DNA methylation signatures distinguish extranodal NK/T-cell lymphoma and EBV-positive nodal T/NK-cell lymphoma and identify prognostic subgroups.

Extranodal NK/T-cell lymphoma (ENKTL) and primary Epstein-Barr virus (EBV)-positive nodal T/NK-cell lymphoma (nodal-TNKL) are aggressive lymphomas with overlapping clinicopathologic features but distinct underlying biology. While their genomic landscapes have been increasingly defined, comparative epigenetic characterization remains limited. We performed methylated DNA immunoprecipitation sequencing (MeDIP-seq) on formalin-fixed paraffin-embedded samples from ENKTL, nodal-TNKL, ENKTL cell lines, and control tissues. ENKTL displayed extensive promoter hypermethylation associated with repression of tumor suppressor genes, lineage regulators, and lymphoid signaling genes, including LEF1 and BANK1, together with focal hypomethylation of immune- and interferon-responsive genes such as IFITM1. In contrast, nodal-TNKL showed global hypomethylation, particularly affecting cytotoxicity, immune-response, and antigen-presentation pathways; TET2-mutated nodal-TNKL cases exhibited locus-specific methylation changes. Across all samples, global DNA methylation levels correlated with genomic instability. Unsupervised clustering identified two epigenetically distinct ENKTL subgroups, one characterized by higher global methylation, TP53 loss, increased copy number alterations and loss of heterozygosity and significantly poorer overall survival. Together, this study defines fundamental epigenetic differences between ENKTL and nodal-TNKL and links DNA methylation dynamics to genomic instability and clinical outcome, highlighting the value of methylation profiling for refined classification, risk stratification and therapeutic guidance.