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On-line Access: 2022-11-15

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 ORCID:

Zifang SHANG

https://orcid.org/0000-0001-9062-0999

Dongli MA

https://orcid.org/0000-0001-5299-6207

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Journal of Zhejiang University SCIENCE B

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Recent advances in the use of the CRISPR-Cas system for the detection of infectious pathogens


Author(s):  Hongdan GAO, Zifang SHANG, Siew Yin CHAN, Dongli MA

Affiliation(s):  Institute of Pediatrics, Shenzhen Children’s Hospital, Shenzhen 518026, China; more

Corresponding email(s):  madl1234@126.com

Key Words:  CRISPR-Cas; Diagnosis; Disease detection; Infectious disease; Pathogen


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Hongdan GAO, Zifang SHANG, Siew Yin CHAN, Dongli MA. Recent advances in the use of the CRISPR-Cas system for the detection of infectious pathogens[J]. Journal of Zhejiang University Science B, 2022, 23(1): 881-898.

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year="2022",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.B2200068"
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Abstract: 
Infectious diseases cause great economic loss and individual and even social anguish. Existing detection methods lack sensitivity and specificity, have a poor turnaround time, and are dependent on expensive equipment. In recent years, the clustered regularly interspaced short palindromic repeats (CRISPR)‍-CRISPR-associated protein (Cas) system has been widely used in the detection of pathogens that cause infectious diseases owing to its high specificity, sensitivity, and speed, and good accessibility. In this review, we discuss the discovery and development of the CRISPR-Cas system, summarize related analysis and interpretation methods, and discuss the existing applications of CRISPR-based detection of infectious pathogens using Cas proteins. We conclude the challenges and prospects of the CRISPR-Cas system in the detection of pathogens.

CRISPR-CAS系统检测传染病病原体的研究进展

高宏丹1,尚子方1,2,曾筱莹3,马东礼1
1深圳市儿童医院儿科研究所,中国深圳,518026
2中国科学院微生物研究所病原微生物学重点实验室,中国北京,100101
3西北工业大学柔性电子研究院,中国西安,710072
概要:感染性疾病对个人乃至社会均可造成极大的经济损失和精神痛苦。现有检测方法在灵敏度与特异性、检测时间、昂贵仪器设备依赖方面或多或少存在不足。成簇的规律间隔的短回文重复序列(CRISPR)-相关蛋白(Cas)系统,因其具备特异、灵敏、快速、便捷等优势,近年来被尝试应用于感染性疾病病原体的检测。本文首先回顾了CRISPR-Cas系统的发现发展进程,并列举可与之结合获得检测结果的检测结果阅读方式,之后从检测过程中所应用的不同Cas蛋白的角度简要描述了目前已有的基于CRISRP检测感染性疾病病原体的应用,最后还展望了CRISPR/Cas系统未来在检测方面的应用前景及挑战。

关键词组:CRISPR-Cas;诊断;疾病检测;传染病;病原体

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

[1]AbudayyehOO, GootenbergJS, KonermannS, et al., 2016. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science, 353(6299):aaf5573.

[2]AckermanCM, MyhrvoldC, ThakkuSG, et al., 2020. Massively multiplexed nucleic acid detection with Cas13. Nature, 582(7811):277-282.

[3]AliZ, AmanR, MahasA, et al., 2020. iSCAN: an RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2. Virus Res, 288:198129.

[4]AnantharamanV, MakarovaKS, BurroughsAM, et al., 2013. Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing. Biol Direct, 8:15.

[5]Aquino-JarquinG, 2019. CRISPR-Cas14 is now part of the artillery for gene editing and molecular diagnostic. Nanomedicine, 18:428-431.

[6]Arizti-SanzJ, FreijeCA, StantonAC, et al., 2020. Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2. Nat Commun, 11:5921.

[7]AumillerWM, CakmakFP, DavisBW, et al., 2016. RNA-based coacervates as a model for membraneless organelles: formation, properties, and interfacial liposome assembly. Langmuir, 32(39):10042-10053.

[8]BhattacharyyaRP, ThakkuSG, HungDT, 2018. Harnessing CRISPR effectors for infectious disease diagnostics. ACS Infect Dis, 4(9):1278-1282.

[9]BroughtonJP, DengXD, YuGX, et al., 2020. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol, 38(7):870-874.

[10]CaiQQ, WangR, QiaoZH, et al., 2021. Single-digit Salmonella detection with the naked eye using bio-barcode immunoassay coupled with recombinase polymerase amplification and a CRISPR-Cas12a system. Analyst, 146(17):5271-5279.

[11]ChangYF, DengY, LiTY, et al., 2020. Visual detection of porcine reproductive and respiratory syndrome virus using CRISPR-Cas13a. Transbound Emerg Dis, 67(2):564-571.

[12]ChenJS, MaEB, HarringtonLB, et al., 2018. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science, 360(6387):436-439.

[13]DaiYF, LiuCC, 2019. Recent advances on electrochemical biosensing strategies toward universal point-of-care systems. Angew Chem Int Ed Engl, 131(36):12483-12496.

[14]DaiYF, SomozaRA, WangL, et al., 2019. Exploring the trans-cleavage activity of CRISPR-Cas12a (cpf1) for the development of a universal electrochemical biosensor. Angew Chem Int Ed Engl, 131(48):17560-17566.

[15]DingX, YinK, LiZY, et al., 2020. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat Commun, 11:4711.

[16]East-SeletskyA, O'ConnellMR, KnightSC, et al., 2016. Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection. Nature, 538(7624):270-273.

[17]FozouniP, SonS, de León DerbyMD, et al., 2021. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell, 184(2):323-333.e9.

[18]GeXL, MengT, TanX, et al., 2021. Cas14a1-mediated nucleic acid detectifon platform for pathogens. Biosens Bioelectron, 189:113350.

[19]GootenbergJS, AbudayyehOO, LeeJW, et al., 2017. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science, 356(6336):438-442.

[20]GootenbergJS, AbudayyehOO, KellnerMJ, et al., 2018. Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. Science, 360(6387):439-444.

[21]GuoL, SunXH, WangXE, et al., 2020. SARS-CoV-2 detection with CRISPR diagnostics. Cell Discov, 6:34.

[22]HaftDH, SelengutJ, MongodinEF, et al., 2005. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol, 1(6):e60.

[23]HajianR, BalderstonS, TranT, et al., 2019. Detection of unamplified target genes via CRISPR-Cas9 immobilized on a graphene field-effect transistor. Nat Biomed Eng, 3(6):427-437.

[24]HammJN, ErdmannS, Eloe-FadroshEA, et al., 2019. Unexpected host dependency of Antarctic Nanohaloarchaeota. Proc Natl Acad Sci USA, 116(29):14661-14670.

[25]HarringtonLB, BursteinD, ChenJS, et al., 2018. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science, 362(6416):839-842.

[26]HeQ, YuDM, BaoMD, et al., 2020. High-throughput and all-solution phase African Swine Fever Virus (ASFV) detection using CRISPR-Cas12a and fluorescence based point-of-care system. Biosens Bioelectron, 154:112068.

[27]HouTY, ZengWQ, YangML, et al., 2020. Development and evaluation of a rapid CRISPR-based diagnostic for COVID-19. PLoS Pathog, 16(8):e1008705.

[28]HuangY, GuD, XueH, et al., 2021. Rapid and accurate Campylobacter jejuni detection with CRISPR-Cas12b based on newly identified Campylobacter jejuni-specific and -conserved genomic signatures. Front Microbiol, 12:649010.

[29]HwangH, HwangBY, BuenoJ, 2018. Biomarkers in infectious diseases. Dis Markers, 2018:8509127.

[30]HymanAA, WeberCA, JülicherF, 2014. Liquid-liquid phase separation in biology. Ann Rev Cell Dev Biol, 30:39-58.

[31]IshinoY, ShinagawaH, MakinoK, et al., 1987. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol, 169(12):5429-5433.

[32]IwaiK, WwhrsM, GarberM, et al., 2022. Scalable and automated CRISPR-based strain engineering using droplet microfluidics. Microsyst Nanoeng, 8:31.

[33]JansenR, van EmbdenJDA, GaastraW, et al., 2002. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol, 43(6):‍1565-1575.

[34]JoungJ, LadhaA, SaitoM, et al., 2020. Detection of SARS-CoV-2 with SHERLOCK one-pot testing. N Engl J Med, 383(15):1492-1494.

[35]KarvelisT, BigelyteG, YoungJK, et al., 2020. PAM recognition by miniature CRISPR-Cas12f nucleases triggers programmable double-stranded DNA target cleavage. Nucleic Acids Res, 48(9):5016-5023.

[36]KonermannS, LotfyP, BrideauNJ, et al., 2018. Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell, 173(3):665-676.e14.

[37]KooninEV, MakarovaKS, ZhangF, 2017. Diversity, classification and evolution of CRISPR-Cas systems. Curr Opin Microbiol, 37:67-78.

[38]KostyushevaA, BrezginS, BabinY, et al., 2022. CRISPR-Cas systems for diagnosing infectious diseases. Methods, 203:431-446.

[39]LeungRKK, ChengQX, WuZL, et al., 2022. CRISPR-Cas12-based nucleic acids detection systems. Methods, 203:276-281.

[40]LiF, YeQH, ChenMT, et al., 2021a. Cas12aFDet: a CRISPR/Cas12a-based fluorescence platform for sensitive and specific detection of Listeria monocytogenes serotype 4c. Anal Chim Acta, 1151:338248.

[41]LiF, YeQH, ChenMT, et al., 2021b. An ultrasensitive CRISPR/Cas12a based electrochemical biosensor for Listeria monocytogenes detection. Biosens Bioelectron, 179:‍113073.

[42]LiLX, LiSY, WuN, et al., 2019. HOLMESv2: a CRISPR-Cas12b-assisted platform for nucleic acid detection and DNA methylation quantitation. ACS Synth Biol, 8(10):2228-2237.

[43]LiSY, ChengQX, WangJM, et al., 2018a. CRISPR-Cas12a-assisted nucleic acid detection. Cell Discov, 4:20.

[44]LiSY, ChengQX, LiuJK, et al., 2018b. CRISPR-Cas12a has both cis- and trans-cleavage activities on single-stranded DNA. Cell Res, 28(4):491-493.

[45]LiuL, XuZH, AwaydaK, et al., 2022. Gold nanoparticle-labeled CRISPR-Cas13a assay for the sensitive solid-state nanopore molecular counting. Adv Mater Technol, 7(3):2101550.

[46]LiuXY, LinL, TangLC, et al., 2021. Lb2Cas12a and its engin

[47]eered variants mediate genome editing in human cells. FASEB J, 35(4):e21270.

[48]LiuYF, XuHP, LiuC, et al., 2019. CRISPR-Cas13a nanomachine based simple technology for avian influenza a (H7N9) virus on-site detection. J Biomed Nanotechnol, 15(4):790-798.

[49]LozanoR, NaghaviM, ForemanK, et al., 2012. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet, 380(9859):2095-2128.

[50]MaL, PengL, YinLJ, et al., 2021. CRISPR-Cas12a-powered dual-mode biosensor for ultrasensitive and cross-validating detection of pathogenic bacteria. ACS Sens, 6(8):2920-2927.

[51]MaL, YinLJ, LiXY, et al., 2022. A smartphone-based visual biosensor for CRISPR-Cas powered SARS-CoV-2 diagnostics. Biosens Bioelectron, 195:113646.

[52]MaQN, WangM, ZhengLB, et al., 2021. RAA-Cas12a-Tg: a nucleic acid detection system for Toxoplasma gondii based on CRISPR-Cas12a combined with recombinase-aided amplification (RAA). Microorganisms, 9(8):1644.

[53]MaffertP, ReverchonS, NasserW, et al., 2017. New nucleic acid testing devices to diagnose infectious diseases in resource-limited settings. Eur J Clin Microbiol Infect Dis, 36(10):1717-1731.

[54]MakarovaKS, WolfYI, AlkhnbashiOS, et al., 2015. An updated evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol, 13(11):722-736.

[55]MatthijsG, SoucheE, AldersM, et al., 2016. Guidelines for diagnostic next-generation sequencing. Eur J Hum Genet, 24(1):2-5.

[56]MohanrajuP, MakarovaKS, ZetscheB, et al., 2016. Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. Science, 353(6299):aad5147.

[57]MyhrvoldC, FreijeCA, GootenbergJS, et al., 2018. Field-deployable viral diagnostics using CRISPR-Cas13. Science, 360(6387):444-448.

[58]NguyenLT, SmithBM, JainPK, 2020. Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection. Nat Commun, 11:4906.

[59]O'ConnellMR, 2019. Molecular mechanisms of RNA targeting by Cas13-containing type VI CRISPR-Cas systems. J Mol Biol, 431(1):66-87.

[60]PardeeK, GreenAA, TakahashiMK, et al., 2016. Rapid, low-cost detection of Zika virus using programmable biomolecular components. Cell, 165(5):1255-1266.

[61]PauschP, Al-ShayebB, Bisom-RappE, et al., 2020. CRISPR-CasΦ from huge phages is a hypercompact genome editor. Science, 369(6501):333-337.

[62]QinPW, ParkM, AlfsonKJ, et al., 2019. Rapid and fully microfluidic ebola virus detection with CRISPR-Cas13a. ACS Sens, 4(4):1048-1054.

[63]SamIK, ChenYY, MaJ, et al., 2021. TB-QUICK: CRISPR-Cas12b-assisted rapid and sensitive detection of Mycobacterium tuberculosis. J Infect, 83(1):54-60.

[64]SanoT, SmithCL, CantorCR, 1992. Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates. Science, 258(5079):120-122.

[65]SchelerO, GlynnB, KurgA, 2014. Nucleic acid detection technologies and marker molecules in bacterial diagnostics. Expert Rev Mol Diagn, 14(4):489-500.

[66]SchnellC, 2019. Quantum imaging in biological samples. Nat Methods, 16(3):214.

[67]ShenJJ, ZhouXM, ShanYY, et al., 2020. Sensitive detection of a bacterial pathogen using allosteric probe-initiated catalysis and CRISPR-Cas13a amplification reaction. Nat Commun, 11:267.

[68]ShinodaH, TaguchiY, NakagawaR, et al., 2021. Amplification-free RNA detection with CRISPR-Cas13. Commun Biol, 4:476.

[69]ShmakovS, AbudayyehOO, MakarovaKS, et al., 2015. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol Cell, 60(3):385-397.

[70]SmargonAA, CoxDBT, PyzochaNK, et al., 2017. Cas13b is a type VI-B CRISPR-associated RNA-guided rnase differentially regulated by accessory proteins Csx27 and Csx28. Mol Cell, 65(4):618-630.e7.

[71]SunYY, YuL, LiuCX, et al., 2021. One-tube SARS-CoV-2 detection platform based on RT-RPA and CRISPR/Cas12a. J Transl Med, 19:74.

[72]TaylorSC, LaperriereG, GermainH, 2017. Droplet Digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data. Sci Rep, 7:2409.

[73]TengF, GuoL, CuiTT, et al., 2019. CDetection: CRISPR-Cas12b-based DNA detection with sub-attomolar sensitivity and single-base specificity. Genome Biol, 20:132.

[74]TernsMP, TernsRM, 2011. CRISPR-based adaptive immune systems. Curr Opin Microbiol, 14(3):321-327.

[75]TsouJH, LengQX, JiangF, 2019. A CRISPR test for detection of circulating nuclei acids. Transl Oncol, 12(12):1566-1573.

[76]WangB, WangR, WangDQ, et al., 2019. Cas12aVDet: a CRISPR/Cas12a-based platform for rapid and visual nucleic acid detection. Anal Chem, 91(19):12156-12161.

[77]WangR, QianCY, PangYN, et al., 2021. opvCRISPR: one-pot visual RT-LAMP-CRISPR platform for SARS-cov-2 detection. Biosens Bioelectron, 172:112766.

[78]WangS, LiH, KouZ, et al., 2021. Highly sensitive and specific detection of hepatitis B virus DNA and drug resistance mutations utilizing the PCR-based CRISPR-Cas13a system. Clin Microbiol Infect, 27(3):443-450.

[79]WangXJ, JiPP, FanHY, et al., 2020a. CRISPR/Cas12a technology combined with immunochromatographic strips for portable detection of African swine fever virus. Commun Biol, 3:62.

[80]WangXJ, ShangXY, HuangXX, 2020b. Next-generation pathogen diagnosis with CRISPR/Cas-based detection methods. Emerg Microbes Infect, 9(1):1682-1691.

[81]WangXJ, ZhongMT, LiuY, et al., 2020c. Rapid and sensitive detection of COVID-19 using CRISPR/Cas12a-based detection with naked eye readout, CRISPR/Cas12a-NER. Sci Bull, 65(17):1436-1439.

[82]WeiYD, TaoZZ, WanL, et al., 2022. Aptamer-based Cas14a1 biosensor for amplification-free live pathogenic detection. Biosens Bioelectron, 211:114282.

[83]WuJH, MukamaO, WuW, et al., 2020. A CRISPR/Cas12a based universal lateral flow biosensor for the sensitive and specific detection of African swine-fever viruses in whole blood. Biosensors, 10(12):203.

[84]WuYT, LiuSX, WangF, et al., 2019. Room temperature detection of plasma Epstein-Barr virus DNA with CRISPR-Cas13. Clin Chem, 65(4):591-592.

[85]XuW, JinT, DaiYF, et al., 2020. Surpassing the detection limit and accuracy of the electrochemical DNA sensor through the application of CRISPR Cas systems. Biosens Bioelectron, 155:112100.

[86]YanFC, WangW, ZhangJQ, 2019. CRISPR-Cas12 and Cas13: the lesser known siblings of CRISPR-Cas9. Cell Biol Toxicol, 35(6):489-492.

[87]YanWX, ChongSR, ZhangHB, et al., 2018. Cas13d is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL-domain-containing accessory protein. Mol Cell, 70(2):327-339.e5.

[88]YanWX, HunnewellP, AlfonseLE, et al., 2019. Functionally diverse type V CRISPR-Cas systems. Science, 363(6422):88-91.

[89]YouY, ZhangPP, WuGS, et al., 2021. Highly specific and sensitive detection of Yersinia pestis by portable Cas12a-UPTLFA platform. Front Microbiol, 12:700016.

[90]YuACH, VatcherG, YueX, et al., 2012. Nucleic acid-based diagnostics for infectious diseases in public health affairs. Front Med, 6(2):173-186.

[91]ZetscheB, GootenbergJS, AbudayyehOO, et al., 2015. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell, 163(3):759-771.

[92]ZhangF, AbudayyehOO, GootenbergJS, 2020. A protocol for detection of COVID-19 using CRISPR diagnostics. https://broad.io/sherlockprotocol

[93]ZhangYQ, ChenMY, LiuCR, et al., 2021. Sensitive and rapid on-site detection of SARS-CoV-2 using a gold nanoparticle-based high-throughput platform coupled with CRISPR/Cas12-assisted RT-LAMP. Sens Actuators B Chem, 345:130411.

[94]ZhaoYX, ChenF, LiQ, et al., 2015. Isothermal amplification of nucleic acids. Chem Rev, 115(22):‍12491-12545.

[95]ZhouJ, YinLJ, DongYN, et al., 2020. CRISPR-Cas13a based bacterial detection platform: sensing pathogen Staphylococcus aureus in food samples. Anal Chim Acta, 1127:225-233.

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