A de novo IKZF4 Variant Underlies Hypogammaglobulinemia and Increased Infection Susceptibility through Downregulating the NF-κB Pathway

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 is a group of C2H2 zinc-finger transcription factors that includes IKAROS ( IKZF1 ), HELIOS ( IKZF2 ), AIOLOS ( IKZF3 ), EOS ( IKZF4 ), and PEGASUS ( IKZF5 ). Variants in IKZF have been reported to cause human IEI except IKZF4 . This research aimed to identify the pathogenicity and underlying mechanisms of IKZF4 as a novel candidate gene for IEI. Here, we used whole-exome sequencing to identify candidate variants of IEI. Western blotting, quantitative polymerase chain reaction, immune staining, co-immunoprecipitation, flow cytometry, Luminex assays, and single-cell RNA sequencing were used to explore the phenotypes and functional effects in cell and mouse models. An 11-month-old patient presented with repeated fever and convulsions accompanied by persistently reduced immunoglobulin levels and abnormal immune indices, which supported the diagnosis of IEI. A de novo c.1472delG variant (GRCh37/hg19, NM_022465.3) in IKZF4 was selected as the candidate variant for IEI. The c.1472delG variant caused reduced EOS expression and truncated protein (predicted molecular weight ~ 57 kDa), defective pericentromeric heterochromatin targeting, and impaired protein interactions of EOS. A mouse model harboring the corresponding variant in Ikzf4 ( Ikzf4 + /c.1475delG ) showed a proinflammatory switch in regulatory T cells, accompanied by reduced levels of immunoglobulins and a decreased ratio of marginal zone B cells after lipopolysaccharide stimulation, which were potentially caused by the down-regulated transcriptional regulation of EOS on the nuclear factor kappa-B pathway. This research identified IKZF4 as a novel candidate gene for IEI, advancing our knowledge of the IKZF family and the complexity of human IEI.