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Castañeda Cataña MA, Dodes Traian MM, Rivas Marquina AP, Marquez AB, Arrúa EC, Carlucci MJ, Damonte EB, Pérez OE, Sepúlveda CS. Design and characterization of BSA-mycophenolic acid nanocomplexes: Antiviral activity exploration. Int J Biol Macromol 2024; 265:131023. [PMID: 38513897 DOI: 10.1016/j.ijbiomac.2024.131023] [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: 11/03/2023] [Revised: 03/01/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
The interactions between bovine serum albumin (BSA) and mycophenolic acid (MPA) were investigated in silico through molecular docking and in vitro, using fluorescence spectroscopy. Dynamic light scattering and scanning electron microscopy were used to figure out the structure of MPA-Complex (MPA-C). The binding affinity between MPA and BSA was determined, yielding a Kd value of (12.0 ± 0.7) μM, and establishing a distance of 17 Å between the BSA and MPA molecules. The presence of MPA prompted protein aggregation, leading to the formation of MPA-C. The cytotoxicity of MPA-C and its ability to fight Junín virus (JUNV) were tested in A549 and Vero cell lines. It was found that treating infected cells with MPA-C decreased the JUNV yield and was more effective than free MPA in both cell line models for prolonged time treatments. Our results represent the first report of the antiviral activity of this type of BSA-MPA complex against JUNV, as assessed in cell culture model systems. MPA-C shows promise as a candidate for drug formulation against human pathogenic arenaviruses.
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Affiliation(s)
- Mayra A Castañeda Cataña
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). UBA-CONICET, 1428 Buenos Aires, Argentina
| | - Martín M Dodes Traian
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). UBA-CONICET, 1428 Buenos Aires, Argentina
| | - Andrea P Rivas Marquina
- Centro de Investigación y Desarrollo en Materiales Avanzados y Almacenamiento de Energía de Jujuy-CIDMEJu (CONICET-Universidad Nacional de Jujuy), Centro de Desarrollo Tecnológico General Savio, 4612 Palpalá, Jujuy, Argentina
| | - Agostina B Marquez
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). UBA-CONICET, 1428 Buenos Aires, Argentina
| | - Eva C Arrúa
- Centro de Investigación y Desarrollo en Materiales Avanzados y Almacenamiento de Energía de Jujuy-CIDMEJu (CONICET-Universidad Nacional de Jujuy), Centro de Desarrollo Tecnológico General Savio, 4612 Palpalá, Jujuy, Argentina
| | - María J Carlucci
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). UBA-CONICET, 1428 Buenos Aires, Argentina
| | - Elsa B Damonte
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), 1428 Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). UBA-CONICET, 1428 Buenos Aires, Argentina
| | - Oscar E Pérez
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), 1428 Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). UBA-CONICET, 1428 Buenos Aires, Argentina
| | - Claudia S Sepúlveda
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), 1428 Buenos Aires, Argentina; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN). UBA-CONICET, 1428 Buenos Aires, Argentina.
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2
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Tyumentseva M, Tyumentsev A, Akimkin V. CRISPR/Cas9 Landscape: Current State and Future Perspectives. Int J Mol Sci 2023; 24:16077. [PMID: 38003266 PMCID: PMC10671331 DOI: 10.3390/ijms242216077] [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: 10/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a unique genome editing tool that can be easily used in a wide range of applications, including functional genomics, transcriptomics, epigenetics, biotechnology, plant engineering, livestock breeding, gene therapy, diagnostics, and so on. This review is focused on the current CRISPR/Cas9 landscape, e.g., on Cas9 variants with improved properties, on Cas9-derived and fusion proteins, on Cas9 delivery methods, on pre-existing immunity against CRISPR/Cas9 proteins, anti-CRISPR proteins, and their possible roles in CRISPR/Cas9 function improvement. Moreover, this review presents a detailed outline of CRISPR/Cas9-based diagnostics and therapeutic approaches. Finally, the review addresses the future expansion of genome editors' toolbox with Cas9 orthologs and other CRISPR/Cas proteins.
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Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (A.T.); (V.A.)
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3
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Borase H, Shukla D. The Interplay of Genital Herpes with Cellular Processes: A Pathogenesis and Therapeutic Perspective. Viruses 2023; 15:2195. [PMID: 38005873 PMCID: PMC10675801 DOI: 10.3390/v15112195] [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: 09/27/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Genital herpes, primarily caused by herpes simplex virus-2 (HSV-2), remains a pressing global health concern. Its remarkable ability to intertwine with cellular processes, from harnessing host machinery for replication to subverting antiviral defenses like autophagy and programmed cell death, exemplifies the intricate interplay at the heart of its pathogenesis. While the biomedical community has extensively researched antiviral interventions, the efficiency of these strategies in managing HSV-2 remains suboptimal. Recognizing this, attention has shifted toward leveraging host cellular components to regulate HSV-2 replication and influence the cell cycle. Furthermore, innovative interventional strategies-including drug repurposing, microbivacs, connecting the host microbiome, and exploiting natural secondary metabolites-are emerging as potential game changers. This review summarizes the key steps in HSV-2 pathogenesis and newly discovered cellular interactions, presenting the latest developments in the field, highlighting existing challenges, and offering a fresh perspective on HSV-2's pathogenesis and the potential avenues for its treatment by targeting cellular proteins and pathways.
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Affiliation(s)
- Hemant Borase
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | - Deepak Shukla
- Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA;
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
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4
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Keng CT, Yogarajah T, Lee RCH, Muhammad IBH, Chia BS, Vasandani SR, Lim DS, Guo K, Wong YH, Mok CK, Chu JJH, Chew WL. AAV-CRISPR-Cas13 eliminates human enterovirus and prevents death of infected mice. EBioMedicine 2023; 93:104682. [PMID: 37390772 PMCID: PMC10363442 DOI: 10.1016/j.ebiom.2023.104682] [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: 02/15/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND RNA viruses account for many human diseases and pandemic events but are often not targetable by traditional therapeutics modalities. Here, we demonstrate that adeno-associated virus (AAV) -delivered CRISPR-Cas13 directly targets and eliminates the positive-strand EV-A71 RNA virus in cells and infected mice. METHODS We developed a Cas13gRNAtor bioinformatics pipeline to design CRISPR guide RNAs (gRNAs) that cleave conserved viral sequences across the virus phylogeny and developed an AAV-CRISPR-Cas13 therapeutics using in vitro viral plaque assay and in vivo EV-A71 lethally-infected mouse model. FINDINGS We show that treatment with a pool of AAV-CRISPR-Cas13-gRNAs designed using the bioinformatics pipeline effectively blocks viral replication and reduces viral titers in cells by >99.99%. We further demonstrate that AAV-CRISPR-Cas13-gRNAs prophylactically and therapeutically inhibited viral replication in infected mouse tissues and prevented death in a lethally challenged EV-A71-infected mouse model. INTERPRETATION Our results show that the bioinformatics pipeline designs efficient CRISPR-Cas13 gRNAs for direct viral RNA targeting to reduce viral loads. Additionally, this new antiviral AAV-CRISPR-Cas13 modality represents an effective direct-acting prophylactic and therapeutic agent against lethal RNA viral infections. FUNDING Agency for Science, Technology and Research (A∗STAR) Assured Research Budget, A∗STAR Central Research Fund UIBR SC18/21-1089UI, A∗STAR Industrial Alignment Fund Pre-Positioning (IAF-PP) grant H17/01/a0/012, MOE Tier 2 2017 (MOE2017-T2-1-078; MOE-T2EP30221-0005), and NUHSRO/2020/050/RO5+5/NUHS-COVID/4.
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Affiliation(s)
- Choong Tat Keng
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Thinesshwary Yogarajah
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Irfan Bin Hajis Muhammad
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Bing Shao Chia
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Suraj Rajan Vasandani
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Daryl Shern Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Ke Guo
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore
| | - Yi Hao Wong
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore
| | - Chee Keng Mok
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore
| | - Justin Jang Hann Chu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos #06-05, 138673, Singapore; Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Infectious Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore; NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore.
| | - Wei Leong Chew
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore 138672, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore.
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5
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Li S, Sun Y, Du M, Shangguan A, Liu Z, Li W, Lina L, Liu W, Zhang S, Han H. Graphene Oxide Nanoparticles Combined with CRISPR/Cas9 System Enable Efficient Inhibition of Pseudorabies Virus. Bioconjug Chem 2023; 34:326-332. [PMID: 36629744 DOI: 10.1021/acs.bioconjchem.2c00570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We describe an application where graphene oxide nanoparticles (GONs) enable combined inhibition of Pseudorabies Virus (PRV) through delivery of a CRISPR/Cas9 system for targeted cleaving of a PRV genome and direct interaction with viral particles. The sheeted GONs could load CRISPR plasmid DNA (pDNA) to form a small sized, near-spheroidal GONs-CRISPR complex, which enables CRISPR pDNA efficient intracellular delivery and transient expression under serum conditions. Cell studies showed that GONs-CRISPR could allow rapid cellular uptake, endolysosomes escape, and nucleus transport within 3 h. Virus studies demonstrated that the pure GONs have antiviral activity and GONs-CRISPR could significantly inhibit PRV replication and result in progeny PRV decreasing by approximately 4000 times in infected host cells. Transmission electron microscopy (TEM) imaging showed that GONs-CRISPR could destroy the PRV structures by directly interacting with viral particles. This GONs-based strategy may extend the advanced application of the CRISPR system for antiviral action.
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Affiliation(s)
- Shuojun Li
- State Key Laboratory of Agriculture Microbiology, College of life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yumei Sun
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China.,State Key Laboratory of Agriculture Microbiology, School of Animal Science and Technology, School of Animal Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Moqing Du
- State Key Laboratory of Agriculture Microbiology, College of Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Aishao Shangguan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongzhu Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Wentao Li
- State Key Laboratory of Agriculture Microbiology, School of Animal Science and Technology, School of Animal Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liu Lina
- Department of Biotechnology, School of Biology and Engineering, Guizhou Medical University, Guiyang, Guizhou 550025, China
| | - Wenju Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Shujun Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Heyou Han
- State Key Laboratory of Agriculture Microbiology, College of life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,State Key Laboratory of Agriculture Microbiology, College of Science, Huazhong Agricultural University, Wuhan, 430070, China
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6
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Tao S, Chen H, Li N, Fang Y, Xu Y, Liang W. Association of CRISPR-Cas System with the Antibiotic Resistance and Virulence Genes in Nosocomial Isolates of Enterococcus. Infect Drug Resist 2022; 15:6939-6949. [PMID: 36474907 PMCID: PMC9719680 DOI: 10.2147/idr.s388354] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/26/2022] [Indexed: 04/07/2024] Open
Abstract
PURPOSE This study aimed to investigate the prevalence of the CRISPR-Cas system in nosocomial isolates of Enterococcus and their possible association with antibiotic resistance and virulence genes. MATERIALS AND METHODS Identification and antimicrobial susceptibility of the microorganism were performed by the automatized VITEK 2 Compact system (bioMerieux, France). A total of 100 Enterococcus isolates were collected and identified by VITEK 2 Compact automatic microbial identification drug susceptibility analyzer. The prevalence of various CRISPR-Cas systems, antibiotic resistance genes and virulence genes were investigated by polymerase chain reaction (PCR). The prevalence of CRISPR-Cas systems associated with antibiotic resistance and virulence genes was performed by appropriate statistical tests. RESULTS A total of 100 isolates of Enterococcus were identified and there were 62/100(62.0%) Enterococcus faecalis isolates and 38/100(38.0%) Enterococcus faecalis isolates. In total, 46 (46.0%) of 100 isolates had at least one CRISPR-Cas locus. CRISPR elements were more prevalent in Enterococcus faecalis isolates. The results of PCR demonstrated that CRISPR1-Cas, orphan CRISPR2, and CRISPR3-Cas were present in 23 (23.0%), 42 (42.0%) and 5 (5.0%) Enterococcus isolates, respectively. Compared with CRISPR-Casnegative isolates, the CRISPR-Cas positive isolates showed significant lower resistance rates against ampicillin, erythromycin, levofloxacin, tetracycline, vancomycin, gentamicin, streptomycin, and rifampicin. Presumably consistent with drug susceptibility, fewer CRISPR loci were identified in vanA, tetM, ermB, aac6'-aph(2"), aadE, and ant(6) positive isolates. There was a significant negative correlation between the CRISPR-Cas locus and the enterococcal virulence factors enterococcal surface protein (esp) gene. CONCLUSION In conclusion, the results indicated that the absence of the CRISPR-Cas system was negatively associated with some antibiotic resistance in clinical isolates of Enterococcus faecalis and Enterococcus faecium. Also, there was a negative correlation with the carriage of antibiotic resistance genes. Furthermore, CRISPR-Cas may prevent some isolates from acquiring certain virulence factors.
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Affiliation(s)
- Shuan Tao
- School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, People’s Republic of China
| | - Huimin Chen
- School of Medicine, Jiangsu University, Zhenjiang, People’s Republic of China
| | - Na Li
- Bengbu Medical College, Bengbu, People’s Republic of China
| | - Yewei Fang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, People’s Republic of China
| | - Yao Xu
- School of Medicine, Ningbo University, Ningbo, People’s Republic of China
| | - Wei Liang
- Department of Clinical Laboratory, Ningbo First Hospital, Ningbo, People’s Republic of China
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7
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Wang D, Chen L, Li C, Long Q, Yang Q, Huang A, Tang H. CRISPR/Cas9 delivery by NIR-responsive biomimetic nanoparticles for targeted HBV therapy. J Nanobiotechnology 2022; 20:27. [PMID: 34991617 PMCID: PMC8740473 DOI: 10.1186/s12951-021-01233-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/29/2021] [Indexed: 12/17/2022] Open
Abstract
Background Currently, there are no curative drugs for hepatitis B virus (HBV). Complete elimination of HBV covalently closed circular DNA (cccDNA) is key to the complete cure of hepatitis B virus infection. The CRISPR/Cas9 system can directly destroy HBV cccDNA. However, a CRISPR/Cas9 delivery system with low immunogenicity and high efficiency has not yet been established. Moreover, effective implementation of precise remote spatiotemporal operations in CRISPR/Cas9 is a major limitation. Results In this work, we designed NIR-responsive biomimetic nanoparticles (UCNPs-Cas9@CM), which could effectively deliver Cas9 RNP to achieve effective genome editing for HBV therapy. HBsAg, HBeAg, HBV pgRNA and HBV DNA along with cccDNA in HBV-infected cells were found to be inhibited. These findings were confirmed in HBV-Tg mice, which did not exhibit significant cytotoxicity and minimal off-target DNA damage. Conclusions The UCNPs-based biomimetic nanoplatforms achieved the inhibition of HBV replication via CRISPR therapy and it is a potential system for efficient treatment of human HBV diseases. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-021-01233-4.
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Affiliation(s)
- Dan Wang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, 1 Yi Xue Yuan Road, Chongqing, 400016, China.,The People's Hospital of Rongchang District, Chongqing, 402460, China
| | - Ling Chen
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, 1 Yi Xue Yuan Road, Chongqing, 400016, China
| | - Chengbi Li
- The People's Hospital of Rongchang District, Chongqing, 402460, China
| | - Quanxin Long
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, 1 Yi Xue Yuan Road, Chongqing, 400016, China
| | - Qing Yang
- The People's Hospital of Rongchang District, Chongqing, 402460, China
| | - Ailong Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, 1 Yi Xue Yuan Road, Chongqing, 400016, China
| | - Hua Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, 1 Yi Xue Yuan Road, Chongqing, 400016, China.
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8
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Chan KG, Ang GY, Yu CY, Yean CY. Harnessing CRISPR-Cas to Combat COVID-19: From Diagnostics to Therapeutics. Life (Basel) 2021; 11:1210. [PMID: 34833086 PMCID: PMC8623262 DOI: 10.3390/life11111210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 10/31/2021] [Accepted: 11/03/2021] [Indexed: 12/24/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global threat with an ever-increasing death toll even after a year on. Hence, the rapid identification of infected individuals with diagnostic tests continues to be crucial in the on-going effort to combat the spread of COVID-19. Viral nucleic acid detection via real-time reverse transcription polymerase chain reaction (rRT-PCR) or sequencing is regarded as the gold standard for COVID-19 diagnosis, but these technically intricate molecular tests are limited to centralized laboratories due to the highly specialized instrument and skilled personnel requirements. Based on the current development in the field of diagnostics, the programmable clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system appears to be a promising technology that can be further explored to create rapid, cost-effective, sensitive, and specific diagnostic tools for both laboratory and point-of-care (POC) testing. Other than diagnostics, the potential application of the CRISPR-Cas system as an antiviral agent has also been gaining attention. In this review, we highlight the recent advances in CRISPR-Cas-based nucleic acid detection strategies and the application of CRISPR-Cas as a potential antiviral agent in the context of COVID-19.
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Affiliation(s)
- Kok Gan Chan
- International Genome Centre, Jiangsu University, Zhenjiang 212013, China;
- Institute of Marine Sciences, Shantou University, Shantou 515063, China
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Geik Yong Ang
- Faculty of Sports Science and Recreation, Universiti Teknologi MARA, Shah Alam 40450, Malaysia
| | - Choo Yee Yu
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - Chan Yean Yean
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Malaysia
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9
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Andrei G. Vaccines and Antivirals: Grand Challenges and Great Opportunities. FRONTIERS IN VIROLOGY 2021. [DOI: 10.3389/fviro.2021.666548] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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10
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Haddad CO, Kalt I, Shovman Y, Xia L, Schlesinger Y, Sarid R, Parnas O. Targeting the Kaposi's sarcoma-associated herpesvirus genome with the CRISPR-Cas9 platform in latently infected cells. Virol J 2021; 18:56. [PMID: 33731154 PMCID: PMC7966637 DOI: 10.1186/s12985-021-01527-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/04/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Kaposi's sarcoma-associated herpesvirus (KSHV) is a transforming gammaherpesvirus. Like other herpesviruses, KSHV infection is for life long and there is no treatment that can cure patients from the virus. In addition, there is an urgent need to target viral genes to study their role during the infection cycle. The CRISPR-Cas9 technology offers a means to target viral genomes and thus may offer a novel strategy for viral cure as well as for better understanding of the infection process. We evaluated the suitability of this platform for the targeting of KSHV. METHODS We have used the recombinat KSHV BAC16 genome, which contains an expression cassette encoding hygromycin-resistance and a GFP marker gene. Three genes were targeted: gfp, which serves as a marker for infection; orf45 encoding a lytic viral protein; and orf73, encoding LANA which is crucial for latent infection. The fraction of cells expressing GFP, viral DNA levels and LANA expression were monitored and viral genomes were sequenced. RESULTS We found that KSHV episomes can be targeted by CRISPR-Cas9. Interestingly, the quantity of KSHV DNA declined, even when target sites were not functionally important for latency. In addition, we show that antibiotic selection, used to maintain infection, interferes with the outcome of targeting. CONCLUSIONS Our study provides insights into the use of this fundamental approach for the study and manipulation of KSHV. It provides guidelines for the targeting CRISPR-Cas9 to the viral genome and for outcomes interpretation.
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Affiliation(s)
- Coral Orel Haddad
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Inna Kalt
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, 5290002, Ramat-Gan, Israel
| | - Yehuda Shovman
- The Concern Foundation at the Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University Faculty of Medicine, 91120, Jerusalem, Israel
| | - Lei Xia
- The Concern Foundation at the Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University Faculty of Medicine, 91120, Jerusalem, Israel
| | - Yehuda Schlesinger
- The Concern Foundation at the Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University Faculty of Medicine, 91120, Jerusalem, Israel
| | - Ronit Sarid
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, 5290002, Ramat-Gan, Israel.
| | - Oren Parnas
- The Concern Foundation at the Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University Faculty of Medicine, 91120, Jerusalem, Israel.
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11
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Koganti R, Yadavalli T, Naqvi RA, Shukla D, Naqvi AR. Pathobiology and treatment of viral keratitis. Exp Eye Res 2021; 205:108483. [PMID: 33556334 DOI: 10.1016/j.exer.2021.108483] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/12/2021] [Accepted: 01/29/2021] [Indexed: 12/17/2022]
Abstract
Keratitis is one of the most prevalent ocular diseases manifested by partial or total loss of vision. Amongst infectious (viz., microbes including bacteria, fungi, amebae, and viruses) and non-infectious (viz., eye trauma, chemical exposure, and ultraviolet exposure, contact lens) risk factors, viral keratitis has been demonstrated as one of the leading causes of corneal opacity. While many viruses have been shown to cause keratitis (such as rhabdoviruses, coxsackieviruses, etc.), herpesviruses are the predominant etiologic agent of viral keratitis. This chapter will summarize current knowledge on the prevalence, diagnosis, and pathobiology of viral keratitis. Virus-mediated immunomodulation of host innate and adaptive immune components is critical for viral persistence, and dysfunctional immune responses may cause destruction of ocular tissues leading to keratitis. Immunosuppressed or immunocompromised individuals may display recurring disease with pronounced severity. Early diagnosis of viral keratitis is beneficial for disease management and response to treatment. Finally, we have discussed current and emerging therapies to treat viral keratitis.
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Affiliation(s)
- Raghuram Koganti
- Department of Ophthalmology and Visual Sciences, University of Illinois Medical Center, Chicago, IL, 60612, USA
| | - Tejabhiram Yadavalli
- Department of Ophthalmology and Visual Sciences, University of Illinois Medical Center, Chicago, IL, 60612, USA
| | - Raza Ali Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Deepak Shukla
- Department of Ophthalmology and Visual Sciences, University of Illinois Medical Center, Chicago, IL, 60612, USA; Department of Microbiology and Immunology, University of Illinois at Chicago, IL, 60612, USA.
| | - Afsar R Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, IL, 60612, USA.
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Désaulniers K, Ortiz L, Dufour C, Claudel A, Plourde MB, Merindol N, Berthoux L. Editing of the TRIM5 Gene Decreases the Permissiveness of Human T Lymphocytic Cells to HIV-1. Viruses 2020; 13:E24. [PMID: 33375604 PMCID: PMC7824555 DOI: 10.3390/v13010024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 12/20/2020] [Accepted: 12/22/2020] [Indexed: 01/08/2023] Open
Abstract
Tripartite-motif-containing protein 5 isoform α (TRIM5α) is a cytoplasmic antiretroviral effector upregulated by type I interferons (IFN-I). We previously showed that two points mutations, R332G/R335G, in the retroviral capsid-binding region confer human TRIM5α the capacity to target and strongly restrict HIV-1 upon overexpression of the mutated protein. Here, we used clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-mediated homology-directed repair (HDR) to introduce these two mutations in the endogenous human TRIM5 gene. We found 6 out of 47 isolated cell clones containing at least one HDR-edited allele. One clone (clone 6) had both alleles containing R332G, but only one of the two alleles containing R335G. Upon challenge with an HIV-1 vector, clone 6 was significantly less permissive compared to unmodified cells, whereas the cell clones with monoallelic modifications were only slightly less permissive. Following interferon (IFN)-β treatment, inhibition of HIV-1 infection in clone 6 was significantly enhanced (~40-fold inhibition). TRIM5α knockdown confirmed that HIV-1 was inhibited by the edited TRIM5 gene products. Quantification of HIV-1 reverse transcription products showed that inhibition occurred through the expected mechanism. In conclusion, we demonstrate the feasibility of potently inhibiting a viral infection through the editing of innate effector genes. Our results also emphasize the importance of biallelic modification in order to reach significant levels of inhibition by TRIM5α.
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Affiliation(s)
| | | | | | | | | | | | - Lionel Berthoux
- Department of Medical Biology, Université du Québec à Trois-Rivières, Trois-Rivières, QC G9A 5H7, Canada; (K.D.); (L.O.); (C.D.); (A.C.); (M.B.P.); (N.M.)
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13
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Le TK, Paris C, Khan KS, Robson F, Ng WL, Rocchi P. Nucleic Acid-Based Technologies Targeting Coronaviruses. Trends Biochem Sci 2020; 46:351-365. [PMID: 33309323 PMCID: PMC7691141 DOI: 10.1016/j.tibs.2020.11.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently creating a global health emergency. This crisis is driving a worldwide effort to develop effective vaccines, prophylactics, and therapeutics. Nucleic acid (NA)-based treatments hold great potential to combat outbreaks of coronaviruses (CoVs) due to their rapid development, high target specificity, and the capacity to increase druggability. Here, we review key anti-CoV NA-based technologies, including antisense oligonucleotides (ASOs), siRNAs, RNA-targeting clustered regularly interspaced short palindromic repeats-CRISPR-associated protein (CRISPR-Cas), and mRNA vaccines, and discuss improved delivery methods and combination therapies with other antiviral drugs.
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Affiliation(s)
- Thi Khanh Le
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes Marseille, France; Department of Life Sciences, University of Science and Technology of Hanoi (USTH), Hanoi, Vietnam
| | - Clément Paris
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes Marseille, France
| | - Khadija Shahed Khan
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Fran Robson
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Wai-Lung Ng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong.
| | - Palma Rocchi
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm UMR1068, CNRS UMR7258, Aix-Marseille University U105, Institut Paoli-Calmettes Marseille, France.
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Shiri I, Abdollahi H, Atashzar MR, Rahmim A, Zaidi H. A theranostic approach based on radiolabeled antiviral drugs, antibodies and CRISPR-associated proteins for early detection and treatment of SARS-CoV-2 disease. Nucl Med Commun 2020; 41:837-840. [PMID: 32796470 PMCID: PMC7485524 DOI: 10.1097/mnm.0000000000001269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/04/2020] [Indexed: 01/18/2023]
Affiliation(s)
- Isaac Shiri
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
| | - Hamid Abdollahi
- Department of Radiologic Sciences and Medical Physics, Faculty of Allied Medicine, Kerman University of Medical Science, Kerman
| | - Mohammad Reza Atashzar
- Department of Immunology, School of Medicine, Fasa University of Medical Science, Fasa, Iran
| | - Arman Rahmim
- Departments of Radiology and Physics, University of British Columbia
- Department of Integrative Oncology, BC Cancer Research Centre, Vancouver BC, Canada
| | - Habib Zaidi
- Division of Nuclear Medicine and Molecular Imaging, Geneva University Hospital, Geneva, Switzerland
- Geneva University Neurocenter, Geneva University, Geneva, Switzerland
- Department of Nuclear Medicine and Molecular Imaging, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Nuclear Medicine, University of Southern Denmark, Odense, Denmark
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15
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Naqvi AR. Immunomodulatory roles of human herpesvirus-encoded microRNA in host-virus interaction. Rev Med Virol 2020; 30:e2081. [PMID: 31432608 PMCID: PMC7398577 DOI: 10.1002/rmv.2081] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/18/2022]
Abstract
Human herpesviruses (HHV) are large, double stranded, DNA viruses with high seroprevalence across the globe. Clinical manifestation of primary HHV infection resolve shortly, however, this period is prolonged in immunocompromised patients or individuals with suppressed immunity. Examining molecular mechanisms of HHV-encoded virulence factors can provide finer details of HHV-host interaction. A unique genetic feature of most members of HHV is that they encode multiple microRNAs (miR). In this review, I will provide mechanistic insights into the immunomodulatory functions of herpesvirus-encoded viral miR (v-miR) that favor viral persistence and spread by ingenious immune evasion schemes. Similar to host miR, v-miR can simultaneously regulate expression of multiple transcripts including host- and virus-derived. V-miRs, by virtue of their direct interaction with various transcripts, can regulate expression of critical components of host innate and adaptive immune system. V-miRs are also exported through exosomal route and gain entry into various cells even at distant sites, thereby allowing HHV to manipulate cellular and tissue immunity. Targeting v-miR may serve as a novel and promising therapeutic candidate to mitigate HHV-mediated clinical manifestations.
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Affiliation(s)
- Afsar R Naqvi
- Mucosal Immunology Lab, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
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Delviks-Frankenberry KA, Ackerman D, Timberlake ND, Hamscher M, Nikolaitchik OA, Hu WS, Torbett BE, Pathak VK. Development of Lentiviral Vectors for HIV-1 Gene Therapy with Vif-Resistant APOBEC3G. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:1023-1038. [PMID: 31778955 PMCID: PMC6889484 DOI: 10.1016/j.omtn.2019.10.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/17/2019] [Accepted: 10/23/2019] [Indexed: 12/29/2022]
Abstract
Strategies to control HIV-1 replication without antiviral therapy are needed to achieve a functional cure. To exploit the innate antiviral function of restriction factor cytidine deaminase APOBEC3G (A3G), we developed self-activating lentiviral vectors that efficiently deliver HIV-1 Vif-resistant mutant A3G-D128K to target cells. To circumvent APOBEC3 expression in virus-producing cells, which diminishes virus infectivity, a vector containing two overlapping fragments of A3G-D128K was designed that maintained the gene in an inactive form in the virus-producer cells. However, during transduction of target cells, retroviral recombination between the direct repeats reconstituted an active A3G-D128K in 89%-98% of transduced cells. Lentiviral vectors that expressed A3G-D128K transduced CD34+ hematopoietic stem and progenitor cells with a high efficiency (>30%). A3G-D128K expression in T cell lines CEM, CEMSS, and PM1 potently inhibited spreading infection of several HIV-1 subtypes by C-to-U deamination leading to lethal G-to-A hypermutation and inhibition of reverse transcription. SIVmac239 and HIV-2 were not inhibited, since their Vifs degraded A3G-D128K. A3G-D128K expression in CEM cells potently suppressed HIV-1 replication for >3.5 months without detectable resistant virus, suggesting a high genetic barrier for the emergence of A3G-D128K resistance. Because of this, A3G-D128K expression in HIV-1 target cells is a potential anti-HIV gene therapy approach that could be combined with other therapies for the treatment and functional cure of HIV-1 infection.
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Affiliation(s)
- Krista A Delviks-Frankenberry
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Daniel Ackerman
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | | | - Maria Hamscher
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Olga A Nikolaitchik
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA
| | | | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute at Frederick, Frederick, MD 21702, USA.
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