Human Papillomavirus 42 Drives Digital Papillary Adenocarcinoma and Elicits a Germ Cell-like Program Conserved in HPV-Positive Cancers

Digital Papillary Adenocarcinoma at the Site of 5 Years of Recurrent Paronychia: Case Report and Literature Review

Digital papillary adenocarcinoma (DPA) is a rare malignant eccrine tumor often misdiagnosed as a benign condition. A 57-year-old Caucasian male with recurrent paronychia and a subcutaneous mass on the distal phalanx of the right fourth digit was diagnosed with DPA after seeking hand surgery evaluation 5 years following onset. A marginal excisional biopsy was positive for Staphylococcus aureus infection and DPA, leading to surgical excision with transmiddle phalangeal amputation for negative margins. DPA, while rare, often presents insidiously, leading to delayed diagnosis and increased risk of metastasis. This tumor has high rates of recurrence and metastasis, most commonly to pulmonary and lymphatic sites. Accurate diagnosis of DPA is challenging due to its resemblance to multiple benign cutaneous conditions. Current treatments focus on surgical excision, with an emphasis on negative margins. Sentinel lymph node biopsy is not routinely performed, although guidelines are difficult to establish due to the rarity of DPA. Diagnosing and treating DPA minimizes metastasis and recurrence. DPA should be considered in patients presenting with recalcitrant or recurring cutaneous lesions. Surgical management remains the primary treatment strategy, with ongoing research needed to optimize treatment protocols and follow-up care.

The HPV101 E7 protein shares host cellular targets and biological activities with high-risk HPV16 E7

Human papillomaviruses (HPVs) are a diverse family of viruses with over 450 members that have been identified and fully sequenced. They are classified into five phylogenetic genera: alpha, beta, gamma, mu, and nu. The high-risk alpha HPVs, such as HPV16, have been studied the most extensively due to their medical significance as cancer-causing agents. However, while nearly 70% of all HPVs are members of the gamma genus, they are almost entirely unstudied. This is because gamma HPVs have been considered medically irrelevant commensals as most of them infect the skin and are not known to cause significant clinical lesions in immunocompetent individuals. Members of the gamma 6 HPVs, however, have been detected in the anogenital tract mucosa and HPV101 has been isolated from a premalignant cervical lesion. Moreover, gamma 6 HPVs have a unique genome structure. They lack E6 proteins but in place of E6, they encode unique, small hydrophobic proteins without any close viral or cellular homologs that have been termed E10. Here, we report that HPV101 E7 shares biochemical activities with the high-risk alpha HPV16 E7, including the ability to target the pRB and PTPN14 tumor suppressors for degradation. This study underscores the importance of further characterizing HPV101 and other unstudied HPV species.

Detection of human papillomavirus (HPV) in malignant melanoma

The most common type of melanoma is cutaneous melanoma (CM). The predominant mutational signature is that of ultraviolet radiation (UVR) exposure. The Cancer Genome Atlas (TCGA) molecular classification includes four major subtypes of CM based on common genetic alterations involving the following genes: BRAF, NRAS, and NF1, with a small fraction being "triple" wild-type. The two main signaling pathway abnormalities in CM are the mitogen-activated protein kinase (MAPK) pathway and the phosphoinositol-3-kinase (PI3K) pathway. Other less common types include mucosal melanomas (MM) and uveal melanoma (UM), which have a significantly different genomic landscape. Although few studies reported rare cases with HPV-positive (HPV+) melanoma, the clinicopathological and molecular characteristic of this entity has not been well-described. Among the 2084 melanoma cases queried at our institution, we identified seven patients diagnosed with HPV+ melanoma (prevalence 0.03 %), including five instances of CM and two of MM. The majority of cases were positive for HPV16 (n = 6). Most of the patients were elderly and with advanced disease (n = 6), although this finding may be attributed to the relative frequency of our institution testing advanced-stage tumors. Histologically, most cases showed high degree of pleomorphism and high mitotic count (5 or more mitoses/mm2) (n = 6). UVR signature was present in the CM, but not in the MM cases. Alterations in either MAPK and/or PI3K pathways were detected in the majority of cases (n = 6). The most common genetic abnormalities detected in this study occurred in the TERT promoter (TERTp) (n = 5), a finding that has been reported to be associated with aggressive disease. Our data shows that while HPV+ melanoma is rare, identifying this disease entity could help guide therapy given the demonstrated genomic alterations.

Why HPV16? Why, now, HPV42? How the discovery of HPV42 in rare cancers provides an opportunity to challenge our understanding about the transition between health and disease for common members of the healthy microbiota

In 2022, a bioinformatic, agnostic approach identified HPV42 as causative agent of a rare cancer, later confirmed experimentally. This unexpected association offers an opportunity to reconsider our understanding about papillomavirus infections and cancers. We have expanded our knowledge about the diversity of papillomaviruses and the diseases they cause. Yet, we still lack answers to fundamental questions, such as what makes HPV16 different from the closely related HPV31 or HPV33; or why the very divergent HPV13 and HPV32 cause focal epithelial hyperplasia, while HPV6 or HPV42 do not, despite their evolutionary relatedness. Certain members of the healthy skin microbiota are associated to rare clinical conditions. We propose that a focus on cellular phenotypes, most often transient and influenced by intrinsic and extrinsic factors, may help understand the continuum between health and disease. A conceptual switch is required towards an interpretation of biology as a diversity of states connected by transition probabilities, rather than quasi-deterministic programs. Under this perspective, papillomaviruses may only trigger malignant transformation when specific viral genotypes interact with precise cellular states. Drawing on Canguilhem's concepts of normal and pathological, we suggest that understanding the transition between fluid cellular states can illuminate how commensal-like infections transition from benign to malignant.

National epidemiology of digital papillary adenocarcinoma in England 2013-2020: a population-based registry study

BACKGROUND

Digital papillary adenocarcinoma (DPA), formerly known as aggressive DPA, is a rare adnexal cancer of sweat gland differentiation with metastatic potential. DPA epidemiology and patient outcome data are prerequisites for developing diagnostic and therapeutic guidance, which are lacking for this rare cancer.

OBJECTIVES

To report the incidence, patient demographics and treatment of patients with DPA in England from 1 January 2013 to 31 December 2020 using national cancer registry data.

METHODS

DPA diagnoses in England during 2013-2020 were identified from the National Cancer Registration and Analysis Service dataset using morphology and behaviour codes. These were registered from routinely collected pathology reports, along with cancer outcomes and services datasets. The 2013 European age-standardized incidence rates (EASRs) were calculated.

RESULTS

In total, 36 cases of DPA (7 in women and 29 in men) were diagnosed. The median age at diagnosis for the cohort was 54 years (interquartile range 46-64). The most frequently affected sites were the upper limbs (81%). All patients in the cohort received surgical excisions. The EASR was 0.10 (95% confidence interval 0.07-0.14) per 1 000 000 person-years.

CONCLUSIONS

This study reports the incidence and variation of DPA in England between 2013 and 2020. DPA was more common in older men and predominantly affected the upper limbs. This finding supports the need to develop a national policy for the reporting and management of DPA as well as development of a clinical guideline.

Hidrocystoma-like tumours with RET or ALK fusion: a study of four cases

Hidrocystoma is thought to be a benign retention cyst of sweat ductal units. The lesion is usually located in the periorbital skin; however, lesions with similar histopathological features are rarely observed in extra-facial sites. Herein, we present four cases of hidrocystoma-like tumours in extra-facial skin sites that harboured a RET or ALK rearrangement. This study features a 67-year-old female with a 10 mm-sized digital tumour (Case 1), a 62-year-old male with an 8 mm-sized clavicular tumour (Case 2), a 61-year-old male with a 19 mm-sized digital tumour (Case 3), and an 11-year-old female with a 10 mm-size lower leg tumour (Case 4) as well as five control cases (Cases 5-9) of classical periorbital hidrocystoma. In Cases 1-4, multicystic tumours comprising a two-cell layer of inner cuboidal ductoglandular (p63- and SOX10+/-) and outer flat myoepithelial (p63+ and SOX10+) cells were observed. The inner ductoglandular tumour cells exhibited micropapillary projections and Roman bridging structures. No apparent atypical cells were observed. NCOA4::RET in Cases 1 and 3, CCDC6::RET in Case 2, and SLC12A2::ALK in Case 4 were revealed by next-generation sequencing or Sanger sequencing. In contrast, control cases of classical hidrocystoma (Cases 5-9) did not show intracystic proliferation, abundant cytoplasm, ALK immunoreactivity, or NCOA4::RET detection in the tumour cells. RET/ALK-rearranged hidrocystoma-like tumours are tumour entities that can be distinguished from classical hidrocystoma. This RET/ALK-rearranged neoplasm is benign and is frequently observed in the digits. Future studies will establish the concept, detailed clinicopathological characteristics, and genetic variations of hidrocystoma-like tumours.

Correlation between breast cancer and human papillomavirus (HPV) infection

Breast cancer (BC), the most common malignant tumor in women worldwide, has been increasing in incidence and mortality year by year. While significant progress has been made in understanding the pathogenesis of breast cancer, certain aspects remain under investigation. Human papillomavirus (HPV) is known to be closely associated with a variety of cancers, including cervical, vulvar, anal, and head and neck cancers. It is important to note that while HPV is associated with the mentioned cancers, its direct association with breast cancer remains a topic of debate and research. In this paper, we review the research progress on the correlation between breast cancer and HPV infection, and put forward the problems in the current research. This review aims to shed light on the current understanding and controversies surrounding the correlation between HPV infection and breast cancer, providing insights for future research aimed at enhancing prevention and treatment strategies.

Are There More Human Cancer Viruses Left to Be Found?

Of the thousands of viruses infecting humans, only seven cause cancer in the general population. Tumor sequencing is now a common cancer medicine procedure, and so it seems likely that more human cancer viruses already would have been found if they exist. Here, we review cancer characteristics that can inform a dedicated search for new cancer viruses, focusing on Kaposi sarcoma herpesvirus and Merkel cell polyomavirus as the most recent examples of successful genomic and transcriptomic searches. We emphasize the importance of epidemiology in determining which cancers to examine and describe approaches to virus discovery. Barriers to virus discovery, such as novel genomes and viral suppression of messenger RNA expression, may exist that prevent virus discovery using existing approaches. Optimally virus hunting should be performed in such a way that if no virus is found, the tumor can be reasonably excluded from having an infectious etiology and new information about the biology of the tumor can be found.

Ancillary immunohistochemical and molecular testing in the classification of cutaneous sweat gland/duct neoplasms: A validation study with emphasis on histomorphologic correlation and pathological diagnosis

Sweat gland neoplasms represent a challenging area of dermatopathology, as they are relatively uncommon and often histopathologically complex. Recent studies have uncovered distinct immunohistochemical and molecular profiles in several sweat gland neoplasms, including digital papillary adenocarcinoma (DPA), papillary eccrine adenoma/tubular apocrine adenoma (PEA/TAA), poroid family tumors (PFT)/porocarcinoma, and clear cell hidradenoma (CCH)/clear cell hidradenocarcinoma (CCHCa). To further evaluate the diagnostic utility of ancillary studies in various sweat gland neoplasms, we performed an independent validation study in a cohort of patients with acral and non-acral tumors (9 DPA, 8 PEA/TAA, 13 PFT, 5 porocarcinoma, 23 CCH, 7 CCHCa, 6 sweat gland carcinoma not otherwise specified). p63 immunohistochemistry (IHC) demonstrated a myoepithelial pattern in 8/8 DPA and 4 of 4 tested PEA/TAA cases, and showed a ductal pattern in all tested PFT/porocarcinoma and CCH/CCHCa cases (42/42). All PEA/TAA (8/8) cases were positive for BRAF V600E IHC. 5 of 12 tested PFT and 5/5 porocarcinoma cases showed either positive staining with NUT IHC or harbored YAP1::NUTM1 fusion gene by RNA sequencing. MAML2 fluorescence in situ hybridization (FISH) was positive in all CCH and CCHCa cases (23/23 and 7/7, respectively). Our results further support the usefulness of appropriate ancillary studies in precise classification of sweat gland tumors, which may be routinely applied in diagnostic pathology practice when morphologic evaluation is in doubt.

High-risk human papilloma virus status & outcomes for penile squamous cell carcinoma: A single institution experience

OBJECTIVES

There is a paucity of data on North American cohorts of patients with penile squamous cell carcinoma (pSCC). Herein, we aimed to assess the sensitivity of various modalities to identify human papillomavirus (HPV) status, determine the prevalence of high-risk HPV-positivity, and evaluate the prognostic impact of relevant clinicopathologic variables.

METHODS

Patients with pSCC (n = 121) consecutively treated with partial/total penectomy (2000-2022) at a single institution were included. HPV status (based on immunohistochemistry [IHC], in situ hybridization [ISH], and panviral metagenomic sequencing [PMS]), histologic features, and outcomes were reviewed. Outcome events included death due to disease and progression.

RESULTS

The majority of patients were white (105/121, 86.8%). Thirty-seven (30.6%) were high-risk HPV-positive, and morphologic evaluation had a sensitivity of 97.3% (95% confidence interval [CI], 86.2-99.5) for predicting high-risk HPV status compared to IHC/ISH/PMS. Disease progression was more common among high-risk HPV-negative compared to high-risk HPV-positive patients (HR 2.74, CI 1.12-8.23, P = 0.03). Moreover, among high-risk HPV-negative patients, those with moderate-poorly differentiated tumors had increased disease-specific mortality (32.6%, CI 17.1-48.1) compared to those with well-differentiated tumors (0%). Among high-risk HPV-positive patients, those with basaloid morphology had lower disease-specific mortality (0% vs 14.4%, CI 0.0-33.1).

CONCLUSIONS

We demonstrate high-risk HPV-positivity in approximately one-third of patients with pSCC. Morphologic evaluation alone had a high sensitivity in correctly determining HPV status. Our results suggest that high-risk HPV status and morphologic features (differentiation in high-risk HPV-negative, and basaloid subtype in high-risk HPV-positive pSCC) may have prognostic value.

Digital Papillary Adenocarcinoma: The Detection of Low-Risk Human Papillomaviruses and the BRAF p.V600E Mutation in a Subset of Cases

Digital papillary adenocarcinoma (DPA) is a rare malignant neoplasm which arises from the sweat glands and has metastatic potential. DPA exhibits a wide range of architectural features and exhibits low-grade to high-grade features, so distinguishing DPA from benign skin neoplasms, including acral hidradenoma, poses significant diagnostic challenges. The recent literature suggests a strong association between DPA and human papillomavirus (HPV) 42, a low-risk HPV (LR-HPV) subtype, and a possible association between DPA and BRAF p.V600E. To explore these associations, we assessed the utility of in situ hybridization (ISH) for LR-HPV (types 6, 11, 40, 42, 43, 44) and immunohistochemistry (IHC) for BRAF p.V600E in diagnosing DPA and distinguishing DPA from acral hidradenoma. With institutional review board approval, we retrospectively identified 15 specimens of DPA (from 13 patients) and 3 cases of acral hidradenoma. Of the 13 DPA cases, 6 were negative for LR-HPV and BRAF p.V600E; 6 were positive for only LR-HPV; and 1 was positive for only BRAF p.V600E but negative for LR-HPV. All three cases of acral hidradenoma were negative for LR-HPV and BRAF p.V600E. As our sample size is limited, larger studies are needed to assess the value of detecting LR-HPV and BRAF p.V600E in the distinction of DPA and acral hidradenoma. However, our findings indicate a stronger association of DPA with LR-HPV than with BRAF p.V600E.

[Cutaneous adnexal tumours: Development and synthesis of diagnostic fusion genes]

Cutaneous adnexal tumours are a heterogeneous group of epithelial lesions that includes tumours with follicular, sudoral and/or sebaceous differentiation, or even several combined lines of differentiation. Over the last few years, molecular analysis of these lesions has allowed to identify specific molecular events responsible for tumour development in an increasing number of tumour types. Like other rare neoplasms, such as soft tissue tumours, adnexal tumours display fusion genes resulting from chromosomal translocations that may be specific for the diagnosis if molecular data are properly integrated in the clinical and morphological setting. Molecular testing of adnexal tumours is valuable as it allows to strengthen the robustness of the diagnosis for a group of tumours displaying a wide morphological spectrum. It has allowed to refine the diagnostic criteria and to develop increasingly specific diagnostic immunostainings. Finally, molecular testing has been responsible for the identification of new entities or morphological subtypes of previously known entities. The aim of this review is to provide an update on cutaneous adnexal tumours associated with fusion genes and to evaluate the impact of molecular data on the diagnosis of these lesions.

Epidermodysplasia verruciformis-associated eccrine neoplasm: a rare entity with distinctive clinical and histopathologic features

Most tumors are caused by inherited or acquired genetic changes. However, a subset of tumors is driven by viral infection including Kaposi sarcoma, nasopharyngeal carcinoma, and others. Human papillomavirus (HPV) is an especially common cause of epithelial cancers and hyperplasias. Epidermodysplasia verruciformis (EDV) is a rare type of HPV infection with characteristic histopathologic features and a unique spectrum of HPV subtypes. We report here a distinctive form of EDV-associated eccrine neoplasia. Seven tumors from two patients were analyzed and show highly uniform features including multiple clustered clinical lesions, multifocal epidermal origin, eccrine differentiation with close association with the acrosyringium, an anastomosing growth pattern, and a bland monotonous poroid-to-basaloid cytomorphology. Clinical follow-up for one patient has been benign to date. These tumors show strong similarity to two previously reported cases, suggesting that this type of EDV-associated eccrine neoplasia may represent a rare but reproducible form of skin adnexal tumor with distinctive clinicopathologic features.

Deep learning based histological classification of adnex tumors

BACKGROUND

Cutaneous adnexal tumors are a diverse group of tumors arising from structures of the hair appendages. Although often benign, malignant entities occur which can metastasize and lead to patients´ death. Correct diagnosis is critical to ensure optimal treatment and best possible patient outcome. Artificial intelligence (AI) in the form of deep neural networks has recently shown enormous potential in the field of medicine including pathology, where we and others have found common cutaneous tumors can be detected with high sensitivity and specificity. To become a widely applied tool, AI approaches will also need to reliably detect and distinguish less common tumor entities including the diverse group of cutaneous adnexal tumors.

METHODS

To assess the potential of AI to recognize cutaneous adnexal tumors, we selected a diverse set of these entities from five German centers. The algorithm was trained with samples from four centers and then tested on slides from the fifth center.

RESULTS

The neural network was able to differentiate 14 different cutaneous adnexal tumors and distinguish them from more common cutaneous tumors (i.e. basal cell carcinoma and seborrheic keratosis). The total accuracy on the test set for classifying 248 samples into these 16 diagnoses was 89.92 %. Our findings support AI can distinguish rare tumors, for morphologically distinct entities even with very limited case numbers (< 50) for training.

CONCLUSION

This study further underlines the enormous potential of AI in pathology which could become a standard tool to aid pathologists in routine diagnostics in the foreseeable future. The final diagnostic responsibility will remain with the pathologist.

Artificial intelligence-assisted dermatology diagnosis: From unimodal to multimodal

Artificial Intelligence (AI) is progressively permeating medicine, notably in the realm of assisted diagnosis. However, the traditional unimodal AI models, reliant on large volumes of accurately labeled data and single data type usage, prove insufficient to assist dermatological diagnosis. Augmenting these models with text data from patient narratives, laboratory reports, and image data from skin lesions, dermoscopy, and pathologies could significantly enhance their diagnostic capacity. Large-scale pre-training multimodal models offer a promising solution, exploiting the burgeoning reservoir of clinical data and amalgamating various data types. This paper delves into unimodal models' methodologies, applications, and shortcomings while exploring how multimodal models can enhance accuracy and reliability. Furthermore, integrating cutting-edge technologies like federated learning and multi-party privacy computing with AI can substantially mitigate patient privacy concerns in dermatological datasets and further fosters a move towards high-precision self-diagnosis. Diagnostic systems underpinned by large-scale pre-training multimodal models can facilitate dermatology physicians in formulating effective diagnostic and treatment strategies and herald a transformative era in healthcare.

Human papillomaviruses: Knowns, mysteries, and unchartered territories

There has been an explosion in the number of papillomaviruses that have been identified and fully sequenced. Yet only a minute fraction of these has been studied in any detail. Most of our molecular research efforts have focused on the E6 and E7 proteins of "high-risk," cancer-associated human papillomaviruses (HPVs). Interactions of the high-risk HPV E6 and E7 proteins with their respective cellular targets, the p53 and the retinoblastoma tumor suppressors, have been investigated in minute detail. Some have thus questioned if research on papillomaviruses remains an exciting and worthwhile area of investigation. However, fundamentally new insights on the biological activities and cellular targets of the high-risk HPV E6 and E7 proteins have been discovered and previously unstudied HPVs have been newly associated with human diseases. HPV infections continue to be an important cause of human morbidity and mortality and since there are no antivirals to combat HPV infections, research on HPVs should remain attractive to new investigators and biomedical funding agencies, alike.

Digital Papillary Adenocarcinoma in Nonacral Skin: Clinicopathologic and Genetic Characterization of 5 Cases

Digital papillary adenocarcinoma (DPA) is a rare sweat gland neoplasm that has exceptionally been reported outside acral locations. Recently, human papillomavirus 42 was identified as the main oncogenic driver of DPA. Herein, we report 5 tumors arising in extra-acral locations predominantly in the female anogenital skin. Four patients were female and 1 patient was male. The mean age at the diagnosis time was 65 years (range: 55 to 82 y). Tumors were located on the vulva (n=3), perianal area (n=1), and forearm (n=1). Histologically, all tumors were lobular and mainly solid and composed of sheets of cells with rare focal papillae and frequent glandular structures in a "back-to-back" pattern and lined by atypical basophilic cells. Immunohistochemistry showed diffuse positivity for SOX10. Epithelial membrane antigen and carcinoembryonic antigen highlighted the luminal cells and staining for p63 and p40 revealed a consistent and continuous myoepithelial component around glandular structures. Follow-up was available in 3 cases (mean duration: 12 mo [range: 8 to 16 mo]). One patient developed local recurrence and 1 experienced regional lymph node metastases. HPV Capture Next-generation sequencing revealed the presence of the HPV42 genome in all samples. Viral reads distributions were compatible in the 5 cases with an episomal nature of the viral genome, with a recurrent deletion in the E1 and/or E2 open reading frames. In conclusion, this study demonstrates that digital DPA may rarely present in nonacral locations mainly in the female anogenital area, usually with a more solid pattern as compared with those cases presenting on the digits and it is also associated with HPV42.

HPV prevalence and genotype distribution among 38 056 women in Weifang, China: a cross-sectional study

OBJECTIVES

Human papillomavirus (HPV) infection is closely associated with cervical cancer, especially the persistent infection of high-risk HPV (HR-HPV) genotypes. Therefore, investigating the HPV prevalence, age-specific, genotype distribution and the impact of the COVID-19 pandemic among large populations was essential for HPV screening and optimising vaccination.

DESIGN

This was a cross-sectional study.

METHODS

A total of 38 056 cervical epithelial cell specimens were collected in Weifang city from January 2018 to December 2022. The study was divided into seven age groups based on the age of the participants. HPV genotype testing was performed by using a commercial kit which is designed for the detection of 23 HPV genotypes.

RESULT

A total of 8998 women were infected with HPV, with an overall positive rate of 23.64% (8998/38 056). Single infection of HPV was dominant among different age groups, which accounted for 71.33% of total infections. The most prevalent genotype was HR-HPV 16 (4.33%), followed by 52, 58, 53 and 68. Low-risk HPV (LR-HPV) 42 exhibited the highest prevalence (2.19%) among six LR-HPV genotypes, representing a novel finding. There was a significant difference in the prevalence across different age groups (p<0.01), with the highest prevalence in the group under 25 years old. During the 3 year COVID-19 breakout period, the number of HPV samples received in 2020, 2021 and 2022 was reduced by 24.03%, 14.79% and 24.76%, respectively. In 2018-2022, the annual prevalence varied between 21.09% and 25.30%, with a decreasing trend, while the prevalence of HR-HPV 39, 56, 31 and LR-HPV 42 increased.

CONCLUSION

This study indicates a high-HPV infection rate and age-specific distribution characteristics of HPV genotype infections, as well as analyses of the impact of the COVID-19 outbreak on the HPV prevalence, which provides an epidemiological basis for the control and prevention of HPV infection in this region.

A nodular lesion on a finger: an unusual site for a cyst

We report a greyish nodule on the pad of the second finger of the right hand. High-resolution ultrasound showed a predominantly cystic lesion with an intralesional peripheral solid component with a mamelonated pseudonodular appearance.

Genomic landscape of virus-associated cancers

It has been estimated that 15%-20% of human cancers are attributable to infections, mostly by carcinogenic viruses. The incidence varies worldwide, with a majority affecting developing countries. Here, we present a comparative analysis of virus-positive and virus-negative tumors in nine cancers linked to five viruses. We find that virus-positive tumors occur more frequently in males and show geographical disparities in incidence. Genomic analysis of 1,658 tumors reveals virus-positive tumors exhibit distinct mutation signatures and driver gene mutations and possess a lower somatic mutation burden compared to virus-negative tumors of the same cancer type. For example, compared to the respective virus-negative counterparts, virus-positive cases across different cancer histologies had less often mutations of TP53 and deletions of 9p21.3/ CDKN2 A- CDKN1A ; Epstein-Barr virus-positive (EBV+) gastric cancer had more frequent mutations of EIF4A1 and ARID1A and less marked mismatch repair deficiency signatures; and EBV-positive cHL had fewer somatic genetic lesions of JAK-STAT, NF-κB, PI3K-AKT and HLA-I genes and a less pronounced activity of the aberrant somatic hypermutation signature. In cHL, we also identify germline homozygosity in HLA class I as a potential risk factor for the development of EBV-positive Hodgkin lymphoma. Finally, an analysis of clinical trials of PD-(L)1 inhibitors in four virus-associated cancers suggested an association of viral infection with higher response rate in patients receiving such treatments, which was particularly evident in gastric cancer and head and neck squamous cell carcinoma. These results illustrate the epidemiological, genetic, prognostic, and therapeutic trends across virus-associated malignancies.

Serial Genotyping of the Human Papillomavirus in Cervical Cancer: An Insight Into Virome Dynamics During Chemoradiation Therapy

PURPOSE

Human papillomavirus (HPV) is the primary driver of cervical cancer. Although studies in other malignancies correlated peripheral blood DNA clearance with favorable outcomes, research on the prognostic value of HPV clearance in gynecologic cancers using intratumoral HPV is scarce. We aimed to quantify the intratumoral HPV virome in patients undergoing chemoradiation therapy (CRT) and associate this with clinical characteristics and outcomes.

METHODS AND MATERIALS

This prospective study enrolled 79 patients with stage IB-IVB cervical cancer undergoing definitive CRT. Cervical tumor swabs collected at baseline and week 5 (end of intensity modulated radiation therapy) were sent for shotgun metagenome sequencing and processed via VirMAP, a viral genome sequencing and identification tool for all known HPV types. The data were categorized into HPV groups (16, 18, high risk [HR], and low risk [LR]). We used independent t tests and Wilcoxon signed-rank to compare continuous variables and χ² and Fisher exact tests to compare categorical variables. Kaplan-Meier survival modeling was performed with log-rank testing. HPV genotyping was verified using quantitative polymerase chain reaction to validate VirMAP results using receiver operating characteristic curve and Cohen's kappa.

RESULTS

At baseline, 42%, 12%, 25%, and 16% of patients were positive for HPV 16, HPV 18, HPV HR, and HPV LR, respectively, and 8% were HPV negative. HPV type was associated with insurance status and CRT response. Patients with HPV 16+ and other HPV HR+ tumors were significantly more likely to have a complete response to CRT versus patients with HPV 18 and HPV LR/HPV-negative tumors. Overall HPV viral loads predominantly decreased throughout CRT, except for HPV LR viral load.

CONCLUSIONS

Rarer, less well-studied HPV types in cervical tumors are clinically significant. HPV 18 and HPV LR/negative tumors are associated with poor CRT response. This feasibility study provides a framework for a larger study of intratumoral HPV profiling to predict outcomes in patients with cervical cancer.