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Wang M, Liang H, Yan Y, Bian R, Huang W, Zhang X, Nie J. Distribution of HPV types among women with HPV-related diseases and exploration of lineages and variants of HPV 52 and 58 among HPV-infected patients in China: A systematic literature review. Hum Vaccin Immunother 2024; 20:2343192. [PMID: 38745409 DOI: 10.1080/21645515.2024.2343192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/11/2024] [Indexed: 05/16/2024] Open
Abstract
To summarize the distribution of types of human papillomavirus (HPV) associated with HPV-related diseases and investigate the potential causes of high prevalence of HPV 52 and 58 by summarizing the prevalence of lineages, sub-lineages, and mutations among Chinese women. We searched PubMed, EMBASE, CNKI, and WanFang from January, 2012 to June, 2023 to identify all the eligible studies. We excluded patients who had received HPV vaccinations. Data were summarized in tables and cloud/rain maps. A total of 102 studies reporting HPV distribution and 15 studies reporting HPV52/HPV58 variants were extracted. Among Chinese women, the top five prevalent HPV types associated with cervical cancer (CC) were HPV16, 18, 58, 52, and 33. In patients with vaginal cancers and precancerous lesions, the most common HPV types were 16 and 52 followed by 58. For women with condyloma acuminatum (CA), the most common HPV types were 11 and 6. In Chinese women with HPV infection, lineage B was the most prominently identified for HPV52, and lineage A was the most common for HPV58. In addition to HPV types 16, which is prevalent worldwide, our findings revealed the unique high prevalence of HPV 52/58 among Chinese women with HPV-related diseases. HPV 52 variants were predominantly biased toward lineage B and sub-lineage B2, and HPV 58 variants were strongly biased toward lineage A and sub-lineage A1. Further investigations on the association between the high prevalent lineage and sub-lineage in HPV 52/58 and the risk of cancer risk are needed. Our findings underscore the importance of vaccination with the nine-valent HPV vaccine in China.
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Affiliation(s)
- Meng Wang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, WHO Collaborating Center for Standardization and Evaluation of Biologicals, State Key Laboratory of Drug Regulatory Science, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Haoyu Liang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, WHO Collaborating Center for Standardization and Evaluation of Biologicals, State Key Laboratory of Drug Regulatory Science, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Yue Yan
- Merck Research Laboratories (MRL) Global Medical Affairs, MSD China, Shanghai, China
| | - Rui Bian
- Merck Research Laboratories (MRL) Global Medical Affairs, MSD China, Shanghai, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, WHO Collaborating Center for Standardization and Evaluation of Biologicals, State Key Laboratory of Drug Regulatory Science, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Xingxing Zhang
- Merck Research Laboratories (MRL) Global Medical Affairs, MSD China, Shanghai, China
| | - Jianhui Nie
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, WHO Collaborating Center for Standardization and Evaluation of Biologicals, State Key Laboratory of Drug Regulatory Science, NHC Key Laboratory of Research on Quality and Standardization of Biotech Products and NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China
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Kogure G, Tanaka K, Matsui T, Onuki M, Matsumoto K, Iwata T, Kukimoto I. Intra-Patient Genomic Variations of Human Papillomavirus Type 31 in Cervical Cancer and Precancer. Viruses 2023; 15:2104. [PMID: 37896881 PMCID: PMC10612030 DOI: 10.3390/v15102104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023] Open
Abstract
Human papillomavirus type 31 (HPV31) is detected less frequently in cervical cancer than two major causative types, HPV16 and HPV18. Here, we report a comprehensive analysis of HPV31 genome sequences in cervical lesions collected from Japanese women. Of 52 HPV31-positive cervical specimens analyzed by deep sequencing, 43 samples yielded complete genome sequences of around 7900 base pairs and 9 samples yielded partially deleted genome sequences. Phylogenetic analysis showed that HPV31 variant distribution was lineage A in 19 samples (36.5%), lineage B in 28 samples (53.8%), and lineage C in 5 samples (9.6%), indicating that lineage B variants are dominant among HPV31 infections in Japan. Deletions in the viral genome were found in the region from the E1 to L1 genes, but all the deleted genomes retained the E6/E7 genes. Among intra-patient nucleotide variations relative to a consensus genome sequence in each sample, C-to-T substitutions were most frequently detected, followed by T-to-C and C-to-A substitutions. High-frequency, intra-patient mutations (>10%) in cervical cancer samples were found in the E1, E2, and E7 genes, and all of them were nonsynonymous substitutions. The enrichment of high-frequency nonsynonymous substitutions strongly suggests that these intra-patient mutations are positively selected during the development of cervical cancer/precancer.
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Affiliation(s)
- Gota Kogure
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo 142-8666, Japan; (G.K.); (M.O.); (K.M.)
| | - Kohsei Tanaka
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-0016, Japan; (K.T.); (T.M.); (T.I.)
| | - Tomoya Matsui
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-0016, Japan; (K.T.); (T.M.); (T.I.)
| | - Mamiko Onuki
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo 142-8666, Japan; (G.K.); (M.O.); (K.M.)
| | - Koji Matsumoto
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo 142-8666, Japan; (G.K.); (M.O.); (K.M.)
| | - Takashi Iwata
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-0016, Japan; (K.T.); (T.M.); (T.I.)
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
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Chagas BS, Tibúrcio Júnior E, Silva RCDO, dos Santos DL, Barros Junior MR, de Lima RDCP, Invenção MDCV, Santos VEP, França Neto PL, Silva Júnior AH, Silva Neto JC, Batista MVDA, de Freitas AC. E7 Oncogene HPV58 Variants Detected in Northeast Brazil: Genetic and Functional Analysis. Microorganisms 2023; 11:1915. [PMID: 37630475 PMCID: PMC10458125 DOI: 10.3390/microorganisms11081915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Cervical cancer is associated with persistent infections by high-risk Human Papillomavirus (HPV) types that may have nucleotide polymorphisms and, consequently, different oncogenic potentials. Therefore, this study aimed to evaluate the genetic variability and structural effects of the E7 oncogene of HPV58 in cervical scraping samples from Brazilian women. The study was developed with patients from hospitals in the metropolitan area of Recife, PE, Brazil. The most frequent HPV types were, in descending order of abundance, HPV16, 31, and 58. Phylogenetic analysis demonstrated that the isolates were classified into sublineages A2, C1, and D2. Two positively selected mutations were found in E7: 63G and 64T. The mutations G41R, G63D, and T64A in the E7 protein reduced the stability of the protein structure. Utilizing an NF-kB reporter assay, we observed a decrease in the NK-kB pathway activity with the HPV58-E7 variant 54S compared to the WT E7. The other detected E7 HPV58 variants presented similar NF-kB pathway activity compared to the WT E7. In this study, it was possible to identify mutations that may interfere with the molecular interaction between the viral oncoproteins and host proteins.
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Affiliation(s)
- Bárbara Simas Chagas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Elias Tibúrcio Júnior
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Ruany Cristyne de Oliveira Silva
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Daffany Luana dos Santos
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Marconi Rego Barros Junior
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Rita de Cássia Pereira de Lima
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Maria da Conceição Viana Invenção
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Vanessa Emanuelle Pereira Santos
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Pedro Luiz França Neto
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Antônio Humberto Silva Júnior
- Center for Biological and Health Sciences, Federal University of Campina Grande, Campina Grande 58429-900, PB, Brazil;
| | - Jacinto Costa Silva Neto
- Laboratory of Molecular and Cytological Research, Department of Histology, Federal University of Pernambuco, Recife 50670-901, PE, Brazil;
| | - Marcus Vinícius de Aragão Batista
- Laboratory of Molecular Genetics and Biotechnology, Department of Biology, Federal University of Sergipe, São Cristóvão 49100-000, SE, Brazil;
| | - Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
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Characteristics of human papillomavirus infection among females and the genetic variations of HPV18 and HPV58 in Henan province, China. Sci Rep 2023; 13:2252. [PMID: 36755053 PMCID: PMC9908864 DOI: 10.1038/s41598-022-24641-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/17/2022] [Indexed: 02/10/2023] Open
Abstract
The present study aims to investigate the genotype distribution of Human papillomavirus (HPV) and variations of HPV18 and HPV58 infection among 6538 females in Luoyang city during 2019-2021. The overall positive rate of females with HPV infection was 12.34%, with 9.74% were infected with single HPV and 2.60% with multiple HPVs. The prevalent rate of high-risk HPV (HR-HPV) was 9.85% and the top five HR-HPV genotypes were HPV52 (1.94%), HPV16 (1.93%), HPV58 (1.48%), HPV51 (1.02%) and HPVV39 (0.99%). Two peaks of HPV infections rates were observed in females aged ≤ 20 and 61-65 years old. To characterize mutations, 39 HPV18 and 56 HPV58 L1, E6 and E7 genes were sequenced and submitted to GenBank. In the HPV18 E6-E7-L1 sequences, 38 nucleotides changes were observed with 10/38 were non-synonymous mutations (5 in E6 gene, 1 in E7 gene and 4 in L1 gene). In the HPV58 E6-E7-L1 sequences, 53 nucleotides changes were observed with 23/53 were non-synonymous mutations (3 in E6 gene, 5 in E7 gene and 15 in L1 gene). Phylogenetic analysis based on L1 gene showed that 92.3% (36/39) of HPV18 isolates fell into sublineage A1 and 7.7% (3/39) belonged to A5. For HPV58, 75.0% (42/56) isolates belonged to sublineage A1 and 25.0% (14/56) were sublineage A2. There was no association between amino mutation and cervical lesions. The present study provides basic information about the distribution, genotypes and variations of HPV among females population in Luoyang city, which would assist in the formulation of HPV screening and vaccination programs and preventive strategies for HPV-attributable cancer in this region.
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Yang Z, He ZH, Zhang Y, Di XH, Zheng DF, Xu HH. Genetic variability in the E6 and E7 oncogenes of HPV52 and its prevalence in the Taizhou area, China. Virol J 2022; 19:194. [PMID: 36415002 PMCID: PMC9682741 DOI: 10.1186/s12985-022-01929-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022] Open
Abstract
Background Human papillomavirus (HPV) 52 is one of the prevalent oncogenic HPV genotypes in East Asia. Chinese women have the highest susceptibility to the HPV52 type, but research data on HPV52 genetic variability and its carcinogenicity in China is lacking. Methods The present study aimed to investigate the genetic variability of HPV52 currently circulating among Chinese women by PCR sequencing the entire E6 and E7 oncogenes. HPV52 sequence alignment, genetic heterogeneity analyses and maximum-likelihood phylogenetic tree construction were performed by BioEdit software and MEGA X software. Results Between 2016 and 2018, the overall HPV infection rate was 21.3%, of which HPV52 was the most prevalent high-risk type (17.2%) in the Taizhou area, China. A total of 339 single HPV52-positive samples were included in this study. We obtained 27 distinct variation patterns of HPV52 with the accession GenBank numbers ON529577-ON529603. Phylogenetic analysis showed that 96.6% of HPV52 variants belonged to lineage B, which seemed to be uniquely defined by G350T, A379G (K93R) in the E6 gene and C751T, A801G in the E7 gene. Due to the dominance of lineage B in our study population, the results could not be used to assess the association of the HPV52 (sub)lineage with the risk of cervical lesions. In addition, no significant trends were observed between the nucleotide substitutions of HPV52 variants and the risk of cervical carcinogenesis. Conclusion Our data showed that HPV52 variants were strongly biased towards lineage B. These results confirmed that cervical lesions in the Taizhou area are highly attributable to HPV52, which may be due to the high infection rate of lineage B in the population. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-022-01929-5.
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Affiliation(s)
- Zhi Yang
- grid.268099.c0000 0001 0348 3990Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000 Zhejiang China
| | - Zhe-Hang He
- grid.268099.c0000 0001 0348 3990Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000 Zhejiang China
| | - Yang Zhang
- grid.268099.c0000 0001 0348 3990Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000 Zhejiang China
| | - Xing-Hong Di
- grid.268099.c0000 0001 0348 3990Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000 Zhejiang China
| | - Die-Fei Zheng
- grid.268099.c0000 0001 0348 3990Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000 Zhejiang China
| | - Hui-Hui Xu
- grid.268099.c0000 0001 0348 3990Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000 Zhejiang China ,grid.268099.c0000 0001 0348 3990Scientific Research Department, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, 317000 Zhejiang China
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Palmer M, Katanoda K, Saito E, Acuti Martellucci C, Tanaka S, Ikeda S, Sakamoto H, Machelek D, Ml Brotherton J, Hocking JS. Genotype prevalence and age distribution of human papillomavirus from infection to cervical cancer in Japanese women: A systematic review and meta-analysis. Vaccine 2022; 40:5971-5996. [PMID: 36085257 DOI: 10.1016/j.vaccine.2022.07.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/31/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND National HPV vaccination coverage in Japan is less than one percent of the eligible population and cervical cancer incidence and mortality are increasing. This systematic review and meta-analysis aimed to provide a comprehensive estimate of HPV genotype prevalence for Japan. METHODS English and Japanese databases were searched to March 2021 for research reporting HPV genotypes in cytology and histology samples from Japanese women. Summary estimates were calculated by disease stage from cytology only assessment - Normal, ASCUS, LSIL, HSIL and from histological assessment - CIN1, CIN2, CIN3/AIS, ICC (ICC-SCC, and ICC-ADC), and other. A random-effects meta-analysis was used to calculate summary prevalence estimates of any-HPV, high-risk (HR) and low-risk (LR) vaccine types, and vaccine genotypes (bivalent, quadrivalent, or nonavalent). This study was registered with PROSPERO: CRD42018117596. RESULTS A total of 57759 women with normal cytology, 1766 ASCUS, 3764 LSIL, 2017 HSIL, 3130 CIN1, 1219 CIN2, 869 CIN3/AIS, and 4306 ICC (which included 1032 ICC-SCC, and 638 ICC-ADC) were tested for HPV. The summary estimate of any-HPV genotype in women with normal cytology was 15·6% (95% CI: 12·3-19·4) and in invasive cervical cancer (ICC) was 85·6% (80·7-89·8). The prevalence of HR-HPV was 86·0% (95% CI: 73·9-94·9) for cytological cases of HSIL, 76·9% (52·1-94·7) for histological cases of CIN3/AIS, and 75·7% (68·0-82·6) for ICC. In women with ICC, the summary prevalence of bivalent vaccine genotypes was 58·5% (95% CI: 52·1-64·9), for quadrivalent genotypes was 58·6% (52·2-64·9) and for nonavalent genotypes was 71·5% (64·9-77·6), and of ICC cases that were HPV positive over 90% of infections are nonavalent vaccine preventable. There was considerable heterogeneity in all HPV summary estimates and for ICC, this heterogeneity was not explained by variability in study design, sample type, HPV assay type, or HPV DNA detection method, although studies published in the 1990s had lower prevalence estimates of any-HPV and HR HPV genotypes. INTERPRETATIONS HPV prevalence is high among Japanese women. The nonavalent vaccine is likely to have the greatest impact on reducing cervical cancer incidence and mortality in Japan.
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Affiliation(s)
- Matthew Palmer
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne Australia; Division of Surveillance and Policy Evaluation, National Cancer Center Institute for Cancer Control, Tokyo, Japan.
| | - Kota Katanoda
- Division of Surveillance and Policy Evaluation, National Cancer Center Institute for Cancer Control, Tokyo, Japan
| | - Eiko Saito
- Institute for Global Health Policy Research, National Center for Global Health Medicine, Tokyo, Japan
| | | | - Shiori Tanaka
- Department of Global Health Policy, Graduate School of Medicine, The University of Teokyo, Tokyo, Japan; Division of Prevention, Center for Public Health Sciences, National Cancer Center, Japan
| | - Sayaka Ikeda
- Division of Surveillance and Policy Evaluation, National Cancer Center Institute for Cancer Control, Tokyo, Japan
| | - Haruka Sakamoto
- Department of Global Health Policy, Graduate School of Medicine, The University of Teokyo, Tokyo, Japan
| | | | - Julia Ml Brotherton
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne Australia; Australian Centre for the Prevention of Cervical Cancer, Carlton, Australia
| | - Jane S Hocking
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne Australia
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Kukimoto I, Onuki M, Yamamoto K, Yahata H, Aoki Y, Yokota H, Konnai K, Nio A, Takehara K, Kamiura S, Tsuda N, Takei Y, Shimada M, Nakai H, Yoshida H, Motohara T, Yamazaki H, Nakamura K, Okunomiya A, Tasaka N, Ishikawa M, Hirashima Y, Shimoji Y, Mori M, Iwata T, Takahashi F, Yoshikawa H, Yaegashi N, Matsumoto K. Regional differences in human papillomavirus type 52 prevalence among Japanese women with cervical intraepithelial neoplasia†. Jpn J Clin Oncol 2022; 52:1242-1247. [PMID: 35938523 DOI: 10.1093/jjco/hyac127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Although geographical differences in the distribution of human papillomavirus genotypes have been observed worldwide, no studies have reported on national differences in the prevalence of human papillomavirus types in Japan. Here, we report a cross-sectional study to explore regional differences in the prevalence of human papillomavirus types among Japanese women with cervical intraepithelial neoplasia or invasive cervical cancer. Using human papillomavirus genotyping data from the nationwide prospective study on human papillomavirus vaccine effectiveness, we compared the frequency of detection of 15 high-risk and two low-risk human papillomavirus types in each disease category between the women who visited hospitals located in eastern Japan and those who visited hospitals located in western Japan. The risk of cervical intraepithelial neoplasia progression was assessed by calculating a prevalence ratio of each human papillomavirus type for cervical intraepithelial neoplasia grade 2/3 versus grade 1. Among the human papillomavirus types studied, human papillomavirus 52 was detected significantly more frequently in western hospitals than in eastern hospitals in cervical intraepithelial neoplasia grade 1 patients, but was less frequent in cervical intraepithelial neoplasia grade 2/3. The prevalence of particular human papillomavirus types was not significantly different between patients in hospitals in eastern Japan and those in hospitals in western Japan for invasive cervical cancer. In both eastern and western hospitals, a higher risk of cervical intraepithelial neoplasia progression was observed in patients infected with human papillomavirus 16, 31 or 58. In contrast, there was a significantly higher prevalence of human papillomavirus 52 infection in women with cervical intraepithelial neoplasia grade 2/3 than in those with cervical intraepithelial neoplasia grade 1 in eastern hospitals (prevalence ratio, 1.93; 95% confidence interval, 1.48-2.58), but not in western hospitals (prevalence ratio, 1.03; 95% confidence interval, 0.83-1.30). Regional differences of human papillomavirus 52 prevalence in cervical intraepithelial neoplasia lesions may exist and emphasize the importance of continuous monitoring of human papillomavirus type prevalence throughout the country in order to accurately assess the efficacy of human papillomavirus vaccines.
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Affiliation(s)
- Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mamiko Onuki
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Kasumi Yamamoto
- Department of Gynecologic Oncology, Hyogo Cancer Center, Akashi, Japan
| | - Hideaki Yahata
- Department of Gynecology and Obstetrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoichi Aoki
- Department of Gynecology, Cancer Institute Hospital, Tokyo, Japan
| | | | - Katsuyuki Konnai
- Department of Gynecology, Kanagawa Cancer Center, Kanagawa, Japan
| | - Ai Nio
- Gynecology Service, NHO Kyushu Cancer Center, Fukuoka, Japan
| | - Kazuhiro Takehara
- Department of Gynecologic Oncology, National Hospital Organization Shikoku Cancer Center, Matsuyama, Japan
| | - Shoji Kamiura
- Department of Gynecology, Osaka International Cancer Institute, Osaka, Japan
| | - Naotake Tsuda
- Department of Obstetrics and Gynecology, Kurume University School of Medicine, Kurume, Japan
| | - Yuji Takei
- Department of Obstetrics and Gynecology, Jichi Medical University, Tochigi, Japan
| | - Muneaki Shimada
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hidekatsu Nakai
- Department of Obstetrics and Gynecology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Hiroyuki Yoshida
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Takeshi Motohara
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Yamazaki
- Department of Obstetrics and Gynecology, Faculty of Medicine, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Keiichiro Nakamura
- Department of Obstetrics and Gynecology, Dentistry and Pharmaceutical Sciences, Okayama University Graduate School of Medicine, Okayama, Japan
| | - Asuka Okunomiya
- Department of Gynecology and Obstetrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Nobutaka Tasaka
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Mitsuya Ishikawa
- Department of Gynecology, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuyuki Hirashima
- Division of Gynecology, Shizuoka Cancer Center Hospital, Shizuoka, Japan
| | - Yuko Shimoji
- Department of Obstetrics and Gynecology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Mayuyo Mori
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takashi Iwata
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Fumiaki Takahashi
- Division of Medical Engineering, Department of Information Science, Iwate Medical University, Yahaba, Japan
| | - Hiroyuki Yoshikawa
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Nobuo Yaegashi
- Department of Obstetrics and Gynecology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Koji Matsumoto
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
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Tanaka K, Kogure G, Onuki M, Matsumoto K, Iwata T, Aoki D, Kukimoto I. Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan. Viruses 2022; 14:v14030464. [PMID: 35336870 PMCID: PMC8953638 DOI: 10.3390/v14030464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022] Open
Abstract
Human papillomavirus (HPV) is a sexually transmitted virus with an approximately 8-kilo base DNA genome, which establishes long-term persistent infection in anogenital tissues. High levels of genetic variations, including viral genotypes and intra-type variants, have been described for HPV genomes, together with geographical differences in the distribution of genotypes and variants. Here, by employing a maximum likelihood method, we performed phylogenetic analyses of the complete genome sequences of HPV16, HPV18 and HPV58 available from GenBank (n = 627, 146 and 157, respectively). We found several characteristic clusters that exclusively contain HPV genomes from Japan: two for HPV16 (sublineages A4 and A5), one for HPV18 (sublineage A1) and two for HPV58 (sublineages A1 and A2). Bayesian phylogenetic analyses of concatenated viral gene sequences showed that divergence of the most recent common ancestor of these Japan-specific clades was estimated to have occurred ~98,000 years before present (YBP) for HPV16 A4, ~39,000 YBP for HPV16 A5, ~38,000 YBP for HPV18 A1, ~26,000 for HPV58 A1 and ~25,000 YBP for HPV58 A2. This estimated timeframe for the divergence of the Japan-specific clades suggests that the introduction of these HPV variants into the Japanese archipelago dates back to at least ~25,000 YBP and provides a scenario of virus co-migration with ancestral Japanese populations from continental Asia during the Upper Paleolithic period.
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Affiliation(s)
- Kohsei Tanaka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (K.T.); (G.K.)
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-0016, Japan; (T.I.); (D.A.)
| | - Gota Kogure
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (K.T.); (G.K.)
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo 142-8666, Japan; (M.O.); (K.M.)
| | - Mamiko Onuki
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo 142-8666, Japan; (M.O.); (K.M.)
| | - Koji Matsumoto
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo 142-8666, Japan; (M.O.); (K.M.)
| | - Takashi Iwata
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-0016, Japan; (T.I.); (D.A.)
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-0016, Japan; (T.I.); (D.A.)
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (K.T.); (G.K.)
- Correspondence: ; Tel.: +81-42-561-0771
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9
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Genetic characteristics of human papillomavirus type 16, 18, 52 and 58 in southern China. Genomics 2021; 113:3895-3906. [PMID: 34555497 DOI: 10.1016/j.ygeno.2021.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/15/2021] [Accepted: 09/09/2021] [Indexed: 11/21/2022]
Abstract
Persistent infections of high-risk human papillomaviruses (HPVs) are the leading cause of cervical cancers. We collected cervical exfoliated cell samples from females in Changsha city, Hunan Province and obtained 338 viral genomes of four major HPV types, including HPV 16 (n = 82), 18 (n = 35), 52 (n = 121) and 58 (n = 100). The lineage/sublineage distribution of the four HPVs confirmed previous epidemiological reports, with the predominant prevailing sublineage as A4 (50%), A1 (37%) and A3 (13%) for HPV16, A1 (83%) for HPV18, B2 (86%) for HPV52 and A1 (65%), A3 (19%) and A2 (12%) for HPV58. We also identified two potentially novel HPV18 sublineages, i.e. A6 and A7. Virus mutation analysis further revealed the presence of HPV16 and HPV58 sublineages associated with potentially high oncogenicity. These findings expanded our knowledge of the HPV genetic diversity in China, providing valuable evidence to facilitate HPV DNA screening, vaccine effectiveness evaluation and control strategy development.
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10
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Bee KJ, Gradissimo A, Chen Z, Harari A, Schiffman M, Raine-Bennett T, Castle PE, Clarke M, Wentzensen N, Burk RD. Genetic and Epigenetic Variations of HPV52 in Cervical Precancer. Int J Mol Sci 2021; 22:ijms22126463. [PMID: 34208758 PMCID: PMC8234014 DOI: 10.3390/ijms22126463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022] Open
Abstract
The goal of this study was to identify human papillomavirus (HPV) type 52 genetic and epigenetic changes associated with high-grade cervical precancer and cancer. Patients were selected from the HPV Persistence and Progression (PaP) cohort, a cervical cancer screening program at Kaiser Permanente Northern California (KPNC). We performed a nested case-control study of 89 HPV52-positive women, including 50 cases with predominantly cervical intraepithelial neoplasia grade 3 (CIN3) and 39 controls without evidence of abnormalities. We conducted methylation analyses using Illumina sequencing and viral whole genome Sanger sequencing. Of the 24 CpG sites examined, increased methylation at CpG site 5615 in HPV52 L1 region was the most significantly associated with CIN3, with a difference in median methylation of 17.9% (odds ratio (OR) = 4.8, 95% confidence interval (CI) = 1.9–11.8) and an area under the curve of 0.73 (AUC; 95% CI = 0.62–0.83). Complete genomic sequencing of HPV52 isolates revealed associations between SNPs present in sublineage C2 and a higher risk of CIN3, with ORs ranging from 2.8 to 3.3. This study identified genetic and epigenetic HPV52 variants associated with high risk for cervical precancer, improving the potential for early diagnosis of cervical neoplasia caused by HPV52.
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Affiliation(s)
- Katharine J. Bee
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.J.B.); (A.G.); (Z.C.); (A.H.)
- DBV Technologies, 92120 Montrouge, France
| | - Ana Gradissimo
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.J.B.); (A.G.); (Z.C.); (A.H.)
| | - Zigui Chen
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.J.B.); (A.G.); (Z.C.); (A.H.)
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ariana Harari
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.J.B.); (A.G.); (Z.C.); (A.H.)
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; (M.S.); (P.E.C.); (M.C.); (N.W.)
| | - Tina Raine-Bennett
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA;
| | - Philip E. Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; (M.S.); (P.E.C.); (M.C.); (N.W.)
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA
| | - Megan Clarke
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; (M.S.); (P.E.C.); (M.C.); (N.W.)
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA; (M.S.); (P.E.C.); (M.C.); (N.W.)
| | - Robert D. Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; (K.J.B.); (A.G.); (Z.C.); (A.H.)
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Microbiology & Immunology, and Obstetrics, Gynecology & Women’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Correspondence: ; Tel.: +1-718-430-3720
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11
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Song Z, Cui Y, Li Q, Deng J, Ding X, He J, Liu Y, Ju Z, Fang L. The genetic variability, phylogeny and functional significance of E6, E7 and LCR in human papillomavirus type 52 isolates in Sichuan, China. Virol J 2021; 18:94. [PMID: 33941222 PMCID: PMC8091156 DOI: 10.1186/s12985-021-01565-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 04/23/2021] [Indexed: 11/10/2022] Open
Abstract
Background Variations in human papillomavirus (HPV) E6 and E7 have been shown to be closely related to the persistence of the virus and the occurrence and development of cervical cancer. Long control region (LCR) of HPV has been shown multiple functions on regulating viral transcription. In recent years, there have been reports on E6/E7/LCR of HPV-16 and HPV-58, but there are few studies on HPV-52, especially for LCR. In this study, we focused on gene polymorphism of the HPV-52 E6/E7/LCR sequences, assessed the effects of variations on the immune recognition of viral E6 and E7 antigens, predicted the effect of LCR variations on transcription factor binding sites and provided more basic date for further study of E6/E7/LCR in Chengdu, China. Methods LCR/E6/E7 of the HPV-52 were amplified and sequenced to do polymorphic and phylogenetic analysis. Sequences were aligned with the reference sequence by MEGA 7.0 to identify SNP. A neighbor-joining phylogenetic tree was constructed by MEGA 7.0, followed by the secondary structure prediction of the related proteins using PSIPRED 4.0. The selection pressure of E6 and E7 coding regions were estimated by Bayes empirical Bayes analysis of PAML 4.9. The HLA class-I and II binding peptides were predicted by the Immune Epitope Database server. The B cell epitopes were predicted by ABCpred server. Transcription factor binding sites in LCR were predicted by JASPAR database. Results 50 SNP sites (6 in E6, 10 in E7, 34 in LCR) were found. From the most variable to the least variable, the nucleotide variations were LCR > E7 > E6. Two deletions were found between the nucleotide sites 7387–7391 (TTATG) and 7698–7700 (CTT) in all samples. A deletion was found between the nucleotide sites 7287–7288 (TG) in 97.56% (40/41) of the samples. The combinations of all the SNP sites and deletions resulted in 12 unique sequences. As shown in the neighbor-joining phylogenetic tree, except for one belonging to sub-lineage C2, others sequences clustered into sub-lineage B2. No positive selection was observed in E6 and E7. 8 non-synonymous amino acid substitutions (including E3Q and K93R in the E6, and T37I, S52D, Y59D, H61Y, D64N and L99R in the E7) were potential affecting multiple putative epitopes for both CD4+ and CD8+ T-cells and B-cells. A7168G was the most variable site (100%) and the binding sites for transcription factor VAX1 in LCR. In addition, the prediction results showed that LCR had the high probability binding sites for transcription factors SOX9, FOS, RAX, HOXA5, VAX1 and SRY. Conclusion This study provides basic data for understanding the relation among E6/E7/LCR mutations, lineages and carcinogenesis. Furthermore, it provides an insight into the intrinsic geographical relatedness and biological differences of the HPV-52 variants, and contributes to further research on the HPV-52 therapeutic vaccine development. Supplementary Information The online version contains supplementary material available at 10.1186/s12985-021-01565-5.
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Affiliation(s)
- Zhilin Song
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-Resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China
| | - Yanru Cui
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-Resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China
| | - Qiufu Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-Resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China
| | - Junhang Deng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-Resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China
| | - Xianping Ding
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China. .,Bio-Resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China.
| | - Jiaoyu He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-Resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China
| | - Yiran Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-Resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China
| | - Zhuang Ju
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-Resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China
| | - Liyuan Fang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.,Bio-Resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing, People's Republic of China
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12
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Genetic signatures for lineage/sublineage classification of HPV16, 18, 52 and 58 variants. Virology 2020; 553:62-69. [PMID: 33238224 DOI: 10.1016/j.virol.2020.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 11/20/2022]
Abstract
Increasing evidences indicate that high-risk HPV variants are heterogeneous in carcinogenicity and ethnic dispersion. In this work, we identified genetic signatures for convenient determination of lineage/sublineage of HPV16, 18, 52 and 58 variants. Using publicly available genomes, we found that E2 of HPV16, L2 of HPV18, L1 and LCR of HPV52, and L2, LCR and E1 of HPV58 contain the proper genetic signature for lineage/sublineage classification. Sets of hierarchical signature nucleotide positions were further confirmed for high accuracy (>95%) by classifying HPV genomes obtained from Chinese females, which included 117 HPV16 variants, 48 HPV18 variants, 117 HPV52 variants and 89 HPV58 variants. The circulation of HPV variants posing higher cancer risk in Eastern China, such as HPV16 A4 and HPV58 A3, calls for continuous surveillance in this region. The marker genes and signature nucleotide positions may facilitate cost-effective diagnostic detections of HPV variants in clinical settings.
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13
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Zhao J, Zhan Q, Guo J, Liu M, Ruan Y, Zhu T, Han L, Li F. Phylogeny and polymorphism in the E6 and E7 of human papillomavirus: alpha-9 (HPV16, 31, 33, 52, 58), alpha-5 (HPV51), alpha-6 (HPV53, 66), alpha-7 (HPV18, 39, 59, 68) and alpha-10 (HPV6, 44) in women from Shanghai. Infect Agent Cancer 2019; 14:38. [PMID: 31832087 PMCID: PMC6873513 DOI: 10.1186/s13027-019-0250-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/21/2019] [Indexed: 12/13/2022] Open
Abstract
Background Persistent infection with human papillomaviruses (HPVs) has been associated with cervical intraepithelial neoplasia (CIN) and cervical cancer. However, why only a fraction of HPV cases progress to cancer is still unclear. Methods We focused on the heterogeneity, classification, evolution and dispersal of variants for 14 common HPV types in 262 HPV-positive patients with cervical lesions. The E6 and E7 genes of HPV were sequenced and compared with the HPV reference for sequence analysis. Phylogenetic trees were constructed using the neighbour-joining tree method with MEGA 7.0. Results In this study, 233 E6 and 212 E7 sequences were successfully amplified by PCR, and these sequences were divided into 5 species groups: alpha-9 (HPV16, 31, 33, 52, 58), alpha-5 (HPV51), alpha-6 (HPV53, 66), alpha-7 (HPV18, 39, 59, 68) and alpha-10 (HPV6, 44). The incidence of high-grade squamous intraepithelial lesion (HSIL) in patients infected with alpha-9 HPV was significantly increased compared with other groups (P < 0.0001), especially HPV16 (P < 0.0001). Strikingly, E7 had significantly fewer nonsynonymous variants in the HSIL compared to <HSIL groups (P = 3.17× 10- 4). The A388C (K93 N) variation in HPV58 E6 can significantly reduce the risk of HSIL (P = 0.015). However, T7220G (D32E) variation in HPV16 E6 and A7689G (N29S) in HPV16 E7 increased the incidence of HSIL compared to the <HSIL group (P = 0.036 and 0.022). Conclusions Strict conservation of E7 is important for HPV carcinogenicity, especially N29 of HPV16. The findings in this work provide preventative/therapeutic interventions for HPV infections and CIN.
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Affiliation(s)
- Junwei Zhao
- 1Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, 150 Jimo Rd, Shanghai, 200120 People's Republic of China
| | - Qin Zhan
- 2Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 201204 China
| | - Junhan Guo
- 1Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, 150 Jimo Rd, Shanghai, 200120 People's Republic of China
| | - Min Liu
- 1Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, 150 Jimo Rd, Shanghai, 200120 People's Republic of China
| | - Yetian Ruan
- 1Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, 150 Jimo Rd, Shanghai, 200120 People's Republic of China
| | - Tailin Zhu
- 3School of Physics HH Wills Physics Laboratory, University of Bristol, Bristol, UK
| | - Lingfei Han
- 2Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 201204 China
| | - Fang Li
- 1Department of Obstetrics and Gynecology, East Hospital, Tongji University School of Medicine, 150 Jimo Rd, Shanghai, 200120 People's Republic of China
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Within-Host Variations of Human Papillomavirus Reveal APOBEC Signature Mutagenesis in the Viral Genome. J Virol 2018; 92:JVI.00017-18. [PMID: 29593040 DOI: 10.1128/jvi.00017-18] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/08/2018] [Indexed: 01/05/2023] Open
Abstract
Persistent infection with oncogenic human papillomaviruses (HPVs) causes cervical cancer, accompanied by the accumulation of somatic mutations into the host genome. There are concomitant genetic changes in the HPV genome during viral infection; however, their relevance to cervical carcinogenesis is poorly understood. Here, we explored within-host genetic diversity of HPV by performing deep-sequencing analyses of viral whole-genome sequences in clinical specimens. The whole genomes of HPV types 16, 52, and 58 were amplified by type-specific PCR from total cellular DNA of cervical exfoliated cells collected from patients with cervical intraepithelial neoplasia (CIN) and invasive cervical cancer (ICC) and were deep sequenced. After constructing a reference viral genome sequence for each specimen, nucleotide positions showing changes with >0.5% frequencies compared to the reference sequence were determined for individual samples. In total, 1,052 positions of nucleotide variations were detected in HPV genomes from 151 samples (CIN1, n = 56; CIN2/3, n = 68; ICC, n = 27), with various numbers per sample. Overall, C-to-T and C-to-A substitutions were the dominant changes observed across all histological grades. While C-to-T transitions were predominantly detected in CIN1, their prevalence was decreased in CIN2/3 and fell below that of C-to-A transversions in ICC. Analysis of the trinucleotide context encompassing substituted bases revealed that TpCpN, a preferred target sequence for cellular APOBEC cytosine deaminases, was a primary site for C-to-T substitutions in the HPV genome. These results strongly imply that the APOBEC proteins are drivers of HPV genome mutation, particularly in CIN1 lesions.IMPORTANCE HPVs exhibit surprisingly high levels of genetic diversity, including a large repertoire of minor genomic variants in each viral genotype. Here, by conducting deep-sequencing analyses, we show for the first time a comprehensive snapshot of the within-host genetic diversity of high-risk HPVs during cervical carcinogenesis. Quasispecies harboring minor nucleotide variations in viral whole-genome sequences were extensively observed across different grades of CIN and cervical cancer. Among the within-host variations, C-to-T transitions, a characteristic change mediated by cellular APOBEC cytosine deaminases, were predominantly detected throughout the whole viral genome, most strikingly in low-grade CIN lesions. The results strongly suggest that within-host variations of the HPV genome are primarily generated through the interaction with host cell DNA-editing enzymes and that such within-host variability is an evolutionary source of the genetic diversity of HPVs.
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15
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Ito Y, Ogata D, Shimizu A, Arai E, Tsuchida T. Detection of human papillomavirus type 52 in a case of gluteal squamous cell carcinoma. J Dermatol 2018; 45:e154-e155. [PMID: 29315778 DOI: 10.1111/1346-8138.14197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Yui Ito
- Department of Dermatology, Saitama Medical University, Saitama, Japan
| | - Dai Ogata
- Department of Dermatology, Saitama Medical University, Saitama, Japan
| | - Akira Shimizu
- Department of Dermatology, Gunma University School of Medicine, Maebashi, Japan
| | - Eiichi Arai
- Department of Pathology, Saitama Medical University International Medical Center, Yamane, Japan
| | - Tetsuya Tsuchida
- Department of Dermatology, Saitama Medical University, Saitama, Japan
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