Ka-Yue Chow L, Lai-Shun Chung D, Tao L, Chan KF, Tung SY, Cheong Ngan RK, Ng WT, Wing-Mui Lee A, Yau CC, Lai-Wan Kwong D, Ho-Fun Lee V, Lam KO, Liu J, Chen H, Dai W, and Lung ML
Background: Epstein-Barr virus (EBV) latent infection is associated with genome-wide epigenomic changes in several malignancies, but its role in epigenetic dysregulation remains unclear in nasopharyngeal carcinoma (NPC)., Methods: To investigate EBV-associated epigenetic dysregulation, we performed a multi-omics study by integrating whole-genome bisulfite sequencing (WGBS), assay for transposase-accessible chromatin using sequencing (ATAC-Seq), whole-exome sequencing (WES), and single-cell RNA sequencing (scRNA-Seq) data., Findings: In addition to the known global DNA hypermethylated subtype, we discovered a novel subtype with global hypomethylation in EBV + NPC. The consistent EBV-specific differentially methylated regions (EBV-DMRs) in the human genome were identified from both subtypes and associated with loss of CTCF binding (P < 2.2e-16). Importantly, CTCF is a master chromatin regulator and CTCF protein was reduced in 45% of NPC cases, especially in those with advanced NPC (Stage IV vs. others: 62% vs. 38%, P = 0.034). This result links EBV with chromatin changes. The ATAC-Seq data suggest regulatory epigenome reprogramming through chromatin accessibility changes in EBV + NPC with altered CTCF binding and the switch of transcription factor binding from differentiation-associated KLF/SP family to the innate and adaptive immunity-related NF-ĸB and IRF families. Detailed chromatin accessibility analysis identified a potential EBV target gene CD74, which mediated EBV-specific cell-cell communications in the tumor microenvironment (TME) and was strongly correlated with T cell exhaustion (r 2 = 0.55)., Interpretation: Our study reveals the unexpected epigenetic heterogeneity, providing insights into NPC pathogenesis and highlighting the involvement of host factors in virus-associated epigenetic changes. EBV infection is associated with epigenome reprogramming and may promote immune evasion., Funding: This study was funded by the Hong Kong Research Grants Council grant (AoE/M-06/08) to MLL, General Research Fund (17103218 and 17102619) and seed funding for basic research (201611159158) to WD, and General Research Fund (17119618) to HC., Competing Interests: Declaration of interests R.K.C.N. is an Advisory Board member or a Data Safety Monitoring Board member of Nuance (ShenZhen, China), received consultation fees from Pfizer, Novartis, Sanofi, AstraZeneca, Eli Lilly, Merck Sharp & Dohme, ZailLab, Roche, Eisai, and Merck, received payment for lectures, presentations, speakers bureaus, manuscript writing, or educational events from Novartis, AstraZeneca, Sanofi, Pfizer, ZaiLab, Eisai, Eli Lilly, and Merck Sharp & Dohme, and received funding for travel or attending meetings from Pfizer, Astellas, Novartis, MSD, Roche, Eisai, Merck, Sanofi, Bristol-Myers Squibb, and ZaiLab. V.H.F.L. is an Advisory Board member or a Data Safety Monitoring Board member of Amgen, AstraZeneca, Merck Sharp & Dohme, Pfizer, and Takeda, received consultation fees from AQUILAB, received payment and honoraria for lectures, presentations, speakers bureaus, manuscript writing or education events from Amgen, AstraZeneca, Boston Scientific, Eli Lilly, Merck Sharpe & Dohme, Novartis, Pfizer, and Takeda, received traveling funding from AstraZeneca and Takeda, received receipt of equipment, materials, drugs, medical writing, gifts, or other services from AstraZeneca, and received grants and contracts from AstraZeneca for his institution. The remaining authors have declared that no conflict of interest exists., (Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.)