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Nair DM, Vajravelu LK, Thulukanam J, Paneerselvam V, Vimala PB, Lathakumari RH. Tackling hepatitis B Virus with CRISPR/Cas9: advances, challenges, and delivery strategies. Virus Genes 2024:10.1007/s11262-024-02105-3. [PMID: 39196289 DOI: 10.1007/s11262-024-02105-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
Hepatitis B virus (HBV) infection remains a significant global health challenge, with chronic HBV leading to severe liver diseases, including cirrhosis and hepatocellular carcinoma. Current treatments often fail to eradicate the virus, highlighting the need for innovative therapeutic strategies. The CRISPR/Cas9 system has emerged as a dynamic tool for precise genome editing and presents a promising approach to targeting and eliminating HBV infection. This review provides a comprehensive overview of the advances, challenges, and delivery strategies associated with CRISPR/Cas9-based therapies for HBV. We begin by elucidating the mechanism of the CRISPR/Cas9 system and then explore HBV pathogenesis, focusing on the role of covalently closed circular DNA (cccDNA) and integrated HBV DNA in maintaining chronic infection. CRISPR/Cas9 can disrupt these key viral reservoirs, which are critical for persistent HBV replication and associated liver damage. The application of CRISPR/Cas9 in HBV treatment faces significant challenges, such as off-target effects, delivery efficiency, and immune responses. These challenges are addressed by examining current approaches to enhance the specificity, safety, and efficacy of CRISPR/Cas9. A future perspective on the development and clinical translation of CRISPR/Cas9 therapies for HBV is provided, emphasizing the requirement for further research to improve delivery methods and ensure durable safety and effectiveness. This review underscores the transformative potential of CRISPR/Cas9 in combating HBV and sets the stage for future breakthroughs in the field.
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Affiliation(s)
- Dakshina M Nair
- Department of Microbiology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India.
| | - Leela Kakithakara Vajravelu
- Department of Microbiology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India
| | - Jayaprakash Thulukanam
- Department of Microbiology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India
| | - Vishnupriya Paneerselvam
- Department of Microbiology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India
| | - Poornima Baskar Vimala
- Department of Microbiology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India
| | - Rahul Harikumar Lathakumari
- Department of Microbiology, SRM Medical College Hospital and Research Centre, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu, Tamil Nadu, India
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2
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Matsuzaki S, Sakuma T, Yamamoto T. REMOVER-PITCh: microhomology-assisted long-range gene replacement with highly multiplexed CRISPR-Cas9. In Vitro Cell Dev Biol Anim 2024; 60:697-707. [PMID: 38334880 PMCID: PMC11297102 DOI: 10.1007/s11626-024-00850-1] [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: 11/14/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024]
Abstract
A variety of CRISPR-Cas9-based gene editing technologies have been developed, including gene insertion and gene replacement, and applied to the study and treatment of diseases. While numerous studies have been conducted to improve the efficiency of gene insertion and to expand the system in various ways, there have been relatively few reports on gene replacement technology; therefore, further improvements are still needed in this context. Here, we developed the REMOVER-PITCh system to establish an efficient long-range gene replacement method and demonstrated its utility at two genomic loci in human cultured cells. REMOVER-PITCh depends on microhomology-assisted gene insertion technology called PITCh with highly multiplexed CRISPR-Cas9. First, we achieved gene replacement of about 20-kb GUSB locus using this system. Second, by applying the previously established knock-in-enhancing platform, the LoAD system, along with REMOVER-PITCh, we achieved the replacement of a longer gene region of about 200 kb at the ARSB locus. Our REMOVER-PITCh system will make it possible to remove and incorporate a variety of sequences from and into the genome, respectively, which will facilitate the generation of various disease and humanized models.
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Affiliation(s)
- Shu Matsuzaki
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
- Drug Discovery Laboratory, Wakunaga Pharmaceutical Co., Ltd., 1624 Shimokotachi, Koda-Cho, Akitakata-Shi, Hiroshima, 739-1195, Japan
| | - Tetsushi Sakuma
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan.
| | - Takashi Yamamoto
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
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3
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Zahedipour F, Zahedipour F, Zamani P, Jaafari MR, Sahebkar A. Harnessing CRISPR technology for viral therapeutics and vaccines: from preclinical studies to clinical applications. Virus Res 2024; 341:199314. [PMID: 38211734 PMCID: PMC10825633 DOI: 10.1016/j.virusres.2024.199314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
The CRISPR/Cas system, identified as a type of bacterial adaptive immune system, have attracted significant attention due to its remarkable ability to precisely detect and eliminate foreign genetic material and nucleic acids. Expanding upon these inherent capabilities, recent investigations have unveiled the potential of reprogrammed CRISPR/Cas 9, 12, and 13 systems for treating viral infections associated with human diseases, specifically targeting DNA and RNA viruses, respectively. Of particular interest is the RNA virus responsible for the recent global outbreak of coronavirus disease 2019 (COVID-19), which presents a substantial public health risk, coupled with limited efficacy of current prophylactic and therapeutic techniques. In this regard, the utilization of CRISPR/Cas technology offers a promising gene editing approach to overcome the limitations of conventional methods in managing viral infections. This comprehensive review provides an overview of the latest CRISPR/Cas-based therapeutic and vaccine strategies employed to combat human viral infections. Additionally, we discuss significant challenges and offer insights into the future prospects of this cutting-edge gene editing technology.
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Affiliation(s)
- Farzaneh Zahedipour
- Microbiology Department, Medical Sciences Branch, Islamic Azad University (IAU), Tehran, Iran
| | - Fatemeh Zahedipour
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parvin Zamani
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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4
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Bartosh UI, Dome AS, Zhukova NV, Karitskaya PE, Stepanov GA. CRISPR/Cas9 as a New Antiviral Strategy for Treating Hepatitis Viral Infections. Int J Mol Sci 2023; 25:334. [PMID: 38203503 PMCID: PMC10779197 DOI: 10.3390/ijms25010334] [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: 11/15/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatitis is an inflammatory liver disease primarily caused by hepatitis A (HAV), B (HBV), C (HCV), D (HDV), and E (HEV) viruses. The chronic forms of hepatitis resulting from HBV and HCV infections can progress to cirrhosis or hepatocellular carcinoma (HCC), while acute hepatitis can lead to acute liver failure, sometimes resulting in fatality. Viral hepatitis was responsible for over 1 million reported deaths annually. The treatment of hepatitis caused by viral infections currently involves the use of interferon-α (IFN-α), nucleoside inhibitors, and reverse transcriptase inhibitors (for HBV). However, these methods do not always lead to a complete cure for viral infections, and chronic forms of the disease pose significant treatment challenges. These facts underscore the urgent need to explore novel drug developments for the treatment of viral hepatitis. The discovery of the CRISPR/Cas9 system and the subsequent development of various modifications of this system have represented a groundbreaking advance in the quest for innovative strategies in the treatment of viral infections. This technology enables the targeted disruption of specific regions of the genome of infectious agents or the direct manipulation of cellular factors involved in viral replication by introducing a double-strand DNA break, which is targeted by guide RNA (spacer). This review provides a comprehensive summary of our current knowledge regarding the application of the CRISPR/Cas system in the regulation of viral infections caused by HAV, HBV, and HCV. It also highlights new strategies for drug development aimed at addressing both acute and chronic forms of viral hepatitis.
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Affiliation(s)
| | | | | | | | - Grigory A. Stepanov
- The Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia; (U.I.B.); (A.S.D.); (N.V.Z.); (P.E.K.)
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5
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Zhang H, Tu T. Targeting Hepatitis B Virus DNA Using Designer Gene Editors. Clin Liver Dis 2023; 27:895-916. [PMID: 37778776 DOI: 10.1016/j.cld.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Chronic hepatitis B virus (HBV) infection is a serious disease that currently has no cure. Key forms of HBV include covalently closed circular DNA, which mediates chronic persistence, and integrated DNA, which contributes to immune evasion and carcinogenesis. These forms are not targeted by current therapies; however, gene editing technologies have emerged as promising tools for disrupting HBV DNA. Gene editor-induced double-stranded breaks at precise locations within the HBV genome can induce effects ranging from inactivation of target genes to complete degradation of the target genome. Although promising, several challenges remain in efficacy and safety that require solutions.
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Affiliation(s)
- Henrik Zhang
- Westmead Institute for Medical Research, University of Sydney School of Medicine and Health, 176 Hawkesbury Road, Westmead, NSW 2145, Australia
| | - Thomas Tu
- Westmead Institute for Medical Research, University of Sydney School of Medicine and Health, 176 Hawkesbury Road, Westmead, NSW 2145, Australia.
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Ebrahimi S, Khosravi MA, Raz A, Karimipoor M, Parvizi P. CRISPR-Cas Technology as a Revolutionary Genome Editing tool: Mechanisms and Biomedical Applications. IRANIAN BIOMEDICAL JOURNAL 2023; 27:219-46. [PMID: 37873636 PMCID: PMC10707817 DOI: 10.61186/ibj.27.5.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/14/2023] [Indexed: 12/17/2023]
Abstract
Programmable nucleases are powerful genomic tools for precise genome editing. These tools precisely recognize, remove, or change DNA at a defined site, thereby, stimulating cellular DNA repair pathways that can cause mutations or accurate replacement or deletion/insertion of a sequence. CRISPR-Cas9 system is the most potent and useful genome editing technique adapted from the defense immune system of certain bacteria and archaea against viruses and phages. In the past decade, this technology made notable progress, and at present, it has largely been used in genome manipulation to make precise gene editing in plants, animals, and human cells. In this review, we aim to explain the basic principle, mechanisms of action, and applications of this system in different areas of medicine, with emphasizing on the detection and treatment of parasitic diseases.
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Affiliation(s)
- Sahar Ebrahimi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Ali Khosravi
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abbasali Raz
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
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Mayes CM, Santarpia JL. Pan-Coronavirus CRISPR-CasRx Effector System Significantly Reduces Viable Titer in HCoV-OC43, HCoV-229E, and SARS-CoV-2. CRISPR J 2023; 6:359-368. [PMID: 36912815 PMCID: PMC10457650 DOI: 10.1089/crispr.2022.0095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/07/2023] [Indexed: 03/14/2023] Open
Abstract
CRISPR-based technology has become widely used as an antiviral strategy, including as a broad-spectrum human coronavirus (HCoV) therapeutic. In this work, we have designed a CRISPR-CasRx effector system with guide RNAs (gRNAs) that are cross-reactive among several HCoV species. We tested the efficacy of this pan-coronavirus effector system by evaluating the reduction in viral viability associated with different CRISPR targets in HCoV-OC43, HCoV-229E, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We determined that several CRISPR targets significantly reduce viral titer, despite the presence of single nucleotide polymorphisms in the gRNA when compared with a non-targeting, negative control gRNA. CRISPR targets reduced viral titer between 85% and >99% in HCoV-OC43, between 78% and >99% in HCoV-229E, and between 70% and 94% in SARS-CoV-2 when compared with an untreated virus control. These data establish a proof-of-concept for a pan-coronavirus CRISPR effector system that is capable of reducing viable virus in both Risk Group 2 and Risk Group 3 HCoV pathogens.
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Affiliation(s)
- Cathryn M. Mayes
- WMD Threats and Aerosol Science, Sandia National Laboratories, Albuquerque, New Mexico, USA; National Strategic Research Institute, Omaha, Nebraska, USA
| | - Joshua L. Santarpia
- University of Nebraska Medical Center, Omaha, Nebraska, USA; and National Strategic Research Institute, Omaha, Nebraska, USA
- Chemical & Biological Threat Detection & Countermeasure Development, National Strategic Research Institute, Omaha, Nebraska, USA
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8
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Yang H, Yao W, Yang J. Overview of the development of HBV small molecule inhibitors. Eur J Med Chem 2023; 249:115128. [PMID: 36709647 DOI: 10.1016/j.ejmech.2023.115128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/28/2023]
Abstract
Like tuberculosis and Acquired Immune Deficiency Syndrome (AIDS), hepatitis B is a globally recognized major public health threat. Although there are many small-molecule drugs for the treatment of hepatitis B, the approved drugs cannot eradicate the pathogenic culprit covalently closed circular DNA in patients, so the patients need long-term medication to control HBV amplification. Driven by a high unmet medical need, many pharmaceutical companies and research institutions have been engaged in the development of anti-HBV drugs to achieve a functional cure for chronic hepatitis B as soon as possible. This review summarizes the pathogenesis of hepatitis B virus and the research progress in the development of anti-HBV small molecule drugs, and introduces the cccDNA formation and transcription inhibitors and core inhibitors in detail, especially emphasizes the role of chinese herbal medicine in the treatment of chronic hepatitis B. Furthermore, this review proposes three potential strategies for cccDNA eradication in the future. We believe this review will provide meaningful guidance to achieve a functional cure for viral hepatitis B in the future.
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Affiliation(s)
- Huihui Yang
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266001, China
| | - Weiwei Yao
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266001, China
| | - Jinfei Yang
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266001, China.
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9
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Jacobs R, Singh P, Smith T, Arbuthnot P, Maepa MB. Prospects of viral vector-mediated delivery of sequences encoding anti-HBV designer endonucleases. Gene Ther 2022:10.1038/s41434-022-00342-5. [PMID: 35606493 DOI: 10.1038/s41434-022-00342-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 11/09/2022]
Abstract
Available treatment for chronic hepatitis B virus (HBV) infection offers modest functional curative efficacy. The viral replicative intermediate comprising covalently closed circular DNA (cccDNA) is responsible for persistent chronic HBV infection. Hence, current efforts have focused on developing therapies that disable cccDNA. Employing gene editing tools has emerged as an attractive strategy, with the end goal of establishing permanently inactivated cccDNA. Although anti-HBV designer nucleases are effective in vivo, none has yet progressed to clinical trial. Lack of safe and efficient delivery systems remains the limiting factor. Several vectors may be used to deliver anti-HBV gene editor-encoding sequences, with viral vectors being at the forefront. Despite the challenges associated with packaging large gene editor-encoding sequences into viral vectors, advancement in the field is overcoming such limitations. Translation of viral vector-mediated gene editing against HBV to clinical application is within reach. This review discusses the prospects of delivering HBV targeted designer nucleases using viral vectors.
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Affiliation(s)
- Ridhwaanah Jacobs
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Prashika Singh
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tiffany Smith
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mohube Betty Maepa
- Wits/SAMRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Martinez MG, Combe E, Inchauspe A, Mangeot PE, Delberghe E, Chapus F, Neveu G, Alam A, Carter K, Testoni B, Zoulim F. CRISPR-Cas9 Targeting of Hepatitis B Virus Covalently Closed Circular DNA Generates Transcriptionally Active Episomal Variants. mBio 2022; 13:e0288821. [PMID: 35389262 PMCID: PMC9040760 DOI: 10.1128/mbio.02888-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
Chronic hepatitis B virus (HBV) infection persists due to the lack of therapies that effectively target the HBV covalently closed circular DNA (cccDNA). We used HBV-specific guide RNAs (gRNAs) and CRISPR-Cas9 and determined the fate of cccDNA after gene editing. We set up a ribonucleoprotein (RNP) delivery system in HBV-infected HepG2-NTCP cells. HBV parameters after Cas9 editing were analyzed. Southern blot (SB) analysis and DNA/RNA sequencing (DNA/RNA-seq) were performed to determine the consequences of cccDNA editing and transcriptional activity of mutated cccDNA. Treatment of infected cells with HBV-specific gRNAs showed that CRISPR-Cas9 can efficiently affect HBV replication. The appearance of episomal HBV DNA variants after dual gRNA treatment was observed by PCR, SB analysis, and DNA/RNA-seq. These transcriptionally active variants are the products of simultaneous Cas9-induced double-strand breaks in two target sites, followed by repair and religation of both short and long fragments. Following suppression of HBV DNA replicative intermediates by nucleoside analogs, mutations and formation of smaller transcriptionally active HBV variants were still observed, suggesting that established cccDNA is accessible to CRISPR-Cas9 editing. Targeting HBV DNA with CRISPR-Cas9 leads to cleavage followed by appearance of episomal HBV DNA variants. Effects induced by Cas9 were sustainable after RNP degradation/loss of detection, suggesting permanent changes in the HBV genome instead of transient effects due to transcriptional interference. IMPORTANCE Hepatitis B virus infection can develop into chronic infection, cirrhosis, and hepatocellular carcinoma. Treatment of chronic hepatitis B requires novel approaches to directly target the viral minichromosome, which is responsible for the persistence of the disease. Designer nuclease approaches represent a promising strategy to treat chronic infectious diseases; however, comprehensive knowledge about the fate of the HBV minichromosome is needed before this potent tool can be used as a potential therapeutic approach. This study provides an in-depth analysis of CRISPR-Cas9 targeting of HBV minichromosome.
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Affiliation(s)
| | - Emmanuel Combe
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon, Lyon, France
| | - Aurore Inchauspe
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon, Lyon, France
- Evotec, Lyon, France
| | - Philippe Emmanuel Mangeot
- Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR-5308, INSERM and Ecole Normale Superieure de Lyon, Lyon, France
| | - Elodie Delberghe
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon, Lyon, France
| | - Fleur Chapus
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon, Lyon, France
| | | | | | | | - Barbara Testoni
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon, Lyon, France
| | - Fabien Zoulim
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon, Lyon, France
- University of Lyon, Université Claude-Bernard, Lyon, France
- Hospices Civils de Lyon, Lyon, France
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11
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Zhang Y, Li Z, Milon Essola J, Ge K, Dai X, He H, Xiao H, Weng Y, Huang Y. Biosafety materials: Ushering in a new era of infectious disease diagnosis and treatment with the CRISPR/Cas system. BIOSAFETY AND HEALTH 2022; 4:70-78. [PMID: 35310559 PMCID: PMC8920088 DOI: 10.1016/j.bsheal.2022.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 01/07/2023] Open
Abstract
Despite multiple virus outbreaks over the past decade, including the devastating coronavirus disease 2019 (COVID-19) pandemic, the lack of accurate and timely diagnosis and treatment technologies has wreaked havoc on global biosecurity. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system has the potential to address these critical needs for tackling infectious diseases to detect viral nucleic acids and inhibit viral replication. This review summarizes how the CRISPR/Cas system is being utilized for the treatment and diagnosis of infectious diseases with the help of biosafety materials and highlights the design principle and in vivo and in vitro efficacy of advanced biosafety materials used to deal with virus attacks.
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Affiliation(s)
- Yuquan Zhang
- School of Life Science, School of Medical Technology, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Ziyue Li
- School of Life Science, School of Medical Technology, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Julien Milon Essola
- School of Life Science, School of Medical Technology, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Kun Ge
- Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of the Ministry of Education, Hebei University, Baoding 071000, China
| | - Xuyan Dai
- Hunan Agricultural University, Changsha 410128, China
| | - Huining He
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Haihua Xiao
- Beijing National Laboratory for Molecular Science, State Key Laboratory of Polymer Physical and Chemistry, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, China
| | - Yuhua Weng
- School of Life Science, School of Medical Technology, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yuanyu Huang
- School of Life Science, School of Medical Technology, Advanced Research Institute of Multidisciplinary Science, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
- School of Materials and the Environment, Beijing Institute of Technology, Zhuhai 519085, China
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12
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Recent Progress and Future Prospective in HBV Cure by CRISPR/Cas. Viruses 2021; 14:v14010004. [PMID: 35062208 PMCID: PMC8781244 DOI: 10.3390/v14010004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/09/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) infection remains an important issue of global public health. Although current antiviral therapy has dramatically reduced the mortality and morbidity of chronic hepatitis B (CHB), it fails to cure it. Rebound viremia often occurs after stopping antiviral therapy. Persistent HBV covalently closed circular DNA (cccDNA) and integrated DNA under antiviral therapy form the major barrier to eradication of HBV infection. CRISPR-mediated genome editing has emerged as a promising therapeutic approach to specifically destroy persistent HBV genomes, both cccDNA and integrated DNA, for HBV cure. However, the cleavage of integrated HBV DNA by CRISPR-Cas9 will cause double-strand break (DSB) of host genome, raising a serious safety concern about genome instability and carcinogenesis. The newly developed CRISPR-derived base editors (BEs), which fuse a catalytically disabled nuclease with a nucleobase deaminase enzyme, can be used to permanently inactivate HBV genome by introducing irreversible point mutations for generation of premature stop codons without DSBs of host genome. Although promising, CRISPR-mediated base editing still faces daunting challenges before its clinical application, including the base-editing efficacy, the off-target effect, the difficulty in finding conserved target HBV sequences, and in vivo delivery efficiency. Several strategies have been adopted to optimize the efficiency and specificity of CRISPR-BEs and to improve in vivo delivery efficacy through novel viral and non-viral delivery approaches. Particularly, the non-viral delivery of Cas9 mRNA and ribonucleoprotein by lipid nanoparticles exhibits attractive potential for liver-targeted delivery in clinical. Along with all progress above, the CRISPR-mediated gene therapy will ultimately achieve HBV cure.
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Kostyushev D, Kostyusheva A, Ponomareva N, Brezgin S, Chulanov V. CRISPR/Cas and Hepatitis B Therapy: Technological Advances and Practical Barriers. Nucleic Acid Ther 2021; 32:14-28. [PMID: 34797701 DOI: 10.1089/nat.2021.0075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
After almost a decade of using CRISPR/Cas9 systems to edit target genes, CRISPR/Cas9 and related technologies are rapidly moving to clinical trials. Hepatitis B virus (HBV), which causes severe liver disease, cannot be cleared by modern antivirals, but represents an ideal target for CRISPR/Cas9 systems. Early studies demonstrated very high antiviral potency of CRISPR/Cas9 and supported its use for developing a cure against chronic HBV infection. This review discusses the key issues that must be solved to make CRISPR/Cas9 an anti-HBV therapy.
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Affiliation(s)
- Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia.,Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia
| | - Natalia Ponomareva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia.,Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia.,Department of Infectious Diseases, Sechenov University, Moscow, Russia
| | - Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia.,Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
| | - Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow, Russia.,Division of Biotechnology, Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia.,Department of Infectious Diseases, Sechenov University, Moscow, Russia
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14
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Watanabe T, Inoue T, Tanaka Y. Hepatitis B Core-Related Antigen and New Therapies for Hepatitis B. Microorganisms 2021; 9:microorganisms9102083. [PMID: 34683404 PMCID: PMC8537336 DOI: 10.3390/microorganisms9102083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 02/06/2023] Open
Abstract
The hepatitis B core-related antigen (HBcrAg) is an unprecedented novel HBV biomarker that plays an essential role in reflecting covalently closed circular DNA (cccDNA) in chronic hepatitis B (CHB) because its levels correlate with intrahepatic cccDNA and serum HBV DNA. In this review, we describe the clinical application of serum HBcrAg in CHB patients, with a particular focus on new therapies targeting intrahepatic HBV replication. (1) HBcrAg can be detected in clinical cases where serum HBV DNA is undetectable during anti-HBV therapy. (2) A highly sensitive HBcrAg assay (iTACT-HBcrAg) may be useful for monitoring HBV reactivation, as an alternative to HBV DNA. (3) Decreased HBcrAg levels have been significantly associated with promising outcomes in CHB patients, reducing the risk of progression or recurrence of hepatocellular carcinoma. Additionally, we focus on and discuss several drugs in development that target HBV replication, and monitoring HBcrAg may be useful for determining the therapeutic efficacies of such novel drugs. In conclusion, HBcrAg, especially when measured by the recently developed iTACT-HBcrAg assay, may be the most appropriate surrogate marker, over other HBV biomarkers, to predict disease progression and treatment response in CHB patients.
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Affiliation(s)
- Takehisa Watanabe
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan;
| | - Takako Inoue
- Department of Clinical Laboratory Medicine, Nagoya City University Hospital, Nagoya 467-8602, Japan;
| | - Yasuhito Tanaka
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan;
- Correspondence:
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15
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Lin H, Li G, Peng X, Deng A, Ye L, Shi L, Wang T, He J. The Use of CRISPR/Cas9 as a Tool to Study Human Infectious Viruses. Front Cell Infect Microbiol 2021; 11:590989. [PMID: 34513721 PMCID: PMC8430244 DOI: 10.3389/fcimb.2021.590989] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/04/2021] [Indexed: 12/12/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) systems are a set of versatile gene-editing toolkit that perform diverse revolutionary functions in various fields of application such as agricultural practices, food industry, biotechnology, biomedicine, and clinical research. Specially, as a novel antiviral method of choice, CRISPR/Cas9 system has been extensively and effectively exploited to fight against human infectious viruses. Infectious diseases including human immunodeficiency virus (HIV), hepatitis B virus (HBV), human papillomavirus (HPV), and other viruses are still global threats with persistent potential to probably cause pandemics. To facilitate virus removals, the CRISPR/Cas9 system has already been customized to confer new antiviral capabilities into host animals either by modifying host genome or by directly targeting viral inherent factors in the form of DNA. Although several limitations and difficulties still need to be conquered, this technology holds great promises in the treatment of human viral infectious diseases. In this review, we will first present a brief biological feature of CRISPR/Cas9 systems, which includes a description of CRISPR/Cas9 structure and composition; thereafter, we will focus on the investigations and applications that employ CRISPR/Cas9 system to combat several human infectious viruses and discuss challenges and future perspectives of using this new platform in the preclinical and clinical settings as an antiviral strategy.
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Affiliation(s)
- Huafeng Lin
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, Changsha, China.,Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Gang Li
- Institute of Biomedicine and Department of Cell Biology, Jinan University, Guangzhou, China
| | - Xiangwen Peng
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, Changsha, China
| | - Aimin Deng
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, Changsha, China
| | - Lei Ye
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
| | - Tuanmei Wang
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, Changsha, China
| | - Jun He
- Changsha Hospital for Maternal and Child Health Care of Hunan Normal University, Changsha, China
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16
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Smith T, Singh P, Chmielewski KO, Bloom K, Cathomen T, Arbuthnot P, Ely A. Improved Specificity and Safety of Anti-Hepatitis B Virus TALENs Using Obligate Heterodimeric FokI Nuclease Domains. Viruses 2021; 13:v13071344. [PMID: 34372550 PMCID: PMC8310341 DOI: 10.3390/v13071344] [Citation(s) in RCA: 10] [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: 06/18/2021] [Accepted: 07/02/2021] [Indexed: 01/04/2023] Open
Abstract
Persistent hepatitis B virus (HBV) infection remains a serious medical problem worldwide, with an estimated global burden of 257 million carriers. Prophylactic and therapeutic interventions, in the form of a vaccine, immunomodulators, and nucleotide and nucleoside analogs, are available. Vaccination, however, offers no therapeutic benefit to chronic sufferers and has had a limited impact on infection rates. Although immunomodulators and nucleotide and nucleoside analogs have been licensed for treatment of chronic HBV, cure rates remain low. Transcription activator-like effector nucleases (TALENs) designed to bind and cleave viral DNA offer a novel therapeutic approach. Importantly, TALENs can target covalently closed circular DNA (cccDNA) directly with the potential of permanently disabling this important viral replicative intermediate. Potential off-target cleavage by engineered nucleases leading to toxicity presents a limitation of this technology. To address this, in the context of HBV gene therapy, existing TALENs targeting the viral core and surface open reading frames were modified with second- and third-generation FokI nuclease domains. As obligate heterodimers these TALENs prevent target cleavage as a result of FokI homodimerization. Second-generation obligate heterodimeric TALENs were as effective at silencing viral gene expression as first-generation counterparts and demonstrated an improved specificity in a mouse model of HBV replication.
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Affiliation(s)
- Tiffany Smith
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa; (T.S.); (P.S.); (K.B.); (P.A.)
| | - Prashika Singh
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa; (T.S.); (P.S.); (K.B.); (P.A.)
| | - Kay Ole Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg & Medical Faculty, University of Freiburg, 79106 Freiburg, Germany; (K.O.C.); (T.C.)
| | - Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa; (T.S.); (P.S.); (K.B.); (P.A.)
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg & Medical Faculty, University of Freiburg, 79106 Freiburg, Germany; (K.O.C.); (T.C.)
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa; (T.S.); (P.S.); (K.B.); (P.A.)
| | - Abdullah Ely
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa; (T.S.); (P.S.); (K.B.); (P.A.)
- Correspondence: ; Tel.: +27-(0)11-717-2561
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17
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Ramirez-Phillips AC, Liu D. Therapeutic Genome Editing and In Vivo Delivery. AAPS JOURNAL 2021; 23:80. [PMID: 34080099 DOI: 10.1208/s12248-021-00613-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/20/2021] [Indexed: 11/30/2022]
Abstract
Improvements in the understanding of human genetics and its roles in disease development and prevention have led to an increased interest in therapeutic genome editing via the use of engineered nucleases. Various approaches have been explored in the past focusing on the development of an effective and safe system for sequence-specific editing. Compared to earlier nucleases such as zinc finger nuclease and transcription activator-like effector nuclease, the relatively low cost and ease of producing clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR/Cas9) systems have made therapeutic genome editing significantly more feasible. CRISPR/Cas9 genome editing has shown great potential to correct genetic mutations implicated in monogenic diseases and to eradicate latent or chronic viral infections in preclinical studies. Several CRISPR/Cas9-based therapeutics have reached the clinical stage, including treatments for inherited red blood cell disorders and Leber Congenital Amaurosis 10, as well as CRISPR/Cas9-edited T cells designed to target and destroy cancer cells. Further advances in therapeutic genome editing will rely on a safe and more efficient method of in vivo CRISPR/Cas9 delivery and improved efficiency of homology-directed repair for site-specific gene insertion or replacement. While other reviews have focused on one or two aspects of CRISPR/Cas9 genome editing, this review aims to provide a summary of the mechanisms of genome editing, the reasons for the emerging interest in CRISPR/Cas9 compared to other engineered nucleases, the current progress in developing CRISPR/Cas9 delivery systems, and the current preclinical and clinical applications of CRISPR/Cas9 genome editing.
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Affiliation(s)
| | - Dexi Liu
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, 30602, USA.
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18
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Latest Advances of Virology Research Using CRISPR/Cas9-Based Gene-Editing Technology and Its Application to Vaccine Development. Viruses 2021; 13:v13050779. [PMID: 33924851 PMCID: PMC8146441 DOI: 10.3390/v13050779] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 02/07/2023] Open
Abstract
In recent years, the CRISPR/Cas9-based gene-editing techniques have been well developed and applied widely in several aspects of research in the biological sciences, in many species, including humans, animals, plants, and even in viruses. Modification of the viral genome is crucial for revealing gene function, virus pathogenesis, gene therapy, genetic engineering, and vaccine development. Herein, we have provided a brief review of the different technologies for the modification of the viral genomes. Particularly, we have focused on the recently developed CRISPR/Cas9-based gene-editing system, detailing its origin, functional principles, and touching on its latest achievements in virology research and applications in vaccine development, especially in large DNA viruses of humans and animals. Future prospects of CRISPR/Cas9-based gene-editing technology in virology research, including the potential shortcomings, are also discussed.
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19
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Maepa MB, Bloom K, Ely A, Arbuthnot P. Hepatitis B virus: promising drug targets and therapeutic implications. Expert Opin Ther Targets 2021; 25:451-466. [PMID: 33843412 DOI: 10.1080/14728222.2021.1915990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Current therapy for infection with hepatitis B virus (HBV) rarely clears the virus, and viremia commonly resurges following treatment withdrawal. To prevent serious complications of the infection, research has been aimed at identifying new viral and host targets that can be exploited to inactivate HBV replication.Areas covered: This paper reviews the use of these new molecular targets to advance anti-HBV therapy. Emphasis is on appraising data from pre-clinical and early clinical studies described in journal articles published during the past 10 years and available from PubMed.Expert opinion: The wide range of viral and host factors that can be targeted to disable HBV is impressive and improved insight into HBV molecular biology continues to provide the basis for new drug design. In addition to candidate therapies that have direct or indirect actions on HBV covalently closed circular DNA (cccDNA), compounds that inhibit HBsAg secretion, viral entry, destabilize viral RNA and effect enhanced immune responses to HBV show promise. Preclinical and clinical evaluation of drug candidates, as well as investigating use of treatment combinations, are encouraging. The field is poised at an interesting stage and indications are that reliably achieving functional cure from HBV infection is a tangible goal.
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Affiliation(s)
- Mohube Betty Maepa
- School of Pathology, Faculty of Health Sciences, Wits/SAMRC Antiviral Gene Therapy Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Kristie Bloom
- School of Pathology, Faculty of Health Sciences, Wits/SAMRC Antiviral Gene Therapy Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Abdullah Ely
- School of Pathology, Faculty of Health Sciences, Wits/SAMRC Antiviral Gene Therapy Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Patrick Arbuthnot
- School of Pathology, Faculty of Health Sciences, Wits/SAMRC Antiviral Gene Therapy Research Unit, University of the Witwatersrand, Johannesburg, South Africa
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20
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Escalona‐Noguero C, López‐Valls M, Sot B. CRISPR/Cas technology as a promising weapon to combat viral infections. Bioessays 2021; 43:e2000315. [PMID: 33569817 PMCID: PMC7995209 DOI: 10.1002/bies.202000315] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 12/13/2022]
Abstract
The versatile clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system has emerged as a promising technology for therapy and molecular diagnosis. It is especially suited for overcoming viral infections outbreaks, since their effective control relies on an efficient treatment, but also on a fast diagnosis to prevent disease dissemination. The CRISPR toolbox offers DNA- and RNA-targeting nucleases that constitute dual weapons against viruses. They allow both the manipulation of viral and host genomes for therapeutic purposes and the detection of viral nucleic acids in "Point of Care" sensor devices. Here, we thoroughly review recent advances in the use of the CRISPR/Cas system for the treatment and diagnosis of viral deleterious infections such as HIV or SARS-CoV-2, examining their strengths and limitations. We describe the main points to consider when designing CRISPR antiviral strategies and the scientific efforts to develop more sensitive CRISPR-based viral detectors. Finally, we discuss future prospects to improve both applications. Also see the video abstract here: https://www.youtube.com/watch?v=C0z1dLpJWl4.
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Affiliation(s)
| | | | - Begoña Sot
- Fundación IMDEA‐NanocienciaMadridSpain
- Nanobiotecnología (IMDEA‐Nanociencia)Unidad Asociada al Centro Nacional de Biotecnología (CSIC)MadridSpain
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21
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CRISPR-Cas9 gene editing of hepatitis B virus in chronically infected humanized mice. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 20:258-275. [PMID: 33473359 PMCID: PMC7803634 DOI: 10.1016/j.omtm.2020.11.014] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Chronic hepatitis B virus (HBV) infection is a major public health problem. New treatment approaches are needed because current treatments do not target covalently closed circular DNA (cccDNA), the template for HBV replication, and rarely clear the virus. We harnessed adeno-associated virus (AAV) vectors and CRISPR-Staphylococcus aureus (Sa)Cas9 to edit the HBV genome in liver-humanized FRG mice chronically infected with HBV and receiving entecavir. Gene editing was detected in livers of five of eight HBV-specific AAV-SaCas9-treated mice, but not control mice, and mice with detectable HBV gene editing showed higher levels of SaCas9 delivery to HBV+ human hepatocytes than those without gene editing. HBV-specific AAV-SaCas9 therapy significantly improved survival of human hepatocytes, showed a trend toward decreasing total liver HBV DNA and cccDNA, and was well tolerated. This work provides evidence for the feasibility and safety of in vivo gene editing for chronic HBV infections, and it suggests that with further optimization, this approach may offer a plausible way to treat or even cure chronic HBV infections.
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22
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Duraisamy GS, Bhosale D, Lipenská I, Huvarova I, Růžek D, Windisch MP, Miller AD. Advanced Therapeutics, Vaccinations, and Precision Medicine in the Treatment and Management of Chronic Hepatitis B Viral Infections; Where Are We and Where Are We Going? Viruses 2020; 12:v12090998. [PMID: 32906840 PMCID: PMC7552065 DOI: 10.3390/v12090998] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
The management of chronic hepatitis B virus (CHB) infection is an area of massive unmet clinical need worldwide. In spite of the development of powerful nucleoside/nucleotide analogue (NUC) drugs, and the widespread use of immune stimulators such as interferon-alpha (IFNα) or PEGylated interferon-alpha (PEG-IFNα), substantial improvements in CHB standards of care are still required. We believe that the future for CHB treatment now rests with advanced therapeutics, vaccination, and precision medicine, if all are to bring under control this most resilient of virus infections. In spite of a plethora of active drug treatments, anti-viral vaccinations and diagnostic techniques, the management of CHB infection remains unresolved. The reason for this is the very complexity of the virus replication cycle itself, giving rise to multiple potential targets for therapeutic intervention some of which remain very intractable indeed. Our review is focused on discussing the potential impact that advanced therapeutics, vaccinations and precision medicine could have on the future management of CHB infection. We demonstrate that advanced therapeutic approaches for the treatment of CHB, in the form of gene and immune therapies, together with modern vaccination strategies, are now emerging rapidly to tackle the limitations of current therapeutic approaches to CHB treatment in clinic. In addition, precision medicine approaches are now gathering pace too, starting with personalized medicine. On the basis of this, we argue that the time has now come to accelerate the design and creation of precision therapeutic approaches (PTAs) for CHB treatment that are based on advanced diagnostic tools and nanomedicine, and which could maximize CHB disease detection, treatment, and monitoring in ways that could genuinely eliminate CHB infection altogether.
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Affiliation(s)
- Ganesh Selvaraj Duraisamy
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
| | - Dattatry Bhosale
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
| | - Ivana Lipenská
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
| | - Ivana Huvarova
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
| | - Daniel Růžek
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 České Budějovice, Czech Republic
| | - Marc P. Windisch
- Applied Molecular Virology Laboratory, Institut Pasteur Korea, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, Gyeonggi-do 463-400, Korea;
- Division of Bio-Medical Science and Technology, University of Science and Technology, Daejeon 305-350, Korea
| | - Andrew D. Miller
- Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; (G.S.D.); (D.B.); (I.L.); (I.H.); (D.R.)
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1, Černá Pole, CZ-61300 Brno, Czech Republic
- KP Therapeutics (Europe) s.r.o., Purkyňova 649/127, CZ-61200 Brno, Czech Republic
- Correspondence:
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23
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Ligat G, Goto K, Verrier E, Baumert TF. Targeting Viral cccDNA for Cure of Chronic Hepatitis B. CURRENT HEPATOLOGY REPORTS 2020; 19:235-244. [PMID: 36034467 PMCID: PMC7613435 DOI: 10.1007/s11901-020-00534-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Purpose of Review Chronic hepatitis B (CHB), caused by hepatitis B virus (HBV), is a major cause of advanced liver disease and hepatocellular carcinoma (HCC) worldwide. HBV replication is characterized by the synthesis of covalently closed circular (ccc) DNA which is not targeted by antiviral nucleos(t)ide analogues (NUCs) the key modality of standard of care. While HBV replication is successfully suppressed in treated patients, they remain at risk for developing HCC. While functional cure, characterized by loss of HBsAg, is the first goal of novel antiviral therapies, curative treatments eliminating cccDNA remain the ultimate goal. This review summarizes recent advances in the discovery and development of novel therapeutic strategies and their impact on cccDNA biology. Recent Findings Within the last decade, substantial progress has been made in the understanding of cccDNA biology including the discovery of host dependency factors, epigenetic regulation of cccDNA transcription and immune-mediated degradation. Several approaches targeting cccDNA either in a direct or indirect manner are currently at the stage of discovery, preclinical or early clinical development. Examples include genome-editing approaches, strategies targeting host dependency factors or epigenetic gene regulation, nucleocapsid modulators and immune-mediated degradation. Summary While direct-targeting cccDNA strategies are still largely at the preclinical stage of development, capsid assembly modulators and immune-based approaches have reached the clinical phase. Clinical trials are ongoing to assess their efficacy and safety in patients including their impact on viral cccDNA. Combination therapies provide additional opportunities to overcome current limitations of individual approaches.
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Affiliation(s)
- Gaëtan Ligat
- Université de Strasbourg, 67000 Strasbourg, France
- Institut de Recherche sur les Maladies Virales et Hépatiques, Inserm U1110, 3 Rue Koeberlé, 67000 Strasbourg, France
| | - Kaku Goto
- Université de Strasbourg, 67000 Strasbourg, France
- Institut de Recherche sur les Maladies Virales et Hépatiques, Inserm U1110, 3 Rue Koeberlé, 67000 Strasbourg, France
| | - Eloi Verrier
- Université de Strasbourg, 67000 Strasbourg, France
- Institut de Recherche sur les Maladies Virales et Hépatiques, Inserm U1110, 3 Rue Koeberlé, 67000 Strasbourg, France
| | - Thomas F. Baumert
- Université de Strasbourg, 67000 Strasbourg, France
- Institut de Recherche sur les Maladies Virales et Hépatiques, Inserm U1110, 3 Rue Koeberlé, 67000 Strasbourg, France
- Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, 67000 Strasbourg, France
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24
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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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25
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El-Kenawy A, Benarba B, Neves AF, de Araujo TG, Tan BL, Gouri A. Gene surgery: Potential applications for human diseases. EXCLI JOURNAL 2019; 18:908-930. [PMID: 31762718 PMCID: PMC6868916 DOI: 10.17179/excli2019-1833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
Gene therapy became in last decade a new emerging therapeutic era showing promising results against different diseases such as cancer, cardiovascular diseases, diabetes, and neurological disorders. Recently, the genome editing technique for eukaryotic cells called CRISPR-Cas (Clustered Regulatory Interspaced Short Palindromic Repeats) has enriched the field of gene surgery with enhanced applications. In the present review, we summarized the different applications of gene surgery for treating human diseases such as cancer, diabetes, nervous, and cardiovascular diseases, besides the molecular mechanisms involved in these important effects. Several studies support the important therapeutic applications of gene surgery in a large number of health disorders and diseases including β-thalassemia, cancer, immunodeficiencies, diabetes, and neurological disorders. In diabetes, gene surgery was shown to be effective in type 1 diabetes by triggering different signaling pathways. Furthermore, gene surgery, especially that using CRISPR-Cas possessed important application on diagnosis, screening and treatment of several cancers such as lung, liver, pancreatic and colorectal cancer. Nevertheless, gene surgery still presents some limitations such as the design difficulties and costs regarding ZFNs (Zinc Finger Nucleases) and TALENs (Transcription Activator-Like Effector Nucleases) use, off-target effects, low transfection efficiency, in vivo delivery-safety and ethical issues.
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Affiliation(s)
- Ayman El-Kenawy
- Department of Pathology, College of Medicine, Taif University, Saudi Arabia
- Department of Molecular Biology, GEBRI, University of Sadat City, P.O. Box 79, Sadat City, Egypt
| | - Bachir Benarba
- Laboratory Research on Biological Systems and Geomatics, Faculty of Nature and Life Sciences, University of Mascara, Algeria
| | - Adriana Freitas Neves
- Institute of Biotechnology, Molecular Biology Laboratory, Universidade Federal de Goias, Catalao, Brazil
| | - Thaise Gonçalves de Araujo
- Laboratory of Genetics and Biotechnology, Institute of Biotechnology, Federal University of Uberlandia, Patos de Minas, MG, Brazil
| | - Bee Ling Tan
- Department of Nutrition and Dietetics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Adel Gouri
- Laboratory of Medical Biochemistry, Faculty of Medicine, University of Annaba, Algeria
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Dong Z, Qin Q, Hu Z, Chen P, Huang L, Zhang X, Tian T, Lu C, Pan M. Construction of a One-Vector Multiplex CRISPR/Cas9 Editing System to Inhibit Nucleopolyhedrovirus Replication in Silkworms. Virol Sin 2019; 34:444-453. [PMID: 31218589 DOI: 10.1007/s12250-019-00121-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/25/2019] [Indexed: 12/15/2022] Open
Abstract
Recently the developed single guide (sg)RNA-guided clustered regularly interspaced short palindromic repeats/associated protein 9 nuclease (CRISPR/Cas9) technology has opened a new avenue for antiviral therapy. The CRISPR/Cas9 system uniquely allows targeting of multiple genome sites simultaneously. However, there are relatively few applications of CRISPR/Cas9 multigene editing to target insect viruses. To address the need for sustained delivery of a multiplex CRISPR/Cas9-based genome-editing vehicle against insect viruses, we developed a one-vector (pSL1180-Cas9-U6-sgRNA) system that expresses multiple sgRNA and Cas9 protein to excise Bombyx mori nucleopolyhedrovirus (BmNPV) in insect cells. We screened the immediate-early-1 gene (ie-1), the major envelope glycoprotein gene (gp64), and the late expression factor gene (lef-11), and identified multiple sgRNA editing sites through flow cytometry and viral DNA replication analysis. In addition, we constructed a multiplex editing vector (PSL1180-Cas9-sgIE1-sgLEF11-sgGP64, sgMultiple) to efficiently regulate multiplex gene-editing and inhibit BmNPV replication after viral infection. This is the first report of the application of a multiplex CRISPR/Cas9 system to inhibit insect virus replication. This multiplex system can significantly enhance the potential of CRISPR/Cas9-based multiplex genome engineering in insect virus.
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Affiliation(s)
- Zhanqi Dong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Qi Qin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Zhigang Hu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Peng Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Liang Huang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Xinling Zhang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Ting Tian
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, 400716, China.
| | - Minhui Pan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, 400716, China.
- Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, 400716, China.
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Inoue T, Tanaka Y. The Role of Hepatitis B Core-Related Antigen. Genes (Basel) 2019; 10:genes10050357. [PMID: 31075974 PMCID: PMC6562807 DOI: 10.3390/genes10050357] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) cannot be completely eliminated from infected hepatocytes due to the existence of intrahepatic covalently closed circular DNA (cccDNA). Serological biomarkers reflect intrahepatic viral replicative activity as non-invasive alternatives to liver biopsy. Hepatitis B core-related antigen (HBcrAg) is a novel biomarker that has an important role in chronic hepatitis B (CHB), because it correlates with serum HBV DNA and intrahepatic cccDNA. In clinical cases with undetectable serum HBV DNA or loss of HBsAg, HBcrAg still can be detected and the decrease in HBcrAg levels is significantly associated with promising outcomes for CHB patients. HBcrAg can predict spontaneous or treatment-induced hepatitis B envelope antigen (HBeAg) seroconversion, persistent responses before and after cessation of nucleos(t)ide analogues, potential HBV reactivation, HBV reinfection after liver transplantation, and risk of hepatocellular carcinoma progression or recurrence. In this review, the clinical applications of HBcrAg in CHB patients based on its virological features are described. Furthermore, new potential therapeutic anti-HBV agents that affect intrahepatic cccDNA are under development, and the monitoring of HBcrAg might be useful to judge therapeutic effects. In conclusion, HBcrAg might be a suitable surrogate marker beyond other HBV markers to predict the disease progression and treatment responses of CHB patients.
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Affiliation(s)
- Takako Inoue
- Department of Clinical Laboratory Medicine, Nagoya City University Hospital, Nagoya 467-8602, Japan.
| | - Yasuhito Tanaka
- Department of Clinical Laboratory Medicine, Nagoya City University Hospital, Nagoya 467-8602, Japan.
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan.
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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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Qin K, Liang X, Sun G, Shi X, Wang M, Liu H, Chen Y, Liu X, He Z. Highly efficient correction of structural mutations of 450 kb KIT locus in kidney cells of Yorkshire pig by CRISPR/Cas9. BMC Mol Cell Biol 2019; 20:4. [PMID: 31041890 PMCID: PMC6446502 DOI: 10.1186/s12860-019-0184-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 03/11/2019] [Indexed: 11/23/2022] Open
Abstract
The white coat colour of Yorkshire and Landrace pig breeds is caused by the dominant white I allele of KIT, associated with 450-kb duplications and a splice mutation (G > A) at the first base in intron 17. To test whether genome editing can be employed to correct this structural mutation, and to investigate the role of KIT in the control of porcine coat colour, we designed sgRNAs targeting either intron 16 or intron 17 of KIT, and transfected Cas9/sgRNA co-expression plasmids into the kidney cells of Yorkshire pigs. The copy number of KIT was reduced by about 13%, suggesting the possibility of obtaining cells with corrected structural mutations of the KIT locus. Using single cell cloning, from 24 successfully expanded single cell clones derived from cells transfected with sgRNA targeting at intron 17, we obtained 3 clones with a single copy of KIT without the splice mutation. Taken together, the 12.5% (3/24) efficiency of correction of structural mutations of 450 kb fragments is highly efficient, providing a solid basis for the generation of genome edited Yorkshire pigs with a normal KIT locus. This provides an insight into the underlying genetic mechanisms of porcine coat colour.
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Affiliation(s)
- Ke Qin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Xinyu Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Guanjie Sun
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Xuan Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Min Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Hongbo Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, People's Republic of China.
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Rodríguez-Rodríguez DR, Ramírez-Solís R, Garza-Elizondo MA, Garza-Rodríguez MDL, Barrera-Saldaña HA. Genome editing: A perspective on the application of CRISPR/Cas9 to study human diseases (Review). Int J Mol Med 2019; 43:1559-1574. [PMID: 30816503 PMCID: PMC6414166 DOI: 10.3892/ijmm.2019.4112] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 08/01/2018] [Indexed: 02/06/2023] Open
Abstract
Genome editing reemerged in 2012 with the development of CRISPR/Cas9 technology, which is a genetic manipulation tool derived from the defense system of certain bacteria against viruses and plasmids. This method is easy to apply and has been used in a wide variety of experimental models, including cell lines, laboratory animals, plants, and even in human clinical trials. The CRISPR/Cas9 system consists of directing the Cas9 nuclease to create a site-directed double-strand DNA break using a small RNA molecule as a guide. A process that allows a permanent modification of the genomic target sequence can repair the damage caused to DNA. In the present study, the basic principles of the CRISPR/Cas9 system are reviewed, as well as the strategies and modifications of the enzyme Cas9 to eliminate the off-target cuts, and the different applications of CRISPR/Cas9 as a system for visualization and gene expression activation or suppression. In addition, the review emphasizes on the potential application of this system in the treatment of different diseases, such as pulmonary, gastrointestinal, hematologic, immune system, viral, autoimmune and inflammatory diseases, and cancer.
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Affiliation(s)
- Diana Raquel Rodríguez-Rodríguez
- Universidad Autónoma de Nuevo León, Department of Biochemistry and Molecular Medicine, School of Medicine and University Hospital 'Dr. José E. González', Monterrey, Nuevo León 64460, México
| | - Ramiro Ramírez-Solís
- Institutional Core Laboratories, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Mario Alberto Garza-Elizondo
- Universidad Autónoma de Nuevo León, Service of Rheumatology, School of Medicine and University Hospital 'Dr. José E. González', Monterrey, Nuevo León 64460, México
| | - María De Lourdes Garza-Rodríguez
- Universidad Autónoma de Nuevo León, Department of Biochemistry and Molecular Medicine, School of Medicine and University Hospital 'Dr. José E. González', Monterrey, Nuevo León 64460, México
| | - Hugo Alberto Barrera-Saldaña
- Universidad Autónoma de Nuevo León, Department of Biochemistry and Molecular Medicine, School of Medicine and University Hospital 'Dr. José E. González', Monterrey, Nuevo León 64460, México
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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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Kostyusheva A, Kostyushev D, Brezgin S, Volchkova E, Chulanov V. Clinical Implications of Hepatitis B Virus RNA and Covalently Closed Circular DNA in Monitoring Patients with Chronic Hepatitis B Today with a Gaze into the Future: The Field Is Unprepared for a Sterilizing Cure. Genes (Basel) 2018; 9:E483. [PMID: 30301171 PMCID: PMC6210151 DOI: 10.3390/genes9100483] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 09/30/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022] Open
Abstract
. Chronic hepatitis B virus (HBV) infection has long remained a critical global health issue. Covalently closed circular DNA (cccDNA) is a persistent form of the HBV genome that maintains HBV chronicity. Decades of extensive research resulted in the two therapeutic options currently available: nucleot(s)ide analogs and interferon (IFN) therapy. A plethora of reliable markers to monitor HBV patients has been established, including the recently discovered encapsidated pregenomic RNA in serum, which can be used to determine treatment end-points and to predict the susceptibility of patients to IFN. Additionally, HBV RNA splice variants and cccDNA and its epigenetic modifications are associated with the clinical course and risks of hepatocellular carcinoma (HCC) and liver fibrosis. However, new antivirals, including CRISPR/Cas9, APOBEC-mediated degradation of cccDNA, and T-cell therapies aim at completely eliminating HBV, and it is clear that the diagnostic arsenal for defining the long-awaited sterilizing cure is missing. In this review, we discuss the currently available tools for detecting and measuring HBV RNAs and cccDNA, as well as the state-of-the-art in clinical implications of these markers, and debate needs and goals within the context of the sterilizing cure that is soon to come.
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Affiliation(s)
| | | | - Sergey Brezgin
- Central Research Institute of Epidemiology, Moscow, 111123, Russia.
- National Research Centre, Institute of Immunology, Federal Medical Biological Agency, Moscow, 115478, Russia.
| | - Elena Volchkova
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of the Russian Federation, Moscow, 119146, Russia.
| | - Vladimir Chulanov
- Central Research Institute of Epidemiology, Moscow, 111123, Russia.
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of the Russian Federation, Moscow, 119146, Russia.
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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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Bloom K, Maepa MB, Ely A, Arbuthnot P. Gene Therapy for Chronic HBV-Can We Eliminate cccDNA? Genes (Basel) 2018; 9:E207. [PMID: 29649127 PMCID: PMC5924549 DOI: 10.3390/genes9040207] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 02/06/2023] Open
Abstract
Chronic infection with the hepatitis B virus (HBV) is a global health concern and accounts for approximately 1 million deaths annually. Amongst other limitations of current anti-HBV treatment, failure to eliminate the viral covalently closed circular DNA (cccDNA) and emergence of resistance remain the most worrisome. Viral rebound from latent episomal cccDNA reservoirs occurs following cessation of therapy, patient non-compliance, or the development of escape mutants. Simultaneous viral co-infections, such as by HIV-1, further complicate therapeutic interventions. These challenges have prompted development of novel targeted hepatitis B therapies. Given the ease with which highly specific and potent nucleic acid therapeutics can be rationally designed, gene therapy has generated interest for antiviral application. Gene therapy strategies developed for HBV include gene silencing by harnessing RNA interference, transcriptional inhibition through epigenetic modification of target DNA, genome editing by designer nucleases, and immune modulation with cytokines. DNA-binding domains and effectors based on the zinc finger (ZF), transcription activator-like effector (TALE), and clustered regularly interspaced short palindromic repeat (CRISPR) systems are remarkably well suited to targeting episomal cccDNA. This review discusses recent developments and challenges facing the field of anti-HBV gene therapy, its potential curative significance and the progress towards clinical application.
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Affiliation(s)
- Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Private Bag 3, Johannesburg, WITS 2050, South Africa.
| | - Mohube Betty Maepa
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Private Bag 3, Johannesburg, WITS 2050, South Africa.
| | - Abdullah Ely
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Private Bag 3, Johannesburg, WITS 2050, South Africa.
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Private Bag 3, Johannesburg, WITS 2050, South Africa.
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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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Kostyushev DS, Zueva AP, Brezgin SA, Lipatnikov AD, Simirskii VN, Glebe D, Volchkova EV, Shipulin GA, Chulanov VP. [Overexpression of DNA-methyltransferases in persistency of cccDNA pool in chronic hepatitis B]. TERAPEVT ARKH 2018; 89:21-26. [PMID: 29260742 DOI: 10.17116/terarkh2017891121-26] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AIM To define the role of DNA-methyltransferases of type 1 and type 3A in hepatitis B viral cycle. MATERIAL AND METHODS Human hepatoma cells HepG2 with stable expression of 1.1-mer HBV genome were transfected with vectors encoding DNA-methyltransferase 1 (DNMT1), DNA-methyltransferase 3A (DNMT3A) or were co-transfected with these vectors. Total HBV DNA copy number, relative expression of pregenomic RNA (pgRNA), S-protein-encoding RNA (S-RNA) and cccDNA were analyzed by quantitative and semi-quantitative real-time PCR-analysis with TaqMan probes for assessment of DNMTs-mediated effects on HBV. RESULTS DNMT1 and DNMT3A suppress HBV transcription and replication, though to different magnitude. cccDNA pool is enlarged statistically significantly ≈2-fold (P<0.005) after transfection of DNMT3A, but is unaltered under DNMT1 treatment. CONCLUSION DNMT3A regulates the size of cccDNA pool and is important for persistency of HBV infection.
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Affiliation(s)
- D S Kostyushev
- Central Research Institute of Epidemiology, Moscow, Russia
| | - A P Zueva
- Central Research Institute of Epidemiology, Moscow, Russia; M.V. Lomonosov Moscow State University, Moscow, Russia
| | - S A Brezgin
- Central Research Institute of Epidemiology, Moscow, Russia; I.M. Sechenov First State Medical University, Moscow, Russia
| | - A D Lipatnikov
- Central Research Institute of Epidemiology, Moscow, Russia; D.I. Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - V N Simirskii
- N.K. Koltzov Institute of Developmental Biology, Moscow, Russia
| | - D Glebe
- Justus-Liebig University of Giessen, Institute of Medical Virology, Giessen, Germany
| | - E V Volchkova
- I.M. Sechenov First State Medical University, Moscow, Russia
| | - G A Shipulin
- Central Research Institute of Epidemiology, Moscow, Russia
| | - V P Chulanov
- Central Research Institute of Epidemiology, Moscow, Russia; I.M. Sechenov First State Medical University, Moscow, Russia
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Thompson DB, Aboulhouda S, Hysolli E, Smith CJ, Wang S, Castanon O, Church GM. The Future of Multiplexed Eukaryotic Genome Engineering. ACS Chem Biol 2018; 13:313-325. [PMID: 29241002 PMCID: PMC5880278 DOI: 10.1021/acschembio.7b00842] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multiplex genome editing is the simultaneous introduction of multiple distinct modifications to a given genome. Though in its infancy, maturation of this field will facilitate powerful new biomedical research approaches and will enable a host of far-reaching biological engineering applications, including new therapeutic modalities and industrial applications, as well as "genome writing" and de-extinction efforts. In this Perspective, we focus on multiplex editing of large eukaryotic genomes. We describe the current state of multiplexed genome editing, the current limits of our ability to multiplex edits, and provide perspective on the many applications that fully realized multiplex editing technologies would enable in higher eukaryotic genomes. We offer a broad look at future directions, covering emergent CRISPR-based technologies, advances in intracellular delivery, and new DNA assembly approaches that may enable future genome editing on a massively multiplexed scale.
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Affiliation(s)
- David B. Thompson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Soufiane Aboulhouda
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Eriona Hysolli
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Cory J. Smith
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Stan Wang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
| | - Oscar Castanon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau, France
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA
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Chen P, You L, Lu Y. Applications of CRISPR-Cas9 Technology in Translational Research on Solid-Tumor Cancers. CRISPR J 2018; 1:47-54. [PMID: 31021191 DOI: 10.1089/crispr.2017.0001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Since its introduction to genome editing, CRISPR-Cas9 has been used to generate cell and animal models of disease, investigate relations between genomes and phenotypes, and interfere with disease development. Although most of its applications have been in basic research, efforts are underway to move CRISPR-Cas9 from bench to bedside. This review summarizes current and prospective applications of the CRISPR-Cas9 system in biomedical and translational research on solid tumors, as well as the challenges of expanding this technology into clinical use.
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Affiliation(s)
- Patricia Chen
- 1 Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China .,2 Drexel University College of Medicine , Philadelphia, Pennsylvania
| | - Liting You
- 1 Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - You Lu
- 1 Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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Moyo B, Bloom K, Scott T, Ely A, Arbuthnot P. Advances with using CRISPR/Cas-mediated gene editing to treat infections with hepatitis B virus and hepatitis C virus. Virus Res 2018; 244:311-320. [PMID: 28087399 DOI: 10.1016/j.virusres.2017.01.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 12/21/2022]
Abstract
Chronic infections with hepatitis B and hepatitis C viruses (HBV and HCV) account for the majority of cases of cirrhosis and hepatocellular carcinoma. Current therapies for the infections have limitations and improved efficacy is necessary to prevent complications in carriers of the viruses. In the case of HBV persistence, the replication intermediate comprising covalently closed circular DNA (cccDNA) is particularly problematic. Licensed therapies have little effect on cccDNA and HBV replication relapses following treatment withdrawal. Disabling cccDNA is thus key to curing HBV infections and application of gene editing technology, such as harnessing the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system, has curative potential. Several studies have reported good efficacy when employing CRISPR/Cas technologies to disable HBV replication in cultured cells and in hydrodynamically injected mice. Recent advances with HCV drug development have revolutionized treatment of the infection. Nevertheless, individuals may be refractory to treatment. Targeting RNA from HCV with CRISPR/Cas isolated from Francisella novicida may have therapeutic utility. Although preclinical work shows that CRISPR/Cas technology has potential to overcome infection with HBV and HCV, significant challenges need to be met. Ensuring specificity for viral targets and efficient delivery of the gene editing sequences to virus-infected cells are particularly important. The field is at an interesting stage and the future of curative antiviral drug regimens, particularly for treatment of chronic HBV infection, may well entail use of combinations that include derivatives of CRISPR/Cas.
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MESH Headings
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Associated Protein 9
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA Cleavage
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Endonucleases/genetics
- Endonucleases/metabolism
- Hepacivirus/genetics
- Hepacivirus/growth & development
- Hepacivirus/metabolism
- Hepatitis B virus/genetics
- Hepatitis B virus/growth & development
- Hepatitis B virus/metabolism
- Hepatitis B, Chronic/therapy
- Hepatitis B, Chronic/virology
- Hepatitis C, Chronic/therapy
- Hepatitis C, Chronic/virology
- Humans
- Molecular Targeted Therapy/methods
- Patient Safety
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Virus Replication
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Affiliation(s)
- Buhle Moyo
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Tristan Scott
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa; Center for Gene Therapy, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Abdullah Ely
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa.
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Yang HC, Chen PJ. The potential and challenges of CRISPR-Cas in eradication of hepatitis B virus covalently closed circular DNA. Virus Res 2018; 244:304-310. [PMID: 28627393 DOI: 10.1016/j.virusres.2017.06.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 12/16/2022]
Abstract
Current antiviral therapy fails to cure chronic hepatitis B virus (HBV) infection, primarily because of the persistence of covalently closed circular DNA (cccDNA). Although nucleos(t)ide analogues (NAs) can inhibit the reverse transcriptase of HBV and suppress its replication to levels below the detection limit, viremia often rebounds after cessation of therapy. Nuclear cccDNA serves as the HBV replicative template and exhibits extraordinary stability, and is not affected by NAs. Therefore, curing chronic hepatitis B (CHB) requires novel therapy for purging cccDNA from patients. The CRISPR/Cas9 system is a newly developed programmable genome-editing tool and allows for sequence-specific cleavage of DNA. Compared to other genome-editing tools, the CRIPSR/Cas9 system is advantageous for its simplicity and flexibility of design. Theoretically, Cas9 can be redirected to specifically cleave any desired genome sequences simply by designing guide RNAs with about 20 nucleotides that match the particular sequences of genomes with downstream protospacer adjacent motifs. Recently, it has been demonstrated that the CRIPSR/Cas9 system can specifically destruct HBV genomes in vitro and in vivo. Although promising, the CRISPR/Cas9 system faces several challenges that need to be overcome for the clinical application, namely, off-target cleavage and the in vivo delivery efficiency. Cutting integrated HBV genomes by CRISPR/Cas9 also raises serious concern because this has the risk of genome instability. In summary, the CRISPR/Cas9 system bears the potential for curing CHB as long as several challenging issues can be successfully solved.
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MESH Headings
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Associated Protein 9
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA Cleavage
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Endonucleases/genetics
- Endonucleases/metabolism
- Genomic Instability
- Hepatitis B virus/genetics
- Hepatitis B virus/growth & development
- Hepatitis B virus/metabolism
- Hepatitis B, Chronic/therapy
- Hepatitis B, Chronic/virology
- Humans
- Molecular Targeted Therapy/methods
- Patient Safety
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Virus Replication
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Affiliation(s)
- Hung-Chih Yang
- Department of Microbiology, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei, Taiwan; Hepatitis Research Center, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei, Taiwan; Department of Medical Research, National Taiwan University College of Medicine and National Taiwan University Hospital, Taipei, Taiwan.
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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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Cebrian-Serrano A, Davies B. CRISPR-Cas orthologues and variants: optimizing the repertoire, specificity and delivery of genome engineering tools. Mamm Genome 2017; 28:247-261. [PMID: 28634692 PMCID: PMC5569134 DOI: 10.1007/s00335-017-9697-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022]
Abstract
Robust and cost-effective genome editing in a diverse array of cells and model organisms is now possible thanks to the discovery of the RNA-guided endonucleases of the CRISPR-Cas system. The commonly used Cas9 of Streptococcus pyogenes shows high levels of activity but, depending on the application, has been associated with some shortcomings. Firstly, the enzyme has been shown to cause mutagenesis at genomic sequences resembling the target sequence. Secondly, the stringent requirement for a specific motif adjacent to the selected target site can limit the target range of this enzyme. Lastly, the physical size of Cas9 challenges the efficient delivery of genomic engineering tools based on this enzyme as viral particles for potential therapeutic applications. Related and parallel strategies have been employed to address these issues. Taking advantage of the wealth of structural information that is becoming available for CRISPR-Cas effector proteins, Cas9 has been redesigned by mutagenizing key residues contributing to activity and target recognition. The protein has also been shortened and redesigned into component subunits in an attempt to facilitate its efficient delivery. Furthermore, the CRISPR-Cas toolbox has been expanded by exploring the properties of Cas9 orthologues and other related effector proteins from diverse bacterial species, some of which exhibit different target site specificities and reduced molecular size. It is hoped that the improvements in accuracy, target range and efficiency of delivery will facilitate the therapeutic application of these site-specific nucleases.
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Affiliation(s)
| | - Benjamin Davies
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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Kurihara T, Fukuhara T, Ono C, Yamamoto S, Uemura K, Okamoto T, Sugiyama M, Motooka D, Nakamura S, Ikawa M, Mizokami M, Maehara Y, Matsuura Y. Suppression of HBV replication by the expression of nickase- and nuclease dead-Cas9. Sci Rep 2017; 7:6122. [PMID: 28733609 PMCID: PMC5522428 DOI: 10.1038/s41598-017-05905-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/05/2017] [Indexed: 12/26/2022] Open
Abstract
Complete removal of hepatitis B virus (HBV) DNA from nuclei is difficult by the current therapies. Recent reports have shown that a novel genome-editing tool using Cas9 with a single-guide RNA (sgRNA) system can cleave the HBV genome in vitro and in vivo. However, induction of a double-strand break (DSB) on the targeted genome by Cas9 risks undesirable off-target cleavage on the host genome. Nickase-Cas9 cleaves a single strand of DNA, and thereby two sgRNAs are required for inducing DSBs. To avoid Cas9-induced off-target mutagenesis, we examined the effects of the expressions of nickase-Cas9 and nuclease dead Cas9 (d-Cas9) with sgRNAs on HBV replication. The expression of nickase-Cas9 with a pair of sgRNAs cleaved the target HBV genome and suppressed the viral-protein expression and HBV replication in vitro. Moreover, nickase-Cas9 with the sgRNA pair cleaved the targeted HBV genome in mouse liver. Interestingly, d-Cas9 expression with the sgRNAs also suppressed HBV replication in vitro without cleaving the HBV genome. These results suggest the possible use of nickase-Cas9 and d-Cas9 with a pair of sgRNAs for eliminating HBV DNA from the livers of chronic hepatitis B patients with low risk of undesirable off-target mutation on the host genome.
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Affiliation(s)
- Takeshi Kurihara
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Graduate School of Medicine, Department of Surgery and Science, Kyushu University, Fukuoka, Japan
| | - Takasuke Fukuhara
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
| | - Chikako Ono
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Satomi Yamamoto
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Laboratory of Veterinary Microbiology, School of Veterinary Medicine, Kitasato University, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
| | - Kentaro Uemura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Toru Okamoto
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Masaya Sugiyama
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Masato Ikawa
- Center for Genetic Analysis of Biological Responses, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Masashi Mizokami
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Yoshihiko Maehara
- Graduate School of Medicine, Department of Surgery and Science, Kyushu University, Fukuoka, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
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Ko C, Michler T, Protzer U. Novel viral and host targets to cure hepatitis B. Curr Opin Virol 2017; 24:38-45. [DOI: 10.1016/j.coviro.2017.03.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/06/2017] [Accepted: 03/30/2017] [Indexed: 02/07/2023]
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He ZY, Men K, Qin Z, Yang Y, Xu T, Wei YQ. Non-viral and viral delivery systems for CRISPR-Cas9 technology in the biomedical field. SCIENCE CHINA. LIFE SCIENCES 2017; 60:458-467. [PMID: 28527117 DOI: 10.1007/s11427-017-9033-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/16/2017] [Indexed: 02/08/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system provides a novel genome editing technology that can precisely target a genomic site to disrupt or repair a specific gene. Some CRISPR-Cas9 systems from different bacteria or artificial variants have been discovered or constructed by biologists, and Cas9 nucleases and single guide RNAs (sgRNA) are the major components of the CRISPR-Cas9 system. These Cas9 systems have been extensively applied for identifying therapeutic targets, identifying gene functions, generating animal models, and developing gene therapies. Moreover, CRISPR-Cas9 systems have been used to partially or completely alleviate disease symptoms by mutating or correcting related genes. However, the efficient transfer of CRISPR-Cas9 system into cells and target organs remains a challenge that affects the robust and precise genome editing activity. The current review focuses on delivery systems for Cas9 mRNA, Cas9 protein, or vectors encoding the Cas9 gene and corresponding sgRNA. Non-viral delivery of Cas9 appears to help Cas9 maintain its on-target effect and reduce off-target effects, and viral vectors for sgRNA and donor template can improve the efficacy of genome editing and homology-directed repair. Safe, efficient, and producible delivery systems will promote the application of CRISPR-Cas9 technology in human gene therapy.
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Affiliation(s)
- Zhi-Yao He
- Department of Pharmacy, and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Ke Men
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Zhou Qin
- Department of Pharmacy, and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Ting Xu
- Department of Pharmacy, and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
| | - Yu-Quan Wei
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
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Rapid generation of genetic diversity by multiplex CRISPR/Cas9 genome editing in rice. SCIENCE CHINA-LIFE SCIENCES 2017; 60:506-515. [DOI: 10.1007/s11427-017-9008-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 12/20/2016] [Indexed: 12/26/2022]
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48
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Horie N, Hikita A, Nishizawa S, Uto S, Takato T, Hoshi K. Impairment of the transition from proliferative stage to prehypertrophic stage in chondrogenic differentiation of human induced pluripotent stem cells harboring the causative mutation of achondroplasia in fibroblast growth factor receptor 3. Regen Ther 2017; 6:15-20. [PMID: 30271835 PMCID: PMC6134919 DOI: 10.1016/j.reth.2016.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 11/15/2016] [Indexed: 11/01/2022] Open
Abstract
Introduction Achondroplasia (ACH) is a congenital disease which causes dwarfism and many symptoms resulting from skeletal dysplasia. Because present therapeutic strategies are mainly surgical procedures as symptomatic treatments, development of a radical treatment is desired. Clarification of the ACH pathology is essential for creating a new remedy. However, there are many questions about the disease mechanisms that have not been answered. Methods As a single base substitution of the FGFR3 gene had been proved to be the ACH causing genome mutation, our group established disease specific iPS cells by introducing the causative mutation of achondroplasia into human iPS cells by CRISPR/Cas9 based genome editing. These cells were differentiated towards chondrocytes, then the gene and protein expressions were examined by real time RT-PCR and Western blotting, respectively. Results Based on the western blotting analysis, the FGFR3 protein and phosphorylated ERK were increased in the FGFR3 mutated iPS cells compared to the control cells, while the FGFR3 gene expression was suppressed in the FGFR3 mutated iPS cells. According to chondrogenic differentiation experiments, the IHH expression level was increased in the control cells as the differentiation progressed. On the other hand, up-regulation of the IHH gene expression was suppressed in the FGFR3 mutated iPS cells. Conclusions These results suggested that chondrocyte maturation was impaired between the proliferative stage and prehypertrophic stage in the chondrocytes of ACH. The development of chemical compounds which affect the specific maturation stage of chondrocytes is expected to contribute to the ACH treatment, and FGFR3 genome-edited hiPSCs will be a valuable tool in such research studies.
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Affiliation(s)
- Naohiro Horie
- Department of Sensory and Motor System Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Atsuhiko Hikita
- Department of Cartilage and Bone Regeneration (Fujisoft), Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Satoru Nishizawa
- Translational Research Center, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Sakura Uto
- Department of Cartilage and Bone Regeneration (Fujisoft), Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Tsuyoshi Takato
- Department of Sensory and Motor System Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazuto Hoshi
- Department of Sensory and Motor System Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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