To validate the SCENIC results, we isolated CD8+ T cells and NK cells from the NPC tissue samples by flow cytometry (FACS), and identified a significantly higher percentage of cytotoxic GZMB+ or perforin+ phenotypes in the EOMES+, RUNX3+, and XBP1+ CD8+ T cells and NK cells (Supplementary information, Fig. S10a, b). Here, RUNX3 is linked to nasopharyngeal carcinoma.