A de novo IKZF4 variant impairs marginal zone B cells and regulatory T cells by downregulating the NF-κB pathway

Purpose Inborn errors of immunity (IEI) are a group of complex diseases characterized by reduced immunity and increased susceptibility to external pathogens, autoinflammation, autoimmune conditions, and/or malignancy. The IKAROS zinc-finger ( IKZF ) family belongs to the C2H2 zinc-finger transcription factors composed of IKAROS ( IKZF1 ), HELIOS ( IKZF2 ), AIOLOS ( IKZF3 ), EOS ( IKZF4 ), and PEGASUS ( IKZF5 ). Variants in IKZF have been reported to cause human IEI except for IKZF4 . This research aimed to identify the pathogenicity and pathogenic mechanism of IKZF4 as a novel causative gene for IEI. Methods Here, we use whole-exome sequencing to screen out the candidate variant of IEI. Western blotting, quantitative polymerase chain reaction, immune staining, co-immunoprecipitation, flow cytometry, Luminex assay, and single-cell RNA-sequencing were used to explore the phenotypes and functional effects in the cell model and the mouse model. Results A de novo c.1472delG variant in IKZF4 was selected as the candidate variant for IEI. The c.1472delG variant caused defective pericentromeric heterochromatin targeting and impaired protein interaction of EOS. Mouse model harboring the corresponding variant in Ikzf4 ( Ikzf4 ^+/c.1475delG ) showed a pro-inflammatory switch in the regulatory T cells, accompanied by reduced levels of immunoglobulins and a decreased ratio of marginal zone B cells after lipopolysaccharide stimulation, which were probably caused by the down-regulated transcriptional regulation of EOS on the nuclear factor kappa-B pathway. Conclusion This research identified IKZF4 as a novel causative gene for IEI, which advances our knowledge of the IKZF family and the complexity of human IEI.