Treatment of GATA2 deficiency by allele-specific CRISPR-Cas9-directed gene correction in hematopoietic stem cells.

GATA2 deficiency is a rare inborn error of immunity caused by monoallelic variants in the GATA2 gene, leading to dysfunction of hematopoietic stem and progenitor cells (HSPCs). Here, we investigate a potential therapeutic strategy for GATA2 deficiency based on CRISPR-Cas9-based gene correction, utilizing recombinant adeno-associated virus serotype 6 (rAAV6) as a template for homology-directed repair (HDR). For a 7-base pair (bp) deletion giving rise to GATA2 deficiency, we identify a single guide RNA (sgRNA) supporting allele-specific cleavage in the disease allele. Initially, we observe high cytotoxicity in HSPCs upon Cas9/sgRNA ribonucleoprotein nucleofection and rAAV6 transduction, but this is mitigated by co-administering mRNA-based modulators of the DNA damage response combined with a 10-fold reduction in rAAV6 dose. Using this protocol, we achieve efficient HDR (>80%) in HSPCs derived from a patient carrying the 7-bp deletion and show increased engraftment potential after GATA2 correction. Using DISCOVER-seq, we find limited off-target activity. However, with PCR-free long-read sequencing, we detect frequent large aberrations at the on-target site in HSPCs, primarily attributed to the integration of AAV concatemers identified in 15% of the targeted alleles. Our findings describe the effect of gene correction on GATA2 deficiency and highlight potential on-target aberrations following HDR-mediated gene correction.