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DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods. PLoS Negl Trop Dis 2016; 10:e0005017. [PMID: 27654806 PMCID: PMC5031435 DOI: 10.1371/journal.pntd.0005017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/31/2016] [Indexed: 01/06/2023] Open
Abstract
Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n = 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods.
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Das S, Rundell MS, Mirza AH, Pingle MR, Shigyo K, Garrison AR, Paragas J, Smith SK, Olson VA, Larone DH, Spitzer ED, Barany F, Golightly LM. A Multiplex PCR/LDR Assay for the Simultaneous Identification of Category A Infectious Pathogens: Agents of Viral Hemorrhagic Fever and Variola Virus. PLoS One 2015; 10:e0138484. [PMID: 26381398 PMCID: PMC4575071 DOI: 10.1371/journal.pone.0138484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 08/30/2015] [Indexed: 02/04/2023] Open
Abstract
CDC designated category A infectious agents pose a major risk to national security and require special action for public health preparedness. They include viruses that cause viral hemorrhagic fever (VHF) syndrome as well as variola virus, the agent of smallpox. VHF is characterized by hemorrhage and fever with multi-organ failure leading to high morbidity and mortality. Smallpox, a prior scourge, has been eradicated for decades, making it a particularly serious threat if released nefariously in the essentially non-immune world population. Early detection of the causative agents, and the ability to distinguish them from other pathogens, is essential to contain outbreaks, implement proper control measures, and prevent morbidity and mortality. We have developed a multiplex detection assay that uses several species-specific PCR primers to generate amplicons from multiple pathogens; these are then targeted in a ligase detection reaction (LDR). The resultant fluorescently-labeled ligation products are detected on a universal array enabling simultaneous identification of the pathogens. The assay was evaluated on 32 different isolates associated with VHF (ebolavirus, marburgvirus, Crimean Congo hemorrhagic fever virus, Lassa fever virus, Rift Valley fever virus, Dengue virus, and Yellow fever virus) as well as variola virus and vaccinia virus (the agent of smallpox and its vaccine strain, respectively). The assay was able to detect all viruses tested, including 8 sequences representative of different variola virus strains from the CDC repository. It does not cross react with other emerging zoonoses such as monkeypox virus or cowpox virus, or six flaviviruses tested (St. Louis encephalitis virus, Murray Valley encephalitis virus, Powassan virus, Tick-borne encephalitis virus, West Nile virus and Japanese encephalitis virus).
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Affiliation(s)
- Sanchita Das
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Mark S. Rundell
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aashiq H. Mirza
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Maneesh R. Pingle
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Kristi Shigyo
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Aura R. Garrison
- United States Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Jason Paragas
- Integrated Research Facility, Division of Clinical Research, NIAID, NIH, Fort Detrick, Maryland, United States of America
| | - Scott K. Smith
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Victoria A. Olson
- Poxvirus Team, Poxvirus and Rabies Branch, Division of High Consequence Pathogens and Pathology, National Center of Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Davise H. Larone
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, NY, United States of America
| | - Eric D. Spitzer
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, New York, United States of America
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
| | - Linnie M. Golightly
- Department of Medicine, Division of Infectious Diseases, Weill Medical College of Cornell University, New York, New York, United States of America
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, New York, United States of America
- * E-mail:
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Ferguson BD, Carol Tan YH, Kanteti RS, Liu R, Gayed MJ, Vokes EE, Ferguson MK, John Iafrate A, Gill PS, Salgia R. Novel EPHB4 Receptor Tyrosine Kinase Mutations and Kinomic Pathway Analysis in Lung Cancer. Sci Rep 2015; 5:10641. [PMID: 26073592 PMCID: PMC4466581 DOI: 10.1038/srep10641] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 04/28/2015] [Indexed: 12/11/2022] Open
Abstract
Lung cancer outcomes remain poor despite the identification of several potential therapeutic targets. The EPHB4 receptor tyrosine kinase (RTK) has recently emerged as an oncogenic factor in many cancers, including lung cancer. Mutations of EPHB4 in lung cancers have previously been identified, though their significance remains unknown. Here, we report the identification of novel EPHB4 mutations that lead to putative structural alterations as well as increased cellular proliferation and motility. We also conducted a bioinformatic analysis of these mutations to demonstrate that they are mutually exclusive from other common RTK variants in lung cancer, that they correspond to analogous sites of other RTKs’ variations in cancers, and that they are predicted to be oncogenic based on biochemical, evolutionary, and domain-function constraints. Finally, we show that EPHB4 mutations can induce broad changes in the kinome signature of lung cancer cells. Taken together, these data illuminate the role of EPHB4 in lung cancer and further identify EPHB4 as a potentially important therapeutic target.
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Affiliation(s)
- Benjamin D Ferguson
- Department of Surgery, University of Chicago, Chicago, Illinois, United States of America
| | - Yi-Hung Carol Tan
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America
| | - Rajani S Kanteti
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America
| | - Ren Liu
- Department of Medicine, Division of Medical Oncology, University of Southern California, Los Angeles, California, United States of America
| | - Matthew J Gayed
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America
| | - Everett E Vokes
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America
| | - Mark K Ferguson
- Department of Surgery, University of Chicago, Chicago, Illinois, United States of America.,Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, United States of America
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Parkash S Gill
- Department of Medicine, Division of Medical Oncology, University of Southern California, Los Angeles, California, United States of America
| | - Ravi Salgia
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, Illinois, United States of America.,Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, United States of America
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