Projects / Programmes
Molecular characterization of the genomic variants of human papillomavirus genotypes HPV-6, HPV-11, HPV-16, HPV-18, HPV-31, and HPV-53
| Code |
Science |
Field |
Subfield |
| 3.01.00 |
Medical sciences |
Microbiology and immunology |
|
| Code |
Science |
Field |
| B230 |
Biomedical sciences |
Microbiology, bacteriology, virology, mycology |
Human papillomaviruses, HPV, genetic diversity, HPV variants, pathogenicity, PCR
Researchers (1)
| no. |
Code |
Name and surname |
Research area |
Role |
Period |
No. of publicationsNo. of publications |
| 1. |
23430 |
PhD Boštjan Kocjan |
Microbiology and immunology |
Head |
2008 - 2010 |
231 |
Organisations (1)
Abstract
Human papillomaviruses (HPV) are remarkably diverse DNA viruses associated with various benign and malignant tumorous lesions of mucosal and cutaneous epithelia. Currently, more than 95 HPV genotypes have been completely characterized. HPV genotypes show tissue tropism and induce type-specific lesions. Since the HPV associated lesions develop only in the minority of infected subjects, there are indications that variants of the same HPV genotype may differ biologically and etiologically. Variants of HPV-16 and HPV-18 have been particularly well studied, although their role in the etiopathogenesis of specific diseases (e.g., cervical cancer) still requires substantial research before final conclusions can be drawn.
Within the proposed research project the genetic diversity, the oncopathogenicity and the evolution of variants of HPV-6, HPV-11, HPV-16, HPV-18, HPV-31, and HPV-53 genotypes will be investigated. HPV-6 and HPV-11 are etiologically most commonly associated with genital warts and laryngeal papillomas. HPV-16, HPV-18, and HPV-31 are found with the highest frequencies in cervical cancers; HPV-16 and HPV-18 account for approximately two thirds of all cervical carcinomas worldwide. The role of HPV-53 in a process of cervical carcinogenesis still remains controversial and therefore further research is needed. All the isolates that will be included in the study - except for the HPV-53 isolates - were previously collected in Slovenia from patients with different benign and malignant neoplastic lesions of mucosal epithelium, and are part of the DNA sample collection of the Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana. HPV-53 isolates - obtained from women with normal cervical cytology, different grades of cervical dysplasia, and cervical cancer – have been collected with the help of our collaborating research groups from Europe and USA. The identification and characterized of HPV-6, HPV-11, HPV-16, HPV-18, HPV-31, and HPV-53 variants will be performed by PCR sequencing of the HPV coding and non-coding genomic regions.
Based on the overall results, we will most probably prove that HPV-6 induced anal warts are - similarly as genital warts and laryngeal papillomas - exclusively caused by the non-prototypic HPV-6 variants. Furthermore, it will be possible to answer if there are variants of HPV-11 significantly associated with diseases caused by HPV-11. Sequencing of HPV-53 isolates collected in 7 European countries and USA will most probably identify several novel HPV-53 variants. We also expect to answer the question whether there are HPV-53 variants significantly associated with cervical cancer. Molecular analysis of the three most commonly isolated HPV genotypes from Slovenian women with cervical cancer will - according to the previously published data - identify several HPV-16, HPV-18, and HPV-31 variants. Their association with cervical cancer will be investigated. The results of this study will also help us to answer the question regarding the age and the origin of Slovenian HPV-6, HPV-11, HPV-16, HPV-18, HPV-31, and HPV-53 isolates (variants).
Our study - where several novel HPV variants will be most probably identified - will significantly expand the missing knowledge about intratype genomic diversity of six clinically very important HPV genotypes and their association with specific diseases.
Significance for science
Based on the overall results of this research project we have importantly contributed to the basic knowledge about the number, the pathogenicity and the evolution of genomic variants of five in Slovenia as well as in the world clinically important human papillomavirus (HPV) genotypes: HPV-6, HPV-11, HPV-16, HPV-18, and HPV-33. We have shown that in Slovenia nonprototypic genomic variants of HPV-6 and HPV-11 are the main etiological agents of genital (GW) and anal warts (AW) and laryngeal papillomas (LP). In addition, LCR based phylogenetic comparison showed that the majority of Slovenian HPV-6 and HPV-11 isolates were identical to several phylogenetically diverse HPV-6 and HPV-11 genomes identified previously in other parts of the world. Thus, in contrast to HPV-16 and HPV-18, the existence of specific and geographically restricted HPV-6 and HPV-11 genomic variants seems highly unlikely. On the basis of analysis of L1 protein sequence of 140 HPV-6 (N=77) and HPV-11 (N=63) isolates obtained from GW, AW, and LP we conclude that the majority of these tumors could be prevented by use of a quadrivalent prophylactic vaccine against HPV-6, HPV-11, HPV-16 and HPV-18. However, specific amino acid alternations of the HPV-6 L1 protein (which serves as a base for the quadrivalent HPV vaccine in addition to L1 proteins of HPV-11, -16, and -18) that were identified in 16.9% (13/77) of analyzed HPV-6 isolates from GW and LP could theoretically lower the efficiency of this vaccine against infection with HPV-6 in Slovenia as well as on the other parts of the world. In the second part of the project we have investigated genomic diversity of HPV-16, HPV-18 and HPV-33, the three most commonly encountered high-risk HPV genotypes in Slovenian women with cervical cancer (CC). A total of 40 randomly selected isolates of HPV-16, 20 isolates of HPV-18 and 11 isolates of HPV-33 were included in the study. We identified several genomic variants of these HPV genotypes and showed for the first time that the majority of HPV-16 and HPV-18 variants/isolates from Slovenian patients with CC belong to the European branches, what is in line with previous studies performed in several European countries. In addition, European HPV-16 genomic variant E6 T350G (L83V), with presumably higher oncogenic potential, was found in 25/40 (60%) HPV-16 isolates. Similarly, presumably more pathogenic nonprototypic HPV-33 genomic variants were identified in 6/11 (54.4%) HPV-33 isolates. The results of our study confirm previous observations that specific genomic variants of HPV-16 and HPV-18 have increased prevalence in some parts of the world and correlate with the predominant ethnic group of that geographic region. The nucleotide sequence data of HPV genotypes HPV-6, HPV-11, HPV-16, HPV-18, and HPV-33 obtained in this project will be important for the development of new as well as for the improvement of the existing HPV detection and genotyping methods. Thus, on the basis of newly obtained E1 sequences of HPV-6 and HPV-11 we have already developed a unique PCR-RFLP method for the detection and reliable differentiation of HPV-6, HPV-11, HPV-32, HPV-42, HPV-43, HPV-44, and HPV-55, as well as prototypic and no-prototypic HPV-6 genomic variants. This method, which targets 7 with benign tumors (GW, AW, LP, and oral tumors (HPV-32)) most frequently associated low-risk HPV genotypes (the most important are HPV-6 and HPV-11), gives good complementary information to the commercially available HPV genotyping methods and may be of great value for clinical and epidemiological studies of low-risk HPV infections. Similarly, using the newly obtained E2 sequences of HPV-11, we have already improved our original RT-PCR method for detection and differentiation of prototypic and nonprototypic HPV-6 genomic variants to additionally detect HPV11.
Significance for the country
The results of our study provide important national data (and in some cases the first data) regarding the number, the pathogenicity, and the evolution of HPV variants of some of the - in Slovenia - clinically most important HPV genotypes. In addition, by determining the distribution of HPV genotypes among a representative group of Slovenian women with cervical cancer, we estimate that 77.1% of this cancer (caused by HPV-16 and HPV-18) in Slovenia could be prevented by use of a quadrivalent prophylactic vaccine against HPV-6, HPV-11, HPV-16 and HPV-18. Similarly, on the basis of analysis of L1 protein sequence of 140 HPV-6 and HPV-11 isolates obtained from genital and anal warts and laryngeal papillomas we conclude that in Slovenia the majority of these tumors could be also prevented by this vaccine. However, specific amino acid alternations of the HPV-6 L1 protein (which serves as a base for the quadrivalent vaccine in addition to L1 proteins of HPV-11, -16, and -18) that were identified in 16.9% (13/77) of analyzed HPV-6 isolates from genital warts and laryngeal papillomas could theoretically lower the efficiency of a quadrivalent HPV vaccine against infection with HPV-6. The results of this research project will be also important for the future development of basic molecular methods for the determination of HPV genomic variants as well as for the development of new and improvement of the existing HPV detection and genotyping methods.
Most important scientific results
Annual report
2008,
final report,
complete report on dLib.si
Most important socioeconomically and culturally relevant results
Annual report
2008,
final report,
complete report on dLib.si
