Development of evolutionarily conserved viral integration sites as safe harbors for human gene therapy

Abstract

Gene transfer into hematopoietic stem and progenitor cells (HSPCs) involving indiscriminately integrating viral vectors has unpredictable outcomes including potential adverse events such as leukemogenesis, resulting from insertional mutagenesis. Therefore, identifying and characterizing genomic safe harbor (GSH) sites where exogenous genetic information can be integrated safely into adult progenitor and stem cells is critically important for therapeutic gene addition. Here, we present a novel approach to identify new GSH sites based on a proven system of stable transgene insertion: the evolutionarily conserved integration of parvovirus DNA into the germlines of host species. From a dataset of 199 unique endogenous parvovirus element (EPV) integration events identified in host genomes, 102 loci were mapped to the human genome with 17 being evaluated for potential use as GSHs in primary human CD34+ HSPCs. Six of the edited loci resulted in sustained transgene expression in both erythroid and myeloid phenotypes while three exhibited myeloid specific-expression and the remaining four loci resulted in a subset of myeloid and erythroid lineages. Following this approach, a minimum of nine promising GSH sites suitable for gene therapy of blood disorders were identified and additional GSH sites are likely to emerge from the remaining mapped loci which may be suitable for gene addition in stem and progenitor cells other than hematopoietic tissues. This novel approach extends the options for gene knock-ins while reducing the risks of insertional mutagenesis, unpredictable expression profiles, and increasing the safety and therapeutic effects.