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Mouse Mammary Tumour Virus (MMTV) in Human Breast Cancer—The Value of Bradford Hill Criteria. Viruses 2022; 14:v14040721. [PMID: 35458452 PMCID: PMC9028876 DOI: 10.3390/v14040721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/27/2023] Open
Abstract
For many decades, the betaretrovirus, mouse mammary tumour virus (MMTV), has been a causal suspect for human breast cancer. In recent years, substantial new evidence has been developed. Based on this evidence, we hypothesise that MMTV has a causal role. We have used an extended version of the classic A. Bradford Hill causal criteria to assess the evidence. 1. Identification of MMTV in human breast cancers: The MMTV 9.9 kb genome in breast cancer cells has been identified. The MMTV genome in human breast cancer is up to 98% identical to MMTV in mice. 2. Epidemiology: The prevalence of MMTV positive human breast cancer is about 35 to 40% of breast cancers in Western countries and 15 to 20% in China and Japan. 3. Strength of the association between MMTV and human breast cancer: Consistency—MMTV env gene sequences are consistently five-fold higher in human breast cancer as compared to benign and normal breast controls. 4. Temporality (timing) of the association: MMTV has been identified in benign and normal breast tissues up to 10 years before the development of MMTV positive breast cancer in the same patient. 5. Exposure: Exposure of humans to MMTV leads to development of MMTV positive human breast cancer. 6. Experimental evidence: MMTVs can infect human breast cells in culture; MMTV proteins are capable of malignantly transforming normal human breast epithelial cells; MMTV is a likely cause of biliary cirrhosis, which suggests a link between MMTV and the disease in humans. 7. Coherence—analogy: The life cycle and biology of MMTV in humans is almost the same as in experimental and feral mice. 8. MMTV Transmission: MMTV has been identified in human sputum and human milk. Cereals contaminated with mouse fecal material may transmit MMTV. These are potential means of transmission. 9. Biological plausibility: Retroviruses are the established cause of human cancers. Human T cell leukaemia virus type I (HTLV-1) causes adult T cell leukaemia, and human immunodeficiency virus infection (HIV) is associated with lymphoma and Kaposi sarcoma. 10. Oncogenic mechanisms: MMTV oncogenesis in humans probably differs from mice and may involve the enzyme APOBEC3B. Conclusion: In our view, the evidence is compelling that MMTV has a probable causal role in a subset of approximately 40% of human breast cancers.
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Song Y, Tang W, Li H. Identification of KIF4A and its effect on the progression of lung adenocarcinoma based on the bioinformatics analysis. Biosci Rep 2021; 41:BSR20203973. [PMID: 33398330 PMCID: PMC7823194 DOI: 10.1042/bsr20203973] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/25/2020] [Accepted: 01/04/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the most frequent histological type of lung cancer, and its incidence has displayed an upward trend in recent years. Nevertheless, little is known regarding effective biomarkers for LUAD. METHODS The robust rank aggregation method was used to mine differentially expressed genes (DEGs) from the gene expression omnibus (GEO) datasets. The Search Tool for the Retrieval of Interacting Genes (STRING) database was used to extract hub genes from the protein-protein interaction (PPI) network. The expression of the hub genes was validated using expression profiles from TCGA and Oncomine databases and was verified by real-time quantitative PCR (qRT-PCR). The module and survival analyses of the hub genes were determined using Cytoscape and Kaplan-Meier curves. The function of KIF4A as a hub gene was investigated in LUAD cell lines. RESULTS The PPI analysis identified seven DEGs including BIRC5, DLGAP5, CENPF, KIF4A, TOP2A, AURKA, and CCNA2, which were significantly upregulated in Oncomine and TCGA LUAD datasets, and were verified by qRT-PCR in our clinical samples. We determined the overall and disease-free survival analysis of the seven hub genes using GEPIA. We further found that CENPF, DLGAP5, and KIF4A expressions were positively correlated with clinical stage. In LUAD cell lines, proliferation and migration were inhibited and apoptosis was promoted by knocking down KIF4A expression. CONCLUSION We have identified new DEGs and functional pathways involved in LUAD. KIF4A, as a hub gene, promoted the progression of LUAD and might represent a potential therapeutic target for molecular cancer therapy.
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Affiliation(s)
- Yexun Song
- Department of Otolaryngology-Head Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Wenfang Tang
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha 410000, Hunan Province, China
| | - Hui Li
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha 410000, Hunan Province, China
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3
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Lawson JS, Glenn WK. Evidence for a causal role by human papillomaviruses in prostate cancer - a systematic review. Infect Agent Cancer 2020; 15:41. [PMID: 32684946 PMCID: PMC7359253 DOI: 10.1186/s13027-020-00305-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/25/2020] [Indexed: 12/17/2022] Open
Abstract
It is hypothesised that high risk for cancer human papillomaviruses (HPVs) have a causal role in prostate cancer. In 26 case control studies, high risk HPVs have been identified in benign and prostate cancers. High risk HPVs were identified in 325 (22.6%) of 1284 prostate cancers and in 113 (8.6%) of 1313 normal or benign prostate controls (p = 0.001). High risk HPVs of the same type have been identified in both normal and benign prostate tissues prior to the development of HPV positive prostate cancer. High risk HPVs can be associated with inflammatory prostatitis leading to benign prostate hyperplasia and later prostate cancer. Normal human prostate epithelial cells can be immortalised by experimental exposure to HPVs. HPVs are probably sexually transmitted. The role of HPVs in prostate cancer is complex and differs from HPVs associated cervical cancer. HPV infections may initiate prostate oncogenesis directly and influence oncogenesis indirectly via APOBEC enzymes. HPVs may collaborate with other pathogens in prostate oncogenesis. Although HPVs are only one of many pathogens that have been identified in prostate cancer, they are the only infectious pathogen which can be prevented by vaccination. A causal role for HPVs in prostate cancer is highly likely.
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Affiliation(s)
- James S Lawson
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
| | - Wendy K Glenn
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
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4
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Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir KR, Fridholm H, Hansen TA, Herrera JAR, Barnes CJ, Jensen RH, Richter SR, Nielsen IB, Pietroni C, Alquezar-Planas DE, Rey-Iglesia A, Olsen PVS, Rajpert-De Meyts E, Groth-Pedersen L, von Buchwald C, Jensen DH, Gniadecki R, Høgdall E, Langhoff JL, Pete I, Vereczkey I, Baranyai Z, Dybkaer K, Johnsen HE, Steiniche T, Hokland P, Rosenberg J, Baandrup U, Sicheritz-Pontén T, Willerslev E, Brunak S, Lund O, Mourier T, Vinner L, Izarzugaza JMG, Nielsen LP, Hansen AJ. High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach. J Infect Dis 2020; 220:1312-1324. [PMID: 31253993 PMCID: PMC6743825 DOI: 10.1093/infdis/jiz318] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/27/2019] [Indexed: 01/10/2023] Open
Abstract
Background Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data. Methods In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads. Results Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found. Conclusions Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.
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Affiliation(s)
- Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Maria Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jens Friis-Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | | | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - José Alejandro Romero Herrera
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Stine Raith Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ida Broman Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Carlotta Pietroni
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Pernille V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Ewa Rajpert-De Meyts
- Department of Growth and Reproduction, Copenhagen University Hospital (Rigshospitalet), Denmark
| | - Line Groth-Pedersen
- Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - David H Jensen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen University Hospital
| | - Robert Gniadecki
- Department of Dermato-Venerology, Faculty of Health Sciences, Copenhagen University Hospital, Bispebjerg Hospital, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Jill Levin Langhoff
- Department of Pathology, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Imre Pete
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Ildikó Vereczkey
- National Institute of Oncology, Department of Gynecology, Budapest, Hungary
| | - Zsolt Baranyai
- 1st Department of Surgery, Semmelweis University, Budapest, Hungary
| | - Karen Dybkaer
- Department of Clinical Medicine, Aalborg University, Denmark
| | | | | | - Peter Hokland
- Department of Clinical Medicine, Department of Haematology, Aarhus University Hospital, Denmark
| | - Jacob Rosenberg
- Department of Surgery, Herlev and Gentofte Hospital, University of Copenhagen, Denmark
| | - Ulrik Baandrup
- Center for Clinical Research, North Denmark Regional Hospital and Department of Clinical Medicine, Aalborg University, Hjørring, Denmark
| | - Thomas Sicheritz-Pontén
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Kedah, Malaysia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Søren Brunak
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
| | - Jose M G Izarzugaza
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen S, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Denmark
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Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related deaths in both the USA and the world. Recent research has demonstrated the involvement of the gut microbiota in CRC development and progression. Microbial biomarkers of disease have focused primarily on the bacterial component of the microbiome; however, the viral portion of the microbiome, consisting of both bacteriophages and eukaryotic viruses, together known as the virome, has been lesser studied. Here we review the recent advancements in high-throughput sequencing (HTS) technologies and bioinformatics, which have enabled scientists to better understand how viruses might influence the development of colorectal cancer. We discuss the contemporary findings revealing modulations in the virome and their correlation with CRC development and progression. While a variety of challenges still face viral HTS detection in clinical specimens, we consider herein numerous next steps for future basic and clinical research. Clinicians need to move away from a single infectious agent model for disease etiology by grasping new, more encompassing etiological paradigms, in which communities of various microbial components interact with each other and the host. The reporting and indexing of patient health information, socioeconomic data, and other relevant metadata will enable identification of predictive variables and covariates of viral presence and CRC development. Altogether, the virome has a more profound role in carcinogenesis and cancer progression than once thought, and viruses, specific for either human cells or bacteria, are clinically relevant in understanding CRC pathology, patient prognosis, and treatment development.
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6
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Singanallur NB, Anderson DE, Sessions OM, Kamaraj US, Bowden TR, Horsington J, Cowled C, Wang LF, Vosloo W. Probe capture enrichment next-generation sequencing of complete foot-and-mouth disease virus genomes in clinical samples. J Virol Methods 2019; 272:113703. [PMID: 31336142 DOI: 10.1016/j.jviromet.2019.113703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/04/2019] [Accepted: 07/17/2019] [Indexed: 01/02/2023]
Abstract
Next-generation sequencing (NGS) techniques offer an unprecedented "step-change" increase in the quantity and quality of sequence data rapidly generated from a sample and can be applied to obtain ultra-deep coverage of viral genomes. This is not possible with the routinely used Sanger sequencing method that gives the consensus reads, or by cloning approaches. In this study, a targeted-enrichment methodology for the simultaneous acquisition of complete foot-and-mouth disease virus (FMDV) genomes directly from clinical samples is presented. Biotinylated oligonucleotide probes (120 nt) were used to capture and enrich viral RNA following library preparation. To create a virus capture panel targeting serotype O and A simultaneously, 18 baits targeting the highly conserved regions of the 8.3 kb FMDV genome were synthesised, with 14 common to both serotypes, 2 specific to serotype O and 2 specific to serotype A. These baits were used to capture and enrich FMDV RNA (as cDNA) from samples collected during one pathogenesis and two vaccine efficacy trials, where pigs were infected with serotype O or A viruses. After enrichment, FMDV-specific sequencing reads increased by almost 3000-fold. The sequence data were used in variant call analysis to identify single nucleotide polymorphisms (SNPs). This methodology was robust in its ability to capture diverse sequences, was shown to be highly sensitive, and can be easily scaled for large-scale epidemiological studies.
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Affiliation(s)
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - October M Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore
| | - Uma S Kamaraj
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Timothy R Bowden
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Jacquelyn Horsington
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Christopher Cowled
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wilna Vosloo
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
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7
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Fischer TK, Rasmussen LD, Fonager J. Taking gastro-surveillance into the 21st century. J Clin Virol 2019; 117:43-48. [PMID: 31176211 DOI: 10.1016/j.jcv.2019.05.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/20/2019] [Accepted: 05/30/2019] [Indexed: 01/04/2023]
Abstract
Enteric viruses, particularly rotaviruses and noroviruses, are leading causes of gastroenteritis worldwide. Human rotaviruses are ubiquitous and globally almost every child has been infected by 3-5 years of age. Noroviruses affect people of all ages and is the leading cause of foodborne outbreaks. Rota- and noroviruses account for ˜40% and ˜17% of diarrhea-associated hospitalizations, and ˜200,000 deaths annually respectively, with most deaths occurring in developing countries. Two rotavirus vaccines have currently been implemented in ˜95 countries and several norovirus vaccine candidates are currently in development and/or clinical testing. Surveillance of enteric viruses is an important part of outbreak investigations as well as pre- and post-vaccine impact studies but is even in developed countries often limited to investigation of sporadic cases or comprehensive outbreaks. Conventional methods for enteric virus detection and subtyping relies on standard RT-PCR methods, supplemented with Sanger-sequencing. However, for viruses with even moderate mutationrates, PCR-based-typing of only limited parts of the virus genome is challenging and requires regular update of primers. Full-genomecharacterization technologies based on sequence independent methods based on next generation sequencing (NGS), have demonstrated great potential for enteric virus detection and/or typing in both clinical and environmental samples. However, cost-benefits must balance for such methods to be widely accepted for public health purposes. In Europe as also globally, routine use of NGS-methods for surveillance of enteric viruses is currently limited to few national public health laboratories. What important lessons can be learned from these and what is the future of NGS-based surveillance?
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Affiliation(s)
- Thea K Fischer
- Department of Clinical Research, Nordsjaellands Hospital, Hilleroed, Denmark; Departments of Infectious Diseases and Global Health, Clinical Institute, University of Southern Denmark, Denmark; National Virus Surveillance and WHO Reference Laboratories, Dept of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark.
| | - Lasse D Rasmussen
- National Virus Surveillance and WHO Reference Laboratories, Dept of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus Research & Development Laboratory, Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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8
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Application of a targeted-enrichment methodology for full-genome sequencing of Dengue 1-4, Chikungunya and Zika viruses directly from patient samples. PLoS Negl Trop Dis 2019; 13:e0007184. [PMID: 31022183 PMCID: PMC6504110 DOI: 10.1371/journal.pntd.0007184] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 05/07/2019] [Accepted: 01/23/2019] [Indexed: 11/19/2022] Open
Abstract
The frequency of epidemics caused by Dengue viruses 1-4, Zika virus and Chikungunya viruses have been on an upward trend in recent years driven primarily by uncontrolled urbanization, mobility of human populations and geographical spread of their shared vectors, Aedes aegypti and Aedes albopictus. Infections by these viruses present with similar clinical manifestations making them challenging to diagnose; this is especially difficult in regions of the world hyperendemic for these viruses. In this study, we present a targeted-enrichment methodology to simultaneously sequence the complete viral genomes for each of these viruses directly from clinical samples. Additionally, we have also developed a customized computational tool (BaitMaker) to design these enrichment baits. This methodology is robust in its ability to capture diverse sequences and is amenable to large-scale epidemiological studies. We have applied this methodology to two large cohorts: a febrile study based in Colombo, Sri Lanka taken during the 2009-2015 dengue epidemic (n = 170) and another taken during the 2016 outbreak of Zika virus in Singapore (n = 162). Results from these studies indicate that we were able to cover an average of 97.04% ± 0.67% of the full viral genome from samples in these cohorts. We also show detection of one DENV3/ZIKV co-infected patient where we recovered full genomes for both viruses.
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9
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Amarante MK, de Sousa Pereira N, Vitiello GAF, Watanabe MAE. Involvement of a mouse mammary tumor virus (MMTV) homologue in human breast cancer: Evidence for, against and possible causes of controversies. Microb Pathog 2019; 130:283-294. [PMID: 30905715 DOI: 10.1016/j.micpath.2019.03.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/26/2019] [Accepted: 03/15/2019] [Indexed: 01/01/2023]
Abstract
Breast cancer (BC) is a complex and heterogeneous disease whose evolution depends on the tumor-host interaction. This type of cancer occurs when the mammary cells begin to grow wildly and become able to invade nearby tissues and/or promote metastases. Mouse mammary tumor virus (MMTV) is the accepted etiological agent of mammary tumors in mice. The identification of MMTV-like sequences and antigens in human mammary carcinoma has supported the theory that a virus homologous to MMTV (namely, HMTV) may be involved in human BC, but the role of retroviral elements in this disease remains elusive, as results from different research groups were contradictory. In the present review we present works for and against the involvement of HMTV in BC and discuss possible causes of divergences among studies. In the final section we fit current data regarding this issue to stablished causality criteria. We conclude that there is convincing data supporting the association of HMTV with BC, however there is still a need for epidemiological and basic research studies focusing on carcinogenic mechanisms for this virus in humans to fully understand its role in BC. This knowledge may open the way for the development of new preventive and therapeutic approaches in human BC.
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Affiliation(s)
- Marla Karine Amarante
- Laboratory of DNA Polymorphisms and Immunology, Department of Pathological Sciences, Biological Sciences Center, Londrina State University, Londrina, Paraná, Brazil.
| | - Nathalia de Sousa Pereira
- Laboratory of DNA Polymorphisms and Immunology, Department of Pathological Sciences, Biological Sciences Center, Londrina State University, Londrina, Paraná, Brazil
| | - Glauco Akelinghton Freire Vitiello
- Laboratory of DNA Polymorphisms and Immunology, Department of Pathological Sciences, Biological Sciences Center, Londrina State University, Londrina, Paraná, Brazil
| | - Maria Angelica Ehara Watanabe
- Laboratory of DNA Polymorphisms and Immunology, Department of Pathological Sciences, Biological Sciences Center, Londrina State University, Londrina, Paraná, Brazil
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10
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Metagenomic analysis of viruses in toilet waste from long distance flights-A new procedure for global infectious disease surveillance. PLoS One 2019; 14:e0210368. [PMID: 30640944 PMCID: PMC6331095 DOI: 10.1371/journal.pone.0210368] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/20/2018] [Indexed: 01/01/2023] Open
Abstract
Human viral pathogens are a major public health threat. Reliable information that accurately describes and characterizes the global occurrence and transmission of human viruses is essential to support national and global priority setting, public health actions, and treatment decisions. However, large areas of the globe are currently without surveillance due to limited health care infrastructure and lack of international cooperation. We propose a novel surveillance strategy, using metagenomic analysis of toilet material from international air flights as a method for worldwide viral disease surveillance. The aim of this study was to design, implement, and evaluate a method for viral analysis of airplane toilet waste enabling simultaneous detection and quantification of a wide range of human viral pathogens. Toilet waste from 19 international airplanes was analyzed for viral content, using viral capture probes followed by high-throughput sequencing. Numerous human pathogens were detected including enteric and respiratory viruses. Several geographic trends were observed with samples originating from South Asia having significantly higher viral species richness as well as higher abundances of salivirus A, aichivirus A and enterovirus B, compared to samples originating from North Asia and North America. In addition, certain city specific trends were observed, including high numbers of rotaviruses in airplanes departing from Islamabad. Based on this study we believe that central sampling and analysis at international airports could be a useful supplement for global viral surveillance, valuable for outbreak detection and for guiding public health resources.
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11
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Martinez Cuesta L, Lendez PA, Nieto Farias MV, Dolcini GL, Ceriani MC. Can Bovine Leukemia Virus Be Related to Human Breast Cancer? A Review of the Evidence. J Mammary Gland Biol Neoplasia 2018; 23:101-107. [PMID: 29777406 DOI: 10.1007/s10911-018-9397-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/09/2018] [Indexed: 02/07/2023] Open
Abstract
The incidence of breast cancer is continuously increasing worldwide, as influenced by many factors that act synergistically. In the last decade there was an increasing interest in the possible viral etiology of human breast cancer. Since then, many viruses have been associated with this disease (murine mammary tumor virus, MMTV; Epstein-Barr virus, EBV; and human papillomavirus, HPV). Recently, BLV has been identified in human breast cancers giving rise to the hypothesis that it could be one of the causative agents of this condition. BLV is a retrovirus distributed worldwide that affects cattle, causing lymphosarcoma in a small proportion of infected animals. Because of its similarity with human retroviruses like HTLV and HIV, BLV was assumed to also be involved in tumor emergence. Based on this assumption, studies were focused on the possible role of BLV in human breast cancer development. We present a compilation of the current knowledge on the subject and some prospective analysis that is required to fully end this controversy.
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Affiliation(s)
- Lucia Martinez Cuesta
- Laboratorio de Virología, Facultad de Cs. Veterinarias-UNCPBA, CIVETAN-CONICET, CICPBA, Campus Universitario, Paraje Arroyo Seco s/n, 7000, Tandil, Argentina
| | - Pamela Anahi Lendez
- Laboratorio de Virología, Facultad de Cs. Veterinarias-UNCPBA, CIVETAN-CONICET, CICPBA, Campus Universitario, Paraje Arroyo Seco s/n, 7000, Tandil, Argentina
| | - Maria Victoria Nieto Farias
- Laboratorio de Virología, Facultad de Cs. Veterinarias-UNCPBA, CIVETAN-CONICET, CICPBA, Campus Universitario, Paraje Arroyo Seco s/n, 7000, Tandil, Argentina
| | - Guillermina Laura Dolcini
- Laboratorio de Virología, Facultad de Cs. Veterinarias-UNCPBA, CIVETAN-CONICET, CICPBA, Campus Universitario, Paraje Arroyo Seco s/n, 7000, Tandil, Argentina
| | - Maria Carolina Ceriani
- Laboratorio de Virología, Facultad de Cs. Veterinarias-UNCPBA, CIVETAN-CONICET, CICPBA, Campus Universitario, Paraje Arroyo Seco s/n, 7000, Tandil, Argentina.
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McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, van Driem G, Gram Wilken U, Seguin-Orlando A, de la Fuente Castro C, Wasef S, Shoocongdej R, Souksavatdy V, Sayavongkhamdy T, Saidin MM, Allentoft ME, Sato T, Malaspinas AS, Aghakhanian FA, Korneliussen T, Prohaska A, Margaryan A, de Barros Damgaard P, Kaewsutthi S, Lertrit P, Nguyen TMH, Hung HC, Minh Tran T, Nghia Truong H, Nguyen GH, Shahidan S, Wiradnyana K, Matsumae H, Shigehara N, Yoneda M, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Hanihara T, Nakagome S, Deviese T, Bacon AM, Duringer P, Ponche JL, Shackelford L, Patole-Edoumba E, Nguyen AT, Bellina-Pryce B, Galipaud JC, Kinaston R, Buckley H, Pottier C, Rasmussen S, Higham T, Foley RA, Lahr MM, Orlando L, Sikora M, Phipps ME, Oota H, Higham C, Lambert DM, Willerslev E. The prehistoric peopling of Southeast Asia. Science 2018; 361:88-92. [DOI: 10.1126/science.aat3628] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022]
Abstract
The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
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Affiliation(s)
- Hugh McColl
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fabrice Demeter
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- National Museum of Natural History, Ecoanthropology and Ethnobiology, Musée de l’Homme, Paris, France
| | - Takashi Gakuhari
- Center for Cultural Resource Studies, Kanazawa University, Kanazawa, Japan
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | | | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
- University of New England, Armidale, NSW, Australia
| | - Uffe Gram Wilken
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | | | - Sally Wasef
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Rasmi Shoocongdej
- Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, Thailand
| | - Viengkeo Souksavatdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Thongsa Sayavongkhamdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Mohd Mokhtar Saidin
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | - Morten E. Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Farhang A. Aghakhanian
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | | | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | | | - Supannee Kaewsutthi
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patcharee Lertrit
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thi Mai Huong Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Hsiao-chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia
| | - Thi Minh Tran
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Huu Nghia Truong
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Giang Hai Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Shaiful Shahidan
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Hiromi Matsumae
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Nobuo Shigehara
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | - Minoru Yoneda
- University Museum, University of Tokyo, Tokyo, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | | | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Thibaut Deviese
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Anne-Marie Bacon
- Laboratoire AMIS, Université Paris Descartes, Faculté de Chirurgie Dentaire, Montrouge, France
| | - Philippe Duringer
- École et Observatoire des Sciences de la Terre, Université de Strasbourg, Strasbourg, France
- Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UDS UMR 7516), Strasbourg, France
| | - Jean-Luc Ponche
- Laboratory “Image Ville et Environnement LIVE,” UMR7362, CNRS and Université de Strasbourg, Strasbourg, France
| | - Laura Shackelford
- Department of Anthropology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | | | - Anh Tuan Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Bérénice Bellina-Pryce
- CNRS, UMR7055 “Préhistoire et Technologie,” Maison Archéologie et Ethnologie, Nanterre, France
| | - Jean-Christophe Galipaud
- Research Institute for Development, National Museum of Natural History, UMR Paloc, Paris, France
| | - Rebecca Kinaston
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hallie Buckley
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Robert A. Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | - Hiroki Oota
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Charles Higham
- Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand
- St. Catharine’s College, University of Cambridge, Cambridge, UK
| | - David M. Lambert
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
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13
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Lawson JS, Salmons B, Gunzburg WH. Commentary regarding Gannon et al. “Viral infections and breast cancer – A current perspective”. Cancer Lett 2018; 424:117-118. [DOI: 10.1016/j.canlet.2018.03.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 10/17/2022]
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Lawson JS, Mazzanti C, Civita P, Menicagli M, Ngan CC, Whitaker NJ, Hochman J, Braitbard O, Yosufi B, Glenn WK. Association of Mouse Mammary Tumor Virus With Human Breast Cancer: Histology, Immunohistochemistry and Polymerase Chain Reaction Analyses. Front Oncol 2018; 8:141. [PMID: 29868468 PMCID: PMC5950654 DOI: 10.3389/fonc.2018.00141] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/18/2018] [Indexed: 12/18/2022] Open
Abstract
Purpose The purpose of this study is to determine whether mouse mammary tumor virus (MMTV)-associated human breast cancer has the same or similar histology to MMTV-associated mouse mammary tumors. Such associations may indicate a role for MMTV in human breast cancer. Methods Immunohistochemical techniques (using antibodies directed against the signal peptide p14 of the envelope precursor protein of MMTV) and polymerase chain reaction (PCR) analyses were used to identify MMTV proteins and MMTV-like envelope gene sequences in a series of breast cancers from Australian women. The histological characteristics of these human breast cancer specimens were compared with MMTV positive mouse mammary tumors. The same methods were used to study benign breast tissues which 1–11 years later developed into breast cancer. Results MMTV p14 proteins were identified in 27 (54%) of 50 human breast cancers. MMTV env gene sequences were identified by PCR in 12 (27%) of 45 human breast cancers. There was a significant correlation between the presence of MMTV (identified by p14 immunohistochemistry) in human breast cancers and histological characteristics similar to MMTV positive mouse mammary tumors (p = 0.001). There was a non-significant correlation between the presence of MMTV env gene sequences (identified by PCR) in human breast cancers and histological characteristics similar to MMTV positive mouse mammary tumors (p = 0.290). MMTV p14 proteins were identified in 7 (54%) of 13 benign breast specimens that later developed into human breast cancers. MMTV by PCR was identified in two benign specimens one of whom later developed MMTV positive breast cancer. Discussion These observations offer evidence that MMTV may be associated with characteristic human breast cancer histology. p14-based immunohistochemistry appears to be a more reliable technique than PCR for the identification of MMTV in human breast cancer. Identification of MMTV-associated p14 proteins in benign breast tissues confirms prior PCR-based studies that MMTV infection occurs before the development of MMTV positive breast cancer. Conclusion Many MMTV positive human breast cancers have similar histology to MMTV positive mouse mammary tumors. MMTV infection identified in benign breast tissues precedes development of MMTV positive human breast cancer. When considered in the context of prior studies, these observations indicate a likely role for MMTV in human breast cancer.
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Affiliation(s)
| | | | | | | | | | | | - Jacob Hochman
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ori Braitbard
- Department of Cell and Developmental Biology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Benafsha Yosufi
- Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia
| | - Wendy K Glenn
- University of New South Wales, Sydney, NSW, Australia
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15
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Cappellini E, Prohaska A, Racimo F, Welker F, Pedersen MW, Allentoft ME, de Barros Damgaard P, Gutenbrunner P, Dunne J, Hammann S, Roffet-Salque M, Ilardo M, Moreno-Mayar JV, Wang Y, Sikora M, Vinner L, Cox J, Evershed RP, Willerslev E. Ancient Biomolecules and Evolutionary Inference. Annu Rev Biochem 2018; 87:1029-1060. [PMID: 29709200 DOI: 10.1146/annurev-biochem-062917-012002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past three decades, studies of ancient biomolecules-particularly ancient DNA, proteins, and lipids-have revolutionized our understanding of evolutionary history. Though initially fraught with many challenges, today the field stands on firm foundations. Researchers now successfully retrieve nucleotide and amino acid sequences, as well as lipid signatures, from progressively older samples, originating from geographic areas and depositional environments that, until recently, were regarded as hostile to long-term preservation of biomolecules. Sampling frequencies and the spatial and temporal scope of studies have also increased markedly, and with them the size and quality of the data sets generated. This progress has been made possible by continuous technical innovations in analytical methods, enhanced criteria for the selection of ancient samples, integrated experimental methods, and advanced computational approaches. Here, we discuss the history and current state of ancient biomolecule research, its applications to evolutionary inference, and future directions for this young and exciting field.
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Affiliation(s)
- Enrico Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Frido Welker
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | | | - Morten E Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Peter de Barros Damgaard
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Petra Gutenbrunner
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Julie Dunne
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Simon Hammann
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom; .,Department of Anthropology and Archaeology, University of Bristol, Bristol BS8 1UU, United Kingdom
| | - Mélanie Roffet-Salque
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Melissa Ilardo
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - J Víctor Moreno-Mayar
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Yucheng Wang
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; ,
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom;
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; , .,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom.,Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
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16
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Lawson JS, Salmons B, Glenn WK. Oncogenic Viruses and Breast Cancer: Mouse Mammary Tumor Virus (MMTV), Bovine Leukemia Virus (BLV), Human Papilloma Virus (HPV), and Epstein-Barr Virus (EBV). Front Oncol 2018; 8:1. [PMID: 29404275 PMCID: PMC5786831 DOI: 10.3389/fonc.2018.00001] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/03/2018] [Indexed: 12/18/2022] Open
Abstract
Background Although the risk factors for breast cancer are well established, namely female gender, early menarche and late menopause plus the protective influence of early pregnancy, the underlying causes of breast cancer remain unknown. The development of substantial recent evidence indicates that a handful of viruses may have a role in breast cancer. These viruses are mouse mammary tumor virus (MMTV), bovine leukemia virus (BLV), human papilloma viruses (HPVs), and Epstein–Barr virus (EBV-also known as human herpes virus type 4). Each of these viruses has documented oncogenic potential. The aim of this review is to inform the scientific and general community about this recent evidence. The evidence MMTV and human breast cancer—the evidence is detailed and comprehensive but cannot be regarded as conclusive. BLV and human breast cancer—the evidence is limited. However, in view of the emerging information about BLV in human breast cancer, it is prudent to encourage the elimination of BLV in cattle, particularly in the dairy industry. HPVs and breast cancer—the evidence is substantial but not conclusive. The availability of effective preventive vaccines is a major advantage and their use should be encouraged. EBV and breast cancer—the evidence is also substantial but not conclusive. Currently, there are no practical means of either prevention or treatment. Although there is evidence of genetic predisposition, and cancer in general is a culmination of events, there is no evidence that inherited genetic traits are causal. Conclusion The influence of oncogenic viruses is currently the major plausible hypothesis for a direct cause of human breast cancer.
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Affiliation(s)
- James S Lawson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | | | - Wendy K Glenn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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17
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Lawson JS, Glenn WK. Multiple oncogenic viruses are present in human breast tissues before development of virus associated breast cancer. Infect Agent Cancer 2017; 12:55. [PMID: 29075317 PMCID: PMC5644159 DOI: 10.1186/s13027-017-0165-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/09/2017] [Indexed: 02/07/2023] Open
Abstract
Background Multiple oncogenic viruses including, mouse mammary tumor virus, bovine leukemia virus, human papilloma virus, and Epstein Barr virus, have been identified as separate infectious pathogens in human breast cancer. Here we demonstrate that these four viruses may be present in normal and benign breast tissues 1 to 11 years before the development of same virus breast cancer in the same patients. Methods We combined the data we developed during investigations of the individual four oncogenic viruses and breast cancer. Patients who had benign breast biopsies 1–11 years prior to developing breast cancer were identified by pathology reports from a large Australian pathology service (Douglas Hanly Moir Pathology). Archival formalin fixed specimens from these patients were collected. The same archival specimens were used for (i) investigations of mouse mammary tumour virus (also known as human mammary tumour virus) conducted at the Icahn School of Medicine at Mount Sinai, New York and at the University of Pisa, Italy, (ii) bovine leukemia virus conducted at the University of California at Berkeley,(iii) human papilloma virus and Epstein Barr virus conducted at the University of New South Wales, Sydney, Australia. Seventeen normal breast tissues from cosmetic breast surgery conducted on Australian patients were used as controls. These patients were younger than those with benign and later breast cancer. Results Standard and in situ polymerase chain reaction (PCR) methods were used to identify the four viruses. The detailed methods are outlined in the separate publications.: mouse mammary tumor virus, human papilloma virus and Epstein Barr virus (Infect Agent Cancer 12:1, 2017, PLoS One 12:e0179367, 2017, Front Oncol 5:277, 2015, PLoS One 7:e48788, 2012). Epstein Barr virus and human papilloma virus were identified in the same breast cancer cells by in situ PCR. Mouse mammary tumour virus was identified in 6 (24%) of 25 benign breast specimens and in 9 (36%) of 25 breast cancer specimens which subsequently developed in the same patients. Bovine leukemia virus was identified in 18 (78%) of 23 benign breast specimens and in 20 (91%) of 22 subsequent breast cancers in the same patients. High risk human papilloma viruses were identified in 13 (72%) of 17 benign breast specimens and in 13 (76%) of 17 subsequent breast cancers in the same patients. Epstein Barr virus was not identified in any benign breast specimens but was identified in 3 (25%) of 12 subsequent breast cancers in the same patients. Mouse mammary tumour virus 3 (18%), bovine leukemia virus 6 (35%), high risk human papilloma virus 3 (18%) and Epstein Barr virus 5 (29%) were identified in 17 normal control breast specimens. Conclusions These findings add to the evidence that multiple oncogenic viruses have potential roles in human breast cancer. This is an important observation because evidence of prior infection before the development of disease is a key criterion when assessing causation.
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Affiliation(s)
- James S Lawson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052 Australia.,School of BABS, University of NSW, Sydney, NSW 2110 Australia
| | - Wendy K Glenn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052 Australia
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18
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Fonager J, Stegger M, Rasmussen LD, Poulsen MW, Rønn J, Andersen PS, Fischer TK. A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants. Sci Rep 2017; 7:813. [PMID: 28400558 PMCID: PMC5429772 DOI: 10.1038/s41598-017-00926-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 03/21/2017] [Indexed: 12/16/2022] Open
Abstract
Norovirus (NoV) is the most common cause of non-bacterial gastroenteritis and is a major agent associated with outbreaks of gastroenteritis. Conventional molecular genotyping analysis of NoV, used for the identification of transmission routes, relies on standard typing methods (STM) by Sanger-sequencing of only a limited part of the NoV genome, which could lead to wrong conclusions. Here, we combined a NoV capture method with next generation sequencing (NGS), which increased the proportion of norovirus reads by ~40 fold compared to NGS without prior capture. Of 15 NoV samples from 6 single-genotype outbreaks, near full-genome coverage (>90%) was obtained from 9 samples. Fourteen polymerase (RdRp) and 15 capsid (cap) genotypes were identified compared to 12 and 13 for the STM, respectively. Analysis of 9 samples from two mixed-genotype outbreaks identified 6 RdRp and 6 cap genotypes (two at >90% NoV genome coverage) compared to 4 and 2 for the STM, respectively. Furthermore, complete or partial sequences from the P2 hypervariable region were obtained from 7 of 8 outbreaks and a new NoV recombinant was identified. This approach could therefore strengthen outbreak investigations and could be applied to other important viruses in stool samples such as hepatitis A and enterovirus.
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Affiliation(s)
- Jannik Fonager
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark.
| | - Marc Stegger
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Lasse Dam Rasmussen
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Mille Weismann Poulsen
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Jesper Rønn
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Paal Skytt Andersen
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
- Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thea Kølsen Fischer
- Virology Surveillance and Research Section, Department of Microbiological diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Department of Infectious Diseases and Centre for Global health, Clinical Unit, University of Southern Denmark, Odense, Denmark
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19
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Nartey T, Mazzanti CM, Melana S, Glenn WK, Bevilacqua G, Holland JF, Whitaker NJ, Lawson JS, Pogo BGT. Mouse mammary tumor-like virus (MMTV) is present in human breast tissue before development of virally associated breast cancer. Infect Agent Cancer 2017; 12:1. [PMID: 28053656 PMCID: PMC5209856 DOI: 10.1186/s13027-016-0113-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/16/2016] [Indexed: 12/18/2022] Open
Abstract
Background There is substantial evidence that a virus homologous to mouse mammary tumor virus (MMTV) may have a role in human breast cancer. The present study indicates that those who developed breast cancer associated with an MMTV-like virus had this virus in their non-cancerous breast tissues years before the cancer developed. Methods Polymerase chain reaction (PCR) techniques and sequencing were used to identify MMTV-like envelope gene sequences (MMTV-like env sequences) in Australian benign breast biopsy specimens from women who several years later developed breast cancer. Murine contamination was excluded by stringent laboratory procedures, and the absence of intracisternal A particle sequences and mitochondrial cyclooxygenase sequences. Results MMTV-like env sequences (also called HMTV sequences to denote their source) were found in 9 of 25 breast cancer specimens (36%). Among 25 non-cancerous breast biopsies of these same patients taken 1 to 11 years earlier, six contained MMTV-like sequences (24%). Five of the six were among the nine virally-associated breast cancers. In two pairs of specimens, benign and malignant, env sequences were 97% identical. Conclusions The identification of MMTV (MMTV-like) sequences in breast tissues prior to the development of MMTV positive breast cancer fulfills a key criterion for a possible causal role for the MMTV-like virus in human breast cancer.
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Affiliation(s)
- Teiko Nartey
- Icahn School of Medicine at Mount Sinai, New York, NY USA
| | | | - Stella Melana
- Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Wendy K Glenn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | | | | | - Noel J Whitaker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - James S Lawson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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20
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Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms. Proc Natl Acad Sci U S A 2016; 113:15066-15071. [PMID: 27956618 DOI: 10.1073/pnas.1615819114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome.
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21
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Lawson JS, Glenn WK, Whitaker NJ. Human Papilloma Viruses and Breast Cancer - Assessment of Causality. Front Oncol 2016; 6:207. [PMID: 27747193 PMCID: PMC5040724 DOI: 10.3389/fonc.2016.00207] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/13/2016] [Indexed: 12/22/2022] Open
Abstract
High risk human papilloma viruses (HPVs) may have a causal role in some breast cancers. Case-control studies, conducted in many different countries, consistently indicate that HPVs are more frequently present in breast cancers as compared to benign breast and normal breast controls (odds ratio 4.02). The assessment of causality of HPVs in breast cancer is difficult because (i) the HPV viral load is extremely low, (ii) HPV infections are common but HPV associated breast cancers are uncommon, and (iii) HPV infections may precede the development of breast and other cancers by years or even decades. Further, HPV oncogenesis can be indirect. Despite these difficulties, the emergence of new evidence has made the assessment of HPV causality, in breast cancer, a practical proposition. With one exception, the evidence meets all the conventional criteria for a causal role of HPVs in breast cancer. The exception is "specificity." HPVs are ubiquitous, which is the exact opposite of specificity. An additional reservation is that the prevalence of breast cancer is not increased in immunocompromised patients as is the case with respect to HPV-associated cervical cancer. This indicates that HPVs may have an indirect causal influence in breast cancer. Based on the overall evidence, high-risk HPVs may have a causal role in some breast cancers.
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Affiliation(s)
| | - Wendy K Glenn
- School of BABS, University of New South Wales , Sydney, NSW , Australia
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22
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Kawada JI, Okuno Y, Torii Y, Okada R, Hayano S, Ando S, Kamiya Y, Kojima S, Ito Y. Identification of Viruses in Cases of Pediatric Acute Encephalitis and Encephalopathy Using Next-Generation Sequencing. Sci Rep 2016; 6:33452. [PMID: 27625312 PMCID: PMC5022051 DOI: 10.1038/srep33452] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/22/2016] [Indexed: 12/27/2022] Open
Abstract
Acute encephalitis/encephalopathy is a severe neurological syndrome that is occasionally associated with viral infection. Comprehensive virus detection assays are desirable because viral pathogens have not been identified in many cases. We evaluated the utility of next-generation sequencing (NGS) for detecting viruses in clinical samples of encephalitis/encephalopathy patients. We first determined the sensitivity and quantitative performance of NGS by comparing the NGS-determined number of sequences of human herpesvirus-6 (HHV-6) in clinical serum samples with the HHV-6 load measured using real-time PCR. HHV-6 was measured as it occasionally causes neurologic disorders in children. The sensitivity of NGS for detection of HHV-6 sequences was equivalent to that of real-time PCR, and the number of HHV-6 reads was significantly correlated with HHV-6 load. Next, we investigated the ability of NGS to detect viral sequences in 18 pediatric patients with acute encephalitis/encephalopathy of unknown etiology. A large number of Coxsackievirus A9 and mumps viral sequences were detected in the cerebrospinal fluid of 2 and 1 patients, respectively. In addition, Torque teno virus and Pepper mild mottle viral sequences were detected in the sera of one patient each. These data indicate that NGS is useful for detection of causative viruses in patients with pediatric encephalitis/encephalopathy.
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Affiliation(s)
- Jun-Ichi Kawada
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yusuke Okuno
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yuka Torii
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Ryo Okada
- Horticultural Research Institute, Ibaraki Agricultural Center, 3165-1 Ago, Kasama, 319-0292, Japan
| | - Satoshi Hayano
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Shotaro Ando
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yasuko Kamiya
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Seiji Kojima
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
| | - Yoshinori Ito
- Departments of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan
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23
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Holst-Jensen A, Spilsberg B, Arulandhu AJ, Kok E, Shi J, Zel J. Application of whole genome shotgun sequencing for detection and characterization of genetically modified organisms and derived products. Anal Bioanal Chem 2016; 408:4595-614. [PMID: 27100228 PMCID: PMC4909802 DOI: 10.1007/s00216-016-9549-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 12/13/2022]
Abstract
The emergence of high-throughput, massive or next-generation sequencing technologies has created a completely new foundation for molecular analyses. Various selective enrichment processes are commonly applied to facilitate detection of predefined (known) targets. Such approaches, however, inevitably introduce a bias and are prone to miss unknown targets. Here we review the application of high-throughput sequencing technologies and the preparation of fit-for-purpose whole genome shotgun sequencing libraries for the detection and characterization of genetically modified and derived products. The potential impact of these new sequencing technologies for the characterization, breeding selection, risk assessment, and traceability of genetically modified organisms and genetically modified products is yet to be fully acknowledged. The published literature is reviewed, and the prospects for future developments and use of the new sequencing technologies for these purposes are discussed.
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Affiliation(s)
- Arne Holst-Jensen
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750, Sentrum, 0106, Oslo, Norway.
| | - Bjørn Spilsberg
- Norwegian Veterinary Institute, Ullevaalsveien 68, P.O. Box 750, Sentrum, 0106, Oslo, Norway
| | - Alfred J Arulandhu
- RIKILT, Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Esther Kok
- RIKILT, Wageningen UR, P.O. Box 230, 6700 AE, Wageningen, The Netherlands
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Jana Zel
- National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
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24
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Miyazato P, Katsuya H, Fukuda A, Uchiyama Y, Matsuo M, Tokunaga M, Hino S, Nakao M, Satou Y. Application of targeted enrichment to next-generation sequencing of retroviruses integrated into the host human genome. Sci Rep 2016; 6:28324. [PMID: 27321866 PMCID: PMC4913254 DOI: 10.1038/srep28324] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/31/2016] [Indexed: 12/20/2022] Open
Abstract
The recent development and advancement of next-generation sequencing (NGS) technologies have enabled the characterization of the human genome at extremely high resolution. In the retrovirology field, NGS technologies have been applied to integration-site analysis and deep sequencing of viral genomes in combination with PCR amplification using virus-specific primers. However, virus-specific primers are not available for some epigenetic analyses, like chromatin immunoprecipitation sequencing (ChIP-seq) assays. Viral sequences are poorly detected without specific PCR amplification because proviral DNA is very scarce compared to human genomic DNA. Here, we have developed and evaluated the use of biotinylated DNA probes for the capture of viral genetic fragments from a library prepared for NGS. Our results demonstrated that viral sequence detection was hundreds or thousands of times more sensitive after enrichment, enabling us to reduce the economic burden that arises when attempting to analyze the epigenetic landscape of proviruses by NGS. In addition, the method is versatile enough to analyze proviruses that have mismatches compared to the DNA probes. Taken together, we propose that this approach is a powerful tool to clarify the mechanisms of transcriptional and epigenetic regulation of retroviral proviruses that have, until now, remained elusive.
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Affiliation(s)
- Paola Miyazato
- Center for AIDS Research, Kumamoto University, Japan.,International Research Center for Medical Sciences, Kumamoto University, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, Japan
| | - Hiroo Katsuya
- Center for AIDS Research, Kumamoto University, Japan.,International Research Center for Medical Sciences, Kumamoto University, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, Japan
| | - Asami Fukuda
- Center for AIDS Research, Kumamoto University, Japan.,International Research Center for Medical Sciences, Kumamoto University, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, Japan
| | - Yoshikazu Uchiyama
- Department of Medical Physics, Faculty of Life Sciences, Kumamoto University, Japan
| | - Misaki Matsuo
- Center for AIDS Research, Kumamoto University, Japan.,International Research Center for Medical Sciences, Kumamoto University, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, Japan
| | - Michiyo Tokunaga
- Center for AIDS Research, Kumamoto University, Japan.,International Research Center for Medical Sciences, Kumamoto University, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, Japan
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute for Molecular Biology and Embryology, Kumamoto University, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute for Molecular Biology and Embryology, Kumamoto University, Japan.,Core Research for Evolutionary Science and Technology (CREST), Japan Science of Technology Agency, Tokyo, Japan
| | - Yorifumi Satou
- Center for AIDS Research, Kumamoto University, Japan.,International Research Center for Medical Sciences, Kumamoto University, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, Japan
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25
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Mayer C, Sann M, Donath A, Meixner M, Podsiadlowski L, Peters RS, Petersen M, Meusemann K, Liere K, Wägele JW, Misof B, Bleidorn C, Ohl M, Niehuis O. BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design. Mol Biol Evol 2016; 33:1875-86. [PMID: 27009209 DOI: 10.1093/molbev/msw056] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Target DNA enrichment combined with high-throughput sequencing technologies is a powerful approach to probing a large number of loci in genomes of interest. However, software algorithms that explicitly consider nucleotide sequence information of target loci in multiple reference species for optimizing design of target enrichment baits to be applicable across a wide range of species have not been developed. Here we present an algorithm that infers target DNA enrichment baits from multiple nucleotide sequence alignments. By applying clustering methods and the combinatorial 1-center sequence optimization to bait design, we are able to minimize the total number of baits required to efficiently probe target loci in multiple species. Consequently, more loci can be probed across species with a given number of baits. Using transcript sequences of 24 apoid wasps (Hymenoptera: Crabronidae, Sphecidae) from the 1KITE project and the gene models of Nasonia vitripennis, we inferred 57,650, 120-bp-long baits for capturing 378 coding sequence sections of 282 genes in apoid wasps. Illumina reduced-representation library sequencing confirmed successful enrichment of the target DNA when applying these baits to DNA of various apoid wasps. The designed baits furthermore enriched a major fraction of the target DNA in distantly related Hymenoptera, such as Formicidae and Chalcidoidea, highlighting the baits' broad taxonomic applicability. The availability of baits with broad taxonomic applicability is of major interest in numerous disciplines, ranging from phylogenetics to biodiversity monitoring. We implemented our new approach in a software package, called BaitFisher, which is open source and freely available at https://github.com/cmayer/BaitFisher-package.git.
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Affiliation(s)
- Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Manuela Sann
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Lars Podsiadlowski
- University of Bonn, Institute of Evolutionary Biology and Ecology, Bonn, Germany
| | - Ralph S Peters
- Department Arthropoda, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Karen Meusemann
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany Australian National Insect Collection, CSIRO National Research Collections Australia, Acton, Canberra, ACT, Australia
| | - Karsten Liere
- Services in Molecular Biology GmbH, Rüdersdorf, Germany
| | | | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Christoph Bleidorn
- Molecular Evolution and Systematics of Animals, Institute for Biology, University of Leipzig, Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), Madrid, Spain
| | - Michael Ohl
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Oliver Niehuis
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
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26
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Munro AC, Houldcroft C. Human cancers and mammalian retroviruses: should we worry about bovine leukemia virus? Future Virol 2016. [DOI: 10.2217/fvl.16.5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Andrew C Munro
- School of Clinical Medicine, University of Cambridge, Long Road, Cambridge, CB2 0SP, UK
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27
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Friis-Nielsen J, Kjartansdóttir KR, Mollerup S, Asplund M, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Nielsen IB, Alquezar-Planas DE, Olsen PVS, Vinner L, Fridholm H, Nielsen LP, Willerslev E, Sicheritz-Pontén T, Lund O, Hansen AJ, Izarzugaza JMG, Brunak S. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers. Viruses 2016; 8:E53. [PMID: 26907326 PMCID: PMC4776208 DOI: 10.3390/v8020053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 12/17/2022] Open
Abstract
Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32 non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified inhabitants of the healthy tissue flora as well as experimental contaminants. Unmapped sequences that co-occur with high statistical significance potentially represent the unknown sequence space where novel pathogens can be identified.
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Affiliation(s)
- Jens Friis-Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Kristín Rós Kjartansdóttir
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Maria Asplund
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Alba Rey-Iglesia
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Stine Raith Richter
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Ida Broman Nielsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - David E Alquezar-Planas
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Pernille V S Olsen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Lars Peter Nielsen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, DK-2300 Copenhagen S, Denmark.
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen, Denmark.
| | - Jose M G Izarzugaza
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
- NNF Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark.
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28
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Mourier T, Mollerup S, Vinner L, Hansen TA, Kjartansdóttir KR, Guldberg Frøslev T, Snogdal Boutrup T, Nielsen LP, Willerslev E, Hansen AJ. Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads. Sci Rep 2015; 5:15644. [PMID: 26493184 PMCID: PMC4616055 DOI: 10.1038/srep15644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 09/21/2015] [Indexed: 02/06/2023] Open
Abstract
From Illumina sequencing of DNA from brain and liver tissue from the lion, Panthera leo, and tumor samples from the pike-perch, Sander lucioperca, we obtained two assembled sequence contigs with similarity to known retroviruses. Phylogenetic analyses suggest that the pike-perch retrovirus belongs to the epsilonretroviruses, and the lion retrovirus to the gammaretroviruses. To determine if these novel retroviral sequences originate from an endogenous retrovirus or from a recently integrated exogenous retrovirus, we assessed the genetic diversity of the parental sequences from which the short Illumina reads are derived. First, we showed by simulations that we can robustly infer the level of genetic diversity from short sequence reads. Second, we find that the measures of nucleotide diversity inferred from our retroviral sequences significantly exceed the level observed from Human Immunodeficiency Virus infections, prompting us to conclude that the novel retroviruses are both of endogenous origin. Through further simulations, we rule out the possibility that the observed elevated levels of nucleotide diversity are the result of co-infection with two closely related exogenous retroviruses.
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Affiliation(s)
- Tobias Mourier
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Mollerup
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Kristín Rós Kjartansdóttir
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Tobias Guldberg Frøslev
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Torsten Snogdal Boutrup
- Section for Virology, National Veterinary Institute, Technical University of Denmark, Frederiksberg, Denmark
| | - Lars Peter Nielsen
- Department for Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, Museum of Natural History of Denmark, University of Copenhagen, Copenhagen, Denmark
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29
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Jensen RH, Mollerup S, Mourier T, Hansen TA, Fridholm H, Nielsen LP, Willerslev E, Hansen AJ, Vinner L. Target-dependent enrichment of virions determines the reduction of high-throughput sequencing in virus discovery. PLoS One 2015; 10:e0122636. [PMID: 25853649 PMCID: PMC4390369 DOI: 10.1371/journal.pone.0122636] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
Viral infections cause many different diseases stemming both from well-characterized viral pathogens but also from emerging viruses, and the search for novel viruses continues to be of great importance. High-throughput sequencing is an important technology for this purpose. However, viral nucleic acids often constitute a minute proportion of the total genetic material in a sample from infected tissue. Techniques to enrich viral targets in high-throughput sequencing have been reported, but the sensitivity of such methods is not well established. This study compares different library preparation techniques targeting both DNA and RNA with and without virion enrichment. By optimizing the selection of intact virus particles, both by physical and enzymatic approaches, we assessed the effectiveness of the specific enrichment of viral sequences as compared to non-enriched sample preparations by selectively looking for and counting read sequences obtained from shotgun sequencing. Using shotgun sequencing of total DNA or RNA, viral targets were detected at concentrations corresponding to the predicted level, providing a foundation for estimating the effectiveness of virion enrichment. Virion enrichment typically produced a 1000-fold increase in the proportion of DNA virus sequences. For RNA virions the gain was less pronounced with a maximum 13-fold increase. This enrichment varied between the different sample concentrations, with no clear trend. Despite that less sequencing was required to identify target sequences, it was not evident from our data that a lower detection level was achieved by virion enrichment compared to shotgun sequencing.
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Affiliation(s)
- Randi Holm Jensen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
| | - Sarah Mollerup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Tobias Mourier
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Arn Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Helena Fridholm
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lars Peter Nielsen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Anders Johannes Hansen
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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