Ikaros regulates gene expression programs required for proper BCR-activation in mature B cells

Abstract

Abstract The zinc-finger (ZnF) transcription factor Ikaros (encoded by Ikzf1) plays an essential role in regulating transcriptional programs required for B cell development, as Ikzf1null/null mice do not develop B cells. Ikaros contains two ZnF domains which function in DNA-binding and protein-protein interactions, respectively. Recently, mutations within the central DNA-binding ZnF domain of the IKZF1 gene has been linked to autoimmunity. Likewise, our murine model containing a germ-line deletion of the fourth ZnF (Ikzf1DF4/DF4) displays a B cell hyper-reactive (HR) phenotype, with B cells activated by anti-IgM without the requirement for a second co-stimulatory signal. Although Ikaros has been well-studied in early developing B cells, how loss-of-function mutations in Ikzf1 impacts downstream effector functions of mature B cells, remains largely unknown. Here, we investigated the role of Ikaros in regulating an epigenetic program required for co-stimulation-restricted activation of B cells. We utilized transcriptomic and epigenomic approaches (RNA-seq and ATAC-seq) to define transcriptional programs which dynamically change upon ex vivo stimulation and investigated their Ikaros-dependency. Interestingly, we found that the largest subset of genes deregulated between wt and Ikzf1DF4/DF4 B cells, occur prior to stimulation. In addition, CUT&RUN performed in wt B cells shows Ikaros binding to a large subset of genes expressed upon stimulation with anti-IgM and CD40L. Together, these results demonstrate that Ikaros regulates the transcriptional landscape of BCR-activated mature B cells. In the future, we will be integrating single cell RNA-seq analysis to investigate B cell heterogeneity in wt and Ikzf1DF4/DF4 B cells.