Immune dysregulation and prognostic signatures associated with Epstein–Barr virus in acute lymphoblastic leukemia: an integrated transcriptomic and single-cell analysis

Background Epstein–Barr virus (EBV) is associated with lymphoid malignancies; however, its contribution to acute lymphoblastic leukemia (ALL) is unclear. Therefore, we investigated the associations between EBV-related transcriptional activity and immune remodeling in ALL across publicly available cohorts. Methods This study integrated transcriptomics, weighted gene co-expression network analysis, protein–protein interaction network analyses, and single-cell RNA sequencing (scRNA-seq). Results We identified 401 EBV-related differentially expressed genes and constructed a prognostic model comprising the following nine critical immune-related genes: interleukin (IL)-18, Toll-like receptor 1, perforin 1 [ PRF1 ], IL-6 receptor, C-C motif chemokine ligand 2 [ CCL2 ], TTK protein kinase [ TTK ], CD19 molecule [ CD19 ], cathepsin S, and C-C motif chemokine ligand 4 [ CCL4 ]. Our model robustly stratified patients into high- and low-risk groups. The high-risk group exhibited significantly poorer survival than did the low-risk group ( P  = 0.015). External validation confirmed the predictive accuracy of the model (area under the curve values: 0.82, 0.68, and 0.68 for 1-, 3-, and 5-year survival, respectively). scRNA-seq further revealed distinct expression patterns of the nine prognostic genes across immune cell subsets: TTK was enriched in B and T cells; PRF1 was predominantly expressed in T and natural killer cells; and CCL2, CCL4 , and CD19 were highly expressed in monocytes and B cells. Conclusions Associations between these genes, immune composition/proliferation signals, and survival in ALL were highlighted. These findings are hypothesis-generating and may reflect EBV-related transcriptional activity as well as lineage and immune-infiltration states; causal roles require validation in clinically EBV-characterized cohorts.