A novel GATA2 enhancer single nucleotide mutation results in the MonoMAC syndrome phenotype in two second cousins

Inherited or sporadic mutations in the transcription factor GATA2 have been shown to be responsible for MonoMAC syndrome, a GATA2 deficiency disease characterized by a constellation of findings including disseminated non-tuberculous mycobacterial infections, severe deficiencies of monocytes, natural killer cells, and B-lymphocytes, and myelodysplastic syndrome. Mutations in the GATA2 gene are found in ~90% of patients with a GATA2 deficiency phenotype and are largely missense mutations in the conserved second zinc-finger domain or truncation mutations elsewhere in the coding sequence. Mutations in an intron 5 regulatory enhancer element are also well described in GATA2 deficiency. Here we present a large multigeneration kindred with the clinical features of GATA2 deficiency but lacking an apparent GATA2 mutation. Whole Genome Sequencing revealed a unique Adenine-to-Thymine variant in the GATA2 -110 enhancer 116,855bp upstream of the GATA2 gene. The mutation creates a new E-box consensus in position with an existing GATA-box to generate a new hematopoietic regulatory composite element. The mutation segregates with the disease pattern in five generations of the family pedigree. Cell-type specific allelic imbalance of GATA2 expression is observed in a patient’s bone marrow with higher expression from the mutant-linked allele. Allele-specific overexpression of GATA2 is observed in CRISPR/Cas9-modified HL60 cultured cells and in luciferase assays with the enhancer mutation. This study demonstrates overexpression of GATA2 resulting from a single nucleotide change in an upstream regulatory enhancer element in patients with MonoMAC syndrome. RNA-sequencing of a HL-60 promyelocytic leukemia cell line engineered to harbor an A-to-T inversion in the GATA2 -110 enhancer 116,855bp upstream of the GATA2 gene via CRISPR/Cas-9-mediated genome editing compared to WT control measured over four days.