title: Detection of hypermutated human papillomavirus type 16 genome by Next-Generation Sequencing.
abstract: Human papillomavirus type 16 (HPV16) is a major cause of cervical cancer. We previously demonstrated that C-to-T and G-to-A hypermutations accumulated in the HPV16 genome by APOBEC3 expression in vitro. To investigate in vivo characteristics of hypermutation, differential DNA denaturation-PCR (3D-PCR) was performed using three clinical specimens obtained from HPV16-positive cervical dysplasia, and detected hypermutation from two out of three specimens. One sample accumulating hypermutations in both E2 and the long control region (LCR) was further subjected to Next-Generation Sequencing, revealing that hypermutations spread across the LCR and all early genes. Notably, hypermutation was more frequently observed in the LCR, which contains a viral replication origin and the early promoter. APOBEC3 expressed abundantly in an HPV16-positive cervix, suggesting that single-stranded DNA exposed during viral replication and transcription may be efficient targets for deamination. The results further strengthen a role of APOBEC3 in introducing HPV16 hypermutation in vivo.
authors.affiliation: Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
authors.forename: Kousho
authors.initials: K
authors.lastname: Wakae
authors.affiliation: Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan; Tokyo Medical and Dental University Hospital Faculty of Medicine, Tokyo 113-8510, Japan.
authors.forename: Satoru
authors.initials: S
authors.lastname: Aoyama
authors.affiliation: Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan; Division of Medical Oncology, Affiliated Zhongshan Hospital of Dalian University, 116001, China.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
authors.forename: Kouichi
authors.initials: K
authors.lastname: Kitamura
authors.affiliation: Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
authors.forename: Guangyan
authors.initials: G
authors.lastname: Liu
authors.affiliation: Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
authors.forename: Ahasan Md
authors.initials: AM
authors.lastname: Monjurul
authors.affiliation: Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
authors.forename: Miki
authors.initials: M
authors.lastname: Koura
authors.affiliation: Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
authors.forename: Mieko
authors.initials: M
authors.lastname: Imayasu
authors.affiliation: Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
authors.forename: Naoya
authors.initials: N
authors.lastname: Sakamoto
authors.affiliation: Department of Obstetrics and Gynecology, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
authors.forename: Mitsuhiro
authors.initials: M
authors.lastname: Nakamura
authors.affiliation: Department of Obstetrics and Gynecology, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan; Department of Obstetrics and Gynecology, Shimane University Faculty of Medicine, Izumo, Shimane 693-8501, Japan.
authors.forename: Satoru
authors.initials: S
authors.lastname: Kyo
authors.affiliation: Division of Otorhinolaryngology and Head and Neck Surgery, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
authors.forename: Satoru
authors.initials: S
authors.lastname: Kondo
authors.affiliation: Department of Obstetrics and Gynecology, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Fujiwara
authors.affiliation: Division of Otorhinolaryngology and Head and Neck Surgery, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan.
authors.forename: Tomokazu
authors.initials: T
authors.lastname: Yoshizaki
authors.affiliation: Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-murayama, Tokyo 208-0011, Japan.
authors.forename: Iwao
authors.initials: I
authors.lastname: Kukimoto
authors.affiliation: Functional Genomic Facility, National Institute of Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.
authors.forename: Katsushi
authors.initials: K
authors.lastname: Yamaguchi
authors.affiliation: Functional Genomic Facility, National Institute of Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.
authors.forename: Shuji
authors.initials: S
authors.lastname: Shigenobu
authors.affiliation: Advanced Science Research Center, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan. Electronic address: tomoakin@staff.kanazawa-u.ac.jp.
authors.forename: Tomoaki
authors.initials: T
authors.lastname: Nishiyama
authors.affiliation: Department of Molecular Genetics, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 920-8640, Japan. Electronic address: muramatu@med.kanazawa-u.ac.jp.
authors.forename: Masamichi
authors.initials: M
authors.lastname: Muramatsu
mesh_terms: D000071478:APOBEC Deaminases; D016022:Case-Control Studies; D003564:Cytidine Deaminase; D043525:Cytosine Deaminase / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D005260:Female; D015870:Gene Expression; D005814:Genes, Viral; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D052162:Human papillomavirus 16 / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D009154:Mutation; D009856:Oncogene Proteins, Viral / Q000235:genetics; D030361:Papillomavirus Infections / Q000235:genetics / Q000821:virology; D002578:Uterine Cervical Dysplasia / Q000175:diagnosis / Q000235:genetics / Q000821:virology
chemical_list: D004279:DNA, Viral; D004268:DNA-Binding Proteins; C054855:E2 protein, Human papillomavirus type 16; D009856:Oncogene Proteins, Viral; D043525:Cytosine Deaminase; D000071478:APOBEC Deaminases; C502889:APOBEC3 proteins, human; D003564:Cytidine Deaminase
keywords: APOBEC3; Cervical cancer; HPV16; Hypermutation; Next-Generation Sequencing