Infections with highly pathogenic avian H5N1 influenza A viruses (lAV) or Ebola viruses (EBOV) cause severe respiratory disease or hemorrhagic fever with high mortality rates in humans. The limited understanding of how these viruses dysregulate the host response impairs effective treatments for virus induced disease. We hypothesize that comparing host responses to H5N1 lAV, EBOV and a range of virulence mutants will allow delineation of common and virus-specific mechanisms of immune subversion and pathogenicity. Here, we propose a highly integrated systems biology approach to address this hypothesis. We will leverage our existing transcriptome and proteome data from cells and mouse lungs infected with H5N1 lAV and mutant viruses, and in Aim 1, similar proteomics and transcriptomics datasets will be acquired for EBOV-infected cells and mice. In addition, we will perform miRNA profiling, phosphoproteomics, metabolomics and lipidomics analyses for both viruses;quantify immune cell trafficking into infected lung or liver tissues;collect transcriptomics data for immune cell populations isolated from lAV infected lungs;and provide comprehensive data for lAV and EBOV protein interactions with host proteins. Datasets will be acquired with the assistance of several Cores for sample processing, statistical and computational analyses, and integration with data generated for West Nile virus (WNV) under the second Research Project of this contract. The Computational Modeling Core will produce prioritized regulatory target lists for follow-up analysis, and in Aim 2, targets will be experimentally validated using in vitro systems coupled with perturbation of host factor expression or activity. Selected targets then will be validated in vivo by generation of knockout (KO) mice and assessment of the effects of gene KO on the outcome of infection. To allow refinement of computational models and completion of the systems biology paradigm, we will also obtain samples from KO mice for iterative OMICs studies. Collectively, this strategy is expected to facilitate predictive modeling of disease states associated with severe human viral pathogens and identify important regulators of viral pathogenesis that may be targeted for novel intervention strategies.

Public Health Relevance

Ebola viruses (EBOV) and influenza A viruses (lAV) are classified as 'Category A'and 'Category C priority agents, respectively, by the National Institute of Allergy and Infectious Diseases (NIAID). Both viruses have the ability to cause severe and/or fatal infections in humans, although the mechanisms are not clearly defined. Here, we seek to identify these mechanisms using a highly collaborative state-of-the-art systems biology methodology, to facilitate better understanding and treatment of EBOV and lAV infections in humans.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
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Special Emphasis Panel (ZAI1-EC-M)
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University of Wisconsin Madison
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Kyle, Jennifer E; Aly, Noor; Zheng, Xueyun et al. (2018) Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry. Bioanalysis 10:279-289
Gralinski, Lisa E; Sheahan, Timothy P; Morrison, Thomas E et al. (2018) Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis. MBio 9:
Menachery, Vineet D; Gralinski, Lisa E; Mitchell, Hugh D et al. (2018) Combination Attenuation Offers Strategy for Live Attenuated Coronavirus Vaccines. J Virol 92:
Menachery, Vineet D; Schäfer, Alexandra; Burnum-Johnson, Kristin E et al. (2018) MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape. Proc Natl Acad Sci U S A 115:E1012-E1021
Agnihothram, Sudhakar; Menachery, Vineet D; Yount Jr, Boyd L et al. (2018) Development of a Broadly Accessible Venezuelan Equine Encephalitis Virus Replicon Particle Vaccine Platform. J Virol 92:
Thackray, Larissa B; Handley, Scott A; Gorman, Matthew J et al. (2018) Oral Antibiotic Treatment of Mice Exacerbates the Disease Severity of Multiple Flavivirus Infections. Cell Rep 22:3440-3453.e6
Couvillion, Sneha P; Zhu, Ying; Nagy, Gabe et al. (2018) New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells. Analyst :
White, James P; Xiong, Shanshan; Malvin, Nicole P et al. (2018) Intestinal Dysmotility Syndromes following Systemic Infection by Flaviviruses. Cell 175:1198-1212.e12
Wojcik, Roza; Webb, Ian K; Deng, Liulin et al. (2017) Lipid and Glycolipid Isomer Analyses Using Ultra-High Resolution Ion Mobility Spectrometry Separations. Int J Mol Sci 18:
Burnum-Johnson, Kristin E; Kyle, Jennifer E; Eisfeld, Amie J et al. (2017) MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. Analyst 142:442-448

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