U.S. patent application number 09/254747 was filed with the patent office on 2003-11-20 for aav4 vector and uses thereof.
Invention is credited to CHIORINI, JOHN A., KOTIN, ROBERT M., SAFER, BRIAN.
Application Number | 20030215422 09/254747 |
Document ID | / |
Family ID | 21828864 |
Filed Date | 2003-11-20 |
United States Patent
Application |
20030215422 |
Kind Code |
A1 |
CHIORINI, JOHN A. ; et
al. |
November 20, 2003 |
AAV4 VECTOR AND USES THEREOF
Abstract
The present invention provides an adeno-associated virus 4
(AAV4) virus and vectors and particles derived therefrom. In
addition, the present invention provides methods of delivering a
nucleic acid to a cell using the AAV4 vectors and particles.
Inventors: |
CHIORINI, JOHN A.; (SILVER
SPRINGS, MD) ; KOTIN, ROBERT M.; (BETHESDA, MD)
; SAFER, BRIAN; (SILVER SPRINGS, MD) |
Correspondence
Address: |
NEEDLE & ROSENBERG, P.C.
SUITE 1000
999 PEACHTREE STREET
ATLANTA
GA
30309-3915
US
|
Family ID: |
21828864 |
Appl. No.: |
09/254747 |
Filed: |
November 26, 1999 |
PCT Filed: |
September 11, 1997 |
PCT NO: |
PCT/US97/16266 |
Current U.S.
Class: |
424/93.2 ;
435/235.1; 435/456 |
Current CPC
Class: |
C12N 15/63 20130101;
C12N 2750/14141 20130101; C12N 15/86 20130101; C12N 2750/14143
20130101; C07K 14/005 20130101; C12N 2750/14122 20130101; A61K
48/00 20130101; C12N 7/00 20130101 |
Class at
Publication: |
424/93.2 ;
435/235.1; 435/456 |
International
Class: |
A61K 048/00; C12N
007/00; C12N 015/861 |
Foreign Application Data
Date |
Code |
Application Number |
Sep 11, 1996 |
US |
60025934 |
Claims
What is claimed is:
1. A nucleic acid vector comprising a pair of adeno-associated
virus 4 (AAV4) inverted terminal repeats and a promoter between the
inverted terminal repeats.
2. A nucleic acid vector comprising a pair of adeno-associated
virus 4 (AAV4) inverted terminal repeats and a promoter between the
inverted terminal repeats, wherein the AAV4 inverted terminal
repeats comprise the nucleotide sequence set forth in SEQ ID
NO:6.
3. A nucleic acid vector comprising a pair of adeno-associated
virus 4 (AAV4) inverted terminal repeats and a promoter between the
inverted terminal repeats, wherein the AAV4 inverted terminal
repeats comprise the nucleotide sequence set forth in SEQ ID
NO:20.
4. The vector of claim 2, wherein the promoter is an AAV promoter
p5.
5. The vector of claim 4, wherein the p5 promoter is AAV4 p5
promoter.
6. The vector of claim 2, further comprising an exogenous nucleic
acid functionally linked to the promoter.
7. The vector of claim 2 encapsidated in an adeno-associated virus
particle.
8. The particle of claim 7, wherein the particle is an AAV4
particle, comprising a capsid protein comprising an amino acid
sequence defined by amino acids 438-601 shown in SEQ ID NO:4.
9. The particle of claim 7, wherein the particle is an AAV1
particle, an AAV2 particle, an AAV3 particle or an AAV5
particle.
10. An AAV4 particle, comprising a capsid protein comprising an
amino acid sequence defined by amino acids 438-601 shown in SEQ ID
NO:4.
11. The particle of claim 10, wherein the vector further comprises
an exogenous nucleic acid inserted between the inverted terminal
repeats.
12. An isolated nucleic acid comprising the nucleotide sequence set
forth in SEQ ID NO:1.
13. An isolated nucleic acid consisting essentially of the
nucleotide sequence set forth in SEQ ID NO:1.
14. An isolated nucleic acid that selectively hybridizes with the
nucleic acid of claim 13.
15. An isolated nucleic acid encoding an adeno-associated virus 4
Rep protein.
16. The nucleic acid of claim 15, wherein the adeno-associated
virus 4 Rep protein has the amino acid sequence set forth in SEQ D
NO:2.
17. The nucleic acid of claim 15, wherein the adeno-associated
virus 4 Rep protein has the amino acid sequence set forth in SEQ ID
NO:8.
18. The nucleic acid of claim 15, wherein the adeno-associated
virus 4 Rep protein has the amino acid sequence set forth in SEQ ID
NO:9.
19. The nucleic acid of claim 15, wherein the adeno-associated
virus 4 Rep protein has the amino acid sequence set forth in SEQ ID
NO:10.
20. The nucleic acid of claim 15, wherein the adeno-associated
virus 4 Rep protein has the amino acid sequence set forth in SEQ ID
NO:11.
21. The nucleic acid of claim 15, wherein the nucleic acid
comprises the nucleotide sequence set forth in SEQ ID NO:3.
22. The nucleic acid of claim 15, wherein the nucleic acid consists
essentially of the nucleotide sequence set forth in SEQ ID
NO:3.
23. An isolated nucleic acid that selectively hybridizes with the
nucleic acid of claim 22.
24. The nucleic acid of claim 15, wherein the nucleic acid
comprises the nucleotide sequence set forth in SEQ ID NO:12.
25. The nucleic acid of claim 15, wherein the nucleic acid
comprises the nucleotide sequence set forth in SEQ ID NO:13.
26. The nucleic acid of claim 15, wherein the nucleic acid
comprises the nucleotide sequence set forth in SEQ ID NO:14.
27. The nucleic acid of claim 15, wherein the nucleic acid
comprises the nucleotide sequence set forth in SEQ ID NO:15.
28. An isolated AAV4 Rep protein having the amino acid sequence set
forth in SEQ ID NO:2, or a unique fragment thereof.
29. An isolated AAV4 Rep protein having the amino acid sequence set
forth in SEQ ID NO:8, or a unique fragment thereof.
30. An isolated AAV4 Rep protein having the amino acid sequence set
forth in SEQ ID NO:9, or a unique fragment thereof.
31. An isolated AAV4 Rep protein having the amino acid sequence set
forth in SEQ ID NO:10, or a unique fragment thereof.
32. An isolated AAV4 Rep protein having the amino acid sequence set
forth in SEQ ID NO:11, or a unique fragment thereof.
33. An isolated antibody that specifically binds the protein of
claim 28.
34. An isolated AAV4 capsid protein having the amino acid sequence
set forth in SEQ ID NO:4.
35. An isolated antibody that specifically binds the protein of
claim 34.
36. An isolated AAV4 capsid protein having the amino acid sequence
set forth in SEQ ID NO:16.
37. An isolated antibody that specifically binds the protein of
claim 36.
38. An isolated AAV4 capsid protein having, the amino acid sequence
set forth in SEQ ID NO:18.
39. An isolated antibody that specifically binds the protein of
claim 38.
40. An isolated nucleic acid encoding the adeno-associated virus 4
capsid protein of SEQ ID NO:16.
41. An isolated nucleic acid encoding the adeno-associated virus 4
capsid protein of SEQ ID NO:4.
42. The nucleic acid of claim 41, wherein the nucleic acid
comprises the nucleic acid sequence set forth in SEQ D NO:5.
43. The nucleic acid of claim 41, wherein the nucleic acid consists
essentially of the nucleic acid sequence set forth in SEQ ID
NO:5.
44. An isolated nucleic acid that selectively hybridizes with the
nucleic acid of claim 39.
45. An isolated nucleic acid that selectively hybridizes with the
nucleic acid of SEQ ID NO:4.
46. An isolated nucleic acid comprising the AAV4 p5 promoter
comprising nucleotides 130-291 of SEQ ID NO:1.
47. A method of screening a cell for infectivity by AAV4 comprising
contacting the cell with an AAV4 particle comprising a capsid
protein comprising an amino acid sequence defined by amino acids
438-601 shown in SEQ ID NO:4 and detecting the presence of the AAV4
particle in the cells.
48. A method of screening a cell for infectivity by AAV4 comprising
contacting the cell with an AAV4 vector comprising an AAV4 particle
comprising a capsid protein comprising an amino acid sequence
defined by amino acids 438-601 shown in SEQ ID NO:4 and comprising
a known nucleic acid, wherein the presence of the AAV4 vector is
detected in the cells by detecting the presence of the known
nucleic acid.
49. A method of determining the suitability of an AAV4 vector for
administration to a subject comprising administering to an
antibody-containing sample from the subject an antigenic protein
comprising an amino acid sequence selected from the group
consisting of SEQ ID NO:4, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:2,
SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11 and residues
438-601of SEQ ID NO:2 and detecting an antibody-antigen reaction in
the sample, the presence of a reaction indicating the AAV4 vector
to be unsuitable for use in the subject.
50. A method of determining the presence in a subject of an
AAV4-specific antibody comprising administering to an
antibody-containing sample from the subject an antigenic protein
comprising an amino acid sequence selected from the group
consisting of SEQ ID NO:4, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:2,
SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11 and residues
438-601 SEQ ID NO:4 and detecting an antibody-antigen reaction in
the sample, the presence of a reaction-indicating the presence of
an AAV4-specific antibody in the subject.
51. A method of delivering a nucleic acid to a cell comprising
administering to the cell an AAV4 particle, comprising a capsid
protein comprising an amino acid sequence defined by amino acids
438-601 shown in SEQ ID NO:4, containing a vector comprising the
nucleic acid inserted between a pair of AAV inverted terminal
repeats, thereby delivering the nucleic acid to the cell.
52. The method of claim 52, wherein the AAV inverted terminal
repeats are AAV4 inverted terminal repeats.
53. The method of claim 52, wherein the AAV inverted terminal
repeats are AAV2 inverted terminal repeats.
54. A method of delivering a nucleic acid to a subject comprising
administering to a cell from the subject an AAV4 particle,
comprising a capsid protein comprising an amino acid sequence
defined by amino acids 438-601 shown in SEQ ID NO:4, comprising the
nucleic acid inserted between a pair of AAV inverted terminal
repeats, and returning the cell to the subject, thereby delivering
the nucleic acid to the subject.
55. A method of delivering a nucleic acid to a cell in a subject
comprising administering to the subject an AAV4 particle,
comprising a capsid protein comprising an amino acid sequence
defined by amino acids 438-601 shown in SEQ ID NO:4, comprising the
nucleic acid inserted between a pair of AAV inverted terminal
repeats, thereby delivering the nucleic acid to a cell in the
subject.
56. A method of delivering a nucleic acid to a cell in a subject
having antibodies to AAV2 comprising administering to the subject
an AAV4 particle, comprising a capsid protein comprising an amino
acid sequence defined by amino acids 438-601 shown in SEQ ID NO:4,
comprising the nucleic acid, thereby delivering the nucleic acid to
a cell in the subject.
57. The vector of claim 3, wherein the promoter is an AAV promoter
p5.
58. The vector of claim 3, wherein the p5 promoter is AAV4 p5
promoter.
59. The vector of claim 3, further comprising an exogenous nucleic
acid functionally linked to the promoter.
60. The vector of claim 3, encapsidated in an adeno-associated
virus particle.
61. The particle of claim 61, wherein the particle is an AAV4
particle, comprising a capsid protein comprising an amino acid
sequence defined by amino acids 43 8-601 shown in SEQ ID NO:4.
62. The particle of claim 61, wherein the particle is an AAV1
particle, an AAV2 particle, an AAV3 particle or an AAV5
particle.
63. An isolated nucleic acid encoding, the adeno-associated virus 4
capsid protein of SEQ ID NO:18.
64. The particle of claim 7, wherein the particle is an AAV4
particle, comprising a capsid protein comprising an amino acid
sequence selected from the group consisting of SEQ ID NO:4, SEQ ID
NO:16 and SEQ ID NO:18.
65. An AAV4 particle, comprising a capsid protein consisting
essentially of an amino acid sequence selected from the group
consisting of SEQ ID NO:4, SEQ ID NO:16 and SEQ ID NO:18,
containing a vector comprising a pair of AAV2 inverted terminal
repeats.
66. A method of delivering a nucleic acid to a cell comprising
administering to the cell an AAV4 particle, comprising a capsid
protein consisting essentially of an amino acid sequence selected
from the group consisting of SEQ ID NO:4, SEQ ID NO:16 and SEQ ID
NO:18, containing a vector comprising the nucleic acid inserted
between a pair of AAV-inverted terminal repeats, thereby delivering
the nucleic acid to the cell.
67. A method of delivering a nucleic acid to a subject comprising
administering to a cell from the subject an AAV4 particle,
comprising a capsid protein consisting essentially of an amino acid
sequence selected from the group consisting of SEQ ID NO:4, SEQ ID
NO:16 and SEQ ID NO:18, comprising the nucleic acid inserted
between a pair of AAV inverted terminal repeats, and returning the
cell to the subject, thereby delivering the nucleic acid to the
subject.
68. A method of delivering a nucleic acid to a cell in a subject
comprising administering to the subject an AAV4 particle,
comprising a capsid protein consisting essentially of an amino acid
sequence selected from the group consisting of SEQ ID NO:4, SEQ ID
NO:16 and SEQ ID NO:18, comprising the nucleic acid inserted
between a pair of AAV inverted terminal repeats, thereby delivering
the nucleic acid to a cell in the subject.
69. A method of delivering a nucleic acid to a cell in a subject
having antibodies to AAV2 comprising administering to the subject
an AAV4 particle, comprising a capsid protein consisting
essentially of an amino acid sequence selected from the group
consisting of SEQ ID NO:4, SEQ ID NO:16 and SEQ ID NO:18,
comprising the nucleic acid, thereby delivering the nucleic acid to
a cell in the subject.
70. An AAV4 vector, comprising a nucleic acid selected from the
group consisting of SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID
NO:7, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ
ID NO:17, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21 and SEQ ID
NO:22.
71. An isolated adeno-associated virus 4 Rep protein.
Description
BACKGROUND OF THE INVENTION
[0001] 1. Field of the Invention
[0002] The present invention provides adeno-associated virus 4
(AAV4) and vectors derived therefrom. Thus, the present invention
relates to AAV4 vectors for and methods of delivering nucleic acids
to cells of subjects.
[0003] 1. Background Art
[0004] Adeno associated virus (AAV) is a small nonpathogenic virus
of the parvoviridae family (for review see 28). AAV is distinct
from the other members of this family by its dependence upon a
helper virus for replication. In the absence of a helper virus, AAV
may integrate in a locus specific manner into the q arm of
chromosome 19 (21). The approximately 5 kb genome of AAV consists
of one segment of single stranded DNA of either plus or minus
polarity. The ends of the genome are short inverted terminal
repeats which can fold into hairpin structures and serve as the
origin of viral DNA replication. Physically, the parvovirus virion
is non-enveloped and its icosohedral capsid is approximately 20 nm
in diameter.
[0005] To date 7 serologically distinct AAVs have been identified
and 5 have been isolated from humans or primates and are referred
to as AAV types 1-5 (1). The most extensively studied of these
isolates is AAV type 2 (AAV2). The genome of AAV2 is 4680
nucleotides in length and contains two open reading frames (ORFs).
The left ORF encodes the non-structural Rep proteins, Rep40, Rep
52, Rep68 and Rep 78, which are involved in regulation of
replication and transcription in addition to the production of
single-stranded progeny genomes (5-8, 11, 12, 15, 17, 19, 21-23,
25, 34, 37-40). Furthermore, two of the Rep proteins have been
associated with the preferential integration of AAV genomes into a
region of the q arm of human chromosome 19. Rep68/78 have also been
shown to possess NTP binding activity as well as DNA and RNA
helicase activities. The Rep proteins possess a nuclear
localization signal as well as several potential phosphorylation
sites. Mutation of one of these kinase sites resulted in a loss of
replication activity.
[0006] The ends of the genome are short inverted terminal repeats
which have the potential to fold into T-shaped hairpin structures
that serve as the origin of viral DNA replication. Within the ITR
region two elements have been described which are central to the
function of the ITR, a GAGC repeat motif and the terminal
resolution site (trs). The repeat motif has been shown to bind Rep
when the ITR is in either a linear or hairpin conformation (7, 8,
26). This binding serves to position Rep68/78 for cleavage at the
trs which occurs in a site- and strand-specific manner. In addition
to their role in replication, these two elements appear to be
central to viral integration. Contained within the chromosome 19
integration locus is a Rep binding site with an adjacent trs. These
elements have been shown to be functional and necessary for locus
specific integration.
[0007] The AAV2 virion is a non-enveloped, icosohedral particle
approximately 25 nm in diameter, consisting of three related
proteins referred to as VPI,2 and 3. The right ORF encodes the
capsid proteins, VP1, VP2, and VP3. These proteins are found in a
ratio of 1:1:10 respectively and are all derived from the
right-hand ORF. The capsid proteins differ from each other by the
use of alternative splicing and an unusual start codon. Deletion
analysis has shown that removal or alteration of VP1 which is
translated from an alternatively spliced message results in a
reduced yield of infections particles (15, 16, 38). Mutations
within the VP3 coding region result in the failure to produce any
single-stranded progeny DNA or infectious particles (15, 16,
38).
[0008] The following features of AAV have made it an attractive
vector for gene transfer (16). AAV vectors have been shown in vitro
to stably integrate into the cellular genome; possess a broad host
range; transduce both dividing and non dividing cells in vitro and
in vivo (13, 20, 30, 32) and maintain high levels of expression of
the transduced genes (41). Viral particles are heat stable,
resistant to solvents, detergents, changes in pH, temperature, and
can be concentrated on CsCl gradients (1,2). Integration of AAV
provirus is not associated with any long term negative effects on
cell growth or differentiation (3,42). The ITRs have been shown to
be the only cis elements required for replication, packaging and
integration (3 5) and may contain some promoter activities
(14).
[0009] Initial data indicate that AAV4 is a unique member of this
family. DNA hybridization data indicated a similar level of
homology for AAV1-4 (31). However, in contrast to the other AAVs
only one ORF corresponding to the capsid proteins was identified in
AAV4 and no ORF was detected for the Rep proteins (27).
[0010] AAV2 was originally thought to infect a wide variety of cell
types provided the appropriate helper virus was present. Recent
work has shown that some cell lines are transduced very poorly by
AAV2 (30). While the receptor has not been completely
characterized, binding studies have indicated that it is poorly
expressed on erythroid cells (26). Recombinant AAV2 transduction of
CD34.sup.+, bone marrow pluripotent cells, requires a multiplicity
of infection (MOI) of 10.sup.4 particles per cell (A. W. Nienhuis
unpublished results). This suggests that transduction is occurring
by a non-specific mechanism or that the density of receptors
displayed on the cell surface is low compared to other cell
types.
[0011] The present invention provides a vector comprising the AAV4
virus as well as AAV4 viral particles. While AAV4 is similar to
AAV2, the two viruses are found herein to be physically and
genetically distinct. These differences endow AAV4 with some unique
advantages which better suit it as a vector for gene therapy. For
example, the wt AAV4 genome is larger than AAV2, allowing for
efficient encapsidation of a larger recombinant genome.
Furthermore, wt AAV4 particles have a greater buoyant density than
AAV2 particles and therefore are more easily separated from
contaminating helper virus and empty AAV particles than AAV2-based
particles. Additionally, in contrast to AAV1, 2, and 3, AAV4, is
able to hemagglutinate human, guinea pig, and sheep erythrocytes
(18).
[0012] Furthermore, as shown herein, AAV4 capsid protein, again
surprisingly, is distinct from AAV2 capsid protein and exhibits
different tissue tropism. AAV2 and AAV4 have been shown to be
serologically distinct and thus, in a gene therapy application,
AAV4 would allow for transduction of a patient who already possess
neutralizing antibodies to AAV2 either as a result of natural
immunological defense or from prior exposure to AAV2 vectors. Thus,
the present invention, by providing these new recombinant vectors
and particles based on AAV4 provides a new and highly useful series
of vectors.
SUMMARY OF THE INVENTION
[0013] The present invention provides a nucleic acid vector
comprising a pair of adeno-associated virus 4 (AAV4) inverted
terminal repeats and a promoter between the inverted terminal
repeats.
[0014] The present invention further provides an AAV4 particle
containing a vector comprising a pair of AAV2 inverted terminal
repeats.
[0015] Additionally, the instant invention provides an isolated
nucleic acid comprising the nucleotide sequence set forth in SEQ ID
NO:1 [AAV4 genome]. Furthermore, the present invention provides an
isolated nucleic acid consisting essentially of the nucleotide
sequence set forth in SEQ ID NO:1 [AAV4 genome].
[0016] The present invention provides an isolated nucleic acid
encoding an adeno-associated virus 4 Rep protein. Additionally
provided is an isolated AAV4 Rep protein having the amino acid
sequence set forth in SEQ ID NO:2, or a unique fragment thereof.
Additionally provided is an isolated AAV4 Rep protein having the
amino acid sequence set forth in SEQ ID NO:8, or a unique fragment
thereof. Additionally provided is an isolated AAV4 Rep protein
having the amino acid sequence set forth in SEQ ID NO:9, or a
unique fragment thereof. Additionally provided is an isolated AAV4
Rep protein having the amino acid sequence set forth in SEQ ID
NO:10, or a unique fragment thereof. Additionally provided is an
isolated AAV4 Rep protein having the amino acid sequence set forth
in SEQ ID NO:11, or a unique fragment thereof.
[0017] The present invention further provides an isolated AAV4
capsid protein having the amino acid sequence set forth in SEQ ID
NO:4. Additionally provided is an isolated AAV4 capsid protein
having the amino acid sequence set forth in SEQ ID NO:16. Also
provided is an isolated AAV4 capsid protein having the amino acid
sequence set forth in SEQ ID NO:18.
[0018] The present invention additionally provides an isolated
nucleic acid encoding adeno-associated virus 4 capsid protein.
[0019] The present invention further provides an AAV4 particle
comprising a capsid protein consisting essentially of the amino
acid sequence set forth in SEQ ID NO:4.
[0020] Additionally provided by the present invention is an
isolated nucleic acid comprising an AAV4 p5 promoter.
[0021] The instant invention provides a method of screening a cell
for infectivity by AAV4 comprising contacting the cell with AAV4
and detecting the presence of AAV4 in the cells.
[0022] The present invention further provides a method of
delivering a nucleic acid to a cell comprising administering to the
cell an AAV4 particle containing a vector comprising the nucleic
acid inserted between a pair of AAV inverted terminal repeats,
thereby delivering the nucleic acid to the cell.
[0023] The present invention also provides a method of delivering a
nucleic acid to a subject comprising administering to a cell from
the subject an AAV4 particle comprising the nucleic acid inserted
between a pair of AAV inverted terminal repeats, and returning the
cell to the subject, thereby delivering the nucleic acid to the
subject.
[0024] The present invention further provides a method of
delivering a nucleic acid to a subject comprising administering to
a cell from the subject an AAV4 particle comprising the nucleic
acid inserted between a pair of AAV inverted terminal repeats, and
returning the cell to the subject, thereby delivering the nucleic
acid to the subject.
[0025] The present invention also provides a method of delivering a
nucleic acid to a cell in a subject comprising administering to the
subject an AAV4 particle comprising the nucleic acid inserted
between a pair of AAV inverted terminal repeats, thereby delivering
the nucleic acid to a cell in the subject.
[0026] The instant invention further provides a method of
delivering a nucleic acid to a cell in a subject having antibodies
to AAV2 comprising administering to the subject an AAV4 particle
comprising the nucleic acid, thereby delivering the nucleic acid to
a cell in the subject.
BRIEF DESCRIPTION OF THE DRAWINGS
[0027] FIG. 1 shows a schematic outline of AAV 4. Promoters are
indicated by horizontal arrows with their corresponding map
positions indicated above. The polyadenylation site is indicated by
a vertical arrow and the two open reading frames are indicated by
black boxes. The splice region is indicated by a shaded box.
[0028] FIG. 2 shows AAV4 ITR. The sequence of the ITR (SEQ ID
NO:20) is shown in the hairpin conformation. The putative Rep
binding site is boxed. The cleavage site in the trs is indicated by
an arrow. Bases which differ from the ITR of AAV2 are outlined.
[0029] FIG. 3 shows cotransduction of rAAV2 and rAAV4. Cos cells
were transduced with a constant amount of rAAV2 or rAAV4 expressing
beta galactosidase and increasing amounts of rAAV2 expressing human
factor IX (rAAV2FIX) . For the competition the number of positive
cells detected in the cotransduced wells was divided by the number
of positive cells in the control wells (cells transduced with only
rAAV2LacZ or rAAV4LacZ) and expressed as a percent of the control.
This value was plotted against the number of particles of
rAAV2FIX.
[0030] FIG. 4 shows effect of trypsin treatment on cos cell
transduction. Cos cell monolayers were trypsinized and diluted in
complete media. Cells were incubated with virus at an MOI of 260
and following cell attachment the virus was removed. As a control
an equal number of cos cells were plated and allowed to attach
overnight before transduction with virus for the same amount of
time. The number of positive cells was determined by staining 50
hrs post transduction. The data is presented as a ratio of the
number of positive cells seen with the trypsinized group and the
control group.
DETAILED DESCRIPTION OF THE INVENTION
[0031] As used in the specification and in the claims, "a" can mean
one or more, depending upon the context in which it is used.
[0032] The present invention provides the nucleotide sequence of
the adeno-associated virus 4 (AAV4) genome and vectors and
particles derived therefrom. Specifically, the present invention
provides a nucleic acid vector comprising a pair of AAV4 inverted
terminal repeats (ITRs) and a promoter between the inverted
terminal repeats. The AAV4 ITRs are exemplified by the nucleotide
sequence set forth in SEQ ID NO:6 and SEQ ID NO:20; however, these
sequences can have minor modifications and still be contemplated to
constitute AAV4 ITRs. The nucleic acid listed in SEQ ID NO:6
depicts the ITR in the "flip" orientation of the ITR. The nucleic
acid listed in SEQ ID NO:20 depicts the ITR in the "flop"
orientation of the ITR. Minor modifications in an ITR of either
orientation are those that will not interfere with the hairpin
structure formed by the AAV4 ITR as described herein and known in
the art. Furthermore, to be considered within the term "AAV4 ITRs"
the nucleotide sequence must retain the Rep binding site described
herein and exemplified in SEQ ID NO:6 and SEQ ID NO:20, i.e., it
must retain one or both features described herein that distinguish
the AAV4 ITR from the AAV2 ITR: (1) four (rather than three as in
AAV2) "GAGC" repeats and (2) in the AAV4 ITR Rep binding site the
fourth nucleotide in the first two "GAGC" repeats is a T rather
than a C.
[0033] The promoter can be any desired promoter, selected by known
considerations, such as the level of expression of a nucleic acid
functionally linked to the promoter and the cell type in which the
vector is to be used. Promoters can be an exogenous or an
endogenous promoter. Promoters can include, for example, known
strong promoters such as SV40 or the inducible metallothionein
promoter, or an AAV promoter, such as an AAV p5 promoter.
Additional examples of promoters include promoters derived from
actin genes, immunoglobulin genes, cytomegalovirus (CMV),
adenovirus, bovine papilloma virus, adenoviral promoters, such as
the adenoviral major late promoter, an inducible heat shock
promoter, respiratory syncytial virus, Rous sarcomas virus (RSV),
etc. Specifically, the promoter can be AAV2 p5 promoter or AAV4 p5
promoter. More specifically, the AAV4 p5 promoter can be about
nucleotides 130 to 291 of SEQ ID NO:1. Additionally, the p5
promoter may be enhanced by nucleotides 1-130. Furthermore, smaller
fragments of p5 promoter that retain promoter activity can readily
be determined by standard procedures including, for example,
constructing a series of deletions in the p5 promoter, linking the
deletion to a reporter gene, and determining whether the reporter
gene is expressed, i.e., transcribed and/or translated.
[0034] It should be recognized that the nucleotide and amino acid
sequences set forth herein may contain minor sequencing errors.
Such errors in the nucleotide sequences can be corrected, for
example, by using the hybridization procedure described above with
various probes derived from the described sequences such that the
coding sequence can be reisolated and resequenced. The
corresponding amino acid sequence can then be corrected
accordingly.
[0035] The AAV4 vector can further comprise an exogenous nucleic
acid functionally linked to the promoter. By "heterologous nucleic
acid" is meant that any heterologous or exogenous nucleic acid can
be inserted into the vector for transfer into a cell, tissue or
organism. The nucleic acid can encode a polypeptide or protein or
an antisense RNA, for example. By "functionally linked" is meant
such that the promoter can promote expression of the heterologous
nucleic acid, as is known in the art, such as appropriate
orientation of the promoter relative to the heterologous nucleic
acid. Furthermore, the heterologous nucleic acid preferably has all
appropriate sequences for expression of the nucleic acid, as known
in the art, to functionally encode, i.e., allow the nucleic acid to
be expressed. The nucleic acid can include, for example, expression
control sequences, such as an enhancer, and necessary information
processing sites, such as ribosome binding sites, RNA splice sites,
polyadenylation sites, and transcriptional terminator
sequences.
[0036] The heterologous nucleic acid can encode beneficial proteins
that replace missing or defective proteins required by the subject
into which the vector in transferred or can encode a cytotoxic
polypeptide that can be directed, e.g., to cancer cells or other
cells whose death would be beneficial to the subject. The
heterologous nucleic acid can also encode antisense RNAs that can
bind to, and thereby inactivate, mRNAs made by the subject that
encode harmful proteins. In one embodiment, antisense
polynucleotides can be produced from a heterologous expression
cassette in an AAV4 viral construct where the expression cassette
contains a sequence that promotes cell-type specific expression
(Wirak et al., EMBO 10:289 (1991)). For general methods relating to
antisense polynucleotides, see Antisense RNA and DNA, D. A. Melton,
Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
(1988).
[0037] Examples of heterologous nucleic acids which can be
administered to a cell or subject as part of the present AAV4
vector can include, but are not limited to the following: nucleic
acids encoding therapeutic agents, such as tumor necrosis factors
(TNF), such as TNF-.alpha.; interferons, such as
interferon-.alpha., interferon-.beta., and interferon-.gamma.;
interleukins, such as IL-1, IL-1.beta., and ILs -2 through -14;
GM-CSF; adenosine deaminase; cellular growth factors, such as
lymphokines; soluble CD4; Factor VIII; Factor IX; T-cell receptors;
LDL receptor; ApoE; ApoC; alpha-1 antitrypsin; ornithine
transcarbamylase (OTC); cystic fibrosis transmembrane receptor
(CFTR); insulin; Fc receptors for antigen binding domains of
antibodies, such as immunoglobulins; and antisense sequences which
inhibit viral replication, such as antisense sequences which
inhibit replication of hepatitis B or hepatitis non-A, non-B virus.
The nucleic acid is chosen considering several factors, including
the cell to be transfected. Where the target cell is a blood cell,
for example, particularly useful nucleic acids to use are those
which allow the blood cells to exert a therapeutic effect, such as
a gene encoding a clotting factor for use in treatment of
hemophilia. Furthermore, the nucleic acid can encode more than one
gene product, limited only, if the nucleic acid is to be packaged
in a capsid, by the size of nucleic acid that can be packaged.
[0038] Furthermore, suitable nucleic acids can include those that,
when transferred into a primary cell, such as a blood cell, cause
the transferred cell to target a site in the body where that cell's
presence would be beneficial. For example, blood cells such as TIL
cells can be modified, such as by transfer into the cell of a Fab
portion of a monoclonal antibody, to recognize a selected antigen.
Another example would be to introduce a nucleic acid that would
target a therapeutic blood cell to tumor cells. Nucleic acids
useful in treating cancer cells include those encoding chemotactic
factors which cause an inflammatory response at a specific site,
thereby having a therapeutic effect.
[0039] Cells, particularly blood cells, having such nucleic acids
transferred into them can be useful in a variety of diseases,
syndromes and conditions. For example, suitable nucleic acids
include nucleic acids encoding soluble CD4, used in the treatment
of AIDS and .alpha.-antitrypsin, used in the treatment of emphysema
caused by .alpha.-antitrypsin deficiency. Other diseases, syndromes
and conditions in which such cells can be useful include, for
example, adenosine deaminase deficiency, sickle cell deficiency,
brain disorders such as Alzheimer's disease, thalassemia,
hemophilia, diabetes, phenylketonuria, growth disorders and heart
diseases, such as those caused by alterations in cholesterol
metabolism, and defects of the immune system.
[0040] As another example, hepatocytes can be transfected with the
present vectors having useful nucleic acids to treat liver disease.
For example, a nucleic acid encoding OTC can be used to transfect
hepatocytes (ex vivo and returned to the liver or in vivo) to treat
congenital hyperammonemia, caused by an inherited deficiency in
OTC. Another example is to use a nucleic acid encoding LDL to
target hepatocytes ex vivo or in vivo to treat inherited LDL
receptor deficiency. Such transfected hepatocytes can also be used
to treat acquired infectious diseases, such as diseases resulting
from a viral infection. For example, transduced hepatocyte
precursors can be used to treat viral hepatitis, such as hepatitis
B and non-A, non-B hepatitis, for example by transducing the
hepatocyte precursor with a nucleic acid encoding an antisense RNA
that inhibits viral replication. Another example includes
transferring a vector of the present invention having a nucleic
acid encoding a protein, such as .alpha.-interferon, which can
confer resistance to the hepatitis virus.
[0041] For a procedure using transfected hepatocytes or hepatocyte
precursors, hepatocyte precursors having a vector of the present
invention transferred in can be grown in tissue culture, removed
form the tissue culture vessel, and introduced to the body, such as
by a surgical method. In this example, the tissue would be placed
directly into the liver, or into the body cavity in proximity to
the liver, as in a transplant or graft. Alternatively, the cells
can simply be directly injected into the liver, into the portal
circulatory system, or into the spleen, from which the cells can be
transported to the liver via the circulatory system. Furthermore,
the cells can be attached to a support, such as microcarrier beads,
which can then be introduced, such as by injection, into the
peritoneal cavity. Once the cells are in the liver, by whatever
means, the cells can then express the nucleic acid and/or
differentiate into mature hepatocytes which can express the nucleic
acid.
[0042] The present invention also contemplates any unique fragment
of these AAV4 nucleic acids, including the AAV4 nucleic acids set
forth in SEQ ID NOs: 1, 3, 5, 6, 7, 12-15, 17 and 19. To be unique,
the fragment must be of sufficient size to distinguish it from
other known sequences, most readily determined by comparing any
nucleic acid fragment to the nucleotide sequences of nucleic acids
in computer databases, such as GenBank. Such comparative searches
are standard in the art. Typically, a unique fragment useful as a
primer or probe will be at least about 8 or 10 to about 20 or 25
nucleotides in length, depending upon the specific nucleotide
content of the sequence. Additionally, fragments can be, for
example, at least about 30, 40, 50, 75, 100, 200 or 500 nucleotides
in length. The nucleic acid can be single or double stranded,
depending upon the purpose for which it is intended.
[0043] The present invention further provides an AAV4 capsid
protein. In particular, the present invention provides not only a
polypeptide comprising all three AAV4 coat proteins, i.e., VP1, VP2
and VP3, but also a polypeptide comprising each AAV4 coat protein
individually. Thus an AAV4 particle comprising an AAV4 capsid
protein comprises at least one AAV4 coat protein VP1, VP2 or VP3.
An AAV4 particle comprising an AAV4 capsid protein can be utilized
to deliver a nucleic acid vector to a cell, tissue or subject. For
example, the herein described AAV4 vectors can be encapsulated in
an AAV4 particle and utilized in a gene delivery method.
Furthermore, other viral nucleic acids can be encapsidated in the
AAV4 particle and utilized in such delivery methods. For example,
an AAV2 vector can be encapsidated in an AAV4 particle and
administered. Furthermore, a chimeric capsid protein incorporating
both AAV2 and AAV4 sequences can be generated, by standard cloning
methods, selecting regions from each protein as desired. For
example, particularly antigenic regions of the AAV2 capsid protein
can be replaced with the corresponding region of the AAV4 capsid
protein.
[0044] The herein described AAV4 nucleic acid vector can be
encapsidated in an AAV particle. In particular, it can be
encapsidated in an AAV1 particle, an AAV2 particle, an AAV3
particle, an AAV4 particle, or an AAV5 particle by standard methods
using the appropriate capsid proteins in the encapsidation process,
as long as the nucleic acid vector fits within the size limitation
of the particle utilized. The encapsidation process itself is
standard in the art.
[0045] An AAV4 particle is a viral particle comprising an AAV4
capsid protein. An AAV4 capsid polypeptide encoding the entire VP1,
VP2, and VP3 polypeptide can overall have at least about 63%
homology to the polypeptide having the amino acid sequence encoded
by nucleotides 2260-4464 set forth in SEQ ID NO:1 (AAV4 capsid
protein). The capsid protein can have about 70% homology, about 75%
homology, 80% homology, 85% homology, 90% homology, 95% homology,
98% homology, 99% homology, or even 100% homology to the protein
having the amino acid sequence encoded by nucleotides 2260-4464 set
forth in SEQ ID NO:1. The particle can be a particle comprising
both AAV4 and AAV2 capsid protein, i.e., a chimeric protein.
Variations in the amino acid sequence of the AAV4 capsid protein
are contemplated herein, as long as the resulting viral particle
comprising the AAV4 capsid remains antigenically or immunologically
distinct from AAV2, as can be routinely determined by standard
methods. Specifically, for example, ELISA and Western blots can be
used to determine whether a viral particle is antigenically or
immunologically distinct from AAV2. Furthermore, the AAV4 viral
particle preferably retains tissue tropism distinction from AAV2,
such as that exemplified in the examples herein, though an AAV4
chimeric particle comprising at least one AAV4 coat protein may
have a different tissue tropism from that of an AAV4 particle
consisting only of AAV4 coat proteins.
[0046] The invention further provides an AAV4 particle containing,
i.e., encapsidating, a vector comprising a pair of AAV2 inverted
terminal repeats. The nucleotide sequence of AAV2 ITRs is known in
the art. Furthermore, the particle can be a particle comprising
both AAV4 and AAV2 capsid protein, i.e., a chimeric protein. The
vector encapsidated in the particle can further comprise an
exogenous nucleic acid inserted between the inverted terminal
repeats.
[0047] The present invention further provides an isolated nucleic
acid comprising the nucleotide sequence set forth in SEQ ID NO:1
(AAV4 genome). This nucleic acid, or portions thereof, can be
inserted into other vectors, such as plasmids, yeast artificial
chromosomes, or other viral vectors, if desired, by standard
cloning methods. The present invention also provides an isolated
nucleic acid consisting essentially of the nucleotide sequence set
forth in SEQ ID NO:1. The nucleotides of SEQ ID NO:1 can have minor
modifications and still be contemplated by the present invention.
For example, modifications that do not alter the amino acid encoded
by any given codon (such as by modification of the third, "wobble,"
position in a codon) can readily be made, and such alterations are
known in the art. Furthermore, modifications that cause a resulting
neutral amino acid substitution of a similar amino acid can be made
in a coding region of the genome. Additionally, modifications as
described herein for the AAV4 components, such as the ITRs, the p5
promoter, etc. are contemplated in this invention.
[0048] The present invention additionally provides an isolated
nucleic acid that selectively hybridizes with an isolated nucleic
acid consisting essentially of the nucleotide sequence set forth in
SEQ ID NO:1 (AAV4 genome). The present invention further provides
an isolated nucleic acid that selectively hybridizes with an
isolated nucleic acid comprising the nucleotide sequence set forth
in SEQ ID NO:1 (AAV4 genome). By "selectively hybridizes" as used
in the claims is meant a nucleic acid that specifically hybridizes
to the particular target nucleic acid under sufficient stringency
conditions to selectively hybridize to the target nucleic acid
without significant background hybridization to a nucleic acid
encoding an unrelated protein, and particularly, without detectably
hybridizing to AAV2. Thus, a nucleic acid that selectively
hybridizes with a nucleic acid of the present invention will not
selectively hybridize under stringent conditions with a nucleic
acid encoding a different protein, and vice versa. Therefore,
nucleic acids for use, for example, as primers and probes to detect
or amplify the target nucleic acids are contemplated herein.
Nucleic acid fragments that selectively hybridize to any given
nucleic acid can be used, e.g., as primers and or probes for
further hybridization or for amplification methods (e.g.,
polymerase chain reaction (PCR), ligase chain reaction (LCR)).
Additionally, for example, a primer or probe can be designed that
selectively hybridizes with both AAV4 and a gene of interest
carried within the AAV4 vector (i.e., a chimeric nucleic acid).
[0049] Stringency of hybridization is controlled by both
temperature and salt concentration of either or both of the
hybridization and washing steps. Typically, the stringency of
hybridization to achieve selective hybridization involves
hybridization in high ionic strength solution (6.times.SSC or
6.times.SSPE) at a temperature that is about 12-25.degree. C. below
the T.sub.m (the melting temperature at which half of the molecules
dissociate from its partner) followed by washing at a combination
of temperature and salt concentration chosen so that the washing
temperature is about 5.degree. C. to 20.degree. C. below the
T.sub.m The temperature and salt conditions are readily determined
empirically in preliminary experiments in which samples of
reference DNA immobilized on filters are hybridized to a labeled
nucleic acid of interest and then washed under conditions of
different stringencies. Hybridization temperatures are typically
higher for DNA-RNA and RNA-RNA hybridizations. The washing
temperatures can be used as described above to achieve selective
stringency, as is known in the art. (Sambrook et al., Molecular
Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor
Laboratory, Cold Spring Harbor, N.Y., 1989; Kunkel et al. Methods
Enzymol. 1987:154:367, 1987). A preferable stringent hybridization
condition for a DNA:DNA hybridization can be at about 68.degree. C.
(in aqueous solution) in 6.times.SSC or 6.times.SSPE followed by
washing at 68.degree. C. Stringency of hybridization and washing,
if desired, can be reduced accordingly as homology desired is
decreased, and further, depending upon the G-C or A-T richness of
any area wherein variability is searched for. Likewise, stringency
of hybridization and washing, if desired, can be increased
accordingly as homology desired is increased, and further,
depending upon the G-C or A-T richness of any area wherein high
homology is desired, all as known in the art.
[0050] A nucleic acid that selectively hybridizes to any portion of
the AAV4 genome is contemplated herein. Therefore, a nucleic acid
that selectively hybridizes to AAV4 can be of longer length than
the AAV4 genome, it can be about the same length as the AAV4 genome
or it can be shorter than the AAV4 genome. The length of the
nucleic acid is limited on the shorter end of the size range only
by its specificity for hybridization to AAV4, i.e., once it is too
short, typically less than about 5 to 7 nucleotides in length, it
will no longer bind specifically to AAV4, but rather will hybridize
to numerous background nucleic acids. Additionally contemplated by
this invention is a nucleic acid that has a portion that
specifically hybridizes to AAV4 and a portion that specifically
hybridizes to a gene of interest inserted within AAV4.
[0051] The present invention further provides an isolated nucleic
acid encoding an adeno-associated virus 4 Rep protein. The AAV4 Rep
proteins are encoded by open reading frame (ORF) 1 of the AAV4
genome. The AAV4 Rep genes are exemplified by the nucleic acid set
forth in SEQ ID NO:3 (AAV4 ORF1), and include a nucleic acid
consisting essentially of the nucleotide sequence set forth in SEQ
ID NO:3 and a nucleic acid comprising the nucleotide sequence set
forth in SEQ ID NO:3. The present invention also includes a nucleic
acid encoding the amino acid sequence set forth in SEQ ID NO:2
(polypeptide encoded by AAV4 ORF1). However, the present invention
includes that the Rep genes nucleic acid can include any one, two,
three, or four of the four Rep proteins, in any order, in such a
nucleic acid. Furthermore, minor modifications are contemplated in
the nucleic acid, such as silent mutations in the coding sequences,
mutations that make neutral or conservative changes in the encoded
amino acid sequence, and mutations in regulatory regions that do
not disrupt the expression of the gene. Examples of other minor
modifications are known in the art. Further modifications can be
made in the nucleic acid, such as to disrupt or alter expression of
one or more of the Rep proteins in order to, for example, determine
the effect of such a disruption; such as to mutate one or more of
the Rep proteins to determine the resulting effect, etc. However,
in general, a modified nucleic acid encoding all four Rep proteins
will have at least about 90%, about 93%, about 95%, about 98% or
100% homology to the sequence set forth in SEQ ID NO:3, and the Rep
polypeptide encoded therein will have overall about 93%, about 95%,
about 98%, about 99% or 100% homology with the amino acid sequence
set forth in SEQ ID NO:2.
[0052] The present invention also provides an isolated nucleic acid
that selectively hybridizes with a nucleic acid consisting
essentially of the nucleotide sequence set forth in SEQ ID NO:3 and
an isolated nucleic acid that selectively hybridizes with a nucleic
acid comprising the nucleotide sequence set forth in SEQ ID NO:3.
"Selectively hybridizing" is defined elsewhere herein.
[0053] The present invention also provides each individual AAV4 Rep
protein and the nucleic acid encoding each. Thus the present
invention provides the nucleic acid encoding a Rep 40 protein, and
in particular an isolated nucleic acid comprising the nucleotide
sequence set forth in SEQ ID NO:12, an isolated nucleic acid
consisting essentially of the nucleotide sequence set forth in SEQ
ID NO:12, and a nucleic acid encoding the adeno-associated virus 4
Rep protein having the amino acid sequence set forth in SEQ ID
NO:8. The present invention also provides the nucleic acid encoding
a Rep 52 protein, and in particular an isolated nucleic acid
comprising the nucleotide sequence set forth in SEQ ID NO:13, an
isolated nucleic acid consisting essentially of the nucleotide
sequence set forth in SEQ ID NO:13, and a nucleic acid encoding the
adeno-associated virus 4 Rep protein having the amino acid sequence
set forth in SEQ ID NO:9. The present invention further provides
the nucleic acid encoding a Rep 68 protein, and in particular an
isolated nucleic acid comprising the nucleotide sequence set forth
in SEQ ID NO:14, an isolated nucleic acid consisting essentially of
the nucleotide sequence set forth in SEQ ID NO:14, and a nucleic
acid encoding the adeno-associated virus 4 Rep protein having the
amino acid sequence set forth in SEQ ID NO:10. And, further, the
present invention provides the nucleic acid encoding a Rep 78
protein, and in particular an isolated nucleic acid comprising the
nucleotide sequence set forth in SEQ ID NO:15, an isolated nucleic
acid consisting essentially of the nucleotide sequence set forth in
SEQ ID NO:15, and a nucleic acid encoding the adeno-associated
virus 4 Rep protein having the amino acid sequence set forth in SEQ
ID NO:11. As described elsewhere herein, these nucleic acids can
have minor modifications, including silent nucleotide
substitutions, mutations causing neutral amino acid substitutions
in the encoded proteins, and mutations in control regions that do
not or minimally affect the encoded amino acid sequence.
[0054] The present invention further provides a nucleic acid
encoding the entire AAV4 Capsid polypeptide. Specifically, the
present invention provides a nucleic acid having the nucleotide
sequence set for the nucleotides 2260-4464 of SEQ ID NO:1.
Furthermore, the present invention provides a nucleic acid encoding
each of the three AAV4 coat proteins, VP1, VP2, and VP3. Thus, the
present invention provides a nucleic acid encoding AAV4 VP1, a
nucleic acid encoding AAV4 VP2, and a nucleic acid encoding AAV4
VP3. Thus, the present invention provides a nucleic acid encoding
the amino acid sequence set forth in SEQ ID NO:4 (VP1); a nucleic
acid encoding the amino acid sequence set forth in SEQ ID NO:16
(VP2), and a nucleic acid encoding the amino acid sequence set
forth in SEQ ID NO:18 (VP3). The present invention also
specifically provides a nucleic acid comprising SEQ ID NO:5 (VP1
gene); a nucleic acid comprising SEQ ID NO:17 (VP2 gene); and a
nucleic acid comprising SEQ ID NO:19 (VP3 gene). The present
invention also specifically provides a nucleic acid consisting
essentially of SEQ ID NO:5 (VP1 gene), a nucleic acid consisting
essentially of SEQ ID NO:17 (VP2 gene), and a nucleic acid
consisting essentially of SEQ ID NO:19 (VP3 gene). Furthermore, a
nucleic acid encoding an AAV4 capsid protein VP1 is set forth as
nucleotides 2157-4361 of SEQ ID NO:1; a nucleic acid encoding an
AAV4 capsid protein VP2 is set forth as nucleotides 2565-4361 of
SEQ ID NO:1; and a nucleic acid encoding an AAV4 capsid protein VP3
is set forth as nucleotides 2745-4361 of SEQ ID NO:1. Minor
modifications in the nucleotide sequences encoding the capsid, or
coat, proteins are contemplated, as described above for other AAV4
nucleic acids.
[0055] The present invention also provides a cell containing one or
more of the herein described nucleic acids, such as the AAV4
genome, AAV4 ORF1 and ORF2, each AAV4 Rep protein gene, and each
AAV4 capsid protein gene. Such a cell can be any desired cell and
can be selected based upon the use intended. For example, cells can
include human HeLa cells, cos cells, other human and mammalian
cells and cell lines. Primary cultures as well as established
cultures and cell lines can be used. Nucleic acids of the present
invention can be delivered into cells by any selected means, in
particular depending upon the target cells. Many delivery means are
well-known in the art. For example, electroporation, calcium
phosphate precipitation, microinjection, cationic or anionic
liposomes, and liposomes in combination with a nuclear localization
signal peptide for delivery to the nucleus can be utilized, as is
known in the art. Additionally, if in a viral particle, the cells
can simply be transfected with the particle by standard means known
in the art for AAV transfection.
[0056] The term "polypeptide" as used herein refers to a polymer of
amino acids and includes fill-length proteins and fragments
thereof. Thus, "protein," "polypeptide," and "peptide" are often
used interchangeably herein. Substitutions can be selected by known
parameters to be neutral (see, e.g., Robinson W E Jr, and Mitchell
W M., AIDS 4:S151-S162 (1990)). As will be appreciated by those
skilled in the art, the invention also includes those polypeptides
having slight variations in amino acid sequences or other
properties. Such variations may arise naturally as allelic
variations (e.g., due to genetic polymorphism) or may be produced
by human intervention (e.g., by mutagenesis of cloned DNA
sequences), such as induced point, deletion, insertion and
substitution mutants. Minor changes in amino acid sequence are
generally preferred, such as conservative amino acid replacements,
small internal deletions or insertions, and additions or deletions
at the ends of the molecules. Substitutions may be designed based
on, for example, the model of Dayhoff, et al. (in Atlas of Protein
Sequence and Structure 1978, Nat'l Biomed. Res. Found., Washington,
D.C.). These modifications can result in changes in the amino acid
sequence, provide silent mutations, modify a restriction site, or
provide other specific mutations.
[0057] A polypeptide of the present invention can be readily
obtained by any of several means. For example, polypeptide of
interest can be synthesized mechanically by standard methods.
Additionally, the coding regions of the genes can be expressed and
the resulting polypeptide isolated by standard methods.
Furthermore, an antibody specific for the resulting polypeptide can
be raised by standard methods (see, e.g., Harlow and Lane,
Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory,
Cold Spring Harbor, N.Y., 1988), and the protein can be isolated
from a cell expressing the nucleic acid encoding the polypeptide by
selective hybridization with the antibody. This protein can be
purified to the extent desired by standard methods of protein
purification (see, e.g., Sambrook et al., Molecular Cloning: A
Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold
Spring Harbor, N.Y., 1989).
[0058] Typically, to be unique, a polypeptide fragment of the
present invention will be at least about 5 amino acids in length;
however, unique fragments can be 6, 7, 8, 9, 10, 20, 30, 40, 50,
60, 70, 80, 90, 100 or more amino acids in length. A unique
polypeptide will typically comprise such a unique fragment;
however, a unique polypeptide can also be determined by its overall
homology. A unique polypeptide can be 6, 7, 8, 9, 10, 20, 30, 40,
50, 60, 70, 80, 90, 100 or more amino acids in length. Uniqueness
of a polypeptide fragment can readily be determined by standard
methods such as searches of computer databases of known peptide or
nucleic acid sequences or by hybridization studies to the nucleic
acid encoding the protein or to the protein itself, as known in the
art.
[0059] The present invention provides an isolated AAV4 Rep protein.
AAV4 Rep polypeptide is encoded by ORF1 of AAV4. Specifically, the
present invention provides an AAV4 Rep polypeptide comprising the
amino acid sequence set forth in SEQ ID NO:2, or a unique fragment
thereof. The present invention also provides an AAV4 Rep
polypeptide consisting essentially of the amino acid sequence set
forth in SEQ ID NO:2, or a unique fragment thereof Additionally,
nucleotides 291-2306 of the AAV4 genome, which genome is set forth
in SEQ ID NO:1, encode the AAV4 Rep polypeptide. The present
invention also provides each AAV4 Rep protein. Thus the present
invention provides AAV4 Rep 40, or a unique fragment thereof. The
present invention particularly provides Rep 40 having the amino
acid sequence set forth in SEQ ID NO:8. The present invention
provides AAV4 Rep 52, or a unique fragment thereof. The present
invention particularly provides Rep 52 having the amino acid
sequence set forth in SEQ ID NO:9. The present invention provides
AAV4 Rep 68, or a unique fragment thereof The present invention
particularly provides Rep 68 having the amino acid sequence set
forth in SEQ ID NO:10. The present invention provides AAV4 Rep 78,
or a unique fragment thereof The present invention particularly
provides Rep 78 having the amino acid sequence set forth in SEQ ID
NO:11. By "unique fragment thereof" is meant any smaller
polypeptide fragment encoded by AAV rep gene that is of sufficient
length to be unique to the Rep polypeptide. Substitutions and
modifications of the amino acid sequence can be made as described
above and, further, can include protein processing modifications,
such as glycosylation, to the polypeptide. However, a polypeptide
including all four Rep proteins will encode a polypeptide having at
least about 91% overall homology to the sequence set forth in SEQ
ID NO:2, and it can have about 93%, about 95%, about 98%, about 99%
or 100% homology with the amino acid sequence set forth in SEQ ID
NO:2.
[0060] The present invention further provides an AAV4 Capsid
polypeptide or a unique fragment thereof AAV4 capsid polypeptide is
encoded by ORF 2 of AAV4. Specifically, the present invention
provides an AAV4 Capsid protein comprising the amino acid sequence
encoded by nucleotides 2260-4464 of the nucleotide sequence set
forth in SEQ ID NO:1, or a unique fragment of such protein. The
present invention also provides an AAV4 Capsid protein consisting
essentially of the amino acid sequence encoded by nucleotides
2260-4464 of the nucleotide sequence set forth in SEQ ID NO:1, or a
unique fragment of such protein. The present invention further
provides the individual AAV4 coat proteins, VP1, VP2 and VP3. Thus,
the present invention provides an isolated polypeptide having the
amino acid sequence set forth in SEQ ID NO:4 (VP1). The present
invention additionally provides an isolated polypeptide having the
amino acid sequence set forth in SEQ ID NO:16 (VP2). The present
invention also provides an isolated polypeptide having the amino
acid sequence set forth in SEQ ID NO:18 (VP3). By "unique fragment
thereof" is meant any smaller polypeptide fragment encoded by any
AAV4 capsid gene that is of sufficient length to be unique to the
AAV4 Capsid protein. Substitutions and modifications of the amino
acid sequence can be made as described above and, further, can
include protein processing modifications, such as glycosylation, to
the polypeptide. However, an AAV4 Capsid polypeptide including all
three coat proteins will have at least about 63% overall homology
to the polypeptide encoded by nucleotides 2260-4464 of the sequence
set forth in SEQ ID NO:1. The protein can have about 65%, about
70%, about 75%, about 80%, about 85%, about 90%, about 95% or even
100% homology to the amino acid sequence encoded by the nucleotides
2260-4464 of the sequence set forth in SEQ ID NO:4. An AAV4 VP2
polypeptide can have at least about 58%, about 60%, about 70%,
about 80%, about 90% about 95% or about 100% homology to the amino
acid sequence set forth in SEQ ID NO:16. An AAV4 VP3 polypeptide
can have at least about 60%, about 70%, about 80%, about 90% about
95% or about 100% homology to the amino acid sequence set forth in
SEQ ID NO:18.
[0061] The present invention further provides an isolated antibody
that specifically binds AAV4 Rep protein. Also provided is an
isolated antibody that specifically binds the AAV4 Rep protein
having the amino acid sequence set forth in SEQ ID NO:2, or that
specifically binds a unique fragment thereof. Clearly, any given
antibody can recognize and bind one of a number of possible
epitopes present in the polypeptide; thus only a unique portion of
a polypeptide (having the epitope) may need to be present in an
assay to determine if the antibody specifically binds the
polypeptide.
[0062] The present invention additionally provides an isolated
antibody that specifically binds any adeno-associated virus 4
Capsid protein or the polypeptide comprising all three AAV4 coat
proteins. Also provided is an isolated antibody that specifically
binds the AAV4 Capsid protein having the amino acid sequence set
forth in SEQ ID NO:4, or that specifically binds a unique fragment
thereof. The present invention further provides an isolated
antibody that specifically binds the AAV4 Capsid protein having the
amino acid sequence set forth in SEQ ID NO:16, or that specifically
binds a unique fragment thereof. The invention additionally
provides an isolated antibody that specifically binds the AAV4
Capsid protein having the amino acid sequence set forth in SEQ ID
NO:18, or that specifically binds a unique fragment thereof. Again,
any given antibody can recognize and bind one of a number of
possible epitopes present in the polypeptide; thus only a unique
portion of a polypeptide (having the epitope) may need to be
present in an assay to determine if the antibody specifically binds
the polypeptide.
[0063] The antibody can be a component of a composition that
comprises an antibody that specifically binds the AAV4 protein. The
composition can further comprise, e.g., serum, serum-free medium,
or a pharmaceutically acceptable carrier such as physiological
saline, etc.
[0064] By "an antibody that specifically binds" an AAV4 polypeptide
or protein is meant an antibody that selectively binds to an
epitope on any portion of the AAV4 peptide such that the antibody
selectively binds to the AAV4 polypeptide, i.e., such that the
antibody binds specifically to the corresponding AAV4 polypeptide
without significant background. Specific binding by an antibody
further means that the antibody can be used to selectively remove
the target polypeptide from a sample comprising the polypeptide or
and can readily be determined by radioimmuno assay (RIA), bioassay,
or enzyme-linked immunosorbant (ELISA) technology. An ELISA method
effective for the detection of the specific antibody-antigen
binding can, for example, be as follows: (1) bind the antibody to a
substrate; (2) contact the bound antibody with a sample containing
the antigen; (3) contact the above with a secondary antibody bound
to a detectable moiety (e.g., horseradish peroxidase enzyme or
alkaline phosphatase enzyme); (4) contact the above with the
substrate for the enzyme; (5) contact the above with a color
reagent; (6) observe the color change.
[0065] An antibody can include antibody fragments such as Fab
fragments which retain the binding activity. Antibodies can be made
as described in, e.g., Harlow and Lane, Antibodies: A Laboratory
Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
(1988). Briefly, purified antigen can be injected into an animal in
an amount and in intervals sufficient to elicit an immune response.
Antibodies can either be purified directly, or spleen cells can be
obtained from the animal. The cells are then fused with an immortal
cell line and screened for antibody secretion. Individual
hybridomas are then propagated as individual clones serving as a
source for a particular monoclonal antibody.
[0066] The present invention additionally provides a method of
screening a cell for infectivity by AAV4 comprising contacting the
cell with AAV4 and detecting the presence of AAV4 in the cells.
AAV4 particles can be detected using any standard physical or
biochemical methods. For example, physical methods that can be used
for this detection include 1) polymerase chain reaction (PCR) for
viral DNA or RNA, 2) direct hybridization with labeled probes, 3)
antibody directed against the viral structural or non-structural
proteins. Catalytic methods of viral detection include, but are not
limited to, detection of site and strand specific DNA nicking
activity of Rep proteins or replication of an AAV origin-containing
substrate. Additional detection methods are outlined in Fields,
Virology, Raven Press, New York, N.Y. 1996.
[0067] For screening a cell for infectivity by AAV4 wherein the
presence of AAV4 in the cells is determined by nucleic acid
hybridization methods, a nucleic acid probe for such detection can
comprise, for example, a unique fragment of any of the AAV4 nucleic
acids provided herein. The uniqueness of any nucleic acid probe can
readily be determined as described herein for unique nucleic acids.
The nucleic acid can be, for example, the nucleic acid whose
nucleotide sequence is set forth in SEQ ID NO:1, 3, 5, 6, 7, 12,
13, 14, 15, 17 or 19, or a unique fragment thereof.
[0068] The present invention includes a method of determining the
suitability of an AAV4 vector for administration to a subject
comprising administering to an antibody-containing sample from the
subject an antigenic fragment of an isolated AAV4 capsid protein,
and detecting an antibody-antigen reaction in the sample, the
presence of a reaction indicating the AAV4 vector to be unsuitable
for use in the subject. The AAV4 capsid protein from which an
antigenic fragment is selected can have the amino acid sequence set
forth in SEQ ID NO:4. An immunogenic fragment of an isolated AAV4
capsid protein can also be used in these methods. The AAV4 capsid
protein from which an antigenic fragment is selected can have the
amino acid sequence set forth in SEQ ID NO:17. The AAV4 capsid
protein from which an antigenic fragment is selected can have the
amino acid sequence set forth in SEQ ID NO:19.
[0069] Alternatively, or additionally, an antigenic fragment of an
isolated AAV4 Rep protein can be utilized in this determination
method. An immunogenic fragment of an isolated AAV4 Rep protein can
also be used in these methods. Thus the present invention further
provides a method of determining the suitability of an AAV4 vector
for administration to a subject comprising administering to an
antibody-containing sample from the subject an antigenic fragment
of an AAV4 Rep protein and detecting an antibody-antigen reaction
in the sample, the presence of a reaction indicating the AAV4
vector to be unsuitable for use in the subject. The AAV4 Rep
protein from which an antigenic fragment is selected can have the
amino acid sequence set forth in SEQ ID NO:2. The AAV4 Rep protein
from which an antigenic fragment is selected can have the amino
acid sequence set forth in SEQ ID NO:8. The AAV4 Rep protein from
which an antigenic fragment is selected can have the amino acid
sequence set forth in SEQ ID NO:9. The AAV4 Rep protein from which
an antigenic fragment is selected can have the amino acid sequence
set forth in SEQ ID NO:10. The AAV4 Rep protein from which an
antigenic fragment is selected can have the amino acid sequence set
forth in SEQ ID NO:11.
[0070] An antigenic or immunoreactive fragment is typically an
amino acid sequence of at least about 5 consecutive amino acids,
and it can be derived from the AAV4 polypeptide amino acid
sequence. An antigenic fragment is any fragment unique to the AAV4
protein, as described herein, against which an AAV4-specific
antibody can be raised, by standard methods. Thus, the resulting
antibody-antigen reaction should be specific for AAV4.
[0071] The AAV4 polypeptide fragments can be analyzed to determine
their antigenicity, immunogenicity and/or specificity. Briefly,
various concentrations of a putative immunogenically specific
fragment are prepared and administered to a subject and the
immunological response (e.g., the production of antibodies or cell
mediated immunity) of an animal to each concentration is
determined. The amounts of antigen administered depend on the
subject, e.g. a human, rabbit or a guinea pig, the condition of the
subject, the size of the subject, etc. Thereafter an animal so
inoculated with the antigen can be exposed to the AAV4 viral
particle or AAV4 protein to test the immunoreactivity or the
antigenicity of the specific immunogenic fragment. The specificity
of a putative antigenic or immunogenic fragment can be ascertained
by testing sera, other fluids or lymphocytes from the inoculated
animal for cross reactivity with other closely related viruses,
such as AAV1, AAV2, AAV3 and AAV5.
[0072] As will be recognized by those skilled in the art, numerous
types of immunoassays are available for use in the present
invention to detect binding between an antibody and an AAV4
polypeptide of this invention. For instance, direct and indirect
binding assays, competitive assays, sandwich assays, and the like,
as are generally described in, e.g., U.S. Pat. Nos. 4,642,285;
4,376,110; 4,016,043; 3,879,262; 3,852,157; 3,850,752; 3,839,153;
3,791,932; and Harlow and Lane, Antibodies, A Laboratory Manual,
Cold Spring Harbor Publications, N.Y. (1988). For example, enzyme
immunoassays such as immunofluorescence assays (IFA), enzyme linked
immunosorbent assays (ELISA) and immunoblotting can be readily
adapted to accomplish the detection of the antibody. An ELISA
method effective for the detection of the antibody bound to the
antigen can, for example, be as follows: (1) bind the antigen to a
substrate; (2) contact the bound antigen with a fluid or tissue
sample containing the antibody; (3) contact the above with a
secondary antibody specific for the antigen and bound to a
detectable moiety (e.g., horseradish peroxidase enzyme or alkaline
phosphatase enzyme); (4) contact the above with the substrate for
the enzyme; (5) contact the above with a color reagent; (6) observe
color change.
[0073] The antibody-containing sample of this method can comprise
any biological sample which would contain the antibody or a cell
containing the antibody, such as blood, plasma, serum, bone marrow,
saliva and urine.
[0074] By the "suitability of an AAV4 vector for administration to
a subject" is meant a determination of whether the AAV4 vector will
elicit a neutralizing immune response upon administration to a
particular subject. A vector that does not elicit a significant
immune response is a potentially suitable vector, whereas a vector
that elicits a significant, neutralizing immune response is thus
indicated to be unsuitable for use in that subject. Significance of
any detectable immune response is a standard parameter understood
by the skilled artisan in the field. For example, one can incubate
the subject's serum with the virus, then determine whether that
virus retains its ability to transduce cells in culture. If such
virus cannot transduce cells in culture, the vector likely has
elicited a significant immune response.
[0075] The present method further provides a method of delivering a
nucleic acid to a cell comprising administering to the cell an AAV4
particle containing a vector comprising the nucleic acid inserted
between a pair of AAV inverted terminal repeats, thereby delivering
the nucleic acid to the cell. Administration to the cell can be
accomplished by any means, including simply contacting the
particle, optionally contained in a desired liquid such as tissue
culture medium, or a buffered saline solution, with the cells. The
particle can be allowed to remain in contact with the cells for any
desired length of time, and typically the particle is administered
and allowed to remain indefinitely. For such in vitro methods, the
virus can be administered to the cell by standard viral
transduction methods, as known in the art and as exemplified
herein. Titers of virus to administer can vary, particularly
depending upon the cell type, but will be typical of that used for
AAV transduction in general. Additionally the titers used to
transduce the particular cells in the present examples can be
utilized. The cells can include any desired cell, such as the
following cells and cells derived from the following tissues, in
humans as well as other mammals, such as primates, horse, sheep,
goat, pig, dog, rat, and mouse: Adipocytes, Adenocyte, Adrenal
cortex, Amnion, Aorta, Ascites, Astrocyte, Bladder, Bone, Bone
marrow, Brain, Breast, Bronchus, Cardiac muscle, Cecum, Cervix,
Chorion, Colon, Conjunctiva, Connective tissue, Cornea, Dermis,
Duodenum, Endometrium, Endothelium, Epithelial tissue, Epidermis,
Esophagus, Eye, Fascia, Fibroblasts, Foreskin, Gastric, Glial
cells, Glioblast, Gonad, Hepatic cells, Histocyte, Ileum,
Intestine, small Intestine, Jejunum, Keratinocytes, Kidney, Larynx,
Leukocytes, Lipocyte, Liver, Lung, Lymph node, Lymphoblast,
Lymphocytes, Macrophages, Mammary alveolar nodule, Mammary gland,
Mastocyte, Maxilla, Melanocytes, Monocytes, Mouth, Myelin, Nervous
tissue, Neuroblast, Neurons, Neuroglia, Osteoblasts, Osteogenic
cells, Ovary, Palate, Pancreas, Papilloma, Peritoneum, Pituicytes,
Pharynx, Placenta, Plasma cells, Pleura, Prostate, Rectum, Salivary
gland, Skeletal muscle, Skin, Smooth muscle, Somatic, Spleen,
Squamous, Stomach, Submandibular gland, Submaxillary gland,
Synoviocytes, Testis, Thymus, Thyroid, Trabeculae, Trachea,
Turbinate, Umbilical cord, Ureter, and Uterus.
[0076] The AAV inverted terminal repeats in the vector for the
herein described delivery methods can be AAV4 inverted terminal
repeats. Specifically, they can comprise the nucleic acid whose
nucleotide sequence is set forth in SEQ ID NO:6 or the nucleic acid
whose nucleotide sequence is set forth in SEQ ID NO:20, or any
fragment thereof demonstrated to have ITR functioning. The ITRs can
also consist essentially of the nucleic acid whose nucleotide
sequence is set forth in SEQ ID NO:6 or the nucleic acid whose
nucleotide sequence is set forth in SEQ ID NO:20. Furthermore, the
AAV inverted terminal repeats in the vector for the herein
described nucleic acid delivery methods can also comprise AAV2
inverted terminal repeats. Additionally, the AAV inverted terminal
repeats in the vector for this delivery method can also consist
essentially of AAV2 inverted terminal repeats.
[0077] The present invention also includes a method of delivering a
nucleic acid to a subject comprising administering to a cell from
the subject an AAV4 particle comprising the nucleic acid inserted
between a pair of AAV inverted terminal repeats, and returning the
cell to the subject, thereby delivering the nucleic acid to the
subject. The AAV ITRs can be any AAV ITRs, including AAV4 ITRs and
AAV2 ITRs. For such an ex vivo administration, cells are isolated
from a subject by standard means according to the cell type and
placed in appropriate culture medium, again according to cell type
(see, e.g., ATCC catalog). Viral particles are then contacted with
the cells as described above, and the virus is allowed to transfect
the cells. Cells can then be transplanted back into the subject's
body, again by means standard for the cell type and tissue (e. g.,
in general, U.S. Pat. No. 5,399,346; for neural cells, Dunnett, S.
B. and Bjorklund, A., eds., Transplantation: Neural
Transplantation-A Practical Approach, Oxford University Press,
Oxford (1992)). If desired, prior to transplantation, the cells can
be studied for degree of transfection by the virus, by known
detection means and as described herein. Cells for ex vivo
transfection followed by transplantation into a subject can be
selected from those listed above, or can be any other selected
cell. Preferably, a selected cell type is examined for its
capability to be transfected by AAV4. Preferably, the selected cell
will be a cell readily transduced with AAV4 particles; however,
depending upon the application, even cells with relatively low
transduction efficiencies can be useful, particularly if the cell
is from a tissue or organ in which even production of a small
amount of the protein or antisense RNA encoded by the vector will
be beneficial to the subject.
[0078] The present invention further provides a method of
delivering a nucleic acid to a cell in a subject comprising
administering to the subject an AAV4 particle comprising the
nucleic acid inserted between a pair of AAV inverted terminal
repeats, thereby delivering the nucleic acid to a cell in the
subject. Administration can be an ex vivo administration directly
to a cell removed from a subject, such as any of the cells listed
above, followed by replacement of the cell back into the subject,
or administration can be in vivo administration to a cell in the
subject. For ex vivo administration, cells are isolated from a
subject by standard means according to the cell type and placed in
appropriate culture medium, again according to cell type (see,
e.g., ATCC catalog). Viral particles are then contacted with the
cells as described above, and the virus is allowed to transfect the
cells. Cells can then be transplanted back into the subject's body,
again by means standard for the cell type and tissue (e. g., for
neural cells, Dunnett, S. B. and Bjorklund, A., eds.,
Transplantation: Neural Transplantation-A Practical Approach,
Oxford University Press, Oxford (1992)). If desired, prior to
transplantation, the cells can be studied for degree of
transfection by the virus, by known detection means and as
described herein.
[0079] In vivo administration to a human subject or an animal model
can be by any of many standard means for administering viruses,
depending upon the target organ, tissue or cell. Virus particles
can be administered orally, parenterally (e.g., intravenously), by
intramuscular injection, by direct tissue or organ injection, by
intraperitoneal injection, topically, transdermally, or the like.
Viral nucleic acids (non-encapsidated) can be administered, e.g.,
as a complex with cationic liposomes, or encapsulated in anionic
liposomes. Compositions can include various amounts of the selected
viral particle or non-encapsidated viral nucleic acid in
combination with a pharmaceutically acceptable carrier and, in
addition, if desired, may include other medicinal agents,
pharmaceutical agents, carriers, adjuvants, diluents, etc. Parental
administration, if used, is generally characterized by injection.
Injectables can be prepared in conventional forms, either as liquid
solutions or suspensions, solid forms suitable for solution or
suspension in liquid prior to injection, or as emulsions. Dosages
will depend upon the mode of administration, the disease or
condition to be treated, and the individual subject's condition,
but will be that dosage typical for and used in administration of
other AAV vectors, such as AAV2 vectors. Often a single dose can be
sufficient; however, the dose can be repeated if desirable.
[0080] The present invention further provides a method of
delivering a nucleic acid to a cell in a subject having antibodies
to AAV2 comprising administering to the subject an AAV4 particle
comprising the nucleic acid, thereby delivering the nucleic acid to
a cell in the subject. A subject that has antibodies to AAV2 can
readily be determined by any of several known means, such as
contacting AAV2 protein(s) with an antibody-containing sample, such
as blood, from a subject and detecting an antigen-antibody reaction
in the sample. Delivery of the AAV4 particle can be by either ex
vivo or in vivo administration as herein described. Thus, a subject
who might have an adverse immunogenic reaction to a vector
administered in an AAV2 viral particle can have a desired nucleic
acid delivered using an AAV4 particle. This delivery system can be
particularly useful for subjects who have received therapy
utilizing AAV2 particles in the past and have developed antibodies
to AAV2. An AAV4 regimen can now be substituted to deliver the
desired nucleic acid.
STATEMENT OF UTILITY
[0081] The present invention provides recombinant vectors based on
AAV4. Such vectors may be useful for transducing erythroid
progenitor cells which is very inefficient with AAV2 based vectors.
In addition to transduction of other cell types, transduction of
erythroid cells would be useful for the treatment of cancer and
genetic diseases which can be corrected by bone marrow transplants
using matched donors. Some examples of this type of treatment
include, but are not limited to, the introduction of a therapeutic
gene such as genes encoding interferons, interleukins, tumor
necrosis factors, adenosine deaminase, cellular growth factors such
as lymphokines, blood coagulation factors such as factor VIII and
IX, cholesterol metabolism uptake and transport protein such as
EpoE and LDL receptor, and antisense sequences to inhibit viral
replication of, for example, hepatitis or HIV.
[0082] The present invention provides a vector comprising the AAV4
virus as well as AAV4 viral particles. While AAV4 is similar to
AAV2, the two viruses are found herein to be physically and
genetically distinct. These differences endow AAV4 with some unique
advantages which better suit it as a vector for gene therapy. For
example, the wt AAV4 genome is larger than AAV2, allowing for
efficient encapsidation of a larger recombinant genome.
Furthermore, wt AAV4 particles have a greater buoyant density than
AAV2 particles and therefore are more easily separated from
contaminating helper virus and empty AAV particles than AAV2-based
particles.
[0083] Furthermore, as shown herein, AAV4 capsid protein is
distinct from AAV2 capsid protein and exhibits different tissue
tropism. AAV2 and AAV4 are shown herein to utilize distinct
cellular receptors. AAV2 and AAV4 have been shown to be
serologically distinct and thus, in a gene therapy application,
AAV4 would allow for transduction of a patient who already possess
neutralizing antibodies to AAV2 either as a result of natural
immunological defense or from prior exposure to AAV2 vectors.
[0084] The present invention is more particularly described in the
following examples which are intended as illustrative only since
numerous modifications and variations therein will be apparent to
those skilled in the art.
EXAMPLES
[0085] To understand the nature of AAV4 virus and to determine its
usefulness as a vector for gene transfer, it was cloned and
sequenced.
[0086] Cell Culture and Virus Propagation
[0087] Cos and HeLa cells were maintained as monolayer cultures in
D10 medium (Dulbecco's modified Eagle's medium containing 10% fetal
calf serum, loo ug/ml penicillin, 100 units/ml streptomycin and IX
Fungizone as recommended by the manufacturer; (GIBCO, Gaithersburg,
Md., USA) . All other cell types were grown under standard
conditions which have been previously reported. AAV4 stocks were
obtained from American Type Culture Collection #VR-64 6.
[0088] Virus was produced as previously described for AAV2 using
the Beta galactosidase vector plasmid and a helper plasmid
containing the AAV4 Rep and Cap genes (9). The helper plasmid was
constructed in such a way as not to allow any homologous sequence
between the helper and vector plasmids. This step was taken to
minimize the potential for wild-type (wt) particle formation by
homologous recombination.
[0089] Virus was isolated from 5.times.10.sup.7 cos cells by CsCl
banding (9), and the distribution of Beta galactosidase genomes
across the genome was determined by DNA dot blots of aliquots of
gradient fractions. The majority of packaged genomes were found in
fractions with a density of 1.43 which is similar to that reported
for wt AAV4. This preparation of virus yielded 2.5.times.10.sup.11
particles or 5000 particles/producer cell. In comparison AAV2
isolated and CsCl banded from 8.times.10.sup.7 cells yielded
1.2.times.10.sup.11 particles or 1500 particles/producer cell.
Thus, typical yields of rAAV4 particles/producer cell were 3-5 fold
greater than that of rAAV2 particles.
[0090] DNA Cloning and Sequencing and Analysis
[0091] In order to clone the genome of AAV4, viral lysate was
amplified in cos cells and then HeLa cells with the resulting viral
particles isolated by CsCl banding. DNA dot blots of aliquots of
the gradient fractions indicated that peak genomes were contained
in fractions with a density of 1.41-1.45. This is very similar to
the buoyant density previously reported for AAV4 (29). Analysis of
annealed DNA obtained from these fractions indicated a major
species of 4.8 kb in length which upon restriction analysis gave
bands similar in size to those previously reported. Additional
restriction analysis indicated the presence of BssHII restriction
sites near the ends of the DNA. Digestion with BssHII yielded a 4.5
kb fragment which was then cloned into Bluescript SKII+ and two
independent clones were sequenced.
[0092] The viral sequence is now available through Genebank,
accession number U89790. DNA sequence was determined using an ABI
373A automated sequencer and the FS dye terminator chemistry. Both
strands of the plasmids were sequenced and confirmed by sequencing
of a second clone. As further confirmation of the authenticity of
the sequence, bases 91-600 were PCR amlified from the original seed
material and directly sequenced. The sequence of this region, which
contains a 56 base insertion compared to AAV2 and 3, was found to
be identical to that derived from the cloned material. The ITR was
cloned using Deep Vent Polymerase (New England Biolabs) according
to the manufactures instructions using the following primers,
primer 1: 5'TCTAGTCTAGACTTGGCCACTCCCTCTCTGCGCGC(SEQ ID NO:21);
primer 2: 51 AGGCCTTAAGAGCAGTCGTCCACCACCTTGTTCC (SEQ ID NO:22).
Cycling conditions were 97.degree. C. 20 sec, 65.degree. C. 30 sec,
75.degree. C. 1 min for 35 rounds. Following the PCR reaction, the
mixture was treated with XbaI and EcoRI endonucleases and the
amplified band purified by agarose gel electrophoresis. The
recovered DNA fragment was ligated into Bluescript SKII+
(Stratagene) and transformed into competent Sure strain bacteria
(Stratagene). The helper plasmid (pSV40oriAAV.sub.4-2) used for the
production of recombinant virus, which contains the rep and cap
genes of AAV4, was produced by PCR with Pfu polymerase (Stratagene)
according to the manufactures instructions. The amplified sequence,
nt 216-4440, was ligated into a plasmid that contains the SV40
origin of replication previously described (9, 10). Cycling
conditions were 95.degree. C. 30 sec, 55.degree. C. 30 sec,
72.degree. C. 3 min for 20 rounds. The final clone was confirmed by
sequencing. The .beta.gal reporter vector has been described
previously (9, 10).
[0093] Sequencing of this fragment revealed two open reading frames
(ORF) instead of only one as previously suggested. In addition to
the previously identified Capsid ORF in the right-hand side of the
genome, an additional ORF is present on the left-hand side.
Computer analysis indicated that the left-hand ORF has a high
degree of homology to the Rep gene of AAV2. At the amino acid level
the ORF is 90% identical to that of AAV2 with only 5% of the
changes being non-conserved (SEQ ID NO:2). In contrast, the right
ORF is only 62% identical at the amino acid level when compared to
the corrected AAV2 sequence. While the internal start site of VP2
appears to be conserved, the start site for VP3 is in the middle of
one of the two blocks of divergent sequence. The second divergent
block is in the middle of VP3. By using three dimensional structure
analysis of the canine parvovirus and computer aided sequence
comparisons, regions of AAV2 which might be exposed on the surface
of the virus have been identified. Comparison of the AAV2 and AAV4
sequences indicates that these regions are not well conserved
between the two viruses and suggests altered tissue tropism for the
two viruses.
[0094] Comparison of the p5 promoter region of the two viruses
shows a high degree of conservation of known functional elements
(SEQ ID NO:7). Initial work by Chang et al. identified two YY1
binding sites at -60 and +1 and a TATA Box at -30 which are all
conserved between AAV2 and AAV4 (4). A binding site for the Rep has
been identified in the p5 promoter at -17 and is also conserved
(24). The only divergence between the two viruses in this region
appears to be in the sequence surrounding these elements. AAV4 also
contains an additional 56 bases in this region between the p5
promoter and the TRS (nt 209-269). Based on its positioning in the
viral genome and efficient use of the limited genome space, this
sequence may possess some promoter activity or be involved in
rescue, replication or packaging of the virus.
[0095] The inverted terminal repeats were cloned by PCR using a
probe derived from the terminal resolution site (TRS)of the BssHII
fragment and a primer in the Rep ORF. The TRS is a sequence at the
end of the stem of the ITR and the reverse compliment of TRS
sequence was contained within the BssHII fragment. The resulting
fragments were cloned and found to contain a number of sequence
changes compared to AAV2. However, these changes were found to be
complementary and did not affect the ability of this region to fold
into a hairpin structure (FIG. 2). While the TRS site was conserved
between AAV2 and AAV4 the Rep binding site contained two
alterations which expand the binding site from 3 GAGC repeats to 4.
The first two repeats in AAV4 both contain a T in the fourth
position instead of a C. This type of repeat is present in the p5
promoter and is present in the consensus sequence that has been
proposed for Rep binding (10) and its expansion may affect its
affinity for Rep. Methylation interference data has suggested the
importance of the CTTTG motif found at the tip of one palindrome in
Rep binding with the underlined T residues clearly affecting Rep
binding to both the flip and flop forms. While most of this motif
is conserved in AAV4 the middle T residue is changed to a C
(33).
[0096] Hemagglutination Assays
[0097] Hemagglutination was measured essentially as described
previously (18). Serial two fold dilutions of virus in
Veronal-buffered saline were mixed with an equal volume of 0.4%
human erythrocytes (type 0) in plastic U bottom 96 well plates. The
reaction was complete after a 2 hr incubation at 8.degree. C. HA
units (HAU) are defined as the reciprocal of the dilution causing
50% hemagglutination.
[0098] The results show that both the wild type and recombinant
AAV4 viruses can hemagglutinate human red blood cells (RBCS) with
HA titers of approximately 1024 HAU/.mu.l and 512 HAU/.mu.l
respectively. No HA activity was detected with AAV type 3 or
recombinant AAV type 2 as well as the helper adenovirus. If the
temperature was raised to 22.degree. C., HA activity decreased
32-fold. Comparison of the viral particle number per RBC at the end
point dilution indicated that approximately 1-10 particles per RBC
were required for hemagglutination. This value is similar to that
previously reported (18).
[0099] Tissue Tropism Analysis
[0100] The sequence divergence in the capsid proteins ORF which are
predicted to be exposed on the surface of the virus may result in
an altered binding specificity for AAV4 compared to AAV2. Very
little is known about the tissue tropism of any dependovirus. While
it had been shown to hemagglutinate human, guinea pig, and sheep
erythrocytes, it is thought to be exclusively a simian virus (18).
Therefore, to examine AAV4 tissue tropism and its species
specificity, recombinant AAV4 particles which contained the gene
for nuclear localized Beta galactosidase were constructed. Because
of the similarity in genetic organization of AAV4 and AAV2, it was
determined whether AAV4 particles could be constructed containing a
recombinant genome. Furthermore, because of the structural
similarities of the AAV type 2 and type 4 ITRs, a genome containing
AAV2 ITRs which had been previously described was used.
[0101] Tissue Tropism Analysis 1.
[0102] To study AAV transduction, a variety of cell lines were
transduced with 5 fold serial dilutions of either recombinant AAV2
or AAV4 particles expressing the gene for nuclear localized Beta
galactosidase activity (Table 1). Approximately 4.times.10.sup.4
cells were exposed to virus in 0.5 ml serum free media for 1 hour
and then 1 ml of the appropriate complete media was added and the
cells were incubated for 48-60 hours. The cells were then fixed and
stained for .beta.-galactosidase activity with
5-Bromo-4-Chloro-3-Indolyl-.beta.-D-galactopyranoside (Xgal) (ICN
Biomedicals) (36). Biological titers were determined by counting
the number of positive cells in the different dilutions using a
calibrated microscope ocular (3.1 mm.sup.2) then multiplying by the
area of the well and the dilution of the virus. Typically dilutions
which gave 1-10 positive cells per field (100-1000 positive cells
per 2 cm well) were used for titer determination. Titers were
determined by the average number of cells in a minimum of 10
fields/well.
[0103] To examine difference in tissue tropism, a number of cell
lines were transduced with serial dilutions of either AAV4 or AAV2
and the biological titers determined. As shown in Table 1, when Cos
cells were transduced with a similar number of viral particles, a
similar level of transduction was observed with AAV2 and AAV4.
However, other cell lines exhibited differential transducibility by
AAV2 or AAV4. Transduction of the human colon adenocarcinoma cell
line SW480 with AAV2 was over 100 times higher than that obtained
with AAV4. Furthermore, both vectors transduced SW1116, SW1463 and
NIH3T3 cells relatively poorly.
1TABLE 1 Cell type AAV2 AAV4 Cos 4.5 .times. 10.sup.7 1.9 .times.
10.sup.7 SW480 3.8 .times. 10.sup.6 2.8 .times. 10.sup.4 SW1116 5.2
.times. 10.sup.4 8 .times. 10.sup.3 SW1463 8.8 .times. 10.sup.4 8
.times. 10.sup.3 SW620 8.8 .times. 10.sup.4 ND NIH3T3 2 .times.
10.sup.4 8 .times. 10.sup.3
[0104] Tissue Tropism Analysis 2.
[0105] A. Transduction of Cells.
[0106] Exponentially growing cells (2.times.10.sup.4) were plated
in each well of a 12 well plate and transduced with serial
dilutions of virus in 200 .mu.l of medium for 1 hr. After this
period, 800 .mu.l of additional medium was added and incubated for
48 hrs. The cells were then fixed and stained for
.beta.-galactosidase activity overnight with
5-bromo-4-chloro-3-indolyl-.beta.-D-galactopyranoside (Xgal) (ICN
Biomedicals) (36). No endogenous .beta.-galactosidase activity was
visible after 24 hr incubation in Xgal solution. Infectious titers
were determined by counting the number of positive cells in the
different dilutions using a calibrated microscope ocular (diameter
3.1 mm.sup.2 ) then multiplying by the area of the well and the
dilution of the virus. Titers were determined by the average number
of cells in a minimum of 10 fields/well.
[0107] As shown in Table 2, cos cells transduced with equivalent
amounts of rAAV2 and rAAV4particles resulted in similar
transduction levels. However, other cell lines exhibited
differential transducibility. Transduction of the human colon
adenocarcinoma cell line, SW480, with rAAV2 was 60 times higher
than that obtained with rAAV4. Hela and SW620 cells were also
transduced more efficiently with rAAV2 than rAAV4. In contrast,
transduction of primary rat brain cultures exhibited a greater
transduction of glial and neuronal cells with rAAV4 compared to
rAAV2. Because of the heterogeneous nature of the cell population
in the rat brain cultures, only relative transduction efficiencies
are reported (Table 2).
[0108] As a control for adenovirus contamination of the viral
preparations cos and Hela cells were coinfected with RAAV and
adenovirus then stained after 24 hr. While the titer of rAAV2
increased in the presence of Ad in both cos and Hela, adenovirus
only increased the titer in the cos cells transduced with rAAV4 and
not the HeLa cells, suggesting the difference in transduction
efficiencies is not the result of adenovirus contamination.
Furthermore, both vectors transduced SW1116, SW1463, NIH3T3 and
monkey fibroblasts FL2 cells very poorly. Thus AAV4 may utilize a
cellular receptor distinct from that of AAV2.
2TABLE 2 CELL TYPE AAV2 AAV4 Primary Rat Brain 1 4.3 .+-. 0.7 cos
4.2 .times. 10.sup.7 .+-. 4.6 .times. 10.sup.6 2.2 .times. 10.sup.7
.+-. 2.5 .times. 10.sup.6 SW480 7.75 .times. 10.sup.6 .+-. 1.7
.times. 10.sup.6 1.3 .times. 10.sup.5 .+-. 6.8 .times. 10.sup.4
Hela 2.1 .times. 10.sup.7 .+-. 1 .times. 10.sup.6 1.3 .times.
10.sup.6 .+-. 1 .times. 10.sup.5 SW620 1.2 .times. 10.sup.5 .+-.
3.9 .times. 10.sup.4 4 .times. 10.sup.4 KLEB 1.2 .times. 10.sup.5
.+-. 3.5 .times. 10.sup.4 9 .times. 10.sup.4 .+-. 1.4 .times.
10.sup.4 HB 5.6 .times. 10.sup.5 .+-. 2 .times. 10.sup.5 3.8
.times. 10.sup.4 .+-. 1.8 .times. 10.sup.4 SW1116 5.2 .times.
10.sup.4 8 .times. 10.sup.3 SW1463 8.8 .times. 10.sup.4 8 .times.
10.sup.3 NIH3T3 3 .times. 10.sup.3 2 .times. 10.sup.3
[0109] B. Competition Assay.
[0110] Cos cells were plated at 2.times.10.sup.4/well in 12 well
plates 12-24 hrs prior to transduction. Cells were transduced with
0.5.times.10.sup.7 particles of rAAV2 or rAAV4 (containing the LacZ
gene) in 200 .mu.l of DMEM and increasing amounts of rAAV2
containing the gene for the human coagulation factor IX. Prior to
transduction the CsCl was removed from the virus by dialysis
against isotonic saline. After 1 hr incubation with the recombinant
virus the culture medium was supplemented with complete medium and
allowed to incubate for 48-60 hrs. The cells were then stained and
counted as described above.
[0111] AAV4 utilization of a cellular receptor distinct from that
of AAV2 was further examined by cotransduction experiments with
rAAV2 and rAAV4. Cos cells were transduced with an equal number of
rAAV2 or rAAV4 particles containing the LacZ gene and increasing
amounts of rAAV2 particles containing the human coagulation factor
IX gene (rAAV2FIX). At a 72:1 ratio of rAAV2FIX:rAAV4LacZ only a
two-fold effect on the level of rAAV4LacZ transduction was obtained
(FIG. 3). However this same ratio of rAAV2FIX:rAAV2LacZ reduced the
transduction efficiency of rAAV2LacZ approximately 10 fold.
Comparison of the 50% inhibition points for the two viruses
indicated a 7 fold difference in sensitivity.
[0112] C. Trypsinization of Cells.
[0113] An 80% confluent monolayer of cos cells (1.times.10.sup.7)
was treated with 0.05% trypsin/0.02% versene solution (Biofluids)
for 3-5 min at 37.degree. C. Following detachment the trypsin was
inactivated by the addition of an equal volume of media containing
10% fetal calf serum. The cells were then further diluted to a
final concentration of 1.times.10.sup.4/ml. One ml of cells was
plated in a 12 well dish and incubated with virus at a multiplicity
of infection (MOI) of 260 for 1-2 hrs. Following attachment of the
cells the media containing the virus was removed, the cells washed
and fresh media was added. Control cells were plated at the same
time but were not transduced until the next day. Transduction
conditions were done as described above for the trypsinized cell
group. The number of transduced cells was determined by staining
48-60 hrs post transduction and counted as described above.
[0114] Previous research had shown that binding and infection of
AAV2 is inhibited by trypsin treatment of cells (26). Transduction
of cos cells with rAAV21acZ gene was also inhibited by trypsin
treatment prior to transduction (FIG. 4). In contrast trypsin
treatment had a minimal effect on rAAV41acZ transduction. This
result and the previous competition experiment are both consistent
with the utilization of distinct cellular receptors for AAV2 and
AAV4.
[0115] AAV4 is a distinct virus based on sequence analysis,
physical properties of the virion, hemagglutination activity, and
tissue tropism. The sequence data indicates that AAV4 is a distinct
virus from that of AAV2. In contrast to original reports, AAV4
contains two open reading frames which code for either Rep proteins
or Capsid proteins. AAV4 contains additional sequence upstream of
the p5 promoter which may affect promoter activity, packaging or
particle stability. Furthermore, AAV4 contains an expanded Rep
binding site in its ITR which could alter its activity as an origin
of replication or promoter. The majority of the differences in the
Capsid proteins lies in regions which have been proposed to be on
the exterior surface of the parvovirus. These changes are most
likely responsible for the lack of cross reacting antibodies,
hemagglutinate activity, and the altered tissue tropism compared to
AAV2. Furthermore, in contrast to previous reports AAV4 is able to
transduce human as well as monkey cells.
[0116] Throughout this application, various publications are
referenced. The disclosures of these publications in their
entireties are hereby incorporated by reference into this
application in order to more fully describe the state of the art to
which this invention pertains.
[0117] Although the present process has been described with
reference to specific details of certain embodiments thereof, it is
not intended that such details should be regarded as limitations
upon the scope of the invention except as and to the extent that
they are included in the accompanying claims.
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Sequence CWU 1
1
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