The genetic variability and Individual variations in immune status dictate responses to vaccinations, infections, and contribute to disease severity. The sequencing of the human genome and generation of the Haplotype Map now enables a mechanistic understanding of how genetic variation influences human immune responses. Yet manifold non-genetic factors also interact to maintain the healthy immune system, and complex analysis will be required to form predictions for its response to perturbations. Here, we will employ systems approaches and novel, high throughput and high-fidelity technologies such as multiplexed gene expression, automated multidimensional flow cytometry, and integrated single-cell assays in nanowells to quantitatively assess leukocyte function to ultimately identify the molecular signatures defining individual immune responses. We will address immune profiles in three related studies. In Research Project 1, we will develop immunologic signatures of influenza vaccine responsiveness and determine the effect of aging and functional status on these signatures. We will identify gene signatures and biological pathways that can distinguish between strong and weak immune responses to vaccination and that predict effective responses. In Research Project 2, we will investigate resistance to flaviviral infections using West Nile virus, and hepatitis C virus;through analysis of responses in patients from stratified cohorts, we will establish correlations between gene expression, immune cell responses and clinical outcome. In Research Project 3, we will generate mathematical models that detect connectivity and predict dynamic functional responses of the immune system. This approach will link data collected on both populations and individuals using multivariate statistical approaches to integrate cohort-wide data including genome wide association studies and novel single-cell analyses to assess immune responsiveness in relationship to genetic variation. Our functional systems immunology approach will allow us to define baseline human immune signatures following viral infection and vaccination along with deviations from this baseline, with the goal of identifying future targets for intervention and establishing sets of biomarkers that predict responses to vaccination.

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-QV-I (M2))
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Dong, Gang
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Yale University
Schools of Medicine
New Haven
United States
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Cahill, Megan E; Yao, Yi; Nock, David et al. (2017) West Nile Virus Seroprevalence, Connecticut, USA, 2000-2014. Emerg Infect Dis 23:708-710
Shaham, Uri; Stanton, Kelly P; Zhao, Jun et al. (2017) Removal of batch effects using distribution-matching residual networks. Bioinformatics 33:2539-2546
Montgomery, R R (2017) Age-related alterations in immune responses to West Nile virus infection. Clin Exp Immunol 187:26-34
Herndler-Brandstetter, Dietmar; Shan, Liang; Yao, Yi et al. (2017) Humanized mouse model supports development, function, and tissue residency of human natural killer cells. Proc Natl Acad Sci U S A 114:E9626-E9634
Molony, Ryan D; Malawista, Anna; Montgomery, Ruth R (2017) Reduced dynamic range of antiviral innate immune responses in aging. Exp Gerontol :
Shalek, Alex K; Benson, Mikael (2017) Single-cell analyses to tailor treatments. Sci Transl Med 9:
HIPC-CHI Signatures Project Team; HIPC-I Consortium (2017) Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses. Sci Immunol 2:
Molony, Ryan D; Nguyen, Jenny T; Kong, Yong et al. (2017) Aging impairs both primary and secondary RIG-I signaling for interferon induction in human monocytes. Sci Signal 10:
Goldberg, Emily L; Asher, Jennifer L; Molony, Ryan D et al. (2017) ?-Hydroxybutyrate Deactivates Neutrophil NLRP3 Inflammasome to Relieve Gout Flares. Cell Rep 18:2077-2087
Montgomery, Ruth R (2016) High standards for high dimensional investigations. Cytometry A 89:886-888

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