EDIT-301: An Experimental Autologous Cell Therapy Comprising Cas12a-RNP Modified mPB-CD34+ Cells for the Potential Treatment of SCD

Sickle cell disease (SCD) is an inherited blood disorder affecting approximately 100,000 individuals in the United States. Fetal hemoglobin (HbF) is a major modifier of SCD severity. Studies showed that individuals with compound heterozygosity for sickle hemoglobin (HbS) and hereditary persistence of fetal hemoglobin (HPFH) that expressed approximately 30% HbF did not show features of SCD. Therefore, we are developing EDIT-301, an experimental autologous cell therapy comprising CD34+ cells genetically modified using a Cas12a RNP (ribonucleoprotein) to promote HbF expression to treat SCD.

Several HPFH mutations have been reported at the HBG locus. In particular, disruption of the distal CCAAT-box region of the HBG1/2 promoters was associated with elevated levels of HbF, suggesting that this region is a relevant genome editing target for the treatment of SCD. Genotype to phenotype analysis at the distal CCAAT-box region of the HBG1/2 promoters identified the mutations leading to elevated HbF expression. Indels disrupting more than 3 nucleotides were generally associated with elevated HbF expression while smaller indels had lower to no impact. We evaluated editing at this site using several RNP configurations, based on either SpCas9 or Cas12a (also known as Cpf1). Cas12a RNP resulted in larger deletions and a higher frequency of productive indels than SpCas9 RNP. Furthermore, productive indels generated with SpCas9 RNP relied predominantly on microhomology mediated end joining (MMEJ) mechanism. As the MMEJ repair mechanism is not frequently used by hematopoietic stem cells (HSC), productive editing may be low in vivo. In contrast, Cas12a RNP generated more productive indels at the HBG1/2 promoters target site irrespective of the DNA repair mechanism. We therefore postulated that editing at the distal CCAAT-box region with Cas12a would better support long-term persistence of productive indels and robust HbF expression.

Consistent with this hypothesis, 80-90% editing was observed after electroporation of mobilized peripheral blood CD34+ cells (mPB-CD34+ cells) from healthy donors with a Cas12a RNP targeting the HBG1/2 promoters, resulting in approximately 40% of HbF expression in their erythroid progeny. Infusion of the modified CD34+ cells into NBSGW mice resulted in long-term multi-lineage reconstitution at 16 weeks post-infusion, with no reduction in editing levels compared to those at the time of infusion. A diverse on-target editing profile was observed in all animals, indicative of a polyclonal engraftment. Erythroid cells purified from the bone marrow of animals that received Cas12a-RNP treated cells demonstrated robust HbF expression averaging 40-50% compared to ~5% observed in the vehicle-treated control group.

Off-target activity of the Cas12a RNP was also evaluated. A set of candidate off-target sites was first determined using orthogonal methods, including: in-silico prediction, Digenome-Seq and GUIDE-Seq. Each candidate site was then analyzed for editing by targeted PCR-NGS in electroporated CD34+ cells. No off-target editing was verified, demonstrating the specificity of this Cas12a RNP.

Taken together, we identified a specific Cas12a RNP that efficiently edited the distal CCAAT-box region at the HBG1/2 promoters in CD34+ cells. These edited CD34+ cells led to long-term polyclonal multilineage engraftment and therapeutically meaningful levels of 40-50% HbF in vivo. Based on these results, IND-enabling activities have been initiated for EDIT-301: an experimental autologous cell therapy comprising Cas12a-RNP modified mPB-CD34+ cells for the potential treatment of SCD.