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Galati L, Di Bonito P, Marinaro M, Chiantore MV, Gheit T. HPV16 Phylogenetic Variants in Anogenital and Head and Neck Cancers: State of the Art and Perspectives. Viruses 2024; 16:904. [PMID: 38932197 PMCID: PMC11209046 DOI: 10.3390/v16060904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
HPV16 is responsible for approximately 60% and 90% of global HPV-induced cervical and oropharyngeal cancers, respectively. HPV16 intratype variants have been identified by HPV genome sequencing and classified into four phylogenetic lineages (A-D). Our understanding of HPV16 variants mostly derives from epidemiological studies on cervical cancer (CC) in which HPV16 B, C, and D lineages (previously named "non-European" variants) were mainly associated with high-grade cervical lesions and cancer. Although a predominance of HPV16 lineage A (previously named "European variants") has been observed in head and neck squamous cell carcinoma (HNSCC), epidemiological and in vitro biological studies are still limited for this tumor site. Next Generation Sequencing (NGS) of the entire HPV genome has deepened our knowledge of the prevalence and distribution of HPV variants in CC and HNSCC. Research on cervical cancer has shown that certain HPV16 sublineages, such as D2, D3, A3, and A4, are associated with an increased risk of cervical cancer, and sublineages A4, D2, and D3 are linked to a higher risk of developing adenocarcinomas. Additionally, lineage C and sublineages D2 or D3 of HPV16 show an elevated risk of developing premalignant cervical lesions. However, it is still crucial to conduct large-scale studies on HPV16 variants in different HPV-related tumor sites to deeply evaluate their association with disease development and outcomes. This review discusses the current knowledge and updates on HPV16 phylogenetic variants distribution in HPV-driven anogenital and head and neck cancers.
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Affiliation(s)
- Luisa Galati
- International Agency for Research on Cancer, 69007 Lyon, France
| | - Paola Di Bonito
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (P.D.B.); (M.M.); (M.V.C.)
| | - Mariarosaria Marinaro
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (P.D.B.); (M.M.); (M.V.C.)
| | - Maria Vincenza Chiantore
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (P.D.B.); (M.M.); (M.V.C.)
| | - Tarik Gheit
- International Agency for Research on Cancer, 69007 Lyon, France
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Clarke MA. HPV Testing and its Role in Cervical Cancer Screening. Clin Obstet Gynecol 2023; 66:448-469. [PMID: 37650662 DOI: 10.1097/grf.0000000000000793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The recognition that persistent infection with carcinogenic human papillomavirus (HPV) is a necessary cause of cervical precancer and cancer has led to the introduction of HPV testing into cervical cancer screening, either as a primary screening test or in conjunction with cervical cytology (i.e., co-testing). HPV testing has much higher sensitivity for detection of cervical precancer and provides greater long-term reassurance if negative compared to cytology. However, most HPV infections are transient, and do not progress to invasive cancer, thus triage tests are required to identify individuals who should be referred to colposcopy for diagnostic evaluation. This chapter begins with a description of the biology, natural history, and epidemiology of HPV as a foundation for understanding the role of HPV in cervical carcinogenesis. This section is followed by a detailed discussion regarding the introduction of HPV-based testing and triage into cervical cancer screening and management. Summarized triage tests include cervical cytology, HPV genotyping, p16/Ki-67 dual stain, and HPV and cellular methylation markers. The final section of this chapter includes an important discussion on cervical cancer disparities, particularly within the United States, followed by concluding remarks.
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Affiliation(s)
- Megan A Clarke
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Rockville, Maryland
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Nelson CW, Mirabello L. Human papillomavirus genomics: Understanding carcinogenicity. Tumour Virus Res 2023; 15:200258. [PMID: 36812987 PMCID: PMC10063409 DOI: 10.1016/j.tvr.2023.200258] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Human papillomavirus (HPV) causes virtually all cervical cancers and many cancers at other anatomical sites in both men and women. However, only 12 of 448 known HPV types are currently classified as carcinogens, and even the most carcinogenic type - HPV16 - only rarely leads to cancer. HPV is therefore necessary but insufficient for cervical cancer, with other contributing factors including host and viral genetics. Over the last decade, HPV whole genome sequencing has established that even fine-scale within-type HPV variation influences precancer/cancer risks, and that these risks vary by histology and host race/ethnicity. In this review, we place these findings in the context of the HPV life cycle and evolution at various levels of viral diversity: between-type, within-type, and within-host. We also discuss key concepts necessary for interpreting HPV genomic data, including features of the viral genome; events leading to carcinogenesis; the role of APOBEC3 in HPV infection and evolution; and methodologies that use deep (high-coverage) sequencing to characterize within-host variation, as opposed to relying on a single representative (consensus) sequence. Given the continued high burden of HPV-associated cancers, understanding HPV carcinogenicity remains important for better understanding, preventing, and treating cancers attributable to infection.
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Affiliation(s)
- Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA; Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, 20850, USA.
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Lang Kuhs KA, Faden DL, Chen L, Smith DK, Pinheiro M, Wood CB, Davis S, Yeager M, Boland JF, Cullen M, Steinberg M, Bass S, Wang X, Liu P, Mehrad M, Tucker T, Lewis JS, Ferris RL, Mirabello L. Genetic variation within the human papillomavirus type 16 genome is associated with oropharyngeal cancer prognosis. Ann Oncol 2022; 33:638-648. [PMID: 35306154 PMCID: PMC9350957 DOI: 10.1016/j.annonc.2022.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 01/02/2023] Open
Abstract
PURPOSE A significant barrier to adoption of de-escalated treatment protocols for human papillomavirus-driven oropharyngeal cancer (HPV-OPC) is that few predictors of poor prognosis exist. We conducted the first large whole-genome sequencing (WGS) study to characterize the genetic variation of the HPV type 16 (HPV16) genome and to evaluate its association with HPV-OPC patient survival. PATIENTS AND METHODS A total of 460 OPC tumor specimens from two large United States medical centers (1980-2017) underwent HPV16 whole-genome sequencing. Site-specific variable positions [single nucleotide polymorphisms (SNPs)] across the HPV16 genome were identified. Cox proportional hazards model estimated hazard ratios (HRs) and 95% confidence intervals (CIs) for overall survival by HPV16 SNPs. Harrell C-index and time-dependent positive predictive value (PPV) curves and areas under the PPV curves were used to evaluate the predictive accuracy of HPV16 SNPs for overall survival. RESULTS A total of 384 OPC tumor specimens (83.48%) passed quality control filters with sufficient depth and coverage of HPV16 genome sequencing to be analyzed. Some 284 HPV16 SNPs with a minor allele frequency ≥1% were identified. Eight HPV16 SNPs were significantly associated with worse survival after false discovery rate correction (individual prevalence: 1.0%-5.5%; combined prevalence: 15.10%); E1 gene position 1053 [HR for overall survival (HRos): 3.75, 95% CI 1.77-7.95; Pfdr = 0.0099]; L2 gene positions 4410 (HRos: 5.32, 95% CI 1.91-14.81; Pfdr = 0.0120), 4539 (HRos: 6.54, 95% CI 2.03-21.08; Pfdr = 0.0117); 5050 (HRos: 6.53, 95% CI 2.34-18.24; Pfdr = 0.0030), and 5254 (HRos: 7.76, 95% CI 2.41-24.98; Pfdr = 0.0030); and L1 gene positions 5962 (HRos: 4.40, 95% CI 1.88-10.31; Pfdr = 0.0110) and 6025 (HRos: 5.71, 95% CI 2.43-13.41; Pfdr = 0.0008) and position 7173 within the upstream regulatory region (HRos: 9.90, 95% CI 3.05-32.12; Pfdr = 0.0007). Median survival time for patients with ≥1 high-risk HPV16 SNPs was 3.96 years compared with 18.67 years for patients without a high-risk SNP; log-rank test P < 0.001. HPV16 SNPs significantly improved the predictive accuracy for overall survival above traditional factors (age, smoking, stage, treatment); increase in C-index was 0.069 (95% CI 0.019-0.119, P < 0.001); increase in area under the PPV curve for predicting 5-year survival was 0.068 (95% CI 0.015-0.111, P = 0.008). CONCLUSIONS HPV16 genetic variation is associated with HPV-OPC prognosis and can improve prognostic accuracy.
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Affiliation(s)
- K A Lang Kuhs
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, USA; Department of Medicine, Vanderbilt University Medical Cancer, Nashville, USA.
| | - D L Faden
- Department of Otolaryngology, Massachusetts Eye and Ear, Massachusetts General Hospital, Harvard Medical School, Boston, USA; Broad Institute of MIT and Harvard, Cambridge, USA
| | - L Chen
- Division of Cancer Biostatistics, Department of Internal Medicine and Biostatistics and Bioinformatics Shared Resource Facility, Markey Cancer Center, University of Kentucky, Lexington, USA
| | - D K Smith
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, USA
| | - M Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA
| | - C B Wood
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, USA; Department of Otolaryngology - Head and Neck Surgery, University of Tennessee Health Science Center, Memphis, USA
| | - S Davis
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, USA
| | - M Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, USA
| | - J F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, USA
| | - M Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, USA
| | - M Steinberg
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, USA
| | - S Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, USA
| | - X Wang
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, Chicago, USA
| | - P Liu
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, USA
| | - M Mehrad
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, USA
| | - T Tucker
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, USA
| | - J S Lewis
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, USA
| | - R L Ferris
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, USA; Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - L Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA
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Wang X, Han S, Li X, Wang X, Wang S, Ma L. Prevalence and distribution of human papillomavirus (HPV) in Luoyang city of Henan province during 2015-2021 and the genetic variability of HPV16 and 52. Virol J 2022; 19:37. [PMID: 35246180 PMCID: PMC8896270 DOI: 10.1186/s12985-022-01759-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/05/2022] [Indexed: 12/09/2022] Open
Abstract
Background Persistent high-risk Human papillomavirus (HPV) subtypes infection has been implicated as a causative of cervical cancer. Distribution and genotypes of HPV infection among females and their variations would assist in the formulation of preventive strategy for cervical cancer. The purpose of the present study is to investigate the prevalence of HPV among females in central China. Methods The distribution and genotypes of HPV among 9943 females attending the gynecological examinations in central of China during 2015–2021 were investigated. HPV genotypes were detected using a commercial kit. Nucleotides sequences of L1, E6 and E7 genes in HPV16 or HPV52 positive samples collected in 2021 were amplified by polymerase chain reaction (PCR). Variations of L1, E6 and E7 in HPV16 and HPV52 were gained by sequencing and compared with the reference sequence. Sublineages of HPV16 and HPV52 were determined by the construction of phylogenetic tree based on L1 gene. Results The overall prevalence of HPV infection was 22.81%, with the infection rate of high-risk human papillomavirus (HR-HPV) was 19.02% and low-risk human papillomavirus (LR-HPV) was 6.40%. The most top five genotypes of HPV infection were HPV16 (7.49%), HPV52 (3.04%), HPV58 (2.36%), HPV18 (1.65%) and HPV51 (1.61%). Plots of the age-infection rate showed that the single HPV, multiple HPV, HR-HPV, LR-HPV infection revealed the same tendency with two peaks of HPV infection were observed among females aged ≤ 20 year-old and 60–65 year-old. The predominant sublineage of HPV16 was A1 and B2 for HPV52. For HPV16, The most prevalent mutations were T266A (27/27) and N181T (7/27) for L1, D32E for E6 and S63F for E7 in HPV16. For HPV52, all of the nucleotide changes were synonymous mutation in L1 (except L5S) and E7 genes. The K93R mutation was observed in most HPV52 E6 protein. Conclusions The present study provides basic information about the distribution, genotypes and variations of HPV among females population in Henan province, which would assist in the formulation of preventive strategies and improvements of diagnostic probe and vaccine for HPV in this region.
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Affiliation(s)
- Xiuli Wang
- Department of Blood Transfusion and Clinical Laboratory, No.989 Hospital of the Joint Logistic Support Force of Chinese PLA, Luoyang, Henan Province, China
| | - Shuizhong Han
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xingwei Li
- Department of Blood Transfusion and Clinical Laboratory, No.989 Hospital of the Joint Logistic Support Force of Chinese PLA, Luoyang, Henan Province, China
| | - Xiaochuan Wang
- Department of Blood Transfusion and Clinical Laboratory, No.989 Hospital of the Joint Logistic Support Force of Chinese PLA, Luoyang, Henan Province, China
| | - Shan Wang
- Department of Blood Transfusion and Clinical Laboratory, No.989 Hospital of the Joint Logistic Support Force of Chinese PLA, Luoyang, Henan Province, China
| | - Li Ma
- Department of Blood Transfusion and Clinical Laboratory, No.989 Hospital of the Joint Logistic Support Force of Chinese PLA, Luoyang, Henan Province, China.
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Repurposing the Hybrid Capture 2 (HC2) screening test for whole-genome sequencing of human papillomaviruses. Arch Virol 2021; 166:3421-3425. [PMID: 34618227 DOI: 10.1007/s00705-021-05259-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Simple and standardized approaches for genome analysis of human papillomavirus (HPV) by next-generation sequencing are needed. The aim of the study was to develop a protocol for direct deep sequencing of high-risk (hr) HPV strains, based on the widely used commercial Hybrid Capture 2 (QIAGEN) test, without any additional probe design. This protocol was applied to 15 HPV-positive and two HPV-negative cervical samples or cell lines and validated at the genotype level by comparing the sequencing results to those obtained using a commercial genotyping kit. The performance of our protocol, presented in this proof-of-principle study, supports its use for accurate characterization of genetic variants of hrHPV.
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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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APOBEC Mutagenesis Is Concordant between Tumor and Viral Genomes in HPV-Positive Head and Neck Squamous Cell Carcinoma. Viruses 2021; 13:v13081666. [PMID: 34452530 PMCID: PMC8402723 DOI: 10.3390/v13081666] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
APOBEC is a mutagenic source in human papillomavirus (HPV)-mediated malignancies, including HPV+ oropharyngeal squamous cell carcinoma (HPV + OPSCC), and in HPV genomes. It is unknown why APOBEC mutations predominate in HPV + OPSCC, or if the APOBEC-induced mutations observed in both human cancers and HPV genomes are directly linked. We performed sequencing of host somatic exomes, transcriptomes, and HPV16 genomes from 79 HPV + OPSCC samples, quantifying APOBEC mutational burden and activity in both host and virus. APOBEC was the dominant mutational signature in somatic exomes. In viral genomes, there was a mean of five (range 0-29) mutations per genome. The mean of APOBEC mutations in viral genomes was one (range 0-5). Viral APOBEC mutations, compared to non-APOBEC mutations, were more likely to be low-variant allele fraction mutations, suggesting that APOBEC mutagenesis actively occurrs in viral genomes during infection. HPV16 APOBEC-induced mutation patterns in OPSCC were similar to those previously observed in cervical samples. Paired host and viral analyses revealed that APOBEC-enriched tumor samples had higher viral APOBEC mutation rates (p = 0.028), and APOBEC-associated RNA editing (p = 0.008), supporting the concept that APOBEC mutagenesis in host and viral genomes is directly linked and occurrs during infection. Using paired sequencing of host somatic exomes, transcriptomes, and viral genomes, we demonstrated for the first-time definitive evidence of concordance between tumor and viral APOBEC mutagenesis. This finding provides a missing link connecting APOBEC mutagenesis in host and virus and supports a common mechanism driving APOBEC dysregulation.
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Arizmendi-Izazaga A, Navarro-Tito N, Jiménez-Wences H, Mendoza-Catalán MA, Martínez-Carrillo DN, Zacapala-Gómez AE, Olea-Flores M, Dircio-Maldonado R, Torres-Rojas FI, Soto-Flores DG, Illades-Aguiar B, Ortiz-Ortiz J. Metabolic Reprogramming in Cancer: Role of HPV 16 Variants. Pathogens 2021; 10:pathogens10030347. [PMID: 33809480 PMCID: PMC7999907 DOI: 10.3390/pathogens10030347] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/13/2021] [Accepted: 03/14/2021] [Indexed: 12/12/2022] Open
Abstract
Metabolic reprogramming is considered one of the hallmarks in cancer and is characterized by increased glycolysis and lactate production, even in the presence of oxygen, which leads the cancer cells to a process called “aerobic glycolysis” or “Warburg effect”. The E6 and E7 oncoproteins of human papillomavirus 16 (HPV 16) favor the Warburg effect through their interaction with a molecule that regulates cellular metabolism, such as p53, retinoblastoma protein (pRb), c-Myc, and hypoxia inducible factor 1α (HIF-1α). Besides, the impact of the E6 and E7 variants of HPV 16 on metabolic reprogramming through proteins such as HIF-1α may be related to their oncogenicity by favoring cellular metabolism modifications to satisfy the energy demands necessary for viral persistence and cancer development. This review will discuss the role of HPV 16 E6 and E7 variants in metabolic reprogramming and their contribution to developing and preserving the malignant phenotype of cancers associated with HPV 16 infection.
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Affiliation(s)
- Adán Arizmendi-Izazaga
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (A.A.-I.); (M.A.M.-C.); (A.E.Z.-G.); (F.I.T.-R.); (D.G.S.-F.); (B.I.-A.)
| | - Napoleón Navarro-Tito
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (N.N.-T.); (M.O.-F.)
| | - Hilda Jiménez-Wences
- Laboratorio de Investigación en Biomoléculas, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (H.J.-W.); (D.N.M.-C.)
- Laboratorio de Investigación Clínica, Facultad de Ciencias, Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico;
| | - Miguel A. Mendoza-Catalán
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (A.A.-I.); (M.A.M.-C.); (A.E.Z.-G.); (F.I.T.-R.); (D.G.S.-F.); (B.I.-A.)
- Laboratorio de Investigación en Biomoléculas, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (H.J.-W.); (D.N.M.-C.)
| | - Dinorah N. Martínez-Carrillo
- Laboratorio de Investigación en Biomoléculas, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (H.J.-W.); (D.N.M.-C.)
- Laboratorio de Investigación Clínica, Facultad de Ciencias, Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico;
| | - Ana E. Zacapala-Gómez
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (A.A.-I.); (M.A.M.-C.); (A.E.Z.-G.); (F.I.T.-R.); (D.G.S.-F.); (B.I.-A.)
| | - Monserrat Olea-Flores
- Laboratorio de Biología Celular del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (N.N.-T.); (M.O.-F.)
| | - Roberto Dircio-Maldonado
- Laboratorio de Investigación Clínica, Facultad de Ciencias, Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico;
- Laboratorio de Diagnóstico e Investigación en Salud, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico
| | - Francisco I. Torres-Rojas
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (A.A.-I.); (M.A.M.-C.); (A.E.Z.-G.); (F.I.T.-R.); (D.G.S.-F.); (B.I.-A.)
| | - Diana G. Soto-Flores
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (A.A.-I.); (M.A.M.-C.); (A.E.Z.-G.); (F.I.T.-R.); (D.G.S.-F.); (B.I.-A.)
| | - Berenice Illades-Aguiar
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (A.A.-I.); (M.A.M.-C.); (A.E.Z.-G.); (F.I.T.-R.); (D.G.S.-F.); (B.I.-A.)
- Laboratorio de Diagnóstico e Investigación en Salud, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico
| | - Julio Ortiz-Ortiz
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (A.A.-I.); (M.A.M.-C.); (A.E.Z.-G.); (F.I.T.-R.); (D.G.S.-F.); (B.I.-A.)
- Laboratorio de Investigación en Biomoléculas, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Av. Lázaro Cárdenas S/N, Ciudad Universitaria, Colonia La Haciendita, Chilpancingo C.P. 39090, Guerrero, Mexico; (H.J.-W.); (D.N.M.-C.)
- Correspondence: ; Tel.: +52-747-471-0901
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10
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High prevalence of human papillomavirus and European variants of HPV 16 infecting concomitantly to cervix and oral cavity in HIV positive women. PLoS One 2020; 15:e0227900. [PMID: 32320400 PMCID: PMC7176371 DOI: 10.1371/journal.pone.0227900] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 01/02/2020] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Identify the prevalence of HPV infections in the uterine cervix and oral cavity and HPV16 variants in HIV+ women. METHODS A total of 174 HIV+ women attended an HIV+ specialized clinic in Mexico City. Cells were obtained from the oral cavity and cervix to extract DNA. Polymerase chain reaction (PCR) was used to amplify the HPV sequence with generic primers. We detected specific HPV types using the INNO-LiPA HPV Genotyping Extra II Kit (INNOGENETICS). The identification of variants was studied by sequencing the E6 gene with a Big Dye Terminator Kit and an Applied Biosystems 3500/3500xL genetic analyzer. RESULTS HPV infection was very high in the uterine cervix (168/174, 96.6%) and oral cavity (161/174, 92.5%). The prevalence of HPV concurrent infections in the cervix and oral cavity was 155/174 (89.1%). We found hrHPVs to be more prevalent than low-risk HPVs (lrHPVs) in the oral cavity (90.2% versus 45.4%) and that infections simultaneously affected the cervix (94.3% versus 36.2%) and oral cavity (85.1% versus 20.1%). Surprisingly, only European variants of HPV type 16 were found in the uterine cervix of women and the oral cavity of all tested samples (52 oral cavity samples and 52 uterine cervix samples). CONCLUSIONS The high prevalence of HPV, multiple infections and presence of the EP350G intravariant in both anatomical regions are strongly related to the persistence of the virus, which is fundamental for the development of cancer. Therefore, it is very important to control and monitor this high-risk population as well as implement programs for the early detection of HPV and vaccination.
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11
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Zhu B, Xiao Y, Yeager M, Clifford G, Wentzensen N, Cullen M, Boland JF, Bass S, Steinberg MK, Raine-Bennett T, Lee D, Burk RD, Pinheiro M, Song L, Dean M, Nelson CW, Burdett L, Yu K, Roberson D, Lorey T, Franceschi S, Castle PE, Walker J, Zuna R, Schiffman M, Mirabello L. Mutations in the HPV16 genome induced by APOBEC3 are associated with viral clearance. Nat Commun 2020; 11:886. [PMID: 32060290 PMCID: PMC7021686 DOI: 10.1038/s41467-020-14730-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 01/28/2020] [Indexed: 12/24/2022] Open
Abstract
HPV16 causes half of cervical cancers worldwide; for unknown reasons, most infections resolve within two years. Here, we analyze the viral genomes of 5,328 HPV16-positive case-control samples to investigate mutational signatures and the role of human APOBEC3-induced mutations in viral clearance and cervical carcinogenesis. We identify four de novo mutational signatures, one of which matches the COSMIC APOBEC-associated signature 2. The viral genomes of the precancer/cancer cases are less likely to contain within-host somatic HPV16 APOBEC3-induced mutations (Fisher's exact test, P = 6.2 x 10-14), and have a 30% lower nonsynonymous APOBEC3 mutation burden compared to controls. We replicate the low prevalence of HPV16 APOBEC3-induced mutations in 1,749 additional cases. APOBEC3 mutations also historically contribute to the evolution of HPV16 lineages. We demonstrate that cervical infections with a greater burden of somatic HPV16 APOBEC3-induced mutations are more likely to be benign or subsequently clear, suggesting they may reduce persistence, and thus progression, within the host.
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Affiliation(s)
- Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Yanzi Xiao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gary Clifford
- Infections and Cancer Epidemiology Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372, Lyon, Cedex 08, France
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mia K Steinberg
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tina Raine-Bennett
- Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - DongHyuk Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Robert D Burk
- Departments of Pediatrics, Microbiology and Immunology, and Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Chase W Nelson
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - David Roberson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Thomas Lorey
- Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA, USA
| | | | - Philip E Castle
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joan Walker
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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12
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Méndez-Martínez R, Maldonado-Frías S, Vázquez-Vega S, Caro-Vega Y, Rendón-Maldonado JG, Guido-Jiménez M, Crabtree-Ramírez B, Sierra-Madero JG, García-Carrancá A. High prevalent human papillomavirus infections of the oral cavity of asymptomatic HIV-positive men. BMC Infect Dis 2020; 20:27. [PMID: 31924186 PMCID: PMC6954555 DOI: 10.1186/s12879-019-4677-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/29/2019] [Indexed: 12/24/2022] Open
Abstract
Background Incidence of anal and oral infections with Human Papillomavirus (HPV) is increasing, particularly among Human Immunodeficiency Virus-positive (HIV+) men. HPV type 16 has exhibited the highest incidence and only limited data is available on other prevalent types, variants of HPV16, as well as associated factors. We were interested in identifying prevalent HPV types, variants of type 16, as well as factors associated with HPV16 infections in the oral cavity of HIV+ men who have sex with men (MSM). Methods A cross-sectional study of oral cavity samples from HIV+ MSM, that in a previous study were identified as positive for HPV16 in the anal canal. Cells from the oral cavity (102 samples, paired with 102 from the anal canal of same patient) were used to extract DNA and detect HPV infections using INNO-LiPA HPV Genotyping Extra II, and PCR. From these, 80 samples (paired, 40 anal and 40 oral) were used to identify variants of type 16 by sequencing. Statistical differences were estimated by the X2 test, and p values equal to or less than 0.05 were considered significant. SPSS ver. Twenty-four statistical software (IBM Corp) was used. Results We found a high prevalence of High-Risk HPV (HR-HPV) and Low-Risk HPV (LR-HPV). Patients were positive in the oral cavity for HR types; 16, 39 and 18 (80.4, 61.8 and 52.9% respectively) and LR types 11 and 6 (53.9 and 34.3% respectively). Surprisingly, only European variants of type 16 were found in the oral cavity, although American Asian (22.5%) and African (2.5%) variants were identified in the anal canal. The analysis showed that CD4 counts could be the most important risk factor associated with HR-HPV infections in the oral cavity, anal canal or both anatomical regions. The risk of infection of the oral cavity with type 18 increased in men diagnosed with HIV for more than 6 years. Conclusions Prevalence of both HR and LR HPV’s in the oral cavity of Mexican HIV+ MSM is very high. The fact that only European variants of HPV16 were found in the oral cavity suggest a possible tropism not previously described.
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Affiliation(s)
- Rocío Méndez-Martínez
- División de Investigación Básica, Instituto Nacional de Cancerología, Av. San Fernando #22, Tlalpan, 2do piso, Torre de Investigación Básica, 14080, CDMX, México City, Mexico.,Doctorado en Biotecnología & Doctorado en Ciencias Biomédicas, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, Mexico
| | - Silvia Maldonado-Frías
- División de Estudios de Posgrado e Investigación, Facultad de Odontología, Universidad Nacional Autónoma de México, Universidad 3000, Coyoacán, Copilco Universidad, 04360 Ciudad de México, CDMX, México City, Mexico
| | - Salvador Vázquez-Vega
- Unidad de Investigación Epidemiológica y en Servicios de Salud, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Doctores 330, Cuauhtemoc, 06720, Ciudad de México, CDMX, Mexico
| | - Yanink Caro-Vega
- Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán" (INCMNSZ), Secretaría de Salud, México City, Mexico
| | - José Guadalupe Rendón-Maldonado
- Facultad de Ciencias Químico-Biológicas- UAS, Universidad Autónoma de Sinaloa, Calz. de las Américas Norte 2771, Burócrata, 80030, Culiacán, Sinaloa, Mexico
| | - Miriam Guido-Jiménez
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México & Instituto Nacional de Cancerología, Av. San Fernando #22, Tlalpan, 2do piso, Torre de Investigación Básica, 14080, CDMX, México City, Mexico
| | - Brenda Crabtree-Ramírez
- Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán" (INCMNSZ), Secretaría de Salud, México City, Mexico
| | - Juan G Sierra-Madero
- Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán" (INCMNSZ), Secretaría de Salud, México City, Mexico
| | - Alejandro García-Carrancá
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México & Instituto Nacional de Cancerología, Av. San Fernando #22, Tlalpan, 2do piso, Torre de Investigación Básica, 14080, CDMX, México City, Mexico.
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13
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Tan G, Duan M, Li Y, Zhang N, Zhang W, Li B, Qu P. Distribution of HPV 16 E6 gene variants in screening women and its associations with cervical lesions progression. Virus Res 2019; 273:197740. [PMID: 31493439 DOI: 10.1016/j.virusres.2019.197740] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 11/28/2022]
Abstract
The aim of this study is to investigate distribution of human papillomavirus (HPV) 16 variants in screening healthy women and the potential association between HPV 16 variants and progression of cervical lesions. For this study a total of 2000 healthy women in Tianjin urban area and 212 patients who were HPV 16 positive and underwent colposcopy were analyzed for HPV 16 variants by pyrosequencing. The results show that the HPV 16 was the most prevalent genotype in Tianjin healthy women and five HPV 16 variant types were detected. The HPV 16 variants were determined by sequencing parital E6 region and the detected variants were European prototype E-T350 (E-p), E-G350, E-C109 G, Asian (As) and Asian-American (AA), among which the E-p variant was the most prevalent (82.76%) followed by As variant. Interestingly, in patients with suspected cervical lesions the most prevalent variant was As variant (54.9%) by increasing significance with severity of cervical diseases (OR 4.337; 95% CI 1.248-15.067; P = 0.021), and followed by HPV 16 E-p variant while E-G350 variant only appeared in HSIL and cervical cancer. Our results show that HPV 16 E-p variant was more prevalent than As in Tianjin healthy screening women while As variant was the most frequently type in HSIL and cervical cancer. It is suggested that the mutation of HPV 16 Asian variants, comparing with HPV 16 E-p variants, might contribute to the transformation from HPV 16 persistent infection to cervical cancer.
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Affiliation(s)
- Guichun Tan
- Tianjin Medical University, No. 22 Meteorological Observatory Road, Heping District, Tianjin, China; Tianjin Central Hospital of Gynecology Obstetrics, No. 156 Nankai San Ma Road, Nankai District, Tianjin, China
| | - Meng Duan
- Jining No.1 People's Hospital, Shandong, No. 6 Health Road, Rencheng District, Jining, China
| | - Yan'e Li
- Tianjin Medical University, No. 22 Meteorological Observatory Road, Heping District, Tianjin, China; Tianjin Central Hospital of Gynecology Obstetrics, No. 156 Nankai San Ma Road, Nankai District, Tianjin, China
| | - Na Zhang
- Tianjin Central Hospital of Gynecology Obstetrics, No. 156 Nankai San Ma Road, Nankai District, Tianjin, China
| | - Wenwen Zhang
- Tianjin Central Hospital of Gynecology Obstetrics, No. 156 Nankai San Ma Road, Nankai District, Tianjin, China
| | - Bohan Li
- Tianjin Central Hospital of Gynecology Obstetrics, No. 156 Nankai San Ma Road, Nankai District, Tianjin, China
| | - Pengpeng Qu
- Tianjin Central Hospital of Gynecology Obstetrics, No. 156 Nankai San Ma Road, Nankai District, Tianjin, China.
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14
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Álvarez-Paredes L, Santibañez M, Galiana A, Rodríguez Díaz JC, Parás-Bravo P, Andrada-Becerra ME, Ruiz García MM, Rodríguez-Ingelmo JM, Portilla-Sogorb J, Paz-Zulueta M. Association of Human Papillomavirus Genotype 16 Viral Variant and Viral Load with Cervical High-grade Intraepithelial Lesions. Cancer Prev Res (Phila) 2019; 12:547-556. [PMID: 31208965 DOI: 10.1158/1940-6207.capr-18-0397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 05/15/2019] [Accepted: 06/11/2019] [Indexed: 11/16/2022]
Abstract
Human papillomavirus genotype 16 (HPV16) is by far the genotype most strongly associated with cervical cancer; viral variant and/or viral load of HPV16 could modulate this association. The objective was to determine the association between the viral variant and viral load of HPV16 and the presence of cervical high-grade lesions. This cross-sectional study included all women in whom HPV infection was found by cervical smear during routine gynecologic health checks. Women with single or multiple HPV16 infections (n = 176) were selected for viral variant and viral load analysis. Smear results were classified using the Bethesda system. HPV types were classified according to the International Agency for Research on Cancer. Odds ratios (OR) with their 95% confidence intervals (CI) were estimated by logistic regression, adjusted for age, immigrant status, and coinfection with other high-risk genotypes. No statistically significant associations were found regarding the detected viral variants. A viral load above the median (>1,367.79 copies/cell) was associated with a significant risk of high-grade epithelial lesion or carcinoma, after adjusting for age, immigrant status, coinfections, and viral variant: (adjusted OR 7.89; 95% CI: 2.75-22.68). This relationship showed a statistically significant dose-response pattern after categorizing by viral load tertiles: adjusted OR for a viral load greater than the third tertile was 17.23 (95% CI: 4.20-70.65), with adjusted linear P trend = 0.001. In patients infected with HPV16, viral load is associated with high-grade intraepithelial lesions or cervical carcinoma. This could be useful as prognostic biomarker of neoplastic progression and as screening for cervical cancer.
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Affiliation(s)
| | - Miguel Santibañez
- Department of Nursing, Nursing Research Group-IDIVAL, University of Cantabria, Cantabria, Spain
| | - Antonio Galiana
- Department of Microbiology, University General Hospital of Elche, Alicante, Spain
| | | | - Paula Parás-Bravo
- Department of Nursing, Nursing Research Group-IDIVAL, University of Cantabria, Cantabria, Spain
| | | | | | | | | | - María Paz-Zulueta
- Department of Nursing, University of Cantabria, Cantabria, Spain. IDIVAL, GI Derecho Sanitario y Bioetica, GRIDES, Cantabria, Spain.
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15
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Clifford GM, Tenet V, Georges D, Alemany L, Pavón MA, Chen Z, Yeager M, Cullen M, Boland JF, Bass S, Steinberg M, Raine-Bennett T, Lorey T, Wentzensen N, Walker J, Zuna R, Schiffman M, Mirabello L. Human papillomavirus 16 sub-lineage dispersal and cervical cancer risk worldwide: Whole viral genome sequences from 7116 HPV16-positive women. PAPILLOMAVIRUS RESEARCH (AMSTERDAM, NETHERLANDS) 2019; 7:67-74. [PMID: 30738204 PMCID: PMC6374642 DOI: 10.1016/j.pvr.2019.02.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/03/2019] [Indexed: 01/23/2023]
Abstract
BACKGROUND Human papillomavirus (HPV)16 can be separated into genetic sub-lineages (A1-4, B1-4, C1-4, D1-4) which may have differential cervical cancer risk. METHODS A next-generation sequencing assay was used to whole-genome sequence 7116 HPV16-positive cervical samples from well-characterised international epidemiological studies, including 2076 controls, 1878 squamous cell carcinoma (SCC) and 186 adenocarcinoma/adenosquamous cell carcinoma (ADC), and to assign HPV16 sub-lineage. Logistic regression was used to estimate region-stratified country-adjusted odds ratios (OR) and 95%CI. RESULTS A1 was the most globally widespread sub-lineage, with others showing stronger regional specificity (A3 and A4 for East Asia, B1-4 and C1-4 for Africa, D2 for the Americas, B4, C4 and D4 for North Africa). Increased cancer risks versus A1 were seen for A3, A4 and D (sub)lineages in regions where they were common: A3 in East Asia (OR=2.2, 95%CI:1.0-4.7); A4 in East Asia (6.6, 3.1-14.1) and North America (3.8, 1.7-8.3); and D in North (6.2, 4.1-9.3) and South/Central America (2.2, 0.8-5.7), where D lineages were also more frequent in ADC than SCC (3.2, 1.5-6.5; 12.1, 5.7-25.6, respectively). CONCLUSIONS HPV16 genetic variation can strongly influence cervical cancer risk. However, burden of cervical cancer attributable to different sub-lineages worldwide is largely driven by historical HPV16 sub-lineage dispersal.
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Affiliation(s)
| | - Vanessa Tenet
- International Agency for Research on Cancer, Lyon, France.
| | - Damien Georges
- International Agency for Research on Cancer, Lyon, France.
| | - Laia Alemany
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology, Bellvitge Institute of Biomedical Research, Barcelona, Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.
| | - Miquel Angel Pavón
- Infections and Cancer Unit, Cancer Epidemiology Research Program, Catalan Institute of Oncology, Bellvitge Institute of Biomedical Research, Barcelona, Spain; CIBER en Oncología (CIBERONC), Barcelona, Spain.
| | - Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA.
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA.
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA.
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA.
| | - Mia Steinberg
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD, USA.
| | - Tina Raine-Bennett
- Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA.
| | - Thomas Lorey
- Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA, USA.
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
| | - Joan Walker
- University of Oklahoma Health Sciences Center, Oklahoma City, USA.
| | - Rosemary Zuna
- University of Oklahoma Health Sciences Center, Oklahoma City, USA.
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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16
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Zhou Z, Yang H, Yang L, Yao Y, Dai S, Shi L, Li C, Yang L, Yan Z, Yao Y. Human papillomavirus type 16 E6 and E7 gene variations associated with cervical cancer in a Han Chinese population. INFECTION GENETICS AND EVOLUTION 2019; 73:13-20. [PMID: 30981880 DOI: 10.1016/j.meegid.2019.04.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUD Human papillomavirus type 16 (HPV16) is a high-risk HPV subtype and a potent carcinogen. The HPV16 E6 and E7 genes are considered oncogenes that play a core role in the development of cervical cancer. METHODS In the current study, we enrolled 97 HPV16-positive cervical cancer patients (case group) and 136 HPV16-positive asymptomatic individuals (control group) in a study to analyse the association between HPV16 E6 and E7 gene variations and cervical cancer. RESULTS Our results showed that three HPV16 sub-lineages (A1-A3, A4 and D3) were present; the distribution of these variants between the case and control group was not significantly different (P = 0.178). When the distribution of the HPV16 E6 and E7 gene variations was compared, the distribution of only A131C (R10R) in the E6 gene showed a different trend between the case and control groups and C749T (S63F) in the E7 gene was significantly different between the case and control groups (P = 0.071 and P = 4.861 × 10-10, respectively). Regarding the sub-lineages, no variations in the E6 gene were significantly different between the case and control group for the A4 (As) and A1-A3 (EUR) sub-lineages. However, the distribution of C749T (S63F) in the E7 gene was significantly different between the case and control groups for the A4 (As) and A1-A3 (EUR) sub-lineages (P = 1.815 × 10-8 and P = 0.008). In the current study, we found that the C749T (S63F) variation in the HPV16 E7 gene was associated with cervical cancer not only in the A4 (As) sub-lineage but also in the A1-A3 (EUR) sub-lineage. CONCLUSION Our study will provide a good reference for further functional studies of the relationship between cervical cancer carcinogenesis and the HPV16 E6 and E7 genes.
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Affiliation(s)
- Ziyun Zhou
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Hongying Yang
- Department of Gynaecologic Oncology, The 3rd Affiliated Hospital of Kunming Medical University, Kunming 650118, China
| | - Lijuan Yang
- Department of Gynaecologic Oncology, The 3rd Affiliated Hospital of Kunming Medical University, Kunming 650118, China
| | - Yueting Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Shuying Dai
- School of Basic Medical Science, Kunming Medical University, Kunming 650500, China
| | - Li Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Chuanyin Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Longyu Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China
| | - Zhiling Yan
- Department of Gynaecologic Oncology, The 3rd Affiliated Hospital of Kunming Medical University, Kunming 650118, China.
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming 650118, Yunnan, China.
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17
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Galati L, Equestre M, Bruni R, Accardi L, Torti C, Fiorillo MT, Surace G, Barreca GS, Liberto MC, Focà A, Ciccaglione AR, Di Bonito P. Identification of human papillomavirus type 16 variants circulating in the Calabria region by sequencing and phylogenetic analysis of HPV16 from cervical smears. INFECTION GENETICS AND EVOLUTION 2018; 68:185-193. [PMID: 30578936 DOI: 10.1016/j.meegid.2018.12.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 02/04/2023]
Abstract
Sequence analysis of HPV16 isolates reveals the presence of genome variants with characteristic mutations. The HPV16 variants have different geographical distribution and diverge into four phylogenetic lineages (A, B, C and D) and 16 sub-lineages: A1, A2, A3 (previously known as European variants), A4 (Asian variant), B1, B2, B3, B4, C1, C2, C3, and C4 (African variants), D1 (North-American variant), D2, D3 (Asian-American variants) and D4. Population studies showed that infections with viruses belonging to specific HPV16 sublineages confer different risks of viral persistence and cancer. In this study, 39 HPV16-positive cervical smears from European women living in Calabria (Italy) were analyzed for the presence of HPV16 variants. Cervical DNA extracts were processed by PCR to amplify L1, the Long Control Region (LCR), E6 and E7, which were sequenced. The sequences were concatenated and the 3169 nucleotides long fragments were characterized by BLAST and phylogenetic analysis. A total of 96 Single Nucleotide Polymorphism (SNPs) were detected, 29 of which mapping in the L1, 45 in the LCR, 15 in the E6 and 7 in the E7. The most common SNP was the T350G (29/39 samples, 74.4%), causing the L83 V amino acid change in the E6. Most of the HPV16 isolates (89.7%) had 99% of nucleotide (nt) identity to members of the A1 and A2 sublineages, while 4 isolates had 99% nt identity to members of the B2, B4, C1 and D4 sublineages. In conclusion, viruses belonging to the A1, A2, B2, B4, C1 and D4 HPV16 sublineages were found to circulate in the Calabria region.
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Affiliation(s)
- Luisa Galati
- Department Infectious Diseases, EVOR unit, Istituto Superiore di Sanità, Rome, Italy; Institute of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Michele Equestre
- Department Cell Biology and Neurosciences, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Bruni
- Department Infectious Diseases, EVOR unit, Istituto Superiore di Sanità, Rome, Italy
| | - Luisa Accardi
- Department Infectious Diseases, EVOR unit, Istituto Superiore di Sanità, Rome, Italy
| | - Carlo Torti
- Department of Medical and Surgical Sciences, Unit of Infectious and Tropical Diseases, School of Medicine, University of "Magna Graecia", Catanzaro, Italy
| | - Maria Teresa Fiorillo
- Unit of Microbiology and Virology, Polo Sanitario Nord ASP 5, Reggio Calabria, Italy
| | - Giovanni Surace
- Unit of Microbiology and Virology, Polo Sanitario Nord ASP 5, Reggio Calabria, Italy
| | - Giorgio Settimo Barreca
- Institute of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Maria Carla Liberto
- Institute of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Alfredo Focà
- Institute of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Anna Rita Ciccaglione
- Department Infectious Diseases, EVOR unit, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Di Bonito
- Department Infectious Diseases, EVOR unit, Istituto Superiore di Sanità, Rome, Italy.
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Cuschieri K, Ronco G, Lorincz A, Smith L, Ogilvie G, Mirabello L, Carozzi F, Cubie H, Wentzensen N, Snijders P, Arbyn M, Monsonego J, Franceschi S. Eurogin roadmap 2017: Triage strategies for the management of HPV-positive women in cervical screening programs. Int J Cancer 2018; 143:735-745. [PMID: 29341110 DOI: 10.1002/ijc.31261] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/20/2017] [Accepted: 01/03/2018] [Indexed: 01/04/2023]
Abstract
Cervical cancer screening will rely, increasingly, on HPV testing as a primary screen. The requirement for triage tests which can delineate clinically significant infection is thus prescient. In this EUROGIN 2017 roadmap, justification behind the most evidenced triages is outlined, as are challenges for implementation. Cytology is the triage with the most follow-up data; the existence of an HR-HPV-positive, cytology-negative group presents a challenge and retesting intervals for this group (and choice of retest) require careful consideration. Furthermore, cytology relies on subjective skills and while adjunctive dual-staining with p16/Ki67 can mitigate inter-operator/-site disparities, clinician-taken samples are required. Comparatively, genotyping and methylation markers are objective and are applicable to self-taken samples, offering logistical advantages including in low and middle income settings. However, genotyping may have diminishing returns in immunised populations and type(s) included must balance absolute risk for disease to avoid low specificity. While viral and cellular methylation markers show promise, more prospective data are needed in addition to refinements in automation. Looking forward, systems that detect multiple targets concurrently such as next generation sequencing platforms will inform the development of triage tools. Additionally, multistep triage strategies may be beneficial provided they do not create complex, unmanageable pathways. Inevitably, the balance of risk to cost(s) will be key in decision making, although defining an acceptable risk will likely differ between settings. Finally, given the significant changes to cervical screening and the variety of triage strategies, appropriate education of both health care providers and the public is essential.
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Affiliation(s)
- Kate Cuschieri
- Scottish HPV Reference Laboratory, Department of Laboratory Medicine, NHS Lothian, Royal Infirmary of Edinburgh, 51 Little France Crescent, Edinburgh, EH16 4SA, United Kingdom
| | - Guglielmo Ronco
- Centre for Cancer Prevention (CPO), AOU Città della Salute e della Scienza via Cavour 39, Torino, 10123, Italy
| | - Attila Lorincz
- Wolfson Institute of Preventive Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, United Kingdom
| | - Laurie Smith
- University of British Columbia and BC Women's Hospital and Health Centre, 4500 Oak Street, Vancouver, British Columbia, V6H 3N1, Canada
| | - Gina Ogilvie
- Faculty of Medicine, University of British Columbia, British Columbia, Canada
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Francesca Carozzi
- Cancer Prevention Regional Laboratory, ISPO, Cancer Prevention and Research Institute, Florence, Italy
| | - Heather Cubie
- Global Health Academy, University of Edinburgh, Teviot Quad, Edinburgh, EH8 9PG, United Kingdom
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Peter Snijders
- Department of Pathology, VU University Medical Center (VUmc), Amsterdam, The Netherlands
| | - Marc Arbyn
- Unit of Cancer Epidemiology, Belgian Cancer Centre, Scientific Institute of Public Health, Brussels, Belgium
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Pham TTT, Bi X, Hoang HTT, Ishizaki A, Nguyen MTP, Nguyen CH, Nguyen HP, Pham TV, Ichimura H. Human Papillomavirus Genotypes and HPV16 E6/E7 Variants among Patients with Genital Cancers in Vietnam. Jpn J Infect Dis 2018; 71:419-426. [PMID: 29962490 DOI: 10.7883/yoken.jjid.2018.206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We previously reported human papillomavirus type 52 (HPV52) as the most prevalent high-risk genotype in non-cancer individuals in Vietnam. This study aimed to evaluate HPV genotypes and HPV16 E6 and E7 (E6/E7) gene variations in Vietnamese patients with genital cancers. Biopsy samples were collected from 124 Vietnamese patients with genital cancers (20 with vaginal, 50 with vulvar, and 54 with penile cancer). The HPV-DNA was amplified and genotyped, and HPV16 E6/E7 genes were compared with those previously reported for women with normal cervical cytology (N = 23). HPV-DNA was detected in 80.6% (100/124) of the cancer patients (80.0% of vaginal, 82.0% of vulvar, and 79.6% of penile), with HPV16/18 in 86.0% (86/100) and HPV52 in 7.0% (7/100) of the HPV-positive samples. The HPV-DNA prevalence and HPV genotype distribution did not significantly differ among the genital cancer patients (both P = 0.95). Significantly fewer instances of the HPV16 A4 sublineage (34.8% vs. 82.6%, P < 0.0001) and HPV16 E7 29S (36.4% vs. 87.0%, P = 0.0002) occurred in the cancer patients than in the women with normal cytology. Our results indicate that HPV16/18 accounts for more than 85% of genital cancers in Vietnam, and the HPV16 sublineage A4 containing E7 29S may be less oncogenic.
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Affiliation(s)
- Trang Thi Thu Pham
- Department of Viral Infection and International Health, Graduate School of Medical Sciences/Advanced Preventive Medical Sciences, Kanazawa University
| | - Xiuqiong Bi
- Department of Viral Infection and International Health, Graduate School of Medical Sciences/Advanced Preventive Medical Sciences, Kanazawa University
| | | | - Azumi Ishizaki
- Department of Viral Infection and International Health, Graduate School of Medical Sciences/Advanced Preventive Medical Sciences, Kanazawa University
| | | | | | | | | | - Hiroshi Ichimura
- Department of Viral Infection and International Health, Graduate School of Medical Sciences/Advanced Preventive Medical Sciences, Kanazawa University
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20
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Combes JD, Franceschi S. Human papillomavirus genome variants and head and neck cancers: a perspective. Infect Agent Cancer 2018; 13:13. [PMID: 29643933 PMCID: PMC5891965 DOI: 10.1186/s13027-018-0185-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 03/27/2018] [Indexed: 12/22/2022] Open
Abstract
Human papillomaviruses (HPV) cause infections that are responsible for diverse clinical manifestations from benign conditions to invasive cancer. As different HPV types are associated with variable pathogenic potential, minor genetic variations within a given high-risk HPV type might also be associated with distinct oncogenic capacities, through variable ability of persistence or risk of progression to precancer/cancer. Most recent HPV variant studies in the cervix using latest sequencing technology confirmed that minor changes in the HPV genome can have a major influence on carcinogenesis and have revealed key data that help better understand the carcinogenicity of HPV at a molecular level. Here we review the limited number of studies on HPV genome variants in head and neck cancers (HNC) and discuss their implications for cancer research in the light of accumulated knowledge for the cervix. Challenges in transposing HPV variant studies from the lower anogenital to the upper aerodigestive tract are also discussed, highlighting the main gaps of knowledge in the field of HPV-induced HNC. Specifically in the head and neck region, the lack of characterisation of precancerous lesions and the difficulty in sampling normal tissue will challenge the development of accurate studies. Although there is so far no indication that HPV variant research in HNC could directly translate into clinical application, such research is expected to be useful to disentangle unanswered questions in the pathogenesis of HNC. Yet, history of HPV variant research suggests that, to be successful, studies will require large international collaborative efforts.
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Affiliation(s)
- Jean-Damien Combes
- International Agency for Research on Cancer, 150 cours Albert Thomas, 69372 Cedex 08 Lyon, France
| | - Silvia Franceschi
- Cancer Epidemiology Unit, CRO Aviano National Cancer Institute IRCCS, Via Franco Gallini 2, 33081 Aviano, PN Italy
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21
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Mirabello L, Clarke MA, Nelson CW, Dean M, Wentzensen N, Yeager M, Cullen M, Boland JF, Schiffman M, Burk RD. The Intersection of HPV Epidemiology, Genomics and Mechanistic Studies of HPV-Mediated Carcinogenesis. Viruses 2018; 10:v10020080. [PMID: 29438321 PMCID: PMC5850387 DOI: 10.3390/v10020080] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/24/2018] [Accepted: 02/12/2018] [Indexed: 12/14/2022] Open
Abstract
Of the ~60 human papillomavirus (HPV) genotypes that infect the cervicovaginal epithelium, only 12–13 “high-risk” types are well-established as causing cervical cancer, with HPV16 accounting for over half of all cases worldwide. While HPV16 is the most important carcinogenic type, variants of HPV16 can differ in their carcinogenicity by 10-fold or more in epidemiologic studies. Strong genotype-phenotype associations embedded in the small 8-kb HPV16 genome motivate molecular studies to understand the underlying molecular mechanisms. Understanding the mechanisms of HPV genomic findings is complicated by the linkage of HPV genome variants. A panel of experts in various disciplines gathered on 21 November 2016 to discuss the interdisciplinary science of HPV oncogenesis. Here, we summarize the discussion of the complexity of the viral–host interaction and highlight important next steps for selected applied basic laboratory studies guided by epidemiological genomic findings.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
- Correspondence: (L.M.); (R.D.B.)
| | - Megan A. Clarke
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
| | - Chase W. Nelson
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Joseph F. Boland
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | | | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute, National Institutes of Health, Rockville, MD 20850, USA; (M.A.C.); (C.W.N.); (M.D.); (N.W.); (M.Y.); (M.C.); (J.F.B.); (M.S.)
| | - Robert D. Burk
- Departments of Pediatrics, Microbiology and Immunology, Epidemiology and Population Health, and Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Correspondence: (L.M.); (R.D.B.)
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22
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Islam S, Mazumder Indra D, Basu M, Roychowdhury A, Das P, Dasgupta H, Roy A, Alam N, Mondal RK, Roychoudhury S, Panda CK. Phylogenetic analysis of Human papillomavirus 16 variants isolated from Indian Breast cancer patients showed difference in genetic diversity with that of cervical cancer isolates. Virus Res 2017; 243:1-9. [PMID: 28988982 DOI: 10.1016/j.virusres.2017.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/21/2017] [Accepted: 10/04/2017] [Indexed: 11/29/2022]
Abstract
The genetic variations of HPV16 in Breast Cancer (BC) are not well studied unlike HPV16 in Cervical Cancer (CACX). In this study, the genetic variations of HPV16 in BC were compared with HPV16 in CACX. In sequencing analysis of LCR, E6 and E7 regions of HPV16 in BC and CACX the A lineage was seen to be 64.2% and 66.6% respectively. The other lineages showed differential frequency in BC and CACX. The mutation frequency index of the regions in BC and CACX was in the following order: LCR>E6>E7. However, the inter-patient genetic diversity in LCR and E6/E7 regions was high in BC than CACX. The LCR region showed more variations than the E6/E7 region in BC. Apart from some common variations, some unique tissue specific variants in LCR and E6/E7 region were seen in BC and in CACX. Besides the selection of some common variants in both BC and CACX, some unique variants in BC (D98Y; 395 G>T) and CACX (R48W; 245 G>T) were observed. The 7521 G>A variant of LCR showed association with Luminal B subtype of BC and progression of CACX. Whereas, 145 G>T (Q14H) and 335 C>T (H78Y) variants of E6 showed association with either early invasiveness of BC and/or poor outcome of the patients. Thus, this study indicates that there may be a difference in the genetic variation of HPV16 in BC and in CACX.
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Affiliation(s)
- Saimul Islam
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, West Bengal 700026, India
| | | | - Mukta Basu
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, West Bengal 700026, India
| | - Anirban Roychowdhury
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, West Bengal 700026, India
| | - Pijush Das
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, West Bengal 700032, India
| | - Hemantika Dasgupta
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, West Bengal 700026, India
| | - Anup Roy
- Department of Pathology, NilRatan Sircar Medical College and Hospital, Sealdah, Raja Bazar, 138, Acharya Jagadish Chandra Bose Rd, Kolkata, West Bengal 700014, India
| | - Neyaz Alam
- Department of Surgical Oncology, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, West Bengal 700026, India
| | - Ranajit Kumar Mondal
- Department of Gynaecology Oncology, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, West Bengal 700026, India
| | - Susanta Roychoudhury
- Saroj Gupta Cancer Centre and Research Institute, Thakurpukur, Kolkata 700 063, India
| | - Chinmay Kumar Panda
- Department of Oncogene Regulation, Chittaranjan National Cancer Institute, 37, S.P. Mukherjee Road, Kolkata, West Bengal 700026, India.
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23
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Jackson R, Rosa BA, Lameiras S, Cuninghame S, Bernard J, Floriano WB, Lambert PF, Nicolas A, Zehbe I. Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology. BMC Genomics 2016; 17:851. [PMID: 27806689 PMCID: PMC5094076 DOI: 10.1186/s12864-016-3203-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Human papillomaviruses (HPVs) are a worldwide burden as they are a widespread group of tumour viruses in humans. Having a tropism for mucosal tissues, high-risk HPVs are detected in nearly all cervical cancers. HPV16 is the most common high-risk type but not all women infected with high-risk HPV develop a malignant tumour. Likely relevant, HPV genomes are polymorphic and some HPV16 single nucleotide polymorphisms (SNPs) are under evolutionary constraint instigating variable oncogenicity and immunogenicity in the infected host. RESULTS To investigate the tumourigenicity of two common HPV16 variants, we used our recently developed, three-dimensional organotypic model reminiscent of the natural HPV infectious cycle and conducted various "omics" and bioinformatics approaches. Based on epidemiological studies we chose to examine the HPV16 Asian-American (AA) and HPV16 European Prototype (EP) variants. They differ by three non-synonymous SNPs in the transforming and virus-encoded E6 oncogene where AAE6 is classified as a high- and EPE6 as a low-risk variant. Remarkably, the high-risk AAE6 variant genome integrated into the host DNA, while the low-risk EPE6 variant genome remained episomal as evidenced by highly sensitive Capt-HPV sequencing. RNA-seq experiments showed that the truncated form of AAE6, integrated in chromosome 5q32, produced a local gene over-expression and a large variety of viral-human fusion transcripts, including long distance spliced transcripts. In addition, differential enrichment of host cell pathways was observed between both HPV16 E6 variant-containing epithelia. Finally, in the high-risk variant, we detected a molecular signature of host chromosomal instability, a common property of cancer cells. CONCLUSIONS We show how naturally occurring SNPs in the HPV16 E6 oncogene cause significant changes in the outcome of HPV infections and subsequent viral and host transcriptome alterations prone to drive carcinogenesis. Host genome instability is closely linked to viral integration into the host genome of HPV-infected cells, which is a key phenomenon for malignant cellular transformation and the reason for uncontrolled E6 oncogene expression. In particular, the finding of variant-specific integration potential represents a new paradigm in HPV variant biology.
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Affiliation(s)
- Robert Jackson
- Probe Development and Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada.,Biotechnology Program, Lakehead University, Thunder Bay, Ontario, Canada
| | - Bruce A Rosa
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Sonia Lameiras
- NGS platform, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris, Cedex, France
| | - Sean Cuninghame
- Probe Development and Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada.,Northern Ontario School of Medicine, Lakehead University, Thunder Bay, Ontario, Canada
| | - Josee Bernard
- Probe Development and Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada.,Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
| | - Wely B Floriano
- Department of Chemistry, Lakehead University, Thunder Bay, Ontario, Canada
| | - Paul F Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Alain Nicolas
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique UMR3244, Sorbonne Universités, Paris, France
| | - Ingeborg Zehbe
- Probe Development and Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada. .,Northern Ontario School of Medicine, Lakehead University, Thunder Bay, Ontario, Canada. .,Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada.
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24
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Makowsky R, Lhaki P, Wiener HW, Bhatta MP, Cullen M, Johnson DC, Perry RT, Lama M, Boland JF, Yeager M, Ghimire S, Broker TR, Shrestha S. Genomic diversity and phylogenetic relationships of human papillomavirus 16 (HPV16) in Nepal. INFECTION GENETICS AND EVOLUTION 2016; 46:7-11. [PMID: 27725301 DOI: 10.1016/j.meegid.2016.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 11/30/2022]
Abstract
OBJECTIVES/BACKGROUND Sequence variants in HPV16 confer differences in oncogenic potential; however, to date there have not been any HPV sequence studies performed in Nepal. The objective of this study was to characterize HPV16 viral genome sequences from Nepal compared to a reference sequence in order to determine their lineages. Additionally, we sought to determine if five High-grade Squamous Intraepithelial Lesion (HSIL) subjects were genetically distinct from the non-HSIL subjects. METHODS DNA was isolated from exfoliated cervical cells from 17 individuals in Nepal who were previously identified to be HPV16-positive. A custom HPV16 Ion Ampliseq panel of multiplexed degenerate primers was designed that generated 47 overlapping amplicons and covered 99% of the viral genome for all known HPV16 variant lineages. All sequence data were processed through a custom quality control and analysis pipeline of sequence comparisons and phylogenetic analysis. RESULTS There were high similarities across the genomes, with two major indels observed in the non-coding region between E5 and L2. Compared to the PAVE reference HPV16 genome, there were up to 9, 4, 38, 27, 8, 7, 52, and 32 nucleotide variants in the E6, E7, E1, E2, E4, E5, L2, and L1 genes in the Nepalese samples, respectively. Based on sequence variation, HPV16 from Nepal falls across the A, C, and D lineages in this study. We found no evidence of genetic distinctness between HSIL and non-HSIL subjects. CONCLUSIONS The evolutionary and pathological characteristics of the representative HPV16 genomes from Nepal seem similar to results from other parts of the world and provide the basis for further studies.
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Affiliation(s)
- Robert Makowsky
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, AL, USA
| | | | - Howard W Wiener
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA
| | - Madhav P Bhatta
- Department of Biostatistics, Environmental Health Sciences, and Epidemiology, College of Public Health, Kent State University, OH, USA
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Gaithersburg, MD, USA
| | - Derek C Johnson
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA
| | - Rodney T Perry
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA
| | | | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Gaithersburg, MD, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA; Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Gaithersburg, MD, USA
| | - Sarita Ghimire
- Cancer Screening Center, Nepal Cancer Care Foundation, Lalitpur, Nepal
| | - Thomas R Broker
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sadeep Shrestha
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, AL, USA.
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Mirabello L, Yeager M, Cullen M, Boland JF, Chen Z, Wentzensen N, Zhang X, Yu K, Yang Q, Mitchell J, Roberson D, Bass S, Xiao Y, Burdett L, Raine-Bennett T, Lorey T, Castle PE, Burk RD, Schiffman M. HPV16 Sublineage Associations With Histology-Specific Cancer Risk Using HPV Whole-Genome Sequences in 3200 Women. J Natl Cancer Inst 2016; 108:djw100. [PMID: 27130930 PMCID: PMC5939630 DOI: 10.1093/jnci/djw100] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/19/2016] [Accepted: 02/24/2016] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND HPV16 is a common sexually transmitted infection although few infections lead to cervical precancer/cancer; we cannot distinguish nor mechanistically explain why only certain infections progress. HPV16 can be classified into four main evolutionary-derived variant lineages (A, B, C, D) that have been previously suggested to have varying disease risks. METHODS We used a high-throughput HPV16 whole-genome sequencing assay to investigate variant lineage risk among 3215 HPV16-infected women. Using sublineages A1/A2 as the reference, we assessed all variant lineage associations with infection outcome over three or more years of follow-up: 1107 control subjects ( RESULTS A4 sublineage was associated with an increased risk of cancer, specifically adenocarcinoma (OR = 9.81, 95% CI = 2.02 to 47.69, P = 4.7x10(-03)). Lineage B had a lower risk of CIN3 (OR = 0.51, 95% CI = 0. 28 to 0.91, P = 02) while lineage C showed increased risk (OR = 2.06, 95% CI = 1.09 to 3.89, P = 03). D2/D3 sublineages were strongly associated with an increased risk of CIN3 and cancer, particularly D2 (OR for cancer = 28.48, 95% CI = 9.27 to 87.55, P = 5.0x10(-09)). D2 had the strongest increased risk of glandular lesions, AIS (OR = 29.22, 95% CI = 8.94 to 95.51, P = 2.3x10(-08)), and adenocarcinomas (OR = 137.34, 95% CI = 37.21 to 506.88, P = 1.5x10(-13)). Moreover, the risk of precancer and cancer for specific variant lineages varied by a women's race/ethnicity; those women whose race/ethnicity matched that of the infecting HPV16 variant had an increased risk of CIN3 + (P < 001). CONCLUSIONS Specific HPV16 variant sublineages strongly influence risk of histologic types of precancer and cancer, and viral genetic variation may help explain its unique carcinogenic properties.
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Affiliation(s)
- Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Michael Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Joseph F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Zigui Chen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Xijun Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Qi Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Jason Mitchell
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - David Roberson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Sara Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Yanzi Xiao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Tina Raine-Bennett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Thomas Lorey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Philip E Castle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Robert D Burk
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
| | - Mark Schiffman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD (LM, MY, MC, JFB, NW, XZ, KY, QY, JM, DR, SB, LB, YX, MS); Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, MD (MY, MC, JFB, XZ, QY, JM, DR, SB, LB); Department of Microbiology, The Chinese University of Hong Kong, Hong Kong (ZC); Women's Health Research Institute, Division of Research, Kaiser Permanente Northern California, Oakland CA (TRB); Regional Laboratory, Kaiser Permanente Northern California, Oakland, CA (TL); Department of Epidemiology and Population Health, at Albert Einstein College of Medicine, Bronx, NY (PEC, RDB); Departments of Pediatrics; Microbiology & Immunology; and, Obstetrics, Gynecology and Women's Health, at Albert Einstein College of Medicine, Bronx, NY (RDB)
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Variants of human papillomaviruses 16 (HPV16) in Uigur women in Xinjiang, China. Infect Agent Cancer 2016; 11:44. [PMID: 27540411 PMCID: PMC4989296 DOI: 10.1186/s13027-016-0089-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Persistent infection of high-risk human papillomaviruses 16 (HPV16) has been considered as the leading cause of cervical cancer. In this study we assessed HPV16 sequence variation and genetic diversity of HPV16 variants in cervical cancer in Uigur women in Xinjiang, China. We analyzed the nucleotide sequences of the open reading frames of E6 and E7, and part of the open reading frames of L1 of HPV16 in Uigur women. METHODS Biopsies of histologically confirmed HPV16 infections with cervical cancer were obtained from 43 Uigur women in Xinjiang, China. E6, E7 and L1 genes of HPV16 of all samples were amplified and sequenced; the sequences were used in phylogenetic analysis of HPV16 variants. RESULTS Our analysis revealed nine nucleotide changes in E6 (five changes), E7 (one change) and L1 (three changes) gene. The most frequently observed variations were T350G (79.1 %). One variation T295G (D64E) at E6 were detected in 6 cases (KT959536, KT959542, KT959546, KT959550, KT959553, KT959558). Deletion (464Asp) along with insertion (448Ser) were observed in L1 (100 %). Most variants were European lineage (97.7 %); only one belongs to Asia variants with common T178G (D25E) in E6 and A647G (N29S) in E7. CONCLUSION The most prevalent HPV16 variants in the Uigur women we studied were of the European lineage. Our results indicate that HPV16 European lineage may serve as a harmful factor associated with the development and progression of cervical cancer.
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Togtema M, Jackson R, Richard C, Niccoli S, Zehbe I. The human papillomavirus 16 European-T350G E6 variant can immortalize but not transform keratinocytes in the absence of E7. Virology 2015; 485:274-82. [PMID: 26318249 DOI: 10.1016/j.virol.2015.07.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/05/2015] [Accepted: 07/30/2015] [Indexed: 11/25/2022]
Abstract
Human papillomavirus type 16 is commonly implicated in HPV-related cancers. However, only a small number of infected individuals progress to this stage. Epidemiological evidence demonstrated that oncogenic risk is population-specific and variations within the viral oncogene, E6, have been suggested to play a role in these findings. Of focus in this study is the European-T350G variant, which is characterized by an L>V amino acid substitution at residue 83 of the prototype E6 protein. To elucidate the functional effects of this polymorphism, we followed keratinocytes transduced with E-T350G E6 for over 60 passages and compared them to keratinocytes transduced, in parallel, with prototype or Asian-American (Q14H/L83V/H78Y) E6. We found that although E-T350G E6 immortalized transduced keratinocytes in the absence of E7, these cells were not fully transformed. We also found that E-T350G down-regulated E-cadherin compared to the other variants, providing a possible link between its population-based oncogenicity and host genetic variations.
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Affiliation(s)
- Melissa Togtema
- Probe Development and Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, ON, Canada; Biotechnology Program, Lakehead University, Thunder Bay, ON, Canada
| | - Robert Jackson
- Probe Development and Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, ON, Canada; Biotechnology Program, Lakehead University, Thunder Bay, ON, Canada
| | - Christina Richard
- Regional Cancer Care, Thunder Bay Regional Health Sciences Centre, Thunder Bay, ON, Canada
| | - Sarah Niccoli
- Probe Development and Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, ON, Canada; Department of Biology, Lakehead University, Thunder Bay, ON, Canada
| | - Ingeborg Zehbe
- Probe Development and Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, ON, Canada; Department of Biology, Lakehead University, Thunder Bay, ON, Canada.
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Kukimoto I, Muramatsu M. Genetic variations of human papillomavirus type 16: implications for cervical carcinogenesis. Jpn J Infect Dis 2015; 68:169-75. [PMID: 25766614 DOI: 10.7883/yoken.jjid.2014.584] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Human papillomaviruses (HPVs) are the causative agent of cervical cancer, and among approximately 15 high-risk genotypes, HPV16 accounts for more than half the cases of cervical cancer worldwide. Recent progress in determining HPV genomic sequences from clinical samples has revealed a wide variety in HPV16 genome sequences, and has allowed for comprehensive classification of intratype HPV16 variants. These consist of four variant lineages containing nucleotide variations in 1.0%-10.0% of the complete viral genome sequence. Epidemiological data suggest that the non-European-Asian lineages of HPV16 entail a higher risk of progression to invasive cervical cancer than the European-Asian lineage. Deep sequencing analysis has recently demonstrated that HPV16 genome sequences are highly homogeneous in individual clinical specimens compared with those of RNA viruses. However, an extremely sensitive PCR method, differential DNA denaturation PCR, has detected hypermutations from C to T or G to A in the E2 gene and the long control region of the HPV16 genome, which suggests the involvement of cellular apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) proteins in this hypermutation. The quasispecies status of the HPV16 genome in the infected cervix may affect the development of cervical cancer and warrants further investigation.
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Affiliation(s)
- Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases
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Yang L, Yang H, Wu K, Shi X, Ma S, Sun Q. Prevalence of HPV and variation of HPV 16/HPV 18 E6/E7 genes in cervical cancer in women in South West China. J Med Virol 2014; 86:1926-36. [PMID: 25111286 DOI: 10.1002/jmv.24043] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Lijuan Yang
- Institute of Medical Biology; Chinese Academy of Medical Sciences, and Peking Union Medical College; Kunming China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases; Kunming China
| | - Hongying Yang
- The Third Affiliated Hospital of Kunming Medical University (Yunnan Provincial Tumor Hospital); Kunming China
| | - Kun Wu
- The First Affiliated Hospital of Kunming Medical University; Kunming China
| | - Xinan Shi
- Southwest Guizhou Vocational and Technical College for Nationalities; Xingyi China
| | - Shaohui Ma
- Institute of Medical Biology; Chinese Academy of Medical Sciences, and Peking Union Medical College; Kunming China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases; Kunming China
| | - Qiangming Sun
- Institute of Medical Biology; Chinese Academy of Medical Sciences, and Peking Union Medical College; Kunming China
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases; Kunming China
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Human papillomavirus 16 non-European variants are preferentially associated with high-grade cervical lesions. PLoS One 2014; 9:e100746. [PMID: 24983739 PMCID: PMC4077691 DOI: 10.1371/journal.pone.0100746] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/29/2014] [Indexed: 01/10/2023] Open
Abstract
HPV16 accounts for 50–70% of cervical cancer cases worldwide. Characterization of HPV16 variants previously indicated that they differ in risks for viral persistence, progression to cervical precancer and malignant cancer. The aim of this study was to examine the association of severity of disease with HPV16 variants identified in specimens (n = 281) obtained from a Cervical Pathology and Colposcopy outpatient clinic in the University Hospital of Espírito Santo State, Southeastern Brazil, from April 2010 to November 2011. All cytologic and histologic diagnoses were determined prior to definitive treatment. The DNA was isolated using QIAamp DNA Mini Kit and HPV was detected by amplification with PGMY09/11 primers and positive samples were genotyped by RFLP analyses and reverse line blot. The genomes of the HPV16 positive samples were sequenced, from which variant lineages were determined. Chi2 statistics was performed to test the association of HPV16 variants between case and control groups. The prevalence of HR-HPV types in <CIN1, CIN2 and CIN3+ were 33.7%, 84.4% and 91.6%, respectively. Thirty-eight of 49 (78%) HPV16 positive samples yielded HPV16 sequence information; of which, 32 complete genomes were sequenced and an additional 6 samples were partially sequenced. Phylogenetic analysis and patterns of variations identified 65.8% (n = 25) as HPV16 European (E) and 34.2% (n = 13) as non-European (NE) variants. Classification of disease into CIN3+ vs. <CIN3 indicated that NE types were associated with high-grade disease with an OR = 4.6 (1.07–20.2, p = 0.05). The association of HPV16 NE variants with an increased risk of CIN3+ is consistent with an HPV16 genetically determined enhanced oncogenicity. The prevalence of genetic variants of HPV16 is distributed across different geographical areas and with recent population admixture, only empiric data will provide information on the highest risk HPV16 variants within a given population.
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Jackson R, Togtema M, Lambert PF, Zehbe I. Tumourigenesis driven by the human papillomavirus type 16 Asian-American e6 variant in a three-dimensional keratinocyte model. PLoS One 2014; 9:e101540. [PMID: 24983759 PMCID: PMC4077794 DOI: 10.1371/journal.pone.0101540] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 04/30/2014] [Indexed: 12/22/2022] Open
Abstract
Infection with a transforming human papillomavirus (HPV) such as type 16 (of species Alphapapillomavirus 9) causes ano-genital and oral tumours via viral persistence in human squamous cell epithelia. Epidemiological studies showed that the naturally occurring HPV16 Asian-American (AA) variant (sublineage D2/D3) is found more often than the European Prototype (EP) (sublineage A1) in high-grade cervical neoplasia and tumours compared to non-cancer controls. Just three amino acid changes within the early gene, E6, of HPV16 AA have been linked to this augmented tumourigenicity. The AAE6 variant's greater immortalizing and transforming potential over EPE6 has recently been confirmed in retrovirally-transduced keratinocytes expressing the E6 gene only. However, the tumourigenic role of the full-length viral genome of HPV16 has not yet been addressed with regard to these E6 variants. To investigate this process in the context of these two HPV16 E6 genotypes, an organotypic tissue culture model was used to simulate the HPV infectious life cycle. The AAE6 variant demonstrated an enhanced ability over EPE6 to drive the viral life cycle toward tumourigenesis, as evidenced phenotypically—by a more severe grade of epithelial dysplasia with higher proliferation and deregulated differentiation, and molecularly—by high viral oncogene E6 and E7 expression, but lack of productive viral life cycle markers. In contrast, EPE6 had low E6 and E7 but high E1∧E4 expression, indicative of a productive life cycle. We suggest increased viral integration into the host genome for AAE6 as one possible mechanism for these observed differences from EPE6. Additionally, we found downstream effects on immortalization and host innate immune evasion. This study highlights how minor genomic variations in transforming viruses can have a significant affect on their tumourigenic ability.
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Affiliation(s)
- Robert Jackson
- Probe Development & Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
| | - Melissa Togtema
- Probe Development & Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Ingeborg Zehbe
- Probe Development & Biomarker Exploration, Thunder Bay Regional Research Institute, Thunder Bay, Ontario, Canada
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
- * E-mail:
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HPV16 E6 variants: Frequency, association with HPV types and in silico analysis of the identified novel variants. J Med Virol 2014; 86:968-74. [DOI: 10.1002/jmv.23924] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2014] [Indexed: 11/07/2022]
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Chang YJ, Chen HC, Pan MH, Lee BH, You SL, Lin CY, Chou YC, Hsieh CY, Cheng YJ, Liaw KL, Hsing AW, Schiffman M, Chen CJ. Intratypic variants of human papillomavirus type 16 and risk of cervical neoplasia in Taiwan. J Med Virol 2014; 85:1567-76. [PMID: 23852681 DOI: 10.1002/jmv.23651] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2013] [Indexed: 11/06/2022]
Abstract
The associations between variants of human papillomavirus (HPV) 16 and risk of cervical neoplasia have been reported, but nucleotide variations of HPV 16 in Asian populations and their association with cervical neoplasia have not been evaluated extensively. During 1991-1992, 11,923 women from seven townships in Taiwan were enrolled. The HPV DNA in cervical cells was detected and genotyped using EasyChip HPV blot. Nucleotide variations in the long control region (LCR), E6, and E7 genes were determined using DNA sequencing for 170 HPV 16-positive cervical samples. The Asian variant was the most prevalent variant (81.8%) of HPV 16 in Taiwan, and was also associated with increased prevalence of histologically confirmed cervical intraepithelial neoplasia grade 3 or worse, showing an age-adjusted odds ratio (exact confidence limits) of 10.70 (1.62-451.05; P = 0.0049) compared to the HPV 16 European variant. Similar significant associations with cervical intraepithelial neoplasia grade 3 or worse were also observed for distinct nucleotide substitutions, including T178A/G, A647G, A7730C/G, T7781C, G7842A, and C24T/G. These results demonstrate that non-European variants (non-E) of HPV 16, predominantly Asian variants, are associated with increased risk for severe cervical neoplasia, compared with European variants. Molecular mechanisms accounting for varied cervical neoplasia risk among different HPV 16 variants warrant further investigation.
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Affiliation(s)
- Ya-Ju Chang
- Graduate Institute of Epidemiology, National Taiwan University, Taipei, Taiwan
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Hang D, Gao L, Sun M, Liu Y, Ke Y. Functional effects of sequence variations in the E6 and E2 genes of human papillomavirus 16 European and Asian variants. J Med Virol 2013; 86:618-26. [PMID: 24150786 DOI: 10.1002/jmv.23792] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Dong Hang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Laboratory of Genetics; Peking University Cancer Hospital & Institute; Beijing China
| | - Lei Gao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Laboratory of Genetics; Peking University Cancer Hospital & Institute; Beijing China
| | - Min Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Laboratory of Genetics; Peking University Cancer Hospital & Institute; Beijing China
| | - Ying Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Laboratory of Genetics; Peking University Cancer Hospital & Institute; Beijing China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education); Laboratory of Genetics; Peking University Cancer Hospital & Institute; Beijing China
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Qmichou Z, Khyatti M, Berraho M, Ennaji MM, Benbacer L, Nejjari C, Benjaafar N, Benider A, Attaleb M, El Mzibri M. Analysis of mutations in the E6 oncogene of human papillomavirus 16 in cervical cancer isolates from Moroccan women. BMC Infect Dis 2013; 13:378. [PMID: 23953248 PMCID: PMC3751500 DOI: 10.1186/1471-2334-13-378] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 08/15/2013] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Worldwide, cervical cancer is the second most common cancer in women. High-risk human papillomavirus (HPV) play a crucial role in the etiology of cervical cancer and the most prevalent genotype is HPV16. HPV 16 intratypic variants have been reported to differ in their prevalence, biological and biochemical properties. The present study was designed to analyze and identify HPV type 16 E6 variants among patients with cervical cancer in Morocco. METHODS A total of 103 HPV16 positive samples were isolated from 129 cervical cancer cases, and variant status was subsequently determined by DNA sequencing of the E6 gene. RESULTS Isolates from patients were grouped into the European (E), African (Af) and North-American (NA1) phylogenetic clusters with a high prevalence of E lineage (58.3%). The Af and NA1 variants were detected in 31.1% and 11.6% of the HPV16 positive specimens, respectively, whereas, only 3% of cases were prototype E350T. No European-Asian (EA), Asian (As) or Asian-American (AA) variants were observed in our HPV16-positive specimens. At the amino acid level, the most prevalent non-synonymous variants were L83V (T350G), H78Y (C335T), E113D (A442C), Q14D (C143G/G145T) and R10I (G132T), and were observed respectively in 65%, 41.8%, 38.8%, 30.1% and 23.3% of total samples.Moreover, HPV16 European variants were mostly identified in younger women at early clinical diagnosis stages. Whereas, HPV16 Af variants were most likely associated with cervical cancer development in older women with pronounced aggressiveness. CONCLUSION This study suggests a predominance of E lineage strains among Moroccan HPV 16 isolates and raises the possibility that HPV16 variants have a preferential role in progression to malignancy and could be associated with the more aggressive nature of cervical cancer.
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Affiliation(s)
- Zineb Qmichou
- Unité de Biologie et Recherche Médicale, Centre National de l'Energie, des Sciences et des Techniques Nucléaires, (CNESTEN), BP 1382 RP, 10001 Rabat, Morocco
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Kuppuswamy M, Subramanian T, Kostas-Polston E, Vijayalingam S, Zhao LJ, Varvares M, Chinnadurai G. Functional similarity between E6 proteins of cutaneous human papillomaviruses and the adenovirus E1A tumor-restraining module. J Virol 2013; 87:7781-6. [PMID: 23637414 PMCID: PMC3700293 DOI: 10.1128/jvi.00037-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 04/24/2013] [Indexed: 11/20/2022] Open
Abstract
The adenovirus E1A C-terminal region restrains oncogenic transformation through interaction with three distinct cellular protein complexes that include the DYRK1A/1B/HAN11 complex. The E6 proteins of beta-human papillomaviruses (beta-HPVs) also interact with the DYRK1/HAN11 complex. A variant of HPV5 E6 frequently found in epidermodysplasia verruciformis skin lesions interacted less efficiently with DYRK1A/HAN11. The E6 variant and E7 of HPV5 efficiently coimmortalized primary epithelial cells, suggesting that naturally arising variants may contribute potential oncogenic activities of beta-HPV E6 proteins.
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Affiliation(s)
- Mohan Kuppuswamy
- Institute for Molecular Virology, Saint Louis University School of Medicine, Doisy Research Center, St. Louis, Missouri, USA
| | - T. Subramanian
- Institute for Molecular Virology, Saint Louis University School of Medicine, Doisy Research Center, St. Louis, Missouri, USA
| | | | - S. Vijayalingam
- Institute for Molecular Virology, Saint Louis University School of Medicine, Doisy Research Center, St. Louis, Missouri, USA
| | - Ling-jun Zhao
- Institute for Molecular Virology, Saint Louis University School of Medicine, Doisy Research Center, St. Louis, Missouri, USA
| | - Mark Varvares
- Saint Louis University Cancer Center, St. Louis, Missouri, USA
| | - G. Chinnadurai
- Institute for Molecular Virology, Saint Louis University School of Medicine, Doisy Research Center, St. Louis, Missouri, USA
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Novel E6 and E7 oncogenes variants of human papillomavirus type 31 in Brazilian women with abnormal cervical cytology. INFECTION GENETICS AND EVOLUTION 2013; 16:13-8. [DOI: 10.1016/j.meegid.2013.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/31/2013] [Accepted: 02/01/2013] [Indexed: 11/22/2022]
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Yao Y, Huang W, Yang X, Sun W, Liu X, Cun W, Ma Y. HPV-16 E6 and E7 protein T cell epitopes prediction analysis based on distributions of HLA-A loci across populations: an in silico approach. Vaccine 2013; 31:2289-94. [PMID: 23499609 DOI: 10.1016/j.vaccine.2013.02.065] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Revised: 02/06/2013] [Accepted: 02/28/2013] [Indexed: 11/16/2022]
Abstract
Human papillomavirus type 16 (HPV-16) is the most prevalent virus in human cervical cancers, as it is present in more than half of all cases. Many studies have found continued expression of E6 and E7 proteins in the majority of cervical cancer cases, but not in normal tissues. These results indicated that the E6 and E7 proteins could be ideal candidate therapeutic vaccines against HPV-16 infection and cervical cancer. Using the Immune Epitope Database Analysis Resource, cytotoxic T lymphocyte (CTL) epitopes of the HPV-16 E6 and E7 proteins were predicted according to worldwide frequency distributions of HLA-A alleles (HLA-A*01:01, -A*02:01, -A*02:06, -A*03:01, -A*11:01, -A*24:02, -A*26:01, -A*31:01 and -A*33:03). Our results predicted a total of 81 epitopes of HPV-16 E6 (n=59) and E7 (n=22). Epitope cluster analysis showed that among the 20 clusters of HPV-16 E6, cluster 3 contained the most epitopes (10 epitopes), which was represented by HLA-A*31:01 and -A*33:03. Of the 10 clusters of HPV-16 E7, cluster 3 contained the most epitopes (5 epitopes), which was represented by HLA-A*01:01 and -A*26:01. Our results indicated that the combination of epitopes FAFRDLCIVYR₅₂₋₆₂ of E6 (HLA-A*02:06, HLA-A*31:01, and HLA-A*33:03), PYAVCDKCLKF₆₆₋₇₆ of E6 (HLA-A*11:01 and HLA-A*24:02), HGDTPTLHEY₂₋₁₁ of E7 (HLA-A*01:01 and HLA-A*26:01), and YMLDLQPETT₁₁₋₂₀ of E7 (HLA-A*02:01) could vaccinate >50% of all individuals worldwide. Our results propose CTL epitopes or combinations of them predicted in current study for candidate therapeutic vaccines to effectively control HPV-16 infection and development of cervical cancer.
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Affiliation(s)
- Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Diseases, Yunnan Engineering Research Center of Vaccine Research & Development on Severe Infectious Diseases, Kunming 650118, China
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Yi JW, Jang M, Kim SJ, Kim SS, Rhee JE. Degradation of p53 by natural variants of the E6 protein of human papillomavirus type 16. Oncol Rep 2013; 29:1617-22. [PMID: 23404471 DOI: 10.3892/or.2013.2281] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 12/17/2012] [Indexed: 11/05/2022] Open
Abstract
The degradation of p53 by high-risk human papillomavirus (HR-HPV) E6 proteins is recognized as necessary for the immortalization of mammary epithelial cells and the progression of cancer. The HR-HPV type 16 E6 proteins exhibit numerous variants associated with different risk factors for the development of cervical cancer. Two variants of E6 proteins, D25E and L83V, are common in cervical carcinomas among Asian and European populations. In the present study, we compared the effect of two E6 variants on p53 degradation by a prototype E6 protein. We demonstrate that both the D25E and L83V variants downregulate p53 through a ubiquitin-proteasome pathway, and that the effect is very similar to that of the prototype E6 protein. The reduction in the p53 protein levels was induced through the ubiquitin-proteasome pathway via interaction with E6 proteins. The expression of p21 CIP1/WAF1, a downstream molecule of p53, was similarly reduced in both prototype and variant E6 protein-expressing cell lines, leading to aberrant G1/S cell cycle arrest. These results suggest that the natural variants, E6 D25E and L83V, similar to the prototype E6 protein, contribute to tumorigenesis by degrading p53.
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Affiliation(s)
- Ja Woon Yi
- Division of AIDS, Center for Immunology and Pathology, Korea National Institute of Health, Seoul, Republic of Korea
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40
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Pientong C, Wongwarissara P, Ekalaksananan T, Swangphon P, Kleebkaow P, Kongyingyoes B, Siriaunkgul S, Tungsinmunkong K, Suthipintawong C. Association of human papillomavirus type 16 long control region mutation and cervical cancer. Virol J 2013; 10:30. [PMID: 23343096 PMCID: PMC3599568 DOI: 10.1186/1743-422x-10-30] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 12/28/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The variation of human papillomavirus (HPV) genes or HPV variants demonstrates different risks of cervical cancer. Mutation in the long control region (LCR) at YY1-motifs is one of the mechanisms for enhancing viral oncogene expression during the course of cancer cell progression. In Thai women, cervical cancers are almost always associated with HPV16 variant sub-lineage Asian (HPV16As); however, the mechanism involved remains elusive. The aim of this study was to understand further the oncogenic potential of HPV16As. METHODS A total of 82 HPV16-positive specimens from Thai women were selected from formalin-fixed paraffin-embedded cervical tissues, and the full length E6 gene of each specimen was amplified and sequenced. LCRs of the HPV16As-positive cases were amplified and sequenced to analyze their polymorphisms. Transcriptional activities of the HPV16As LCRs were then compared with sub-lineage European (EUR), sub-lineage Asian-American 1 (AA1) and HPV16 prototype by insertion of the LCRs into the pGL3-Basic vector. RESULTS The HPV16 DNA sequences were classified as HPV16 prototype (18.3%), Asian (As, 61%), Asian American-1 (AA1, 8.5%), European (EUR, 7.3%), Asian African-2 (AFR2, 3.7%) and Java-135C (J135C, 1.2%). The prevalence of HPV16As was 30% in low-grade squamous intraepithelial lesion (LSIL), while that in high-grade squamous intraepithelial lesion (HSIL) and squamous cell cervical carcinoma (SCC) were 63.9% and 66.7%, respectively, which demonstrates a significant association of HPV16As with the disease severity. LCR polymorphisms from 43 HPV16As positive cases were analyzed by PCR-sequencing. Thirty-eight nucleotide variation positions spanned nucleotide positions 7157-82. Ten new mutations found in the HPV16As LCRs were located predominantly at the enhancer and proximal to the 3'-end of the early promoter. The LCRs of the common HPV16As, EUR and AA1 showed 5, 13 and 23-fold higher activity than the HPV16 prototype LCR, while those of the new nucleotide variations of As showed 19 (As-sv1) and 30 (As-sv14) -fold higher activity than the HPV16 prototype. CONCLUSIONS HPV16As DNA sequence variation, especially at the proximal to early promoter in the LCR, enhances transcriptional activity. This could be one of the possible mechanisms for HPV16As-associated cervical cancer development.
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Affiliation(s)
- Chamsai Pientong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Burroni E, Bisanzi S, Sani C, Puliti D, Carozzi F. Codon 72 polymorphism of p53 and HPV type 16 E6 variants as risk factors for patients with squamous epithelial lesion of the uterine cervix. J Med Virol 2012; 85:83-90. [PMID: 23124863 DOI: 10.1002/jmv.23417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2012] [Indexed: 11/09/2022]
Abstract
The Arg/Arg genotype versus Arg/Pro or Pro/Pro at codon 72 of the p53 gene in association with human papillomavirus (HPV) 16 E6 variants has been implicated as a risk marker in cervical neoplasia. However, research on this topic has produced controversial results. The association of p53 codon 72 polymorphism alone and in combination with specific HPV 16 E6 variants with risk of developing squamous intraepithelial cervical lesion has been investigated in low and high-grade squamous intraepithelial lesions and in HPV-negative controls from an Italian population. The data obtained showed statistically significant different distribution of p53 genotypes between healthy controls and precursor lesions, with the p53 arginine homozygous increased in high-grade squamous intraepithelial lesions. The T350G HPV 16 variant was the most frequent variant observed in the analyzed group of Italian women, showing a slight decreasing with the severity of the lesion. At the same time, the number of the prototype T350 slightly increased with the severity of the cytological lesions. In conclusion, p53 arginine homozygous was found to be increased in high-grade lesions, supporting the results of previous investigations indicating that HPV-positive patients with p53 Arg/Arg have an increased risk of developing pre-cancerous lesions. In addition, T350G HPV 16 variant was over-represented in p53 Arg homozygous women with cervical lesions. When p53 genotype and HPV 16 variants are considered together, no difference emerges between cases and controls so is not possible to assess that the oncogenic effect of HPV 16 T350G variant may be influenced by the p53 genotype.
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Affiliation(s)
- E Burroni
- Unit of Analytical and Biomolecular Cytology, ISPO, Florence, Italy.
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Sichero L, Simão Sobrinho J, Lina Villa L. Oncogenic potential diverge among human papillomavirus type 16 natural variants. Virology 2012; 432:127-32. [DOI: 10.1016/j.virol.2012.06.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 03/30/2012] [Accepted: 06/05/2012] [Indexed: 01/21/2023]
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Liu JH, Lu ZT, Wang GL, Zhou WQ, Liu C, Yang LX, Sun ZR, Ruan Q. Variations of human papillomavirus type 58 E6, E7, L1 genes and long control region in strains from women with cervical lesions in Liaoning province, China. INFECTION GENETICS AND EVOLUTION 2012; 12:1466-72. [DOI: 10.1016/j.meegid.2012.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 05/08/2012] [Accepted: 05/13/2012] [Indexed: 12/26/2022]
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Matsumoto K, Yoshikawa H. Human papillomavirus infection and the risk of cervical cancer in Japan. J Obstet Gynaecol Res 2012; 39:7-17. [PMID: 22925027 DOI: 10.1111/j.1447-0756.2012.01977.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Infection with a high-risk human papillomavirus (HPV) is established as a major risk factor for cervical cancer. In Japan, eight HPV genotypes (16, 18, 31, 33, 35, 45, 52 and 58) confer a much higher risk of cervical cancer and its immediate premalignant lesions (cervical intraepithelial neoplasia grade 3 [CIN 3]) than do other high-risk and the low-risk HPV types. However, only a small fraction of infected women develop CIN 3 or invasive cervical cancer, suggesting the involvement of additional cofactors in cervical carcinogenesis. A multicenter prospective cohort study of Japanese women with low-grade cervical abnormalities has demonstrated that tobacco smoking is significantly associated with an increased risk of persistent low-grade cervical lesions, while the presence of human leukocyte antigen Class II DRB1*1302 protects against progression to CIN 3. Understanding the epidemiology of HPV infections and cervical cancer may improve prevention and lead to novel clinical management strategies for cervical precursor lesions. Viral and host factors that affect the risk of cervical cancer are discussed in this review.
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Affiliation(s)
- Koji Matsumoto
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan.
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Sabol I, Matovina M, Si-Mohamed A, Grce M. Characterization and whole genome analysis of human papillomavirus type 16 e1-1374^63nt variants. PLoS One 2012; 7:e41045. [PMID: 22911739 PMCID: PMC3404080 DOI: 10.1371/journal.pone.0041045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 06/20/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The variation of the most common Human papillomavirus (HPV) type found in cervical cancer, the HPV16, has been extensively investigated in almost all viral genes. The E1 gene variation, however, has been rarely studied. The main objective of the present investigation was to analyze the variability of the E6 and E1 genes, focusing on the recently identified E1-1374^63nt variant. METHODOLOGY/PRINCIPAL FINDINGS Variation within the E6 of 786 HPV16 positive cervical samples was analyzed using high-resolution melting, while the E1-1374^63nt duplication was assayed by PCR. Both techniques were supplemented with sequencing. The E1-1374^63nt duplication was linked with the E-G350 and the E-C109/G350 variants. In comparison to the referent HPV16, the E1-1374^63nt E-G350 variant was significantly associated with lower grade cervical lesions (p = 0.029), while the E1-1374^63nt E-C109/G350 variant was equally distributed between high and low grade lesions. The E1-1374^63nt variants were phylogenetically closest to E-G350 variant lineage (A2 sub-lineage based on full genome classification). The major differences between E1-1374^63nt variants were within the LCR and the E6 region. On the other hand, changes within the E1 region were the major differences from the A2 sub-lineage, which has been historically but inconclusively associated with high grade cervical disease. Thus, the shared variations cannot explain the particular association of the E1-1374^63nt variant with lower grade cervical lesions. CONCLUSIONS/SIGNIFICANCE The E1 region has been thus far considered to be well conserved among all HPVs and therefore uninteresting for variability studies. However, this study shows that the variations within the E1 region could possibly affect cervical disease, since the E1-1374^63nt E-G350 variant is significantly associated with lower grade cervical lesions, in comparison to the A1 and A2 sub-lineage variants. Furthermore, it appears that the silent variation 109T>C of the E-C109/G350 variant might have a significant role in the viral life cycle and warrants further study.
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Affiliation(s)
- Ivan Sabol
- Division of Molecular Medicine, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Mihaela Matovina
- Department of Microbiology and Parasitology, School of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ali Si-Mohamed
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Paris, France
| | - Magdalena Grce
- Division of Molecular Medicine, Rudjer Boskovic Institute, Zagreb, Croatia
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Cornet I, Gheit T, Franceschi S, Vignat J, Burk RD, Sylla BS, Tommasino M, Clifford GM. Human papillomavirus type 16 genetic variants: phylogeny and classification based on E6 and LCR. J Virol 2012; 86:6855-61. [PMID: 22491459 PMCID: PMC3393538 DOI: 10.1128/jvi.00483-12] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Naturally occurring genetic variants of human papillomavirus type 16 (HPV16) are common and have previously been classified into 4 major lineages; European-Asian (EAS), including the sublineages European (EUR) and Asian (As), African 1 (AFR1), African 2 (AFR2), and North-American/Asian-American (NA/AA). We aimed to improve the classification of HPV16 variant lineages by using a large resource of HPV16-positive cervical samples collected from geographically diverse populations in studies on HPV and/or cervical cancer undertaken by the International Agency for Research on Cancer. In total, we sequenced the entire E6 genes and long control regions (LCRs) of 953 HPV16 isolates from 27 different countries worldwide. Phylogenetic analyses confirmed previously described variant lineages and subclassifications. We characterized two new sublineages within each of the lineages AFR1 and AFR2 that are robustly classified using E6 and/or the LCR. We could differentiate previously identified AA1, AA2, and NA sublineages, although they could not be distinguished by E6 alone, requiring the LCR for correct phylogenetic classification. We thus provide a classification system for HPV16 genomes based on 13 and 32 phylogenetically distinguishing positions in E6 and the LCR, respectively, that distinguish nine HPV16 variant sublineages (EUR, As, AFR1a, AFR1b, AFR2a, AFR2b, NA, AA1, and AA2). Ninety-seven percent of all 953 samples fitted this classification perfectly. Other positions were frequently polymorphic within one or more lineages but did not define phylogenetic subgroups. Such a standardized classification of HPV16 variants is important for future epidemiological and biological studies of the carcinogenic potential of HPV16 variant lineages.
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Affiliation(s)
- Iris Cornet
- International Agency for Research on Cancer, Lyon, France
| | - Tarik Gheit
- International Agency for Research on Cancer, Lyon, France
| | | | - Jerome Vignat
- International Agency for Research on Cancer, Lyon, France
| | - Robert D. Burk
- Albert Einstein College of Medicine, Bronx, New York, USA
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López-Urrutia E, Valdés J, Bonilla-Moreno R, Martínez-Salazar M, Martínez-Garcia M, Berumen J, Villegas-Sepúlveda N. A few nucleotide polymorphisms are sufficient to recruit nuclear factors differentially to the intron 1 of HPV-16 intratypic variants. Virus Res 2012; 166:43-53. [DOI: 10.1016/j.virusres.2012.02.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 02/28/2012] [Accepted: 02/28/2012] [Indexed: 01/24/2023]
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48
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Jang M, Rhee JE, Jang DH, Kim SS. Gene expression profiles are altered in human papillomavirus-16 E6 D25E-expressing cell lines. Virol J 2011; 8:453. [PMID: 21943319 PMCID: PMC3203858 DOI: 10.1186/1743-422x-8-453] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 09/25/2011] [Indexed: 01/18/2023] Open
Abstract
Previously, we have reported that the human papillomavirus (HPV) type 16 E6 D25E is the most prevalent variant in Korean women at high risk for cervical cancers. Several studies have identified an association between the increased frequency of this variant and the elevated risk of cervical intraepithelial neoplasia and invasive cervical carcinoma. To investigate whether the HPV-16 E6 D25E variant might influence cervical cancer progression, we used an oligonucleotide microarray approach to identify transcriptionally altered gene expression patterns in recombinant wild-type E6 or E6 D25E variant-expressing HPV-negative cancer cells. We found that 211 genes were significantly up- or down-regulated (at least 1.5-fold, p < 0.05). We identified 14 genes, nine down-regulated and five up-regulated upon E6 D25E expression, compared with wild-type E6 expression. These results further emphasize the unique biological activity of the HPV-16 E6 D25E variant.
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Affiliation(s)
- Mi Jang
- Division of AIDS, Center for Immunology and Pathology, Korea National Institute of Health, Seoul, Republic of Korea
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Shang Q, Wang Y, Fang Y, Wei L, Chen S, Sun Y, Li B, Zhang F, Gu H. Human papillomavirus type 16 variant analysis of E6, E7, and L1 [corrected] genes and long control region in [corrected] cervical carcinomas in patients in northeast China. J Clin Microbiol 2011; 49:2656-63. [PMID: 21593270 PMCID: PMC3147813 DOI: 10.1128/jcm.02203-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 05/03/2011] [Indexed: 11/20/2022] Open
Abstract
Human papillomavirus type 16 (HPV 16) plays a cardinal role in the pathogenesis of cervical cancer. HPV 16 has intratypic variants which show different geographical distributions and different oncogenic potentials. To analyze the presence of sequence variations of HPV 16 variants in northeast China, 71 cervical carcinomas were identified by HPV typing. HPV 16-positive specimens were analyzed by PCR-directed sequencing in the E6, E7, and L1 genes and the LCR (long control region). The variation data were compared with those of neighboring districts. In this hospital-based study, HPV 16 was the most common type (73.24%). In HPV 16-positive specimens, 67.31% belonged to the European (E) lineage, while 32.69% were Asian (As) variants. The Asian-American (AA), African-1 (Af-1), African-2 (Af-2), and northern American (NA) lineages were not detected. The most frequently observed variation sites were T178G (32.69%) in E6; A647G (34.62%), G666A (38.46%), and T846C (32.69%) in E7; C6826T (36.17%) and G7060A (61.70%) in L1; and G7521A (98.08%) in the LCR. The most prevalent amino acid variations were D25E in E6 and N29S in E7. In addition, 28 novel variations of HPV 16 were reported. Some covariations between different genes were obtained. In this study, HPV 16 variants belonged to the European lineage and the Asian lineage. Compared with neighboring districts, the distribution of HPV 16 variants in northeast China had a typical pattern. As the first report on HPV 16 variants in northeast China, it should be helpful for designing a HPV vaccine and HPV vaccination program in China.
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Affiliation(s)
- Qinglong Shang
- Department of Microbiology, Harbin Medical University, Heilongjiang Key Laboratory of Infection and Immunity, Heilongjiang Province, Pathogenic-Biological Key Laboratory, Heilongjiang Higher Education Institutions, Harbin 150081, People's Republic of China
| | - Yan Wang
- Department of Microbiology, Harbin Medical University, Heilongjiang Key Laboratory of Infection and Immunity, Heilongjiang Province, Pathogenic-Biological Key Laboratory, Heilongjiang Higher Education Institutions, Harbin 150081, People's Republic of China
| | - Yong Fang
- Department of Microbiology, Harbin Medical University, Heilongjiang Key Laboratory of Infection and Immunity, Heilongjiang Province, Pathogenic-Biological Key Laboratory, Heilongjiang Higher Education Institutions, Harbin 150081, People's Republic of China
| | - Lanlan Wei
- Department of Microbiology, Harbin Medical University, Heilongjiang Key Laboratory of Infection and Immunity, Heilongjiang Province, Pathogenic-Biological Key Laboratory, Heilongjiang Higher Education Institutions, Harbin 150081, People's Republic of China
| | - Sijia Chen
- Department of Microbiology, Harbin Medical University, Heilongjiang Key Laboratory of Infection and Immunity, Heilongjiang Province, Pathogenic-Biological Key Laboratory, Heilongjiang Higher Education Institutions, Harbin 150081, People's Republic of China
| | - Yuhui Sun
- Department of Gynecology, First Affiliated Hospital, Harbin Medical University, Harbin 150001, People's Republic of China
| | - Baoxin Li
- Department of Pharmacology, Harbin Medical University, and Bio-pharmacological Key Laboratory of Heilongjiang Province, Harbin 150081, People's Republic of China
| | - Fengmin Zhang
- Department of Microbiology, Harbin Medical University, Heilongjiang Key Laboratory of Infection and Immunity, Heilongjiang Province, Pathogenic-Biological Key Laboratory, Heilongjiang Higher Education Institutions, Harbin 150081, People's Republic of China
| | - Hongxi Gu
- Department of Microbiology, Harbin Medical University, Heilongjiang Key Laboratory of Infection and Immunity, Heilongjiang Province, Pathogenic-Biological Key Laboratory, Heilongjiang Higher Education Institutions, Harbin 150081, People's Republic of China
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Zehbe I, Lichtig H, Westerback A, Lambert PF, Tommasino M, Sherman L. Rare human papillomavirus 16 E6 variants reveal significant oncogenic potential. Mol Cancer 2011; 10:77. [PMID: 21702904 PMCID: PMC3144020 DOI: 10.1186/1476-4598-10-77] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Accepted: 06/24/2011] [Indexed: 01/01/2023] Open
Abstract
The aim of this study was to determine whether low prevalence human papillomavirus (HPV) 16 E6 variants differ from high prevalence types in their functional abilities. We evaluated functions relevant to carcinogenesis for the rarely-detected European variants R8Q, R10G and R48W as compared to the commonly detected L83V. Human immortalized keratinocytes (NIKS) stably transduced with the E6 variants were used in most functional assays. Low and high prevalence E6 variants displayed similar abilities in abrogation of growth arrest and inhibition of p53 elevation induced by actinomycin D. Differences were detected in the abilities to dysregulate stratification and differentiation of NIKS in organotypic raft cultures, modulate detachment induced apoptosis (anoikis) and hyperactivate Wnt signaling. No distinctive phenotype could be assigned to include all rare variants. Like L83V, raft cultures derived from variants R10G and R48W similarly induced hyperplasia and aberrantly expressed keratin 5 in the suprabasal compartment with significantly lower expression of keratin 10. Unlike L83V, both variants, and particularly R48W, induced increased levels of anoikis upon suspension in semisolid medium. R8Q induced a unique phenotype characterized by thin organotypic raft cultures, low expression of keratin 10, and high expression of keratins 5 and 14 throughout all raft layers. Interestingly, in a reporter based assay R8Q exhibited a higher ability to augment TCF/β-catenin transcription. The data suggests that differences in E6 variant prevalence in cervical carcinoma may not be related to the carcinogenic potential of the E6 protein.
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Affiliation(s)
- Ingeborg Zehbe
- Thunder Bay Regional Research Institute, Probe Development & Biomarker Exploration, Thunder Bay, Ontario, Canada
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