14. Absence of T-Shaped Structure and Deletions of B and C Hairpins Have Minimal Effects on Essential Functions of AAV Inverted Terminal Repeats
Authors: Hiroyuki Nakai, Xiaolin Wu, Sally Fuess, Theresa Storm, Shawn Burgess, Markus Grompe, Mark A. Kay
Journal: Molecular Therapy (2004)

Recent reports on severe adverse effects induced by retroviral integration into the LMO2 proto-oncogene in humans and the demonstration of preferential AAV serotype 2 (rAAV2) vector integration into genes in our previous study with a limited number of integration sites in mice1, have raised a possible concern about rAAV-mediated insertional mutagenesis. In order to further address this issue, we have expanded our previous study and performed a high-throughput analysis of rAAV2 integration sites isolated from in vivo selected hereditary tyrosinemia type I (HTI) mouse hepatocytes transduced with a human fumaryl acetoacetate hydrolase (FAH)-expressing rAAV2 shuttle vector, AAV-EF1α-hFAH.AOS. Briefly, total liver DNA was isolated from 4 HTI mice that underwent a 7-month in vivo selection of transplanted hepatocytes isolated from the donor HTI mice having received 3.0×1011 vector genomes of AAV-EF1α-hFAH.AOS via the portal vein and undergone an 8-week in vivo selection. The whole proviral rAAV2 vector genome and flanking genomic DNA sequences were isolated as a plasmid from the liver DNA by a plasmid rescue technique as previously described1. All four mice had a different donor HTI mouse, therefore, any integrations found in different mice should be considered as independent integration events. To date, we have characterized 307 independent integration events and found: 1) 191 of 307 (62%) of integrations occurred in genes; 2) there was a strong bias toward integrating into host genomes around transcription start sites, as has been observed in murine leukemia virus integrations (approximately a quarter of the total rAAV2 integrations occurred within ±1 kb from transcription start sites); 3) rAAV integration involved large genomic deletions of over 1 kb in 15% of the cases, suggesting that such large deletions may not be rare events associated with rAAV2 integration. The most striking finding was that among the 307 independent integration events, at least 4 integrations from 3 different mice (1.5 % of total integrations and 2.1 % of the genes targeted by rAAV) were found within a 30-kb region in the mouse ubiquitin C gene, and at least 4 integrations from 4 different mice fell on another sequence stretch of approximately 2.5 kb. Our preliminary analysis by restriction enzyme mapping and sequencing over a thousand base pairs has indicated that the hot spot of 2.5 kb in length likely resides in a proto-oncogene, the Evi-1 gene. It should be noted that murine leukemia found in a retroviral gene marking study was induced by insertional mutagenesis at this locus. Although the oncogenic potential of this gene in the liver is not known, overexpression of this gene can transform not only hematopoietic cells but also other cell types. Thus, the preliminary results in our high-throughput rAAV2 integration site analysis further emphasize the importance of pursuing the study on the elucidation of the mechanisms of rAAV vector integration and its consequences in the host.