Lentivector integration sites in ependymal cells from a model of metachromatic leukodystrophy: non-B DNA as a new factor influencing integration

Robert G McAllister; Jiahui Liu; Matthew W Woods; Sean K Tom; C Anthony Rupar; Stephen D Barr

doi:10.1038/mtna.2014.39

Lentivector integration sites in ependymal cells from a model of metachromatic leukodystrophy: non-B DNA as a new factor influencing integration

Mol Ther Nucleic Acids. 2014 Aug 26;3(8):e187. doi: 10.1038/mtna.2014.39.

Authors

Robert G McAllister¹, Jiahui Liu², Matthew W Woods¹, Sean K Tom¹, C Anthony Rupar³, Stephen D Barr¹

Affiliations

¹ Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Center for Human Immunology, Western University, London, Ontario, Canada.
² Department of Biochemistry, Western University, London, Ontario, Canada.
³ 1] Department of Biochemistry, Western University, London, Ontario, Canada [2] Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada [3] Department of Pediatrics, Western University, London, Ontario, Canada [4] Children's Health Research Institute, Western University, London, Ontario, Canada.

Abstract

The blood-brain barrier controls the passage of molecules from the blood into the central nervous system (CNS) and is a major challenge for treatment of neurological diseases. Metachromatic leukodystrophy is a neurodegenerative lysosomal storage disease caused by loss of arylsulfatase A (ARSA) activity. Gene therapy via intraventricular injection of a lentiviral vector is a potential approach to rapidly and permanently deliver therapeutic levels of ARSA to the CNS. We present the distribution of integration sites of a lentiviral vector encoding human ARSA (LV-ARSA) in murine brain choroid plexus and ependymal cells, administered via a single intracranial injection into the CNS. LV-ARSA did not exhibit a strong preference for integration in or near actively transcribed genes, but exhibited a strong preference for integration in or near satellite DNA. We identified several genomic hotspots for LV-ARSA integration and identified a consensus target site sequence characterized by two G-quadruplex-forming motifs flanking the integration site. In addition, our analysis identified several other non-B DNA motifs as new factors that potentially influence lentivirus integration, including human immunodeficiency virus type-1 in human cells. Together, our data demonstrate a clinically favorable integration site profile in the murine brain and identify non-B DNA as a potential new host factor that influences lentiviral integration in murine and human cells.