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Journal of Virology, April 2003, p. 4881-4887, Vol. 77, No. 8
0022-538X/03/$08.00+0 DOI: 10.1128/JVI.77.8.4881-4887.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Packaging of Human Chromosome 19-Specific Adeno-Associated Virus (AAV) Integration Sites in AAV Virions during AAV Wild-Type and Recombinant AAV Vector Production
Daniela Hüser, Stefan Weger, and Regine Heilbronn*
Department of Virology, Institute of Infectious Diseases, Free University of Berlin, 12203 Berlin, Germany
Received 15 August 2002/
Accepted 17 January 2003

ABSTRACT
Adeno-associated virus type 2 (AAV-2) establishes latency by
site-specific integration into a unique locus on human chromosome
19, called AAVS1. During the development of a sensitive real-time
PCR assay for site-specific integration, AAV-AAVS1 junctions
were reproducibly detected in highly purified AAV wild-type
and recombinant AAV vector stocks. A series of controls documented
that the junctions were packaged in AAV capsids and were newly
generated during a single round of AAV production. Cloned junctions
displayed variable AAV sequences fused to AAVS1. These data
suggest that packaged junctions represent footprints of AAV
integration during productive infection. Apparently, AAV latency
established by site-specific integration and the helper virus-dependent,
productive AAV cycle are more closely related than previously
thought.

INTRODUCTION
Adeno-associated virus (AAV) has evolved a biphasic life cycle
to ensure persistence in its primate host. It needs an unrelated
helper virus, adenovirus (Ad), or herpesvirus for productive
infection (
16). In the absence of a helper, AAV establishes
latency by preferential integration into a specific site on
human chromosome 19 (chr.19), 19q13.3q-ter, called AAVS1 (
10).
AAV type 2 (AAV-2) contains a linear single-stranded DNA genome
of 4.7 kb that covers the genes
rep and
cap, flanked by 145-bp
inverted terminal repeats (ITRs) (
27) that serve as origins
of replication and as
cis elements for chromosomal integration.
The AAV regulatory proteins Rep78 and/or Rep68 (Rep78/68) are
necessary for AAV DNA replication both in vivo and in vitro.
Rep78/68 binds to the Rep-binding site (RBS) on the AAV-ITR
(
26) and nicks and unwinds the ITR at the terminal resolution
site (
trs) (
7). Rep78/68 also mediates site-specific AAV integration
at AAVS1 on chr.19 that comprises DNA sequences homologous to
the RBS and the
trs of the AAV-ITR (
9,
23). In vitro studies
showed ternary complex formation of Rep68 with the AAV-ITR and
AAVS1 (
31) and Rep68-mediated initiation of DNA replication
starting from an origin sequence comprised of AAVS1 (
29). A
33-bp sequence spanning the chr.19 RBS, a spacer sequence, and
a
trs homology element are sufficient to mediate site-specific
AAV integration in vivo (
12,
14). chr.19 integration sites have
been analyzed either in selected cell clones or in 293 cells
carrying AAVS1 on an Epstein-Barr virus-based episome (
1,
2,
9,
17,
20,
23,
28,
32). To analyze integration into the authentic
chr.19 preintegration locus early after AAV-2 infection, we
have recently developed a sensitive and quantitative real-time
PCR assay for AAV-ITR/AAVS1 junctions. Within 4 days postinfection
(p.i.) site-specific integration frequency reached 10 to 20%
of unselected HeLa cells. Further analysis showed that at least
1 in 1,000 infectious AAV-2 integrated site specifically (
5,
6).

MATERIALS AND METHODS
Plasmids.
The following plasmids have been described: pTAV2-0 (
4), pDG
(
3), pAAVS1-TR (
6), and p
sub201 (
22). Plasmid psub
gfpneo was
generated by inserting the
gfpneo cassette derived from pTR-UF5
(
36) between the 190-bp,
XbaI-flanked AAV-ITRs of p
sub201.
Preparation of highly purified AAV wild-type stocks.
Conventional AAV-2 stocks were produced and titrated as described previously (6). Cells were infected at a multiplicity of infection (MOI) of 500 unless otherwise stated. Highly purified AAV stocks were generated on pTAV2-0 transfected and Ad type 2 (Ad2)-infected HeLa cells. The corresponding AAV-negative control preparations were generated in parallel without pTAV2-0 transfection. Virus purification was done according to a protocol published previously (35). In brief, phosphate-buffered saline (PBS)-washed cells were pelleted by low-speed centrifugation, resuspended in PBS, and adjusted to 0.5% deoxycholic acid. Unencapsidated nucleic acids were degraded by treatment with 5,000 U of benzonase (Purity Grade II; Merck) for 90 min at 37°C. Cell debris was pelleted at 8,100 x g for 30 min. Supernatants were frozen, thawed, centrifuged again, and then purified on iodixanol discontinuous density gradients. The 40% fraction containing AAV was aspirated and subjected to heparin affinity chromatography. Eluted virions were dialyzed against PBS and stored at -80°C.
Preparation of highly purified rAAV stocks.
Recombinant AAV-2 (rAAV-2) stocks were prepared on 293 cells by cotransfection of pDG and psubgfpneo as described by Huser et al. (6). Highly purified rAAV was prepared according to the protocol described above for the AAV wild type.
Quantitative, real-time PCR for the determination of site-specific integration.
Targeted integration of AAV-2 into AAVS1 was detected by real-time PCR of virus-cell junctions and calculated with the aid of known concentrations of a standard plasmid, as described previously (6). For calculations of AAV-ITR/chr.19 junction copy numbers per cell, a DNA content of 10 pg per cell was assumed, reflecting the hypertriploid (3n+) karyotype of HeLa cells (13).
Quantitative, real-time PCR for the determination of virion genome copies.
Genome copy numbers of AAV-2 wild-type or rAAV vector stocks were quantified by by real-time PCR as follows. Aliquots of highly purified (benzonase-treated) virion stocks (see above) were digested with proteinase K, extracted with phenol, precipitated, and resuspended in Tris-EDTA. DNAs were purified by adsorption chromatography on QIAquick spin columns (Qiagen, Hilden, Germany). Real-time LightCycler PCR was performed with aliquots diluted to a final volume of 20 µl. The reaction mixture included polymerase (LightCycler Kit-Fast Start DNA Master SYBR Green I; Roche) and 5 mM MgCl2. For the determination of AAV-2 wild-type genomes, a 500 nM concentration of primer PAAV-F1 (GCCAACTCCATCACTAGGGG; AAV-2 nucleotides 121 to 140) and a 500 nM concentration of primer PAAV-W1 (CCCGCTTCAAAATGGAGACC; AAV-2 nucleotides 299 to 280) were used. For the determination of rAAV-gfp, a primer pair specific for the cytomegalovirus promoter, PAAV-F3 (TGGGCGTGGATAGCGGTTTG) and PAAV-B3 (AACAGCGTGGATGGCGTCTC), were used. Amplification was done at 95°C for 10 min to activate the polymerase, followed by 40 cycles at 95°C for 0 s, 60°C for 4 s, and 72°C for 15 s.
Detection of virus-cell junctions in purified AAV preparations.
Samples of the highly purified AAV stock (1 ml) or of the purified negative-control preparation (1 ml) spiked with 4 x 107 copies of pAAVS1-TR were digested for 30 min at 37°C with 250 U of benzonase as indicated above. Controls without benzonase were run in parallel. Samples were pelleted by using the S55-S rotor and the RC-M120 GX ultracentrifuge (Sorvall) at 120,000 x g and 4°C for 2 h. Each pellet was resuspended in 2 ml of PBS, centrifuged again, and resuspended in 300 µl of Tris-EDTA. Samples were adjusted to 1% sodium lauryl sarcosinate, digested with proteinase K for 2 h at 56°C, and then extracted with phenol-chloroform. DNA samples were precipitated with ethanol, purified with the QIAquick PCR purification kit (Qiagen, Hilden, Germany), and eluted with 30 µl of Tris-Cl. Then, 5-µl aliquots were used for the determination of junction copy numbers by real-time PCR as described previously (6).
Analysis of PCR products.
Aliquots of the PCR products were cloned into pCR4-TOPO (Invitrogen) and subjected to DNA sequencing as described previously (6).

RESULTS
Detection of AAV-ITR/AAVS1 junctions in highly purified AAV preparations.
The recently established real-time PCR assay for site-specific
AAV-2 integration (Fig.
1) regularly detects targeted integration
by 8 h p.i. (
6). Repeated analyses of earlier time points led
to the consistent finding that in AAV-2-infected cells (MOI,
500) harvested immediately after the 45-min adsorption period,
low but specific PCR signals of AAV-ITR/AAVS1 junctions were
detected, whereas mock-infected parallel cultures were negative.
To exclude the possibility that the PCR signals resulted from
fragmented genomic DNA possibly contaminating AAV freeze-thaw
stocks, AAV stocks were purified to the high purification grade
developed for rAAV gene therapy vectors as outlined in Materials
and Methods (
35). As seen in Table
1 no (0) junctions were detected
in 1 µg of uninfected HeLa cell DNA. AAV-infected HeLa
cell DNA extracted immediately after removal of the virus (0
h p.i.) gave rise to 173 junction copies that increased to 2,150
junction copies at 72 h p.i. The data are similar to the results
obtained with conventional AAV preparations. Analysis of the
highly purified AAV preparation alone yielded 124 junction copies
per 2
x 10
8 virion genomes, whereas the controls remained negative
(Table
1). Thus, highly purified AAV-2 preparations contain
low levels of AAV-ITR/AAVS1 junction DNAs that survive a rigorous
virus purification scheme. Efficient protection of the AAV-ITR/AAVS1
junctions by AAV capsids appears to be the most likely explanation
for this finding.
To verify this assumption, the efficiency of the benzonase digestion
step during AAV preparation had to be evaluated, ideally by
the demonstration of efficient enzymatic degradation of an excess
of added junction DNA. To address this point, a highly purified
AAV-2 preparation and an AAV-negative control preparation were
generated and purified step by step in parallel, as outlined
in Materials and Methods. No AAV-ITR/AAVS1 junction copies were
detected in the AAV-negative control preparation, whereas the
purified AAV-2 preparation (AAV titer, 5
x 10
8 infectious units/ml)
was positive. This finding excluded DNA or virus contamination
during the preparation procedure. To demonstrate that an excess
of added unprotected junction DNA is efficiently degraded during
benzonase digestion, the AAV-negative control preparation was
spiked with the plasmid pAAVS1-TR that covers a cloned AAV-ITR/AAVS1
junction (Fig.
2). After benzonase digestion (250 U for 30 min)
real-time PCR detected 10
3 junction copies/ml, whereas the undigested
sample had 6
x 10
6 junction copies/ml. The efficient, >5,000-fold
reduction of unprotected DNA was in contrast to an only 2-fold
reduction of junction copy number in the highly purified AAV
preparation (Fig.
2). This minor reduction may result from junctions
packaged in leaky or otherwise defective capsids. Benzonase
accessibility of one primer-binding site is already sufficient
to render the template undetectable by the PCR assay. In summary,
the obvious explanation for the benzonase resistance of AAV-ITR/AAVS1
junctions in highly purified AAV preparations is efficient protection
by packaging in AAV capsids.
Additional AAV wild-type preparations were produced on PCR-tested
HeLa or 293 cells by (i) coinfection of AAV-2 and Ad2, (ii)
transfection of pTAV2-0 followed by Ad2 infection, or (iii)
cotransfection of pTAV2-0 and pDG, a plasmid covering the Ad
helper genes. In seven of nine virus preparations packaged AAV-ITR/AAVS1
junctions were detected (Table
1 displays the quantification
for three independent preparations). Junction copy numbers per
10
9 virion genomes were highly variable, possibly reflecting
differences in the infection kinetics. Furthermore, rAAV vector
stocks were analyzed that were prepared as described in Materials
and Methods. Three out of three independently generated rAAV
preparations contained junctions detected by real-time PCR (Table
1). The ratios of packaged junctions compared to virion genome
titers were similar to those of AAV-2 wild-type preparations.
The results, taken together, show that both AAV wild-type and
rAAV vector stocks regularly contain packaged AAV-ITR/AAVS1
junctions at variable copy numbers. Since virus stocks were
produced by plasmid transfections with tested reagents, packaged
junctions were newly generated during a single AAV production
round.
DNA sequence analysis of packaged junctions.
To analyze the packaged DNA sequences, PCR products were cloned into pCR4-TOPO as described previously (6). DNAs of randomly selected clones were subjected to DNA sequence analysis (Fig. 3). AAV-ITR sequences fused to variable integration sites of AAVS1 were found. Although the PCR assay detects only the right-hand AAV-ITR (6), AAV p5 promoter sequences were detected in one clone and parts of AAV cap and the polyadenylation signal in two others. These findings point to extensive rearrangements of the entire AAV genome. Although the cloning procedure and sequence analysis were identical to those in the study of AAV site-specific integration at AAVS1 on chr.19, the DNA structures of the packaged junctions were more rearranged than the ones derived from latently infected HeLa cells after AAV infection (5, 6). We therefore favor the interpretation that the detected sequence rearrangements indicate that the integration, rescue, replication, and/or recombination events took place before packaging rather than during PCR amplification and subcloning of the junctions. Since we were able to reisolate junctions with identical rearrangements from the same AAV preparation, this notion is further underlined. Either of the rearranged sequences in Fig. 3 can be explained as an intermediate of AAV integration into AAVS1. None of the clones analyzed contained unrelated DNA sequences as described recently for DNAs cloned from rAAV-transduced cells (15).

DISCUSSION
The current concept of site-specific AAV integration.
Targeted AAV integration requires three essential components:
Rep78/68 in
trans and both the AAV-ITR and the AAVS1 of chr.19
in
cis, which together form a ternary complex (
31). A recent
report suggests that that the AAV p5 promoter elements add to
the effect (
19). Typical AAV DNA replication intermediates have
a head-to-head or tail-to-tail genome conformation (
16). This
is also true for AAV wild-type genomes (
8). Other studies have
demonstrated integrated AAV genomes preferentially displaying
head-to-tail concatemeric structures (
1,
32). These findings
led Linden et al. (
12) to propose a circular AAV intermediate
as a template for limited rolling circle replication, thereby
explaining the generation of head-to-tail concatemers. After
ternary complex formation of Rep78/68, the AAV RBS and the chr.19
RBS Rep-mediated nicking of the chr.19
trs is assumed to initiate
targeting. Rep is then assumed to attach to the free 5' end
of the chr.19 single-stranded nick, in analogy to the single-stranded
AAV genome in which covalent Rep binding to the free 5' end
has been described (
25). The free 3' end of the nicked chr.19
sequence may serve as primer for the polymerase that replicates
along the gap. To explain AAV integration, Rep is postulated
to switch templates between the circular AAV genome and the
chr.19 preintegration site (
11), a critical component of the
model that remains to be proven. Young and Samulski (
34) recently
showed that in cell culture nicking of the AAV-ITR,
trs was
not required for targeted integration and that overexpression
of Rep alone was sufficient to induce rearrangements at AAVS1
(
33). Based on these findings, Rep78/68 is assumed to initiate
replication on chr.19 by interaction with RBS and
trs. The AAV
genome will be attracted to enter the Rep-AAVS1 complex. Integration
of the AAV genome is assumed to rely on cellular recombination
mechanisms also active in gene amplification (
34). This assumption
is backed by previous in vitro studies that not only demonstrated
ternary complex formation of Rep with the AAV-ITR and AAVS1
(
31) but also demonstrated Rep-dependent initiation of DNA synthesis
starting off a DNA sequence within AAVS1 that serves as the
origin sequence (
29). Thus, the described ability of Rep not
only to site specifically nick DNA but also to ligate free single-stranded
DNAs (
24) in conjunction with ternary complex formation could
explain our finding of covalently attached AAV-ITRs and AAVS1
of chr.19. Irrespective of the mode of AAV integration, free
AAV-ITR/AAVS1 junction sequences can be viewed as episomal integration
intermediates that, due to the presence of packaging signals
within the AAV-ITR, can be encapsidated in AAV virions. The
recent description of chr.19 containing AAV particles rescued
from a latently infected cell clone established by a
trs-defective
AAV genome (
34) further supports the notion of AAV/AAVS1 junctions
being aberrant replication intermediates. Thus far, we could
only analyze the DNA sequences between the defined primers on
chr.19 and on the AAV-ITR. At present, we have no experimental
data demonstrating whether other covalently attached genomic
DNAs can be packaged. Due to the low percentage of packaged
junctions in the virion stocks, cloning of complete packaged
genomes and detection of "unknown" DNAs, e.g., with some combinations
of degenerate primers, is beyond the scope of this study.
Potential mechanisms of AAV-ITR/AAVS1 generation during productive AAV infection.
The generally accepted concept of the bipartite AAV life cycle is represented in Fig. 4. Targeted AAV integration leads to the establishment of latency in AAV-infected cells. The helper virus-dependent, productive AAV cycle is viewed as separate in the sense that an unrelated helper virus, typically Ad or herpesvirus, induces high-level AAV replication of the episomal AAV template (16). In the case of a latently infected cell line, Ad will rescue AAV from the integrated state. It is unclear whether this involves excision of the AAV copy, followed by replication of the AAV episome, or whether DNA replication uses the integrated AAV copy as a template.
The data presented here point to a closer relationship between
AAV latency and productive AAV replication as outlined in Fig.
4. Packaged AAV-ITR/AAVS1 junctions can be viewed as aberrant
integration intermediates of productive infection. AAV appears
to have an inherent potential to integrate at AAVS1 irrespective
of the presence of a helper virus. We assume that after AAV
infection the p5 promoter is able to express enough Rep to initiate
site-specific integration before the cascade of Ad helper functions
has been fully expressed and the AAV genome starts replication.
Ad-induced Rep78 expression and AAV DNA replication were detected
at 10 to 12 h p.i. (
21). In our study of Rep expression in the
absence of a helper virus, we were able to detect Rep78 on Western
blots as early as 8 h p.i. In addition, by using sensitive immunofluorescence
protocols, an occasional Rep-positive cell could be detected
as early as 5 h p.i. (R. Heilbronn et al., unpublished data).
In latently infected cell clones under conditions of autoregulated
Rep expression, a few thousand Rep molecules per cell have been
measured (
33). In addition, a low level of targeted AAV integration
has been detected by 8 h p.i. (
6). Thus, limited targeted integration
may occur very early after AAV infection, before the onset of
Ad-stimulated AAV replication. A recent report describing site-specific
integration of an AAV-ITR-containing Ad vector expressing Rep78
(
18) and our preliminary data on limited AAV integration in
the presence of replicating wild-type Ad (D. Hüser and
R. Heilbronn, unpublished data) support this notion. However,
upon AAV replication, the increasing copy number of the AAV-ITR
is assumed to compete for binding with the chr.19 RBS, which
has been shown to bind to Rep in vitro with reduced affinity
(
33). In addition, the nuclear compartmentalization of the AAV
genome and of Rep in Ad replication centers at later time points
postinfection (
30) presumedly limits chr.19 targeting. Based
on these findings, we assume that chr.19-specific AAV targeting
is limited to the first few hours after AAV and Ad coinfection.
In addition, due to cell lysis AAV integration in the presence
of Ad will remain without consequences for the infected cell.
In summary, the packaged AAV-ITR/AAVS1 junctions detected in AAV virion stocks can be viewed as footprints of integration events during productive AAV replication. Interestingly, packaged junctions were detected irrespective of the AAV production method. Ad2 infection, as well as transfection of the defined Ad5 helper genes, into 293 cells led to formation of these junctions. Obviously, the latent and the productive AAV replication cycles are more closely related than previously thought.
Implications for gene therapy and rAAV production protocols.
Packaged AAV-ITR/AAVS1 junctions were not only found in AAV wild-type preparations but rAAV vector stocks were also found to harbor comparable amounts of packaged junctions. Typical inoculation doses in mice and rats range between 1011 and 1013 genome equivalents. With this dose it is expected that 104 to 106 packaged junctions will be transferred. Due to restrictions in primer design, we only analyzed vectors based on psub201 (22). It will be interesting to see how optimized rAAV vectors such as the pUF2 series (36) and the rAAVs derived from them will perform. We have to envision that many, if not most, rAAV preparations harbor low and as-yet-undetected levels of packaged junctions. This point has to be reevaluated critically. However, to our knowledge unwanted side effects attributable to the presence of ITR/chr.19 junctions have not been documented so far.

ACKNOWLEDGMENTS
We thank M. Gere for skilled technical assistance, R. Joncker
for secretarial support, and M. Boshart for helpful discussions
and critical reading of the manuscript. We also thank J. Kleinschmidt,
N. Muzyczka, and R. J. Samulski for plasmids.
This work was supported by the Deutsche Forschungsgemeinschaft (SFB 506).

FOOTNOTES
* Corresponding author. Mailing address: Institut für Infektionsmedizin, Abteilung Virologie, Universitätsklinikum Benjamin Franklin, Freie Universität Berlin, Hindenburgdamm 27, 12203 Berlin, Germany. Phone: 030-8445-3696. Fax: 030-8445-4485. E-mail:
regine.heilbronn{at}ukbf.fu-berlin.de.


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Journal of Virology, April 2003, p. 4881-4887, Vol. 77, No. 8
0022-538X/03/$08.00+0 DOI: 10.1128/JVI.77.8.4881-4887.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
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