplex detection requirements. Therefore, various strategies have been applied to optimize the LFIA for DENV detection, including label material improvement, optical enhancement and novel structure design. In this review, we comprehensively presented the snapshot of dengue, the principle of LFIA, and recent progress in the LFIA optimization for dengue diagnoses. Furthermore, this review also discusses insights into the prospect of LFIA dengue diagnostic methods, such as microfluidics, multiplex design, nucleic acid-typed probes and smartphone-assisted result analysis.
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Affiliation(s)
- Ziting Ma
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, 510006, China
| | - Jinnian Guo
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, 510006, China
| | - Lu Jiang
- Department of Biomedical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, 510006, China.
| | - Suqing Zhao
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong, 510006, China.
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11
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Zhang Z, Wang C, Chen X, Zhang Z, Shi G, Zhai X, Zhang T. Based on CRISPR-Cas13a system, to establish a rapid visual detection method for avian influenza viruses. Front Vet Sci 2024; 10:1272612. [PMID: 38260192 PMCID: PMC10800881 DOI: 10.3389/fvets.2023.1272612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
To rapidly, specifically, and sensitively detect avian influenza virus (AIV), this research established a visual detection method of recombinase-aided amplification (RAA) based on Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated proteins 13a (Cas13a) system. In this study, specific primers and CRISPR RNA (crRNA) were designed according to the conservative sequence of AIV Nucleprotein (NP) gene. RAA technology was used to amplify the target sequence, and the amplification products were visually detected by lateral flow dipstick (LFD). The specificity, sensitivity, and reproducibility of RAA-CRISPR-Cas13a-LFD were evaluated. At the same time, this method and polymerase chain reaction (PCR)-agarose electrophoresis method were used to detect clinical samples, and the coincidence rate of the two detection methods was calculated. The results showed that the RAA-CRISPR-Cas13a-LFD method could achieve specific amplification of the target gene fragments, and the detection results could be visually observed through the LFD. Meanwhile, there was no cross-reaction with infectious bronchitis virus (IBV), infectious laryngotracheitis virus (ILTV), and Newcastle disease virus (NDV). The sensitivity reached 100 copies/μL, which was 1,000-fold higher than that of PCR-agarose electrophoresis method. The coincidence rate of clinical tests was 98.75 %, and the total reaction time was ~1 h. The RAA-CRISPR-Cas13a-LFD method established in this study had the advantages of rapid, simple, strong specificity, and high sensitivity, which provided a new visual method for AIV detection.
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Affiliation(s)
- Zongshu Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Chunguang Wang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Xi Chen
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Zichuang Zhang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Guoqiang Shi
- Hebei Sanshi Biotechnology Co., Ltd., Shijiazhuang, China
| | - Xianghe Zhai
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
| | - Tie Zhang
- College of Veterinary Medicine, Hebei Agricultural University, Baoding, China
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Yang Z, Wang J, Qi Y, Shi Y, Li F, Wang W, Tian X, Mei X, Zhang Z, Wang S. A novel detection method based on MIRA-CRISPR/Cas13a-LFD targeting the repeated DNA sequence of Trichomonas vaginalis. Parasit Vectors 2024; 17:14. [PMID: 38191422 PMCID: PMC10775430 DOI: 10.1186/s13071-023-06106-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/18/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Trichomonas vaginalis is a protozoan parasite, widely recognized as the most prevalent non-viral sexually transmitted infection (STI) globally. This infection is linked to various complications, including pelvic inflammatory disease, adverse pregnancy outcomes, and an increased risk of acquiring HIV. Current molecular detection methods for T. vaginalis are often costly and technically challenging. METHODS We developed a novel detection method for T. vaginalis using a multi-enzyme isothermal rapid amplification-clustered regularly interspaced short palindromic repeats (MIRA-CRISPR)/Cas13a-lateral flow device (LFD). This assay targets the repeated DNA sequence (GenBank: L23861.1) of T. vaginalis and is performed at a constant temperature of 37 °C for approximately 1 hour. RESULTS The detection limit of genomic DNA (gDNA) using our protocol was 1 × 10-4 ng/μl. Specificity was confirmed by the absence of cross-reaction with gDNA from various other microorganisms such as Staphylococcus aureus, Lactobacillus taiwanensis, Escherichia coli, Monilia albicans, Giardia lamblia, or Toxoplasma gondii. Among 30 clinical samples tested, the positive rates of T. vaginalis detection were 33.33% (10/30) by wet mount microscopy, 40% (12/30) by nested polymerase chain reaction (PCR), 40% (12/30) by MIRA-CRISPR/Cas13a-LFD, and 40% (12/30) by the culture method. Compared with the culture method, the gold standard for diagnosing trichomoniasis, wet mount microscopy showed a sensitivity of 83.3% and moderate diagnostic agreement (kappa value = 0.87). Both nested PCR and MIRA-CRISPR/Cas13a-LFD exhibited 100% sensitivity and excellent diagnostic agreement (kappa value = 1). CONCLUSIONS The MIRA-CRISPR/Cas13a-LFD method is a convenient, rapid, stable, and accurate diagnostic tool for detecting T. vaginalis. This method has the potential to enhance the diagnosis and management of vaginitis, offering a significant improvement over existing diagnostic techniques.
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Affiliation(s)
- Zhenke Yang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Jinghui Wang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Yiming Qi
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Yiping Shi
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Fakun Li
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Weijuan Wang
- Third Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Xiaowei Tian
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Xuefang Mei
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Zhenchao Zhang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China.
| | - Shuai Wang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China.
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Nie X, Wang D, Pan Y, Hua Y, Lü P, Yang Y. Discovery, classification and application of the CPISPR-Cas13 system. Technol Health Care 2024; 32:525-544. [PMID: 37545273 DOI: 10.3233/thc-230258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
BACKGROUND The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is an acquired immune system of bacteria and archaea. Continued research has resulted in the identification of other Cas13 proteins. OBJECTIVE This review briefly describes the discovery, classification, and application of the CRISPR-Cas13 system, including recent technological advances in addition to factors affecting system performance. METHODS Cas13-based molecular therapy of human, animal, and plant transcriptomes was discussed, including regulation of gene expression to combat pathogenic RNA viruses. In addition, the latest progress, potential shortcomings, and challenges of the CRISPR-Cas system for treatment of animal and plant diseases are reviewed. RESULTS The CRISPR-Cas system VI is characterized by two RNA-guided higher eukaryotes and prokaryotes nucleotide-binding domains. CRISPR RNA can cleave specific RNA through the interaction between the stem-loop rich chain of uracil residues and the Cas13a protein. The CRISPR-Cas13 system has been applied for gene editing in animal and plant cells, in addition to biological detection via accurate targeting of single-stranded RNA. CONCLUSION The CRISPR-Cas13 system offers a high-throughput and convenient technology for detection of viruses and potentially the development of anti-cancer drugs in the near future.
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Affiliation(s)
- Xiaojuan Nie
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Dandan Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ye Pan
- School of Experimental Animal Center, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ye Hua
- Institute of Oncology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Peng Lü
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yanhua Yang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
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He Y, Hu Q, San S, Kasputis T, Splinter MGD, Yin K, Chen J. CRISPR-based Biosensors for Human Health: A Novel Strategy to Detect Emerging Infectious Diseases. Trends Analyt Chem 2023; 168:117342. [PMID: 37840598 PMCID: PMC10571337 DOI: 10.1016/j.trac.2023.117342] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Infectious diseases (such as sepsis, influenza, and malaria), caused by various pathogenic bacteria and viruses, are widespread across the world. Early and rapid detection of disease-related pathogens is necessary to reduce their spread in the world and prevent their potential global pandemics. The clustered regularly interspaced short palindromic repeats (CRISPR) technology, as the next-generation molecular diagnosis technique, holds immense promise in the detection of infectious diseases because of its remarkable advantages, including supreme flexibility, sensitivity, and specificity. While numerous CRISPR-based biosensors have been developed for application in environmental monitoring, food safety, and point-of-care diagnosis, there remains a critical need to summarize and explore their potential in human health. This review aims to address this gap by focusing on the latest advancements in CRISPR-based biosensors for infectious disease detection. We provide an overview of the current status, pre-amplification methods, the unique feature of each CRISPR system, and the design of CRISPR-based biosensing strategies to detect disease-associated nucleic acids. Last but not least, the review analyzes the current challenges and provides future perspectives, which will contribute to developing more effective CRISPR-based biosensors for human health.
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Affiliation(s)
- Yawen He
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Qinqin Hu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People’s Republic of China
| | - Samantha San
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | - Tom Kasputis
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Kun Yin
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
- One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People’s Republic of China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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Mohammad N, Talton L, Hetzler Z, Gongireddy M, Wei Q. Unidirectional trans-cleaving behavior of CRISPR-Cas12a unlocks for an ultrasensitive assay using hybrid DNA reporters containing a 3' toehold. Nucleic Acids Res 2023; 51:9894-9904. [PMID: 37650631 PMCID: PMC10570054 DOI: 10.1093/nar/gkad715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/04/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023] Open
Abstract
CRISPR-Cas12a can induce nonspecific trans-cleavage of dsDNA substrate, including long and stable λ DNA. However, the mechanism behind this is still largely undetermined. In this study, we observed that while trans-activated Cas12a didn't cleave blunt-end dsDNA within a short reaction time, it could degrade dsDNA reporters with a short overhang. More interestingly, we discovered that the location of the overhang also affected the susceptibility of dsDNA substrate to trans-activated Cas12a. Cas12a trans-cleaved 3' overhang dsDNA substrates at least 3 times faster than 5' overhang substrates. We attributed this unique preference of overhang location to the directional trans-cleavage behavior of Cas12a, which may be governed by RuvC and Nuc domains. Utilizing this new finding, we designed a new hybrid DNA reporter as nonoptical substrate for the CRISPR-Cas12a detection platform, which sensitively detected ssDNA targets at sub picomolar level. This study not only unfolded new insight into the trans-cleavage behavior of Cas12a but also demonstrated a sensitive CRISPR-Cas12a assay by using a hybrid dsDNA reporter molecule.
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Affiliation(s)
- Noor Mohammad
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
- Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
| | - Logan Talton
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Zach Hetzler
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Megha Gongireddy
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
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16
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Jiang W, Aman R, Ali Z, Rao GS, Mahfouz M. PNA-Pdx: Versatile Peptide Nucleic Acid-Based Detection of Nucleic Acids and SNPs. Anal Chem 2023; 95:14209-14218. [PMID: 37696750 PMCID: PMC10535012 DOI: 10.1021/acs.analchem.3c01809] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/11/2023] [Indexed: 09/13/2023]
Abstract
Monitoring diseases caused by pathogens or by mutations in DNA sequences requires accurate, rapid, and sensitive tools to detect specific nucleic acid sequences. Here, we describe a new peptide nucleic acid (PNA)-based nucleic acid detection toolkit, termed PNA-powered diagnostics (PNA-Pdx). PNA-Pdx employs PNA probes that bind specifically to a target and are then detected in lateral flow assays. This can precisely detect a specific pathogen or genotype genomic sequence. PNA probes can also be designed to invade double-stranded DNAs (dsDNAs) to produce single-stranded DNAs for precise CRISPR-Cas12b-based detection of genomic SNPs without requiring the protospacer-adjacent motif (PAM), as Cas12b requires PAM sequences only for dsDNA targets. PNA-Pdx identified target nucleic acid sequences at concentrations as low as 2 copies/μL and precisely detected the SARS-CoV-2 genome in clinical samples in 40 min. Furthermore, the specific dsDNA invasion by the PNA coupled with CRISPR-Cas12b precisely detected genomic SNPs without PAM restriction. Overall, PNA-Pdx provides a novel toolkit for nucleic acid and SNP detection as well as highlights the benefits of engineering PNA probes for detecting nucleic acids.
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Affiliation(s)
- Wenjun Jiang
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Rashid Aman
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gundra S. Rao
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering and
Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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Bao M, Waitkus J, Liu L, Chang Y, Xu Z, Qin P, Chen J, Du K. Micro- and nanosystems for the detection of hemorrhagic fever viruses. LAB ON A CHIP 2023; 23:4173-4200. [PMID: 37675935 DOI: 10.1039/d3lc00482a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Hemorrhagic fever viruses (HFVs) are virulent pathogens that can cause severe and often fatal illnesses in humans. Timely and accurate detection of HFVs is critical for effective disease management and prevention. In recent years, micro- and nano-technologies have emerged as promising approaches for the detection of HFVs. This paper provides an overview of the current state-of-the-art systems for micro- and nano-scale approaches to detect HFVs. It covers various aspects of these technologies, including the principles behind their sensing assays, as well as the different types of diagnostic strategies that have been developed. This paper also explores future possibilities of employing micro- and nano-systems for the development of HFV diagnostic tools that meet the practical demands of clinical settings.
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Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Jacob Waitkus
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Li Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Yu Chang
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Zhiheng Xu
- Department of Industrial Engineering, Rochester Institute of Technology, Rochester, NY, USA
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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18
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Li X, Zhong J, Li H, Qiao Y, Mao X, Fan H, Zhong Y, Imani S, Zheng S, Li J. Advances in the application of CRISPR-Cas technology in rapid detection of pathogen nucleic acid. Front Mol Biosci 2023; 10:1260883. [PMID: 37808520 PMCID: PMC10552857 DOI: 10.3389/fmolb.2023.1260883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are widely used as gene editing tools in biology, microbiology, and other fields. CRISPR is composed of highly conserved repetitive sequences and spacer sequences in tandem. The spacer sequence has homology with foreign nucleic acids such as viruses and plasmids; Cas effector proteins have endonucleases, and become a hotspot in the field of molecular diagnosis because they recognize and cut specific DNA or RNA sequences. Researchers have developed many diagnostic platforms with high sensitivity, high specificity, and low cost by using Cas proteins (Cas9, Cas12, Cas13, Cas14, etc.) in combination with signal amplification and transformation technologies (fluorescence method, lateral flow technology, etc.), providing a new way for rapid detection of pathogen nucleic acid. This paper introduces the biological mechanism and classification of CRISPR-Cas technology, summarizes the existing rapid detection technology for pathogen nucleic acid based on the trans cleavage activity of Cas, describes its characteristics, functions, and application scenarios, and prospects the future application of this technology.
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Affiliation(s)
- Xiaoping Li
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
- Faculty of Medicine, Macau University of Science and Technology, Avenida Wai Long Taipa, Macau, China
| | - Jiaye Zhong
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Haoyu Li
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Yinbiao Qiao
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
| | - Xiaolei Mao
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Huayan Fan
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Yiwu Zhong
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Saber Imani
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Shulan International Medical College, Zhejiang Shuren University, Hangzhou, China
| | - Shusen Zheng
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Jianhui Li
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, China
- NHC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou, China
- The Organ Repair and Regeneration Medicine Institute of Hangzhou, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- Zhejiang Chinese Medical University, Hangzhou, China
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Wang M, Chen M, Wu X, Huang X, Yu B. CRISPR applications in cancer diagnosis and treatment. Cell Mol Biol Lett 2023; 28:73. [PMID: 37674114 PMCID: PMC10481571 DOI: 10.1186/s11658-023-00483-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/17/2023] [Indexed: 09/08/2023] Open
Abstract
Cancer remains a significant global health challenge, necessitating the exploration of novel and more precise therapeutic options beyond conventional treatments. In this regard, clustered regularly interspaced short palindromic repeats (CRISPR) systems have emerged as highly promising tools for clinical gene editing applications. The CRISPR family encompasses diverse CRISPR-associated (Cas) proteins that possess the ability to recognize specific target sequences. The initial CRISPR system consisted of the Cas9 protein and a single-guide RNA, which guide Cas9 to the desired target sequence, facilitating precise double-stranded cleavage. In addition to the traditional cis-cleavage activity, the more recently discovered Cas12 and Cas13 proteins exhibit trans-cleavage activity, which expands their potential applications in cancer diagnosis. In this review, we provide an overview of the functional characteristics of Cas9, Cas12, and Cas13. Furthermore, we highlight the latest advancements and applications of these CRISPR systems in cancer gene therapy and molecular diagnosis. We also emphasize the importance of understanding the strengths and limitations of each CRISPR system to maximize their clinical utility. By providing a comprehensive overview of the current state of CRISPR technology in cancer research, we aim to inspire further exploration and innovation in this rapidly evolving field.
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Affiliation(s)
- Mingxia Wang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Shenzhen Key Laboratory of Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Menghui Chen
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Xia Wu
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Xinbo Huang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
| | - Bo Yu
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
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Shashank PR, Parker BM, Rananaware SR, Plotkin D, Couch C, Yang LG, Nguyen LT, Prasannakumar NR, Braswell WE, Jain PK, Kawahara AY. CRISPR-based diagnostics detects invasive insect pests. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541004. [PMID: 37292907 PMCID: PMC10245733 DOI: 10.1101/2023.05.16.541004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rapid identification of organisms is essential across many biological and medical disciplines, from understanding basic ecosystem processes and how organisms respond to environmental change, to disease diagnosis and detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta, and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than other real time-PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a lab setting, reduces the risk of cross-contamination, and can be completed in less than one hour. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.
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Affiliation(s)
- Pathour R. Shashank
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Division of Entomology, ICAR-Indian Agricultural Research Institution, New Delhi 110012, India
| | - Brandon M. Parker
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
- U.S. Environmental Protection Agency, Office of Research and Development, RTP, NC, 27709, USA
| | - Santosh R. Rananaware
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - David Plotkin
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Christian Couch
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Lilia G. Yang
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Long T. Nguyen
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - N. R. Prasannakumar
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research, Bengaluru 560089, India
| | - W. Evan Braswell
- Insect Management and Molecular Diagnostics Laboratory, USDA APHIS PPQ S&T, 22675 North Moorefield Road, Edinburg, Texas 78541, USA
| | - Piyush K. Jain
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida, USA
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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21
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Grant DS, Samuels RJ, Garry RF, Schieffelin JS. Lassa Fever Natural History and Clinical Management. Curr Top Microbiol Immunol 2023. [PMID: 37106159 DOI: 10.1007/82_2023_263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Lassa fever is caused by Lassa virus (LASV), an Old World Mammarenavirus that is carried by Mastomys natalensis and other rodents. It is endemic in Sierra Leone, Nigeria, and other countries in West Africa. The clinical presentation of LASV infection is heterogenous varying from an inapparent or mild illness to a fatal hemorrhagic fever. Exposure to LASV is usually through contact with rodent excreta. After an incubation period of 1-3 weeks, initial symptoms such as fever, headache, and fatigue develop that may progress to sore throat, retrosternal chest pain, conjunctival injection, vomiting, diarrhea, and abdominal pain. Severe illness, including hypotension, shock, and multiorgan failure, develops in a minority of patients. Patient demographics and case fatality rates are distinctly different in Sierra Leone and Nigeria. Laboratory diagnosis relies on the detection of LASV antigens or genomic RNA. LASV-specific immunoglobulin G and M assays can also contribute to clinical management. The mainstay of treatment for Lassa fever is supportive care. The nucleoside analog ribavirin is commonly used to treat acute Lassa fever but is considered useful only if treatment is begun early in the disease course. Drugs in development, including a monoclonal antibody cocktail, have the potential to impact the management of Lassa fever.
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Affiliation(s)
- Donald S Grant
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health, Kenema, Sierra Leone
- College of Medicine and Allied Health Sciences (COMAHS), University of Sierra Leone, Freetown, Sierra Leone
| | - Robert J Samuels
- Lassa Fever Program, Kenema Government Hospital, Ministry of Health, Kenema, Sierra Leone
| | - Robert F Garry
- School of Medicine, Department of Microbiology and Immunology, Tulane University, New Orleans, LA, 70112, USA
- Zalgen Labs, Frederick, MD, 21703, USA
- Global Virus Network (GVN), Baltimore, MD, 21201, USA
| | - John S Schieffelin
- School of Medicine, Department of Pediatrics, Tulane University, New Orleans, LA, 70112, USA.
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22
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Leski TA, Spangler JR, Wang Z, Schultzhaus Z, Taitt CR, Dean SN, Stenger DA. Machine learning for design of degenerate Cas13a crRNAs using lassa virus as a model of highly variable RNA target. Sci Rep 2023; 13:6506. [PMID: 37081092 PMCID: PMC10119381 DOI: 10.1038/s41598-023-33494-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/13/2023] [Indexed: 04/22/2023] Open
Abstract
The design of minimum CRISPR RNA (crRNA) sets for detection of diverse RNA targets using sequence degeneracy has not been systematically addressed. We tested candidate degenerate Cas13a crRNA sets designed for detection of diverse RNA targets (Lassa virus). A decision tree machine learning (ML) algorithm (RuleFit) was applied to define the top attributes that determine the specificity of degenerate crRNAs to elicit collateral nuclease activity. Although the total number of mismatches (0-4) is important, the specificity depends as well on the spacing of mismatches, and their proximity to the 5' end of the spacer. We developed a predictive algorithm for design of candidate degenerate crRNA sets, allowing improved discrimination between "included" and "excluded" groups of related target sequences. A single degenerate crRNA set adhering to these rules detected representatives of all Lassa lineages. Our general ML approach may be applied to the design of degenerate crRNA sets for any CRISPR/Cas system.
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Affiliation(s)
- T A Leski
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA.
| | - J R Spangler
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
| | - Z Wang
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
| | - Z Schultzhaus
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
- U.S. Department of Agriculture, Riverdale, MD, USA
| | - C R Taitt
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
- Nova Research Inc., Alexandria, VA, USA
| | - S N Dean
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
| | - D A Stenger
- Center for Bio/Molecular Science & Engineering, U.S. Naval Research Laboratory, Washington, USA
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23
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Fang L, Yang L, Han M, Xu H, Ding W, Dong X. CRISPR-cas technology: A key approach for SARS-CoV-2 detection. Front Bioeng Biotechnol 2023; 11:1158672. [PMID: 37214290 PMCID: PMC10198440 DOI: 10.3389/fbioe.2023.1158672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/31/2023] [Indexed: 05/24/2023] Open
Abstract
The CRISPR (Clustered Regularly Spaced Short Palindromic Repeats) system was first discovered in prokaryotes as a unique immune mechanism to clear foreign nucleic acids. It has been rapidly and extensively used in basic and applied research owing to its strong ability of gene editing, regulation and detection in eukaryotes. Hererin in this article, we reviewed the biology, mechanisms and relevance of CRISPR-Cas technology and its applications in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis. CRISPR-Cas nucleic acid detection tools include CRISPR-Cas9, CRISPR-Cas12, CRISPR-Cas13, CRISPR-Cas14, CRISPR nucleic acid amplification detection technology, and CRISPR colorimetric readout detection system. The above CRISPR technologies have been applied to the nucleic acid detection, including SARS-CoV-2 detection. Common nucleic acid detection based on CRISPR derivation technology include SHERLOCK, DETECTR, and STOPCovid. CRISPR-Cas biosensing technology has been widely applied to point-of-care testing (POCT) by targeting recognition of both DNA molecules and RNA Molecules.
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Affiliation(s)
- Lijuan Fang
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Lusen Yang
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Mingyue Han
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Huimei Xu
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Wenshuai Ding
- Department of Laboratory Medicine, Hangzhou Ninth People’s Hospital, Hangzhou, Zhejiang Province, China
| | - Xuejun Dong
- Medical Laboratory, Zhejiang University Shaoxing Hospital, Shaoxing, China
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24
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Lock EH, Lee J, Choi DS, Bedford RG, Karna SP, Roy AK. Materials Innovations for Quantum Technology Acceleration: A Perspective. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2201064. [PMID: 37021584 DOI: 10.1002/adma.202201064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 01/16/2023] [Indexed: 06/19/2023]
Abstract
A broad perspective of quantum technology state of the art is provided and critical stumbling blocks for quantum technology development are identified. Innovations in demonstrating and understanding electron entanglement phenomena using bulk and low-dimensional materials and structures are summarized. Correlated photon-pair generation via processes such as nonlinear optics is discussed. Application of qubits to current and future high-impact quantum technology development is presented. Approaches for realizing unique qubit features for large-scale encrypted communication, sensing, computing, and other technologies are still evolving; thus, materials innovation is crucially important. A perspective on materials modeling approaches for quantum technology acceleration that incorporate physics-based AI/ML, integrated with quantum metrology is discussed.
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Affiliation(s)
- Evgeniya H Lock
- Materials Science and Technology Division, U. S. Naval Research Laboratory, Washington, DC, 20375, USA
| | - Jonghoon Lee
- Air Force Research Laboratory, Materials and Manufacturing Directorate, AFRL/RXAN, 2179 12th St, WPAFB, OH, 45433, USA
- ARCTOS Technology Solutions, 1270 N Fairfield Rd, Beavercreek, OH, 45432, USA
| | - Daniel S Choi
- DEVCOM Army Research Laboratory, Weapons and Materials Research Directorate, FCDD-RLW, Aberdeen Proving Ground, Beavercreek, MD, 21015, USA
| | - Robert G Bedford
- Air Force Research Laboratory, Materials and Manufacturing Directorate, AFRL/RXAN, 2179 12th St, WPAFB, OH, 45433, USA
| | - Shashi P Karna
- DEVCOM Army Research Laboratory, Weapons and Materials Research Directorate, FCDD-RLW, Aberdeen Proving Ground, Beavercreek, MD, 21015, USA
| | - Ajit K Roy
- Air Force Research Laboratory, Materials and Manufacturing Directorate, AFRL/RXAN, 2179 12th St, WPAFB, OH, 45433, USA
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25
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Microfluidics: the propellant of CRISPR-based nucleic acid detection. Trends Biotechnol 2023; 41:557-574. [PMID: 35989112 DOI: 10.1016/j.tibtech.2022.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/18/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022]
Abstract
Since the discovery of collateral cleavage activity, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems have become the new generation of nucleic acid detection tools. However, their widespread application remains limited. A pre-amplification step is required to improve the sensitivity of CRISPR systems, complicating the operating procedure and limiting quantitative precision. In addition, nonspecific collateral cleavage activity makes it difficult to realize multiplex detection in a one-pot CRISPR reaction with a single Cas protein. Microfluidics, which can transfer nucleic acid analysis process to a chip, has the advantages of miniaturization, integration, and automation. Microfluidics coupled with CRISPR systems improves the detection ability of CRISPR, enabling fast, high-throughput, integrated, multiplex, and digital detection, which results in the further popularization of CRISPR for a range of scenarios.
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26
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Liu FX, Cui JQ, Wu Z, Yao S. Recent progress in nucleic acid detection with CRISPR. LAB ON A CHIP 2023; 23:1467-1492. [PMID: 36723235 DOI: 10.1039/d2lc00928e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Recent advances in CRISPR-based biotechnologies have greatly expanded our capabilities to repurpose CRISPR for the development of molecular diagnostic systems. The key attribute that allows CRISPR to be widely utilized is its programmable and highly specific nature. In this review, we first illustrate the principle of the class 2 CRISPR nucleases for molecular diagnostics which originates from their immunologic defence systems. Next, we present the CRISPR-based schemes in the application of diagnostics with amplification-assisted or amplification-free strategies. By highlighting some of the recent advances we interpret how general bioengineering methodologies can be integrated with CRISPR. Finally, we discuss the challenges and exciting prospects for future CRISPR-based biosensing development. We hope that this review will guide the reader to systematically learn the start-of-the-art development of CRISPR-mediated nucleic acid detection and understand how to apply the CRISPR nucleases with different design concepts to more general applications in diagnostics and beyond.
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Affiliation(s)
- Frank X Liu
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Johnson Q Cui
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| | - Zhihao Wu
- IIP-Advanced Materials, Interdisciplinary Program Office (IPO), Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Shuhuai Yao
- Department of Mechanical and Aerospace Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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27
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Avaro AS, Santiago JG. A critical review of microfluidic systems for CRISPR assays. LAB ON A CHIP 2023; 23:938-963. [PMID: 36601854 DOI: 10.1039/d2lc00852a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Reviewed are nucleic acid detection assays that incorporate clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics and microfluidic devices and techniques. The review serves as a reference for researchers who wish to use CRISPR-Cas systems for diagnostics in microfluidic devices. The review is organized in sections reflecting a basic five-step workflow common to most CRISPR-based assays. These steps are analyte extraction, pre-amplification, target recognition, transduction, and detection. The systems described include custom microfluidic chips and custom (benchtop) chip control devices for automated assays steps. Also included are partition formats for digital assays and lateral flow biosensors as a readout modality. CRISPR-based, microfluidics-driven assays offer highly specific detection and are compatible with parallel, combinatorial implementation. They are highly reconfigurable, and assays are compatible with isothermal and even room temperature operation. A major drawback of these assays is the fact that reports of kinetic rates of these enzymes have been highly inconsistent (many demonstrably erroneous), and the low kinetic rate activity of these enzymes limits achievable sensitivity without pre-amplification. Further, the current state-of-the-art of CRISPR assays is such that nearly all systems rely on off-chip assays steps, particularly off-chip sample preparation.
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Affiliation(s)
- Alexandre S Avaro
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Juan G Santiago
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305, USA.
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28
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Jiang W, Aman R, Ali Z, Mahfouz M. Bio-SCAN V2: A CRISPR/dCas9-based lateral flow assay for rapid detection of theophylline. Front Bioeng Biotechnol 2023; 11:1118684. [PMID: 36741753 PMCID: PMC9893010 DOI: 10.3389/fbioe.2023.1118684] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
Rapid, specific, and robust diagnostic strategies are needed to develop sensitive biosensors for small molecule detection, which could aid in controlling contamination and disease transmission. Recently, the target-induced collateral activity of Cas nucleases [clustered regularly interspaced short palindromic repeats (CRISPR)-associated nucleases] was exploited to develop high-throughput diagnostic modules for detecting nucleic acids and small molecules. Here, we have expanded the diagnostic ability of the CRISPR-Cas system by developing Bio-SCAN V2, a ligand-responsive CRISPR-Cas platform for detecting non-nucleic acid small molecule targets. The Bio-SCAN V2 consists of an engineered ligand-responsive sgRNA (ligRNA), biotinylated dead Cas9 (dCas9-biotin), 6-carboxyfluorescein (FAM)-labeled amplicons, and lateral flow assay (LFA) strips. LigRNA interacts with dCas9-biotin only in the presence of sgRNA-specific ligand molecules to make a ribonucleoprotein (RNP). Next, the ligand-induced ribonucleoprotein is exposed to FAM-labeled amplicons for binding, and the presence of the ligand (small molecule) is detected as a visual signal [(dCas9-biotin)-ligRNA-FAM labeled DNA-AuNP complex] at the test line of the lateral flow assay strip. With the Bio-SCAN V2 platform, we are able to detect the model molecule theophylline with a limit of detection (LOD) up to 2 μM in a short time, requiring only 15 min from sample application to visual readout. Taken together, Bio-SCAN V2 assay provides a rapid, specific, and ultrasensitive detection platform for theophylline.
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29
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Mammarenavirus Genetic Diversity and Its Biological Implications. Curr Top Microbiol Immunol 2023; 439:265-303. [PMID: 36592249 DOI: 10.1007/978-3-031-15640-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Members of the family Arenaviridae are classified into four genera: Antennavirus, Hartmanivirus, Mammarenavirus, and Reptarenavirus. Reptarenaviruses and hartmaniviruses infect (captive) snakes and have been shown to cause boid inclusion body disease (BIBD). Antennaviruses have genomes consisting of 3, rather than 2, segments, and were discovered in actinopterygian fish by next-generation sequencing but no biological isolate has been reported yet. The hosts of mammarenaviruses are mainly rodents and infections are generally asymptomatic. Current knowledge about the biology of reptarenaviruses, hartmaniviruses, and antennaviruses is very limited and their zoonotic potential is unknown. In contrast, some mammarenaviruses are associated with zoonotic events that pose a threat to human health. This review will focus on mammarenavirus genetic diversity and its biological implications. Some mammarenaviruses including lymphocytic choriomeningitis virus (LCMV) are excellent experimental model systems for the investigation of acute and persistent viral infections, whereas others including Lassa (LASV) and Junin (JUNV) viruses, the causative agents of Lassa fever (LF) and Argentine hemorrhagic fever (AHF), respectively, are important human pathogens. Mammarenaviruses were thought to have high degree of intra-and inter-species amino acid sequence identities, but recent evidence has revealed a high degree of mammarenavirus genetic diversity in the field. Moreover, closely related mammarenavirus can display dramatic phenotypic differences in vivo. These findings support a role of genetic variability in mammarenavirus adaptability and pathogenesis. Here, we will review the molecular biology of mammarenaviruses, phylogeny, and evolution, as well as the quasispecies dynamics of mammarenavirus populations and their biological implications.
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30
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Yang J, Song Y, Deng X, Vanegas JA, You Z, Zhang Y, Weng Z, Avery L, Dieckhaus KD, Peddi A, Gao Y, Zhang Y, Gao X. Engineered LwaCas13a with enhanced collateral activity for nucleic acid detection. Nat Chem Biol 2023; 19:45-54. [PMID: 36138140 DOI: 10.1038/s41589-022-01135-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 08/08/2022] [Indexed: 12/31/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 13 (Cas13) has been rapidly developed for nucleic-acid-based diagnostics by using its characteristic collateral activity. Despite the recent progress in optimizing the Cas13 system for the detection of nucleic acids, engineering Cas13 protein with enhanced collateral activity has been challenging, mostly because of its complex structural dynamics. Here we successfully employed a novel strategy to engineer the Leptotrichia wadei (Lwa)Cas13a by inserting different RNA-binding domains into a unique active-site-proximal loop within its higher eukaryotes and prokaryotes nucleotide-binding domain. Two LwaCas13a variants showed enhanced collateral activity and improved sensitivity over the wild type in various buffer conditions. By combining with an electrochemical method, our variants detected the SARS-CoV-2 genome at attomolar concentrations from both inactive viral and unextracted clinical samples, without target preamplification. Our engineered LwaCas13a enzymes with enhanced collateral activity are ready to be integrated into other Cas13a-based platforms for ultrasensitive detection of nucleic acids.
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Affiliation(s)
- Jie Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Yang Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA.,Institute of Materials Science, University of Connecticut, Storrs, CT, USA
| | - Xiangyu Deng
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Jeffrey A Vanegas
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Zheng You
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Yuxuan Zhang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA.,Institute of Materials Science, University of Connecticut, Storrs, CT, USA
| | - Zhengyan Weng
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA.,Institute of Materials Science, University of Connecticut, Storrs, CT, USA
| | - Lori Avery
- Department of Pathology and Laboratory Medicine, UConn Health, Farmington, CT, USA
| | - Kevin D Dieckhaus
- Division of Infectious Diseases, Department of Medicine, UConn Health, Farmington, CT, USA
| | - Advaith Peddi
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, TX, USA.
| | - Yi Zhang
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT, USA. .,Polymer Program, Institute of Materials Science, University of Connecticut, Storrs, CT, USA.
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA. .,Department of Bioengineering, Rice University, Houston, TX, USA. .,Department of Chemistry, Rice University, Houston, TX, USA.
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31
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Tripathi S, Khatri P, Fatima Z, Pandey RP, Hameed S. A Landscape of CRISPR/Cas Technique for Emerging Viral Disease Diagnostics and Therapeutics: Progress and Prospects. Pathogens 2022; 12:pathogens12010056. [PMID: 36678404 PMCID: PMC9863163 DOI: 10.3390/pathogens12010056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022] Open
Abstract
Viral diseases have emerged as a serious threat to humanity and as a leading cause of morbidity worldwide. Many viral diagnostic methods and antiviral therapies have been developed over time, but we are still a long way from treating certain infections caused by viruses. Acquired immunodeficiency syndrome (AIDS) is one of the challenges where current medical science advancements fall short. As a result, new diagnostic and treatment options are desperately needed. The CRISPR/Cas9 system has recently been proposed as a potential therapeutic approach for viral disease treatment. CRISPR/Cas9 is a specialised, effective, and adaptive gene-editing technique that can be used to modify, delete, or correct specific DNA sequences. It has evolved into an advanced, configurable nuclease-based single or multiple gene-editing tool with a wide range of applications. It is widely preferred simply because its operational procedures are simple, inexpensive, and extremely efficient. Exploration of infectious virus genomes is required for a comprehensive study of infectious viruses. Herein, we have discussed the historical timeline-based advancement of CRISPR, CRISPR/Cas9 as a gene-editing technology, the structure of CRISPR, and CRISPR as a diagnostic tool for studying emerging viral infections. Additionally, utilizing CRISPR/Cas9 technology to fight viral infections in plants, CRISPR-based diagnostics of viruses, pros, and cons, and bioethical issues of CRISPR/Cas9-based genomic modification are discussed.
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Affiliation(s)
- Shyam Tripathi
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
| | - Purnima Khatri
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Department of Microbiology, SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
| | - Zeeshan Fatima
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram 122413, India
| | - Ramendra Pati Pandey
- Centre for Drug Design Discovery and Development (C4D), SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Department of Microbiology, SRM University, Delhi-NCR, Rajiv Gandhi Education City, Sonepat 131029, India
- Correspondence: (R.P.P.); (S.H.)
| | - Saif Hameed
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram 122413, India
- Correspondence: (R.P.P.); (S.H.)
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32
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Zahra A, Shahid A, Shamim A, Khan SH, Arshad MI. The SHERLOCK Platform: An Insight into Advances in Viral Disease Diagnosis. Mol Biotechnol 2022; 65:699-714. [PMID: 36494593 PMCID: PMC9735230 DOI: 10.1007/s12033-022-00625-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022]
Abstract
Persistence and prevalence of microbial diseases (pandemics, epidemics) is the most alarming threats to the human resulting in huge health and economic losses. Rapid detection and understanding of the disease dynamics by molecular biotechnology tools allow for robust reporting, treatment and control of diseases. As per WHO, the optimal diagnostic approach should be quick, specific, sensitive, without a stringed instrument, and low cost. The drawbacks of traditional detection techniques promote the use of CRISPR-mediated nucleic acid detection methods such as SHERLOCK as detection method. It takes advantage of the unexpected in vitro features of CRISPR-Cas system to develop field-deployable sensitive detection tools. Previously, CRISPR-mediated diagnostic methods have extensively been reviewed particularly for SARS-COV-2 detection, but it fails to provide the insight into advances of this technique. This study is the first attempt to review the advances of SHERLOCK approach as diagnostic tool for viral diseases detection. Variations of SHERLOCK mechanism for improved efficiency are discussed. Particularly integrated SHERLOCK approaches in terms of extraction-free assay and Bluetooth-enabled detection are reviewed to access their feasibility for the development of simpler and cost-effective diagnostic toolkits. Insight in to perks and limitations of diagnostic methods indicates its potential as ultimate diagnostic instrument for disease management.
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Affiliation(s)
- Ambreen Zahra
- Center for Advanced Studies (CAS) for Agriculture and Food Security, One Health Lab, University of Agriculture, Faisalabad, 38000 Pakistan
| | - Ayesha Shahid
- Center for Advanced Studies (CAS) for Agriculture and Food Security, One Health Lab, University of Agriculture, Faisalabad, 38000 Pakistan
| | - Amen Shamim
- Center for Advanced Studies (CAS) for Agriculture and Food Security, One Health Lab, University of Agriculture, Faisalabad, 38000 Pakistan
| | - Sultan Habibullah Khan
- Center for Advanced Studies (CAS) for Agriculture and Food Security, One Health Lab, University of Agriculture, Faisalabad, 38000 Pakistan
| | - Muhammad Imran Arshad
- Center for Advanced Studies (CAS) for Agriculture and Food Security, One Health Lab, University of Agriculture, Faisalabad, 38000 Pakistan ,Institute of Microbiology, University of Agriculture, Faisalabad, 38000 Pakistan
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33
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Zhao L, Qiu M, Li X, Yang J, Li J. CRISPR-Cas13a system: A novel tool for molecular diagnostics. Front Microbiol 2022; 13:1060947. [PMID: 36569102 PMCID: PMC9772028 DOI: 10.3389/fmicb.2022.1060947] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system is a natural adaptive immune system of prokaryotes. The CRISPR-Cas system is currently divided into two classes and six types: types I, III, and IV in class 1 systems and types II, V, and VI in class 2 systems. Among the CRISPR-Cas type VI systems, the CRISPR/Cas13a system has been the most widely characterized for its application in molecular diagnostics, gene therapy, gene editing, and RNA imaging. Moreover, because of the trans-cleavage activity of Cas13a and the high specificity of its CRISPR RNA, the CRISPR/Cas13a system has enormous potential in the field of molecular diagnostics. Herein, we summarize the applications of the CRISPR/Cas13a system in the detection of pathogens, including viruses, bacteria, parasites, chlamydia, and fungus; biomarkers, such as microRNAs, lncRNAs, and circRNAs; and some non-nucleic acid targets, including proteins, ions, and methyl groups. Meanwhile, we highlight the working principles of some novel Cas13a-based detection methods, including the Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK) and its improved versions, Cas13a-based nucleic acid amplification-free biosensors, and Cas13a-based biosensors for non-nucleic acid target detection. Finally, we focus on some issues that need to be solved and the development prospects of the CRISPR/Cas13a system.
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Affiliation(s)
- Lixin Zhao
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China,Institute of Immunology, PLA, Army Medical University, Chongqing, China
| | - Minyue Qiu
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China,Institute of Immunology, PLA, Army Medical University, Chongqing, China
| | - Xiaojia Li
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China
| | - Juanzhen Yang
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China
| | - Jintao Li
- Department of Biosafety, School of Basic Medicine, Army Medical University, Chongqing, China,Institute of Immunology, PLA, Army Medical University, Chongqing, China,*Correspondence: Jintao Li,
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34
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Wu S, Tian P, Tan T. CRISPR-Cas13 technology portfolio and alliance with other genetic tools. Biotechnol Adv 2022; 61:108047. [DOI: 10.1016/j.biotechadv.2022.108047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/03/2022] [Accepted: 09/29/2022] [Indexed: 11/02/2022]
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35
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Xie Y, Li H, Chen F, Udayakumar S, Arora K, Chen H, Lan Y, Hu Q, Zhou X, Guo X, Xiu L, Yin K. Clustered Regularly Interspaced short palindromic repeats-Based Microfluidic System in Infectious Diseases Diagnosis: Current Status, Challenges, and Perspectives. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2204172. [PMID: 36257813 PMCID: PMC9731715 DOI: 10.1002/advs.202204172] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/16/2022] [Indexed: 06/02/2023]
Abstract
Mitigating the spread of global infectious diseases requires rapid and accurate diagnostic tools. Conventional diagnostic techniques for infectious diseases typically require sophisticated equipment and are time consuming. Emerging clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) detection systems have shown remarkable potential as next-generation diagnostic tools to achieve rapid, sensitive, specific, and field-deployable diagnoses of infectious diseases, based on state-of-the-art microfluidic platforms. Therefore, a review of recent advances in CRISPR-based microfluidic systems for infectious diseases diagnosis is urgently required. This review highlights the mechanisms of CRISPR/Cas biosensing and cutting-edge microfluidic devices including paper, digital, and integrated wearable platforms. Strategies to simplify sample pretreatment, improve diagnostic performance, and achieve integrated detection are discussed. Current challenges and future perspectives contributing to the development of more effective CRISPR-based microfluidic diagnostic systems are also proposed.
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Affiliation(s)
- Yi Xie
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Huimin Li
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Fumin Chen
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Srisruthi Udayakumar
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Khyati Arora
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Hui Chen
- Division of Engineering in MedicineDepartment of MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02139USA
| | - Yang Lan
- Centre for Nature‐Inspired EngineeringDepartment of Chemical EngineeringUniversity College LondonLondonWC1E 7JEUK
| | - Qinqin Hu
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Xiaonong Zhou
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Xiaokui Guo
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Leshan Xiu
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
| | - Kun Yin
- School of Global HealthChinese Center for Tropical Diseases ResearchShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- One Health CenterShanghai Jiao Tong University‐The University of EdinburghShanghai200025P. R. China
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36
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Gleerup JL, Mogensen TH. CRISPR-Cas in Diagnostics and Therapy of Infectious Diseases. J Infect Dis 2022; 226:1867-1876. [PMID: 35446391 DOI: 10.1093/infdis/jiac145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/11/2022] [Indexed: 12/31/2022] Open
Abstract
Infectious diseases are a major threat to the global health. The rise in antimicrobial-resistant organisms, incurable chronic infections, and an increasing demand for rapid accurate diagnostics have prompted researchers to experiment with new approaches. Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) is a naturally occurring adaptive immune system in bacteria that has been developed as a tool for performing genomic alterations in any genome of interest, including humans and microbes. Accordingly, several studies have been conducted to investigate how the technology can be utilized in infectious diseases to improve diagnostics, disrupt antimicrobial resistance, and cure chronic infections. This review provides an overview of the CRISPR-Cas system and how it has been applied in studies on infectious diseases. The review also investigates the current challenges of the technology and the improvements that are needed for the platform to be adopted for clinical use in patients.
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Affiliation(s)
| | - Trine H Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
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37
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Mohammad N, Katkam SS, Wei Q. A Sensitive and Nonoptical CRISPR Detection Mechanism by Sizing Double‐Stranded λ DNA Reporter. Angew Chem Int Ed Engl 2022; 61:e202213920. [PMID: 36239984 PMCID: PMC10100359 DOI: 10.1002/anie.202213920] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Indexed: 11/12/2022]
Abstract
CRISPR-based biosensors often rely on colorimetric, fluorescent, or electrochemical signaling mechanism, which involves expensive reporters and/or sophisticated equipment. Here, we demonstrated a simple, inexpensive, nonoptical, and sensitive CRISPR-Cas12a-based sensing platform to detect ssDNA targets by sizing double-stranded λ DNA as novel report molecules. In this platform, the size reduction of λ DNA was quantified by gel electrophoresis analysis. We hypothesize that the massive trans-nuclease activity of Cas12a toward λ DNA is due to the presence of single-stranded looped structures along the λ DNA sequence. In addition, we observed a strong binding affinity between Cas12a and λ DNA, which further promotes the trans-cleavage activity and helps achieve sub-picomolar detection sensitivity, ≈100 times more sensitive than the fluorescent counterpart. The concept of utilizing the physical size change of λ DNA unlocks the possibility of using a variety of dsDNA as CRISPR reporters.
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Affiliation(s)
- Noor Mohammad
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh NC 27695 USA
- Department of Chemical Engineering Bangladesh University of Engineering and Technology 1000 Dhaka Bangladesh
| | - Shrinivas S. Katkam
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh NC 27695 USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh NC 27695 USA
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38
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Zhu Y, Xing C, Yang L, Li Q, Wang X, Zhou J, Zhang C, Ren C, Liu F, He J, Shen B, Du Y, Liu Y. Dual-gene detection in a single-tube system based on CRISPR-Cas12a/Cas13a for severe fever thrombocytopenia syndrome virus. Front Microbiol 2022; 13:977382. [PMID: 36406407 PMCID: PMC9668895 DOI: 10.3389/fmicb.2022.977382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/17/2022] [Indexed: 09/12/2023] Open
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease, which is caused by severe fever with thrombocytopenia syndrome virus (SFTSV). The disease results in high mortality and increased morbidity and threatens global public health. Rapid detection of SFTSV is crucial for epidemic prevention in low-resource settings. Here we developed deployable, sensitive and rapid detection methods based on CRISPR/Cas12a or Cas13a technologies. The CRISPR/Cas12a-based detection assay could stably detect the SFTSV L or M genes at 10 cp/μl. The Cas13a-based method could detect the L gene as low as 0.75 cp/μl. For point-of-care testing, we combined fluorescence visualization and lateral flow detection with CRISPR/Cas-based assays. Furthermore, using the orthogonal DNA/RNA collateral activity of the Cas12a/Cas13a system, we present the dual-gene detection platform for SFTSV, which can simultaneously detect the L and M genes in a single tube. Based on the dual-gene detection, we designed multiplexed test strips to detect SFTSV. All our methods were initially validated using 52 clinical samples, showing 100% sensitivity and specificity. These new CRISPR/Cas-based detection methods are promising candidates for on-site detection of SFTSV.
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Affiliation(s)
- Yating Zhu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Anhui Provincial Laboratory of Microbiology and Parasitology, Department of Microbiology and Parasitology, Anhui Medical University, Hefei, China
| | - Chen Xing
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Li Yang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Qian Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Anhui Provincial Laboratory of Microbiology and Parasitology, Department of Microbiology and Parasitology, Anhui Medical University, Hefei, China
| | - Xiaofeng Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Anhui Provincial Laboratory of Microbiology and Parasitology, Department of Microbiology and Parasitology, Anhui Medical University, Hefei, China
| | - Jing Zhou
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Cong Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Cuiping Ren
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Anhui Provincial Laboratory of Microbiology and Parasitology, Department of Microbiology and Parasitology, Anhui Medical University, Hefei, China
| | - Fahu Liu
- Department of Clinical Laboratory, The Affiliated Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Jun He
- Microbiological Laboratory, Anhui Center for Disease Control and Prevention, Hefei, China
| | - Bing Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yinan Du
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- Anhui Provincial Laboratory of Microbiology and Parasitology, Department of Microbiology and Parasitology, Anhui Medical University, Hefei, China
| | - Yan Liu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
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Álvarez-Rodríguez A, Jin BK, Radwanska M, Magez S. Recent progress in diagnosis and treatment of Human African Trypanosomiasis has made the elimination of this disease a realistic target by 2030. Front Med (Lausanne) 2022; 9:1037094. [PMID: 36405602 PMCID: PMC9669443 DOI: 10.3389/fmed.2022.1037094] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Human African Trypanosomiasis (HAT) is caused by unicellular flagellated protozoan parasites of the genus Trypanosoma brucei. The subspecies T. b. gambiense is mainly responsible for mostly chronic anthroponotic infections in West- and Central Africa, accounting for roughly 95% of all HAT cases. Trypanosoma b. rhodesiense results in more acute zoonotic infections in East-Africa. Because HAT has a two-stage pathogenesis, treatment depends on clinical assessment of patients and the determination whether or not parasites have crossed the blood brain barrier. Today, ultimate confirmation of parasitemia is still done by microscopy analysis. However, the introduction of diagnostic lateral flow devices has been a major contributor to the recent dramatic drop in T. b. gambiense HAT. Other techniques such as loop mediated isothermal amplification (LAMP) and recombinant polymerase amplification (RPA)-based tests have been published but are still not widely used in the field. Most recently, CRISPR-Cas technology has been proposed to improve the intrinsic diagnostic characteristics of molecular approaches. This will become crucial in the near future, as preventing the resurgence of HAT will be a priority and will require tools with extreme high positive and negative predicted values, as well as excellent sensitivity and specificity. As for treatment, pentamidine and suramin have historically been the drugs of choice for the treatment of blood-stage gambiense-HAT and rhodesiense-HAT, respectively. For treatment of second-stage infections, drugs that pass the blood brain barrier are needed, and melarsoprol has been effectively used for both forms of HAT in the past. However, due to the high occurrence of post-treatment encephalopathy, the drug is not recommended for use in T. b. gambiense HAT. Here, a combination therapy of eflornithine and nifurtimox (NECT) has been the choice of treatment since 2009. As this treatment requires IV perfusion of eflornithine, efforts were launched in 2003 by the drugs for neglected disease initiative (DNDi) to find an oral-only therapy solution, suitable for rural sub-Saharan Africa treatment conditions. In 2019 this resulted in the introduction of fexinidazole, with a treatment regimen suitable for both the blood-stage and non-severe second-stage T. b. gambiense infections. Experimental treatment of T. b. rhodesiense HAT has now been initiated as well.
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Affiliation(s)
- Andrés Álvarez-Rodríguez
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bo-Kyung Jin
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
| | - Magdalena Radwanska
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Stefan Magez
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- *Correspondence: Stefan Magez,
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40
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CRISPR-Cas-mediated diagnostics. Trends Biotechnol 2022; 40:1326-1345. [PMID: 35595574 DOI: 10.1016/j.tibtech.2022.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 01/21/2023]
Abstract
An ideal molecular diagnostic method should be sensitive, specific, low cost, rapid, portable, and easy to operate. Traditional nucleic acid detection methods based mainly on PCR technology have not only high sensitivity and specificity, but also some limitations, such as the need for expensive equipment and skilled technicians, being both time and labor intensive, and difficult to implement in some regions. However, with the continuous development of CRISPR-Cas technology and its application in molecular diagnosis, new approaches have been used for the construction of molecular diagnostic systems. In this review, we discuss recent advances in CRISPR-based molecular diagnostic technologies and highlight the revolution they bring to the field of molecular diagnostics.
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41
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Huang Z, Fang J, Zhou M, Gong Z, Xiang T. CRISPR-Cas13: A new technology for the rapid detection of pathogenic microorganisms. Front Microbiol 2022; 13:1011399. [PMID: 36386639 PMCID: PMC9650447 DOI: 10.3389/fmicb.2022.1011399] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/10/2022] [Indexed: 08/03/2023] Open
Abstract
Pathogenic microorganisms have major impacts on human lives. Rapid and sensitive diagnostic tools are urgently needed to facilitate the early treatment of microbial infections and the effective control of microbial transmission. CRISPR-Cas13 employs programmable RNA to produce a sensitive and specific method with high base resolution and thus to provide a novel tool for the rapid detection of microorganisms. The review aims to provide insights to spur further development by summarizing the characteristics of effectors of the CRISPR-Cas13 system and by describing the latest research into its application in the rapid detection of pathogenic microorganisms in combination with nucleic acid extraction, isothermal amplification, and product detection.
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Affiliation(s)
- Zhanchao Huang
- Medical Center for Major Public Health Events in Jiangxi Province, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianhua Fang
- Medical Center for Major Public Health Events in Jiangxi Province, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Min Zhou
- Jiangxi Zhongke Yanyuan Biotechnology Co., Ltd., Nanchang, China
| | - Zhenghua Gong
- Jiangxi Zhongke Yanyuan Biotechnology Co., Ltd., Nanchang, China
| | - Tianxin Xiang
- Medical Center for Major Public Health Events in Jiangxi Province, The First Affiliated Hospital of Nanchang University, Nanchang, China
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42
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Flórez-Álvarez L, de Souza EE, Botosso VF, de Oliveira DBL, Ho PL, Taborda CP, Palmisano G, Capurro ML, Pinho JRR, Ferreira HL, Minoprio P, Arruda E, de Souza Ferreira LC, Wrenger C, Durigon EL. Hemorrhagic fever viruses: Pathogenesis, therapeutics, and emerging and re-emerging potential. Front Microbiol 2022; 13:1040093. [PMID: 36386719 PMCID: PMC9640979 DOI: 10.3389/fmicb.2022.1040093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/06/2022] [Indexed: 01/29/2023] Open
Abstract
Hemorrhagic fever viruses (HFVs) pose a threat to global public health owing to the emergence and re-emergence of highly fatal diseases. Viral hemorrhagic fevers (VHFs) caused by these viruses are mostly characterized by an acute febrile syndrome with coagulation abnormalities and generalized hemorrhage that may lead to life-threatening organ dysfunction. Currently, the events underlying the viral pathogenicity associated with multiple organ dysfunction syndrome still underexplored. In this minireview, we address the current knowledge of the mechanisms underlying VHFs pathogenesis and discuss the available development of preventive and therapeutic options to treat these infections. Furthermore, we discuss the potential of HFVs to cause worldwide emergencies along with factors that favor their spread beyond their original niches.
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Affiliation(s)
| | | | | | | | - Paulo Lee Ho
- Virology Laboratory, Butantan Institute, São Paulo, Brazil
| | | | - Giuseppe Palmisano
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - João Renato Rebello Pinho
- Albert Einstein Institute for Teaching and Research (IIEP), Hospital Israelita Albert Einstein, São Paulo, Brazil,Hospital das Clínicas da Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
| | - Helena Lage Ferreira
- Faculty of Animal Science and Food Engineering, University of São Paulo, São Paulo, Brazil
| | | | - Eurico Arruda
- Faculty of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Luís Carlos de Souza Ferreira
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil,Scientific Platform Pasteur-USP, São Paulo, Brazil
| | - Carsten Wrenger
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil,*Correspondence: Carsten Wrenger, ; Edison Luiz Durigon,
| | - Edison Luiz Durigon
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil,Scientific Platform Pasteur-USP, São Paulo, Brazil,*Correspondence: Carsten Wrenger, ; Edison Luiz Durigon,
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43
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Xu JH, Kang L, Yuan B, Feng ZH, Li SQ, Wang J, Wang YR, Xin WW, Gao S, Li JX, Sun YS, Wang JL, Yuan Y. Development and evaluation of a rapid RPA/CRISPR-based detection of Francisella tularensis. Front Microbiol 2022; 13:901520. [PMID: 36033876 PMCID: PMC9399789 DOI: 10.3389/fmicb.2022.901520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Francisella tularensis is a dangerous pathogen that causes an extremely contagious zoonosis in humans named tularemia. Given its low-dose morbidity, the potential to be fatal, and aerosol spread, it is regarded as a severe threat to public health. The US Centers for Disease Control and Prevention (CDC) has classified it as a category A potential agent for bioterrorism and a Tier 1 Select Agent. Herein, we combined recombinase polymerase amplification (RPA) with CRISPR/Cas12a system to select the F. tularensis target gene (TUL4), creating a two-pronged rapid and ultrasensitive diagnostic method for detecting F. tularensis. The real-time RPA (RT-RPA) assay detected F. tularensis within 10 min at a sensitivity of 5 copies/reaction, F. tularensis genomic DNA of 5 fg, and F. tularensis of 2 × 102 CFU/ml; the RPA-CRISPR/Cas12a assay detects F. tularensis within 40 min at a sensitivity of 0.5 copies/reaction, F. tularensis genomic DNA of 1 fg, and F. tularensis of 2 CFU/ml. Furthermore, the evaluation of specificity showed that both assays were highly specific to F. tularensis. More importantly, in a test of prepared simulated blood and sewage samples, the RT-RPA assay results were consistent with RT-PCR assay results, and the RPA-CRISPR/Cas12a assay could detect a minute amount of F. tularensis genomic DNA (2.5 fg). There was no nonspecific detection with blood samples and sewage samples, giving the tests a high practical application value. For example, in on-site and epidemic areas, the RT-RPA was used for rapid screening and the RPA-CRISPR/Cas12a assay was used for more accurate diagnosis.
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Affiliation(s)
- Jian-Hao Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Bing Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Zi-Han Feng
- Department of Disease Control and Prevention, The No. 96609 Hospital of Chinese People's Liberation Army, Yinchuan, China
| | - Shi-Qing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jing Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Ya-Ru Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Wen-Wen Xin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Shan Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Jia-Xin Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yan-Song Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- *Correspondence: Yan-Song Sun
| | - Jing-Lin Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Jing-Lin Wang
| | - Yuan Yuan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- Yuan Yuan
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44
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Mohammad N, Katkam SS, Wei Q. Recent Advances in Clustered Regularly Interspaced Short Palindromic Repeats-Based Biosensors for Point-of-Care Pathogen Detection. CRISPR J 2022; 5:500-516. [PMID: 35856644 DOI: 10.1089/crispr.2021.0146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Infectious pathogens are pressing concerns due to their heavy toll on global health and socioeconomic infrastructure. Rapid, sensitive, and specific pathogen detection methods are needed more than ever to control disease spreading. The fast evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics (CRISPR-Dx) has opened a new horizon in the field of molecular diagnostics. This review highlights recent efforts in configuring CRISPR technology as an efficient diagnostic tool for pathogen detection. It starts with a brief introduction of different CRISPR-Cas effectors and their working principles for disease diagnosis. It then focuses on the evolution of laboratory-based CRISPR technology toward a potential point-of-care test, including the development of new signaling mechanisms, elimination of preamplification and sample pretreatment steps, and miniaturization of CRISPR reactions on digital assay chips and lateral flow devices. In addition, promising examples of CRISPR-Dx for pathogen detection in various real samples, such as blood, saliva, nasal swab, plant, and food samples, are highlighted. Finally, the challenges and perspectives of future development of CRISPR-Dx for infectious disease monitoring are discussed.
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Affiliation(s)
- Noor Mohammad
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA.,Department of Chemical Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | | | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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45
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Rossetti M, Merlo R, Bagheri N, Moscone D, Valenti A, Saha A, Arantes PR, Ippodrino R, Ricci F, Treglia I, Delibato E, van der Oost J, Palermo G, Perugino G, Porchetta A. Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters. Nucleic Acids Res 2022; 50:8377-8391. [PMID: 35822842 PMCID: PMC9371913 DOI: 10.1093/nar/gkac578] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 12/24/2022] Open
Abstract
The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based detection. Here, we report on the enhancement of trans-cleavage activity of Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate of trans-cleavage activity of Cas12a due to its improved affinity (Km) for hairpin DNA structures, and provide mechanistic insights of our findings through Molecular Dynamics simulations. Using hairpin DNA probes we significantly enhance FRET-based signal transduction compared to the widely used linear single stranded DNA reporters. Our signal transduction enables faster detection of clinically relevant double stranded DNA targets with improved sensitivity and specificity either in the presence or in the absence of an upstream pre-amplification step.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Neda Bagheri
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Danila Moscone
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Aakash Saha
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Pablo R Arantes
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Rudy Ippodrino
- Ulisse BioMed S.r.l. Area Science Park, 34149 Trieste, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
| | - Ida Treglia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA 52512 USA
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.,Department of Biology, University of Naples "Federico II", Complesso Universitario di Monte Sant'Angelo, Ed. 7, Via Cintia 26, 80126 Naples, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome, Tor Vergata, Via della Ricerca Scientifica 00133, Rome, Italy
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46
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Abstract
Type VI CRISPR-Cas systems have been repurposed for various applications such as gene knockdown, viral interference, and diagnostics. However, the identification and characterization of thermophilic orthologs will expand and unlock the potential of diverse biotechnological applications. Herein, we identified and characterized a thermostable ortholog of the Cas13a family from the thermophilic organism Thermoclostridium caenicola (TccCas13a). We show that TccCas13a has a close phylogenetic relation to the HheCas13a ortholog from the thermophilic bacterium Herbinix hemicellulosilytica and shares several properties such as thermostability and inability to process its own pre-CRISPR RNA. We demonstrate that TccCas13a possesses robust cis and trans activities at a broad temperature range of 37 to 70 °C, compared with HheCas13a, which has a more limited range and lower activity. We harnessed TccCas13a thermostability to develop a sensitive, robust, rapid, and one-pot assay, named OPTIMA-dx, for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. OPTIMA-dx exhibits no cross-reactivity with other viruses and a limit of detection of 10 copies/μL when using a synthetic SARS-CoV-2 genome. We used OPTIMA-dx for SARS-CoV-2 detection in clinical samples, and our assay showed 95% sensitivity and 100% specificity compared with qRT-PCR. Furthermore, we demonstrated that OPTIMA-dx is suitable for multiplexed detection and is compatible with the quick extraction protocol. OPTIMA-dx exhibits critical features that enable its use at point of care (POC). Therefore, we developed a mobile phone application to facilitate OPTIMA-dx data collection and sharing of patient sample results. This work demonstrates the power of CRISPR-Cas13 thermostable enzymes in enabling key applications in one-pot POC diagnostics and potentially in transcriptome engineering, editing, and therapies.
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47
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Wang Y, Huang C, Zhao W. Recent advances of the biological and biomedical applications of CRISPR/Cas systems. Mol Biol Rep 2022; 49:7087-7100. [PMID: 35705772 PMCID: PMC9199458 DOI: 10.1007/s11033-022-07519-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/19/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022]
Abstract
The clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated endonuclease (Cas) system, referred to as CRISPR/Cas system, has attracted significant interest in scientific community due to its great potential in translating into versatile therapeutic tools in biomedical field. For instance, a myriad of studies has demonstrated that the CRISPR/Cas system is capable of detecting various types of viruses, killing antibiotic-resistant bacteria, treating inherited genetic diseases, and providing new strategies for cancer therapy. Furthermore, CRISPR/Cas systems are also exploited as research tools such as genome engineering tool that allows researchers to interrogate the biological roles of unexplored genes or uncover novel functions of known genes. Additionally, the CRISPR/Cas system has been employed to edit the genome of a wide range of eukaryotic, prokaryotic organisms and experimental models, including but not limited to mammalian cells, mice, zebrafish, plants, yeast, and Escherichia coli. The present review mainly focuses on summarizing recent discoveries regarding the type II CRISPR/Cas9 and type VI CRISPR/Cas13a systems to give researchers a glimpse of their potential applications in the biological and biomedical field.
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Affiliation(s)
- Yaya Wang
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, 58 Yanta Zhonglu, 710054, Xi'an, Shaanxi, China.
- State Key Laboratory of Cancer Biology, Department of Physiology and Pathophysiology, Air Force Medical University, Xi'an, China.
| | - Chun Huang
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, 58 Yanta Zhonglu, 710054, Xi'an, Shaanxi, China
| | - Weiqin Zhao
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, 58 Yanta Zhonglu, 710054, Xi'an, Shaanxi, China
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48
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Metsky HC, Welch NL, Pillai PP, Haradhvala NJ, Rumker L, Mantena S, Zhang YB, Yang DK, Ackerman CM, Weller J, Blainey PC, Myhrvold C, Mitzenmacher M, Sabeti PC. Designing sensitive viral diagnostics with machine learning. Nat Biotechnol 2022; 40:1123-1131. [PMID: 35241837 PMCID: PMC9287178 DOI: 10.1038/s41587-022-01213-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 01/07/2022] [Indexed: 12/20/2022]
Abstract
Design of nucleic acid-based viral diagnostics typically follows heuristic rules and, to contend with viral variation, focuses on a genome's conserved regions. A design process could, instead, directly optimize diagnostic effectiveness using a learned model of sensitivity for targets and their variants. Toward that goal, we screen 19,209 diagnostic-target pairs, concentrated on CRISPR-based diagnostics, and train a deep neural network to accurately predict diagnostic readout. We join this model with combinatorial optimization to maximize sensitivity over the full spectrum of a virus's genomic variation. We introduce Activity-informed Design with All-inclusive Patrolling of Targets (ADAPT), a system for automated design, and use it to design diagnostics for 1,933 vertebrate-infecting viral species within 2 hours for most species and within 24 hours for all but three. We experimentally show that ADAPT's designs are sensitive and specific to the lineage level and permit lower limits of detection, across a virus's variation, than the outputs of standard design techniques. Our strategy could facilitate a proactive resource of assays for detecting pathogens.
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Affiliation(s)
- Hayden C Metsky
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA.
| | - Nicole L Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Virology Program, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | | | - Nicholas J Haradhvala
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biophysics Program, Harvard Medical School, Boston, MA, USA
| | - Laurie Rumker
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Bioinformatics and Integrative Genomics Program, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Sreekar Mantena
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Yibin B Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - David K Yang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cheri M Ackerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | | | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA
| | - Cameron Myhrvold
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael Mitzenmacher
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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49
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Kostyusheva A, Brezgin S, Babin Y, Vasilyeva I, Glebe D, Kostyushev D, Chulanov V. CRISPR-Cas systems for diagnosing infectious diseases. Methods 2022; 203:431-446. [PMID: 33839288 PMCID: PMC8032595 DOI: 10.1016/j.ymeth.2021.04.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 03/15/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Infectious diseases are a global health problem affecting billions of people. Developing rapid and sensitive diagnostic tools is key for successful patient management and curbing disease spread. Currently available diagnostics are very specific and sensitive but time-consuming and require expensive laboratory settings and well-trained personnel; thus, they are not available in resource-limited areas, for the purposes of large-scale screenings and in case of outbreaks and epidemics. Developing new, rapid, and affordable point-of-care diagnostic assays is urgently needed. This review focuses on CRISPR-based technologies and their perspectives to become platforms for point-of-care nucleic acid detection methods and as deployable diagnostic platforms that could help to identify and curb outbreaks and emerging epidemics. We describe the mechanisms and function of different classes and types of CRISPR-Cas systems, including pros and cons for developing molecular diagnostic tests and applications of each type to detect a wide range of infectious agents. Many Cas proteins (Cas3, Cas9, Cas12, Cas13, Cas14 etc.) have been leveraged to create highly accurate and sensitive diagnostic tools combined with technologies of signal amplification and fluorescent, potentiometric, colorimetric, lateral flow assay detection and other. In particular, the most advanced platforms -- SHERLOCK/v2, DETECTR, CARMEN or CRISPR-Chip -- enable detection of attomolar amounts of pathogenic nucleic acids with specificity comparable to that of PCR but with minimal technical settings. Further developing CRISPR-based diagnostic tools promises to dramatically transform molecular diagnostics, making them easily affordable and accessible virtually anywhere in the world. The burden of socially significant diseases, frequent outbreaks, recent epidemics (MERS, SARS and the ongoing COVID-19) and outbreaks of zoonotic viruses (African Swine Fever Virus etc.) urgently need the developing and distribution of express-diagnostic tools. Recently devised CRISPR-technologies represent the unprecedented opportunity to reshape epidemiological surveillance and molecular diagnostics.
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Affiliation(s)
- Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia.
| | - Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia,Institute of Immunology, Moscow, Russia
| | - Yurii Babin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia
| | - Irina Vasilyeva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia
| | - Dieter Glebe
- Institute of Medical Virology, University of Giessen, Giessen, Germany
| | - Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia,Sirius University of Science and Technology, Sochi, Russia
| | - Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia,Sechenov University, Moscow, Russia
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50
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Xue Y, Chen Z, Zhang W, Zhang J. Engineering CRISPR/Cas13 System against RNA Viruses: From Diagnostics to Therapeutics. Bioengineering (Basel) 2022; 9:bioengineering9070291. [PMID: 35877342 PMCID: PMC9312194 DOI: 10.3390/bioengineering9070291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 12/23/2022] Open
Abstract
Over the past decades, RNA viruses have been threatened people’s health and led to global health emergencies. Significant progress has been made in diagnostic methods and antiviral therapeutics for combating RNA viruses. ELISA and RT-qPCR are reliable methods to detect RNA viruses, but they suffer from time-consuming procedures and limited sensitivities. Vaccines are effective to prevent virus infection and drugs are useful for antiviral treatment, while both need a relatively long research and development cycle. In recent years, CRISPR-based gene editing and modifying tools have been expanded rapidly. In particular, the CRISPR-Cas13 system stands out from the CRISPR-Cas family due to its accurate RNA-targeting ability, which makes it a promising tool for RNA virus diagnosis and therapy. Here, we review the current applications of the CRISPR-Cas13 system against RNA viruses, from diagnostics to therapeutics, and use some medically important RNA viruses such as SARS-CoV-2, dengue virus, and HIV-1 as examples to demonstrate the great potential of the CRISPR-Cas13 system.
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