Title of Invention

COMPOSITIONS AND METHODS TO PREVENT AAV VECTOR AGGREGATION

Abstract The invention discloses a method of preventing aggregation of adeno-associated virions (AAV) virions in a purified preparation of AAV virions, comprising: a) providing a lysate comprising rAAV virions; b) purifying rAAV virions from the lysate using ultracentrifugation and/or chromatography, wherein said virions are purified; and c) adding one or more excipients comprising multivalent ions to the preparation of virions to achieve an ionic strength of at least about 200 mM. The invention is also for a composition for storage of purified adeno-associated virus (AAV) comprising purified AAV particles, a pH buffer and excipients comprising salt(s) of multivalent ions, wherein the said composition has ionic strength of greater than 200 mM.
Full Text FIELD OF THE INVENTION
The present invention relates to compositions and methods of preparing and storing
AAV virions that prevent aggregation.
BACKGROUND
Recombinant adeno-associated virus (rAAV) is a promising vector for human gene
transfer. Grimm, D., and Kleinschmidt, J. A. (1999) Hum Gene Ther. 10: 2445-2450; High,
K. A. (2001) Ann. N. Y. Acad. Sci. 953: 64-67; Pfeifer, A., and Verma, I. M. (2001) Ann. Rev.
Genomics Hum. Genet. 2: 177-211. AAV is a member of the Dependovirus genus of the
parvoviruses. AAV serotype 2 (AAV2) is composed of a single-strand DNA molecule of
4680 nucleotides encoding replication {rep) and encapsidation (cap) genes flanked by
inverted terminal repeat (ITR) sequences. Berns, K. I. (1996) in Fields Virology (B. N.
Fields et. al. Eds.), pp. 2173-2197. Lippincott-Raven Publishers, Philadelphia. The genome
is packaged by three capsid proteins (VP1, VP2 and VP3), which are amino-terminal variants
of the cap gene product. The resulting icosahedral virus particle has a diameter of ~26 nm.
A high resolution crystal structure of AAV2 has been reported. Xie, Q. et al. (2002) Proc. Natl.
Acad. Sci. U.S.A. 99: 10405-10410.
The solubility of purified AAV2 virus particles is limited, and aggregation of AAV2
particles has been described as a problem. Croyle, M. A. et al. (2001) Gene Therapy 8: 1281-
1290; Huang, J. et al. (2000) Mol. Therapy 1: S286; Wright, J. F. et al. (2003) Curr. Opin.
Drug Disc. Dev. 6: 174-178; Xie, Q. et al. (2004) J. Virol. Methods 122: 17-27. In
commonly used buffered-saline solutions, significant aggregation occurs at concentrations of

1013 particles/mL, and aggregation increases at higher concentrations. Huang and co-workers
reported that AAV vectors undergo concentration-dependent aggregation. Huang, J. et al.
(2000) Mol. Therapy 1: S286. Xie and coworkers (Xie, Q. et al. (2004) J. Virol. Methods
122: 17-27) similarly reported that at concentrations exceeding 0.1mg/mL, AAV2 vectors
require elevated concentrations of salt to prevent aggregation. Aggregation of AAV2 vectors
occurs at particle concentrations exceeding 1013 particles/mL in commonly used neutral-
buffered solutions such as phosphate- and Tris-buffered saline. This corresponds to a protein
concentration of~0.06 mg/mL, and emphasizes the low solubility of AAV2 under these
conditions. The effective vector concentration limit may be even lower for vectors purified
using column chromatography techniques because excess empty capsids are co-purified and
contribute to particle concentration.
Particle aggregation is a significant and not fully resolved issue for adenovirus vectors
as well. Stability of a recently established adenovirus reference material (ARM) was recently
reported. Adadevoh, K. et al. (2002) BioProcessing 1(2): 62-69. Aggregation of the
reference material, formulated in 20mM Tris, 25 mM NaCl, and 2.5% glycerol at pH 8.0, was
assessed by dynamic light scattering, photon correlation spectroscopy and visual appearance.
A variable level of vector aggregation following either freeze-thaw cycling or non-frozen
storage was observed, resulting in restrictive protocols for the use of the ARM.
Aggregation can lead to losses during purification and inconsistencies in testing of
purified vector preparations. The in vivo administration of AAV2 vectors to certain sites,
such as the central nervous system, may require small volumes of highly concentrated vector,
and the maximum achievable dose may be limited by low vector solubility.
Vector aggregation is also likely to influence biodistribution following in vivo
administration, and cause adverse immune responses to vectors following their
administration. As has been reported for proteins (Braun, A. et al. (1997) Pharm. Res. 14:

1472-1478), aggregation of vector may increase immunogenicity by targeting the vector to
antigen presenting cells, and inducing enhanced immune responses to the capsid proteins and
transgene product. The reports of immune responses to AAV vectors in pre-clinical
(Chenuaud, P. et al. (2004) Blood 103: 3303-3304; Flotte, T. R. (2004) Human Gene Ther.
15: 716-717; Gao, G. et al. (2004) Blood 103: 3300-3302) and clinical (High, K. A. et al.
(2004) Blood 104: 121a) studies illustrate the need to address all factors that may contribute
to vector immunogenicity.
Testing protocols to characterize purified vectors are also likely to be affected by
vector aggregation. Determination of the infectivity titer of vector was reported to be highly
sensitive to vector aggregation. Zhen, Z. et al. (2004) Human Gene Ther. 15: 709-715. An
important concern is that vector aggregates may have deleterious consequences following
their in vivo administration because their transduction efficiency, biodistribution and
immunogenicity may differ from monomelic particles. For example, intravascular delivery
of AAV vectors to hepatocytes requires that the vectors pass through the fenestrated
endothelial cell lining of hepatic sinusoids. These fenestrations have a radius ranging from
50 to 150 nm (Meijer, K. D. F., and Molema, G. (1995) Sent. Liver Dis. 15: 206) that is
predicted to allow the passage of monomelic AAV vectors (diameter ~26 nm), but prevent
the passage of larger vector aggregates. In biodistribution studies in mice, aggregated AAV2
vectors labeled with the fluorescent molecule Cy3 were sequestered in liver macrophages
following vascular delivery. Huang, J. et al. (2000) Mol. Therapy 1: S286.
Formulation development for virus-based gene transfer vectors is a relatively recent
area of investigation, and only a few studies have been reported describing systematic efforts
to optimize AAV vector formulation and stability. Croyle, M. A. et al. (2001) Gene Therapy
8: 1281-1290; Wright, J. F. et al. (2003) Curr. Opin. Drug Disc. Dev. 6: 174-178; Xie, Q. et
al. (2004)J. Virol. Methods 122: 17-27. Defining formulations compatible with pre-clinical

and clinical applications that minimize changes in vector preparations is an important
requirement to achieve consistently high vector safety and functional characteristics. As is
well established for protein therapeutics (Chen, B. et al. (1994) J. Pharm. Sci. 83: 1657-1661;
Shire, S. J. et al. (2004) J. Pharm. Sci. 93:1390-1402; Wang, W. (1999) Int. J. Pharm. 185:
129-188; Won, C. M. et al. (1998) Int. J. Pharm. 167: 25-36), an important aspect of vector -
stability is solubility during preparation and storage, and vector aggregation is a problem that
needs to be fully addressed. Vector aggregation leads to losses during vector purification,
and while aggregates can be removed by filtration, the loss in yield results in higher costs and
capacity limitations when producing vector for pre-clinical and clinical studies. Even after
filtration to remove aggregates, new aggregates can form in concentrated preparations of
AAV2 vector in buffered-saline solutions.
The need exists for improved formulations and methods for purification and storage
of AAV vectors, such as rAAV2, that prevent aggregation of virus particles.
SUMMARY OF THE INVENTION
These and other needs in the art are met by the present invention, which provides high
ionic strength solutions for use in preparing and storing AAV vectors that maintain high
infectivity titer and transduction efficiency, even after freeze-thaw cycles.
In one aspect the invention relates to methods of preventing aggregation of virions in
a preparation of virions by adding excipients to achieve an ionic strength high enough to
prevent aggregation. In another aspect the invention relates to compositions of virions having
an ionic strength high enough to prevent aggregation.
In some embodiments of the invention, the ionic strength is at least about 150mM,
200mM, 250mM, 300mM, 350mM, 400mM, 450mM, 500mM, 600mM, 700mM or more. In

some embodiments this ionic strength is accomplished using excipients comprising one or
more multivalent ions, for example citrate, sulfate, magnesium or phosphate.
In additional embodiments, the osmolality of the preparation of virions is maintained
at near isotonic levels, for example 200mOsm, 250mOsm, 280mOsm, 300mOsm, 350mOsm
or 400mOsm, even though the ionic strength is high enough to prevent virion aggregation.
In some embodiments the virions are adeno-associated virus (AAV) virions, for
example AAV-2.
In other embodiments of the methods of the present invention preparations of virions
are treated with a nuclease, for example Benzonase®. In further embodiments, nuclease
treatment is combined with addition of excipients that achieve an ionic strength high enough
to prevent aggregation.
In some embodiments of the present invention, the surfactant Pluronic® F68 is added
to a preparation of virions, for example to 0.001%. In one embodiment, the composition
comprises purified virus particles, 10 mM Tris pH 8.0, 100mM sodium citrate and 0.001%
Pluronic® F68.
In one embodiment, AAV vectors can be stored as compositions of the present
invention at concentrations exceeding 1x1013 vg/mL, for example 2x1013, 3x1013, 4x1013,
5x1013 and up to 6.4x1013 vg/mL, without significant aggregation. In some embodiments,
AAV vectors stored using the methods and compositions of the invention do not exhibit
significant aggregation when stored at 4°C for five days. In other embodiments, AAV
vectors that are stored as such compositions do not exhibit significant aggregation after,one,
five, ten or more freeze-thaw cycles at -20°C or at -80°C.
In some embodiments, preparations of virions stored according to the methods and
compositions of the invention exhibit an average particle radius (Rh), as measured by
dynamic light scattering, indicating that no significant aggregation of virions has taken place.

In some embodiments, preparations of virions stored according to the methods and
compositions of the invention exhibit an average particle radius (Rh) greater than about
15nm, 20nm, or 30nm.
In some embodiments, recovery of virions from preparations of virions stored
according to the methods and compositions of the invention is greater than about 85%, 90%
or 95% following filtration through a 0.22µm filter.
In yet another aspect, the invention relates to kits comprising the high ionic strength
formulations of the invention. In one embodiment the kit comprises a pre-mixed solution of
excipients. In another embodiment the kit comprises two or more separate components of a
high ionic strength composition of the present invention to be mixed by a user. In some
embodiments the kit comprises sodium citrate, Tris® and Pluronic® F68. In other
embodiments, the kit further comprises instructions for making a composition or performing
a method of the present invention.

DESCRIPTION OF THE ACCOMPANYINGRAWINGS
FIGS. 1A and 1B present data showing aggregation of AAV2-FIX particles as a
function of osmolality (FIG. 1A) or ionic strength (FIG. 1B) for various buffer compositions.
AAV2-FIX vectors are prepared by Method 2 of Example 1. Average particle radius is
measured by dynamic light scattering (DLS) following vector dilution in varying
concentrations of excipients buffered with 10 mM sodium phosphate at pH 7.5. Excipients
include sodium chloride ( ), sodium citrate ( ), sodium phosphate ( ), sodium sulfate ( ),
magnesium sulfate ( ), and glycerol ( ).
FIG. 2 presents data on AAV2-FIX aggregation as a function of the method of
purification. The average particle radius is measured by DLS following vector dilution in
varying concentrations of sodium chloride buffered with 10mM sodium phosphate at pH 7.5.

Vectors are purified by Method 1 (double CsCl gradient) ( ); Method 2 (cation exchange
chromatography) ( ); Method 2 plus nuclease digestion ( ); or Method 3 (chromatography
plus one CsCl gradient) ( ). Purification Methods 1-3 are described in Example 1.
FIG. 3 presents data on transgene expression from D7/4 cells transduced with
rAAV2-AADC virions prepared and stored in high ionic strength formulation ( ) or in a
control formulation ( ). The concentration of AADC was measured by ELISA (in triplicate
for each data point) 72 hours post-transduction. Error bars represent standard deviations.
DETAILED DESCRIPTION OF THE INVENTION
AAV2 vector aggregation is frequently observed in concentrated preparations of
vectors and can affect purification recovery, and in vivo potency and safety. Hence, an
important objective for the development-AAV2 vectors is to identify methods and
formulations that prevent aggregation of vectors when concentrated stocks are prepared.
Unless otherwise indicated, the term "vector" as used herein refers to a recombinant
AAV virion, or virus particle, regardless of the frequent use of "vector" to also refer to non-
viral DNA molecules, such as plasmids, in other contexts.
The present invention is based in part on the observation that solution ionic strength is
an important parameter in AAV vector aggregation, implicating the involvement of ionic
interactions between virus particles in the aggregation process. The observation that elevated
ionic strength increases AAV2 vector solubility regardless of the identity of the charged
excipient supports the hypothesis that ionic strength of solution per se, rather than
interactions involving a specific ionic species, is the relevant physico-chemical parameter. A
threshold ionic strength of at least 200mM is required to prevent aggregation at vector
particle concentrations examined herein.

Of practical concern, commonly used buffered saline solutions have insufficient ionic
strength to prevent AAV2 vector aggregation at concentrations exceeding 1013 particles/mL.
It is known that high salt concentrations increase AAV2 vector solubility (e.g. highly
concentrated AAV2 vectors recovered from gradients generally remain soluble in
concentrated CsCl). However, optimal formulations for pre-clinical and clinical studies
should be close to isotonic (280-400 mOsm), especially for in vivo administration of vector to
sites where dilution of hypertonic solutions may be slow. In embodiments of the present
invention the exponential relationship of ionic strength with charge valency is used to
develop isotonic formulations with high ionic strengths. Salt species with multiple charge
valencies (e.g. salts of sulfate, citrate, and phosphate) that are commonly used as excipients in
human parenteral formulations can provide the level of ionic strength needed to prevent
AAV2 vector aggregation when used at isotonic concentrations. While isotonic (150mM)
sodium chloride has an ionic strength of 150mM, a value insufficient to maintain AAV2
solubility at high vector concentrations, isotonic sodium citrate, with an ionic strength of
~500mM, can support AAV2 vector concentrations of at least 6.4 x 1013 vg/mL without
aggregation.
Without intending to be limited by theory, the low solubility of AAV2 particles may
be caused by their highly symmetrical nature in conjunction with the stabilizing effect of
complementary charged regions between neighbouring particles in aggregates. The surface
charge density based on the crystal structure of AAV2 (Xie, Q. et al. (2002) Proc. Natl. Acad.
Sci. U.S.A. 99: 10405-10410) reveals a pattern of positive and negative charges on the virus
surface. Previous reports have shown that AAV2 vector aggregation is pH dependent, and
hypothesized that amino acids with charged side groups are involved in inter-particle binding.
Qu, G. et al. (2003) Mol. Therapy 7: S238. These reports hypothesized that if charged amino
acid side chains are involved in vector aggregation, high concentrations of free amino acids

could block vector particle interactions. However, we have found that amino acids with
charged side chains are not effective in preventing AAV2 vector aggregation beyond their
contribution to ionic strength.
Vector aggregation at low ionic strength was also found to be reduced but not
prevented by efficient nuclease treatment of purified vector particles. Digestion at an earlier
stage of the purification process (clarified HEK cell lysate) did not reduce aggregation
following vector purification. It is likely that digestion of already purified virions is more
efficient because of a higher enzyme to nucleic acid substrate ratio. One mechanism to
explain these results is that residual nucleic acid impurities (e.g. host cell and plasmid DNA)
bound to the vector surface can bridge to binding sites on neighbouring virus particles and
thus cause aggregation. Purified AAV2 vectors (empty capsid free) have been reported to
contain approximately 1% non-vector DNA. Smith, P. et al. (2003) Mo/. Therapy 7: S348.
While >50% of this non-vector DNA was reported to be nuclease resistant and was packaged
within capsid particles, some impurity DNA was nuclease resistant and appeared to be
associated with the surface of purified vector particles. The observation that efficient
nuclease treatment can reduce vector aggregation suggests that nucleic acids associated with
the vector surface at an average level not greater than ~25 nucleotides per vector particle can
contribute to AAV vector aggregation.
In summary, the use of high ionic strength solutions during AAV2 vector purification
and final formulation, and efficient removal of residual vector surface DNA are two effective
strategies to achieve highly concentrated solutions of AAV2 vectors for use in pre-clinical
and clinical studies. High ionic strength solutions and nuclease treatment can be used in
combination or separately. Although data were obtained using AAV2 vectors, the
composition and methods of the present invention may also be useful with other AAV
serotypes / variants, or other viral vectors such as adenoviruses, lentiviruses and retroviruses.


AA V Aggregation as a Function of Excipient Concentration
Initial screening experiments are performed to elucidate the mechanism of AAV
vector aggregation and to identify classes of excipients that can reduce / prevent aggregation.
Vector aggregation can be caused by dilution (5-fold) of vector in neutral-buffered saline
with low concentration buffer (20mM sodium phosphate, pH 7.2). Excipients are screened
using this "dilution-stress" method to identify excipients that are able to prevent vector
aggregation when included in the diluent. For screening, aggregation is measured by
dynamic light scattering (DLS). Classes of excipients examined included selected inorganic
salts, amino acids, uncharged carbohydrates, and surfactants. Results are presented in
Table 1.



As illustrated in Table 1, charged excipients (inorganic salts and amino acids) prevent
aggregation when present at sufficient concentrations. However, salt concentrations required
to prevent vector aggregation vary, ranging from 180 mOsrn for magnesium sulfate, to 320
mOsm for sodium chloride. The amino acids arginine, aspartic acid, glutamic acid, glycine,
histidine, and lysine do not prevent aggregation at 200 mOsm, but lysine, aspartic acid, and
glutamic acid prevent aggregation at 300-320 mOsm. Arginine, glycine and histidine were
not tested at concentrations other than 200 mOsm. Selected carbohydrates have no effect on
vector particle aggregation when present at concentrations up to 5% w/v. For example, 5%
w/v glycerol (543 mOsm) does not prevent aggregation. The surfactants Polysorbate80 (1%
w/v) and Pluronic® F68 (10% w/v) similarly have no effect on aggregation using the
"dilution-stress" method.
AAV Aggregation as a Function of Osmolarity and Ionic Strength
FIGS. 1A and 1B show the results of a more detailed analysis of vector aggregation as
a function of the concentration of various salts. FIG. 1A shows vector aggregation as a
function of the osmolarity of selected excipients. For charged species a concentration-
dependent inhibition of AAV2 vector aggregation is observed. Salts with multivalent ions
achieve a similar degree of inhibition of aggregation at lower concentrations than monovalent
sodium chloride. For example, magnesium sulfate prevents aggregation at 200 mOsm
whereas sodium chloride requires 350 mOsm to achieve a similar effect. Sodium citrate,
sodium sulfate, and sodium phosphate are intermediate in their potency to prevent vector
aggregation.
Although the results in FIG. 1A and Table 1 show no effect of glycerol and certain
sugars at concentrations up to 5% on AAV2 vector aggregation induced by low ionic


strength, the data cannot rule out improvement of AAV2 solubility at glycerol concentrations
above 5%. For example, Xie and co-workers reported that 25% (w/v) glycerol enabled
concentration of AAV2 to very high concentrations (4.4 to 18 x 1014 particles/ml) in low
ionic strength solutions. Xie, Q. et al. (2004) J. Virol. Methods 122: 17-27.
FIG. 1B shows the data of FIG. 1A plotted as a function of the calculated ionic
strength, rather than osmolality, for each excipient. FIG. 1B demonstrates that vector
aggregation is prevented when ionic strength is ~200 mM or greater regardless of which salt
is used. These data suggested that the ionic strength (µ) of a solution, a parameter that
depends on both solute concentration and charge valency, is the primary factor affecting
aggregation.
Ionic strengths useful to prevent aggregation in embodiments of the present invention
include, for example, 250 mM, 300 mM, 350 mM, 400 mM, 450 mM, 500 mM, 600 mM,
700 mM or higher ionic strengths. Multivalent ions are preferred to achieve these ionic
strengths in methods and formulations of the present invention, such as divalent, trivalent,
tetravalent, pentavalent ions and ions of even higher valency. The pH buffer in solutions and
formulations of the present invention may be phosphate, Tris, or HEPES (or other Good's
buffers), but any other suitable pH buffer may be used. In preferred embodiments, the
multivalent ions and buffer are selected to be compatible with the target tissue for the vector
being prepared.
Use of multivalent ions in the methods and compositions of the invention makes it
possible to create compositions of high ionic strength but relatively low osmolality. High
ionic strength compositions of the present invention may be nearly isotonic, and may be, for
example, about 200mOsm, 250mOsm, 280mOsm, 300mOsm, 350mOsm or 400mOsm,
although other osmolalities may be acceptable for some uses of the compositions.
13

AA V Aggregation as a Function of the Method of AA V Purification
Recombinant AAV2 purified using different methods (e.g. density gradient
purification versus ion-exchange chromatography) would be expected to have different
impurity profiles. FIG. 2 shows vector aggregation as a function of ionic strength for several
preparations of AAV differing in the purification method. Purification methods are described
in Example 1. Sodium chloride is used to vary the ionic strength. AAV2-FIX vectors
purified by double cesium chloride gradient ultracentrifugation (Method 1), by cation
exchange column chromatography (Method 2), or by combined column and cesium chloride
gradient ultracentrifugation (Method 3) each demonstrate similar aggregation responses as
ionic strength is decreased. In contrast, AAV2-FIX purified by the column method and then
subjected to a nuclease digestion step (Method 2 + nuclease) shows reduced aggregation at
low ionic strength.
AAV Aggregation at Preparative Scale
The data in Table 1 and FIGS. 1 A, 1B and 2 involve vector aggregation at an
analytical scale, employing DLS to measure aggregation. Table 2, in contrast, shows the
effects of elevated ionic strength and nuclease treatment on AAV2 vector aggregation at a
larger scale, using methods to induce and quantify vector aggregation that are relevant to
preparative scale vector purification. Experimental details are provided in Example 2.
Purified AAV vectors are diafiltered into solutions of various ionic strengths, the volume is
reduced to achieve high vector concentrations, and aggregation is then assessed by measuring
vector recovery after filtration through a 0.22µm filter. Aliquots from a single pool of
AAV2-AADC vector purified by Method 1 through the second CsCl gradient centrifugation
step (1.8xl015 vg in 91mL, 1.8xl013 vg/mL, in ~3M CsCl) are used as starting material in the
diafiltration experiments. Tangential flow filtration using hollow fibers is used for


diafiltration because it is scalable and yet it still enables preparation of volumes (min.
1,4mL), and thus AAV concentrations, at which aggregation would be expected in neutral
buffered saline.
In Experiment 1, three hollow fiber units are used to diafilter AAV2-AADC vector in
formulations CF, TF1, or TF2, and the volume is reduced to a target of 2.5xl013 vg/mL. See
Example 2. The samples are then filtered through a 0.22um filter. Results are shown in
Table 2. Vector recovery ("Yield %") for both elevated ionic strength formulations TF1 (95
± 7.4%) and TF2 (93 ± 7.4%) are significantly higher than the recovery using the control
formulation CF.(77 ± 6.6%).

In Experiment 2, AAV2-AADC is concentrated to a higher target value (6.7x1013
vg/mL) in CF or.TF2. Vector recovery using TF2 (96 ± 4.4%) is again significantly higher
than recovery using CF (59 ± 6.0%). Within the variability of the assays used, vector was
recovered fully at both target concentrations using TF2, indicating that aggregation was
prevented. In contrast, significant aggregation was observed at both target concentrations
using CF, and the extent of aggregation (i.e. loss following 0.22 µm filtration) was higher at
the higher target vector concentration. In an additional experiment (not shown), 50 µL

samples of AAV2 vector are taken following concentration but prior to the 0.22µm filtration
step of Experiment 2, and examined by light microscopy. Vector concentrated in CF contains
obvious amounts of visible material (not shown), while no such material is seen in vector
concentrated in TF2.
Experiment 3 examines the effect of prior nuclease digestion of purified vector on
aggregation. In the absence of nuclease digestion recovery of AAV2-AADC in CF is 68 ±
11%, similar to the recoveries in Experiments 1 and 2. In contrast, purified vector treated
with nuclease and then concentrated in CF gives higher recovery (91 ± 12%). These prep
scale results reflect the same effect of nuclease digestion shown in FIG. 2 using the "dilution-
stress" (analytical scale) method.
The results presented in Table 2 demonstrate that the methods and compositions of
the present invention increase the recovery of AAV vector recovery. For example, in various
embodiments of the present invention, recovery is improved from less than about 80% to at
least about 85%, 90%, 95% or more.
AA V Stability and Activity Following Storage or Freeze-Thaw Cycling
Croyle and coworkers reported a significant loss of titer of AAV and adenovirus
following multiple freeze-thaw cycling in sodium phosphate buffer, and demonstrated that
the better pH buffering provided by potassium phosphate during freeze-thaw cycling
prevented titer loss. Croyle, M. A. et al. (2001) Gene Therapy 8: 1281-1290. Results of our
freeze-thaw stability study using sodium phosphate support these findings. We find that
while 150mM sodium phosphate provides sufficient ionic strength to prevent aggregation
during preparation and non-frozen storage of concentrated AAV2-AADC vector, even a
single freeze-thaw cycle at -20 or -80 °C results in aggregation.

AAV stability after storage or freeze-thaw (F/T) cycling is assessed in buffers of the
present invention as follows. The concentrated vectors prepared in CF, TF1, and TF2 (Table
2, Experiment 1) are subjected to a short stability study to investigate whether aggregation
will occur during refrigerated storage, or following multiple freeze-thaw (F/T) cycles.
Aggregation is assessed by DLS using undiluted samples, and Rh values >20nm are deemed
to indicate the occurrence of some level of aggregation.

As shown in Table 3, AAV2-AADC vector prepared in CF shows some aggregation
after 5 days of storage at 4 °C, as well as following one or more F/T cycles at -20 or -80°C.
For vector prepared in TF1, no aggregation occurs after 5 days at 4°C, but aggregation occurs
following a single F/T cycle at -20 or -80 °C as indicated by a DLS signal intensity that is too
high to measure. Visual inspection of these samples reveals slight cloudiness, which is
consistent with aggregation. For vector prepared in TF2, no aggregation is observed at 4 °C,
or following up to 10 F/T cycles at -20 °C. Some aggregation is observed following 5 and 10
F/T cycles at -80 °C.

AAV activity after storage or F/T cycling in TF2 is assessed as follows. As described
above, the high ionic strength, isotonic formulation TF2 effectively prevents vector
aggregation during concentration and storage, and therefore represents a promising candidate
for further study. An important question is whether preparation and storage of the vector in
high ionic strength TF2 would adversely affect its functional activity. To assess this, assays
are performed to measure the infectious titer and the transduction efficiency of vectors
prepared and stored for an extended period of time in TF2.
For infectivity, a highly sensitive infectivity assay capable of detecting single
infectious events is used. Zhen, Z. et al (2004) Human Gene Ther. 15: 709-715. AAV2-
AADC is prepared in TF2 at a concentration of 6.4x1013 vg/mL. After being stored for 45
days at 4 °C the preparation has a vector genome to infectious unit ratio (vg/IU) of 13,
compared to a value of 16 vg/IU for the reference vector.. This difference is not significant
given the reported variability of this assay (RSD -50%).
Transduction efficiency is assessed by measuring the expression of AADC protein by
ELISA following transduction of D7/4 cells. FIG. 3 shows no significant difference between
vector prepared in TF2 and the reference control for vector input ranging from 10 to 105
vg/cell. Together, these data indicate that preparation and storage of AAV2 vectors in high
ionic strength TF2 does not have a deleterious effect on vector infectivity or transduction
efficiency.
Conclusion
The effect of ionic strength (µ) on virus particle interactions is determined to elucidate
the mechanism of vector aggregation. The ionic strength of neutral-buffered isotonic saline
(µ = 150mM) is insufficient to prevent aggregation of AAV2 vectors purified by gradient
ultracentrifugation or by cation exchange chromatography at concentrations exceeding ~1013


particles/mL. Inclusion of sugars (sorbitol, sucrose, mannitol, trehalose, glycerol) at
concentrations up to 5% (w/v) or of surfactants Tween80® (1%) or Pluronic® F68 (10%) does
not prevent aggregation of vector particles.
In contrast, vector particles remain soluble when elevated ionic strength solutions (µ >
200mM) are used during purification and for final vector formulation. Elevated ionic
strength solutions using isotonic excipient concentrations for in vivo administration are
prepared with salts of multivalent ions, including sodium citrate, sodium phosphate, and
magnesium sulfate. An isotonic formulation containing 10mM Tris, 100mM sodium citrate,
0.001% Pluronic® F68, pH 8.0 (µ ~500mM) enables concentration of AAV2-AADC vectors
to 6.4x1013 vg/mL with no aggregation observed during preparation and following ten freeze-
thaw cycles at -20 °C. See Table 3, below, and accompanying discussion. AAV2-AADC
vectors prepared and stored for an extended period in elevated ionic strength formulation
retain high infectivity titer (13 IU/vg) and transduction efficiency.
Nuclease treatment of purified AAV2 vectors reduces the degree of vector
aggregation, implicating vector surface nucleic acid impurities in inter-particle interactions.
Hence, purification methods to efficiently remove vector surface residual nucleic acids,
coupled with the use of elevated ionic strength isotonic formulations, are useful methods to
prevent AAV2 vector aggregation.
EXAMPLE 1
AAV PURIFICATION METHODS
AAV2 vectors expressing human coagulation factor IX (FIX) or human amino acid
decarboxylase (AADC) are produced by triple transfection of HEK293 cells as previously
described (Matsushita, T. et al. (1998) Gene Therapy 5: 938-945), with modifications. For


the large scale preparations, cells are cultured and transfected in 850 mm2 roller bottles
(Corning). Vectors are purified by one of three methods.
In purification Method 1, modified from Matsushita, transfected HEK293 cells in
roller bottles are collected by centrifugation (1000g, 15min), resuspended in 10mM sodium
phosphate, 500mM sodium chloride, pH 7.2, and lysed by three freeze / thaw cycles
(alternating an ethanol / dry ice bath and a 37°C water bath). The cell lysate is clarified by
centrifugation (8,000g, 15 min). The supernatant is then diluted to 200mM NaCl by addition
of lOmM sodium phosphate, pH 7.2, and digested with Benzonase® (Merck, Purity Grade 1;
200 U/mL, 1h, 37 °C). The lysate is adjusted to 25mM CaCl2 using a IM stock solution, and
incubated at 4°C for one hour.
The mixture is centrifuged (8,000g, 15 min), and the supernatant containing vector is
collected. To precipitate virus from the clarified cell lysate, polyethylene glycol (PEG8000)
is added to a final concentration of 8%, the mixture incubated at 4°C for three hours, and then
centrifuged (8,000g, 15 min). The pellets containing vector are re-suspended with mixing in
0.15M NaCl, 50mM Hepes, 25mM EDTA, pH 8.0 and incubated at 4°C for 16 hours. The
resuspended material is pooled, and solid cesium chloride is added to a final density of 1.40
gm/ml. Vector is then banded by ultracentrifugation (SW28,27,000rpm, 24h, 20°C) using a
Beckman model LE-80 centrifuge. The centrifugation tubes are fractionated, and densities
from 1.38 to 1.42 gm/mL containing vector are pooled. This material is banded a second
time by ultracentrifugation (NVT65 rotor, 65,000 rpm, 16h, 20°C), and fractions containing
purified AAV2 vectors are pooled. To concentrate vector and to perform buffer exchange,
vectors in concentrated cesium chloride solution are subjected to ultrafiltration / diafiltration
(UF/DF) by tangential flow filtration as described below (Example 2).
In purification Method 2, cell harvests containing AAV are microfluidized and
filtered sequentially through 0.65 and 0.22 µm filters (Sartorius). Virus is purified from the


clarified cell lysates by cation exchange chromatography using Poros HS50 resin as
previously described. U.S. Pat. No. 6,593,123. For the nuclease digestion described in
FIG. 2, column-purified vectors are incubated (4h, RT) with 100 U/mL Benzonase and 10
U/mL DNAse I (RNAse free, Roche Diagnostics, Indianapolis, Indiana).
For purification Method 3, AAV2 vectors purified by cation exchange
chromatography are subjected to an additional cesium chloride gradient ultracentrifugation
step (SW28,27,000rpm, 20h) to remove empty capsids prior to UF/DF.
Real time quantitative PCR (Q-PCR) is used to quantify AAV preparations as
previously described. Sommer, J. M. et al. (2003) Mol. Therapy 7: 122-128. Vectors
purified by each of the three methods are analyzed by SDS-PAGE / silver staining analysis,
and in all cases VP1, VP2 and VP3 are present in the expected ratios, with the capsid proteins
representing >95% of total proteins as determined by scanning densitometry. However,
unlike gradient-purified AAV2 vectors purified using Methods 1 and 3, vectors purified by
Method 2 (column chromatography) contain empty capsids, ranging from 3-10 empty capsids
per vector genome.
EXAMPLE 2
ULTRAFILTRATION AND DIAFILTRATION TO DETECT AAV AGGREGATION
Disposable hollow fiber tangential flow filtration devices (Amersham BioSciences 8"
Midgee, 100 kDa nominal pore size) are used to concentrate and diafilter AAV2 vectors
purified by the methods described above, and for the UF/DF experiments described in Table
2. For all UF/DF procedures a volume of diafiltration buffer corresponding to 10x the
product volume is used, and it is added in ~1mL increments to approximate continuous
diafiltration. Using this method, the calculated residual CsCl after diafiltration is 21

The following three formulations were used for UF/DF: Control Formulation (CF:
140mM sodium chloride, 10mM sodium phosphate, 5% sorbitol, pH 7.3); Test Formulation 1
(TF1: 150mM sodium phosphate, pH7.5); and Test Formulation 2 (TF2: 100mM sodium
citrate, 10mM Tris, pH8.0). For Experiment 1 shown in Table 2, diafiltration is performed at
a volume corresponding to a vector concentration of 1x 1013 vg/mL, and following
diafiltration the volume is reduced to a value corresponding to 2.5x1013 vg/mL (assuming no
vector loss).
For Experiment 2, diafiltration is performed at a volume corresponding to a 2x1013
vg/mL, and the volume is then reduced to a value corresponding to 6.7x1013 vg/mL.
For Experiment 3 (CF ± Bz), AAV2-AADC (approximately 1.2x1014 vg) is first
diafiltered into TF1 (a formulation compatible with nuclease activity) and then passed
through a 0.22 µm filter. The titer of this material is determined, and the volume is adjusted
to correspond to a concentration of 1x1013 vg/mL. To 10 mL of this material, MgCl2 is added
to a concentration of 2 mM, and then divided into two equal aliquots. One aliquot is
incubated with Benzonase (200 U/mL, 4h, RT), and the second is mock-incubated. Each
aliquot is then diafiltered at a volume corresponding to a vector concentration 2x1013 vg/mL,
and then concentrated to a 3.6x1013 vg/mL target. Following all UF/DF protocols, Pluronic®
F-68 (BASF Corp., Mount Olive, NJ) from a 1% stock is added to the vector product to a
final concentration of 0.001%, and the solution is passed through a 0.22µm syringe filter
(Sartorius). All UF/DF procedures are performed in a laminar flow cabinet.

EXAMPLE 3
MEASUREMENT OF VECTOR AGGREGATION BY
DYNAMIC LIGHT SCATTERING
Purified vectors are analyzed for aggregation by dynamic light scattering (DLS) using
a Protein Solutions DynaPro 99 (λ=825.4 nm). Primary data (particle radius - Rh, average
value measured over 30 cycles, 10 cycles/min) are used for all analyses reported. A
"dilution-stress" method is used to assess the effect of varying excipients on vector
aggregation. In this method, 80 µL of test diluent is added to 20 µL of vector solution with
mixing in the actual cuvette used for DLS measurement, and data collection is initiated
within 10 seconds of mixing. Prior to addition of test diluents, the Rh value for AAV2 vector
preparations is measured and confirmed to be monomeric. Samples that are not 100% monomelic are passed through a 0.22µm syringe
disc filter (Sartorius, low protein binding) to remove aggregates.
The osmolarity and ionic strength values given in FIGS. 1 and 2 are calculated using
all excipients present in the mixture (i.e. weighted: test diluent (80%) and starting vector
formulation (20%)). Osmolarity is calculated according to the equation: Osmolarity = ci,
where ci is the molar concentration of each solute species. The ionic strength (µ) is
calculated according to the equation: µ = ½ ciz2, where zi is the charge on each species. In
conditions that resulted in vector aggregation (e.g. low µ) a progressive increase in Rh is
observed over the course of data collection. To validate the use of the average Rh measured
over the 3 minute interval following dilution as a reliable measure of aggregation, the average
rate of increase of Rh (ΔRh I At) over the same time interval is also determined (not shown).
Analysis of ΔRh / Δt gives results concordant with those obtained using the average Rh value
reported in FIGS. 1 and 2.


EXAMPLE 4
AAV VIRION rNFECTIVITY
Infectivity of AAV2-AADC vectors is determined using a highly sensitive assay as
previously described. Zhen, Z. et ah (2004) Human Gene Ther. 15: 709-715. Briefly,
samples are serially diluted (10-fold dilutions, 10 replicates / dilution) and added to D7/4
cells (modified HeLa cells expressing AAV rep and cap) grown in 96 well tissue culture
plates (Falcon, cat. #353227) in DMEM medium containing 10% FBS. Adenovirus (Ad-5,
100 vp/cell) is added to each well to provide helper functions. After 48h, replication of AAV
vector in each well is quantified by Q-PCR using transgene-specific primers and probes, and
the frequency of infection at limiting dilution is analyzed by the Karber method to calculate
the infectivity titer. The test sample is run concurrently with an AAV2-AADC reference
previously prepared in CF and stored at -80 °C.
The transduction efficiency of AAV2 vectors is quantified by a whole cell ELISA.
D7/4 cells grown in 96 well plates are infected with 10-fold serial dilutions of the test sample
and reference vector, corresponding to 10 to 105 vg / cell input (5 replicates / dilution). After
48h, the culture medium is removed, and cells are washed twice with 200 µL PBS (10 mM
sodium phosphate, 140mM sodium chloride, pH 7.2). Cells are then permeabilized and fixed
by addition of 100µL of PBS containing 0.5% Triton X-100 and 4% paraformaldehyde to
each well (15 min). The fixing solution is removed, and the cells are washed twice with PBS
containing 0.5% Triton X-100. Non-specific sites are blocked by adding PBS containing 3%
bovine serum albumin (BSA) and 0.5% Triton X-100 (60min).
After washing, cells are incubated for one hour with rabbit anti-AADC IgG antibody
(Chemicon, AB136), and washed. Cells are then incubated for one hour with alkaline
phosphatase-conjugated goat anti-rabbit IgG, and washed. Antibodies are diluted 1:1000 in
PBS containing 1% BSA, 0.5% Triton X-100. Substrate (PNPP, Pierce, cat. #34047) is then


added (1 mg/mL in IX diethanolamine substrate buffer, Pierce, cat. #34064), and after
incubation for 30min the concentration of cleaved substrate is measured
spectrophotometrically (λ=405nm). Human AADC expression as a function of vector input
is fitted using a spline curve (SigmaPlot). The AAV2-AADC reference vector is measured
concurrently with the test sample.
While preferred illustrative embodiments of the present invention are described, it
will be apparent to one skilled in the art that various changes and modifications may be made
therein without departing from the invention, and it is intended in the appended claims to
cover all such changes and modifications that fall within the true spirit and scope of the
invention.


We Claim:
1. A method of preventing aggregation of adeno-associated virions (AAV) virions in a
purified preparation of AAV virions, comprising:
a) providing a lysate comprising rAAV virions;
b) purifying rAAV virions from the lysate using ultracentrifugation and/or
chromatography, wherein said virions are purified; and
c) adding one or more excipients comprising multivalent ions such as herein described
to the preparation of virions to achieve an ionic strength of at least 200 mM.

2. The method as claimed in claim 1, optionally comprising treating said preparation of
virions with a nuclease.
3. The method as claimed in claim 2, wherein the nuclease is "Serratia marcescens
endonuclease" (Benzonase).
4. The method as claimed in claim 1, wherein one of the one or more multivalent ions is
citrate.
5. The method as claimed in claim 1, wherein the osmolarity of the preparations of
virions after addition of the one or more excipients is no greater than 280mOsm.
6. The method as claimed in claim 1, wherein, after addition of the one or more
excipients, the average particle radius (Rh) of the virions in the preparation of virions is less
than 20nm as measured by dynamic light scattering.
7. The method as claimed in claim 1, wherein, after addition of the one or more
excipients, recovery of the virions is at least 90% following filtration of the preparations of
virions through a 0.22pm filter.

8. A composition for the storage of purified adeno-associated virus(AAV) particles,
comprising: purified AAV particles; a pH buffer; and excipients comprising one or more salts
of multivalent ions; wherein the ionic strength of the composition is greater than 200 mM.
9. The composition as claimed in claim 8, wherein one of the one or more multivalent
ions is citrate.
10. The composition as claimed in claim 8, optionally comprising "methyl-oxirane
polymer" (Pluronic® F68).
11. The composition as claimed in claim 10, wherein the "methyl-oxirane polymer"
(Pluronic® F68) is present at 0.001%.
12. The composition as claimed in claim 8, wherein the pH buffer is 10 mM Tris, pH 8.0
and the excipients comprise 100 mM sodium citrate.
13. The composition as claimed in claim 8, wherein the average particle radius (Rh) of the
purified virus particles is less than 20nm as measured by dynamic light scattering.
14. The composition as claimed in claim 8, wherein recovery of the purified virus
particles is at least 90% following filtration of the composition of virions through a 0.22µm
filter.


The invention discloses a method of preventing aggregation of adeno-associated virions
(AAV) virions in a purified preparation of AAV virions, comprising: a) providing a lysate
comprising rAAV virions; b) purifying rAAV virions from the lysate using ultracentrifugation
and/or chromatography, wherein said virions are purified; and c) adding one or more
excipients comprising multivalent ions to the preparation of virions to achieve an ionic
strength of at least about 200 mM.
The invention is also for a composition for storage of purified adeno-associated virus (AAV)
comprising purified AAV particles, a pH buffer and excipients comprising salt(s) of
multivalent ions, wherein the said composition has ionic strength of greater than 200 mM.

Documents:

03646-kolnp-2006-abstract.pdf

03646-kolnp-2006-claims.pdf

03646-kolnp-2006-correspondence others.pdf

03646-kolnp-2006-description(complete).pdf

03646-kolnp-2006-drawings.pdf

03646-kolnp-2006-form-1.pdf

03646-kolnp-2006-form-3.pdf

03646-kolnp-2006-form-5.pdf

03646-kolnp-2006-international publication.pdf

03646-kolnp-2006-international search authority report.pdf

3646-KOLNP-2006-(29-08-2011)-ABSTRACT.pdf

3646-KOLNP-2006-(29-08-2011)-AMANDED CLAIMS.pdf

3646-KOLNP-2006-(29-08-2011)-CERTIFIED COPIES(OTHER COUNTRIES).pdf

3646-KOLNP-2006-(29-08-2011)-DESCRIPTION (COMPLETE).pdf

3646-KOLNP-2006-(29-08-2011)-DRAWINGS.pdf

3646-KOLNP-2006-(29-08-2011)-EXAMINATION REPORT REPLY RECIEVED.pdf

3646-KOLNP-2006-(29-08-2011)-FORM 1.pdf

3646-KOLNP-2006-(29-08-2011)-FORM 2.pdf

3646-KOLNP-2006-(29-08-2011)-OTHERS.pdf

3646-KOLNP-2006-(29-08-2011)-PA.pdf

3646-KOLNP-2006-(29-08-2011)-PETITION UNDER RULE 137-1.1.pdf

3646-KOLNP-2006-(29-08-2011)-PETITION UNDER RULE 137.pdf

3646-KOLNP-2006-ASSIGNMENT.pdf

3646-KOLNP-2006-CORRESPONDENCE.pdf

3646-KOLNP-2006-EXAMINATION REPORT.pdf

3646-KOLNP-2006-FORM 18 1.1.pdf

3646-kolnp-2006-form 18.pdf

3646-KOLNP-2006-FORM 3.pdf

3646-KOLNP-2006-FORM 5.pdf

3646-KOLNP-2006-GPA.pdf

3646-KOLNP-2006-GRANTED-ABSTRACT.pdf

3646-KOLNP-2006-GRANTED-CLAIMS.pdf

3646-KOLNP-2006-GRANTED-DESCRIPTION (COMPLETE).pdf

3646-KOLNP-2006-GRANTED-DRAWINGS.pdf

3646-KOLNP-2006-GRANTED-FORM 1.pdf

3646-KOLNP-2006-GRANTED-FORM 2.pdf

3646-KOLNP-2006-GRANTED-SPECIFICATION.pdf

3646-KOLNP-2006-OTHERS.pdf

3646-KOLNP-2006-REPLY TO EXAMINATION REPORT.pdf

3646-KOLNP-2006-TRANSLATED COPY OF PRIORITY DOCUMENT.pdf

3686-KOLNP-2008-(29-08-2011)-FORM 2.pdf


Patent Number 252936
Indian Patent Application Number 3646/KOLNP/2006
PG Journal Number 24/2012
Publication Date 15-Jun-2012
Grant Date 11-Jun-2012
Date of Filing 05-Dec-2006
Name of Patentee GENZYME CORPORATION
Applicant Address 500 KENDALL STREET , CAMBRIDGE,MA 02142, U.S.A.
Inventors:
# Inventor's Name Inventor's Address
1 WRIGHT JOHN FRASER 68 RIVER BIRCH CIRCLE, PRINCETON,NEW YORK 08540, U.S.A.
2 QU GUANG 1103 REGENT STREET, APARTMENT D, ALAMEDA,CALIFORNIA 94501, U.S.A.
PCT International Classification Number C12N7/02
PCT International Application Number PCT/US2005/019235
PCT International Filing date 2005-06-01
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/575,997 2004-06-01 U.S.A.
2 60/639,222 2004-12-22 U.S.A.