HPV-DNA Positive Samples Research Articles

The clinical importance of IFN-γ and human epididymis protein 4 in Egyptian patients with epithelial ovarian cancer combined with HPV infection

BackgroundHigh-grade Epithelial Ovarian Cancer (HGEOC) is an aggressive disease that usually presents at an advanced stage. Thus, detecting the circulating cytokines (IFNγ and TNF-α) may serve as a biomarker to identify malignancy and manage therapeutic decisions. ObjectivesAssessing the clinical importance of inflammatory mediators and tumor markers in EOC Egyptian patients compared with benign cases. Moreover, identifying the distinct inflammatory mediators in EOC patients combined with HPV infection. MethodsThis study was conducted on 61 Egyptian patients, divided into 25 patients with HGEOC, 22 patients with LGEOC, and 14 benign ovarian tumor cases. Measurements of serum HE4, CA125, CEA, and CA19-9 were determined by Roche Elecsys immunoassays. Serum levels of TNF-α and IFN-γ were measured using quantitative sandwich ELISA. Quantitative genotyping of HPV DNA types 16, 18, and 45 was assessed for the HPV DNA-positive samples. ResultsHPV DNA was detected in 25.53 % of malignant cases, HPV 16 was detected in 50 % of HPV-positive cases, and only 1 case of HPV 18 was detected out of 12 positive cases. The Human Epididymis protein 4 (HE4) was statistically different between patients with EOC and benign cases (p-value = 0.007) and between HPV DNA positive and HPV DNA negative cases (p-value = 0.008). The serum levels of IFN- γ were statistically different between HGEOC and LGEOC (p-value < 0.001), while the serum levels of TNF-α didn’t differ statistically between the two groups. ConclusionIFN-γ could be used as a biomarker to discriminate HGEOC and LGEOC. Initial evidence for the possible association between HE4 and the progression of HPV-associated EOC was speculated.

Abstract 81: The Introduction of a High Risk HPV DNA Test for the Cervical Cancer Screening Among Mongolian Women

Abstract Purpose: A global strategy developed by the World Health Organization aims to reduce cervical cancer burden by screening 70% of women with high performance tests at least twice during their lifetime. While Mongolia has implemented a PAP test-based cervical cancer screening program over the past few decades, cervical cancer remains the leading cause of death in the country. Therefore, it is necessary to introduce high-risk HPV DNA detection tests in cervical cancer screening program. Methods: Cervical screening was conducted in 6 districts of the UB and in 4 regional provinces between March 01 and July 01, 2019. A high risk HPV DNA test was conducted on all women using the careHPV test, and then all positive samples were double-tested using the PAP test. All positive women were followed by HPV genotyping test and colposcopy with direct biopsy or endocervical curettage as necessary. Results: A total of 2725 women were screened for HPV DNA, with 8.5%(239) of these detecting high risk HPV DNA, and 61% (138) of positive results having a negative result for intraepithelial neoplasia as determined by PAP tests. It was determined that 10% of samples contained atypical squamous cells of undetermined significance, 4% contained atypical squamous cells of unknown significance, and cannot exclude high grade, 17% of the samples contained low grade squamous intraepithelial lesions, and 10% contained high grade squamous intraepithelial lesions. A colposcopy examination was performed on 181 women who were high-risk HPV DNA positive. An abnormal colonoscopy result was observed in 18% of the women, for which biopsies were taken. A total of 31% of them were confirmed with CIN I, 31% with CIN II, 9% with CIN III, 11% with CIS, and 6% with SCC. Additionally, 105 high-risk HPV DNA-positive samples were genotyped for HPV. There were 25.7% of individuals who were found to have HPV genotype 16, 4.7% who were found to have HPV genotype 18, and 69.6% who were found to have other high-risk genotypes. Conclusion: By incorporating high-risk HPV DNA tests into cervical cancer screening program, its coverage and effectiveness could be increased. Citation Format: Enkhjargal Bayarsaikan. The Introduction of a High Risk HPV DNA Test for the Cervical Cancer Screening Among Mongolian Women [abstract]. In: Proceedings of the 11th Annual Symposium on Global Cancer Research; Closing the Research-to-Implementation Gap; 2023 Apr 4-6. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(6_Suppl):Abstract nr 81.

Cervical, anal and oral HPV detection and HPV type concordance among women referred for colposcopy

BackgroundInfection with human papillomaviruses (HPVs) can cause benign and malignant tumours in the anogenital tract and the oropharynx both in men and women. The aim of the presented study was to investigate cervical, anal, and oral HPV-detection rates among women referred to colposcopy for abnormal Cervical Cancer (CaCx) screening results and assess the concordance of HPV-types among these anatomical sites.MethodsWomen referred to colposcopy at a single centre due to abnormal cytology, conducted for CaCx screening, were subjected to cervical Liquid-based Cytology (LBC) smear testing, anal and oral sampling. Routine colposcopy consisted in multiple biopsies and/or Endocervical Curettage (ECC). HPV-detection was performed by PCR genotyping in all three anatomical sites. In high-risk (hr) HPV-DNA positive samples either from anal canal or oral cavity, anal LBC cytology and anoscopy were performed, or oral cavity examination respectively. Descriptive statistics was used for the analysis of HPV-detection rates and phi-coefficient for the determination of HPV-positivity concordance between the anatomical sites.ResultsOut of 118 referred women, hr. HPV-DNA was detected in 65 (55.1%), 64 (54.2%) and 3 (2.5%) at cervix, anal canal and oral cavity respectively while low-risk HPV-DNA was detected in 14 (11.9%) and 11 (9.3%) at cervix and anal canal respectively. The phi-coefficient for cervix/anal canal was 0.392 for HPV16, 0.658 for HPV31, 0.758 for HPV33, − 0.12 for HPV45, 0.415 for HPV52 and 0.473 for HPV58. All values were statistically significant (p < 0.001).ConclusionsThe results suggest that most HPV-types, high-risk and low-risk, detected in the cervix of women with prevalent cervical dysplasia, correlate with the ones detected in their anal canal. This particularly applies for the HPV-types included in the nonavalent HPV-vaccine (HPVs 6/11/16/18/31/33/45/52/58).

Human Papillomavirus and Factors Associated with Recurrence in Sinonasal Inverted Papillomas from Poland and Spain.

Sinonasal inverted papilloma (SNIP) is a benign but locally aggressive tumor that has a tendency for recurrence and malignant transformation. The role of human papillomavirus (HPV) in SNIP is controversial. To determine the HPV-DNA prevalence and type distribution in SNIP in two different geographic areas and assess the association between SNIP recurrence and HPV infection, as well as additional potential etiologic factors. Two retrospective cohorts of SNIP patients from Poland and Spain were evaluated. Demographic, tobacco/alcohol use, clinical, and follow-up data were collected. All samples were subject to histopathologic evaluation, DNA quality control, and HPV-DNA detection by PCR. HPV-DNA positive samples and a random sample of HPV-DNA negative cases were further subject to p16INK4a analysis. Proportional-hazards models were used to evaluate the risk of recurrence by selected variables. Seventy-nine SNIP patients (46 from Spain diagnosed between 1995 and 2014, and 33 from Poland diagnosed between 2012 and 2017) were included in the study. HPV-DNA was detected in four patients (5.1%), two from each region, and all four were positive for the HPV11 subtype. Seventeen patients (21.5%) experienced recurrence, with a median time to recurrence of 14months. No association was identified between lesional HPV-DNA positivity, toxic habits, Krouse stage, or malignant transformation and a higher risk of recurrence. The low prevalence of HPV-DNA in SNIPs suggests that HPV is not a main etiology for development of these lesions. With a lack of association between the evaluated factors and recurrence, further research with larger number of patients and additional biomarkers is warranted to further understand predisposing risk factors.

Risk of second primary neoplasia in patients with oropharyngeal carcinoma: Role of HPV status in the outcome.

e17544 Background: Patients with HPV-positive oropharyngeal cancer (OPC) have better prognosis and a lower risk of appearance of second primary neoplasm (SPN) than HPV-negative OPC patients. The aim of our study was to analyze the risk of developing SPN in a large group of patients with OPC according to HPV status in the primary tumor and its relationship with toxic habits. Methods: This study includes patients from a prospective data-base: 484 OPC patients were treated from 1991 to 2017 for which the HPV DNA positivity was evaluated by PCR in available tumor specimens. HPV DNA positive samples were further tested for HPV E6*I mRNA detection and/or p16INK4a immunohistochemistry. The mean follow-up of patients included in the study was 4.9 years (SD 5.1 years). We estimated the incidence of SPN in all cancer sites and in cancer sites related to tobacco and alcohol consumption according to the HPV status in the primary tumor. Results: Ninety-nine (20.5%) out of 484 OPCs included in the study were HPV-related. During the follow-up period, 127 patients with HPV-negative tumors (33.0%) and 19 patients with HPV-positive tumors (19.2%) had a SPN. Considering only the tobacco/alcohol-related SPNs, 106 of the patients with HPV-negative tumors (27.5%), and 12 patients with HPV-positive tumors (12.1%) had a tobacco/alcohol-related SPN (P &lt; 0.0001). Five-year and 10-year SPN-free survival for HPV-negative versus HPV-positive OPC patients was 61.0% versus 81.5%, and 37.6% versus 73.8%, respectively (P &lt; 0.001). When restricting the analyses to tobacco/alcohol-related SPNs, the corresponding survival rates were 66.6% versus 86.8% and 45.9% versus 83.5% for 5-year and 10-year survival rates, respectively (P &lt; 0.0001). The frequency of tobacco/alcohol-related SPNs occurrence throughout the follow-up period for patients with HPV-negative OPC was 27.5%, for patients with HPV-positive tumors with a previous history of severe tobacco and/or alcohol use was 21.4%, and for patients with HPV-positive tumors without a history of severe tobacco and/or alcohol consumption it was 8.5% (P &lt; 0.0001). Conclusions: HPV status and previous toxic habits might allow classifying patients regarding the risk of tobacco/alcohol-related SPNs. HPV-related OPC patients without previous history of severe tobacco and/or alcohol use have a significant low risk of SPN development, particularly in those locations related to tobacco use or alcohol consumption

Human papillomavirus in premalignant oral lesions: No evidence of association in a Spanish cohort.

BackgroundHuman papillomavirus (HPV) is the cause of a fraction of head and neck squamous cell carcinoma. Although this relation is well-known, it is still not clear the role of HPV in premalignant oral lesions such as oral lichen planus (OLP) and dysplasia. We aimed to evaluate the HPV-DNA prevalence and type distribution in a set of oral biopsies obtained from patients diagnosed with OLP and dysplasia, as well as the role of HPV in these lesions.MethodsA retrospective cohort of all premalignant oral lesions consecutively diagnosed from March 30th 1995 to May 21st 2014 at Hospital of Bellvitge and Odontological University Hospital of Bellvitge was identified and classified in four groups: OLP (groups 1 and 2) and dysplasias (groups 3 and 4) that progressed or not to invasive cancer during follow-up. A random selection targeting 25 cases was aimed to be performed for each group. All selected cases were subjected to pathological evaluation, DNA quality control and HPV-DNA detection. HPV-DNA positive samples were further subject to p16INK4a analysis.ResultsA total of 83 cases yielded a valid HPV-DNA result. From those, 7 and 34 cases were OLP that progressed or not to invasive cancer during follow-up, whereas 24 and 18 cases were displasias that progressed or not to invasive cancer during follow-up, respectively. HPV-DNA was detected in 4 samples (3 dysplastic lesions and 1 OLP). Two samples were HPV16 positive (2%), 1 sample HPV18 positive (1%) and 1 sample (1%) was HPV indeterminate. Two out of four HPV-DNA positive cases had high p16INK4a expression and none of the HPV positive cases progressed to invasive cancer during long-term follow-up.ConclusionsWe found a low HPV-DNA attributable fraction in premalignant lesions of the oral cavity, suggesting that HPV is unlikely to play a significant role in oral carcinogenesis in our setting.

Incident genital HPV infections and potential impact of HPV vaccines in adult women living with HIV/AIDS

ABSTRACT This study aims to describe and characterize incident HR-HPV infections and associated diseases in HIV-infected women. 805 HIV-infected women enrolled in the VALHIDATE Study were screened and followed-up for HPV by co-testing. Social, behavioral and health data were collected. HPV-DNA positive samples were typed using a commercial kit or RFLP analysis. Conventional Pap-smears were evaluated using the 2001 Bethesda System. The participants with abnormal cytological results were referred for colposcopy. 565 HIV-infected women (median age: 43 years) were analysed, 40.9% had >5 lifetime sexual partners, 77.2% contracted HIV through sexual intercourse, 93% were receiving antiretroviral treatment and 77.3% had undetectable HIV-RNA. The women underwent 1254 follow-ups (median follow-up: 33 months) for 1430.6 PersonYear-Follow-Up. 37.4% of baseline HPV-negative women acquired incident HPV-infections, 69.6% of which were HR-HPVs. HPV-53 was the most common HPV type detected (9.3%). 18.2% of women showed incident or progressive cytological abnormalities (7.8% ASC-US, 9.7% LSIL and 0.6% HSIL) and colposcopy revealed CIN2 (N = 2), CIN1 (N = 2) and VIN3 (N = 1). The preventable fraction of incident infections was 11.3%, 16.7%, and 35.2% for the 2v-4v-9v-HPV vaccines respectively (χ2 p < 0.0001). The overall burden of incident lesions attributable to the vaccine types were 9.1% for 2v-, 14.5% for 4v- and 30.9% for 9v-vaccine. High HPV incidence rates and high percentages of multiple HR-HPV infections were observed in a cohort of HIV-infected women receiving effective antiretroviral treatment. Primary prevention strategies based on the new 9v-HPV vaccine may help to prevent incident infections and disease progression in this cohort of women.

Abstract 49: Simultaneous quantification of HPV oncogene (E6, E7 mRNA) and PD-L1 protein expression in oral cancer samples using flow cytometry

Abstract Background: Human papillomaviruses are a family of DNA viruses that infect the epithelium leading to the formation of lesions with the ability to progress into carcinoma in many forms. Research into causality of head and neck cancers has found a link to HPV infections affiliated with better prognosis. In addition, advances in immuno-oncology have brought immunotherapy to the forefront of cancer treatment across cancer types. Here we present data that demonstrate a combined diagnostic approach to quantify two markers important in the management of head and neck cancer. Methods: Swabs were collected from patients of Institut Gustave Roussy with lesions of the oral pharynx. Swabs were collected and placed into a collection vial with a proprietary fixation/permeabilization solution (IncellCollect, IncellDx, Inc.) and shipped overnight on cold packs for processing. Upon receipt, samples were passed through a 35 µM filter to remove aggregates. Cells were labeled with CD45 antibodies to separate epithelial from immune cells, RNA in situ hybridization with E6, E7 mRNA probes (HPV OncoTect) was performed, and these cells were labeled with PD-L1 Ab (clone 28-8) prior to analysis on the flow cytometer (CytoFlex, Beckman Coulter, Inc). Samples were also stained with DAPI to identify single nucleated cells, and to analyze cell cycle. Results: We analyzed samples from 8 patients with oral cancer with the combined E6, E7 mRNA/PD-L1 protein assay by flow cytometry. The percentage of tumor cells expressing PD-L1 averaged 9.1% in all of the samples. Of the HPV DNA positive tumor samples, the percentage of cells overexpressing HPV E6, E7 mRNA was 4.8%. Interestingly, the percentage of cells overexpressing E6, E7 mRNA that also expressed PD-L1 was statistically lower (1.4%) than the percentage of all tumor cells that expressed PD-L1 (P=0.01). Conclusions: We report a novel flow cytometric assay to quantify both HPV E6, E7 mRNA and PD-L1 simultaneously in single cells. Further, we found the expression of PD-L1 in tumor cells with HPV E6, E7 mRNA to be significantly lower than the expression of PD-L1 in tumor cells not expressing HPV E6, E7 mRNA. These findings may influence prognosis and treatment strategies. Note: This abstract was not presented at the conference. Citation Format: Rian J. Morgan, Amanda N. Chargin, Haitham Mirghani, Bruce K. Patterson. Simultaneous quantification of HPV oncogene (E6, E7 mRNA) and PD-L1 protein expression in oral cancer samples using flow cytometry [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; April 23-25, 2017; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(23_Suppl):Abstract nr 49.

The role of HPV on the risk of second primary neoplasia in patients with oropharyngeal carcinoma

ObjectivesIt has been reported that patients with HPV-positive oropharyngeal cancer (OPC) have a lower risk of appearance of second primary neoplasm (SPN) than HPV-negative OPC patients. The aim of our study was to analyze the risk of developing SPN in a large group of patients with OPC according to HPV status in the primary tumor. Materials and methodsWe included 412 OPC patients treated at our center from 1991 to 2014 for which the HPV DNA positivity was evaluated by PCR in available tumor specimens. HPV DNA positive samples were further tested for HPV E6∗I mRNA detection and/or p16INK4a immunohistochemistry. We estimated the incidence of SPN in all cancer sites and in cancer sites related to tobacco and alcohol consumption according to the HPV status in the primary tumor. ResultsFifty-one (12.4%) out of 412 OPCs included in the study were HPV-related. Five-year SPN-free survival for HPV-negative versus HPV-positive OPC patients was 57.0% and 89.0% (P<0.001), respectively. Corresponding estimates for 10-year SPN-free survival were 35.2% versus 78.5% (P<0.001). When restricting the analyses to tobacco/alcohol-related SPNs, the corresponding survival rates where 62.0% versus 97.6% (P<0.001) and 42.2% versus 97.6%, (P<0.001), for 5-year and 10-year survival rates, respectively. HPV status and previous toxic habits might allow classifying patients regarding the risk of tobacco/alcohol-related SPNs. ConclusionHPV-related OPC patients have a significant lower risk of SPN development, particularly in those locations related to tobacco use or alcohol consumption.

Presence of high risk HPV DNA but indolent transcription of E6/E7 oncogenes in invasive ductal carcinoma of breast

Background and aimsThe causative role of high risk human papillomavirus (HR-HPV) in breast cancer development is controversial, though a number of reports have identified HR-HPV DNA in breast cancer specimens. Nevertheless, most studies to date have focused primarily on viral DNA rather than the viral transcription. The aim of this study was to investigate the presence of HR-HPV in breast cancer tissues at HPV DNA level and HPV oncogenes mRNA level by in situ hybridization (ISH). MethodsOne hundred and forty six (146) cases of breast invasive ductal carcinoma(IDC) and 83 cases of benign breast lesions were included in the study. Type specific oligonucleotide probes were used for the DNA detection of HPV 16,18 and 58 by ISH. HR-HPV oncogenes mRNA was assayed by novel RNAscope HR-HPV HR7 assay ISH. p16 protein expression was evaluated by immunohistochemistry (IHC). ResultsHR-HPV 16,18 and 58 DNA were detected in 52 out of 146 (35.6%) IDC and in 3 out of 83 (3.6%) benign breast lesions by ISH. The HR-HPV mRNAs was detected only in a few specimens with strong HPV DNA positivity(4/25) in a few scattered cancer cells with very weak punctate nuclear and/or cytoplasmic staining. p16 over-expression did not correlate with the HPV DNA positive breast cancer samples(17/52 HPVDNA+ vs 28/94 HPV DNA-, p=0.731). ConclusionsHR-HPVs certainly exist in breast cancer tissue with less active transcription, which implies that the causal role of HPV in breast cancer development need further study.

Association between human papillomavirus (HPV) DNA and micronuclei in normal cervical cytology.

The aim of the present study was to investigate the association between HPV-DNA and micronucleus (MN) frequency in women with normal cervical cytology. A total of 158 normal cervical smears were analyzed cytologically. The HPV genome was amplified using the GP5+/bioGP6+ consensus primers. HPV-DNA of high-risk types 16, 18, 31, 33, 39, 45 and 59 were also investigated. Of the 158 samples, 20 (12.7%) and 47 (29.7%) were positive for HPV-DNA and MN, respectively. Evidence for MN was found in 11 out of 20 (55%) HPV-DNA positive samples and in 36 out of 138 (26.1%) HPV-DNA negative ones. MN presence was significantly higher in HPV-DNA positive samples (p = 0.016). On the other hand, the absence of MN observed in a considerable number of HPV-DNA negative samples (102) may be of great value in predicting the absence of HPV. The mean age of HPV-DNA positive women (34.2 ± 12.6) was significantly lower than the mean age of HPV-DNA negative women (43.9 ± 13.7) (p = 0.003). Infection by one or multiple HPV types was found in 11 out of 20 (55.0%) and 9 out of 20 (45.0%) samples, respectively. The evaluation of MN using cervical smears collected for cytology tests could, thus, be used as additional information to monitor a population's exposure to HPV.

Risk of cervical HPV infection and prevalence of vaccine-type and other high-risk HPV types among sexually active teens and young women (13–26 years) enrolled in the VALHIDATE study

HPV vaccination is expected to reduce the incidence of cervical cancer. The greatest and the earliest health gains will be ensured by high vaccine coverage among all susceptible people. The high costs and the risk of a reduced cost/effectiveness ratio in sexually active girls still represent the main obstacles for a more widespread use of HPV vaccination in many countries. Data on the rate, risk factors, and HPV types in sexually active women could provide information for the evaluation of vaccination policies extended to broader age cohorts.Sexually active women aged 13–26 years enrolled in an Italian cohort study were screened for cervical HPV infections; HPV-DNA positive samples were genotyped by InnoLipa HPV Genotyping Extra or by RFLP genotype analysis.Among the 796 women meeting the inclusion criteria, 10.80% (95% CI 8.65–12.96) were HPV-DNA infected. Age >18 years, lifetime sexual partners >1, and history of STIs were associated to higher risk of HPV infection in the multivariable models adjusted for age, lifetime sexual partners, and time of sexual exposure. The global prevalence of the four HPV vaccine-types was 3.02% (95% CI 1.83–4.20) and the cumulative probability of infection from at least one vaccine-type was 12.82% in 26-years-old women and 0.78% in 18-years-old women.Our data confirm most of the previously reported findings on the risk factors for HPV infections. The low prevalence of the HPV vaccine-types found may be useful for the evaluation of the cost/efficacy and the cost/effectiveness of broader immunization programs beyond the 12-years-old cohort.

A Simple Approach for Determining Presence of HPV DNA from Slides Previously Stained for P16ink4a

Background: HPV is a favorable prognostic factor in oropharyngeal squamous cell carcinoma (OSCC), where tonsillar and base of tongue squamous cell carcinoma (TSCC and BOTSCC) dominate. Hence. HPV DNA testing as a predictive marker is desirable even when FFPE material is unavailable. Glass slides with p16 staining, often used as a surrogate marker for HPV, are however generally available. Furthermore, the combination of HPV DNA and p16 positivity is established as being better than testing for HPV DNA, or p16 alone, and almost equivalent as testing for E6 and E7 mRNA for determining HPV driven OSCC. Presence of HPV DNA was therefore examined in cells from glass slides previously stained for p16. Materials and methods: DNA extracted from cells scraped off glass slides from 23 TSCC; 24 BOTSCC and 50 cancers of unknown primary (CUP) of the head and neck, with known HPV DNA and p16 status was tested for presence of HPV by a bead-based multiplex assay. Results: DNA was obtained from 95.9% of the TSCC/BOTSCC/CUP slides and exhibited 93.5% (87/93) concordance with the HPV DNA status of the original FFPEs, with 38/42 (90.5%) of the originally HPV DNA positive/p16 positive remaining HPV DNA positive and all HPV DNA negative samples staying negative. Conclusion: A 93.5% concordance was obtained between the HPV DNA status of the original FFPEs and DNA obtained from p16 stained glass slides. Of the HPV DNA positive IHC samples 38/38 100% were derived from HPV DNA positive/p16 positive FFPE biopsies, while all HPV DNA negative samples stayed HPV-negative. This approach allows for safer identification of HPV-positive tumors, and useful for following patients with HPV-positive tumors in retrospective studies and for future decision-making.

The comparative results of three different real-time PCR assays: MY09/11 primers failed to detect multiple infections

HPV-DNA testing is widely used worldwide today and it has become an important part of cervical cancer screening programs. The aim of this study is re-evaluating the effectiveness of MY09/11 consensus primer system, which is one of the most widely used HPV-DNA tests, by using a different approach. In this study, MY09/11 consensus PCR and two different TaqMan-based type-specific PCR assays were used for investigation of the presence of 17 different HPV types in cervical smear samples. Of the 470 samples, 33.2% (156/470) were HPV-DNA positive by at least one of the three methods and remains were negative by all methods. A total of 220 different HPV isolates were identified in 149 samples by the type specific PCR, while the nine samples were positive by consensus PCR only. A single HPV type was detected in 64.4% (96/149) of the genotyped samples, and multiple HPV types were detected in the remaining 35.6% (53/149). MY09/11 PCR failed to detect 21.2% (33/156) of all HPV-DNA positive samples and the rates of false negative results were 18.75% (18/96) and 28.3% (15/53) in single and multiple infections, respectively. We conclude that highly sensitive type-specific PCR tests may be a useful tool for screening of cervical cancer.

Detection of major HPVs by a new multiplex real-time PCR assay using type-specific primers

In this study, we aimed to develop a cost-effective, practical, and sensitive method to be used for the diagnosis of HPV infections. The presence of HPV-DNA was investigated in cervical smear samples using three different methods: MY09/11 consensus PCR, TaqMan-based type-specific real-time PCR, and SYBR Green-based multiplex PCR. Of the 315 samples, 21.6% (68/315) were HPV-DNA positive by using at least one of the three methods. The relative sensitivities of MY09/11 PCR, type-specific PCR, and multiplex PCR were found to be 86.8% (59/68), 91.2% (62/68), and 91.2% (62/68), respectively. Genotyping analyses were successfully carried out in 62 of 68 HPV-DNA positive samples, and 77 isolates (8 low-risk and 69 high-risk HPV) were identified, while six samples were determined to be positive by consensus PCR only and could not be genotyped. The type distribution of the 69 high-risk HPV strains was as follows: 37.7% HPV 16, 13.0% HPV 52, 11.6% HPV 58, 7.2% HPV 18, 7.2% HPV 31, 7.2% HPV 68, 4.3% HPV 35, 4.3% HPV 39, 4.3% HPV 82, 1.4% HPV 33, and 1.4% HPV 45. Our data suggests that the diagnosis of HPV infections using only consensus PCR may lead to epidemiologically significant data loss, and that our multiplex PCR is more sensitive than consensus PCR and lower in cost than the type-specific PCR. We believe that the SYBR Green-based multiplex PCR may be useful and cost-effective for other microbiological fields. In addition, type-specific screening of HPV-DNA gives more reliable results, but it may also be used in combination with consensus PCR if the type spectrum of the test is not large enough.

HPV involvement in tonsillar cancer: Prognostic significance and clinically relevant markers

The association of high-risk human papillomaviruses (HR HPVs) with tonsillar cancer (TC) has been documented. Because patients with HPV-associated tumors show better survival rates, modification of their treatment regimen is being considered. It is therefore crucial to find markers for the identification of patients whose tumors are linked to viral infection. A cohort of 109 patients with primary TC was screened for HPV DNA presence in the tumor tissues and HPV-specific antibodies in sera. Data regarding risk factors and clinical parameters were collected. Forty-five specimens were analyzed for the expression of viral E6 and E2-region mRNA, and the p16 and p53 protein expression status was assessed by immunohistochemistry. The overall prevalence of HPV DNA in TC tissues was 65.1%. Ninety-three percent of HR HPV DNA-positive samples expressed E6*I mRNA. E2-region mRNA expression was detected in 36% of positive samples, which implies that the virus is integrated in 64% of HPV DNA/RNA-positive tumors. p16 overexpression and the presence of antibodies specific to HPV16 E6/E7 oncoproteins correlated well with HPV DNA and RNA presence. The disease-specific survival rate of patients with HPV DNA-positive tumors was significantly higher than that of HPV DNA-negative patients. In addition to providing further evidence of the involvement of HPV infection in the etiopathogenesis of a proportion of TC cases, our study demonstrates that p16 immunostaining and anti-E6/E7 antibodies as surrogate markers of HPV involvement represent specific, sensitive and clinically accessible assays for the identification of TC patients who have a considerably better prognosis.

Detection and typing of low-risk human papillomavirus genotypes HPV 6, HPV 11, HPV 42, HPV 43 and HPV 44 by polymerase chain reaction and restriction fragment length polymorphism

A novel PCR-restriction fragment length polymorphism assay (PCR-RFLP) was developed for sensitive detection and reliable differentiation of five low-risk human papillomavirus (lr-HPV) genotypes: HPV 6, HPV 11, HPV 42, HPV 43 and HPV 44, as well as differentiation of prototypic and non-prototypic HPV 6 genomic variants. The assay is based on the amplification of a 320-bp fragment of the HPV E1 gene and subsequent analysis of PCR-products with BsaJI and HinFI. Testing on plasmid standards showed that PCR-RFLP enabled simple and reliable identification and differentiation of five targeted lr-HPV genotypes and could detect reproducibly down to 10 copies of viral genome equivalents per PCR. The PCR-RFLP showed almost complete agreement with previously obtained genotyping results on 42 HPV-DNA negative samples and 223 HPV-DNA positive samples (45 HPV 6, 34 HPV 11, 35 HPV 42, 10 HPV 43, 24 HPV 44 positive samples and 75 samples containing 28 non-targeted HPV genotypes). The novel assay is simple and robust, does not require any sophisticated equipment and can be of great value for epidemiological studies, particularly in settings in which financial resources are limited.

Universal ProbeLibrary based real-time PCR assay for detection and confirmation of human papillomavirus genotype 52 infections

A novel TaqMan real-time PCR (RT-PCR) assay for sensitive and specific detection of HPV 52 infection and confirmation/exclusion of the presence of HPV 52 in clinical specimens positive with a Roche HPV Linear Array cross-reactive probe was developed. Sensitivity of the assay at a 95% detection level was 3.9 DNA copies/reaction and the dynamic range was seven orders of magnitude, discriminating 10–10 7 viral genome equivalents/reaction. Testing 45 HPV-DNA negative samples and 102 HPV-DNA positive samples (42 HPV 52 positive samples and 60 samples containing 30 other HPV genotypes), showed complete agreement with results obtained with GP5+/GP6+ or PGMY09/PGMY0911 PCR-based screening and sequencing. Of the 27 HPV 31/33/58 positive samples cross-reacting with the Linear Array HPV 52 probe, 4 (14.8%) were identified as also containing HPV 52 using RT-PCR. All 16 Linear Array “true HPV 52-positive” samples were confirmed to contain HPV 52 DNA in RT-PCR testing.

OP5-7 Diversification of HIV-1 subtypes in Turkey – a country with a low HIV endemicity

As a part of our continuous search for oncogenic viruses in bronchial cancer, we extended our HPV studies to analyse also SV40, BKV, JCV and HCMV sequences in bronchial cancer and related these data with p53 codon 72 polymorphism. Fresh tumor samples from 78 patients with lung cancer were analysed for SV40, BKV, JCV, HCMV and HPV sequences by PCR. HPV genotypes were determined using reverse blot hybridization and sequencing, and all HPV-positive tumors were tested for the presence of E6/E7 transcripts by RT-PCR. All samples were analysed for p53 codon 72 polymorphism, using PCR-based RFLP method.Of the 78 cases studied, 11 (14.1%) were positive for T-Ag gene of SV40, while BKV and JCV sequences were both amplified in 1 tumor only. Altogether, 10/78 lesions were HPV-positive; six HPV16, one HPV31, two HPV6/53 and one HPV16/18. All HPV DNA-positive samples except one also expressed E6 and E7 transcripts. HCMV was amplified in 18 (23%) cases. RFLP analysis of p53 codon 72 revealed 32 homozygotes for arg/arg allele (50.8%), 26 heterozygotes for arg/pro allele (41.3%), and 5 homozygotes for pro/pro allele (7.9%). P53 codon 72 polymorphism was not significantly different between cases (n = 63) and controls (n = 50) (p = 0.455), among virus positive and negative patients, nor was it related to HPV genotypes (p = 0.384), expression of E6 (p = 0.384) and E7 oncogenes (p = 0.293). Of all possible combinations of virus co-detection, only SV40-HCMV association was statistically significant (OR = 5.500, 95%CI 1.43–21.02; p = 0.015). Taken the known mechanisms of these individual viruses, there is a chance that these viruses could affect cell cycle control and inhibit apoptosis, thus potentially causing genetic instability and promote oncogenesis.

RNA (E6 and E7) Assays versus DNA (E6 and E7) Assays for Risk Evaluation for Women Infected with Human Papillomavirus

In the majority of cases, high-risk human papillomavirus (HR HPV) infections regress spontaneously, with only a small percentage progressing to high-grade lesions. Current screening methods are based on DNA detection. An alternative would be to monitor expression of the E6 and E7 viral oncogenes continuously expressed by malignant phenotypes. In the work reported in this paper, we compared the two methods for a group of women with high-risk HPV infections. Cervical specimens from 400 women, previously found to be HPV DNA positive, were analyzed for HPV DNA by a liquid hybridization assay and typed by multiplex PCR (for types 16, 18, 31, and 33). Identification of HR HPV E6 and E7 RNA transcripts was performed using real-time reverse transcription-PCR and nucleic acid sequence-based amplification assays. Results were compared with concurrent cytological data. HR HPVs were found in 61.2% of patients. The most common genotype was HPV type 16 (HPV-16) (47.1%), followed by HPV-18, HPV-31, and HPV-33. Nine percent of cases involved other genotypes. Among 223 HPV DNA-positive samples, only 118 were positive in the RNA test. Among HPV DNA-positive patients with normal cytology, we detected E6 and E7 RNA transcripts in two cases (18.2%). The rate of detection increased gradually with the grade of the observed lesions, rising from 20% for patients with atypical squamous cells of undetermined significance to 48.1% for women with low-grade squamous intraepithelial lesions and 86.3% for those with high-grade squamous intraepithelial lesions. These results suggest that testing for HPV E6 and E7 transcripts could be a useful tool for screening and patient management, providing more accurate predictions of risk than those obtained by DNA testing.