Transcriptome-wide Association Study of Circulating IgE Levels Identifies Novel Targets for Asthma and Allergic Diseases

Measurement of circulating immunoglobulin E (IgE) concentration is helpful for diagnosing and treating asthma and allergic diseases. Identifying gene expression signatures associated with IgE might elucidate novel pathways for IgE regulation. To this end, we performed a discovery transcriptome-wide association study (TWAS) to identify differentially expressed genes associated with circulating IgE levels in whole-blood derived RNA from 5,345 participants in the Framingham Heart Study (FHS) across 17,873 mRNA gene-level transcripts. We identified 216 significant transcripts at a false discovery rate (FDR)< 0.05. We conducted replication using the meta-analysis of two independent external studies: the Childhood Asthma Management Program (n = 610) and the Genetic Epidemiology of Asthma in Costa Rica Study (n = 326); we then reversed the discovery and replication cohorts, which revealed 59 significant genes that bidirectionally replicated. Gene ontology analysis revealed that many of these genes were implicated in immune function pathways, including defense response, inflammatory response, and cytokine production. Mendelian randomization (MR) analysis revealed four genes (CLC, CCDC21, S100A13, and GCNT1) as putatively causal (p< 0.05) regulators of IgE levels. GCNT1 (beta = 1.5, p = 0.01)--which is a top result in the MR analysis of expression in relation to asthma and allergic diseases--plays a role in regulating T helper type 1 (Th1) cell homing, lymphocyte trafficking, and B cell differentiation. Our findings build upon prior knowledge of IgE regulation and provide a deeper understanding of underlying molecular mechanisms. The IgE-associated genes that we identified--particularly those implicated in MR analysis--can be explored as promising therapeutic targets for asthma and IgE-related diseases.