High Prevalence of the EBER Variant EB-8m in Endemic Nasopharyngeal Carcinomas

Abstract

Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) are the most highly expressed transcripts in all EBV-associated tumors and are involved in both lymphoid and epithelioid carcinogenesis. Our previous study on Chinese isolates from non-endemic area of nasopharyngeal carcinoma (NPC) identified new EBER variants (EB-8m and EB-10m) which were less common but relatively more frequent in NPC cases than healthy donors. In the present study, we determined the EBER variants in NPC cases and healthy donors from endemic and non-endemic areas of NPC within China and compared the EBER variants, in relation to the genotypes at BamHI F region (prototype F and f variant), between population groups and between two areas. According to the phylogenetic tree, four EBER variants (EB-6m, EB-8m, EB-10m and B95-8) were identified. EB-6m was dominant in all population groups except for endemic NPC group, in which EB-8m was dominant. EB-8m was more common in endemic NPC cases (82.0%, 41/50) than non-endemic NPC cases (33.7%, 32/95) (p<0.0001), and it was also more frequent in healthy donors from endemic area (32.4%, 24/74) than healthy donors from non-endemic area (1.1%, 1/92) (p<0.0001). More importantly, the EB-8m was more prevalent in NPC cases than healthy donors in both areas (p<0.0001). The f variant, which has been suggested to associate with endemic NPC, demonstrated preferential linkage with EB-8m in endemic isolates, however, the EB-8m variant seemed to be more specific to NPC isolates than f variant. These results reveal high prevalence of EBER EB-8m variant in endemic NPC cases, suggesting an association between NPC development and EBV isolates carrying EB-8m variant. Our finding identified a small healthy population group that shares the same viral strain which predominates in NPC cases. It could be interesting to carry extensive cohort studies following these individuals to evaluate the risk to develop NPC.

High risk Epstein‐Barr virus variants characterized by distinct polymorphisms in the EBER locus are strongly associated with nasopharyngeal carcinoma

“…Whilst polymorphisms in EBER, EBNA1 (V‐Val), BZLF1 promoter (Zp‐V3), RPMS1 and LMP1 had been proposed to be associated with NPC and other EBV‐associated malignancies, these studies were based on data derived from pre‐selected candidate genes and are prone to detect spurious association due to failure to adjust for the effects of population stratification . To illustrate this point, we analysed the association of these polymorphisms with NPC by chi‐square test in our case–control dataset without considering the population structure.…”

“…The results of our GWAS suggested that the variations in the EBER region, designated as HKNPC‐EBERvar, are the most robust ones in the context of the genetic background of EBV variants harbored in Hong Kong Chinese. Apparent association between some of these variations in the EBER region and NPC by a candidate gene approach in individuals of South China has been reported . Functionally, several studies have indicated the link between EBERs and NPC by their abilities to promote cell growth and survival and modulate the expression of LMP1 and LMP2 genes .…”

“…Previous case–control studies based on the analyses of candidate EBV genes have reported association between various genetic polymorphisms and NPC . However, these studies are prone to detect spurious association due to the failure to adjust for the confounding effects of population stratification .…”

“…Previous case-control studies based on the analyses of candidate EBV genes have reported association between various genetic polymorphisms and NPC. 11,39,41,42 However, these studies are prone to detect spurious association due to the failure to adjust for the confounding effects of population stratification. 38 To minimize the confounding effects, it is essential to analyse individual SNP of EBV genome in the context of genome-wide sequence data in order to accurately identify significant variations associated with NPC.…”

Geographic Population Structure in Epstein-Barr Virus Revealed by Comparative Genomics

“…Indeed, an apparent association an LMP1 variant carrying a 30 bp deletion with Asian NPC was later shown to likely be a consequence of geographic biases in allele frequencies (Zhang et al 2002). One of the most compelling associations of an EBV genotype with a particular human disease is the finding that particular variants in the non-coding EBER RNAs are consistently present in NPC isolates from both high and intermediate incidence areas in China, but at lower proportions in the background population in intermediate incidence areas (Shen et al 2015). However, the lack of complete genome data for these isolates does not exclude the potential presence of additional tightly linked variants that may show higher association with the disease.…”