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Bhardwaj P, Kant R, Behera SP, Dwivedi GR, Singh R. Next-Generation Diagnostic with CRISPR/Cas: Beyond Nucleic Acid Detection. Int J Mol Sci 2022; 23:6052. [PMID: 35682737 PMCID: PMC9180940 DOI: 10.3390/ijms23116052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 02/07/2023] Open
Abstract
The early management, diagnosis, and treatment of emerging and re-emerging infections and the rising burden of non-communicable diseases (NCDs) are necessary. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas system has recently acquired popularity as a diagnostic tool due to its ability to target specific genes. It uses Cas enzymes and a guide RNA (gRNA) to cleave target DNA or RNA. The discovery of collateral cleavage in CRISPR-Cas effectors such as Cas12a and Cas13a was intensively repurposed for the development of instrument-free, sensitive, precise and rapid point-of-care diagnostics. CRISPR/Cas demonstrated proficiency in detecting non-nucleic acid targets including protein, analyte, and hormones other than nucleic acid. CRISPR/Cas effectors can provide multiple detections simultaneously. The present review highlights the technical challenges of integrating CRISPR/Cas technology into the onsite assessment of clinical and other specimens, along with current improvements in CRISPR bio-sensing for nucleic acid and non-nucleic acid targets. It also highlights the current applications of CRISPR/Cas technologies.
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Affiliation(s)
| | | | | | - Gaurav Raj Dwivedi
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (R.K.); (S.P.B.)
| | - Rajeev Singh
- ICMR-Regional Medical Research Centre, BRD Medical College Campus, Gorakhpur 273013, India; (P.B.); (R.K.); (S.P.B.)
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Wei J, Li Y, Cao Y, Liu Q, Yang K, Song X, Shao Y, Qi K, Tu J. Rapid and Visual Detection of Porcine Parvovirus Using an ERA-CRISPR/Cas12a System Combined With Lateral Flow Dipstick Assay. Front Cell Infect Microbiol 2022; 12:879887. [PMID: 35646725 PMCID: PMC9131491 DOI: 10.3389/fcimb.2022.879887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/11/2022] [Indexed: 12/26/2022] Open
Abstract
Porcine parvovirus (PPV) is one of the important causes of pig reproductive diseases. The most prevalent methods for PPV authentication are the polymerase chain reaction (PCR), enzyme-linked immunosorbent assay, and quantitative real-time PCR. However, these procedures have downsides, such as the fact that they take a long time and require expensive equipment. As a result, a rapid, visible, and economical clinical diagnostic strategy to detect PPV is necessary. In this study, three pairs of crRNA primers were designed to recognize the VP2 gene, and an ERA-CRISPR/Cas12a system for PPV detection was successfully developed. The approach involved isothermal detection at 37°C, and the method can be used for visual inspection. The detection limit of the ERA-CRISPR/Cas12a system was 3.75 × 102 copies/μL, and no cross reactions with other porcine viruses were found. In view of the preceding, a rapid, visible, and low-cost nucleic acid testing approach for PPV has been developed using the ERA-CRISPR/Cas12a system.
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Affiliation(s)
- Jing Wei
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
| | - Yanan Li
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
| | - Yingli Cao
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
| | - Qi Liu
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
| | - Kankan Yang
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
| | - Xiangjun Song
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
| | - Ying Shao
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
| | - Kezong Qi
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
| | - Jian Tu
- Anhui Province Engineering Laboratory for Animal Food Quality and Bio-safety, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, China
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Habimana JDD, Huang R, Muhoza B, Kalisa YN, Han X, Deng W, Li Z. Mechanistic insights of CRISPR/Cas nucleases for programmable targeting and early-stage diagnosis: A review. Biosens Bioelectron 2022; 203:114033. [DOI: 10.1016/j.bios.2022.114033] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/21/2022]
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Zheng F, Chen Z, Li J, Wu R, Zhang B, Nie G, Xie Z, Zhang H. A Highly Sensitive CRISPR-Empowered Surface Plasmon Resonance Sensor for Diagnosis of Inherited Diseases with Femtomolar-Level Real-Time Quantification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105231. [PMID: 35343100 PMCID: PMC9108660 DOI: 10.1002/advs.202105231] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/21/2022] [Indexed: 05/25/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) molecular system has emerged as a promising technology for the detection of nucleic acids. Herein, the development of a surface plasmon resonance (SPR) sensor that is functionalized with a layer of locally grown graphdiyne film, achieving excellent sensing performance when coupled with catalytically deactivated CRISPR-associated protein 9 (dCas9), is reported. dCas9 protein is immobilized on the sensor surface and complexed with a specific single-guide RNA, enabling the amplification-free detection of target sequences within genomic DNA. The sensor, termed CRISPR-SPR-Chip, is used to successfully analyze recombinant plasmids with only three-base mutations with a limit of detection as low as 1.3 fM. Real-time monitoring CRISPR-SPR-Chip is used to analyze clinical samples of patients with Duchenne muscular dystrophy with two exon deletions, which are detected without any pre-amplification step, yielding significantly positive results within 5 min. The ability of this novel CRISPR-empowered SPR (CRISPR-eSPR) sensing platform to rapidly, precisely, sensitively, and specifically detect a target gene sequence provides a new on-chip optic approach for clinical gene analysis.
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Affiliation(s)
- Fei Zheng
- Shenzhen Engineering Laboratory of phosphorene and OptoelectronicsInternational Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of EducationShenzhen Institute of Translational MedicineDepartment of OtolaryngologyShenzhen Second People's Hospitalthe First Affiliated HospitalInstitute of Microscale OptoelectronicsShenzhen UniversityShenzhen518060P.R. China
| | - Zhi Chen
- Shenzhen Engineering Laboratory of phosphorene and OptoelectronicsInternational Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of EducationShenzhen Institute of Translational MedicineDepartment of OtolaryngologyShenzhen Second People's Hospitalthe First Affiliated HospitalInstitute of Microscale OptoelectronicsShenzhen UniversityShenzhen518060P.R. China
| | - Jingfeng Li
- Shenzhen Engineering Laboratory of phosphorene and OptoelectronicsInternational Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of EducationShenzhen Institute of Translational MedicineDepartment of OtolaryngologyShenzhen Second People's Hospitalthe First Affiliated HospitalInstitute of Microscale OptoelectronicsShenzhen UniversityShenzhen518060P.R. China
- Shenzhen International Institute for Biomedical ResearchShenzhen518110China
| | - Rui Wu
- Laboratory of Robotics and SystemHarbin Institute of TechnologyHarbin150001P. R. China
| | - Bin Zhang
- Shenzhen Engineering Laboratory of phosphorene and OptoelectronicsInternational Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of EducationShenzhen Institute of Translational MedicineDepartment of OtolaryngologyShenzhen Second People's Hospitalthe First Affiliated HospitalInstitute of Microscale OptoelectronicsShenzhen UniversityShenzhen518060P.R. China
| | - Guohui Nie
- Shenzhen Engineering Laboratory of phosphorene and OptoelectronicsInternational Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of EducationShenzhen Institute of Translational MedicineDepartment of OtolaryngologyShenzhen Second People's Hospitalthe First Affiliated HospitalInstitute of Microscale OptoelectronicsShenzhen UniversityShenzhen518060P.R. China
| | - Zhongjian Xie
- Institute of PediatricsShenzhen Children's HospitalShenzhenGuangdong518038P. R. China
- Shenzhen International Institute for Biomedical ResearchShenzhenGuangdong518116P. R. China
| | - Han Zhang
- Shenzhen Engineering Laboratory of phosphorene and OptoelectronicsInternational Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of EducationShenzhen Institute of Translational MedicineDepartment of OtolaryngologyShenzhen Second People's Hospitalthe First Affiliated HospitalInstitute of Microscale OptoelectronicsShenzhen UniversityShenzhen518060P.R. China
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Huang H, Song D, Zhang W, Fang S, Zhou Q, Zhang H, Liang Z, Li Y. Choline Oxidase-Integrated Copper Metal-Organic Frameworks as Cascade Nanozymes for One-Step Colorimetric Choline Detection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5228-5236. [PMID: 35411770 DOI: 10.1021/acs.jafc.2c00746] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Choline is an important factor for regulating human health and is widely present in various foods. In this work, a sensor strategy based on a choline oxidase-integrated copper(II) metal-organic framework with peroxidase-like activity is constructed for one-step cascade detection of choline. The one-step cascade strategy can avoid intermediate product transferring in general multi-step reactions, and the multi-enzyme activities can be well exerted under one condition, thus exhibiting excellent catalytic activity and enhanced stability. In the integrated system, choline is catalyzed by ChOx to produce betaine and H2O2, which eventually got converted to hydroxyl radicals by the peroxidase nanozyme, oxidized the chromogenic substrate ABTS, and produced an observable absorption peak at 420 nm. A new choline detection method was thus established and showed a satisfactory linear relationship at 6-300 μM, which has been used for the choline analysis in milk.
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Affiliation(s)
- Hui Huang
- College of Food Science and Engineering, Jilin University, Changchun 130025, China
| | - Donghui Song
- College of Food Science and Engineering, Jilin University, Changchun 130025, China
| | - Wenjing Zhang
- College of Food Science and Engineering, Jilin University, Changchun 130025, China
| | - Shuaizhen Fang
- College of Food Science and Engineering, Jilin University, Changchun 130025, China
| | - Qianxi Zhou
- College of Food Science and Engineering, Jilin University, Changchun 130025, China
| | - Haoyu Zhang
- College of Food Science and Engineering, Jilin University, Changchun 130025, China
| | - Zheng Liang
- College of Food Science and Engineering, Jilin University, Changchun 130025, China
| | - Yongxin Li
- Key Lab of Groundwater Resources and Environment of Ministry of Education, Key Lab of Water Resources and Aquatic Environment of Jilin Province, College of New Energy and Environment, Jilin University, Changchun 130021, China
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Wan Y, Zong C, Li X, Wang A, Li Y, Yang T, Bao Q, Dubow M, Yang M, Rodrigo LA, Mao C. New Insights for Biosensing: Lessons from Microbial Defense Systems. Chem Rev 2022; 122:8126-8180. [PMID: 35234463 DOI: 10.1021/acs.chemrev.1c01063] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microorganisms have gained defense systems during the lengthy process of evolution over millions of years. Such defense systems can protect them from being attacked by invading species (e.g., CRISPR-Cas for establishing adaptive immune systems and nanopore-forming toxins as virulence factors) or enable them to adapt to different conditions (e.g., gas vesicles for achieving buoyancy control). These microorganism defense systems (MDS) have inspired the development of biosensors that have received much attention in a wide range of fields including life science research, food safety, and medical diagnosis. This Review comprehensively analyzes biosensing platforms originating from MDS for sensing and imaging biological analytes. We first describe a basic overview of MDS and MDS-inspired biosensing platforms (e.g., CRISPR-Cas systems, nanopore-forming proteins, and gas vesicles), followed by a critical discussion of their functions and properties. We then discuss several transduction mechanisms (optical, acoustic, magnetic, and electrical) involved in MDS-inspired biosensing. We further detail the applications of the MDS-inspired biosensors to detect a variety of analytes (nucleic acids, peptides, proteins, pathogens, cells, small molecules, and metal ions). In the end, we propose the key challenges and future perspectives in seeking new and improved MDS tools that can potentially lead to breakthrough discoveries in developing a new generation of biosensors with a combination of low cost; high sensitivity, accuracy, and precision; and fast detection. Overall, this Review gives a historical review of MDS, elucidates the principles of emulating MDS to develop biosensors, and analyzes the recent advancements, current challenges, and future trends in this field. It provides a unique critical analysis of emulating MDS to develop robust biosensors and discusses the design of such biosensors using elements found in MDS, showing that emulating MDS is a promising approach to conceptually advancing the design of biosensors.
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Affiliation(s)
- Yi Wan
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Chengli Zong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, Schools of Medicine and Pharmacy, University of California, San Francisco, 1700 Fourth Street, Byers Hall 303C, San Francisco, California 94158, United States
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Pharmaceutical Sciences, Marine College, Hainan University, Haikou 570228, P. R. China
| | - Yan Li
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Qing Bao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Michael Dubow
- Institute for Integrative Biology of the Cell (I2BC), UMR 9198 CNRS, CEA, Université Paris-Saclay, Campus C.N.R.S, Bâtiment 12, Avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Mingying Yang
- College of Animal Science, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
| | - Ledesma-Amaro Rodrigo
- Imperial College Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States.,School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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Zhang Y, Bai X, Li J, Xie J, Li H, Yang L, Li P, Li P, Dong H, Chen Q, Hu X, Wang Y, Jiang T, Song H, Jia L, Li L. A CRISPR-based nucleic acid detection method for severe fever with thrombocytopenia syndrome virus. Virus Res 2022; 311:198691. [PMID: 35143909 DOI: 10.1016/j.virusres.2022.198691] [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: 10/09/2021] [Revised: 01/02/2022] [Accepted: 01/25/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Fever with thrombocytopenia syndrome virus (SFTS) is a tick-borne infection now known to spread among humans as an aerosol, which has resulted in several outbreaks across Asia over the past decade. As mortality is substantial, it is vital to establish a rapid, on-site nucleic acid detection method for diagnosis. Here we describe such a method for SFTSV (Dabie bandavirus) based on CRISPR-Cas13a. METHODS Specific recombinase-aided amplification (RAA) primers and CRISPR (cr)RNA nucleic acid detection targets were designed and synthesized for the conserved sequence of the SFTSV genome, and fluorescent CRISPR detection was used to screen for high-sensitivity crRNAs. Colloidal immunochromatography test paper was used to read CRISPR detection results. Sensitivity and specificity were evaluated by running tests on gradient dilutions of SFTSV nucleic acid and the nucleic acids of other pathogens with similar transmission routes or clinical manifestations. RESULTS One crRNA with high detection sensitivity was screened out of 5 crRNAs with conserved sequences from the SFTSV genome. This CRISPR nucleic acid-based detection method was able to detect a single crRNA copy per microliter but not the nucleic acids of similar pathogens. CONCLUSION This CRISPR test strip detection method permits rapid, sensitive, and specific diagnosis of SFTS without the need for advanced nucleic acid detection equipment, thus allowing for on-site application.
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Affiliation(s)
- Yansong Zhang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xuanyang Bai
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jinhui Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Jing Xie
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Huan Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Lang Yang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Peihan Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Peng Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hao Dong
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Qichao Chen
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Xinyan Hu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yun Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Tingting Jiang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongbin Song
- Chinese PLA Center for Disease Control and Prevention, Beijing, China.
| | - Leili Jia
- Chinese PLA Center for Disease Control and Prevention, Beijing, China.
| | - Lizhong Li
- Chinese PLA Center for Disease Control and Prevention, Beijing, China.
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Qian S, Chen Y, Xu X, Peng C, Wang X, Wu H, Liu Y, Zhong X, Xu J, Wu J. Advances in amplification-free detection of nucleic acid: CRISPR/Cas system as a powerful tool. Anal Biochem 2022; 643:114593. [DOI: 10.1016/j.ab.2022.114593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/28/2022] [Accepted: 02/05/2022] [Indexed: 12/26/2022]
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Liao B, Chen X, Zhou X, Zhou Y, Shi Y, Ye X, Liao M, Zhou Z, Cheng L, Ren B. Applications of CRISPR/Cas gene-editing technology in yeast and fungi. Arch Microbiol 2021; 204:79. [DOI: 10.1007/s00203-021-02723-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/20/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022]
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Kim H, Lee S, Yoon J, Song J, Park HG. CRISPR/Cas12a collateral cleavage activity for simple and rapid detection of protein/small molecule interaction. Biosens Bioelectron 2021; 194:113587. [PMID: 34455224 DOI: 10.1016/j.bios.2021.113587] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 12/26/2022]
Abstract
To realize the full potential of the CRISPR/Cas system and expand its applicability up to the detection of molecular interactions, we herein describe a novel method to identify protein/small molecule interactions by utilizing the CRISPR/Cas12a collateral cleavage activity. This technique employs a single-stranded activator DNA modified with a specific small molecule, which would switch on the CRISPR/Cas12a collateral cleavage activity upon binding to crRNA within the CRISPR/Cas12a system. When the target protein binds to the small molecule on the activator DNA, the bound protein sterically hinders the access of the activator DNA to crRNA, thereby promoting less collateral cleavage activity of CRISPR/Cas12a. As a consequence, fewer reporter probes nearby are cleaved to produce accordingly reduced fluorescence signals in response to target protein. Based on this unique design principle, the two model protein/small molecule interactions, streptavidin/biotin and anti-digoxigenin/digoxigenin, were successfully determined down to 0.03 nM and 0.09 nM, respectively, with a fast and simple detection workflow (11 min). The practical applicability of this method was also verified by reliably detecting target streptavidin spiked in heterogeneous human serum. This work would provide great insight to construct novel strategies to identify protein/small molecule interaction by making the most of the CRISPR/Cas12a system beyond its superior capabilities in genome editing and molecular diagnostics.
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Affiliation(s)
- Hansol Kim
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Seoyoung Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Junhyeok Yoon
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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Wang Z, Zhong C. Cas12c-DETECTOR: A specific and sensitive Cas12c-based DNA detection platform. Int J Biol Macromol 2021; 193:441-449. [PMID: 34715203 DOI: 10.1016/j.ijbiomac.2021.10.167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/26/2022]
Abstract
The robust and precise nucleic acid detection platform enormously influences the clinical diagnosis of human and plant pathogens, drastically affecting disease pandemic control. CRISPR-based nucleic acid detection tools have been successfully applied for rapid and sensitive nucleic acid detection. However, the T-rich protospacer adjacent motif (PAM), specificity, and sensitivity of the CRISPR-based nucleic acid detection tools limited its wide application. We first developed a new Cas12c-based nucleic acid detection platform (Cas12c-DETECTOR), recognizing a 5'-TG PAM and showing high sensitivity and specificity on examined targets. Our results indicate that Cas12c-DETECTOR coupling with the optimized single-guide RNA (sgRNA) can be applied to specifically identity single nucleotide polymorphism (SNP). Moreover, combined with pre-amplification and lateral flow strips or the visual fluorescence detection method, Cas12c-DETECTOR can be used to diagnose human and plant pathogens in practice. Therefore, our findings illustrated that Cas12c-DETECTOR is a robust, sensitive, precise, and practiced nucleic acid detection platform.
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Affiliation(s)
- Zupeng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Engineering Laboratory for Kiwifruit Industrial Technology, Chinese Academy of Sciences, Wuhan 430074, China.
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; Engineering Laboratory for Kiwifruit Industrial Technology, Chinese Academy of Sciences, Wuhan 430074, China.
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63
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Yuan M, Ding R, Chen S, Duan G. Advances in Field Detection Based on CRISPR/Cas System. ACS Synth Biol 2021; 10:2824-2832. [PMID: 34714068 DOI: 10.1021/acssynbio.1c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid and accurate diagnostic methods are essential to interrupt outbreaks of infectious diseases such as COVID-19. However, the most commonly used nucleic acid detection method, qPCR or RT-qPCR, takes several hours to complete and requires highly sophisticated equipment. Recently, an emerging nucleic acid detection method based on the CRISPR/Cas system has reduced the reliance on qPCR. It has several important features that make it suitable for on-site POCT (point-of-care testing), including short detection cycles, low cost, high sensitivity, and the ability to be combined with different readout methods. This review briefly introduces the steps of CRISPR/Cas detection and then summarizes the current advances of CRISPR/Cas-based POCT from four steps: nucleic acid extraction, target amplification, CRISPR/Cas-based signal generation, and signal output. Finally, we discuss the advantages and challenges of CRISPR-based POCT and describe the future research perspectives for CRISPR.
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Affiliation(s)
- Mingzhu Yuan
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
| | - Ronghua Ding
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, Henan Province 450000, China
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Wang SY, Du YC, Wang DX, Ma JY, Tang AN, Kong DM. Signal amplification and output of CRISPR/Cas-based biosensing systems: A review. Anal Chim Acta 2021; 1185:338882. [PMID: 34711321 DOI: 10.1016/j.aca.2021.338882] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/30/2021] [Accepted: 07/23/2021] [Indexed: 12/14/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) proteins are powerful gene-editing tools because of their ability to accurately recognize and manipulate nucleic acids. Besides gene-editing function, they also show great promise in biosensing applications due to the superiority of easy design and precise targeting. To improve the performance of CRISPR/Cas-based biosensing systems, various nucleic acid-based signal amplification techniques are elaborately incorporated. The incorporation of these amplification techniques not only greatly increases the detection sensitivity and specificity, but also extends the detectable target range, as well as makes the use of various signal output modes possible. Therefore, summarizing the use of signal amplification techniques in sensing systems and elucidating their roles in improving sensing performance are very necessary for the development of more superior CRISPR/Cas-based biosensors for various applications. In this review, CRISPR/Cas-based biosensors are summarized from two aspects: the incorporation of signal amplification techniques in three kinds of CRISPR/Cas-based biosensing systems (Cas9, Cas12 and Cas13-based ones) and the signal output modes used by these biosensors. The challenges and prospects for the future development of CRISPR/Cas-based biosensors are also discussed.
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Affiliation(s)
- Si-Yuan Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China
| | - Yi-Chen Du
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China
| | - Dong-Xia Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China
| | - Jia-Yi Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China
| | - An-Na Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China
| | - De-Ming Kong
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, 300071, People's Republic of China.
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Hillary VE, Ignacimuthu S, Ceasar SA. Potential of CRISPR/Cas system in the diagnosis of COVID-19 infection. Expert Rev Mol Diagn 2021; 21:1179-1189. [PMID: 34409907 PMCID: PMC8607542 DOI: 10.1080/14737159.2021.1970535] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Emerging novel infectious diseases and persistent pandemics with potential to destabilize normal life remain a public health concern for the whole world. The recent outbreak of pneumonia caused by Coronavirus infectious disease-2019 (COVID-19) resulted in high mortality due to a lack of effective drugs or vaccines. With a constantly increasing number of infections with mutated strains and deaths across the globe, rapid, affordable and specific detections with more accurate diagnosis and improved health treatments are needed to combat the spread of this novel pathogen COVID-19. AREAS COVERED Researchers have started to utilize the recently invented clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR/Cas)-based tools for the rapid detection of novel COVID-19. In this review, we summarize the potential of CRISPR/Cas system for the diagnosis and enablement of efficient control of COVID-19. EXPERT OPINION Multiple groups have demonstrated the potential of utilizing CRISPR-based diagnosis tools for the detection of SARS-CoV-2. In coming months, we expect more novel and rapid CRISPR-based kits for mass detection of COVID-19-infected persons within a fraction of a second. Therefore, we believe science will conquer COVID-19 in the near future.
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Affiliation(s)
- V. Edwin Hillary
- Division of Biotechnology, Entomology Research Institute, Loyola College, University of Madras, Chennai, India
| | | | - S. Antony Ceasar
- Department of Biosciences, Bharath Institute of Higher Education and Research, Chennai, India
- Department of Biosciences, Rajagiri College of Social Sciences, Cochin, India
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66
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Tang Y, Gao L, Feng W, Guo C, Yang Q, Li F, Le XC. The CRISPR-Cas toolbox for analytical and diagnostic assay development. Chem Soc Rev 2021; 50:11844-11869. [PMID: 34611682 DOI: 10.1039/d1cs00098e] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) systems have revolutionized biological and biomedical sciences in many ways. The last few years have also seen tremendous interest in deploying the CRISPR-Cas toolbox for analytical and diagnostic assay development because CRISPR-Cas is one of the most powerful classes of molecular machineries for the recognition and manipulation of nucleic acids. In the short period of development, many CRISPR-enabled assays have already established critical roles in clinical diagnostics, biosensing, and bioimaging. We describe in this review the recent advances and design principles of CRISPR mediated analytical tools with an emphasis on the functional roles of CRISPR-Cas machineries as highly efficient binders and molecular scissors. We highlight the diverse engineering approaches for molecularly modifying CRISPR-Cas machineries and for devising better readout platforms. We discuss the potential roles of these new approaches and platforms in enhancing assay sensitivity, specificity, multiplexity, and clinical outcomes. By illustrating the biochemical and analytical processes, we hope this review will help guide the best use of the CRISPR-Cas toolbox in detecting, quantifying and imaging biologically and clinically important molecules and inspire new ideas, technological advances and engineering strategies for addressing real-world challenges such as the on-going COVID-19 pandemic.
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Affiliation(s)
- Yanan Tang
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Lu Gao
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Wei Feng
- Department of Chemistry, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - Chen Guo
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Qianfan Yang
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China.
| | - Feng Li
- Analytical & Testing Center, College of Chemistry, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610064, China. .,Department of Chemistry, Brock University, St. Catharines, Ontario, L2S 3A1, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Alberta, T6G 2G3, Canada
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67
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Fu J, Li J, Chen J, Li Y, Liu J, Su X, Shi S. Ultra-specific nucleic acid testing by target-activated nucleases. Crit Rev Biotechnol 2021; 42:1061-1078. [PMID: 34706599 DOI: 10.1080/07388551.2021.1983757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Specific and sensitive detection of nucleic acids is essential to clinical diagnostics and biotechnological applications. Currently, amplification steps are necessary for most detection methods due to the low concentration of nucleic acid targets in real samples. Although amplification renders high sensitivity, poor specificity is prevalent because of the lack of highly accurate precise strategies, resulting in significant false positives and false negatives. Nucleases exhibit high catalytic activity for nucleic acid cleavage which is regulated in a programmable manner. This review focuses on the latest progress in nucleic acid testing methods based on the target-activated nucleases. It summarizes the property of enzymes such as CRISPR/Cas, Argonautes, and some gene-editing irrelevant nucleases, which have been leveraged to create highly specific and sensitive nucleic acid testing tools. We elaborate on recent advances in the field of nuclease-mediated DNA recognition techniques for nucleic acid detection, and discuss its future applications and challenges in molecular diagnostics.
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Affiliation(s)
- Jinyu Fu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Junjie Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jing Chen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yabei Li
- Department of Neurosurgery, People's Hospital of Shijiazhuang, Shijiazhuang, China
| | - Jiajia Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xin Su
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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68
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Wang S, Dong H, Shen W, Yang Y, Li Z, Liu Y, Wang C, Gu B, Zhang L. Rapid SERS identification of methicillin-susceptible and methicillin-resistant Staphylococcus aureus via aptamer recognition and deep learning. RSC Adv 2021; 11:34425-34431. [PMID: 35494737 PMCID: PMC9042729 DOI: 10.1039/d1ra05778b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/15/2021] [Indexed: 12/27/2022] Open
Abstract
Here, we report a label-free surface-enhanced Raman scattering (SERS) method for the rapid and accurate identification of methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) based on aptamer-guided AgNP enhancement and convolutional neural network (CNN) classification. Sixty clinical isolates of Staphylococcus aureus (S. aureus), comprising 30 strains of MSSA and 30 strains of MRSA were used to build the CNN classification model. The developed method exhibited 100% identification accuracy for MSSA and MRSA, and is thus a promising tool for the rapid detection of drug-sensitive and drug-resistant bacterial strains.
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Affiliation(s)
- Shu Wang
- Hefei Institute of Physical Science, Chinese Academy of Sciences Hefei 230036 P. R China .,University of Science and Technology of China Hefei 230036 P. R China
| | - Hao Dong
- Hefei Institute of Physical Science, Chinese Academy of Sciences Hefei 230036 P. R China .,University of Science and Technology of China Hefei 230036 P. R China
| | - Wanzhu Shen
- Anhui Agricultural University Hefei 230036 P. R China
| | - Yong Yang
- Hefei Institute of Physical Science, Chinese Academy of Sciences Hefei 230036 P. R China .,University of Science and Technology of China Hefei 230036 P. R China
| | - Zhigang Li
- Hefei Institute of Physical Science, Chinese Academy of Sciences Hefei 230036 P. R China
| | - Yong Liu
- Hefei Institute of Physical Science, Chinese Academy of Sciences Hefei 230036 P. R China .,University of Science and Technology of China Hefei 230036 P. R China
| | - Chongwen Wang
- Anhui Agricultural University Hefei 230036 P. R China
| | - Bing Gu
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou 510000 P. R China
| | - Long Zhang
- Hefei Institute of Physical Science, Chinese Academy of Sciences Hefei 230036 P. R China .,University of Science and Technology of China Hefei 230036 P. R China
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69
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Zhang J, Lv H, Li L, Chen M, Gu D, Wang J, Xu Y. Recent Improvements in CRISPR-Based Amplification-Free Pathogen Detection. Front Microbiol 2021; 12:751408. [PMID: 34659186 PMCID: PMC8515055 DOI: 10.3389/fmicb.2021.751408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/09/2021] [Indexed: 12/26/2022] Open
Abstract
Molecular diagnostic (MDx) methods directly detect target nucleic acid sequences and are therefore an important approach for precise diagnosis of pathogen infection. In comparison with traditional MDx techniques such as PCR, the recently developed CRISPR-based diagnostic technologies, which employ the single-stranded nucleic acid trans-cleavage activities of either Cas12 or Cas13, show merits in both sensitivity and specificity and therefore have great potential in both pathogen detection and beyond. With more and more efforts in improving both the CRISPR trans-cleavage efficiencies and the signal detection sensitivities, CRISPR-based direct detection of target nucleic acids without preamplification can be a possibility. Here in this mini-review, we summarize recent research progresses of amplification-free CRISPR-Dx systems and explore the potential changes they will lead to pathogen diagnosis. In addition, discussion of the challenges for both detection sensitivity and cost of the amplification-free systems will also be covered.
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Affiliation(s)
- Jian Zhang
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hailong Lv
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, China
| | - Linxian Li
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Minjie Chen
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Dayong Gu
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jin Wang
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yong Xu
- Department of Clinical Laboratory, Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
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70
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Gupta R, Kazi TA, Dey D, Ghosh A, Ravichandiran V, Swarnakar S, Roy S, Biswas SR, Ghosh D. CRISPR detectives against SARS-CoV-2: a major setback against COVID-19 blowout. Appl Microbiol Biotechnol 2021; 105:7593-7605. [PMID: 34542686 PMCID: PMC8450312 DOI: 10.1007/s00253-021-11583-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 12/26/2022]
Abstract
The emergence of SARS-CoV-2 has brought the world to a standstill, and till date, effective treatments and diagnostics against this idiosyncratic pathogen are lacking. As compared to the standard WHO/CDC qPCR detection method, which consumes several hours for detection, CRISPR-based SHERLOCK, DETECTR, and FELUDA have emerged as rapid diagnostic tools for the detection of the RNA genome of SARS-CoV-2 within an hour with 100% accuracy, specificity, and sensitivity. These attributes of CRISPR-based detection technologies have taken themselves one step ahead of available detection systems and are emerging as an inevitable tool for quick detection of the virus. Further, the discovery of Cas13s nucleases and their orthologs has opened a new corridor for exploitation of Cas13s as an antiviral therapy against SARS-CoV-2 and other viral diseases. One such approach is Prophylactic Antiviral CRISPR in huMAN cells (PACMAN), which needs a long haul to bring into therapy. The approval of SHERLOCK as the first CRISPR-based SARS-CoV-2 test kit by the FDA, for emergency diagnosis of COVID-19 patients, has given positive hope to scientists that sooner human trials of CRISPR-based therapy will be ratified. In this review, we have extensively reviewed the present CRISPR-based approaches, challenges, and future prospects in the light of diagnostics and therapeutics against SARS-CoV-2. KEY POINTS: • The discovery of Cas12 and Cas13 siblings allowed scientists to detect the viral genes. • Cas13d's identification aided scientists in precisely cleaving the SARS-CoV-2 ssRNA. • CRISPR-Cas system acts as "molecular detector and antiviral proctor."
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Affiliation(s)
- Rahul Gupta
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | | | - Dhritiman Dey
- National Institute of Pharmaceutical Education and Research, Kolkata, India
| | | | - V Ravichandiran
- National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Snehasikta Swarnakar
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Syamal Roy
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | | | - Dipanjan Ghosh
- National Institute of Pharmaceutical Education and Research, Kolkata, India.
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71
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Kim S, Ji S, Koh HR. CRISPR as a Diagnostic Tool. Biomolecules 2021; 11:1162. [PMID: 34439828 PMCID: PMC8391464 DOI: 10.3390/biom11081162] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has recently gained growing attention as a diagnostic tool due to its capability of specific gene targeting. It consists of Cas enzymes and a guide RNA (gRNA) that can cleave the target DNA or RNA based on the sequence of the gRNA, making it an attractive genetic engineering technique. In addition to the target-specific binding and cleavage, the trans-cleavage activity was reported for some Cas proteins, including Cas12a and Cas13a, which is to cleave the surrounding single-stranded DNA or RNA upon the target binding of Cas-gRNA complex. All these activities of the CRISPR-Cas system are based on its target-specific binding, making it applied to develop diagnostic methods by detecting the disease-related gene as well as microRNAs and the genetic variations such as single nucleotide polymorphism and DNA methylation. Moreover, it can be applied to detect the non-nucleic acids target such as proteins. In this review, we cover the various CRISPR-based diagnostic methods by focusing on the activity of the CRISPR-Cas system and the form of the target. The CRISPR-based diagnostic methods without target amplification are also introduced briefly.
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Affiliation(s)
| | | | - Hye Ran Koh
- Department of Chemistry, Chung-Ang University, Seoul 06974, Korea; (S.K.); (S.J.)
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72
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Qiu E, Jin S, Xiao Z, Chen Q, Wang Q, Liu H, Xie C, Chen C, Li Z, Han S. CRISPR-based detection of Helicobacter pylori in stool samples. Helicobacter 2021; 26:e12828. [PMID: 34117655 DOI: 10.1111/hel.12828] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Noninvasive detection of Helicobacter pylori plays an important role in clinical practice. However, few noninvasive methods have been applied in epidemiological studies due to the requirement for expensive equipment and complicated processes. The aim of this study was to establish a reliable, fast, and inexpensive noninvasive method based on CRISPR-Cas12a technology for the detection of Helicobacter pylori in stool specimens. METHOD A novel detection method based on CRISPR-Cas12a technology was established and validated with 41 stool specimens collected from Zhujiang Hospital and compared with reliable Helicobacter pylori detection assays, such as the rapid urease test and urea breath test. RESULT A CRISPR-Cas12a system-based method was established, and its sensitivity and specificity were evaluated. Utilizing a lateral flow biosensor, the limit of detection was 5 copies/μl, and our method could successfully distinguish Helicobacter pylori from other pathogens, suggesting no cross-reactivity with other pathogens. Furthermore, lateral flow biosensor strips were utilized to test stool specimens, which could display the detection results in an accessible way. CONCLUSION Our CRISPR-Cas12a system-based method successfully detected Helicobacter pylori in stool specimens. It is a rapid, simple, and inexpensive method for the detection and screening of Helicobacter pylori, which makes it a very promising supplemental test. However, its sensitivity and specificity compared with those of the gold standard test still need to be examined.
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Affiliation(s)
- Enming Qiu
- General Surgery Center, Department of Gastrointestinal Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shaoqin Jin
- Department of Gastroenterology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Zhuo Xiao
- Guangzhou Pluslife Technology Co, Ltd, Guangzhou, China
| | - Qianyun Chen
- General Surgery Center, Department of Gastrointestinal Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qiaohui Wang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Huayong Liu
- Guangzhou Pluslife Technology Co, Ltd, Guangzhou, China
| | - Chanfang Xie
- Guangzhou Pluslife Technology Co, Ltd, Guangzhou, China
| | - Chong Chen
- Guangzhou Pluslife Technology Co, Ltd, Guangzhou, China
| | - Zhou Li
- General Surgery Center, Department of Gastrointestinal Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shuai Han
- General Surgery Center, Department of Gastrointestinal Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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73
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Bao M, Chen Q, Xu Z, Jensen EC, Liu C, Waitkus JT, Yuan X, He Q, Qin P, Du K. Challenges and Opportunities for Clustered Regularly Interspaced Short Palindromic Repeats Based Molecular Biosensing. ACS Sens 2021; 6:2497-2522. [PMID: 34143608 DOI: 10.1021/acssensors.1c00530] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Clustered regularly interspaced short palindromic repeats, CRISPR, has recently emerged as a powerful molecular biosensing tool for nucleic acids and other biomarkers due to its unique properties such as collateral cleavage nature, room temperature reaction conditions, and high target-recognition specificity. Numerous platforms have been developed to leverage the CRISPR assay for ultrasensitive biosensing applications. However, to be considered as a new gold standard, several key challenges for CRISPR molecular biosensing must be addressed. In this paper, we briefly review the history of biosensors, followed by the current status of nucleic acid-based detection methods. We then discuss the current challenges pertaining to CRISPR-based nucleic acid detection, followed by the recent breakthroughs addressing these challenges. We focus upon future advancements required to enable rapid, simple, sensitive, specific, multiplexed, amplification-free, and shelf-stable CRISPR-based molecular biosensors.
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Affiliation(s)
- Mengdi Bao
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Qun Chen
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Zhiheng Xu
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Erik C. Jensen
- HJ Science & Technology Inc., San Leandro, California 94710, United States
| | - Changyue Liu
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Jacob T. Waitkus
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Xi Yuan
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Qian He
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Peiwu Qin
- Center of Precision Medicine and Healthcare, Tsinghua-Berkeley Shenzhen Institute, Shenzhen, Guangdong Province 518055, China
| | - Ke Du
- Department of Mechanical Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- Department of Microsystems Engineering, Rochester Institute of Technology, Rochester, New York 14623, United States
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
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74
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Diao M, Lang L, Feng J, Li R. Molecular detections of coronavirus: current and emerging methodologies. Expert Rev Anti Infect Ther 2021; 20:199-210. [PMID: 34225540 DOI: 10.1080/14787210.2021.1949986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Seven coronavirus species have been identified that can infect humans. While human coronavirus infections had been historically associated with only mild respiratory symptoms similar to the common cold, three coronaviruses identified since 2003, Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and SARS-CoV-2, cause life-threatening severe respiratory syndromes. The coronavirus disease 2019 (COVID-19) caused by the highly transmissible SARS-CoV-2 has triggered a worldwide health emergency. Due to the lack of effective drugs and vaccination, rapid and reliable detection is of vital importance to control coronavirus epidemics/pandemics.Area covered: A literature search was performed in Pubmed covering the detections and diagnostics of SARS, MERS and SARS-CoV-2. This review summarized the current knowledge of established and emerging methods for coronavirus detection. The characteristics of different diagnostic approaches were described, and the strengths and weaknesses of each method were analyzed and compared. In addition, future trends in the field of coronavirus detection were also discussed.Expert opinion: Nucleic acid-based RT-PCR is the current golden-standard of coronavirus detection, while immunoassays provide history of coronavirus infection besides diagnostic information. Integrated high-throughput system holds the great potential and is the trend of future detection and diagnosis of virus infection.
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Affiliation(s)
- Mingkun Diao
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China
| | - Lang Lang
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China
| | - Juan Feng
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China
| | - Rongsong Li
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen, China
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75
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Kaminski MM, Abudayyeh OO, Gootenberg JS, Zhang F, Collins JJ. CRISPR-based diagnostics. Nat Biomed Eng 2021; 5:643-656. [PMID: 34272525 DOI: 10.1038/s41551-021-00760-7] [Citation(s) in RCA: 442] [Impact Index Per Article: 147.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 06/02/2021] [Indexed: 02/02/2023]
Abstract
The accurate and timely diagnosis of disease is a prerequisite for efficient therapeutic intervention and epidemiological surveillance. Diagnostics based on the detection of nucleic acids are among the most sensitive and specific, yet most such assays require costly equipment and trained personnel. Recent developments in diagnostic technologies, in particular those leveraging clustered regularly interspaced short palindromic repeats (CRISPR), aim to enable accurate testing at home, at the point of care and in the field. In this Review, we provide a rundown of the rapidly expanding toolbox for CRISPR-based diagnostics, in particular the various assays, preamplification strategies and readouts, and highlight their main applications in the sensing of a wide range of molecular targets relevant to human health.
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Affiliation(s)
- Michael M Kaminski
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA
| | - Feng Zhang
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.,Massachusetts Consortium for Pathogen Readiness, Boston, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - James J Collins
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, MIT, Cambridge, MA, USA. .,Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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76
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Banerjee A, Mukherjee S, Maji BK. Manipulation of genes could inhibit SARS-CoV-2 infection that causes COVID-19 pandemics. Exp Biol Med (Maywood) 2021; 246:1643-1649. [PMID: 33899542 PMCID: PMC8090827 DOI: 10.1177/15353702211008106] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The year 2020 witnessed an unpredictable pandemic situation due to novel coronavirus (COVID-19) outbreaks. This condition can be more severe if the patient has comorbidities. Failure of viable treatment for such viral infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to lack of identification. Thus, modern and productive biotechnology-based tools are being used to manipulate target genes by introducing the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas (CRISPR-associated) system. Moreover, it has now been used as a tool to inhibit viral replication. Hence, it can be hypothesized that the CRISPR/Cas system can be a viable tool to target both the SARS-CoV-2 genome with specific target RNA sequence and host factors to destroy the SARS-CoV-2 community via inhibition of viral replication and infection. Moreover, comorbidities and COVID-19 escalate the rate of mortality globally, and as a result, we have faced this pandemic. CRISPR/Cas-mediated genetic manipulation to knockdown viral sequences may be a preventive strategy against such pandemic caused by SARS-CoV-2. Furthermore, prophylactic antiviral CRISPR in human cells (PAC-MAN) along with CRISPR/Cas13d efficiently degrades the specific RNA sequence to inhibit viral replication. Therefore, we suggest that CRISPR/Cas system with PAC-MAN could be a useful tool to fight against such a global pandemic caused by SARS-CoV-2. This is an alternative preventive approach of management against the pandemic to destroy the target sequence of RNA in SARS-CoV-2 by viral inhibition.
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Affiliation(s)
- Arnab Banerjee
- Department of Physiology (UG & PG),
Serampore College, Serampore, Hooghly 712201, India
| | - Sandip Mukherjee
- Department of Physiology (UG & PG),
Serampore College, Serampore, Hooghly 712201, India
| | - Bithin K Maji
- Department of Physiology (UG & PG),
Serampore College, Serampore, Hooghly 712201, India
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77
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Li P, Wang L, Yang J, Di LJ, Li J. Applications of the CRISPR-Cas system for infectious disease diagnostics. Expert Rev Mol Diagn 2021; 21:723-732. [PMID: 33899643 DOI: 10.1080/14737159.2021.1922080] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Rapid and accurate diagnostic approaches are essential for impeding the spread of infectious diseases. This review aims to summarize current progress of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) systems in the applications for diagnostics of infectious diseases including the ongoing COVID-19 epidemic. AREAS COVERED In this review, we discuss class 2 CRISPR-Cas biosensing systems-based diagnostics in various emerging and reemerging infectious diseases, CRISPR-Cas systems have created a new era for early diagnostics of infectious diseases, especially with the discovery of the collateral cleavage activity of Cas12 and Cas13. We mainly focus on different CRISPR-Cas effectors for the detection of pathogenic microorganisms as well as provide a detailed explanation of the pros and cons of CRISPR-Cas biosensing systems. In addition, we also introduce future research perspectives. EXPERT COMMENTARY However, further improvement of newly discovered systems and engineering existing ones should be developed to increase the specificity, sensitivity or stability of the diagnostic tools. It may be a long journey to finish the clinical transition from research use. CRISPR-Cas approaches will emerge as more promising and robust tools for infectious disease diagnosis in the future.
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Affiliation(s)
- Peipei Li
- Kobilka Institute of Innovative Drug Discovery, Faculty of Life and Health Sciences, the Chinese University of Hong Kong, Shenzhen, Guangdong, China.,Cancer Center, Faculty of Health Sciences, University of Macau, China
| | - Li Wang
- Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, SAR of China
| | - Junning Yang
- Frontage Laboratories Inc, Exton, Pennsylvania, USA
| | - Li-Jun Di
- Cancer Center, Faculty of Health Sciences, University of Macau, China
| | - Jingjing Li
- Jinming Yu Academician Workstation of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China.,Cancer Center, Faculty of Health Sciences, University of Macau, China
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78
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Nouri R, Tang Z, Dong M, Liu T, Kshirsagar A, Guan W. CRISPR-based detection of SARS-CoV-2: A review from sample to result. Biosens Bioelectron 2021; 178:113012. [PMID: 33497879 PMCID: PMC7826142 DOI: 10.1016/j.bios.2021.113012] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/10/2021] [Accepted: 01/17/2021] [Indexed: 12/23/2022]
Abstract
The current pandemic of the 2019 novel coronavirus (COVID-19) caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) has raised significant public health concern. Rapid, affordable, and accurate diagnostics of SARS-CoV-2 is essential for early treatment and control of the disease spread. In the past few years, CRISPR technology has shown great potential for highly sensitive and specific molecular diagnostics. Amid the ongoing COVID-19 pandemic, there is an increasing interest in implementing CRISPR-based diagnostic principles to develop fast and precise methods for detecting SARS-CoV-2. In this work, we reviewed and summarized these CRISPR-based diagnostic systems as well as their characteristics and challenges. We also provided future perspectives of CRISPR-based sensing towards point-of-care molecular diagnosis applications.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Zifan Tang
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Aneesh Kshirsagar
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, 16802, United States; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, 16802, United States.
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79
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Zhang Y, Wu Y, Wu Y, Chang Y, Liu M. CRISPR-Cas systems: From gene scissors to programmable biosensors. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116210] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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80
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Dhar BC, Steimberg N, Mazzoleni G. Point-of-Care Pathogen Detection with CRISPR-based Programmable Nucleic Acid Binding Proteins. ChemMedChem 2021; 16:1566-1575. [PMID: 33258314 DOI: 10.1002/cmdc.202000782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Indexed: 12/24/2022]
Abstract
The contemporary discovery of extremely versatile engineered nucleic acid-binding proteins has transformed a brave new world in the genome-editing scientific area. Clustered regularly interspaced short palindromic repeats (CRISPR)-mediated programmable nucleic acid-binding proteins have brought about a revolution in diagnostic platforms. The groundbreaking finding that bacteria and archaea that harbored prokaryotes have transmitted adaptive immunity through CRISPR and CRISPR-associated (Cas) proteins has driven revolutionary advances in molecular biology. Importantly, advances in gene editing focus how expanding visions in CRISPR-Cas biology are revolutionizing the area of molecular diagnostics for identifying DNA and RNA in emerging microbiological pathogens, for single nucleotide polymorphism (SNP) identifications, and for cell-free mutation. Recent advances, such as improvements in multiplexing and quantitative capabilities as well as instrument-free detection of nucleic acids, will potentially leverage the introduction of these novel technologies to detecting bacteria and viruses at the point of care (POC). In this review, we highlight the fundamental features of CRISPR/Cas-based molecular diagnostic technologies and summarize a vision of the next applications for identifying pathogens in POC settings.
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Affiliation(s)
- Bidhan C Dhar
- Lineberger Comprehensive Cancer Center, University of North Carolina (UNC), 205 S Columbia St., Chapel Hill, NC, 27514, USA
| | - Nathalie Steimberg
- Department of Clinical and Experimental Sciences, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.,Interuniversity Research Center "Integrated Models for Prevention and Protection in Environmental and Occupational Health" (MISTRAL), University of Brescia/ University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Giovanna Mazzoleni
- Department of Clinical and Experimental Sciences, University of Brescia, Viale Europa 11, 25123, Brescia, Italy.,Interuniversity Research Center "Integrated Models for Prevention and Protection in Environmental and Occupational Health" (MISTRAL), University of Brescia/ University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
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81
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Bhattacharjee G, Gohil N, Lam NL, Singh V. CRISPR-based diagnostics for detection of pathogens. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:45-57. [PMID: 34127201 DOI: 10.1016/bs.pmbts.2021.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The improved sensitivity and superior specificity associated with the use of molecular assays has improved the fate of disease diagnosis by bestowing the clinicians with outcomes that are both rapid and precise. In recent years, CRISPR has made considerable progress in in vitro diagnostic platform which has paved its way for developing rapid and sensitive CRISPR-based diagnostic tools. Improved perception and better understanding of diverse CRISPR-Cas systems has broadened the reach of CRISPR applications for not just early detection of pathogens but also for early onset of diseases such as cancer. The inherent allele specificity of CRISPR is the predominant reason for its application in designing a diagnostic-tool that is field-deployable, portable, sensitive, specific and rapid. In this chapter, we highlight various CRISPR-based diagnostic platforms, its applications, challenges and future prospects of the CRISPR-Cas system.
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Affiliation(s)
- Gargi Bhattacharjee
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Navya Lavina Lam
- The J. David Gladstone Institutes, San Francisco, CA, United States
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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82
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Roy S, Naha S, Rao A, Basu S. CRISPR-Cas system, antibiotic resistance and virulence in bacteria: Through a common lens. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 178:123-174. [PMID: 33685595 DOI: 10.1016/bs.pmbts.2020.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CRISPR-Cas system, antibiotic resistance and virulence are different modes of survival for the bacteria. CRISPR-Cas is an adaptive immune system that can degrade foreign DNA, antibiotic resistance helps bacteria to evade drugs that can threaten their existence and virulence determinants are offensive tools that can facilitate the establishment of infection by pathogens. This chapter focuses on these three aspects, providing insights about the CRISPR system and resistance mechanisms in brief, followed by understanding the synergistic or antagonistic relationship of resistance and virulence determinants in connection to the CRISPR system. We have addressed the discussion of this evolving topic through specific examples and studies. Different approaches for successful detection of this unique defense system in bacteria and various applications of the CRISPR-Cas systems to show how it can be harnessed to tackle the increasing problem of antibiotic resistance have been put forth. World Health Organization has declared antibiotic resistance as a serious global problem of the 21st century. As antibiotic-resistant bacteria increase their footprint across the globe, newer tools such as the CRISPR-Cas system hold immense promise to tackle this problem.
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Affiliation(s)
- Subhasree Roy
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Scheme XM, Beliaghata, Kolkata, India
| | - Sharmi Naha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Scheme XM, Beliaghata, Kolkata, India
| | - Ankur Rao
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Scheme XM, Beliaghata, Kolkata, India
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Scheme XM, Beliaghata, Kolkata, India.
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83
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Satish L, Lavanya G, Kasthuri T, Kalaivaani A, Shamili S, Muthuramalingam P, Gowrishankar S, Pandian SK, Singh V, Sitrit Y, Kushmaro A. CRISPR based development of RNA editing and the diagnostic platform. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 179:117-159. [PMID: 33785175 DOI: 10.1016/bs.pmbts.2020.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Clustered Regularly Interspersed Short Palindromic Repeat-CRISPR-Associated (CRISPR-Cas) system has improved the ability to edit and control gene expression as desired. Genome editing approaches are currently leading the biomedical research with improved focus on direct nuclease dependent editing. So far, the research was predominantly intended on genome editing over the DNA level, recent adapted techniques are initiating to secure momentum through their proficiency to provoke modifications in RNA sequence. Integration of this system besides to lateral flow method allows reliable, quick, sensitive, precise and inexpensive diagnostic. These interesting methods illustrate only a small proportion of what is technically possible for this novel technology, but several technological obstacles need to be overcome prior to the CRISPR-Cas genome editing system can meet its full ability. This chapter covers the particulars on recent advances in CRISPR-Cas9 genome editing technology including diagnosis and technical advancements, followed by molecular mechanism of CRISPR-based RNA editing and diagnostic tools and types, and CRISPR-Cas-based biosensors.
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Affiliation(s)
- Lakkakula Satish
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel; The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Bergman Campus, Beer Sheva, Israel
| | - Gunamalai Lavanya
- Department of Postharvest and Fresh Produce, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Thirupathi Kasthuri
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Aruchamy Kalaivaani
- Department of Postharvest and Fresh Produce, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Sasanala Shamili
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Bergman Campus, Beer Sheva, Israel
| | | | | | | | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Yaron Sitrit
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Bergman Campus, Beer Sheva, Israel
| | - Ariel Kushmaro
- Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel.
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84
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CRISPR/Cas9-Based Lateral Flow and Fluorescence Diagnostics. Bioengineering (Basel) 2021; 8:bioengineering8020023. [PMID: 33673107 PMCID: PMC7918862 DOI: 10.3390/bioengineering8020023] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/06/2021] [Accepted: 02/09/2021] [Indexed: 12/23/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR/Cas) proteins can be designed to bind specified DNA and RNA sequences and hold great promise for the accurate detection of nucleic acids for diagnostics. We integrated commercially available reagents into a CRISPR/Cas9-based lateral flow assay that can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences with single-base specificity. This approach requires minimal equipment and represents a simplified platform for field-based deployment. We also developed a rapid, multiplex fluorescence CRISPR/Cas9 nuclease cleavage assay capable of detecting and differentiating SARS-CoV-2, influenza A and B, and respiratory syncytial virus in a single reaction. Our findings provide proof-of-principle for CRISPR/Cas9 point-of-care diagnosis as well as a scalable fluorescent platform for identifying respiratory viral pathogens with overlapping symptomology.
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85
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Kwarteng A, Sylverken A, Asiedu E, Ahuno ST. Genome editing as control tool for filarial infections. Biomed Pharmacother 2021; 137:111292. [PMID: 33581654 DOI: 10.1016/j.biopha.2021.111292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/11/2021] [Accepted: 01/13/2021] [Indexed: 12/26/2022] Open
Abstract
Human filarial infections are vector-borne nematode infections, which include lymphatic filariasis, onchocerciasis, loiasis, and mansonella filariasis. With a high prevalence in developing countries, filarial infections are responsible for some of the most debilitating morbidities and a vicious cycle of poverty and disease. Global initiatives set to eradicate these infections include community mass treatments, vector control, provision of care for morbidity, and search for vaccines. However, there are growing challenges associated with mass treatments, vector control, and antifilarial vaccine development. With the emergence of genome editing tools and successful applications in other infectious diseases, the integration of genetic editing techniques in future control strategies for filarial infections would offer the best option for eliminating filarial infections. In this review, we briefly discuss the mechanisms of the three main genetic editing techniques and explore the potential applications of these powerful tools to control filarial infections.
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Affiliation(s)
- Alexander Kwarteng
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana; Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana.
| | - Augustina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana; Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana
| | - Ebenezer Asiedu
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana
| | - Samuel Terkper Ahuno
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana; Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, KNUST, Kumasi, Ghana
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86
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Wu H, Chen X, Zhang M, Wang X, Chen Y, Qian C, Wu J, Xu J. Versatile detection with CRISPR/Cas system from applications to challenges. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2020.116150] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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87
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Daisy PS, Shreyas KS, Anitha TS. Will CRISPR-Cas9 Have Cards to Play Against Cancer? An Update on its Applications. Mol Biotechnol 2021; 63:93-108. [PMID: 33386579 PMCID: PMC7775740 DOI: 10.1007/s12033-020-00289-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 02/06/2023]
Abstract
Genome editing employs targeted nucleases as powerful tools to precisely alter the genome of target cells and regulate functional genes. Various strategies have been risen so far as the molecular scissors-mediated genome editing that includes zinc finger nuclease, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats-CRISPR-related protein 9. These tools allow researchers to understand the basics of manipulating the genome, create animal models to study human diseases, understand host-pathogen interactions and design disease targets. Targeted genome modification utilizing RNA-guided nucleases are of recent curiosity, as it is a fast and effective strategy that enables the researchers to manipulate the gene of interest, carry out functional studies, understand the molecular basis of the disease and design targeted therapies. CRISPR-Cas9, a bacterial defense system employed against viruses, consists of a single-strand RNA-guided Cas9 nuclease connected to the corresponding complementary target sequence. This powerful and versatile tool has gained tremendous attention among the researchers, owing to its ability to correct genetic disorders. To help illustrate the potential of this gene editor in unexplored corners of oncology, we describe the history of CRISPR-Cas9, its rapid progression in cancer research as well as future perspectives.
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Affiliation(s)
- Precilla S Daisy
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed To-Be University), Mahatma Gandhi Medical College and Research Institute Campus, Pillaiyarkuppam, Puducherry, 607403, India
| | - Kuduvalli S Shreyas
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed To-Be University), Mahatma Gandhi Medical College and Research Institute Campus, Pillaiyarkuppam, Puducherry, 607403, India
| | - T S Anitha
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed To-Be University), Mahatma Gandhi Medical College and Research Institute Campus, Pillaiyarkuppam, Puducherry, 607403, India.
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88
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Yadav N, Narang J, Chhillar AK, Rana JS. CRISPR: A new paradigm of theranostics. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 33:102350. [PMID: 33359413 PMCID: PMC7831819 DOI: 10.1016/j.nano.2020.102350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/09/2020] [Accepted: 12/15/2020] [Indexed: 12/26/2022]
Abstract
Infectious and hereditary diseases are the primary cause of human mortality globally. Applications of conventional techniques require significant improvement in sensitivity and specificity in therapeutics. However, clustered regularly interspaced short palindromic repeats (CRISPRs) is an innovative genome editing technology which has provided a significant therapeutic tool exhibiting high sensitivity, fast and precise investigation of distinct pathogens in an epidemic. CRISPR technology has also facilitated the understanding of the biology and therapeutic mechanism of cancer and several other hereditary diseases. Researchers have used the CRISPR technology as a theranostic approach for a wide range of diseases causing pathogens including distinct bacteria, viruses, fungi and parasites and genetic mutations as well. In this review article, besides various therapeutic applications of infectious and hereditary diseases we have also explained the structure and mechanism of CRISPR tools and role of CRISPR integrated biosensing technology in provoking diagnostic applications.
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Affiliation(s)
- Neelam Yadav
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonepat; Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana.
| | - Jagriti Narang
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi, India.
| | | | - Jogender Singh Rana
- Department of Biotechnology, Deenbandhu Chhotu Ram University of Science and Technology, Murthal, Sonepat.
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89
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Bonini A, Poma N, Vivaldi F, Kirchhain A, Salvo P, Bottai D, Tavanti A, Di Francesco F. Advances in biosensing: The CRISPR/Cas system as a new powerful tool for the detection of nucleic acids. J Pharm Biomed Anal 2021; 192:113645. [PMID: 33039910 PMCID: PMC7513908 DOI: 10.1016/j.jpba.2020.113645] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/26/2022]
Abstract
A main challenge in the development of biosensing devices for the identification and quantification of nucleic acids is to avoid the amplification of the genetic material from the sample by polymerase chain reaction (PCR), which is at present necessary to enhance sensitivity and selectivity of assays. PCR has undoubtedly revolutionized genetic analyses, but it requires careful purification procedures that are not easily implemented in point of care (POC) devices. In recent years, a new strategy for nucleic acid detection based on clustered regularly interspaced short palindromic repeats (CRISPR) and associated protein systems (Cas) seems to offer unprecedented possibilities. The coupling of the CRISPR/Cas system with recent isothermal amplification methods is fostering the development of innovative optical and electrochemical POC devices. In this review, the mechanisms of action of several new CRISRP/Cas systems are reported together with their use in biosensing of nucleic acids.
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Affiliation(s)
- Andrea Bonini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, Pisa, Italy.
| | - Noemi Poma
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, Pisa, Italy
| | - Federico Vivaldi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, Pisa, Italy,Institute of Clinical Physiology, National Research Council, Via G. Moruzzi 1, Pisa, Italy
| | - Arno Kirchhain
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, Pisa, Italy
| | - Pietro Salvo
- Institute of Clinical Physiology, National Research Council, Via G. Moruzzi 1, Pisa, Italy
| | - Daria Bottai
- Department of Biology, University of Pisa, Via San Zeno 35-39, Pisa, Italy
| | - Arianna Tavanti
- Department of Biology, University of Pisa, Via San Zeno 35-39, Pisa, Italy
| | - Fabio Di Francesco
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, Pisa, Italy
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90
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Moon J, Kwon HJ, Yong D, Lee IC, Kim H, Kang H, Lim EK, Lee KS, Jung J, Park HG, Kang T. Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. ACS Sens 2020; 5:4017-4026. [PMID: 33270431 DOI: 10.1021/acssensors.0c0192910.1021/acssensors.0c01929.s001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Viruses have been a continuous threat to human beings. The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a pandemic that is still ongoing worldwide. Previous pandemic influenza A virus (pH1N1) might be re-emerging through a drug-resistant mutation. We report a colorimetric viral detection method based on the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 endonuclease dead (dCas9) system. In this method, RNA in the viral lysate was directly recognized by the CRISPR/dCas9 system with biotin-protospacer adjacent motif (PAM)-presenting oligonucleotide (PAMmer). Streptavidin-horseradish peroxidase then bound to biotin-PAMmer, inducing a color change through the oxidation of 3,3',5,5'-tetramethylbenzidine. Using the developed method, we successfully identified SARS-CoV-2, pH1N1, and pH1N1/H275Y viruses by the naked eye. Moreover, the detection of viruses in human nasopharyngeal aspirates and sputum was demonstrated. Finally, clinical samples from COVID-19 patients led to a successful diagnosis. We anticipate that the current method can be employed for simple and accurate diagnosis of viruses.
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Affiliation(s)
- Jeong Moon
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | | | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | | | | | | | - Eun-Kyung Lim
- Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | | | - Juyeon Jung
- Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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91
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Moon J, Kwon HJ, Yong D, Lee IC, Kim H, Kang H, Lim EK, Lee KS, Jung J, Park HG, Kang T. Colorimetric Detection of SARS-CoV-2 and Drug-Resistant pH1N1 Using CRISPR/dCas9. ACS Sens 2020; 5:4017-4026. [PMID: 33270431 PMCID: PMC7724983 DOI: 10.1021/acssensors.0c01929] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/19/2020] [Indexed: 12/13/2022]
Abstract
Viruses have been a continuous threat to human beings. The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a pandemic that is still ongoing worldwide. Previous pandemic influenza A virus (pH1N1) might be re-emerging through a drug-resistant mutation. We report a colorimetric viral detection method based on the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 endonuclease dead (dCas9) system. In this method, RNA in the viral lysate was directly recognized by the CRISPR/dCas9 system with biotin-protospacer adjacent motif (PAM)-presenting oligonucleotide (PAMmer). Streptavidin-horseradish peroxidase then bound to biotin-PAMmer, inducing a color change through the oxidation of 3,3',5,5'-tetramethylbenzidine. Using the developed method, we successfully identified SARS-CoV-2, pH1N1, and pH1N1/H275Y viruses by the naked eye. Moreover, the detection of viruses in human nasopharyngeal aspirates and sputum was demonstrated. Finally, clinical samples from COVID-19 patients led to a successful diagnosis. We anticipate that the current method can be employed for simple and accurate diagnosis of viruses.
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Affiliation(s)
- Jeong Moon
- Bionanotechnology Research Center and
Functional Biomaterial Research Center,
KRIBB, 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic of Korea
- Department of Chemical and
Biomolecular Engineering, KAIST, 291
Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of
Korea
| | - Hyung-Jun Kwon
- Bionanotechnology Research Center and
Functional Biomaterial Research Center,
KRIBB, 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and
Research Institute of Bacterial Resistance, Yonsei
University College of Medicine, 50-1 Yonsei-ro,
Seodaemun-gu, Seoul 03722, Republic of Korea
| | - In-Chul Lee
- Bionanotechnology Research Center and
Functional Biomaterial Research Center,
KRIBB, 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic of Korea
| | - Hongki Kim
- Bionanotechnology Research Center and
Functional Biomaterial Research Center,
KRIBB, 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic of Korea
| | - Hyunju Kang
- Bionanotechnology Research Center and
Functional Biomaterial Research Center,
KRIBB, 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center and
Functional Biomaterial Research Center,
KRIBB, 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic of Korea
- Department of Nanobiotechnology,
KRIBB School of Biotechnology, UST,
217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of
Korea
| | - Kyu-Sun Lee
- Bionanotechnology Research Center and
Functional Biomaterial Research Center,
KRIBB, 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center and
Functional Biomaterial Research Center,
KRIBB, 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic of Korea
- Department of Nanobiotechnology,
KRIBB School of Biotechnology, UST,
217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of
Korea
| | - Hyun Gyu Park
- Department of Chemical and
Biomolecular Engineering, KAIST, 291
Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of
Korea
| | - Taejoon Kang
- Bionanotechnology Research Center and
Functional Biomaterial Research Center,
KRIBB, 125 Gwahak-ro, Yuseong-gu,
Daejeon 34141, Republic of Korea
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92
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Kim H, Lee S, Seo HW, Kang B, Moon J, Lee KG, Yong D, Kang H, Jung J, Lim EK, Jeong J, Park HG, Ryu CM, Kang T. Clustered Regularly Interspaced Short Palindromic Repeats-Mediated Surface-Enhanced Raman Scattering Assay for Multidrug-Resistant Bacteria. ACS NANO 2020; 14:17241-17253. [PMID: 33216524 DOI: 10.1021/acsnano.0c07264] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Antimicrobial resistance and multidrug resistance are slower-moving pandemics than the fast-spreading coronavirus disease 2019; however, they have potential to cause a much greater threat to global health. Here, we report a clustered regularly interspaced short palindromic repeats (CRISPR)-mediated surface-enhanced Raman scattering (SERS) assay for multidrug-resistant (MDR) bacteria. This assay was developed via a synergistic combination of the specific gene-recognition ability of the CRISPR system, superb sensitivity of SERS, and simple separation property of magnetic nanoparticles. This assay detects three multidrug-resistant (MDR) bacteria, species Staphylococcus aureus, Acinetobacter baumannii, and Klebsiella pneumoniae, without purification or gene amplification steps. Furthermore, MDR A. baumannii-infected mice were successfully diagnosed using the assay. Finally, we demonstrate the on-site capture and detection of MDR bacteria through a combination of the three-dimensional nanopillar array swab and CRISPR-mediated SERS assay. This method may prove effective for the accurate diagnosis of MDR bacterial pathogens, thus preventing severe infection by ensuring appropriate antibiotic treatment.
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Affiliation(s)
| | | | | | | | - Jeong Moon
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyoung G Lee
- Nanobio Application Team, National NanoFab Center (NNFC), 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | | | | | | | | | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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93
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Wang X, Shang X, Huang X. Next-generation pathogen diagnosis with CRISPR/Cas-based detection methods. Emerg Microbes Infect 2020; 9:1682-1691. [PMID: 32643563 PMCID: PMC7473117 DOI: 10.1080/22221751.2020.1793689] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 02/06/2023]
Abstract
Ideal methods for detecting pathogens should be sensitive, specific, rapid, cost-effective and instrument-free. Conventional nucleic acid pathogen detection strategies, mostly PCR-based techniques, have various limitations, such as expensive equipment, reagents and skilled performance. Recently, CRISPR/Cas-based methods have burst onto the scene, with the potential to power the pathogen detection field. Here we introduce these unique methods and discuss its hurdles and promises.
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Affiliation(s)
- Xinjie Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, People’s Republic of China
| | - Xiaoyun Shang
- Suzhou Maximum Bio-tech Co., Ltd., Suzhou, People’s Republic of China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, People’s Republic of China
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94
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Vatankhah M, Azizi A, Sanajouyan Langeroudi A, Ataei Azimi S, Khorsand I, Kerachian MA, Motaei J. CRISPR-based biosensing systems: a way to rapidly diagnose COVID-19. Crit Rev Clin Lab Sci 2020; 58:225-241. [PMID: 33245685 DOI: 10.1080/10408363.2020.1849010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The outbreak of the emerging SARS-CoV-2 virus has highlighted the challenges of detecting viral infections, especially in resource-limited settings. The SARS-CoV-2 virus transmission chain is interrupted when screening and diagnosis can be performed on a large scale by identifying asymptomatic or moderately symptomatic patients. Diagnosis of COVID-19 with reverse transcription polymerase chain reaction (RT-PCR) has been limited due to inadequate access to complex, expensive equipment and reagents, which has impeded efforts to reduce the spread of virus transmission. Recently, the development of several diagnostic platforms based on the CRISPR-Cas system has reduced the dependence on RT-PCR. The first CRISPR-based diagnostic test for SARS-CoV-2 was recently approved by the U.S. Food and Drug Administration. The biosensing systems have several important features that make them suitable for point-of-care tests, including the speed of design and synthesis of each platform in less than a few days, an assay time of 1-2 h, and the cost of materials and reagents less than one dollar per test. The HUDSON-SHERLOCK and STOPCovid biosensing systems, as field-deployable and rapid diagnostic tests, can detect low-copy viruses in body fluids without nucleic acid extraction and with minimal equipment. In addition, Cas13-based treatment strategies could potentially be an effective antiviral strategy for the prevention and treatment of emerging pandemic viruses such as SARS-CoV-2. In this review, we describe recent advances in CRISPR-based diagnostic platforms with an emphasis on their use in the rapid diagnosis and potential treatment of COVID-19.
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Affiliation(s)
- Majid Vatankhah
- Department of Anesthesiology, Critical Care and Pain Management Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Amir Azizi
- Department of Biology, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran
| | | | - Sajad Ataei Azimi
- Department of Internal Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Imaneh Khorsand
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Jamshid Motaei
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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95
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Cheng M, Xiong E, Tian T, Zhu D, Ju HQ, Zhou X. A CRISPR-driven colorimetric code platform for highly accurate telomerase activity assay. Biosens Bioelectron 2020; 172:112749. [PMID: 33160233 DOI: 10.1016/j.bios.2020.112749] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/20/2020] [Accepted: 10/19/2020] [Indexed: 12/26/2022]
Abstract
Telomeric repeat amplification protocol (TRAP) has been the most widely used method for assessing the telomerase activity from cells and tissues. However, cell lysates, body fluid samples, or tumor tissue samples often contain high concentrations of protein or other complex matrices, which are usually inhibiting the TRAP response, thus leading to false-negative results. Internal control (IC) involved TRAP enables reliable telomerase activity assay but requires time consuming and laborious electrophoretic separation to visualize telomeric repeat DNA and internal control products from TRAP reaction, severely limiting its application in clinical diagnosis. Herein, a colorimetric code system based on programmable CRISPR-Cas12a technology and gold nano-particles (AuNPs) probe has been developed to analyse telomeric repeat DNA and internal control in TRAP products, enabling the rapid detection of telomerase activity and identification of false-negatives with naked-eye. We transform the detection results into three typical colorimetric codes-positive (P), negative (N) and false-negative (FN), making the judgement of detection results more convenient and user-friendly. The platform has also been applied in accurate detection of clinical liver cancer specimens for telomerase activity with a detection sensitivity of 93.75% and a specificity of 93.75% based on Youden index analysis. As a proof of concept, we further demonstrated the feasibility of Cas9-mediated triple-line lateral flow assay (TL-LFA), which enabled the detection of telomeric repeat DNA and internal control on a single triple-line test strip, achieving convenient and accurate telomerase activity assay.
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Affiliation(s)
- Meng Cheng
- School of Life Science & College of Biophotonics, South China Normal University, Guangzhou, 510631, PR China
| | - Erhu Xiong
- School of Life Science & College of Biophotonics, South China Normal University, Guangzhou, 510631, PR China
| | - Tian Tian
- School of Life Science & College of Biophotonics, South China Normal University, Guangzhou, 510631, PR China
| | - Debin Zhu
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry, South China Normal University, Guangzhou, 510006, China
| | - Huai-Qiang Ju
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China.
| | - Xiaoming Zhou
- School of Life Science & College of Biophotonics, South China Normal University, Guangzhou, 510631, PR China.
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96
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Fernandez-Garcia L, Pacios O, González-Bardanca M, Blasco L, Bleriot I, Ambroa A, López M, Bou G, Tomás M. Viral Related Tools against SARS-CoV-2. Viruses 2020; 12:E1172. [PMID: 33081350 PMCID: PMC7589879 DOI: 10.3390/v12101172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
At the end of 2019, a new disease appeared and spread all over the world, the COVID-19, produced by the coronavirus SARS-CoV-2. As a consequence of this worldwide health crisis, the scientific community began to redirect their knowledge and resources to fight against it. Here we summarize the recent research on viruses employed as therapy and diagnostic of COVID-19: (i) viral-vector vaccines both in clinical trials and pre-clinical phases; (ii) the use of bacteriophages to find antibodies specific to this virus and some studies of how to use the bacteriophages themselves as a treatment against viral diseases; and finally, (iii) the use of CRISPR-Cas technology both to obtain a fast precise diagnose of the patient and also the possible use of this technology as a cure.
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Affiliation(s)
- Laura Fernandez-Garcia
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Olga Pacios
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Mónica González-Bardanca
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Lucia Blasco
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Inés Bleriot
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - Antón Ambroa
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - María López
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
| | - German Bou
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
- Spanish Network for the Research in Infectious Diseases (REIPI), 41071 Sevilla, Spain
| | - Maria Tomás
- Microbiology Department-Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), 15006 A Coruña, Spain; (L.F.-G.); (O.P.); (M.G.-B.); (L.B.); (I.B.); (A.A.); (M.L.); (G.B.)
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA) of Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), 28003 Madrid, Spain
- Spanish Network for the Research in Infectious Diseases (REIPI), 41071 Sevilla, Spain
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97
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van Dongen JE, Berendsen JTW, Steenbergen RDM, Wolthuis RMF, Eijkel JCT, Segerink LI. Point-of-care CRISPR/Cas nucleic acid detection: Recent advances, challenges and opportunities. Biosens Bioelectron 2020; 166:112445. [PMID: 32758911 PMCID: PMC7382963 DOI: 10.1016/j.bios.2020.112445] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/02/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022]
Abstract
With the trend of moving molecular tests from clinical laboratories to on-site testing, there is a need for nucleic acid based diagnostic tools combining the sensitivity, specificity and flexibility of established diagnostics with the ease, cost effectiveness and speed of isothermal amplification and detection methods. A promising new nucleic acid detection method is Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated nuclease (Cas)-based sensing. In this method Cas effector proteins are used as highly specific sequence recognition elements that can be combined with many different read-out methods for on-site point-of-care testing. This review covers the technical aspects of integrating CRISPR/Cas technology in miniaturized sensors for analysis on-site. We start with a short introduction to CRISPR/Cas systems and the different effector proteins and continue with reviewing the recent developments of integrating CRISPR sensing in miniaturized sensors for point-of-care applications. Finally, we discuss the challenges of point-of-care CRISPR sensing and describe future research perspectives.
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Affiliation(s)
- Jeanne E van Dongen
- BIOS Lab on a Chip group, Technical Medical Centre, MESA+ Institute for Nanotechnology, University of Twente, P.O. box 217, 7500, AE, Enschede, the Netherlands.
| | - Johanna T W Berendsen
- BIOS Lab on a Chip group, Technical Medical Centre, MESA+ Institute for Nanotechnology, University of Twente, P.O. box 217, 7500, AE, Enschede, the Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Rob M F Wolthuis
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Clinical Genetics, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands
| | - Jan C T Eijkel
- BIOS Lab on a Chip group, Technical Medical Centre, MESA+ Institute for Nanotechnology, University of Twente, P.O. box 217, 7500, AE, Enschede, the Netherlands
| | - Loes I Segerink
- BIOS Lab on a Chip group, Technical Medical Centre, MESA+ Institute for Nanotechnology, University of Twente, P.O. box 217, 7500, AE, Enschede, the Netherlands
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98
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Wang M, Zhang R, Li J. CRISPR/cas systems redefine nucleic acid detection: Principles and methods. Biosens Bioelectron 2020; 165:112430. [PMID: 32729545 PMCID: PMC7341063 DOI: 10.1016/j.bios.2020.112430] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
Methods that enable rapid, sensitive and specific analyses of nucleic acid sequences have positive effects on precise disease diagnostics and effective clinical treatments by providing direct insight into clinically relevant genetic information. Thus far, many CRISPR/Cas systems have been repurposed for diagnostic functions and are revolutionizing the accessibility of robust diagnostic tools due to their high flexibility, sensitivity and specificity. As RNA-guided targeted recognition effectors, Cas9 variants have been utilized for a variety of diagnostic applications, including biosensing assays, imaging assays and target enrichment for next-generation sequencing (NGS), thereby enabling the development of flexible and cost-effective tests. In addition, the ensuing discovery of Cas proteins (Cas12 and Cas13) with collateral cleavage activities has facilitated the development of numerous diagnostic tools for rapid and portable detection, and these tools have great potential for point-of-care settings. However, representative reviews proposed on this topic are mainly confined to classical biosensing applications; thus, a comprehensive and systematic description of this fast-developing field is required. In this review, based on the detection principle, we provide a detailed classification and comprehensive discussion of recent works that harness these CRISPR-based diagnostic tools from a new perspective. Furthermore, current challenges and future perspectives of CRISPR-based diagnostics are outlined.
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Affiliation(s)
- Meng Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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99
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Li H, Xing S, Xu J, He Y, Lai Y, Wang Y, Zhang G, Guo S, Deng M, Zeng M, Liu W. Aptamer-based CRISPR/Cas12a assay for the ultrasensitive detection of extracellular vesicle proteins. Talanta 2020; 221:121670. [PMID: 33076176 DOI: 10.1016/j.talanta.2020.121670] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/24/2020] [Accepted: 09/12/2020] [Indexed: 12/15/2022]
Abstract
Tumor-derived extracellular vesicles (TEVs) have emerged as promising sources of diagnostic and prognostic biomarkers for nasopharyngeal carcinoma (NPC). However, the lack of high-sensitivity analytic methods for ultratrace membrane proteins on TEVs hamper their clinical application of TEVs. Herein, by combining aptamers that specifically bind to protein targets on TEVs, PCR-based exponential amplification and CRISPR/Cas12a real-time DNA detection, we developed a novel technique, termed the aptamer-CRISPR/Cas12a assay, to detect CD109+ and EGFR+ TEVs from cell lines and complex biofluids. The platform enables highly sensitive detection of CD109+ and EGFR+ TEVs at as low as 100 particles/mL with a linear range spanning 6 orders of magnitude (102-108 particles/mL), which was found to be sufficient to effectively detect TEV proteins directly in low-volume (50 μl) samples. Furthermore, clinical serum sample analysis verified that the combination of serum CD109+ and EGFR+ TEV levels yielded high diagnostic accuracy, with an AUC of 0.934 (95% CI: 0.868-1.000), a sensitivity of 84.1% and a specificity of 85.0%, in discriminating NPC from healthy controls. Moreover, the dramatic decrease in both biomarkers in responders after radiotherapy indicated their potential roles in radiotherapy surveillance. Given that the aptamer-CRISPR/Cas12a assay rapidly and conveniently detects ultralow concentrations of CD109+ and EGFR+ TEVs directly in serum, it could be useful in NPC diagnosis and prognosis.
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Affiliation(s)
- Huilan Li
- Department of Clinical Laboratory, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, PR China
| | - Shan Xing
- Department of Clinical Laboratory, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, PR China
| | - Jianhua Xu
- Laboratory of Oncology Science and Molecular Biology, ShunDe Hospital of the Guangzhou University of Chinese Medicine, No. 12 Jinsha Avenue, Shunde District, Foshan, 528333, PR China
| | - Yi He
- Department of Clinical Laboratory, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, PR China
| | - Yanzhen Lai
- Department of Clinical Laboratory, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, PR China; Heyuan People's Hospital, Heyuan, China
| | - Yu Wang
- Department of Clinical Laboratory, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, PR China
| | - Ge Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, No. 132 Waihuandong Road, University Town, Guangzhou, 510006, PR China
| | - Songhe Guo
- School of Pharmaceutical Sciences, Sun Yat-sen University, No. 132 Waihuandong Road, University Town, Guangzhou, 510006, PR China
| | - Min Deng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, No. 78, Hengzhigang Road, Guangzhou, 510095, PR China.
| | - Musheng Zeng
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, PR China.
| | - Wanli Liu
- Department of Clinical Laboratory, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, Guangzhou, 510060, PR China.
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George JT, Azhar M, Aich M, Sinha D, Ambi UB, Maiti S, Chakraborty D, Srivatsan SG. Terminal Uridylyl Transferase Mediated Site-Directed Access to Clickable Chromatin Employing CRISPR-dCas9. J Am Chem Soc 2020; 142:13954-13965. [PMID: 32658470 PMCID: PMC7611130 DOI: 10.1021/jacs.0c06541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Locus-specific interrogation of target genes employing functional probes such as proteins and small molecules is paramount in decoding the molecular basis of gene function and designing tools to modulate its downstream effects. In this context, CRISPR-based gene editing and targeting technologies have proved tremendously useful, as they can be programmed to target any gene of interest by simply changing the sequence of the single guide RNA (sgRNA). Although these technologies are widely utilized in recruiting genetically encoded functional proteins, display of small molecules using CRISPR system is not well developed due to the lack of adequate techniques. Here, we have devised an innovative technology called sgRNA-Click (sgR-CLK) that harnesses the power of bioorthogonal click chemistry for remodeling guide RNA to display synthetic molecules on target genes. sgR-CLK employs a novel posttranscriptional chemoenzymatic labeling platform wherein a terminal uridylyl transferase (TUTase) was repurposed to generate clickable sgRNA of choice by site-specific tailoring of multiple azide-modified nucleotide analogues at the 3' end. The presence of a minimally invasive azide handle assured that the sgRNAs are indeed functional. Notably, an azide-tailed sgRNA targeting the telomeric repeat served as a Trojan horse on the CRISPR-dCas9 system to guide synthetic tags (biotin) site-specifically on chromatin employing copper-catalyzed or strain-promoted click reactions. Taken together, sgR-CLK presents a significant advancement on the utility of bioorthogonal chemistry, TUTase, and the CRISPR toolbox, which could offer a simplified solution for site-directed display of small molecule probes and diagnostic tools on target genes.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | | | | | | | - Uddhav B Ambi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Souvik Maiti
- Institute of Genomics and Integrative Biology (IGIB)-National Chemical Laboratory (NCL) Joint Center, Council of Scientific and Industrial Research-NCL, Pune 411008, India
| | | | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
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