Genetic factors affecting EBV copy number in lymphoblastoid cell lines derived from the 1000 Genome Project samples

Abstract

Epstein-Barr virus (EBV), human herpes virus 4, has been classically associated with infectious mononucleosis, multiple sclerosis and several types of cancers. Many of these diseases show marked geographical differences in prevalence, which points to underlying genetic and/or environmental factors. Those factors may include a different susceptibility to EBV infection and viral copy number among human populations. Since EBV is commonly used to transform B-cells into lymphoblastoid cell lines (LCLs) we hypothesize that differences in EBV copy number among individual LCLs may reflect differential susceptibility to EBV infection. To test this hypothesis, we retrieved whole-genome sequenced EBV-mapping reads from 1,753 LCL samples derived from 19 populations worldwide that were sequenced within the context of the 1000 Genomes Project. An in silico methodology was developed to estimate the number of EBV copy number in LCLs and validated these estimations by real-time PCR. After experimentally confirming that EBV relative copy number remains stable over cell passages, we performed a genome wide association analysis (GWAS) to try detecting genetic variants of the host that may be associated with EBV copy number. Our GWAS has yielded several genomic regions suggestively associated with the number of EBV genomes per cell in LCLs, unraveling promising candidate genes such as CAND1, a known inhibitor of EBV replication. While this GWAS does not unequivocally establish the degree to which genetic makeup of individuals determine viral levels within their derived LCLs, for which a larger sample size will be needed, it potentially highlighted human genes affecting EBV-related processes, which constitute interesting candidates to follow up in the context of EBV related pathologies.

A reliable Epstein-Barr Virus classification based on phylogenomic and population analyses

“…22 had to blanked out more than 20 repeat regions from 71 virus genomes to increase the assembly accuracy of repetitive region and thus facilitate comparisons between the strains. Previous studies have shown that cell passages have scarce influence to change the EBV copy number within EBV-transformed lymphoblastoid cell lines 67 ; however, this viral culture could induce small artificial nucleotide changes in the EBV genome 13 .…”

The Microenvironment in Epstein–Barr Virus-Associated Malignancies

“…In two large studies, suggestive associations with SNPs and specific genomic regions were observed for EBV copy numbers in cohorts of more than 900 and 1700 lymphoblastoid cell lines (LCLs). These LCLs were derived from individuals with different ethnicities, and clear differences were observed for EBV copy numbers and ethnicity [ 178 ].…”

An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease

“…The correlation is weaker for intracellular survival and replication phenotypes (correlation to S. Typhimurium replication, R=0.36 for S. Typhi and R=0.34 for S. Typhimurium ∆ sifA ), reflecting the different replications niches for ∆ sifA (host cell cytoplasm) and wild-type Typhimurium (membrane bound vacuole) (Beuzon et al, 2000) or the use of a different repertoire of effectors by S. Typhi (Parkhill et al, 2001). In contrast, we observed almost no correlation between EBV copy number (from (Mandage et al, 2017) for 284 LCLs also used in H2P2) and H2P2 traits (Figure S3; Table S2), indicating these phenotypes are not being driven by the LCL immortalization method. Thus, clustering based on phenotypic diversity verified reliability of measurements and confirmed biological relatedness established by much previous work.…”