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

HPV-KITE: sequence analysis software for rapid HPV genotype detection

Human papillomaviruses (HPVs) are among the most diverse viral families that infect humans. Fortunately, only a small number of closely related HPV types affect human health, most notably by causing nearly all cervical cancers, as well as some oral and other anogenital cancers, particularly when infections with high-risk HPV types become persistent. Numerous viral polymerase chain reaction-based diagnostic methods as well as sequencing protocols have been developed for accurate, rapid, and efficient HPV genotyping. However, due to the large number of closely related HPV genotypes and the abundance of nonviral DNA in human derived biological samples, it can be challenging to correctly detect HPV genotypes using high throughput deep sequencing. Here, we introduce a novel HPV detection algorithm, HPV-KITE (HPV K-mer Index Tversky Estimator), which leverages k-mer data analysis and utilizes Tversky indexing for DNA and RNA sequence data. This method offers a rapid and sensitive alternative for detecting HPV from both metagenomic and transcriptomic datasets. We assessed HPV-KITE using three previously analyzed HPV infection-related datasets, comprising a total of 1430 sequenced human samples. For benchmarking, we compared our method's performance with standard HPV sequencing analysis algorithms, including general sequence-based mapping, and k-mer-based classification methods. Parallelization demonstrated fast processing times achieved through shingling, and scalability analysis revealed optimal performance when employing multiple nodes. Our results showed that HPV-KITE is one of the fastest, most accurate, and easiest ways to detect HPV genotypes from virtually any next-generation sequencing data. Moreover, the method is also highly scalable and available to be optimized for any microorganism other than HPV.

Cervical Human Papillomavirus-Independent Squamous Cell Carcinoma: A Clinicopathological Review and Outcomes Analysis Compared With Human Papillomavirus-Associated Squamous Cell Carcinoma

Human papillomavirus (HPV)-independent cervical squamous cell carcinomas (HPVI SCCs) represent a poorly characterized entity. We aimed to explore the clinicopathological and survival features in the largest series of HPVI SCCs and compare them to HPV-associated (HPVA) SCCs. Eighty-nine cases of SCC previously tested negative for high-risk and low-risk HPV were collected from 22 institutions. A total of 363 HPVA SCCs were retrieved from a previously published database. Demographic and clinicopathological features, including p16 and p53 immunohistochemistry, and follow-up data were recorded. Forty-nine of 89 cases were classified as "true" HPVI SCC (HPV-/p16-), whereas 40 were equivocal HPVI SCC (HPV-/p16+ or HPV-/p16 not performed) and were excluded. The median age of true HPVI SCCs was 68 (range, 36-88) years and 38 (77.6%) patients were diagnosed aged 60 years or older. Seven (14.2%) had a history of uterine prolapse. Compared with HPVA SCC, patients with HPVI SCCs were older (P < .001), had larger tumors (P < .001), were diagnosed at higher Federation of Gynecology and Obstetrics stage (P < .001), recurred more frequently (P < .001) and had worse survival (P < .001). True HPVI SCCs also more frequently had keratinizing histology (P = .001) and abnormal p53 (P < .001). In a bivariate analysis adjusted for Federation of Gynecology and Obstetrics stage, HPVI p53-abnormal SCC had a higher risk of recurrence (P = .068; P < .001) and death of disease (P = .062; P < .001) than HPVI p53-wild type SCC and HPVA SCC. Survival outcomes (recurrence and disease-specific survival) in HPVI SCC and HPVA SCC differed significantly when comparing surgically treated HPVI SCC and HPVA SCC (P < .0001 for both). Even with the challenges associated with an analysis of a heterogeneous study set, we confirm that HPVI cervical SCCs have distinctive clinicopathological features. p53-Abnormal and p53-wild type HPVI SCC neoplasms exist in the uterine cervix, and p53-abnormal tumors are more aggressive. Although HPVI SCC is more frequently keratinizing than HPVA SCC neoplasms, there is substantial morphologic overlap, so HPV testing (or p16 at least) and p53 should be considered in cervical SCC, especially in patients over the age of 60 years.

Virusplot: a web server for viral integration analysis and visualization

The integration of viral DNA into the human genome is a critical event in the pathogenesis of various cancers. This process leads to genomic instability, disrupts cellular regulatory mechanisms, and activates oncogenes or inactivates tumor suppressor genes. Despite significant advancements in genome sequencing technologies, there remains a notable lack of computational tools, particularly web-based applications, specifically designed for viral integration analysis and visualization. To address this gap, we present virusPlot, a web server with the following functional modules: (i) automatic retrieval of virus genome sequences and their annotation; (ii) visualization of virus integration locations and read counts through a graphical representation that links viral and host genome integration sites, facilitating the interpretation of integration patterns; (iii) analysis of virus integration hotspots using Fisher's exact test; and (iv) integration of various functions into an interactive web platform via shinyapp. VirusPlot efficiently processes and visualizes integration data from viruses and host genomes, providing researchers with an intuitive and user-friendly analytical tool that simplifies the complexity of virus integration analysis.

Dual lateral flow assay based on PdRu nanocages for human Papillomavirus detection

Cervical cancer is one of the most common gynecological malignancies, with the vast majority of which being caused by persistent infection with Human Papillomavirus (HPV) 16 and 18. The current available HPV detection methods are sensitive and genotyped but are restricted by expensive instruments and skilled personnel. The development of an easy-to-use, rapid, and cost-friendly analysis method for HPV is of great need. Herein, hollow palladium-ruthenium nanocages modified with two oligonucleotides (PdRu capture probes) were constructed for genotyping and simultaneous detection of target nucleic acids HPV16 and HPV18 by dual lateral flow assay (DLFA). PdRu capture probes were endowed with bi-functions for the first time, which could be used to output signals and hybridize target nucleic acids. Under optimized conditions, the PdRu based-DLFA with detection limits of 0.93 nM and 0.19 nM, respectively, exhibited convenient operation, and high sensitivity. Meanwhile, the DLFA achieved excellent rapid detection within 20 min, which was attributed to capture probes that can be directly bound to amplification-free target nucleic acids. Therefore, the development of PdRu-based DLFA can be utilized for rapid, sensitive, and simultaneous genotyping detection of HPV16 and HPV18, showing great application for nucleic acid detection.

Identification of transcriptionally-active human papillomavirus integrants through nanopore sequencing reveals viable targets for gene therapy against cervical cancer

Integration of the human papillomavirus (HPV) genome into the cellular genome is a key event that leads to constitutive expression of viral oncoprotein E6/E7 and drives the progression of cervical cancer. However, HPV integration patterns differ on a case-by-case basis among related malignancies. Next-generation sequencing technologies still face challenges for interrogating HPV integration sites. In this study, utilizing Nanopore long-read sequencing, we identified 452 and 108 potential integration sites from the cervical cancer cell lines (CaSki and HeLa) and five tissue samples, respectively. Based on long Nanopore chimeric reads, we were able to analyze the methylation status of the HPV long control region (LCR), which controls oncogene E6/E7 expression, and to identify transcriptionally-active integrants among the numerous integrants. As a proof of concept, we identified an active HPV integrant in between RUNX2 and CLIC5 on chromosome 6 in the CaSki cell line, which was supported by ATAC-seq, H3K27Ac ChIP-seq, and RNA-seq analysis. Knockout of the active HPV integrant, by the CRISPR/Cas9 system, dramatically crippled cell proliferation and induced cell senescence. In conclusion, identifying transcriptionally-active HPV integrants with Nanopore sequencing can provide viable targets for gene therapy against HPV-associated cancers.

Menstrual Blood as a Diagnostic Specimen for Human Papillomavirus Genotyping and Genital Tract Infection Using Next-Generation Sequencing as a Novel Diagnostic Tool

BACKGROUND

Menstrual blood (MB) is a convenient specimen type that can be self-collected easily and non-invasively by women. This study assessed the potential application of MB as a diagnostic specimen to detect genital tract infections (GTIs) and human papillomavirus (HPV) infections in women.

METHOD

Genomic DNA was extracted from MB samples. Pacific Bioscience (Pacbio) 16S ribosomal DNA (rDNA) high-fidelity (HiFi) long-read sequencing and HPV PCR were performed.

RESULTS

MB samples were collected from women with a pathological diagnosis of CIN1, CIN2, CIN3 or HPV infection. The sensitivity and positive predictive value (PPV) of high-risk HPV detection using MB were found to be 66.7%. A shift in vaginal flora and a significant depletion in Lactobacillus spp. in the vaginal microbiota communities were observed in the MB samples using 16S rDNA sequencing.

CONCLUSIONS

In this study, we demonstrated that MB is a proper diagnostic specimen of consideration for non-invasive detection of HPV DNA and genotyping using PCR and the diagnosis of GTIs using metagenomic next-generation sequencing (mNGS). MB testing is suitable for all women who menstruate and this study has opened up the possibility of the use of MB as a diagnostic specimen to maintain women's health.

The International Human Papillomavirus Reference Center: Standardization, collaboration, and quality assurance in HPV research and diagnostics

The International Human Papillomavirus (HPV) Reference Center (IHRC) confirms and assigns type numbers to novel HPV types, maintains a reference clone repository, and issues international proficiency panels for HPV screening and genotyping. Furthermore, the Center coordinates the Global HPV Reference Laboratory Network that promotes collaboration and international exchange of experiences among national HPV reference laboratories, to further international standardization and quality assurance in the HPV field. The established HPV types (n = 225) belong to 5 different genera: alpha (n = 65), beta (n = 54), gamma (n = 102), mu (n = 3) and nu (n = 1). Since the last published IHRC overview in 2018, 6 novel types have been established, with 5/6 belonging to the gamma genus and 1/6 to beta genus. Also, 474 reference clones have been provided to 55 different research laboratories and the global proficiency program for HPV genotyping has seen an increasing proficiency (despite a decrease seen in 2019), from 68% proficiency in 2017 to 77.3% in 2022. The first proficiency study for HPV screening found an international proficiency of up to 77%. In summary, increasing complexity of the HPVs and demands on quality assurance in the era of cervical cancer elimination requires international efforts to support proficiency and recognized quality and order among HPV types.

Incidence and Clinicopathologic Characteristics of Human Papillomavirus-independent Invasive Squamous Cell Carcinomas of the Cervix: A Morphologic, Immunohistochemical, and Human Papilloma-Virologic Study of 670 Cases

We aimed to determine the frequency of human papillomavirus-independent (HPVI) cervical squamous cell carcinoma (SCC) and to describe clinicopathologic characteristics. Among 670 patients with surgically treated SCCs in an established multi-institutional cohort, 447 had available tissue. Tissue microarrays were constructed and studied by in situ hybridization (ISH) for high-risk and low-risk human papillomavirus (HPV) mRNA and immunohistochemistry for p16 and p53. Tumors were HPVI if negative by HPV ISH and they failed to show diffuse p16 positivity by immunohistochemistry, and human papillomavirus-associated (HPVA) if positive by HPV ISH. Ten HPVI SCCs and 435 HPVA SCCs were identified; 2 cases were equivocal and excluded from analysis. The overall rate of HPVI SCC was low (2%) but was higher among older patients (7% in patients above 60 y of age and 17% in patients above 70 y of age). Compared with HPVA, patients with HPVI SCC were significantly older (median age, 72 vs. 49, P <0.001) and diagnosed at a higher stage (40% vs. 18% with stage III/IV disease, P =0.055). p53 expression was varied; 2 cases (20%) had null expression and 8 (80%) had wild-type expression. HPVI SCCs were heterogenous, with keratinizing, nonkeratinizing, and warty morphologies observed. Several cases had a precursor lesion reminiscent of differentiated vulvar intraepithelial neoplasia, with prominent basal atypia and hypereosinophilia or a basaloid-like morphology. Two patients (20%) had distant recurrences within 12 months, and 3 (30%) died of disease during follow-up. HPVI SCCs are rare tumors that are more common among older patients with higher stage disease and have important clinical and histologic differences from HPVA SCCs.

Next-Generation sequencing transforming clinical practice and precision medicine

Next-generation sequencing (NGS) has revolutionized the field of genomics and is rapidly transforming clinical diagnosis and precision medicine. This advanced sequencing technology enables the rapid and cost-effective analysis of large-scale genomic data, allowing comprehensive exploration of the genetic landscape of diseases. In clinical diagnosis, NGS has proven to be a powerful tool for identifying disease-causing variants, enabling accurate and early detection of genetic disorders. Additionally, NGS facilitates the identification of novel disease-associated genes and variants, aiding in the development of targeted therapies and personalized treatment strategies. NGS greatly benefits precision medicine by enhancing our understanding of disease mechanisms and enabling the identification of specific molecular markers for disease subtypes, thus enabling tailored medical interventions based on individual characteristics. Furthermore, NGS contributes to the development of non-invasive diagnostic approaches, such as liquid biopsies, which can monitor disease progression and treatment response. The potential of NGS in clinical diagnosis and precision medicine is vast, yet challenges persist in data analysis, interpretation, and protocol standardization. This review highlights NGS applications in disease diagnosis, prognosis, and personalized treatment strategies, while also addressing challenges and future prospects in fully harnessing genomic potential within clinical practice.

Broad-Spectrum Detection of HPV in Male Genital Samples Using Target-Enriched Whole-Genome Sequencing

Most human papillomavirus (HPV) surveillance studies target 30-50 of the more than 200 known types. We applied our recently described enriched whole-genome sequencing (eWGS) assay to demonstrate the impact of detecting all known and novel HPV types in male genital samples (n = 50). HPV was detected in nearly all (82%) samples, (mean number of types/samples 13.6; range 1-85), and nearly all HPV-positive samples included types in multiple genera (88%). A total of 560 HPV detections (237 unique HPV types: 46 alpha, 55 beta, 135 gamma, and 1 mu types) were made. The most frequently detected HPV types were alpha (HPV90, 43, and 74), beta (HPV115, 195, and 120), and gamma (HPV134, mSD2, and HPV50). High-risk alpha types (HPV16, 18, 31, 39, 52, and 58) were not common. A novel gamma type was identified (now officially HPV229) along with 90 unclassified types. This pilot study demonstrates the utility of the eWGS assay for broad-spectrum type detection and suggests a significantly higher type diversity in males compared to females that warrants further study.

Joint detection of multiple HPV-testing technologies and evaluation of clinicopathological characteristics discriminate between HPV-independent and low-copy HPV-associated cervical squamous cell carcinoma (CSCC) -an analysis of 3869 cases

OBJECTIVES

This study aimed to investigate the frequency and clinicopathological characteristics of HPV-independent cervical squamous cell carcinoma (CSCC).

METHODS

A total of 3869 patients with CSCC from 2017 to 2021 were searched. p16^INK4a immunochemistry (IHC), two HPV-DNA(L1) polymerase chain reactions and HPV mRNA in situ hybridization were performed. Viral copies were detected using the 21 HPV quantitative test.

RESULTS

Six cases showed negative results in all four assays (group 1, 0.16%). Twenty-seven cases showed discordant results (group 2), and 3836 cases presented all-positive results (group 3). p16^INK4a IHC showed similar sensitivity, specificity, and positive predictive value compared to the other three direct HPV assays. 21 HPV genotyping showed 100% of negative predictive value. HPV copies were extremely lower in Group 2 than in Group 3 (P < 0.01), but were not significantly different from those in Group 1. Older age, advanced FIGO stage (III-IV) and abnormal p53 (p53abn) IHC were independent predictors of HPV-negative status in univariate and multivariate logistic regression. Group 2 had similar proportions of age >60 years and p53abn IHC with Group 1, but had fewer cases with advanced FIGO stage (P < 0.05) and TILs (P < 0.05). Groups 1 and 2 had worse disease-free survival (DFS) and disease-specific survival (DSS) than Group 3 (P < 0.01), while no significant difference was found between these two groups. HPV-negative status was a risk factor for both DFS (P < 0.05) and DSS (P < 0.01) in univariate but not multivariate Cox regression.

CONCLUSIONS

Joint detection of multiple technologies and evaluation of clinicopathological characteristics discriminate between HPV-independent and low-copy HPV-associated CSCC cases that present similar prognoses. Additional attention should be paid to these low-copy HPV-associated cases in clinical practice.

The Future of Cervical Cancer Prevention: From "One-Size-Fits-All" to Personalized Screening

Cervical cancer screening represents an excellent model system for the development of personalized cancer-prevention strategies [...].

The role of liquid biopsy in management of the neck with indeterminate response on post-treatment imaging following non-surgical management of oropharyngeal cancer

INTRODUCTION

This study aimed to determine if post-treatment HPV cell-free DNA (cfDNA) can assist in the decision-making process for salvage neck dissection in patients following non-surgical treatment of oropharyngeal squamous cell carcinoma (OPSCC) with a partial response in the neck on imaging at 12 weeks post-treatment.

METHODS

86 patients who completed treatment were prospectively recruited through the regional multidisciplinary team (MDT). Treatment response was categorised as complete response (CR), partial response (PR) or progressive disease on 12-week post-treatment imaging. Pre- and post-treatment blood samples were assessed for HPV cfDNA through droplet digital PCR (ddPCR).

RESULTS

Eight patients had an isolated partial response in the neck. One (12.5%) had detectable HPV cfDNA (22.96 copies/ml) at ∼12 weeks post-treatment with positive disease on subsequent neck dissection (positive predictive value; PPV = 100%). Of the seven patients with undetectable HPV cfDNA, two patients had evidence of regional disease recurrence at 23.9 and 27.4 months respectively (negative predictive value; NPV = 71%).

CONCLUSION

The detection of HPV cfDNA may help target salvage therapy in patients with a partial response in the neck. Follow-up studies in larger cohorts would be required to further validate the use of post-treatment HPV cfDNA in the management of OPSCC.

Exploration of biomarkers for the diagnosis, treatment and prognosis of cervical cancer: a review

As the fourth most diagnosed cancer, cervical cancer (CC) is one of the major causes of cancer-related mortality affecting females globally, particularly when diagnosed at advanced stage. Discoveries of CC biomarkers pave the road to precision medicine for better patient outcomes. High throughput omics technologies, characterized by big data production further accelerate the process. To date, various CC biomarkers have been discovered through the advancement in technologies. Despite, very few have successfully translated into clinical practice due to the paucity of validation through large scale clinical studies. While vast amounts of data are generated by the omics technologies, challenges arise in identifying the clinically relevant data for translational research as analyses of single-level omics approaches rarely provide causal relations. Integrative multi-omics approaches across different levels of cellular function enable better comprehension of the fundamental biology of CC by highlighting the interrelationships of the involved biomolecules and their function, aiding in identification of novel integrated biomarker profile for precision medicine. Establishment of a worldwide Early Detection Research Network (EDRN) system helps accelerating the pace of biomarker translation. To fill the research gap, we review the recent research progress on CC biomarker development from the application of high throughput omics technologies with sections covering genomics, transcriptomics, proteomics, and metabolomics.

Metatranscriptome analysis in human papillomavirus negative cervical cancers

Human papillomavirus (HPV) negative cancers are associated with symptomatic detection, late-stage diagnosis, and worse prognosis. It is thus essential to investigate all possible infectious agents and biomarkers that could early identify these HPV negative cancers. We aimed to analyze and compare the metatranscriptome present in HPV positive and HPV negative cervical cancers. We analyzed the whole RNA sequencing files from 223 HPV negative cervical cancers (negativity established after confirming cervical cancer diagnosis, sample adequacy and subjecting specimens to PCR and unbiased RNA sequencing), 223 HPV positive tumors and 11 blank paraffin block pools (used as controls) using Kraken2 software. Overall, 84 bacterial genera were detected, with 6/84 genera showing a positive median number of reads/sample and being present in both cervical tumor groups (HPV positive and negative). Viral reads belonged to 63 different viral genera, with 6/63 genera showing a positive median annotated read/sample value. No significant difference among genera was detected except for the presence of alpha-papillomaviruses. Metatranscriptome of bacteria and viruses present in HPV positive and HPV negative cervical cancers show no significant difference, except for HPV. Further studies are needed to early identify this biologically distinct group of cervical cancers.

Using HPV-meta for human papillomavirus RNA quality detection

In the era of cervical cancer elimination, accurate and validated pipelines to detect human papillomavirus are essential to elucidate and understand HPV association with human cancers. We aimed to provide an open-source pipeline, "HPV-meta", to detect HPV transcripts in RNA sequencing data, including several steps to warn operators for possible viral contamination. The "HPV-meta" pipeline automatically performs several steps, starting with quality trimming, human genome filtering, HPV detection (blastx), cut-off settlement (10 reads and 690 bp coverage to make an HPV call) and finishing with fasta sequence generation for HPV positive samples. Fasta sequences can then be aligned to assess sequence diversity among HPV positive samples. All RNA sequencing files (n = 10,908) present in the cancer genome atlas (TCGA) were analyzed. "HPV-meta" identified 25 different HPV types being present in 488/10,904 specimens. Validation of results showed 99.98% agreement (10,902/10,904). Multiple alignment from fasta files warned about high sequence identity between several HPV 18 and 38 positive samples, whose contamination had previously been reported. The "HPV-meta" pipeline is a robust and validated pipeline that detects HPV in RNA sequencing data. Obtaining the fasta files enables contamination investigation, a non very rare occurrence in next generation sequencing.