EBV genome analysis of NPC268 reveals resemblance with those commonly found in NPC from endemic regions. A, PCA of the 213 EBV genomes was performed. PC2 was plotted against PC1, each dot represents a previously published EBV genome [142 healthy control saliva (orange) and 62 NPC patient biopsies (green) from Hui et al. 2019; other published EBV genomes (blue) including those from NPC cell lines, saliva or biopsies (C666-1, NPC43, GD1, GD2, M81) and commonly reported non-NPC EBV strains such as Akata and B95.8/Raji. EBV from NPC268 tumor or cell line were indicated in red. B, Maximum-likelihood phylogenetic tree of 213 whole EBV genomes was performed. Type I and type II EBV are separated by the gray dotted line. Color panel at the bottom indicated the source of the EBV genomes.
ARTICLE ABSTRACT
Nasopharyngeal carcinoma (NPC), a cancer that is etiologically associated with the Epstein-Barr virus (EBV), is endemic in Southern China and Southeast Asia. The scarcity of representative NPC cell lines owing to the frequent loss of EBV episomes following prolonged propagation and compromised authenticity of previous models underscores the critical need for new EBV-positive NPC models. Herein, we describe the establishment of a new EBV-positive NPC cell line, designated NPC268 from a primary non-keratinizing, differentiated NPC tissue. NPC268 can undergo productive lytic reactivation of EBV and is highly tumorigenic in immunodeficient mice. Whole-genome sequencing revealed close similarities with the tissue of origin, including large chromosomal rearrangements, while whole-genome bisulfite sequencing and RNA sequencing demonstrated a hypomethylated genome and enrichment in immune-related pathways, respectively. Drug screening of NPC268 together with six other NPC cell lines using 339 compounds, representing the largest high-throughput drug testing in NPC, revealed biomarkers associated with specific drug classes. NPC268 represents the first and only available EBV-positive non-keratinizing differentiated NPC model, and extensive genomic, methylomic, transcriptomic, and drug response data should facilitate research in EBV and NPC, where current models are limited.
NPC268 is the first and only EBV-positive cell line derived from a primary non-keratinizing, differentiated nasopharyngeal carcinoma, an understudied but important subtype in Southeast Asian countries. This model adds to the limited number of authentic EBV-positive lines globally that will facilitate mechanistic studies and drug development for NPC.
