1. A Direct Comparison of Foamy and Lentiviral Vector Genotoxicity in SCID-Repopulating Cells Shows Foamy Vectors Are Less Prone to Clonal Dominance

Abstract

Hematopoietic stem cell (HSC) gene therapy has immense potential for numerous diseases including primary immunodeficiencies. However, in some SCID-X1 patients treated with gammaretroviral vectors, leukemia occurred as a result of vector mediated genotoxicity. Lentiviral vectors are less genotoxic than gammaretroviral vectors and have become the retroviral vector of choice in HSC clinical trials. Foamy retroviral vectors have a promising integration profile and are less prone to read-through transcription when directly compared to gammaretroviral or lentiviral vectors. Here we directly compared the safety and efficacy of foamy vectors to lentiviral vectors in human cord blood CD34+ repopulating cells in immunodeficient mice (NSG). To increase their genotoxic potential, foamy and lentiviral vectors with identical transgene cassettes that utilized a known genotoxic spleen focus forming virus promoter were used. Our rationale was that in order to compare the relative safety of these two vector systems in normal human CD34+ cells, within the relatively short time span of repopulating cells in mice, a highly genotoxic promoter would be the best way to elicit differences in genotoxicity. Both foamy and lentiviral vectors resulted in efficient marking in vivo with 12.2% of peripheral blood human CD45+ cells expressing EGFP for foamy vectors, and 9.6% for lentiviral vectors at 19 weeks after transplantation. A total of 837 foamy vector and 423 lentiviral vector unique integration sites were recovered in human SCID repopulating cells 19 weeks after transplantation. Foamy vector proviruses were observed less often within genes (40%) than lentiviral vectors (74%), and were also observed less often within proto-oncogenes (6.6%) than lentiviral vectors (9.7%). Analysis of clonality in repopulating cells within individual mice showed that the foamy vector group was more polyclonal with fewer dominant clones (2/6 mice) than in the lentiviral vector group (8/8 mice) (Figure 1Figure 1). Dominant clones were defined as a single integration site having over 20% of captures. Five of the thirteen dominant clones from the lentiviral group had integrations near known proto-oncogenes (Table 1) but in the foamy vector group, none of the three dominant clones had a known proto-oncogene near the integration site. In summary, in a direct comparison in human CD34+ SCID repopulating cells, foamy vectors resulted in fewer dominant clones and more polyclonal repopulation than lentiviral vectors. Our data further supports the relative safety of foamy vectors for HSC gene therapy.View Large Image | Download PowerPoint Slide