1
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Kondo S, Okuno Y, Murata T, Dochi H, Wakisaka N, Mizokami H, Moriyama-Kita M, Kobayashi E, Kano M, Komori T, Hirai N, Ueno T, Nakanishi Y, Endo K, Sugimoto H, Kimura H, Yoshizaki T. EBV genome variations enhance clinicopathological features of nasopharyngeal carcinoma in a non-endemic region. Cancer Sci 2022; 113:2446-2456. [PMID: 35485636 PMCID: PMC9277247 DOI: 10.1111/cas.15381] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/17/2022] [Accepted: 04/20/2022] [Indexed: 11/17/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is caused by infection with Epstein–Barr virus (EBV) and endemic in certain geographic regions. EBV lytic gene, BALF2, closely associates with viral reactivation and BALF2 gene variation, the H‐H‐H strain, causes NPC in endemic region, southern China. Here, we investigate whether such EBV variations also affect NPC in a non‐endemic region, Japan. Viral genome sequencing with 47 EBV isolates of Japanese NPC were performed and compared with those of other EBV‐associated diseases from Japan or NPC in Southern China. EBV genomes of Japanese NPC are different from those of other diseases in Japan or endemic NPC; Japanese NPC was not affected by the endemic strain (the BALF2 H‐H‐H) but frequently carried the type 2 EBV or the strain with intermediate risk of endemic NPC (the BALF2 H‐H‐L). Seven single nucleotide variations were specifically associated with Japanese NPC, of which six were present in both type 1 and 2 EBV genomes, suggesting the contribution of the type 2 EBV‐derived haplotype. This observation was supported by a higher viral titer and stronger viral reactivation in NPC with either type 2 or H‐H‐L strains. Our results highlight the importance of viral strains and viral reactivation in the pathogenesis of non‐endemic NPC.
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Affiliation(s)
- Satoru Kondo
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan.,These authors contributed equally to this work
| | - Yusuke Okuno
- Department of Virology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Aichi, Japan.,Pediatric Cancer Treatment Center, Nagoya University Hospital, Nagoya, Aichi, Japan.,These authors contributed equally to this work
| | - Takayuki Murata
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Hirotomo Dochi
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Naohiro Wakisaka
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Harue Mizokami
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Makiko Moriyama-Kita
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Eiji Kobayashi
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Makoto Kano
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Takeshi Komori
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Nobuyuki Hirai
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Takayoshi Ueno
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Yosuke Nakanishi
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Kazuhira Endo
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Hisashi Sugimoto
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
| | - Hiroshi Kimura
- Department of Virology, Nagoya University, Graduate school of Medicine, Nagoya, Aichi, Japan
| | - Tomokazu Yoshizaki
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical science, Kanazawa University. Kanazawa, Ishikawa, Japan
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2
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Xu M, Yao Y, Chen H, Zhang S, Cao SM, Zhang Z, Luo B, Liu Z, Li Z, Xiang T, He G, Feng QS, Chen LZ, Guo X, Jia WH, Chen MY, Zhang X, Xie SH, Peng R, Chang ET, Pedergnana V, Feng L, Bei JX, Xu RH, Zeng MS, Ye W, Adami HO, Lin X, Zhai W, Zeng YX, Liu J. Genome sequencing analysis identifies Epstein-Barr virus subtypes associated with high risk of nasopharyngeal carcinoma. Nat Genet 2019; 51:1131-1136. [PMID: 31209392 PMCID: PMC6610787 DOI: 10.1038/s41588-019-0436-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 05/07/2019] [Indexed: 12/13/2022]
Abstract
Epstein-Barr virus (EBV) infection is ubiquitous worldwide and is
associated with multiple cancers, including nasopharyngeal carcinoma (NPC). The
importance of EBV viral genomic variation in NPC development and its striking
epidemic in southern China has been poorly explored. Through large-scale genome
sequencing of 270 EBV isolates and two-stage association study of EBV isolates
from China, we identified two non-synonymous EBV variants within
BALF2 strongly associated with the risk of NPC (odds ratio
(OR) = 8.69, P=9.69×10−25 for SNP
162476_C; OR = 6.14, P=2.40×10−32 for
SNP 163364_T). The cumulative effects of these variants contributed to 83% of
the overall risk of NPC in southern China. Phylogenetic analysis of the risk
variants revealed a unique origin in Asia, followed by clonal expansion in
NPC-endemic regions. Our results provide novel insights into NPC endemic in
southern China and also enable the identification of high-risk individuals for
NPC prevention. Whole-genome sequencing and association analysis of 270 Epstein-Barr
virus (EBV) isolates from China identify two non-synonymous EBV variants within
BALF2 strongly associated with the risk of nasopharyngeal carcinoma.
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Affiliation(s)
- Miao Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Youyuan Yao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Comprehensive Medical Oncology, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, Hangzhou, China
| | - Hui Chen
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shanshan Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Su-Mei Cao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhe Zhang
- Department of Otolaryngology/Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Bing Luo
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Zhiwei Liu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Zilin Li
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tong Xiang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guiping He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qi-Sheng Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Li-Zhen Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiang Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ming-Yuan Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shang-Hang Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Roujun Peng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ellen T Chang
- Center for Health Sciences, Exponent, Menlo Park, CA, USA.,Stanford Cancer Institute, Stanford, CA, USA
| | - Vincent Pedergnana
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lin Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jin-Xin Bei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rui-Hua Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Weiwei Zhai
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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10
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Makhov AM, Sen A, Yu X, Simon MN, Griffith JD, Egelman EH. The bipolar filaments formed by herpes simplex virus type 1 SSB/recombination protein (ICP8) suggest a mechanism for DNA annealing. J Mol Biol 2008; 386:273-9. [PMID: 19138689 DOI: 10.1016/j.jmb.2008.12.059] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 12/08/2008] [Accepted: 12/11/2008] [Indexed: 10/21/2022]
Abstract
Herpes simplex virus type 1 encodes a multifunctional protein, ICP8, which serves both as a single-strand binding protein and as a recombinase, catalyzing reactions involved in replication and recombination of the viral genome. In the presence of divalent ions and at low temperature, previous electron microscopic studies showed that ICP8 will form long left-handed helical filaments. Here, electron microscopic image reconstruction reveals that the filaments are bipolar, with an asymmetric unit containing two subunits of ICP8 that constitute a symmetrical dimer. This organization of the filament has been confirmed using scanning transmission electron microscopy. The pitch of the filaments is approximately 250 A, with approximately 6.2 dimers per turn. Docking of a crystal structure of ICP8 into the reconstructed filament shows that the C-terminal domain of ICP8, attached to the body of the subunit by a flexible linker containing approximately 10 residues, is packed into a pocket in the body of a neighboring subunit in the crystal in a similar manner as in the filament. However, the interactions between the large N-terminal domains are quite different in the filament from that observed in the crystal. A previously proposed model for ICP8 binding single-stranded DNA (ssDNA), based upon the crystal structure, leads to a model for a continuous strand of ssDNA near the filament axis. The bipolar nature of the ICP8 filaments means that a second strand of ssDNA would be running through this filament in the opposite orientation, and this provides a potential mechanism for how ICP8 anneals complementary ssDNA into double-stranded DNA, where each strand runs in opposite directions.
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Affiliation(s)
- Alexander M Makhov
- Lineberger Comprehensive Cancer Center, Department Microbiology and Immunology, University of North Carolina at Chapel Hill, 27517, USA
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