Epstein-Barr virus induced epigenetic reprogramming drives cancer stem cell emergence in breast cancer

Summary Basal breast cancers display stem cell associated basal programs, but originate from luminal progenitors. This lineage paradox may be created by Epstein–Barr virus (EBV) infection. Across more than 2,000 breast cancer genomes, coordinated methyla-tion changes appeared in cis-regulatory elements governing stem cell differentiation. Methylation positions followed EBV-associated malignancies with striking accuracy independent of whether ER-status marked a luminal or basal cancer. EBV-driven epigenetic reprogramming was incompatible with tumor infiltrating lymphocytes and disrupted lineage specification before tumorigenesis. Breast cancers commonly showed coordinated viral response indicators that tracked with antigen presentation and stem cell differentiation programs. Non-malignant keratinocytes with resolved EBV infections retained some aberrantly methylated loci. Analyses of non-EBV skin carcinoma, randomized genomic sites, endogenous retroelements, DUX4, and repli-cation clocks confirmed the specificity of EBV-linked alterations. These findings posi-tion EBV as a developmental lineage hijacker that reprograms cells into premalignant stem-like states. Abstract Figure EBV infection reprograms the methylome of breast luminal progenitors to generate or select for cancer stem-like cells. In Brief Epstein-Barr virus (EBV) rewires developmental programs that specify cell identity, creating cancer stem-like cells with malignant potential. This targeted reshaping of progenitors links viral infection to the earliest steps of breast cancer development. Highlights Epstein-Barr virus (EBV) infection reprograms the methylome of lu-minal progenitors generating breast cancer stem-like cells. EBV-driven methylation sites overlap luminal and basal breast cancer signatures that regulate stem cell differentiation. Characteristic responses to viral infection are common in breast can-cer and they correlate with gene programs needed to differentiate progenitor cells. Even after viral clearance, EBV leaves persistent methylation scars in non-malignant cells that may increase risks for future malignancy.