Epstein-Barr virus strain variation and cancer

Abstract

Epstein-Barr virus (EBV) is a human tumor virus and is etiologically linked to various malignancies. Certain EBV-associated diseases, such as Burkitt lymphomas and nasopharyngeal carcinomas, are endemic and exhibit biased geographic distribution worldwide. Recent advances in deep sequencing technology enabled high-throughput sequencing of the EBV genome from clinical samples. Rapid cloning and sequencing of cancer-derived EBV genomes, followed by reconstitution of infectious virus, have also become possible. These developments have revealed that various EBV strains are differentially distributed throughout the world, and that the behavior of cancer-derived EBV strains is different from that of the prototype EBV strain of non-cancerous origin. In this review, we summarize recent progress and future perspectives regarding the association between EBV strain variation and cancer.

Keywords: Epstein-Barr virus; geographic distribution; nasopharyngeal carcinoma; sequencing; strain variation.

Figure 1

Epstein‐Barr virus (EBV) association frequencies of nasopharyngeal carcinomas (NPC) and Burkitt lymphomas are presented for different geographic areas. The sizes of the circles roughly represent the disease incidence relative to that in other geographic regions. Adapted from Chang et al3 and Cohen et al.13 Blue means EBV‐positive. Burkitt lym, Burkitt lymphoma

Figure 2

Schematic illustration of the Epstein‐Barr virus (EBV) genome and viral gene products. A linear EBV genome, viral genes, non‐coding RNA (EBV‐encoded RNA [EBER] and BART), and viral microRNA genes (miR‐BHRF1 and miR‐BART) are illustrated. The BamHI restriction map is based on the sequence of the SNU‐719 strain of EBV.46 The scale of DNA sizes is at the top. EBV latent gene products and lytic gene products (selected, green) are illustrated below. Repetitive sequences are shaded in purple. Viral gene promoters are indicated with arrows. Details of mRNA splicing are not faithfully represented. EBNA, EBV nuclear antigen; FR, family of repeats; IR, internal repeats; LMP, latent membrane protein; TR, terminal repeats

Figure 3

Experimental strategies to sequence whole Epstein‐Barr virus (EBV) genomes. (Left) For the hybrid capture‐mediated sequencing, the prepared DNA, consisting of host cell DNA (black) and viral DNA (red), were fragmented and hybridized with biotin (green)‐labeled RNA probes spanning the EBV genome. Captured EBV DNA were then subjected to deep sequencing using a short‐read sequencer. (Right) For EBV‐bacterial artificial chromosome (BAC) cloning, a linear targeting vector was transfected into EBV latently infected cells to obtain homologous recombinants. Alternatively, a circular donor plasmid and a CRISPR/Cas9 plasmid were co‐transfected into the cells to increase the homologous recombination efficiency.46, 47 Episomal DNA were prepared and used to transform bacterial cells and obtain EBV‐BAC clones

Figure 4

Epstein‐Barr virus (EBV) sequencing milestones and the recent explosive increase in EBV whole genome sequences. Green dots indicate EBV strains whose sequences were completely determined, whereas gray circles indicate those in which genome sequences were determined except for the repetitive regions. Red squares indicate EBV strains that were cloned as bacterial artificial chromosome (BAC) clones and completely sequenced. GC, gastric cancer. References (Ref.) are indicated. NPC, nasopharyngeal carcinomas

Figure 5

Summary of Epstein‐Barr virus (EBV) gene heterogeneity possibly affecting EBV‐mediated carcinogenesis. References (Ref.) are indicated. EBER, EBV‐encoded RNA; EBNA, EBV nuclear antigen; FR, family of repeats; IR, internal repeats; LMP1, latent membrane protein 1; SNP, single nucleotide polymorphism; TR, terminal repeats