Fig. 6

Epigenomic profiling of EBV and host cells in EBVaGCs and their precursor lesions. a Bar plots showing the mean coverage of human (hollow bar) and EBV genomes (solid bar) in each sample. Histological types of samples are shown in different colors. b Dot plots of EBV genome copies in 5 normal tissues and LDs used for whole-genome bisulfite sequencing (WGBS). The LD sample in patient P13 (P13-LD) is not shown due to the lack of DNA for measurement of EBV genome copies by qPCR (see the “Methods” section). c Three-dimensional diagram showing the heterogeneity index, Euclidean distance of CCF, and Euclidean distance of methylation level (β value) between pairwise samples in each patient. All pairwise samples are divided into 4 groups. d Heatmap of 6316 differentially methylated regions (DMRs) between EBVaGCs and precursor lesions. e Bar plots of the fractions of DMRs overlapping with different genomic elements. f Diagram exhibiting the methylation level of DMRs encompassed by the region of transcript start site (TSS) ± 2000 bp in LDs and normal tissues (left) and EBVaGCs (right). g Enrichment of biological processes (Gene Ontology) for genes with hypermethylated promoters. Genes of interests were selected and indicated. h The promoter region of CDKN2A showing hypermethylation in EBVaGCs in comparison with that in normal tissues and LDs. Black dots represent each CpG site. Different colors of the areas indicate the histological types of samples (pink, normal tissues; green, LDs; blue, EBVaGCs). The transcription strand is indicated by the arrow orientation (left, reverse strand; right, forward strand). The statistical significance is shown (Student’s t test). i Genes encoding Ras GTPase-activating proteins (RasGAP) showing hypermethylated promotors in EBVaGCs in comparison with that in normal tissues and LDs. j Bar plots comparing the mRNA expression levels of RASA4, RASSF1A, and RASAL3 in AGS cell line with or without EBV infection. Student’s t test, **P < 0.01, ***P < 0.001. Data are shown as mean ± SD. k Western blotting of p-cRaf, p-MEK, and p-ERK1/2 in AGS cell line with or without EBV infection