MTHFD1L-associated branched-chain amino acid degradation transcriptional signature represents a conserved metabolic program in Epstein-Barr virus-associated malignancies.

Epstein-Barr virus (EBV)-associated malignancies encompass multiple tumor types with distinct tissue origins, yet the extent to which they share conserved metabolic programs remains poorly understood. Here, we performed an integrated cross-cancer transcriptomic analysis of nasopharyngeal carcinoma, EBV-associated gastric cancer, and EBV-associated plasmablastic lymphoma to identify conserved metabolic programs, followed by independent cohort validation and single-cell transcriptomic characterization. We identified 103 consensus differentially expressed genes and 72 conserved gene-metabolic pathway pairs across the three discovery cohorts. Among them, only the MTHFD1L-associated Valine, leucine and isoleucine degradation program was consistently preserved in both the discovery and validation cohorts. Single-cell analysis further demonstrated that this conserved metabolic program was predominantly enriched in CD4+ T cells, γδ T cells, and NK cells, and was accompanied by cell state-dependent metabolic remodeling, altered cell-cell communication, and distinct MTHFD1L-centered regulatory networks across immune cell populations. Collectively, our study identifies an MTHFD1L-associated branched-chain amino acid degradation transcriptional co-expression signature as a conserved metabolic program shared across EBV-associated malignancies and reveals its immune cell-specific and dynamic characteristics. These findings provide new insight into the metabolic adaptation of EBV-associated malignancies and offer a conceptual framework for the development of metabolism-targeted therapeutic strategies for virus-associated cancers.