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Wang J, Guo Y, Wang H, Li Y, Zhang L, Wang Z, Song L, Liu H. Genetic diversity of E6, E7 and the long control region in human papillomavirus type 16 variants in Beijing, China. Biochem Biophys Rep 2022; 31:101286. [PMID: 35655951 PMCID: PMC9151740 DOI: 10.1016/j.bbrep.2022.101286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 12/02/2022] Open
Abstract
Background High-risk human papillomavirus type 16 (HPV16) is a risk factor for cervical cancer. The progression from initial infection to cervical cancer has been linked to properties of the viral sequences. However, the distribution of HPV16 variants among Chinese women has not been extensively addressed and the role of HPV16 variants in the risk of cervical carcinogenesis remains poorly understood. Methods HPV16 positive cervical exfoliated cell samples were collected from 249 women living in Beijing, China. PCR products from two fragments of E6-E7 and LCR of HPV16 in these samples were sequenced and analyzed. Results Lineage A was found in the subjects, including A1, A2, A3 and A4 sublineages. Based on the HPV16 reference sequences, 26 nucleotide mutations of A4 sublineage and 39 nucleotide mutations of A1-3 sublineages were found in the E6, E7 and LCR of HPV16 isolates. Point mutations T843C, A7287C and A7872G of A4 sublineage were significantly associated with high-grade cervical lesions. The high-frequency sites in HPV16 LCR located at regions that can bind to multiple transcription factors. Conclusions This study contributes to the identification of unique variants in the E6, E7 and LCR of HPV16 isolates infected in Chinese women. Mutations of T843C, A7287C and A7872G in A4 sublineages were significantly associated with high-grade cervical lesions, suggesting that mutations in the E7 and LCR region have potential effects on viral replication and progression of cervical cancer. Lineage A is the predominant HPV16 variant in Chinese women. Based on the HPV16 prototype, 25 nucleotide mutations in E6 and E7 were found and 41 nucleotide mutations in LCR were found. The mutations of C843T, A7287C and A7872G were significantly correlated with the cervical lesions.
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Affiliation(s)
- Jiao Wang
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
| | - Yifan Guo
- Department of Obstetrics and Gynaecology, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572013, Hainan Province, China
| | - Hui Wang
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
| | - Ying Li
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
| | - Li Zhang
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
| | - Zhan Wang
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
| | - Lei Song
- Department of Obstetrics and Gynaecology, Chinese PLA General Hospital, Beijing, 100048, China
| | - Hongtu Liu
- Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China
- Center for Biosafety Mega-Science, Chinese Academy of Science, Wuhan, 430071, Hubei Province, China
- Chinese Center for Disease Control and Prevention-Wuhan Institute of Virology, Chinese Academy of Sciences Joint Research Center for Emerging Infectious Diseases and Biosafety, Wuhan, 430071, Hubei Province, China
- Corresponding author. Department of Tumor-Associated Virus, National Institute for Viral Disease Control and Prevention, Beijing, 102206, China.
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Escobar-Escamilla N, González-Martínez BE, Araiza-Rodríguez A, Fragoso-Fonseca DE, Pedroza-Torres A, Landa-Flores MG, Garcés-Ayala F, Mendieta-Condado E, Díaz-Quiñonez JA, Castro-Escarpulli G, Ramírez-González JE. Mutational landscape and intra-host diversity of human papillomavirus type 16 long control region and E6 variants in cervical samples. Arch Virol 2019; 164:2953-2961. [PMID: 31552532 DOI: 10.1007/s00705-019-04407-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/17/2019] [Indexed: 11/24/2022]
Abstract
Human papillomavirus genotype 16 (HPV16) is the most frequent high-risk HPV (HR-HPV) identified in cervical precursor lesions and cervical cancer (CC) worldwide. The oncogenic potential of HPV16 is partly dependent on the lineage involved in the infection and the presence of clinically relevant mutations. In this report, we present the distribution of HR-HPV and the mutational profile and intra-host variability of HPV16 lineages, based on analysis of the long control region (LCR) and the E6 gene in samples with normal cytology (n = 39), squamous intraepithelial lesions (n = 25), and CC (n = 39). HR-HPV genotyping was performed using multiplex real-time PCR. HPV16 lineage assignments and mutation frequencies were determined by conventional PCR and Sanger DNA sequencing, and intra-patient viral populations were analyzed using next-generation sequencing (NGS). The most frequent HR-HPV type was HPV16, followed by HPV31 and HPV18. The frequency of HPV16 sublineages was A1/A2 > D2 > D3 and B1. Moreover, the most frequent mutations, both in samples from this study and in the available sequences from Mexican isolates in the GenBank database were LCR-G7518A, which is involved in carcinogenesis, and E6-T350G (producing L83V), associated with persistence of infection. Otherwise, deep sequencing revealed high conservation of viral lineages and mutations, independently of the stages studied. In conclusion, the high frequency and stability of these molecular markers, as well as the circulating viral lineages, could be related to the incidence of CC associated with HPV16. Hence, they deserve a broader analysis to determine the risk of specific populations for progression of the disease.
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Affiliation(s)
- Noé Escobar-Escamilla
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico. .,Laboratorio de Investigación Clínica y Ambiental, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico.
| | - Blanca Estela González-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - Adnan Araiza-Rodríguez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - David Esaú Fragoso-Fonseca
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - Abraham Pedroza-Torres
- Cátedra CONACyT, Clínica de Cáncer Hereditario, Instituto Nacional de Cancerología (INCan), Secretaría de Salud, Mexico City, Mexico
| | - Magaly Guadalupe Landa-Flores
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - Fabiola Garcés-Ayala
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - Edgar Mendieta-Condado
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico
| | - José Alberto Díaz-Quiñonez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico.,División de Estudios de Posgrado, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Graciela Castro-Escarpulli
- Laboratorio de Investigación Clínica y Ambiental, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - José Ernesto Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) "Dr. Manuel Martínez Báez", Secretaría de Salud, Mexico City, Mexico.
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Ahmed HG, Bensumaidea SH, Ashankyty IM. Frequency of Human Papilloma Virus (HPV) subtypes 31,33,35,39 and 45 among Yemeni women with cervical cancer. Infect Agent Cancer 2015; 10:29. [PMID: 26347799 PMCID: PMC4561418 DOI: 10.1186/s13027-015-0026-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/19/2015] [Indexed: 11/18/2022] Open
Abstract
Background Identification of different HPV subtypes in unidentified communities provides sufficient information for screening and monitoring potential impact of a vaccination program. Therefore, the aim of this study was to screen for the presence of HPVs subtypes 31,33,35,39 and 45 among Yemeni women with Cervical Cancer. Methodology A total of 200 (150 malignant and 50 benign) tissue samples were obtained from Yemeni women with cervical cancer, were investigated for the presence of HPV subtypes 31,33,35,39 and 45 by Polymerase Chain Reaction (PCR). Results Of the 150 cervical cancer tissue specimens, HPV 31, HPV 33, HPV35, HPV 39 and HPV45 were identified in 10/150 (6.7 %), 6/150 (4 %), 6/150 (4 %), 5/150 (3.3 %) and 10/150 (6.7 %), respectively. The frequency of these HPV subtypes among Yemeni women with cervical cancer was 24 %. Conclusion: HPV 31, HPV 33, HPV35, HPV 39 and HPV45 were prevalent among Yemeni women with cervical cancer.
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Affiliation(s)
- Hussain Gadelkarim Ahmed
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, Kingdom of Saudi Arabia ; Department of Pathology, College of Medicine, University of Ha'il, 2240 Hai'l, Kingdom of Saudi Arabia ; Department of Histopathology and Cytology, FMLS, University of Khartoum, Khartoum, Sudan
| | - Saleh Hussein Bensumaidea
- Department of Pathology, College of Medicine, Hadhramout University of Science and Technology, Hadhramout, Yemen
| | - Ibraheem M Ashankyty
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha'il, Ha'il, Kingdom of Saudi Arabia ; Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Ha'il, Ha'il, Kingdom of Saudi Arabia
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Kumar A, Hussain S, Yadav IS, Gissmann L, Natarajan K, Das BC, Bharadwaj M. Identification of human papillomavirus-16 E6 variation in cervical cancer and their impact on T and B cell epitopes. J Virol Methods 2015; 218:51-8. [PMID: 25800725 DOI: 10.1016/j.jviromet.2015.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 12/26/2014] [Accepted: 03/12/2015] [Indexed: 12/22/2022]
Abstract
The infection with high-risk human papillomavirus (HR-HPV) is the most important risk factor for development of cervical cancer. The intra-type variations of HPV have different biological and pathological consequences with respect to disease progression. In the present study, six major Indian variants were experimentally identified in E6 gene of HPV-16 and showed their impact on immunogenicity by in silico methods. Four different phylogenetic lineages were observed in sequences including European (E) prototype, European variant, Asian and American Asian variant classes and complete absence of African phylogenetic lineages. On the prediction of B- and T-cell epitopes, 18 and 23 potent epitopes for MHC-II alleles, 10 potent MHC-I and 15 B-cell epitopes in each reference and variant sequence were identified. Interestingly, the presence of variation H78Y and L83V result in creation of four new epitopes for the HLA-DQA1*0101/DQB1*0501. Out of 15 B-cell predicted epitopes, three most potent epitopes were identified in both reference and variant sequence. Notably the amino acid stretch from amino acid 16-60 and 76-94 are very important for the immunological properties of E6 protein because these regions contain majority of the predicted epitopes. In future, this could control the cervical cancer by targeting these amino acid stretches for the development of HPV-16 vaccine.
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Affiliation(s)
- Anoop Kumar
- Division of Molecular Genetics & Biochemistry, Institute of Cytology & Preventive Oncology (ICMR), Noida, Uttar Pradesh, India; Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi (North Campus), New Delhi, India
| | - Showket Hussain
- Division of Molecular Genetics & Biochemistry, Institute of Cytology & Preventive Oncology (ICMR), Noida, Uttar Pradesh, India
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Lutz Gissmann
- Division of Genome Modification and Carcinogenesis, German Cancer Center, DKFZ, Heidelberg, Germany
| | - K Natarajan
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi (North Campus), New Delhi, India
| | - Bhudev C Das
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi (North Campus), New Delhi, India
| | - Mausumi Bharadwaj
- Division of Molecular Genetics & Biochemistry, Institute of Cytology & Preventive Oncology (ICMR), Noida, Uttar Pradesh, India.
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Liu T, Pan X, Chao L, Tan W, Qu S, Yang L, Wang B, Mei H. Subangstrom accuracy in pHLA-I modeling by Rosetta FlexPepDock refinement protocol. J Chem Inf Model 2014; 54:2233-42. [PMID: 25050981 DOI: 10.1021/ci500393h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Flexible peptides binding to human leukocyte antigen (HLA) play a key role in mediating human immune responses and are also involved in idiosyncratic adverse drug reactions according to recent research. However, the structural determinations of pHLA complexes remain challenging under the present conditions. In this paper, the performance of a new peptide docking method, namely FlexPepDock, was systematically investigated by a benchmark of 30 crystallized structures of peptide-HLA class I complexes. The docking results showed that the near-native pHLA-I models with peptide bb-RMSD less than 2 Å were ranked in the top 1 model for 100% (70/70) docking cases, and the subangstrom models with peptide bb-RMSD less than 1 Å were ranked in the top 5 lowest-energy models for 65.7% (46/70) docking cases. Furthermore, 10 out of 70 docking cases ranked the subangstrom all-atom models in the top 5 lowest-energy models. The results showed that the FlexPepDock can generate high-quality models of pHLA-I complexes and can be widely applied to pHLA-I modeling and mechanism research of peptide-mediated immune responses.
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Affiliation(s)
- Tengfei Liu
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), Chongqing University , Chongqing 400044, China
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