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Lou H, Wang X, Jiang Q, Li X, Yao Y, Chen Q, Chen L, Zhang S, Yu Y, Liu C, Zhou H. Clinical evaluation of a highly multiplexed CRISPR-based diagnostic assay for diagnosing lower respiratory tract infection: a prospective cohort study. Infect Dis (Lond) 2024:1-11. [PMID: 39264585 DOI: 10.1080/23744235.2024.2402921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/28/2024] [Accepted: 09/06/2024] [Indexed: 09/13/2024] Open
Abstract
OBJECTIVE Accurate and rapid identification of causative pathogens is essential to guide the clinical management of lower respiratory tract infections (LRTIs). Here we conducted a single-centre prospective study in 284 patients suspected of lower respiratory tract infections to evaluate the utility of a nucleic acid test based on highly multiplexed polymerase chain reaction (PCR) and CRISPR-Cas12a. METHODS We determined the analytical and diagnostic performance of the CRISPR assay using a combination of reference standards, including conventional microbiological tests (CMTs), metagenomic Next-Generation Sequencing (mNGS), and clinical adjudication by a panel of experts on infectious diseases and microbiology. RESULTS The CRISPR assay showed a higher detection rate (63.0%) than conventional microbiological tests (38.4%) and was lower than metagenomic Next-Generation Sequencing (72.9%). In detecting polymicrobial infections, the positivity rate of the CRISPR assay (19.4%) was higher than conventional microbiological tests (3.5%) and lower than metagenomic Next-Generation Sequencing (28.9%). The overall diagnostic sensitivity of the CRISPR assay (67.8%) was higher than conventional microbiological tests (41.8%), and lower than metagenomic Next-Generation Sequencing (93.2%). CONCLUSIONS Considering the low cost, ease of operation, short turnaround time, and broad range of pathogens detected in a single test, the CRISPR assay has the potential to be implemented as a screening tool for the aetiological diagnosis of lower respiratory tract infections patients, especially in cases where atypical bacteria or coinfections are suspected.
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Affiliation(s)
- Hui Lou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaojia Wang
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Qiuting Jiang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Li
- Department of Clinical Laboratory, Laboratory Medicine Center, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yake Yao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Linxing Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shanshan Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chao Liu
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, Zhejiang, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Kim J, Lee GH, Nam D, Park KS. Enhancing multiplex detection capabilities of the Cas12a/blocker DNA system. Talanta 2024; 281:126864. [PMID: 39270605 DOI: 10.1016/j.talanta.2024.126864] [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: 04/18/2024] [Revised: 08/27/2024] [Accepted: 09/08/2024] [Indexed: 09/15/2024]
Abstract
In the field of molecular diagnostics, the demand for multiplex detection, aimed at reducing overall analysis costs and streamlining procedures, is on the rise, prompting ongoing developments in various technologies. In this study, we developed a novel system, the split T7 promoter-based three-way junction-transcription, coupled with Cas12a/Blocker DNA (T3-CaB), for the multiplex detection of target nucleic acids. The T3-CaB system builds upon the foundation of the T3 system, generating numerous RNA transcripts upon encountering target nucleic acids. Subsequently, these RNA transcripts displace the blocker DNA from reporter DNA, allowing active Cas12a to engage in efficient trans-cleavage reaction on the reporter DNA, resulting in a strong fluorescence signal. Importantly, the proposed system operates at the isothermal condition (37 °C), with the entire analysis completed within 90 min. Further, the detection performance of the proposed system surpasses that of the preceding Cas12a/Blocker DNA system. Model targets, namely the 16S rRNA of Staphylococcus aureus and Escherichia coli, were selected, and a successful demonstration of multiplex detection was achieved. This technology holds promise for broadening the applicability of CRISPR/Cas-based diagnostics, especially in settings necessitating multiplex detection capabilities.
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Affiliation(s)
- Junhyeong Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Gun Haeng Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Daehan Nam
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea.
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3
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Feng Y, Yang J, He Z, Liu X, Ma C. CRISPR-Cas-based biosensors for the detection of cancer biomarkers. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39258950 DOI: 10.1039/d4ay01446d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Along with discovering cancer biomarkers, non-invasive detection methods have played a critical role in early cancer diagnosis and prognostic improvement. Some traditional detection methods have been used for detecting cancer biomarkers, but they are time-consuming and involve materials and human costs. With great flexibility, sensitivity and specificity, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated system provides a wide range of application prospects in this field. Herein, we introduce the background of the CRISPR-Cas (CRISPR-associated) system and comprehensively summarize the diagnosis strategies of cancer mediated by the CRISPR-Cas system, including four kinds of biochemical-based markers: nucleic acid, enzyme, tumor-specific protein and exosome. Furthermore, we discuss the challenges in implementing the CRISPR-Cas system in clinical applications.
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Affiliation(s)
- Yuxin Feng
- School of Life Sciences, Central South University, Changsha 410013, China.
- Clinical Medicine Eight-year Program, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Jinmeng Yang
- School of Life Sciences, Central South University, Changsha 410013, China.
- Clinical Medicine Eight-year Program, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Ziping He
- School of Life Sciences, Central South University, Changsha 410013, China.
- Clinical Medicine Eight-year Program, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Xinfa Liu
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China.
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4
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Nguyen GT, Schelling MA, Raju A, Buscher KA, Sritharan A, Sashital DG. CRISPR-Cas12a exhibits metal-dependent specificity switching. Nucleic Acids Res 2024; 52:9343-9359. [PMID: 39019776 PMCID: PMC11381342 DOI: 10.1093/nar/gkae613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/19/2024] Open
Abstract
Cas12a is the immune effector of type V-A CRISPR-Cas systems and has been co-opted for genome editing and other biotechnology tools. The specificity of Cas12a has been the subject of extensive investigation both in vitro and in genome editing experiments. However, in vitro studies have often been performed at high magnesium ion concentrations that are inconsistent with the free Mg2+ concentrations that would be present in cells. By profiling the specificity of Cas12a orthologs at a range of Mg2+ concentrations, we find that Cas12a switches its specificity depending on metal ion concentration. Lowering Mg2+ concentration decreases cleavage defects caused by seed mismatches, while increasing the defects caused by PAM-distal mismatches. We show that Cas12a can bind seed mutant targets more rapidly at low Mg2+ concentrations, resulting in faster cleavage. In contrast, PAM-distal mismatches cause substantial defects in cleavage following formation of the Cas12a-target complex at low Mg2+ concentrations. We observe differences in Cas12a specificity switching between three orthologs that results in variations in the routes of phage escape from Cas12a-mediated immunity. Overall, our results reveal the importance of physiological metal ion conditions on the specificity of Cas effectors that are used in different cellular environments.
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Affiliation(s)
- Giang T Nguyen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Michael A Schelling
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Akshara Raju
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Kathryn A Buscher
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Aneisha Sritharan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
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Testa U, Leone G, Cappellini MD. Therapeutic Gene Editing for Hemoglobinopathies. Mediterr J Hematol Infect Dis 2024; 16:e2024068. [PMID: 39258178 PMCID: PMC11385271 DOI: 10.4084/mjhid.2024.068] [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: 07/13/2024] [Accepted: 08/07/2024] [Indexed: 09/12/2024] Open
Abstract
In the last ten years, a consistent number of clinical studies have evaluated different gene approaches for the treatment of patients with sickle cell disease (SCD) and transfusion-dependent β-thalassemia (TDT). Initial studies of gene therapy for hemoglobinopathies involved the use of lentiviral vectors to add functional copies of the gene encoding β-globin in defective CD34 cells; more recently, gene editing techniques have been used involving either CRISPR-Cas9, transcription activation-like effector protein nuclease, zinc finger nuclease, and base editing to either induce fetal hemoglobin production at therapeutic levels or to genetically repair the underlying molecular defect causing the disease. Here, we review recent gene editing studies that have started the development of a new era in the treatment of hemoglobinopathies and, in general, monoallelic hereditary diseases.
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Affiliation(s)
- Ugo Testa
- Istituto Superiore Sanità, Roma, Italy
| | - Giuseppe Leone
- Department of Radiological and Hematological Sciences, Catholic University, Rome, Italy
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca' Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
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6
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Daskalakis V, Papapetros S. Engineering salt-tolerant Cas12f1 variants for gene-editing applications. J Biomol Struct Dyn 2024; 42:7421-7431. [PMID: 37526217 DOI: 10.1080/07391102.2023.2240418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
CRISPR has revolutionized the field of genome editing in life sciences by serving as a versatile and state-of-the-art tool. Cas12f1 is a small nuclease of the bacterial immunity CRISPR system with an ideal size for cellular delivery, in contrast to CRISPR-associated (Cas) proteins like Cas9 or Cas12. However, Cas12f1 works best at low salt concentrations. In this study, we find that the plasticity of certain Cas12f1 regions (K196-Y202 and I452-L515) is negatively affected by increased salt concentrations. On this line, key protein domains (REC1, WED, Nuc, lid) that are involved in the DNA-target recognition and the activation of the catalytic RuvC domain are in turn also affected. We suggest that salt concentration should be taken in to consideration for activity assessments of Cas engineered variants, especially if the mutations are on the protospacer adjacent motif interacting domain. The results can be exploited for the engineering of Cas variants and the assessment of their activity at varying salt concentrations. We propose that the K198Q mutation can restore at great degree the compromised plasticity and could potentially lead to salt-tolerant Cas12f1 variants. The methodology can be also employed for the study of biomolecules in terms of their salinity tolerance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, Limassol, Cyprus
| | - Spyridon Papapetros
- Department of Chemical Engineering, Cyprus University of Technology, Limassol, Cyprus
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7
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Abavisani M, Karbas Foroushan S, Khayami R, Sahebkar A. Mycobacterium tuberculosis Detection Using CRISPR Technology: An Updated Systematic Review and Meta-analysis. Mol Diagn Ther 2024:10.1007/s40291-024-00741-x. [PMID: 39212838 DOI: 10.1007/s40291-024-00741-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Rapid and precise detection of Mycobacterium tuberculosis (MTB) is paramount for effective management and control of tuberculosis. Clustered regularly interspaced short palindromic repeats (CRISPR) technology has emerged as a promising tool for pathogenic diagnosis owing to its specificity and adaptability. This systematic review and meta-analysis aimed to appraise the diagnostic accuracy of CRISPR-based techniques in identifying MTB. METHODS A meticulous search was conducted in Medline, Scopus, Embase, and ISI Web of Science to retrieve relevant studies, adhering to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Quality was assessed using the Joanna Briggs Institute checklist. Data synthesis and analyses, including subgroup analyses, were performed with R v 4.3.1, examining variables like CRISPR variants, gene targets, pre-amplification techniques, and signal readout methods. RESULTS From 389 identified studies, 14 met the inclusion criteria, encompassing 2175 MTB strains. The pooled sensitivity and specificity of CRISPR-based techniques were 0.93 (95% CI 0.85-0.99) and 0.97 (95% CI 0.94-0.99), respectively. The pooled diagnostic odds ratio was 273.4379 (95% CI 103.3311-723.5794), with an area under the curve of 0.97 for the summary receiver operating characteristic (SROC) curve, denoting excellent diagnostic accuracy. Subgroup analyses illustrated variations in diagnostic metrics based on factors like CRISPR variant utilized, target gene, and pre-amplification methods. For instance, CRISPR-Cas12 exhibited a sensitivity and specificity of 0.93 (95% CI 0.78-0.98) and 0.98 (95% CI 0.93-1), respectively. Moreover, this technology showed a sensitivity of 96% and specificity of 100% in detecting resistant MTB. CONCLUSION CRISPR-based methods exhibit substantial diagnostic sensitivity and specificity for detecting MTB, with notable variances across different CRISPR variants and methodological approaches. Further studies must be conducted to optimize CRISPR's potential as a diagnostic tool for MTB in a variety of clinical and research settings.
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Affiliation(s)
- Mohammad Abavisani
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Reza Khayami
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India.
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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8
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Yogi D, Ashok K, Anu CN, Shashikala T, Pradeep C, Bhargava CN, Parvathy MS, Jithesh MN, Manamohan M, Jha GK, Asokan R. CRISPR/Cas12a ribonucleoprotein mediated editing of tryptophan 2,3-dioxygenase of Spodoptera frugiperda. Transgenic Res 2024:10.1007/s11248-024-00406-9. [PMID: 39210187 DOI: 10.1007/s11248-024-00406-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
In insect genome editing CRISPR/Cas9 is predominantly employed, while the potential of several classes of Cas enzymes such as Cas12a largely remain untested. As opposed to Cas9 which requires a GC-rich protospacer adjacent motif (PAM), Cas12a requires a T-rich PAM and causes staggered cleavage in the target DNA, opening possibilities for multiplexing. In this regard, the utility of Cas12a has been shown in only a few insect species such as fruit flies and the silkworm, but not in non-model insects such as the fall armyworm, Spodoptera frugiperda, a globally important invasive pest that defies most of the current management methods. In this regard, a more recent genetic biocontrol method known as the precision-guided sterile insect technique (pgSIT) has shown successful implementation in Drosophila melanogaster, with certain thematic adaptations required for application in agricultural pests. However, before the development of a controllable gene drive for a non-model species, it is important to validate the activity of Cas12a in that species. In the current study we have, for the first time, demonstrated the potential of Cas12a by editing an eye color gene, tryptophan 2,3-dioxygenase (TO) of S. frugiperda by microinjecting ribonucleoprotein complex into pre-blastoderm (G0) eggs. Analysis of G0 mutants revealed that all five mutants (two male and three female) exhibited distinct edits consisting of both deletion and insertion events. All five edits were further validated through in silico modeling to understand the changes at the protein level and further corroborate with the range of eye-color phenotypes observed in the present study.
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Affiliation(s)
- Dhawane Yogi
- ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, 560089, India
- Jain University, Bengaluru, Karnataka, 560069, India
| | - Karuppannasamy Ashok
- ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, 560089, India.
- Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, 641003, India.
| | - Cholenahalli Narayanappa Anu
- ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, 560089, India
- University of Agricultural Sciences, Bengaluru, Karnataka, 560065, India
| | - Thalooru Shashikala
- ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, 560089, India
- University of Agricultural Sciences, Bengaluru, Karnataka, 560065, India
| | - Chalapathy Pradeep
- ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, 560089, India
- University of Agricultural Sciences, Bengaluru, Karnataka, 560065, India
| | - Chikmagalur Nagaraja Bhargava
- ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, 560089, India
- University of Agricultural Sciences, Bengaluru, Karnataka, 560065, India
| | - Madhusoodanan Sujatha Parvathy
- ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, 560089, India
- University of Agricultural Sciences, Bengaluru, Karnataka, 560065, India
| | - M N Jithesh
- Jain University, Bengaluru, Karnataka, 560069, India
| | | | - Girish Kumar Jha
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Ramasamy Asokan
- ICAR-Indian Institute of Horticultural Research, Bengaluru, Karnataka, 560089, India.
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9
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Lei W, Hao L, Qiu H, Bian K, Cui T, Zeng W, Zhang Y, Yang W, Zhang B. Quantum-Dot-Encoded Beads-Enhanced CRISPR/Cas-Based Lateral-Flow Assay for the Amplification-Free, Sensitive, and Rapid Detection of Nucleic Acids in Breast Cancer. ACS APPLIED MATERIALS & INTERFACES 2024; 16:44399-44408. [PMID: 39145508 DOI: 10.1021/acsami.4c05388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Nucleic acid detection plays a pivotal role in the accurate diagnosis of diseases. The CRISPR/Cas detection system, noted for its significant utility in a variety of applications, often necessitates enhanced sensitivity or specific signal amplification strategies, particularly for detecting low-abundance biomarkers. In this study, we present a quantum-dot-encoded beads (QDB)-energized CRISPR/Cas12-based lateral-flow assay (QDB-CRISPR-LFA). This method enables amplification-free, sensitive, and rapid detection (<40 min) of BRCA-1. We validated our method using contrived reference samples and nucleic acids extracted from tumor cells. The QDB-CRISPR-LFA provides a visual, more rapid alternative to the traditional BRCA-1 real-time RT-PCR assay. Significantly, through the integration of CRISPR's specificity and the high signal output of QDB, the detection threshold for BRCA-1 has been reduced to the femtomolar level, representing an enhancement of 2-4 orders of magnitude over existing CRISPR/Cas detection methods. This advancement underscores the potential of our approach in advancing nucleic acid detection techniques, which is crucial for the early and precise diagnosis of diseases.
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Affiliation(s)
- Wenjing Lei
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Liangwen Hao
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Han Qiu
- Galactophore Department, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou 434200, China
| | - Kexin Bian
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Tianming Cui
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Weiwei Zeng
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Yu Zhang
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Weitao Yang
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
| | - Bingbo Zhang
- Department of Radiology, Tongji Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, The Institute for Biomedical Engineering &Nano Science, School of Medicine, Tongji University, Shanghai 200065, China
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10
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Rahimi S, Balusamy SR, Perumalsamy H, Ståhlberg A, Mijakovic I. CRISPR-Cas target recognition for sensing viral and cancer biomarkers. Nucleic Acids Res 2024:gkae736. [PMID: 39189452 DOI: 10.1093/nar/gkae736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/08/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024] Open
Abstract
Nucleic acid-based diagnostics is a promising venue for detection of pathogens causing infectious diseases and mutations related to cancer. However, this type of diagnostics still faces certain challenges, and there is a need for more robust, simple and cost-effective methods. Clustered regularly interspaced short palindromic repeats (CRISPRs), the adaptive immune systems present in the prokaryotes, has recently been developed for specific detection of nucleic acids. In this review, structural and functional differences of CRISPR-Cas proteins Cas9, Cas12 and Cas13 are outlined. Thereafter, recent reports about applications of these Cas proteins for detection of viral genomes and cancer biomarkers are discussed. Further, we highlight the challenges associated with using these technologies to replace the current diagnostic approaches and outline the points that need to be considered for designing an ideal Cas-based detection system for nucleic acids.
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Affiliation(s)
- Shadi Rahimi
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Sri Renukadevi Balusamy
- Department of Food Science and Biotechnology, Sejong University, Gwangjin-gu, Seoul, Republic of Korea
| | - Haribalan Perumalsamy
- Center for Creative Convergence Education, Hanyang University, Seoul 04763, Republic of Korea
- Research Institute for Convergence of Basic Science, Hanyang University, Seoul 04763, South Korea
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Ivan Mijakovic
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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11
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Xu P, Saito M, Faure G, Maguire S, Chau-Duy-Tam Vo S, Wilkinson ME, Kuang H, Wang B, Rice WJ, Macrae RK, Zhang F. Structural insights into the diversity and DNA cleavage mechanism of Fanzor. Cell 2024:S0092-8674(24)00844-4. [PMID: 39208796 DOI: 10.1016/j.cell.2024.07.050] [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: 03/13/2024] [Revised: 05/19/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
Fanzor (Fz) is an ωRNA-guided endonuclease extensively found throughout the eukaryotic domain with unique gene editing potential. Here, we describe the structures of Fzs from three different organisms. We find that Fzs share a common ωRNA interaction interface, regardless of the length of the ωRNA, which varies considerably across species. The analysis also reveals Fz's mode of DNA recognition and unwinding capabilities as well as the presence of a non-canonical catalytic site. The structures demonstrate how protein conformations of Fz shift to allow the binding of double-stranded DNA to the active site within the R-loop. Mechanistically, examination of structures in different states shows that the conformation of the lid loop on the RuvC domain is controlled by the formation of the guide/DNA heteroduplex, regulating the activation of nuclease and DNA double-stranded displacement at the single cleavage site. Our findings clarify the mechanism of Fz, establishing a foundation for engineering efforts.
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Affiliation(s)
- Peiyu Xu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Makoto Saito
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Samantha Maguire
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Samuel Chau-Duy-Tam Vo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Max E Wilkinson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Huihui Kuang
- Cryo-Electron Microscopy Core, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - William J Rice
- Cryo-Electron Microscopy Core, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Rhiannon K Macrae
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
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12
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Jung H, Inaba Y, Banta S. CRISPR/dCas12a knock-down of Acidithiobacillus ferrooxidans electron transport chain bc 1 complexes enables enhanced metal sulfide bioleaching. J Biol Chem 2024:107703. [PMID: 39173952 DOI: 10.1016/j.jbc.2024.107703] [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: 07/06/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024] Open
Abstract
Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotroph that plays an important role in biogeochemical iron and sulfur cycling and is a member of the consortia used in industrial hydrometallurgical processing of copper. Metal sulfide bioleaching is catalyzed by the regeneration of ferric iron, however, bioleaching of chalcopyrite, the dominant unmined form of copper on Earth, is inhibited by surface passivation. Here, we report the implementation of CRISPR interference (CRISPRi) using the catalytically inactive Cas12a (dCas12a) in A. ferrooxidans to knockdown the expression of genes in the petI and petII operons. These operons encode bc1 complex proteins and knockdown of these genes enabled the manipulation (enhancement or repression) of iron oxidation. The petB2 gene knockdown strain enhanced iron oxidation, leading to enhanced pyrite and chalcopyrite oxidation, which correlated with reduced biofilm formation and decreased surface passivation of the minerals. These findings highlight the utility of CRISPRi/dCas12a technology for engineering A. ferrooxidans while unveiling a new strategy to manipulate and improve bioleaching efficiency.
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Affiliation(s)
- Heejung Jung
- Department of Chemical Engineering, Columbia University, New York, New York
| | - Yuta Inaba
- Department of Chemical Engineering, Columbia University, New York, New York
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, New York.
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13
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Lawrenson T, Clarke M, Kirby R, Forner M, Steuernagel B, Brown JKM, Harwood W. An optimised CRISPR Cas9 and Cas12a mutagenesis toolkit for Barley and Wheat. PLANT METHODS 2024; 20:123. [PMID: 39138524 PMCID: PMC11321142 DOI: 10.1186/s13007-024-01234-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 07/08/2024] [Indexed: 08/15/2024]
Abstract
BACKGROUND CRISPR Cas9 and Cas12a are the two most frequently used programmable nucleases reported in plant systems. There is now a wide range of component parts for both which likely have varying degrees of effectiveness and potentially applicability to different species. Our aim was to develop and optimise Cas9 and Cas12a based systems for highly efficient genome editing in the monocotyledons barley and wheat and produce a user-friendly toolbox facilitating simplex and multiplex editing in the cereal community. RESULTS We identified a Zea mays codon optimised Cas9 with 13 introns in conjunction with arrayed guides driven by U6 and U3 promoters as the best performer in barley where 100% of T0 plants were simultaneously edited in all three target genes. When this system was used in wheat > 90% of T0 plants were edited in all three subgenome targets. For Cas12a, an Arabidopsis codon optimised sequence with 8 introns gave the best editing efficiency in barley when combined with a tRNA based multiguide array, resulting in 90% mutant alleles in three simultaneously targeted genes. When we applied this Cas12a system in wheat 86% & 93% of T0 plants were mutated in two genes simultaneously targeted. We show that not all introns contribute equally to enhanced mutagenesis when inserted into a Cas12a coding sequence and that there is rationale for including multiple introns. We also show that the combined effect of two features which boost Cas12a mutagenesis efficiency (D156R mutation and introns) is more than the sum of the features applied separately. CONCLUSION Based on the results of our testing, we describe and provide a GoldenGate modular cloning system for Cas9 and Cas12a use in barley and wheat. Proven Cas nuclease and guide expression cassette options found in the toolkit will facilitate highly efficient simplex and multiplex mutagenesis in both species. We incorporate GRF-GIF transformation boosting cassettes in wheat options to maximise workflow efficiency.
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Affiliation(s)
- Tom Lawrenson
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Martha Clarke
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rachel Kirby
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Macarena Forner
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - James K M Brown
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wendy Harwood
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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14
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Roth GV, Gengaro IR, Qi LS. Precision epigenetic editing: Technological advances, enduring challenges, and therapeutic applications. Cell Chem Biol 2024:S2451-9456(24)00309-X. [PMID: 39137782 DOI: 10.1016/j.chembiol.2024.07.007] [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: 03/04/2024] [Revised: 05/31/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024]
Abstract
The epigenome is a complex framework through which gene expression is precisely and flexibly modulated to incorporate heritable memory and responses to environmental stimuli. It governs diverse cellular processes, including cell fate, disease, and aging. The need to understand this system and precisely control gene expression outputs for therapeutic purposes has precipitated the development of a diverse set of epigenetic editing tools. Here, we review the existing toolbox for targeted epigenetic editing, technical considerations of the current technologies, and opportunities for future development. We describe applications of therapeutic epigenetic editing and their potential for treating disease, with a discussion of ongoing delivery challenges that impede certain clinical interventions, particularly in the brain. With simultaneous advancements in available engineering tools and appropriate delivery technologies, we predict that epigenetic editing will increasingly cement itself as a powerful approach for safely treating a wide range of disorders in all tissues of the body.
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Affiliation(s)
- Goldie V Roth
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Isabella R Gengaro
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Lei S Qi
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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15
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Ou X, Li K, Liu M, Song J, Zuo Z, Guo Y. EXPAR for biosensing: recent developments and applications. Analyst 2024; 149:4135-4157. [PMID: 39034763 DOI: 10.1039/d4an00609g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Emerging as a promising novel amplification technique, the exponential amplification reaction (EXPAR) offers significant advantages due to its potent exponential amplification capability, straightforward reaction design, rapid reaction kinetics, and isothermal operation. The past few years have witnessed swift advancements and refinements in EXPAR-based technologies, with numerous high-performance biosensing systems documented. A deeper understanding of the EXPAR mechanism has facilitated the proposal of novel strategies to overcome limitations inherent to traditional EXPAR. Furthermore, the synergistic integration of EXPAR with diverse amplification methodologies, including the use of a CRISPR/Cas system, metal nanoparticles, aptamers, alternative isothermal amplification techniques, and enzymes, has significantly bolstered analytical efficacy, aiming to enhance specificity, sensitivity, and amplification efficiency. This comprehensive review presents a detailed exposition of the EXPAR mechanism and analyzes its primary challenges. Additionally, we summarize the latest research advancements in the biomedical field concerning the integration of EXPAR with diverse amplification technologies for sensing strategies. Finally, we discuss the challenges and future prospects of EXPAR technology in the realms of biosensing and clinical applications.
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Affiliation(s)
- Xinyi Ou
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
| | - Kunxiang Li
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
| | - Miao Liu
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
| | - Jiajun Song
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
| | - Zhihua Zuo
- Department of Clinical Laboratory, Nanchong Central Hospital, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, Sichuan, 637003, PR China.
| | - Yongcan Guo
- Nanobiosensing and Microfluidic Point-of-Care Testing, Key Laboratory of Luzhou, Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, PR China.
- Department of Laboratory Medicine, The Affiliated Hospital, Southwest Medical University, PR China
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16
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Elliott K, Veley KM, Jensen G, Gilbert KB, Norton J, Kambic L, Yoder M, Weil A, Motomura-Wages S, Bart RS. CRISPR/Cas9-generated mutations in a sugar transporter gene reduce cassava susceptibility to bacterial blight. PLANT PHYSIOLOGY 2024; 195:2566-2578. [PMID: 38701041 PMCID: PMC11288762 DOI: 10.1093/plphys/kiae243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/05/2024]
Abstract
Bacteria from the genus Xanthomonas are prolific phytopathogens that elicit disease in over 400 plant species. Xanthomonads carry a repertoire of specialized proteins called transcription activator-like (TAL) effectors that promote disease and pathogen virulence by inducing the expression of host susceptibility (S) genes. Xanthomonas phaseoli pv. manihotis (Xpm) causes bacterial blight on the staple food crop cassava (Manihot esculenta Crantz). The Xpm effector TAL20 induces ectopic expression of the S gene Manihot esculenta Sugars Will Eventually be Exported Transporter 10a (MeSWEET10a), which encodes a sugar transporter that contributes to cassava bacterial blight (CBB) susceptibility. We used CRISPR/Cas9 to generate multiple cassava lines with edits to the MeSWEET10a TAL20 effector binding site and/or coding sequence. In several of the regenerated lines, MeSWEET10a expression was no longer induced by Xpm, and in these cases, we observed reduced CBB disease symptoms post Xpm infection. Because MeSWEET10a is expressed in cassava flowers, we further characterized the reproductive capability of the MeSWEET10a promoter and coding sequence mutants. Lines were crossed to themselves and to wild-type plants. The results indicated that expression of MeSWEET10a in female, but not male, flowers is critical to produce viable F1 seed. In the case of promoter mutations that left the coding sequence intact, viable F1 progeny were recovered. Taken together, these results demonstrate that blocking MeSWEET10a induction is a viable strategy for decreasing cassava susceptibility to CBB and that ideal lines will contain promoter mutations that block TAL effector binding while leaving endogenous expression of MeSWEET10a unaltered.
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Affiliation(s)
- Kiona Elliott
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
- Division of Biological and Biomedical Sciences, Washington University in Saint Louis, St. Louis, MO 63110, USA
| | - Kira M Veley
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Greg Jensen
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | | | - Joanna Norton
- College of Tropical Agriculture & Human Resources, University of Hawaii at Manoa, Hilo, HI 96720, USA
| | - Lukas Kambic
- College of Tropical Agriculture & Human Resources, University of Hawaii at Manoa, Hilo, HI 96720, USA
| | - Marisa Yoder
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Alex Weil
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Sharon Motomura-Wages
- College of Tropical Agriculture & Human Resources, University of Hawaii at Manoa, Hilo, HI 96720, USA
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
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17
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Hu K, Yin W, Bai Y, Zhang J, Yin J, Zhu Q, Mu Y. CRISPR-Based Biosensors for Medical Diagnosis: Readout from Detector-Dependence Detection Toward Naked Eye Detection. BIOSENSORS 2024; 14:367. [PMID: 39194596 DOI: 10.3390/bios14080367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/22/2024] [Accepted: 07/26/2024] [Indexed: 08/29/2024]
Abstract
The detection of biomarkers (such as DNA, RNA, and protein) plays a vital role in medical diagnosis. The CRISPR-based biosensors utilize the CRISPR/Cas system for biometric recognition of targets and use biosensor strategy to read out biological signals without the employment of professional operations. Consequently, the CRISPR-based biosensors demonstrate great potential for the detection of biomarkers with high sensitivity and specificity. However, the signal readout still relies on specialized detectors, limiting its application in on-site detection for medical diagnosis. In this review, we summarize the principles and advances of the CRISPR-based biosensors with a focus on medical diagnosis. Then, we review the advantages and progress of CRISPR-based naked eye biosensors, which can realize diagnosis without additional detectors for signal readout. Finally, we discuss the challenges and further prospects for the development of CRISPR-based biosensors.
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Affiliation(s)
- Kai Hu
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
| | - Weihong Yin
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
| | - Yunhan Bai
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
| | - Jiarui Zhang
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
| | - Juxin Yin
- Academy of Edge Intelligence, Hangzhou City University, Hangzhou 310015, China
| | - Qiangyuan Zhu
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
| | - Ying Mu
- State Key Laboratory of Industrial Control Technology, Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, Zhejiang University, Hangzhou 310027, China
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18
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Ye X, Wu H, Liu J, Xiang J, Feng Y, Liu Q. One-pot diagnostic methods based on CRISPR/Cas and Argonaute nucleases: strategies and perspectives. Trends Biotechnol 2024:S0167-7799(24)00156-2. [PMID: 39034177 DOI: 10.1016/j.tibtech.2024.06.009] [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: 02/28/2024] [Revised: 05/27/2024] [Accepted: 06/18/2024] [Indexed: 07/23/2024]
Abstract
CRISPR/Cas and Argonaute (Ago) proteins, which target specific nucleic acid sequences, can be applied as diagnostic tools. Despite high specificity and efficiency, achieving sensitive detection often necessitates a preamplification step that involves opening the lid and multistep operation, which may elevate the risk of contamination and prove inadequate for point-of-care testing. Hence, various one-pot detection strategies have been developed that enable preamplification and sensing in a single operation. We outline the challenges of one-pot detection with Cas and Ago proteins, present several main implementation strategies, and discuss future prospects. This review offers comprehensive insights into this vital field and explores potential improvements to detection methods that will be beneficial for human health.
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Affiliation(s)
- Xingyu Ye
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haoyang Wu
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinghan Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiayi Xiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Qian Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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19
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Chen Y, Yan B, Chen W, Zhang X, Liu Z, Zhang Q, Li L, Hu M, Zhao X, Xu X, Lv Q, Luo Y, Cai Y, Liu Y. Development of the CRISPR-Cas12a system for editing of Pseudomonas aeruginosa phages. iScience 2024; 27:110210. [PMID: 39055914 PMCID: PMC11269290 DOI: 10.1016/j.isci.2024.110210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/26/2024] [Accepted: 06/04/2024] [Indexed: 07/28/2024] Open
Abstract
Pseudomonas aeruginosa is a common opportunistic pathogen. The potential efficacy of phage therapy has attracted the attention of researchers, but efficient gene-editing tools are lacking, limiting the study of their biological properties. Here, we designed a type V CRISPR-Cas12a system for the gene editing of P. aeruginosa phages. We first evaluated the active cutting function of the CRISPR-Cas12a system in vitro and discovered that it had a higher gene-cutting efficiency than the type II CRISPR-Cas9 system in three different P. aeruginosa phages. We also demonstrated the system's ability to precisely edit genes in Escherichia coli phages, Salmonella phages, and P. aeruginosa phages. Using the aforementioned strategies, non-essential P. aeruginosa phage genes can be efficiently deleted, resulting in a reduction of up to 5,215 bp (7.05%). Our study has provided a rapid, efficient, and time-saving tool that accelerates progress in phage engineering.
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Affiliation(s)
- Yibao Chen
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
- Shandong Vamph Animal Health Products Co., LTD, Jinan, China
| | - Bingjie Yan
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Weizhong Chen
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xue Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Zhengjie Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Qing Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Lulu Li
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Ming Hu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
- Shandong Vamph Animal Health Products Co., LTD, Jinan, China
| | - Xiaonan Zhao
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Xiaohui Xu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Qianghua Lv
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Yanbo Luo
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
| | - Yumei Cai
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Yuqing Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
- China-UK Joint Laboratory of Bacteriophage Engineering, Jinan, China
- Shandong Vamph Animal Health Products Co., LTD, Jinan, China
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20
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Zhou J, Pan Q, Xue Y, Dong Y, Chen Y, Huang L, Zhang B, Liu ZQ, Zheng Y. Synthetic biology for Monascus: From strain breeding to industrial production. Biotechnol J 2024; 19:e2400180. [PMID: 39014924 DOI: 10.1002/biot.202400180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/25/2024] [Accepted: 06/29/2024] [Indexed: 07/18/2024]
Abstract
Traditional Chinese food therapies often motivate the development of modern medicines, and learning from them will bring bright prospects. Monascus, a conventional Chinese fungus with centuries of use in the food industry, produces various metabolites, including natural pigments, lipid-lowering substances, and other bioactive ingredients. Recent Monascus studies focused on the metabolite biosynthesis mechanisms, strain modifications, and fermentation process optimizations, significantly advancing Monascus development on a lab scale. However, the advanced manufacture for Monascus is lacking, restricting its scale production. Here, the synthetic biology techniques and their challenges for engineering filamentous fungi were summarized, especially for Monascus. With further in-depth discussions of automatic solid-state fermentation manufacturing and prospects for combining synthetic biology and process intensification, the industrial scale production of Monascus will succeed with the help of Monascus improvement and intelligent fermentation control, promoting Monascus applications in food, cosmetic, agriculture, medicine, and environmental protection industries.
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Affiliation(s)
- Junping Zhou
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Qilu Pan
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yinan Xue
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yaping Dong
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yihong Chen
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Lianggang Huang
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Bo Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yuguo Zheng
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
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21
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Madugula SS, Pujar P, Nammi B, Wang S, Jayasinghe-Arachchige VM, Pham T, Mashburn D, Artiles M, Liu J. Identification of Family-Specific Features in Cas9 and Cas12 Proteins: A Machine Learning Approach Using Complete Protein Feature Spectrum. J Chem Inf Model 2024; 64:4897-4911. [PMID: 38838358 DOI: 10.1021/acs.jcim.4c00625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
The recent development of CRISPR-Cas technology holds promise to correct gene-level defects for genetic diseases. The key element of the CRISPR-Cas system is the Cas protein, a nuclease that can edit the gene of interest assisted by guide RNA. However, these Cas proteins suffer from inherent limitations such as large size, low cleavage efficiency, and off-target effects, hindering their widespread application as a gene editing tool. Therefore, there is a need to identify novel Cas proteins with improved editing properties, for which it is necessary to understand the underlying features governing the Cas families. In this study, we aim to elucidate the unique protein features associated with Cas9 and Cas12 families and identify the features distinguishing each family from non-Cas proteins. Here, we built Random Forest (RF) binary classifiers to distinguish Cas12 and Cas9 proteins from non-Cas proteins, respectively, using the complete protein feature spectrum (13,494 features) encoding various physiochemical, topological, constitutional, and coevolutionary information on Cas proteins. Furthermore, we built multiclass RF classifiers differentiating Cas9, Cas12, and non-Cas proteins. All the models were evaluated rigorously on the test and independent data sets. The Cas12 and Cas9 binary models achieved a high overall accuracy of 92% and 95% on their respective independent data sets, while the multiclass classifier achieved an F1 score of close to 0.98. We observed that Quasi-Sequence-Order (QSO) descriptors like Schneider.lag and Composition descriptors like charge, volume, and polarizability are predominant in the Cas12 family. Conversely Amino Acid Composition descriptors, especially Tripeptide Composition (TPC), predominate the Cas9 family. Four of the top 10 descriptors identified in Cas9 classification are tripeptides PWN, PYY, HHA, and DHI, which are seen to be conserved across all Cas9 proteins and located within different catalytically important domains of the Streptococcus pyogenes Cas9 (SpCas9) structure. Among these, DHI and HHA are well-known to be involved in the DNA cleavage activity of the SpCas9 protein. Mutation studies have highlighted the significance of the PWN tripeptide in PAM recognition and DNA cleavage activity of SpCas9, while Y450 from the PYY tripeptide plays a crucial role in reducing off-target effects and improving the specificity in SpCas9. Leveraging our machine learning (ML) pipeline, we identified numerous Cas9 and Cas12 family-specific features. These features offer valuable insights for future experimental and computational studies aiming at designing Cas systems with enhanced gene-editing properties. These features suggest plausible structural modifications that can effectively guide the development of Cas proteins with improved editing capabilities.
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Affiliation(s)
- Sita Sirisha Madugula
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
| | - Pranav Pujar
- Department of Industrial, Manufacturing and Systems Engineering, University of Texas at Arlington, 701 South Nedderman Drive, Arlington, Texas 76019, United States
| | - Bharani Nammi
- Department of Industrial, Manufacturing and Systems Engineering, University of Texas at Arlington, 701 South Nedderman Drive, Arlington, Texas 76019, United States
| | - Shouyi Wang
- Department of Industrial, Manufacturing and Systems Engineering, University of Texas at Arlington, 701 South Nedderman Drive, Arlington, Texas 76019, United States
| | - Vindi M Jayasinghe-Arachchige
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
| | - Tyler Pham
- School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
| | - Dominic Mashburn
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
| | - Maria Artiles
- School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
- School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, Texas 76107, United States
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22
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Wei C, Lei X, Yu S. Multiplexed Detection Strategies for Biosensors Based on the CRISPR-Cas System. ACS Synth Biol 2024; 13:1633-1646. [PMID: 38860462 DOI: 10.1021/acssynbio.4c00161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
A growing number of applications require simultaneous detection of multiplexed nucleic acid targets in a single reaction, which enables higher information density in combination with reduced assay time and cost. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-Cas system have broad applications for the detection of nucleic acids due to their strong specificity, high sensitivity, and excellent programmability. However, realizing multiplexed detection is still challenging for the CRISPR-Cas system due to the nonspecific collateral cleavage activity, limited signal reporting strategies, and possible cross-reactions. In this review, we summarize the principles, strategies, and features of multiplexed detection based on the CRISPR-Cas system and further discuss the challenges and perspective.
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Affiliation(s)
- Cong Wei
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Xueying Lei
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
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23
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Liu Z, Liu H, Huang C, Zhou Q, Luo Y. Hybrid Cas12a Variants with Relaxed PAM Requirements Expand Genome Editing Compatibility. ACS Synth Biol 2024; 13:1809-1819. [PMID: 38819403 DOI: 10.1021/acssynbio.4c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Cas12a is a widely used programmable nuclease for genome editing across a variety of organisms, but its application is limited by its PAM recognition restriction. To alleviate these PAM constraints, protein engineering efforts have been applied to expand the PAM recognition range. In this study, we designed and constructed 990 synthetic hybrid Cas12a chimeras through domain shuffling and screened an efficient hybrid Cas12a (ehCas12a) that could recognize a broad range PAM of 5'-TYYN-3' (Y is T or C and N is A, T, C, or G). Furthermore, we constructed an ehCas12a variant, ehCas12a RRVR (T167R/N572R/K578V/N582R), with expanded PAM preference to 5'-TNYN, TWRV-3' (W is A or T, R is A or G, and V is A, C, or G), which can efficiently recognize -2* A/G PAMs that are barely recognized by Cas12a-type proteins and their mutants. Finally, we demonstrated that the DNase-inactivated ehCas12a RRVR base editor (dehCas12a RRVR-BE) was capable of targeting noncanonical PAMs in vivo and disease-related loci for potential therapeutic applications. Overall, our findings highlight the modular design and reconfiguration of Cas proteins for enhanced functionality.
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Affiliation(s)
- Zhenyu Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Huayi Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Chaoqun Huang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Qun Zhou
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yunzi Luo
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Tangxing Road 133, Nanshan District, Shenzhen 518071, China
- Haihe Laboratory of Sustainable Chemical Transformations, Tianjin 300192, China
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24
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He W, Liao K, Li R, Peng W, Qian B, Zeng D, Tang F, Xue F, Jung YS, Dai J. Development of a CRISPR/Cas12a-based fluorescent detection method of Senecavirus A. BMC Vet Res 2024; 20:258. [PMID: 38877537 PMCID: PMC11179212 DOI: 10.1186/s12917-024-04116-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Senecavirus A (SVA), identified in 2002, is known to cause porcine idiopathic vesicular disease (PIVD), which presents with symptoms resembling other vesicular diseases. This similarity complicates field diagnosis. Conventional molecular diagnostic techniques are limited by their cost, sensitivity, and requirement for complicated instrumentation. Therefore, developing an effective and accurate diagnostic method is crucial for timely identification and isolation of affected pigs, thereby preventing further disease spread. METHODS In this study, we developed a highly-specific and ultra-sensitive SVA detection method powered by CRISPR/Cas12a. To enhance the availability in laboratories with varied equipment conditions, microplate reader and ultraviolet light transilluminator were introduced. Moreover, PCR amplification has also been incorporated into this method to improve sensitivity. The specificity and sensitivity of this method were determined following the preparation of the recombinant Cas12a protein and optimization of the CRISPR/Cas12a-based trans-cleavage system. RESULTS The method demonstrated no cross-reactivity with ten kinds of viruses of swine. The minimum template concentration required to activate substantial trans-cleavage activity was determined to be 106 copies/µL of SVA templates. However, when PCR amplification was incorporated, the method achieved a detection limit of one copy of SVA templates per reaction. It also exhibited 100% accuracy in simulated sample testing. The complete testing process does not exceed three hours. CONCLUSIONS Importantly, this method utilizes standard laboratory equipment, making it accessible for use in resource-limited settings and facilitating widespread and ultra-sensitive screening during epidemics. Overall, the development of this method not only broadens the array of tools available for detecting SVA but also holds significant promise for controlling the spread of PIVD.
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Affiliation(s)
- Wei He
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
- Ningxia Hui Autonomous Region Food Testing and Research Institute, Yinchuan, 750002, China
| | - Kai Liao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruixue Li
- Ningxia Hui Autonomous Region Food Testing and Research Institute, Yinchuan, 750002, China
| | - Wanqing Peng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingxu Qian
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dexin Zeng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China.
- Sanya Institute of Nanjing Agricultural University, Sanya, 572024, China.
| | - Yong Sam Jung
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianjun Dai
- China Pharmaceutical University, Nanjing, 211198, China
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25
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Moradi V, Khodabandehloo E, Alidadi M, Omidkhoda A, Ahmadbeigi N. Progress and pitfalls of gene editing technology in CAR-T cell therapy: a state-of-the-art review. Front Oncol 2024; 14:1388475. [PMID: 38912057 PMCID: PMC11190338 DOI: 10.3389/fonc.2024.1388475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 05/21/2024] [Indexed: 06/25/2024] Open
Abstract
CAR-T cell therapy has shown remarkable promise in treating B-cell malignancies, which has sparked optimism about its potential to treat other types of cancer as well. Nevertheless, the Expectations of CAR-T cell therapy in solid tumors and non-B cell hematologic malignancies have not been met. Furthermore, safety concerns regarding the use of viral vectors and the current personalized production process are other bottlenecks that limit its widespread use. In recent years the use of gene editing technology in CAR-T cell therapy has opened a new way to unleash the latent potentials of CAR-T cell therapy and lessen its associated challenges. Moreover, gene editing tools have paved the way to manufacturing CAR-T cells in a fully non-viral approach as well as providing a universal, off-the-shelf product. Despite all the advantages of gene editing strategies, the off-target activity of classical gene editing tools (ZFNs, TALENs, and CRISPR/Cas9) remains a major concern. Accordingly, several efforts have been made in recent years to reduce their off-target activity and genotoxicity, leading to the introduction of advanced gene editing tools with an improved safety profile. In this review, we begin by examining advanced gene editing tools, providing an overview of how these technologies are currently being applied in clinical trials of CAR-T cell therapies. Following this, we explore various gene editing strategies aimed at enhancing the safety and efficacy of CAR-T cell therapy.
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Affiliation(s)
- Vahid Moradi
- Hematology and Blood Transfusion Science Department, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Elnaz Khodabandehloo
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mehdi Alidadi
- Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Azadeh Omidkhoda
- Hematology and Blood Transfusion Science Department, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Naser Ahmadbeigi
- Gene Therapy Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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26
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Saleh EAM, Ali E, Muxamadovna GM, Kassem AF, Kaur I, Kumar A, Jabbar HS, Alwaily ER, Elawady A, Omran AA. CRISPR/Cas-based colorimetric biosensors: a promising tool for the diagnosis of bacterial foodborne pathogens in food products. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3448-3463. [PMID: 38804827 DOI: 10.1039/d4ay00578c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Some physical phenomena and various chemical substances newly introduced in nanotechnology have allowed scientists to develop valuable devices in the field of food sciences. Regarding such progress, the identification of foodborne pathogenic microorganisms is an imperative subject nowadays. These bacterial species have been found to cause severe health impacts after food ingestion and can result in high mortality in acute cases. The rapid detection of foodborne bacterial species at low concentrations is in high demand in recent diagnostics. CRISPR/Cas-mediated biosensors possess the potential to overcome several challenges in classical assays such as complex pretreatments, long turnaround time, and insensitivity. Among them, colorimetric nanoprobes based on the CRISPR strategy afford promising devices for POCT (point-of-care testing) since they can be visualized with the naked eye and do not require diagnostic apparatus. In this study, we briefly classify and discuss the working principles of the different CRISPR/Cas protein agents that have been employed in biosensors so far. We assess the current status of the CRISPR system, specifically focusing on colorimetric biosensing platforms. We discuss the utilization of each Cas effector in the detection of foodborne pathogens and examine the restrictions of the existing technology. The challenges and future opportunities are also indicated and addressed.
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Affiliation(s)
- Ebraheem Abdu Musad Saleh
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia.
| | - Eyhab Ali
- Al-Zahraa University for Women, Karbala, Iraq
| | | | - Asmaa F Kassem
- Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Irwanjot Kaur
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka-560069, India
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan-303012, India
| | - Abhinav Kumar
- Department of Nuclear and Renewable Energy, Ural Federal University Named After the First President of Russia Boris Yeltsin, Yekaterinburg 620002, Russia
| | - Hijran Sanaan Jabbar
- Department of Chemistry, College of Science, Salahaddin University-Erbil, Erbil, Kurdistan Region, Iraq
| | - Enas R Alwaily
- Microbiology Research Group, College of Pharmacy, Al-Ayen University, Thi-Qar, Iraq
| | - Ahmed Elawady
- College of Technical Engineering, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- College of Technical Engineering, The Islamic University, Najaf, Iraq
- College of Technical Engineering, The Islamic University of Babylon, Babylon, Iraq
| | - Alaa A Omran
- Department of Engineering, AL-Nisour University College, Baghdad, Iraq
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27
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Kim HJ, Cho IS, Choi SR, Jeong RD. Identification of an Isolate of Citrus Tristeza Virus by Nanopore Sequencing in Korea and Development of a CRISPR/Cas12a-Based Assay for Rapid Visual Detection of the Virus. PHYTOPATHOLOGY 2024; 114:1421-1428. [PMID: 38079355 DOI: 10.1094/phyto-10-23-0354-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Citrus tristeza virus (CTV) is a highly destructive viral pathogen posing a significant threat to citrus crops worldwide. Disease management and crop protection strategies necessitate the development of rapid and accurate detection methods. In this study, we employed Oxford Nanopore sequencing to detect CTV in Citrus unshiu samples. Subsequently, we developed a specific and sensitive detection assay combining CRISPR/Cas12a with reverse transcription-recombinase polymerase amplification. The CRISPR-Cas12a assay exhibited exceptional specificity for CTV, surpassing conventional RT-PCR by at least 10-fold in sensitivity. Remarkably, the developed assay detected CTV in field samples, with zero false negatives. This diagnostic approach is user-friendly, cost-effective, and offers tremendous potential for rapid onsite detection of CTV. Therefore, the CRISPR-Cas12a assay plays a significant role in managing and preserving citrus trees that are free from viruses in the industry.
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Affiliation(s)
- Hae-Jun Kim
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Republic of Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Se-Ryung Choi
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Chonnam National University, Gwangju 61185, Republic of Korea
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28
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Hebert JD, Xu H, Tang YJ, Ruiz PA, Detrick CR, Wang J, Hughes NW, Donosa O, Andrejka L, Karmakar S, Aboiralor I, Tang R, Sage J, Cong L, Petrov DA, Winslow MM. Efficient and multiplexed somatic genome editing with Cas12a mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583774. [PMID: 38496463 PMCID: PMC10942438 DOI: 10.1101/2024.03.07.583774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Somatic genome editing in mouse models has increased our understanding of the in vivo effects of genetic alterations in areas ranging from neuroscience to cancer biology and beyond. However, existing models are limited in their ability to create multiple targeted edits. Thus, our understanding of the complex genetic interactions that underlie development, homeostasis, and disease remains incomplete. Cas12a is an RNA-guided endonuclease with unique attributes that enable simple targeting of multiple genes with crRNA arrays containing tandem guides. To accelerate and expand the generation of complex genotypes in somatic cells, we generated transgenic mice with Cre-regulated and constitutive expression of enhanced Acidaminococcus sp. Cas12a (enAsCas12a). In these mice, enAsCas12a-mediated somatic genome editing robustly generated compound genotypes, as exemplified by the initiation of diverse cancer types driven by homozygous inactivation of trios of tumor suppressor genes. We further integrated these modular crRNA arrays with clonal barcoding to quantify the size and number of tumors with each array, as well as the efficiency of each crRNA. These Cas12a alleles will enable the rapid generation of disease models and broadly facilitate the high-throughput investigation of coincident genomic alterations in somatic cells in vivo .
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29
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Rananaware SR, Meister KS, Shoemaker GM, Vesco EK, Sandoval LSW, Lewis JG, Bodin AP, Karalkar VN, Lange IH, Pizzano BLM, Chang M, Ahmadimashhadi MR, Flannery SJ, Nguyen LT, Wang GP, Jain PK. PAM-free diagnostics with diverse type V CRISPR-Cas systems. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.02.24306194. [PMID: 38746294 PMCID: PMC11092703 DOI: 10.1101/2024.05.02.24306194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Type V CRISPR-Cas effectors have revolutionized molecular diagnostics by facilitating the detection of nucleic acid biomarkers. However, their dependence on the presence of protospacer adjacent motif (PAM) sites on the target double-stranded DNA (dsDNA) greatly limits their flexibility as diagnostic tools. Here we present a novel method named PICNIC that solves the PAM problem for CRISPR-based diagnostics with just a simple ∼10-min modification to contemporary CRISPR-detection protocols. Our method involves the separation of dsDNA into individual single-stranded DNA (ssDNA) strands through a high- temperature and high-pH treatment. We then detect the released ssDNA strands with diverse Cas12 enzymes in a PAM-free manner. We show the utility of PICNIC by successfully applying it for PAM-free detection with three different subtypes of the Cas12 family- Cas12a, Cas12b, and Cas12i. Notably, by combining PICNIC with a truncated 15-nucleotide spacer containing crRNA, we demonstrate PAM-independent detection of clinically important single- nucleotide polymorphisms with CRISPR. We apply this approach to detect the presence of a drug-resistant variant of HIV-1, specifically the K103N mutant, that lacks a PAM site in the vicinity of the mutation. Additionally, we successfully translate our approach to clinical samples by detecting and genotyping HCV-1a and HCV-1b variants with 100% specificity at a PAM-less site within the HCV genome. In summary, PICNIC is a simple yet groundbreaking method that enhances the flexibility and precision of CRISPR-Cas12-based diagnostics by eliminating the restriction of the PAM sequence.
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30
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Lei X, Cao S, Liu T, Wu Y, Yu S. Non-canonical CRISPR/Cas12a-based technology: A novel horizon for biosensing in nucleic acid detection. Talanta 2024; 271:125663. [PMID: 38232570 DOI: 10.1016/j.talanta.2024.125663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
Nucleic acids are essential biomarkers in molecular diagnostics. The CRISPR/Cas system has been widely used for nucleic acid detection. Moreover, canonical CRISPR/Cas12a based biosensors can specifically recognize and cleave target DNA, as well as single-strand DNA serving as reporter probe, which have become a super star in recent years in the field of nucleic acid detection due to its high specificity, universal programmability and simple operation. However, canonical CRISPR/Cas12a based biosensors are hard to meet the requirements of higher sensitivity, higher specificity, higher efficiency, larger target scope, easier operation, multiplexing, low cost and diversified signal reading. Then, advanced non-canonical CRISPR/Cas12a based biosensors emerge. In this review, applications of non-canonical CRISPR/Cas12a-based biosensors in nucleic acid detection are summarized. And the principles, peculiarities, performances and perspectives of these non-canonical CRISPR/Cas12a based biosensors are also discussed.
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Affiliation(s)
- Xueying Lei
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Shengnan Cao
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Tao Liu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Yongjun Wu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China
| | - Songcheng Yu
- . College of Public Health, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, PR China.
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31
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Locatelli F, Cavazzana M, Frangoul H, Fuente JDL, Algeri M, Meisel R. Autologous gene therapy for hemoglobinopathies: From bench to patient's bedside. Mol Ther 2024; 32:1202-1218. [PMID: 38454604 PMCID: PMC11081872 DOI: 10.1016/j.ymthe.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 01/31/2024] [Accepted: 03/05/2024] [Indexed: 03/09/2024] Open
Abstract
In recent years, a growing number of clinical trials have been initiated to evaluate gene therapy approaches for the treatment of patients with transfusion-dependent β-thalassemia and sickle cell disease (SCD). Therapeutic modalities being assessed in these trials utilize different molecular techniques, including lentiviral vectors to add functional copies of the gene encoding the hemoglobin β subunit in defective cells and CRISPR-Cas9, transcription activator-like effector protein nuclease, and zinc finger nuclease gene editing strategies to either directly address the underlying genetic cause of disease or induce fetal hemoglobin production by gene disruption. Here, we review the mechanisms of action of these various gene addition and gene editing approaches and describe the status of clinical trials designed to evaluate the potentially for these approaches to provide one-time functional cures to patients with transfusion-dependent β-thalassemia and SCD.
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Affiliation(s)
- Franco Locatelli
- Department of Pediatric Haematology/Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, 00165 Rome, Italy; Catholic University of the Sacred Heart, 00168 Rome, Italy.
| | - Marina Cavazzana
- Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), University of Paris, 75006 Paris, France
| | - Haydar Frangoul
- Sarah Cannon Center for Blood Cancer at The Children's Hospital at TriStar Centennial, Nashville, TN 37203, USA
| | - Josu de la Fuente
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London W21NY, UK
| | - Mattia Algeri
- Department of Pediatric Haematology/Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, 00165 Rome, Italy; Department of Health Sciences, Magna Graecia University, 88100 Catanzaro, Italy
| | - Roland Meisel
- Division of Pediatric Stem Cell Therapy, Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, Heinrich-Heine-University, 40225 Duesseldorf, Germany
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32
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Zhao C, Yang Z, Hu T, Liu J, Zhao Y, Leng D, Yang K, An G. CRISPR-Cas12a based target recognition initiated duplex-specific nuclease enhanced fluorescence and colorimetric analysis of cell-free DNA (cfDNA). Talanta 2024; 271:125717. [PMID: 38281430 DOI: 10.1016/j.talanta.2024.125717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
The significant role of cell-free DNA (cfDNA) for disease diagnosis, including cancer, has garnered a lot of attention. The challenges of creating target-specific primers and the possibility of false-positive signals make amplification-based detection methods problematic. Fluorescent biosensors based on CRISPR-Cas have been widely established, however they still require an amplification step before they can be used for detection. To detect cfDNA, researchers have created a CRISPR-Cas12a-based nucleic acid amplification-free fluorescent biosensor that uses a combination of fluorescence and colorimetric signaling improved by duplex-specific nuclease (DSN). DSN-assisted signal recycling is initiated in H1@MBs when the target cfDNA activates the CRISPR-Cas12a complex, leading to the degradation of single-strand DNA (ssDNA) sequences. This method has an extremely high detection limit for the BRCA-1 breast cancer gene. In addition to measuring viral DNA in a field-deployable and point-of-care testing (POCT) platform, this fast and highly selective sensor can be used to evaluate additional nucleic acid biomarkers.
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Affiliation(s)
- Chenglong Zhao
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, No. 23, Post Street, Nangang District, Harbin City, Heilongjiang Province, 150000, China
| | - Zhipeng Yang
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, No. 23, Post Street, Nangang District, Harbin City, Heilongjiang Province, 150000, China
| | - Tengfei Hu
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, No. 23, Post Street, Nangang District, Harbin City, Heilongjiang Province, 150000, China
| | - Jingwei Liu
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, No. 23, Post Street, Nangang District, Harbin City, Heilongjiang Province, 150000, China
| | - Yibo Zhao
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, No. 23, Post Street, Nangang District, Harbin City, Heilongjiang Province, 150000, China
| | - Dongming Leng
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, No. 23, Post Street, Nangang District, Harbin City, Heilongjiang Province, 150000, China
| | - Kun Yang
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, No. 23, Post Street, Nangang District, Harbin City, Heilongjiang Province, 150000, China; Sichuan Rehabilitation Hospital Affiliated of Chengdu University of Traditional Chinese Medicine Sichuan Bayi Rehabilitation Center, Chengdu, Sichuan province, 611100, China
| | - Gang An
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, No. 23, Post Street, Nangang District, Harbin City, Heilongjiang Province, 150000, China.
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Sen A, Masetty M, Weerakoon S, Morris C, Yadav JS, Apewokin S, Trannguyen J, Broom M, Priye A. Paper-based loop-mediated isothermal amplification and CRISPR integrated platform for on-site nucleic acid testing of pathogens. Biosens Bioelectron 2024; 257:116292. [PMID: 38653014 DOI: 10.1016/j.bios.2024.116292] [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: 02/06/2024] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
We report the development and initial validation of a paper-based nucleic acid testing platform that integrates Loop-mediated isothermal amplification (LAMP) with clustered regularly interspaced short palindromic repeats (CRISPR) technology, referred to as PLACID (Paper-based LAMP-CRISPR Integrated Diagnostics). LAMP eliminates the need for thermal cycling, resulting in simplified instrumentation, and the CRISPR-associated protein (Cas 12a) system eliminates false positive signals from LAMP products, resulting in highly selective and sensitive assays. We optimized the assay to perform both amplification and detection entirely on paper, eliminating the need for complex fluid handling steps and lateral flow assay transfers. Additionally, we engineered a smartphone-operated system that includes a low-powered, non-contact IR heating chamber to actuate paper-based LAMP and CRISPR reactions and enable the detection of fluorescent signals from the paper. The platform demonstrates high specificity and sensitivity in detecting nucleic acid targets with a limit of detection of 50 copies/μL. We integrate an equipment-free sample preparation separation technology designed to streamline the preparation of crude samples prior to nucleic acid testing. The practical utility of our platform is demonstrated by the successful detection of spiked SARS-CoV-2 RNA fragments in saliva, E. Coli in soil, and pathogenic E. Coli in clinically fecal samples of infected patients. Furthermore, we demonstrate that the paper-based LAMP CRISPR chips employed in our assays possess a shelf life of several weeks, establishing them as viable candidates for on-site diagnostics.
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Affiliation(s)
- Anindita Sen
- DNAiTECH Ltd, Marlborough Research Center, 2650 State Highway 1, Grovetown, Blenheim, Marlborough, 7202, New Zealand
| | - Manaswini Masetty
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Sasanka Weerakoon
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Calum Morris
- DNAiTECH Ltd, Marlborough Research Center, 2650 State Highway 1, Grovetown, Blenheim, Marlborough, 7202, New Zealand
| | - Jagjit S Yadav
- Department of Environmental & Public Health Sciences, College of Medicine, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Senu Apewokin
- Division of Infectious Diseases, College of Medicine, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Jennifer Trannguyen
- Division of Infectious Diseases, College of Medicine, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Murray Broom
- DNAiTECH Ltd, Marlborough Research Center, 2650 State Highway 1, Grovetown, Blenheim, Marlborough, 7202, New Zealand.
| | - Aashish Priye
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, OH, 45221, USA; Digital Futures, University of Cincinnati, Cincinnati, OH, 45221, USA.
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Webster LJ, Villa-Gomez D, Brown R, Clarke W, Schenk PM. A synthetic biology approach for the treatment of pollutants with microalgae. Front Bioeng Biotechnol 2024; 12:1379301. [PMID: 38646010 PMCID: PMC11032018 DOI: 10.3389/fbioe.2024.1379301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
The increase in global population and industrial development has led to a significant release of organic and inorganic pollutants into water streams, threatening human health and ecosystems. Microalgae, encompassing eukaryotic protists and prokaryotic cyanobacteria, have emerged as a sustainable and cost-effective solution for removing these pollutants and mitigating carbon emissions. Various microalgae species, such as C. vulgaris, P. tricornutum, N. oceanica, A. platensis, and C. reinhardtii, have demonstrated their ability to eliminate heavy metals, salinity, plastics, and pesticides. Synthetic biology holds the potential to enhance microalgae-based technologies by broadening the scope of treatment targets and improving pollutant removal rates. This review provides an overview of the recent advances in the synthetic biology of microalgae, focusing on genetic engineering tools to facilitate the removal of inorganic (heavy metals and salinity) and organic (pesticides and plastics) compounds. The development of these tools is crucial for enhancing pollutant removal mechanisms through gene expression manipulation, DNA introduction into cells, and the generation of mutants with altered phenotypes. Additionally, the review discusses the principles of synthetic biology tools, emphasizing the significance of genetic engineering in targeting specific metabolic pathways and creating phenotypic changes. It also explores the use of precise engineering tools, such as CRISPR/Cas9 and TALENs, to adapt genetic engineering to various microalgae species. The review concludes that there is much potential for synthetic biology based approaches for pollutant removal using microalgae, but there is a need for expansion of the tools involved, including the development of universal cloning toolkits for the efficient and rapid assembly of mutants and transgenic expression strains, and the need for adaptation of genetic engineering tools to a wider range of microalgae species.
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Affiliation(s)
- Luke J. Webster
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Denys Villa-Gomez
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- School of Civil Engineering, The University of Queensland, Brisbane, QLD, Australia
| | - Reuben Brown
- Algae Biotechnology Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - William Clarke
- School of Civil Engineering, The University of Queensland, Brisbane, QLD, Australia
| | - Peer M. Schenk
- Algae Biotechnology Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
- Algae Biotechnology, Sustainable Solutions Hub, Global Sustainable Solutions Pty Ltd, Brisbane, QLD, Australia
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Sutipatanasomboon A, Wongsantichon J, Sakdee S, Naksith P, Watthanadirek A, Anuracpreeda P, Blacksell SD, Saisawang C. RPA-CRISPR/Cas12a assay for the diagnosis of bovine Anaplasma marginale infection. Sci Rep 2024; 14:7820. [PMID: 38570576 PMCID: PMC10991388 DOI: 10.1038/s41598-024-58169-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Anaplasma marginale infection is one of the most common tick-borne diseases, causing a substantial loss in the beef and dairy production industries. Once infected, the pathogen remains in the cattle for life, allowing the parasites to spread to healthy animals. Since clinical manifestations of anaplasmosis occur late in the disease, a sensitive, accurate, and affordable pathogen identification is crucial in preventing and controlling the infection. To this end, we developed an RPA-CRISPR/Cas12a assay specific to A. marginale infection in bovines targeting the msp4 gene. Our assay is performed at one moderately high temperature, producing fluorescent signals or positive readout of a lateral flow dipstick, which is as sensitive as conventional PCR-based DNA amplification. This RPA-CRISPR/Cas12a assay can detect as few as 4 copies/μl of Anaplasma using msp4 marker without cross-reactivity to other common bovine pathogens. Lyophilized components of the assay can be stored at room temperature for an extended period, indicating its potential for field diagnosis and low-resource settings of anaplasmosis in bovines.
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Affiliation(s)
- Arpaporn Sutipatanasomboon
- Molecular Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Salaya, Thailand
| | - Jantana Wongsantichon
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Somsri Sakdee
- Center for Advanced Therapeutics, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, 25/25 Phuttamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Piyaporn Naksith
- Center for Advanced Therapeutics, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, 25/25 Phuttamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Amaya Watthanadirek
- Molecular Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Salaya, Thailand
| | - Panat Anuracpreeda
- Molecular Biosciences Cluster, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Salaya, Thailand
| | - Stuart D Blacksell
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Chonticha Saisawang
- Center for Advanced Therapeutics, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, 25/25 Phuttamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand.
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Wang M, Rieber L, van Baaren J, Morgan M, Merrett S, McDowell I, Bowen T. Diverse Class 2 CRISPR Effectors as Active Nucleases with Expanded Targeting Capabilities. CRISPR J 2024; 7:120-130. [PMID: 38635326 DOI: 10.1089/crispr.2023.0058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
CRISPR-Cas systems have proven effective in a variety of applications due to their ease of use and relatively high editing efficiency. Yet, any individual CRISPR-Cas system has inherent limitations, necessitating a diversity of RNA-guided nucleases to suit applications with distinct needs. We searched through metagenomic sequences to identify RNA-guided nucleases and found enzymes from diverse CRISPR-Cas types and subtypes, the most promising of which we developed into gene-editing platforms. Based on prior annotations of the metagenomic sequences, we establish the likely taxa and sampling locations where Class 2 CRISPR-Cas systems active in eukaryotes may be found. The newly discovered systems show robust capabilities as gene editors and base editors.
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Affiliation(s)
- Meng Wang
- UCB Biosciences Inc, Early Solutions, Cambridge, Massachusetts, USA
| | - Lila Rieber
- UCB Biosciences Inc, Early Solutions, Durham, North Carolina, USA
| | | | - Meaghan Morgan
- UCB Biosciences Inc, Early Solutions, Durham, North Carolina, USA
| | | | - Ian McDowell
- UCB Biosciences Inc, Early Solutions, Durham, North Carolina, USA
| | - Tyson Bowen
- UCB Biosciences Inc, Early Solutions, Durham, North Carolina, USA
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Riedl MA, Bordone L, Revenko A, Newman KB, Cohn DM. Clinical Progress in Hepatic Targeting for Novel Prophylactic Therapies in Hereditary Angioedema. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2024; 12:911-918. [PMID: 38142864 DOI: 10.1016/j.jaip.2023.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/09/2023] [Accepted: 12/08/2023] [Indexed: 12/26/2023]
Abstract
Hereditary angioedema (HAE) is typically caused by a deficiency of the protease inhibitor C1 inhibitor (C1INH). The absence of C1INH activity on plasma kallikrein and factor XIIa leads to overproduction of the vasoactive peptide bradykinin, with resulting angioedema. As the primary site of C1INH and prekallikrein production, the liver is recognized as an important therapeutic target in HAE, leading to the development of hepatic-focused treatment strategies such as GalNAc-conjugated antisense technology and gene modification. This report reviews currently available data on hepatic-focused interventions for HAE that have advanced into human trials. Donidalorsen is an investigational GalNAc3-conjugated antisense oligonucleotide that binds to prekallikrein mRNA in the liver and reduces the expression of prekallikrein. Phase 2 data with subcutaneous donidalorsen demonstrated a significant reduction in HAE attack rate compared with placebo. Phase 3 trials are underway. ADX-324 is a GalNAc3-conjugated short-interfering RNA being investigated in HAE. BMN 331 is an investigational AAV5-based gene therapy vector that expresses wild-type human C1INH and is targeted to hepatocytes. A single intravenous dose of BMN 331 is intended to replace the defective SERPING1 gene and enable patients to produce functional C1INH. A first-in-human phase 1/2 study is ongoing with BMN 331. NTLA-2002 is an investigational in vivo clustered regularly interspaced short palindromic repeats/Cas9-based therapy designed to knock out the prekallikrein-coding KLKB1 gene in hepatocytes; a phase 1/2 study is ongoing. Findings from these and other ongoing studies are highly anticipated with the expectation of expanding the array of treatment options in HAE.
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Affiliation(s)
- Marc A Riedl
- Division of Allergy and Immunology, University of California, San Diego, La Jolla, Calif.
| | | | | | | | - Danny M Cohn
- Department of Vascular Medicine, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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38
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Recktenwald M, Hutt E, Davis L, MacAulay J, Daringer NM, Galie PA, Staehle MM, Vega SL. Engineering transcriptional regulation for cell-based therapies. SLAS Technol 2024; 29:100121. [PMID: 38340892 DOI: 10.1016/j.slast.2024.100121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/10/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
A major aim in the field of synthetic biology is developing tools capable of responding to user-defined inputs by activating therapeutically relevant cellular functions. Gene transcription and regulation in response to external stimuli are some of the most powerful and versatile of these cellular functions being explored. Motivated by the success of chimeric antigen receptor (CAR) T-cell therapies, transmembrane receptor-based platforms have been embraced for their ability to sense extracellular ligands and to subsequently activate intracellular signal transduction. The integration of transmembrane receptors with transcriptional activation platforms has not yet achieved its full potential. Transient expression of plasmid DNA is often used to explore gene regulation platforms in vitro. However, applications capable of targeting therapeutically relevant endogenous or stably integrated genes are more clinically relevant. Gene regulation may allow for engineered cells to traffic into tissues of interest and secrete functional proteins into the extracellular space or to differentiate into functional cells. Transmembrane receptors that regulate transcription have the potential to revolutionize cell therapies in a myriad of applications, including cancer treatment and regenerative medicine. In this review, we will examine current engineering approaches to control transcription in mammalian cells with an emphasis on systems that can be selectively activated in response to extracellular signals. We will also speculate on the potential therapeutic applications of these technologies and examine promising approaches to expand their capabilities and tighten the control of gene regulation in cellular therapies.
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Affiliation(s)
- Matthias Recktenwald
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Evan Hutt
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Leah Davis
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - James MacAulay
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Nichole M Daringer
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Peter A Galie
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Mary M Staehle
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA
| | - Sebastián L Vega
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ 08028, USA; Department of Orthopaedic Surgery, Cooper Medical School of Rowan University, Camden, NJ 08103, USA.
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Coppola U, Kenney J, Waxman JS. A Foxf1-Wnt-Nr2f1 cascade promotes atrial cardiomyocyte differentiation in zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584759. [PMID: 38558972 PMCID: PMC10980076 DOI: 10.1101/2024.03.13.584759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Nr2f transcription factors (TFs) are conserved regulators of vertebrate atrial cardiomyocyte (AC) differentiation. However, little is known about the mechanisms directing Nr2f expression in ACs. Here, we identified a conserved enhancer 3' to the nr2f1a locus, which we call 3'reg1-nr2f1a (3'reg1), that can promote Nr2f1a expression in ACs. Sequence analysis of the enhancer identified putative Lef/Tcf and Foxf TF binding sites. Mutation of the Lef/Tcf sites within the 3'reg1 reporter, knockdown of Tcf7l1a, and manipulation of canonical Wnt signaling support that Tcf7l1a is derepressed via Wnt signaling to activate the transgenic enhancer and promote AC differentiation. Similarly, mutation of the Foxf binding sites in the 3'reg1 reporter, coupled with gain- and loss-of-function analysis supported that Foxf1 promotes expression of the enhancer and AC differentiation. Functionally, we find that Wnt signaling acts downstream of Foxf1 to promote expression of the 3'reg1 reporter within ACs and, importantly, both Foxf1 and Wnt signaling require Nr2f1a to promote a surplus of differentiated ACs. CRISPR-mediated deletion of the endogenous 3'reg1 abrogates the ability of Foxf1 and Wnt signaling to produce surplus ACs in zebrafish embryos. Together, our data support that downstream members of a conserved regulatory network involving Wnt signaling and Foxf1 function on a nr2f1a enhancer to promote AC differentiation in the zebrafish heart.
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Affiliation(s)
- Ugo Coppola
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jennifer Kenney
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Joshua S. Waxman
- Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Developmental Biology Division, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45229, USA
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40
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Liu Y, Chao Z, Ding W, Fang T, Gu X, Xue M, Wang W, Han R, Sun W. A multiplex RPA-CRISPR/Cas12a-based POCT technique and its application in human papillomavirus (HPV) typing assay. Cell Mol Biol Lett 2024; 29:34. [PMID: 38459454 PMCID: PMC10921630 DOI: 10.1186/s11658-024-00548-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 02/09/2024] [Indexed: 03/10/2024] Open
Abstract
Persistent infection with high-risk human papillomavirus (HR-HPV) is the primary and initiating factor for cervical cancer. With over 200 identified HPV types, including 14 high-risk types that integrate into the host cervical epithelial cell DNA, early determination of HPV infection type is crucial for effective risk stratification and management. Presently, on-site immediate testing during the HPV screening stage, known as Point of Care Testing (POCT), remains immature, severely limiting the scope and scenarios of HPV screening. This study, guided by the genomic sequence patterns of HPV, established a multiplex recombinase polymerase amplification (RPA) technology based on the concept of "universal primers." This approach achieved the multiple amplification of RPA, coupled with the CRISPR/Cas12a system serving as a medium for signal amplification and conversion. The study successfully constructed a POCT combined detection system, denoted as H-MRC12a (HPV-Multiple RPA-CRISPR/Cas12a), and applied it to high-risk HPV typing detection. The system accomplished the typing detection of six high-risk HPV types (16, 18, 31, 33, 35, and 45) can be completed within 40 min, and the entire process, from sample loading to result interpretation, can be accomplished within 45 min, with a detection depth reaching 1 copy/μL for each high-risk type. Validation of the H-MRC12a detection system's reproducibility and specificity was further conducted through QPCR on 34 clinical samples. Additionally, this study explored and optimized the multiplex RPA amplification system and CRISPR system at the molecular mechanism level. Furthermore, the primer design strategy developed in this study offers the potential to enhance the throughput of H-MRC12a detection while ensuring sensitivity, providing a novel research avenue for high-throughput detection in Point-of-Care molecular pathogen studies.
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Affiliation(s)
- Yan Liu
- Laboratory of Molecular Diagnostics, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215000, Jiangsu, People's Republic of China
| | - Zhujun Chao
- Soochow University, Suzhou Medical College of Soochow University, Suzhou, 215000, Jiangsu, People's Republic of China
| | - Wei Ding
- Laboratory of Molecular Diagnostics, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215000, Jiangsu, People's Republic of China
| | - Tanfeng Fang
- Laboratory of Molecular Diagnostics, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215000, Jiangsu, People's Republic of China
| | - Xinxian Gu
- Dushu Lake Hospital, Affiliated to Soochow University, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, 215004, Jiangsu, People's Republic of China.
| | - Man Xue
- Biological Products and Biochemical Drugs, Suzhou Institute for Food and Drug Control, Suzhou, 215101, Jiangsu, People's Republic of China
| | - Wei Wang
- Laboratory of Molecular Diagnostics, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215000, Jiangsu, People's Republic of China
| | - Rong Han
- Laboratory of Molecular Diagnostics, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215000, Jiangsu, People's Republic of China
| | - Wanping Sun
- Laboratory of Molecular Diagnostics, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215000, Jiangsu, People's Republic of China.
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Yang P, Tian J, Zhang L, Zhang H, Yang G, Ren Y, Fang J, Gu Y, Jiang W. A toolbox for genetic manipulation in intestinal Clostridium symbiosum. Synth Syst Biotechnol 2024; 9:43-54. [PMID: 38234413 PMCID: PMC10793094 DOI: 10.1016/j.synbio.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/08/2023] [Accepted: 12/24/2023] [Indexed: 01/19/2024] Open
Abstract
Gut microbes are closely related with human health, but remain much to learn. Clostridium symbiosum is a conditionally pathogenic human gut bacterium and regarded as a potential biomarker for early diagnosis of intestinal tumors. However, the absence of an efficient toolbox that allows diverse genetic manipulations of this bacterium limits its in-depth studies. Here, we obtained the complete genome sequence of C. symbiosum ATCC 14940, a representative strain of C. symbiosum. On this basis, we further developed a series of genetic manipulation methods for this bacterium. Firstly, following the identification of a functional replicon pBP1 in C. symbiosum ATCC 14940, a highly efficient conjugative DNA transfer method was established, enabling the rapid introduction of exogenous plasmids into cells. Next, we constructed a dual-plasmid CRISPR/Cas12a system for genome editing in this bacterium, reaching over 60 % repression for most of the chosen genes as well as efficient deletion (>90 %) of three target genes. Finally, this toolbox was used for the identification of crucial functional genes, involving growth, synthesis of important metabolites, and virulence of C. symbiosum ATCC 14940. Our work has effectively established and optimized genome editing methods in intestinal C. symbiosum, thereby providing strong support for further basic and application research in this bacterium.
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Affiliation(s)
- Pengjie Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinzhong Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Xianghu Laboratory, Hangzhou, 311231, China
| | - Lu Zhang
- NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai, 200001, China
| | - Hui Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Gaohua Yang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Bruna Straket 16, Gothenburg, 41345, Sweden
| | - Yimeng Ren
- NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai, 200001, China
| | - Jingyuan Fang
- NHC Key Laboratory of Digestive Diseases, Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai, 200001, China
| | - Yang Gu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Weihong Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
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Larriba E, Yaroshko O, Pérez-Pérez JM. Recent Advances in Tomato Gene Editing. Int J Mol Sci 2024; 25:2606. [PMID: 38473859 DOI: 10.3390/ijms25052606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
The use of gene-editing tools, such as zinc finger nucleases, TALEN, and CRISPR/Cas, allows for the modification of physiological, morphological, and other characteristics in a wide range of crops to mitigate the negative effects of stress caused by anthropogenic climate change or biotic stresses. Importantly, these tools have the potential to improve crop resilience and increase yields in response to challenging environmental conditions. This review provides an overview of gene-editing techniques used in plants, focusing on the cultivated tomatoes. Several dozen genes that have been successfully edited with the CRISPR/Cas system were selected for inclusion to illustrate the possibilities of this technology in improving fruit yield and quality, tolerance to pathogens, or responses to drought and soil salinity, among other factors. Examples are also given of how the domestication of wild species can be accelerated using CRISPR/Cas to generate new crops that are better adapted to the new climatic situation or suited to use in indoor agriculture.
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Affiliation(s)
- Eduardo Larriba
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
| | - Olha Yaroshko
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain
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43
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Valdivia-Francia F, Sendoel A. No country for old methods: New tools for studying microproteins. iScience 2024; 27:108972. [PMID: 38333695 PMCID: PMC10850755 DOI: 10.1016/j.isci.2024.108972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Abstract
Microproteins encoded by small open reading frames (sORFs) have emerged as a fascinating frontier in genomics. Traditionally overlooked due to their small size, recent technological advancements such as ribosome profiling, mass spectrometry-based strategies and advanced computational approaches have led to the annotation of more than 7000 sORFs in the human genome. Despite the vast progress, only a tiny portion of these microproteins have been characterized and an important challenge in the field lies in identifying functionally relevant microproteins and understanding their role in different cellular contexts. In this review, we explore the recent advancements in sORF research, focusing on the new methodologies and computational approaches that have facilitated their identification and functional characterization. Leveraging these new tools hold great promise for dissecting the diverse cellular roles of microproteins and will ultimately pave the way for understanding their role in the pathogenesis of diseases and identifying new therapeutic targets.
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Affiliation(s)
- Fabiola Valdivia-Francia
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
- Life Science Zurich Graduate School, Molecular Life Science Program, University of Zurich/ ETH Zurich, Schlieren-Zurich, Switzerland
| | - Ataman Sendoel
- University of Zurich, Institute for Regenerative Medicine (IREM), Wagistrasse 12, 8952 Schlieren-Zurich, Switzerland
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44
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Storz U. The CRISPR Cas patent files, part 2: Is Cpf1/Cas12a a less conflict- prone alternative to Cas9? J Biotechnol 2024; 381:67-75. [PMID: 38181979 DOI: 10.1016/j.jbiotec.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/11/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
CRISPR Cpf1/Cas12a has been discussed as a less conflict prone alternative, patent-wise, to Cas9. This article investigates whether or not this assumption is correct, and comes to the conclusion that the promise that CRISPR Cpf1/Cas12 would make things easier, and be less conflict-prone, is fragile.
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Affiliation(s)
- Ulrich Storz
- Michalski Hüttermann & Partner Patentanwälte mbB Düsseldorf, München, Germany.
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45
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Zeng D, Jiao J, Mo T. Combination of nucleic acid amplification and CRISPR/Cas technology in pathogen detection. Front Microbiol 2024; 15:1355234. [PMID: 38380103 PMCID: PMC10877009 DOI: 10.3389/fmicb.2024.1355234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024] Open
Abstract
Major health events caused by pathogenic microorganisms are increasing, seriously jeopardizing human lives. Currently PCR and ITA are widely used for rapid testing in food, medicine, industry and agriculture. However, due to the non-specificity of the amplification process, researchers have proposed the combination of nucleic acid amplification technology with the novel technology CRISPR for detection, which improves the specificity and credibility of results. This paper summarizes the research progress of nucleic acid amplification technology in conjunction with CRISPR/Cas technology for the detection of pathogens, which provides a reference and theoretical basis for the subsequent application of nucleic acid amplification technology in the field of pathogen detection.
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Affiliation(s)
| | | | - Tianlu Mo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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46
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Li D, Yao Y, Cheng W, Hou Z, Wang Z, Xiang Y. Self-Priming Cyclic Amplification Accelerating CRISPR Sensor for Sensitive and Specific MicroRNA Analysis with No Background. Anal Chem 2024; 96:1717-1724. [PMID: 38217876 DOI: 10.1021/acs.analchem.3c04866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2024]
Abstract
In this work, we demonstrate for the first time the application of the phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) reaction for miRNA assays. A self-priming amplification accelerating CRISPR sensor was well-established for sensitive and specific miRNA detection by integrating the PS-THSP reaction and CRISPR/Cas12a system. The sensor consists of three steps: (1) the formation of a complete PS-THSP template in the presence of target miRNA and ligase; (2) the exponential isothermal amplification of the PS-THSP reaction under the action of DNA polymerase; (3) the activation of the CRISPR/Cas12a fluorescence system to generate signals. We used miR-21 as a model target. The sensor can achieve sensitive detection of miR-21 without the involvement of any primers, and the special design of the CRISPR proto-spacer neighbor motif (PAM) sequence effectively avoids the interference of the background signal. In addition, the sensor can not only identify single-base mutant homologous sequences but also show stable performance in complex biological matrices. We have successfully used this sensor to accurately analyze miR-21 in different cell lines and real clinical samples, demonstrating its great potential in clinical diagnosis.
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Affiliation(s)
- Dayong Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Yanheng Yao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Wenting Cheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Zhiqiang Hou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Zhongyun Wang
- Department of Anesthesiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, P. R. China
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47
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Madugula SS, Pujar P, Bharani N, Wang S, Jayasinghe-Arachchige VM, Pham T, Mashburn D, Artilis M, Liu J. Identification of Family-Specific Features in Cas9 and Cas12 Proteins: A Machine Learning Approach Using Complete Protein Feature Spectrum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576286. [PMID: 38328240 PMCID: PMC10849529 DOI: 10.1101/2024.01.22.576286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The recent development of CRISPR-Cas technology holds promise to correct gene-level defects for genetic diseases. The key element of the CRISPR-Cas system is the Cas protein, a nuclease that can edit the gene of interest assisted by guide RNA. However, these Cas proteins suffer from inherent limitations like large size, low cleavage efficiency, and off-target effects, hindering their widespread application as a gene editing tool. Therefore, there is a need to identify novel Cas proteins with improved editing properties, for which it is necessary to understand the underlying features governing the Cas families. In the current study, we aim to elucidate the unique protein attributes associated with Cas9 and Cas12 families and identify the features that distinguish each family from the other. Here, we built Random Forest (RF) binary classifiers to distinguish Cas12 and Cas9 proteins from non-Cas proteins, respectively, using the complete protein feature spectrum (13,495 features) encoding various physiochemical, topological, constitutional, and coevolutionary information of Cas proteins. Furthermore, we built multiclass RF classifiers differentiating Cas9, Cas12, and Non-Cas proteins. All the models were evaluated rigorously on the test and independent datasets. The Cas12 and Cas9 binary models achieved a high overall accuracy of 95% and 97% on their respective independent datasets, while the multiclass classifier achieved a high F1 score of 0.97. We observed that Quasi-sequence-order descriptors like Schneider-lag descriptors and Composition descriptors like charge, volume, and polarizability are essential for the Cas12 family. More interestingly, we discovered that Amino Acid Composition descriptors, especially the Tripeptide Composition (TPC) descriptors, are important for the Cas9 family. Four of the identified important descriptors of Cas9 classification are tripeptides PWN, PYY, HHA, and DHI, which are seen to be conserved across all the Cas9 proteins and were located within different catalytically important domains of the Cas9 protein structure. Among these four tripeptides, tripeptides DHI and HHA are well-known to be involved in the DNA cleavage activity of the Cas9 protein. We therefore propose the the other two tripeptides, PWN and PYY, may also be essential for the Cas9 family. Our identified important descriptors enhanced the understanding of the catalytic mechanisms of Cas9 and Cas12 proteins and provide valuable insights into design of novel Cas systems to achieve enhanced gene-editing properties.
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Affiliation(s)
- Sita Sirisha Madugula
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, United States
| | - Pranav Pujar
- Department of Industrial, Manufacturing and Systems Engineering, University of Texas at Arlington, Arlington, Texas, United States
| | - Nammi Bharani
- Department of Industrial, Manufacturing and Systems Engineering, University of Texas at Arlington, Arlington, Texas, United States
| | - Shouyi Wang
- Department of Industrial, Manufacturing and Systems Engineering, University of Texas at Arlington, Arlington, Texas, United States
| | - Vindi M. Jayasinghe-Arachchige
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, United States
| | - Tyler Pham
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas
| | - Dominic Mashburn
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, United States
| | - Maria Artilis
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, United States
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas, United States
- Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas
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48
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Harsij Z, Ghafoorzadeh Z, Goharian E. The CRISPR Revolution: Unraveling the mysteries of Life's genetic code. Gene 2024; 892:147870. [PMID: 37797781 DOI: 10.1016/j.gene.2023.147870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 10/07/2023]
Abstract
A biotechnological revolution is triggered by CRISPR-Cas systems' variety, measured quality, and proficiency. Identifying nucleic acid biomarkers, one of the methods that use CRISPR for diagnosis, is an extremely sensitive diagnostic method.A broad range of infectious and noninfecting diseases, mutations, and CRISPR deletions associated with genetic disorders have been detected using diagnostics. Furthermore, this technology is used to test proteins and micromolecules. We focus on how Cas proteins can be used to detect diseases in genes, agriculture, and cancer therapy. Furthermore, CRISPR technology has many negative impacts on the health of living organisms, environmental and population structures in spite of its numerous contributions to biomedical science. Therefore, an investigation into the impact of genome editing on nontargeted species is important for these reasons. CRISPR in the future is briefly discussed towards the end of this review.
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Affiliation(s)
- Zohreh Harsij
- Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan 81746-73441, Iran.
| | - Zahra Ghafoorzadeh
- Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan 81746-73441, Iran
| | - Elahe Goharian
- Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan 81746-73441, Iran
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49
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Nguyen GT, Schelling MA, Buscher KA, Sritharan A, Sashital DG. CRISPR-Cas12a exhibits metal-dependent specificity switching. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.29.569287. [PMID: 38076861 PMCID: PMC10705449 DOI: 10.1101/2023.11.29.569287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Cas12a is the immune effector of type V-A CRISPR-Cas systems and has been co-opted for genome editing and other biotechnology tools. The specificity of Cas12a has been the subject of extensive investigation both in vitro and in genome editing experiments. However, in vitro studies have often been performed at high magnesium ion concentrations that are inconsistent with the free Mg2+ concentrations that would be present in cells. By profiling the specificity of Cas12a orthologs at a range of Mg2+ concentrations, we find that Cas12a switches its specificity depending on metal ion concentration. Lowering Mg2+ concentration decreases cleavage defects caused by seed mismatches, while increasing the defects caused by PAM-distal mismatches. We show that Cas12a can bind seed mutant targets more rapidly at low Mg2+ concentrations, resulting in faster cleavage. In contrast, PAM-distal mismatches cause substantial defects in cleavage following formation of the Cas12a-target complex at low Mg2+ concentrations. We observe differences in Cas12a specificity switching between three orthologs that results in variations in the routes of phage escape from Cas12a-mediated immunity. Overall, our results reveal the importance of physiological metal ion conditions on the specificity of Cas effectors that are used in different cellular environments.
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Affiliation(s)
- Giang T. Nguyen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Equal contribution
| | - Michael A. Schelling
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Equal contribution
| | - Kathryn A. Buscher
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Current address: Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Aneisha Sritharan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
- Current address: Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Dipali G. Sashital
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
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50
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Li Y, Zhou S, Wu Q, Gong C. CRISPR/Cas gene editing and delivery systems for cancer therapy. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1938. [PMID: 38456346 DOI: 10.1002/wnan.1938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 03/09/2024]
Abstract
CRISPR/Cas systems stand out because of simplicity, efficiency, and other superiorities, thus becoming attractive and brilliant gene-editing tools in biomedical field including cancer therapy. CRISPR/Cas systems bring promises for cancer therapy through manipulating and engineering on tumor cells or immune cells. However, there have been concerns about how to overcome the numerous physiological barriers and deliver CRISPR components to target cells efficiently and accurately. In this review, we introduced the mechanisms of CRISPR/Cas systems, summarized the current delivery strategies of CRISPR/Cas systems by physical methods, viral vectors, and nonviral vectors, and presented the current application of CRISPR/Cas systems in cancer clinical treatment. Furthermore, we discussed prospects related to delivery approaches of CRISPR/Cas systems. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.
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Affiliation(s)
- Yingjie Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Shiyao Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Qinjie Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Changyang Gong
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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