Loss-of-function mutation in ZNF74 is associated with a novel primary immunodeficiency and T cell intrinsic BHLHE40 de-repression

KRAB zinc finger proteins (KZFP) are a large family of epigenetic repressors with pleiotropic functions. While the KZFP co-factor KAP-1 has been extensively studied, the physiologic function of individual KZFP members is largely unknown. Within a cohort of patients with primary immunodeficiency (PID), we identified two brothers carrying a homozygosity region on chromosome 22q11 with a truncating loss-of-function mutation in ZNF74 combined with a known disease-associated variant in ADA2. As deficiency of ADA2 (DADA2) has a very variable clinical phenotype, incomplete penetrance and is likely influenced by mutations in modifying genes, we tested the possible influence of the truncating loss-of-function mutation in ZNF74 on the observed clinical phenotype. Analyzing published ChIP-exo-seq data of ZNF74 revealed a binding peak close to an enhancer cluster of BHLHE40, a transcription factor which was highly up-regulated in CD4+ T cell subsets from the index patient. Wild type but not mutant ZNF74 bound to the specific BHLHE40 enhancer site and repressed BHLHE40 in vitro underlining that the BHLHE40 up-regulation seen in the index patient is likely caused by the ZNF74 loss-of-function. Furthermore, transcriptomic analysis of CD4+ T cell subsets from the index patient revealed a tissue resident memory (Trm)-like signature of circulating T cells likely activated by the BHLHE40 de-repression. This could be clinically linked to excessive lymphoma-like T cell infiltrations in skin and bone marrow and an altered memory T cell compartment. Thus, we report the first homozygous loss-of-function mutation in a human KZFP contributing to immune-dysregulation.