Efficient CRISPR/Cas9-Mediated Gene Editing of Pklr in Human Hematopoietic Progenitors and Stem Cells for the Gene Therapy of Pyruvate Kinase Deficiency

Pyruvate kinase deficiency (PKD) is the most common erythroid inherited enzymatic defect causing chronic nonspherocytic hemolytic anemia. PKD is an autosomal recessive disorder caused by mutations in the PKLR gene, which led in a total or partial reduction of the activity of the erythroid pyruvate kinase (RPK) protein. To date, more than 200 different mutations in the PKLR gene have been related with PKD. The disease is associated with reticulocytosis, splenomegaly and iron overload, and may be life-threatening in severely affected patients. Treatments for PKD are mainly palliative, including regular red blood cell transfusion, splenectomy and iron chelation therapy. Allogeneic hematopoietic stem cell transplant (HSCT) represents the only curative treatment for severely affected patients, so far. Autologous HSCT of genetically corrected cells would offer a durable and curative clinical option. Over the last years, gene editing has emerged as a promising gene therapy approach for blood cell disorders, where genetic alterations can be accurately corrected. The high level of correction got in hematopoietic progenitors and stem cells without remarkable off-target effects suggests that the clinical use of gene editing therapy to correct genetic hematopoietic diseases is highly likely in a short term. Here, we present two gene editing approaches to correct PKD in human hematopoietic cells based of specific point mutation correction and in cDNA knock-in of a codon optimized version the RPK cDNA. We have designed both strategies to maintain the endogenous regulation of RPK once the gene editing has been carried out. First, we designed specific sgRNA targeting NM_000298.5(PKLR):c.359C>T mutation reported as pathogenic in PKD patients, and a single-stranded donor oligonucleotide (ssODN) to correct this mutation. When both sgRNA/Cas9 ribonucleoprotein (RNP) and ssODN were nucleofected together in a heterozygous PKD patient-lymphoblastic cell line (PKD LCL), around 5% of total alleles were correctly edited.

In a second strategy, we developed a knock-in gene editing strategy at the genomic starting site of the PKLR gene by combining RNP electroporation and the adeno-associated viral vector (AAV) delivery of the recombination matrix. Specific gRNAs generating up to 60% indels at the RPK starting site were generated. Two different AAV constructs flanked by specific homologous arms were generated to delivery either a TurboGFP expression cassette or a promotor-less therapeutic coRPK. Up to 60% donor integration and stable expression of turbo EGFP and of coRPK driven by PKLR endogenous promoter was obtained in K562 erythroleukemia cells. Similar gene editing efficacies were obtained in human CB-CD34⁺. Specific integration and stable expression of the transgenes were detected in up to 30% colony forming units (CFUs). Moreover, gene edited cells engrafted efficiently in NSG mice. These results demonstrate the feasibility of editing the PKLR locus in hematopoietic progenitors and hematopoietic stem cells at efficiencies that could be clinically applicable to treat Pyruvate Kinase deficiency.