Bulk RNA-seq analysis of WT and tristetraprolin (TTP)-knockout basophils treated with antigen/IgE stimulation

Basophils play crucial roles in type 2 immune responses, such as chronic allergic inflammation and protective immunity against parasites. However, the molecular mechanisms regulating basophil activation and effector molecule production remain poorly understood. To investigate the role of RNA-binding proteins (RBPs), we first analyzed the gene expression of CCCH zinc finger proteins in antigen/IgE-stimulated basophils. Among these proteins, we identified that Zfp36, encoding tristetraprolin (TTP), was the most significantly upregulated gene. Therefore, we focused on the functions of TTP in basophils. We generated TTP-KO mice using the CRISPR-Cas9 method and conducted bulk RNA-seq analysis of antigen/IgE-stimulated basophils from wild-type (WT) and TTP-knockout (TTP-KO) mice. TTP-KO basophils exhibited elevated mRNA expression of pro-inflammatory mediators, such as Il4, Il13, Areg, Ccl3, and Cxcl2, compared to WT basophils. These data suggest that TTP is a key regulator of basophil activation, controlling the mRNA expression of inflammatory mediators. Overall design: To examine the effect of TTP deficiency on gene expression profiles in antigen/IgE-stimulated basophils, WT and TTP-KO basophils sensitized with hapten TNP-specific IgE were treated with control OVA for 2 hours or TNP-conjugated OVA for 2 and 4 hours and then subjected to bulk RNA-seq analysis.