Molecular tests potentially improving HPV screening and genotyping for cervical cancer prevention

In Situ Colorimetric LAMP Based on One-Step Modified Filter Paper to Screen Human Papillomavirus (HPV)16/18 from Clinical Samples

Cervical cancer is among the most common malignant tumors in women. The development of rapid screening techniques plays an important role in early screening for cancer treatment. We have developed an HPV screening method, which effectively combines the high-efficiency nucleic acid enrichment of chitosan-modified filter paper and the rapid visual detectability of colorimetric LAMP, along with the enhancement of the tolerance ability of the pH-sensitive LAMP reagent to acidic original samples, making the detection of HPV 16/18 easy to carry out and reliable, which is helpful for the epidemiological prevention and control strategies of HPV-induced cancer. This technique can simultaneously exhibit the "in situ amplification" capability of chitosan-modified filter paper and the nontemperature cycle dependence of visual LAMP detection. Therefore, DNA extraction and amplification can be performed efficiently and quickly within a single reaction where all DNA is concentrated in the QF paper disc. By embedding amino-modified filter paper into the plastic chip, a simple and reliable disposable chip was prepared for rapid HPV16 and HPV18 detection from clinical endometrial samples, and the results were 100% consistent with clinical diagnosis. More importantly, even after the sample was diluted 100-fold, HPV16/18-infected cells could be accurately identified, showing the advantages of the system in early cancer screening. Moreover, for endometrial samples containing plenty of cells, the filter paper could be used to enrich cells by filtration, preventing the acidic fluid from impacting pH-induced colorimetric LAMP detection and realizing direct amplification for HPV identification without nucleic acid extraction. This easy-to-operate system that can analyze a wide range of samples will be suitable for routine on-site HPV screening, dramatically extending the applications and utility for rapid, near-patient nucleic acid testing.

Cervical Cancer Genetic Profile through Circulating Tumor DNA: What Can We Learn from Blood?

Cervical cancer (CC) is one of the deadliest gynecological cancers worldwide. Human papillomavirus is the main etiological agent responsible for the initiation and development of most CC cases. The standard method utilized for CC screening in the global population is the cytological Pap smear test. Despite its effective validity in detecting precancerous lesions and its response to layer stages of this disease, greater screening and diagnostic reliability are needed, as well as an improvement in specificity and sensitivity. In this context, the use of liquid biopsies, like blood, for the isolation of circulating tumor DNA (ctDNA) in CC screening, diagnosis, prognosis, and surveillance could fill the gaps that still exist. In the present review, we aim to study the literature in order to collect knowledge on blood-based liquid biopsy based on descriptions of its precious molecular content and its utilization as a potential tool for CC patients' management. We will mainly focus on the important role of the novel ctDNA and the unique possibilities to additionally use HPV-ctDNA in CC at various stages of clinical application.

Portable Device with Nicking Enzyme Enhanced Special RCA on μPADs toward Sensitive Detection of High-Risk HPV Infection

Development of an accurate, rapid, and cost-effective portable device is in high demand for point-of-care molecular diagnosis toward disease screening. Here we report a one-pot homogeneous isothermal assay that leverages nicking endonuclease and minimum secondary structured rolling circle amplification (N-MSSRCA) for fast and sensitive quantification of nucleic acids on distance microfluidic paper-based analytical devices (dμPAD) by a portable custom-made fluorescence detector. Human papillomavirus (HPV) oncogenic E7 mRNA as the biomarker for cervical cancer was used as the model analyte. N-MSSRCA integrates ligase for target recognition, the nicking enzyme for primer generation, and the dual function of the Phi29 DNA polymerase for both on- and off-loop amplification. The proposed method was capable of detecting 1 and 10 fM of the analyte using the microplate reader and portable detector with dμPAD, respectively, with ∼1 h assay time. A cohort study of 40 cervical swab samples shows N-MSSRCA reached positive and negative predictive values of 87.5% and 93.5% using the portable detector with dμPAD, compared to 91.67% and 100% using the microplate reader. N-MSSRCA demonstrates potential in early screening of high-risk HPV infection as a generic strategy to detect various nucleic acids in point-of-care scenarios.

Discovery and technical validation of high-performance methylated DNA markers for the detection of cervical lesions at risk of malignant progression in low- and middle-income countries

BACKGROUND

Cervical cancer remains a leading cause of death, particularly in developing countries. WHO screening guidelines recommend human papilloma virus (HPV) detection as a means to identify women at risk of developing cervical cancer. While HPV testing identifies those at risk, it does not specifically distinguish individuals with neoplasia. We investigated whether a quantitative molecular test that measures methylated DNA markers could identify high-risk lesions in the cervix with accuracy.

RESULTS

Marker discovery was performed in TCGA-CESC Infinium Methylation 450 K Array database and verified in three other public datasets. The panel was technically validated using Quantitative Multiplex-Methylation-Specific PCR in tissue sections (N = 252) and cervical smears (N = 244) from the USA, South Africa, and Vietnam. The gene panel consisted of FMN2, EDNRB, ZNF671, TBXT, and MOS. Cervical tissue samples from all three countries showed highly significant differential methylation in squamous cell carcinoma (SCC) with a sensitivity of 100% [95% CI 74.12-100.00], and specificity of 91% [95% CI 62.26-99.53] to 96% [95% CI 79.01-99.78], and receiver operating characteristic area under the curve (ROC AUC) = 1.000 [95% CI 1.00-1.00] compared to benign cervical tissue, and cervical intraepithelial neoplasia 2/3 with sensitivity of 55% [95% CI 37.77-70.84] to 89% [95% CI 67.20-98.03], specificity of 93% [95% CI 84.07-97.38] to 96% [95% CI 79.01-99.78], and a ROC AUC ranging from 0.793 [95% CI 0.68-0.89] to 0.99 [95% CI 0.97-1.00] compared to CIN1. In cervical smears, the marker panel detected SCC with a sensitivity of 87% [95% CI 77.45-92.69], specificity 95% [95% CI 88.64-98.18], and ROC AUC = 0.925 [95% CI 0.878-0.974] compared to normal, and high-grade squamous intraepithelial lesion (HSIL) at a sensitivity of 70% (95% CI 58.11-80.44), specificity of 94% (95% CI 88.30-97.40), and ROC AUC = 0.884 (95% CI 0.822-0.945) compared to low-grade intraepithelial lesion (LSIL)/normal in an analysis of pooled data from the three countries. Similar to HPV-positive, HPV-negative cervical carcinomas were frequently hypermethylated for these markers.

CONCLUSIONS

This 5-marker panel detected SCC and HSIL in cervical smears with a high level of sensitivity and specificity. Molecular tests with the ability to rapidly detect high-risk HSIL will lead to timely treatment for those in need and prevent unnecessary procedures in women with low-risk lesions throughout the world. Validation of these markers in prospectively collected cervical smear cells followed by the development of a hypermethylated marker-based cervical cancer detection test is warranted.

Qualitative and quantitative changes in mitochondrial DNA associated with cervical cancer: A comprehensive review

Cervical cancer is the fourth most commonly diagnosed cancer in women and is considered a preventable disease, as vaccination and screening programs effectively reduce its incidence and mortality rates. Disease physiopathology and malignant cell transformation is a complex process, but it is widely known that high-risk HPV (hrHPV) infection is a necessary risk factor for cancer development. Mitochondria, cell organelles with important bioenergetic and biosynthetic functions, are important for cell energy production, cell growth, and apoptosis. Mitochondrial DNA is a structure that is particularly susceptible to quantitative (mtDNA copy number variation) and qualitative (sequence variations) alterations that are associated with various types of cancer. Novel biomarkers with diagnostic and prognostic value in cervical cancer can be evaluated to provide higher specificity and complement hrHPV molecular testing, which is the most recommended method for primary screening. In accordance with this, this review aimed to assess mitochondrial alterations associated with cervical cancer in clinical cervicovaginal samples, in order to unravel their possible role as specific diagnostic and prognostic biomarkers for cervical malignancy, and also to guide the understanding of their involvement in carcinogenesis, HPV infection, and disease progression.

Development and validation of real-time recombinase polymerase amplification-based assays for detecting HPV16 and HPV18 DNA

IMPORTANCE

HPV DNA screening is an effective approach for the prevention of cervical cancer. The novel real-time recombinase polymerase amplification-based HPV detection systems we developed constitute an improvement over the HPV detection methods currently used in clinical practice and should help to extend cervical cancer screening in the future, particularly in point-of-care test settings.

A novel human papillomavirus and host DNA methylation score and detection of cervical adenocarcinoma

BACKGROUND

The widespread introduction of Pap testing in the 1960s was followed by substantial reductions in the incidence of cervical squamous cell cancer (SCC). However, the incidence of cervical adenocarcinoma (ADC) did not decrease, likely because of low Pap test sensitivity for ADC and adenocarcinoma in situ (AIS). This study assessed a novel human papillomavirus (HPV) and host DNA Methylation Score for AIS and ADC screening.

METHODS

We measured methylation levels at CpG sites in the L2/L1 open reading frames of HPV16, HPV18, and HPV45-as well as 2 human loci, DCC and HS3ST2. Specifically, we tested exfoliated cervicovaginal cells from women in the HPV Persistence and Progression (PaP) cohort who were positive for 1 of HPV16, 18, or 45, including: 1) 176 with AIS/ADC, 2) 353 with cervical intraepithelial neoplasia-3 (CIN3) or SCC, and 3) controls who either cleared (HPV-Clearers; n = 579) or had persistent HPV16, 18, or 45 infection (HPV-Persisters; n = 292). CpG site-specific methylation percentages were measured using our reported next-generation methods. The Methylation Score was the average methylation percentage across all 35 CpG sites tested.

RESULTS

Each individual CpG site had higher methylation percentages in exfoliated cervicovaginal cells collected from patients with AIS/ADC, and as well as those with CIN3/SCC, relative to either control group (weakest P  = .004). The Methylation Score for AIS/ADC had a sensitivity of 74% and specificity of 89%. The multivariate odds ratio (OR) between the Methylation Score (4th vs 1st quartile) for AIS/ADC was ORq4-q1 = 49.01 (PBenjamini-Hochberg = 4.64E-12), using HPV-Clearers as controls. CIN3/SCC had similar, albeit weaker, associations with the Methylation Score.

CONCLUSIONS

HPV16/18/45-infected women with Methylation Scores in the highest quartile had very high odds of AIS/ADC, suggesting they may warrant careful histologic evaluation of the cervical transition zone (eg, conization or loop electrosurgical excision procedure [LEEP]).

Assessing the Genomic Landscape of Cervical Cancers: Clinical Opportunities and Therapeutic Targets

PURPOSE

Tumor genomic profiling is increasingly used to guide treatment strategy in patients with cancer. We integrated tumor genomic, clinical demographic, and treatment response data to assess how prospective tumor-normal sequencing impacted treatment selection in patients with cervical cancer.

EXPERIMENTAL DESIGN

Cervical cancers were prospectively analyzed using the MSK-IMPACT (Memorial Sloan Kettering Cancer Center - Integrated Mutation Profiling of Actionable Cancer Targets) next-generation sequencing panel. Clinical data, including histology, stage at diagnosis, treatment history, clinical trial enrollment and outcomes, date of last follow-up, and survival status were obtained from medical records.

RESULTS

A total of 177 patients with cervical cancer (squamous, 69; endocervical adenocarcinoma, 50; gastric type, 22; adenosquamous, 21; and other, 15) underwent MSK-IMPACT testing. The most prevalent genomic alterations were somatic mutations or amplifications in PIK3CA (25%), ERBB2 (12%), KMT2C (10%), and KMT2D (9%). Furthermore, 13% of patients had high tumor mutational burden (TMB >10 mut/Mb), 3 of which were also microsatellite instability-high (MSI-H). Thirty-seven percent of cases had at least one potentially actionable alteration designated as a level 3B mutational event according to the FDA-recognized OncoKB tumor mutation database and treatment classification system. A total of 30 patients (17%) were enrolled on a therapeutic clinical trial, including 18 (10%) who were matched with a study based on their MSK-IMPACT results. Twenty patients (11%) participated in an immune checkpoint inhibition study for metastatic disease; 2 remain progression free at >5 years follow-up.

CONCLUSIONS

Tumor genomic profiling can facilitate the selection of targeted/immunotherapies, as well as clinical trial enrollment, for patients with cervical cancer.

Target-mediated rolling circle transcription coupling with CRISPR/Cas12a-Cas13a for simultaneous detection of HPV16 and HPV18

Simultaneous detection of multiple targets can provide important data support for clinical diagnosis and treatment. Here, we report a facile isothermal assay based on target-mediated rolling circle transcription coupling with CRISPR/Cas12a-Cas13a (TM-RCT/Cas12a-Cas13a). Through facile one-step amplification (TM-RCT), two target DNAs are converted to RNA amplified products. The simultaneous detection of HPV16 and HPV18 is then achieved by combining two CRISPR/Cas systems. This system shows excellent sensing performance and provides a universal method for simultaneous detection.

Team-Based Approach to Reduce Malignancies in People with Diabetes and Obesity

PURPOSE OF REVIEW

Numerous observations have indicated an increased risk of developing various types of cancers, as well as cancer-related mortality, among patients with diabetes and obesity. The purpose of this review is to outline multiple-cancer screening among these patients through a team-based approach and to present the findings of a pioneering integrated care program designed for patients with obesity with a specific emphasis on cancer prevention.

RECENT FINDINGS

A community-based multi-cancer prevention program, which provides all services in one location and utilizes team-based approaches, is reported to be feasible and has the potential to enhance the uptake rate of multiple cancers screening among patients with diabetes and obesity. The team-based approach is a commonly utilized method for managing patients with diabetes, obesity, and cancer, and has been shown to be efficacious. Nevertheless, research on team-based cancer screening programs for patients with diabetes and obesity remains limited. Providing a comprehensive screening for colorectal, prostate, and breast cancer, as well as metabolic syndrome, during a single clinic visit has been proven effective and well-received by participants.

Prevalence of high-risk HPV among marginalized urban women in India and its implications on vaccination: A cross sectional study

OBJECTIVE

To discover the prevalence and distribution of high-risk human papilloma virus (HPV) subtypes in urban slums and their implications.

METHODS

A cross-sectional study was performed to discover prevalence and distribution of high-risk HPV subtypes. We screened 956 women. Data were analyzed using SPSS v.25. Inclusion criterion was married women between 30 and 45 years of age. Exclusion criteria were women with known cervical cancer at the time of the survey or those who had undergone hysterectomy.

RESULTS

Of the women, 32.47% were HPV positive and of these, about 84.50% were positive for high-risk HPV. HPV type 6 (HPV 6) and HPV 11 were not seen in the population. After HPV 16 and HPV 18, type 58 was the most common variant seen in our study. Currently-used vaccines in India do not cover HPV 58.

CONCLUSION

Knowing and understanding the distribution of high-risk HPV are necessary for an effective strategy to eliminate cervical cancer from India. Deoxyribonucleic acid-based HPV screening is a useful method along with vaccination to prevent cervical cancer.

Development of a simplified and cost-effective sample preparation method for genotyping of human papillomavirus by next-generation sequencing

High-risk human papillomavirus (HPV) infection is the most common cause of cervical cancer, but low-risk HPV strains can sometimes also be involved. Although HPV genotyping techniques used in clinical diagnosis cannot detect low-risk HPV, next-generation sequencing (NGS) can detect both types. However, DNA library preparation is complicated and expensive. The aim of this study was to develop a simplified, cost-effective sample preparation procedure for HPV genotyping based on next-generation sequencing (NGS). After DNA extraction, a first round of PCR was performed using modified MY09/11 primers specific for the L1 region of the HPV genome, followed by a second round of PCR to add the indexes and adaptors. Then, the DNA libraries were purified and quantified, and high-throughput sequencing was performed using an Illumina MiSeq platform. The sequencing reads were compared with reference sequences for HPV genotyping. The limit of detection for HPV amplification was 100 copies/µl. Analysis of the correlation of pathological cytology with the HPV genotype in individual clinical samples showed that HPV66 was the most common genotype found in the normal stage, whereas HPV16 was the main genotype found in low-grade squamous intraepithelial lesions, high-grade squamous intraepithelial lesions, and cervical cancer. This NGS method can detect and identify several HPV genotypes with 92% accuracy and 100% reproducibility, and it shows potential as a simplified and cost-effective technique for large-scale HPV genotyping in clinical samples.

Prevalence and genotype distribution of HPV infection among women in Xiamen, China

Objective

This study aimed to evaluate the prevalence of HPV and genotype distribution among female populations in Xiamen, Fujian Province, China, which can be conducive for local governments to formulate cervical cancer screening and HPV vaccine strategies.

Methods

Cervical swabs were collected from 47,926 participants aged 16-92 years at the Women and Children's Hospital, Xiamen University, from November 2019 to June 2020. HPV DNA was extracted and detected using conventional PCR, followed by HPV subtype-specific hybridisation. HPV infection rates based on different groups were compared using the χ2 test. HPV prevalence and the corresponding 95% confidence intervals (95% CI) were calculated using SPSS 19.0.

Results

The overall HPV prevalence among the 47,926 cervical swabs that were analysed was 15.13%, of which single, double, and multiple infections accounted for 76.83, 16.70 and 6.47%, respectively. The age-specific prevalence of HPV infection presented a "U" curve with a HPV prevalence peak observed in women aged <20 years. The gynaecology clinic group had significantly higher HPV positive rates than the health examination group (p < 0.001). The five most common HR-HPV subtypes in Xiamen were HPV52, 58, 16, 51, and 39 (2.69, 1.63, 1.23, 1.05, and 0.98%, respectively). The five most common LR-HPV subtypes were HPV54, 61, 81, 70, 34, and 84 (0.92, 0.86, 0.71, 0.45 and 0.35%, respectively).

Conclusion

Our findings demonstrate that the 9-valent HPV vaccine is recommended for regular immunisation in Xiamen. It is necessary for elderly women to participate in HPV screening to decrease the morbidity and mortality of cervical cancer.

High prevalence of HPV 18 and multiple infections with oncogenic HPV genotypes in women at risk of cervical cancer examined in Manaus, Brazil

Cervical cancer is a serious public health problem in Brazil, especially in Manaus (Amazonas), the city with the highest incidence rate of cervical cancer in the country. Persistent infection with oncogenic human papillomavirus (HPV) genotypes is the cause of disease development. The aim of this study was to investigate the prevalence of oncogenic genotypes in women at high risk for cervical precancer examined in two policlinics in Manaus. One hundred and two patients who underwent colposcopy took part in the research. The DNA samples obtained from the cervical epithelium were analyzed by PCR with type-specific primers for the detection of eight oncogenic genotypes, which were chosen based on previous studies. The presence of HPV virus was detected in all samples. The most prevalent oncogenic genotypes were 18 (47.1%) and 16 (45.1%). Interestingly, HPV 18 was considered uncommon in this region. In addition to these, genotypes 31 (19.6%), 58 (19.6%), 33 (18.6%), and 45 (15.7%) also had a relatively high frequency in this population. Fifty-six women (54.9%) had multiple infections with up to five oncogenic types. Also, the presence of genotypes other than 16 and 18 was observed in most samples (57.8%), which also deserves attention since they are not covered by currently available vaccines against HPV in Brazil. The high prevalence and multiple infections with several oncogenic HPV genotypes in association with precursor lesions for cervical cancer highlighted the need to improve strategies to prevent this disease in Amazonas.

Detection of high-grade cervical neoplasia using extended genotyping: Performance data from the longitudinal phase of the Onclarity trial

OBJECTIVES

The Onclarity cervical cancer screening trial was designed to establish the clinical validity of the Onclarity HPV assay for extended genotyping (xGT) during detection of high-grade cervical neoplasia grades 2 or 3 (≥CIN2 or ≥CIN3). Here, three-year follow up data is presented to evaluate the overall efficacy of these screening strategies, compared to the baseline data.

METHODS

At baseline 29,513 women, ≥25 years, had evaluable cytology and valid high-risk HPV results. Women with atypical squamous cells-undetermined significance or worse cytology or a positive HPV test were referred for colposcopy/biopsy. Participants that did not reach the study end point (treatment for ≥CIN2) continued into the longitudinal phase that included the same protocol as baseline.

RESULTS

The three-year cumulative incident risk (CIR) for ≥CIN3 in HPV-negative women was 0.15% [95%CI: 0.06, 0.26] and for HPV- and cytology-negative women was 0.12% [95% CI: 0.03,0.23]. HPV16 carried the highest baseline and three-year ≥CIN3 CIR, followed by HPV31 and HPV18. At least one year of genotype-specific persistence increased ≥CIN3 risk for xGT results compared to genotype non-persistence, HPV clearance, or new infection over the same time period. Risk-based screening with immediate colposcopy for HPV16/18/31 and further xGT triage resulted in better ≥CIN3 sensitivity (79.2% versus 72.3%; relative difference of 6.9 [95%CI: 3.3, 10.4]) and a lower colposcopy/≥CIN3 ratio (9.2 versus 11.2; relative difference of -1.9 [95%CI: -2.6, -1.3]) when compared to primary HPV16/18-based screening.

CONCLUSIONS

An HPV-negative result offers the same assurance of no disease over three years of follow up as that offered by a negative co-testing result. xGT facilitates risk-based screening and persistence tracking and can help optimize disease detection during screening without excessive colposcopic procedures.

Impact of human papillomavirus vaccine on cervical cancer epidemic: Evidence from the surveillance, epidemiology, and end results program

Introduction

Since 2006, the human papillomavirus (HPV) vaccine has been recommended for females aged 9-26 years in the United States. Aiming to evaluate the early effect of the HPV vaccine on cervical cancer, this study assessed the incidence of cervical cancer by age and histology before and after the introduction of HPV vaccination.

Methods

Data on cervical cancer incidence from 1975-2019 were extracted from the Surveillance, Epidemiology, and End Results Program. Joinpoint regression was used to determine temporal trends over time. Future cervical cancer incidence (2015-2039) was projected using Bayesian age-period-cohort analysis. Age-period-cohort (APC) models were created to evaluate age, period, and cohort effects.

Results

For overall cervical cancer and cervical squamous cell carcinoma (SCC), incidence rate showed decreasing trends (-0.7%, and -1.0% annually, respectively), whereas cervical adenocarcinoma (AC) incidence continuously increased (2.6% annually). The incidence trends for AC were stable in the 20-24 and 25-29-year age groups, whereas there was an increasing trend in older age groups. Similarly, the projected trend for AC in females aged 20-30 years exhibited a decline, whereas an increase was predicted in the 31-40-year age group, especially in the 35-44 year age group. The birth cohort and period effects in SCC and AC were extracted from APC models.

Discussion

During the period of 1975-2019, the incidence of cervical AC remained almost unchanged in the age groups receiving HPV vaccines while increased in the age groups not receiving HPV vaccines. The birth cohort effects of SCC and AC of the cervix provided evidence supporting the effectiveness of the HPV vaccine in preventing cervical cancer.

Highlights from the 7th Oncological Pathology Conference 'Pathological Anatomy in the context of the National Cancer Law: An overview of the Latin American experience', 15, 22 and 23 July 2022, Trujillo, Peru

The seventh session of the Oncological Pathology Conference (JoPaO) entitled 'Pathological Anatomy in the context of the National Cancer Law: An overview of the Latin American experience', was held virtually on July 15, 22 and 23. Peru was the headquarters for this event, where 17 national and international professors of high academic standing participated. They interacted in a multidisciplinary context through talks with national panellists and the general public. The recent promulgation of the 'National Cancer Law' fosters the development of discussion forums to analyse the national realities and uphold continuous learning about experiences in other Latin American countries with successful cancer programmes, in which pathology holds a principal role. The topics addressed during this JoPaO included the exchange of Latin American cancer management experiences, an emphasis on investments in and the development of strategic plans to improve care, the use of new technologies, laboratory quality control, and the need to advance scientific research.

Identification of cervical squamous cell carcinoma feature genes and construction of a prognostic model based on immune-related features

As heterogeneity of cervical squamous cell carcinoma (CSCC), prognosis assessment for CSCC patients remain challenging. To develop novel prognostic strategies for CSCC patients, associated biomarkers are urgently needed. This study aimed to cluster CSCC samples from a molecular perspective. CSCC expression data sets were obtained from The Cancer Genome Atlas and based on the accessed expression profile, a co-expression network was constructed with weighted gene co-expression network analysis to form different gene modules. Tumor microenvironment was evaluated using ESTIMATE algorithm, observing that the brown module was highly associated with tumor immunity. CSCC samples were clustered into three subtypes by consensus clustering based on gene expression profiles in the module. Gene set variation analysis showed differences in immune-related pathways among the three subtypes. CIBERSORT and single-sample gene set enrichment analysis analyses showed the difference in immune cell infiltration among subtype groups. Also, Human leukocyte antigen protein expression varied considerably among subtypes. Subsequently, univariate, Lasso and multivariate Cox regression analyses were performed on the genes in the brown module and an 8-gene prognostic model was constructed. Kaplan-Meier analysis illuminated that the low-risk group manifested a favorable prognosis, and receiver operating characteristic curve showed that the model has good predictive performance. qRT-PCR was used to examine the expression status of the prognosis-associated genes. In conclusion, this study identified three types of CSCC from a molecular perspective and established an effective prognostic model for CSCC, which will provide guidance for clinical subtype identification of CSCC and treatment of patients.

Current Status of Human Papillomavirus Infection and Cervical Cancer in the Philippines

Cervical cancer is estimated to cause 341,831 deaths each year, with 9 of 10 deaths occurring in developing countries. Over the past decade, there has been a significant increase in cervical cancer incidence among women in the Philippines. Persistent infection with high-risk human papillomavirus (HPV) is the well-established necessary cause of cervical cancer. Based on limited studies conducted in the Philippines, the prevalence of infection with any HPV genotype was 93.8% for cervical squamous cell carcinoma and 90.9% for cervical adenocarcinomas. HPV types 16 and 18 were the most common HPV genotypes among Filipino patients with cervical cancer. On the other hand, the incidence of HPV infection among Filipino women with normal cervices was 9.2%. The World Health Organization has launched a global agenda of eliminating HPV infection by 2030. One of its key milestones is to vaccinate 90% of girls with the HPV vaccine by 15 years. However, the HPV vaccination rate among Filipino women remains to be unsatisfactory. HPV vaccination has only been included in the Philippine Department of Health's community-based National Immunization Program in 2015. Despite these efforts, the Philippines currently ranks last on HPV program coverage among low-middle income countries, with coverage of only 23% of the target female population for the first dose and 5% for the final dose. The principal reason for the non-acceptance of HPV vaccines was the perceived high cost of vaccination. The low utilization of available cervical cancer screening tests such as Pap smear and visual inspection with acetic acid hampered the Philippines' control and prevention of HPV infection and cervical cancer. Among those diagnosed with cervical cancer in the Philippines, only an estimated 50% to 60% receive some form of treatment. To this end, we summarize the burden of HPV infection and cervical cancer on Filipinos and the risk factors associated with the disease. We present the current screening, diagnostics, treatment, and prevention of HPV-related diseases in the Philippines. Lastly, we also propose solutions on how each building block in health systems can be improved to eliminate HPV infection and reduce the burden of cervical cancer in the Philippines.

Detection of Host Cell Gene/HPV DNA Methylation Markers: A Promising Triage Approach for Cervical Cancer

Cervical cancer is the most prevalent gynecologic malignancy, especially in women of low- and middle-income countries (LMICs). With a better understanding of the etiology and pathogenesis of cervical cancer, it has been well accepted that this type of cancer can be prevented and treated via early screening. Due to its higher sensitivity than cytology to identify precursor lesions of cervical cancer, detection of high-risk human papillomavirus (HR-HPV) DNA has been implemented as the primary screening approach. However, a high referral rate for colposcopy after HR-HPV DNA detection due to its low specificity in HR-HPV screening often leads to overtreatment and thus increases the healthcare burden. Emerging evidence has demonstrated that detection of host cell gene and/or HPV DNA methylation represents a promising approach for the early triage of cervical cancer in HR-HPV-positive women owing to its convenience and comparable performance to cytology, particularly in LMICs with limited healthcare resources. While numerous potential markers involving DNA methylation of host cell genes and the HPV genome have been identified thus far, it is crucial to define which genes or panels involving host and/or HPV are feasible and appropriate for large-scale screening and triage. An ideal approach for screening and triage of CIN/ICC requires high sensitivity and adequate specificity and is suitable for self-sampling and inexpensive to allow population-based screening, particularly in LMICs. In this review, we summarize the markers of host cell gene/HR-HPV DNA methylation and discuss their triage performance and feasibility for high-grade precancerous cervical intraepithelial neoplasia or worse (CIN2+ and CIN3+) in HR-HPV-positive women.

Diagnostic value of colposcopy in patients with cytology-negative and HR-HPV-positive cervical lesions

PURPOSE

High-risk human papillomavirus (HR-HPV)-positive but cytology-negative cervical cancer screening results are not uncommon. This study aimed to investigate colposcopy's accuracy and diagnostic value in patients with cytology-negative HR-HPV-positive screening results.

METHODS

This retrospective study included patients with HR-HPV-positive cytology-negative screening results who underwent electronic colposcopy with acetic acid and multi-point cervical biopsy, HPV typing (24 HPV subtypes), and quantitative HPV detection.

RESULTS

Among 229 patients, 130 had chronic cervicitis, and 99 had cervical lesions (CIN1, n = 37; CIN2/3, n = 55; invasive carcinoma, n = 7). Using colposcopy as a reference, the cervical cytology false-negative rate was 43.2% (99/229). Colposcopy was more accurate in patients with HR-HPV16/18 or high viral loads. Multivariable analyses showed HPV viral load and childbearing history were the independent factors affecting the accuracy of colposcopy (P < 0.05).

CONCLUSION

Colposcopy in HR-HPV-positive cytology-negative patients has a moderate diagnostic accuracy. The type of cervical transformation zone and HPV viral load are independent factors affecting the accuracy of colposcopy-based diagnosis.

Preliminary establishment and validation of a loop-mediated isothermal amplification assay for convenient screening of 13 types of high-risk human papillomaviruses in cervical secretions

BACKGROUND

The detection of human papillomaviruses (HPV) is a well-recognized strategy in early screening and prevention of cervical cancer. However, it's hard to carry out in undeveloped area because the sophisticated equipment that required in traditional methods is usually unavailable. To overcome this situation, we aim to establish a loop-mediated isothermal amplification (LAMP) method, which is simple and reliable for on-site detection of HPV.

METHODS

At least 3 sets of LAMP primers for each of the 13 types of high risk HPV were designed. After preliminary validation, the candidate primers were used in the detection of clinical samples and the results were head-to-head compared with a clinically approved real-time PCR assay. The performance of the LAMP method was assessed by kappa concordance test.

RESULTS

Cervical secretions samples from 1412 patients were included, with 224 samples were used in the preliminary screening of the LAMP primers and the other 1188 samples were used in the verification. Compared with real-time PCR method, the specificity of our LAMP method for each type of HPV were 100 %, and 11 of the 13 types had a sensitivity greater than 80 %. Among them, HPV 31 and 52 demonstrated the best performance, both with Kappa value of 0.913 (P < 0.0001). Besides, HPV 18, 35 and 56 only achieved a Kappa value less than 0.7, indicating their primers or reaction conditions may need further optimization. In general, the sensitivity, specificity, positive predictive value, negative predictive value and agreement of the LAMP assay in all HPV types was 86.9 %, 100 %, 100 %, 71.4 %, and 90.2 %, respectively (Kappa = 0.766, P < 0.0001).

CONCLUSION

In present study, we preliminary established and validated a LAMP method for HPV detection. This method could combine with self-sampling, thermostatic device, and appropriate dyes to form a simple and effective assay in the future, which would has good prospect and practical value in cervical cancer prevention, especially in undeveloped area.

Management of Early-Stage Cervical Cancer: A Literature Review

Simple Summary

Despite being a preventable disease, cervical cancer still causes morbidity and deaths worldwide. In the early stages (FIGO IA1 with lymph-vascular space invasion-IIA1), the disease is highly curable. The primary treatment for early-stage cervical cancer is radical hysterectomy with pelvic lymphadenectomy. This surgical treatment has changed during the past decades, and we aimed to review and discuss the advances in the literature. We performed a literature review through PubMed focusing on English articles about the topic of surgical management of early-stage cervical cancer. The emergent topics considered here are the FIGO 2018 staging system update, conservative management for selected patients, sentinel lymph node mapping, fertility preservation, surgical approach, and management of tumors up to 2 cm. These topics show an evolvement to a more tailored treatment to prevent morbidity and assure oncologic safety.

Abstract

Cervical cancer (CC) remains a public health issue worldwide despite preventive measures. Surgical treatment in the early-stage CC has evolved during the last decades. Our aim was to review the advances in the literature and summarize the ongoing studies on this topic. To this end, we conducted a literature review through PubMed focusing on English-language articles on the surgical management of early-stage CC. The emergent topics considered here are the FIGO 2018 staging system update, conservative management with less radical procedures for selected patients, lymph node staging, fertility preservation, preferred surgical approach, management of tumors up to 2 cm, and prognosis. In terms of updating FIGO, we highlight the inclusion of lymph node status on staging and the possibility of imaging. Regarding the preferred surgical approach, we emphasize the LACC trial impact worldwide in favor of open surgery; however, we discuss the controversial application of this for tumors < 2 cm. In summary, all topics show a tendency to provide patients with tailored treatment that avoids morbidity while maintaining oncologic safety, which is already possible in high-income countries. We believe that efforts should focus on making this a reality for low-income countries as well.

Cervical Cancer Screening Postpandemic: Self-Sampling Opportunities to Accelerate the Elimination of Cervical Cancer

The persisting burden of cervical cancer in underserved populations and low-resource regions worldwide, worsened by the onset of the COVID-19 pandemic, requires proactive strategies and expanded screening options to maintain and improve screening coverage and its effects on incidence and mortality from cervical cancer. Self-sampling as a screening strategy has unique advantages from both a public health and individual patient perspective. Some of the barriers to screening can be mitigated by self-sampling, and resources can be better allocated to patients at the highest risk of developing cervical cancer. This review summarizes the implementation options for self-sampling and associated challenges, evidence in support of self-sampling, the available devices, and opportunities for expansion beyond human papillomavirus testing.

Causes and Consequences of HPV Integration in Head and Neck Squamous Cell Carcinomas: State of the Art

A constantly increasing incidence in high-risk Human Papillomaviruses (HPV)s driven head and neck squamous cell carcinomas (HNSCC)s, especially of oropharyngeal origin, is being observed. During persistent infections, viral DNA integration into the host genome may occur. Studies are examining if the physical status of the virus (episomal vs. integration) affects carcinogenesis and eventually has further-reaching consequences on disease progression and outcome. Here, we review the literature of the most recent five years focusing on the impact of HPV integration in HNSCCs, covering aspects of detection techniques used (from PCR up to NGS approaches), integration loci identified, and associations with genomic and clinical data. The consequences of HPV integration in the human genome, including the methylation status and deregulation of genes involved in cell signaling pathways, immune evasion, and response to therapy, are also summarized.

Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures

Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.

The Potential Clinical and Economic Value of a Human Papillomavirus Primary Screening Test That Additionally Identifies Genotypes 31, 45, 51, and 52 Individually

BACKGROUND

Although current human papillomavirus (HPV) genotype screening tests identify genotypes 16 and 18 and do not specifically identify other high-risk types, a new extended genotyping test identifies additional individual (31, 45, 51, and 52) and groups (33/58, 35/39/68, and 56/59/66) of high-risk genotypes.

METHODS

We developed a Markov model of the HPV disease course and evaluated the clinical and economic value of HPV primary screening with Onclarity (BD Diagnostics, Franklin Lakes, NJ) capable of extended genotyping in a cohort of women 30 years or older. Women with certain genotypes were later rescreened instead of undergoing immediate colposcopy and varied which genotypes were rescreened, disease progression rate, and test cost.

RESULTS

Assuming 100% compliance with screening, HPV primary screening using current tests resulted in 25,194 invasive procedures and 48 invasive cervical cancer (ICC) cases per 100,000 women. Screening with extended genotyping (100% compliance) and later rescreening women with certain genotypes averted 903 to 3163 invasive procedures and resulted in 0 to 3 more ICC cases compared with current HPV primary screening tests. Extended genotyping was cost-effective ($2298-$7236/quality-adjusted life year) when costing $75 and cost saving (median, $0.3-$1.0 million) when costing $43. When the probabilities of disease progression increased (2-4 times), extended genotyping was not cost-effective because it resulted in more ICC cases and accrued fewer quality-adjusted life years.

CONCLUSIONS

Our study identified the conditions under which extended genotyping was cost-effective and even cost saving compared with current tests. A key driver of cost-effectiveness is the risk of disease progression, which emphasizes the need to better understand such risks in different populations.

A Sample-In-Answer-Out Microfluidic System for the Molecular Diagnostics of 24 HPV Genotypes Using Palm-Sized Cartridge

This paper proposes an automated microfluidic system for molecular diagnostics that integrates the functions of a traditional polymerase chain reaction (PCR) laboratory into a palm-sized microfluidic cartridge (CARD) made of polystyrene. The CARD integrates 4 independent microfluidic sample lanes, which can independently complete a sample test, and each sample lane integrates the 3 functional areas of the sample preparation area, PCR amplification area, and product analysis area. By using chemical cell lysis, magnetic silica bead-based DNA extraction, combined with multi-PCR-reverse dot hybridization with microarray, 24 HPV genotypes can be typing tested in CARD. With a custom-made automated CARD operating platform, the entire process can be automatically carried out, achieving sample-in-answer-out. The custom-made operation platform is developed based on a liquid handling station-type, which can automatically load off-chip reagents without placing reagents in CARD in advance. The platform can control six CARDs to work simultaneously, detect 24 samples at a time. The results show that the limit of detection of the microfluidic system is 200 copies/test, and the positive detection rate of clinical samples by this system is 100%, which is an effective method for detection of HPV.

The accuracy of HPV genotyping in isolation and in combination with CD4 and HIV viral load for the identification of HIV-infected women at risk for developing cervical cancer

BACKGROUND

Human papillomavirus (HPV) genotype testing has limited utility to identify human immunodeficiency virus-infected (HIV+) women's risk for developing cervical cancer (CC) due to high positivity rate of high-risk (HR) HPVs. We investigated the accuracy of HPV testing in isolation/in combination with CD4 and HIV viral load (VL) to identify HIV+ women at risk for developing CC.

METHODS

Study consisted of 344 HIV+ women on combination antiretroviral therapy (cART), tested for cervical cytology/HPV using the Cobas test and had data on absolute CD4 count and VL measurements. We calculated the positive predictive value (PPV) and negative predictive value (NPV) of HPV testing, pre-, post-cART, and current CD4 and VL in isolation and in combinations to identify those with or free of higher than atypical squamous cells of unknown significance (ASCUS+) or low-grade intraepithelial lesions (LSIL+).

RESULTS

HPV test in combination with pre-/post-cART or current CD4 counts and VL had higher PPVs compared to HPV test alone for identifying ASCUS+ or LSIL+. PPV of HPV-CD4 combinations yielded higher PPVs compared to HPV-VL combinations. The NPVs with pre-, post-cART, or current CD4 count and VL in isolation or in combinations were comparable to that of HPV test alone.

CONCLUSIONS

Our results provide a more accurate tool for managing HIV+ women by combining Cobas HPV with CD4 and VL, especially those who had an undesirable pre-cART CD4 and VL status. Our results also indicate the usefulness of CD4 and VL measurements to identify those at lower risk in the absence of HPV testing.

Human Papillomavirus Coinfection in the Cervical Intraepithelial Lesions and Cancer of Mexican Patients

According to their oncogenic properties, Human Papillomaviruses (HPVs) are classified into two types: Low-Risk (LR-HPVs) and High-Risk Human Papillomaviruses (HR-HPVs). The immune system naturally controls the majority of HPV infections; however, when the HR-HPV infection is persistent, the risk of developing cervical cancer increases. Previous studies indicate that multiple-infection or coinfection with HR-HPV occurs frequently and can potentiate the development of cervical lesions. This study aimed to establish the HPV coinfection rate in squamous intraepithelial lesions from Mexican patients. For HPV detection, we performed PCR on 55 cervical lesions diagnosed by colposcopy. We detected the presence of HPV infection in 87.27% (48/55) of the lesions; interestingly, HPV coinfection was observed in 70.83% (34/48) of these samples. We also evaluated HPV infection in adjacent areas without morphological changes from 25 samples. The results showed that 80% (20/25) of these were HPV-positive and, curiously, all presented HPV-16 infection. In conclusion, our results revealed a high prevalence of HPV coinfection in cervical lesions in Mexican patients, and these results contribute to future research focused on the role that HPV coinfection plays in the development of cervical cancer.

TMEM48 promotes cell proliferation and invasion in cervical cancer via activation of the Wnt/β-catenin pathway

Transmembrane proteins (TMEMs), spanning the entire width of lipid bilayers and anchored to them permanently, exist in diverse cell types to implement a series of essential physiological functions. Recently, TMEM48, a member of the TMEM family, has been demonstrated to be closely associated with tumorigenesis. However, little is known about the specific role of TMEM48 in cervical cancer (CC). This study aimed to investigate the biological functions of TMEM48 in CC. The CCK-8 assay was performed to detect CC cell proliferation. The wound healing and transwell assays were conducted to measure cell migration and invasion, respectively. The levels of TMEM48, β-catenin, T cell factor 1(TCF1) and axis formation inhibitor 2 (AXIN2) were examined by the western blot analysis. Xenograft models were established for the tumorigenesis assay in vivo. The results showed that TMEM48 was overexpressed in CC tissues and cell lines. Knockdown of TMEM48 significantly inhibited CC cell proliferation, migration and invasion in vitro and suppressed CC cell growth in vivo. In addition, the investigation on the molecular mechanisms indicated that TMEM48 down-regulation remarkably decreased the protein levels of β-catenin, TCF1 and AXIN2 in CC cells and TMEM48 exerted its promoting effect on CC progression via activation of the Wnt/β-catenin pathway. Taken together, our study suggested TMEM48 as a promising therapeutic target for CC treatment.

Human papillomavirus genotyping as a tool for cervical cancer prevention: from commercially available human papillomavirus DNA test to next-generation sequencing

The biological importance of human papillomavirus (HPV) in the field of medicine – related to cervical carcinogenesis – has been extensively reported in the last decades. For the first time, a direct correlation between cause and effect to explain a cancer development was completely achieved in medical research. Consequently, the Nobel Prize was awarded to HZ Hausen in 2008 for his efforts to understand the effects of persistent infection of oncogenic types of HPV and malignancy transformation. The aim of the present review was to summarize the principal elements of HPV characteristics and their importance in oncology.

It is established that HPV is the main etiologic agent for the development of cervical cancer. With the evolution of diagnosis and molecular biology, many tools have become essential for an early diagnosis and thereby, considerably reducing mortality. Molecular biology continues to advance and provide new perspectives with the use of reverse-transcription PCR in automation and genotyping through next-generation sequencing. This article aims to provide an overview of what is currently used in HPV diagnostic and research and future perspectives with the help of technologies such as next-generation sequencing for screening and vaccination.

Persistent High-Risk HPV Infection and Molecular Changes Related to the Development of Cervical Cancer

This article is a preliminary investigational study that is aimed at giving hints about the interesting biomarkers involved in the transition process from low-grade cervix lesion to invasive cervical cancer. Our study focuses on the risk factors and tumour molecular changes in one patient. First in 1986, she was diagnosed a preinvasive cervix lesion. Then, 16 years later, she was diagnosed an invasive cervical cancer. The 2002 diagnosis was a squamous cell carcinoma of the cervix, stage IIIB (FIGO), whereas in 1986, she had been diagnosed a high-grade squamous intraepithelial cervical lesion. Retrospectively, the analysis of samples of preneoplastic lesions and invasive cervical cancer confirmed the histopathological diagnoses and detected the presence of HPV type and HPV-16 variants, as well as the overexpression of proteins such as hTERT, IGF1Rα, IGF1Rβ, CAIX, and GLUT1. Finally, the Arg72Pro polymorphism was detected in TP53. The role of high-risk HPV and HPV-16 variants and of hTERT, IGF1Rα, IGF1Rβ, CAIX, and GLUT1 variations seemed confirmed in the development and progression of cervical cancer. As a result, analyzing the molecular changes in one and same tumour that progresses from a low-grade cervix lesion to invasive cervical cancer could provide valuable information in order to improve detection, diagnosis, and treatment in the future.

Emerging biomarkers and clinical significance of HPV genotyping in prevention and management of cervical cancer

Cervical cancer is a growing and serious problem world-wide in women, but more acute in developing countries especially in Indian subcontinent. The main causative agent for the disease is Human Papilloma Virus (HPV). The history of the cervical cancer goes back to eighteenth century as the HPV infection is reported since 1800s. Presently, the genetic structure of HPV is well defined. Several screening tests including cytology and visual based screening and high risk HPV testing are available. Also available are various clinical and commercial diagnostic tests. However due to the lack of awareness and population-based screening programs, the morbidity and mortality rate is alarmingly high. There are new emerging biomarkers including E6/E7 mRNA, p16^ink4a, markers of aberrant S-phase induction, chromosomal abnormalities and miRNAs along with advanced genotyping methods. These markers have clinical significance and are helpful in disease prevention and management. Further, recent advancement in the field of metagenomics has increased the prospects of identifying newer microbes, viruses hitherto reported thus far in the context of HPV infection. Analysis of HPV cases using modern tools including genotyping using more powerful biomarkers is envisaged to enhance the prospects of early diagnosis, better prognosis, more reliable treatment and eventual management of the disease.

HPV 6-associated HSIL/Squamous Carcinoma in the Anogenital Tract

Human papillomavirus (HPV) type 6 is historically classified as low-risk HPV type and associates with low-grade squamous intraepithelial lesions of the anogenital tract. Rare squamous carcinomas have been reported in association with these HPV types but the mechanism(s) behind this carcinogenic sequence have been unclear. We report 4 cases of low risk anogenital HPV infections-3 cervical (immature low-grade squamous intraepithelial lesion with metaplastic phenotype) and one anal (exophytic condyloma) lesion-that manifested with high-grade squamous intraepithelial lesion/squamous cell carcinoma. Two were associated with invasion one of which metastasized to a regional node. Two cases exhibited strong p53 positivity in the high-grade squamous intraepithelial lesion/squamous cell carcinoma component analogous to that seen in HPV-negative differentiated intraepithelial lesions of the external genitalia. This series of cases adds to the literature on low risk HPV-associated cervical squamous carcinomas. It underscores the similarities between the baseline cyto-morphology and benign mimics (low-grade squamous intraepithelial lesions), the subtle cytologic and immunohistochemical (MIB1) features heralding biologic aggressiveness, and in some potential pathways (p53) not usually involved in HPV-related anogenital neoplasia.

Epigenetic IVD Tests for Personalized Precision Medicine in Cancer

Epigenetic alterations play a key role in the initiation and progression of cancer. Therefore, it is possible to use epigenetic marks as biomarkers for predictive and precision medicine in cancer. Precision medicine is poised to impact clinical practice, patients, and healthcare systems. The objective of this review is to provide an overview of the epigenetic testing landscape in cancer by examining commercially available epigenetic-based in vitro diagnostic tests for colon, breast, cervical, glioblastoma, lung cancers, and for cancers of unknown origin. We compile current commercial epigenetic tests based on epigenetic biomarkers (i.e., DNA methylation, miRNAs, and histones) that can actually be implemented into clinical practice.

Trends in cervical cancer incidence rates by age, race/ethnicity, histological subtype, and stage at diagnosis in the United States

Recent trends of cervical cancer incidence by histology and age in the United States (U.S.) have not been reported. We examined contemporary trends in cervical squamous cell carcinoma (SCC) and adenocarcinoma (AC) incidence rates in the U.S. by age group, race/ethnicity, and stage at diagnosis after accounting for hysterectomy. Incidence data (1999-2015) were obtained from the U.S. Cancer Statistics Incidence Analytic Database. Hysterectomy prevalence was estimated using National Health Interview Survey data (2000-2015). Overall SCC incidence rates continued to decrease in all racial/ethnic groups except among non-Hispanic whites in whom rates stabilized in the 2010s, largely driven by stable trends in ages <50 years and a slower pace of decrease in ages 50-59 years. After a stable trend between 1999 and 2002, AC incidence rates among non-Hispanic whites rose during 2002-2015 (1.3% per year), mostly due to increases in ages 40-49 (4.4% annually since 2004) and 50-59 years (5.5% annually since 2011). Overall AC incidence rates during 1999-2015 decreased in blacks and Hispanics but were stable in Asian/Pacific Islanders; in all these race/ethnicities, rates were generally stable in ages <50 years but decreasing in older ages. Rates of distant stage cervical SCC and AC among non-Hispanic whites increased in several age groups but were generally stable in non-whites. Increasing or stabilized incidence trends for AC and attenuation of earlier declines for SCC in several subpopulations underscore the importance of intensifying efforts to reverse the increasing trends and further reduce the burden of cervical cancer in the U.S.

Screening for Human Papillomavirus in a Low- and Middle-Income Country

PURPOSE

Low- and middle-income countries have high incidences of cervical cancer linked to human papillomavirus (HPV), and without resources for cancer screenings these countries bear 85% of all cervical cancer cases. To address some of these needs, brigade-style screening combined with sensitive polymerase chain reaction–based HPV testing to detect common high-risk HPV genotypes may be necessary.

METHODS

We deployed an inexpensive DNA extraction technique and a real-time polymerase chain reaction–based HPV genotyping assay, as well as Papanicolaou testing, in a factory in San Pedro Sula, Honduras, where 1,732 women were screened for cervical cancer.

RESULTS

We found that 28% of participants were positive for high-risk HPV, with 26% of HPV-positive participants having more than one HPV infection. Moreover, the most common HPV genotypes detected were different than those routinely found in the United States.

CONCLUSION

This work demonstrates a deployable protocol for HPV screening in low- and middle-income countries with limited resources to perform cytopathology assessment of Pap smears.

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis

The composition of the vaginal microbiome, including both the presence of pathogens involved in sexually transmitted infections (STI) as well as commensal microbiota, has been shown to have important associations for a woman's reproductive and general health. Currently, healthcare providers cannot offer comprehensive vaginal microbiome screening, but are limited to the detection of individual pathogens, such as high-risk human papillomavirus (hrHPV), the predominant cause of cervical cancer. There is no single test on the market that combines HPV, STI, and microbiome screening. Here, we describe a novel inclusive vaginal health assay that combines self-sampling with sequencing-based HPV detection and genotyping, vaginal microbiome analysis, and STI-associated pathogen detection. The assay includes genotyping and detection of 14 hrHPV types, 5 low-risk HPV types (lrHPV), as well as the relative abundance of 31 bacterial taxa of clinical importance, including Lactobacillus, Sneathia, Gardnerella, and 3 pathogens involved in STI, with high sensitivity, specificity, and reproducibility. For each of these taxa, reference ranges were determined in a group of 50 self-reported healthy women. The HPV sequencing portion of the test was evaluated against the digene High-Risk HPV HC2 DNA test. For hrHPV genotyping, agreement was 95.3% with a kappa of 0.804 (601 samples); after removal of samples in which the digene hrHPV probe showed cross-reactivity with lrHPV types, the sensitivity and specificity of the hrHPV genotyping assay were 94.5% and 96.6%, respectively, with a kappa of 0.841. For lrHPV genotyping, agreement was 93.9% with a kappa of 0.788 (148 samples), while sensitivity and specificity were 100% and 92.9%, respectively. This novel assay could be used to complement conventional cervical cancer screening, because its self-sampling format can expand access among women who would otherwise not participate, and because of its additional information about the composition of the vaginal microbiome and the presence of pathogens.

WarmStart colorimetric LAMP for the specific and rapid detection of HPV16 and HPV18 DNA

BACKGROUND AND OBJECTIVES

Persistent infection with High-Risk HPV genotypes is the principal cause for the development of cervical cancer with HPV16 and HPV18 to be the most frequently identified HPV genotypes observed in approximately 70% of cervical cancer cases worldwide. The present study focused on the development of a simple molecular methodology based on WarmStart colorimetric LAMP for the specific identification of HPV16 and HPV18.

METHODS

The method was developed by designing LAMP type-specific primer sets that target the E6 gene. The assay was applied using HPV-positive clinical samples along with control cases in order to evaluate the specificity of the newly designed isothermal protocol. In addition, an experimental cutoff value was estimated through reconstitution experiments with HPV-DNA plasmids. LAMP amplicons were visualized by color changes, thus eliminating the requirement for post-amplification processing steps.

RESULTS

The WarmStart colorimetric LAMP facilitates the isothermal amplification of 10 copies per reaction of both HPV16 and HPV18 DNA, while it exhibits 100% specificity for the detection of the corresponding genotypes in LSIL and HSIL cases. Moreover, the assay demonstrates 100% PPV and 100% NPV. Finally, the sensitivity of conventional PCR with the type-specific LAMP primer sets (B3/F3) for the HPV16, HPV18 DNA detection was 100 copies/reaction and 10 copies/reaction, respectively.

CONCLUSIONS

The newly established WarmStart colorimetric LAMP can be considered as a powerful molecular tool that it can be easily implemented in small clinical and research laboratories for a rapid and efficient identification of the most tumorigenic HPV genotypes.

Universal human papillomavirus typing by whole genome sequencing following target enrichment: evaluation of assay reproducibility and limit of detection

BACKGROUND

We recently described a method for unbiased detection of all known human papillomaviruses (HPV) types with the potential for the determination of their variant and integration from the resulting whole genome sequence data. Considering the complex workflow for target-enriched next generation sequencing (NGS), we focused on the reproducibility and limit of detection (LOD) of this new universal HPV typing assay in this study.

RESULTS

We evaluated the reproducibility and LOD for HPV genotyping based on our recently published method that used RNA-baits targeting whole genomes of 191 HPV types, Agilent SureSelect protocol for target enrichment and Illumina HiSeq 2500 for sequencing (eWGS, enriched whole genome sequencing). Two libraries, prepared from pooled plasmids representing 9 vaccine HPV types at varying input (1-625 copies/reaction), were sequenced twice giving four replicates for evaluating reproducibility and LOD. eWGS showed high correlation in the number of reads mapped to HPV reference genomes between the two flow-cell lanes within (R² = 1) and between experiments (R² = 0.99). The number of mapped reads was positively correlated to copy number (β = 13.9, p < 0.0001). The limit of blank (LOB) could be calculated based on mapped reads to HPV types not included in each sample. HPV genotyping was reproducible for all 9 types at 625 copies using multiple cut-off criteria but LOD was 25 copies based on number of reads above LOB even when multiple types were present. eWGS showed no bias for HPV genotyping under single or multiple infection (p = 0.16-0.99).

CONCLUSIONS

The universal eWGS method for HPV genotyping has sensitivity, competitive with widely used consensus PCR methods with reduced type competition, and with the potential for determination of variant and integration status. The protocol used in this study, using defined samples varying in complexity and copy number, analyzed in replicate and duplicate assays, is applicable to most WGS methods.

Human Plasma Levels of Vascular Endothelial Growth Factor, Matrix Metalloproteinase 9, and Tissue Inhibitor of Matrix Metalloproteinase 1 and Their Applicability as Tumor Markers in Diagnoses of Cervical Cancer Based on ROC Analysis

Cervical cancer (CC) remains a major diagnostic problem. The introduction of human papillomavirus vaccination significantly reduced the number of new cases; however, the search for new methods that would earlier indicate the development of cancerous changes is vital. The aim of this study was to investigate the diagnostic power of those parameters in comparison to Cancer Antigen 125 (CA 125) and Squamous Cell Carcinoma Antigen (SCC-Ag) in patients with CC and in relation to the control group. The study included 100 patients with CC and 50 healthy women. Plasma levels of tested parameters were determined by enzyme-linked immunosorbent assay, CA 125, and SCC-Ag by chemiluminescent microparticle immunoassay. Plasma levels of all parameters in the total cancer group showed statistical significance (in all cases P < .05). In stage I cancer, only vascular endothelial growth factor (VEGF) and tissue inhibitors of metalloproteinase 1; in stage II, all the tested parameters and CA 125; and in stage III + IV, VEGF, matrix metalloproteinase 9 (MMP-9), and CA 125 showed statistical significance when compared to the healthy volunteers group. Vascular endothelial growth factor showed the highest value of sensitivity from all tested parameters (I: 75%, II: 76%, III + IV: 94%, and 82% in total CC group). The highest specificity was obtained by MMP-9 (94%). In the total CC, stage I, and stage II groups, all tested parameters showed statistically significant area under the receiver operating characteristics curve (AUC), but maximum range was obtained for the combination VEGF + SCC-Ag (I: 0.9146, II: 0.8941, III + IV: 0.9139, total CC group: 0.9347). The combined analysis of tested parameters and tumor markers resulted in an increase in sensitivity and AUC values, which provides hope for developing new panel of biomarkers that may be used in the diagnosis of CC in the future.

Methylation of High-Risk Human Papillomavirus Genomes Are Associated with Cervical Precancer in HIV-Positive Women

BACKGROUND

HIV-positive women are at substantial risk of HPV-associated cervical neoplasia caused by high-risk (HR) HPVs. Methylation of the HPV genome is associated with cervical intraepithelial neoplasia grade 3 (CIN3) in HIV-negative women, yet it is unknown whether this holds true for HIV-positive women.

METHODS

We designed a case-control study within the Women's Interagency HIV Study (WIHS) cohort comparing HIV-positive CIN3 cases (N = 72) to HIV-positive controls without detectable CIN2+. The unit of analysis and matching was HPV-type infection. Cases with ≥2 HR-HPV types (N = 23; 32%) had a separate control for each HR-HPV type. We developed and utilized next-generation sequencing (NGS) methylation assays for 12 different HR-HPVs, focusing on CpG sites in the L1/L2 regions.

RESULTS

Significant case-control differences in individual CpG site methylation levels were observed for multiple alpha-9 (HPV16/31/35/58) and alpha-7 HPV (HPV18/39/45) types, based on dichotomization of tertile levels (T3 vs. T1 and T2). Analyses combining homologous CpG sites [e.g., HPV16-L1-5608/HPV31-L1-5521/HPV35-L2L1-5570; OR = 7.28; 95% confidence interval (CI): 2.75-19.3], and (e.g., HPV18-L1-7062/HPV45-L1-7066; OR = 6.94; 95% CI: 1.23-39.3) were significant in separate case-control comparisons. In cases with multiple HR-HPVs, we tested and confirmed the hypothesis that one HR-HPV type would have higher methylation than other types detected, consistent with there being a single HR-HPV causally related to a lesion.

CONCLUSIONS

CIN3 is associated with elevated L1/L2 CpG methylation levels in HIV-positive women.

IMPACT

HPV DNA CpG methylation is a promising triage option in HIV-positive women testing positive for HR-HPV types and provides risk attribution in women with multiple HPV type infections.

Screening of Cervical Cancer with Self-Collected Cervical Samples and Next-Generation Sequencing

Cervical cancer is the second leading cause of death in female genital malignancies. Persistent infection with high-risk HPV is closely related to cervical intraepithelial neoplasia (CIN). Wide-scale HPV screening has already been implemented in developed countries. However, with advances in HPV testing methods, there are presently no better methods for the management of the increasing number of high-risk HPV-positive women except for periodic review. In order to improve screening coverage and achieve better triage of those women, we present current HPV testing methods with self-collected cervical samples, focusing on recent advances in next-generation sequencing (NGS) technologies as a promising screening technology for cervical cancer precursors.

DNA methylation markers as a triage test for identification of cervical lesions in a high risk human papillomavirus positive screening cohort

Objective triage strategies are required to prevent unnecessary referrals for colposcopy in population‐based screening programs using primary high‐risk human papillomavirus (hrHPV) testing. We have identified several DNA methylation markers with high sensitivity and specificity for detection of high‐grade cervical intraepithelial neoplasia or worse (CIN2+) in women referred for colposcopy. Our study assessed diagnostic potential of these methylation markers in a hrHPV‐positive screening cohort. All six markers (JAM3, EPB41L3, C13orf18, ANKRD18CP, ZSCAN1 and SOX1) showed similar association across histology in the hrHPV‐positive cohort when compared to the Dutch cohort (each p > 0.15). Sensitivity for CIN2+ was higher using methylation panel C13orf18/EPB41L3/JAM3 compared to the other 2 panels (80% vs. 60% (ANKRD18CP/C13orf18/JAM3) and 63% (SOX1/ZSCAN1), p = 0.01). For CIN3+ all three methylation panels showed comparable sensitivity ranging from 68% (13/19) to 95% (18/19). Specificity of SOX1/ZSCAN1 panel (84%, 167/200) was considerably higher compared to ANKRD18CP/C13orf18/JAM3 (68%, 136/200, p = 2 × 10⁻⁵) and C13orf18/EPB41L3/JAM3 (66%, 132/200, p = 2 × 10⁻⁷). High negative predictive value (NPV) (91–95% and 96–99%) was observed for CIN2+ and CIN3+, for all three methylation panels, while positive predictive value (PPV) varied from 25 to 40% for CIN2+ and 15–27% for CIN3+. Interestingly, 118/235 samples were negative for all six markers (including 106 controls (89.8%), 6 CIN1 (5.1%), 5 CIN2 (4.2%) and 1 CIN3 (0.8%)). Methylation results from both independent cohorts were comparable as well as high sensitivity for detection of cervical cancer and its high‐grade precursors in hrHPV‐positive population. Our study therefore validates these methylation marker panels as triage test either in hrHPV‐based or abnormal cytology‐based screening programs.

What's new?

In cervical cancer screening, HPV testing provides greater sensitivity than cytology, but its lower specificity leads to some unnecessary treatment referrals. DNA methylation assays could potentially provide better specificity for identifying CIN2+ in women carrying high risk HPV. These authors investigated six previously identified CIN2+ methylation markers. They tested three different combinations of markers, and found high levels of sensitivity and specificity, making these markers potentially useful as part of a population‐based screening program.

Human Papillomavirus DNA Methylation as a Biomarker for Cervical Precancer: Consistency across 12 Genotypes and Potential Impact on Management of HPV-Positive Women

Purpose: Human papillomavirus (HPV) DNA methylation testing is a promising triage option for women testing HPV positive during cervical cancer screening. However, the extent to which methylation indicates precancer for all 12 carcinogenic HPV types has not been evaluated.Experimental Design: In this nested case-control study, we tested up to 30 cases of precancer [cervical intraepithelial neoplasia grade 3 (CIN3)/adenocarcinoma in situ (AIS)] and 30 normal controls for each carcinogenic type (single infections with 16/18/31/33/35/39/45/51/52/56/58/59). Next-generation bisulfite sequencing was performed on CpG sites within the L1 and L2 genes. We calculated differences in methylation, ORs, and AUC. Using a fixed sensitivity of 80%, we evaluated the specificity and the risk of CIN3/AIS for best performing CpG sites, and compared the performance of an explorative multi-type methylation assay with current triage strategies.Results: Methylation was positively associated with CIN3/AIS across all 12 types. AUCs for the top sites ranged from 0.71 (HPV51 and HPV56) to 0.86 (HPV18). A combined 12-type methylation assay had the highest Youden index (0.46), compared with cytology (0.31) and a 5-type methylation assay, including only previously described types (0.26). The 12-type methylation assay had higher sensitivity (80% vs. 76.6%) and lower test positivity compared with cytology (38.5% vs. 48.7%). The risk of CIN3/AIS was highest for methylation positives and lowest for cytology or HPV16/18 positives.Conclusions: HPV DNA methylation is a general phenomenon marking the transition from HPV infection to precancer for all 12 carcinogenic types. Development of a combined multitype methylation assay may serve as a triage test for HPV-positive women. Clin Cancer Res; 24(9); 2194-202. ©2018 AACR.