title: Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome sequencing.
abstract: The latent expression pattern of Epstein-Barr Virus (EBV) genes in nasopharyngeal carcinoma (NPC) has been extensively investigated, and the expression of several lytic genes in NPC has been reported. However, comprehensive information through EBV transcriptome analysis in NPC is limited. We performed paired-end RNA-seq to systematically and comprehensively characterize the expression of EBV genes in NPC tissue and C666-1 NPC cell line, which consistently carries EBV. In addition to the transcripts restricted to type II latency infection, the type III latency EBNA3s genes and a substantial number of lytic genes, such as BZLF1, BRLF1, and BMRF1, were detected through RNA-seq and were further verified in C666-1 cells and NPC tissue through realtime PCR.We also performed clustering analysis to classify NPC patient groups in terms of EBV gene expression, which presented two subtypes of NPC samples. Results revealed interesting patterns of EBV gene expression in NPC patients. This clustering was correlated with many signaling pathways, such as those related to heterotrimeric G-protein signaling, inflammation mediated by chemokine and cytokine signaling, ribosomes, protein metabolism, influenza infection, and ECM-receptor interaction. Our combined findings suggested that the expression of EBV genes in NPC is restricted not only to type II latency genes but also to type III latency and lytic genes. This study provided further insights into the potential role of EBV in the development of NPC.
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Medical Oncology, Affiliated Tumor Hospital of Guangzhou Medical University, Guangzhou, 510095, China.
authors.forename: Lijuan
authors.initials: L
authors.lastname: Hu
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
authors.forename: Zhirui
authors.initials: Z
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
authors.forename: Yanheng
authors.initials: Y
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
authors.forename: Juqin
authors.initials: J
authors.lastname: Dong
authors.affiliation: Division of Infectious Disease, Brigham and Women's Hospital and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Zhao
authors.affiliation: Beijing Genomics Institute Co., Ltd., Shenzhen, 518083, China.
authors.forename: Yanbing
authors.initials: Y
authors.lastname: Cheng
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
authors.forename: Peiyu
authors.initials: P
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Oncology and Hematology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China.
authors.forename: Lihua
authors.initials: L
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
authors.forename: Tianliang
authors.initials: T
authors.lastname: Xia
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Xiong
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
authors.forename: Hongbo
authors.initials: H
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
authors.forename: Manzhi
authors.initials: M
authors.lastname: Li
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Guo
authors.affiliation: Division of Infectious Disease, Brigham and Women's Hospital and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.
authors.forename: Elliott
authors.initials: E
authors.lastname: Kieff
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.|Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
authors.forename: Yixin
authors.initials: Y
authors.lastname: Zeng
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China. zhongqian@sysucc.org.cn.|Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China. zhongqian@sysucc.org.cn.
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhong
authors.affiliation: State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China. zengmsh@mail.sysu.edu.cn.|Department of Experimental Research, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China. zengmsh@mail.sysu.edu.cn.
authors.forename: Musheng
authors.initials: M
authors.lastname: Zeng
mesh_terms: D045744:Cell Line, Tumor; D020869:Gene Expression Profiling / Q000379:methods*; D004854:Herpesvirus 4, Human / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D017874:Immediate-Early Proteins / Q000378:metabolism; D009303:Nasopharyngeal Neoplasms / Q000378:metabolism / Q000821:virology*; D060888:Real-Time Polymerase Chain Reaction; D015398:Signal Transduction; D015534:Trans-Activators / Q000378:metabolism; D017735:Virus Latency / Q000235:genetics
chemical_list: C068382:BRLF1 protein, Human herpesvirus 4; C063676:BZLF1 protein, Herpesvirus 4, Human; D017874:Immediate-Early Proteins; D015534:Trans-Activators
keywords: Epstein-Barr virus; latency genes; lytic genes; nasopharyngeal carcinoma; paired-end transcriptome sequencing