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Galati L, Gupta P, Tufaro A, Marinaro M, Saponaro C, Escobar Marcillo DI, Loisi D, Sen R, Robitaille A, Brancaccio RN, Cuenin C, McKay-Chopin S, Paradiso AV, Liška V, Souček P, Zito FA, Hughes DJ, Tommasino M, Gheit T. Evaluation of human papillomavirus DNA in colorectal cancer and adjacent mucosal tissue samples. Infect Agent Cancer 2023; 18:71. [PMID: 37941001 PMCID: PMC10634082 DOI: 10.1186/s13027-023-00552-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/02/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Although the role of viral agents, such as human papillomavirus (e.g. HPV16, HPV18) in colorectal cancer (CRC) has been previously investigated, results remain inconclusive. METHODS To further evaluate the involvement of oncogenic HPV types in CRC, 40 frozen neoplastic and 40 adjacent colonic tissues collected from Italian patients were analyzed by Luminex-based assays that detect a broad spectrum of HPV types, i.e. Alpha (n = 21), Beta (n = 46) and Gamma HPVs (n = 52). In addition, 125 frozen CRC samples and 70 surrounding mucosal tissues were collected from Czech patients and analyzed by broad spectrum PCR protocols: (i) FAP59/64, (ii) FAPM1 and (iii) CUT combined with Next Generation Sequencing (NGS). RESULTS Using Luminex-basedassays, DNA from HPV16 was detected in 5% (2/40) CRC tissues from Italian patients. One HPV16 DNA-positive CRC case was subsequently confirmed positive for E6*I mRNA. Cutaneous beta HPV types were detected in 10% (4/40) adjacent tissues only, namely HPV111 (n = 3) and HPV120 (n = 1), while gamma HPV168 (n = 1) and HPV199 (n = 1) types were detected in adjacent and in tumor tissues, respectively. The NGS analysis of the CRC Czech samples identified HPV sequences from mucosal alpha-3 (HPV89), alpha-7 (HPV18, 39, 68 and 70) and alpha-10 species (HPV11), as well as cutaneous beta-1 (HPV20, 24, 93, 98, 105,124) beta-2 (HPV23), beta-3 (HPV49) and gamma-1 species (HPV205). CONCLUSIONS Our findings indicate that HPV types belonging to the mucosal alpha, and the 'cutaneous' beta and gamma genera can be detected in the colonic mucosal samples with a low prevalence rate and a low number of HPV reads by Luminex and NGS, respectively. However, additional studies are required to corroborate these findings.
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Affiliation(s)
- Luisa Galati
- International Agency for Research on Cancer (IARC), 25 Avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Purnima Gupta
- International Agency for Research on Cancer (IARC), 25 Avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
| | - Antonio Tufaro
- Institutional BioBank, Istituto Tumori "Giovanni Paolo II", IRCCS, Bari, Italy
| | - Mariarosaria Marinaro
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy
| | - Concetta Saponaro
- Pathology Department, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | | | - Donato Loisi
- Pathology Department, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Rajdip Sen
- International Agency for Research on Cancer (IARC), 25 Avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
| | - Alexis Robitaille
- International Agency for Research on Cancer (IARC), 25 Avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
- Leibniz Institute of Virology, Hamburg, Germany
| | - Rosario N Brancaccio
- International Agency for Research on Cancer (IARC), 25 Avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC), 25 Avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
| | - Sandrine McKay-Chopin
- International Agency for Research on Cancer (IARC), 25 Avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
| | | | - Václav Liška
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Surgery, Faculty Hospital and Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Pavel Souček
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | | | - David J Hughes
- Cancer Biology and Therapeutics Group, School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - Massimo Tommasino
- International Agency for Research on Cancer (IARC), 25 Avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France
| | - Tarik Gheit
- International Agency for Research on Cancer (IARC), 25 Avenue Tony Garnier, CS 90627, 69366, Lyon Cedex 07, France.
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Zhu Y, Yu X, Cheng G. Human skin bacterial microbiota homeostasis: A delicate balance between health and disease. MLIFE 2023; 2:107-120. [PMID: 38817619 PMCID: PMC10989898 DOI: 10.1002/mlf2.12064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/30/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2024]
Abstract
As the largest organ of the body, the skin acts as a barrier to prevent diseases and harbors a variety of beneficial bacteria. Furthermore, the skin bacterial microbiota plays a vital role in health and disease. Disruption of the barrier or an imbalance between symbionts and pathogens can lead to skin disorders or even systemic diseases. In this review, we first provide an overview of research on skin bacterial microbiota and human health, including the composition of skin bacteria in a healthy state, as well as skin bacterial microbiota educating the immune system and preventing the invasion of pathogens. We then discuss the diseases that result from skin microbial dysbiosis, including atopic dermatitis, common acne, chronic wounds, psoriasis, viral transmission, cutaneous lupus, cutaneous lymphoma, and hidradenitis suppurativa. Finally, we highlight the progress that utilizes skin microorganisms for disease therapeutics, such as bacteriotherapy and skin microbiome transplantation. A deeper knowledge of the interaction between human health and disease and the homeostasis of the skin bacterial microbiota will lead to new insights and strategies for exploiting skin bacteria as a novel therapeutic target.
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Affiliation(s)
- Yibin Zhu
- Tsinghua University‐Peking University Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
- Shenzhen Bay LaboratoryInstitute of Infectious DiseasesShenzhenChina
| | - Xi Yu
- Tsinghua University‐Peking University Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
- Shenzhen Bay LaboratoryInstitute of Infectious DiseasesShenzhenChina
| | - Gong Cheng
- Tsinghua University‐Peking University Joint Center for Life Sciences, School of MedicineTsinghua UniversityBeijingChina
- Shenzhen Bay LaboratoryInstitute of Infectious DiseasesShenzhenChina
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3
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Gallego C, Jaracz-Ros A, Laganà M, Mercier-Nomé F, Domenichini S, Fumagalli A, Roingeard P, Herfs M, Pidoux G, Bachelerie F, Schlecht-Louf G. Reprogramming of connexin landscape fosters fast gap junction intercellular communication in human papillomavirus-infected epithelia. Front Cell Infect Microbiol 2023; 13:1138232. [PMID: 37260709 PMCID: PMC10228504 DOI: 10.3389/fcimb.2023.1138232] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/26/2023] [Indexed: 06/02/2023] Open
Abstract
Human papillomaviruses (HPVs) are highly prevalent commensal viruses that require epithelial stratification to complete their replicative cycle. While HPV infections are most often asymptomatic, certain HPV types can cause lesions, that are usually benign. In rare cases, these infections may progress to non-replicative viral cycles associated with high HPV oncogene expression promoting cell transformation, and eventually cancer when not cleared by host responses. While the consequences of HPV-induced transformation on keratinocytes have been extensively explored, the impact of viral replication on epithelial homeostasis remains largely unexplored. Gap junction intercellular communication (GJIC) is critical for stratified epithelium integrity and function. This process is ensured by a family of proteins named connexins (Cxs), including 8 isoforms that are expressed in stratified squamous epithelia. GJIC was reported to be impaired in HPV-transformed cells, which was attributed to the decreased expression of the Cx43 isoform. However, it remains unknown whether and how HPV replication might impact on the expression of Cx isoforms and GJIC in stratified squamous epithelia. To address this question, we have used 3D-epithelial cell cultures (3D-EpCs), the only model supporting the productive HPV life cycle. We report a transcriptional downregulation of most epithelial Cx isoforms except Cx45 in HPV-replicating epithelia. At the protein level, HPV replication results in a reduction of Cx43 expression while that of Cx45 increases and displays a topological shift toward the cell membrane. To quantify GJIC, we pioneered quantitative gap-fluorescence loss in photobleaching (FLIP) assay in 3D-EpCs, which allowed us to show that the reprogramming of Cx landscape in response to HPV replication translates into accelerated GJIC in living epithelia. Supporting the pathophysiological relevance of our observations, the HPV-associated Cx43 and Cx45 expression pattern was confirmed in human cervical biopsies harboring HPV. In conclusion, the reprogramming of Cx expression and distribution in HPV-replicating epithelia fosters accelerated GJIC, which may participate in epithelial homeostasis and host immunosurveillance.
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Affiliation(s)
- Carmen Gallego
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
| | - Agnieszka Jaracz-Ros
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
| | - Marta Laganà
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
| | - Françoise Mercier-Nomé
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
- US31-UMS3679-Plateforme PHIC, Ingénierie et Plateformes au Service de l’Innovation Thérapeutique (IPSIT), INSERM, CNRS, Université Paris-Saclay, Orsay, France
| | - Séverine Domenichini
- UMS-IPSIT Plateforme MIPSIT, Université Paris-Saclay, CNRS, Inserm, Ingénierie et Plateformes au Service de l’Innovation Thérapeutique, Orsay, France
| | - Amos Fumagalli
- CNRS, UMR-5203, Institut de Génomique Fonctionnelle, Montpellier, France
| | - Philippe Roingeard
- INSERM U1259, Université de Tours et CHRU de Tours & Plateforme IBiSA des Microscopies, PPF ASB, CHRU de Tours, Tours, France
| | - Michael Herfs
- Laboratory of Experimental Pathology, GIGA-Cancer, University of Liège, Liège, Belgium
| | | | - Françoise Bachelerie
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
| | - Géraldine Schlecht-Louf
- Inflammation, Microbiome and Immunosurveillance, INSERM UMR-996, Université Paris-Saclay, Orsay, France
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4
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Saeidian AH, Youssefian L, Naji M, Mahmoudi H, Barnada SM, Huang C, Naghipoor K, Hozhabrpour A, Park JS, Manzo Margiotta F, Vahidnezhad F, Saffarian Z, Kamyab-Hesari K, Tolouei M, Faraji N, Azimi SZ, Namdari G, Mansouri P, Casanova JL, Béziat V, Jouanguy E, Uitto J, Vahidnezhad H. Whole transcriptome-based skin virome profiling in typical epidermodysplasia verruciformis reveals α-, β-, and γ-HPV infections. JCI Insight 2023; 8:e162558. [PMID: 36602881 PMCID: PMC10077487 DOI: 10.1172/jci.insight.162558] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023] Open
Abstract
HPVs are DNA viruses include approximately 450 types that are classified into 5 genera (α-, β-, γ-, μ-, and ν-HPV). The γ- and β-HPVs are present in low copy numbers in healthy individuals; however, in patients with an inborn error of immunity, certain species of β-HPVs can cause epidermodysplasia verruciformis (EV), manifesting as recalcitrant cutaneous warts and skin cancer. EV presents as either typical or atypical. Manifestations of typical EV are limited to the skin and are caused by abnormal keratinocyte-intrinsic immunity to β-HPVs due to pathogenic sequence variants in TMC6, TMC8, or CIB1. We applied a transcriptome-based computational pipeline, VirPy, to RNA extracted from normal-appearing skin and wart samples of patients with typical EV to explore the viral and human genetic determinants. In 26 patients, 9 distinct biallelic mutations were detected in TMC6, TMC8, and CIB1, 7 of which are previously unreported to our knowledge. Additionally, 20 different HPV species, including 3 α-HPVs, 16 β-HPVs, and 1 γ-HPV, were detected, 8 of which are reported here for the first time to our knowledge in patients with EV (β-HPV-37, -47, -80, -151, and -159; α-HPV-2 and -57; and γ-HPV-128). This study expands the TMC6, TMC8, and CIB1 sequence variant spectrum and implicates new HPV subtypes in the pathogenesis of typical EV.
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Affiliation(s)
- Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Mahtab Naji
- University of California, Riverside, School of Medicine, California, USA
| | - Hamidreza Mahmoudi
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Samantha M. Barnada
- Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Charles Huang
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Karim Naghipoor
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Hozhabrpour
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Jason S. Park
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Geisinger Commonwealth School of Medicine, Scranton, Pennsylvania, USA
| | | | - Fatemeh Vahidnezhad
- UCSC Silicon Valley Extension, University of California, Santa Cruz, California, USA
| | - Zahra Saffarian
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
- Imam Khomeini Hospital, Tehran University of Medical Science, Tehran, Iran
| | - Kambiz Kamyab-Hesari
- Department of Dermatology, Razi Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Niloofar Faraji
- Razi Clinical Research Development Unit, Razi Hospital, Guilan University of Medical Science, Rasht, Iran
| | - Seyyede Zeinab Azimi
- Center for Research and Training in Skin Diseases and Leprosy, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghazal Namdari
- Department of Dermatology, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Parvin Mansouri
- Department of Research, Skin and Stem Cell Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Paris University, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, New York, USA
| | - Vivien Béziat
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Paris University, Paris, France
| | - Emmanuelle Jouanguy
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Paris University, Paris, France
| | - Jouni Uitto
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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5
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Zhou Z, Hou Y, Qing W, Shi Y, Zhang Y, Chen R, Ou J, Zhou H, Chen M. The association of HPV infection and vaginal microbiota of reproductive women in China: A multicenter cohort study protocol. MEDICINE IN MICROECOLOGY 2022. [DOI: 10.1016/j.medmic.2022.100072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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6
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A broadly protective vaccine against cutaneous human papillomaviruses. NPJ Vaccines 2022; 7:116. [PMID: 36216845 PMCID: PMC9550855 DOI: 10.1038/s41541-022-00539-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 09/08/2022] [Indexed: 11/19/2022] Open
Abstract
Skin colonization by human papillomavirus (HPV) is typically related to inconspicuous cutaneous infections without major disease or complications in immunocompetent individuals. However, in immunosuppressed patients, especially organ transplanted recipients, cutaneous HPV infections may cause massive, highly spreading and recurrent skin lesions upon synergism with UV-exposure. Current HPV prophylactic vaccines are not effective against cutaneous HPV types (cHPV). By applying a modular polytope-based approach, in this work, we explored different vaccine candidates based on selected, tandemly arranged cHPV-L2 epitopes fused to thioredoxin (Trx) as a scaffold protein. Upon conversion to heptameric nanoparticles with the use of a genetically fused oligomerization domain, our candidate Trx-L2 vaccines induce broadly neutralizing immune responses against 19 cHPV in guinea pigs. Similar findings were obtained in mice, where protection against virus challenge was also achieved via passive transfer of immune sera. Remarkably, immunization with the candidate cHPV vaccines also induced immune responses against several mucosal low- and high-risk HPV types, including HPV16 and 18. Based on cumulative immunogenicity data but also on ease and yield of production, we identified a lead vaccine candidate bearing 12 different cHPV-L2 epitopes that holds great promise as a scalable and GMP production-compatible lead molecule for the prevention of post-transplantation skin lesions caused by cHPV infection.
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7
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Castro-Oropeza R, Piña-Sánchez P. Epigenetic and Transcriptomic Regulation Landscape in HPV+ Cancers: Biological and Clinical Implications. Front Genet 2022; 13:886613. [PMID: 35774512 PMCID: PMC9237502 DOI: 10.3389/fgene.2022.886613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Human Papillomavirus (HPV) is an oncogenic virus that causes the highest number of viral-associated cancer cases and deaths worldwide, with more than 690,000 new cases per year and 342,000 deaths only for cervical cancer (CC). Although the incidence and mortality rates for CC are declining in countries where screening and vaccination programs have been implemented, other types of cancer in which HPV is involved, such as oropharyngeal cancer, are increasing, particularly in men. Mutational and transcriptional profiles of various HPV-associated neoplasms have been described, and accumulated evidence has shown the oncogenic capacity of E6, E7, and E5 genes of high-risk HPV. Interestingly, transcriptomic analysis has revealed that although a vast majority of the human genome is transcribed into RNAs, only 2% of transcripts are translated into proteins. The remaining transcripts lacking protein-coding potential are called non-coding RNAs. In addition to the transfer and ribosomal RNAs, there are regulatory non-coding RNAs classified according to size and structure in long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and small RNAs; such as microRNAs (miRNAs), piwi-associated RNAs (piRNAs), small nucleolar RNAs (snoRNAs) and endogenous short-interfering RNAs. Recent evidence has shown that lncRNAs, miRNAs, and circRNAs are aberrantly expressed under pathological conditions such as cancer. In addition, those transcripts are dysregulated in HPV-related neoplasms, and their expression correlates with tumor progression, metastasis, poor prognosis, and recurrence. Nuclear lncRNAs are epigenetic regulators involved in controlling gene expression at the transcriptional level through chromatin modification and remodeling. Moreover, disruption of the expression profiles of those lncRNAs affects multiple biological processes such as cell proliferation, apoptosis, and migration. This review highlights the epigenetic alterations induced by HPV, from infection to neoplastic transformation. We condense the epigenetic role of non-coding RNA alterations and their potential as biomarkers in transformation’s early stages and clinical applications. We also summarize the molecular mechanisms of action of nuclear lncRNAs to understand better their role in the epigenetic control of gene expression and how they can drive the malignant phenotype of HPV-related neoplasia. Finally, we review several chemical and epigenetic therapy options to prevent and treat HPV-associated neoplasms.
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Vanni C, Schechter MS, Acinas SG, Barberán A, Buttigieg PL, Casamayor EO, Delmont TO, Duarte CM, Eren AM, Finn RD, Kottmann R, Mitchell A, Sánchez P, Siren K, Steinegger M, Gloeckner FO, Fernàndez-Guerra A. Unifying the known and unknown microbial coding sequence space. eLife 2022; 11:67667. [PMID: 35356891 PMCID: PMC9132574 DOI: 10.7554/elife.67667] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40–60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71 M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for Cand. Patescibacteria (also known as Candidate Phyla Radiation, CPR), which provides a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data. It is estimated that scientists do not know what half of microbial genes actually do. When these genes are discovered in microorganisms grown in the lab or found in environmental samples, it is not possible to identify what their roles are. Many of these genes are excluded from further analyses for these reasons, meaning that the study of microbial genes tends to be limited to genes that have already been described. These limitations hinder research into microbiology, because information from newly discovered genes cannot be integrated to better understand how these organisms work. Experiments to understand what role these genes have in the microorganisms are labor-intensive, so new analytical strategies are needed. To do this, Vanni et al. developed a new framework to categorize genes with unknown roles, and a computational workflow to integrate them into traditional analyses. When this approach was applied to over 400 million microbial genes (both with known and unknown roles), it showed that the share of genes with unknown functions is only about 30 per cent, smaller than previously thought. The analysis also showed that these genes are very diverse, revealing a huge space for future research and potential applications. Combining their approach with experimental data, Vanni et al. were able to identify a gene with a previously unknown purpose that could be involved in antibiotic resistance. This system could be useful for other scientists studying microorganisms to get a more complete view of microbial systems. In future, it may also be used to analyze the genetics of other organisms, such as plants and animals.
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Affiliation(s)
- Chiara Vanni
- Microbial Genomics and Bioinformatics Research G, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar-CMIMA (CSIC), Barcelona, Spain
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, United States
| | - Pier Luigi Buttigieg
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Bremerhaven, Germany
| | - Emilio O Casamayor
- Center for Advanced Studies of Blanes CEAB-CSIC, Spanish Council for Research, Blanes, Spain
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Paris, France
| | - Carlos M Duarte
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, United States
| | - Robert D Finn
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, United Kingdom
| | - Renzo Kottmann
- Microbial Genomics and Bioinformatics Research G, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Alex Mitchell
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Hinxton, United Kingdom
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar-CMIMA (CSIC), Barcelona, Spain
| | - Kimmo Siren
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Frank Oliver Gloeckner
- MARUM, Helmholtz Center for Polar and Marine Research, University of Bremen, Bremen, Germany
| | - Antonio Fernàndez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
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9
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The Chemokine System in Oncogenic Pathways Driven by Viruses: Perspectives for Cancer Immunotherapy. Cancers (Basel) 2022; 14:cancers14030848. [PMID: 35159113 PMCID: PMC8834488 DOI: 10.3390/cancers14030848] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Oncoviruses are viruses with oncogenic potential, responsible for almost 20% of human cancers worldwide. They are from various families, some of which belong to the microbial communities that inhabit several sites in the body of healthy humans. As a result, they most often establish latent infections controlled by the arsenal of human host responses that include the chemokine system playing key roles at the interface between tissue homeostasis and immune surveillance. Yet, chemokines and their receptors also contribute to oncogenic processes as they are targeted by the virus-induced deregulations of host responses and/or directly encoded by viruses. Thus, the chemokine system offers a strong rationale for therapeutic options, some few already approved or in trials, and future ones that we are discussing in view of the pharmacological approaches targeting the different functions of chemokines operating in both cancer cells and the tumor microenvironment. Abstract Chemokines interact with glycosaminoglycans of the extracellular matrix and activate heptahelical cellular receptors that mainly consist of G Protein-Coupled Receptors and a few atypical receptors also with decoy activity. They are well-described targets of oncogenic pathways and key players in cancer development, invasiveness, and metastasis acting both at the level of cancer cells and cells of the tumor microenvironment. Hence, they can regulate cancer cell proliferation and survival and promote immune or endothelial cell migration into the tumor microenvironment. Additionally, oncogenic viruses display the potential of jeopardizing the chemokine system by encoding mimics of chemokines and receptors as well as several products such as oncogenic proteins or microRNAs that deregulate their human host transcriptome. Conversely, the chemokine system participates in the host responses that control the virus life cycle, knowing that most oncoviruses establish asymptomatic latent infections. Therefore, the deregulated expression and function of chemokines and receptors as a consequence of acquired or inherited mutations could bias oncovirus infection toward pro-oncogenic pathways. We here review these different processes and discuss the anticancer therapeutic potential of targeting chemokine availability or receptor activation, from signaling to decoy-associated functions, in combination with immunotherapies.
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10
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Di Donato V, Caruso G, Bogani G, Cavallari EN, Palaia G, Perniola G, Ralli M, Sorrenti S, Romeo U, Pernazza A, Pierangeli A, Clementi I, Mingoli A, Cassoni A, Tanzi F, Cuccu I, Recine N, Mancino P, de Vincentiis M, Valentini V, d’Ettorre G, Della Rocca C, Mastroianni CM, Antonelli G, Polimeni A, Muzii L, Palaia I. HPV Vaccination after Primary Treatment of HPV-Related Disease across Different Organ Sites: A Multidisciplinary Comprehensive Review and Meta-Analysis. Vaccines (Basel) 2022; 10:vaccines10020239. [PMID: 35214697 PMCID: PMC8879645 DOI: 10.3390/vaccines10020239] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
Objective: To assess evidence on the efficacy of adjuvant human papillomavirus (HPV) vaccination in patients treated for HPV-related disease across different susceptible organ sites. Methods: A systematic review was conducted to identify studies addressing the efficacy of adjuvant HPV vaccination on reducing the risk of recurrence of HPV-related preinvasive diseases. Results were reported as mean differences or pooled odds ratios (OR) with 95% confidence intervals (95% CI). Results: Sixteen studies were identified for the final analysis. Overall, 21,472 patients with cervical dysplasia were included: 4132 (19.2%) received the peri-operative HPV vaccine, while 17,340 (80.8%) underwent surgical treatment alone. The recurrences of CIN 1+ (OR 0.45, 95% CI 0.27 to 0.73; p = 0.001), CIN 2+ (OR 0.33, 95% CI 0.20 to 0.52; p < 0.0001), and CIN 3 (OR 0.28, 95% CI 0.13 to 0.59; p = 0.0009) were lower in the vaccinated than in unvaccinated group. Similarly, adjuvant vaccination reduced the risk of developing anal intraepithelial neoplasia (p = 0.005) and recurrent respiratory papillomatosis (p = 0.004). No differences in anogenital warts and vulvar intraepithelial neoplasia recurrence rate were observed comparing vaccinated and unvaccinated individuals. Conclusions: Adjuvant HPV vaccination is associated with a reduced risk of CIN recurrence, although there are limited data regarding its role in other HPV-related diseases. Further research is warranted to shed more light on the role of HPV vaccination as adjuvant therapy after primary treatment.
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Affiliation(s)
- Violante Di Donato
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (V.D.D.); (G.B.); (G.P.); (S.S.); (F.T.); (I.C.); (N.R.); (P.M.); (L.M.); (I.P.)
| | - Giuseppe Caruso
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (V.D.D.); (G.B.); (G.P.); (S.S.); (F.T.); (I.C.); (N.R.); (P.M.); (L.M.); (I.P.)
- Correspondence:
| | - Giorgio Bogani
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (V.D.D.); (G.B.); (G.P.); (S.S.); (F.T.); (I.C.); (N.R.); (P.M.); (L.M.); (I.P.)
| | - Eugenio Nelson Cavallari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (E.N.C.); (G.d.); (C.M.M.)
| | - Gaspare Palaia
- Department of Oral and Maxillofacial Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (G.P.); (U.R.); (A.C.); (M.d.V.); (V.V.); (A.P.)
| | - Giorgia Perniola
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (V.D.D.); (G.B.); (G.P.); (S.S.); (F.T.); (I.C.); (N.R.); (P.M.); (L.M.); (I.P.)
| | - Massimo Ralli
- Department of Sense Organs, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy;
| | - Sara Sorrenti
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (V.D.D.); (G.B.); (G.P.); (S.S.); (F.T.); (I.C.); (N.R.); (P.M.); (L.M.); (I.P.)
| | - Umberto Romeo
- Department of Oral and Maxillofacial Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (G.P.); (U.R.); (A.C.); (M.d.V.); (V.V.); (A.P.)
| | - Angelina Pernazza
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (A.P.); (C.D.R.)
| | - Alessandra Pierangeli
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (A.P.); (G.A.)
| | - Ilaria Clementi
- Department of Emergency, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy;
| | - Andrea Mingoli
- Department of Surgery “Pietro Valdoni”, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy;
| | - Andrea Cassoni
- Department of Oral and Maxillofacial Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (G.P.); (U.R.); (A.C.); (M.d.V.); (V.V.); (A.P.)
| | - Federica Tanzi
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (V.D.D.); (G.B.); (G.P.); (S.S.); (F.T.); (I.C.); (N.R.); (P.M.); (L.M.); (I.P.)
| | - Ilaria Cuccu
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (V.D.D.); (G.B.); (G.P.); (S.S.); (F.T.); (I.C.); (N.R.); (P.M.); (L.M.); (I.P.)
| | - Nadia Recine
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (V.D.D.); (G.B.); (G.P.); (S.S.); (F.T.); (I.C.); (N.R.); (P.M.); (L.M.); (I.P.)
| | - Pasquale Mancino
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (V.D.D.); (G.B.); (G.P.); (S.S.); (F.T.); (I.C.); (N.R.); (P.M.); (L.M.); (I.P.)
| | - Marco de Vincentiis
- Department of Oral and Maxillofacial Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (G.P.); (U.R.); (A.C.); (M.d.V.); (V.V.); (A.P.)
| | - Valentino Valentini
- Department of Oral and Maxillofacial Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (G.P.); (U.R.); (A.C.); (M.d.V.); (V.V.); (A.P.)
| | - Gabriella d’Ettorre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (E.N.C.); (G.d.); (C.M.M.)
| | - Carlo Della Rocca
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (A.P.); (C.D.R.)
| | - Claudio Maria Mastroianni
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (E.N.C.); (G.d.); (C.M.M.)
| | - Guido Antonelli
- Department of Molecular Medicine, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (A.P.); (G.A.)
| | - Antonella Polimeni
- Department of Oral and Maxillofacial Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (G.P.); (U.R.); (A.C.); (M.d.V.); (V.V.); (A.P.)
| | - Ludovico Muzii
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (V.D.D.); (G.B.); (G.P.); (S.S.); (F.T.); (I.C.); (N.R.); (P.M.); (L.M.); (I.P.)
| | - Innocenza Palaia
- Department of Maternal and Child Health and Urological Sciences, Sapienza University of Rome, Policlinico Umberto I, 00161 Rome, Italy; (V.D.D.); (G.B.); (G.P.); (S.S.); (F.T.); (I.C.); (N.R.); (P.M.); (L.M.); (I.P.)
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González A, Sánchez R, Camargo M, Soto-De León SC, Del Río-Ospina L, Mora LH, Ramírez E, Rodríguez AA, Hurtado P, Patarroyo ME, Patarroyo MA. Cervical cancer screening programme attendance and compliance predictors regarding Colombia’s Amazon region. PLoS One 2022; 17:e0262069. [PMID: 35077465 PMCID: PMC8789105 DOI: 10.1371/journal.pone.0262069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/17/2021] [Indexed: 12/04/2022] Open
Abstract
Background Cervical cancer (CC) promotion and prevention (P&P) programmes’ challenge lies in guaranteeing that follow-up strategies have a real impact on reducing CC-related mortality rates. CC P&P programme compliance and coverage rates are relevant indicators for evaluating their success and good performance; however, such indicators’ frequency rates are considerably lower among women living in rural and border areas. This study was aimed at identifying factors associated with CC screening programme attendance for women living in Colombia’s Amazon region. Methods This study (qualitative and quantitative phases) was carried out between September 2015 and November 2016; women residing in the border towns of Leticia and Puerto Nariño participated in it. The first phase (qualitative) involved interviews and focus group discussions; this led to establishing factors related to CC P&P programme attendance which were used in the quantitative phase for designing a survey for determining the strength of association in a logistic regression model. The terms attendance and compliance were considered to apply to women who had followed the 1–1–3 scheme throughout their lives, i.e. a cytology examination every 3 years after receiving two consecutive negative annual cytology results. Results Inclusion criteria were met by 309 women (≥18-year-olds having an active sexual life, having resided in the target community for at least one year); 15.2% had suitable P&P programme follow-up. Screening programme attendance was positively associated with first intercourse after becoming 20 years-old (aOR: 3.87; 1.03–9.50 95%CI; p = 0.045), frequent contraceptive use (aOR: 3.11; 1.16–8.33 95%CI; p = 0.023), awareness of the age to participate in P&P programmes (aOR: 2.69; 1.08–6.68 95%CI; p = 0.032), awareness of cytology’s usefulness in identifying cervical abnormalities (aOR: 2.43; 1.02–5.77 95%CI; p = 0.043) and considering cytology important (aOR: 2.64; 1.12–6.19 95%CI; p = 0.025). Women living in rural areas had a lower probability (aOR 0.43: 0.24–0.79 95%CI; p = 0.006) of adhering to CC P&P programmes. Conclusions This study’s findings suggested the need for including novel strategies in screening programmes which will promote CC P&P activities going beyond hospital outpatient attendance to reach the most remote or widely scattered communities, having the same guarantees regarding access, opportunity and quality. Including education-related activities and stimulating the population’s awareness regarding knowledge about CC prevention could be one of the main tools for furthering the impact of attendance at and compliance with P&P programmes.
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Affiliation(s)
- Alejandra González
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Ricardo Sánchez
- Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Milena Camargo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia
| | - Sara Cecilia Soto-De León
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Luisa Del Río-Ospina
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | | | - Edwin Ramírez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Anny Alejandra Rodríguez
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Paula Hurtado
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Manuel Elkin Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- Health Sciences Division, Main Campus, Universidad Santo Tomás, Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
- Health Sciences Division, Main Campus, Universidad Santo Tomás, Bogotá, Colombia
- * E-mail:
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12
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Howard B, Bascom CC, Hu P, Binder RL, Fadayel G, Huggins TG, Jarrold BB, Osborne R, Rocchetta HL, Swift D, Tiesman JP, Song Y, Wang Y, Wehmeyer K, Kimball AB, Isfort RJ. Aging Associated Changes in the Adult Human Skin Microbiome and the Host Factors That Affect Skin Microbiome Composition. J Invest Dermatol 2021; 142:1934-1946.e21. [PMID: 34890626 DOI: 10.1016/j.jid.2021.11.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 11/01/2021] [Accepted: 11/16/2021] [Indexed: 01/16/2023]
Abstract
Understanding changes in the skin microbiome and their relationship to host skin factors during aging remains largely unknown. To better understand this phenomenon, we collected samples for metagenomic and host skin factor analyses from forearm, buttock, and facial skin from 158 Caucasian females at 20-24, 30-34, 40-44, 50-54, 60-64, and 70-74 years of age. Metagenomics analysis was performed using 16S rRNA gene sequencing, while host sebocyte gland area, skin lipids, natural moisturizing factors (NMFs) and anti-microbial peptides (AMPs) measurements were also performed. These analyses demonstrated that skin bacterial diversity increased at all the skin sites with increasing age. Of the bacterial genera with average relative abundance of >1%, only Lactobacillus and Cutibacterium demonstrated a significant change (decrease) in abundance at all sampled skin sites with increasing age. Additional bacterial genera demonstrated significant age and site-specific changes in abundance. Analysis of sebocyte area, NMFs, lipids and AMPs demonstrated an age-related decrease in sebocyte area and increases in NMFs/AMPs/skin lipids, all which correlated with changes in specific bacterial genera. In conclusion, the human skin microbiome undergoes age-associated alterations that may reflect underlying age-related changes in cutaneous biology.
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Affiliation(s)
- Brian Howard
- The Procter & Gamble Company, Cincinnati, OH USA
| | | | - Ping Hu
- The Procter & Gamble Company, Cincinnati, OH USA
| | | | - Gina Fadayel
- The Procter & Gamble Company, Cincinnati, OH USA
| | | | | | | | | | - Dionne Swift
- The Procter & Gamble Company, Cincinnati, OH USA
| | | | - Yuli Song
- The Procter & Gamble Company, Cincinnati, OH USA
| | - Yu Wang
- The Procter & Gamble Company, Cincinnati, OH USA
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13
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Pistone D, Meroni G, Panelli S, D’Auria E, Acunzo M, Pasala AR, Zuccotti GV, Bandi C, Drago L. A Journey on the Skin Microbiome: Pitfalls and Opportunities. Int J Mol Sci 2021; 22:9846. [PMID: 34576010 PMCID: PMC8469928 DOI: 10.3390/ijms22189846] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/22/2022] Open
Abstract
The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the "core" and "transient" types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.
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Affiliation(s)
- Dario Pistone
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
| | - Gabriele Meroni
- Department of Biomedical Surgical and Dental Sciences-One Health Unit, University of Milan, 20133 Milan, Italy;
| | - Simona Panelli
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
| | - Enza D’Auria
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Miriam Acunzo
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Ajay Ratan Pasala
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
| | - Gian Vincenzo Zuccotti
- Pediatric Clinical Research Center “Invernizzi”, Department of Biomedical and Clinical Sciences “L. Sacco”, University of Milan, 20157 Milan, Italy; (S.P.); (A.R.P.); (G.V.Z.)
- Department of Pediatrics, Children’s Hospital Vittore Buzzi, University of Milan, 20154 Milan, Italy; (E.D.); (M.A.)
| | - Claudio Bandi
- Pediatric Clinical Research Center “Invernizzi”, Department of Biosciences, University of Milan, 20133 Milan, Italy;
| | - Lorenzo Drago
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
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Chen Z, Utro F, Platt D, DeSalle R, Parida L, Chan PKS, Burk RD. K-Mer Analyses Reveal Different Evolutionary Histories of Alpha, Beta, and Gamma Papillomaviruses. Int J Mol Sci 2021; 22:9657. [PMID: 34502564 PMCID: PMC8432194 DOI: 10.3390/ijms22179657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/04/2021] [Accepted: 09/05/2021] [Indexed: 12/31/2022] Open
Abstract
Papillomaviruses (PVs) are a heterogeneous group of DNA viruses that can infect fish, birds, reptiles, and mammals. PVs infecting humans (HPVs) phylogenetically cluster into five genera (Alpha-, Beta-, Gamma-, Mu- and Nu-PV), with differences in tissue tropism and carcinogenicity. The evolutionary features associated with the divergence of Papillomaviridae are not well understood. Using a combination of k-mer distributions, genetic metrics, and phylogenetic algorithms, we sought to evaluate the characteristics and differences of Alpha-, Beta- and Gamma-PVs constituting the majority of HPV genomes. A total of 640 PVs including 442 HPV types, 27 non-human primate PV types, and 171 non-primate animal PV types were evaluated. Our analyses revealed the highest genetic diversity amongst Gamma-PVs compared to the Alpha and Beta PVs, suggesting reduced selective pressures on Gamma-PVs. Using a sequence alignment-free trimer (k = 3) phylogeny algorithm, we reconstructed a phylogeny that grouped most HPV types into a monophyletic clade that was further split into three branches similar to alignment-based classifications. Interestingly, a subset of low-risk Alpha HPVs (the species Alpha-2, 3, 4, and 14) split from other HPVs and were clustered with non-human primate PVs. Surprisingly, the trimer-constructed phylogeny grouped the Gamma-6 species types originally isolated from the cervicovaginal region with the main Alpha-HPV clade. These data indicate that characterization of papillomavirus heterogeneity via orthogonal approaches reveals novel insights into the biological understanding of HPV genomes.
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Affiliation(s)
- Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China;
- Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Filippo Utro
- Computational Genomics, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA; (F.U.); (D.P.); (L.P.)
| | - Daniel Platt
- Computational Genomics, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA; (F.U.); (D.P.); (L.P.)
| | - Rob DeSalle
- Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA;
| | - Laxmi Parida
- Computational Genomics, IBM T. J. Watson Research, Yorktown Heights, NY 10598, USA; (F.U.); (D.P.); (L.P.)
| | - Paul K. S. Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China;
- Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Robert D. Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Obstetrics, Gynecology and Woman’s Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Dong J, Li Y, Xiao H, Cui M, Fan S. Commensal microbiota in the digestive tract: a review of its roles in carcinogenesis and radiotherapy. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0476. [PMID: 34369136 PMCID: PMC8763002 DOI: 10.20892/j.issn.2095-3941.2020.0476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/27/2021] [Indexed: 11/11/2022] Open
Abstract
The human microflora is a complex ecosystem composed of diverse microorganisms mainly distributed in the epidermal and mucosal habitats of the entire body, including the mouth, lung, intestines, skin, and vagina. These microbial communities are involved in many essential functions, such as metabolism, immunity, host nutrition, and diseases. Recent studies have focused on the microbiota associated with cancers, particularly the oral and intestinal microbiota. Radiotherapy, the most effective cytotoxic modality available for solid tumors, contributes to the treatment of cancer patients. Mounting evidence supports that the microbiota plays pivotal roles in the efficacy and prognosis of tumor radiotherapy. Here, we review current research on the microbiota and cancer development, and describe knowledge gaps in the study of radiotherapy and the microbiota. Better understanding of the effects of the microbiome in tumorigenesis and radiotherapy will shed light on future novel prevention and treatment strategies based on modulating the microbiome in cancer patients.
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Affiliation(s)
- Jiali Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Yuan Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Huiwen Xiao
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Ming Cui
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
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16
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Maura D, Elmekki N, Goddard CA. The ammonia oxidizing bacterium Nitrosomonas eutropha blocks T helper 2 cell polarization via the anti-inflammatory cytokine IL-10. Sci Rep 2021; 11:14162. [PMID: 34238943 PMCID: PMC8266879 DOI: 10.1038/s41598-021-93299-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
The prevalence of atopic diseases has been steadily increasing since the mid twentieth century, a rise that has been linked to modern hygienic lifestyles that limit exposure to microbes and immune system maturation. Overactive type 2 CD4+ helper T (Th2) cells are known to be closely associated with atopy and represent a key target for treatment. In this study, we present an initial characterization of ammonia oxidizing bacteria (AOB) Nitrosomonas eutropha D23, an environmental microbe that is not associated with human pathology, and show AOB effectively suppress the polarization of Th2 cells and production of Th2-associated cytokines (IL-5, IL-13, and IL-4) by human peripheral blood mononuclear cells (PBMC). We show that AOB inhibit Th2 cell polarization not through Th1-mediated suppression, but rather through mechanisms involving the anti-inflammatory cytokine IL-10 and the potential inhibition of dendritic cells, as evidenced by a reduction in Major Histocompatibility Complex Class II (MHC II) and CD86 expression following AOB treatment. This is the first report of immunomodulatory properties of AOB, and provides initial support for the development of AOB as a potential therapeutic for atopic diseases.
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17
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Boero E, Mnich ME, Manetti AGO, Soldaini E, Grimaldi L, Bagnoli F. Human Three-Dimensional Models for Studying Skin Pathogens. Curr Top Microbiol Immunol 2021; 430:3-27. [PMID: 32601967 DOI: 10.1007/82_2020_219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Skin is the most exposed surface of the human body, separating the microbe-rich external environment, from the sterile inner part. When skin is breached or its homeostasis is perturbed, bacterial, fungal and viral pathogens can cause local infections or use the skin as an entry site to spread to other organs. In the last decades, it has become clear that skin provides niches for permanent microbial colonization, and it actively interacts with microorganisms. This crosstalk promotes skin homeostasis and immune maturation, preventing expansion of harmful organisms. Skin commensals, however, are often found to be skin most prevalent and dangerous pathogens. Despite the medical interest, mechanisms of colonization and invasion for most skin pathogens are poorly understood. This limitation is due to the lack of reliable skin models. Indeed, animal models do not adequately mimic neither the anatomy nor the immune response of human skin. Human 3D skin models overcome these limitations and can provide new insights into the molecular mechanisms of microbial pathogenesis. Herein, we address the strengths and weaknesses of different types of human skin models and we review the main findings obtained using these models to study skin pathogens.
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Affiliation(s)
| | | | | | | | - Luca Grimaldi
- Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
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18
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Comprehensive metagenomic analysis of blastic plasmacytoid dendritic cell neoplasm. Blood Adv 2021; 4:1006-1011. [PMID: 32182365 DOI: 10.1182/bloodadvances.2019001260] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022] Open
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a hematologic malignancy believed to originate from plasmacytoid dendritic cells (pDCs), the immune cells responsible for producing type 1 interferons during infection. Nearly all patients with BPDCN have prominent skin involvement, with cutaneous infiltration occupying the dermis and subcutis. One half of patients present with BPDCN cells only in the skin, with no evidence of disease elsewhere. Because normal pDCs are rare or absent in cutaneous sites, and they only traffic to the skin after activation by pathogen or inflammation, our aim was to determine if a microorganism is associated with BPDCN. We performed RNA sequencing in BPDCN skin and bone marrow, with cutaneous T-cell lymphoma (CTCL) and normal skin as controls. GATK-PathSeq was used to identify known microbial sequences. Bacterial reads in BPDCN skin were components of normal flora and did not distinguish BPDCN from controls. We then developed a new computational tool, virID (Viral Identification and Discovery; https://github.com/jnoms/virID), for identification of microbial-associated reads remaining unassigned after GATK-PathSeq. We found no evidence for a known or novel virus in BPDCN skin or bone marrow, despite confirming that virID could identify Merkel cell polyomavirus in Merkel cell carcinoma, human papillomavirus in head and neck squamous cell carcinoma, and Kaposi's sarcoma herpesvirus in Kaposi's sarcoma in a blinded fashion. Thus, at the level of sensitivity used here, we found no clear pathogen linked to BPDCN.
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19
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Hošnjak L, Kocjan BJ, Pirš B, Seme K, Poljak M. The genetic diversity of human papillomavirus types from the species Gammapapillomavirus 15: HPV135, HPV146, and HPV179. PLoS One 2021; 16:e0249829. [PMID: 33956809 PMCID: PMC8101917 DOI: 10.1371/journal.pone.0249829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/25/2021] [Indexed: 11/29/2022] Open
Abstract
Objectives To determine the prevalence, viral load, tissue tropism, and genetic variability of novel human papillomavirus (HPV) type 179, which is etiologically associated with sporadic cases of common warts in immunocompromised patients, and phylogenetically related HPV types 135 and 146. Methods The representative collection of 850 HPV-associated clinical samples (oral/nasopharyngeal/anal, archival specimens of oral/oropharyngeal/conjunctival/cervical/skin cancer, benign lesions of the larynx/conjunctiva/skin, and eyebrows), obtained from immunocompetent individuals, was tested for the presence of HPV179, HPV135, and HPV146 using type-specific real-time PCRs. To assess the genetic diversity of the HPVs investigated in the non-coding long control region (LCR), several highly sensitive nested PCR protocols were developed for each HPV type. The genetic diversity of HPV179 was additionally determined in 12 HPV179 isolates from different anatomical sites of an only immunocompromised patient included in the study. Results HPV179, HPV135, and HPV146 were detected in 1.4, 2.0, and 1.5% of the samples tested, respectively, with no preference for cutaneous or mucosal epithelial cells. One (with five single nucleotide polymorphisms; SNPs), four (with one to six SNPs), and four (with one to eight SNPs) genetic variants of HPV179, HPV135, and HPV146, respectively, were identified among eligible samples. HPV179 isolates from the immunocompromised patient exhibited the identical LCR nucleotide sequence, suggesting that HPV179 can cause generalized HPV infections. Conclusions HPV179, HPV135, and HPV146 have a mucocutaneous tissue tropism and are associated with sporadic infections in immunocompromised and immunocompetent individuals. Because the majority of mutations were found outside the major functional domains of the respective LCRs, we assume that HPV179, HPV135, and HPV146 genetic variants pathogenically do not differ from their prototypes. In addition, no association was found between specific HPV179, HPV135, and HPV146 genetic variants and anatomical sites of infection and/or specific neoplasms.
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Affiliation(s)
- Lea Hošnjak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Boštjan J. Kocjan
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | | | - Katja Seme
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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20
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Ganly I, Pei Z, Hao Y, Ma Y, Rosenthal M, Wu Z, Migliacci J, Huang B, Katabi N, Tseng W, Brown S, Tang YW, Yang L. Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing. Sci Rep 2021; 11:3867. [PMID: 33594114 PMCID: PMC7886861 DOI: 10.1038/s41598-021-83197-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 01/27/2021] [Indexed: 12/13/2022] Open
Abstract
The aim of this study was to carry out a case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma (OC-SCC) to normal patients using metagenomic shotgun sequencing. We recruited 50 OC-SCC cases which were then matched with a control patient by age, gender, race, smoking status and alcohol status. DNA was extracted from oral wash samples from all patients and whole genome shotgun sequencing performed. The raw sequence data was cleaned, reads aligned with the human genome (GRCH38), nonhuman reads identified and then HPV genotypes identified using HPViewer. In the 50 patients with OC-SCC, the most common subsite was tongue in 26 (52%). All patients were treated with primary resection and neck dissection. All but 2 tumors were negative on p16 immunohistochemistry. There were no statistically significant differences between the cases and controls in terms of gender, age, race/ethnicity, alcohol drinking, and cigarette smoking. There was no statistically significant difference between the cancer samples and control samples in the nonhuman DNA reads (medians 4,228,072 vs. 5,719,715, P value = 0.324). HPV was detected in 5 cases (10%) of OC-SCC (genotypes 10, 16, 98) but only 1 tumor sample (genotype 16) yielded a high number of reads to suggest a role in the etiology of OC-SCC. HPV was detected in 4 control patients (genotypes 16, 22, 76, 200) but all had only 1–2 HPV reads per human genome. Genotypes of HPV are rarely found in patients with oral cancer.
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Affiliation(s)
- Ian Ganly
- Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, USA.
| | - Zhiheng Pei
- Department of Pathology, New York University School of Medicine, New York, 10016, USA.,Department of Medicine, New York University School of Medicine, New York, 10016, USA.,Department of Veterans Affairs, New York Harbor Healthcare System, New York, USA
| | - Yuhan Hao
- Department of Pathology, New York University School of Medicine, New York, 10016, USA.,Applied Bioinformatics Laboratories, New York University School of Medicine, New York, 10016, USA.,Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10016, USA
| | - Yingfei Ma
- Department of Medicine, New York University School of Medicine, New York, 10016, USA.,Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518000, China
| | - Matthew Rosenthal
- Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Zhenglin Wu
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Jocelyn Migliacci
- Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Bin Huang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Nora Katabi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Wenzhi Tseng
- Department of Pathology, New York University School of Medicine, New York, 10016, USA
| | - Stuart Brown
- Applied Bioinformatics Laboratories, New York University School of Medicine, New York, 10016, USA
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.,Medical Affairs, Cepheid, Danaher Diagnostic Platform, Shanghai, China
| | - Liying Yang
- Department of Pathology, New York University School of Medicine, New York, 10016, USA. .,Department of Medicine, New York University School of Medicine, New York, 10016, USA.
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21
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Jackson WD, Gulino A, Fossati-Jimack L, Castro Seoane R, Tian K, Best K, Köhl J, Belmonte B, Strid J, Botto M. C3 Drives Inflammatory Skin Carcinogenesis Independently of C5. J Invest Dermatol 2021; 141:404-414.e6. [PMID: 32682912 PMCID: PMC8150327 DOI: 10.1016/j.jid.2020.06.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/30/2020] [Accepted: 06/10/2020] [Indexed: 11/17/2022]
Abstract
Nonmelanoma skin cancer such as cutaneous squamous cell carcinoma (cSCC) is the most common form of cancer and can occur as a consequence of DNA damage to the epithelium by UVR or chemical carcinogens. There is growing evidence that the complement system is involved in cancer immune surveillance; however, its role in cSCC remains unclear. Here, we show that complement genes are expressed in tissue from patients with cSCC, and C3 activation fragments are present in cSCC biopsies, indicating complement activation. Using a range of complement-deficient mice in a two-stage mouse model of chemically-induced cSCC, where a subclinical dose of 7,12-dimethylbenz[a]anthracene causes oncogenic mutations in epithelial cells and 12-O-tetradecanoylphorbol-13-acetate promotes the outgrowth of these cells, we found that C3-deficient mice displayed a significantly reduced tumor burden, whereas an opposite phenotype was observed in mice lacking C5aR1, C5aR2, and C3a receptor. In addition, in mice unable to form the membrane attack complex, the tumor progression was unaltered. C3 deficiency did not affect the cancer response to 7,12-dimethylbenz[a]anthracene treatment alone but reduced the epidermal hyperplasia during 12-O-tetradecanoylphorbol-13-acetate-induced inflammation. Collectively, these data indicate that C3 drives tumorigenesis during chronic skin inflammation, independently of the downstream generation of C5a or membrane attack complex.
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MESH Headings
- 9,10-Dimethyl-1,2-benzanthracene/administration & dosage
- 9,10-Dimethyl-1,2-benzanthracene/toxicity
- Animals
- Carcinogens/administration & dosage
- Carcinogens/toxicity
- Carcinoma, Squamous Cell/chemically induced
- Carcinoma, Squamous Cell/immunology
- Carcinoma, Squamous Cell/pathology
- Complement Activation/genetics
- Complement Activation/immunology
- Complement C3/genetics
- Complement C3/metabolism
- Complement C5/metabolism
- Complement Membrane Attack Complex/metabolism
- Disease Models, Animal
- Disease Progression
- Humans
- Mice
- Mice, Knockout
- Mice, Transgenic
- Neoplasms, Experimental/blood
- Neoplasms, Experimental/chemically induced
- Neoplasms, Experimental/immunology
- Neoplasms, Experimental/pathology
- Receptor, Anaphylatoxin C5a/genetics
- Receptor, Anaphylatoxin C5a/metabolism
- Receptors, Complement/genetics
- Receptors, Complement/metabolism
- Signal Transduction/genetics
- Signal Transduction/immunology
- Skin/drug effects
- Skin/immunology
- Skin/pathology
- Skin Neoplasms/chemically induced
- Skin Neoplasms/immunology
- Skin Neoplasms/pathology
- Tumor Escape
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Affiliation(s)
- William D Jackson
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, United Kingdom
| | - Alessandro Gulino
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo School of Medicine, Palermo, Italy
| | - Liliane Fossati-Jimack
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, United Kingdom
| | - Rocio Castro Seoane
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, United Kingdom
| | - Kunyuan Tian
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, United Kingdom
| | - Katie Best
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Jörg Köhl
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany; Division of Immunobiology, Cincinnati Children's Hospital and College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Beatrice Belmonte
- Tumor Immunology Unit, Department of Health Sciences, University of Palermo School of Medicine, Palermo, Italy
| | - Jessica Strid
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, United Kingdom.
| | - Marina Botto
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, United Kingdom
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22
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Li H, Zang Y, Wang C, Li H, Fan A, Han C, Xue F. The Interaction Between Microorganisms, Metabolites, and Immune System in the Female Genital Tract Microenvironment. Front Cell Infect Microbiol 2020; 10:609488. [PMID: 33425785 PMCID: PMC7785791 DOI: 10.3389/fcimb.2020.609488] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/18/2020] [Indexed: 12/24/2022] Open
Abstract
The female reproductive tract microenvironment includes microorganisms, metabolites, and immune components, and the balance of the interactions among them plays an important role in maintaining female reproductive tract homeostasis and health. When any one of the reproductive tract microorganisms, metabolites, or immunity is out of balance, it will affect the other two, leading to the occurrence and development of diseases and the appearance of corresponding symptoms and signs, such as infertility, miscarriage, premature delivery, and gynecological tumors caused by infectious diseases of the reproductive tract. Nutrients in the female reproductive tract provide symbiotic and pathogenic microorganisms with a source of nutrients for their own reproduction and utilization. At the same time, this interaction with the host forms a variety of metabolites. Changes in metabolites in the host reproductive tract are related not only to the interaction between the host and microbiota under dysbiosis but also to changes in host immunity or the environment, all of which will participate in the pathogenesis of diseases and lead to disease-related phenotypes. Microorganisms and their metabolites can also interact with host immunity, activate host immunity, and change the host immune status and are closely related to persistent genital pathogen infections, aggravation of infectious diseases, severe pregnancy outcomes, and even gynecological cancers. Therefore, studying the interaction between microorganisms, metabolites, and immunity in the reproductive tract cannot only reveal the pathogenic mechanisms that lead to inflammation of the reproductive tract, adverse pregnancy outcomes and tumorigenesis but also provide a basis for further research on the diagnosis and treatment of targets.
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Affiliation(s)
- Huanrong Li
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China.,Department of Gynecology and Obstetrics, Tianjin Key Laboratory of Female Reproductive Health and Eugenic, Tianjin Medical University General Hospital, Tianjin, China
| | - Yuqin Zang
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China.,Department of Gynecology and Obstetrics, Tianjin Key Laboratory of Female Reproductive Health and Eugenic, Tianjin Medical University General Hospital, Tianjin, China
| | - Chen Wang
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China.,Department of Gynecology and Obstetrics, Tianjin Key Laboratory of Female Reproductive Health and Eugenic, Tianjin Medical University General Hospital, Tianjin, China
| | - Huiyang Li
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China.,Department of Gynecology and Obstetrics, Tianjin Key Laboratory of Female Reproductive Health and Eugenic, Tianjin Medical University General Hospital, Tianjin, China
| | - Aiping Fan
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China.,Department of Gynecology and Obstetrics, Tianjin Key Laboratory of Female Reproductive Health and Eugenic, Tianjin Medical University General Hospital, Tianjin, China
| | - Cha Han
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China.,Department of Gynecology and Obstetrics, Tianjin Key Laboratory of Female Reproductive Health and Eugenic, Tianjin Medical University General Hospital, Tianjin, China
| | - Fengxia Xue
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China.,Department of Gynecology and Obstetrics, Tianjin Key Laboratory of Female Reproductive Health and Eugenic, Tianjin Medical University General Hospital, Tianjin, China
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23
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Galati L, Combes JD, Gupta P, Sen R, Robitaille A, Brancaccio RN, Atsou K, Cuenin C, McKay-Chopin S, Tornesello ML, Buonaguro FM, Clifford G, Gheit T, Tommasino M. Detection of a large spectrum of viral infections in conjunctival premalignant and malignant lesions. Int J Cancer 2020; 147:2862-2870. [PMID: 32525572 DOI: 10.1002/ijc.33149] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/24/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022]
Abstract
To study the interaction between HIV and other carcinogenic infections in conjunctival squamous cell carcinoma (SCC), we evaluated the presence of a broad spectrum of human viruses in conjunctiva specimens. Beta Human papillomavirus (HPV; n = 46), gamma HPV (n = 52), polyomaviruses (n = 12) and herpes viruses (n = 3) was determined in DNA extracted from 67 neoplastic and 55 non-neoplastic conjunctival tissues of HIV-positive and HIV negative subjects by Luminex-based assays. Next-generation sequencing (NGS) was also used to further characterize the presence of cutaneous HPVs. Detection of beta-2 HPV infections was associated with the risk of neoplasia (adjusted odds ratio [aOR] 3.0; 95% confidence interval [CI] 1.3-6.8), regardless of HIV status (HIV positive, aOR 2.6, 95% CI 0.9-7.7; HIV negative, aOR 3.5, 95% CI 0.9-14.4). EBV was strongly associated with the risk of neoplasia (aOR 12.0, 95% CI 4.3-33.5; P < .01) mainly in HIV individuals (HIV positive, aOR 57.5; 95% CI: 10.1-327.1; HIV negative aOR 2.6; 95% CI: 0.2-34.7). NGS allowed to identify 13 putative novel HPVs in cases and controls. Our findings suggest a role of beta HPV types and EBV, in conjunctival SCC. However, additional studies of viral expression in tumor tissue are required to confirm the causal association.
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Affiliation(s)
- Luisa Galati
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
| | - Jean Damien Combes
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
| | - Purnima Gupta
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
| | - Rajdip Sen
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
| | - Alexis Robitaille
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
| | - Rosario Nicola Brancaccio
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
| | - Kueshivi Atsou
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
| | - Sandrine McKay-Chopin
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
| | - Maria Lina Tornesello
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori, IRCCS "Fondazione Pascale", Naples, Italy
| | - Franco Maria Buonaguro
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori, IRCCS "Fondazione Pascale", Naples, Italy
| | - Gary Clifford
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
| | - Tarik Gheit
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
| | - Massimo Tommasino
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon Cedex 08, France
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24
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Squarzanti DF, Zavattaro E, Pizzimenti S, Amoruso A, Savoia P, Azzimonti B. Non-Melanoma Skin Cancer: news from microbiota research. Crit Rev Microbiol 2020; 46:433-449. [PMID: 32692305 DOI: 10.1080/1040841x.2020.1794792] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Recently, research has been deeply focusing on the role of the microbiota in numerous diseases, either affecting the skin or other organs. What it is well established is that its dysregulation promotes several cutaneous disorders (i.e. psoriasis and atopic dermatitis). To date, little is known about its composition, mediators and role in the genesis, progression and response to therapy of Non-Melanoma Skin Cancer (NMSC). Starting from a bibliographic study, we classified the selected articles into four sections: i) normal skin microbiota; ii) in vitro study models; iii) microbiota and NMSC and iv) probiotics, antibiotics and NMSC. What has emerged is how skin microflora changes, mainly represented by increases of Staphylococcus aureus, Streptococcus pyogenes and Pseudomonas aeruginosa strains, modifications in the mutual quantity of β-Human papillomavirus genotypes, of Epstein Barr Virus and Malassezia or candidiasis, may contribute to the induction of a state of chronic self-maintaining inflammation, leading to cancer. In this context, the role of S. aureus and that of specific antimicrobial peptides look to be prominent. Moreover, although antibiotics may contribute to carcinogenesis, due to their ability to influence the microbiota balance, specific probiotics, such as Lacticaseibacillus rhamnosus GG, Lactobacillus johnsonii NCC 533 and Bifidobacteria spp., may be protective.
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Affiliation(s)
- Diletta Francesca Squarzanti
- Department of Health Sciences (DiSS), University of Piemonte Orientale (UPO), Novara, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases (CAAD), DiSS, UPO, Novara, Italy
| | - Elisa Zavattaro
- Department of Translational Medicine (DiMeT), UPO, Novara, Italy
| | - Stefania Pizzimenti
- Department of Clinical and Biological Sciences (DSCB), University of Turin, Turin, Italy
| | | | - Paola Savoia
- Department of Health Sciences (DiSS), University of Piemonte Orientale (UPO), Novara, Italy
| | - Barbara Azzimonti
- Department of Health Sciences (DiSS), University of Piemonte Orientale (UPO), Novara, Italy.,Center for Translational Research on Autoimmune and Allergic Diseases (CAAD), DiSS, UPO, Novara, Italy
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25
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Sharma VR, Singh M, Kumar V, Yadav M, Sehrawat N, Sharma DK, Sharma AK. Microbiome dysbiosis in cancer: Exploring therapeutic strategies to counter the disease. Semin Cancer Biol 2020; 70:61-70. [PMID: 32693015 DOI: 10.1016/j.semcancer.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/11/2020] [Accepted: 07/11/2020] [Indexed: 02/09/2023]
Abstract
Cancer being a multiplex disease which involves many genomic and physiological alterations that occur consistently in the cancerous tissue, making the treatment and management of the disease even more complicated. The human gut microbiota (GM) harbors collective genomes of microbes comprising of trillions of bacteria along with fungi, archaea, and viruses that have the tendency to affect the development and progression of cancer. Moreover, inter-microbial interactions, diversity and distinct differences among the GM populations could influence the course of disease, making the microbiome an ideal target or to be modulated in such a way so as to improve cancer therapeutics with better efficacy and reduced toxicity. Current review focuses upon exploring the association of gut microbiota with the progression of cancer for which a structured search of bibliographic databases for peer-reviewed research literature has been carried out using focused review questions and inclusion/exclusion criteria. Through this review one could envisage a wide-spectrum role of microbiota in maintaining host metabolism, immune homeostasis paving the way for an anticancer diagnostic and therapeutic solution that has the potential to counter the menace of anti-cancer drug resistance as well.
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Affiliation(s)
- Var Ruchi Sharma
- Department of Biotechnology, Sri Guru Gobind Singh College Sector-26, Chandigarh UT, 160019, India
| | - Manoj Singh
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala Haryana, 133207, India
| | - Vikas Kumar
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala Haryana, 133207, India
| | - Mukesh Yadav
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala Haryana, 133207, India
| | - Nirmala Sehrawat
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala Haryana, 133207, India
| | | | - Anil K Sharma
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala Haryana, 133207, India.
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Development of a β-HPV vaccine: Updates on an emerging frontier of skin cancer prevention. J Clin Virol 2020; 126:104348. [PMID: 32334327 DOI: 10.1016/j.jcv.2020.104348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/22/2020] [Accepted: 03/29/2020] [Indexed: 12/11/2022]
Abstract
Human papillomaviruses (HPVs) are small, non-enveloped, doublestranded DNA viruses. Over 200 subtypes of HPV have been identified, organized into five major genera. β-HPVs are a group of approximately 50 HPV subtypes that preferentially infect cutaneous sites. While α-HPVs are primarily responsible for genital lesions and mucosal cancers, growing evidence has established an association between β-HPVs and the development of cutaneous squamous cell carcinomas. Given this association, the development of a vaccine against β-HPVs has become an important topic of research; however, currently licensed vaccines only provide coverage for genital HPVs, leaving β-HPV infections and their associated skin cancers unaddressed. In this review, we summarize the current advances in β-HPV vaccine development, including progress made in preclinical testing and limited clinical data. We also discuss novel findings in the viral pathomechanisms involved in β-HPV cutaneous tumorigenesis that may play a large role in future vaccine development. We hope that synthesizing the available data and advances surrounding β- HPV vaccine development will not only lead to increased dedication to vaccine development, but also heightened awareness of a future vaccine among clinicians and the public.
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Gupta I, Nasrallah GK, Sharma A, Jabeen A, Smatti MK, Al-Thawadi HA, Sultan AA, Alkhalaf M, Vranic S, Moustafa AEA. Co-prevalence of human Papillomaviruses (HPV) and Epstein-Barr virus (EBV) in healthy blood donors from diverse nationalities in Qatar. Cancer Cell Int 2020; 20:107. [PMID: 32265596 PMCID: PMC7118960 DOI: 10.1186/s12935-020-01190-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 03/27/2020] [Indexed: 12/31/2022] Open
Abstract
Background Infections by both human oncoviruses, human Papillomaviruses (HPV) and Epstein–Barr virus (EBV) are very common in the adult human population and are associated with various malignancies. While HPV is generally transmitted sexually or via skin-to-skin contact, EBV is frequently transmitted by oral secretions, blood transfusions and organ transplants. This study aims to determine the prevalence and circulating genotypes of HPV and EBV in healthy blood donors in Qatar. Methods We explored the co-prevalence of high-risk HPVs and EBV in 378 males and only 7 females blood donors of different nationalities (mainly from Qatar, Egypt, Syria, Jordan, Pakistan, and India) residing in Qatar, using polymerase chain reaction (PCR). DNA was extracted from the buffy coat and genotyping was performed using PCR and nested-PCR targeting E6 and E7 as well as LMP-1 of HPV and EBV, respectively. Results We found that from the total number of 385 cases of healthy blood donors studied, 54.8% and 61% of the samples are HPVs and EBV positive, respectively. Additionally, our data revealed that the co-presence of both high-risk HPVs and EBV is 40.4% of the total samples. More significantly, this study pointed out for the first time that the most frequent high-risk HPV types in Qatar are 59 (54.8%), 31 (53.7%), 52 (49.1%), 51 (48.6%), 58 (47%) and 35 (45.5%), while the most commonly expressed low-risk HPV types are 53 (50.6%), 11 (45.5), 73 (41.7%) and 6 (41.3%), with all the cases showing multiple HPVs infection. Conclusion In this study, we demonstrated for the first time that HPV and EBV are commonly co-present in healthy blood donors in Qatar. On the other hand, it is important to highlight that these oncoviruses can also be co-present in several types of human cancers where they can cooperate in the initiation and/or progression of these cancers. Therefore, more studies regarding the co-presence of these oncoviruses and their interaction are necessary to understand their cooperative role in human diseases.
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Affiliation(s)
- Ishita Gupta
- 1College of Medicine, QU Health, Qatar University, Doha, Qatar
| | | | - Anju Sharma
- 1College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Ayesha Jabeen
- 1College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Maria K Smatti
- 2Biomedical Research Centre, Qatar University, Doha, Qatar
| | | | | | - Moussa Alkhalaf
- 4Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Semir Vranic
- 1College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Ala-Eddin Al Moustafa
- 1College of Medicine, QU Health, Qatar University, Doha, Qatar.,2Biomedical Research Centre, Qatar University, Doha, Qatar
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Shah UJ, Nasiruddin M, Dar SA, Khan MKA, Akhter MR, Singh N, Rabaan AA, Haque S. Emerging biomarkers and clinical significance of HPV genotyping in prevention and management of cervical cancer. Microb Pathog 2020; 143:104131. [PMID: 32169490 DOI: 10.1016/j.micpath.2020.104131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/10/2020] [Accepted: 03/06/2020] [Indexed: 12/15/2022]
Abstract
Cervical cancer is a growing and serious problem world-wide in women, but more acute in developing countries especially in Indian subcontinent. The main causative agent for the disease is Human Papilloma Virus (HPV). The history of the cervical cancer goes back to eighteenth century as the HPV infection is reported since 1800s. Presently, the genetic structure of HPV is well defined. Several screening tests including cytology and visual based screening and high risk HPV testing are available. Also available are various clinical and commercial diagnostic tests. However due to the lack of awareness and population-based screening programs, the morbidity and mortality rate is alarmingly high. There are new emerging biomarkers including E6/E7 mRNA, p16ink4a, markers of aberrant S-phase induction, chromosomal abnormalities and miRNAs along with advanced genotyping methods. These markers have clinical significance and are helpful in disease prevention and management. Further, recent advancement in the field of metagenomics has increased the prospects of identifying newer microbes, viruses hitherto reported thus far in the context of HPV infection. Analysis of HPV cases using modern tools including genotyping using more powerful biomarkers is envisaged to enhance the prospects of early diagnosis, better prognosis, more reliable treatment and eventual management of the disease.
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Affiliation(s)
- Ushma Jaykamal Shah
- MedGenome Labs Ltd., Kailash Cancer Hospital and Research Center, Muni Seva Ashram, P.O. Goraj, Tal. Waghodia, Dist. Vadodara, 391760, Gujarat, India
| | - Mohammad Nasiruddin
- Anand Diagnostic Laboratory (A Neuberg Associate), Neuberg Anand Reference Laboratory, Anand Tower, 54, Bowring Hospital Road, Shivajinagar, Bangalore - 560001, India.
| | - Sajad Ahmad Dar
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia
| | - Md Khurshid Alam Khan
- School of Life Sciences, BS Abdur Rahman Crescent Institute of Science and Technology, Chennai, 600048, Tamil Nadu, India
| | - Mohammad Riyaz Akhter
- MedGenome Labs Ltd., 3rd Floor, Narayana Nethralaya Building, Narayana Health City, # 258/A, Bommasandra, Hosur Road, Bangalore, 560099, Karnataka, India
| | - Nidhi Singh
- Department of Obstetrics and Gynecology, Prasad Institute of Medical Sciences, Lucknow, 226401, Uttar Pradesh, India
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Saudi Aramco, Dhahran, 31311, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, 45142, Saudi Arabia.
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Abstract
The discovery of bacteria in the female urinary bladder has fundamentally changed current dogma regarding the urinary tract and related urinary disorders. Previous research characterized many of the bacterial components of the female urinary tract, but the viral fraction of this community is largely unknown. Viruses within the human microbiota far outnumber bacterial cells, with the most abundant viruses being those that infect bacteria (bacteriophages). Similar to observations within the microbiota of the gut and oral cavity, preliminary surveys of the urinary tract and bladder microbiota indicate a rich diversity of uncharacterized bacteriophage (phage) species. Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome using phages has therapeutic potential for lower urinary tract symptoms. Furthermore, as natural predators of bacteria, phages have garnered renewed interest for their use as antimicrobial agents, for instance, in the treatment of urinary tract infections.
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Human Papillomavirus and carcinogenesis: Novel mechanisms of cell communication involving extracellular vesicles. Cytokine Growth Factor Rev 2020; 51:92-98. [PMID: 31973992 PMCID: PMC7108386 DOI: 10.1016/j.cytogfr.2019.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/18/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022]
Abstract
A group of mucosal HPVs are the causative agents of cervical cancer and are associated to other cancers. Certain cutaneous HPVs are involved in the development of cutaneous squamous cell carcinoma. EVs released by HPV+ cells convey a specific cargo of mRNAs and microRNAs. The EV delivery from HPV+ cells to non-infected recipient cells may represent a novel mechanism of tumorigenesis promotion.
A small group of mucosal Human Papillomaviruses are the causative agents of cervical cancer and are also associated with other types of cancers. Certain cutaneous Human Papillomaviruses seem to have a role as co-factors in the UV-induced carcinogenesis of the skin. The main mechanism of the tumorigenesis induced by Human Papillomaviruses is linked to the transforming activity of the viral E6 and E7 oncoproteins. However, other mechanisms, such as the gene expression control by specific microRNAs expression and deregulation of immune inflammatory mediators, may be important in the process of transformation. In this context, the release of Extracellular Vesicles with a specific cargo (microRNAs involved in tumorigenesis, mRNAs of viral oncoproteins, cytokines, chemokines) appears to play a key role.
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Ranjeva SL, Mihaljevic JR, Joseph MB, Giuliano AR, Dwyer G. Untangling the dynamics of persistence and colonization in microbial communities. THE ISME JOURNAL 2019; 13:2998-3010. [PMID: 31444482 PMCID: PMC6863904 DOI: 10.1038/s41396-019-0488-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 07/23/2019] [Accepted: 08/02/2019] [Indexed: 01/19/2023]
Abstract
A central goal of community ecology is to infer biotic interactions from observed distributions of co-occurring species. Evidence for biotic interactions, however, can be obscured by shared environmental requirements, posing a challenge for statistical inference. Here, we introduce a dynamic statistical model, based on probit regression, that quantifies the effects of spatial and temporal covariance in longitudinal co-occurrence data. We separate the fixed pairwise effects of species occurrences on persistence and colonization rates, a potential signal of direct interactions, from latent pairwise correlations in occurrence, a potential signal of shared environmental responses. We first validate our modeling framework with several simulation studies. Then, we apply the approach to a pressing epidemiological question by examining how human papillomavirus (HPV) types coexist. Our results suggest that while HPV types respond similarly to common host traits, direct interactions are sparse and weak, so that HPV type diversity depends largely on shared environmental drivers. Our modeling approach is widely applicable to microbial communities and provides valuable insights that should lead to more directed hypothesis testing and mechanistic modeling.
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Affiliation(s)
- Sylvia L Ranjeva
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Joseph R Mihaljevic
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA.
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | | | - Anna R Giuliano
- Center for Immunization and Infection in Cancer Research (CIIRC), Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Greg Dwyer
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
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Mitochondrial somatic mutations and the lack of viral genomic variation in recurrent respiratory papillomatosis. Sci Rep 2019; 9:16625. [PMID: 31719597 PMCID: PMC6851396 DOI: 10.1038/s41598-019-53148-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022] Open
Abstract
Recurrent Respiratory Papillomatosis (RRP) is a rare disease of the aerodigestive tract caused by the Human Papilloma Virus (HPV) that manifests as profoundly altered phonatory and upper respiratory anatomy. Current therapies are primarily symptomatic; enhanced insight regarding disease-specific biology of RRP is critical to improved therapeutics for this challenging population. Multiplex PCR was performed on oral rinses collected from twenty-three patients with adult-onset RRP every three months for one year. Twenty-two (95.6%) subjects had an initial HPV positive oral rinse. Of those subjects, 77.2% had an additional positive oral rinse over 12 months. A subset of rinses were then compared to tissue samples in the same patient employing HPViewer to determine HPV subtype concordance. Multiple HPV copies (60–787 per human cell) were detected in RRP tissue in each patient, but a single dominant HPV was found in individual samples. These data confirm persistent oral HPV infection in the majority of patients with RRP. In addition, three novel HPV6 isolates were found and identical HPV strains, at very low levels, were identified in oral rinses in two patients suggesting potential HPV subtype concordance. Finally, somatic heteroplasmic mtDNA mutations were observed in RRP tissue with 1.8 mutations per sample and two nonsynonymous variants. These data provide foundational insight into both the underlying pathophysiology of RRP, but also potential targets for intervention in this challenging patient cohort.
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Aints A, Mölder S, Salumets A. EXTL3-interacting endometriosis-specific serum factors induce colony formation of endometrial stromal cells. Sci Rep 2019; 9:12562. [PMID: 31467315 PMCID: PMC6715673 DOI: 10.1038/s41598-019-48840-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 08/12/2019] [Indexed: 12/30/2022] Open
Abstract
Endometriosis is a benign chronic condition characterized by the existence of endometrial-like stroma and glandular tissue in extrauterine locations. The molecular mechanisms of its pathogenesis have not been elucidated. We have studied the role of EXTL3 (exostosin-like 3) in endometriosis and found that it is expressed in endometrial tissue as well as endometriosis lesions. We have found that serum from endometriosis patients contains a factor or factors, which interact with EXTL3 resulting in strongly increased colony formation in regenerating cell culture. We also found increased anti-EXTL3 antibodies in endometriosis patients’ sera. EXTL3 is an N-acetyl glucosamine (GlcNAc) transferase, performing a key step in heparan sulfate (HS) glucosaminoglycan synthesis. Many viruses replicate in regenerating epithelial cells and use HS as a receptor for cell entry. We measured antibody titres to viruses, which use HS as a receptor for cell entry, and found rarely increased titres for these viruses in endometriosis sera, whereas titres to viruses using other receptors were equally distributed in study groups. The data indicate that perturbation of HS metabolism is associated with endometriosis.
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Affiliation(s)
- Alar Aints
- Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, 51014, Estonia. .,Kvintest OÜ, Tartu, 50410, Estonia.
| | - Signe Mölder
- Competence Centre on Health Technologies AS, Tartu, 50410, Estonia
| | - Andres Salumets
- Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, 51014, Estonia.,Competence Centre on Health Technologies AS, Tartu, 50410, Estonia.,Institute of Bio- and Translational Medicine, University of Tartu, Tartu, 50411, Estonia.,Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, 00014, Finland
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Hao Y, Yang L, Galvao Neto A, Amin MR, Kelly D, Brown SM, Branski RC, Pei Z. HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA. Bioinformatics 2019; 34:1986-1995. [PMID: 29377990 DOI: 10.1093/bioinformatics/bty037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 01/23/2018] [Indexed: 01/02/2023] Open
Abstract
Motivation Shotgun DNA sequencing provides sensitive detection of all 182 HPV types in tissue and body fluid. However, existing computational methods either produce false positives misidentifying HPV types due to shared sequences among HPV, human and prokaryotes, or produce false negative since they identify HPV by assembled contigs requiring large abundant of HPV reads. Results We designed HPViewer with two custom HPV reference databases masking simple repeats and homology sequences respectively and one homology distance matrix to hybridize these two databases. It directly identified HPV from short DNA reads rather than assembled contigs. Using 100 100 simulated samples, we revealed that HPViewer was robust for samples containing either high or low number of HPV reads. Using 12 shotgun sequencing samples from respiratory papillomatosis, HPViewer was equal to VirusTAP, and Vipie and better than HPVDetector with the respect to specificity and was the most sensitive method in the detection of HPV types 6 and 11. We demonstrated that contigs-based approaches had disadvantages of detection of HPV. In 1573 sets of metagenomic data from 18 human body sites, HPViewer identified 104 types of HPV in a body-site associated pattern and 89 types of HPV co-occurring in one sample with other types of HPV. We demonstrated HPViewer was sensitive and specific for HPV detection in metagenomic data. Availability and implementation HPViewer can be accessed at https://github.com/yuhanH/HPViewer/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yuhan Hao
- Department of Pathology.,Applied Bioinformatics Laboratories
| | - Liying Yang
- Department of Pathology.,Department of Medicine
| | | | - Milan R Amin
- Department of Otolaryngology-Head and Neck Surgery
| | | | - Stuart M Brown
- Applied Bioinformatics Laboratories.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | | | - Zhiheng Pei
- Department of Pathology.,Department of Medicine.,Department of Veterans Affairs New York Harbor Healthcare System, New York, NY, USA
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Di Bonito P, Galati L, Focà A, Brambilla M, Bisaglia C, Bonanno Ferraro G, Mancini P, Iaconelli M, Veneri C, La Rosa G. Evidence for swine and human papillomavirus in pig slurry in Italy. J Appl Microbiol 2019; 127:1246-1254. [PMID: 31251456 PMCID: PMC7166630 DOI: 10.1111/jam.14363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/15/2019] [Accepted: 06/20/2019] [Indexed: 01/10/2023]
Abstract
AIMS The diversity and the geographical distribution of swine papillomaviruses (PVs) are virtually unknown. The occurrence and the diversity of swine PV were therefore investigated in pig slurry collected in Italy, to contribute towards filling this gap in knowledge. METHODS AND RESULTS Twenty-two slurry samples underwent analysis by nested PCR and DNA sequencing using published and newly designed specific primer pairs for Sus scrofa papillomavirus (SsPV) type 1 and 2 (SsPV1 and 2), along with degenerate PV-specific primers targeting the major coat protein L1 and the helicase protein E1. Overall, three samples (13·6%) were positive for SsPV1 by specific primers, and nucleotide (nt) sequences showed 99-100% nt identity with SsPV1 variant a (EF395818), while SsPV2 was not found in any sample. Using generic primers, eight samples (36·4%) were tested positive for human papillomavirus (HPV), and were characterized as follows: β1-HPV8, β1-HPV14, β1-HPV206, β2-HPV113, β2-HPV120 and γ1-HPV173. Moreover, one unclassified γ-type was detected. CONCLUSIONS Both swine and human PVs were detected in pig slurry in this study. The unexpected presence of HPV in pig waste could be explained as the result of an improper use of the sewage collection pits and/or with improper procedures of the operators. SIGNIFICANCE AND IMPACT OF THE STUDY This study reports the first detection of SsPV1 in Italy, along with the first detection of HPVs in pig slurry samples in Italy, and expands our knowledge about PV diversity and geographic distribution.
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Affiliation(s)
- P Di Bonito
- Viral Hepatitis, Oncoviruses and Retroviruses (EVOR) Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - L Galati
- Viral Hepatitis, Oncoviruses and Retroviruses (EVOR) Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - A Focà
- School of medicine, "Magna Graecia" University, Catanzaro, Italy
| | - M Brambilla
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Research Centre for Engineering and Agri Food Processing, Treviglio, BG, Italy
| | - C Bisaglia
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA), Research Centre for Engineering and Agri Food Processing, Treviglio, BG, Italy
| | - G Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - P Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - M Iaconelli
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - C Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - G La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
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Brusselaers N, Shrestha S, van de Wijgert J, Verstraelen H. Vaginal dysbiosis and the risk of human papillomavirus and cervical cancer: systematic review and meta-analysis. Am J Obstet Gynecol 2019; 221:9-18.e8. [PMID: 30550767 DOI: 10.1016/j.ajog.2018.12.011] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 01/16/2023]
Abstract
OBJECTIVE The vaginal microbiota proposedly influence the association between human papillomavirus and cervical cancer. Our aim was to assess whether vaginal dysbiosis affects human papilloma virus acquisition, persistence, and progression to related cervical premalignancy. DATA SORUCES MEDLINE, Embase, CINAHL, Cochrane Library, and Web of Science (inception until June 2018) were used for this study. The study protocol was registered at PROSPERO (CRD42016035620). STUDY ELIGIBILITY CRITERIA This systematic review included all observational studies reporting on incident human papilloma virus, persistent human papilloma virus, and/or related cervical disease in women with or without vaginal dysbiosis prior to outcome assessment. STUDY APPRAISAL AND SYNTHESIS METHODS We used random-effects models for meta-analyses and report pooled relative risks with 95% confidence intervals. The risk for incident and/or persistent human papilloma virus or related cervical disease based on longitudinal results was determined. RESULTS Of 1645 unique articles, 15 mainly prospective cohort studies were included, published between 2003 and 2017, including a total of 101,049 women. Vaginal dysbiosis was associated with an increased risk of incident human papilloma virus (overall relative risk, 1.33, 1.18-1.50, I2 = 0%; among young women relative risk, 1.43, 1.10-1.85, I2 = 0%), human papilloma virus persistence (overall relative risk, 1.14, 1.01-1.28, I2 = 44.2%; for oncogenic types relative risk, 1.18, 1.01-1.38, I2 = 0%), and high-grade lesions and cancer (relative risk, 2.01, 1.40-3.01, I2 = 0%), but women with lesions/cancer were compared with those without, regardless of their oncogenic human papilloma virus status. Overall, comparable results were found in the molecular vaginal microbiota studies. CONCLUSION This study supports a causal link between vaginal dysbiosis and cervical cancer along the oncogenic human papillomavirus acquisition, persistence, and cervicovaginal dysplasia development pathway.
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Farina R, Severi M, Carrieri A, Miotto E, Sabbioni S, Trombelli L, Scapoli C. Whole metagenomic shotgun sequencing of the subgingival microbiome of diabetics and non-diabetics with different periodontal conditions. Arch Oral Biol 2019; 104:13-23. [PMID: 31153098 DOI: 10.1016/j.archoralbio.2019.05.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 01/01/2023]
Abstract
OBJECTIVE The aim of this study was to use high-resolution whole metagenomic shotgun sequencing to characterize the subgingival microbiome of patients with/without type 2 Diabetes Mellitus and with/without periodontitis. DESIGN Twelve subjects, falling into one of the four study groups based on the presence/absence of poorly controlled type 2 Diabetes Mellitus and moderate-severe periodontitis, were selected. For each eligible subject, subgingival plaque samples were collected at 4 sites, all representative of the periodontal condition of the individual (i.e., non-bleeding sulci in subjects without a history of periodontitis, bleeding pockets in patients with moderate-severe periodontitis). The subgingival microbiome was evaluated using high-resolution whole metagenomic shotgun sequencing. RESULTS The results showed that: (i) the presence of type 2 Diabetes Mellitus and/or periodontitis were associated with a tendency of the subgingival microbiome to decrease in richness and diversity; (ii) the presence of type 2 Diabetes Mellitus was not associated with significant differences in the relative abundance of one or more species in patients either with or without periodontitis; (iii) the presence of periodontitis was associated with a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in type 2 Diabetes Mellitus patients. CONCLUSIONS Whole metagenomic shotgun sequencing of the subgingival microbiome was extremely effective in the detection of low-abundant taxon. Our results point out a significantly higher relative abundance of Anaerolineaceae bacterium oral taxon 439 in patients with moderate to severe periodontitis vs patients without history of periodontitis, which was maintained when the comparison was restricted to type 2 diabetics.
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Affiliation(s)
- Roberto Farina
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Italy; Operative Unit of Dentistry, University-Hospital of Ferrara, Italy.
| | - Mattia Severi
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Italy
| | - Alberto Carrieri
- Department of Life Sciences and Biotechnology - Section of Biology and Evolution, University of Ferrara, Italy
| | - Elena Miotto
- Department of Life Sciences and Biotechnology - Section of Pathology and Applied Microbiology,University of Ferrara, Italy
| | - Silvia Sabbioni
- Department of Life Sciences and Biotechnology - Section of Pathology and Applied Microbiology,University of Ferrara, Italy
| | - Leonardo Trombelli
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Italy; Operative Unit of Dentistry, University-Hospital of Ferrara, Italy
| | - Chiara Scapoli
- Research Centre for the Study of Periodontal and Peri-Implant Diseases, University of Ferrara, Italy; Department of Life Sciences and Biotechnology - Section of Biology and Evolution, University of Ferrara, Italy
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Siqueira JD, Curty G, Xutao D, Hofer CB, Machado ES, Seuánez HN, Soares MA, Delwart E, Soares EA. Composite Analysis of the Virome and Bacteriome of HIV/HPV Co-Infected Women Reveals Proxies for Immunodeficiency. Viruses 2019; 11:v11050422. [PMID: 31067713 PMCID: PMC6563245 DOI: 10.3390/v11050422] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/26/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023] Open
Abstract
The human cervical microbiome is complex, and its role in health and disease has just begun to be elucidated. In this study, 57 cervical swab samples from 19 HIV/HPV co-infected women were analyzed for both virome and bacteriome composition. Virome analysis focused on circular DNA viruses through rolling circle amplification followed by next-generation sequencing (NGS). Data were assigned to virus families and genera, and HPV types were identified. NGS data of bacterial 16S from a subset of 24 samples were assigned to operational taxonomic units and classified according to vaginal microbiome community state types (CSTs). Four viral families were found: Papillomaviridae, Anelloviridae, Genomoviridae, and Herpesviridae. Papillomavirus reads were more abundant in women with premalignant cervical lesions, which were also strongly associated with multiple (≥3) high-risk HPV infection. Anellovirus read abundance was negatively correlated with host CD4+ T-cell counts. The bacteriome revealed the presence of CST III and CST IV, and women with ≥1% frequency of genomovirus or herpesvirus reads displayed an increased risk of carrying CST IV. By characterizing the composition of the cervical circular DNA viruses and the bacteriome of HIV/HPV co-infected women, we identified putative interactions between these two microorganism communities and their associations with patients’ clinical characteristics, notably immunodeficiency status.
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Affiliation(s)
- Juliana D Siqueira
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Gislaine Curty
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
| | - Deng Xutao
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Cristina B Hofer
- Instituto de Ginecologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20211-340, Brazil.
| | - Elizabeth S Machado
- Instituto de Puericultura e Pediatria Martagão Gesteira, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-912, Brazil.
| | - Héctor N Seuánez
- Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21944-970, Brazil.
| | - Marcelo A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
- Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21944-970, Brazil.
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Esmeralda A Soares
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro 20231-050, Brazil.
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de Lourdes Mora-García M, López-Cisneros S, Gutiérrez-Serrano V, García-Rocha R, Weiss-Steider B, Hernández-Montes J, Sánchez-Peña HI, Ávila-Ibarra LR, Don-López CA, Muñóz-Godínez R, Pineda DBT, Chacón-Salinas R, Vallejo-Castillo L, Pérez-Tapia SM, Monroy-García A. HPV-16 Infection Is Associated with a High Content of CD39 and CD73 Ectonucleotidases in Cervical Samples from Patients with CIN-1. Mediators Inflamm 2019; 2019:4651627. [PMID: 31205451 PMCID: PMC6530152 DOI: 10.1155/2019/4651627] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/14/2019] [Accepted: 04/09/2019] [Indexed: 01/26/2023] Open
Abstract
The development of cervical cancer (CeCa) is associated with high-risk human papilloma virus (HR-HPV) infections, mainly HPV-16, which is present in more than 50% of cases. The presence of immunosuppressive factors in the early stages of the disease is also strongly linked to CeCa progression. In this context, it is unknown whether ectonucleotidases CD39 and CD73, which are involved in the production of adenosine (Ado) that suppresses the specific antitumor immune response, are present in precursor lesions of CeCa. In this pilot study, we analyzed the presence of CD39 and CD73 and their capacity to generate Ado in 25 cervical samples from patients with grade 1 cervical intraepithelial neoplasms (CIN-1) and 25 samples from normal donors (NDs) free of HPV infection. Cells obtained from cervical samples of CIN-1 patients positive for HPV-16 showed higher CD39 and CD73 contents compared to samples obtained from CIN-1 patients negative for HPV-16 and NDs. Interestingly, solubilized cervical mucus from these patients also showed higher contents of soluble CD39 and CD73, which were associated with a greater capacity to produce Ado from the hydrolysis of adenosine triphosphate (ATP) and adenosine monophosphate (AMP). In addition, serum samples of these patients showed higher levels of TGF-β than those of CIN-1 patients negative for HPV-16 and ND. These results suggest that persistent infection with HR-HPV, mostly HPV-16, in CIN-1 patients may promote the expression of CD39 and CD73 through the production of TGF-β in precursor lesions to generate an immunosuppressive microenvironment and allow its progression to CeCa.
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Affiliation(s)
| | - Sofía López-Cisneros
- Laboratorio de Inmunología y Cáncer, Unidad de Investigación Médica en Enfermedades Oncológicas, CMN SXXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Vianey Gutiérrez-Serrano
- Laboratorio de Inmunobiología, UIDCC-UMIEZ, FES-Zaragoza, UNAM, Ciudad de México, Mexico
- Laboratorio de Inmunología y Cáncer, Unidad de Investigación Médica en Enfermedades Oncológicas, CMN SXXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Rosario García-Rocha
- Laboratorio de Inmunobiología, UIDCC-UMIEZ, FES-Zaragoza, UNAM, Ciudad de México, Mexico
- Laboratorio de Inmunología y Cáncer, Unidad de Investigación Médica en Enfermedades Oncológicas, CMN SXXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Benny Weiss-Steider
- Laboratorio de Inmunobiología, UIDCC-UMIEZ, FES-Zaragoza, UNAM, Ciudad de México, Mexico
| | - Jorge Hernández-Montes
- Laboratorio de Inmunobiología, UIDCC-UMIEZ, FES-Zaragoza, UNAM, Ciudad de México, Mexico
| | | | - Luis Roberto Ávila-Ibarra
- Laboratorio de Inmunología y Cáncer, Unidad de Investigación Médica en Enfermedades Oncológicas, CMN SXXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
- Programa de Posgrado en Ciencias Biológicas, UNAM, Ciudad de México, Mexico
| | | | - Ricardo Muñóz-Godínez
- Laboratorio de Inmunología y Cáncer, Unidad de Investigación Médica en Enfermedades Oncológicas, CMN SXXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
- Programa de Posgrado en Ciencias Biológicas, UNAM, Ciudad de México, Mexico
| | - Daniela Berenice Torres Pineda
- Laboratorio de Inmunología y Cáncer, Unidad de Investigación Médica en Enfermedades Oncológicas, CMN SXXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
- Programa de Posgrado en Ciencias Biológicas, UNAM, Ciudad de México, Mexico
| | - Rommel Chacón-Salinas
- Unidad de Desarrollo e Investigación en Bioprocesos (UDIBI), Instituto Politécnico Nacional, Ciudad de México, Mexico
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional (ENCB-IPN), Ciudad de México, Mexico
| | - Luis Vallejo-Castillo
- Unidad de Desarrollo e Investigación en Bioprocesos (UDIBI), Instituto Politécnico Nacional, Ciudad de México, Mexico
- Departamento de Farmacología, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav-IPN), Ciudad de México, Mexico
| | - Sonia Mayra Pérez-Tapia
- Unidad de Desarrollo e Investigación en Bioprocesos (UDIBI), Instituto Politécnico Nacional, Ciudad de México, Mexico
- Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional (ENCB-IPN), Ciudad de México, Mexico
| | - Alberto Monroy-García
- Laboratorio de Inmunobiología, UIDCC-UMIEZ, FES-Zaragoza, UNAM, Ciudad de México, Mexico
- Laboratorio de Inmunología y Cáncer, Unidad de Investigación Médica en Enfermedades Oncológicas, CMN SXXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
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Clarke EL, Taylor LJ, Zhao C, Connell A, Lee JJ, Fett B, Bushman FD, Bittinger K. Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. MICROBIOME 2019; 7:46. [PMID: 30902113 PMCID: PMC6429786 DOI: 10.1186/s40168-019-0658-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 03/11/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND Analysis of mixed microbial communities using metagenomic sequencing experiments requires multiple preprocessing and analytical steps to interpret the microbial and genetic composition of samples. Analytical steps include quality control, adapter trimming, host decontamination, metagenomic classification, read assembly, and alignment to reference genomes. RESULTS We present a modular and user-extensible pipeline called Sunbeam that performs these steps in a consistent and reproducible fashion. It can be installed in a single step, does not require administrative access to the host computer system, and can work with most cluster computing frameworks. We also introduce Komplexity, a software tool to eliminate potentially problematic, low-complexity nucleotide sequences from metagenomic data. A unique component of the Sunbeam pipeline is an easy-to-use extension framework that enables users to add custom processing or analysis steps directly to the workflow. The pipeline and its extension framework are well documented, in routine use, and regularly updated. CONCLUSIONS Sunbeam provides a foundation to build more in-depth analyses and to enable comparisons in metagenomic sequencing experiments by removing problematic, low-complexity reads and standardizing post-processing and analytical steps. Sunbeam is written in Python using the Snakemake workflow management software and is freely available at github.com/sunbeam-labs/sunbeam under the GPLv3.
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Affiliation(s)
- Erik L. Clarke
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Louis J. Taylor
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Andrew Connell
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Jung-Jin Lee
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Bryton Fett
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
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Murahwa AT, Meiring TL, Mbulawa ZZA, Williamson AL. Discovery, characterisation and genomic variation of six novel Gammapapillomavirus types from penile swabs in South Africa. PAPILLOMAVIRUS RESEARCH 2019; 7:102-111. [PMID: 30844514 PMCID: PMC6416656 DOI: 10.1016/j.pvr.2019.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 02/14/2019] [Accepted: 02/25/2019] [Indexed: 12/21/2022]
Abstract
Six novel human papillomaviruses from penile swabs were characterised. Multiple full genome clones for each novel type were generated, and complete genome sizes were: HPV211 (7253bp), HPV212 (7208bp), HPV213 (7096bp), HPV214 (7357), HPV215 (7186bp) and HPV216 (7233bp). Phylogenetically the novel papillomaviruses all clustered with Gammapapillomaviruses: HPV211 is most closely related to HPV168 (72% identity in the L1 nucleotide sequence) of the Gamma-8 species, HPV212 is most closely related to HPV144 (82.9%) of the Gamma-17 species, HPV213 is most closely related to HPV153 (71.8%) of the Gamma-13 species, HPV214 is most closely related to HPV103 (75.3%) of the Gamma-6 species, HPV215 and HPV216 are most closely related to HPV129 (76.8% and 79.2% respectively) of the Gamma-9 species. The novel HPV types demonstrated the classical genomic organisation of Gammapapillomavirusess, with seven open reading frames (ORFs) encoding five early (E1, E2, E4, E6 and E7) and two late (L1 and L2) proteins. Typical of Gammapapillomavirusess the novel types all lacked the E5 ORF and HPV214 also lacked the E6 ORF. HPV212 had nine unique variants, HPV213 had five and HPV215 had four variants. Conserved domains observed among the novel types are the Zinc finger Binding Domain and PDZ domains. A retinoblastoma binding domain (pRB) binding domain in E7 protein was additionally identified in HPV214. This study expands the knowledge of the rapidly growing Gammapapillomavirus genus.
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Affiliation(s)
- Alltalents T Murahwa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Tracy L Meiring
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Zizipho Z A Mbulawa
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Center for HIV and STIs, National Institute for Communicable Disease, National Health Laboratory Service, Johannesburg, South Africa; SAMRC Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anna-Lise Williamson
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; SAMRC Gynaecological Cancer Research Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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Abstract
Malignancies were one of the earliest recognized manifestations that led to the description of the acquired immune deficiency syndrome (AIDS). The majority of cancers in AIDS patients are associated with coinfection with oncogenic viruses, such as Epstein-Barr virus, human herpesvirus 8, and human papillomavirus, with resulting malignancies occurring secondary to diminished immune surveillance against viruses and virus-infected tumor cells. Over 50% of AIDS lymphomas are associated with Epstein-Barr virus (EBV) and/or HHV8 infection. HHV8-associated diseases include Kaposi sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman disease (MCD). EBV is associated with several malignancies, including Hodgkin lymphoma (HL) and non-Hodgkin lymphoma (NHL). Coinfection with HIV and HPV is associated with an increased risk of various squamous cell carcinomas of epithelial tissues. HAART has significantly impacted the incidence, management, and prognosis of AIDS-related malignancies. In addition to changing the natural history of HIV infection in regard to incidence and survival, HAART has dramatically decreased the incidence of certain virally mediated HIV-associated malignancies such as KS and primary CNS lymphoma. The beneficial effects of HAART on these tumors are attributed to drug-mediated HIV suppression and immune reconstitution. However, HAART has had a less favorable impact on EBV- and HPV-related malignancies. This chapter presents an overview of HIV-associated malignancies mediated by HHV-8, EBV, and HPV, and reviews the effect of HAART on the epidemiology, presentation, treatment, and outcomes of these cancers.
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Annunziata C, Stellato G, Greggi S, Sanna V, Curcio MP, Losito S, Botti G, Buonaguro L, Buonaguro FM, Tornesello ML. Prevalence of "unclassified" HPV genotypes among women with abnormal cytology. Infect Agent Cancer 2018; 13:26. [PMID: 30061920 PMCID: PMC6056927 DOI: 10.1186/s13027-018-0199-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/13/2018] [Indexed: 12/16/2022] Open
Abstract
Background High risk human papillomaviruses (HPVs) have been unequivocally recognised as the necessary cause of squamous intraepithelial lesions (SIL) and invasive carcinoma of the cervix. The distribution and the role of unclassified risk HPV genotypes in cervical neoplasia has not been fully elucidated. Methods Liquid-based cytological samples were collected from 337 women referred for colposcopy following an abnormal cytological diagnosis. HPV DNA was detected by broad-spectrum PCR and genotypes identified by nucleotide sequencing analysis and reverse line blot (RLB). Results The overall frequency of HPV infection was 36.5% (35 out of 96) in samples negative for intraepithelial lesions or malignancy (NILM), 80% (181 out of 226) in low grade SIL and 93.3% (14 out of 15) in high grade SIL (P < 0.001). Thirty-five different genotypes were identified among the 230 HPV-positive cases. The Group 1 oncogenic viruses (HPV16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58 and 59) were found in 21.9, 46.5, and 86.7% of NILM, low grade SIL and high grade SIL, respectively. The Group 2A, including the probably oncogenic virus HPV68, was found in 1 and 0.8% of NILM and low grade SIL, respectively. The Group 2b possibly oncogenic HPVs (HPV34, 53, 66, 67, 70, 73, 82 and 85) were found in 4.2, 21.7 and 26.7% of NILM, low grade SIL and high grade SIL, respectively. The unclassified viruses (HPV12, 42, 54, 55, 61, 62, 81, 83, 84, 89, 90, 91) were detected in 8.3 and 14.6% of NILM and low grade SIL, respectively, and never in high grade SIL. Conclusions Group 1 HPVs were mainly prevalent in high grade SIL and low grade SIL while Group 2B were equally distributed among the two groups. The dominant frequency of unclassified HPVs in low grade SIL and NILM and their rarity in high grade SIL suggests their marginal role in cervical neoplasia of the studied population.
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Affiliation(s)
- Clorinda Annunziata
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", via M Semmola, 80131 Naples, Italy
| | - Giovanni Stellato
- Gynecology Oncology Unit, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", 80131 Naples, Italy
| | - Stefano Greggi
- Gynecology Oncology Unit, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", 80131 Naples, Italy
| | - Veronica Sanna
- 3Department of Pathology, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", 80131 Naples, Italy
| | - Maria Pia Curcio
- 3Department of Pathology, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", 80131 Naples, Italy
| | - Simona Losito
- 3Department of Pathology, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", 80131 Naples, Italy
| | - Gerardo Botti
- 3Department of Pathology, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", 80131 Naples, Italy
| | - Luigi Buonaguro
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", via M Semmola, 80131 Naples, Italy
| | - Franco Maria Buonaguro
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", via M Semmola, 80131 Naples, Italy
| | - Maria Lina Tornesello
- Molecular Biology and Viral Oncology Unit, Istituto Nazionale Tumori IRCCS "Fondazione G. Pascale", via M Semmola, 80131 Naples, Italy
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Nagar P, Hasija Y. Metagenomic approach in study and treatment of various skin diseases: a brief review. BIOMEDICAL DERMATOLOGY 2018. [DOI: 10.1186/s41702-018-0029-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Hasche D, Vinzón SE, Rösl F. Cutaneous Papillomaviruses and Non-melanoma Skin Cancer: Causal Agents or Innocent Bystanders? Front Microbiol 2018; 9:874. [PMID: 29770129 PMCID: PMC5942179 DOI: 10.3389/fmicb.2018.00874] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/16/2018] [Indexed: 12/12/2022] Open
Abstract
There is still controversy in the scientific field about whether certain types of cutaneous human papillomaviruses (HPVs) are causally involved in the development of non-melanoma skin cancer (NMSC). Deciphering the etiological role of cutaneous HPVs requires - besides tissue culture systems - appropriate preclinical models to match the obtained results with clinical data from affected patients. Clear scientific evidence about the etiology and underlying mechanisms involved in NMSC development is fundamental to provide reasonable arguments for public health institutions to classify at least certain cutaneous HPVs as group 1 carcinogens. This in turn would have implications on fundraising institutions and health care decision makers to force - similarly as for anogenital cancer - the implementation of a broad vaccination program against "high-risk" cutaneous HPVs to prevent NMSC as the most frequent cancer worldwide. Precise knowledge of the multi-step progression from normal cells to cancer is a prerequisite to understand the functional and clinical impact of cofactors that affect the individual outcome and the personalized treatment of a disease. This overview summarizes not only recent arguments that favor the acceptance of a viral etiology in NMSC development but also reflects aspects of causality in medicine, the use of empirically meaningful model systems and strategies for prevention.
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Affiliation(s)
- Daniel Hasche
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center, Heidelberg, Germany
| | - Sabrina E Vinzón
- Laboratory of Molecular and Cellular Therapy, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Frank Rösl
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center, Heidelberg, Germany
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Bouwes Bavinck JN, Feltkamp MCW, Green AC, Fiocco M, Euvrard S, Harwood CA, Nasir S, Thomson J, Proby CM, Naldi L, Diphoorn JCD, Venturuzzo A, Tessari G, Nindl I, Sampogna F, Abeni D, Neale RE, Goeman JJ, Quint KD, Halk AB, Sneek C, Genders RE, de Koning MNC, Quint WGV, Wieland U, Weissenborn S, Waterboer T, Pawlita M, Pfister H. Human papillomavirus and posttransplantation cutaneous squamous cell carcinoma: A multicenter, prospective cohort study. Am J Transplant 2018; 18:1220-1230. [PMID: 29024374 PMCID: PMC5947129 DOI: 10.1111/ajt.14537] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/20/2017] [Accepted: 10/03/2017] [Indexed: 01/25/2023]
Abstract
Organ transplant recipients (OTRs) have a 100-fold increased risk of cutaneous squamous cell carcinoma (cSCC). We prospectively evaluated the association between β genus human papillomaviruses (βPV) and keratinocyte carcinoma in OTRs. Two OTR cohorts without cSCC were assembled: cohort 1 was transplanted in 2003-2006 (n = 274) and cohort 2 was transplanted in 1986-2002 (n = 352). Participants were followed until death or cessation of follow-up in 2016. βPV infection was assessed in eyebrow hair by using polymerase chain reaction-based methods. βPV IgG seroresponses were determined with multiplex serology. A competing risk model with delayed entry was used to estimate cumulative incidence of histologically proven cSCC and the effect of βPV by using a multivariable Cox regression model. Results are reported as adjusted hazard ratios (HRs). OTRs with 5 or more different βPV types in eyebrow hair had 1.7 times the risk of cSCC vs OTRs with 0 to 4 different types (HR 1.7, 95% confidence interval 1.1-2.6). A similar risk was seen with high βPV loads (HR 1.8, 95% confidence interval 1.2-2.8). No significant associations were seen between serum antibodies and cSCC or between βPV and basal cell carcinoma. The diversity and load of βPV types in eyebrow hair are associated with cSCC risk in OTRs, providing evidence that βPV is associated with cSCC carcinogenesis and may present a target for future preventive strategies.
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Affiliation(s)
| | - Mariet C. W. Feltkamp
- Department of Medical MicrobiologyLeiden University Medical CenterLeidenThe Netherlands
| | - Adele C. Green
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Marta Fiocco
- Department of Medical Statistics and BioinformaticsLeiden University Medical CenterLeidenThe Netherlands,Institute of MathematicsLeiden UniversityLeidenThe Netherlands
| | - Sylvie Euvrard
- Department of DermatologyEdouard Herriot HospitalHospices Civils de LyonLyonFrance
| | - Catherine A. Harwood
- Centre for Cell Biology and Cutaneous ResearchBlizard Institute, Barts and The London School of Medicine and DentistryQueen Mary University of LondonUK
| | - Shaaira Nasir
- Centre for Cell Biology and Cutaneous ResearchBlizard Institute, Barts and The London School of Medicine and DentistryQueen Mary University of LondonUK
| | - Jason Thomson
- Centre for Cell Biology and Cutaneous ResearchBlizard Institute, Barts and The London School of Medicine and DentistryQueen Mary University of LondonUK
| | - Charlotte M. Proby
- Division of Cancer ResearchUniversity of DundeeNinewells Hospital and Medical SchoolDundeeUK
| | - Luigi Naldi
- Department of DermatologyAzienda Ospedaliera papa Giovanni XXIII, and GISED Study CenterBergamoItaly
| | - Janouk C. D. Diphoorn
- Department of DermatologyAzienda Ospedaliera papa Giovanni XXIII, and GISED Study CenterBergamoItaly
| | - Anna Venturuzzo
- Department of DermatologyAzienda Ospedaliera papa Giovanni XXIII, and GISED Study CenterBergamoItaly
| | - Gianpaolo Tessari
- Department of MedicineSection of DermatologyUniversity of Veronac/o Ospedale Civile MaggioreVeronaItaly
| | - Ingo Nindl
- Department of DermatologyUniversity Hospital CharitéSkin Cancer Center CharitéBerlinGermany
| | | | | | | | - Jelle J. Goeman
- Department of Medical Statistics and BioinformaticsLeiden University Medical CenterLeidenThe Netherlands
| | - Koen D. Quint
- Department of DermatologyLeiden University Medical CenterLeidenThe Netherlands
| | - Anne B. Halk
- Department of DermatologyLeiden University Medical CenterLeidenThe Netherlands
| | - Carmen Sneek
- Department of DermatologyLeiden University Medical CenterLeidenThe Netherlands
| | - Roel E. Genders
- Department of DermatologyLeiden University Medical CenterLeidenThe Netherlands
| | | | | | - Ulrike Wieland
- Institute of VirologyUniversity of CologneCologneGermany
| | | | - Tim Waterboer
- German Cancer Research Center (DKFZ)HeidelbergGermany
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Dutta S, Robitaille A, Aubin F, Fouéré S, Galicier L, Boutboul D, Luzi F, Di Bonito P, Tommasino M, Gheit T. Identification and characterization of two novel Gammapapillomavirus genomes in skin of an immunosuppressed Epidermodysplasia Verruciformis patient. Virus Res 2018; 249:66-68. [PMID: 29526719 DOI: 10.1016/j.virusres.2018.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/03/2018] [Accepted: 03/04/2018] [Indexed: 01/19/2023]
Abstract
Two novel human gamma-papillomavirus genomes (HPV_MTS3, and HPV_MTS4) were isolated from the skin of an immunosuppressed, late-onset Epidermodysplasia Verruciformis patient and fully cloned. The L1 open reading frames of HPV_MTS3 and HPV_MTS4 were 77% and 91% identical to their closest HPV full genome isolates w18c39 and EV03c60, which belong to the species gamma-22and gamma-7 of the genus Gammapapillomavirus, respectively.
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Affiliation(s)
- Sankhadeep Dutta
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
| | - Alexis Robitaille
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
| | - François Aubin
- Dermatology Department and EA3181, Centre National de Référence HPV, Centre Hospitalier Universitaire, Université de Franche-Comté, Besançon, France
| | - Sébastien Fouéré
- STD Unit (Centre des MST) Dermatology Department (Service de Dermatologie), Saint Louis University Hospital, Paris, France
| | - Lionel Galicier
- Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - David Boutboul
- Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris (APHP), Paris, France
| | - Fabiola Luzi
- Plastic and Reconstructive Surgery, San Gallicano Dermatologic Institute, IRCCS, Rome, Italy
| | - Paola Di Bonito
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Massimo Tommasino
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France
| | - Tarik Gheit
- Infections and Cancer Biology Group, International Agency for Research on Cancer, Lyon, France.
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Huang X, Li C, Li F, Zhao J, Wan X, Wang K. Cervicovaginal microbiota composition correlates with the acquisition of high-risk human papillomavirus types. Int J Cancer 2018; 143:621-634. [PMID: 29479697 DOI: 10.1002/ijc.31342] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 01/05/2018] [Accepted: 02/08/2018] [Indexed: 12/29/2022]
Abstract
High-risk (hr) human papillomavirus (HPV) infection is closely associated with the clinical conditions of both squamous intraepithelial lesions (SILs) and cervical carcinoma. However, it remains unclear what factors determine the type of hrHPV infection. Here, we have comprehensively investigated the bacterial composition of the cervicovaginal microbiota of 280 women infected with one type of hrHPV (HPV 16, 52 or 58) by the pyrosequencing of barcoded 16S rRNA genes. Differential microbiota composition was observed among various SIL groups and within the subgroups of each group. This result showed that it is not the microbiota diversity or the common microbiota, but rather agents that are specific to each SIL that might have a positive influence on the acquisition of hrHPV types, independent of abundance. Specifically, a composition of Oribacterium, Lachnobacterium and Thermus in the cervicovaginal microbiota is more likely to be associated with HPV 16, while a composition of Motilibacter in the cervicovaginal microbiota is more likely to be associated with HPV 52, and a composition of Litorilinea and Paludibaculum with a concomitant paucity of L. iners in the cervicovaginal microbiota is more likely to be associated with HPV 58. Furthermore, functional predictions regarding infectious diseases and cancer-related genes disclosed significant differences (p < 0.01) among the different (sub)groups. Our study provides an elucidation of the relationship between the composition of the cervicovaginal microbiota and the type of hrHPV acquired.
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Affiliation(s)
- Xiaojie Huang
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Chao Li
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Fang Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Junwei Zhao
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Xiaoping Wan
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Kai Wang
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
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Hansen BT, Campbell S, Nygård M. Long-term incidence trends of HPV-related cancers, and cases preventable by HPV vaccination: a registry-based study in Norway. BMJ Open 2018; 8:e019005. [PMID: 29476028 PMCID: PMC5855252 DOI: 10.1136/bmjopen-2017-019005] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES Examine long-term incidence trends of human papillomavirus (HPV)-related cancer in Norway, and estimate the number of cancer cases preventable by vaccines against HPV 16/18 or HPV 16/18/31/33/45/52/58. DESIGN Observational registry-based study. We extracted incident cases of HPV-related cancer during 1953-2015 from the Cancer Registry of Norway. Tumour HPV prevalence estimates from large international meta-analyses or from Norway were used to estimate the protective potential of HPV vaccines. PARTICIPANTS AND SETTING The Norwegian population. PRIMARY OUTCOME MEASURES Incidence trend analyses during 1953-2015 for squamous cell carcinoma (SCC) of the cervix, vulva, vagina, oropharynx, anus and penis, and adenocarcinoma of the cervix. Additionally, the number of cancer cases preventable by HPV vaccination. RESULTS Among women, incidences of SCC of the anus, oropharynx, vulva and cervical adenocarcinoma increased, while vaginal SCC showed no trend. For these cancers combined, the average annual percentage change (AAPC) during 1953-2015 was 1.2 (95% CI 0.7 to 1.6). The incidence of cervical SCC generally decreased during 1976-2004 and remained stable thereafter. Among men, incidences of SCC of the anus, oropharynx and penis increased. The AAPC during 1953-2015 combined for all male HPV-related cancer was 1.9 (95% CI 1.3 to 2.5). A vaccine against HPV 16/18 might yearly prevent 402 (95% CI 382 to 420) cancers. A vaccine against HPV 16/18/31/33/45/52/58 might yearly prevent 478 (95% CI 464 to 490) cancers, of which 206 (95% CI 202 to 209) occur in non-cervical organs, and 113 (95% CI 110 to 115) occur among men. CONCLUSIONS The incidences of HPV-related cancers that are not effectively prevented by screening have generally increased during 1953-2015. HPV vaccination can prevent a substantial number of cancers in Norway, in cervical and non-cervical organs, among women and men.
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Affiliation(s)
- Bo T Hansen
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | | | - Mari Nygård
- Department of Research, Cancer Registry of Norway, Oslo, Norway
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Truchado DA, Moens MAJ, Callejas S, Pérez-Tris J, Benítez L. Genomic characterization of the first oral avian papillomavirus in a colony of breeding canaries (Serinus canaria). Vet Res Commun 2018; 42:111-120. [PMID: 29446002 DOI: 10.1007/s11259-018-9713-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 01/31/2018] [Indexed: 01/08/2023]
Abstract
Papillomaviruses are non-enveloped, DNA viruses that infect skin and mucosa of a wide variety of vertebrates, causing neoplasias or simply persisting asymptomatically. Avian papillomaviruses, with six fully sequenced genomes, are the second most studied group after mammalian papillomaviruses. In this study, we describe the first oral avian papillomavirus, detected in the tongue of a dead Yorkshire canary (Serinus canaria) and in oral swabs of the same bird and other two live canaries from an aviary in Madrid, Spain. Its genome is 8,071 bp and presents the canonical papillomavirus architecture with six early (E6, E7, E1, E9, E2, E4) and two late open reading frames (L1 and L2) and a long control region between L1 and E6. This new avian papillomavirus L1 gene shares a 64% pairwise identity with FcPV1 L1, so it has been classified as a new species (ScPV1) within the Ethapapillomavirus genus. Although the canary died after showing breathing problems, there is no evidence that the papillomavirus caused those symptoms so it could be part of the oral microbiota of the birds. Hence, future investigations are needed to evaluate the clinical relevance of the virus.
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Affiliation(s)
- Daniel A Truchado
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología, Universidad Complutense de Madrid, Calle José Antonio Novais 12, 28040, Madrid, Spain. .,Departamento de Fisiología, Genética y Microbiología, Facultad de Biología, Calle José Antonio Novais 12, 28040, Madrid, Spain.
| | - Michaël A J Moens
- Fundación de Conservación Jocotoco, Lizardo García E9-104 y Andrés Xaura, 170143, Quito, Ecuador
| | - Sergio Callejas
- Unidad de Genómica, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Calle Melchor Fernández Almagro, 3, 28029, Madrid, Spain
| | - Javier Pérez-Tris
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Biología, Universidad Complutense de Madrid, Calle José Antonio Novais 12, 28040, Madrid, Spain
| | - Laura Benítez
- Departamento de Fisiología, Genética y Microbiología, Facultad de Biología, Calle José Antonio Novais 12, 28040, Madrid, Spain
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