Enhancer infestation drives tumorigenic activation of inactive B compartment in Epstein-Barr virus-positive nasopharyngeal carcinomaResearch in context
Harue Mizokami,
Atsushi Okabe,
Ruchi Choudhary,
Masato Mima,
Kenta Saeda,
Masaki Fukuyo,
Bahityar Rahmutulla,
Motoaki Seki,
Boon-Cher Goh,
Satoru Kondo,
Hirotomo Dochi,
Makiko Moriyama-Kita,
Kiyoshi Misawa,
Toyoyuki Hanazawa,
Patrick Tan,
Tomokazu Yoshizaki,
Melissa Jane Fullwood,
Atsushi Kaneda
Affiliations
Harue Mizokami
Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan; Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
Atsushi Okabe
Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan; Health and Disease Omics Center, Chiba University, Chiba, 260-8670, Japan
Ruchi Choudhary
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
Masato Mima
Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan; Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Hamamatsu University School of Medicine, Shizuoka, 431-3125, Japan
Kenta Saeda
Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan; Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
Masaki Fukuyo
Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
Bahityar Rahmutulla
Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
Motoaki Seki
Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
Boon-Cher Goh
Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore; Department of Haematology-Oncology, National University Cancer Institute, Singapore, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Blk MD3, 16 Medical Drive, Singapore, 117600, Singapore
Satoru Kondo
Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
Hirotomo Dochi
Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
Makiko Moriyama-Kita
Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
Kiyoshi Misawa
Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Hamamatsu University School of Medicine, Shizuoka, 431-3125, Japan
Toyoyuki Hanazawa
Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
Patrick Tan
Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
Tomokazu Yoshizaki
Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
Melissa Jane Fullwood
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore; Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, 117599, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore; Corresponding author. School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
Atsushi Kaneda
Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan; Health and Disease Omics Center, Chiba University, Chiba, 260-8670, Japan; Corresponding author. Department of Molecular Oncology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
Summary: Background: Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV)-associated malignant epithelial tumor endemic to Southern China and Southeast Asia. While previous studies have revealed a low frequency of gene mutations in NPC, its epigenomic aberrations are not fully elucidated apart from DNA hypermethylation. Epigenomic rewiring and enhancer dysregulation, such as enhancer hijacking due to genomic structural changes or extrachromosomal DNA, drive cancer progression. Methods: We conducted Hi-C, 4C-seq, ChIP-seq, and RNA-seq analyses to comprehensively elucidate the epigenome and interactome of NPC using C666-1 EBV(+)-NPC cell lines, NP69T immortalized nasopharyngeal epithelial cells, clinical NPC biopsy samples, and in vitro EBV infection in HK1 and NPC-TW01 EBV(−) cell lines. Findings: In C666-1, the EBV genome significantly interacted with inactive B compartments of host cells; the significant association of EBV-interacting regions (EBVIRs) with B compartment was confirmed using clinical NPC and in vitro EBV infection model. EBVIRs in C666-1 showed significantly higher levels of active histone modifications compared with NP69T. Aberrant activation of EBVIRs after EBV infection was validated using in vitro EBV infection models. Within the EBVIR-overlapping topologically associating domains, 14 H3K4me3(+) genes were significantly upregulated in C666-1. Target genes of EBVIRs including PLA2G4A, PTGS2 and CITED2, interacted with the enhancers activated in EBVIRs and were highly expressed in NPC, and their knockdown significantly reduced cell proliferation. Interpretation: The EBV genome contributes to NPC tumorigenesis through “enhancer infestation” by interacting with the inactive B compartments of the host genome and aberrantly activating enhancers. Funding: The funds are listed in the Acknowledgements section.
