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Chagas BS, Tibúrcio Júnior E, Silva RCDO, dos Santos DL, Barros Junior MR, de Lima RDCP, Invenção MDCV, Santos VEP, França Neto PL, Silva Júnior AH, Silva Neto JC, Batista MVDA, de Freitas AC. E7 Oncogene HPV58 Variants Detected in Northeast Brazil: Genetic and Functional Analysis. Microorganisms 2023; 11:1915. [PMID: 37630475 PMCID: PMC10458125 DOI: 10.3390/microorganisms11081915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Cervical cancer is associated with persistent infections by high-risk Human Papillomavirus (HPV) types that may have nucleotide polymorphisms and, consequently, different oncogenic potentials. Therefore, this study aimed to evaluate the genetic variability and structural effects of the E7 oncogene of HPV58 in cervical scraping samples from Brazilian women. The study was developed with patients from hospitals in the metropolitan area of Recife, PE, Brazil. The most frequent HPV types were, in descending order of abundance, HPV16, 31, and 58. Phylogenetic analysis demonstrated that the isolates were classified into sublineages A2, C1, and D2. Two positively selected mutations were found in E7: 63G and 64T. The mutations G41R, G63D, and T64A in the E7 protein reduced the stability of the protein structure. Utilizing an NF-kB reporter assay, we observed a decrease in the NK-kB pathway activity with the HPV58-E7 variant 54S compared to the WT E7. The other detected E7 HPV58 variants presented similar NF-kB pathway activity compared to the WT E7. In this study, it was possible to identify mutations that may interfere with the molecular interaction between the viral oncoproteins and host proteins.
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Affiliation(s)
- Bárbara Simas Chagas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Elias Tibúrcio Júnior
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Ruany Cristyne de Oliveira Silva
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Daffany Luana dos Santos
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Marconi Rego Barros Junior
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Rita de Cássia Pereira de Lima
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Maria da Conceição Viana Invenção
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Vanessa Emanuelle Pereira Santos
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Pedro Luiz França Neto
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
| | - Antônio Humberto Silva Júnior
- Center for Biological and Health Sciences, Federal University of Campina Grande, Campina Grande 58429-900, PB, Brazil;
| | - Jacinto Costa Silva Neto
- Laboratory of Molecular and Cytological Research, Department of Histology, Federal University of Pernambuco, Recife 50670-901, PE, Brazil;
| | - Marcus Vinícius de Aragão Batista
- Laboratory of Molecular Genetics and Biotechnology, Department of Biology, Federal University of Sergipe, São Cristóvão 49100-000, SE, Brazil;
| | - Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife 50670-901, PE, Brazil; (B.S.C.); (E.T.J.); (R.C.d.O.S.); (D.L.d.S.); (M.R.B.J.); (R.d.C.P.d.L.); (M.d.C.V.I.); (V.E.P.S.); (P.L.F.N.)
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Yu M, Wu S, Wang S, Cui C, Lu Y, Sun Z. Polymorphism of E6 and E7 Genes in Human Papillomavirus Types 31 and 33 in Northeast China. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:9338294. [PMID: 36950084 PMCID: PMC10027458 DOI: 10.1155/2023/9338294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/04/2023] [Accepted: 01/30/2023] [Indexed: 03/14/2023]
Abstract
Persistent infection with human papillomavirus (HPV) types 31 and 33 is an important causative factor for cervical cancer. The E6/E7 genes are key oncogenes involved in the immortalization and transformation of human epithelial cells. Genetic polymorphism may lead to differences in the virus' carcinogenic potential, the immune reaction of the host, and the potencies of vaccines. Few studies on HPV31/33 E6/E7 genetic polymorphism have been carried out. To study the genetic polymorphism of HPV31 and HPV33 E6/E7 genes in northeast China, these genes (HPV31 E6/E7, n = 151; HPV33 E6/E7, n = 136) were sequenced and compared to reference sequences (J04353.1, M12732.1) using BioEdit. Phylogenetic trees were constructed by the neighbor-joining method using MegaX. The diversity of the secondary structure was estimated using the PSIPred server. The positively selected sites were analyzed using PAML4.9. The major histocompatibility complex (MHC) class I and MHCII epitopes were predicted using the ProPred-I server and ProPredserver. B-cell epitopes were predicted using the ABCpred server. In the 151 HPV31E6 sequences, 25 (25/450) single-nucleotide mutations were found, 14 of which were synonymous mutations and 11 were nonsynonymous. In the 151 HPV31E7 sequences, 8 (8/297) nucleotide mutations were found, 3 of which were synonymous mutations and 5 were nonsynonymous. In the 136 HPV33E6 sequences, 17 (17/450) nucleotide mutations were observed, 7 of which were synonymous mutations and 10 were nonsynonymous. C14T/G (T5I/S) was a triallelic mutation. Finally, in the 136 HPV33E7 sequences, 9 (9/294) nucleotide mutations were observed, 3 of which were synonymous mutations and 6 were nonsynonymous. C134T/A (A45V/E) and C278G/A (T93S/N) were triallelic mutations. Lineage A was the most common lineage in both HPV31 and HPV33. In all of the sequences, we only identified one positively selected site, HPV33 E6 (K93N). Most nonsynonymous mutations were localized at sites belonging to MHC and/or B-cell predicted epitopes. Data obtained in this study should contribute to the development and application of detection probes, targeted drugs, and vaccines.
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Affiliation(s)
- Miao Yu
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Si Wu
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Shuang Wang
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Changwan Cui
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yiping Lu
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhengrong Sun
- Department of BioBank, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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Hosseini N, Shoja Z, Younesi S, Shafiei-Jandaghi NZ, Jalilvand S. Lineage analysis of human papillomavirus types 31 and 45 in cervical samples of Iranian women. J Med Virol 2021; 93:3857-3864. [PMID: 33368429 DOI: 10.1002/jmv.26748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 12/05/2020] [Accepted: 12/19/2020] [Indexed: 01/23/2023]
Abstract
Knowing the regional lineages/sublineages of human papillomavirus 31 (HPV 31) and 45 would be of great importance for further evolutionary, epidemiological, and biological analysis. In this regard, to characterize more common lineages and sublineages of HPV 31 and 45, the sequence variations of E6 gene were investigated in normal, premalignant, and malignant samples collected from the cervix in Iran. In total, 54 HPV 31- and 24 HPV 45-positive samples were analyzed by hemi-nested polymerase chain reaction (PCR) and nested-PCR, respectively. All PCR products were subjected to direct sequencing analysis. The results indicated that all three lineages A, B, and C were detected in HPV 31-positive samples; among which HPV 31 lineage A was dominant as it was found in 66.7% of all samples. HPV 31 lineages B and C were identified in 5.5% and 27.8% of samples, respectively. In HPV 45-infected samples, lineage B comprised of 62.5% of all samples and the remaining 37.5% belonged to lineage A. In conclusion, our findings showed that lineage A of HPV 31 was predominant in Iran. Lineage B of HPV 45 was also dominant among Iranian women. However, further studies with larger sample size should be addressed to estimate the pathogenicity risk of HPV 31 or HPV 45 lineages/sublineages in the development of cervical cancer among Iranian women.
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Affiliation(s)
- Neda Hosseini
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Sarang Younesi
- Department of Clinical Laboratory Sciences, Nilou Medical Laboratory, Tehran, Iran
| | | | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Silva RCDO, da Silva Júnior AHP, Gurgel APAD, Barros Junior MR, Santos DL, de Lima RDCP, Batista MVA, Pena LJ, Chagas BS, Freitas AC. Structural and functional impacts of E5 genetic variants of human papillomavirus type 31. Virus Res 2020; 290:198143. [PMID: 32871208 DOI: 10.1016/j.virusres.2020.198143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 11/29/2022]
Abstract
Persistent infections caused by high-risk human papillomavirus (HR-HPV) are important, for the development of cervical lesions, but environmental and genetic factors are also related in the process of carcinogenesis. Among the genetic factors, the genetic variants of HR-HPV appear to be related to the risk of persistent infections. Therefore, the present study investigates variants of HPV31 E5 oncogene in cervical scraping samples from Brazilian women to assess their functional and structural effects, in order to identify possible repercussions of these variants on the infectious and carcinogenic process. Our results detected nucleotide changes previously described in the HPV31 E5 oncogene, which may play a critical role in the development of cancer due to its ability to promote cell proliferation and signal transmission. In our study, the interaction percentage of the 31E5 sequence generated by the Immune Epitope Server database and the Analysis Resource (IEDB) allowed us to include possible immunogenic epitopes with the MHC-I and MHC-II molecules, which may represent a possible relationship between protein suppression of the immune system. In the structural analysis of the HPV31 E5 oncoprotein, the N5D, I48 V, P56A, F80I and V64I polymorphisms can be found inserted within transmembrane regions. The P56A mutation has been predicted to be highly stabilizing and, therefore, can cause a change in protein function. Regarding the interaction of the E5 protein from HPV31 with the signaling of NF-kB pathway, we observed that in all variants of the E5 gene from HPV-31, the activity of the NF-kB pathway was increased compared to the prototype. Our study contributes to a more refined design of studies with the E5 gene from HPV31 and provides important data for a better understanding of how variants can be distinguished under their clinical consequences.
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Affiliation(s)
- Ruany C de O Silva
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil
| | | | - Ana P A D Gurgel
- Department of Engineering and Environment, Federal University of Paraiba, Paraiba, Brazil
| | - Marconi R Barros Junior
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil
| | - Daffany L Santos
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil
| | - Rita de C P de Lima
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil
| | - Marcus V A Batista
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Federal University of Sergipe, Sergipe, Brazil
| | - Lindomar J Pena
- Department of Virology and Experimental Therapy, Research Center Aggeu Magalhães, Oswaldo Cruz Foundation, Pernambuco, Brazil
| | - Bárbara S Chagas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil
| | - Antonio C Freitas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Pernambuco, Brazil.
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de Oliveira THA, do Amaral CM, de França São Marcos B, Nascimento KCG, de Miranda Rios AC, Quixabeira DCA, Muniz MTC, Silva Neto JDC, de Freitas AC. Presence and activity of HPV in primary lung cancer. J Cancer Res Clin Oncol 2018; 144:2367-2376. [DOI: 10.1007/s00432-018-2748-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 09/08/2018] [Indexed: 12/11/2022]
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Zhang J, Zhang S, Wang M, Ding X, Wen Q, Chen Z, Cao M, Jing Y, Zhang S. Genetic variability in E5, E6, E7 and L1 genes of human papillomavirus type 31. Mol Med Rep 2018; 17:5498-5507. [PMID: 29393441 DOI: 10.3892/mmr.2018.8500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 12/13/2016] [Indexed: 11/05/2022] Open
Abstract
Human papillomavirus (HPV) type 31 is an important pathogenic subtype associated with cervical cancer. The aims of the present study were to analyze E5, E6, E7 and L1 gene mutations of HPV‑31 among females, and to elucidate the evolutionary associations between them. In total, 87 positive samples were collected. The E5, E6, E7 and L1 genes were amplified by polymerase chain reaction and sequenced. Subsequently, two phylogenetic trees were constructed from the nucleotide sequences of the E5, E6 and E7 and the L1 variants of HPV‑31. In total, 31 mutation sites of E5, E6 and E7 genes were identified, of which 16 were non‑synonymous. T4053A (F80I), C285T (H60Y), C520T (A138V) and A743G (K62E) were the most common non‑synonymous mutations. A total of 30 mutation sites of L1 genes were identified, of which four were non‑synonymous. The most common non‑synonymous mutations of L1 genes were A6350G (T29A) and C6372A (T36N). By phylogenetic analysis, A and C variants were most frequently detected, while B variants were less frequently detected in this population. The sequence variation data obtained in the present study provides a foundation for future research regarding HPV‑induced oncogenesis, and may prove valuable for developing diagnostic probes and in the design of HPV vaccines for targeted populations.
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Affiliation(s)
- Jianhui Zhang
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Shaohong Zhang
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Mengting Wang
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Xianping Ding
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Qiang Wen
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Zuyi Chen
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Man Cao
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Yaling Jing
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Shun Zhang
- Key Laboratory of Bio‑Resources and Eco‑Environment, Ministry of Education, Institute of Medical Genetics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
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Association Study between Cervical Lesions and Single or Multiple Vaccine-Target and Non-Vaccine Target Human Papillomavirus (HPV) Types in Women from Northeastern Brazil. PLoS One 2015; 10:e0132570. [PMID: 26176537 PMCID: PMC4503727 DOI: 10.1371/journal.pone.0132570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/16/2015] [Indexed: 01/05/2023] Open
Abstract
We performed an association between high-grade squamous intraepithelial lesions (HSIL), low-grade squamous intraepithelial lesions (LSIL) and single or multiple vaccine-target as well as non-vaccine target Human papillomavirus (HPV) types. Using bead-based HPV genotyping, 594 gynecological samples were genotyped. An association between squamous intraepithelial lesion (SIL) and presence of HPV16, 18, 31, 58 and 56 types were calculated. The risk was estimated by using odds ratio (OR) and 95% of confidence intervals (CI). A total of 370 (62.3%) women were HPV positive. Among these, 157 (42.7%) presented a single HPV infection, and 212 (57.3%) were infected by more than one HPV type. HPV31 was the most prevalent genotype, regardless single and multiple HPV infections. Single infection with HPV31 was associated with LSIL (OR=2.32; 95%CI: 1.01 to 5.32; p=0.04); HPV31 was also associated with LSIL (OR=3.28; 95%CI: 1.74 to 6.19; p= 0.0002) and HSIL (OR=3.82; 95%CI: 2.10 to 6.97; p<0.001) in multiple HPV infections. Risk to harbor cervical lesions was observed in multiple HPV infections with regard to the HPV56 (OR=5.39; 95%CI: 2.44 to 11.90; p<0.001for LSIL; OR=5.37; 95%CI: 2.71 to 10.69; p<0.001) and HPV58 (OR=3.29; 95%CI: 1.34 to 8.09; p=0.0091 for LSIL; OR=3.55; 95%CI: 1.56 to 8.11; p=0.0026) genotypes. In addition, women coinfected with HPV16/31/56 types had 6 and 5-fold increased risk of HSIL (OR=6.46; 95%CI: 1.89 to 22.09; p=0.002) and LSIL (OR=5.22; 95%CI: 1.10 to 24.70; p=0.03), respectively. Multiple HPV infections without HPV16/18 has 2-fold increased risk of HSIL (OR=2.57; 95%CI: 1.41 to 4.70; p=0.002) and LSIL OR=2.03; 95%CI: 1.08 to 3.79; p=0.02). The results of this study suggest that single and multiple vaccine target as well as non-vaccine target HPV types are associated with LSIL and HSIL. These finding should be taken into consideration in the design of HPV vaccination strategies.
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Prevalence of human papillomavirus variants and genetic diversity in the L1 gene and long control region of HPV16, HPV31, and HPV58 found in North-East Brazil. BIOMED RESEARCH INTERNATIONAL 2015; 2015:130828. [PMID: 25793187 PMCID: PMC4352477 DOI: 10.1155/2015/130828] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/08/2015] [Indexed: 02/06/2023]
Abstract
This study showed the prevalence of human papillomavirus (HPV) variants as well as nucleotide changes within L1 gene and LCR of the HPV16, HPV31, and HPV58 found in cervical lesions of women from North-East Brazil.
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Leitão MDCG, Coimbra EC, de Lima RDCP, Guimarães MDL, Heráclio SDA, Silva Neto JDC, de Freitas AC. Quantifying mRNA and microRNA with qPCR in cervical carcinogenesis: a validation of reference genes to ensure accurate data. PLoS One 2014; 9:e111021. [PMID: 25365304 PMCID: PMC4217744 DOI: 10.1371/journal.pone.0111021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/23/2014] [Indexed: 01/17/2023] Open
Abstract
A number of recent studies have catalogued global gene expression patterns in a panel of normal, tumoral cervical tissues so that potential biomarkers can be identified. The qPCR has been one of the most widely used technologies for detecting these potential biomarkers. However, few studies have investigated a correct strategy for the normalization of data in qPCR assays for cervical tissues. The aim of this study was to validate reference genes in cervical tissues to ensure accurate quantification of mRNA and miRNA levels in cervical carcinogenesis. For this purpose, some issues for obtaining reliable qPCR data were evaluated such as the following: geNorm analysis with a set of samples which meet all of the cervical tissue conditions (Normal + CIN1 + CIN2 + CIN3 + Cancer); the use of individual Ct values versus pooled Ct values; and the use of a single (or multiple) reference genes to quantify mRNA and miRNA expression levels. Two different data sets were put on the geNorm to assess the expression stability of the candidate reference genes: the first dataset comprised the quantities of the individual Ct values; and the second dataset comprised the quantities of the pooled Ct values. Moreover, in this study, all the candidate reference genes were analyzed as a single “normalizer”. The normalization strategies were assessed by measuring p16INK4a and miR-203 transcripts in qPCR assays. We found that the use of pooled Ct values, can lead to a misinterpretation of the results, which suggests that the maintenance of inter-individual variability is a key factor in ensuring the reliability of the qPCR data. In addition, it should be stressed that a proper validation of the suitability of the reference genes is required for each experimental setting, since the indiscriminate use of a reference gene can also lead to discrepant results.
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Affiliation(s)
- Maria da Conceição Gomes Leitão
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Center for Biological Sciences, Federal University of Pernambuco, Pernambuco, Brazil
| | - Eliane Campos Coimbra
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Center for Biological Sciences, Federal University of Pernambuco, Pernambuco, Brazil
| | - Rita de Cássia Pereira de Lima
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Center for Biological Sciences, Federal University of Pernambuco, Pernambuco, Brazil
| | | | | | - Jacinto da Costa Silva Neto
- Molecular and Cytological Research Laboratory, Department of Histology, Federal University of Pernambuco, Pernambuco, Brazil
| | - Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Center for Biological Sciences, Federal University of Pernambuco, Pernambuco, Brazil
- * E-mail:
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Liu M, He Z, Xi L, Li J, Liu F, Liu Y, Pan Y, Ning T, Guo C, Xu R, Zhang L, Cai H, Ke Y. The distribution and common amino acid polymorphisms of human papillomavirus (HPV)-31 variants in 2700 women from Northern China. PLoS One 2014; 9:e99141. [PMID: 24901850 PMCID: PMC4047102 DOI: 10.1371/journal.pone.0099141] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/10/2014] [Indexed: 11/18/2022] Open
Abstract
To investigate the distribution of Human papillomavirus (HPV)-31 A, B and C variants as well as the common amino acid polymorphisms in Chinese women, all 14 HPV-31 positive cervical exfoliated cell specimens identified from a descriptive study including ∼2700 women from Northern China were analyzed. HPV-31 positive specimens were identified by Mass Spectrometry and the fragments of partial Long Control Region, E6 and E7 were amplified and directly sequenced or cloned into vector and then sequenced to confirm the variant information. HPV-31 prevalence in Northern Chinese female population was 0.52%. Six different sequences represented all 14 isolates, and these isolates were subsequently classified into variant lineage A (9), B (0) and C (5) by phylogenetic analysis. Five common amino acid polymorphism sites (2 in E6 and 3 in E7) and a novel non-synonymous mutation were detected in the current study. Our investigation suggested that HPV-31 was much less detected in Chinese women population than that in western countries. A and C variants were commonly detected while B variants were rarely detected in this population.
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Affiliation(s)
- Mengfei Liu
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Zhonghu He
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Longfu Xi
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Jingjing Li
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Fangfang Liu
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Ying Liu
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Yaqi Pan
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Tao Ning
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Chuanhai Guo
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
| | - Ruiping Xu
- Anyang Cancer Hospital, Anyang, Henan, P. R. China
| | - Lixin Zhang
- Anyang Cancer Hospital, Anyang, Henan, P. R. China
| | - Hong Cai
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
- * E-mail: (HC); (YK)
| | - Yang Ke
- Laboratory of Genetics, Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, P. R. China
- * E-mail: (HC); (YK)
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de Freitas AC, Coimbra EC, Leitão MDCG. Molecular targets of HPV oncoproteins: potential biomarkers for cervical carcinogenesis. Biochim Biophys Acta Rev Cancer 2014; 1845:91-103. [PMID: 24388872 DOI: 10.1016/j.bbcan.2013.12.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 12/10/2013] [Accepted: 12/27/2013] [Indexed: 12/17/2022]
Abstract
Cervical cancer is the second most common cancer among women worldwide and is responsible for 275,000 deaths each year. Persistent infection with high-risk human papillomavirus (HR-HPV) is an essential factor for the development of cervical cancer. Although the process is not fully understood, molecular mechanisms caused by HPV infection are necessary for its development and reveal a large number of potential biomarkers for diagnosis and prognosis. These molecules are host genes and/or proteins, and cellular microRNAs involved in cell cycle regulation that result from disturbed expression of HR-HPV E5, E6 and E7 oncoproteins. One of the current challenges in medicine is to discover potent biomarkers that can correctly diagnose cervical premalignant lesions and standardize clinical management. Currently, studies are showing that some of these molecules are potential biomarkers of cervical carcinogenesis, and it is possible to carry out a more accurate diagnosis and provide more appropriate follow-up treatment for women with cervical dysplasia. In this paper, we review recent research studies on cell cycle molecules deregulated by HPV infections, as well as their potential use for cervical cancer screening.
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Affiliation(s)
- Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy, Department of Genetics, Center for Biological Sciences, Federal University of Pernambuco, Recife, Brazil.
| | - Eliane Campos Coimbra
- Laboratory of Molecular Studies and Experimental Therapy, Department of Genetics, Center for Biological Sciences, Federal University of Pernambuco, Recife, Brazil.
| | - Maria da Conceição Gomes Leitão
- Laboratory of Molecular Studies and Experimental Therapy, Department of Genetics, Center for Biological Sciences, Federal University of Pernambuco, Recife, Brazil.
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Prevalence and genetic variability in capsid L1 gene of rare human papillomaviruses (HPV) found in cervical lesions of women from North-East Brazil. BIOMED RESEARCH INTERNATIONAL 2013; 2013:546354. [PMID: 23865057 PMCID: PMC3705854 DOI: 10.1155/2013/546354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 04/30/2013] [Accepted: 05/09/2013] [Indexed: 12/03/2022]
Abstract
The aim of this study was to examine the prevalence and genetic variability of the capsid L1 gene of rare HPV genotypes that were found in the cervical lesions of women from North-East Brazil. A total number of 263 patients were included in this study. HPV detection was performed using PCR followed by direct sequencing of MY09/11, as well as type-specific PCR to detect the Alpha-9 species. Epitope prediction was performed to determine whether or not the genetic variants are inserted in B-cell and T-cell epitopes. The prevalence of rare HPV types in cervical lesions was found to be 9.47%. The rare HPV genotypes that were detected were HPV-53, 54, 56, 61, 62, 66, 70, and 81. The genetic variability in the L1 gene of rare HPV types involved thirty nucleotide changes, eight of which were detected for the first time in this study. Moreover, some of these variants are embedded in B-cell or T-cell epitope regions. The results of this research suggest that rare HPV types might be involved in cervical lesions and some of these variants can be found in B-cell and T-cell epitopes. Data on the prevalence and variability of rare HPV types will assist in clarifying the role of these viruses in carcinogenesis.
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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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Xi LF, Schiffman M, Koutsky LA, He Z, Winer RL, Hulbert A, Lee SK, Ke Y, Kiviat NB. Persistence of newly detected human papillomavirus type 31 infection, stratified by variant lineage. Int J Cancer 2012; 132:549-55. [PMID: 22729840 DOI: 10.1002/ijc.27689] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/30/2012] [Indexed: 12/31/2022]
Abstract
Variants of human papillomavirus (HPV) type 31 have been shown to be related both to risk of cervical lesions and racial composition of a population. It is largely undetermined whether variants differ in their likelihood of persistence. Study subjects were women who participated in the ASCUS-LSIL Triage Study and who had a newly detected HPV31 infection during a two-year follow-up with six-month intervals. HPV31 isolates were characterized by sequencing and assigned to one of three variant lineages. Loss of the newly detected HPV31 infection was detected in 76 (47.5%) of the 160 women (32/67 with A variants, 16/27 with B variants and 28/66 with C variants). The adjusted hazard ratio associating loss of the infection was 1.2 (95% CI, 0.7-2.1) for women with A variants and 2.1 (95% CI, 1.2-3.5) for women with B variants when compared with those with C variants. Infections with A and C variants were detected in 50 and 41 Caucasian women and in 15 and 23 African-American women, respectively. The likelihood of clearance of the infection was significantly lower in African-American women with C variants than in African-American women with A variants (p = 0.05). There was no difference in the likelihood of clearance between A and C variants among Caucasian women. Our data indicated that infections with B variants were more likely to resolve than those with C variants. The difference in clearance of A vs. C variants in African-Americans, but not in Caucasians, suggests a possibility of the race-related influence in retaining the variant-specific infection.
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Affiliation(s)
- Long Fu Xi
- Department of Pathology, School of Medicine, School of Public Health, University of Washington, Seattle, WA 98104, USA.
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Xi LF, Schiffman M, Koutsky LA, Hulbert A, Lee SK, Defilippis V, Shen Z, Kiviat NB. Association of human papillomavirus type 31 variants with risk of cervical intraepithelial neoplasia grades 2-3. Int J Cancer 2012; 131:2300-7. [PMID: 22396129 DOI: 10.1002/ijc.27520] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 02/24/2012] [Indexed: 11/09/2022]
Abstract
Although the lineages of human papillomavirus type 31 (HPV31) variants are recognized, their clinical relevance is unknown. The purpose of our study was to examine risk of cervical intraepithelial neoplasia Grades 2-3 (CIN2/3) by HPV31 variants. Study subjects were women who participated in the atypical squamous cells of undetermined significance and low-grade squamous intraepithelial lesion Triage Study and who had HPV31 infections detected at one or more visits. They were followed semi-annually over 2 years for detection of HPV DNA and cervical lesion. HPV31 isolates were characterized by DNA sequencing and assigned into 1 of 3 variant lineages. CIN2/3 was histologically confirmed in 127 (27.0%) of the 470 HPV31-positive women, 83 diagnosed at the first HPV31-positive visit and 44 thereafter. The odds ratio for the association of 2-year cumulative risk of CIN2/3 was 1.7 (95% CI: 1.0-2.9) for infections with A variants and 2.2 (95% CI: 1.2-3.9) for infections with B variants as compared to those with C variants. Among women without CIN2/3 at the first HPV31-positive visit, the risk of subsequent CIN2/3 was 2.2-fold greater for those with A variants (95% CI: 1.0-4.8) and 2.0-fold greater for those with B variants (95% CI: 0.9-4.9) as compared to those with C variants. Similar associations were observed when CIN3 was used as the endpoint. The findings from our study help to tag HPV31 variants that differ in risk of CIN2/3 and to explain in part why some HPV31 infections regress spontaneously and others lead to disease progression.
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Affiliation(s)
- Long Fu Xi
- Department of Pathology, School of Medicine, University of Washington, Seattle, WA 98104, USA.
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