Molecular dynamics of genome editing with CRISPR-Cas9 and rAAV6 virus in human HSPCs to treat sickle cell disease

Authors:
Liwen Xu, Premanjali Lahiri, Jason Skowronski, Neehar Bhatia, Annalisa Lattanzi, and Matthew H. Porteus
In:
Source: Mol Ther Methods Clin Dev.
Publication Date: (2023)
Issue: 30:  P317-331
Research Area:
Cancer Research/Cell Biology
Immunotherapy / Hematology
Cells used in publication:
CD34+ cell, human
Species: human
Tissue Origin: blood
Platform:
4D-Nucleofector® X-Unit
Experiment

Briefly, CD34+ HSPCs were cultured and pre-stimulated for 72 h after thaw and before genome editing except when specifically indicated. Chemically modified HBB sgRNA was synthesized by Agilent Technologies (Santa Clara, CA, USA). SpyFi Cas9 was purchased from Aldevron (Fargo, ND, USA). HBB donor rAAV6 virus was purchased from Viralgen VC (Donostia, Gipuzkoa, Spain). Electroporation of Cas9-RNP complex was performed using Lonza 4DNucleofector (Lonza Group, Alpharetta, GA, USA) in P3 Primary Cell Solution with program DZ-100 as described previously. Electroporated cells were then plated at 2.5 x 10^5 cells/mL in HSPC culture medium supplemented with cytokines. For RNP/rAAV6 or rAAV6 treatment, HBB donor rAAV6 was immediately dispensed onto cells at an MOI of 2.5 x10^3 vg/cell based on the titer determined by ddPCR except for special indications. After incubation for 24 h, a medium addition or medium exchange was performed to dilute or remove residual HBB donor rAAV6. The CD34+ HSPCs were cultured for an additional 24 h for quantification of genome editing events. 

Abstract

Ex vivo gene correction with CRISPR-Cas9 and a recombinant adeno-associated virus serotype 6 (rAAV6) in autologous hematopoietic stem/progenitor cells (HSPCs) to treat sickle cell disease (SCD) has now entered early-phase clinical investigation. To facilitate the progress of CRISPR-Cas9/rAAV6 genome editing technology, we analyzed the molecular changes in key reagents and cellular responses during and after the genome editing procedure in human HSPCs. We demonstrated the high stability of rAAV6 to serve as the donor DNA template. We assessed the benefit of longer HSPC pre-stimulation in terms of increased numbers of edited cells. We observed that the p53 pathway was transiently activated, peaking at 6 h, and resolved over time. Notably, we revealed a strong correlation between p21 mRNA level and rAAV6 genome number in cells and beneficial effects of transient inhibition of p53 with siRNA on genome editing, cell proliferation, and cell survival. In terms of potential immunogenicity, we found that rAAV6 capsid protein was not detectable, while a trace amount of residual Cas9 protein was still detected at 48 h post-genome editing. We believe this information will provide important insights for future improvements of gene correction protocols in HSPCs.