1. ¹Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
2. ²Division of Infectious Disease, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
3. ³Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
4. ⁴Department of Family and Preventive Medicine, University of California, San Diego School of Medicine, San Diego, California, USA
5. ⁵VIRxSYS Corporation, Gaithersburg, Maryland, USA

Correspondence: Frederic D. Bushman, Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6076, USA. E-mail: bushman@mail.med.upenn.edu

Received 3 December 2008; Accepted 12 January 2009; Published online 3 March 2009.

Abstract

Lentiviral vector-based gene therapy has been used to target the human immunodeficiency virus (HIV) using an antisense env payload. We have analyzed lentiviral-vector integration sites from three treated individuals. We compared integration sites from the ex vivo vector-transduced CD4+ cell products to sites from cells recovered at several times after infusion. Integration sites were analyzed using 454 pyrosequencing, yielding a total of 7,782 unique integration sites from the ex vivo product and 237 unique sites from cells recovered after infusion. Integrated vector copies in both data sets were found to be strongly enriched within active genes and near epigenetic marks associated with active transcription units. Analysis of integration relative to nucleosome structure on target DNA indicated favoring of integration in outward facing DNA major grooves on the nucleosome surface. There was no indication that growth of transduced cells after infusion resulted in enrichment for integration sites near proto-oncogene 5'-ends or within tumor suppressor genes. Thus, this first look at the longitudinal evolution of cells transduced with a lentiviral vector after infusion of gene modified CD4+ cells provided no evidence for abnormal expansions of cells due to vector-mediated insertional activation of proto-oncogenes.