Epstein-Barr virus drives nasopharyngeal carcinoma metastasis via RNA m5C modification of ICAM-1 mediated by NSUN2 and YBX3

Epstein-Barr virus (EBV) is a critical epigenetic regulator in nasopharyngeal carcinoma (NPC) pathogenesis, primarily through well-established mechanisms involving DNA methylation and histone modifications. However, the contribution of RNA modifications, especially RNA 5-methylcytosine (m⁵C), to EBV-driven NPC progression remains largely unclear. Here, we performed RNA bisulfite sequencing (RNA-Bis-seq) on NPC cells and observed a global elevation in RNA m⁵C levels following EBV infection. Notably, EBV infection upregulated NSUN2, a known RNA m⁵C methyltransferase ("writer"), through LMP1-mediated activation of the NF-κB signaling pathway, leading to RNA m⁵C elevation. Functional assays confirmed that NSUN2 significantly enhances NPC cell migration and metastasis through its RNA m⁵C catalytic activity. Furthermore, we identified YBX3 as a novel RNA m⁵C-binding protein ("reader") that was simultaneously upregulated upon EBV infection. Mechanistically, NSUN2 catalyzed m⁵C modification on ICAM-1. Subsequently, YBX3 specifically recognized the modified site, recruiting PABPC1 through interacting with its cold shock domain and thereby enhancing ICAM-1 translation. Consistently, ICAM-1 overexpression effectively rescued the metastasis defects induced by NSUN2 knockdown. Additionally, we observed significant positive correlations among NSUN2, YBX3, and ICAM-1 expression levels in NPC tissues, with their expression strongly associated with tumor progression and poor prognosis. Together, our findings reveal the crucial role of RNA m⁵C modification in EBV-associated NPC progression, delineate the LMP1/NSUN2/YBX3/ICAM-1 signaling cascade, and suggest this regulatory axis as a potential therapeutic target for NPC.