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Gene expression of murine hematopoietic stem and progenitor cells transduced with integrating vectors

ABSTRACT: Gene therapy has emerged as a promising therapeutic strategy, but efficient in vitro assessment of vector safety remains challenging. To create a predictor of vector induced genotoxicity, we developed the Surrogate Assay for Genotoxicity Assessment (SAGA), which uses genetic algorithm-enhanced machine learning to detect the deregulation of a specific gene expression signature in murine hematopoietic stem and progenitor cells (HSPC) transduced with potentially genotoxic vectors. For the SAGA assay, murine lineage negative (Lin-) HSPC are isolated and transduced with high multiplicities of infection (MOI) to reach at least 3 vector copies per cell. Post-transduction, bulk cultures are expanded for a total of 15 days in medium supplemented with cytokines promoting myeloid differentiation. Total RNA is prepared from the bulk cultures on day 15 and gene expression profiles are analyzed on microarrays.SAGA classifies samples based on their gene expression profile by using a support vector machine with a radial kernel on 9 features deduced by a genetic algorithm. SAGA is more robust, sensitive and faster than previous assays and reliably predicts a mutagenic risk for vectors that led to leukemia in clinical trials.

ORGANISM(S): Mus musculus

PROVIDER: GSE109391 | GEO | 2019/01/01

REPOSITORIES: GEO

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