Induction of Fetal Hemoglobin Synthesis By Crispr/Cas9-Mediated Disruption of the β-Globin Locus Architecture

Naturally occurring, large deletions in the β-globin locus result in increased fetal hemoglobin (HbF) expression (HPFH, Hereditary Persistence of Fetal Hemoglobin), a condition that mitigates the clinical severity of Sickle Cell Disease (SCD) and β-thalassemia. Here, we integrated BCL11A and GATA1 transcription factor binding site analysis and HPFH mutational data to identify potential HbF silencers in the β-globin locus. Based on this analysis, we designed a CRISPR/Cas9 strategy to disrupt: (i) a 3.5-kb δγ-intergenic region that is specifically deleted in individuals with HPFH. This region contains BCL11A and GATA1 binding sites in adult, HbF-negative primary erythroblasts, thus representing a potential HbF silencer; (ii) a 7.2-kb region, encompassing the 3.5-kb δγ-intergenic element, which is the minimal naturally occurring deletion associated with HPFH ("Corfù" deletion; Chakalova et al., Blood, 2005); (iii) a 13.6-kb genomic region commonly deleted in HPFH, which includes the δ- and β-globin genes and putative intergenic HbF silencers. Targeted deletion or inversion of the 13.6-kb genomic region caused a substantial increase in γ-globin mRNA levels, re-activation of HbF synthesis and a concomitant decrease in HbA expression in adult human erythroid cells (HUDEP-2). Interestingly, deletion of the Corfù region or of the 3.5-kb putative HbF silencer, increased γ-globin gene transcription but failed to produce accumulation of γ-globin mRNA, suggesting a post-transcriptional regulation of γ-globin synthesis in the presence of an intact and active β-globin gene. We then tested re-activation of HbF synthesis in primary adult hematopoietic stem/progenitor cells differentiated towards the erythroid lineage in liquid and clonogenic cultures. Targeting the 13.6-kb genomic region resulted in a high proportion of γ-globin expressing primary erythroblasts, with HbF representing up to 50% of total hemoglobin. Cell morphology, erythroid marker profile, total hemoglobin levels and erythroid maturation were unaffected, consistent with the asymptomatic phenotype of adult HPFH carriers. These data suggest that this region could serve as target for therapeutic genome editing for HbF induction in β-hemoglobinopathies. Overall, this study contributes to the knowledge of the mechanisms underlying fetal to adult Hb switching, and provides clues for a genome editing approach to the treatment of SCD and β-thalassemia.