Module function and two-way clustering analysis of Epstein-Barr virus-related nasopharyngeal cancer

Chen, F.; Liu, Jun; Mao, Fan; Wei, Xianzhao; Xie, Yanshe; Wang, L.H.; Yang, Huili

doi:10.4238/2014.march.17.10

Cited by 1 publication

(1 citation statement)

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“…This might be partially explained by the heterogeneity of the population or NPC subtype. EBV is highly prevalent in all human populations and is associated with both nonmalignant disease and some human cancers (32); however, only NPC has remarkable ethnic and geographic distribution, indicating that the EBV genome might also exhibit heterogeneity with different subtypes resulting in different diseases (62,63). We hypothesized that the subtype of EBV that is prevalent in southern China might have unique genetic variations that play an important role in the development of NPC as opposed to other diseases.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of 18 Epstein-Barr Viruses Isolated from Primary Nasopharyngeal Carcinoma Biopsy Specimens

Zeng

et al. 2017

J Virol

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Epstein-Barr virus (EBV) is a ubiquitous gammaherpesvirus that is highly prevalent in almost all human populations and is associated with many human cancers, such as nasopharyngeal carcinoma (NPC), Hodgkin's disease, and gastric carcinoma. However, in these EBV-associated cancers, only NPC exhibits remarkable ethnic and geographic distribution. We hypothesized that EBV genomic variations might contribute to the pathogenesis of different human cancers in different geographic areas. In this study, we collected 18 NPC biopsy specimens from the Hunan Province in southern China and assembled 18 NPC biopsy specimen-derived EBV (NPC-EBV) genomes, designated HN1 to HN18. This was achieved through target enrichment of EBV DNA by hybridization, followed by next-generation sequencing, to reveal sequence diversity. These EBV genomes harbored 20,570 variations totally, including 20,328 substitutions, 88 insertions, and 154 deletions, compared to the EBV reference genome. Phylogenetic analysis revealed that all NPC-EBV genomes were distinct from other EBV genomes. Furthermore, HN1 to HN18 had some nonsynonymous variations in EBV genes including genes encoding latent, early lytic, and tegument proteins, such as substitutions within transmembrane domains 1 and 3 of LMP1, FoP_duplication, and zf-AD domains of ENBA1, in addition to aberrations in noncoding regions, especially in BamHI A rightward transcript microRNAs. These variations might have potential biological significance. In conclusion, we reported a genome-wide view of sequence variation in EBV isolated from primary NPC biopsy specimens obtained from the Hunan Province. This might contribute to further understanding of how genomic variations contribute to carcinogenesis, which would impact the treatment of EBV-associated cancer. Nasopharyngeal carcinoma (NPC) is highly associated with Epstein-Barr virus (EBV) infection and exhibits remarkable ethnic and geographic distribution. Hunan Province in southern China has a high incidence rate of NPCs. Here, we report 18 novel EBV genome sequences from viruses isolated from primary NPC biopsy specimens in this region, revealing whole-genome sequence diversity.

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Section: Discussionmentioning

confidence: 99%