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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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Wang C, Chen J, Li J, Xu Z, Huang L, Zhao Q, Chen L, Liang X, Hu H, Li G, Xiong C, Wu B, You H, Du D, Wang X, Li H, Wang Z, Chen L. An EBV-related CD4 TCR immunotherapy inhibits tumor growth in an HLA-DP5+ nasopharyngeal cancer mouse model. J Clin Invest 2024; 134:e172092. [PMID: 38412034 PMCID: PMC11014665 DOI: 10.1172/jci172092] [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: 05/09/2023] [Accepted: 02/24/2024] [Indexed: 02/29/2024] Open
Abstract
Adoptive transfer of T cell receptor-engineered T cells (TCR-T) is a promising strategy for immunotherapy against solid tumors. However, the potential of CD4+ T cells in mediating tumor regression has been neglected. Nasopharyngeal cancer is consistently associated with EBV. Here, to evaluate the therapeutic potential of CD4 TCR-T in nasopharyngeal cancer, we screened for CD4 TCRs recognizing EBV nuclear antigen 1 (EBNA1) presented by HLA-DP5. Using mass spectrometry, we identified EBNA1567-581, a peptide naturally processed and presented by HLA-DP5. We isolated TCR135, a CD4 TCR with high functional avidity, that can function in both CD4+ and CD8+ T cells and recognizes HLA-DP5-restricted EBNA1567-581. TCR135-transduced T cells functioned in two ways: directly killing HLA-DP5+EBNA1+ tumor cells after recognizing EBNA1 presented by tumor cells and indirectly killing HLA-DP5-negative tumor cells after recognizing EBNA1 presented by antigen-presenting cells. TCR135-transduced T cells preferentially infiltrated into the tumor microenvironment and significantly inhibited tumor growth in xenograft nasopharyngeal tumor models. Additionally, we found that 62% of nasopharyngeal cancer patients showed 50%-100% expression of HLA-DP on tumor cells, indicating that nasopharyngeal cancer is well suited for CD4 TCR-T therapy. These findings suggest that TCR135 may provide a new strategy for EBV-related nasopharyngeal cancer immunotherapy in HLA-DP5+ patients.
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Affiliation(s)
- Chenwei Wang
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiewen Chen
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jingyao Li
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhihong Xu
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lihong Huang
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qian Zhao
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
| | - Lei Chen
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong, China
| | - Xiaolong Liang
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hai Hu
- Department of Pathology, Air Force Hospital of Southern Theater Command, Guangzhou, Guangdong, China
| | - Gang Li
- Department of Otolaryngology–Head and Neck Surgery, Huiqiao Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chengjie Xiong
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Bin Wu
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hua You
- Laboratory for Excellence in Systems Biomedicine of Pediatric Oncology, Department of Pediatric Hematology and Oncology, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Danyi Du
- Department of Otolaryngology–Head and Neck Surgery, Precision Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoling Wang
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hongle Li
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Zibing Wang
- Department of Immunotherapy, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, China
| | - Lin Chen
- Guangzhou Medical University–Guangzhou Institute of Biomedicine and Health (GMU-GIBH) Joint School of Life Sciences and Guangdong–Hong Kong–Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, Guangdong, China
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Vafapour Z, Tabatabaie FH, Hosseini SY, Haghighat S, Hashemi SMA, Moattari A, Sarvari J. Sequence variation of the Epstein-Barr virus nuclear antigen 1 (EBNA1) gene in chronic lymphocytic leukemia and healthy volunteer subjects. Arch Virol 2023; 169:1. [PMID: 38063941 DOI: 10.1007/s00705-023-05933-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023]
Abstract
Epstein-Barr virus-related malignancies have been linked to variations in the sequences of EBV genes, notably EBNA1. Therefore, the purpose of this study was to examine the DBD/DD domain and USP7 binding domain sequences at the C-terminus of the EBNA1 gene in patients with chronic lymphocytic leukemia (CLL). This study included 40 CLL patients and 21 healthy volunteers. Using commercial kits, total DNA was extracted from buffy coat samples, and each sample was tested for the presence of the EBV genome. The C-terminus of EBNA1 was then amplified from positive samples, using nested PCR. Sanger sequencing was used to identify mutations in the PCR products, and the results were analyzed using MEGA11 software. The mean ages of CLL patients and healthy individuals were 61.07 ± 10.2 and 59.08 ± 10.3, respectively. In the EBNA-1 amplicons from CLL patients and healthy individuals, 38.5% and 16.7%, respectively, harbored mutations in the DBD/DD domain of the C-terminal region of the EBNA1 gene (P = 0.378). The mutation frequency at locus 97,320 was significantly higher in CLL patients than in healthy individuals (P = 0.039). Three EBV subtypes based on residue 487 were detected. The frequency of alanine, threonine, and valine in both groups was 88, 8, and 4 percent, respectively (P = 0.207). Moreover, all of the isolates from healthy donors had alanine at this position. The findings indicated that the presence of threonine or valine at residue 487 as well as a synonymous substitution at residue 553 in the C-terminal region of EBNA1 might be involved in the pathogenesis of EBV in CLL patients.
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Affiliation(s)
- Zahra Vafapour
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran
| | - Fatemeh Hosseini Tabatabaie
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran
| | - Seyed Younes Hosseini
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran
| | - Shirin Haghighat
- Department of Hematology and Medical Oncology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Ali Hashemi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran
| | - Jamal Sarvari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, P.O. Box: 71345-1735, Shiraz, Iran.
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Wang HM, Qiao YY, Cai BY, Tan J, Na L, Wang Y, Lu H, Tang YD. Genome editing of pseudorabies virus in the CRISPR/Cas9 era: a mini-review. Front Vet Sci 2023; 10:1237186. [PMID: 37476821 PMCID: PMC10354360 DOI: 10.3389/fvets.2023.1237186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 06/22/2023] [Indexed: 07/22/2023] Open
Abstract
Pseudorabies virus (PRV) is an important swine virus that has a significant impact on the global swine industry. PRV is a member of the herpesvirus family, specifically the alphaherpesvirus subfamily, and has been extensively utilized as a prototype herpesvirus. Notably, recent studies have reported that PRV sporadically spills over into humans. The PRV genome is approximately 150 kb in size and is difficult to manipulate at the genomic level. The development of clustered regularly interspaced short palindromic repeat-associated protein (CRISPR/Cas9) technology has revolutionized PRV genome editing. CRISPR/Cas9 has been widely used in the construction of reporter viruses, knock-out/knock-in of genes of interest, single virus tracking and antiviral strategies. Most importantly, for vaccine development, virulence gene knockout PRV vaccine candidates can be obtained within 2 weeks using CRISPR/Cas9. In this mini-review, we provide a concise overview of the application of CRISPR/Cas9 in PRV research and mainly share our experience with methods for efficiently editing the PRV genome. Through this review, we hope to give researchers better insight into the genome editing of pseudorabies virus.
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Affiliation(s)
- Hai-Ming Wang
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Yang-Yang Qiao
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Bing-Yan Cai
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Ju Tan
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Lei Na
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
- Jiangsu Vocational College Agriculture and Forestry, Taizhou, Jiangsu, China
| | - Yu Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Hui Lu
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, China
| | - Yan-Dong Tang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
- Heilongjiang Provincial Research Center for Veterinary Biomedicine, Harbin, China
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Xu M, Zhang L, Feng J, Yang S, Wang Y, Wang Y, Chen M, Zhou L, Zhang J, Qin Q. Establishment and characterization of two Epstein-Barr virus-positive gastric cancer cell lines with epitheliotropic M81 strain undergoing distinct viral and altered cellular expression profiles. J Med Virol 2023; 95:e28387. [PMID: 36478267 DOI: 10.1002/jmv.28387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/09/2022]
Abstract
Epstein-Barr virus (EBV)-associated gastric cancer (EBVaGC) is a distinct subtype of gastric cancer (GC) distinguished by the presence of the EBV genome and limited viral gene expression within malignant epithelial cells. EBV infection is generally thought to be a relatively late event following atrophic gastritis in carcinogenesis, which implies the heterogeneity of EBVaGC. To facilitate the study of the role of EBV in EBVaGC, we established two EBV-positive GC cell lines (AGS-EBV and HGC27-EBV) with an epitheliotropic EBV strain M81 and characterized viral and cellular gene expression profiles in comparison to SNU719, a naturally derived EBV-positive GC cell line. Like SNU719, AGS-EBV and HGC27-EBV stably maintained their EBV genomes and expressed EBV-encoded small RNAs and nuclear antigen EBNA1. Comprehensive analysis of the expression of EBV-encoded miRNAs within the BamHI-A region rightward transcript region, and the transcripts of EBV latent and lytic genes in cell lines, as well as xenografts, reveals that AGS-EBV and HGC27-EBV cells undergo distinct viral expression profiles. A very small fraction of AGS-EBV and SNU719 cells can spontaneously produce infectious progeny virions, while HGC27-EBV does not. AGS-EBV (both M81 and Akata) cells largely mimic SNU719 cells in viral gene expression profiles, and altered cellular functions and pathways perturbed by EBV infection. Phylogenetic analysis of the EBV genome shows both M81 and Akata EBV strains are closely related to clinical EBVaGC isolates. Taken together, these two newly established EBV-positive GC cell lines can serve as models to further investigate the role of EBV in different contexts of gastric carcinogenesis and identify novel therapeutics against EBVaGC.
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Affiliation(s)
- Mingqian Xu
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, Guangdong, China
| | - Liang Zhang
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, Guangdong, China
| | - Jinfu Feng
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, Guangdong, China
| | - Shuaibing Yang
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, Guangdong, China
| | - Yixuan Wang
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, Guangdong, China
| | - Yuyi Wang
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, Guangdong, China
| | - Meiyang Chen
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, Guangdong, China
| | - Li Zhou
- Department of Gynecologic Oncology, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Junjie Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, Hubei, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, Hubei, China
| | - Qingsong Qin
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, Guangdong, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, Guangdong, China
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Shantou University Medical College, Shantou, Guangdong, China
- Center of Pathogen Biology and Immunology, Institute of Basic Medical Research, Shantou University Medical College, Shantou, Guangdong, China
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Abe K, Kitago M, Matsuda S, Shinoda M, Yagi H, Abe Y, Oshima G, Hori S, Endo Y, Yokose T, Miura E, Kubota N, Ueno A, Masugi Y, Ojima H, Sakamoto M, Kitagawa Y. Epstein-Barr virus-associated inflammatory pseudotumor variant of follicular dendritic cell sarcoma of the liver: a case report and review of the literature. Surg Case Rep 2022; 8:220. [PMID: 36484868 PMCID: PMC9733763 DOI: 10.1186/s40792-022-01572-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Follicular dendritic cell sarcoma is a rare stromal tumor with no standard treatment. However, some reports have revealed that follicular dendritic cell sarcoma has an inflammatory pseudotumor variant associated with Epstein-Barr virus infection that has a relatively good prognosis. In this report, we present a case of a resected inflammatory pseudotumor variant of follicular dendritic cell sarcoma of the liver, and have reviewed the literature on the clinicopathological, molecular, and genomic features of this tumor. CASE PRESENTATION The inflammatory pseudotumor variant of follicular dendritic cell sarcoma originates only in the liver or spleen, causes no symptoms, and is more common in middle-aged Asian women. It has no characteristic imaging features, which partially explains why the inflammatory pseudotumor variant of follicular dendritic cell sarcoma is difficult to diagnose. Pathologically, the inflammatory pseudotumor variant of follicular dendritic cell sarcoma has spindle cells mixed with inflammatory cells and is variably positive for follicular dendritic cell markers (CD21, CD23, and CD35) and Epstein-Barr virus-encoded RNA. On genetic analysis, patients with this tumor high levels of latent membrane protein 1 gene expression and extremely low levels of host C-X-C Chemokine Receptor type 7 gene expression, indicating that the inflammatory pseudotumor variant of follicular dendritic cell sarcoma has a latent Epstein-Barr virus type 2 infection. CONCLUSIONS The inflammatory pseudotumor variant of follicular dendritic cell sarcoma is an Epstein-Barr virus-associated tumor and a favorable prognosis by surgical resection, similar to Epstein-Barr virus-associated gastric cancer.
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Affiliation(s)
- K. Abe
- grid.26091.3c0000 0004 1936 9959Department of Surgery, Keio University School of Medicine, Shinanomachi 35, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - M. Kitago
- grid.26091.3c0000 0004 1936 9959Department of Surgery, Keio University School of Medicine, Shinanomachi 35, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - S. Matsuda
- grid.26091.3c0000 0004 1936 9959Department of Surgery, Keio University School of Medicine, Shinanomachi 35, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - M. Shinoda
- grid.26091.3c0000 0004 1936 9959Department of Surgery, Keio University School of Medicine, Shinanomachi 35, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - H. Yagi
- grid.26091.3c0000 0004 1936 9959Department of Surgery, Keio University School of Medicine, Shinanomachi 35, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Y. Abe
- grid.26091.3c0000 0004 1936 9959Department of Surgery, Keio University School of Medicine, Shinanomachi 35, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - G. Oshima
- grid.26091.3c0000 0004 1936 9959Department of Surgery, Keio University School of Medicine, Shinanomachi 35, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - S. Hori
- grid.26091.3c0000 0004 1936 9959Department of Surgery, Keio University School of Medicine, Shinanomachi 35, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - Y. Endo
- grid.26091.3c0000 0004 1936 9959Department of Surgery, Keio University School of Medicine, Shinanomachi 35, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - T. Yokose
- grid.26091.3c0000 0004 1936 9959Department of Surgery, Keio University School of Medicine, Shinanomachi 35, Shinjuku-Ku, Tokyo, 160-8582 Japan
| | - E. Miura
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - N. Kubota
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - A. Ueno
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Y. Masugi
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - H. Ojima
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - M. Sakamoto
- grid.26091.3c0000 0004 1936 9959Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Y. Kitagawa
- grid.26091.3c0000 0004 1936 9959Department of Surgery, Keio University School of Medicine, Shinanomachi 35, Shinjuku-Ku, Tokyo, 160-8582 Japan
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Wang J, Xue H, Chen Z, Wang Q, Yuan H, Zhang X. Safety of Early Oral Feeding After Laparoscopic Gastrectomy for Gastric Cancer: a Systematic Review and Meta-analysis. Indian J Surg 2022. [DOI: 10.1007/s12262-021-03062-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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Wongwiwat W, Fournier B, Bassano I, Bayoumy A, Elgueta Karstegl C, Styles C, Bridges R, Lenoir C, BoutBoul D, Moshous D, Neven B, Kanda T, Morgan RG, White RE, Latour S, Farrell PJ. Epstein-Barr Virus Genome Deletions in Epstein-Barr Virus-Positive T/NK Cell Lymphoproliferative Diseases. J Virol 2022; 96:e0039422. [PMID: 35612313 PMCID: PMC9215254 DOI: 10.1128/jvi.00394-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/02/2022] [Indexed: 12/14/2022] Open
Abstract
The main target cells for Epstein-Barr virus (EBV) infection and persistence are B lymphocytes, although T and NK cells can also become infected. In this paper, we characterize the EBV present in 21 pediatric and adult patients who were treated in France for a range of diseases that involve infection of T or NK cells. Of these 21 cases, 5 pediatric patients (21%) and 11 adult patients (52%) were of Caucasian origin. In about 30% of the cases, some of the EBV genomes contain a large deletion. The deletions are different in every patient but tend to cluster near the BART region of the viral genome. Detailed investigation of a family in which several members have persistent T or NK cell infection by EBV indicates that the virus genome deletions arise or are selected independently in each individual patient. Genome sequence polymorphisms in the EBV in these T or NK cell diseases reflect the geographic origin of the patient and not a distinct type of EBV (the 21 cases studied included examples of both type 1 and type 2 EBV infection). Using virus produced from type 1 or type 2 EBV genomes cloned in bacterial artificial chromosome (BAC) vectors, we demonstrate infection of T cells in cord blood from healthy donors. Our results are consistent with transient infection of some T cells being part of normal asymptomatic infection by EBV in young children. IMPORTANCE EBV contributes to several types of human cancer. Some cancers and nonmalignant lymphoproliferative diseases involving T or NK cells contain EBV. These diseases are relatively frequent in Japan and China and have been shown sometimes to have deletions in the EBV genome in the disease cells. We identify further examples of deletions within the EBV genome associated with T or NK cell diseases, and we provide evidence that the virus genomes with these deletions are most likely selected in the individual cases, rather than being transmitted between people during infection. We demonstrate EBV infection of cord blood T cells by highly characterized, cloned EBV genomes and suggest that transient infection of T cells may be part of normal asymptomatic infection by EBV in young children.
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Affiliation(s)
- Wiyada Wongwiwat
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Benjamin Fournier
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR1163, Institut Imagine, Paris, France
- Department of Pediatric Immunology, Hematology, and Rheumatology, Necker-Enfants-Malades Hospital, APHP, Paris, France
- Université de Paris, Paris, France
| | - Irene Bassano
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Amr Bayoumy
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Claudio Elgueta Karstegl
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Christine Styles
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ray Bridges
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Christelle Lenoir
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR1163, Institut Imagine, Paris, France
| | - David BoutBoul
- Université de Paris, Paris, France
- Department of Clinical Immunology, Saint-Louis Hospital, APHP, Paris, France
| | - Despina Moshous
- Department of Pediatric Immunology, Hematology, and Rheumatology, Necker-Enfants-Malades Hospital, APHP, Paris, France
- Université de Paris, Paris, France
| | - Bénédicte Neven
- Department of Pediatric Immunology, Hematology, and Rheumatology, Necker-Enfants-Malades Hospital, APHP, Paris, France
| | - Teru Kanda
- Division of Microbiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Rhys G. Morgan
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Robert E. White
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, INSERM UMR1163, Institut Imagine, Paris, France
- Université de Paris, Paris, France
| | - Paul J. Farrell
- Section of Virology, Department of Infectious Disease, Imperial College London, London, United Kingdom
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Luthra R, Kaur S, Bhandari K. Applications of CRISPR as a potential therapeutic. Life Sci 2021; 284:119908. [PMID: 34453943 DOI: 10.1016/j.lfs.2021.119908] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 02/06/2023]
Abstract
Genetic disorders and congenital abnormalities are present in 2-5% of births all over the world and can cause up to 50% of all early childhood deaths. The establishment of sophisticated and controlled techniques for customizing DNA manipulation is significant for the therapeutic role in such disorders and further research on them. One such technique is CRISPR that is significant towards optimizing genome editing and therapies, metabolic fluxes as well as artificial genetic systems. CRISPR-Cas9 is a molecular appliance that is applied in the areas of genetic and protein engineering. The CRISPR-CAS system is an integral element of prokaryotic adaptive immunity that allows prokaryotic cells to identify and kill any foreign DNA. The Gene editing property of CRISPR finds various applications like diagnostics and therapeutics in cancer, neurodegenerative disorders, genetic diseases, blindness, etc. This review discusses applications of CRISPR as a therapeutic in various disorders including several genetic diseases (including sickle cell anemia, blindness, thalassemia, cystic fibrosis, hereditary tyrosinemia type I, duchenne muscular dystrophy, mitochondrial disorders), Cancer, Huntington's disease and viral infections (like HIV, COVID, etc.) along with the prospects concerning them. CRISPR-based therapy is also being researched and defined for COVID-19. The related mechanism of CRISPR has been discussed alongside highlighting challenges involved in therapeutic applications of CRISPR.
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Affiliation(s)
- Ritika Luthra
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Simran Kaur
- Department of Biotechnology, Delhi Technological University, Delhi, India
| | - Kriti Bhandari
- Department of Biotechnology, Delhi Technological University, Delhi, India.
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10
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Tang N, Zhang Y, Shen Z, Yao Y, Nair V. Application of CRISPR-Cas9 Editing for Virus Engineering and the Development of Recombinant Viral Vaccines. CRISPR J 2021; 4:477-490. [PMID: 34406035 DOI: 10.1089/crispr.2021.0017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas technology, discovered originally as a bacterial defense system, has been extensively repurposed as a powerful tool for genome editing for multiple applications in biology. In the field of virology, CRISPR-Cas9 technology has been widely applied on genetic recombination and engineering of genomes of various viruses to ask some fundamental questions about virus-host interactions. Its high efficiency, specificity, versatility, and low cost have also provided great inspiration and hope in the field of vaccinology to solve a series of bottleneck problems in the development of recombinant viral vaccines. This review highlights the applications of CRISPR editing in the technological advances compared to the traditional approaches used for the construction of recombinant viral vaccines and vectors, the main factors affecting their application, and the challenges that need to be overcome for further streamlining their effective usage in the prevention and control of diseases. Factors affecting efficiency, target specificity, and fidelity of CRISPR-Cas editing in the context of viral genome editing and development of recombinant vaccines are also discussed.
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Affiliation(s)
- Na Tang
- Shandong Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, P.R. China; University of Oxford, Oxford, United Kingdom
| | - Yaoyao Zhang
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash road, Guildford, Surrey, United Kingdom; University of Oxford, Oxford, United Kingdom
| | - Zhiqiang Shen
- Shandong Binzhou Animal Science and Veterinary Medicine Academy and UK-China Centre of Excellence for Research on Avian Diseases, Binzhou, P.R. China; University of Oxford, Oxford, United Kingdom
| | - Yongxiu Yao
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash road, Guildford, Surrey, United Kingdom; University of Oxford, Oxford, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute and UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash road, Guildford, Surrey, United Kingdom; University of Oxford, Oxford, United Kingdom.,The Jenner Institute Laboratories, University of Oxford, Oxford, United Kingdom; and University of Oxford, Oxford, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
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11
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Binnie A, Fernandes E, Almeida-Lousada H, de Mello RA, Castelo-Branco P. CRISPR-based strategies in infectious disease diagnosis and therapy. Infection 2021; 49:377-385. [PMID: 33393066 PMCID: PMC7779109 DOI: 10.1007/s15010-020-01554-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/06/2020] [Indexed: 12/21/2022]
Abstract
PURPOSE CRISPR gene-editing technology has the potential to transform the diagnosis and treatment of infectious diseases, but most clinicians are unaware of its broad applicability. Derived from an ancient microbial defence system, these so-called "molecular scissors" enable precise gene editing with a low error rate. However, CRISPR systems can also be targeted against pathogenic DNA or RNA sequences. This potential is being combined with innovative delivery systems to develop new therapeutic approaches to infectious diseases. METHODS We searched Pubmed and Google Scholar for CRISPR-based strategies in the diagnosis and treatment of infectious diseases. Reference lists were reviewed and synthesized for narrative review. RESULTS CRISPR-based strategies represent a novel approach to many challenging infectious diseases. CRISPR technologies can be harnessed to create rapid, low-cost diagnostic systems, as well as to identify drug-resistance genes. Therapeutic strategies, such as CRISPR systems that cleave integrated viral genomes or that target resistant bacteria, are in development. CRISPR-based therapies for emerging viruses, such as SARS-CoV-2, have also been proposed. Finally, CRISPR systems can be used to reprogram human B cells to produce neutralizing antibodies. The risks of CRISPR-based therapies include off-target and on-target modifications. Strategies to control these risks are being developed and a phase 1 clinical trials of CRISPR-based therapies for cancer and monogenic diseases are already underway. CONCLUSIONS CRISPR systems have broad applicability in the field of infectious diseases and may offer solutions to many of the most challenging human infections.
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Affiliation(s)
- Alexandra Binnie
- Department of Critical Care, William Osler Health System, Etobicoke, ON, Canada.
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Edificio 2, Ala Norte, Campus Gambelas, 8005-139, Faro, Portugal.
- Algarve Biomedical Center Research Institute, Faro, Portugal.
- Centre for Biomedical Research, University of Algarve, Faro, Portugal.
| | - Emanuel Fernandes
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Edificio 2, Ala Norte, Campus Gambelas, 8005-139, Faro, Portugal
- Algarve Biomedical Center Research Institute, Faro, Portugal
| | - Helder Almeida-Lousada
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Edificio 2, Ala Norte, Campus Gambelas, 8005-139, Faro, Portugal
- Algarve Biomedical Center Research Institute, Faro, Portugal
- Centre for Biomedical Research, University of Algarve, Faro, Portugal
| | - Ramon Andrade de Mello
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Edificio 2, Ala Norte, Campus Gambelas, 8005-139, Faro, Portugal
- Algarve Biomedical Center Research Institute, Faro, Portugal
- ONCOLOGY PRECISION & HEALTH ECONOMICS RESEARCH GROUP (ONCOPRECHE), Departamento de Oncologia Clínica da Escola Paulista de Medicina, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brasil, & Pós-graduação em Medicina da Universidade Nove de Julho (UNINOVE), São Paulo, Brasil
| | - Pedro Castelo-Branco
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Edificio 2, Ala Norte, Campus Gambelas, 8005-139, Faro, Portugal
- Algarve Biomedical Center Research Institute, Faro, Portugal
- Centre for Biomedical Research, University of Algarve, Faro, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
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12
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Chen YC. CRISPR based genome editing and removal of human viruses. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 179:93-116. [PMID: 33785179 DOI: 10.1016/bs.pmbts.2020.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated proteins 9 (Cas9), a gene-editing technology, has been extensively applied as a tool for genetic engineering in basic research. Efficient genome engineering has been performed in viruses, human cells, bacteria, fungi, plants and animals, etc. Currently, it has been employed to edit human viruses for studying viral molecular biology, pathogenesis and oncogenesis, and facilitate the development of antiviral agents and vaccine. The virus is ubiquitous worldwide and elicits global health problems, many human diseases are associated with virus infections. Although traditional drugs can be used to treat or prevent productive viral infections, their efficacy is limited because of toxicity, side effects and other problems. Additionally, no current drugs are approved to be indicated for latent infections. Therefore, the next highlight is to develop antiviral approaches to against both productive and latent infections. Fortunately, CRISPR has been successfully applied in the removal of human viruses ex vivo and/or in vivo, and has the potential to be used to manufacture antiviral agents for clinical application. CRISPR/Cas9 is promising in applications, even though some technical challenges, safety concerns, ethic concerns need to be improved. In this article, the discovery and application of genome editing and removal of human viruses based on CRISPR are explored. Additionally, we evaluate the prospects and limitations of this novel antiviral strategies.
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Affiliation(s)
- Yuan-Chuan Chen
- Jenteh Junior College of Medicine, Nursing and Management, Miaoli County, Taiwan; Program in Comparative Biochemistry, University of California, Berkeley, CA, United States.
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13
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Yajima M, Kakuta R, Saito Y, Kitaya S, Toyoda A, Ikuta K, Yasuda J, Ohta N, Kanda T. A global phylogenetic analysis of Japanese tonsil-derived Epstein-Barr virus strains using viral whole-genome cloning and long-read sequencing. J Gen Virol 2021; 102. [PMID: 33433312 DOI: 10.1099/jgv.0.001549] [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: 12/17/2022] Open
Abstract
Epstein-Barr virus (EBV) establishes lifelong latent infection in the majority of healthy individuals, while it is a causative agent for various diseases, including some malignancies. Recent high-throughput sequencing results indicate that there are substantial levels of viral genome heterogeneity among different EBV strains. However, the extent of EBV strain variation among asymptomatically infected individuals remains elusive. Here, we present a streamlined experimental strategy to clone and sequence EBV genomes derived from human tonsillar tissues, which are the reservoirs of asymptomatic EBV infection. Complete EBV genome sequences, including those of repetitive regions, were determined for seven tonsil-derived EBV strains. Phylogenetic analyses based on the whole viral genome sequences of worldwide non-tumour-derived EBV strains revealed that Asian EBV strains could be divided into several distinct subgroups. EBV strains derived from nasopharyngeal carcinoma-endemic areas constitute different subgroups from a subgroup of EBV strains from non-endemic areas, including Japan. The results could be consistent with biased regional distribution of EBV-associated diseases depending on the different EBV strains colonizing different regions in Asian countries.
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Affiliation(s)
- Misako Yajima
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Risako Kakuta
- Present address: Department of Otolaryngology, Head and Neck Surgery, Tohoku University School of Medicine, Sendai, Miyagi, Japan.,Division of Otolaryngology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Yutaro Saito
- Present address: Department of Otolaryngology, Head and Neck Surgery, Tohoku University School of Medicine, Sendai, Miyagi, Japan.,Division of Otolaryngology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Shiori Kitaya
- Present address: Department of Otolaryngology, Head and Neck Surgery, Tohoku University School of Medicine, Sendai, Miyagi, Japan.,Division of Otolaryngology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Kazufumi Ikuta
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Jun Yasuda
- Present address: Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Miyagi, Japan.,Division of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Nobuo Ohta
- Division of Otolaryngology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Teru Kanda
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
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14
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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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15
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A single nucleotide polymorphism in the BART promoter region of Epstein-Barr virus isolated from nasopharyngeal cancer cells. Biochem Biophys Res Commun 2019; 520:373-378. [DOI: 10.1016/j.bbrc.2019.10.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/21/2022]
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16
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Fu YZ, Guo Y, Zou HM, Su S, Wang SY, Yang Q, Luo MH, Wang YY. Human cytomegalovirus protein UL42 antagonizes cGAS/MITA-mediated innate antiviral response. PLoS Pathog 2019; 15:e1007691. [PMID: 31107917 PMCID: PMC6527189 DOI: 10.1371/journal.ppat.1007691] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) senses viral DNA in the cytosol and then catalyzes synthesis of the second messenger cGAMP, which activates the ER-localized adaptor protein Mediator of IRF3 Activator (MITA) to initiate innate antiviral response. Human cytomegalovirus (HCMV) proteins can antagonize host immune responses to promote latent infection. Here, we identified HCMV UL42 as a negative regulator of cGAS/MITA-dependent antiviral response. UL42-deficiency enhances HCMV-induced production of type I interferons (IFNs) and downstream antiviral genes. Consistently, wild-type HCMV replicates more efficiently than UL42-deficient HCMV. UL42 interacts with both cGAS and MITA. UL42 inhibits DNA binding, oligomerization and enzymatic activity of cGAS. UL42 also impairs translocation of MITA from the ER to perinuclear punctate structures, which is required for MITA activation, by facilitating p62/LC3B-mediated degradation of translocon-associated protein β (TRAPβ). These results suggest that UL42 can antagonize innate immune response to HCMV by targeting the core components of viral DNA-triggered signaling pathways. Recognition of viral DNA by the cytosolic DNA sensor cGAS and subsequent induction of type I IFNs via the cGAS-MITA signaling axis are important for host antiviral innate immunity. The human cytomegalovirus (HCMV) causes complications in immunodeficient populations and is a major cause of birth defects. It is known that HCMV suppresses innate immunity, which is pivotal for establishing immune evasion and latent infection. In this study, we found that HCMV protein UL42 inhibits innate antiviral responses thus promotes HCMV replication. UL42 functions by targeting cGAS and MITA through distinct mechanisms. UL42 inhibits cGAS activation by interrupting its DNA binding and oligomerization, while it targets MITA by interfering trafficking of MITA from the ER to perinuclear punctate structures, a process required for MITA activation. These findings defined an important mechanism for HCMV immune evasion, which may provide a therapeutic target for the treatment of HCMV infection.
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Affiliation(s)
- Yu-Zhi Fu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yi Guo
- Medical Research Institute, School of Medicine, Wuhan University,Wuhan, China
| | - Hong-Mei Zou
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Shan Su
- Medical Research Institute, School of Medicine, Wuhan University,Wuhan, China
| | - Su-Yun Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Qing Yang
- Medical Research Institute, School of Medicine, Wuhan University,Wuhan, China
| | - Min-Hua Luo
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yan-Yi Wang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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17
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Efficient Epstein-Barr Virus Progeny Production Mediated by Cancer-Derived LMP1 and Virally-Encoded microRNAs. Microorganisms 2019; 7:microorganisms7050119. [PMID: 31052238 PMCID: PMC6560388 DOI: 10.3390/microorganisms7050119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/25/2019] [Accepted: 04/28/2019] [Indexed: 12/22/2022] Open
Abstract
Epstein-Barr virus (EBV) genomes, particularly their latent genes, are heterogeneous among strains. The heterogeneity of EBV-encoded latent membrane protein 1 (LMP1) raises the question of whether there are functional differences between LMP1 expressed by cancer-associated EBV and that by non-cancerous strains. Here, we used bacterial artificial chromosome (BAC)-cloned EBV genomes retaining all virally encoded microRNA (miRNA) genes to investigate the functions of cancer-derived LMP1 in the context of the EBV genome. HEK293 cells were stably transfected with EBV-BAC clone DNAs encoding either nasopharyngeal carcinoma (NPC)-derived CAO-LMP1 (LMP1CAO) or LMP1 from a prototype B95-8 strain of EBV (LMP1B95-8). When an EBV-BAC clone DNA encoding LMP1CAO was stably transfected into HEK293 cells, it generated many more stable transformants than the control clone encoding LMP1B95-8. Furthermore, stably transfected HEK293 cells exhibited highly efficient production of progeny virus. Importantly, deletion of the clustered viral miRNA genes compromised the ability to produce progeny viruses. These results indicate that cancer-derived LMP1 and viral miRNAs together are necessary for efficient production of progeny virus, and that the resulting increase in efficiency contributes to EBV-mediated epithelial carcinogenesis.
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18
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Kanda T, Yajima M, Ikuta K. Epstein-Barr virus strain variation and cancer. Cancer Sci 2019; 110:1132-1139. [PMID: 30697862 PMCID: PMC6447851 DOI: 10.1111/cas.13954] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 12/16/2022] Open
Abstract
Epstein‐Barr virus (EBV) is a human tumor virus and is etiologically linked to various malignancies. Certain EBV‐associated diseases, such as Burkitt lymphomas and nasopharyngeal carcinomas, are endemic and exhibit biased geographic distribution worldwide. Recent advances in deep sequencing technology enabled high‐throughput sequencing of the EBV genome from clinical samples. Rapid cloning and sequencing of cancer‐derived EBV genomes, followed by reconstitution of infectious virus, have also become possible. These developments have revealed that various EBV strains are differentially distributed throughout the world, and that the behavior of cancer‐derived EBV strains is different from that of the prototype EBV strain of non‐cancerous origin. In this review, we summarize recent progress and future perspectives regarding the association between EBV strain variation and cancer.
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Affiliation(s)
- Teru Kanda
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Misako Yajima
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Kazufumi Ikuta
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Japan
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19
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Nakayama A, Abe H, Kunita A, Saito R, Kanda T, Yamashita H, Seto Y, Ishikawa S, Fukayama M. Viral loads correlate with upregulation of PD-L1 and worse patient prognosis in Epstein-Barr Virus-associated gastric carcinoma. PLoS One 2019; 14:e0211358. [PMID: 30695048 PMCID: PMC6350976 DOI: 10.1371/journal.pone.0211358] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/13/2019] [Indexed: 12/13/2022] Open
Abstract
Epstein–Barr virus (EBV)-associated gastric carcinoma (EBVaGC), one of four major gastric cancer types, consists of clonal growth of EBV-infected epithelial cells. However, the significance of viral loads in each tumor cell has not been evaluated. EBV-DNA is stably maintained in episomal form in the nucleus of each cancer cell. To estimate EBV copy number per genome (EBV-CN), qPCR of viral EBNA1 and host GAPDH, standardized by Namalwa DNA (one copy/genome), was applied to the formalin-fixed paraffin embedded (FFPE) surgically resected EBVaGC specimens (n = 43) and EBVaGC cell lines (SNU-719 and NCC-24). In surgical specimens, the cancer cell ratio (CCR) was determined with image analysis, and EBV-CN was obtained by adjusting qPCR value with CCR. Fluorescent in situ hybridization (FISH) was also applied to the FFPE sections using the whole EBV-genome as a probe. In surgical specimens, EBV-CN obtained by qPCR/CCR was between 1.2 and 185 copies with a median of 9.9. EBV-CN of SNU-719 and NCC-24 was 42.0 and 1.1, respectively. A linear correlation was observed with qPCR/CCR data up to 20 copies/genome (40 signals/nucleus), the limit of FISH analysis. In addition, substantial variation in the number of EBV foci was observed. Based on qPCR/CCR, high EBV-CN (>10 copies) correlated with PD-L1 expression in cancer cells (P = 0.015), but not with other pathological indicators. Furthermore, EBVaGC with high EBV-CN showed worse disease-specific survival (P = 0.041). Our findings suggest that cancer cell viral loads may contribute to expression of the immune checkpoint molecule and promotion of cancer progression in EBVaGC.
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Affiliation(s)
- Atsuhito Nakayama
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Akiko Kunita
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Ruri Saito
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Teru Kanda
- Department of Microbiology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Hiroharu Yamashita
- Department of Gastrointestinal Surgery, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- * E-mail:
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20
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Zhou H, Tan S, Li H, Lin X. Expression and significance of EBV, ARID1A and PIK3CA in gastric carcinoma. Mol Med Rep 2019; 19:2125-2136. [PMID: 30747208 PMCID: PMC6390055 DOI: 10.3892/mmr.2019.9886] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022] Open
Abstract
AT-rich interaction domain 1A (ARID1A) and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA) serve important roles in the formation and development of numerous malignancies including gastric cancer. Accumulating evidence has demonstrated that Epstein-Barr virus (EBV) is a pathogenic virus associated with gastric cancer. The present study aimed to investigate the association between EBV infection, and the expression levels of ARID1A and PIK3CA in gastric cancer. EBER in situ hybridization was performed to detect EBV infection. Immunohistochemistry was used to assess the expression levels of ARID1A and PIK3CA in gastric cancer and adjacent normal tissues. A total of 58 gastric cancer and 10 adjacent normal tissues were tested for genetic mutations via single nucleotide polymorphism genotyping assays. Fluorescent polymerase chain reaction was used to detect EBV infection; 9.3% (28/300) of gastric cancer samples were positive for EBV, whereas, all adjacent normal tissues were negative. ARID1A and PIK3CA were negatively correlated in gastric cancer (r=−0.167). The expression levels of ARID1A and PIK3CA in gastric cancer were significantly associated with the depth of invasion of gastric cancer. A total of 62.1% (36/58) of tumor samples exhibited mutations in ARID1A, whereas, 13.8% (8/58) presented mutations in PIK3CA. Notably, EBV-associated gastric cancer (EBVaGC) samples with PIK3CA mutations additionally exhibited ARID1A mutations. Although in the present study it was identified that ARID1A and PIK3CA were negatively correlated in EBVaGC, further studies are required to investigate the association among ARID1A, PIK3CA and EBV in gastric cancer.
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Affiliation(s)
- Huan Zhou
- Department of Pathology, Central South University, Xiangya School of Medicine, Affiliated Haikou Hospital, Haikou, Hainan 570208, P.R. China
| | - Shun Tan
- Department of Pathology, Central South University, Xiangya School of Medicine, Affiliated Haikou Hospital, Haikou, Hainan 570208, P.R. China
| | - Hong Li
- Department of Pathology, Central South University, Xiangya School of Medicine, Affiliated Haikou Hospital, Haikou, Hainan 570208, P.R. China
| | - Xiangtao Lin
- Department of Pathology, Central South University, Xiangya School of Medicine, Affiliated Haikou Hospital, Haikou, Hainan 570208, P.R. China
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21
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Bayat H, Naderi F, Khan AH, Memarnejadian A, Rahimpour A. The Impact of CRISPR-Cas System on Antiviral Therapy. Adv Pharm Bull 2018; 8:591-597. [PMID: 30607331 PMCID: PMC6311650 DOI: 10.15171/apb.2018.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 09/08/2018] [Accepted: 09/29/2018] [Indexed: 12/16/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein nuclease (Cas) is identified as an adaptive immune system in archaea and bacteria. Type II of this system, CRISPR-Cas9, is the most versatile form that has enabled facile and efficient targeted genome editing. Viral infections have serious impacts on global health and conventional antiviral therapies have not yielded a successful solution hitherto. The CRISPR-Cas9 system represents a promising tool for eliminating viral infections. In this review, we highlight 1) the recent progress of CRISPR-Cas technology in decoding and diagnosis of viral outbreaks, 2) its applications to eliminate viral infections in both pre-integration and provirus stages, and 3) various delivery systems that are employed to introduce the platform into target cells.
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Affiliation(s)
- Hadi Bayat
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Naderi
- Department of Molecular Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Amjad Hayat Khan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | | | - Azam Rahimpour
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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22
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Abstract
Epstein-Barr virus (EBV) is one of the most widespread human pathogens. EBV infection is usually asymptomatic, and it establishes life-long latent infection. EBV latent infection sometimes causes various tumorigenic diseases, such as EBV-related lymphoproliferative diseases, Burkitt lymphomas, Hodgkin lymphomas, NK/T-cell lymphomas, and epithelial carcinomas. EBV-encoded latent genes are set of viral genes that are expressed in latently infected cells. They include virally encoded proteins, noncoding RNAs, and microRNAs. Different latent gene expression patterns are noticed in different types of EBV-infected cells. Viral latent gene products contribute to EBV-mediated B cell transformation and likely contribute to lymphomagenesis and epithelial carcinogenesis as well. Many biological functions of viral latent gene products have been reported, making difficult to understand a whole view of EBV latency. In this review, we will focus on latent gene functions that have been verified by genetic experiments using EBV mutants. We will also summarize how viral latent genes contribute to EBV-mediated B cell transformation, Burkitt lymphomagenesis, and epithelial carcinogenesis.
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23
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Fukayama M, Kunita A, Kaneda A. Gastritis-Infection-Cancer Sequence of Epstein-Barr Virus-Associated Gastric Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1045:437-457. [PMID: 29896679 DOI: 10.1007/978-981-10-7230-7_20] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Epstein-Barr virus-associated gastric cancer (EBVaGC) is a representative EBV-infected epithelial neoplasm, which is now included as one of the four subtypes of The Cancer Genome Atlas molecular classification of gastric cancer. In this review, we portray a gastritis-infection-cancer sequence of EBVaGC. This virus-associated type of gastric cancer demonstrates clonal growth of EBV-infected epithelial cells within the mucosa of atrophic gastritis. Its core molecular abnormality is the EBV-specific hyper-epigenotype of CpG island promoter methylation, which induces silencing of tumor suppressor genes. This is due to the infection-induced disruption of the balance between DNA methylation and DNA demethylation activities. Abnormalities in the host cell genome, including phosphatidylinositol-4,5-biphosphate 3-kinase catalytic subunit α (PIK3CA), AT-rich interaction domain 1A (ARID1A), and programmed death-ligand 1 (PD-L1), are associated with the development and progression of EBVaGC. Furthermore, posttranscriptional modulation affects the transformation processes of EBV-infected cells, such as epithelial mesenchymal transition and anti-apoptosis, via cellular and viral microRNAs (miRNAs). Once established, cancer cells of EBVaGC remodel their microenvironment, at least partly, via the delivery of exosomes containing cellular and viral miRNAs. After exosomes are incorporated, these molecules change the functions of stromal cells, tuning the microenvironment for EBVaGC. During this series of events, EBV hijacks and uses cellular machineries, such as DNA methylation and the miRNA delivery system. This portrait of gastritis-infection-cancer sequences highlights the survival strategies of EBV in the stomach epithelial cells and may be useful for the integration of therapeutic modalities against EBV-driven gastric cancer.
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Affiliation(s)
- Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Akiko Kunita
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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24
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Stanland LJ, Luftig MA. Molecular features and translational outlook for Epstein-Barr virus-associated gastric cancer. Future Virol 2018; 13:803-818. [PMID: 34367314 PMCID: PMC8345226 DOI: 10.2217/fvl-2018-0071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epstein-Barr Virus (EBV) was the first discovered human tumor virus and is the etiological agent of B cell lymphomas and also epithelial cancers. Indeed, nearly 10% of gastric cancers worldwide are EBV-positive and display unique molecular, epigenetic, and clinicopathological features. EBV-positive gastric cancers display the highest rate of host genome methylation of all tumor types studied and harbor recurrent mutations activating PI3Kα, silencing ARID1A, and amplifying PD-L1. While EBV infection of B cells can be studied efficiently, de novo epithelial cell infection is much more difficult. We propose that new culture models including 3D-based gastric organoids and xenografts can bring new insight into EBV-induced gastric carcinogenesis and will lead to improved precision medicine-based therapies for patients with EBV-positive gastric cancer.
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Affiliation(s)
- Lyla J. Stanland
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University School of Medicine, Durham, NC, 27710, USA
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25
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Sequence Variation of Epstein-Barr Virus: Viral Types, Geography, Codon Usage, and Diseases. J Virol 2018; 92:JVI.01132-18. [PMID: 30111570 PMCID: PMC6206488 DOI: 10.1128/jvi.01132-18] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
Epstein-Barr virus causes most cases of infectious mononucleosis and posttransplant lymphoproliferative disease. It contributes to several types of cancer, including Hodgkin's lymphoma, Burkitt's lymphoma, diffuse large B cell lymphoma, nasopharyngeal carcinoma, and gastric carcinoma. EBV genome variation is important because some of the diseases associated with EBV have very different incidences in different populations and geographic regions, and differences in the EBV genome might contribute to these diseases. Some specific EBV genome alterations that appear to be significant in EBV-associated cancers are already known, and current efforts to make an EBV vaccine and antiviral drugs should also take account of sequence differences in the proteins used as targets. One hundred thirty-eight new Epstein-Barr virus (EBV) genome sequences have been determined. One hundred twenty-five of these and 116 from previous reports were combined to produce a multiple-sequence alignment of 241 EBV genomes, which we have used to analyze variation within the viral genome. The type 1/type 2 classification of EBV remains the major form of variation and is defined mostly by EBNA2 and EBNA3, but the type 2 single-nucleotide polymorphisms (SNPs) at the EBNA3 locus extend into the adjacent gp350 and gp42 genes, whose products mediate infection of B cells by EBV. A small insertion within the BART microRNA region of the genome was present in 21 EBV strains. EBV from saliva of U.S. patients with chronic active EBV infection aligned with the wild-type EBV genome with no evidence of WZhet rearrangements. The V3 polymorphism in the Zp promoter for BZLF1 was found to be frequent in nasopharyngeal carcinoma cases from both Hong Kong and Indonesia. Codon usage was found to differ between latent and lytic cycle EBV genes, and the main forms of variation of the EBNA1 protein have been identified. IMPORTANCE Epstein-Barr virus causes most cases of infectious mononucleosis and posttransplant lymphoproliferative disease. It contributes to several types of cancer, including Hodgkin's lymphoma, Burkitt's lymphoma, diffuse large B cell lymphoma, nasopharyngeal carcinoma, and gastric carcinoma. EBV genome variation is important because some of the diseases associated with EBV have very different incidences in different populations and geographic regions, and differences in the EBV genome might contribute to these diseases. Some specific EBV genome alterations that appear to be significant in EBV-associated cancers are already known, and current efforts to make an EBV vaccine and antiviral drugs should also take account of sequence differences in the proteins used as targets.
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26
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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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27
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Gilani U, Shaukat M, Rasheed A, Shahid M, Tasneem F, Arshad M, Rashid N, Shahzad N. The implication of CRISPR/Cas9 genome editing technology in combating human oncoviruses. J Med Virol 2018; 91:1-13. [PMID: 30133783 DOI: 10.1002/jmv.25292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/31/2018] [Indexed: 12/23/2022]
Abstract
It is evidenced that 20% of all tumors in humans are caused by oncoviruses, including human papilloma viruses, Epstein-Barr virus, Kaposi sarcoma virus, human polyomaviruses, human T-lymphotrophic virus-1, and hepatitis B and C viruses. Human immunodeficiency virus is also involved in carcinogenesis, although not directly, but by facilitating the infection of many oncoviruses through compromising the immune system. Being intracellular parasites with the property of establishing latency and integrating into the host genome, these viruses are a therapeutic challenge for biomedical researchers. Therefore, strategies able to target nucleotide sequences within episomal or integrated viral genomes are of prime importance in antiviral or anticancerous armamentarium. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has emerged as a powerful genome editing tool. Standing out as a precise and efficient oncoviruses method, it has been extensively applied in recent experimental ventures in the field of molecular medicine, particularly in combating infections including tumor inducing viruses. This review is aimed at collating the experimental and clinical advances in CRISPR/Cas9 technology in terms of its applications against oncoviruses. Primarily, it will focus on the application of CRISPR/Cas9 in combating tumor viruses, types of mechanisms targeted, and the significant outcomes till date. The technical pitfalls of the CRISPR/Cas9 and the comparative approaches in evaluating this technique with respect to other available alternatives are also described briefly. Furthermore, the review also discussed the clinical aspects and the ethical, legal, and social issues associated with the use of CRISPR/Cas9.
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Affiliation(s)
- Usman Gilani
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Memoona Shaukat
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Arisha Rasheed
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mehak Shahid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Fareeda Tasneem
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Arshad
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Naveed Shahzad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
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28
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The Natural Large Genomic Deletion Is Unrelated to the Increased Virulence of the Novel Genotype Fowl Adenovirus 4 Recently Emerged in China. Viruses 2018; 10:v10090494. [PMID: 30217040 PMCID: PMC6165077 DOI: 10.3390/v10090494] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 12/31/2022] Open
Abstract
Since 2015, severe hydropericardium-hepatitis syndrome (HHS), caused by a highly pathogenic fowl adenovirus 4 (FAdV-4), emerged in China. In our previous study, the FAdV-4 has been identified as a novel genotype with a unique 1966-bp nucleotide deletion (1966Del) between open reading frame 42 and 43. In this study, the natural 1966Del was frequently identified among 17 clinical isolates and other reported Chinese clinical strains. To investigate the relationship between 1966Del and the increased virulence of the novel FAdV-4, a CRISPR/Cas9 operating platform for FAdV-4 was developed for the first time in this study. Based on this platform, a Re1966 strain was rescued, inserted the relative 1966Del sequence of a nonpathogenic strain KR5. In the pathogenicity study, the Re1966 strain retained high virulence for specific-pathogen-free chickens, similar to the parental wild-type HLJFAd15, although the survival time of chickens infected with Re1966 was much longer. Therefore, the natural 1966Del was identified as a non-essential site for the increased virulence of the emerged novel FAdV-4. Although further research on the virulence-determining region or point within the genome of the novel FAdV-4 is needed, the CRISPR/Cas9 operating platform for the novel FAdV-4 was developed and successfully applied to edit the genomic DNA for the first time, and it provides a novel powerful tool for both basic virology studies and vaccine vector development of FAdVs.
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29
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Xiao H, Liu W, Zhao Z, Zhang Y, Song Y, Luo B. Single nucleotide polymorphism rs2274084 of gap junction protein beta 2 gene among Epstein-Barr virus-associated tumors. Cancer Biomark 2018; 21:499-504. [PMID: 29103018 DOI: 10.3233/cbm-170078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Gap junction protein beta 2 gene (GJB2) encodes one of connexins- Connexin 26 (Cx26), which mainly expressed in epithelial cells. Cx26 is usually considered a channel to exchange information between cells, which plays a critical role in tumor cell proliferation. OBJECTIVE We investigated GJB2 rs2274084 polymorphism in three types of tumors, including nasophoryngeal carcinoma (NPC), gastric cancer (GC) and lymphoma. METHODS Proteinase K digestion and phenolchloroform purification and QIAamp DNA FFPE tissue kit was used for DNA extraction. The genotype of GJB2 gene rs2274084 was detected through Sequenom MassARRAY SNP technique. The Chi-square test and Fisher's exact test were used to compare the differences between two groups. RESULTS The genotype frequency of GJB2 gene rs2274084 was significantly different between EBV-positive NPC and normal control (P< 0.05). However, for EBV-associated gastric cancer (EBVaGC), EBV-negative gastric cancer (EBVnGC) and lymphoma, no significant differences were found in comparison with the normal control. CONCLUSIONS The mutation rate of TT genotype was a risk factor to the occurrence of EBV-positive NPC.
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Affiliation(s)
- Hua Xiao
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao 266021, Shandong, China
| | - Wen Liu
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao 266021, Shandong, China
| | - Zhenzhen Zhao
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao 266021, Shandong, China
| | - Yan Zhang
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao 266021, Shandong, China.,Department of Clinical Laboratory, Central Hospital of Zibo, Zibo 255036, Shandong, China
| | - Yingying Song
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao 266021, Shandong, China
| | - Bing Luo
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao 266021, Shandong, China
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30
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Tang YD, Guo JC, Wang TY, Zhao K, Liu JT, Gao JC, Tian ZJ, An TQ, Cai XH. CRISPR/Cas9-mediated 2-sgRNA cleavage facilitates pseudorabies virus editing. FASEB J 2018; 32:4293-4301. [PMID: 29509513 DOI: 10.1096/fj.201701129r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Several groups have used CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) for DNA virus editing. In most cases, one single-guide RNA (sgRNA) is used, which produces inconsistencies in gene editing. In this study, we used a swine herpesvirus, pseudorabies virus, as a model to systematically explore the application of CRISPR/Cas9 in DNA virus editing. In our current report, we demonstrated that cotransfection of 2 sgRNAs and a viral genome resulted in significantly better knockout efficiency than the transfection-infection-based approach. This method could result in 100% knockout of ≤3500 bp of viral nonessential large fragments. Furthermore, knockin efficiency was significantly improved by using 2 sgRNAs and was also correlated with the number of background viruses. We also demonstrated that the background viruses were all 2-sgRNA-mediated knockout mutants. Finally, this study demonstrated that the efficacy of gene knockin is determined by the replicative kinetics of background viruses. We propose that CRISPR/Cas9 coupled with 2 sgRNAs creates a powerful tool for DNA virus editing and offers great potential for future applications.-Tang, Y.-D., Guo, J.-C., Wang, T.-Y., Zhao, K., Liu, J.-T., Gao, J.-C., Tian, Z.-J., An, T.-Q., Cai, X.-H. CRISPR/Cas9-mediated 2-sgRNA cleavage facilitates pseudorabies virus editing.
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Affiliation(s)
- Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jin-Chao Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Tong-Yun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Kuan Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ji-Ting Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jia-Cong Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhi-Jun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Tong-Qing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xue-Hui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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31
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Bristol JA, Djavadian R, Albright ER, Coleman CB, Ohashi M, Hayes M, Romero-Masters JC, Barlow EA, Farrell PJ, Rochford R, Kalejta RF, Johannsen EC, Kenney SC. A cancer-associated Epstein-Barr virus BZLF1 promoter variant enhances lytic infection. PLoS Pathog 2018; 14:e1007179. [PMID: 30052684 PMCID: PMC6082571 DOI: 10.1371/journal.ppat.1007179] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/08/2018] [Accepted: 06/25/2018] [Indexed: 12/29/2022] Open
Abstract
Latent Epstein-Barr virus (EBV) infection contributes to both B-cell and epithelial-cell malignancies. However, whether lytic EBV infection also contributes to tumors is unclear, although the association between malaria infection and Burkitt lymphomas (BLs) may involve excessive lytic EBV replication. A particular variant of the viral promoter (Zp) that controls lytic EBV reactivation is over-represented, relative to its frequency in non-malignant tissue, in EBV-positive nasopharyngeal carcinomas and AIDS-related lymphomas. To date, no functional differences between the prototype Zp (Zp-P) and the cancer-associated variant (Zp-V3) have been identified. Here we show that a single nucleotide difference between the Zp-V3 and Zp-P promoters creates a binding site for the cellular transcription factor, NFATc1, in the Zp-V3 (but not Zp-P) variant, and greatly enhances Zp activity and lytic viral reactivation in response to NFATc1-inducing stimuli such as B-cell receptor activation and ionomycin. Furthermore, we demonstrate that restoring this NFATc1-motif to the Zp-P variant in the context of the intact EBV B95.8 strain genome greatly enhances lytic viral reactivation in response to the NFATc1-activating agent, ionomycin, and this effect is blocked by the NFAT inhibitory agent, cyclosporine, as well as NFATc1 siRNA. We also show that the Zp-V3 variant is over-represented in EBV-positive BLs and gastric cancers, and in EBV-transformed B-cell lines derived from EBV-infected breast milk of Kenyan mothers that had malaria during pregnancy. These results demonstrate that the Zp-V3 enhances EBV lytic reactivation to physiologically-relevant stimuli, and suggest that increased lytic infection may contribute to the increased prevalence of this variant in EBV-associated malignancies. Whether excessive lytic EBV infection increases the risk of EBV-induced cancers is not clear. A particular variant (Zp-V3) of the viral promoter driving expression of the EBV immediate-early BZLF1 (Z) protein that mediates lytic viral reactivation has been reported to be over-represented (relative to the prototype Zp-P form of the promoter) in certain EBV-positive malignancies, but no functional difference between the two promoter variants has been reported. Here we show that the malignancy-associated Zp-V3 variant (but not the Zp-P variant) contains a binding site for the cellular NFATc1 (nuclear factor of activated T cells c1) transcription factor that allows it to be activated by NFATc1-inducing stimuli such as B-cell receptor stimulation. Furthermore, we demonstrate that restoring this NFATc1-motif to the Zp-P variant in the context of the intact EBV genome greatly enhances lytic viral reactivation in response to the NFATc1-inducing stimuli. We also find that the Zp-V3 variant is over-represented in EBV-positive Burkitt lymphomas and gastric carcinomas, and in lymphoblastoid cell lines transformed by EBV-infected breast milk of Kenyan mothers that had malaria during pregnancy. These findings suggest that the Zp-V3 version of the EBV BZLF1 promoter increases the likelihood of EBV-induced malignancies by increasing lytic EBV infection.
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Affiliation(s)
- Jillian A. Bristol
- Department of Oncology in Wisconsin Institutes for Medical Research, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Reza Djavadian
- Department of Oncology in Wisconsin Institutes for Medical Research, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Emily R. Albright
- Department of Molecular Virology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Carrie B. Coleman
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Denver, Colorado, United States of America
| | - Makoto Ohashi
- Department of Oncology in Wisconsin Institutes for Medical Research, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Mitchell Hayes
- Department of Oncology in Wisconsin Institutes for Medical Research, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - James C. Romero-Masters
- Department of Oncology in Wisconsin Institutes for Medical Research, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- Department of Pathology and Laboratory Medicine, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Elizabeth A. Barlow
- Department of Oncology in Wisconsin Institutes for Medical Research, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Paul J. Farrell
- Molecular Virology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Rosemary Rochford
- Department of Immunology & Microbiology, University of Colorado School of Medicine, Denver, Colorado, United States of America
- Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado United States of America
| | - Robert F. Kalejta
- Department of Molecular Virology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Eric C. Johannsen
- Department of Oncology in Wisconsin Institutes for Medical Research, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- Department of Medicine, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Shannon C. Kenney
- Department of Oncology in Wisconsin Institutes for Medical Research, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- Department of Medicine, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- * E-mail:
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32
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Phylogenetic comparison of Epstein-Barr virus genomes. J Microbiol 2018; 56:525-533. [PMID: 29948828 DOI: 10.1007/s12275-018-8039-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/22/2018] [Accepted: 02/22/2018] [Indexed: 01/06/2023]
Abstract
Technologies used for genome analysis and whole genome sequencing are useful for us to understand genomic characterization and divergence. The Epstein-Barr virus (EBV) is an oncogenic virus that causes diverse diseases such as Burkitt's lymphoma (BL), nasopharyngeal carcinoma (NPC), Hodgkin's lymphoma (HL), and gastric carcinoma (GC). EBV genomes found in these diseases can be classified either by phases of EBV latency (type-I, -II, and -III latency) or types of EBNA2 sequence difference (type-I EBV, type-II EBV or EBV-1, EBV-2). EBV from EBV-transformed lymphoblastoid cell line (LCL) establishes type-III latency, EBV from NPC establishes type-II latency, and EBV from GC establishes type-I latency. However, other important factors play key roles in classifying numerous EBV strains because EBV genomes are highly diverse and not phylogenetically related to types of EBV-associated diseases. Herein, we first reviewed previous studies to describe molecular characteristics of EBV genomes. Then, using comparative and phylogenetic analyses, we phylogenetically analyzed molecular variations of EBV genomes and proteins. The review of previous studies and our phylogenetic analysis showed that EBV genomes and proteins were highly diverse regardless of types of EBV-associated diseases. Other factors should be considered in determining EBV taxonomy. This review will be helpful to understand complicated phylogenetic relationships of EBV genomes.
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33
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Chen YC, Sheng J, Trang P, Liu F. Potential Application of the CRISPR/Cas9 System against Herpesvirus Infections. Viruses 2018; 10:v10060291. [PMID: 29844277 PMCID: PMC6024784 DOI: 10.3390/v10060291] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/19/2018] [Accepted: 05/19/2018] [Indexed: 12/11/2022] Open
Abstract
The CRISPR/Cas9 system has been applied in the genome editing and disruption of latent infections for herpesviruses such as the herpes simplex virus, Epstein⁻Barr virus, cytomegalovirus, and Kaposi's sarcoma-associated herpesvirus. CRISPR/Cas9-directed mutagenesis can introduce similar types of mutations to the viral genome as can bacterial artificial chromosome recombination engineering, which maintains and reconstitutes the viral genome successfully. The cleavage mediated by CRISPR/Cas9 enables the manipulation of disease-associated viral strains with unprecedented efficiency and precision. Additionally, current therapies for herpesvirus productive and latent infections are limited in efficacy and cannot eradicate viruses. CRISPR/Cas9 is potentially adapted for antiviral treatment by specifically targeting viral genomes during latent infections. This review, which focuses on recently published progress, suggests that the CRISPR/Cas9 system is not only a useful tool for basic virology research, but also a promising strategy for the control and prevention of herpesvirus latent infections.
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Affiliation(s)
- Yuan-Chuan Chen
- College of Life Sciences and Technology, Jinan University, Guangzhou 510632, China.
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA.
- National Applied Research Laboratories, Taipei 10636, Taiwan.
| | - Jingxue Sheng
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA.
| | - Phong Trang
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA.
| | - Fenyong Liu
- College of Life Sciences and Technology, Jinan University, Guangzhou 510632, China.
- Program in Comparative Biochemistry, University of California, Berkeley, CA 94720, USA.
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34
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Liu J, Ji X, Shen Z, Wang PhD Y, Luo PhD B. Sequence variations of Epstein-Barr virus-encoded BARF1 gene in nasopharyngeal carcinomas and healthy donors from southern and northern China. J Med Virol 2018; 90:1629-1635. [PMID: 29797589 DOI: 10.1002/jmv.25233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/10/2018] [Indexed: 12/17/2022]
Abstract
The BamHI A rightward frame 1 (BARF1) gene of the Epstein-Barr virus (EBV) is involved in carcinogenesis and immunomodulation of EBV-associated malignancies. The geographical distributions and the disease associations of BARF1 variants remain unclear. In the current study, the BARF1 variants in nasopharyngeal carcinoma (NPC) cases and healthy donors from southern and northern China, the NPC endemic and non-endemic areas, as well as in 153 sequenced EBV genomes from diseased and normal people from around the world, were determined and compared among areas and populations. Only 1 consistent coding change, V29A, and several consistent silent mutations were identified. Two BARF1 types (B95-8 and V29A) and 2 B95-8 subtypes (B95-8t165545c and B95-8P ) were classified. For Chinese isolates, the B95-8 type was dominant in both southern and northern China, but the isolates from southern China showed a higher frequency of the B95-8t165545c subtype than the isolates from northern China (76.0%, 38/50 NPC cases and 50.7%, 37/73 healthy donors vs 26.4%, 24/91 NPC cases and 7.6%, 6/79 healthy donors, P < .0001). Furthermore, the B95-8t165545c subtype was more frequent in NPC cases than healthy donors in both southern China (P = .005) and northern China (P = .001). For EBV genomes, the B95-8P subtype was dominant in northern China, Europe, America, and Australia, while V29A was dominant in Africa. The B95-8t165545c subtype was only identified in Asia and demonstrated high frequency (81.2%, 26/32) in genomes from NPC cases in southern China. These results further reveal conservation and possibly geographically spread variations of BARF1 and may also indicate the preference of EBV strains with the B95-8t165545c subtype in NPC cases, without biological or pathogenic implications.
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Affiliation(s)
- Jincheng Liu
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Xinqiang Ji
- Modern Educational Technology Center, Qingdao University, Qingdao, China
| | - Zhichao Shen
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China.,Department of Clinical Laboratory, The People's Liberation Army 107 Hospital, Yantai, China
| | - Yun Wang PhD
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Bing Luo PhD
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
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35
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Yajima M, Ikuta K, Kanda T. Rapid CRISPR/Cas9-Mediated Cloning of Full-Length Epstein-Barr Virus Genomes from Latently Infected Cells. Viruses 2018; 10:v10040171. [PMID: 29614006 PMCID: PMC5923465 DOI: 10.3390/v10040171] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/28/2018] [Accepted: 03/31/2018] [Indexed: 12/13/2022] Open
Abstract
Herpesviruses have relatively large DNA genomes of more than 150 kb that are difficult to clone and sequence. Bacterial artificial chromosome (BAC) cloning of herpesvirus genomes is a powerful technique that greatly facilitates whole viral genome sequencing as well as functional characterization of reconstituted viruses. We describe recently invented technologies for rapid BAC cloning of herpesvirus genomes using CRISPR/Cas9-mediated homology-directed repair. We focus on recent BAC cloning techniques of Epstein-Barr virus (EBV) genomes and discuss the possible advantages of a CRISPR/Cas9-mediated strategy comparatively with precedent EBV-BAC cloning strategies. We also describe the design decisions of this technology as well as possible pitfalls and points to be improved in the future. The obtained EBV-BAC clones are subjected to long-read sequencing analysis to determine complete EBV genome sequence including repetitive regions. Rapid cloning and sequence determination of various EBV strains will greatly contribute to the understanding of their global geographical distribution. This technology can also be used to clone disease-associated EBV strains and test the hypothesis that they have special features that distinguish them from strains that infect asymptomatically.
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Affiliation(s)
- Misako Yajima
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyagino-ku, Sendai 983-8536, Japan.
| | - Kazufumi Ikuta
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyagino-ku, Sendai 983-8536, Japan.
| | - Teru Kanda
- Division of Microbiology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyagino-ku, Sendai 983-8536, Japan.
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36
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Ren L, Peng Z, Ouyang T, Liu X, Chen X, Ye L, Fan J, Ouyang H, Pang D, Bai J. Subculturing cells have no effect on CRISPR/Cas9-mediated cleavage of UL30 gene in pseudorabies virus. Animal Model Exp Med 2018; 1:74-77. [PMID: 30891550 PMCID: PMC6357676 DOI: 10.1002/ame2.12006] [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: 09/08/2017] [Accepted: 01/22/2018] [Indexed: 01/15/2023] Open
Abstract
CRISPR/Cas9-mediated genome editing can inhibit virus infection by targeting the conserved regions of the viral genomic DNA. Unexpectedly, we found previously that pseudorabies virus (PRV) could escape from CRISPR/Cas9-mediated inhibition. In order to elucidate whether the escape of PRV from Cas9-mediated inhibition was due to cell deficiencies, such as genetic instability of sgRNA or Cas9 protein, the positive cells were passaged ten times, and PRV infection in the sgRNA-expressing cells was evaluated in the present study. The results showed that subculturing cells has no effect on Cas9-mediated cleavage of PRV. Different passages of PX459-PRV cells can stably express sgRNA to facilitate Cas9/sgRNA cleavage on the UL30 gene of PRV, resulting in a pronounced inhibition of PRV infection. Studies to elucidate the mechanism of PRV escape are currently in progress.
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Affiliation(s)
- Lin‐zhu Ren
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Zhi‐yuan Peng
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Ting Ouyang
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Xiao‐hui Liu
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Xin‐rong Chen
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
- The Laboratory Animal CenterThe Academic of Military Medical SciencesBeijingChina
| | - Li Ye
- The Laboratory Animal CenterThe Academic of Military Medical SciencesBeijingChina
| | - Jun‐wen Fan
- The Laboratory Animal CenterThe Academic of Military Medical SciencesBeijingChina
| | - Hong‐sheng Ouyang
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Da‐xin Pang
- Jilin Provincial Key Laboratory of Animal Embryo EngineeringCollege of Animal SciencesJilin UniversityChangchunJilinChina
| | - Jie‐ying Bai
- The Laboratory Animal CenterThe Academic of Military Medical SciencesBeijingChina
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37
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Tsai MH, Lin X, Shumilov A, Bernhardt K, Feederle R, Poirey R, Kopp-Schneider A, Pereira B, Almeida R, Delecluse HJ. The biological properties of different Epstein-Barr virus strains explain their association with various types of cancers. Oncotarget 2018; 8:10238-10254. [PMID: 28052012 PMCID: PMC5354655 DOI: 10.18632/oncotarget.14380] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/15/2016] [Indexed: 12/27/2022] Open
Abstract
The Epstein-Barr virus (EBV) is etiologically associated with the development of multiple types of tumors, but it is unclear whether this diversity is due to infection with different EBV strains. We report a comparative characterization of SNU719, GP202, and YCCEL1, three EBV strains that were isolated from gastric carcinomas, M81, a virus isolated in a nasopharyngeal carcinoma and several well-characterized laboratory type A strains. We found that B95-8, Akata and GP202 induced cell growth more efficiently than YCCEL1, SNU719 and M81 and this correlated positively with the expression levels of the viral BHRF1 miRNAs. In infected B cells, all strains except Akata and B95-8 induced lytic replication, a risk factor for carcinoma development, although less efficiently than M81. The panel of viruses induced tumors in immunocompromised mice with variable speed and efficacy that did not strictly mirror their in vitro characteristics, suggesting that additional parameters play an important role. We found that YCCEL1 and M81 infected primary epithelial cells, gastric carcinoma cells and gastric spheroids more efficiently than Akata or B95-8. Reciprocally, Akata and B95-8 had a stronger tropism for B cells than YCCEL1 or M81. These data suggest that different EBV strains will induce the development of lymphoid tumors with variable efficacy in immunocompromised patients and that there is a parallel between the cell tropism of the viral strains and the lineage of the tumors they induce. Thus, EBV strains can be endowed with properties that will influence their transforming abilities and the type of tumor they induce.
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Affiliation(s)
- Ming-Han Tsai
- German Cancer Research Centre (DKFZ), Unit F100, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
| | - Xiaochen Lin
- German Cancer Research Centre (DKFZ), Unit F100, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
| | - Anatoliy Shumilov
- German Cancer Research Centre (DKFZ), Unit F100, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
| | - Katharina Bernhardt
- German Cancer Research Centre (DKFZ), Unit F100, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
| | - Regina Feederle
- German Cancer Research Centre (DKFZ), Unit F100, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany.,Institute for Diabetes and Obesitas, Monoclonal Antibody Core Facility, German Research Center for Environmental Health, Helmholtz Zentrum München, 81377 Munich, Germany
| | - Remy Poirey
- German Cancer Research Centre (DKFZ), Unit F100, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
| | | | - Bruno Pereira
- Differentiation and Cancer Group, IPATIMUP, Rua Dr Roberto Frias s/n, 4200 - 465 Porto, Portugal
| | - Raquel Almeida
- Differentiation and Cancer Group, IPATIMUP, Rua Dr Roberto Frias s/n, 4200 - 465 Porto, Portugal
| | - Henri-Jacques Delecluse
- German Cancer Research Centre (DKFZ), Unit F100, 69120 Heidelberg, Germany.,Inserm unit U1074, DKFZ, 69120 Heidelberg, Germany
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38
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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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39
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CRISPR-Cas9 Genetic Analysis of Virus-Host Interactions. Viruses 2018; 10:v10020055. [PMID: 29385696 PMCID: PMC5850362 DOI: 10.3390/v10020055] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 01/28/2018] [Accepted: 01/29/2018] [Indexed: 12/12/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) has greatly expanded the ability to genetically probe virus–host interactions. CRISPR systems enable focused or systematic, genomewide studies of nearly all aspects of a virus lifecycle. Combined with its relative ease of use and high reproducibility, CRISPR is becoming an essential tool in studies of the host factors important for viral pathogenesis. Here, we review the use of CRISPR–Cas9 for the loss-of-function analysis of host dependency factors. We focus on the use of CRISPR-pooled screens for the systematic identification of host dependency factors, particularly in Epstein–Barr virus-transformed B cells. We also discuss the use of CRISPR interference (CRISPRi) and gain-of-function CRISPR activation (CRISPRa) approaches to probe virus–host interactions. Finally, we comment on the future directions enabled by combinatorial CRISPR screens.
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40
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Okoli A, Okeke MI, Tryland M, Moens U. CRISPR/Cas9-Advancing Orthopoxvirus Genome Editing for Vaccine and Vector Development. Viruses 2018; 10:E50. [PMID: 29361752 PMCID: PMC5795463 DOI: 10.3390/v10010050] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/17/2018] [Accepted: 01/21/2018] [Indexed: 12/17/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)/associated protein 9 (Cas9) technology is revolutionizing genome editing approaches. Its high efficiency, specificity, versatility, flexibility, simplicity and low cost have made the CRISPR/Cas9 system preferable to other guided site-specific nuclease-based systems such as TALENs (Transcription Activator-like Effector Nucleases) and ZFNs (Zinc Finger Nucleases) in genome editing of viruses. CRISPR/Cas9 is presently being applied in constructing viral mutants, preventing virus infections, eradicating proviral DNA, and inhibiting viral replication in infected cells. The successful adaptation of CRISPR/Cas9 to editing the genome of Vaccinia virus paves the way for its application in editing other vaccine/vector-relevant orthopoxvirus (OPXV) strains. Thus, CRISPR/Cas9 can be used to resolve some of the major hindrances to the development of OPXV-based recombinant vaccines and vectors, including sub-optimal immunogenicity; transgene and genome instability; reversion of attenuation; potential of spread of transgenes to wildtype strains and close contacts, which are important biosafety and risk assessment considerations. In this article, we review the published literature on the application of CRISPR/Cas9 in virus genome editing and discuss the potentials of CRISPR/Cas9 in advancing OPXV-based recombinant vaccines and vectors. We also discuss the application of CRISPR/Cas9 in combating viruses of clinical relevance, the limitations of CRISPR/Cas9 and the current strategies to overcome them.
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Affiliation(s)
- Arinze Okoli
- Biosafety of Genome Editing Research Group, GenØk-Centre for Biosafety, Siva Innovation Centre, N-9294 Tromsø, Norway.
| | - Malachy I Okeke
- Biosafety of Genome Editing Research Group, GenØk-Centre for Biosafety, Siva Innovation Centre, N-9294 Tromsø, Norway.
| | - Morten Tryland
- Biosafety of Genome Editing Research Group, GenØk-Centre for Biosafety, Siva Innovation Centre, N-9294 Tromsø, Norway.
- Artic Infection Biology, Department of Artic and Marine Biology, The Artic University of Norway, N-9037 Tromsø, Norway.
| | - Ugo Moens
- Molecular Inflammation Research Group, Institute of Medical Biology, The Arctic University of Norway, N-9037 Tromsø, Norway.
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41
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Jeanes C, O'Grady J. Diagnosing tuberculosis in the 21st century - Dawn of a genomics revolution? Int J Mycobacteriol 2018; 5:384-391. [PMID: 27931678 DOI: 10.1016/j.ijmyco.2016.11.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Tuberculosis (TB) ranks alongside HIV as the leading cause of death worldwide, killing 1.5million people in 2014. Traditional laboratory techniques do not provide sufficiently rapid results to inform clinicians on appropriate treatment, especially in the face of increasingly prevalent drug-resistant TB. Rapid molecular methods such as PCR and LAMP are vital tools in the fight against TB, however, rapid advances in next generation sequencing (NGS) technology are allowing increasingly rapid and accurate sequencing of entire bacterial genomes at ever decreasing cost, providing unprecedented depth of information. These advances mean NGS stands to revolutionise the diagnosis and epidemiological study of Mycobacterium tuberculosis infection. This review focuses on current applications of NGS for TB diagnosis including sequencing cultured isolates to predict drug resistance and, more desirably, direct diagnostic metagenomic sequencing of clinical samples. Also discussed is the potential impact of NGS on the epidemiological study of TB and some of the key challenges that need to be overcome to enable this promising technology to be translated into routine use.
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Affiliation(s)
- Christopher Jeanes
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norfolk NR4 7TJ, United Kingdom.
| | - Justin O'Grady
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norfolk NR4 7TJ, United Kingdom.
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42
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Moon JW, Kong SK, Kim BS, Kim HJ, Lim H, Noh K, Kim Y, Choi JW, Lee JH, Kim YS. IFNγ induces PD-L1 overexpression by JAK2/STAT1/IRF-1 signaling in EBV-positive gastric carcinoma. Sci Rep 2017; 7:17810. [PMID: 29259270 PMCID: PMC5736657 DOI: 10.1038/s41598-017-18132-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 12/06/2017] [Indexed: 12/21/2022] Open
Abstract
Programmed death-ligand 1 (PD-L1) acts as an immune checkpoint inhibitor in various cancers. PD-L1 is known to be more frequently expressed in EBV (+) gastric cancer (GC). However, the mechanisms underlying the regulation of PD-L1 expression in EBV (+) GC remain unclear. We investigated the basal and inducible PD-L1 expressions in GC cells. PD-L1 expression was upregulated upon treatment with IFNγ in both EBV (-) and EBV (+) GC cells. Upon stimulation with the same concentration of IFNγ for 24 h, EBV (+) SNU-719 cells showed dramatically higher PD-L1 expression levels by activating JAK2/STAT1/IRF-1 signaling than those of EBV (-) AGS cells. PD-L1 promoter assays, chromatin immunoprecipitation, and electrophoretic mobility shift assays revealed that IFNγ-inducible PD-L1 overexpression is primarily mediated by the putative IRF-1α site of the PD-L1 promoter in EBV (+) SNU-719 cells. Moreover, EBNA1 knockdown reduced both constitutive and IFNγ-inducible PD-L1 promoter activity by decreasing the transcript and protein levels of JAK2 and subsequently STAT1/IRF-1/PD-L1 signaling. EBNA1 is suggested to be moderately enhance both constitutive and IFNγ-inducible PD-L1 expression in EBV (+) GC cells. Thus, the signaling proteins and EBNA1 that regulate PD-L1 expression are potential therapeutic targets in EBV (+) GC.
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Affiliation(s)
- Ji Wook Moon
- Department of Pathology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Su-Kang Kong
- Department of Pathology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Byung Soo Kim
- Department of Pathology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyun Ji Kim
- Department of Pathology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyangsoon Lim
- Department of Pathology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kyeonga Noh
- Department of Pathology, Korea University College of Medicine, Seoul, Republic of Korea
| | - Younghye Kim
- Department of Pathology, Korea University Ansan Hospital, Ansan, Republic of Korea
| | - Jung-Woo Choi
- Department of Pathology, Korea University Ansan Hospital, Ansan, Republic of Korea
| | - Ju-Han Lee
- Department of Pathology, Korea University Ansan Hospital, Ansan, Republic of Korea
| | - Young-Sik Kim
- Department of Pathology, Korea University College of Medicine, Seoul, Republic of Korea. .,Department of Pathology, Korea University Ansan Hospital, Ansan, Republic of Korea.
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43
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Ba Abdullah MM, Palermo RD, Palser AL, Grayson NE, Kellam P, Correia S, Szymula A, White RE. Heterogeneity of the Epstein-Barr Virus (EBV) Major Internal Repeat Reveals Evolutionary Mechanisms of EBV and a Functional Defect in the Prototype EBV Strain B95-8. J Virol 2017; 91:e00920-17. [PMID: 28904201 PMCID: PMC5686732 DOI: 10.1128/jvi.00920-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/02/2017] [Indexed: 12/28/2022] Open
Abstract
Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified through both coevolution with its host and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging because of the large number and lengths of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat 1 of EBV (IR1; also known as the BamW repeats) for more than 70 strains. The diversity of the latency protein EBV nuclear antigen leader protein (EBNA-LP) resides predominantly within the exons downstream of IR1. The integrity of the putative BWRF1 open reading frame (ORF) is retained in over 80% of strains, and deletions truncating IR1 always spare BWRF1. Conserved regions include the IR1 latency promoter (Wp) and one zone upstream of and two within BWRF1. IR1 is heterogeneous in 70% of strains, and this heterogeneity arises from sequence exchange between strains as well as from spontaneous mutation, with interstrain recombination being more common in tumor-derived viruses. This genetic exchange often incorporates regions of <1 kb, and allelic gene conversion changes the frequency of small regions within the repeat but not close to the flanks. These observations suggest that IR1-and, by extension, EBV-diversifies through both recombination and breakpoint repair, while concerted evolution of IR1 is driven by gene conversion of small regions. Finally, the prototype EBV strain B95-8 contains four nonconsensus variants within a single IR1 repeat unit, including a stop codon in the EBNA-LP gene. Repairing IR1 improves EBNA-LP levels and the quality of transformation by the B95-8 bacterial artificial chromosome (BAC).IMPORTANCE Epstein-Barr virus (EBV) infects the majority of the world population but causes illness in only a small minority of people. Nevertheless, over 1% of cancers worldwide are attributable to EBV. Recent sequencing projects investigating virus diversity to see if different strains have different disease impacts have excluded regions of repeating sequence, as they are more technically challenging. Here we analyze the sequence of the largest repeat in EBV (IR1). We first characterized the variations in protein sequences encoded across IR1. In studying variations within the repeat of each strain, we identified a mutation in the main laboratory strain of EBV that impairs virus function, and we suggest that tumor-associated viruses may be more likely to contain DNA mixed from two strains. The patterns of this mixing suggest that sequences can spread between strains (and also within the repeat) by copying sequence from another strain (or repeat unit) to repair DNA damage.
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Affiliation(s)
- Mohammed M Ba Abdullah
- Section of Virology, Imperial College Faculty of Medicine, St. Mary's Hospital, Norfolk Place, London, United Kingdom
| | - Richard D Palermo
- Section of Virology, Imperial College Faculty of Medicine, St. Mary's Hospital, Norfolk Place, London, United Kingdom
| | - Anne L Palser
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | | | - Paul Kellam
- Section of Virology, Imperial College Faculty of Medicine, St. Mary's Hospital, Norfolk Place, London, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
- Kymab, Babraham Research Campus, Cambridge, United Kingdom
| | - Samantha Correia
- Section of Virology, Imperial College Faculty of Medicine, St. Mary's Hospital, Norfolk Place, London, United Kingdom
| | - Agnieszka Szymula
- Section of Virology, Imperial College Faculty of Medicine, St. Mary's Hospital, Norfolk Place, London, United Kingdom
| | - Robert E White
- Section of Virology, Imperial College Faculty of Medicine, St. Mary's Hospital, Norfolk Place, London, United Kingdom
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44
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Fitzsimmons L, Kelly GL. EBV and Apoptosis: The Viral Master Regulator of Cell Fate? Viruses 2017; 9:E339. [PMID: 29137176 PMCID: PMC5707546 DOI: 10.3390/v9110339] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022] Open
Abstract
Epstein-Barr virus (EBV) was first discovered in cells from a patient with Burkitt lymphoma (BL), and is now known to be a contributory factor in 1-2% of all cancers, for which there are as yet, no EBV-targeted therapies available. Like other herpesviruses, EBV adopts a persistent latent infection in vivo and only rarely reactivates into replicative lytic cycle. Although latency is associated with restricted patterns of gene expression, genes are never expressed in isolation; always in groups. Here, we discuss (1) the ways in which the latent genes of EBV are known to modulate cell death, (2) how these mechanisms relate to growth transformation and lymphomagenesis, and (3) how EBV genes cooperate to coordinately regulate key cell death pathways in BL and lymphoblastoid cell lines (LCLs). Since manipulation of the cell death machinery is critical in EBV pathogenesis, understanding the mechanisms that underpin EBV regulation of apoptosis therefore provides opportunities for novel therapeutic interventions.
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Affiliation(s)
- Leah Fitzsimmons
- Institute of Cancer and Genomic Sciences and Centre for Human Virology, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Gemma L Kelly
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute for Medical Research, Parkville, Melbourne, VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, Melbourne, VIC 3052, Australia.
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Construction of a highly efficient CRISPR/Cas9-mediated duck enteritis virus-based vaccine against H5N1 avian influenza virus and duck Tembusu virus infection. Sci Rep 2017; 7:1478. [PMID: 28469192 PMCID: PMC5431151 DOI: 10.1038/s41598-017-01554-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/31/2017] [Indexed: 01/05/2023] Open
Abstract
Duck enteritis virus (DEV), duck tembusu virus (DTMUV), and highly pathogenic avian influenza virus (HPAIV) H5N1 are the most important viral pathogens in ducks, as they cause significant economic losses in the duck industry. Development of a novel vaccine simultaneously effective against these three viruses is the most economical method for reducing losses. In the present study, by utilizing a clustered regularly interspaced short palindromic repeats (CRISPR)/associated 9 (Cas9)-mediated gene editing strategy, we efficiently generated DEV recombinants (C-KCE-HA/PrM-E) that simultaneously encode the hemagglutinin (HA) gene of HPAIV H5N1 and pre-membrane proteins (PrM), as well as the envelope glycoprotein (E) gene of DTMUV, and its potential as a trivalent vaccine was also evaluated. Ducks immunized with C-KCE-HA/PrM-E enhanced both humoral and cell-mediated immune responses to H5N1 and DTMUV. Importantly, a single-dose of C-KCE-HA/PrM-E conferred solid protection against virulent H5N1, DTMUV, and DEV challenges. In conclusion, these results demonstrated for the first time that the CRISPR/Cas9 system can be applied for modification of the DEV genome rapidly and efficiently, and that recombinant C-KCE-HA/PrM-E can serve as a potential candidate trivalent vaccine to prevent H5N1, DTMUV, and DEV infections in ducks.
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Abstract
Epstein-Barr virus (EBV) is a common human herpes virus known to infect the majority of the world population. Infection with EBV is often asymptomatic but can manifest in a range of pathologies from infectious mononucleosis to severe cancers of epithelial and lymphocytic origin. Indeed, in the past decade, EBV has been linked to nearly 10% of all gastric cancers. Furthermore, recent advances in high-throughput next-generation sequencing and the development of humanized mice, which effectively model EBV pathogenesis, have led to a wealth of knowledge pertaining to strain variation and host-pathogen interaction. This review highlights some recent advances in our understanding of EBV biology, focusing on new findings on the early events of infection, the role EBV plays in gastric cancer, new strain variation, and humanized mouse models of EBV infection.
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Affiliation(s)
- Brent A Stanfield
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University Medical Center, Durham, NC, USA
| | - Micah A Luftig
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University Medical Center, Durham, NC, USA
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Fu YZ, Su S, Gao YQ, Wang PP, Huang ZF, Hu MM, Luo WW, Li S, Luo MH, Wang YY, Shu HB. Human Cytomegalovirus Tegument Protein UL82 Inhibits STING-Mediated Signaling to Evade Antiviral Immunity. Cell Host Microbe 2017; 21:231-243. [PMID: 28132838 DOI: 10.1016/j.chom.2017.01.001] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 12/02/2016] [Accepted: 01/02/2017] [Indexed: 01/06/2023]
Abstract
Recognition of human cytomegalovirus (HCMV) DNA by the cytosolic sensor cGAS initiates STING-dependent innate antiviral responses. HCMV can antagonize host immune responses to promote latency infection. However, it is unknown whether and how HCMV targets the cGAS-STING axis for immune evasion. Here we identified the HCMV tegument protein UL82 as a negative regulator of STING-dependent antiviral responses. UL82 interacted with STING and impaired STING-mediated signaling via two mechanisms. UL82 inhibited the translocation of STING from the ER to perinuclear microsomes by disrupting the STING-iRhom2-TRAPβ translocation complex. UL82 also impaired the recruitment of TBK1 and IRF3 to the STING complex. The levels of downstream antiviral genes induced by UL82-deficient HCMV were higher than those induced by wild-type HCMV. Conversely, wild-type HCMV replicated more efficiently than the UL82-deficient mutant. These findings reveal an important mechanism of immune evasion by HCMV.
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Affiliation(s)
- Yu-Zhi Fu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China 430072
| | - Shan Su
- Medical Research Institute, Collaborative Innovation Center for Viral Immunology, School of Medicine, Wuhan University, Wuhan, China 430071
| | - Yi-Qun Gao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China 430072
| | - Pei-Pei Wang
- Medical Research Institute, Collaborative Innovation Center for Viral Immunology, School of Medicine, Wuhan University, Wuhan, China 430071
| | - Zhe-Fu Huang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China 430071
| | - Ming-Ming Hu
- Medical Research Institute, Collaborative Innovation Center for Viral Immunology, School of Medicine, Wuhan University, Wuhan, China 430071
| | - Wei-Wei Luo
- Medical Research Institute, Collaborative Innovation Center for Viral Immunology, School of Medicine, Wuhan University, Wuhan, China 430071
| | - Shu Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China 430072
| | - Min-Hua Luo
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China 430071
| | - Yan-Yi Wang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China 430071
| | - Hong-Bing Shu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China 430072; Medical Research Institute, Collaborative Innovation Center for Viral Immunology, School of Medicine, Wuhan University, Wuhan, China 430071.
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48
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Lv YH, Li XQ, Yue CW, Wang M. Application of genome editing technologies in gastrointestinal cancers. Shijie Huaren Xiaohua Zazhi 2016; 24:4772-4780. [DOI: 10.11569/wcjd.v24.i36.4772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Genome editing is a site-directed modification technology for gene targeting and a powerful tool to edit the target DNA by site-specific DNA knockout or knockin. Genome editing has achieved a considerable success from lower microbes to human in the past years and may play a very important role in tumor staging, precision medicine as well as prognosis evaluation in gastrointestinal cancers. This review discusses the mechanisms of different genome-editing strategies and describes each of the common nuclease-based platforms, including transcription activator-like effector nucleases, zinc finger nucleases and the CRISPR/Cas9 system. We also summarize the progress made in applying genome editing to the research of gastrointestinal cancers.
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49
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van Diemen FR, Lebbink RJ. CRISPR/Cas9, a powerful tool to target human herpesviruses. Cell Microbiol 2016; 19. [PMID: 27860066 DOI: 10.1111/cmi.12694] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/07/2016] [Accepted: 11/14/2016] [Indexed: 12/11/2022]
Abstract
Over 90% of the adult population is infected with one or multiple herpesviruses. These viruses are characterized by their ability to establish latency, where the host is unable to clear the invader from infected cells resulting in a lifelong infection. Herpesviruses cause a wide variety of (recurrent) diseases such as cold sores, shingles, congenital defects and several malignancies. Although the productive phase of a herpesvirus infection can often be efficiently limited by nucleoside analogs, these drugs are ineffective during a latent herpesvirus infection and are therefore unable to clear herpesviruses from the human host. Advances in genome engineering using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 facilitates virus research and may hold potential to treat or cure previously incurable herpesvirus infections by directly targeting these viruses within infected cells. Here, we review recent applications of the CRISPR/Cas9 system for herpesviral research and discuss the therapeutic potential of the system to treat, or even cure, productive and latent herpesviral infections.
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Affiliation(s)
- Ferdy R van Diemen
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Utrecht Cornea Research Group, Department of Ophthalmology, 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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Guo JC, Tang YD, Zhao K, Wang TY, Liu JT, Gao JC, Chang XB, Cui HY, Tian ZJ, Cai XH, An TQ. Highly Efficient CRISPR/Cas9-Mediated Homologous Recombination Promotes the Rapid Generation of Bacterial Artificial Chromosomes of Pseudorabies Virus. Front Microbiol 2016; 7:2110. [PMID: 28066407 PMCID: PMC5179515 DOI: 10.3389/fmicb.2016.02110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022] Open
Abstract
Bacterial artificial chromosomes (BACs) are powerful tools for the manipulation of the large genomes of DNA viruses, such as herpesviruses. However, the methods currently used to construct the recombinant viruses, an important intermediate link in the generation of BACs, involve the laborious process of multiple plaque purifications. Moreover, some fastidious viruses may be lost or damaged during these processes, making it impossible to generate BACs from these large-genome DNA viruses. Here, we introduce the CRISPR/Cas9 as a site-specific gene knock-in instrument that promotes the homologs recombination of a linearized transfer vector and the Pseudorabies virus genome through double incisions. The efficiency of recombination is as high as 86%. To our knowledge, this is the highest efficiency ever reported for Pseudorabies virus recombination. We also demonstrate that the positions and distances of the CRISPR/Cas9 single guide RNAs from the homology arms correlate with the efficiency of homologous recombination. Our work show a simple and fast cloning method of BACs with large genome inserted by greatly enhancing the HR efficiencies through CRISPR/Cas9-mediated homology-directed repair mechanism, and this method could be of helpful for manipulating large DNA viruses, and will provide a successful model for insertion of large DNA fragments into other viruses.
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Affiliation(s)
- Jin-Chao Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Kuan Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Tong-Yun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Ji-Ting Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Jia-Cong Gao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Xiao-Bo Chang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Hong-Yu Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Zhi-Jun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Xue-Hui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
| | - Tong-Qing An
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences Harbin, China
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