Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection

Yongsheng Huang¹^,², Aimee K. Zaas³^,⁴, Arvind Rao⁵, Nicolas Dobigeon⁶, Peter J. Woolf¹^,⁷^,⁸, Timothy Veldman⁴, N. Christine Øien⁴, Micah T. McClain³^,⁴, Jay B. Varkey⁹, Bradley Nicholson⁴, Lawrence Carin¹⁰, Stephen Kingsmore¹¹, Christopher W. Woods³^,⁴, Geoffrey S. Ginsburg³^,⁴^*, Alfred O. Hero III¹^,²^,⁷^,¹²^*

1 Center for Computational Biology and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America, 2 Department of Statistics, University of Michigan, Ann Arbor, Michigan, United States of America, 3 Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, United States of America, 4 Department of Medicine, Duke University, Durham, North Carolina, United States of America, 5 Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America, 6 IRIT/INP-ENSEEIHT, University of Toulouse, Toulouse, France, 7 Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America, 8 Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America, 9 Department of Medicine, School of Medicine, Emory University, Atlanta, Georgia, United States of America, 10 Department of Electrical and Computer Engineering, Duke University, Durham, North Carolina, United States of America, 11 Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri, United States of America, 12 Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, United States of America

Abstract

Exposure to influenza viruses is necessary, but not sufficient, for healthy human hosts to develop symptomatic illness. The host response is an important determinant of disease progression. In order to delineate host molecular responses that differentiate symptomatic and asymptomatic Influenza A infection, we inoculated 17 healthy adults with live influenza (H3N2/Wisconsin) and examined changes in host peripheral blood gene expression at 16 timepoints over 132 hours. Here we present distinct transcriptional dynamics of host responses unique to asymptomatic and symptomatic infections. We show that symptomatic hosts invoke, simultaneously, multiple pattern recognition receptors-mediated antiviral and inflammatory responses that may relate to virus-induced oxidative stress. In contrast, asymptomatic subjects tightly regulate these responses and exhibit elevated expression of genes that function in antioxidant responses and cell-mediated responses. We reveal an ab initio molecular signature that strongly correlates to symptomatic clinical disease and biomarkers whose expression patterns best discriminate early from late phases of infection. Our results establish a temporal pattern of host molecular responses that differentiates symptomatic from asymptomatic infections and reveals an asymptomatic host-unique non-passive response signature, suggesting novel putative molecular targets for both prognostic assessment and ameliorative therapeutic intervention in seasonal and pandemic influenza.

Author Summary

The transcriptional responses of human hosts towards influenza viral pathogens are important for understanding virus-mediated immunopathology. Despite great advances gained through studies using model organisms, the complete temporal host transcriptional responses in a natural human system are poorly understood. In a human challenge study using live influenza (H3N2/Wisconsin) viruses, we conducted a clinically uninformed (unsupervised) factor analysis on gene expression profiles and established an ab initio molecular signature that strongly correlates to symptomatic clinical disease. This is followed by the identification of 42 biomarkers whose expression patterns best differentiate early from late phases of infection. In parallel, a clinically informed (supervised) analysis revealed over-stimulation of multiple viral sensing pathways in symptomatic hosts and linked their temporal trajectory with development of diverse clinical signs and symptoms. The resultant inflammatory cytokine profiles were shown to contribute to the pathogenesis because their significant increase preceded disease manifestation by 36 hours. In subclinical asymptomatic hosts, we discovered strong transcriptional regulation of genes involved in inflammasome activation, genes encoding virus interacting proteins, and evidence of active anti-oxidant and cell-mediated innate immune response. Taken together, our findings offer insights into influenza virus-induced pathogenesis and provide a valuable tool for disease monitoring and management in natural environments.

Citation: Huang Y, Zaas AK, Rao A, Dobigeon N, Woolf PJ, et al. (2011) Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection. PLoS Genet 7(8): e1002234. doi:10.1371/journal.pgen.1002234
Editor: Nicholas J. Schork, University of California San Diego and The Scripps Research Institute, United States of America

Received: January 5, 2011; Accepted: June 28, 2011; Published: August 25, 2011
Copyright: © 2011 Huang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This research was partially supported by a grant from the DARPA PHD Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: geoffrey.ginsburg@duke.edu (GSG); hero@eecs.umich.edu (AOH)

PLoS Genetics: Temporal Dynamics of Host Molecular Responses Differentiate Symptomatic and Asymptomatic Influenza A Infection