Systems Biology Approach to Uncover Signaling Defects in Primary Immunodeficiency Diseases

Abstract

Abstract To improve diagnoses and further our understanding of functional defects in subjects with primary immunodeficiency (PI) diseases, we developed a new screen to broadly study the signaling of defective human immune responses to infections. Using time-of-flight mass cytometry (CyTOF) and phospho-specific antibodies, we simultaneously examined the major signaling pathways of all circulating innate and adaptive immune cell types in response to cytokines and TLR agonists to identify signaling responses. We studied healthy controls and developed software tools to generate a systematic map of signaling responses. CyTOF successfully recapitulated established signaling responses, and further, elucidated new pathways that would not have been appreciated with traditional studies. Signaling map of controls was compared to maps generated by analyzing PI subjects with gain-of-function STAT1 and autosomal dominant STAT3 deficiency diseases. CyTOF allowed us to perform unbiased studies to uncover many ex-vivo signaling defects simultaneously to better understand how known genetic etiologies manifest functionally, and exactly which cell subtypes are affected. We identified more glaring defective signaling responses in these subjects aside from the canonical defects, elucidating the true breadth of cell subtypes and pathways affected. Broad, unbiased, functional analysis can complement whole exome sequencing to facilitate identification of novel or rare immune diseases. Comprehensive view of signaling across all immune cell subsets facilitates learning more about abnormal signaling patterns that confer susceptibility to infection or autoimmunity, improving our understanding of immune responses and can lead to new therapies.