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Journal of Virology, September 2006, p. 8820-8823, Vol. 80, No. 17
0022-538X/06/$08.00+0 doi:10.1128/JVI.00719-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Integration Site Choice of a Feline Immunodeficiency Virus Vector
Yubin Kang,1,#
Christopher J. Moressi,2,#
Todd E. Scheetz,3,4,5
Litao Xie,1
Diane Thi Tran,1
Thomas L. Casavant,2,4,5
Prashanth Ak,6
Craig J. Benham,6
Beverly L. Davidson,7 and
Paul B. McCray Jr.1*
Program in Gene Therapy, Department of Pediatrics,1
Department of Electrical and Computer Engineering,2
Department of Ophthalmology,3
Department of Biomedical Engineering,4
Center for Bioinformatics and Computational Biology,5
Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242,7
Genome Center, University of California, Davis, California 95616-88166
Received 9 April 2006/
Accepted 30 May 2006

ABSTRACT
We mapped 226 unique integration sites in human hepatoma cells
following gene transfer with a feline immunodeficiency virus
(FIV)-based lentivirus vector. FIV integrated across the entire
length of the transcriptional units. Microarray data indicated
that FIV integration favored actively transcribed genes. Approximately
21% of FIV integrations within transcriptional units occurred
in genes regulated by the LEDGF/p75 transcriptional coactivator.
DNA in regions of FIV insertion sites exhibited a "bendable"
structure and a pattern of duplex destabilization favoring strand
separation. FIV integration preferences are more similar to
those of primate lentiviruses and distinct from those of Moloney
murine leukemia virus, avian sarcoma leukosis virus, and foamy
virus.

TEXT
Retroviral gene transfer holds promise as a treatment for genetic
diseases. However, integration carries a risk of insertional
mutagenesis, as occurred in a trial for X-linked severe combined
immunodeficiency (
8). This result focused this field towards
understanding integration site preferences for all classes of
vectors under development. Sequencing of the human genome facilitated
large-scale studies of integration patterns for human immunodeficiency
virus type 1 (HIV-1) (
17,
19), simian immunodeficiency virus
(SIV) (
6), murine leukemia virus (MLV) (
26), avian sarcoma leukosis
virus (ASLV) (
17), and foamy virus (FV) (
23). The differences
in integration preferences between vectors of primate lentiviruses,
MLV, ASLV, and FV suggest that it is inadvisable to assume that
all vectors integrate with the same pattern.
Nonprimate lentiviral vectors derived from FIV were developed as an alternative to HIV vectors (18) and transduce a broad range of cells and tissues (3, 7, 10-13, 15, 16, 20, 21, 25). As a model for integration following hepatocyte transduction (12, 13, 21), we cloned, sequenced, and mapped FIV vector integration sites in human hepatoma cells. Vesicular stomatitis virus G protein-pseudotyped FIV encoding enhanced green fluorescence protein (eGFP) driven by a cytomegalovirus promoter/enhancer was produced as described previously (11, 25). HepG2 cells (HB-8065; ATCC, Rockville, MD) were transduced at a multiplicity of infection of
1. We assayed eGFP expression by using a fluorescence-activated cell sorter at various intervals posttransduction. Following an initial decline, the percentage of eGFP-expressing cells remained stable for the interval between 16 days and 1 month posttransduction (
5%). We isolated genomic DNA from nonselected cells 16 days following transduction and cloned FIV integration sites using adaptor-ligated PCR (GenomeWalker kit; BD Biosciences, Palo Alto, CA) as reported previously (19, 26).
We mapped 226 distinct FIV integration events to all chromosomes except chromosome 21 (Fig. 1) (see http://genome.uiowa.edu/SupplementaryData/Kang_JVI2006.html). We asked whether integration favored transcriptional units, defining an integration site as residing within a gene if it occurred between the transcriptional start and stop sites of one of the 23,874 human Reference Sequence (RefSeq) genes (May 2004 UCSC human reference sequence; NCBI Build 35). Of 226 integration sites, 179 (79%) occurred in genes. This percentage increased to 87% if all human mRNAs in GenBank were used. Published retrovirus integration data were downloaded and processed using our analysis pipeline to provide comparable data sets. The frequency of FIV integration in genes was similar to the frequencies reported for HIV and SIV (71% and 76%, respectively) (6, 19) and higher than those for MLV (45%) (26), foamy virus (31%) (23), and random integration (32.2%) (Table 1) (26). Of 179 integrations in RefSeq genes, 172 were in introns and only 7 were in exons or open reading frames (Table 1) (see http://genome.uiowa.edu/SupplementaryData/Kang_JVI2006.html). We identified a single integration hot spot with two events on chromosome 4 at position 123.54 Mb and only one integration event on gene-rich chromosome 19, which had significant affinity for HIV integration (19). A karyotype of the HepG2 cell line revealed that chromosome 19 had a normal size and banding pattern; however, one copy of chromosome 21 was missing (data not shown). FIV integration occurred along the entire length of RefSeq transcripts, and transcriptional start regions were not favored targets (Fig. 2).
The HepG2 cell transcriptional profile was analyzed using published
Affymetrix data sets (
22) (see
http://genome.uiowa.edu/SupplementaryData/Kang_JVI2006.html).
Of the 179 RefSeq genes targeted for integration, 163 were represented
in the data set. The median expression value for all GeneChip
array probes was 41.4, and the median expression value for the
best probe in a RefSeq gene was 57.1. In contrast, the median
expression value for the best probe in a RefSeq gene with an
integration event was 124. For the 163 genes represented on
the array with integration events, there was an approximately
twofold increase in expression compared to that of the set of
all RefSeqs and an approximately threefold increase in expression
compared to that of all probes. Expression was also analyzed
using the expressed sequence tag collection in the human UniGene
set to determine which genes are transcribed in liver cells.
Of the genes that could be correlated to NCBI's UniGene, approximately
95% (170/179) exhibited some level of expression in liver cells.
These findings support the notion that FIV integrates into transcriptionally
active regions of chromatin.
Recent studies indicate that LEDGF/p75 in host cells physically interacts with the integrase protein in HIV and FIV preintegration complexes, directing the complex to specific regions of chromosomal DNA and acting as a tethering protein (4, 14). Interestingly, HIV integration sites correlated with LEDGF/p75-regulated genes, and RNA interference knockdown of LEDGF/p75 expression changed the HIV integration pattern away from LEDGF/p75-regulated genes (5). This approach identified 1,849 LEDGF/p75-regulated Entrez genes on the Affymetrix U133 Plus2 chip (8.7% of the 21,311 Entrez genes represented on the U133 Plus2 chip). Using these same microarray data sets (5), we asked whether FIV integration sites shared a similar preference for LEDGF/p75-regulated genes. As with HIV integrations, the FIV vector integrated at a significantly higher frequency within genes regulated by LEDGF/p75 than within genes not LEDGF/p75 regulated. Of 179 FIV integrations, 38 (21.2%) occurred in LEDGF/p75-regulated genes (P <107 versus random integrations within genes). Of interest, the fraction of FIV integrants that mapped within LEDGF/p75-regulated genes was significantly higher (P < 0.05) than that observed for HIV integrants (
14%). This suggests that FIV may have a greater tendency than HIV to integrate in LEDGF/p75-regulated genes. These data support the idea that LEDGF/p75 is an important modulator of FIV and HIV lentiviral target site selection.
The specific nucleotide composition was analyzed for sequence-specific motifs or base preferences within 20 bases on either side of integration sites (9, 27) (see http://genome.uiowa.edu/SupplementaryData/Kang_JVI2006.html). This analysis identified marked divergence from the expected frequencies of specific bases in the regions. Most interesting was an increase in the prevalence of G's at the sites of integration (Fig. 3). At several positions (from 3 to +1 and from +5 to +8) the deviations from predicted base preferences were very significant (P <107). The overall consensus sequences at these positions are RWRR and YKRY (using standard International Union of Biochemistry codes). While FIV nucleotide preferences shared a symmetry pattern similar to those reported for HIV, SIV, ASLV, and MLV (9, 27), the FIV preferences differed in primary sequence from HIV, MLV, SIV, and ASLV (9, 27). These results suggest that each retrovirus may have distinct, but not absolute, base preferences at integration sites.
We examined 20-base flanking regions on either side of the FIV
insertion sites for physical properties, including B-DNA twist,
A-philicity, DNA bending, and protein-induced deformability
by using previously reported methods (
24). Three sets of randomly
selected control sequences were similarly analyzed and contrasted
with FIV integration regions. No significant differences were
observed in the physical properties of B-DNA twist, A-philicity,
or protein-induced deformability. However, predicted DNA bendability
adjacent to FIV insertion sites deviated significantly from
the DNA bendability of the controls (Fig.
4A, position 18).
In addition, deviations were observed at 6-bp intervals on either
side of the integration site, specifically at positions 12,
18, and 24. A Monte Carlo simulation was performed to assess
the significance of the observed differences in bendability.
The threshold that only 1% of observations are expected to exceed
(
P < 0.01) is indicated in Fig.
4A. Bendability values at
positions 18 and 24 both significantly exceed that threshold,
and bendability at position 12 nearly exceeds that threshold.
DNA bending models the ability of DNA to modify the depth and
width of the major and minor grooves and may correlate with
accessibility for binding by proteins or protein/DNA complexes.
An additional analysis of physical properties was performed
to compare the minimum free energies needed for strand separation
at integration sites to those at control sites (
1,
2) (see
http://genome.uiowa.edu/SupplementaryData/Kang_JVI2006.html).
This analysis revealed that a significantly destabilized region
(
P values in the range of 10
3 to 10
4) occurs roughly
within 150 bp on either side of the insertion points, and a
second destabilized region occurs 600 to 800 bp toward the 5'
end of the insertion site (Fig.
4B). The two median distributions
differ by 1.4 kcal/mol, which makes strand separation at the
insertion sites 9.5 times more frequent at equilibrium. The
probability of this pattern arising by chance is 4.57313
x 10
4 (Kolmogorov-Smirnoff test). These results suggest that FIV integration
sites have distinct physical properties.
The current study provides novel insights into FIV integration
site preferences. Overall, FIV integration preferences were
similar to those reported for HIV (
19) and SIV (
6) and distinct
from those reported for MLV, ASLV (
17,
26), and FV (
23). We
speculate that the primary DNA sequences and physical properties
at FIV target sites provide accessible regions for specific
protein-protein and protein-DNA interactions that favor integration.

ACKNOWLEDGMENTS
We thank Patrick L. Sinn for valuable discussion. We thank Dan
Voytas for helpful discussions and for providing software for
analysis of physical properties of genomic DNA. We thank Mirosalva
Kaloper for technical help with computations. We thank Shivanand
Patil and the UI Chromosome lab for karyotyping the HepG2 cell
line.
This work was supported by the NIH (grants HL-75363, HL-79023, and HL-51670 to P.B.M.; grant GM-68903 to C.J.B.), the National Hemophilia Foundation (Y.K.), the Hemophilia Association of New York (Y.K.), a pilot and feasibility grant from the Center for Gene Therapy for Cystic Fibrosis (Y.K.), a career development award from Research to Prevent Blindness (T.E.S.), and the National Science Foundation (grant DBI-0416764 to C.J.B.).

FOOTNOTES
* Corresponding author. Mailing address: Department of Pediatrics, 240G EMRB, University of Iowa College of Medicine, Iowa City, IA 52242. Phone: (319) 335-6844. Fax: (319) 335-6925. E-mail:
paul-mccray{at}uiowa.edu.

# These authors contributed equally to this work. 

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Journal of Virology, September 2006, p. 8820-8823, Vol. 80, No. 17
0022-538X/06/$08.00+0 doi:10.1128/JVI.00719-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
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