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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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Didara Z, Reithofer F, Zöttl K, Jürets A, Kiss I, Witte A, Klein R. Inhibition of adenovirus replication by CRISPR-Cas9-mediated targeting of the viral E1A gene. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:48-60. [PMID: 36950281 PMCID: PMC10025986 DOI: 10.1016/j.omtn.2023.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
DNA-targeting CRISPR-Cas systems are able to cleave dsDNA in mammalian cells. Accordingly, they have been employed to target the genomes of dsDNA viruses, mostly when present in cells in a non-replicative state with low copy numbers. However, the sheer amount of viral DNA produced within a very short time by certain lytically replicating viruses potentially brings the capacities of CRISPR-Cas systems to their limits. The accessibility of viral DNA replication sites, short time of accessibility of the DNA before encapsidation, or its complexation with shielding proteins are further potential hurdles. Adenoviruses are fast-replicating dsDNA viruses for which no approved antiviral therapy currently exists. We evaluated the potency of CRISPR-Cas9 in inhibiting the replication of human adenovirus 5 in vitro by targeting its master regulator E1A with a set of guide RNAs and observed a decrease in infectious virus particles by up to three orders of magnitude. Target DNA cleavage also negatively impacted the amount of viral DNA accumulated during the infection cycle. This outcome was mainly caused by specific deletions, inversions, and duplications occurring between target sites, which abolished most E1A functions in most cases. Additionally, we compared two strategies for multiplex gRNA expression and obtained comparable results.
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Affiliation(s)
- Zrinka Didara
- Department of Life Sciences, University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria
| | - Florian Reithofer
- Department of Life Sciences, University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria
| | - Karina Zöttl
- Department of Life Sciences, University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria
| | - Alexander Jürets
- Department of Life Sciences, University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria
| | - Izabella Kiss
- Department of Life Sciences, University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria
| | - Angela Witte
- Department of Microbiology, Immunobiology, and Genetics, Max Perutz Labs, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Reinhard Klein
- Department of Life Sciences, University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria
- Corresponding author: Reinhard Klein, Department of Life Sciences, University of Applied Sciences Krems, Piaristengasse 1, 3500 Krems, Austria.
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Prospects for using CRISPR-Cas9 system in the treatment of human viral diseases. ACTA BIOMEDICA SCIENTIFICA 2023. [DOI: 10.29413/abs.2023-8.1.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Abstract
The aim. To analyze the possibility of using the genetic mechanisms of CRISPR-Cas9 technology in the prevention and treatment of certain viral diseases.Materials and methods. The search for publications was carried out in Russian and foreign literature using the following search engines: RSCI, Cyberleninka, eLibrary, PubMed, Cochrane Library, etc. A review of domestic and international scientific papers on the research topic was carried out using search keywords: CRISPR, genetic engineering, genome editing, Cas9, sgRNA.Results. A review of using CRISPR-Cas9 method (“genetic scissors”) as a gene therapy for some viral diseases was carried out, and its main advantages and disadvantages were revealed. An analysis of the data of scientific studies on genetic research methods over the past decade discovers the main aspects of CRISPR-Cas9 technology, modern classification and prospects for using this technology in clinical practice for the treatment and prevention of human viral diseases. The possibilities of creating a more versatile and stable version of the CRISPR-Cas9 technology are considered. Particular attention is paid to the technological difficulties and obstacles that scientists face when implementing this system for targeted use in clinical medicine.Conclusion. One of the rapidly developing areas in science giving promising prospects for modern healthcare is genetic engineering, especially in cases where scientific developments are applied in clinical practice. The discovery of “genetic scissors” technology has revolutionized all medicine. Wide opportunities for developing new treatment methods for many viral diseases and creating conditions for their early prevention opened up for the medical community. In the future, with the introduction of this technology into clinical practice, it will become possible to treat diseases that have not previously responded to ongoing therapy and were considered incurable.
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Rabaan AA, AlSaihati H, Bukhamsin R, Bakhrebah MA, Nassar MS, Alsaleh AA, Alhashem YN, Bukhamseen AY, Al-Ruhimy K, Alotaibi M, Alsubki RA, Alahmed HE, Al-Abdulhadi S, Alhashem FA, Alqatari AA, Alsayyah A, Farahat RA, Abdulal RH, Al-Ahmed AH, Imran M, Mohapatra RK. Application of CRISPR/Cas9 Technology in Cancer Treatment: A Future Direction. Curr Oncol 2023; 30:1954-1976. [PMID: 36826113 PMCID: PMC9955208 DOI: 10.3390/curroncol30020152] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023] Open
Abstract
Gene editing, especially with clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9), has advanced gene function science. Gene editing's rapid advancement has increased its medical/clinical value. Due to its great specificity and efficiency, CRISPR/Cas9 can accurately and swiftly screen the whole genome. This simplifies disease-specific gene therapy. To study tumor origins, development, and metastasis, CRISPR/Cas9 can change genomes. In recent years, tumor treatment research has increasingly employed this method. CRISPR/Cas9 can treat cancer by removing genes or correcting mutations. Numerous preliminary tumor treatment studies have been conducted in relevant fields. CRISPR/Cas9 may treat gene-level tumors. CRISPR/Cas9-based personalized and targeted medicines may shape tumor treatment. This review examines CRISPR/Cas9 for tumor therapy research, which will be helpful in providing references for future studies on the pathogenesis of malignancy and its treatment.
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Affiliation(s)
- Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Hajir AlSaihati
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Rehab Bukhamsin
- Dammam Regional Laboratory and Blood Bank, Dammam 31411, Saudi Arabia
| | - Muhammed A. Bakhrebah
- Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Majed S. Nassar
- Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Abdulmonem A. Alsaleh
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Yousef N. Alhashem
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Ammar Y. Bukhamseen
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi Arabia
| | - Khalil Al-Ruhimy
- Department of Public Health, Ministry of Health, Riyadh 14235, Saudi Arabia
| | - Mohammed Alotaibi
- Department of Public Health, Ministry of Health, Riyadh 14235, Saudi Arabia
| | - Roua A. Alsubki
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Hejji E. Alahmed
- Department of Laboratory and Blood Bank, King Fahad Hospital, Al Hofuf 36441, Saudi Arabia
| | - Saleh Al-Abdulhadi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Riyadh 11942, Saudi Arabia
- Saleh Office for Medical Genetic and Genetic Counseling Services, The House of Expertise, Prince Sattam Bin Abdulaziz University, Dammam 32411, Saudi Arabia
| | - Fatemah A. Alhashem
- Laboratory Medicine Department, Hematopathology Division, King Fahad Hospital of the University, Al-Khobar 31441, Saudi Arabia
| | - Ahlam A. Alqatari
- Hematopathology Department, Clinical Pathology, Al-Dorr Specialist Medical Center, Qatif 31911, Saudi Arabia
| | - Ahmed Alsayyah
- Department of Pathology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | - Rwaa H. Abdulal
- Department of Biology, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Vaccines and Immunotherapy Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ali H. Al-Ahmed
- Dammam Health Network, Eastern Health Cluster, Dammam 31444, Saudi Arabia
| | - Mohd. Imran
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Ranjan K. Mohapatra
- Department of Chemistry, Government College of Engineering, Keonjhar 758002, India
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Prezioso C, Pietropaolo V, Moens U, Ciotti M. JC polyomavirus: a short review of its biology, its association with progressive multifocal leukoencephalopathy, and the diagnostic value of different methods to manifest its activity or presence. Expert Rev Mol Diagn 2023; 23:143-157. [PMID: 36786077 DOI: 10.1080/14737159.2023.2179394] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
INTRODUCTION JC polyomavirus is the causative agent of progressive multifocal leukoencephalopathy (PML), a demyelinating disease resulting from the lytic infection of oligodendrocytes that may develop in immunosuppressed individuals: HIV1 infected or individuals under immunosuppressive therapies. Understanding the biology of JCPyV is necessary for a proper patient management, the development of diagnostic tests, and risk stratification. AREAS COVERED The review covers different areas of expertise including the genomic characterization of JCPyV strains detected in different body compartments (urine, plasma, and cerebrospinal fluid) of PML patients, viral mutations, molecular diagnostics, viral miRNAs, and disease. EXPERT OPINION The implementation of molecular biology techniques improved our understanding of JCPyV biology. Deep sequencing analysis of viral genomes revealed the presence of viral quasispecies in the cerebrospinal fluid of PML patients characterized by noncoding control region rearrangements and VP1 mutations. These neurotropic JCPyV variants present enhanced replication and an altered cell tropism that contribute to PML development. Monitoring these variants may be relevant for the identification of patients at risk of PML. Multiplex realtime PCR targeting both the LTAg and the archetype NCCR could be used to identify them. Failure to amplify NCCR should indicate the presence of a JCPyV prototype speeding up the diagnostic process.
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Affiliation(s)
- Carla Prezioso
- Department of Public Health and Infectious Diseases, "Sapienza" University of Rome Rome, Italy.,IRCSS San Raffaele Roma, Microbiology of Chronic Neuro-Degenerative Pathologies Rome, Italy
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, "Sapienza" University of Rome Rome, Italy
| | - Ugo Moens
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø-The Arctic University of Norway Tromsø, Norway
| | - Marco Ciotti
- Virology Unit, Polyclinic Tor Vergata Rome, Italy
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Bhujbal S, Bhujbal R, Giram P. An overview: CRISPR/Cas-based gene editing for viral vaccine development. Expert Rev Vaccines 2022; 21:1581-1593. [PMID: 35959589 DOI: 10.1080/14760584.2022.2112952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION : Gene-editing technology revolutionized vaccine manufacturing and offers a variety of benefits over traditional vaccinations, such as improved immune response, higher production rate, stability, precise immunogenic activity, and fewer adverse effects. The more recently discovered Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/associated protein 9 (Cas9) system has become the most widely utilized technology based on its efficiency, utility, flexibility, versatility, ease of use, and cheaper compared to other gene-editing techniques. Considering its wider scope for genomic modification, CRISPR/Cas9-based technology's potential is explored for vaccine development. AREAS COVERED : In this review, we will address the recent advances in the CRISPR/Cas system for the development of vaccines and viral vectors for delivery. In addition, we will discuss strategies for the development of the vaccine, as well as the limitations and future prospects of the CRISPR/Cas system. EXPERT OPINION : Human and animal viruses have been exposed to antiviral CRISPR/Cas9-based engineering to prevent infection, which uses knockout, knock-in, gene activation/deactivation, RNA targeting, and editing cell lines strategies for gene editing of viruses. Because of that CRISPR/Cas system is used to boost the vaccine production yield by removing unwanted genes that cause disease or are required for viral infection.
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Affiliation(s)
- Santosh Bhujbal
- Department of Pharmacognosy, Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Sant. Tukaram Nagar Pimpri, Pune, Maharashtra (India) -411018
| | - Rushikesh Bhujbal
- Department of Quality Assurance Technique, Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Sant. Tukaram Nagar Pimpri, Pune, Maharashtra (India) -411018
| | - Prabhanjan Giram
- Department of Pharmaceutics, Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Sant. Tukaram Nagar Pimpri, Pune, Maharashtra (India) -411018.,Department of Pharmaceutics, Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA- 14260-1660
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Mir TUG, Wani AK, Akhtar N, Shukla S. CRISPR/Cas9: Regulations and challenges for law enforcement to combat its dual-use. Forensic Sci Int 2022; 334:111274. [DOI: 10.1016/j.forsciint.2022.111274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 12/15/2022]
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Akram F, Sahreen S, Aamir F, Haq IU, Malik K, Imtiaz M, Naseem W, Nasir N, Waheed HM. An Insight into Modern Targeted Genome-Editing Technologies with a Special Focus on CRISPR/Cas9 and its Applications. Mol Biotechnol 2022; 65:227-242. [PMID: 35474409 PMCID: PMC9041284 DOI: 10.1007/s12033-022-00501-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/13/2022] [Indexed: 01/18/2023]
Abstract
Genome-editing technology has enabled scientists to make changes in model organisms' DNA at the genomic level to get biotechnologically important products from them. Most commonly employed technologies for this purpose are transcription activator like effector nucleases (TALENs), homing-endonucleases or meganucleases, zinc finger nucleases (ZFNs), and clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (Cas9). Among these tools, CRISPR/Cas9 is most preferred because it's easy to use, has a small mutation rate, has great effectiveness, low cost of development, and decreased rate of advancement. CRISPR/Cas9 has a lot of applications in plants, animals, humans, and microbes. It also has applications in many fields such as horticulture, cancer, food biotechnology, and targeted human genome treatments. CRISPR technology has shown great potential for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic to provide early and easy detection methods, possible treatment, and vaccine development. In the present review, genome-editing tools with their basic assembly and features have been discussed. Exceptional notice has been paid to CRISPR technology on basis of its structure and significant applications in humans, plants, animals, and microbes such as bacteria, viruses, and fungi. The review has also shed a little light on current CRISPR challenges and future perspectives.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Sania Sahreen
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Farheen Aamir
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Ikram ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan ,Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Kausar Malik
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Memoona Imtiaz
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Waqas Naseem
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Narmeen Nasir
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
| | - Hafiza Mariam Waheed
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000 Pakistan
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Jamehdor S, Pajouhanfar S, Saba S, Uzan G, Teimoori A, Naserian S. Principles and Applications of CRISPR Toolkit in Virus Manipulation, Diagnosis, and Virus-Host Interactions. Cells 2022; 11:999. [PMID: 35326449 PMCID: PMC8946942 DOI: 10.3390/cells11060999] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 02/04/2023] Open
Abstract
Viruses are one of the most important concerns for human health, and overcoming viral infections is a worldwide challenge. However, researchers have been trying to manipulate viral genomes to overcome various disorders, including cancer, for vaccine development purposes. CRISPR (clustered regularly interspaced short palindromic repeats) is becoming one of the most functional and widely used tools for RNA and DNA manipulation in multiple organisms. This approach has provided an unprecedented opportunity for creating simple, inexpensive, specific, targeted, accurate, and practical manipulations of viruses, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus-1 (HIV-1), and vaccinia virus. Furthermore, this method can be used to make an effective and precise diagnosis of viral infections. Nevertheless, a valid and scientifically designed CRISPR system is critical to make more effective and accurate changes in viruses. In this review, we have focused on the best and the most effective ways to design sgRNA, gene knock-in(s), and gene knock-out(s) for virus-targeted manipulation. Furthermore, we have emphasized the application of CRISPR technology in virus diagnosis and in finding significant genes involved in virus-host interactions.
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Affiliation(s)
- Saleh Jamehdor
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan 989155432609, Iran;
| | - Sara Pajouhanfar
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Sadaf Saba
- Center for Molecular Medicine & Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA;
| | - Georges Uzan
- INSERM UMR-S-MD 1197, Hôpital Paul Brousse, 94800 Villejuif, France;
- Paris-Saclay University, 94800 Villejuif, France
| | - Ali Teimoori
- Department of Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan 6517838738, Iran
| | - Sina Naserian
- INSERM UMR-S-MD 1197, Hôpital Paul Brousse, 94800 Villejuif, France;
- Paris-Saclay University, 94800 Villejuif, France
- CellMedEx, 94100 Saint Maur Des Fossés, France
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Herskovitz J, Hasan M, Patel M, Kevadiya BD, Gendelman HE. Pathways Toward a Functional HIV-1 Cure: Balancing Promise and Perils of CRISPR Therapy. Methods Mol Biol 2022; 2407:429-445. [PMID: 34985679 PMCID: PMC9262118 DOI: 10.1007/978-1-0716-1871-4_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
First identified as a viral defense mechanism, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) has been transformed into a gene-editing tool. It now affords promise in the treatment and potential eradication of a range of divergent genetic, cancer, infectious, and degenerative diseases. Adapting CRISPR-Cas into a programmable endonuclease directed guide RNA (gRNA) has attracted international attention. It was recently awarded the 2020 Nobel Prize in Chemistry. The limitations of this technology have also been identified and work has been made in providing potential remedies. For treatment of the human immunodeficiency virus type one (HIV-1), in particular, a CRISPR-Cas9 approach was adapted to target then eliminate latent proviral DNA. To this end, we reviewed the promise and perils of CRISPR-Cas gene-editing strategies for HIV-1 elimination. Obstacles include precise delivery to reservoir tissue and cell sites of latent HIV-1 as well as assay sensitivity and specificity. The detection and consequent excision of common viral strain sequences and the avoidance of off-target activity will serve to facilitate a final goal of HIV-1 DNA elimination and accelerate testing in infected animals ultimately for use in man.
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Affiliation(s)
- Jonathan Herskovitz
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Mahmudul Hasan
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Milankumar Patel
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Bhavesh D Kevadiya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Howard E Gendelman
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA.
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA.
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Pandey M, Ojha D, Bansal S, Rode AB, Chawla G. From bench side to clinic: Potential and challenges of RNA vaccines and therapeutics in infectious diseases. Mol Aspects Med 2021; 81:101003. [PMID: 34332771 DOI: 10.1016/j.mam.2021.101003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/27/2021] [Accepted: 07/16/2021] [Indexed: 12/14/2022]
Abstract
The functional and structural versatility of Ribonucleic acids (RNAs) makes them ideal candidates for overcoming the limitations imposed by small molecule-based drugs. Hence, RNA-based biopharmaceuticals such as messenger RNA (mRNA) vaccines, antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), microRNA mimics, anti-miRNA oligonucleotides (AMOs), aptamers, riboswitches, and CRISPR-Cas9 are emerging as vital tools for the treatment and prophylaxis of many infectious diseases. Some of the major challenges to overcome in the area of RNA-based therapeutics have been the instability of single-stranded RNAs, delivery to the diseased cell, and immunogenicity. However, recent advancements in the delivery systems of in vitro transcribed mRNA and chemical modifications for protection against nucleases and reducing the toxicity of RNA have facilitated the entry of several exogenous RNAs into clinical trials. In this review, we provide an overview of RNA-based vaccines and therapeutics, their production, delivery, current advancements, and future translational potential in treating infectious diseases.
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Affiliation(s)
- Manish Pandey
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Divya Ojha
- Laboratory of Synthetic Biology, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Sakshi Bansal
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India
| | - Ambadas B Rode
- Laboratory of Synthetic Biology, Regional Centre for Biotechnology, Faridabad, 121001, India.
| | - Geetanjali Chawla
- RNA Biology Laboratory, Regional Centre for Biotechnology, Faridabad, 121001, India.
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12
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May D, Bellizzi A, Kassa W, Cipriaso JM, Caocci M, Wollebo HS. IFNα and β Mediated JCPyV Suppression through C/EBPβ-LIP Isoform. Viruses 2021; 13:v13101937. [PMID: 34696366 PMCID: PMC8537971 DOI: 10.3390/v13101937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/26/2021] [Accepted: 09/22/2021] [Indexed: 12/25/2022] Open
Abstract
Polyomavirus JC (JCPyV) causes the demyelinating disease progressive multifocal leukoencephalopathy (PML). JCPyV infection is very common in childhood and, under conditions of severe immunosuppression, JCPyV may reactivate to cause PML. JC viral proteins expression is regulated by the JCPyV non-coding control region (NCCR), which contains binding sites for cellular transcriptional factors which regulate JCPyV transcription. Our earlier studies suggest that JCPyV reactivation occurs within glial cells due to cytokines such as TNF-α which stimulate viral gene expression. In this study, we examined interferon-α (IFNα) or β (IFNβ) which have a negative effect on JCPyV transcriptional regulation. We also showed that these interferons induce the endogenous liver inhibitory protein (LIP), an isoform of CAAT/enhancer binding protein beta (C/EBPβ). Treatment of glial cell line with interferons increases the endogenous level of C/EBPβ-LIP. Furthermore, we showed that the negative regulatory role of the interferons in JCPyV early and late transcription and viral replication is more pronounced in the presence of C/EBPβ-LIP. Knockdown of C/EBPβ-LIP by shRNA reverse the inhibitory effect on JCPyV viral replication. Therefore, IFNα and IFNβ negatively regulate JCPyV through induction of C/EBPβ-LIP, which together with other cellular transcriptional factors may control the balance between JCPyV latency and activation.
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Affiliation(s)
- Dana May
- Department of Neuroscience, Center for Neurovirology—Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA; (D.M.); (A.B.); (J.M.C.); (M.C.)
| | - Anna Bellizzi
- Department of Neuroscience, Center for Neurovirology—Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA; (D.M.); (A.B.); (J.M.C.); (M.C.)
| | - Workineh Kassa
- Mayo Clinic Hospital and Health Care, 200 First St. S.W., Rochester, MN 55905, USA;
| | - John M. Cipriaso
- Department of Neuroscience, Center for Neurovirology—Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA; (D.M.); (A.B.); (J.M.C.); (M.C.)
| | - Maurizio Caocci
- Department of Neuroscience, Center for Neurovirology—Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA; (D.M.); (A.B.); (J.M.C.); (M.C.)
| | - Hassen S. Wollebo
- Department of Neuroscience, Center for Neurovirology—Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA 19140, USA; (D.M.); (A.B.); (J.M.C.); (M.C.)
- Correspondence: ; Tel.: +1-215-707-7137; Fax: +1-215-707-4888
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Sun J, Wang J, Zheng D, Hu X. Advances in therapeutic application of CRISPR-Cas9. Brief Funct Genomics 2021; 19:164-174. [PMID: 31769791 DOI: 10.1093/bfgp/elz031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/04/2019] [Accepted: 10/03/2019] [Indexed: 02/06/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is one of the most versatile and efficient gene editing technologies, which is derived from adaptive immune strategies for bacteria and archaea. With the remarkable development of programmable nuclease-based genome engineering these years, CRISPR-Cas9 system has developed quickly in recent 5 years and has been widely applied in countless areas, including genome editing, gene function investigation and gene therapy both in vitro and in vivo. In this paper, we briefly introduce the mechanisms of CRISPR-Cas9 tool in genome editing. More importantly, we review the recent therapeutic application of CRISPR-Cas9 in various diseases, including hematologic diseases, infectious diseases and malignant tumor. Finally, we discuss the current challenges and consider thoughtfully what advances are required in order to further develop the therapeutic application of CRISPR-Cas9 in the future.
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Affiliation(s)
- Jinyu Sun
- Sparkfire Scientific Research Group, Nanjing Medical University, China
| | - Jianchu Wang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, No. 18 Zhongshan Road, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Donghui Zheng
- Department of Nephrology, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Xiaorong Hu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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Ghorbani A, Hadifar S, Salari R, Izadpanah K, Burmistrz M, Afsharifar A, Eskandari MH, Niazi A, Denes CE, Neely GG. A short overview of CRISPR-Cas technology and its application in viral disease control. Transgenic Res 2021; 30:221-238. [PMID: 33830423 PMCID: PMC8027712 DOI: 10.1007/s11248-021-00247-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/26/2021] [Indexed: 12/19/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) together with CRISPR-associated (Cas) proteins have catalysed a revolution in genetic engineering. Native CRISPR-Cas systems exist in many bacteria and archaea where they provide an adaptive immune response through sequence-specific degradation of an invading pathogen's genome. This system has been reconfigured for use in genome editing, drug development, gene expression regulation, diagnostics, the prevention and treatment of cancers, and the treatment of genetic and infectious diseases. In recent years, CRISPR-Cas systems have been used in the diagnosis and control of viral diseases, for example, CRISPR-Cas12/13 coupled with new amplification techniques to improve the specificity of sequence-specific fluorescent probe detection. Importantly, CRISPR applications are both sensitive and specific and usually only require commonly available lab equipment. Unlike the canonical Cas9 which is guided to double-stranded DNA sites of interest, Cas13 systems target RNA sequences and thus can be employed in strategies directed against RNA viruses or for transcriptional silencing. Many challenges remain for these approach, including issues with specificity and the requirement for better mammalian delivery systems. In this review, we summarize the applications of CRISPR-Cas systems in controlling mammalian viral infections. Following necessary improvements, it is expected that CRISPR-Cas systems will be used effectively for such applications in the future.
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Affiliation(s)
- Abozar Ghorbani
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran.
| | - Shima Hadifar
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Roya Salari
- Institute of Biotechnology, School of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Michal Burmistrz
- Department of Molecular Microbiology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, 02-089, Warsaw, Poland
| | - Alireza Afsharifar
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Mohammad Hadi Eskandari
- Department of Food Science and Technology, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Christopher E Denes
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW, 2006, Australia
| | - G Gregory Neely
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW, 2006, Australia
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15
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Nidhi S, Anand U, Oleksak P, Tripathi P, Lal JA, Thomas G, Kuca K, Tripathi V. Novel CRISPR-Cas Systems: An Updated Review of the Current Achievements, Applications, and Future Research Perspectives. Int J Mol Sci 2021; 22:3327. [PMID: 33805113 PMCID: PMC8036902 DOI: 10.3390/ijms22073327] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 12/11/2022] Open
Abstract
According to Darwin's theory, endless evolution leads to a revolution. One such example is the Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-Cas system, an adaptive immunity system in most archaea and many bacteria. Gene editing technology possesses a crucial potential to dramatically impact miscellaneous areas of life, and CRISPR-Cas represents the most suitable strategy. The system has ignited a revolution in the field of genetic engineering. The ease, precision, affordability of this system is akin to a Midas touch for researchers editing genomes. Undoubtedly, the applications of this system are endless. The CRISPR-Cas system is extensively employed in the treatment of infectious and genetic diseases, in metabolic disorders, in curing cancer, in developing sustainable methods for fuel production and chemicals, in improving the quality and quantity of food crops, and thus in catering to global food demands. Future applications of CRISPR-Cas will provide benefits for everyone and will save countless lives. The technology is evolving rapidly; therefore, an overview of continuous improvement is important. In this review, we aim to elucidate the current state of the CRISPR-Cas revolution in a tailor-made format from its discovery to exciting breakthroughs at the application level and further upcoming trends related to opportunities and challenges including ethical concerns.
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Affiliation(s)
- Sweta Nidhi
- Department of Genomics and Bioinformatics, Aix-Marseille University, 13007 Marseille, France;
| | - Uttpal Anand
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel;
| | - Patrik Oleksak
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
| | - Pooja Tripathi
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India;
| | - Jonathan A. Lal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India; (J.A.L.); (G.T.)
| | - George Thomas
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India; (J.A.L.); (G.T.)
| | - Kamil Kuca
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, 50003 Hradec Kralove, Czech Republic;
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, Uttar Pradesh, India; (J.A.L.); (G.T.)
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16
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Sar P, Dalai S. CRISPR/Cas9 in epigenetics studies of health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:309-343. [PMID: 34127198 DOI: 10.1016/bs.pmbts.2021.01.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Epigenetics is the heritable phenotypic changes without altering the genotype. Epigenetic processes are such as histone methylation, acetylation, ubiquitination, sumoylation, phosphorylation, ADP ribosylation, DNA methylation and non-coding RNAs interactions associated with structural changes in chromatin. The change of structure is either open chromatin for "active" state or closed chromatin for "inactive" state, that regulates important biological phenomenon like chromatin condensation, gene expression, DNA repair, cellular development, differentiation and homeostasis, etc. However, dysregulation of epigenetic patterns causes diseases like cancer, diabetes, neurological disorder, infectious diseases, autoimmunity etc. Besides, the most important clinical uses of Epigenetics studies are i. identification of disease biomarkers and ii. development of their therapeutics. Epigenetic therapies include epi-drugs, combinatorial therapy, nanocarriers, plant-derived products that are being used for changing the epigenetic pattern to reverse gene expression. However, the developed epi- drugs cause off-target gene and transposable elements activation; promote mutagenesis and carcinogenesis in normal cells, are the major hurdles regarding their clinical use. Therefore, advanced epigenetic therapeutics are required to develop target-specific epigenetic modifications to reverse gene expression pattern. CRISPR-Cas9 (Clustered Regularly Interspaced Palindrome Repeats-associated protein 9) system-mediated gene activation mechanism paves new methods of target-specific epigenetic therapeutics to cure diseases. In this chapter, we discuss how CRISPR/Cas9 and dCas9 have recently been engineered for epigenome editing. Different strategies have been discussed used for epigenome editing based on their efficacy and complexity. Last but not least we have discussed the limitations, different uses of CRISPR/Cas9 and dCas9 in the area of genetic engineering.
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Affiliation(s)
- Pranati Sar
- Institute of Science, NIRMA University, Ahmedabad, India.
| | - Sarat Dalai
- Institute of Science, NIRMA University, Ahmedabad, India.
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17
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Caobi A, Dutta RK, Garbinski LD, Esteban-Lopez M, Ceyhan Y, Andre M, Manevski M, Ojha CR, Lapierre J, Tiwari S, Parira T, El-Hage N. The Impact of CRISPR-Cas9 on Age-related Disorders: From Pathology to Therapy. Aging Dis 2020; 11:895-915. [PMID: 32765953 PMCID: PMC7390517 DOI: 10.14336/ad.2019.0927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 09/27/2019] [Indexed: 12/11/2022] Open
Abstract
With advances in medical technology, the number of people over the age of 60 is on the rise, and thus, increasing the prevalence of age-related pathologies within the aging population. Neurodegenerative disorders, cancers, metabolic and inflammatory diseases are some of the most prevalent age-related pathologies affecting the growing population. It is imperative that a new treatment to combat these pathologies be developed. Although, still in its infancy, the CRISPR-Cas9 system has become a potent gene-editing tool capable of correcting gene-mediated age-related pathology, and therefore ameliorating or eliminating disease symptoms. Deleting target genes using the CRISPR-Cas9 system or correcting for gene mutations may ameliorate many different neurodegenerative disorders detected in the aging population. Cancer cells targeted by the CRISPR-Cas9 system may result in an increased sensitivity to chemotherapeutics, lower proliferation, and higher cancer cell death. Finally, reducing gene targeting inflammatory molecules production through microRNA knockout holds promise as a therapeutic strategy for both arthritis and inflammation. Here we present a review based on how the expanding world of genome editing can be applied to disorders and diseases affecting the aging population.
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Affiliation(s)
- Allen Caobi
- 1Departments of Immunology and Nano-medicine
| | | | - Luis D Garbinski
- 3Cell Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, USA
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18
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Harypursat V, Zhou Y, Tang S, Chen Y. JC Polyomavirus, progressive multifocal leukoencephalopathy and immune reconstitution inflammatory syndrome: a review. AIDS Res Ther 2020; 17:37. [PMID: 32631361 PMCID: PMC7338111 DOI: 10.1186/s12981-020-00293-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 06/29/2020] [Indexed: 01/15/2023] Open
Abstract
The human neurotropic virus JC Polyomavirus, a member of the Polyomaviridae family, is the opportunistic infectious agent causing progressive multifocal leukoencephalopathy, typically in immunocompromised individuals. The spectrum of underlying reasons for the systemic immunosuppression that permits JCV infection in the central nervous system has evolved over the past 2 decades, and therapeutic immunosuppression arousing JCV infection in the brain has become increasingly prominent as a trigger for PML. Effective immune restoration subsequent to human immunodeficiency virus-related suppression is now recognized as a cause for unexpected deterioration of symptoms in patients with PML, secondary to a rebound inflammatory phenomenon called immune reconstitution inflammatory syndrome, resulting in significantly increased morbidity and mortality in a disease already infamous for its lethality. This review addresses current knowledge regarding JC Polyomavirus, progressive multifocal leukoencephalopathy, progressive multifocal leukoencephalopathy-related immune reconstitution inflammatory syndrome, and the immunocompromised states that incite JC Polyomavirus central nervous system infection, and discusses prospects for the future management of these conditions.
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Affiliation(s)
- Vijay Harypursat
- Division of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Geleshan Town, Shapingba District, Chongqing, 400036, People's Republic of China
| | - Yihong Zhou
- Division of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Geleshan Town, Shapingba District, Chongqing, 400036, People's Republic of China
| | - Shengquan Tang
- Division of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Geleshan Town, Shapingba District, Chongqing, 400036, People's Republic of China
| | - Yaokai Chen
- Division of Infectious Diseases, Chongqing Public Health Medical Center, 109 Baoyu Road, Geleshan Town, Shapingba District, Chongqing, 400036, People's Republic of China.
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19
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Dunham SR, Schmidt R, Clifford DB. Treatment of Progressive Multifocal Leukoencephalopathy Using Immune Restoration. Neurotherapeutics 2020; 17:955-965. [PMID: 32166631 PMCID: PMC7641288 DOI: 10.1007/s13311-020-00848-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Progressive multifocal leukoencephalopathy (PML) is a viral disease of the brain associated with immunodeficiency, immune suppressing medications, and malignancy. In the absence of effective anti-viral therapy for the causative JC virus, immune restoration has emerged as the critical therapeutic alternative. The evolving treatment of PML (and other rare JC virus-associated neurologic syndromes) requires consideration of baseline immune functioning and comorbid diseases while selecting from a number of therapeutic options to restore an effective immune response. This review focuses on the current options for management of PML in typical situations where this disease presents, including several where immune restoration is a standard therapeutic approach such as in PML associated with HIV/AIDS and in multiple sclerosis associated with natalizumab. Other circumstances in which PML occurs including associated with primary immunodeficiencies, malignancies, and transplants present greater challenges to immune reconstitution, but emerging concepts may enhance therapeutic options for these situations. Particular attention is focused on recent experience with checkpoint inhibitors, guidance for MS drug discontinuation, and strategies to monitor and facilitate immune restoration.
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Affiliation(s)
- S Richard Dunham
- Department of Neurology, Washington University in St Louis, St. Louis, MO, USA
| | - Robert Schmidt
- Department of Pathology & Immunology, Washington University in St Louis, St. Louis, MO, USA
| | - David B Clifford
- Department of Neurology, Washington University in St Louis, St. Louis, MO, USA.
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20
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Cheng X, Fan S, Wen C, Du X. CRISPR/Cas9 for cancer treatment: technology, clinical applications and challenges. Brief Funct Genomics 2020; 19:209-214. [PMID: 32052006 DOI: 10.1093/bfgp/elaa001] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/08/2019] [Accepted: 01/06/2020] [Indexed: 12/25/2022] Open
Abstract
AbstractClustered regularly interspaced short palindromic repeats (CRISPR) is described as RNA mediated adaptive immune system defense, which is naturally found in bacteria and archaea. CRISPR-Cas9 has shown great promise for cancer treatment in cancer immunotherapy, manipulation of cancer genome and epigenome and elimination or inactivation of carcinogenic viral infections. However, many challenges remain to be addressed to increase its efficacy, including off-target effects, editing efficiency, fitness of edited cells, immune response and delivery methods. Here, we explain CRISPR-Cas classification and its general function mechanism for gene editing. Then, we summarize these preclinical CRISPR-Cas9-based therapeutic strategies against cancer. Moreover, the challenges and improvements of CRISPR-Cas9 clinical applications will be discussed.
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Affiliation(s)
- Xing Cheng
- Spinal Cord Injury Center, Heidelberg University Hospital, Heidelberg, Germany
| | - Shaoyi Fan
- Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine,Guangzhou, China
| | - Chengcai Wen
- Department of Rehabilitation, Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Xianfa Du
- Department of Orthopaedics, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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21
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Bellizzi A, Ahye N, Jalagadugula G, Wollebo HS. A Broad Application of CRISPR Cas9 in Infectious Diseases of Central Nervous System. J Neuroimmune Pharmacol 2019; 14:578-594. [PMID: 31512166 PMCID: PMC6898781 DOI: 10.1007/s11481-019-09878-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/26/2019] [Indexed: 12/16/2022]
Abstract
Virus-induced diseases or neurological complications are huge socio-economic burden to human health globally. The complexity of viral-mediated CNS pathology is exacerbated by reemergence of new pathogenic neurotropic viruses of high public relevance. Although the central nervous system is considered as an immune privileged organ and is mainly protected by barrier system, there are a vast majority of neurotropic viruses capable of gaining access and cause diseases. Despite continued growth of the patient population and a number of treatment strategies, there is no successful viral specific therapy available for viral induced CNS diseases. Therefore, there is an urgent need for a clear alternative treatment strategy that can effectively target neurotropic viruses of DNA or RNA genome. To address this need, rapidly growing gene editing technology based on CRISPR/Cas9, provides unprecedented control over viral genome editing and will be an effective, highly specific and versatile tool for targeting CNS viral infection. In this review, we discuss the application of this system to control CNS viral infection and associated neurological disorders and future prospects. Graphical Abstract CRISPR/Cas9 technology as agent control over CNS viral infection.
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Affiliation(s)
- Anna Bellizzi
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, Room 756 MERB, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Nicholas Ahye
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, Room 756 MERB, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Gauthami Jalagadugula
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, Room 756 MERB, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Hassen S Wollebo
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, Room 756 MERB, 3500 N. Broad Street, Philadelphia, PA, 19140, USA.
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22
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CRISPR/Cas9 Editing of the Polyomavirus Tumor Antigens Inhibits Merkel Cell Carcinoma Growth In Vitro. Cancers (Basel) 2019; 11:cancers11091260. [PMID: 31466237 PMCID: PMC6770690 DOI: 10.3390/cancers11091260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 12/26/2022] Open
Abstract
Merkel cell carcinoma (MCC) is an aggressive type of skin cancer whose main causative agent is Merkel cell polyomavirus (MCPyV). MCPyV is integrated into the genome of the tumor cells in most MCCs. Virus-positive tumor cells constitutively express two viral oncoproteins that promote cell growth: the small (sT) and the large (LT) tumor antigens (TAs). Despite the success of immunotherapies in patients with MCC, not all individuals respond to these treatments. Therefore, new therapeutic options continue to be investigated. Herein, we used CRISPR/Cas9 to target the viral oncogenes in two virus-positive MCC cell lines: MS-1 and WAGA. Frameshift mutations introduced in the target sequence upon repair of the Cas9-induced DNA break resulted in decreased LT protein levels, which subsequently impaired cell proliferation, caused cell cycle arrest, and led to increased apoptosis. Importantly, a virus-negative non-MCC cell line (HEK293T) remained unaffected, as well as those cells expressing a non-targeting single-guide RNA (sgRNA). Thus, we presumed that the noted effects were not due to the off-target activity of the TAs-targeting sgRNAs. Additionally, WAGA cells had altered levels of cellular proteins involved in cell cycle regulation, supporting the observed cell cycle. Taken together, our findings provide evidence for the development of a CRISPR/Cas9-based therapeutic option for virus-positive MCC.
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23
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Del Valle L, Piña-Oviedo S. Human Polyomavirus JCPyV and Its Role in Progressive Multifocal Leukoencephalopathy and Oncogenesis. Front Oncol 2019; 9:711. [PMID: 31440465 PMCID: PMC6694743 DOI: 10.3389/fonc.2019.00711] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/17/2019] [Indexed: 12/12/2022] Open
Abstract
The human neurotropic virus JCPyV, a member of the Polyomaviridiae family, is the opportunistic infectious agent of Progressive Multifocal Leukoencephalopathy (PML), a fatal disease seen in severe immunosuppressive conditions and, during the last decade, in patients undergoing immunotherapy. JCPyV is a ubiquitous pathogen with up to 85% of the adult population word-wide exhibiting antibodies against it. Early experiments demonstrated that direct inoculation of JCPyV into the brain of different species resulted in the development of brain tumors and other neuroectodermal-derived neoplasias. Later, several reports showed the detection of viral sequences in medulloblastomas and glial tumors, as well as expression of the viral protein T-Antigen. Few oncogenic viruses, however, have caused so much controversy regarding their role in the pathogenesis of brain tumors, but the discovery of new Polyomaviruses that cause Merkel cell carcinomas in humans and brain tumors in racoons, in addition to the role of JCPyV in colon cancer and multiple mechanistic studies have shed much needed light on the role of JCPyV in cancer. The pathways affected by the viral protein T-Antigen include cell cycle regulators, like p53 and pRb, and transcription factors that activate pro-proliferative genes, like c-Myc. In addition, infection with JCPyV causes chromosomal damage and T-Antigen inhibits homologous recombination, and activates anti-apoptotic proteins, such as Survivin. Here we review the different aspects of the biology and physiopathology of JCPyV.
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Affiliation(s)
- Luis Del Valle
- Department of Pathology and Stanley S. Scott Cancer Center, Louisiana State University Health, New Orleans, LA, United States
| | - Sergio Piña-Oviedo
- Department of Pathology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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24
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Campbell LA, Richie CT, Maggirwar NS, Harvey BK. Cas9 Ribonucleoprotein Complex Delivery: Methods and Applications for Neuroinflammation. J Neuroimmune Pharmacol 2019; 14:565-577. [PMID: 31172397 DOI: 10.1007/s11481-019-09856-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/02/2019] [Indexed: 12/20/2022]
Abstract
The CRISPR/Cas9 system is a revolutionary gene editing technology that combines simplicity of use and efficiency of mutagenesis. As this technology progresses toward human therapies, valid concerns including off-target mutations and immunogenicity must be addressed. One approach to address these issues is to minimize the presence of the CRISPR/Cas9 components by maintaining a tighter temporal control of Cas9 endonuclease and reducing the time period of activity. This has been achieved to some degree by delivering the CRISPR/Cas9 system via pre-formed Cas9 + gRNA ribonucleoprotein (RNP) complexes. In this review, we first discuss the molecular modifications that can be made using CRISPR/Cas9 and provide an overview of current methods for delivering Cas9 RNP complexes both in vitro and in vivo. We conclude with examples of how Cas9 RNP delivery may be used to target neuroinflammatory processes, namely in regard to viral infections of the central nervous system and neurodegenerative diseases. We propose that Cas9 RNP delivery is a viable approach when considering the CRISPR/Cas9 system for both experimentation and the treatment of disease. Graphical Abstract.
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Affiliation(s)
- Lee A Campbell
- Intramural Research Program, Biomedical Research Center, National Institute on Drug Abuse, Suite 200, 251 Bayview Blvd, Baltimore, MD, 21224, USA.
| | - Christopher T Richie
- Intramural Research Program, Biomedical Research Center, National Institute on Drug Abuse, Suite 200, 251 Bayview Blvd, Baltimore, MD, 21224, USA
| | - Nishad S Maggirwar
- Intramural Research Program, Biomedical Research Center, National Institute on Drug Abuse, Suite 200, 251 Bayview Blvd, Baltimore, MD, 21224, USA
| | - Brandon K Harvey
- Intramural Research Program, Biomedical Research Center, National Institute on Drug Abuse, Suite 200, 251 Bayview Blvd, Baltimore, MD, 21224, USA.
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25
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CRISPR/Cas9-Based Antiviral Strategy: Current Status and the Potential Challenge. Molecules 2019; 24:molecules24071349. [PMID: 30959782 PMCID: PMC6480260 DOI: 10.3390/molecules24071349] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 12/15/2022] Open
Abstract
From its unexpected discovery as a bacterial adaptive immune system to its countless applications as one of the most versatile gene-editing tools, the CRISPR/Cas9 system has revolutionized every field of life science. Virology is no exception to this ever-growing list of CRISPR/Cas9-based applications. Direct manipulation of a virus genome by CRISPR/Cas9 has enabled a systematic study of cis-elements and trans-elements encoded in a virus genome. In addition, this virus genome-specific mutagenesis by CRISPR/Cas9 was further funneled into the development of a novel class of antiviral therapy targeting many incurable chronic viral infections. In this review, a general concept on the CRISPR/Cas9-based antiviral strategy will be described first. To understand the current status of the CRISPR/Cas9-based antiviral approach, a series of recently published antiviral studies involving CRISPR/Cas9-mediated control of several clinically-relevant viruses including human immunodeficiency virus, hepatitis B virus, herpesviruses, human papillomavirus, and other viruses will be presented. Lastly, the potential challenge and future prospect for successful clinical translation of this CRISPR/Cas9-based antiviral method will be discussed.
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Abstract
Infectious diseases remain a global threat contributing to excess morbidity and death annually, with the persistent potential for destabilizing pandemics. Improved understanding of the pathogenesis of bacteria, viruses, fungi, and parasites, along with rapid diagnosis and treatment of human infections, is essential for improving infectious disease outcomes worldwide. Genomic loci in bacteria and archaea, termed clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins, function as an adaptive immune system for prokaryotes, protecting them against foreign invaders. CRISPR-Cas9 technology is now routinely applied for efficient gene editing, contributing to advances in biomedical science. In the past decade, improved understanding of other diverse CRISPR-Cas systems has expanded CRISPR applications, including in the field of infectious diseases. In this review, we summarize the biology of CRISPR-Cas systems and discuss existing and emerging applications to evaluate mechanisms of host-pathogen interactions, to develop accurate and portable diagnostic tests, and to advance the prevention and treatment of infectious diseases.
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Bayat H, Naderi F, Khan AH, Memarnejadian A, Rahimpour A. The Impact of CRISPR-Cas System on Antiviral Therapy. Adv Pharm Bull 2018; 8:591-597. [PMID: 30607331 PMCID: PMC6311650 DOI: 10.15171/apb.2018.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 09/08/2018] [Accepted: 09/29/2018] [Indexed: 12/16/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein nuclease (Cas) is identified as an adaptive immune system in archaea and bacteria. Type II of this system, CRISPR-Cas9, is the most versatile form that has enabled facile and efficient targeted genome editing. Viral infections have serious impacts on global health and conventional antiviral therapies have not yielded a successful solution hitherto. The CRISPR-Cas9 system represents a promising tool for eliminating viral infections. In this review, we highlight 1) the recent progress of CRISPR-Cas technology in decoding and diagnosis of viral outbreaks, 2) its applications to eliminate viral infections in both pre-integration and provirus stages, and 3) various delivery systems that are employed to introduce the platform into target cells.
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Affiliation(s)
- Hadi Bayat
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Naderi
- Department of Molecular Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Amjad Hayat Khan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | | | - Azam Rahimpour
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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28
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Yin L, Hu S, Mei S, Sun H, Xu F, Li J, Zhu W, Liu X, Zhao F, Zhang D, Cen S, Liang C, Guo F. CRISPR/Cas9 Inhibits Multiple Steps of HIV-1 Infection. Hum Gene Ther 2018; 29:1264-1276. [PMID: 29644868 DOI: 10.1089/hum.2018.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CRISPR/Cas9 is an adaptive immune system where bacteria and archaea have evolved to resist the invading viruses and plasmid DNA by creating site-specific double-strand breaks in DNA. This study tested this gene editing system in inhibiting human immunodeficiency virus type 1 (HIV-1) infection by targeting the viral long terminal repeat and the gene coding sequences. Strong inhibition of HIV-1 infection by Cas9/gRNA was observed, which resulted not only from insertions and deletions (indels) that were introduced into viral DNA due to Cas9 cleavage, but also from the marked decrease in the levels of the late viral DNA products and the integrated viral DNA. This latter defect might have reflected the degradation of viral DNA that has not been immediately repaired after Cas9 cleavage. It was further observed that Cas9, when solely located in the cytoplasm, inhibits HIV-1 as strongly as the nuclear Cas9, except that the cytoplasmic Cas9 does not act on the integrated HIV-1 DNA and thus cannot be used to excise the latent provirus. Together, the results suggest that Cas9/gRNA is able to target and edit HIV-1 DNA both in the cytoplasm and in the nucleus. The inhibitory effect of Cas9 on HIV-1 is attributed to both the indels in viral DNA and the reduction in the levels of viral DNA.
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Affiliation(s)
- Lijuan Yin
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Siqi Hu
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Shan Mei
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Hong Sun
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Fengwen Xu
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Jian Li
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Weijun Zhu
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Xiaoman Liu
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Fei Zhao
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Di Zhang
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Shan Cen
- 2 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Chen Liang
- 3 McGill University AIDS Centre , Lady Davis Institute, Jewish General Hospital, Montreal, Canada
| | - Fei Guo
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
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29
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Ebrahimi S, Teimoori A, Khanbabaei H, Tabasi M. Harnessing CRISPR/Cas 9 System for manipulation of DNA virus genome. Rev Med Virol 2018; 29:e2009. [PMID: 30260068 DOI: 10.1002/rmv.2009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/03/2018] [Accepted: 08/07/2018] [Indexed: 12/17/2022]
Abstract
The recent development of the Clustered Regularly Interspaced Palindromic Repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system, a genome editing system, has many potential applications in virology. The possibility of introducing site specific breaks has provided new possibilities to precisely manipulate viral genomics. Here, we provide diagrams to summarize the steps involved in the process. We also systematically review recent applications of the CRISPR/Cas9 system for manipulation of DNA virus genomics and discuss the therapeutic potential of the system to treat viral diseases.
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Affiliation(s)
- Saeedeh Ebrahimi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Virology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Teimoori
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Virology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hashem Khanbabaei
- Medical Physics Department, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Tabasi
- Department of Virology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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30
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Gilani U, Shaukat M, Rasheed A, Shahid M, Tasneem F, Arshad M, Rashid N, Shahzad N. The implication of CRISPR/Cas9 genome editing technology in combating human oncoviruses. J Med Virol 2018; 91:1-13. [PMID: 30133783 DOI: 10.1002/jmv.25292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/31/2018] [Indexed: 12/23/2022]
Abstract
It is evidenced that 20% of all tumors in humans are caused by oncoviruses, including human papilloma viruses, Epstein-Barr virus, Kaposi sarcoma virus, human polyomaviruses, human T-lymphotrophic virus-1, and hepatitis B and C viruses. Human immunodeficiency virus is also involved in carcinogenesis, although not directly, but by facilitating the infection of many oncoviruses through compromising the immune system. Being intracellular parasites with the property of establishing latency and integrating into the host genome, these viruses are a therapeutic challenge for biomedical researchers. Therefore, strategies able to target nucleotide sequences within episomal or integrated viral genomes are of prime importance in antiviral or anticancerous armamentarium. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has emerged as a powerful genome editing tool. Standing out as a precise and efficient oncoviruses method, it has been extensively applied in recent experimental ventures in the field of molecular medicine, particularly in combating infections including tumor inducing viruses. This review is aimed at collating the experimental and clinical advances in CRISPR/Cas9 technology in terms of its applications against oncoviruses. Primarily, it will focus on the application of CRISPR/Cas9 in combating tumor viruses, types of mechanisms targeted, and the significant outcomes till date. The technical pitfalls of the CRISPR/Cas9 and the comparative approaches in evaluating this technique with respect to other available alternatives are also described briefly. Furthermore, the review also discussed the clinical aspects and the ethical, legal, and social issues associated with the use of CRISPR/Cas9.
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Affiliation(s)
- Usman Gilani
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Memoona Shaukat
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Arisha Rasheed
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mehak Shahid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Fareeda Tasneem
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Arshad
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Naveed Shahzad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
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31
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Wilson M, Tyler KL. Emerging Diagnostic and Therapeutic Tools for Central Nervous System Infections. JAMA Neurol 2018; 73:1389-1390. [PMID: 27695862 DOI: 10.1001/jamaneurol.2016.3617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Michael Wilson
- Department of Neurology, University of California, San Francisco
| | - Kenneth L Tyler
- Departments of Neurology, Medicine, and Immunology-Microbiology, University of Colorado School of Medicine, Aurora
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32
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Therapeutic potential of combined viral transduction and CRISPR/Cas9 gene editing in treating neurodegenerative diseases. Neurol Sci 2018; 39:1827-1835. [DOI: 10.1007/s10072-018-3521-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/01/2018] [Indexed: 12/31/2022]
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33
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Donadoni M, Sariyer R, Wollebo H, Bellizzi A, Sariyer IK. Viral tumor antigen expression is no longer required in radiation-resistant subpopulation of JCV induced mouse medulloblastoma cells. Genes Cancer 2018; 9:130-141. [PMID: 30108683 PMCID: PMC6086003 DOI: 10.18632/genesandcancer.174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The human neurotropic polyomavirus JC, JC virus (JCV), infects the majority of human population during early childhood and establishes a latent/persistent infection for the rest of the life. JCV is the etiologic agent of the fatal demyelinating disease of the central nervous system, progressive multifocal leukoencephalopathy (PML) that is seen primarily in immunocompromised individuals. In addition to the PML, JCV has also been shown to transform cells in culture systems and cause a variety of tumors in experimental animals. Moreover, JCV genomic DNA and tumor antigen expression have been shown in a variety of human tumors with CNS origin. Similar to all polyomaviruses, JCV encodes for several tumor antigens from a single transcript of early coding region via alternative splicing. There is little known regarding the characteristics of JCV induced tumors and impact of DNA damage induced by radiation on viral tumor antigen expression and growth of these cells. Here we analyzed the possible impact of ionizing radiation on transformed phenotype and tumor antigen expression by utilizing a mouse medulloblastoma cell line (BSB8) obtained from a mouse transgenic for JCV tumor antigens. Our results suggest that a small subset of BSB8 cells survives and shows radiation resistance. Further analysis of the transformed phenotype of radiation resistant BSB8 cells (BSB8-RR) have revealed that they are capable of forming significantly higher numbers and sizes of colonies under anchorage dependent and independent conditions with reduced viral tumor antigen expression. Moreover, BSB8-RR cells show an increased rate of double-strand DNA break repair by homologous recombination (HR). More interestingly, knockout studies of JCV tumor antigens by utilizing CRISPR/Cas9 gene editing reveal that unlike parental BSB8 cells, BSB8-RR cells are no longer required the expression of viral tumor antigens in order to maintain transformed phenotype.
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Affiliation(s)
- Martina Donadoni
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Rahsan Sariyer
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Hassen Wollebo
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Anna Bellizzi
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Ilker Kudret Sariyer
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
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34
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Luteijn RD, Drexler I, Smith GL, Lebbink RJ, Wiertz EJHJ. Mutagenic repair of double-stranded DNA breaks in vaccinia virus genomes requires cellular DNA ligase IV activity in the cytosol. J Gen Virol 2018; 99:790-804. [PMID: 29676720 PMCID: PMC7614823 DOI: 10.1099/jgv.0.001034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Poxviruses comprise a group of large dsDNA viruses that include members relevant to human and animal health, such as variola virus, monkeypox virus, cowpox virus and vaccinia virus (VACV). Poxviruses are remarkable for their unique replication cycle, which is restricted to the cytoplasm of infected cells. The independence from the host nucleus requires poxviruses to encode most of the enzymes involved in DNA replication, transcription and processing. Here, we use the CRISPR/Cas9 genome engineering system to induce DNA damage to VACV (strain Western Reserve) genomes. We show that targeting CRISPR/Cas9 to essential viral genes limits virus replication efficiently. Although VACV is a strictly cytoplasmic pathogen, we observed extensive viral genome editing at the target site; this is reminiscent of a non-homologous end-joining DNA repair mechanism. This pathway was not dependent on the viral DNA ligase, but critically involved the cellular DNA ligase IV. Our data show that DNA ligase IV can act outside of the nucleus to allow repair of dsDNA breaks in poxvirus genomes. This pathway might contribute to the introduction of mutations within the genome of poxviruses and may thereby promote the evolution of these viruses.
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Affiliation(s)
- Rutger David Luteijn
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Present address: Department of Molecular and Cell Biology, University of California, Berkeley, USA
| | - Ingo Drexler
- Institute for Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | | | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emmanuel J H J Wiertz
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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35
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Abstract
Advances in Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated system (CRISPR/Cas9) has dramatically reshaped our ability to edit genomes. The scientific community is using CRISPR/Cas9 for various biotechnological and medical purposes. One of its most important uses is developing potential therapeutic strategies against diseases. CRISPR/Cas9 based approaches have been increasingly applied to the treatment of human diseases like cancer, genetic, immunological and neurological disorders and viral diseases. These strategies using CRISPR/Cas9 are not only therapy oriented but can also be used for disease modeling as well, which in turn can lead to the improved understanding of mechanisms of various infectious and genetic diseases. In addition, CRISPR/Cas9 system can also be used as programmable antibiotics to kill the bacteria sequence specifically and therefore can bypass multidrug resistance. Furthermore, CRISPR/Cas9 based gene drive may also hold the potential to limit the spread of vector borne diseases. This bacterial and archaeal adaptive immune system might be a therapeutic answer to previous incurable diseases, of course rigorous testing is required to corroborate these claims. In this review, we provide an insight about the recent developments using CRISPR/Cas9 against various diseases with respect to disease modeling and treatment, and what future perspectives should be noted while using this technology.
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36
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Okoli A, Okeke MI, Tryland M, Moens U. CRISPR/Cas9-Advancing Orthopoxvirus Genome Editing for Vaccine and Vector Development. Viruses 2018; 10:E50. [PMID: 29361752 PMCID: PMC5795463 DOI: 10.3390/v10010050] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/17/2018] [Accepted: 01/21/2018] [Indexed: 12/17/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/associated protein 9 (Cas9) technology is revolutionizing genome editing approaches. Its high efficiency, specificity, versatility, flexibility, simplicity and low cost have made the CRISPR/Cas9 system preferable to other guided site-specific nuclease-based systems such as TALENs (Transcription Activator-like Effector Nucleases) and ZFNs (Zinc Finger Nucleases) in genome editing of viruses. CRISPR/Cas9 is presently being applied in constructing viral mutants, preventing virus infections, eradicating proviral DNA, and inhibiting viral replication in infected cells. The successful adaptation of CRISPR/Cas9 to editing the genome of Vaccinia virus paves the way for its application in editing other vaccine/vector-relevant orthopoxvirus (OPXV) strains. Thus, CRISPR/Cas9 can be used to resolve some of the major hindrances to the development of OPXV-based recombinant vaccines and vectors, including sub-optimal immunogenicity; transgene and genome instability; reversion of attenuation; potential of spread of transgenes to wildtype strains and close contacts, which are important biosafety and risk assessment considerations. In this article, we review the published literature on the application of CRISPR/Cas9 in virus genome editing and discuss the potentials of CRISPR/Cas9 in advancing OPXV-based recombinant vaccines and vectors. We also discuss the application of CRISPR/Cas9 in combating viruses of clinical relevance, the limitations of CRISPR/Cas9 and the current strategies to overcome them.
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Affiliation(s)
- Arinze Okoli
- Biosafety of Genome Editing Research Group, GenØk-Centre for Biosafety, Siva Innovation Centre, N-9294 Tromsø, Norway.
| | - Malachy I Okeke
- Biosafety of Genome Editing Research Group, GenØk-Centre for Biosafety, Siva Innovation Centre, N-9294 Tromsø, Norway.
| | - Morten Tryland
- Biosafety of Genome Editing Research Group, GenØk-Centre for Biosafety, Siva Innovation Centre, N-9294 Tromsø, Norway.
- Artic Infection Biology, Department of Artic and Marine Biology, The Artic University of Norway, N-9037 Tromsø, Norway.
| | - Ugo Moens
- Molecular Inflammation Research Group, Institute of Medical Biology, The Arctic University of Norway, N-9037 Tromsø, Norway.
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37
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Lessard S, Francioli L, Alfoldi J, Tardif JC, Ellinor PT, MacArthur DG, Lettre G, Orkin SH, Canver MC. Human genetic variation alters CRISPR-Cas9 on- and off-targeting specificity at therapeutically implicated loci. Proc Natl Acad Sci U S A 2017; 114:E11257-E11266. [PMID: 29229813 PMCID: PMC5748207 DOI: 10.1073/pnas.1714640114] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The CRISPR-Cas9 nuclease system holds enormous potential for therapeutic genome editing of a wide spectrum of diseases. Large efforts have been made to further understanding of on- and off-target activity to assist the design of CRISPR-based therapies with optimized efficacy and safety. However, current efforts have largely focused on the reference genome or the genome of cell lines to evaluate guide RNA (gRNA) efficiency, safety, and toxicity. Here, we examine the effect of human genetic variation on both on- and off-target specificity. Specifically, we utilize 7,444 whole-genome sequences to examine the effect of variants on the targeting specificity of ∼3,000 gRNAs across 30 therapeutically implicated loci. We demonstrate that human genetic variation can alter the off-target landscape genome-wide including creating and destroying protospacer adjacent motifs (PAMs). Furthermore, single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) can result in altered on-target sites and novel potent off-target sites, which can predispose patients to treatment failure and adverse effects, respectively; however, these events are rare. Taken together, these data highlight the importance of considering individual genomes for therapeutic genome-editing applications for the design and evaluation of CRISPR-based therapies to minimize risk of treatment failure and/or adverse outcomes.
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Affiliation(s)
- Samuel Lessard
- Research Center, Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Laurent Francioli
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Jessica Alfoldi
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Jean-Claude Tardif
- Research Center, Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Guillaume Lettre
- Research Center, Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115;
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
- Howard Hughes Medical Institute, Boston, MA 02115
| | - Matthew C Canver
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115;
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
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38
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White MK, Khalili K. CRISPR/Cas9 and cancer targets: future possibilities and present challenges. Oncotarget 2017; 7:12305-17. [PMID: 26840090 PMCID: PMC4914286 DOI: 10.18632/oncotarget.7104] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/23/2016] [Indexed: 02/07/2023] Open
Abstract
All cancers have multiple mutations that can largely be grouped into certain classes depending on the function of the gene in which they lie and these include oncogenic changes that enhance cellular proliferation, loss of function of tumor suppressors that regulate cell growth potential and induction of metabolic enzymes that confer resistance to chemotherapeutic agents. Thus the ability to correct such mutations is an important goal in cancer treatment. Recent research has led to the developments of reagents which specifically target nucleotide sequences within the cellular genome and these have a huge potential for expanding our anticancer armamentarium. One such a reagent is the clustered regulatory interspaced short palindromic repeat (CRISPR)-associated 9 (Cas9) system, a powerful, highly specific and adaptable tool that provides unparalleled control for editing the cellular genome. In this short review, we discuss the potential of CRISPR/Cas9 against human cancers and the current difficulties in translating this for novel therapeutic approaches.
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Affiliation(s)
- Martyn K White
- Department of Neuroscience, Center for Neurovirology and Comprehensive Neuroaids Center, Temple University School of Medicine, Philadelphia, PA, USA
| | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology and Comprehensive Neuroaids Center, Temple University School of Medicine, Philadelphia, PA, USA
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39
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Yang J, Meng X, Pan J, Jiang N, Zhou C, Wu Z, Gong Z. CRISPR/Cas9-mediated noncoding RNA editing in human cancers. RNA Biol 2017; 15:35-43. [PMID: 29028415 DOI: 10.1080/15476286.2017.1391443] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cancer is characterized by multiple genetic and epigenetic alterations, including a higher prevalence of mutations of oncogenes and/or tumor suppressors. Mounting evidences have shown that noncoding RNAs (ncRNAs) are involved in the epigenetic regulation of cancer genes and their associated pathways. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (CRISPR/Cas9) system, a revolutionary genome-editing technology, has shed light on ncRNA-based cancer therapy. Here, we briefly introduce the classifications and mechanisms of CRISPR/Cas9 system. Importantly, we mainly focused on the applications of CRISPR/Cas9 system as a molecular tool for ncRNA (microRNA, long noncoding RNA and circular RNA, etc.) editing in human cancers, and the novel techniques that are based on CRISPR/Cas9 system. Additionally, the off-target effects and the corresponding solutions as well as the challenges toward CRISPR/Cas9 were also evaluated and discussed. Long- and short-ncRNAs have been employed as targets in precision oncology, and CRISPR/Cas9-mediated ncRNA editing may provide an excellent way to cure cancer.
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Affiliation(s)
- Jie Yang
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Xiaodan Meng
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Jinchang Pan
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Nan Jiang
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Chengwei Zhou
- c Department of Thoracic Surgery , The Affiliated Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Zhenhua Wu
- d Department of Otolaryngology Head and Neck Surgery , The Affiliated Ningbo Medical Center Lihuili Eastern Hospital of Medical School of Ningbo University , Ningbo , Zhejiang , China
| | - Zhaohui Gong
- a Department of Biochemistry and Molecular Biology , Medical School of Ningbo University , Ningbo , Zhejiang , China.,b Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University , Ningbo , Zhejiang , China
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Molloy ES, Calabrese CM, Calabrese LH. The Risk of Progressive Multifocal Leukoencephalopathy in the Biologic Era: Prevention and Management. Rheum Dis Clin North Am 2017; 43:95-109. [PMID: 27890176 DOI: 10.1016/j.rdc.2016.09.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Progressive multifocal leukoencephalopathy (PML) is a rare, typically fatal, demyelinating central nervous system infection caused by reactivation of the John Cunningham virus that generally occurs in immunosuppressed patients. With an evolving understanding of a greater clinical heterogeneity of PML and significant implications for therapy, PML should be considered in the differential diagnosis of neurologic presentations of rheumatic diseases. Increased awareness of PML among rheumatologists is required, as earlier diagnosis and restoration of immune function may improve the otherwise grim prognosis associated with PML.
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Affiliation(s)
- Eamonn S Molloy
- Department of Rheumatology, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland.
| | - Cassandra M Calabrese
- RJ Fasenmeyer Center for Clinical Immunology, Department of Rheumatic and Immunologic Diseases, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Leonard H Calabrese
- RJ Fasenmeyer Center for Clinical Immunology, Department of Rheumatic and Immunologic Diseases, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
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41
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Trevisan M, Palù G, Barzon L. Genome editing technologies to fight infectious diseases. Expert Rev Anti Infect Ther 2017; 15:1001-1013. [PMID: 29090592 DOI: 10.1080/14787210.2017.1400379] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Genome editing by programmable nucleases represents a promising tool that could be exploited to develop new therapeutic strategies to fight infectious diseases. These nucleases, such as zinc-finger nucleases, transcription activator-like effector nucleases, clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein 9 (Cas9) and homing endonucleases, are molecular scissors that can be targeted at predetermined loci in order to modify the genome sequence of an organism. Areas covered: By perturbing genomic DNA at predetermined loci, programmable nucleases can be used as antiviral and antimicrobial treatment. This approach includes targeting of essential viral genes or viral sequences able, once mutated, to inhibit viral replication; repurposing of CRISPR-Cas9 system for lethal self-targeting of bacteria; targeting antibiotic-resistance and virulence genes in bacteria, fungi, and parasites; engineering arthropod vectors to prevent vector-borne infections. Expert commentary: While progress has been done in demonstrating the feasibility of using genome editing as antimicrobial strategy, there are still many hurdles to overcome, such as the risk of off-target mutations, the raising of escape mutants, and the inefficiency of delivery methods, before translating results from preclinical studies into clinical applications.
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Affiliation(s)
- Marta Trevisan
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Giorgio Palù
- a Department of Molecular Medicine , University of Padova , Padova , Italy
| | - Luisa Barzon
- a Department of Molecular Medicine , University of Padova , Padova , Italy
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Soppe JA, Lebbink RJ. Antiviral Goes Viral: Harnessing CRISPR/Cas9 to Combat Viruses in Humans. Trends Microbiol 2017; 25:833-850. [PMID: 28522157 DOI: 10.1016/j.tim.2017.04.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/07/2017] [Accepted: 04/19/2017] [Indexed: 12/11/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems are RNA-guided sequence-specific prokaryotic antiviral immune systems. In prokaryotes, small RNA molecules guide Cas effector endonucleases to invading foreign genetic elements in a sequence-dependent manner, resulting in DNA cleavage by the endonuclease upon target binding. A rewired CRISPR/Cas9 system can be used for targeted and precise genome editing in eukaryotic cells. CRISPR/Cas has also been harnessed to target human pathogenic viruses as a potential new antiviral strategy. Here, we review recent CRISPR/Cas9-based approaches to combat specific human viruses in humans and discuss challenges that need to be overcome before CRISPR/Cas9 may be used in the clinic as an antiviral strategy.
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Affiliation(s)
- Jasper Adriaan Soppe
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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43
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Wahid B, Usman S, Ali A, Saleem K, Rafique S, Naz Z, Ahsan Ashfaq H, Idrees M. Therapeutic Strategies of Clustered Regularly Interspaced Palindromic Repeats-Cas Systems for Different Viral Infections. Viral Immunol 2017; 30:552-559. [DOI: 10.1089/vim.2017.0055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Braira Wahid
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sana Usman
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Amjad Ali
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Komal Saleem
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shazia Rafique
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Hafiz Ahsan Ashfaq
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
- Vice Chancellor Hazara University, Mansehra, Pakistan
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White MK, Kaminski R, Young WB, Roehm PC, Khalili K. CRISPR Editing Technology in Biological and Biomedical Investigation. J Cell Biochem 2017; 118:3586-3594. [PMID: 28460414 DOI: 10.1002/jcb.26099] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 01/01/2023]
Abstract
The CRISPR or clustered regularly interspaced short palindromic repeats system is currently the most advanced approach to genome editing and is notable for providing an unprecedented degree of specificity, effectiveness, and versatility in genetic manipulation. CRISPR evolved as a prokaryotic immune system to provide an acquired immunity and resistance to foreign genetic elements such as bacteriophages. It has recently been developed into a tool for the specific targeting of nucleotide sequences within complex eukaryotic genomes for the purpose of genetic manipulation. The power of CRISPR lies in its simplicity and ease of use, its flexibility to be targeted to any given nucleotide sequence by the choice of an easily synthesized guide RNA, and its ready ability to continue to undergo technical improvements. Applications for CRISPR are numerous including creation of novel transgenic cell animals for research, high-throughput screening of gene function, potential clinical gene therapy, and nongene-editing approaches such as modulating gene activity and fluorescent tagging. In this prospect article, we will describe the salient features of the CRISPR system with an emphasis on important drawbacks and considerations with respect to eliminating off-target events and obtaining efficient CRISPR delivery. We will discuss recent technical developments to the system and we will illustrate some of the most recent applications with an emphasis on approaches to eliminate human viruses including HIV-1, JCV and HSV-1 and prospects for the future. J. Cell. Biochem. 118: 3586-3594, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Martyn K White
- Center for Neurovirology and Comprehensive NeuroAIDS Center, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, Pennsylvania, 19140
| | - Rafal Kaminski
- Center for Neurovirology and Comprehensive NeuroAIDS Center, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, Pennsylvania, 19140
| | - Won-Bin Young
- Center for Neurovirology and Comprehensive NeuroAIDS Center, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, Pennsylvania, 19140
| | - Pamela C Roehm
- Center for Neurovirology and Comprehensive NeuroAIDS Center, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, Pennsylvania, 19140
| | - Kamel Khalili
- Center for Neurovirology and Comprehensive NeuroAIDS Center, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, Pennsylvania, 19140
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45
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Antiviral treatment strategies based on gene silencing and genome editing. Curr Opin Virol 2017; 24:46-54. [DOI: 10.1016/j.coviro.2017.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 12/18/2022]
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46
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White MK, Bellizzi A, Ibba G, Pietropaolo V, Palamara AT, Wollebo HS. The DNA damage response promotes polyomavirus JC infection by nucleus to cytoplasm NF- kappaB activation. Virol J 2017; 14:31. [PMID: 28202068 PMCID: PMC5312431 DOI: 10.1186/s12985-017-0707-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 02/10/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Infection of glial cells by human neurotropic polyomavirus JC (JCV), the causative agent of the CNS demyelinating disease progressive multifocal leukoencephalopathy (PML), rapidly inflicts damage to cellular DNA. This activates DNA damage response (DDR) signaling including induction of expression of DNA repair factor Rad51. We previously reported that Rad51 co-operates with the transcription factor NF-κB p65 to activate JCV early transcription. Thus Rad51 induction by JCV infection may provide positive feedback for viral activation early in JCV infection. DDR is also known to stimulate NF-κB activity, a phenomenon known as nucleus to cytoplasm or "inside-out" NF-κB signaling, which is initiated by Ataxia telangiectasia mutated (ATM) protein, a serine/threonine kinase recruited and activated by DNA double-strand breaks. Downstream of ATM, there occurs a series of post-translational modifications of NF-κB essential modulator (NEMO), the γ regulatory subunit of inhibitor of NF-κB (IκB) kinase (IKK), resulting in NF-κB activation. METHODS We analyzed the effects of downstream pathways in the DDR by phosphospecific Western blots and analysis of the subcellular distribution of NEMO by cell fractionation and immunocytochemistry. The role of DDR in JCV infection was analyzed using a small molecule inhibitor of ATM (KU-55933). NEMO sumoylation was investigated by Western and association of ATM and NEMO by immunoprecipitation/Western blots. RESULTS We show that JCV infection caused phosphorylation and activation of ATM while KU-55933 inhibited JCV replication. JCV infection caused a redistribution of NEMO from cytoplasm to nucleus. Co-expression of JCV large T-antigen and FLAG-tagged NEMO showed the occurrence of sumoylation of NEMO, while co-expression of ATM and FLAG-NEMO demonstrated physical association between ATM and NEMO. CONCLUSIONS We propose a model where JCV infection induces both overexpression of Rad51 protein and activation of the nucleus to cytoplasm NF-κB signaling pathway, which then act together to enhance JCV gene expression.
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Affiliation(s)
- Martyn K White
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Anna Bellizzi
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
- Department of Public Health and Infectious Diseases, Institute Pasteur Italia, Cenci-Bolognetti Foundation, Sapienza University of Rome, 5 P.le Aldo Moro, 00185, Rome, Italy
| | - Gabriele Ibba
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, Sapienza University, 5 P.le Aldo Moro, 00185, Rome, Italy
| | - Anna T Palamara
- Department of Public Health and Infectious Diseases, Institute Pasteur Italia, Cenci-Bolognetti Foundation, Sapienza University of Rome, 5 P.le Aldo Moro, 00185, Rome, Italy
- San Raffaele Pisana IRCCS, Telematic University, Rome, Italy
| | - Hassen S Wollebo
- Center for Neurovirology, Department of Neuroscience, Lewis Katz School of Medicine at Temple University, 3500 N. Broad Street, Philadelphia, PA, 19140, USA.
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Anton R, Haas M, Arlett P, Weise M, Balabanov P, Mazzaglia G, Prieto L, Keller-Stanislawski B, Raine J. Drug-induced progressive multifocal leukoencephalopathy in multiple sclerosis: European regulators' perspective. Clin Pharmacol Ther 2017; 102:283-289. [DOI: 10.1002/cpt.604] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/12/2016] [Accepted: 12/13/2016] [Indexed: 01/13/2023]
Affiliation(s)
- R Anton
- European Medicines Agency; London United Kingdom
| | - M Haas
- European Medicines Agency; London United Kingdom
| | - P Arlett
- European Medicines Agency; London United Kingdom
| | - M Weise
- Federal Institute for Drugs and Medical Devices; Bonn Germany
| | - P Balabanov
- European Medicines Agency; London United Kingdom
| | - G Mazzaglia
- European Medicines Agency; London United Kingdom
| | - L Prieto
- European Medicines Agency; London United Kingdom
| | - B Keller-Stanislawski
- Department of Safety of Medicinal Products and Medical Devices; Paul-Ehrlich Institute, Federal Institute for Vaccines and Biomedicines; Langen Germany
| | - J Raine
- Medicines and Healthcare Products Regulatory Agency; London United Kingdom
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48
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Berger JR. Classifying PML risk with disease modifying therapies. Mult Scler Relat Disord 2017; 12:59-63. [PMID: 28283109 DOI: 10.1016/j.msard.2017.01.006] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/02/2017] [Accepted: 01/06/2017] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To catalogue the risk of PML with the currently available disease modifying therapies (DMTs) for multiple sclerosis (MS). BACKGROUND All DMTs perturb the immune system in some fashion. Natalizumab, a highly effective DMT, has been associated with a significant risk of PML. Fingolimod and dimethyl fumarate have also been unquestionably associated with a risk of PML in the MS population. Concerns about PML risk with other DMTs have arisen due to their mechanism of action and pharmacological parallel to other agents with known PML risk. A method of contextualizing PML risk for DMTs is warranted. METHODS Classification of PML risk was predicated on three criteria:: 1) whether the underlying condition being treated predisposes to PML in the absence of the drug; 2) the latency from initiation of the drug to the development of PML; and 3) the frequency with which PML is observed. RESULTS Among the DMTs, natalizumab occupies a place of its own with respect to PML risk. Significantly lesser degrees of risk exist for fingolimod and dimethyl fumarate. Whether PML will be observed with other DMTs in use for MS, such as, rituximab, teriflunomide, and alemtuzumab, remains uncertain. DISCUSSION A logical classification for stratifying DMT PML risk is important for both the physician and patient in contextualizing risk/benefit ratios. As additional experience accumulates regarding PML and the DMTs, this early effort will undoubtedly require revisiting.
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Affiliation(s)
- Joseph R Berger
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, 3400 Spruce Street, Gates 3W, Philadelphia, PA 19104, USA.
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49
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Chin WX, Ang SK, Chu JJH. Recent advances in therapeutic recruitment of mammalian RNAi and bacterial CRISPR-Cas DNA interference pathways as emerging antiviral strategies. Drug Discov Today 2017; 22:17-30. [DOI: 10.1016/j.drudis.2016.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/20/2016] [Accepted: 08/19/2016] [Indexed: 01/01/2023]
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50
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Doerflinger M, Forsyth W, Ebert G, Pellegrini M, Herold MJ. CRISPR/Cas9-The ultimate weapon to battle infectious diseases? Cell Microbiol 2016; 19. [PMID: 27860197 DOI: 10.1111/cmi.12693] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 10/30/2016] [Accepted: 11/04/2016] [Indexed: 12/12/2022]
Abstract
Infectious diseases are a leading cause of death worldwide. Novel therapeutics are urgently required to treat multidrug-resistant organisms such as Mycobacterium tuberculosis and to mitigate morbidity and mortality caused by acute infections such as malaria and dengue fever virus as well as chronic infections such as human immunodeficiency virus-1 and hepatitis B virus. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, which has revolutionized biomedical research, holds great promise for the identification and validation of novel drug targets. Since its discovery as an adaptive immune system in prokaryotes, the CRISPR/Cas9 system has been developed into a multi-faceted genetic modification tool, which can now be used to induce gene deletions or specific gene insertions, such as conditional alleles or endogenous reporters in virtually any organism. The generation of CRISPR/Cas9 libraries that can be used to perform phenotypic whole genome screens provides an important new tool that will aid in the identification of critical host factors involved in the pathogenesis of infectious diseases. In this review, we will discuss the development and recent applications of the CRISPR/Cas9 system used to identify novel regulators, which might become important in the fight against infectious diseases.
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Affiliation(s)
- M Doerflinger
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - W Forsyth
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - G Ebert
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - M Pellegrini
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - M J Herold
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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