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Hong Z, Xiong J, Yang H, Mo YK. Lightweight Low-Rank Adaptation Vision Transformer Framework for Cervical Cancer Detection and Cervix Type Classification. Bioengineering (Basel) 2024; 11:468. [PMID: 38790335 PMCID: PMC11118906 DOI: 10.3390/bioengineering11050468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Cervical cancer is a major health concern worldwide, highlighting the urgent need for better early detection methods to improve outcomes for patients. In this study, we present a novel digital pathology classification approach that combines Low-Rank Adaptation (LoRA) with the Vision Transformer (ViT) model. This method is aimed at making cervix type classification more efficient through a deep learning classifier that does not require as much data. The key innovation is the use of LoRA, which allows for the effective training of the model with smaller datasets, making the most of the ability of ViT to represent visual information. This approach performs better than traditional Convolutional Neural Network (CNN) models, including Residual Networks (ResNets), especially when it comes to performance and the ability to generalize in situations where data are limited. Through thorough experiments and analysis on various dataset sizes, we found that our more streamlined classifier is highly accurate in spotting various cervical anomalies across several cases. This work advances the development of sophisticated computer-aided diagnostic systems, facilitating more rapid and accurate detection of cervical cancer, thereby significantly enhancing patient care outcomes.
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Affiliation(s)
- Zhenchen Hong
- Department of Physics and Astronomy, University of California, Riverside, CA 92521, USA
| | - Jingwei Xiong
- Graduate Group in Biostatistics, University of California, Davis, CA 95616, USA
| | - Han Yang
- Department of Chemistry, Columbia University, New York, NY 10027, USA;
| | - Yu K. Mo
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA;
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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2
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Siqueira JD, Alves BM, Castelo Branco AB, Duque KC, Bustamante-Teixeira MT, Soares EA, Levi JE, Azevedo e Silva G, Soares MA. Comparison of four different human papillomavirus genotyping methods in cervical samples: Addressing method-specific advantages and limitations. Heliyon 2024; 10:e25474. [PMID: 38327440 PMCID: PMC10847660 DOI: 10.1016/j.heliyon.2024.e25474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/05/2023] [Accepted: 01/28/2024] [Indexed: 02/09/2024] Open
Abstract
Since human papillomavirus (HPV) is recognized as the causative agent of cervical cancer and associated with anogenital non-cervical and oropharyngeal cancers, the characterization of the HPV types circulating in different geographic regions is an important tool in screening and prevention. In this context, this study compared four methodologies for HPV detection and genotyping: real-time PCR (Cobas® HPV test), nested PCR followed by conventional Sanger sequencing, reverse hybridization (High + Low PapillomaStrip® kit) and next-generation sequencing (NGS) at an Illumina HiSeq2500 platform. Cervical samples from patients followed at the Family Health Strategy from Juiz de Fora, Minas Gerais, Brazil, were collected and subjected to the real-time PCR. Of those, 114 were included in this study according to the results obtained with the real-time PCR, considered herein as the gold standard method. For the 110 samples tested by at least one methodology in addition to real-time PCR, NGS showed the lowest concordance rates of HPV and high-risk HPV identification compared to the other three methods (67-75 %). Real-time PCR and Sanger sequencing showed the highest rates of concordance (97-100 %). All methods differed in their sensitivity and specificity. HPV genotyping contributes to individual risk stratification, therapeutic decisions, epidemiological studies and vaccine development, supporting approaches in prevention, healthcare and management of HPV infection.
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Affiliation(s)
- Juliana D. Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Brunna M. Alves
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | | | - Kristiane C.D. Duque
- Diretoria de Ensino, Pesquisa e Extensão, Instituto Federal de Santa Catarina, Joinville, SC, Brazil
| | | | - Esmeralda A. Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - José Eduardo Levi
- Instituto de Medicina Tropical de São Paulo Medical School, Universidade de São Paulo, São Paulo, Brazil
- Pesquisa e Desenvolvimento, Dasa Laboratories, Barueri, SP, Brazil
| | - Gulnar Azevedo e Silva
- Departamento de Epidemiologia, Instituto de Medicina Social, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Marcelo A. Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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3
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Cancela F, Marandino A, Panzera Y, Betancour G, Mirazo S, Arbiza J, Ramos N. A combined approach of rolling-circle amplification-single site restriction endonuclease digestion followed by next generation sequencing to characterize the whole genome and intra-host variants of human Torque teno virus. Virus Res 2023; 323:198974. [PMID: 36272542 PMCID: PMC10194382 DOI: 10.1016/j.virusres.2022.198974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
Torque Teno Virus (TTV) was initially associated with post-transfusion hepatitis, but growing evidence of its ubiquity in humans is compatible to no apparent clinical significance. TTV is a small non-enveloped virus with a circular single-negative-stranded DNA genome, belonging to the Anelloviridae family. Currently, TTVs are divided in seven phylogenetic groups and are further classified into 21 species. Studies about diversity of TTV in different conditions are receiving increasing interest and in this sense, sequencing of whole genomes for better genetic characterization becomes even more important. Since its discovery in 1997, few TTV complete genomes have been reported worldwide. This is probably due, among other reasons, to the great genetic heterogeneity among TTV strains that prevents its amplification and sequencing by conventional PCR and cloning methods. In addition, although metagenomics approach is useful in these cases, it remains a challenging tool for viromic analysis. With the aim of contributing to the expansion of the TTV whole genomes dataset and to study intra-host variants, we employed a methodology that combined a rolling-circle amplification approach followed by EcoRI digestion, generating a DNA fragment of ∼4Kb consistent with TTV genome length which was sequenced by Illumina next generation sequencing. A genogroup 3 full-length consensus TTV genome was obtained and co-infection with other species (at least those with a single EcoRI cleavage site) was not identified. Additionally, bioinformatics analysis allowed to identify the spectrum of TTV intra-host variants which provides evidence of a complex evolution dynamics of these DNA circular viruses, similarly to what occurs with RNA viruses.
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Affiliation(s)
- Florencia Cancela
- Sección Virología, Instituto de Biología e Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay
| | - Yanina Panzera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay
| | - Gabriela Betancour
- Sección Virología, Instituto de Biología e Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Santiago Mirazo
- Sección Virología, Instituto de Biología e Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay; Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la Republica, Montevideo, Uruguay
| | - Juan Arbiza
- Sección Virología, Instituto de Biología e Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Ramos
- Sección Virología, Instituto de Biología e Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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4
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Basiletti JA, Valls J, Poklépovich T, Fellner MD, Rol M, Alonso R, Correa RM, Colucci MC, Rodríguez de la Peña M, Falabella PG, Saíno A, Campos J, Herrero R, Almonte M, Picconi MA. Human papillomavirus genotyping using next generation sequencing (NGS) in cervical lesions: Genotypes by histologic grade and their relative proportion in multiple infections. PLoS One 2022; 17:e0278117. [PMID: 36417453 PMCID: PMC9683586 DOI: 10.1371/journal.pone.0278117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022] Open
Abstract
Sensitive and specific genotyping of human papillomaviruses (HPVs) is critical for the surveillance and monitoring of the vaccine effectiveness. Here, HPV genotypes were identified in 137 cervical samples with different histology (79 ≤CIN1 and 58 CIN3+) using Nested-PCR followed by Next-Generation sequencing (NGS) and relative proportions for each genotype in multiple infections were computed. All samples had been previously genotyped by PCR-Reverse Blotting Hybridization (PCR-RBH) thus allowing for a concordance analysis between both techniques. Multiple infections were present in 85% of ≤CIN1 cases compared to only 41% in CIN3+ cases (p<0.001). Among ≤CIN1 cases a towering genotypic diversity was observed, considering both low (LR-) and high risk (HR-) HPV genotypes; while among CIN3+, diversity was lower, HR-HPVs prevailing in most cases, especially HPV16. Furthermore, the predominance of HR-HPV genotypes in the proportions identified in each sample was higher in CIN3+ cases [(HPV16 (62.5%), followed by HPV31 and HPV58 (8.3% each)], than in ≤CIN1 cases [(HPV16 (17.7%), followed by HPV52 (14.7%) and HPV31 (10.3%)]. Agreement between PCR-RBH and NGS was higher than 90% for all genotypes (with an overall Kappa of 0.7), even though NGS identified eighty-nine positive results for HPV genotypes that had not been detected by PCR-RBH, evidencing its greater sensitivity. These results suggest that a reduction in genotypic diversity and/or an increase in the relative proportion of HR-HPVs in multiple infections can be considered as a biomarker for the potential risk of malignant progression.
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Affiliation(s)
- Jorge Alejandro Basiletti
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | - Joan Valls
- Early Detection, Prevention & Infection Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Tomás Poklépovich
- Unidad Operativa Centro de Genómica y Bioinformática, ANLIS "Dr. Malbrán", Buenos Aires, Argentina
| | - María Dolores Fellner
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | - Maryluz Rol
- Early Detection, Prevention & Infection Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Rafael Alonso
- Departamento de Métodos Cuantitativos, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rita Mariel Correa
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | - María Celeste Colucci
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
| | | | - Paula Gabriela Falabella
- Servicio de Ginecología, Hospital Nacional “Prof. Posadas”, El Palomar, Provincia de Buenos Aires, Argentina
| | - Agustina Saíno
- Servicio de Anatomía Patológica, Hospital Nacional “Prof. Posadas”, El Palomar, Provincia de Buenos Aires, Argentina
| | - Josefina Campos
- Unidad Operativa Centro de Genómica y Bioinformática, ANLIS "Dr. Malbrán", Buenos Aires, Argentina
| | - Rolando Herrero
- Agencia Costarricense de Investigaciones Biomédicas, San José, Costa Rica
| | - Maribel Almonte
- Early Detection, Prevention & Infection Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - María Alejandra Picconi
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas-ANLIS “Dr. Malbrán”, Buenos Aires, Argentina
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5
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Correa RM, Baena A, Valls J, Colucci MC, Mendoza L, Rol M, Wiesner C, Ferrera A, Fellner MD, González JV, Basiletti JA, Mongelos P, Rodriguez de la Peña M, Saino A, Kasamatsu E, Velarde C, Macavilca N, Martinez S, Venegas G, Calderón A, Rodriguez G, Barrios H, Herrero R, Almonte M, Picconi MA. Distribution of human papillomavirus genotypes by severity of cervical lesions in HPV screened positive women from the ESTAMPA study in Latin America. PLoS One 2022; 17:e0272205. [PMID: 35905130 PMCID: PMC9337688 DOI: 10.1371/journal.pone.0272205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/15/2022] [Indexed: 11/27/2022] Open
Abstract
The proportion of HPV16 and 18-associated cervical cancer (CC) appears rather constant worldwide (≥70%), but the relative importance of the other HR-HPV differs slightly by geographical region. Here, we studied the HPV genotype distribution of HPV positive Latin American (LA) women by histological grade, in a sub-cohort from the ESTAMPA study; we also explored the association of age-specific HPV genotypes in severe lesions. Cervical samples from 1,252 participants (854 ≤CIN1, 121 CIN2, 194 CIN3 and 83 CC) were genotyped by two PCRs-Reverse Blotting Hybridization strategies: i) Broad-Spectrum General Primers 5+/6+ and ii) PGMY9/11 PCRs. HPV16 was the most frequently found genotype in all histological grades, and increased with the severity of lesions from 14.5% in ≤ CIN1, 19.8% in CIN2, 51.5% in CIN3 to 65.1% in CC (p < 0.001). For the remaining HR-HPVs their frequency in CC did not increase when compared to less severe categories. The nonavalent vaccine HR-types ranked at the top in CC, the dominant ones being HPV16 and HPV45. HR-HPV single infection occurs, respectively, in 57.1% and 57.0% of ≤CIN1 and CIN2, increasing to 72.2% and 91.6% in CIN3 and CC (p<0.001). No association between age and HPV type was observed in CC, although the risk of HPV16 infection in CIN3 cases increased with age. Results confirm the relevance of HPV16 in the whole clinical spectrum, with a strong rise of its proportion in CIN3 and cancer. This information will be relevant in evaluating the impact of HPV vaccination, as a baseline against which to compare genotype changes in HPV type-specific distribution as vaccinated women participate in screening in LA region. Likewise, these data may help select the best HPV testing system for HPV-based efficient, affordable, and sustainable screening programmes.
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Affiliation(s)
- Rita Mariel Correa
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas- ANLIS "Dr. Malbrán", Buenos Aires, Argentina
| | - Armando Baena
- Early Detection, Prevention & Infections Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Joan Valls
- Early Detection, Prevention & Infections Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - María Celeste Colucci
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas- ANLIS "Dr. Malbrán", Buenos Aires, Argentina
| | - Laura Mendoza
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay, San Lorenzo, Paraguay
| | - Maryluz Rol
- Early Detection, Prevention & Infections Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Annabelle Ferrera
- Instituto de Investigaciones en Microbiología, Universidad Nacional Autónoma de Honduras, Tagucigalpa, Honduras
| | - María Dolores Fellner
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas- ANLIS "Dr. Malbrán", Buenos Aires, Argentina
| | - Joaquín Víctor González
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas- ANLIS "Dr. Malbrán", Buenos Aires, Argentina
| | - Jorge Alejandro Basiletti
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas- ANLIS "Dr. Malbrán", Buenos Aires, Argentina
| | - Pamela Mongelos
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay, San Lorenzo, Paraguay
| | | | - Agustina Saino
- Sección Histología, Servicio Anatomía Patológica, Hospital Nacional “Prof. Posadas”, El Palomar, Argentina
| | - Elena Kasamatsu
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay, San Lorenzo, Paraguay
| | - Carlos Velarde
- Instituto Nacional de Enfermedades Neoplásicas, Surquillo, Perú
| | | | | | | | - Alejandro Calderón
- Caja Costarricense de Seguro Social, Región Pacífico Central, San José, Costa Rica
| | | | - Hernán Barrios
- Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, San Lorenzo, Paraguay, San Lorenzo, Paraguay
| | - Rolando Herrero
- Agencia Costarricense de Investigaciones Biomédicas, San José, Costa Rica
| | - Maribel Almonte
- Early Detection, Prevention & Infections Branch, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - María Alejandra Picconi
- Servicio Virus Oncogénicos, Laboratorio Nacional y Regional de Referencia de HPV, Instituto Nacional de Enfermedades Infecciosas- ANLIS "Dr. Malbrán", Buenos Aires, Argentina
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Shen-Gunther J, Cai H, Wang Y. HPV Integration Site Mapping: A Rapid Method of Viral Integration Site (VIS) Analysis and Visualization Using Automated Workflows in CLC Microbial Genomics. Int J Mol Sci 2022; 23:ijms23158132. [PMID: 35897706 PMCID: PMC9331699 DOI: 10.3390/ijms23158132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023] Open
Abstract
Human papillomavirus (HPV) integration within the host genome may contribute to carcinogenesis through various disruptive mechanisms. With next-generation sequencing (NGS), identification of viral and host genomic breakpoints and chimeric sequences are now possible. However, a simple, streamlined bioinformatics workflow has been non-existent until recently. Here, we tested two new, automated workflows in CLC Microbial Genomics, i.e., Viral Hybrid Capture (VHC) Data Analysis and Viral Integration Site (VIS) Identification for software performance and efficiency. The workflows embedded with HPV and human reference genomes were used to analyze a publicly available NGS dataset derived from pre- and cancerous HPV+ cervical cytology of 21 Gabonese women. The VHC and VIS workflow median runtimes were 19 and 7 min per sample, respectively. The VIS dynamic graphical outputs included read mappings, virus-host genomic breakpoints, and virus-host integration circular plots. Key findings, including disrupted and nearby genes, were summarized in an auto-generated report. Overall, the VHC and VIS workflows proved to be a rapid and accurate means of localizing viral-host integration site(s) and identifying disrupted and neighboring human genes. Applying HPV VIS-mapping to pre- or invasive tumors will advance our understanding of viral oncogenesis and facilitate the discovery of prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX 78234, USA
- Correspondence: (J.S.-G.); (Y.W.)
| | - Hong Cai
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Yufeng Wang
- Department of Molecular Microbiology and Immunology, University of Texas at San Antonio, San Antonio, TX 78249, USA;
- South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA
- Correspondence: (J.S.-G.); (Y.W.)
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HPV DeepSeq: An Ultra-Fast Method of NGS Data Analysis and Visualization Using Automated Workflows and a Customized Papillomavirus Database in CLC Genomics Workbench. Pathogens 2021; 10:pathogens10081026. [PMID: 34451490 PMCID: PMC8398645 DOI: 10.3390/pathogens10081026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) has actualized the human papillomavirus (HPV) virome profiling for in-depth investigation of viral evolution and pathogenesis. However, viral computational analysis remains a bottleneck due to semantic discrepancies between computational tools and curated reference genomes. To address this, we developed and tested automated workflows for HPV taxonomic profiling and visualization using a customized papillomavirus database in the CLC Microbial Genomics Module. HPV genomes from Papilloma Virus Episteme were customized and incorporated into CLC “ready-to-use” workflows for stepwise data processing to include: (1) Taxonomic Analysis, (2) Estimate Alpha/Beta Diversities, and (3) Map Reads to Reference. Low-grade (n = 95) and high-grade (n = 60) Pap smears were tested with ensuing collective runtimes: Taxonomic Analysis (36 min); Alpha/Beta Diversities (5 s); Map Reads (45 min). Tabular output conversion to visualizations entailed 1–2 keystrokes. Biodiversity analysis between low- (LSIL) and high-grade squamous intraepithelial lesions (HSIL) revealed loss of species richness and gain of dominance by HPV-16 in HSIL. Integrating clinically relevant, taxonomized HPV reference genomes within automated workflows proved to be an ultra-fast method of virome profiling. The entire process named “HPV DeepSeq” provides a simple, accurate and practical means of NGS data analysis for a broad range of applications in viral research.
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Shen-Gunther J, Xia Q, Stacey W, Asusta HB. Molecular Pap Smear: Validation of HPV Genotype and Host Methylation Profiles of ADCY8, CDH8, and ZNF582 as a Predictor of Cervical Cytopathology. Front Microbiol 2020; 11:595902. [PMID: 33178175 PMCID: PMC7593258 DOI: 10.3389/fmicb.2020.595902] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/22/2020] [Indexed: 12/16/2022] Open
Abstract
Primary high-risk Human Papillomavirus (hrHPV) screening has recently become an accepted standalone or co-test with conventional cytology. Unfortunately, hrHPV singularly lacks specificity for cytopathological grade. However, mechanisms and markers of evolving virus-host interactions at the epigenome level may be harnessed as a better predictor of carcinogenesis. This study aimed to validate and expand the clinical performance of a multiparametric biomarker panel, referred to as the "Molecular Pap smear" based, on HPV genotype and ADCY8, CDH8 and ZNF582 CpG-methylation as a predictive classifier of cervical cytology. This prospective, cross-sectional study used an independent cohort of residual liquid-based cytology for HPV genotyping and epigenetic analysis. Extracted DNA underwent parallel PCR using 3 primer sets for HPV DNA amplification. HPV-infected samples were genotyped by Sanger sequencing. Promoter methylation levels of 3 tumor suppressor genes were quantified by bisulfite-pyrosequencing of genomic DNA on the newest high-resolution PyroMark Q48 platform. Logistic model performance was compared, and model parameters were used to predict and classify binary cytological outcomes. A total of 883 samples were analyzed. HPV DNA positivity correlated with worsening grade: 125/237 (53%) NILM; 136/235 (58%) ASCUS; 222/229 (97%) LSIL; and 157/182 (86%) HSIL samples. The proportion of carcinogenic HPV-types in PCR-positive sequenceable samples correlated with worsening grade: NILM 34/98 (35%); ASCUS 50/113 (44%); LSIL 92/214 (43%); HSIL 129/152 (85%). Additionally, ADCY8, CDH8, and ZNF582 methylation levels increased in direct correlation with worsening grade. Overall, the multi-marker modeling parameters predicted binarized cytological outcomes better than HPV-type alone with significantly higher area under the receiver operator curve (AUC)s, respectively: NILM vs. > NILM (AUC 0.728 vs. 0.709); NILM/ASCUS vs. LSIL/HSIL (AUC 0.805 vs. 0.776); and
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology & Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX, United States
- Department of Molecular Medicine, Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Qingqing Xia
- Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX, United States
| | - Winfred Stacey
- Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX, United States
| | - Heisy B. Asusta
- Department of Obstetrics and Gynecology, Brooke Army Medical Center, Fort Sam Houston, TX, United States
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Karbalaie Niya MH, Mobini Kesheh M, Keshtmand G, Basi A, Rezvani H, Imanzade F, Panahi M, Rakhshani N. Integration rates of human papilloma virus genome in a molecular survey on cervical specimens among Iranian patients. Eur J Cancer Prev 2020; 28:537-543. [PMID: 30444753 DOI: 10.1097/cej.0000000000000498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The human papilloma virus (HPV) as a major causative agent of different cancers is under investigation globally. In this study, we aim to investigate HPV infection in different cytological and pathological stages by different molecular methods, and then the viral genome integration of HPV-16 and -18 is determined by a specific real-time PCR method. The study included women who underwent liquid-based cytology. HPV PCR was conducted by MY09/11 universal primers, HPV genotyping was performed by INNO-LiPA HPV genotyping assay, and the viral genome status was defined by two real-time PCR assays. The statistics were calculated by SPSS v.22 software. In 1668 women included in the study with mean age±std. deviation of 35.6±0.7, HPV was detected in 632 (38%) participants. Following genotyping analyses, 16 HPV types and 713 strains were detected. HPV-16 and HPV-18 from high-risk types and HPV-6 and HPV-11 from low-risk types were the dominant types. We found HPV-16 strains in mixed form (58.8%), and of the HPV-18 strains, the episomal form was prevalent (92.9%). The statistics revealed significant presence of HPV-6 and within normal limits cases; HPV-16 and atypical squamous cells of undetermined significance; HPV-33 as well as HPV-39 and low-grade squamous intraepithelial lesion; HPV-6 and atypical squamous cells of undetermined significance; and HPV-35 as well as HPV-56 and squamous cell carcinoma. Our study showed high prevalence of HPV in low-grade cervical lesions, although it is associated with higher grades. The HPV molecular testing extra to cytology is recommended. HPV-16 and HPV-18 have different programs in genome integration in infected cells.
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Affiliation(s)
| | | | | | - Ali Basi
- Department of Hematology and Oncology, Iran University of Medical Sciences
| | | | - Farid Imanzade
- Pediatrics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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10
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Shen-Gunther J, Cai H, Zhang H, Wang Y. Abundance of HPV L1 Intra-Genotype Variants With Capsid Epitopic Modifications Found Within Low- and High-Grade Pap Smears With Potential Implications for Vaccinology. Front Genet 2019; 10:489. [PMID: 31231420 PMCID: PMC6558378 DOI: 10.3389/fgene.2019.00489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/06/2019] [Indexed: 12/12/2022] Open
Abstract
Background: The aim of this study was to explore the Human Papillomavirus (HPV) genotype composition and intra-genotype variants within individual samples of low- and high-grade cervical cytology by deep sequencing. Clinical, cytological, sequencing, and functional/structural data were forged into an integrated variant profiling pipeline for the detection of potentially vaccine-resistant genotypes or variants. Methods: Low- and high-grade intraepithelial lesion (LSIL and HSIL) cytology samples with +HPV were subjected to amplicon (L1 gene fragment) sequencing by dideoxy (Sanger) and deep methods. Taxonomic, abundance, diversity, and phylogenetic analyses were conducted to determine HPV genotypes/sub-lineages, relative abundance, species diversity and phylogenetic distances within and between samples. Variant detection and functional analysis of translated L1 amino acid sequences determined structural variations of interest. Results: Pure and mixed HPV infections were common among LSIL (n = 6) and HSIL (n = 6) samples. Taxonomic profiling revealed loss of species richness and gain of dominance by carcinogenic genotypes in HSIL samples. Phylogenetic analysis showed excellent correlation between HPV-type specific genetic distances and carcinogenic potential. For combined LSIL/HSIL samples (n = 12), 11 HPV genotypes and 417 mutations were detected: 375 single-nucleotide variants (SNV), 29 insertion/deletion (indel), 12 multi-nucleotide variants (MNV), and 1 replacement variant. The proportion of nonsynonymous mutations was lower for HSIL (0.38) than for LSIL samples (0.51) (p < 0.05). HPV variant analysis pinpointed nucleotide-level mutations and amino acid-level structural modifications. Conclusion: HPV L1 intra-host and intra-genotype variants are abundant in LSIL and HSIL samples with potential functional/structural consequences. An integrated multi-omics approach to variant analysis may provide a sensitive and practical means of detecting changes in HPV evolution and dynamics within individuals or populations.
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Affiliation(s)
- Jane Shen-Gunther
- Gynecologic Oncology and Clinical Investigation, Department of Clinical Investigation, Brooke Army Medical Center, Fort Sam Houston, TX, United States
| | - Hong Cai
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, United States
| | - Hao Zhang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States
| | - Yufeng Wang
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, United States.,South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, United States
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11
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Campos RG, Malacara Rosas A, Gutiérrez Santillán E, Delgado Gutiérrez M, Torres Orozco RE, García Martínez ED, Torres Bernal LF, Rosas Cabral A. Unusual prevalence of high-risk genotypes of human papillomavirus in a group of women with neoplastic lesions and cervical cancer from Central Mexico. PLoS One 2019; 14:e0215222. [PMID: 30998701 PMCID: PMC6474327 DOI: 10.1371/journal.pone.0215222] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/28/2019] [Indexed: 12/18/2022] Open
Abstract
Human papillomavirus has been identified as a main etiological agent in the
development of cervical cancer. HPV 16 and 18 have been reported the most widely
prevalent genotypes worldwide. We conducted a study analyzing the prevalence of
high and low risk human papillomavirus viral types in the Mexican state of
Aguascalientes and neighboring cities in the states of Jalisco and Zacatecas in
central Mexico. Specific viral genotype was determined by a PCR and
hybridization-based detection test. The presence of 37 high- and low-risk HPV
genotypes was evaluated in 883 female participants. Of these, 350 presented
low-grade squamous intraepithelial lesions (LGSIL), 176 presented high-grade
squamous intraepithelial lesions (HGSIL), 107 suffered from cervical cancer and
250 women with negative cytological report for intraepithelial lesion or
malignancy (NILM). HPV 51 was the most prevalent genotype, followed by HPV 16:
overall prevalence of HPV 51, including single infections and co-infections was
31.2% in women with LGSIL, whereas prevalence of HPV 16 was 25.1%. Among women
with HGSIL, HPV 51 prevalence was 47.2% and HPV 16 was 30.1%. Prevalence of HPV
51 in women with cervical cancer was 49.5% and type 16 was 33.6%. Between single
and co-infections, most co-infections were not associated with later stages of
the disease, except 51/16 and some others. HPV 51 showed a significant
correlation with the progression of the disease (OR = 10.81 for LGSIL, 19.38 for
HGSIL and 22.95 for ICC), and when analyzing all other genotypes, five different
groups depending on their correlation with all lesion grades were determined.
According to our findings, HPV genotype 51 has a higher prevalence than HPV 16
and 18 in the Mexican state of Aguascalientes and neighboring cities in the
states of Jalisco and Zacatecas in Central Mexico.
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Affiliation(s)
- Rafael Gutiérrez Campos
- Department of Chemistry, Center for Basic Sciences, Autonomous University
of Aguascalientes, Aguascalientes, Aguascalientes, México
- * E-mail:
| | - Angélica Malacara Rosas
- Department of Chemistry, Center for Basic Sciences, Autonomous University
of Aguascalientes, Aguascalientes, Aguascalientes, México
| | - Elvia Gutiérrez Santillán
- Hospital General de Zona Número 6, Instituto Mexicano del Seguro Social,
Monterrey, Nuevo León, México
| | - Mireya Delgado Gutiérrez
- Hospital General de Zona Número 1, Instituto Mexicano del Seguro Social,
Aguascalientes, Aguascalientes, México
| | - Rusland Enrique Torres Orozco
- Department of Chemistry, Center for Basic Sciences, Autonomous University
of Aguascalientes, Aguascalientes, Aguascalientes, México
| | - Elí Daniel García Martínez
- Department of Chemistry, Center for Basic Sciences, Autonomous University
of Aguascalientes, Aguascalientes, Aguascalientes, México
| | - Luis Fernando Torres Bernal
- Department of Medicine, Center for Health Sciences, Autonomous University
of Aguascalientes, Aguascalientes, México
| | - Alejandro Rosas Cabral
- Department of Medicine, Center for Health Sciences, Autonomous University
of Aguascalientes, Aguascalientes, México
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12
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Lin M, Ye M, Zhou J, Wang ZP, Zhu X. Recent Advances on the Molecular Mechanism of Cervical Carcinogenesis Based on Systems Biology Technologies. Comput Struct Biotechnol J 2019; 17:241-250. [PMID: 30847042 PMCID: PMC6389684 DOI: 10.1016/j.csbj.2019.02.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/29/2019] [Accepted: 02/01/2019] [Indexed: 02/06/2023] Open
Abstract
Cervical cancer is one of the common malignancies in women worldwide. Exploration of pathogenesis and molecular mechanism of cervical cancer is pivotal for development of effective treatment for this disease. Recently, systems biology approaches based on high-throughput technologies have been carried out to investigate the expression of some genes and proteins in genomics, transcriptomics, proteomics, and metabonomics of cervical cancer. Compared with traditional methods,systems biology technology has been shown to provide large of information regarding prognostic biomarkers and therapeutic targets for cervical cancer. These molecular signatures from system biology technology could be useful to understand the molecular mechanisms of cervical cancer development and progression, and help physicians to design targeted therapeutic strategies for patients with cervical cancer.
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Affiliation(s)
- Min Lin
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Miaomiao Ye
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Junhan Zhou
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Z Peter Wang
- Center of Scientific Research, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China.,Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xueqiong Zhu
- Departmant of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
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13
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Savini F, Gallina L, Mazza F, Mariella J, Castagnetti C, Scagliarini A. Molecular Detection of Bovine Papillomavirus DNA in the Placenta and Blood of Healthy Mares and Respective Foals. Vet Sci 2019; 6:vetsci6010014. [PMID: 30736349 PMCID: PMC6466198 DOI: 10.3390/vetsci6010014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/24/2019] [Accepted: 02/03/2019] [Indexed: 12/26/2022] Open
Abstract
Despite the characteristic species specificity of Papillomaviruses (PVs), the bovine papillomavirus (BPV) types 1, 2, and-more rarely-13, can cross-infect equids, where they are involved in the pathogenesis of sarcoid neoplasms. Sarcoids are locally invasive fibroblastic skin tumors that represent the most common skin neoplasms in horses worldwide. The transmission mechanism of BPV is still controversial in horses. Thus far, direct and indirect routes have been implicated, while vertical transmission has been suggested after the detection of viral DNA in the semen of healthy stallions. Testing of the blood and placenta of non-sarcoid baring mares and their respective foals revealed that the equine placenta can harbor BPV DNA, leading us to speculate a possible prenatal vertical DNA transmission in equids.
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Affiliation(s)
- Federica Savini
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50 Ozzano Emilia, Bologna 40064, Italy.
| | - Laura Gallina
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50 Ozzano Emilia, Bologna 40064, Italy.
| | - Francesca Mazza
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50 Ozzano Emilia, Bologna 40064, Italy.
| | - Jole Mariella
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50 Ozzano Emilia, Bologna 40064, Italy.
| | - Carolina Castagnetti
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50 Ozzano Emilia, Bologna 40064, Italy.
| | - Alessandra Scagliarini
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 50 Ozzano Emilia, Bologna 40064, Italy.
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14
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Yang B, Zhang L, Zhang A, Zhou A, Yuan J, Wang Y, Sun L, Cao H, Zheng W. Variant sublineages of human papillomavirus type 16 predispose women to persistent infection characterized by a sequence analysis of the E6, L1, and LCR regions. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2019; 12:337-343. [PMID: 31933750 PMCID: PMC6943999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 10/22/2018] [Indexed: 06/10/2023]
Abstract
BACKGROUND One of the precursors of cervical cancer is persistent infection with human papillomavirus (HPV), especially high-risk HPV. The aim of this study was to verify the relationship between HPV16 variants and persistent viral infection. METHODS Three-hundred and eighty-six Chinese women who had a low-grade squamous intraepithelial lesion (LSIL) or a lesion below LSIL with normal cellular morphology were selected and enrolled in this study. Flow-through hybridization and gene chip technology were applied to identify the HPV type, and a PCR-sequencing assay was performed to detect HPV16 E6, L1, and long control region (LCR) gene variants. The relationship between HPV16 variants and persistent infection was analyzed using Fisher's exact test. RESULTS In this population, 74.09% of HPV16 isolates belonged to the A4 sublineage, 24.87% to the A1/A2 sublineages, and 3.13% to B1/B2 sublineages. In addition, the A4 sublineage T178G (P<0.001) and the A1/A2 sublineages T350G and A442C (P<0.001) were associated with persistent HPV16 infection. L1 and LCR variants were found to be common in this population. Nonetheless, no significant relation was identified between the L1 or LCR variants and the persistence of infection (P>0.05). CONCLUSION HPV16 E6 variants in the Shanghai Pudong District mainly belong to the A4 sublineage, and detection of the specific HPV E6 T178G genotype may be considered a risk factor for viral persistence and progression to other cervical diseases.
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Affiliation(s)
- Binlie Yang
- Department of Obstetrics and Gynecology, Shanghai Pudong New Area People’s HospitalShanghai, China
| | - Lei Zhang
- Department of Obstetrics and Gynecology, Shanghai Pudong New Area People’s HospitalShanghai, China
| | - Ai Zhang
- Department of Obstetrics and Gynecology, Shanghai Pudong New Area People’s HospitalShanghai, China
| | - Aizhi Zhou
- Department of Obstetrics and Gynecology, Shanghai Pudong New Area People’s HospitalShanghai, China
| | - Jieyan Yuan
- Department of Obstetrics and Gynecology, Shanghai Pudong New Area People’s HospitalShanghai, China
| | - Yuhua Wang
- Department of Obstetrics and Gynecology, Shanghai Pudong New Area People’s HospitalShanghai, China
| | - Liyan Sun
- Department of Obstetrics and Gynecology, Shanghai Pudong New Area People’s HospitalShanghai, China
| | - Huimin Cao
- Department of Obstetrics and Gynecology, Shanghai Pudong New Area People’s HospitalShanghai, China
| | - Wenxin Zheng
- Department of Pathology, University of Texas Southwestern Medical Center DallasTX, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center DallasTX, USA
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15
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Murall CL, Jackson R, Zehbe I, Boulle N, Segondy M, Alizon S. Epithelial stratification shapes infection dynamics. PLoS Comput Biol 2019; 15:e1006646. [PMID: 30673699 PMCID: PMC6361466 DOI: 10.1371/journal.pcbi.1006646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/04/2019] [Accepted: 11/16/2018] [Indexed: 02/07/2023] Open
Abstract
Infections of stratified epithelia contribute to a large group of common diseases, such as dermatological conditions and sexually transmitted diseases. To investigate how epithelial structure affects infection dynamics, we develop a general ecology-inspired model for stratified epithelia. Our model allows us to simulate infections, explore new hypotheses and estimate parameters that are difficult to measure with tissue cell cultures. We focus on two contrasting pathogens: Chlamydia trachomatis and Human papillomaviruses (HPV). Using cervicovaginal parameter estimates, we find that key infection symptoms can be explained by differential interactions with the layers, while clearance and pathogen burden appear to be bottom-up processes. Cell protective responses to infections (e.g. mucus trapping) generally lowered pathogen load but there were specific effects based on infection strategies. Our modeling approach opens new perspectives for 3D tissue culture experimental systems of infections and, more generally, for developing and testing hypotheses related to infections of stratified epithelia.
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Affiliation(s)
| | - Robert Jackson
- Probe Development and Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, Ontario, Canada
- Biotechnology Program, Lakehead University, Thunder Bay, Ontario, Canada
| | - Ingeborg Zehbe
- Probe Development and Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, Ontario, Canada
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
| | - Nathalie Boulle
- Pathogenesis and Control of Chronic Infections, INSERM, EFS, Université de Montpellier, Montpellier, France
| | - Michel Segondy
- Pathogenesis and Control of Chronic Infections, INSERM, EFS, Université de Montpellier, Montpellier, France
| | - Samuel Alizon
- Laboratoire MIVEGEC (UMR CNRS 5290, IRD, UM), Montpellier, France
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16
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WYLIE KM, WYLIE TN, CAHILL AG, MACONES GA, TUULI MG, STOUT MJ. The vaginal eukaryotic DNA virome and preterm birth. Am J Obstet Gynecol 2018; 219:189.e1-189.e12. [PMID: 29738749 PMCID: PMC6066425 DOI: 10.1016/j.ajog.2018.04.048] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Despite decades of attempts to link infectious agents to preterm birth, an exact causative microbe or community of microbes remains elusive. Culture-independent sequencing of vaginal bacterial communities demonstrates community characteristics are associated with preterm birth, although none are specific enough to apply clinically. Viruses are important components of the vaginal microbiome and have dynamic relationships with vaginal bacterial communities. We hypothesized that vaginal eukaryotic DNA viral communities (the "vaginal virome") either alone or in the context of bacterial communities are associated with preterm birth. OBJECTIVE The objective of this study was to use high-throughput sequencing to examine the vaginal eukaryotic DNA virome in a cohort of pregnant women and examine associations between vaginal community characteristics and preterm birth. STUDY DESIGN This is a nested case-control study within a prospective cohort study of women with singleton pregnancies, not on supplemental progesterone, and without cervical cerclage in situ. Serial midvaginal swabs were obtained at routine prenatal visits. DNA was extracted, bacterial communities were characterized by 16S ribosomal RNA gene sequencing, and eukaryotic viral communities were characterized by enrichment of viral nucleic acid with the ViroCap targeted sequence capture panel followed by nucleic acid sequencing. Viral communities were analyzed according to presence/absence of viruses, diversity, dynamics over time, and association with bacterial community data obtained from the same specimens. RESULTS Sixty subjects contributed 128 vaginal swabs longitudinally across pregnancy. In all, 24 patients delivered preterm. Participants were predominantly African American (65%). Six families of eukaryotic DNA viruses were detected in the vaginal samples. At least 1 virus was detected in 80% of women. No specific virus or group of viruses was associated with preterm delivery. Higher viral richness was significantly associated with preterm delivery in the full group and in the African American subgroup (P = .0005 and P = .0003, respectively). Having both high bacterial diversity and high viral diversity in the first trimester was associated with the highest risk for preterm birth. CONCLUSION Higher vaginal viral diversity is associated with preterm birth. Changes in vaginal virome diversity appear similar to changes in the vaginal bacterial microbiome over pregnancy, suggesting that underlying physiology of pregnancy may regulate both bacterial and viral communities.
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Affiliation(s)
- Kristine M. WYLIE
- Department of Pediatrics, Washington University School of Medicine, St. Louis
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis
| | - Todd N. WYLIE
- Department of Pediatrics, Washington University School of Medicine, St. Louis
- The McDonnell Genome Institute, Washington University School of Medicine, St. Louis
| | - Alison G. CAHILL
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Washington University School of Medicine, St. Louis
| | - George A. MACONES
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Washington University School of Medicine, St. Louis
| | - Methodius G. TUULI
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Washington University School of Medicine, St. Louis
| | - Molly J. STOUT
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Washington University School of Medicine, St. Louis
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17
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Dube Mandishora RS, Gjøtterud KS, Lagström S, Stray-Pedersen B, Duri K, Chin'ombe N, Nygård M, Christiansen IK, Ambur OH, Chirenje MZ, Rounge TB. Intra-host sequence variability in human papillomavirus. PAPILLOMAVIRUS RESEARCH (AMSTERDAM, NETHERLANDS) 2018; 5:180-191. [PMID: 29723682 PMCID: PMC6047465 DOI: 10.1016/j.pvr.2018.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 03/14/2018] [Accepted: 04/27/2018] [Indexed: 11/20/2022]
Abstract
Human papillomaviruses (HPVs) co-evolve slowly with the human host and each HPV genotype displays epithelial tropisms. We assessed the evolution of intra HPV genotype variants within samples, and their association to anogenital site, cervical cytology and HIV status. Variability in the L1 gene of 35 HPV genotypes was characterized phylogenetically using maximum likelihood, and portrayed by phenotype. Up to a thousand unique variants were identified within individual samples. In-depth analyses of the most prevalent genotypes, HPV16, HPV18 and HPV52, revealed that the high diversity was dominated by a few abundant variants. This suggests high intra-host mutation rates. Clades of HPV16, HPV18 and HPV52 were associated to anatomical site and HIV co-infection. Particularly, we observed that one HPV16 clade was specific to vaginal cells and one HPV52 clade was specific to anal cells. One major HPV52 clade, present in several samples, was strongly associated with cervical neoplasia. Overall, our data suggest that tissue tropism and HIV immunosuppression are strong shapers of HPV evolution.
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Affiliation(s)
- Racheal S Dube Mandishora
- Department of Medical Microbiology, University of Zimbabwe College of Health Sciences, P.O Box A178, Avondale, Harare, Zimbabwe
| | - Kristina S Gjøtterud
- Department of Research, Cancer Registry of Norway, P.O. box 5313 Majorstuen, 0304 Oslo, Norway
| | - Sonja Lagström
- Department of Research, Cancer Registry of Norway, P.O. box 5313 Majorstuen, 0304 Oslo, Norway; Department of Microbiology and Infection Control, The Norwegian HPV Reference Laboratory, Akershus University Hospital, Sykehusveien 25, Lørenskog, Norway
| | - Babill Stray-Pedersen
- Women's clinic, Rikshospitalet, Oslo University Hospital and Institute of Clinical Medicine, P.O Box 4950 Nydalen, 0424 Oslo, Norway
| | - Kerina Duri
- Department of Immunology, University of Zimbabwe College of Health Sciences, P.O Box A178, Avondale, Harare, Zimbabwe
| | - Nyasha Chin'ombe
- Department of Medical Microbiology, University of Zimbabwe College of Health Sciences, P.O Box A178, Avondale, Harare, Zimbabwe
| | - Mari Nygård
- Department of Research, Cancer Registry of Norway, P.O. box 5313 Majorstuen, 0304 Oslo, Norway
| | - Irene Kraus Christiansen
- Department of Microbiology and Infection Control, The Norwegian HPV Reference Laboratory, Akershus University Hospital, Sykehusveien 25, Lørenskog, Norway
| | - Ole Herman Ambur
- Department of Microbiology and Infection Control, The Norwegian HPV Reference Laboratory, Akershus University Hospital, Sykehusveien 25, Lørenskog, Norway; Department of Life Sciences and Health, Oslo and Akershus University College of Applied Sciences, P.O Box 4 St. Olavs plass, N-0130 Oslo, Norway
| | - Mike Z Chirenje
- Department of Obstetrics and Gynaecology, University of Zimbabwe College of Health Sciences, Box A178, Avondale, Harare, Zimbabwe
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, P.O. box 5313 Majorstuen, 0304 Oslo, Norway.
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18
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Togtema M, Jackson R, Grochowski J, Villa PL, Mellerup M, Chattopadhyaya J, Zehbe I. Synthetic siRNA targeting human papillomavirus 16 E6: a perspective on in vitro nanotherapeutic approaches. Nanomedicine (Lond) 2018; 13:455-474. [PMID: 29382252 DOI: 10.2217/nnm-2017-0242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
High-risk human papillomaviruses infect skin and mucosa, causing approximately 5% of cancers worldwide. In the search for targeted nanotherapeutic approaches, siRNAs against the viral E6 transcript have been molecules of interest but have not yet seen successful translation into the clinic. By reviewing the past approximately 15 years of in vitro literature, we identify the need for siRNA validation protocols which concurrently evaluate ranges of key treatment parameters as well as characterize downstream process restoration in a methodical, quantitative manner and demonstrate their implementation using our own data. We also reflect on the future need for more appropriate cell culture models to represent patient lesions as well as the application of personalized approaches to identify optimal treatment strategies.
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Affiliation(s)
- Melissa Togtema
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada.,Biotechnology Program, Lakehead University, Thunder Bay, ON, P7B 5E1, Canada
| | - Robert Jackson
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada.,Biotechnology Program, Lakehead University, Thunder Bay, ON, P7B 5E1, Canada
| | - Jessica Grochowski
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada
| | - Peter L Villa
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada.,Department of Biology, Lakehead University, Thunder Bay, ON, P7B 5E1, Canada
| | - Miranda Mellerup
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada
| | - Jyoti Chattopadhyaya
- Program of Chemical Biology, Institute of Cell & Molecular Biology, Uppsala University, Uppsala, SE-75123, Sweden
| | - Ingeborg Zehbe
- Probe Development & Biomarker Exploration, Thunder Bay Regional Health Research Institute, Thunder Bay, ON, P7B 6V4, Canada.,Department of Biology, Lakehead University, Thunder Bay, ON, P7B 5E1, Canada
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Adenis A, Dufit V, Douine M, Ponty J, Bianco L, Najioullah F, Kilié O, Catherine D, Thomas N, Deshayes JL, Brousse P, Carles G, Grenier C, Lacoste V, Molinie V, Cesaire R, Nacher M. Predictors of abnormal cytology among HPV-infected women in remote territories of French Guiana. BMC WOMENS HEALTH 2018; 18:25. [PMID: 29368607 PMCID: PMC5784667 DOI: 10.1186/s12905-017-0493-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/05/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Cervical cancer prevention using cervical cytology is insufficiently sensitive, a significant proportion of HPV-infected women having normal cytology. The objective of the present study was to try to identify factors associated with abnormal cytology in HPV-infected women living in remote areas of French Guiana. METHODS A study was conducted in women aged 20-65 years having HPV infections confirmed by HPV DNA detection using the GREINER-BIO-ONE kit. In addition to HPV testing, cytology was performed and classified as normal or abnormal. Demographic and life history variables, and infecting genotypes were compared between the normal and abnormal cytology groups. RESULTS None of the demographic and life history variables were associated with cytology results. HPV genotype 53 was significantly associated with absence of cytological abnormalities whereas HPV 52, 58, 16 and perhaps 33 and 66 were independently associated with a greater risk of cytological abnormalities. When grouping HPV genotypes in different species, only species 9 (HPV 16, 31, 33, 35, 52, 58, 67) was significantly associated with abnormal cytology AOR = 5.1 (95% CI = 2.3-11.2), P < 0.001. CONCLUSIONS It was not possible to predict which HPV-infected women will have cytological abnormalities or notfrom anamnesis. In this study HPV 53 seemed more benign than other HPV genotypes. On the contrary, species n°9, containing 5 of the genotypes contained in the nonavalent HPV vaccine, was significantly associated with more cytological abnormalities. HPV testing and vaccination with the nonavalent vaccine should be implemented in these remote parts of French Guiana.
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Affiliation(s)
- Antoine Adenis
- Centre d'Investigation Clinique Antilles-Guyane, CIC INSERM 1424, Centre hospitalier de Cayenne, Ave des Flamboyants, 97300, Cayenne, French Guiana
| | - Valentin Dufit
- Centre d'Investigation Clinique Antilles-Guyane, CIC INSERM 1424, Centre hospitalier de Cayenne, Ave des Flamboyants, 97300, Cayenne, French Guiana
| | - Maylis Douine
- Centre d'Investigation Clinique Antilles-Guyane, CIC INSERM 1424, Centre hospitalier de Cayenne, Ave des Flamboyants, 97300, Cayenne, French Guiana
| | - Jerome Ponty
- Centre d'Investigation Clinique Antilles-Guyane, CIC INSERM 1424, Centre hospitalier de Cayenne, Ave des Flamboyants, 97300, Cayenne, French Guiana
| | - Laure Bianco
- Centre d'Investigation Clinique Antilles-Guyane, CIC INSERM 1424, Centre hospitalier de Cayenne, Ave des Flamboyants, 97300, Cayenne, French Guiana
| | - Fatiha Najioullah
- Laboratoire de Virologie, CHU de la Martinique, Fort de France, Martinique
| | - Odile Kilié
- Laboratoire de Virologie, CHU de la Martinique, Fort de France, Martinique
| | - Dominique Catherine
- Laboratoire d'anatomopathologie, CHU de la Martinique, Fort de France, Martinique
| | - Nadia Thomas
- Service de Gynécologie Obstétrique, Centre hospitalier de Cayenne, Cayenne, French Guiana
| | - Jean Luc Deshayes
- AGDOC Association de Dépistage Organisé des Cancers de Guyane, Cayenne, French Guiana
| | - Paul Brousse
- Département des Centres délocalisés de prévention et de soins, Centre Hospitalier de Cayenne, 97300, Cayenne, French Guiana
| | - Gabriel Carles
- Service de Gynécologie Obstétrique, Centre Hospitalier de l'Ouest Guyanais, Saint Laurent du Maroni, Cayenne, French Guiana
| | - Claire Grenier
- Département des Centres délocalisés de prévention et de soins, Centre Hospitalier de Cayenne, 97300, Cayenne, French Guiana
| | - Vincent Lacoste
- Laboratoire des Interactions Virus-Hôtes, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Vincent Molinie
- Laboratoire d'anatomopathologie, CHU de la Martinique, Fort de France, Martinique
| | - Raymond Cesaire
- Laboratoire de Virologie, CHU de la Martinique, Fort de France, Martinique
| | - Mathieu Nacher
- Centre d'Investigation Clinique Antilles-Guyane, CIC INSERM 1424, Centre hospitalier de Cayenne, Ave des Flamboyants, 97300, Cayenne, French Guiana. .,EA 3593, Ecosystèmes Amazoniens et Pathologie Tropicale, Université de Guyane, Cayenne, French Guiana.
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20
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Rovelli C, Poli A, Galli L, Cernuschi M, Tamburini AM, Racca S, Tambussi G, Rolla S, Albarello L, Rosati R, Lazzarin A, Castagna A, Nozza S. Presence of multiple genotypes in subjects with HPV-16 infection is highly associated with anal squamous intraepithelial lesions in HIV-1 infected males. PLoS One 2017; 12:e0186367. [PMID: 29088236 PMCID: PMC5663371 DOI: 10.1371/journal.pone.0186367] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/29/2017] [Indexed: 12/26/2022] Open
Abstract
Objectives The aim of the study was to determine the prevalence of abnormal cytological findings, high risk (HR)-HPV genotypes and to identify factors associated with an abnormal cytological findings in a cohort of HIV-infected males. Patients and methods Retrospective observational study on HIV-infected male patients who performed screening in the absence of clinical symptoms. Cytological abnormalities were classified as atypical squamous cells of undetermined significance (ASC-US), low-grade(LSIL) or high high-grade squamous intraepithelial lesion (HSIL). Logistic regression models were used to identify predictors of having LSIL/HSIL. Results Among 875 pts, abnormal cytology findings were observed in 254 (29%, 95% CI: 26.1%-32.1%) subjects: 142 (16%) had LSIL and 49 (6%) HSIL. Overall, 581 (66%, 95%CI: 63.2%-69.5%) subjects had ≥1 HR-HPV type and 269 (31%) had ≥2 HR HPV types. Multivariate logistic regression showed that subjects with multiple HR-HPV genotypes (OR = 1.351, 95%CI: 1.005–2.111) and with HPV-16 type (OR = 2.032, 95%CI: 1.313–3.146) were more likely to have LSIL/HSIL in addition to a lower CD4+/CD8+ ratio, a previous diagnosis of syphilis and a positive viral load. In another multivariate model, the presence of multiple HPV types in subjects with HPV-16 type was associated with the highest adjusted OR of having a LSIL/HSIL (OR = 2.598, 95%CI: 1.460–4.624). Conclusions In HIV-infected men, the prevalence of abnormal cytological findings was of 29% and of HR-HPV was 66%. The concomitant presence of HPV-16 and multiple HR genotypes was associated with an increased risk of abnormal cytological findings. These data highlight the importance of screening multiple HPV genotypes in HIV-infected patients.
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Affiliation(s)
| | - Andrea Poli
- Infectious Diseases Department, San Raffaele Scientific Institute, Milan, Italy
| | - Laura Galli
- Infectious Diseases Department, San Raffaele Scientific Institute, Milan, Italy
| | - Massimo Cernuschi
- Infectious Diseases Department, San Raffaele Scientific Institute, Milan, Italy
| | | | - Sara Racca
- Laboratory of Microbiology, San Raffaele Scientific Institute, Milan, Italy
| | - Giuseppe Tambussi
- Infectious Diseases Department, San Raffaele Scientific Institute, Milan, Italy
| | - Serena Rolla
- Laboratory of Microbiology, San Raffaele Scientific Institute, Milan, Italy
| | - Luca Albarello
- Department of Pathology, San Raffaele Scientific Institute, Milan, Italy
| | - Riccardo Rosati
- Università Vita-Salute San Raffaele, Milan, Italy
- Gastrointestinal Surgery, San Raffaele Scientific Institute, Milan, Italy
| | - Adriano Lazzarin
- Università Vita-Salute San Raffaele, Milan, Italy
- Infectious Diseases Department, San Raffaele Scientific Institute, Milan, Italy
| | - Antonella Castagna
- Università Vita-Salute San Raffaele, Milan, Italy
- Infectious Diseases Department, San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Nozza
- Infectious Diseases Department, San Raffaele Scientific Institute, Milan, Italy
- * E-mail:
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21
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Whole-Genome Sequencing and Variant Analysis of Human Papillomavirus 16 Infections. J Virol 2017; 91:JVI.00844-17. [PMID: 28701400 PMCID: PMC5599754 DOI: 10.1128/jvi.00844-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 07/02/2017] [Indexed: 11/20/2022] Open
Abstract
Human papillomavirus (HPV) is a strongly conserved DNA virus, high-risk types of which can cause cervical cancer in persistent infections. The most common type found in HPV-attributable cancer is HPV16, which can be subdivided into four lineages (A to D) with different carcinogenic properties. Studies have shown HPV16 sequence diversity in different geographical areas, but only limited information is available regarding HPV16 diversity within a population, especially at the whole-genome level. We analyzed HPV16 major variant diversity and conservation in persistent infections and performed a single nucleotide polymorphism (SNP) comparison between persistent and clearing infections. Materials were obtained in the Netherlands from a cohort study with longitudinal follow-up for up to 3 years. Our analysis shows a remarkably large variant diversity in the population. Whole-genome sequences were obtained for 57 persistent and 59 clearing HPV16 infections, resulting in 109 unique variants. Interestingly, persistent infections were completely conserved through time. One reinfection event was identified where the initial and follow-up samples clustered differently. Non-A1/A2 variants seemed to clear preferentially (P = 0.02). Our analysis shows that population-wide HPV16 sequence diversity is very large. In persistent infections, the HPV16 sequence was fully conserved. Sequencing can identify HPV16 reinfections, although occurrence is rare. SNP comparison identified no strongly acting effect of the viral genome affecting HPV16 infection clearance or persistence in up to 3 years of follow-up. These findings suggest the progression of an early HPV16 infection could be host related. IMPORTANCE Human papillomavirus 16 (HPV16) is the predominant type found in cervical cancer. Progression of initial infection to cervical cancer has been linked to sequence properties; however, knowledge of variants circulating in European populations, especially with longitudinal follow-up, is limited. By sequencing a number of infections with known follow-up for up to 3 years, we gained initial insights into the genetic diversity of HPV16 and the effects of the viral genome on the persistence of infections. A SNP comparison between sequences obtained from clearing and persistent infections did not identify strongly acting DNA variations responsible for these infection outcomes. In addition, we identified an HPV16 reinfection event where sequencing of initial and follow-up samples showed different HPV16 variants. Based on conventional genotyping, this infection would incorrectly be considered a persistent HPV16 infection. In the context of vaccine efficacy and monitoring studies, such infections could potentially cause reduced reported efficacy or efficiency.
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