Development of a pediatric immune cell atlas and characterization of CD4+ T cells in food allergy.

The immune system undergoes maturation throughout early life, shaped partly by environmental exposures. As a result, pediatric immune responses can be implicated in many diseases including food allergy (FA). This study leveraged publicly available single-cell RNA-sequencing (scRNA-seq) data from eight clinical studies analyzing peripheral blood mononuclear cells to develop a pediatric single-cell reference atlas from 57 individuals. The atlas was used to investigate cellular heterogeneity between healthy children, characterize CD4+ T cells, and CD4+ T cell sub-type specific responses associated with age and allergy. Seven CD4+ T cell subclusters were identified and annotated, a unique subset of cytotoxic Th2-like cells was enriched for both peanut- and egg-allergic gene signatures. Cluster-specific age-associated signatures were identified using multi-variate regression models revealing enrichment of metabolic pathways during early-life. FA gene signatures were identified using bulk and scRNA-seq data and were compared across studies using the developed reference. Finally, Random Forest models were developed to investigate the predictive role of innate immune cells in CD4+ T cell regulation revealing TLR/NOD pathway activities in monocytes associated with gut- and skin-homing Th2 cells. Thus, this study provides a robust single-cell reference atlas of healthy children for pediatric research and further demonstrates three applications of the atlas through cellular mapping and identification of gene signatures in the context of FA.