1Objectives. Infection with oncogenic human papillomaviruses (HPV) is a prerequisite 2 for the development of cervical cancer. In many cases of cervical cancer and all cervical 3 cancer derived cell lines oncogenic HPV DNA is found to be integrated, indicating the 4 importance of integration in disease development. In this study, 176 HPV 16 positive 5 precancerous cervical lesions were analyzed for the physical state of viral genome to 6 determine the sites of integration into a host cell DNA and to evaluate the incidence of the 7 integration in different stages of cervical lesions. 8Methods. The detection of integrated papillomavirus sequences (DIPS) method in 9 combination with the amplification by polymerase chain reaction (PCR) of E1/E2 region was 10 used to identify the physical state of HPV 16 genome. The site of integration within a host 11 cell genome was determined by sequencing of DIPS unusual sized amplicons. 12

Head and neck cancer is the sixth most common malignancy worldwide, predominantly developing from squamous cell epithelia (HNSCC). The main HNSCC risk factors are tobacco, excessive alcohol use, and the presence of human papillomavirus (HPV). HPV positive (+) cancers are etiologically different from other HNSCC and often show better prognosis. The current knowledge regarding HNSCC miRNA profiles is still incomplete especially in the context of HPV+ cancer. Thus, we analyzed 61 freshly collected primary oral (OSCC) and oropharyngeal (OPSCC) SCC samples. HPV DNA and RNA was found in 21% cases. The Illumina whole-genome small-RNA profiling by next-generation sequencing was done on 22 samples and revealed 7 specific miRNAs to HPV+ OSCC, 77 to HPV+ OPSCC, and additional 3 shared with both; 51 miRNAs were specific to HPV− OPSCC, 62 to HPV− OSCC, and 31 shared with both. The results for 9 miRNAs (miR-9, -21, -29a, -100, -106b, -143 and -145) were assessed by reverse transcription-quantitative polymerase chain reaction on the whole study population. The data was additionally confirmed by reanalyzing publicly available miRNA sequencing Cancer Genome Atlas consortium (TCGA) HNSCC data. Cell signaling pathway analysis revealed differences between HPV+ and HPV− HNSCC. Our findings compared with literature data revealed extensive heterogeneity of miRNA deregulation with only several miRNAs consistently affected, and miR-9 being the most likely HPV related miRNA.

Human papillomaviruses (HPVs) have been recognized as etiologic factors in a variety of diseases. Due to the large number of HPV types, methods for HPV genotyping are difficult to standardize. Despite this fact, several methods exist, and some of them are available commercially. In this study, we evaluated the Roche Diagnostics linear array (LA) HPV genotyping assay, the Innogenetics INNO-LiPA (line probe assay [LiPA]), and two noncommercial reverse line blot (RLB) assays based on either primers GP5؉ and GP6؉ (GP) or newly designed broad-spectrum primers BSGP5؉ and BSGP6؉ (BS). The reliabilities of these assays were tested with a wide spectrum of HPV types less prevalent in cervical samples. This is the first study to compare the performance of the most widely used HPV genotyping methods with selected samples positive for low-prevalence HPV types. We focused on interassay agreement, both overall and type specific, in cases with single and/or multiple HPV infections. Interassay agreement was moderate in cases of single HPV infections and poor in cases of multiple HPV infections. The LA and the BS-based RLB assays found a higher rate of cases positive for multiple HPV types than LiPA and the GP-based RLB assay. The weakest capability in detecting multiple HPV infections was observed for LiPA. The use of only one assay in epidemiological and clinical studies might lead to biased conclusions. Therefore, a universally evaluated and agreed upon HPV typing assay or a combination of current assays is needed for possible clinical applications, and knowledge of their limitations is advised.Human papillomaviruses (HPVs) have been recognized as etiologic factors in cervical carcinoma, precancerous lesions of the cervix uteri, and several other anogenital cancers in females and males (for reviews, see references 3 and 24). In addition, about 26% of head and neck cancers are linked to HPV infection (13). HPVs represent an extremely heterogeneous group of DNA viruses. Until now, more than 100 HPV types have been identified and fully sequenced (9). Approximately 40 HPV types infecting the anogenital epithelium are classified as either low risk (LR) or high risk (HR) on the basis of their oncogenic potentials. A recent meta-analysis has designated 15 anogenital HPV types as HR, with an additional 3 HPV types designated as probable HR types (23).Because of their biological properties, HPVs cannot easily be grown in tissue culture, which makes the preparation of antigens for the routine detection of HPV difficult (10). Furthermore, serological assays, which detect HPV-specific antibodies, cannot be used for diagnostic purposes, since these antibodies are markers of a lifetime's cumulative exposure to HPV types (18). For diagnostic purposes, methods based on the detection of HPV-specific nucleic acids are being used. In addition, the typing of HPV isolates is done by means of molecular biological methods (4).Due to the large number of HPV types, methods for HPV genotyping are difficult to standardize. Despite this fact, several met...

The main etiological factor of precancerous lesion and invasive cervical cancer are oncogenic human papillomaviruses types (HPVs). The objective of this study was to establish the distribution of the most common HPVs in different cervical lesions and cancer prior to the implementation of organized population-based cervical screening and HPV vaccination in Croatia. In this study, 4,432 cervical specimens, collected through a 16-year period, were tested for the presence of HPV-DNA by polymerase chain reaction (PCR) with three sets of broad-spectrum primers and type-specific primers for most common low-risk (LR) types (HPV-6, 11) and the most common high-risk (HR) types (HPV-16, 18, 31, 33, 45, 52, 58). Additional 35 archival formalin-fixed, paraffin embedded tissue of cervical cancer specimens were analyzed using LiPA25 assay. The highest age-specific HPV-prevalence was in the group 18–24 years, which decreased continuously with age (P<0.0001) regardless of the cytological diagnosis. The prevalence of HR-HPV types significantly increased (P<0.0001) with the severity of cervical lesions. HPV-16 was the most common type found with a prevalence (with or without another HPV-type) of 6.9% in normal cytology, 15.5% in atypical squamous cells of undetermined significance, 14.4% in low-grade squamous intraepithelial lesions, 33.3% in high-grade squamous intraepithelial lesions, and 60.9% in cervical cancer specimens (P<0.0001). This study provides comprehensive and extensive data on the distribution of the most common HPV types among Croatian women, which will enable to predict and to monitor the impact of HPV-vaccination and to design effective screening strategies in Croatia.

The human papillomavirus (HPV) 16 genome has been studied extensively, although no study has focused on the E1 gene that is implicated in viral DNA replication. After analyzing the E1 region of HPV 16 genomes in 429 cervical samples, 11.2% were found to contain a 63 nucleotides duplication in this region. Sequence analysis of the E6 and the E7 regions has shown that all samples containing this duplication were related to E6‐G350 variant of the HPV 16 (Chi square test, P = 0.0012). A comparison of cervical lesion severity of the examinees having regular or variant E1 genes has shown that the variant group had a significantly (Fischer's exact test, P = 0.0401) lower percentage of high grade disease cases, suggesting that this particular duplication might reduce the oncogenic potential of HPV 16, and also might clarify the differences of E6‐G350 variant oncogenicity observed in European populations. Albeit, a decreased incidence of high grade cervical lesions can be linked to the prevalence of multiple HPV infection, the additional decrease of those cases with the variant E1 gene versus those without (10.5% and 18.6%, respectively) can only be ascribed to the effect of this particular HPV variant. Further research is needed to clarify the biology of these HPV 16 E1 variants. J. Med. Virol. 80:2134–2140, 2008. © 2008 Wiley‐Liss, Inc.