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4. A comprehensive predictive model for radiation-induced brain injury in risk stratification and personalized radiotherapy of nasopharyngeal carcinoma

Author

He, Yong-Qiao, Wang, Tong-Min, Yang, Da-Wei, Xue, Wen-Qiong, Deng, Chang-Mi, Li, Dan-Hua, Zhang, Wen-Li, Liao, Ying, Xiao, Ruo-Wen, Luo, Lu-Ting, Diao, Hua, Tong, Xia-Ting, Wu, Yan-Xia, Chen, Xue-Yin, Zhang, Jiang-Bo, Zhou, Ting, Li, Xi-Zhao, Zhang, Pei-Fen, Zheng, Xiao-Hui, Zhang, Shao-Dan, Hu, Ye-Zhu, Zhou, Guan-Qun, Ma, Jun, Sun, Ying, and Jia, Wei-Hua

Published
2024
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5. High-throughput identification of regulatory elements and functional assays to uncover susceptibility genes for nasopharyngeal carcinoma

Author

Wang, Tong-Min, Xiao, Ruo-Wen, He, Yong-Qiao, Zhang, Wen-Li, Diao, Hua, Tang, Minzhong, Mai, Zhi-Ming, Xue, Wen-Qiong, Yang, Da-Wei, Deng, Chang-Mi, Liao, Ying, Zhou, Ting, Li, Dan-Hua, Wu, Yan-Xia, Chen, Xue-Yin, Zhang, Jiangbo, Li, Xi-Zhao, Zhang, Pei-Fen, Zheng, Xiao-Hui, Zhang, Shao-Dan, Hu, Ye-Zhu, Cai, Yonglin, Zheng, Yuming, Zhang, Zhe, Zhou, Yifeng, Jin, Guangfu, Bei, Jinxin, Mai, Hai-Qiang, Sun, Ying, Ma, Jun, Hu, Zhibin, Liu, Jianjun, Lung, Maria Li, Adami, Hans-Olov, Ye, Weimin, Lam, Tai-Hing, Shen, Hongbing, and Jia, Wei-Hua

Published
2023
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7. The interaction and mediation effects between the host genetic factors and Epstein–Barr virus VCA‐IgA in the risk of nasopharyngeal carcinoma

Author

Diao, Hua, primary, Xue, Wen‐Qiong, additional, Wang, Tong‐Min, additional, Yang, Da‐Wei, additional, Deng, Chang‐Mi, additional, Li, Dan‐Hua, additional, Zhang, Wen‐Li, additional, Liao, Ying, additional, Wu, Yan‐Xia, additional, Chen, Xue‐Yin, additional, Zhou, Ting, additional, Li, Xi‐Zhao, additional, Zhang, Pei‐Fen, additional, Zheng, Xiao‐Hui, additional, Zhang, Shao‐Dan, additional, Hu, Ye‐Zhu, additional, Cao, Su‐Mei, additional, Liu, Qing, additional, Ye, Wei‐Min, additional, He, Yong‐Qiao, additional, and Jia, Wei‐Hua, additional

Published
2023
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12. Oral Microbiota Alteration and Roles in Epstein-Barr Virus Reactivation in Nasopharyngeal Carcinoma

Author

Liao, Ying, primary, Zhang, Jiang-Bo, additional, Lu, Li-Xia, additional, Jia, Yi-Jing, additional, Zheng, Mei-Qi, additional, Debelius, Justine W., additional, He, Yong-Qiao, additional, Wang, Tong-Min, additional, Deng, Chang-Mi, additional, Tong, Xia-Ting, additional, Xue, Wen-Qiong, additional, Cao, Lian-Jing, additional, Wu, Zi-Yi, additional, Yang, Da-Wei, additional, Zheng, Xiao-Hui, additional, Li, Xi-Zhao, additional, Wu, Yan-Xia, additional, Feng, Lin, additional, Ye, Weimin, additional, Mu, Jianbing, additional, and Jia, Wei-Hua, additional

Published
2023
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13. Rare POLN mutations confer risk for familial nasopharyngeal carcinoma through weakened Epstein-Barr virus lytic replication

Author

Xiao, Ruo-Wen, primary, Wang, Fang, additional, Wang, Tong-Min, additional, Zhang, Jiang-Bo, additional, Wu, Zi-Yi, additional, Deng, Chang-Mi, additional, Liao, Ying, additional, Zhou, Ting, additional, Yang, Da-Wei, additional, Dong, Si-Qi, additional, Xue, Wen-Qiong, additional, He, Yong-Qiao, additional, Zheng, Xiao-Hui, additional, Li, Xi-Zhao, additional, Zhang, Pei-Fen, additional, Zhang, Shao-Dan, additional, Hu, Ye-Zhu, additional, Liu, Yu-Ying, additional, Xia, Yun-Fei, additional, Gao, Song, additional, Mu, Jian-Bing, additional, Feng, Lin, additional, and Jia, Wei-Hua, additional

Published
2022
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14. Whole-Exome Sequencing Study of Familial Nasopharyngeal Carcinoma and Its Implication for Identifying High-Risk Individuals

Author

Wang, Tong-Min, primary, He, Yong-Qiao, additional, Xue, Wen-Qiong, additional, Zhang, Jiang-Bo, additional, Xia, Yun-Fei, additional, Deng, Chang-Mi, additional, Zhang, Wen-Li, additional, Xiao, Ruo-Wen, additional, Liao, Ying, additional, Yang, Da-Wei, additional, Zhou, Ting, additional, Li, Dan-Hua, additional, Luo, Lu-Ting, additional, Tong, Xia-Ting, additional, Wu, Yan-Xia, additional, Chen, Xue-Yin, additional, Li, Xi-Zhao, additional, Zhang, Pei-Fen, additional, Zheng, Xiao-Hui, additional, Zhang, Shao-Dan, additional, Hu, Ye-Zhu, additional, Wang, Fang, additional, Wu, Zi-Yi, additional, Zheng, Mei-Qi, additional, Huang, Jing-Wen, additional, Jia, Yi-Jing, additional, Yuan, Lei-Lei, additional, You, Rui, additional, Zhou, Guan-Qun, additional, Lu, Li-Xia, additional, Liu, Yu-Ying, additional, Chen, Ming-Yuan, additional, Feng, Lin, additional, Dai, Wei, additional, Ren, Ze-Fang, additional, Mai, Hai-Qiang, additional, Sun, Ying, additional, Ma, Jun, additional, Zheng, Wei, additional, Lung, Maria Li, additional, and Jia, Wei-Hua, additional

Published
2022
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15. Development and validation of a polygenic hazard score to predict prognosis and adjuvant chemotherapy benefit in early-stage non-small cell lung cancer

Author

Li, Dan-Hua, primary, He, Yong-Qiao, additional, Wang, Tong-Min, additional, Xue, Wen-Qiong, additional, Deng, Chang-Mi, additional, Yang, Da-Wei, additional, Zhang, Wen-Li, additional, Wu, Zi-Yi, additional, Cao, Lian-Jing, additional, Dong, Si-Qi, additional, Jia, Yi-Jing, additional, Yuan, Lei-Lei, additional, Luo, Lu-Ting, additional, Wu, Yan-Xia, additional, Tong, Xia-Ting, additional, Zhang, Jiang-Bo, additional, Zheng, Mei-Qi, additional, Zhou, Ting, additional, Zheng, Xiao-Hui, additional, Li, Xi-Zhao, additional, Zhang, Pei-Fen, additional, Zhang, Shao-Dan, additional, Hu, Ye-Zhu, additional, Cao, Xun, additional, Wang, Xin, additional, and Jia, Wei-Hua, additional

Published
2022
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16. Peptidome‐wide association analysis of Epstein−Barr virus identifies epitope repertoires associated with nasopharyngeal carcinoma.

Author

Deng, Chang‐Mi, Wang, Tong‐Min, He, Yong‐Qiao, Zhang, Wen‐Li, Xue, Wen‐Qiong, Li, Dan‐Hua, Yang, Da‐Wei, Wang, Qiao‐Ling, Liao, Ying, Diao, Hua, Jiang, Cheng‐Tao, Zhang, Jiang‐Bo, Yuan, Lei‐Lei, Chen, Xue‐Yin, Zhou, Ting, Li, Xi‐Zhao, Zhang, Pei‐Fen, Zheng, Xiao‐Hui, Zhang, Shao‐Dan, and Hu, Ye‐Zhu

Subjects
EPSTEIN-Barr virus, NASOPHARYNX cancer, HLA histocompatibility antigens, T cell receptors, PEPTIDES, LOGISTIC regression analysis
Abstract

Human leukocyte antigen (HLA) molecules are essential for presenting Epstein−Barr virus (EBV) antigens and are closely related to nasopharyngeal carcinoma (NPC). This study aims to systematically investigate the association between HLA‐bound EBV peptides and NPC risk through in silico HLA‐peptide binding prediction. A total of 455 NPC patients and 463 healthy individuals in NPC endemic areas were recruited, and HLA‐target sequencing was performed. HLA‐peptide binding prediction for EBV, followed by peptidome‐wide logistic regression and motif analysis, was applied. Binding affinity changes for EBV peptides carrying high‐risk mutations were analyzed. We found that NPC‐associated EBV peptides were significantly enriched in immunogenic proteins and core linkage disequilibrium (LD) proteins related to evolution, especially those binding HLA‐A alleles (p = 3.10 × 10−4 for immunogenic proteins and p = 8.10 × 10−5 for core LD proteins related to evolution). These peptides were clustered and showed binding motifs of HLA supertypes, among which supertype A02 presented an NPC‐risk effect (padj = 3.77 × 10−4) and supertype A03 presented an NPC‐protective effect (padj = 4.89 × 10−4). Moreover, a decreased binding affinity toward risk HLA supertype A02 was observed for the peptide carrying the NPC‐risk mutation BNRF1 V1222I (p = 0.0078), and an increased binding affinity toward protective HLA supertype A03 was observed for the peptide carrying the NPC‐risk mutation BALF2 I613V (p = 0.022). This study revealed the distinct preference of EBV peptides for binding HLA supertypes, which may contribute to shaping EBV population structure and be involved in NPC development. [ABSTRACT FROM AUTHOR]

Published
2023
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17. Transcriptome‐wide association analysis identified candidate susceptibility genes for nasopharyngeal carcinoma

Author

He, Yong‐Qiao, primary, Xue, Wen‐Qiong, additional, Li, Dan‐Hua, additional, Wang, Tong‐Min, additional, Mai, Zhi‐Ming, additional, Yang, Da‐Wei, additional, Deng, Chang‐Mi, additional, Liao, Ying, additional, Zhang, Wen‐Li, additional, Xiao, Ruo‐Wen, additional, Luo, Luting, additional, Diao, Hua, additional, Tong, Xiating, additional, Wu, Yanxia, additional, Zhang, Jiang‐Bo, additional, Zhou, Ting, additional, Li, Xi‐Zhao, additional, Zhang, Pei‐Fen, additional, Zheng, Xiao‐Hui, additional, Zhang, Shao‐Dan, additional, Hu, Ye‐Zhu, additional, Tang, Minzhong, additional, Zheng, Yuming, additional, Cai, Yonglin, additional, Chang, Ellen T., additional, Zhang, Zhe, additional, Huang, Guangwu, additional, Cao, Su‐Mei, additional, Liu, Qing, additional, Feng, Lin, additional, Sun, Ying, additional, Lung, Maria Li, additional, Adami, Hans‐Olov, additional, Ye, Weimin, additional, Lam, Tai‐Hing, additional, and Jia, Wei‐Hua, additional

Published
2022
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18. Genomic landscape of Epstein–Barr virus in familial nasopharyngeal carcinoma

Author

Zhang, Wen-Li, primary, Zhang, Jiang-Bo, additional, Wang, Tong-Min, additional, Wu, Yan-Xia, additional, He, Yong-Qiao, additional, Xue, Wen-Qiong, additional, Liao, Ying, additional, Deng, Chang-Mi, additional, Li, Dan-Hua, additional, Wu, Zi-Yi, additional, Yang, Da-Wei, additional, Zheng, Xiao-Hui, additional, Li, Xi-Zhao, additional, Zhou, Ting, additional, Zhang, Pei-Fen, additional, Zhang, Shao-Dan, additional, Hu, Ye-Zhu, additional, and Jia, Wei-Hua, additional

Published
2022
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19. Genomic Landscapes of Epstein-Barr Virus in Pulmonary Lymphoepithelioma-like Carcinoma

Author

Wu, Yan-Xia, primary, Zhang, Wen-Li, additional, Wang, Tong-Min, additional, Liao, Ying, additional, Zhang, Yi-Jun, additional, Xiao, Ruo-Wen, additional, Jia, Yi-Jing, additional, Wu, Zi-Yi, additional, Deng, Chang-Mi, additional, Yang, Da-Wei, additional, Xue, Wen-Qiong, additional, He, Yong-Qiao, additional, Zheng, Xiao-Hui, additional, Li, Xi-Zhao, additional, Zhou, Ting, additional, Zhang, Pei-Fen, additional, Zhang, Shao-Dan, additional, Hu, Ye-Zhu, additional, Zhang, Jiang-Bo, additional, and Jia, Wei-Hua, additional

Published
2021
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21. Association between HLA alleles and Epstein–Barr virus Zta‐IgA serological status in healthy males from southern China

Author

Yuan, Lei‐Lei, primary, Deng, Chang‐Mi, additional, Xue, Wen‐Qiong, additional, He, Yong‐Qiao, additional, Wang, Tong‐Min, additional, Zhang, Jiang‐Bo, additional, Yang, Da‐Wei, additional, Zhou, Ting, additional, Wu, Zi‐Yi, additional, Liao, Ying, additional, Zheng, Mei‐Qi, additional, Li, Dan‐Hua, additional, Cao, Lian‐Jing, additional, Jia, Yi‐Jing, additional, Zhang, Wen‐Li, additional, Xiao, Ruo‐Wen, additional, Luo, Lu‐Ting, additional, Tong, Xia‐Ting, additional, Wu, Yan‐Xia, additional, Huang, Jing‐Wen, additional, and Jia, Wei‐Hua, additional

Published
2021
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22. Nasopharyngeal Epstein‐Barr virus DNA loads in high‐risk nasopharyngeal carcinoma families: Familial aggregation and host heritability

Author

Zheng, Mei‐Qi, primary, Wang, Tong‐Min, additional, Liao, Ying, additional, Xue, Wen‐Qiong, additional, He, Yong‐Qiao, additional, Wu, Zi‐Yi, additional, Yang, Da‐Wei, additional, Li, Dan‐Hua, additional, Deng, Chang‐Mi, additional, Jia, Yi‐Jing, additional, Yuan, Lei‐Lei, additional, Zhang, Wen‐Li, additional, Luo, Lu‐Ting, additional, Tong, Xia‐Ting, additional, Wu, Yan‐Xia, additional, Zhou, Ting, additional, Li, Xi‐Zhao, additional, Tang, Ling‐Ling, additional, Zhang, Jiang‐Bo, additional, Xia, Yun‐Fei, additional, Mu, Jianbing, additional, and Jia, Wei‐Hua, additional

Published
2020
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23. Peptidome-wide association analysis of Epstein-Barr virus identifies epitope repertoires associated with nasopharyngeal carcinoma.

Author

Deng CM, Wang TM, He YQ, Zhang WL, Xue WQ, Li DH, Yang DW, Wang QL, Liao Y, Diao H, Jiang CT, Zhang JB, Yuan LL, Chen XY, Zhou T, Li XZ, Zhang PF, Zheng XH, Zhang SD, Hu YZ, Xu M, Zeng MS, Feng L, and Jia WH

Subjects
Humans, Epitopes, Herpesvirus 4, Human genetics, Nasopharyngeal Carcinoma genetics, Histocompatibility Antigens Class II, Epstein-Barr Virus Infections complications, Epstein-Barr Virus Infections genetics, Nasopharyngeal Neoplasms genetics
Abstract

Human leukocyte antigen (HLA) molecules are essential for presenting Epstein-Barr virus (EBV) antigens and are closely related to nasopharyngeal carcinoma (NPC). This study aims to systematically investigate the association between HLA-bound EBV peptides and NPC risk through in silico HLA-peptide binding prediction. A total of 455 NPC patients and 463 healthy individuals in NPC endemic areas were recruited, and HLA-target sequencing was performed. HLA-peptide binding prediction for EBV, followed by peptidome-wide logistic regression and motif analysis, was applied. Binding affinity changes for EBV peptides carrying high-risk mutations were analyzed. We found that NPC-associated EBV peptides were significantly enriched in immunogenic proteins and core linkage disequilibrium (LD) proteins related to evolution, especially those binding HLA-A alleles (p = 3.10 × 10 -4 for immunogenic proteins and p = 8.10 × 10 -5 for core LD proteins related to evolution). These peptides were clustered and showed binding motifs of HLA supertypes, among which supertype A02 presented an NPC-risk effect (p adj  = 3.77 × 10 -4 ) and supertype A03 presented an NPC-protective effect (p adj  = 4.89 × 10 -4 ). Moreover, a decreased binding affinity toward risk HLA supertype A02 was observed for the peptide carrying the NPC-risk mutation BNRF1 V1222I (p = 0.0078), and an increased binding affinity toward protective HLA supertype A03 was observed for the peptide carrying the NPC-risk mutation BALF2 I613V (p = 0.022). This study revealed the distinct preference of EBV peptides for binding HLA supertypes, which may contribute to shaping EBV population structure and be involved in NPC development., (© 2023 The Authors. Journal of Medical Virology published by Wiley Periodicals LLC.)

Published
2023
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24. Whole-Exome Sequencing Study of Familial Nasopharyngeal Carcinoma and Its Implication for Identifying High-Risk Individuals.

Author

Wang TM, He YQ, Xue WQ, Zhang JB, Xia YF, Deng CM, Zhang WL, Xiao RW, Liao Y, Yang DW, Zhou T, Li DH, Luo LT, Tong XT, Wu YX, Chen XY, Li XZ, Zhang PF, Zheng XH, Zhang SD, Hu YZ, Wang F, Wu ZY, Zheng MQ, Huang JW, Jia YJ, Yuan LL, You R, Zhou GQ, Lu LX, Liu YY, Chen MY, Feng L, Dai W, Ren ZF, Mai HQ, Sun Y, Ma J, Zheng W, Lung ML, and Jia WH

Subjects
Male, Humans, Nasopharyngeal Carcinoma genetics, Exome Sequencing, Genetic Predisposition to Disease, Herpesvirus 4, Human genetics, Case-Control Studies, Xeroderma Pigmentosum Group D Protein genetics, Nasopharyngeal Neoplasms epidemiology, Nasopharyngeal Neoplasms genetics, Epstein-Barr Virus Infections
Abstract

Background: Nasopharyngeal carcinoma (NPC) is closely associated with genetic factors and Epstein-Barr virus infection, showing strong familial aggregation. Individuals with a family history suffer elevated NPC risk, requiring effective genetic counseling for risk stratification and individualized prevention., Methods: We performed whole-exome sequencing on 502 familial NPC patients and 404 unaffected relatives and controls. We systematically evaluated the established cancer predisposition genes and investigated novel NPC susceptibility genes, making comparisons with 21 other familial cancers in the UK biobank (N = 5218)., Results: Rare pathogenic mutations in the established cancer predisposition genes were observed in familial NPC patients, including ERCC2 (1.39%), TP63 (1.00%), MUTYH (0.80%), and BRCA1 (0.80%). Additionally, 6 novel susceptibility genes were identified. RAD54L, involved in the DNA repair pathway together with ERCC2, MUTYH, and BRCA1, showed the highest frequency (4.18%) in familial NPC. Enrichment analysis found mutations in TP63 were enriched in familial NPC, and RAD54L and EML2 were enriched in both NPC and other Epstein-Barr virus-associated cancers. Besides rare variants, common variants reported in the studies of sporadic NPC were also associated with familial NPC risk. Individuals in the top quantile of common variant-derived genetic risk score while carrying rare variants exhibited increased NPC risk (odds ratio = 13.47, 95% confidence interval = 6.33 to 28.68, P = 1.48 × 10-11); men in this risk group showed a cumulative lifetime risk of 24.19%, much higher than those in the bottom common variant-derived genetic risk score quantile and without rare variants (2.04%)., Conclusions: This study expands the catalog of NPC susceptibility genes and provides the potential for risk stratification of individuals with an NPC family history., (© The Author(s) 2022. Published by Oxford University Press.)

Published
2022
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25. Genomic Landscapes of Epstein-Barr Virus in Pulmonary Lymphoepithelioma-Like Carcinoma.

Author

Wu YX, Zhang WL, Wang TM, Liao Y, Zhang YJ, Xiao RW, Jia YJ, Wu ZY, Deng CM, Yang DW, Xue WQ, He YQ, Zheng XH, Li XZ, Zhou T, Zhang PF, Zhang SD, Hu YZ, Zhang JB, and Jia WH

Subjects
Asian People, China, DNA Methylation, Epitopes, T-Lymphocyte genetics, Genes, Viral genetics, Genetic Variation, Genome-Wide Association Study, Herpesvirus 4, Human isolation & purification, Humans, Virus Integration, Virus Latency genetics, Carcinoma, Non-Small-Cell Lung virology, Epstein-Barr Virus Infections virology, Genome, Viral genetics, Herpesvirus 4, Human genetics, Lung Neoplasms virology
Abstract

Epstein-Barr virus (EBV) infection is associated with multiple malignancies, including pulmonary lymphoepithelioma-like carcinoma (pLELC), a particular subtype of primary lung cancer. However, the genomic characteristics of EBV related to pLELC remain unclear. Here, we obtained the whole-genome data set of EBV isolated from 78 pLELC patients and 37 healthy controls using EBV-captured sequencing. Compared with the reference genome (NC&#95;007605), a total of 3,995 variations were detected across pLELC-derived EBV sequences, with the mutational hot spots located in latent genes. Combined with 180 published EBV sequences derived from healthy people in Southern China, we performed a genome-wide association study and identified 32 variations significantly related to pLELC ( P <  2.56 × 10 -05 , Bonferroni correction), with the top signal of single nucleotide polymorphism (SNP) coordinate T7327C (OR = 1.22, P =  2.39 × 10 -15 ) locating in the origin of plasmid replication (OriP). The results of population structure analysis of EBV isolates in East Asian showed the EBV strains derived from pLELC were more similar to those from nasopharyngeal carcinoma (NPC) than other EBV-associated diseases. In addition, typical latency type-II infection were recognized for EBV of pLELC at both transcription and methylation levels. Taken together, we defined the global view of EBV genomic profiles in pLELC patients for the first time, providing new insights to deepening our understanding of this rare EBV-associated primary lung carcinoma. IMPORTANCE Pulmonary lymphoepithelioma-like carcinoma (pLELC) is a rare, distinctive subtype of primary lung cancer closely associated with Epstein-Barr virus (EBV) infection. Here, we gave the first overview of pLELC-derived EBV at the level of genome, methylation and transcription. We obtained the EBV sequences data set from 78 primary pLELC patients, and revealed the sequences diversity across EBV genome and detected variability in known immune epitopes. Genome-wide association analysis combining 217 healthy controls identifies significant variations related to the risk of pLELC. Meanwhile, we characterized the integration landscapes of EBV at the genome-wide level. These results provided new insight for understanding EBV's role in pLELC tumorigenesis.

Published
2022
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