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Buck CB, Welch N, Belford AK, Varsani A, Pastrana DV, Tisza MJ, Starrett GJ. Widespread Horizontal Gene Transfer Among Animal Viruses. bioRxiv 2024:2024.03.25.586562. [PMID: 38712252 PMCID: PMC11071296 DOI: 10.1101/2024.03.25.586562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzing de novo assemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.
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Blake L, Phillips Savage AC, Soto E, Oura C, Brown-Jordan A, Raines C, Buck CB, Iwanowicz LR. Complete genome sequence of a novel papillomavirus in Siamese fighting fish ( Betta splendens) from Trinidad and Tobago. Microbiol Resour Announc 2024; 13:e0099923. [PMID: 38299841 DOI: 10.1128/mra.00999-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Here, we announce the complete genome of a previously undescribed papillomavirus from a betta fish, Betta splendens. The genome is 5,671 bp with a GC content of 38.2%. Variants were detected in public databases. This genome is most similar to papillomaviruses that infect sea bass (52.9 % nucleotide identity).
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Affiliation(s)
- Lemar Blake
- The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - A Carla Phillips Savage
- The University of the West Indies, St. Augustine, Trinidad and Tobago
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Esteban Soto
- Department of Medicine and Epidemiology, University of California Davis School of Veterinary Medicine, Davis, California, USA
| | - Christopher Oura
- The University of the West Indies, St. Augustine, Trinidad and Tobago
| | | | - Clayton Raines
- US Geological Survey, Eastern Ecological Science Center, Kearneysville, West Virginia, USA
| | - Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Luke R Iwanowicz
- US Geological Survey, Eastern Ecological Science Center, Kearneysville, West Virginia, USA
- USDA-ARS, National Center for Cool and Cold Water Aquaculture, Kearneysville, West Virginia, USA
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3
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McDermott DH, Velez D, Cho E, Cowen EW, DiGiovanna JJ, Pastrana DV, Buck CB, Calvo KR, Gardner PJ, Rosenzweig SD, Stratton P, Merideth MA, Kim HJ, Brewer C, Katz JD, Kuhns DB, Malech HL, Follmann D, Fay MP, Murphy PM. A phase III randomized crossover trial of plerixafor versus G-CSF for treatment of WHIM syndrome. J Clin Invest 2023; 133:e164918. [PMID: 37561579 PMCID: PMC10541188 DOI: 10.1172/jci164918] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 08/08/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUNDWarts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is a primary immunodeficiency disorder caused by heterozygous gain-of-function CXCR4 mutations. Myelokathexis is a kind of neutropenia caused by neutrophil retention in bone marrow and in WHIM syndrome is associated with lymphopenia and monocytopenia. The CXCR4 antagonist plerixafor mobilizes leukocytes to the blood; however, its safety and efficacy in WHIM syndrome are undefined.METHODSIn this investigator-initiated, single-center, quadruple-masked phase III crossover trial, we compared the total infection severity score (TISS) as the primary endpoint in an intent-to-treat manner in 19 patients with WHIM who each received 12 months treatment with plerixafor and 12 months treatment with granulocyte CSF (G-CSF, the standard of care for severe congenital neutropenia). The treatment order was randomized for each patient.RESULTSPlerixafor was nonsuperior to G-CSF for TISS (P = 0.54). In exploratory endpoints, plerixafor was noninferior to G-CSF for maintaining neutrophil counts of more than 500 cells/μL (P = 0.023) and was superior to G-CSF for maintaining lymphocyte counts above 1,000 cells/μL (P < 0.0001). Complete regression of a subset of large wart areas occurred on plerixafor in 5 of 7 patients with major wart burdens at baseline. Transient rash occurred on plerixafor, and bone pain was more common on G-CSF. There were no significant differences in drug preference or quality of life or the incidence of drug failure or serious adverse events.CONCLUSIONPlerixafor was not superior to G-CSF in patients with WHIM for TISS, the primary endpoint. Together with wart regression and hematologic improvement, the infection severity results support continued study of plerixafor as a potential treatment for WHIM syndrome.TRIAL REGISTRATIONClinicaltrials.gov NCT02231879.FUNDINGThis study was funded by the Division of Intramural Research, National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- David H. McDermott
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases
| | - Daniel Velez
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases
| | - Elena Cho
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases
| | - Edward W. Cowen
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases
| | | | | | | | | | - Pamela J. Gardner
- Office of the Clinical Director, National Institute of Dental and Craniofacial Research
| | | | | | | | - H. Jeffrey Kim
- Otolaryngology Branch, National Institute on Deafness and other Communication Disorders, and
| | - Carmen Brewer
- Otolaryngology Branch, National Institute on Deafness and other Communication Disorders, and
| | - James D. Katz
- Rheumatology Fellowship and Training Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, USA
| | | | | | - Dean Follmann
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Michael P. Fay
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Philip M. Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases
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4
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Rao N, Starrett GJ, Piaskowski ML, Butler KE, Golubeva Y, Yan W, Lawrence SM, Dean M, Garcia-Closas M, Baris D, Johnson A, Schwenn M, Malats N, Real FX, Kogevinas M, Rothman N, Silverman DT, Dyrskjøt L, Buck CB, Koutros S, Prokunina-Olsson L. Analysis of Several Common APOBEC-type Mutations in Bladder Tumors Suggests Links to Viral Infection. Cancer Prev Res (Phila) 2023; 16:561-570. [PMID: 37477495 PMCID: PMC10592262 DOI: 10.1158/1940-6207.capr-23-0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/16/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
FGFR3 and PIK3CA are among the most frequently mutated genes in bladder tumors. We hypothesized that recurrent mutations in these genes might be caused by common carcinogenic exposures such as smoking and other factors. We analyzed 2,816 bladder tumors with available data on FGFR3 and/or PIK3CA mutations, focusing on the most recurrent mutations detected in ≥10% of tumors. Compared to tumors with other FGFR3/PIK3CA mutations, FGFR3-Y375C was more common in tumors from smokers than never-smokers (P = 0.009), while several APOBEC-type driver mutations were enriched in never-smokers: FGFR3-S249C (P = 0.013) and PIK3CA-E542K/PIK3CA-E545K (P = 0.009). To explore possible causes of these APOBEC-type mutations, we analyzed RNA sequencing (RNA-seq) data from 798 bladder tumors and detected several viruses, with BK polyomavirus (BKPyV) being the most common. We then performed IHC staining for polyomavirus (PyV) Large T-antigen (LTAg) in an independent set of 211 bladder tumors. Overall, by RNA-seq or IHC-LTAg, we detected PyV in 26 out of 1,010 bladder tumors with significantly higher detection (P = 4.4 × 10-5), 25 of 554 (4.5%) in non-muscle-invasive bladder cancers (NMIBC) versus 1 of 456 (0.2%) of muscle-invasive bladder cancers (MIBC). In the NMIBC subset, the FGFR3/PIK3CA APOBEC-type driver mutations were detected in 94.7% (18/19) of PyV-positive versus 68.3% (259/379) of PyV-negative tumors (P = 0.011). BKPyV tumor positivity in the NMIBC subset with FGFR3- or PIK3CA-mutated tumors was also associated with a higher risk of progression to MIBC (P = 0.019). In conclusion, our results support smoking and BKPyV infection as risk factors contributing to bladder tumorigenesis in the general patient population through distinct molecular mechanisms. PREVENTION RELEVANCE Tobacco smoking likely causes one of the most common mutations in bladder tumors (FGFR3-Y375C), while viral infections might contribute to three others (FGFR3-S249C, PIK3CA-E542K, and PIK3CA-E545K). Understanding the causes of these mutations may lead to new prevention and treatment strategies, such as viral screening and vaccination.
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Affiliation(s)
- Nina Rao
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Gabriel J Starrett
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Mary L Piaskowski
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kelly E Butler
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yelena Golubeva
- Molecular Digital Pathology Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Wusheng Yan
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Scott M Lawrence
- Molecular Digital Pathology Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Dalsu Baris
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | | | - Francisco X Real
- CNIO, Madrid, Spain
- CIBERONC, Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Debra T Silverman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christopher B Buck
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ludmila Prokunina-Olsson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
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5
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Torres C, Correa RM, Picconi MA, Buck CB, Mbayed VA. Identification of a new polyomavirus in distinct human populations and tissues. J Med Virol 2023; 95:e29197. [PMID: 37881064 DOI: 10.1002/jmv.29197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/27/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
Several human polyomaviruses (HPyVs) have been described in the last 15 years. This work aimed to characterize a novel HPyV with cutaneous tropism. Swabs of healthy skin (forehead) of 75 immunocompetent individuals from Argentina were screened for HPyV through sequence amplification techniques. Publicly available metagenomic data sets were also analyzed. A previously unknown polyomavirus sequence was detected in two skin swab samples. A nearly identical sequence was detected in public data sets representing metagenomic surveys of human skin and feces. Further analyses showed that the new polyomavirus diverges from its nearest relative, human polyomavirus 6 (HPyV6), by 17.3%-17.7% (in nucleotides for the large T antigen), which meets criteria for a new species designation in the genus Deltapolyomavirus. The screening also revealed more distant HPyV6 relatives in macaque genital and chimpanzee fecal data sets. Since polyomaviruses are generally thought to cospeciate with mammalian hosts, the high degree of similarity to HPyV6 suggests the new polyomavirus species is human-tropic. Therefore, a novel polyomavirus was identified and characterized from samples of distinct populations and tissues. We suggest the common name human polyomavirus 16 (HPyV16).
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Affiliation(s)
- Carolina Torres
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Rita M Correa
- Servicio Virus Oncogénicos, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - María A Picconi
- Servicio Virus Oncogénicos, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán", Buenos Aires, Argentina
| | - Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Viviana A Mbayed
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Kamminga S, van der Meijden E, Pesavento P, Buck CB, Feltkamp MCW. Serology Identifies LIPyV as a Feline Rather than a Human Polyomavirus. Viruses 2023; 15:1546. [PMID: 37515232 PMCID: PMC10384086 DOI: 10.3390/v15071546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
The number of identified human polyomaviruses (HPyVs) has increased steadily over the last decade. Some of the novel HPyVs have been shown to cause disease in immunocompromised individuals. The Lyon-IARC polyomavirus (LIPyV) belonging to species Alphapolyomavirus quardecihominis was identified in 2017 in skin and saliva samples from healthy individuals. Since its initial discovery, LIPyV has rarely been detected in human clinical samples but has been detected in faeces from cats with diarrhoea. Serological studies show low LIPyV seroprevalence in human populations. To investigate the possibility that LIPyV is a feline rather than a human polyomavirus, we compared serum IgG responses against the VP1 major capsid protein of LIPyV and 13 other HPyVs among cats (n = 40), dogs (n = 38) and humans (n = 87) using an in-house immunoassay. Seropositivity among cats was very high (92.5%) compared to dogs (31.6%) and humans (2.3%). Furthermore, the median antibody titres against LIPyV were 100-10,000x higher in cats compared to dogs and humans. In conclusion, the high prevalence and intensity of measured seroresponses suggest LIPyV to be a feline rather than a human polyomavirus. Whether LIPyV infection induces diarrhoea or other symptoms in cats remains to be established.
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Affiliation(s)
- Sergio Kamminga
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Els van der Meijden
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Patricia Pesavento
- Department of Pathology, Microbiology & Immunology, University California Davis Veterinary Medicine, 5323 Vet Med 3A, Davis, CA 95616, USA
| | - Christopher B Buck
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mariet C W Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
- Department of Donor Medicine Research, Sanquin Research, 1066 CX Amsterdam, The Netherlands
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Abstract
Recent lines of evidence suggest the intriguing hypothesis that consuming common culinary herbs of the mint family might help prevent or treat Covid. Individual citizens could easily explore the hypothesis using ordinary kitchen materials. I offer a philosophical framework to account for the puzzling lack of public health messaging about this interesting idea.
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Affiliation(s)
- Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, Building 37 Room 4118, 9000 Rockville Pike, Bethesda, MD 20892-4263 USA
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8
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Starrett GJ, Yu K, Golubeva Y, Lenz P, Piaskowski ML, Petersen D, Dean M, Israni A, Hernandez BY, Tucker TC, Cheng I, Gonsalves L, Morris CR, Hussain SK, Lynch CF, Harris RS, Prokunina-Olsson L, Meltzer PS, Buck CB, Engels EA. Evidence for virus-mediated oncogenesis in bladder cancers arising in solid organ transplant recipients. eLife 2023; 12:e82690. [PMID: 36961501 PMCID: PMC10446826 DOI: 10.7554/elife.82690] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 03/22/2023] [Indexed: 03/25/2023] Open
Abstract
A small percentage of bladder cancers in the general population have been found to harbor DNA viruses. In contrast, up to 25% of tumors of solid organ transplant recipients, who are at an increased risk of developing bladder cancer and have an overall poorer outcomes, harbor BK polyomavirus (BKPyV). To better understand the biology of the tumors and the mechanisms of carcinogenesis from potential oncoviruses, we performed whole genome and transcriptome sequencing on bladder cancer specimens from 43 transplant patients. Nearly half of the tumors from this patient population contained viral sequences. The most common were from BKPyV (N=9, 21%), JC polyomavirus (N=7, 16%), carcinogenic human papillomaviruses (N=3, 7%), and torque teno viruses (N=5, 12%). Immunohistochemistry revealed variable Large T antigen expression in BKPyV-positive tumors ranging from 100% positive staining of tumor tissue to less than 1%. In most cases of BKPyV-positive tumors, the viral genome appeared to be clonally integrated into the host chromosome consistent with microhomology-mediated end joining and coincided with focal amplifications of the tumor genome similar to other virus-mediated cancers. Significant changes in host gene expression consistent with the functions of BKPyV Large T antigen were also observed in these tumors. Lastly, we identified four mutation signatures in our cases, with those attributable to APOBEC3 and SBS5 being the most abundant. Mutation signatures associated with an antiviral drug, ganciclovir, and aristolochic acid, a nephrotoxic compound found in some herbal medicines, were also observed. The results suggest multiple pathways to carcinogenesis in solid organ transplant recipients with a large fraction being virus-associated.
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Affiliation(s)
| | - Kelly Yu
- DCEG, NCI, NIHRockvilleUnited States
| | | | - Petra Lenz
- Leidos Biomedical Research IncFrederickUnited States
| | | | | | | | - Ajay Israni
- Department of Medicine, Nephrology Division, Hennepin Healthcare System, University of MinnesotaMinneapolisUnited States
| | | | - Thomas C Tucker
- The Kentucky Cancer Registry, University of KentuckyLexingtonUnited States
| | - Iona Cheng
- Department of Epidemiology and Biostatistics,and Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoFremontUnited States
| | - Lou Gonsalves
- Connecticut Tumor Registry, Connecticut Department of Public HealthHartfordUnited States
| | - Cyllene R Morris
- California Cancer Reporting and Epidemiologic Surveillance Program, University of California, DavisDavisUnited States
| | - Shehnaz K Hussain
- Cedars-Sinai Cancer and Department of Medicine, Cedars-Sinai Medical CenterLos AngelesUnited States
| | - Charles F Lynch
- The Iowa Cancer Registry, University of IowaIowa CityUnited States
| | - Reuben S Harris
- Howard Hughes Medical Institute, University of MinnesotaMinneapolisUnited States
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9
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Peretti A, Scorpio DG, Kong WP, Pang YYS, McCarthy MP, Ren K, Jackson M, Graham BS, Buck CB, McTamney PM, Pastrana DV. A multivalent polyomavirus vaccine elicits durable neutralizing antibody responses in macaques. Vaccine 2023; 41:1735-1742. [PMID: 36764908 PMCID: PMC9992340 DOI: 10.1016/j.vaccine.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/10/2023]
Abstract
In 2019, there were about 100,000 kidney transplants globally, with more than a quarter of them performed in the United States. Unfortunately, some engrafted organs are lost to polyomavirus-associated nephropathy (PyVAN) caused by BK and JC viruses (BKPyV and JCPyV). Both viruses cause brain disease and possibly bladder cancer in immunosuppressed individuals. Transplant patients are routinely monitored for BKPyV viremia, which is an accepted hallmark of nascent nephropathy. If viremia is detected, a reduction in immunosuppressive therapy is standard care, but the intervention comes with increased risk of immune rejection of the engrafted organ. Recent reports have suggested that transplant recipients with high levels of polyomavirus-neutralizing antibodies are protected against PyVAN. Virus-like particle (VLP) vaccines, similar to approved human papillomavirus vaccines, have an excellent safety record and are known to induce high levels of neutralizing antibodies and long-lasting protection from infection. In this study, we demonstrate that VLPs representing BKPyV genotypes I, II, and IV, as well as JCPyV genotype 2 produced in insect cells elicit robust antibody titers. In rhesus macaques, all monkeys developed neutralizing antibody titers above a previously proposed protective threshold of 10,000. A second inoculation, administered 19 weeks after priming, boosted titers to a plateau of ≥ 25,000 that was maintained for almost two years. No vaccine-related adverse events were observed in any macaques. A multivalent BK/JC VLP immunogen did not show inferiority compared to the single-genotype VLP immunogens. Considering these encouraging results, we believe a clinical trial administering the multivalent VLP vaccine in patients waiting to receive a kidney transplant is warranted to evaluate its ability to reduce or eliminate PyVAN.
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Affiliation(s)
- Alberto Peretti
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, MD 20892, United States
| | - Diana G Scorpio
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, United States
| | - Wing-Pui Kong
- Virology Core, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, United States
| | - Yuk-Ying S Pang
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, MD 20892, United States
| | - Michael P McCarthy
- Department of Infectious Diseases-Vaccines, MedImmune, Gaithersburg, MD 20878, United States
| | - Kuishu Ren
- Department of Infectious Diseases-Vaccines, MedImmune, Gaithersburg, MD 20878, United States
| | - Moriah Jackson
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, United States
| | - Barney S Graham
- Viral Pathogenesis Laboratory, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, United States
| | - Christopher B Buck
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, MD 20892, United States.
| | - Patrick M McTamney
- Department of Infectious Diseases-Vaccines, MedImmune, Gaithersburg, MD 20878, United States
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, MD 20892, United States
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10
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Kraberger S, Serieys LEK, Riley SPD, Schmidlin K, Newkirk ES, Squires JR, Buck CB, Varsani A. Novel polyomaviruses identified in fecal samples from four carnivore species. Arch Virol 2023; 168:18. [PMID: 36593361 PMCID: PMC10681122 DOI: 10.1007/s00705-022-05675-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/21/2022] [Indexed: 01/04/2023]
Abstract
Polyomaviruses are oncogenic viruses that are generally thought to have co-evolved with their hosts. While primate and rodent polyomaviruses are increasingly well-studied, less is known about polyomaviruses that infect other mammals. In an effort to gain insight into polyomaviruses associated with carnivores, we surveyed fecal samples collected in the USA from bobcats (Lynx rufus), pumas (Puma concolor), Canada lynxes (Lynx canadensis), and grizzly bears (Ursus arctos). Using a viral metagenomic approach, we identified six novel polyomavirus genomes. Surprisingly, four of the six genomes showed a phylogenetic relationship to polyomaviruses found in prey animals. These included a putative rabbit polyomavirus from a bobcat fecal sample and two possible deer-trophic polyomaviruses from Canada lynx feces. One polyomavirus found in a grizzly bear sample was found to be phylogenetically distant from previously identified polyomaviruses. Further analysis of the grizzly bear fecal sample showed that it contained anelloviruses that are known to infect pigs, suggesting that the bear might have preyed on a wild or domestic pig. Interestingly, a polyomavirus genome identified in a puma fecal sample was found to be closely related both to raccoon polyomavirus 1 and to Lyon-IARC polyomavirus, the latter of which was originally identified in human saliva and skin swab specimens but has since been found in samples from domestic cats (Felis catus).
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
| | - Laurel E K Serieys
- Panthera, 8 W 40th St, 18th Floor, New York, NY, 10018, USA
- Santa Monica Mountains National Recreation Area, National Park Service, Thousand Oaks, CA, 91360, USA
| | - Seth P D Riley
- Santa Monica Mountains National Recreation Area, National Park Service, Thousand Oaks, CA, 91360, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | | | - John R Squires
- U.S. Forest Service, Rocky Mountain Research Station, 800 East Beckwith Avenue, Missoula, MT, 59801, USA
| | - Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa.
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11
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Kraberger S, Austin C, Farkas K, Desvignes T, Postlethwait JH, Fontenele RS, Schmidlin K, Bradley RW, Warzybok P, Van Doorslaer K, Davison W, Buck CB, Varsani A. Discovery of novel fish papillomaviruses: From the Antarctic to the commercial fish market. Virology 2022; 565:65-72. [PMID: 34739918 PMCID: PMC8713439 DOI: 10.1016/j.virol.2021.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/23/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023]
Abstract
Fish papillomaviruses form a newly discovered group broadly recognized as the Secondpapillomavirinae subfamily. This study expands the documented genomes of the fish papillomaviruses from six to 16, including one from the Antarctic emerald notothen, seven from commercial market fishes, one from data mining of sea bream sequence data, and one from a western gull cloacal swab that is likely diet derived. The genomes of secondpapillomaviruses are ∼6 kilobasepairs (kb), which is substantially smaller than the ∼8 kb of terrestrial vertebrate papillomaviruses. Each genome encodes a clear homolog of the four canonical papillomavirus genes, E1, E2, L1, and L2. In addition, we identified open reading frames (ORFs) with short linear peptide motifs reminiscent of E6/E7 oncoproteins. Fish papillomaviruses are extremely diverse and phylogenetically distant from other papillomaviruses suggesting a model in which terrestrial vertebrate-infecting papillomaviruses arose after an evolutionary bottleneck event, possibly during the water-to-land transition.
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Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Charlotte Austin
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
| | | | - Rafaela S. Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Russell W. Bradley
- Santa Rosa Island Research Station, California State University Channel Islands, Camarillo CA 93012, USA
| | - Pete Warzybok
- Point Blue Conservation Science, Petaluma, California, CA 94954, USA
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, The BIO5 Institute; Department of Immunobiology; Cancer Biology Graduate Interdisciplinary Program; UA Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - William Davison
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Christopher B. Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA,corresponding authors Christopher B. Buck, Arvind Varsani
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925, Cape Town, South Africa,corresponding authors Christopher B. Buck, Arvind Varsani
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12
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Schmidlin K, Kraberger S, Cook C, DeNardo DF, Fontenele RS, Van Doorslaer K, Martin DP, Buck CB, Varsani A. A novel lineage of polyomaviruses identified in bark scorpions. Virology 2021; 563:58-63. [PMID: 34425496 DOI: 10.1016/j.virol.2021.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/15/2021] [Accepted: 08/15/2021] [Indexed: 11/30/2022]
Abstract
Polyomaviruses are non-enveloped viruses with circular double-stranded DNA genomes (~4-7 kb). Initially identified in mammals, polyomaviruses have now been identified in birds and a few fish species. Although fragmentary polyomavirus-like sequences have been detected as apparent 'hitchhikers' in shotgun genomics datasets of various arthropods, the possible diversity of these viruses in invertebrates remains unclear. Scorpions are predatory arachnids that are among the oldest terrestrial animals. Using high-throughput sequencing and traditional molecular techniques we determine the genome sequences of eight novel polyomaviruses in scorpions (Centruroides sculpturatus) from the greater Phoenix area, Arizona, USA. Analysis of Centruroides transcriptomic datasets elucidated the splicing of the viral late gene array, which is more complex than that of vertebrate polyomaviruses. Phylogenetic analysis provides further evidence of co-divergence of polyomaviruses with their hosts, suggesting that at least one ancestral species of polyomaviruses was circulating amongst the primitive common ancestors of arthropods and chordates.
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Affiliation(s)
- Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Chelsea Cook
- Department of Biological Sciences, Marquette University, 11428 W. Clybourn St, Milwaukee, WI, 53233, USA
| | - Dale F DeNardo
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Koenraad Van Doorslaer
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, 85719, USA; School of Animal and Comparative Biomedical Sciences, The BIO5 Institute, Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, UA Cancer Center, University of Arizona Tucson, Tucson, AZ, 85724, USA
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | - Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA; School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA; Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, 7925, Cape Town, South Africa.
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13
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Abstract
Despite remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This gap persists, even though many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases, and all of them encompass large amounts of viral sequence data. The lack of a comprehensive database for human-associated viruses has historically stymied efforts to interrogate the impact of the virome on human health. This study probes thousands of datasets to uncover sequences from over 45,000 unique virus taxa, with historically high per-genome completeness. Large publicly available case-control studies are reanalyzed, and over 2,200 strong virus-disease associations are found.
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Affiliation(s)
- Michael J Tisza
- Laboratory of Cellular Oncology, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Christopher B Buck
- Laboratory of Cellular Oncology, National Cancer Institute, NIH, Bethesda, MD 20892
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14
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Yang R, Lee EE, Kim J, Choi JH, Kolitz E, Chen Y, Crewe C, Salisbury NJH, Scherer PE, Cockerell C, Smith TR, Rosen L, Verlinden L, Galloway DA, Buck CB, Feltkamp MC, Sullivan CS, Wang RC. Characterization of ALTO-encoding circular RNAs expressed by Merkel cell polyomavirus and trichodysplasia spinulosa polyomavirus. PLoS Pathog 2021; 17:e1009582. [PMID: 33999949 PMCID: PMC8158866 DOI: 10.1371/journal.ppat.1009582] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/27/2021] [Accepted: 04/24/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are a conserved class of RNAs with diverse functions, including serving as messenger RNAs that are translated into peptides. Here we describe circular RNAs generated by human polyomaviruses (HPyVs), some of which encode variants of the previously described alternative large T antigen open reading frame (ALTO) protein. Circular ALTO RNAs (circALTOs) can be detected in virus positive Merkel cell carcinoma (VP-MCC) cell lines and tumor samples. CircALTOs are stable, predominantly located in the cytoplasm, and N6-methyladenosine (m6A) modified. The translation of MCPyV circALTOs into ALTO protein is negatively regulated by MCPyV-generated miRNAs in cultured cells. MCPyV ALTO expression increases transcription from some recombinant promoters in vitro and upregulates the expression of multiple genes previously implicated in MCPyV pathogenesis. MCPyV circALTOs are enriched in exosomes derived from VP-MCC lines and circALTO-transfected 293T cells, and purified exosomes can mediate ALTO expression and transcriptional activation in MCPyV-negative cells. The related trichodysplasia spinulosa polyomavirus (TSPyV) also expresses a circALTO that can be detected in infected tissues and produces ALTO protein in cultured cells. Thus, human polyomavirus circRNAs are expressed in human tumors and infected tissues and express proteins that have the potential to modulate the infectious and tumorigenic properties of these viruses.
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Affiliation(s)
- Rong Yang
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Eunice E. Lee
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Joon H. Choi
- Department of Molecular Biosciences, University of Texas, Austin, Texas, United States of America
| | - Elysha Kolitz
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yating Chen
- Department of Molecular Biosciences, University of Texas, Austin, Texas, United States of America
| | - Clair Crewe
- Touchstone Diabetes Center, Department of Internal Medicine, the UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nicholas J. H. Salisbury
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Philipp E. Scherer
- Touchstone Diabetes Center, Department of Internal Medicine, the UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Clay Cockerell
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Taylor R. Smith
- Department of Dermatology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Leslie Rosen
- Department of Dermatology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Louisa Verlinden
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Denise A. Galloway
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Christopher B. Buck
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Mariet C. Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Christopher S. Sullivan
- Department of Molecular Biosciences, University of Texas, Austin, Texas, United States of America
| | - Richard C. Wang
- Department of Dermatology, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Harold C. Simmons Cancer Center, UT Southwestern Medical Center, Dallas, Texas, United States of America
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15
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Abstract
Viruses, despite their great abundance and significance in biological systems, remain largely mysterious. Indeed, the vast majority of the perhaps hundreds of millions of viral species on the planet remain undiscovered. Additionally, many viruses deposited in central databases like GenBank and RefSeq are littered with genes annotated as 'hypothetical protein' or the equivalent. Cenote-Taker 2, a virus discovery and annotation tool available on command line and with a graphical user interface with free high-performance computation access, utilizes highly sensitive models of hallmark virus genes to discover familiar or divergent viral sequences from user-input contigs. Additionally, Cenote-Taker 2 uses a flexible set of modules to automatically annotate the sequence features of contigs, providing more gene information than comparable tools. The outputs include readable and interactive genome maps, virome summary tables, and files that can be directly submitted to GenBank. We expect Cenote-Taker 2 to facilitate virus discovery, annotation, and expansion of the known virome.
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Affiliation(s)
- Michael J Tisza
- Lab of Cellular Oncology, NCI, NIH, Bethesda, MD 20892-4263, USA
| | - Anna K Belford
- Lab of Cellular Oncology, NCI, NIH, Bethesda, MD 20892-4263, USA
| | | | - Benjamin Bolduc
- Department of Microbiology, Ohio State University, Columbus, OH, USA
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16
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Starrett GJ, Tisza MJ, Welch NL, Belford AK, Peretti A, Pastrana DV, Buck CB. Adintoviruses: a proposed animal-tropic family of midsize eukaryotic linear dsDNA (MELD) viruses. Virus Evol 2021; 7:veaa055. [PMID: 34646575 PMCID: PMC8502044 DOI: 10.1093/ve/veaa055] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA viruses. This supports the inference that at least some polintons are actually viruses capable of cell-to-cell spread. At present, there are no polinton-associated capsid protein genes annotated in public sequence databases. To rectify this deficiency, we used a data-mining approach to investigate the distribution and gene content of polinton-like elements and related DNA viruses in animal genomic and metagenomic sequence datasets. The results define a discrete family-like clade of viruses with two genus-level divisions. We propose the family name Adintoviridae, connoting similarities to adenovirus virion proteins and the presence of a retrovirus-like integrase gene. Although adintovirus-class PolB sequences were detected in datasets for fungi and various unicellular eukaryotes, sequences resembling adintovirus virion proteins and accessory genes appear to be restricted to animals. Degraded adintovirus sequences are endogenized into the germlines of a wide range of animals, including humans.
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Affiliation(s)
| | - Michael J Tisza
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Nicole L Welch
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Anna K Belford
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Alberto Peretti
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, NCI, NIH, Bethesda, MD 20892, USA
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17
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Rosenstein RK, Pastrana DV, Starrett GJ, Sapio MR, Hill NT, Jo JH, Lee CCR, Iadarola MJ, Buck CB, Kong HH, Brownell I, Cowen EW. Host-Pathogen Interactions in Human Polyomavirus 7‒Associated Pruritic Skin Eruption. J Invest Dermatol 2020; 141:1344-1348.e8. [PMID: 33075349 DOI: 10.1016/j.jid.2020.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/16/2020] [Accepted: 09/14/2020] [Indexed: 12/27/2022]
Affiliation(s)
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, NCI/CCR, NIH, Bethesda, Maryland, USA
| | | | - Matthew R Sapio
- Department of Perioperative Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | | | - Jay-Hyun Jo
- Dermatology Branch, NIAMS, NIH, Bethesda, Maryland, USA
| | - Chyi-Chia R Lee
- Laboratory of Pathology, NCI/CCR, NIH, Bethesda, Maryland, USA
| | - Michael J Iadarola
- Department of Perioperative Medicine, Clinical Center, NIH, Bethesda, Maryland, USA
| | | | - Heidi H Kong
- Dermatology Branch, NIAMS, NIH, Bethesda, Maryland, USA
| | | | - Edward W Cowen
- Dermatology Branch, NIAMS, NIH, Bethesda, Maryland, USA.
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18
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Starrett GJ, Yu K, Petersen D, Lenz P, Dyrskjøt L, Meltzer P, Engels E, Buck CB. Abstract IA11: Bladder cancers affecting transplant recipients harbor diverse viruses that associate with overall survival. Cancer Res 2020. [DOI: 10.1158/1538-7445.mvc2020-ia11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BK polyomavirus (BKPyV) is a ubiquitous virus that establishes a lifelong subclinical infection in the urinary tract. In transplant recipients, BKPyV can reactivate and cause kidney and bladder damage. Recent sequencing studies of tumors from transplant recipients have revealed that BKPyV sequences are present in approximately 25% of bladder tumors. This is dramatically higher than the <1% rate of BKPyV detection observed in muscle-invasive bladder cancers affecting the general population. Like cancer-causing human papillomaviruses (HPVs), BKPyV has been shown to upregulate the human cytosine deaminase APOBEC3B, which has emerged as the second most abundant source of point mutations in human cancers. Furthermore, the APOBEC3-associated mutation signature is the most abundant mutational signature in bladder cancer. To comprehensively assess the role of BKPyV and other viruses in bladder cancer from solid organ transplant recipients, we used a database linking US transplant and cancer registries to identify and collect 44 archived primary bladder tumors, 5 metastases, and 15 adjacent normal tissue specimens. Whole-genome and total RNA sequencing was performed on the samples. From these data, we detected BKPyV in 18% of primary tumors. In five cases, there is clear evidence of BKPyV integration into the host cell genome, and all cases show transcription of the viral tumor antigens. In a separate set of analyses, BKPyV transcription was detected in 3.7% of non-muscle-invasive early-stage bladder cancer cases affecting the general population. Our surveys also detected other viruses, including high- and low-risk HPVs, JC polyomavirus (JCPyV), and anelloviruses, at lower frequencies. Two primary-metastatic pairs maintained clonally integrated HPV or BKPyV and respective viral oncogene expression in the metastatic lesions. Nearly all tumors had dominant APOBEC3 signature mutations, and BKPyV-positive tumors expressed significantly more APOBEC3B compared to virus-negative tumors or normal tissues. Tumors from four kidney transplant patients showed high mutation burden consistent with exposure to aristolochic acid, a nephrotoxic carcinogen found in some herbal supplements. Clinical data indicate that BKPyV-positive tumors are predominantly high grade with invasive behavior. Strikingly, survival was significantly shorter for patients whose tumors harbored BKPyV or JCPyV (9.7 and 8.4 months, respectively) compared to patients with tumors harboring HPV or no detectable viruses (65.8 and 50.2 months, respectively). This study comprehensively characterizes the genomes and transcriptomes of tumors, revealing several distinct tumor etiologies that impact patient outcome.
Citation Format: Gabriel J. Starrett, Kelly Yu, David Petersen, Petra Lenz, Lars Dyrskjøt, Paul Meltzer, Eric Engels, Christopher B. Buck. Bladder cancers affecting transplant recipients harbor diverse viruses that associate with overall survival [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA11.
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19
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Tisza MJ, Pastrana DV, Welch NL, Stewart B, Peretti A, Starrett GJ, Pang YYS, Krishnamurthy SR, Pesavento PA, McDermott DH, Murphy PM, Whited JL, Miller B, Brenchley J, Rosshart SP, Rehermann B, Doorbar J, Ta'ala BA, Pletnikova O, Troncoso JC, Resnick SM, Bolduc B, Sullivan MB, Varsani A, Segall AM, Buck CB. Discovery of several thousand highly diverse circular DNA viruses. eLife 2020; 9:51971. [PMID: 32014111 PMCID: PMC7000223 DOI: 10.7554/elife.51971] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/06/2020] [Indexed: 12/18/2022] Open
Abstract
Although millions of distinct virus species likely exist, only approximately 9000 are catalogued in GenBank's RefSeq database. We selectively enriched for the genomes of circular DNA viruses in over 70 animal samples, ranging from nematodes to human tissue specimens. A bioinformatics pipeline, Cenote-Taker, was developed to automatically annotate over 2500 complete genomes in a GenBank-compliant format. The new genomes belong to dozens of established and emerging viral families. Some appear to be the result of previously undescribed recombination events between ssDNA and ssRNA viruses. In addition, hundreds of circular DNA elements that do not encode any discernable similarities to previously characterized sequences were identified. To characterize these ‘dark matter’ sequences, we used an artificial neural network to identify candidate viral capsid proteins, several of which formed virus-like particles when expressed in culture. These data further the understanding of viral sequence diversity and allow for high throughput documentation of the virosphere. When scientists hunt for new DNA sequences, sometimes they get a lot more than they bargained for. Such is the case in metagenomic surveys, which analyze not just DNA of a particular organism, but all the DNA in an environment at large. A vexing problem with these surveys is the overwhelming number of DNA sequences detected that are so different from any known microbe that they cannot be classified using traditional approaches. However, some of these “known unknowns” are undoubtedly viral sequences, because only a fraction of the enormous diversity of viruses has been characterized. This “viral dark matter” is a major obstacle for those studying viruses. This led Tisza et al. to attempt to classify some of the unknown viral sequences in their metagenomic surveys. The search, which specifically focused on viruses with circular DNA genomes, detected over 2,500 circular viral genomes. Intensive analysis revealed that many of these genomes had similar makeup to previously discovered viruses, but hundreds of them were totally different from any known virus, based on typical methods of comparison. Computational analysis of genes that were conserved among some of these brand-new circular sequences often revealed virus-like features. Experiments on a few of these genes showed that they encoded proteins capable of forming particles reminiscent of characteristic viral shells, implying that these new sequences are indeed viruses. Tisza et al. have added the 2,500 newly characterized viral sequences to the publicly accessible GenBank database, and the sequences are being considered for the more authoritative RefSeq database, which currently contains around 9,000 complete viral genomes. The expanded databases will hopefully now better equip scientists to explore the enormous diversity of viruses and help medics and veterinarians to detect disease-causing viruses in humans and other animals.
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Affiliation(s)
- Michael J Tisza
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Diana V Pastrana
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Nicole L Welch
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Brittany Stewart
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Alberto Peretti
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Gabriel J Starrett
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Yuk-Ying S Pang
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Siddharth R Krishnamurthy
- Metaorganism Immunity Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Patricia A Pesavento
- Department of Pathology, Microbiology, and Immunology, University of California, Davis, Davis, United States
| | - David H McDermott
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Philip M Murphy
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Jessica L Whited
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
| | - Bess Miller
- Department of Orthopedic Surgery, Harvard Medical School, The Harvard Stem Cell Institute, Brigham and Women's Hospital, Boston, United States.,Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jason Brenchley
- Barrier Immunity Section, Lab of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Cambridge, United States
| | - Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - John Doorbar
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Olga Pletnikova
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, United States
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Ben Bolduc
- Department of Microbiology, Ohio State University, Columbus, United States
| | - Matthew B Sullivan
- Department of Microbiology, Ohio State University, Columbus, United States.,Civil Environmental and Geodetic Engineering, Ohio State University, Columbus, United States
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, United States.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, South Africa
| | - Anca M Segall
- Viral Information Institute and Department of Biology, San Diego State University, San Diego, United States
| | - Christopher B Buck
- Lab of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, United States
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20
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Abstract
In 2014, the International Agency for Research on Cancer judged Merkel cell polyomavirus (MCPyV) to be a probable human carcinogen. BK polyomavirus (BKPyV, a distant cousin of MCPyV) was ruled a possible carcinogen. In this review, we argue that it has recently become reasonable to view both of these viruses as known human carcinogens. In particular, several complementary lines of evidence support a causal role for BKPyV in the development of bladder carcinomas affecting organ transplant patients. The expansion of inexpensive deep sequencing has opened new approaches to investigating the important question of whether BKPyV causes urinary tract cancers in the general population.
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Affiliation(s)
- Gabriel J Starrett
- National Cancer Institute, Building 37 Room 4118, 9000 Rockville Pike, Bethesda, MD 20892-4263, United States.
| | - Christopher B Buck
- National Cancer Institute, Building 37 Room 4118, 9000 Rockville Pike, Bethesda, MD 20892-4263, United States
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21
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Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM. Mash Screen: high-throughput sequence containment estimation for genome discovery. Genome Biol 2019; 20:232. [PMID: 31690338 PMCID: PMC6833257 DOI: 10.1186/s13059-019-1841-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/27/2019] [Indexed: 11/17/2022] Open
Abstract
The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. Here, we describe an online algorithm capable of measuring the containment of genomes and proteomes within either assembled or unassembled sequencing read sets. We describe several use cases, including contamination screening and retrospective analysis of metagenomes for novel genome discovery. Using this tool, we provide containment estimates for every NCBI RefSeq genome within every SRA metagenome and demonstrate the identification of a novel polyomavirus species from a public metagenome.
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Affiliation(s)
- Brian D. Ondov
- Genome Informatics section, National Human Genome Research Institute, Bethesda, MD USA
- Department of Computer Science, University of Maryland College Park, College Park, MD USA
| | - Gabriel J. Starrett
- Tumor Virus Molecular Biology section, National Cancer Institute, Bethesda, MD USA
| | - Anna Sappington
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Aleksandra Kostic
- Department of Computer Science, Princeton University, Princeton, NJ USA
| | - Sergey Koren
- Genome Informatics section, National Human Genome Research Institute, Bethesda, MD USA
| | - Christopher B. Buck
- Tumor Virus Molecular Biology section, National Cancer Institute, Bethesda, MD USA
| | - Adam M. Phillippy
- Genome Informatics section, National Human Genome Research Institute, Bethesda, MD USA
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22
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Chamseddin BH, Tran BAPD, Lee EE, Pastrana DV, Buck CB, Wang RC, Kirkorian AY. Trichodysplasia spinulosa in a child: Identification of trichodysplasia spinulosa-associated polyomavirus in skin, serum, and urine. Pediatr Dermatol 2019; 36:723-724. [PMID: 31190328 PMCID: PMC8127864 DOI: 10.1111/pde.13857] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A 6-year-old girl with a history of chronic immunosuppression following small bowel and colon transplantation for tufting enteropathy presented with a diffuse, facial-predominant eruption composed of pink-to-skin-colored papules with central white dystrophic spicules. Histology from a punch biopsy and polymerase chain reaction (PCR) from plucked spicules confirmed a diagnosis of trichodysplasia spinulosa (TS). Additional molecular studies identified several strains of the trichodysplasia spinulosa-associated polyomavirus infecting multiple tissues of the patient, confirming the systemic nature of trichodysplasia spinulosa infections.
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Affiliation(s)
- Bahir H Chamseddin
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas
| | | | - Eunice E Lee
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Christopher B Buck
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Richard C Wang
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Anna Yasmine Kirkorian
- Division of Dermatology, Children's National Medical Center, Washington, District of Columbia.,Department of Dermatology, George Washington University School of Medicine, Washington, District of Columbia
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23
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Abstract
Merkel cell polyomavirus (MCPyV) infection can lead to Merkel cell carcinoma (MCC), a highly aggressive form of skin cancer. Mechanistic studies to fully investigate MCPyV molecular biology and oncogenic mechanisms have been hampered by a lack of adequate cell culture models. Here, we describe a set of protocols for performing and detecting MCPyV infection of primary human skin cells. The protocols describe the isolation of human dermal fibroblasts, preparation of recombinant MCPyV virions, and detection of virus infection by both immunofluorescent (IF) staining and in situ DNA-hybridization chain reaction (HCR), which is a highly sensitive fluorescence in situ hybridization (FISH) approach. The protocols herein can be adapted by interested researchers to identify other cell types or cell lines that support MCPyV infection. The described FISH approach could also be adapted for detecting low levels of viral DNAs present in the infected human skin.
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Affiliation(s)
- Wei Liu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Nathan A Krump
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | | | - Jianxin You
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania;
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24
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McDermott DH, Pastrana DV, Calvo KR, Pittaluga S, Velez D, Cho E, Liu Q, Trout HH, Neves JF, Gardner PJ, Bianchi DA, Blair EA, Landon EM, Silva SL, Buck CB, Murphy PM. Plerixafor for the Treatment of WHIM Syndrome. N Engl J Med 2019; 380:163-170. [PMID: 30625055 PMCID: PMC6425947 DOI: 10.1056/nejmoa1808575] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
WHIM syndrome (warts, hypogammaglobulinemia, infections, and myelokathexis), a primary immunodeficiency disorder involving panleukopenia, is caused by autosomal dominant gain-of-function mutations in CXC chemokine receptor 4 (CXCR4). Myelokathexis is neutropenia caused by neutrophil retention in bone marrow. Patients with WHIM syndrome are often treated with granulocyte colony-stimulating factor (G-CSF), which can increase neutrophil counts but does not affect cytopenias other than neutropenia. In this investigator-initiated, open-label study, three severely affected patients with WHIM syndrome who could not receive G-CSF were treated with low-dose plerixafor, a CXCR4 antagonist, for 19 to 52 months. Myelofibrosis, panleukopenia, anemia, and thrombocytopenia were ameliorated, the wart burden and frequency of infection declined, human papillomavirus-associated oropharyngeal squamous-cell carcinoma stabilized, and quality of life improved markedly. Adverse events were mainly infections attributable to the underlying immunodeficiency. One patient died from complications of elective reconstructive surgery. (Funded by the National Institutes of Health.).
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Affiliation(s)
- David H McDermott
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Diana V Pastrana
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Katherine R Calvo
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Stefania Pittaluga
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Daniel Velez
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Elena Cho
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Qian Liu
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Hugh H Trout
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - João F Neves
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Pamela J Gardner
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - David A Bianchi
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Elizabeth A Blair
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Emily M Landon
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Susana L Silva
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Christopher B Buck
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
| | - Philip M Murphy
- From the Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (D.H.M., D.V., E.C., Q.L., P.M.M.), the Laboratories of Cellular Oncology (D.V.P., C.B.B.) and Pathology (S.P.), National Cancer Institute, the Department of Laboratory Medicine, Clinical Center (K.R.C.), the National Institute of Dental and Craniofacial Research (P.J.G.), and the National Institute on Deafness and Other Communication Disorders (D.A.B.), National Institutes of Health, and Kozloff and Trout MDs (H.H.T.), Bethesda, MD; the Infectious Diseases Unit and Primary Immunodeficiencies Unit, Hospital Dona Estefânia, Pediatric University Hospital (J.F.N.), and Centro de Imunodeficiências Primárias, Academic Medical Center of Lisbon (S.L.S.), Lisbon, Portugal; and the University of Chicago Medical Center, Chicago (E.A.B., E.M.L.)
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25
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Wunderink HF, de Brouwer CS, van der Meijden E, Pastrana DV, Kroes ACM, Buck CB, Feltkamp MCW. Development and evaluation of a BK polyomavirus serotyping assay using Luminex technology. J Clin Virol 2018; 110:22-28. [PMID: 30529638 DOI: 10.1016/j.jcv.2018.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/22/2018] [Accepted: 11/30/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND The BK polyomavirus (BKPyV) is subdivided into four genotypes. The consequences of each genotype and of donor-recipient genotype (mis)match for BKPyV-associated nephropathy (BKPyVAN) in kidney transplant recipients (KTRs) are unknown. OBJECTIVES To develop and evaluate a genotype-specific IgG antibody-based BKPyV serotyping assay, in order to classify kidney transplant donors and recipients accordingly. STUDY DESIGN VP1 antigens of six BKPyV variants (Ib1, Ib2, Ic, II, III and IV) were expressed as recombinant glutathione-s-transferase-fusion proteins and coupled to fluorescent Luminex beads. Sera from 87 healthy blood donors and 39 KTRs were used to analyze seroreactivity and serospecificity against the different BKPyV genotypes. Six sera with marked BKPyV serotype profiles were analyzed further for genotype-specific BKPyV pseudovirus neutralizing capacity. RESULTS Seroreactivity was observed against all genotypes, with seropositivity rates above 77% comparable for KTRs and blood donors. Strong cross-reactivity (r > 0.8) was observed among genotype I subtypes, and among genotypes II, III and IV. Seroresponses against genotypes I and IV seemed genuine, while those against II and III could be out(cross)competed. GMT (Luminex) and IC50 (neutralization assay) values showed good agreement in determining the genotype with the strongest seroresponse within an individual. CONCLUSIONS Despite some degree of cross-reactivity, this serotyping assay seems a useful tool to identify the main infecting BKPyV genotype within a given individual. This information, which cannot be obtained otherwise from nonviremic/nonviruric individuals, could provide valuable information regarding the prevalent BKPyV genotype in kidney donors and recipients and warrants further study.
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Affiliation(s)
- Herman F Wunderink
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Caroline S de Brouwer
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Els van der Meijden
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4263, USA
| | - Aloysius C M Kroes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Christopher B Buck
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4263, USA
| | - Mariet C W Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
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26
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Geoghegan EM, Pastrana DV, Schowalter RM, Ray U, Gao W, Ho M, Pauly GT, Sigano DM, Kaynor C, Cahir-McFarland E, Combaluzier B, Grimm J, Buck CB. Infectious Entry and Neutralization of Pathogenic JC Polyomaviruses. Cell Rep 2018; 21:1169-1179. [PMID: 29091757 DOI: 10.1016/j.celrep.2017.10.027] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 08/08/2017] [Accepted: 10/06/2017] [Indexed: 12/24/2022] Open
Abstract
Progressive multifocal leukoencephalopathy (PML) is a lethal brain disease caused by uncontrolled replication of JC polyomavirus (JCV). JCV strains recovered from the brains of PML patients carry mutations that prevent the engagement of sialylated glycans, which are thought to serve as receptors for the infectious entry of wild-type JCV. In this report, we show that non-sialylated glycosaminoglycans (GAGs) can serve as alternative attachment receptors for the infectious entry of both wild-type and PML mutant JCV strains. After GAG-mediated attachment, PML mutant strains engage non-sialylated non-GAG co-receptor glycans, such as asialo-GM1. JCV-neutralizing monoclonal antibodies isolated from patients who recovered from PML appear to block infection by preventing the docking of post-attachment co-receptor glycans in an apical pocket of the JCV major capsid protein. Identification of the GAG-dependent/sialylated glycan-independent alternative entry pathway should facilitate the development of infection inhibitors, including recombinant neutralizing antibodies.
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Affiliation(s)
- Eileen M Geoghegan
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4263, USA
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4263, USA
| | - Rachel M Schowalter
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4263, USA
| | - Upasana Ray
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4263, USA
| | - Wei Gao
- Antibody Therapy Section, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mitchell Ho
- Antibody Therapy Section, Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Gary T Pauly
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Dina M Sigano
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | | | | | | | - Jan Grimm
- Neurimmune Holding AG, Schlieren-Zurich, Switzerland
| | - Christopher B Buck
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-4263, USA.
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27
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Peretti A, Geoghegan EM, Pastrana DV, Smola S, Feld P, Sauter M, Lohse S, Ramesh M, Lim ES, Wang D, Borgogna C, FitzGerald PC, Bliskovsky V, Starrett GJ, Law EK, Harris RS, Killian JK, Zhu J, Pineda M, Meltzer PS, Boldorini R, Gariglio M, Buck CB. Characterization of BK Polyomaviruses from Kidney Transplant Recipients Suggests a Role for APOBEC3 in Driving In-Host Virus Evolution. Cell Host Microbe 2018; 23:628-635.e7. [PMID: 29746834 PMCID: PMC5953553 DOI: 10.1016/j.chom.2018.04.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 12/05/2017] [Accepted: 03/19/2018] [Indexed: 12/31/2022]
Abstract
BK polyomavirus (BKV) frequently causes nephropathy (BKVN) in kidney transplant recipients (KTRs). BKV has also been implicated in the etiology of bladder and kidney cancers. We characterized BKV variants from two KTRs who developed BKVN followed by renal carcinoma. Both patients showed a swarm of BKV sequence variants encoding non-silent mutations in surface loops of the viral major capsid protein. The temporal appearance and disappearance of these mutations highlights the intra-patient evolution of BKV. Some of the observed mutations conferred resistance to antibody-mediated neutralization. The mutations also modified the spectrum of receptor glycans engaged by BKV during host cell entry. Intriguingly, all observed mutations were consistent with DNA damage caused by antiviral APOBEC3 cytosine deaminases. Moreover, APOBEC3 expression was evident upon immunohistochemical analysis of renal biopsies from KTRs. These results provide a snapshot of in-host BKV evolution and suggest that APOBEC3 may drive BKV mutagenesis in vivo.
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Affiliation(s)
- Alberto Peretti
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eileen M Geoghegan
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Diana V Pastrana
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sigrun Smola
- Institute of Virology, Saarland University, Homburg/Saar 66421, Germany
| | - Pascal Feld
- Institute of Virology, Saarland University, Homburg/Saar 66421, Germany
| | - Marlies Sauter
- Institute of Virology, Saarland University, Homburg/Saar 66421, Germany
| | - Stefan Lohse
- Institute of Virology, Saarland University, Homburg/Saar 66421, Germany
| | - Mayur Ramesh
- Division of Infectious Diseases, Henry Ford Hospital, Detroit, MI 48202 USA
| | - Efrem S Lim
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Cinzia Borgogna
- Virology Unit, Department of Translational Medicine, Novara Medical School, Novara 28100, Italy
| | - Peter C FitzGerald
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Valery Bliskovsky
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gabriel J Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Reuben S Harris
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, Institute for Molecular Virology, University of Minnesota, Minneapolis, MN 55455, USA; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - J Keith Killian
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jack Zhu
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marbin Pineda
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul S Meltzer
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Renzo Boldorini
- Pathology Unit, Department of Health Sciences, Novara Medical School, Novara 28100, Italy
| | - Marisa Gariglio
- Virology Unit, Department of Translational Medicine, Novara Medical School, Novara 28100, Italy
| | - Christopher B Buck
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Gupta G, Kuppachi S, Kalil RS, Buck CB, Lynch CF, Engels EA. Treatment for presumed BK polyomavirus nephropathy and risk of urinary tract cancers among kidney transplant recipients in the United States. Am J Transplant 2018; 18:245-252. [PMID: 28980390 PMCID: PMC5739985 DOI: 10.1111/ajt.14530] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/06/2017] [Accepted: 09/18/2017] [Indexed: 02/06/2023]
Abstract
Recent case series describe detection of BK polyomavirus (BKV) in urinary tract cancers in kidney transplant recipients, suggesting that BKV could contribute to the development of these cancers. We assessed risk for urinary tract cancers in kidney recipients with or without treatment for presumed BKV nephropathy (tBKVN) using data from the United States Transplant Cancer Match Study (2003-2013). Among 55 697 included recipients, 2015 (3.6%) were reported with tBKVN. Relative to the general population, incidence was similarly elevated (approximately 4.5-fold) for kidney cancer in recipients with or without tBKVN, and incidence was not increased in either group for prostate cancer. In contrast, for invasive bladder cancer, incidence was more strongly elevated in recipients with versus without tBKVN (standardized incidence ratios 4.5 vs. 1.7; N = 48 cases), corresponding to an incidence rate ratio (IRR) of 2.9 (95% confidence interval [CI] 1.0-8.2), adjusted for sex, age, transplant year, and use of polyclonal antibody induction. As a result, recipients with tBKVN had borderline increased incidence for all urothelial cancers combined (renal pelvis, ureter, and bladder cancers: adjusted IRR 2.2, 95% CI 0.9-5.4; N = 89 cases). Together with reports describing BKV detection in tumor tissues, these results support an association between BKV and urothelial carcinogenesis among kidney transplant recipients.
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Affiliation(s)
- Gaurav Gupta
- Virginia Commonwealth University, Richmond, United States
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Nguyen KD, Lee EE, Yue Y, Stork J, Pock L, North JP, Vandergriff T, Cockerell C, Hosler GA, Pastrana DV, Buck CB, Wang RC. Human polyomavirus 6 and 7 are associated with pruritic and dyskeratotic dermatoses. J Am Acad Dermatol 2016; 76:932-940.e3. [PMID: 28040372 DOI: 10.1016/j.jaad.2016.11.035] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/08/2016] [Accepted: 11/15/2016] [Indexed: 01/21/2023]
Abstract
BACKGROUND Human polyomavirus (HPyV)6 and HPyV7 are shed chronically from human skin. HPyV7, but not HPyV6, has been linked to a pruritic skin eruption of immunosuppression. OBJECTIVE We determined whether biopsy specimens showing a characteristic pattern of dyskeratosis and parakeratosis might be associated with polyomavirus infection. METHODS We screened biopsy specimens showing "peacock plumage" histology by polymerase chain reaction for HPyVs. Cases positive for HPyV6 or HPyV7 were then analyzed by immunohistochemistry, electron microscopy, immunofluorescence, quantitative polymerase chain reaction, and complete sequencing, including unbiased, next-generation sequencing. RESULTS We identified 3 additional cases of HPyV6 or HPyV7 skin infections. Expression of T antigen and viral capsid was abundant in lesional skin. Dual immunofluorescence staining experiments confirmed that HPyV7 primarily infects keratinocytes. High viral loads in lesional skin compared with normal-appearing skin and the identification of intact virions by both electron microscopy and next-generation sequencing support a role for active viral infections in these skin diseases. LIMITATION This was a small case series of archived materials. CONCLUSION We have found that HPyV6 and HPyV7 are associated with rare, pruritic skin eruptions with a distinctive histologic pattern and describe this entity as "HPyV6- and HPyV7-associated pruritic and dyskeratotic dermatoses."
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Affiliation(s)
- Khang D Nguyen
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Eunice E Lee
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yangbo Yue
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Jiri Stork
- Dermatohistopathological Laboratory, Charles University in Prague, Prague, Czech Republic
| | - Lumir Pock
- Bioptical Laboratory, Pilsen, Czech Republic
| | - Jeffrey P North
- Dermatology and Pathology, University of California, San Francisco, California
| | - Travis Vandergriff
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Clay Cockerell
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas; Cockerell Dermatopathology, Dallas, Texas
| | - Gregory A Hosler
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas; ProPath, Dallas, Texas
| | | | | | - Richard C Wang
- Department of Dermatology, University of Texas Southwestern Medical Center, Dallas, Texas.
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Liu W, Yang R, Payne AS, Schowalter RM, Spurgeon ME, Lambert PF, Xu X, Buck CB, You J. Identifying the Target Cells and Mechanisms of Merkel Cell Polyomavirus Infection. Cell Host Microbe 2016; 19:775-87. [PMID: 27212661 DOI: 10.1016/j.chom.2016.04.024] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 03/10/2016] [Accepted: 04/15/2016] [Indexed: 12/20/2022]
Abstract
Infection with Merkel cell polyomavirus (MCPyV) can lead to Merkel cell carcinoma (MCC), a lethal form of skin cancer. However, the skin cell type productively infected by MCPyV remains a central question. We combined cell culture and ex vivo approaches to identify human dermal fibroblasts as natural host cells that support productive MCPyV infection. Based on this, we established a cell culture model for MCPyV infection, which will facilitate investigation of the oncogenic mechanisms for this DNA virus. Using this model, we discovered that induction of matrix metalloproteinase (MMP) genes by the WNT/β-catenin signaling pathway and other growth factors stimulates MCPyV infection. This suggests that MCC risk factors such as UV radiation and aging, which are known to stimulate WNT signaling and MMP expression, may promote viral infection and thus drive MCC. Our study also introduces the FDA-approved MEK antagonist trametinib as an effective inhibitor for controlling MCPyV infection.
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Affiliation(s)
- Wei Liu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruifeng Yang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aimee S Payne
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rachel M Schowalter
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Megan E Spurgeon
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Paul F Lambert
- Department of Oncology, McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Xiaowei Xu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher B Buck
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jianxin You
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Buck CB, Van Doorslaer K, Peretti A, Geoghegan EM, Tisza MJ, An P, Katz JP, Pipas JM, McBride AA, Camus AC, McDermott AJ, Dill JA, Delwart E, Ng TFF, Farkas K, Austin C, Kraberger S, Davison W, Pastrana DV, Varsani A. The Ancient Evolutionary History of Polyomaviruses. PLoS Pathog 2016; 12:e1005574. [PMID: 27093155 PMCID: PMC4836724 DOI: 10.1371/journal.ppat.1005574] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/23/2016] [Indexed: 12/21/2022] Open
Abstract
Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae. Polyomaviruses are a family of DNA-based viruses that are known to infect various terrestrial vertebrates, including humans. In this report, we describe our discovery of highly divergent polyomaviruses associated with various marine fish. Searches of public deep sequencing databases unexpectedly revealed the existence of polyomavirus-like sequences in scorpion and spider datasets. Our analysis of these new sequences suggests that polyomaviruses have slowly co-evolved with individual host animal lineages through an established mechanism known as intrahost divergence. The proposed model is similar to the mechanisms through with other DNA viruses, such as papillomaviruses, are thought to have evolved. Our analysis also suggests that distantly related polyomaviruses sometimes recombine to produce new chimeric lineages. We propose a possible taxonomic scheme that can account for these inferred ancient recombination events.
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Affiliation(s)
- Christopher B. Buck
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
- * E-mail:
| | | | - Alberto Peretti
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Eileen M. Geoghegan
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Michael J. Tisza
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Ping An
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joshua P. Katz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - James M. Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alison A. McBride
- Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Alvin C. Camus
- Department of Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Alexa J. McDermott
- Animal Health Department, Georgia Aquarium, Inc., Atlanta, Georgia, United States of America
| | - Jennifer A. Dill
- Department of Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Terry F. F. Ng
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Kata Farkas
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Charlotte Austin
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - William Davison
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Diana V. Pastrana
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
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Abstract
BK polyomavirus (BKV) is an opportunistic pathogen that poses a serious threat to organ transplant recipients. In this issue of Structure, Hurdiss and colleagues' (Hurdiss et al., 2016) beautiful new high-resolution cryo-EM reconstruction of BKV provides a structural roadmap for the ongoing development of therapeutic antibodies and vaccines targeting this potentially deadly virus. The study also serves as a platform for exploring the basic biology of virion assembly and infectious entry.
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Ray U, Cinque P, Gerevini S, Longo V, Lazzarin A, Schippling S, Martin R, Buck CB, Pastrana DV. JC polyomavirus mutants escape antibody-mediated neutralization. Sci Transl Med 2015; 7:306ra151. [PMID: 26400912 DOI: 10.1126/scitranslmed.aab1720] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/12/2015] [Indexed: 12/15/2022]
Abstract
JC polyomavirus (JCV) persistently infects the urinary tract of most adults. Under conditions of immune impairment, JCV causes an opportunistic brain disease, progressive multifocal leukoencephalopathy (PML). JCV strains found in the cerebrospinal fluid of PML patients contain distinctive mutations in surface loops of the major capsid protein, VP1. We hypothesized that VP1 mutations might allow the virus to evade antibody-mediated neutralization. Consistent with this hypothesis, neutralization serology revealed that plasma samples from PML patients neutralized wild-type JCV strains but failed to neutralize patient-cognate PML-mutant JCV strains. This contrasted with serological results for healthy individuals, most of whom robustly cross-neutralized all tested JCV variants. Mice administered a JCV virus-like particle (VLP) vaccine initially showed neutralizing "blind spots" (akin to those observed in PML patients) that closed after booster immunization. A PML patient administered an experimental JCV VLP vaccine likewise showed markedly increased neutralizing titer against her cognate PML-mutant JCV. The results indicate that deficient humoral immunity is a common aspect of PML pathogenesis and that vaccination may overcome this humoral deficiency. Thus, vaccination with JCV VLPs might prevent the development of PML.
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Affiliation(s)
- Upasana Ray
- Lab of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paola Cinque
- Department of Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Simonetta Gerevini
- Neuroradiology Unit, Head and Neck Department, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Valeria Longo
- Department of Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Adriano Lazzarin
- Department of Infectious Diseases, San Raffaele Scientific Institute, 20132 Milan, Italy. San Raffaele University, 20132 Milan, Italy
| | - Sven Schippling
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University Hospital Zurich, University Zurich, 8091 Zurich, Switzerland
| | - Roland Martin
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University Hospital Zurich, University Zurich, 8091 Zurich, Switzerland
| | - Christopher B Buck
- Lab of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Diana V Pastrana
- Lab of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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Siebrasse EA, Pastrana DV, Nguyen NL, Wang A, Roth MJ, Holland SM, Freeman AF, McDyer J, Buck CB, Wang D. WU polyomavirus in respiratory epithelial cells from lung transplant patient with Job syndrome. Emerg Infect Dis 2015; 21:103-6. [PMID: 25531075 PMCID: PMC4285236 DOI: 10.3201/eid2101.140855] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We detected WU polyomavirus (WUPyV) in a bronchoalveolar lavage sample from lungs transplanted into a recipient with Job syndrome by using immunoassays specific for the WUPyV viral protein 1. Co-staining for an epithelial cell marker identified most WUPyV viral protein 1–positive cells as respiratory epithelial cells.
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Abstract
Epidemiological studies have suggested that consumption of beef may correlate with an increased risk of colorectal cancer. One hypothesis to explain this proposed link might be the presence of a carcinogenic infectious agent capable of withstanding cooking. Polyomaviruses are a ubiquitous family of thermostable non-enveloped DNA viruses that are known to be carcinogenic. Using virion enrichment, rolling circle amplification (RCA) and next-generation sequencing, we searched for polyomaviruses in meat samples purchased from several supermarkets. Ground beef samples were found to contain three polyomavirus species. One species, bovine polyomavirus 1 (BoPyV1), was originally discovered as a contaminant in laboratory FCS. A previously unknown species, BoPyV2, occupies the same clade as human Merkel cell polyomavirus and raccoon polyomavirus, both of which are carcinogenic in their native hosts. A third species, BoPyV3, is related to human polyomaviruses 6 and 7. Examples of additional DNA virus families, including herpesviruses, adenoviruses, circoviruses and gyroviruses were also detected either in ground beef samples or in comparison samples of ground pork and ground chicken. The results suggest that the virion enrichment/RCA approach is suitable for random detection of essentially any DNA virus with a detergent-stable capsid. It will be important for future studies to address the possibility that animal viruses commonly found in food might be associated with disease.
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36
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Gordon SN, Doster MN, Kines RC, Keele BF, Brocca-Cofano E, Guan Y, Pegu P, Liyanage NPM, Vaccari M, Cuburu N, Buck CB, Ferrari G, Montefiori D, Piatak M, Lifson JD, Xenophontos AM, Venzon D, Robert-Guroff M, Graham BS, Lowy DR, Schiller JT, Franchini G. Antibody to the gp120 V1/V2 loops and CD4+ and CD8+ T cell responses in protection from SIVmac251 vaginal acquisition and persistent viremia. J Immunol 2014; 193:6172-83. [PMID: 25398324 DOI: 10.4049/jimmunol.1401504] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The human papillomavirus pseudovirions (HPV-PsVs) approach is an effective gene-delivery system that can prime or boost an immune response in the vaginal tract of nonhuman primates and mice. Intravaginal vaccination with HPV-PsVs expressing SIV genes, combined with an i.m. gp120 protein injection, induced humoral and cellular SIV-specific responses in macaques. Priming systemic immune responses with i.m. immunization with ALVAC-SIV vaccines, followed by intravaginal HPV-PsV-SIV/gp120 boosting, expanded and/or recruited T cells in the female genital tract. Using a stringent repeated low-dose intravaginal challenge with the highly pathogenic SIVmac251, we show that although these regimens did not demonstrate significant protection from virus acquisition, they provided control of viremia in a number of animals. High-avidity Ab responses to the envelope gp120 V1/V2 region correlated with delayed SIVmac251 acquisition, whereas virus levels in mucosal tissues were inversely correlated with antienvelope CD4(+) T cell responses. CD8(+) T cell depletion in animals with controlled viremia caused an increase in tissue virus load in some animals, suggesting a role for CD8(+) T cells in virus control. This study highlights the importance of CD8(+) cells and antienvelope CD4(+) T cells in curtailing virus replication and antienvelope V1/V2 Abs in preventing SIVmac251 acquisition.
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Affiliation(s)
- Shari N Gordon
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892
| | - Melvin N Doster
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892
| | - Rhonda C Kines
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20982
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | | | - Yongjun Guan
- Division of Basic Science and Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Poonam Pegu
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892
| | - Namal P M Liyanage
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892
| | - Monica Vaccari
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892
| | - Nicolas Cuburu
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20982
| | - Christopher B Buck
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20982
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, NC 27710
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710
| | - Michael Piatak
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Anastasia M Xenophontos
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892
| | - David Venzon
- Biostatistics and Data Management Section, National Cancer Institute, Bethesda, MD 20892; and
| | | | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892
| | - Douglas R Lowy
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20982
| | - John T Schiller
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20982
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD 20892;
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Schrama D, Groesser L, Ugurel S, Hafner C, Pastrana DV, Buck CB, Cerroni L, Theiler A, Becker JC. Presence of human polyomavirus 6 in mutation-specific BRAF inhibitor-induced epithelial proliferations. JAMA Dermatol 2014; 150:1180-6. [PMID: 24943872 PMCID: PMC8369517 DOI: 10.1001/jamadermatol.2014.1116] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
IMPORTANCE A frequent adverse effect of mutation-specific BRAF inhibitor therapy is the induction of epithelial proliferations including cutaneous squamous cell carcinomas. To date, the only factor identified contributing to their development is the activation of the mitogen-activated signal transduction cascade by mutations in the RAS genes. However, these mutations explain only 60% of the tumors; hence, it is important to identify what is causing the remaining tumors. OBJECTIVE To test for the presence of human papillomaviruses (HPVs) and the recently identified human polyomaviruses (HPyVs), Merkel cell polyomavirus (MCPyV), and trichodysplasia spinulosa-associated polyomavirus (TSPyV), as well as HPyV-6, HPyV-7, HPyV-9, and HPyV-10, in epithelial proliferations occurring after BRAF inhibitor therapy to determine whether these oncogenic viruses may contribute to BRAF inhibitor-induced skin tumors. DESIGN, SETTING, AND PARTICIPANTS Retrospective study at a university hospital in Austria of epithelial proliferations that developed in patients with melanoma after initiation of treatment with the BRAF inhibitor vemurafenib. Samples were analyzed for (1) presence of the most frequently observed RAS mutations by SNaPshot technology, (2) detection of the viruses by real-time polymerase chain reaction, and (3) presence of capsid proteins of the most abundantly detected virus by immunohistochemical analysis. MAIN OUTCOMES AND MEASURES RAS mutational status, as well as HPV and HPyV presence, in BRAF inhibitor-induced epithelial proliferations. RESULTS Eighteen biopsy samples from 6 patients were retrieved from our hospital's archive. We identified RAS mutations in 10 (62%) of the 16 samples with clear results. DNA of HPyV-9, HPyV-10, and TSPyV were virtually absent in the samples. MCPyV DNA was present in 13 of 18 samples, and HPV, HPyV-6, and HPyV-7 DNA were present in all samples. In general, the amount of DNA encoding the latter viruses was rather low, with the exception of HPyV-6 in several samples of 1 individual patient. Notably, the relevance of the presence of HPyV-6 in the epithelial proliferation was underlined by immunohistochemical detection of the core protein VP1 of HPyV-6. CONCLUSIONS AND RELEVANCE The presence of both high HPyV-6 DNA load and VP1 protein suggests that polyomaviruses may contribute to the epithelial proliferations observed in patients receiving BRAF inhibitor therapy, albeit the relative impact as compared with that of RAS mutations appears circumstantial.
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Affiliation(s)
- David Schrama
- Department of Dermatology, Medical University of Graz, Graz, Austria2Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Leopold Groesser
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Selma Ugurel
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Christian Hafner
- Department of Dermatology, University Hospital Regensburg, Regensburg, Germany
| | - Diana V Pastrana
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland
| | - Christopher B Buck
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland
| | - Lorenzo Cerroni
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Anna Theiler
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Jürgen C Becker
- Department of Dermatology, Medical University of Graz, Graz, Austria
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Ho J, Jedrych JJ, Feng H, Natalie AA, Grandinetti L, Mirvish E, Crespo MM, Yadav D, Fasanella KE, Proksell S, Kuan SF, Pastrana DV, Buck CB, Shuda Y, Moore PS, Chang Y. Human polyomavirus 7-associated pruritic rash and viremia in transplant recipients. J Infect Dis 2014; 211:1560-5. [PMID: 25231015 DOI: 10.1093/infdis/jiu524] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/05/2014] [Indexed: 11/14/2022] Open
Abstract
Human polyomavirus 7 (HPyV7) is one of 11 HPyVs recently discovered through genomic sequencing technologies. Two lung transplant recipients receiving immunosuppressive therapy developed pruritic, brown plaques on the trunk and extremities showing a distinctive epidermal hyperplasia with virus-laden keratinocytes containing densely packed 36-45-nm icosahedral capsids. Rolling circle amplification and gradient centrifugation testing were positive for encapsidated HPyV7 DNA in skin and peripheral blood specimens from both patients, and HPyV7 early and capsid proteins were abundantly expressed in affected tissues. We describe for the first time that HPyV7 is associated with novel pathogenicity in some immunosuppressed individuals.
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Affiliation(s)
| | | | - Huichen Feng
- Cancer Virology Program, Cancer Institute, University of Pittsburgh, Pennsylvania
| | | | | | | | | | | | | | | | | | - Diana V Pastrana
- Laboratory of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Christopher B Buck
- Laboratory of Cellular Oncology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Yoko Shuda
- Cancer Virology Program, Cancer Institute, University of Pittsburgh, Pennsylvania
| | - Patrick S Moore
- Cancer Virology Program, Cancer Institute, University of Pittsburgh, Pennsylvania
| | - Yuan Chang
- Cancer Virology Program, Cancer Institute, University of Pittsburgh, Pennsylvania
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Pastrana DV, Ray U, Magaldi TG, Schowalter RM, Çuburu N, Buck CB. BK polyomavirus genotypes represent distinct serotypes with distinct entry tropism. J Virol 2013; 87:10105-13. [PMID: 23843634 PMCID: PMC3754014 DOI: 10.1128/jvi.01189-13] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 07/01/2013] [Indexed: 12/21/2022] Open
Abstract
BK polyomavirus (BKV) causes significant urinary tract pathogenesis in immunosuppressed individuals, including kidney and bone marrow transplant recipients. It is currently unclear whether BKV-neutralizing antibodies can moderate or prevent BKV disease. We developed reporter pseudoviruses based on seven divergent BKV isolates and performed neutralization assays on sera from healthy human subjects. The results demonstrate that BKV genotypes I, II, III, and IV are fully distinct serotypes. While nearly all healthy subjects had BKV genotype I-neutralizing antibodies, a majority of subjects did not detectably neutralize genotype III or IV. Surprisingly, BKV subgenotypes Ib1 and Ib2 can behave as fully distinct serotypes. This difference is governed by as few as two residues adjacent to the cellular glycan receptor-binding site on the virion surface. Serological analysis of mice given virus-like particle (VLP)-based BKV vaccines confirmed these findings. Mice administered a multivalent VLP vaccine showed high-titer serum antibody responses that potently cross-neutralized all tested BKV genotypes. Interestingly, each of the neutralization serotypes bound a distinct spectrum of cell surface receptors, suggesting a possible connection between escape from recognition by neutralizing antibodies and cellular attachment mechanisms. The finding implies that different BKV genotypes have different cellular tropisms and pathogenic potentials in vivo. Individuals who are infected with one BKV serotype may remain humorally vulnerable to other BKV serotypes after implementation of T cell immunosuppression. Thus, prevaccinating organ transplant recipients with a multivalent BKV VLP vaccine might reduce the risk of developing posttransplant BKV disease.
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Affiliation(s)
- Diana V Pastrana
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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Abstract
The surface of polyomavirus virions is composed of pentameric knobs of the major capsid protein, VP1. In previously studied polyomavirus species, such as SV40, two interior capsid proteins, VP2 and VP3, emerge from the virion to play important roles during the infectious entry process. Translation of the VP3 protein initiates at a highly conserved Met-Ala-Leu motif within the VP2 open reading frame. Phylogenetic analyses indicate that Merkel cell polyomavirus (MCV or MCPyV) is a member of a divergent clade of polyomaviruses that lack the conserved VP3 N-terminal motif. Consistent with this observation, we show that VP3 is not detectable in MCV-infected cells, VP3 is not found in native MCV virions, and mutation of possible alternative VP3-initiating methionine codons did not significantly affect MCV infectivity in culture. In contrast, VP2 knockout resulted in a >100-fold decrease in native MCV infectivity, despite normal virion assembly, viral DNA packaging, and cell attachment. Although pseudovirus-based experiments confirmed that VP2 plays an essential role for infection of some cell lines, other cell lines were readily transduced by pseudovirions lacking VP2. In cell lines where VP2 was needed for efficient infectious entry, the presence of a conserved myristoyl modification on the N-terminus of VP2 was important for its function. The results show that a single minor capsid protein, VP2, facilitates a post-attachment stage of MCV infectious entry into some, but not all, cell types. Merkel cell polyomavirus (MCV or MCPyV) is a recently discovered member of the viral family Polyomaviridae. The virus plays a causal role in Merkel cell carcinoma, a highly lethal form of skin cancer. MCV encodes a major capsid protein, VP1, which forms the non-enveloped surface of the virion. Other polyomavirus species encode two minor capsid proteins, VP2 and VP3, which associate with the inner surface of the capsid and facilitate infectious entry. In this report we show that MCV does not have a VP3 minor capsid protein. Sequence analyses suggest that more than a quarter of known polyomavirus species share MCV's lack of a VP3 protein. In contrast to VP3, VP2-knockout MCV mutants displayed dramatically reduced infectivity. Consistent with native virion findings, MCV pseudovirions lacking VP2 or carrying mutations in the VP2 myristoylation motif displayed reduced infectivity on several cell lines. Puzzlingly, MCV pseudoviruses lacking VP2 successfully transduced other cell lines with high efficiency. Taken together, the data show that the lone MCV minor capsid protein, VP2, plays an important role during infectious entry into some cell types, but is dispensable for entry into other cell types.
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Affiliation(s)
- Rachel M. Schowalter
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christopher B. Buck
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Abstract
The elegant icosahedral surface of the papillomavirus virion is formed by a single protein called L1. Recombinant L1 proteins can spontaneously self-assemble into a highly immunogenic structure that closely mimics the natural surface of native papillomavirus virions. This has served as the basis for two highly successful vaccines against cancer-causing human papillomaviruses (HPVs). During the viral life cycle, the capsid must undergo a variety of conformational changes, allowing key functions including the encapsidation of the ~8 kb viral genomic DNA, maturation into a more stable state to survive transit between hosts, mediating attachment to new host cells, and finally releasing the viral DNA into the newly infected host cell. This brief review focuses on conserved sequence and structural features that underlie the functions of this remarkable protein.
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Çuburu N, Graham BS, Buck CB, Kines RC, Pang YYS, Day PM, Lowy DR, Schiller JT. Intravaginal immunization with HPV vectors induces tissue-resident CD8+ T cell responses. J Clin Invest 2012; 122:4606-20. [PMID: 23143305 DOI: 10.1172/jci63287] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The induction of persistent intraepithelial CD8+ T cell responses may be key to the development of vaccines against mucosally transmitted pathogens, particularly for sexually transmitted diseases. Here we investigated CD8+ T cell responses in the female mouse cervicovaginal mucosa after intravaginal immunization with human papillomavirus vectors (HPV pseudoviruses) that transiently expressed a model antigen, respiratory syncytial virus (RSV) M/M2, in cervicovaginal keratinocytes. An HPV intravaginal prime/boost with different HPV serotypes induced 10-fold more cervicovaginal antigen-specific CD8+ T cells than priming alone. Antigen-specific T cell numbers decreased only 2-fold after 6 months. Most genital antigen-specific CD8+ T cells were intra- or subepithelial, expressed αE-integrin CD103, produced IFN-γ and TNF-α, and displayed in vivo cytotoxicity. Using a sphingosine-1-phosphate analog (FTY720), we found that the primed CD8+ T cells proliferated in the cervicovaginal mucosa upon HPV intravaginal boost. Intravaginal HPV prime/boost reduced cervicovaginal viral titers 1,000-fold after intravaginal challenge with vaccinia virus expressing the CD8 epitope M2. In contrast, intramuscular prime/boost with an adenovirus type 5 vector induced a higher level of systemic CD8+ T cells but failed to induce intraepithelial CD103+CD8+ T cells or protect against recombinant vaccinia vaginal challenge. Thus, HPV vectors are attractive gene-delivery platforms for inducing durable intraepithelial cervicovaginal CD8+ T cell responses by promoting local proliferation and retention of primed antigen-specific CD8+ T cells.
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Affiliation(s)
- Nicolas Çuburu
- Laboratory of Cellular Oncology, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
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Wang X, Li J, Schowalter RM, Jiao J, Buck CB, You J. Bromodomain protein Brd4 plays a key role in Merkel cell polyomavirus DNA replication. PLoS Pathog 2012; 8:e1003021. [PMID: 23144621 PMCID: PMC3493480 DOI: 10.1371/journal.ppat.1003021] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 09/24/2012] [Indexed: 12/15/2022] Open
Abstract
Merkel cell polyomavirus (MCV or MCPyV) is the first human polyomavirus to be definitively linked to cancer. The mechanisms of MCV-induced oncogenesis and much of MCV biology are largely unexplored. In this study, we demonstrate that bromodomain protein 4 (Brd4) interacts with MCV large T antigen (LT) and plays a critical role in viral DNA replication. Brd4 knockdown inhibits MCV replication, which can be rescued by recombinant Brd4. Brd4 colocalizes with the MCV LT/replication origin complex in the nucleus and recruits replication factor C (RFC) to the viral replication sites. A dominant negative inhibitor of the Brd4-MCV LT interaction can dissociate Brd4 and RFC from the viral replication complex and abrogate MCV replication. Furthermore, obstructing the physiologic interaction between Brd4 and host chromatin with the chemical compound JQ1(+) leads to enhanced MCV DNA replication, demonstrating that the role of Brd4 in MCV replication is distinct from its role in chromatin-associated transcriptional regulation. Our findings demonstrate mechanistic details of the MCV replication machinery; providing novel insight to elucidate the life cycle of this newly discovered oncogenic DNA virus. MCV is a novel human polyomavirus that has recently been discovered in Merkel cell carcinoma (MCC), a rare but highly aggressive skin cancer. Several independent studies have confirmed that MCV is present in ∼80% of MCC tumors. However, very little is known about how the interaction between MCV and its human hosts contributes to the virus-induced cancers. Many aspects of the infectious life cycle of MCV are largely unexplored. In this study, we demonstrate that the MCV-encoded large T antigen can bind to host protein Brd4, which in turn serves as a scaffold that functionally recruits cellular DNA replication factors for replication of MCV viral DNA in host cells. This study is the first report to demonstrate mechanistic details of MCV's recruitment of the host cell DNA replication machinery; providing novel insight to elucidate the life cycle of this newly discovered oncogenic DNA virus. Importantly, our work demonstrates that blocking the Brd4 and MCV LT interaction can prevent MCV from replicating in host cells. This study identifies the Brd4-MCV LT interaction as an important target for potential development of effective therapeutic strategies to treat MCV infection.
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Affiliation(s)
- Xin Wang
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jing Li
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Rachel M. Schowalter
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Jing Jiao
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Christopher B. Buck
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Jianxin You
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Handisurya A, Day PM, Thompson CD, Buck CB, Kwak K, Roden RBS, Lowy DR, Schiller JT. Murine skin and vaginal mucosa are similarly susceptible to infection by pseudovirions of different papillomavirus classifications and species. Virology 2012; 433:385-94. [PMID: 22985477 DOI: 10.1016/j.virol.2012.08.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 06/19/2012] [Accepted: 08/27/2012] [Indexed: 01/14/2023]
Abstract
Depending upon viral genotype, productive papillomavirus infection and disease display preferential tropism for cutaneous or mucosal stratified squamous epithelia, although the mechanisms are unclear. To investigate papillomavirus entry tropism, we used reporter pseudovirions based on various cutaneous and mucosal papillomavirus species, including the recently identified murine papillomavirus. Pseudovirus transduction of BALB/c mice was examined using an improved murine skin infection protocol and a previously developed cervicovaginal challenge model. In the skin, HPV5, HPV6, HPV16, BPV1 and MusPV1 pseudovirions preferentially transduced keratinocytes at sites of trauma, similar to the genital tract. Skin infection, visualized by in vivo imaging using a luciferase reporter gene, peaked between days 2-3 and rapidly diminished for all pseudovirion types. Murine cutaneous and genital tissues were similarily permissive for pseudovirions of HPV types 5, 6, 8, 16, 18, 26, 44, 45, 51, 58 and animal papillomaviruses BPV1 and MusPV1, implying that papillomavirus' tissue and host tropism is governed primarily by post-entry regulatory events in the mouse.
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Affiliation(s)
- Alessandra Handisurya
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Abstract
Merkel Cell Polyomavirus (MCV or MCPyV) was recently discovered in an aggressive form of skin cancer known as Merkel cell carcinoma (MCC). Integration of MCV DNA into the host genome likely contributes to the development of MCC in humans. MCV infection is common and many healthy people shed MCV virions from the surface of their skin. MCV DNA has also been detected in samples from a variety of other tissues. Although MCC tumors serve as a record that MCV can infect the Merkel cell lineage, the true tissue tropism and natural reservoirs of MCV infection in the host are not known. In an effort to gain insight into the tissue tropism of MCV, and to possibly identify cellular factors responsible for mediating infectious entry of the virus, the infection potential of human cells derived from a variety of tissues was evaluated. MCV gene transfer vectors (pseudoviruses) carrying reporter plasmid DNA encoding GFP or luciferase genes were used to transduce keratinocytes and melanocytes, as well as lines derived from MCC tumors and the NCI-60 panel of human tumor cell lines. MCV transduction was compared to transduction with pseudoviruses based on the better-studied human BK polyomavirus (BKV). The efficiency of MCV and BKV transduction of various cell types occasionally overlapped, but often differed greatly, and no clear tissue type preference emerged. Application of native MCV virions to a subset of highly transducible cell types suggested that the lines do not support robust replication of MCV, consistent with recent proposals that the MCV late phase may be governed by cellular differentiation in vivo. The availability of carefully curated gene expression data for the NCI-60 panel should make the MCV and BKV transduction data for these lines a useful reference for future studies aimed at elucidation of the infectious entry pathways of these viruses.
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Affiliation(s)
- Rachel M. Schowalter
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - William C. Reinhold
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Christopher B. Buck
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail:
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46
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Neu U, Hengel H, Blaum BS, Schowalter RM, Macejak D, Gilbert M, Wakarchuk WW, Imamura A, Ando H, Kiso M, Arnberg N, Garcea RL, Peters T, Buck CB, Stehle T. Structures of Merkel cell polyomavirus VP1 complexes define a sialic acid binding site required for infection. PLoS Pathog 2012; 8:e1002738. [PMID: 22910713 PMCID: PMC3406085 DOI: 10.1371/journal.ppat.1002738] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 04/21/2012] [Indexed: 11/18/2022] Open
Abstract
The recently discovered human Merkel cell polyomavirus (MCPyV or MCV) causes the aggressive Merkel cell carcinoma (MCC) in the skin of immunocompromised individuals. Conflicting reports suggest that cellular glycans containing sialic acid (Neu5Ac) may play a role in MCPyV infectious entry. To address this question, we solved X-ray structures of the MCPyV major capsid protein VP1 both alone and in complex with several sialylated oligosaccharides. A shallow binding site on the apical surface of the VP1 capsomer recognizes the disaccharide Neu5Ac-α2,3-Gal through a complex network of interactions. MCPyV engages Neu5Ac in an orientation and with contacts that differ markedly from those observed in other polyomavirus complexes with sialylated receptors. Mutations in the Neu5Ac binding site abolish MCPyV infection, highlighting the relevance of the Neu5Ac interaction for MCPyV entry. Our study thus provides a powerful platform for the development of MCPyV-specific vaccines and antivirals. Interestingly, engagement of sialic acid does not interfere with initial attachment of MCPyV to cells, consistent with a previous proposal that attachment is mediated by a class of non-sialylated carbohydrates called glycosaminoglycans. Our results therefore suggest a model in which sialylated glycans serve as secondary, post-attachment co-receptors during MCPyV infectious entry. Since cell-surface glycans typically serve as primary attachment receptors for many viruses, we identify here a new role for glycans in mediating, and perhaps even modulating, post-attachment entry processes.
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Affiliation(s)
- Ursula Neu
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Holger Hengel
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Bärbel S. Blaum
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
- Department of Chemistry, University of Luebeck, Luebeck, Germany
| | - Rachel M. Schowalter
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Dennis Macejak
- Department of Molecular, Cellular, and Developmental Biology, and the Biofrontiers Institute, University of Colorado at Boulder, Boulder, Colorado, United States of America
| | - Michel Gilbert
- National Research Council Canada, Institute for Biological Sciences, Glycobiology Program, Ottawa, Ontario, Canada
| | - Warren W. Wakarchuk
- National Research Council Canada, Institute for Biological Sciences, Glycobiology Program, Ottawa, Ontario, Canada
| | - Akihiro Imamura
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
- Department of Applied Bioorganic Chemistry, Gifu University, Gifu, Japan
| | - Hiromune Ando
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
- Department of Applied Bioorganic Chemistry, Gifu University, Gifu, Japan
| | - Makoto Kiso
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto, Japan
- Department of Applied Bioorganic Chemistry, Gifu University, Gifu, Japan
| | - Niklas Arnberg
- Division of Virology, Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Robert L. Garcea
- Department of Molecular, Cellular, and Developmental Biology, and the Biofrontiers Institute, University of Colorado at Boulder, Boulder, Colorado, United States of America
| | - Thomas Peters
- Department of Chemistry, University of Luebeck, Luebeck, Germany
| | - Christopher B. Buck
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tuebingen, Tuebingen, Germany
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
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Abstract
Mucus is a porous biopolymer matrix that coats all wet epithelia in the human body and serves as the first line of defense against many pathogenic bacteria and viruses. However, under certain conditions viruses are able to penetrate this infection barrier, which compromises the protective function of native mucus. Here, we find that isolated porcine gastric mucin polymers, key structural components of native mucus, can protect an underlying cell layer from infection by small viruses such as human papillomavirus (HPV), Merkel cell polyomavirus (MCV), or a strain of influenza A virus. Single particle analysis of virus mobility inside the mucin barrier reveals that this shielding effect is in part based on a retardation of virus diffusion inside the biopolymer matrix. Our findings suggest that purified mucins may be used as a broad-range antiviral supplement to personal hygiene products, baby formula or lubricants to support our immune system.
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Affiliation(s)
- Oliver Lieleg
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Pastrana DV, Brennan DC, Çuburu N, Storch GA, Viscidi RP, Randhawa PS, Buck CB. Neutralization serotyping of BK polyomavirus infection in kidney transplant recipients. PLoS Pathog 2012; 8:e1002650. [PMID: 22511874 PMCID: PMC3325208 DOI: 10.1371/journal.ppat.1002650] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 03/02/2012] [Indexed: 12/20/2022] Open
Abstract
BK polyomavirus (BKV or BKPyV) associated nephropathy affects up to 10% of kidney transplant recipients (KTRs). BKV isolates are categorized into four genotypes. It is currently unclear whether the four genotypes are also serotypes. To address this issue, we developed high-throughput serological assays based on antibody-mediated neutralization of BKV genotype I and IV reporter vectors (pseudoviruses). Neutralization-based testing of sera from mice immunized with BKV-I or BKV-IV virus-like particles (VLPs) or sera from naturally infected human subjects revealed that BKV-I specific serum antibodies are poorly neutralizing against BKV-IV and vice versa. The fact that BKV-I and BKV-IV are distinct serotypes was less evident in traditional VLP-based ELISAs. BKV-I and BKV-IV neutralization assays were used to examine BKV type-specific neutralizing antibody responses in KTRs at various time points after transplantation. At study entry, sera from 5% and 49% of KTRs showed no detectable neutralizing activity for BKV-I or BKV-IV neutralization, respectively. By one year after transplantation, all KTRs were neutralization seropositive for BKV-I, and 43% of the initially BKV-IV seronegative subjects showed evidence of acute seroconversion for BKV-IV neutralization. The results suggest a model in which BKV-IV-specific seroconversion reflects a de novo BKV-IV infection in KTRs who initially lack protective antibody responses capable of neutralizing genotype IV BKVs. If this model is correct, it suggests that pre-vaccinating prospective KTRs with a multivalent VLP-based vaccine against all BKV serotypes, or administration of BKV-neutralizing antibodies, might offer protection against graft loss or dysfunction due to BKV associated nephropathy.
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Affiliation(s)
- Diana V. Pastrana
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Daniel C. Brennan
- Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Nicolas Çuburu
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Gregory A. Storch
- Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Raphael P. Viscidi
- Department of Pediatrics, Johns Hopkins Medical Center, Baltimore, Maryland, United States of America
| | - Parmjeet S. Randhawa
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Christopher B. Buck
- Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
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Gordon SN, Kines RC, Kutsyna G, Ma ZM, Hryniewicz A, Roberts JN, Fenizia C, Hidajat R, Brocca-Cofano E, Cuburu N, Buck CB, Bernardo ML, Robert-Guroff M, Miller CJ, Graham BS, Lowy DR, Schiller JT, Franchini G. Targeting the vaginal mucosa with human papillomavirus pseudovirion vaccines delivering simian immunodeficiency virus DNA. J Immunol 2012; 188:714-23. [PMID: 22174446 PMCID: PMC3253208 DOI: 10.4049/jimmunol.1101404] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The majority of HIV infections occur via mucosal transmission. Vaccines that induce memory T and B cells in the female genital tract may prevent the establishment and systemic dissemination of HIV. We tested the immunogenicity of a vaccine that uses human papillomavirus (HPV)-based gene transfer vectors, also called pseudovirions (PsVs), to deliver SIV genes to the vaginal epithelium. Our findings demonstrate that this vaccine platform induces gene expression in the genital tract in both cynomolgus and rhesus macaques. Intravaginal vaccination with HPV16, HPV45, and HPV58 PsVs delivering SIV Gag DNA induced Gag-specific Abs in serum and the vaginal tract, and T cell responses in blood, vaginal mucosa, and draining lymph nodes that rapidly expanded following intravaginal exposure to SIV(mac251.) HPV PsV-based vehicles are immunogenic, which warrant further testing as vaccine candidates for HIV and may provide a useful model to evaluate the benefits and risks of inducing high levels of SIV-specific immune responses at mucosal sites prior to SIV infection.
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Affiliation(s)
- Shari N. Gordon
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Rhonda C. Kines
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Galyna Kutsyna
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Zhong-Min Ma
- California National Primate Research Center and Center for Comparative Medicine, University of California Davis, Davis, CA 94118
| | - Anna Hryniewicz
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jeffery N. Roberts
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Claudio Fenizia
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Rachmat Hidajat
- Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Egidio Brocca-Cofano
- Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Nicolas Cuburu
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Christopher B. Buck
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Marcelino L. Bernardo
- Science Applications International Corporation (SAIC)-Frederick, Frederick, MD 21702
| | - Marjorie Robert-Guroff
- Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Christopher J. Miller
- California National Primate Research Center and Center for Comparative Medicine, University of California Davis, Davis, CA 94118
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Douglas R. Lowy
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - John T. Schiller
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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Schowalter RM, Pastrana DV, Buck CB. Glycosaminoglycans and sialylated glycans sequentially facilitate Merkel cell polyomavirus infectious entry. PLoS Pathog 2011; 7:e1002161. [PMID: 21829355 PMCID: PMC3145800 DOI: 10.1371/journal.ppat.1002161] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Accepted: 05/27/2011] [Indexed: 01/04/2023] Open
Abstract
Merkel cell polyomavirus (MCV or MCPyV) appears to be a causal factor in the development of Merkel cell carcinoma, a rare but highly lethal form of skin cancer. Although recent reports indicate that MCV virions are commonly shed from apparently healthy human skin, the precise cellular tropism of the virus in healthy subjects remains unclear. To begin to explore this question, we set out to identify the cellular receptors or co-receptors required for the infectious entry of MCV. Although several previously studied polyomavirus species have been shown to bind to cell surface sialic acid residues associated with glycolipids or glycoproteins, we found that sialylated glycans are not required for initial attachment of MCV virions to cultured human cell lines. Instead, glycosaminoglycans (GAGs), such as heparan sulfate (HS) and chondroitin sulfate (CS), serve as initial attachment receptors during the MCV infectious entry process. Using cell lines deficient in GAG biosynthesis, we found that N-sulfated and/or 6-O-sulfated forms of HS mediate infectious entry of MCV reporter vectors, while CS appears to be dispensable. Intriguingly, although cell lines deficient in sialylated glycans readily bind MCV capsids, the cells are highly resistant to MCV reporter vector-mediated gene transduction. This suggests that sialylated glycans play a post-attachment role in the infectious entry process. Results observed using MCV reporter vectors were confirmed using a novel system for infectious propagation of native MCV virions. Taken together, the findings suggest a model in which MCV infectious entry occurs via initial cell binding mediated primarily by HS, followed by secondary interactions with a sialylated entry co-factor. The study should facilitate the development of inhibitors of MCV infection and help shed light on the infectious entry pathways and cellular tropism of the virus. Strong evidence suggests that Merkel cell polyomavirus (MCV or MCPyV) is a causative factor in the development of a large proportion of cancers arising from epidermal Merkel cells. While Merkel cell carcinoma is rare, it appears that infection with MCV is common, and many healthy people chronically shed MCV virions from the surface of their skin. In an effort to better understand the factors controlling MCV tissue tropism, we sought to characterize the cellular receptors that mediate MCV attachment to cultured cells. Several previously-examined polyomaviruses utilize sialic acid-containing glycolipids and glycoproteins to mediate cell binding and infectious entry. Our results show that, in contrast to other polyomaviruses, MCV does not require sialic acid-bearing glycans for attachment to cells, but instead uses a different group of carbohydrates called glycosaminoglycans for the initial attachment step of the infectious entry process. Interestingly, although sialic acid-bearing glycans are dispensable for initial attachment to cells, data using cells deficient in sialylated glycans suggest that sialic acids may form an essential element of a possible co-receptor that is engaged after the initial attachment of MCV to the cell via glycosaminoglycans.
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Affiliation(s)
- Rachel M. Schowalter
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Diana V. Pastrana
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Christopher B. Buck
- Tumor Virus Molecular Biology Section, Laboratory of Cellular Oncology, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail:
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