title: Large-scale analysis of adeno-associated virus vector integration sites in normal human cells.
abstract: The integration sites of viral vectors used in human gene therapy can have important consequences for safety and efficacy. However, an extensive evaluation of adeno-associated virus (AAV) vector integration sites has not been completed, despite the ongoing use of AAV vectors in clinical trials. Here we have used a shuttle vector system to isolate and analyze 977 unique AAV vector-chromosome integration junctions from normal human fibroblasts and describe their genomic distribution. We found a significant preference for integrating within CpG islands and the first 1 kb of genes, but only a slight overall preference for transcribed sequences. Integration sites were clustered throughout the genome, including a major preference for integration in ribosomal DNA repeats, and 13 other hotspots that contained three or more proviruses within a 500-kb window. Both junctions were localized from 323 proviruses, allowing us to characterize the chromosomal deletions, insertions, and translocations associated with vector integration. These studies establish a profile of insertional mutagenesis for AAV vectors and provide unique insight into the chromosomal distribution of DNA strand breaks that may facilitate integration.
authors.affiliation: Department of Pediatrics, Division of Genetics and Developmental Medicine, University of Washington, Seattle, 98195-7720, USA.
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Miller
authors.forename: Grant D
authors.initials: GD
authors.lastname: Trobridge
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Petek
authors.forename: Michael A
authors.initials: MA
authors.lastname: Jacobs
authors.forename: Rajinder
authors.initials: R
authors.lastname: Kaul
authors.forename: David W
authors.initials: DW
authors.lastname: Russell
mesh_terms: D002874:Chromosome Mapping; D002877:Chromosomes, Human / Q000235:genetics / Q000821:virology; D004268:DNA-Binding Proteins / Q000235:genetics; D000229:Dependovirus / Q000502:physiology*; D005347:Fibroblasts / Q000821:virology*; D005822:Genetic Vectors / Q000502:physiology*; D006801:Humans; D015534:Trans-Activators; D016662:Virus Integration
chemical_list: C409062:CXXC1 protein, human; D004268:DNA-Binding Proteins; D015534:Trans-Activators