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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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Zhang J, Zhang Y, Khanal S, Cao D, Zhao J, Dang X, Nguyen LNT, Schank M, Wu XY, Jiang Y, Ning S, Wang L, El Gazzar M, Moorman JP, Guo H, Yao ZQ. Synthetic gRNA/Cas9 ribonucleoprotein targeting HBV DNA inhibits viral replication. J Med Virol 2023; 95:e28952. [PMID: 37455550 PMCID: PMC10977344 DOI: 10.1002/jmv.28952] [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: 06/07/2022] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
The presence of hepatitis B virus (HBV) covalently closed circular (ccc) DNA (cccDNA), which serves as a template for viral replication and integration of HBV DNA into the host cell genome, sustains liver pathogenesis and constitutes an intractable barrier to the eradication of chronic HBV infection. The current antiviral therapy for HBV infection, using nucleos(t)ide analogues (NAs), can suppress HBV replication but cannot eliminate integrated HBV DNA and episomal cccDNA. Clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 is a powerful genetic tool that can edit integrated HBV DNA and minichromosomal cccDNA for gene therapy, but its expression and delivery require a viral vector, which poses safety concerns for therapeutic applications in humans. In the present study, we used synthetic guide RNA (gRNA)/Cas9-ribonucleoprotein (RNP) as a nonviral formulation to develop a novel CRISPR/Cas9-mediated gene therapy for eradicating HBV infection. We designed a series of gRNAs targeting multiple specific HBV genes and tested their antiviral efficacy and cytotoxicity in different HBV cellular models. Transfection of stably HBV-infected human hepatoma cell line HepG2.2.15 with HBV-specific gRNA/Cas9 RNPs resulted in a substantial reduction in HBV transcripts. Specifically, gRNA5 and/or gRNA9 RNPs significantly reduced HBV cccDNA, total HBV DNA, pregenomic RNA, and HBV antigen (HBsAg, HBeAg) levels. T7 endonuclease 1 (T7E1) cleavage assay and DNA sequencing confirmed specific HBV gene cleavage and mutations at or around the gRNA target sites. Notably, this gene-editing system did not alter cellular viability or proliferation in the treated cells. Because of their rapid DNA cleavage capability, low off-target effects, low risk of insertional mutagenesis, and readiness for use in clinical application, these results suggest that synthetic gRNA/Cas9 RNP-based gene-editing can be utilized as a promising therapeutic drug for eradicating chronic HBV infection.
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Affiliation(s)
- Jinyu Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Yi Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Sushant Khanal
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Dechao Cao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Juan Zhao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Xindi Dang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Lam Ngoc Thao Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Madison Schank
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Xiao Y. Wu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Yong Jiang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
| | - Shunbin Ning
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Ling Wang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Mohamed El Gazzar
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
| | - Jonathan P. Moorman
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
- HCV/HBV/HIV Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, Tennessee 37614
| | - Haitao Guo
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213
| | - Zhi Q. Yao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, Tennessee 37614
- Department of Internal Medicine, Division of Infectious, Inflammatory and Immunologic Diseases, Quillen College of Medicine, ETSU, Johnson City, Tennessee 37614
- HCV/HBV/HIV Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, Tennessee 37614
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Cai B, Chang S, Tian Y, Zhen S. CRISPR/Cas9 for hepatitis B virus infection treatment. Immun Inflamm Dis 2023; 11:e866. [PMID: 37249290 DOI: 10.1002/iid3.866] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/02/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Hepatitis B virus (HBV) infection remains a global health challenge. Despite the availability of effective preventive vaccines, millions of people are at risk of cirrhosis and hepatocellular carcinoma. Current drug therapies inhibit viral replication, slow the progression of liver fibrosis and reduce infectivity, but they rarely remove the covalently sealed circular DNA (cccDNA) of the virus that causes HBV persistence. Alternative treatment strategies, including those based on CRISPR/cas9 knockout virus gene, can effectively inhibit HBV replication, so it has a good prospect. During chronic infection, some virus gene knockouts based on CRISPR/cas9 may even lead to cccDNA inactivation. This paper reviews the progress of different HBV CRISPR/cas9, vectors for delivering to the liver, and the current situation of preclinical and clinical research.
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Affiliation(s)
- Bo Cai
- Center of Medical Genetics, Northwest Women's and Children's Hospital, Xi'an, Shaanxi, PR. China
| | - Shixue Chang
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR. China
| | - Yuhan Tian
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR. China
| | - Shuai Zhen
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR. China
- Genetic Disease Diagnosis Center of Shaanxi province, Xi'an, Shaanxi, PR. China
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Kostyusheva AP, Brezgin SA, Ponomareva NI, Goptar IA, Nikiforova AV, Gegechkori VI, Poluektova VB, Turkadze KA, Sudina AE, Chulanov VP, Kostyushev DS. Antiviral Activity of CRISPR/Cas9 Ribonucleoprotein Complexes on a Hepatitis B Virus Model In Vivo. Mol Biol 2022. [DOI: 10.1134/s0026893322060097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Brezgin SA, Kostyusheva AP, Ponomareva NI, Gegechkori VI, Kirdyashkina NP, Ayvasyan SR, Dmitrieva LN, Kokoreva LN, Chulanov VP, Kostyushev DS. HBx Protein Potentiates Hepatitis B Virus Reactivation. Mol Biol 2022. [DOI: 10.1134/s0026893322050041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Wang D, Chen L, Li C, Long Q, Yang Q, Huang A, Tang H. CRISPR/Cas9 delivery by NIR-responsive biomimetic nanoparticles for targeted HBV therapy. J Nanobiotechnology 2022; 20:27. [PMID: 34991617 PMCID: PMC8740473 DOI: 10.1186/s12951-021-01233-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/29/2021] [Indexed: 12/17/2022] Open
Abstract
Background Currently, there are no curative drugs for hepatitis B virus (HBV). Complete elimination of HBV covalently closed circular DNA (cccDNA) is key to the complete cure of hepatitis B virus infection. The CRISPR/Cas9 system can directly destroy HBV cccDNA. However, a CRISPR/Cas9 delivery system with low immunogenicity and high efficiency has not yet been established. Moreover, effective implementation of precise remote spatiotemporal operations in CRISPR/Cas9 is a major limitation. Results In this work, we designed NIR-responsive biomimetic nanoparticles (UCNPs-Cas9@CM), which could effectively deliver Cas9 RNP to achieve effective genome editing for HBV therapy. HBsAg, HBeAg, HBV pgRNA and HBV DNA along with cccDNA in HBV-infected cells were found to be inhibited. These findings were confirmed in HBV-Tg mice, which did not exhibit significant cytotoxicity and minimal off-target DNA damage. Conclusions The UCNPs-based biomimetic nanoplatforms achieved the inhibition of HBV replication via CRISPR therapy and it is a potential system for efficient treatment of human HBV diseases. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-021-01233-4.
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Affiliation(s)
- Dan Wang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, 1 Yi Xue Yuan Road, Chongqing, 400016, China.,The People's Hospital of Rongchang District, Chongqing, 402460, China
| | - Ling Chen
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, 1 Yi Xue Yuan Road, Chongqing, 400016, China
| | - Chengbi Li
- The People's Hospital of Rongchang District, Chongqing, 402460, China
| | - Quanxin Long
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, 1 Yi Xue Yuan Road, Chongqing, 400016, China
| | - Qing Yang
- The People's Hospital of Rongchang District, Chongqing, 402460, China
| | - Ailong Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, 1 Yi Xue Yuan Road, Chongqing, 400016, China
| | - Hua Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, 1 Yi Xue Yuan Road, Chongqing, 400016, China.
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Baddeley HJE, Isalan M. The Application of CRISPR/Cas Systems for Antiviral Therapy. Front Genome Ed 2021; 3:745559. [PMID: 34723245 PMCID: PMC8549726 DOI: 10.3389/fgeed.2021.745559] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/23/2021] [Indexed: 12/18/2022] Open
Abstract
As CRISPR/Cas systems have been refined over time, there has been an effort to apply them to real world problems, such as developing sequence-targeted antiviral therapies. Viruses pose a major threat to humans and new tools are urgently needed to combat these rapidly mutating pathogens. Importantly, a variety of CRISPR systems have the potential to directly cleave DNA and RNA viral genomes, in a targeted and easily-adaptable manner, thus preventing or treating infections. This perspective article highlights recent studies using different Cas effectors against various RNA viruses causing acute infections in humans; a latent virus (HIV-1); a chronic virus (hepatitis B); and viruses infecting livestock and animal species of industrial importance. The outlook and remaining challenges are discussed, particularly in the context of tacking newly emerging viruses, such as SARS-CoV-2.
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Affiliation(s)
- Helen J E Baddeley
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, United Kingdom
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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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Recent developments with advancing gene therapy to treat chronic infection with hepatitis B virus. Curr Opin HIV AIDS 2021; 15:200-207. [PMID: 32141890 DOI: 10.1097/coh.0000000000000623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW The available vaccine and therapies against hepatitis B virus (HBV) rarely eliminate chronic infection with the virus. High mortality resulting from complicating cirrhosis and hepatocellular carcinoma makes improving anti-HBV therapy an important priority. Recent advances with using gene therapy to counter HBV have potential and are the focus of this review. RECENT FINDINGS The stable replication-competent HBV intermediate comprising covalently closed circular DNA (cccDNA) is the template for expression of all viral genes. Inactivating cccDNA has thus been a focus of research aimed at achieving cure for HBV infection. Many studies have reported profound inhibition of replication of the virus using silencing and editing techniques. Therapeutic gene silencing with synthetic short interfering RNA is now in clinical trials. Ability to mutate and permanently inactivate cccDNA with engineered gene editors, such as those derived from CRISPR/Cas or TALENs, is particularly appealing but has not yet reached clinical evaluation. SUMMARY Gene silencing and gene editing potentially provide the means to cure HBV infection. However, achieving efficient delivery of therapeutic sequences, ensuring their specificity of action and progress with other antiviral strategies are likely to determine utility of gene therapy for chronic HBV infection.
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Zhen S, Qiang R, Lu J, Tuo X, Yang X, Li X. Enhanced antiviral benefit of combination therapy with anti-HBV and anti-PD1 gRNA/cas9 produces a synergistic antiviral effect in HBV infection. Mol Immunol 2021; 130:7-13. [PMID: 33340931 DOI: 10.1016/j.molimm.2020.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/16/2020] [Accepted: 12/02/2020] [Indexed: 02/08/2023]
Abstract
Targeted therapy for patients with hepatitis B virus (HBV) infection can lead to objective responses, although response times may be short. At the same time, the response rate to programmed cell death-1 (PD-1) treatment was more durable. It is speculated that HBV targeted therapy can synergistically enhance the antitumor activity with PD-1 blockade. To test this hypothesis, we evaluated the effect of crispr-cas9 on HBV and PD-1 in vitro and in vivo. We found that HBV targeting gRNA/cas9 induced a decrease in the expression of HBsAg, while the PD-1 gene could be knocked out by electroporation targeting gRNA / cas9 by polymerase chain reaction. In HBV transgenic mice, the immunophenotype and cytokine expression of human dendritic cells (DCS) were detected by crispr-cas9 system stimulation, flow cytometry and polymerase chain reaction. These results indicate that gRNA/cas9 treatment upregulates the expression of CD80, CD83 and CD86, and significantly increases the mRNA levels of IL-6, IL-12, IL-23 and tumor necrosis factor alpha. The combination of anti HBV and anti PD-1 therapy can inhibit HBV expression and significantly improve the survival of HBV transgenic mice. In addition, the combination therapy increased the production of interferon by T cells, and then enhanced the expression of Th1 related immunostimulatory genes, thereby reducing the transcription of regulatory / inhibitory immune genes. In general, this response can reshape the tumor microenvironment from immunosuppression to immune stimulation. Finally, anti HBV therapy can induce the expression of interferon dependent programmed cell death ligand-1 in HBV transgenic mice in vivo. To sum up, these results demonstrate that the combination of HBV targeted therapy and PD-1 immune checkpoint block has a strong synergistic effect, thus supporting the transformation potential of this combined therapy strategy in clinical treatment of HBV infection.
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Affiliation(s)
- Shuai Zhen
- Medical Heredity Research Center, Northwest Women's and Children's Hospital, Shaanxi, PR China.
| | - Rong Qiang
- Medical Heredity Research Center, Northwest Women's and Children's Hospital, Shaanxi, PR China
| | - Jiaojiao Lu
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Xiaoqian Tuo
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Xiling Yang
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
| | - Xu Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China
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Brezgin S, Kostyusheva A, Ponomareva N, Volia V, Goptar I, Nikiforova A, Shilovskiy I, Smirnov V, Kostyushev D, Chulanov V. Clearing of Foreign Episomal DNA from Human Cells by CRISPRa-Mediated Activation of Cytidine Deaminases. Int J Mol Sci 2020; 21:ijms21186865. [PMID: 32962129 PMCID: PMC7557733 DOI: 10.3390/ijms21186865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/07/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023] Open
Abstract
Restriction of foreign DNA is a fundamental defense mechanism required for maintaining genomic stability and proper function of mammalian cells. APOBEC cytidine deaminases are crucial effector molecules involved in clearing pathogenic DNA of viruses and other microorganisms and improperly localized self-DNA (DNA leakages). Mastering the expression of APOBEC provides the crucial means both for developing novel therapeutic approaches for combating infectious and non-infectious diseases and for numerous research purposes. In this study, we report successful application of a CRISPRa approach to effectively and specifically overexpress APOBEC3A and APOBEC3B deaminases and describe their effects on episomal and integrated foreign DNA. This method increased target gene transcription by >6–50-fold in HEK293T cells. Furthermore, CRISPRa-mediated activation of APOBEC3A/APOBEC3B suppressed episomal but not integrated foreign DNA. Episomal GC-rich DNA was rapidly destabilized and destroyed by CRISPRa-induced APOBEC3A/APOBEC3B, while the remaining DNA templates harbored frequent deaminated nucleotides. To conclude, the CRISPRa approach could be readily utilized for manipulating innate immunity and investigating the effects of the key effector molecules on foreign nucleic acids.
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Affiliation(s)
- Sergey Brezgin
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
- Department of Molecular Immunology, Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia; (I.S.); (V.S.)
| | - Anastasiya Kostyusheva
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
| | - Natalia Ponomareva
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
| | - Viktoriia Volia
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
| | - Irina Goptar
- Izmerov Research Institute of Occupational Health, 105275 Moscow, Russia; (I.G.); (A.N.)
| | - Anastasiya Nikiforova
- Izmerov Research Institute of Occupational Health, 105275 Moscow, Russia; (I.G.); (A.N.)
| | - Igor Shilovskiy
- Department of Molecular Immunology, Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia; (I.S.); (V.S.)
| | - Valery Smirnov
- Department of Molecular Immunology, Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia; (I.S.); (V.S.)
| | - Dmitry Kostyushev
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
- Correspondence:
| | - Vladimir Chulanov
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
- Department of Infectious Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
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Mohammadzadeh I, Qujeq D, Yousefi T, Ferns GA, Maniati M, Vaghari-Tabari M. CRISPR/Cas9 gene editing: A new therapeutic approach in the treatment of infection and autoimmunity. IUBMB Life 2020; 72:1603-1621. [PMID: 32344465 DOI: 10.1002/iub.2296] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/19/2022]
Abstract
CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein9) may be viewed as an adaptive bacterial immune system. When a virus infects a bacterium, a fragment of the virus genome is inserted into the CRISPR sequence of the bacterial genome as a memory. When the bacterium becomes infected again with the same virus, an RNA molecule that is a transcript of the memory sequence, directs Cas9, an endonuclease, to the complementary region of the virus genome, and Cas9 disables the virus by a double-strand break. In recent years, studies have shown that by designing synthetic RNA molecules and delivering them along with Cas9 into eukaryotic cells, different regions of the cell's genome can be targeted and manipulated. These findings have drawn much attention to this new technology and it has been shown that CRISPR/Cas9 gene editing can be used to treat some human diseases. These include infectious diseases and autoimmune diseases. In this review article, in addition to a brief overview of the biology of the CRISPR/Cas9 system, we collected the most recent findings on the applications of CRISPR/Cas9 technology for better investigation of the pathogenesis and treatment of viral infections (human immunodeficiency virus infection, hepatitis virus infections, and onco-virus infections), non-viral infections (parasitic, fungal, and bacterial infections), and autoimmune diseases.
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Affiliation(s)
- Iraj Mohammadzadeh
- Non-Communicable Pediatric Diseases Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Durdi Qujeq
- Cellular and Molecular Biology Research Center (CMBRC), Health Research Institute, Babol University of Medical Sciences, Babol, Iran.,Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Tooba Yousefi
- Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Gordon A Ferns
- Department of Medical Education, Brighton & Sussex Medical School, Brighton, UK
| | - Mahmood Maniati
- English Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mostafa Vaghari-Tabari
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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13
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Brezgin S, Kostyusheva A, Bayurova E, Gordeychuk I, Isaguliants M, Goptar I, Nikiforova A, Smirnov V, Volchkova E, Glebe D, Kostyushev D, Chulanov V. Replenishment of Hepatitis B Virus cccDNA Pool Is Restricted by Baseline Expression of Host Restriction Factors In Vitro. Microorganisms 2019; 7:E533. [PMID: 31698767 PMCID: PMC6920784 DOI: 10.3390/microorganisms7110533] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/03/2019] [Accepted: 11/05/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Covalently closed circular DNA (cccDNA) of hepatitis B virus (HBV) is the major cause of viral persistence in patients with chronic HBV infection. Understanding the mechanisms underlying stability and persistence of HBV cccDNA in hepatocytes is critical for developing novel therapeutics and managing chronic hepatitis B. In this study, we observed an unexpected increase in HBV cccDNA levels upon suppression of transcription by de novo DNA methyltransferase DNMT3A and uncovered additional mechanisms potentially involved in HBV cccDNA maintenance. METHODS HBV-expressing cell lines were transfected with a DNMT3A-expressing plasmid. Real-time PCR and HBsAg assays were used to assess the HBV replication rate. Cell cycling was analyzed by fluorescent cell sorting. CRISPR/Cas9 was utilized to abrogate expression of APOBEC3A and APOBEC3B. Alterations in the expression of target genes were measured by real-time PCR. RESULTS Similar to previous studies, HBV replication induced DNMT3A expression, which in turn, led to reduced HBV transcription but elevated HBV cccDNA levels (4- to 6-fold increase). Increased levels of HBV cccDNA were not related to cell cycling, as DNMT3A accelerated proliferation of infected cells and could not contribute to HBV cccDNA expansion by arresting cells in a quiescent state. At the same time, DNMT3A suppressed transcription of innate immunity factors including cytidine deaminases APOBEC3A and APOBEC3B. CRISPR/Cas9-mediated silencing of APOBEC3A and APOBEC3B transcription had minor effects on HBV transcription, but significantly increased HBV cccDNA levels, similar to DNMT3A. In an attempt to further analyze the detrimental effects of HBV and DNMT3A on infected cells, we visualized γ-H2AX foci and demonstrated that HBV inflicts and DNMT3A aggravates DNA damage, possibly by downregulating DNA damage response factors. Additionally, suppression of HBV replication by DNMT3A may be related to reduced ATM/ATR expression. CONCLUSION Formation and maintenance of HBV cccDNA pools may be partially suppressed by the baseline expression of host inhibitory factors including APOBEC3A and APOBEC3B. HBV inflicts DNA damage both directly and by inducing DNMT3A expression.
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Affiliation(s)
- Sergey Brezgin
- National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (A.K.); (V.C.)
- Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia;
| | - Anastasiia Kostyusheva
- National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (A.K.); (V.C.)
| | - Ekaterina Bayurova
- NF Gamaleya Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia; (E.B.); (I.G.); (M.I.)
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia
| | - Ilya Gordeychuk
- NF Gamaleya Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia; (E.B.); (I.G.); (M.I.)
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia
- Sechenov First Moscow State Medical University, 119146 Moscow, Russia;
| | - Maria Isaguliants
- NF Gamaleya Research Center of Epidemiology and Microbiology, 123098 Moscow, Russia; (E.B.); (I.G.); (M.I.)
- Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia
- Riga Stradins University, LV-1007 Riga, Latvia
- Karolinska Institutet, SE-171 76 Stockholm, Sweden
| | - Irina Goptar
- Izmerov Research Institute of Occupational Health, 105275 Moscow, Russia; (I.G.); (A.N.)
| | - Anastasiia Nikiforova
- Izmerov Research Institute of Occupational Health, 105275 Moscow, Russia; (I.G.); (A.N.)
| | - Valery Smirnov
- Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia;
| | - Elena Volchkova
- Sechenov First Moscow State Medical University, 119146 Moscow, Russia;
| | - Dieter Glebe
- Institute of Medical Virology, University of Giessen, 35392 Giessen, Germany;
| | - Dmitry Kostyushev
- National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (A.K.); (V.C.)
| | - Vladimir Chulanov
- National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (A.K.); (V.C.)
- Sechenov First Moscow State Medical University, 119146 Moscow, Russia;
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
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14
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Kostyusheva A, Brezgin S, Bayurova E, Gordeychuk I, Isaguliants M, Goptar I, Urusov F, Nikiforova A, Volchkova E, Kostyushev D, Chulanov V. ATM and ATR Expression Potentiates HBV Replication and Contributes to Reactivation of HBV Infection upon DNA Damage. Viruses 2019; 11:E997. [PMID: 31683589 PMCID: PMC6893526 DOI: 10.3390/v11110997] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023] Open
Abstract
Chronic hepatitis B virus infection (CHB) caused by the hepatitis B virus (HBV) is one of the most common viral infections in the world. Reactivation of HBV infection is a life-threatening condition observed in patients with CHB receiving chemotherapy or other medications. Although HBV reactivation is commonly attributed to immune suppression, other factors have long been suspected to play a role, including intracellular signaling activated in response to DNA damage. We investigated the effects of DNA-damaging factors (doxorubicin and hydrogen peroxide) on HBV reactivation/replication and the consequent DNA-damage response. Dose-dependent activation of HBV replication was observed in response to doxorubicin and hydrogen peroxide which was associated with a marked elevation in the mRNA levels of ataxia-telangiectasia mutated (ATM) and ATM- and RAD3-related (ATR) kinases. Downregulation of ATM or ATR expression by shRNAs substantially reduced the levels of HBV RNAs and DNA. In contrast, transcriptional activation of ATM or ATR using CRISPRa significantly increased HBV replication. We conclude that ATM and ATR are essential for HBV replication. Furthermore, DNA damage leading to the activation of ATM and ATR transcription, results in the reactivation of HBV replication.
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Affiliation(s)
- Anastasiya Kostyusheva
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia.
| | - Sergey Brezgin
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia.
- Institute of Immunology, Federal Medical Biological Agency, Moscow 115522, Russia.
| | - Ekaterina Bayurova
- NF Gamaleya Research Center of Epidemiology and Microbiology, Moscow 123098, Russia.
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
| | - Ilya Gordeychuk
- NF Gamaleya Research Center of Epidemiology and Microbiology, Moscow 123098, Russia.
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
- Sechenov First Moscow State Medical University, Moscow 119146, Russia.
| | - Maria Isaguliants
- NF Gamaleya Research Center of Epidemiology and Microbiology, Moscow 123098, Russia.
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
- Department of Pathology, Riga Stradins University, LV-1007 Riga, Latvia.
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 76 Stockholm, Sweden.
| | - Irina Goptar
- Izmerov Research Institute of Occupational Health, Gene Engineering and Biotechnology, Moscow 105275, Russia.
| | - Felix Urusov
- Izmerov Research Institute of Occupational Health, Gene Engineering and Biotechnology, Moscow 105275, Russia.
| | - Anastasiya Nikiforova
- Izmerov Research Institute of Occupational Health, Gene Engineering and Biotechnology, Moscow 105275, Russia.
| | - Elena Volchkova
- Sechenov First Moscow State Medical University, Moscow 119146, Russia.
| | - Dmitry Kostyushev
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia.
| | - Vladimir Chulanov
- National Medical Research Center of Tuberculosis and Infectious Diseases, Ministry of Health, Moscow 127994, Russia.
- Sechenov First Moscow State Medical University, Moscow 119146, Russia.
- Central Research Institute of Epidemiology, Moscow 111123, Russia.
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