Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection

EBioMedicine - Tập 17 - Trang 172-181 - 2017
Thomas W. Burke1, Ricardo Henao1,2, Erik Soderblom3, Ephraim L. Tsalik1,4,5, J. Will Thompson3, Micah T. McClain1,5,6, Marshall Nichols1, Bradly P. Nicholson4, Timothy Veldman1, Joseph E. Lucas1,2, M. Arthur Moseley1,3, Ronald B. Turner7, Robert Lambkin-Williams8, Alfred O. Hero9, Christopher W. Woods1,5,6, Geoffrey S. Ginsburg1
1Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA
2Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
3Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27708, USA
4Durham Veteran's Affairs Medical Center, Durham, NC 27705, USA
5Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA
6Section for Infectious Diseases, Medicine Service, Durham Veteran's Affairs Medical Center, Durham, NC 27705, USA
7School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
8hVIVO, London, United Kingdom
9Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA

Tài liệu tham khảo

Addona, 2009, Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma, Nat. Biotechnol., 27, 633, 10.1038/nbt.1546 Aebersold, 2013, Western blots versus selected reaction monitoring assays: time to turn the tables?, Mol. Cell. Proteomics, 12, 2381, 10.1074/mcp.E113.031658 Bhoj, 2008, MAVS and MyD88 are essential for innate immunity but not cytotoxic T lymphocyte response against respiratory syncytial virus, Proc. Natl. Acad. Sci. U. S. A., 105, 14046, 10.1073/pnas.0804717105 Boja, 2011, The path to clinical proteomics research: integration of proteomics, genomics, clinical laboratory and regulatory science, Korean J. Lab. Med., 31, 61, 10.3343/kjlm.2011.31.2.61 Byington, 2015, Community surveillance of respiratory viruses among families in the Utah better identification of germs-longitudinal viral epidemiology (BIG-LoVE) study, Clin. Infect. Dis., 61, 1217, 10.1093/cid/civ486 Cameron, 2008, Gene expression analysis of host innate immune responses during Lethal H5N1 infection in ferrets, J. Virol., 82, 11308, 10.1128/JVI.00691-08 Cameron, 2007, Interferon-mediated immunopathological events are associated with atypical innate and adaptive immune responses in patients with severe acute respiratory syndrome, J. Virol., 81, 8692, 10.1128/JVI.00527-07 Fawcett, 2006, An introduction to ROC analysis, Pattern Recogn. Lett., 27, 861, 10.1016/j.patrec.2005.10.010 Friedman, 2010, Regularization paths for generalized linear models via coordinate descent, J. Stat. Softw., 33, 1, 10.18637/jss.v033.i01 Gaboriaud, 2004, Structure and activation of the C1 complex of complement: unraveling the puzzle, Trends Immunol., 25, 368, 10.1016/j.it.2004.04.008 Gerszten, 2010, Integration of proteomic-based tools for improved biomarkers of myocardial injury, Clin. Chem., 56, 194, 10.1373/clinchem.2009.127878 Hong, 2004, Acute respiratory symptoms in adults in general practice, Fam. Pract., 21, 317, 10.1093/fampra/cmh319 House, 2014 Huang da, 2009, Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists, Nucleic Acids Res., 37, 1, 10.1093/nar/gkn923 Huang, 2011, Temporal dynamics of host molecular responses differentiate symptomatic and asymptomatic influenza a infection, PLoS Genet., 7, e1002234, 10.1371/journal.pgen.1002234 Jackson, 1958, Transmission of the common cold to volunteers under controlled conditions. I. The common cold as a clinical entity, AMA Arch. Intern. Med., 101, 267, 10.1001/archinte.1958.00260140099015 Johnston, 1993, Use of polymerase chain reaction for diagnosis of picornavirus infection in subjects with and without respiratory symptoms, J. Clin. Microbiol., 31, 111, 10.1128/JCM.31.1.111-117.1993 Johnstone, 2008, Viral infection in adults hospitalized with community-acquired pneumonia: prevalence, pathogens, and presentation, Chest, 134, 1141, 10.1378/chest.08-0888 Kimura, 2013, Cytokine production and signaling pathways in respiratory virus infection, Front. Microbiol., 4, 276, 10.3389/fmicb.2013.00276 Kiyonami, 2011, Increased selectivity, analytical precision, and throughput in targeted proteomics, Mol. Cell. Proteomics, 10, 002931 Koyama, 2008, Innate immune response to viral infection, Cytokine, 43, 336, 10.1016/j.cyto.2008.07.009 Liu, 2016, An individualized predictor of health and disease using paired reference and target samples, BMC Bioinforma., 17, 1, 10.1186/s12859-016-0889-9 Marion, 2016, Respiratory mucosal proteome quantification in human influenza infections, PLoS One, 11, e0153674, 10.1371/journal.pone.0153674 McClain, 2016, A genomic signature of influenza infection shows potential for presymptomatic detection, guiding early therapy, and monitoring clinical responses, Open Forum Inf. Dis., 3 O'Neill, 2015 Organization, 2015 Oshansky, 2014, Mucosal immune responses predict clinical outcomes during influenza infection independently of age and viral load, Am. J. Respir. Crit. Care Med., 189, 449, 10.1164/rccm.201309-1616OC Pirillo, 2015, HDL in infectious diseases and sepsis, Handb. Exp. Pharmacol., 224, 483, 10.1007/978-3-319-09665-0_15 Ramilo, 2007, Gene expression patterns in blood leukocytes discriminate patients with acute infections, Blood, 109, 2066, 10.1182/blood-2006-02-002477 Ramilo, 2009, Shifting the paradigm: host gene signatures for diagnosis of infectious diseases, Cell Host Microbe, 6, 199, 10.1016/j.chom.2009.08.007 Ricklin, 2010, Complement: a key system for immune surveillance and homeostasis, Nat. Immunol., 11, 785, 10.1038/ni.1923 Thompson, 2010, Estimates of deaths associated with seasonal influenza-United States, 1976–2007, Morb. Mortal. Wkly Rep., 59, 1057 Tsalik, 2016, Host gene expression classifiers diagnose acute respiratory illness etiology, Sci. Transl. Med., 8, 322ra11, 10.1126/scitranslmed.aad6873 Woods, 2013, A host transcriptional signature for presymptomatic detection of infection in humans exposed to influenza H1N1 or H3N2, PLoS One, 8, e52198, 10.1371/journal.pone.0052198 Yoneyama, 2010, Recognition of viral nucleic acids in innate immunity, Rev. Med. Virol., 20, 4, 10.1002/rmv.633 Zaas, 2013, A host-based RT-PCR gene expression signature to identify acute respiratory viral infection, Sci. Transl. Med., 5, 203ra126, 10.1126/scitranslmed.3006280 Zaas, 2009, Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans, Cell Host Microbe, 6, 207, 10.1016/j.chom.2009.07.006 Zaas, 2014, The current epidemiology and clinical decisions surrounding acute respiratory infections, Trends Mol. Med., 20, 579, 10.1016/j.molmed.2014.08.001