ABSTRACT

Severe congenital neutropenia (SCN) is a life-threatening disorder most often caused by dominant mutations of ELANE (encoding neutrophil elastase, NE) that interfere with normal neutrophil maturation. Granulocyte colony stimulating factor (G-CSF) pharmacotherapy alleviates neutropenia but unmasks and accelerates an elevated lifelong risk of myeloid leukemia. Here we perform a pooled CRISPR screen in human hematopoietic stem and progenitor cells (HSPCs) to correlate ELANE mutations with neutrophil maturation potential. Highly efficient ELANE gene editing of early exons elicits nonsense-mediated decay (NMD) and overcomes neutrophil maturation arrest in HSPCs from ELANE mutant SCN patients. Conversely, terminal exon ELANE frameshift alleles that mimic SCN-associated mutations escape NMD and recapitulate neutrophil maturation arrest in healthy donor cells. In mouse xenografts, human HSPCs with early exon gene edits demonstrate normal hematopoietic engraftment function whereas HSPCs with late exon gene edits reproduce selective neutrophil maturation arrest in vivo, establishing the first animal model of ELANE mutant SCN. Surprisingly, only -1 frame indels impede neutrophil maturation, while -2 frame late exon indels repress translation and support neutrophil maturation. Gene editing of primary hematopoietic cells represents a universal therapeutic approach to ELANE mutant neutropenia compatible with HSC function and allows faithful identification of variant pathogenicity that clarifies the molecular pathogenesis of SCN.