Proteomics and Metabolomics Core: IDEAL shapes vaccine response, susceptibility to respiratory infectious disease and asthma

Project Summary: IDEAL Proteomics and Metabolomics Core (PMC) The central premise of the overall proposal Immune Development in Early Life (IDEAL) Shapes Vaccine Response, Respiratory Infectious Disease and Asthma is that childhood immune development generates immunological endotypes with distinct biological mechanisms leading to co-morbidity among the three clinical phenotypes of interest vaccine responsiveness, respiratory infection proneness, and asthma. Our overall hypothesis is that unfavorable immune trajectories in early life result in clinical phenotypes such as low vaccine responsiveness, frequent respiratory infections and development of asthma, with significant overlap. These three clinical phenotypes are the converging clinical manifestations of various immune endotypes, i.e., distinct cellular and molecular signatures associated with the underlying mechanistic processes. The objective of the proposal is to test this hypothesis and to provide multidimensional quantitative molecular maps enabling description of the underlying immunological endotypes, with the ultimate goal to identify biomarkers to identify children at risk for unfavorable immune trajectories and to identify actionable targets for intervention. Given the importance of cytokines/chemokines, proteins and metabolites in modulating immune development, mapping their differential abundances in the context of the three different clinical phenotypes will be essential to understand the underlying immunological endotypes, which will be identified in Project 1 (PR1), further examined in vitro in PR3, and ultimately integrated with epigenetic data from PR2. To enable the proposed research, the Proteomics and Metabolomics Core (PMC) will manage, handle, and aliquot ~1900 plasma and ~600 nasopharyngeal wash samples (provided/collected by the IDEAL Clinical Core; CC) and provide the Data Management Core (DMC) the quantitative cytokine/chemokine, proteome, and metabolome maps. Specific Aim 1 will use a well-established multiplex platform (Luminex; 41-plex Milliplex system) to detect and quantify 41 cytokines and chemokines in plasma and nasopharyngeal wash samples. Specific Aim 2 describes a 2-pronged LC/MS-based plasma proteomics approach yielding ~700 proteins detected per sample, which covers the classical plasma proteome as well as a major fraction of the tissue leakage proteins in plasma. Furthermore, the nasopharyngeal wash proteomes will be mapped using LC/MS- based methods. All LC/MS analyses will be carried out in a high throughput fashion (60 to 100 samples/day) including 96-well plate-based processing. Specific Aim 3 coordinate the aliquoting and shipment of samples to Metabolon, Inc which, as leader in the field of metabolomics services, will perform the LC/MS-based metabolomic analysis of the plasma yielding >1,000 metabolites detected per sample as well as nasopharyngeal wash samples. The PMC will leverage the infrastructure and expertise of management, handling and analyzing 1000s of plasma samples as part of NIAID's IMPACC study to identify immunophenotypes in hospitalized COVID-19 patients.