Systems Biology of Early Atopy (SUNBEAM) Analysis and Bioinformatics Center

1: We will generate immune profiling data on 300 participants for a systems biology analysis of AD and FA. We will conduct flow cytometry (2 x 29-marker panels) and Olink proteomics (92 markers) on 100 non-atopic(NA), 100 AD, and 100 AD + FA subjects at 0, 2, and 5 months of age. Data will be provided to the Bioinformatics and Data Integration Group for integration with datasets from Project 1 and 3. 2: We will identify common innate immune dysfunction that precedes the onset of AD and FA. We hypothesize that there will be a lack of regulatory phenotype in innate cells present at birth that will predict onset of AD and FA in the first year of life. We will focus on myeloid cells (monocytes and DCs) and examine expression of checkpoint markers. We will examine the functional response of cord/peripheral blood mononuclear cells (CBMC/PBMC) to stimulation of innate cells with TLRligands, S. aureus, and anti-CD40. 3: We will identify unique T cell and B cell phenotypes associated with the onset of AD and FA. We hypothesize that the T and B cell response will diverge between AD and FA, specifically at the level of Tfh cells and B cells that support the generation of high-affinity IgE in FA but not in AD without FA. We will examine this by spectral cytometry and functional assays using PMA or S. Aureus stimulated CBMCs/PBMCs. 4: Temporal analysis to identify immune basis of the atopic march. We hypothesize that there will be innate immune dysfunction present at birth that will precede the development of Type 2 T and B cell responses and clinical onset of AD and FA. We will apply integrative analyses, including machine learning and network-based methods to 1) identify combinations of markers and their causal relationships that lead to AD or FA; and 2) identify temporally homogenous subgroups (endotypes) of subjects with distinct longitudinal trajectories of cell types and cytokines and assess their relationship to clinical disease.