Note: Descriptions are shown in the official language in which they were submitted.
CA 02596292 2010-05-05
VECTORS AND VIRAL VECTORS,
AND PACKAGING CELL LINES FOR PROPAGATING SAME
MELD OF THE INVENTION
This invention relates to the field of recombinant nucleic acid technology,
and more
particularly, to the production of gene expression systems involving novel
vectors and viral
vectors as well as unique packaging cell lines for propagating such vectors or
viral vectors
and to the processes for producing them.
BACKGROUND-OF 331E RBXMMN
Virus and nucleic acid vectors provide a means to deliver nucleic acid
sequences to
cells, and they are widely used in gene therapy applications. Critical to
effective gene
therapy is the ability to establish efficient expression of an Exogenous
Nucleic Acid(s) in
the target cell. Expression of exogenous nucleic acid in target cells can take
place when the
Exogenous Nucleic Acid(s) is/are either in an integrated or in an episomal
state. Although
expression in the episomal state can take place in target cells, expression in
most cases
persists for only limited periods of time. In contrast, the expression of
Exogenous Nucleic
Acids in an integrated state can be maintained for much longer periods.
Certain viruses have been of particular interest for use as vectors in gene
therapy
because of their ability to efficiently transfer and/or establish stable
expression of
Exogenous Nucleic Acid in the target cell. Although each particular family of
virus may
possess elements that confer specific advantages for development into a virus
vector, each
virus family also contains inherent features that limit its use as a viable
means of human
gene transfer.
Retroviruses have been a focus for development into virus vectors because they
can
establish stable integration of viral sequences. Current retroviral vectors
can be produced
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CA 02596292 2007-08-23
from packaging cells in which the gag, pol and env elements are provided in
trans through
a plasmid or mutated virus. These vectors can transduce sequences of up to 7.5
to 8.0
kilobases. Nevertheless, several intrinsic features of retroviruses have
hindered their use as
virus vectors, and efforts to modify them to produce safe and efficient
vectors have led to
low yields of virus vector or to the inefficient expression of the exogenous
gene in the
target cell. [Morgenstern, J.P. and Land, Hartmut Methods in Molecular
Biology, Vol. 7:
Gene Transfer and Expression Protocols, 1991, edited by: E. J. Murray The
Humana Press
Inc., Clifton, NJ; Anderson, WF Science 2¾:808-813 (1992); Mulligan, RC
Science
2.0:926-932 (1993)]; Smith, AE, Ann Rev. Microbiol. 42:807-838: Muzyczka, N.,
Curr.
Top. Microbiol. Immunol. LU:97-129(1992); Kotin, R.M., Human Gene Ther. J:793-
801
(1994); and Berliner, K.L., Curr. Top. Microbiol. Immunol. 158:39-66 (1992)].
For
example, it has been demonstrated that in retrovirus vectors the level of
expression directed
by an internal promoter/enhancer can be suppressed up to 50-fold by the
flanking LTRs,
presumably as a result of interference between transcriptional regulatory
units. [Methods in
Molecular Biology, Vol. 7: Gene Transfer and Expression Protocols Edited by:
E.J.
Murray The Humana Press, Inc. Clifton, NJ (1991), supra; Emerman, M. and
Temin,
H.M., Cell 32:459-467 (1984); Emerman, M. and Temin, H.M., Mol. Cell. Bio.
¾:792-800
(1986); Emerman, M. and Temin, H.M., Nucleic Acids Res 14:9381-9396 (1986)].
Attempts to
overcome this suppression and achieve maximum expression of the exogenous
nucleic acid
have been made by deletion of the promoter and enhancer sequences within the
U3 region
of the 3' LTR in the provirus [Yu, S.F. et al. Proc. Natl. Acad Sci. USA
$I:3194-3198
(1986); Hawley, R.G. et al. Proc. Natl. Acad Sci. USA 84:2406-2410 (1987);
Yee, J.K.
et al. Proc. Natl. Acad Sci. USA $4:5197-5201(1987)].
Because the U3 region contains a
polyadenylation signal, any deletions within this region can eliminate
processing of nascent
mRNA. In the absence of 3' RNA processing, such as polyadenylation, newly
transcribed
mRNA is highly unstable and, therefore, subject to immediate degradation. This
accounts
for the observation that provirus mRNA was not detectable in a packaging cell
line
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CA 02596292 2007-08-23
transfected with retrovirus DNA possessing such a deletion (Dougherty, J.P.
and Temin,
H.M., Proc. Natl. Acad Sci. USA $4:1197-1201 [1987]..
Addition of an exogenous SV40 polyadenylation signal to a site downstream from
the 3'
LTR has been used in an attempt to increase the virus mRNA level in the
packaging cells.
Several problems arise from the use of this method. The exogenous
polyadenylation signal
results in a lengthened viral mRNA with additional U5 and SV40 polyadenylation
signal
sequences which are not present in the retrovirus vector RNA in the packaging
cells and in
the target cells. This extra sequence can not only sterically hinder both the
intermolecular
and intramolecular transfer of templates during reverse transcription of the
viral vector
RNA, but can also decrease the packaging efficiency and the size of the
exogenous nucleic
acid sequence which can be inserted into the virus vector due to the size
restriction of the
RNA which can be packaged (Whitcomb, J.M. and Hughes, S.H. [1992] Ann. Rev.
Cell
Biol.$:275-306. In cases where reverse transcription
does occur, the exogenous polyadenylation signal is lost during the process of
reverse
transcription and it cannot be used for polyadenylation of mRNA transcribed
from an
internal gene which does not contain its own polyadenylation signal.
Virus vectors such as retroviruses that can randomly integrate into a cell
genome
have the potential to disrupt the structure and function of cell genes. The
transcriptional
elements within such a randomly integrated virus vector can activate
potentially harmful
genes such as oncogenes or genes triggering programmed cell death [Jaenisch,
R., Harbers,
K, Schnieke, A et al., Cell 12:209-216 (1983); Fung, Y.T. et al., Proc. Natl.
Acad. Sci.
USA 21:3412-3422 (1981); Neel, B.G. et al., Cell 2.:323-334 (1981); Payne,
G.S. et al.
Cell 22:311-322 (1983); Lewin, B., Genes V, Oxford University Press, New York
(1994)].
While removal of the transcriptional activity of the LTRs can reduce or
eliminate the risk of unwanted gene activation by the integrated virus vector,
the
promoters/enhancers of the exogenous nucleic acid can still act to activate
cellular genes
near the site of integration.
Whereas certain viruses possess useful properties for gene transfer, their use
is
limited by the requirement for a helper virus or by an inability to provide
for stable transfer
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CA 02596292 2007-08-23
of Exogenous Nucleic Acid to a target cell. For example, certain defective
viruses can be
propagated in packaging cells that provide the required packaging components
but with the
requirement for use of a helper virus. In order to insure safe use of such a
virus vector
preparation, however, the contaminating helper virus must be removed and the
virus vector
product must be extensively safety tested for the presence of any
contaminating helper
virus. The present invention overcomes these limitations by providing
compositions for
virus metamorphosis which can be used for propagation of virus vectors without
the
requirement of a helper virus.
The ability of a virus vector to integrate into the host genome provides
distinct
advantages for establishing stable expression of Exogenous Nucleic Acid in a
target cell.
The ability to integrate at specific sites is of further advantage by
providing for a reduced
possibility for an integrated vector to alter the structure and function of
cellular genes.
Unlike integrating viruses such as retroviruses, however, adeno-associated
virus (AAV) is a
virus that has been demonstrated to be able to integrate into a specific
region of a cell
genome, namely the q13-ter region of human chromosome 19 [Samulski, R.J. et
at. EMBO
Journal (1991); Kotin, R.M. et at., Genomics 10:831-834 (1991).
This specific integration is directed by the
AAV inverted terminal repeats and the Rep function [(Kotin et al.,.Proc. Natl.
Acad. Sci.
USA 17:2211-2215 (1990), While such specific
integration makes AAV an attractive candidate for use as a virus vector,
existing AAV
vectors cannot integrate at specific sites in a target cell genome. Other
features that hinder
the use of AAV vectors for gene therapy are the size restriction of the
internal gene, the
difficulty in growing virus in large amounts and the risk of helper-virus free
contamination,
all of which stem from the intrinsic mechanism of AAV replication.
By incorporating from different viruses the viral elements that mediate
replication,
virus vectors that derive specific advantages from each virus can be created
to overcome
the limitations associated with each virus vector. For example, the transfer
of site-specific
integration function from AAV into other virus vector systems can provide for
such
properties in a virus vector that may have useful properties for gene transfer
but lacking any
ability to integrate.
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For gene delivery purposes, a virus vector can be developed from a virus that
is native
to a target cell or from a virus that is non-native to a target cell. In
general, it is desirable
to use a non-native virus vector rather than a native virus vector. While
native Vitus
vectors may possess a natural affinity for target cells, such viruses pose a
greater hazard
since they possess a greater potential for propagation in target cells. In
this regard, animal
virus vectors, wherein they are not naturally designed for propagation in
human cells, can
be useful for gene delivery to human cells. In order to obtain sufficient
yields of such
animal virus vectors for use in gene delivery, however, it is necessary to
carry out
production in a native animal packaging cell. Virus vectors produced in this
way, however,
normally lack any components either as part of the envelope or as part of the
capsid that
can provide tropism for human cells. For example, current practices for the
production of
non-human virus vectors, such as ecotropic mouse (murine) retroviruses like
MMLV, are
produced in a mouse packaging cell line. Another component required for human
cell
tropism must be provided.
While non-viral nucleic acid complexes can provide significant advantages for
gene
delivery, these advantages have not or cannot be realized by the use of non-
viral nucleic
acid complexes that rely on non-specific binding components. The present
invention
overcomes these limitations by providing for specific complex formation
between nucleic
acid and protein components wherein the binding of protein molecules that
provide useful
properties for gene transfer can be localized to defined regions of the
nucleic acid
construct. Such localization of specific binding proteins in the nucleic acid
constructs can
reduce or eliminate any interference with the region segments in the
constructs that are
involved in or provide for biological activity. The present invention also
provides for the
controlled displacement of such specific binding proteins from their cognate
binding sites
wherein such displacement can remove any possible interference with biological
function or
can release proteins that can provide useful function in the cell.
S
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SUMMARY OF THE INVENTION
The present invention provides novel vectors and viral vectors for use in
systems for
delivering and expressing desired genes and gene sequences. One such novel
vector is
shown to be capable of expressing an exogenous gene or exogenous nucleic acid
sequences
in a target cell of interest. The vector comprises a viral vector, a viral
vector nucleic acid,
or a nucleic acid construct that comprises a viral vector nucleic acid
sequence. The vector
comprises the following nucleic acid component or components: i) one or more
native
promoter/enhancer regions in which at least one sequence segment has been
modified, (ii)
one or more non-native promoter/enhancers or a non-native promoter's gene or
gene
segment, and (iii) a native viral vector terminator or a processing signal or
segment thereof,
or both.
The present invention also provides a novel viral vector comprising a virus or
viral
portion having at least two adsorbing components on the surfaces or envelopes
thereof.
One adsorbing component is directed to a packaging cell line for the vector,
and the other
adsorbing component is for adsorbing to a target cell for delivering the
vector.
Further provided by this invention is a novel viral vector comprising a virus
or viral
portion thereof in which at least two components on the surfaces or envelopes
are found.
The first component is native to the virus while the second component is
generally
characterized as being non-native to the viral vector, and further, being
capable of
adsorption to a target cell of interest, while being incapable of adsorption
to a cell native
for the same viral vector.
The present invention provides yet further a novel vector selected from the
following
group: a (i) viral vector, (ii) a viral nucleic acid, and (iii) a nucleic acid
construct. The
vector comprises a non-native nucleic acid sequence coding for a segment, the
segment
being capable of integrating into a target cell's genome, and the vector
itself being capable
of producing or introducing a first nucleic acid in the target cell. With
respect to the first
nucleic acid, it is itself capable of producing a second nucleic acid that
comprises a portion
of the first nucleic acid. The second nucleic acid comprises the integration
segment and is
itself capable of expressing an exogenous gene or an exogenous nucleic acid
sequence as
the case may be.
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Also provided by this invention is a novel first vector selected from the
group
consisting of (i) a viral vector comprising a viral nucleic acid and a viral
vector packaging
component or components, (ii) a viral nucleic acid, and (iii) a nucleic acid
construct. When
introduced into a packaging cell, the first vector is capable of producing a
second vector
selected from the group consisting of (a) a second viral vector, (b) a viral
nucleic acid, and
(c) a second nucleic acid construct, each of which group members are capable
of expressing
an exogenous gene or exogenous nucleic acid sequence in a target cell of
interest. The first
vector is capable of producing the second vector in the packaging cell, and
the packaging
cell is capable of providing one or more packaging components for the second
viral nucleic
acid. In this unique vector, the second viral nucleic acid or the second
nucleic acid
construct is structurally different from the first (i) viral nucleic acid or
the first (iii) nucleic
acid construct. Alternatively, more than one packaging component for the
second viral
vector may be different from the first viral vector packaging component or
components (ii).
As a further alternative, both kinds or sets of structural differences may be
present in the
same vector. That is to say, the second viral nucleic acid or the second
nucleic acid
construct may be different from the first, and/or the packaging components for
the second
may be different from the first.
This invention is also directed to novel packaging cell lines for propagating
any of the
foregoing vectors or viral vectors, including the last-mentioned first vector.
Thus, the
packaging cell line of the present invention provides at least two packaging
components for
the surface or envelope of the viral vector. Other packaging cell lines for
propagating other
viral vectors are also provided. In these, the cell line is non-native to the
viral vector
component or components but native to the viral vector nucleic acid. The
packaging cell
line expresses one or more adsorbing components on its membrane or surface.
Such
adsorbing components are for adsorption to the non-native component of the
vector and
broadly comprise receptor(s) or binding partner(s).
Processes for producing any of the novel viral vectors or viral vector nucleic
acid of
this invention are also contemplated and provided in this disclosure. In these
processes, the
desired vector is introduced into an appropriate packaging cell under
conditions sufficient
or appropriate to produce the viral vector or viral vector nucleic acid.
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Still yet provided by this invention are novel and unique packaging cell
lines for propagating viral vectors independent of helper viruses. In such
packaging cell lines, the viral vector comprises a nucleic acid component and
a non-nucleic acid component. The sequence or sequences for the viral vector
nucleic acid component is stably integrated in the genome of the cell line.
The
sequence or sequences for the non-nucleic acid component of the viral vector
are introduced into the packaging cell line by various means. These means
can involve transient expression, episomal expression, stable integration
expression, or any combination of such foregoing means.
Also provided is a first vector comprising:
i) retroviral sequences;
ii) retroviral packaging component or components;
iii) adeno-associated virus (AAV) sequences; and
iv) nucleic acid sequences coding for an exogenous gene or exogenous
nucleic acid sequence;
wherein when introduced into a packaging cell said first vector produces a
second viral vector comprising:
(a) said AAV sequences; and
(b) said exogenous gene or exogenous nucleic acid sequences,
wherein said second viral vector lacks said retroviral sequences (1); and
wherein said packaging cell provides one or more packaging components for
said second viral vector.
Further provided is a packaging cell which comprises a first vector
comprising:
i) retroviral sequences;
ii) retroviral packaging component or components;
iii) adeno-associated virus (AAV) sequences; and
iv) nucleic acid sequences coding for an exogenous gene or exogenous
nucleic acid sequence; wherein said first vector produces a second viral
vector
comprising:
(a) said AAV sequences; and
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CA 02596292 2012-03-08
(b) said exogenous gene or exogenous nucleic acid sequences; and
wherein said packaging cell: (i) lacks a receptor for said first vector, and
(ii)
provides one or more packaging components for said second viral vector.
Additionally provided is a packaging cell which comprises a first vector
comprising:
i) retroviral sequences;
ii) retroviral packaging component or components;
iii) adeno-associated virus (AAV) sequences; and iv) nucleic acid
sequences coding for an exogenous gene or exogenous nucleic acid sequence;
wherein said first vector produces a second viral vector comprising:
(a) said AAV sequences; and (b) said exogenous gene or exogenous
nucleic acid sequences, and wherein said packaging cell (i) lacks a receptor
for
said second vector, and (ii) provides one or more packaging components for
said second viral vector.
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BRIEF DESCRIPTION OF THE FIGURES
FIGURE 1 depicts the general replacement strategy to a retroviral vector
sequence
present in the plasmid pENZ1.
FIGURE 2 shows the wild type 3' LTR native sequence that was removed from the
plasmid pENZ1 as well as the non-native modified 3' LTR sequence that replaced
it. The
modified sequences are designated by bold italics.
FIGURE 3 depicts the general replacement strategy for a retroviral vector
having an
inactivated promoter/enhancer and a non-native polyadenylation signal (the
mouse histone
H2A614 gene).
FIGURE 4 depicts the general replacement strategy for a heterologous
retroviral
vector in which a polyadenylation processing signal from a human gene (G-CSF)
with the
AATAAA and mRNA destabilization elements removed is used to replace a region
of the 3'
U3 snRNA.
FIGURE 5 depicts the general replacement strategy for constructing a
heterologous
retroviral vector for delivering an exogenous nucleic acid that transcribes a
chimeric
molecule composed of antisense RNA and rRNA.
FIGURE 6 also depicts the general replacement strategy for constructing a
heterologous retroviral vector for delivering an exogenous nucleic acid that
transcribes a
chimeric molecule composed of antisense RNA and rRNA.
FIGURE 7 also depicts the general replacement strategy for constructing a
heterologous retroviral vector for delivering an exogenous nucleic acid that
transcribes a
chimeric molecule composed of antisense RNA and rRNA.
FIGURE 8 illustrates the construction of a retroviral vector DNA construct
that
contains two adeno-associated virus (AAV) ITR sequences whereby one sequence
is
inserted into a site immediately downstream from the primer binding site and
the other
sequence is inserted into a site just upstream from the retrovirus origin for
second strand
synthesis (ppt).
FIGURE 9 illustrates the construction of a retroviral vector DNA construct
containing
two AAV ITR sequences whereby one sequence is inserted into a site immediately
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CA 02596292 2007-08-23
downstream from the primer binding site and the other sequence is inserted
into a site from
which the ppt sequences have been deleted.
FIGURE 10 illustrates the construction of a heterologous vector (retrovirus
vector)
DNA construct containing two AAV ITR sequences that flank the primer binding
site
(PBS).
FIGURE 11 illustrates the construction of a heterologous vector (retrovirus
vector)
containing two AAV ITR sequences whereby one sequence is inserted into a site
immediately downstream from the primer binding site and the other sequence is
inserted
into a site just upstream from the retroviral origin for second strand DNA
synthesis (ppt).
FIGURE 12 illustrates the construction of a heterologous vector (retrovirus
vector)
containing two AAV ITR sequences whereby one sequence is inserted into a site
immediately downstream from the primer binding site and the other sequence is
used to
replace the original retroviral sequences for second strand DNA synthesis
(ppt).
FIGURE 13 illustrates the construction of a heterologous vector (retrovirus
vector)
containing two AAV ITR sequences that flank the primer binding site (PBS). The
ppt
sequences are removed and the AAV rep sequences are inserted in their place.
CA 02596292 2007-08-23
DETAILED DESCRIPTION OF THE .NTION
The definitions below are useful to an understanding of the present invention
and this
disclosure.
Definitions
Heterologous Vector: A virus vector or non-virus vector, including non-viral
specific
complex that consists of at least one Non-Native Vector Component and that is
capable of
delivering an Exogenous Nucleic Acid to a cell and which can facilitate
Exogenous Nucleic
Acid expression in a cell. The Heterologous Vector contains a functional
native segment or
segments that interfere with the expression of an exogenous gene or an
exogenous nucleic
acid. The native segment or segments have been modified wherein the
interference is
reduced or eliminated and/or native termination/RNA processing is retained.
Non-Native Vector Component: A nucleic acid sequence derived from any
biological
system, or an altered or modified native element, that forms a component(s) of
a
Heterologous Vector. The component(s) function in or mediate directly or
indirectly in a
cis or trans fashion either in vivo or in vitro to provide or effectuate 1)
expression
(including termination signal) of the Exogenous Gene or Exogenous Nucleic Acid
of the
Heterologous Vector in a target cell of interest; 2) integration; and 3)
propagation, yield
and assembly.
Expression Cassette (or the expression of exogenous nucleic acid sequence or
exogenous gene): A nucleic acid sequence that contains all the elements
required for
exogenous gene expression or the expression of an exogenous nucleic acid
sequence or
segment, and that is inserted into a vector for the purpose of expression in a
target cell of
interest. Such elements embrace both native and non-native vector components
or
combinations thereof, including modified or unmodified promoter/enhancer
sequences for
the expression of Exogenous Nucleic Acid or Exogenous Gene that may contain a
gene or
gene segment corresponding to the non-native promoter/enhancer, modified or
native viral
promoter/enhancers and signals for termination, RNA processing,
polyadenylation and
RNA transport.
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cis effect: The effect exerted by one functional segment of a vector nucleic
acid on the
function of another distal sequence of vector nucleic acid.
Heterologous Virus Vectors
The present invention provides compositions and methods of use for
Heterologous
Vectors that have useful properties for gene delivery to cells, i.e., 1)
efficient propagation
in a packaging cell and 2) the safe and efficient expression of Exogenous
Nucleic Acid in a
cell. These benefits are achieved by the use of Non-Native Vector Components
that can
provide one or more such properties to a virus vector.
Expression of Exogenous Nucleic Acid in a virus vector can in many cases be
inefficient because of the virus vector native promoters/enhancers activity
that interferes
with the function of non-native promoters/enhancers driving Exogenous Nucleic
Acid
expression (Emmerman and Temin, 1986.
Efforts to eliminate this interference by deletion of the virus vector native
promoters/enhancers produce cis effects that occur at sites distal to the
modification site.
Such Cis effects may lead to loss or reduction in termination and/or RNA
processing which
causes reduction or a diminishment in the expression of Exogenous Nucleic Acid
as well as
greatly reduced or an altogether eliminated ability to propagate efficiently
in a packaging
cell. The addition of a non-native polyadenylation signal to a site downstream
from the 3'
LTR has been used in an attempt to restore the lost function (Dougherty and
Temin, 1987).
Such an approach is limited in several critical aspects.
This exogenous polyadenylation signal results in a lengthened viral mRNA with
additional
U5 and SV40 polyadenylation signal sequences which are not present in the
retrovirus
vector RNA in the packaging cells and in the target cells. This extra sequence
can not only
sterically hinder both the intermolecular and intramolecular transfer of
templates during
reverse transcription of the viral vector RNA, but it can also decrease the
packaging
efficiency and the size of the exogenous nucleic acid sequence which can be
inserted into
the virus vector due to the size restriction of the RNA which can be packaged
(Whitcomb
and Hughes, 1992). In cases where reverse transcription
does occur, the exogenous polyadenylation signal is lost during the process of
reverse
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CA 02596292 2007-08-23
transcription and it cannot be used for polyadenylation of mRNA transcribed
from an
exogenous gene which does not contain its own polyadenylation signal.
It is another aspect of this invention to overcome the above limitations in
the art by
providing modification in the natural promoters/enhancers segment through a
variety of
means including substitution, addition, mutation or any combination thereof.
The present
invention overcomes these limitations by providing in one feature the
artificial
reconstitution of the native promoters/enhancers segment of the vector which
has been
demonstrated to reduce or eliminate such Cis effects in the vector. This
reconstitution or
modification is carried out in accordance with this invention, for example,
through the
replacement of Heterologous Vector nucleic acid sequences with Non-Native
Vector
Components that can provide such restoration or even improvement of vector
virus
functions. This reconstitution can be accomplished by replacement of virus
vector
promoter and/or enhancer sequences with Non-Native Vector Components to
provide a
virus vector with an mutated LTR in which the native promoter/enhancer
function is
inactivated in such a manner that eliminates interference with non-native
promoter/enhancer
functions. In this case, the virus vector retains fully active native
termination functions and
native RNA processing functions for expression of virus vector RNA in a
packaging cell
and for expression of Exogenous Nucleic Acid in a target cell.
Thus, the present invention provides a vector comprising a viral vector, a
viral vector
nucleic acid, or a nucleic acid construct that comprises a viral vector
nucleic acid sequence.
The vector is capable of expressing an exogenous gene or exogenous nucleic
acid
sequences in a target cell of interest, the vector comprising a nucleic acid
component or
components. The latter nucleic acid component or components comprise (i) one
or more
native promoter/enhancer regions in which at least one sequence segment has
been
modified, (ii) one or more non-native promoter/enhancers or a non-native
promoter's gene
or gene segment, and (iii) a native viral vector terminator or a processing
signal or segment
thereof, or both. Additionally, the aforementioned viral vector further
comprises a non-
native terminator or two or more modified sequence segments.
Such modifications may take various forms. For example, a native sequence
segment
can be substituted by a non-native sequence segment in the one or more
promoter/enhancer
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CA 02596292 2007-08-23
regions of the vector. Further, the substitution can be of approximately the
same size. In
another aspect, the modification can comprise a mutation selected from any of
the group
members represented by a point mutation, a deletion, an insertion, and a
substitution, or a
combination of any of the foregoing.
In one preferred aspect, the viral vector is a retrovirus. In another, the
terminator, or
processing signal, or both, as the case may be, can include a polyadenylation
signal. In
addition, such a viral vector can comprise a segment of the viral vector
terminator or a
segment of the processing signal, or both. Additionally, the function of the
one or more
promoter/enhancers will have been reduced, inhibited or eliminated in the
present viral
vector.
With respect to the one or more non-native promoters, these are capable of
producing
an RNA lacking a polyadenylation signal. A number of non-native promoters can
be used
in accordance with this invention. Simply by way of example, such non-native
promoters
can be selected from the group of genes represented by or designated as snRNA,
tRNA,
and rRNA, or a combination of any of the foregoing.
In another aspect of this invention, the afore-described viral vector further
comprises
one or more gene or gene segment sequences of the snRNA, tRNA or rRNA gene or
genes. The snRNAs are well described in the literature, and these include, for
example, any
of the members selected from the group consisting of Ui, U2, U3, U4, U5, U6,
U7, U8,
U9, U10 and U11, or a combination of any of the foregoing.
It should also be pointed out that in the viral vector described above, one or
more non-
native promoter's gene or gene segment sequence can or will have been
modified. Such
modifications can also take a number of forms, including the substitution or
replacement of
or addition to the one or more non-native promoter's gene sequence with the
exogenous
gene or an exogenous nucleic acid sequence.
Non-Native Vector Components useful for these purposes include non-native
nucleic
acid sequences in the vector. Such nucleic acid sequences can be derived from
any
biological system or can be chemically synthesized or can be prepared by
recombinant DNA
methods or by any combination of such methods. Such sequences can be
approximately the
same size as the vector virus sequences that are replaced. Thus, such
sequences can range
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CA 02596292 2007-08-23
in size from approximately 2 to approximately 188 bases or base pairs in
length, or longer.
Such sequences can be used to replace one or more sequences in such regions of
the virus
vector as promoter and/or enhancer sequences, or any other native sequences in
which its
ability leads to cis effects. Such replacements can be carried out by the
conventional
methods of recombinant DNA (see Sambrook, J., Fritsch, E.F. and Maniatis, T.
Molecular
Cloning, 2nd ed. Cold Spring Laboratory, Cold Spring Harbor, NY, 1989
and they can be conveniently performed on virus vector nucleic acid genomes
or fragments thereof that are present as double stranded DNA in plasmids.
Modifications to provide reconstitution of cis effects in such vectors as
retroviruses
can, for example, be accomplished by replacements in the U3 region of the 3'
LTR region
of a retrovirus vector genome present in a plasmid, i.e., a vector nucleic
acid construct.
The propagation of retrovirus vectors can proceed by introduction of such a
plasmid into a
packaging cell wherein transcripts of the virus vector genome are produced and
reverse
transcribed after transduction into a target cell. As a result of these
processes,
modifications made to the 3' LTR in a vector plasmid will be present in the 5'
LTR of
propagated retrovirus vectors.
Reconstitution has been accomplished according to the teachings of this
invention in a
retrovirus vector provirus DNA contained in a vector plasmid ( designated pENZ-
1) by
modifications of the 3' LTR. Three separate sequences from the
promoter/enhancer region
were replaced with non-native sequences of approximately the same size. A
sequence of
188 base pairs from the enhancer region of the 3' LTR was replaced with an
unrelated
sequence of 188 base pairs derived from the bacterial neo gene. Two separate
sequences in
the promoter region, one of 2 bases and the other of 6 bases, were also
replaced with
nucleic acid segments of the same size. Introduction of this provirus DNA
construct into a
packaging cell (either GP+E- 86 or PA 317) produced retrovirus vectors at
titers of up to
106 as measured by transduction of G418 resistance. This is illustrated in
Figures 1 and 2.
Thus, the present invention also provides a first vector selected from the
group
consisting of (i) a viral vector comprising a viral nucleic acid and a viral
vector packaging
component or components, (ii) a viral nucleic acid, and (iii) a nucleic acid
construct,
CA 02596292 2007-08-23
wherein when introduced into a packaging cell, the first vector is capable of
producing a
second vector selected from the group consisting of (a) a second viral vector,
(b) a viral
nucleic acid, and (c) a second nucleic acid construct, each being capable of
expressing an
exogenous gene or exogenous nucleic acid sequence in a target cell of
interest. The first
vector is capable of producing in the packaging cell the second vector, and
the packaging
cell is capable of providing one or more packaging components for the second
viral nucleic
acid. The second viral nucleic acid or the second nucleic acid construct is
structurally
different from the first (i) viral nucleic acid or the first (iii) nucleic
acid construct, or more
than one packaging component for the second viral vector is different from the
first viral
vector packaging component or components (ii), or both instances of structural
differences
may be present in this first vector. In one aspect, the first vector comprises
a retrovirus and
the second vector comprises adeno-associated virus (AAV).
With respect to these aforementioned structural differences, these comprise or
take on
any number of forms, including any differences that are selected from the
following group
members: the nucleic acid chemical nature, the nucleic acid form, the nucleic
acid size, and
functional elements, or a combination of any of the foregoing. With respect to
the nucleic
acid chemical nature, the second viral nucleic acid or the second nucleic acid
is selected
from any of the group members consisting of or designated as RNA and DNA, and
the (i)
viral nucleic acid or the (iii) nucleic acid construct comprises a different
member of the
group to impart a structural difference between the elements. With respect to
the nucleic
acid form, the second viral nucleic acid or the second nucleic acid is
selected from any of
the group members consisting of single-stranded, double-stranded and partially
double-
stranded, and the (i) viral nucleic acid or the (iii) nucleic acid construct
comprises a
different member of the group to impart a structural difference therebetween.
With respect
to the nucleic acid size, the second viral nucleic acid or the second nucleic
acid comprises a
segment of the (i) viral nucleic acid or the (iii) nucleic acid construct.
With respect to the
functional elements, the second viral nucleic acid or the second nucleic acid
comprises one
or more promoters, one or more enhancer regions, an integration segment and a
terminator,
or a portion or a segment or a combination of any of the foregoing, and the
(i) viral nucleic
acid or the (iii) nucleic acid construct comprises a different member of the
group to impart
16
CA 02596292 2007-08-23
a structural difference therebetween.
In preferred aspects of this invention, the first vector comprises a
retrovirus and the
second vector comprises adeno-associated virus. In other preferred aspects,
the first vector
comprises adeno-associated virus and the second vector comprises a retrovirus.
Retrovirus vectors can also be reconstituted with a nucleic acid sequence for
a non-
native promoter.
In comparison to a non-reconstituted modified retroviral vector that has
exclusively
lost its propagation capability, the reconstitution of cis effects, as
described earlier, can thus
provide virus vectors with a) the ability to express Exogenous Nucleic Acid at
a maximum
level, and/or b) the ability to propagate efficiently in a packaging cell.
Furthermore, as a
result of the inactivation of virus vector promoter/enhancer function, such
Heterologous
Vector viruses could have properties for safe use in a gene delivery system.
For example,
where said Heterologous Vector contains a non-native promoter which cannot
direct the
transcript of a polyadenylated RNA, then such a vector has a greatly reduced
or lost ability
to activate the expression of polyadenylated mRNA or non-polyadenylated mRNA
from
cellular genes that utilize either polymerase I-dependent, polymerase II-
dependent or
polymerase III-dependent promoters as a result of random integration of the
vector. The
present invention provides additional compositions for the safe use of
Heterologous
Vectors by the use of non-native promoters/enhancers for the expression of
Exogenous
Nucleic Acid wherein such promoters /enhancers lack the ability to provide
poly(A) signal
sequence for activating expression of polyadenylated mRNA. The use of such non-
native
promoters/enhancers for expression of Exogenous Nucleic Acid in such
Heterologous
Vectors can provide safe virus vectors in which the ability to activate
polyadenylated
mRNA synthesis of cellular genes by either virus vector native
promoters/enhancers or by
non-native promoters/ enhancers is markedly reduced or eliminated.
Non-native elements in the vector that provide safe expression of Exogenous
Nucleic
Acid can be derived from any biological system and can include
promoters/enhancers and
compatible processing signals that do not direct the transcription of
polyadenylated RNA.
These promoters/enhancers include such elements that are recognized by RNA
polymerase
I, RNA polymerase II or RNA polymerase III that provide for the synthesis of
cellular
17
CA 02596292 2007-08-23
RNA elements such as ribosomal RNA, transfer RNAs, small nuclear RNAs such as
U1,
U2, U3, U4, U5, U6, U7, U8, U9, U10 and Ui 1. These sequences of cellular RNA
elements can be useful to the practice of this invention wherein they can be
used to form
chimeric RNA molecules with RNA sequences that can provide such biological
functions as
antisense regulation of gene expression, ribozyme activity, sense sequences
for expression
of an exogenous gene or exogenous nucleic acid, and the like.
Such sequences providing for biological activity can be incorporated into such
a
cellular RNA gene or gene segments by partial or complete replacement of some
or all of
the sequences of the cellular RNA gene or gene segments, or by the addition of
such
sequences to the RNA gene sequence. Using the methods of recombinant DNA, such
chimeric molecules can be formed by utilizing the cloned sequences for the
cellular RNA
elements and coding sequence for RNA transcripts of exogenous gene or gene
segments or
exogenous nucleic acid. Such a chimera could be all or in part chemically
synthesized.
Nucleic acid sequences providing for the synthesis of such chimeric RNA
molecules can be
conveniently incorporated into double stranded Heterologous Vector DNA present
in a
plasmid by the methods of recombinant DNA as described above. Heterologous
Vectors
providing for expression of such RNA compositions are presented in Figures 5,
6 and 7.
For the use of such chimeras formed between a cellular RNA gene or gene
segment
and a sequence coding for an exogenous gene or exogenous nucleic acid,
modifications of
the cellular RNA gene may lead to enhanced function of the cassette. For
example, in
chimeric molecules formed between an antisense RNA and a U1snRNA, such
modifications
of the U1 snRNA that could provide a U1 snRNP complex with loss of catalytic
function
and/or loss of transport properties and /or loss of protein interaction could
further the
expression of antisense function in a cell. Modifications that could provide
such properties
could result from deletions, additions or from alterations of one or more
bases of the
sequence of such a molecule. Such a modified Ul system has been prepared from
a Ul
molecule containing an altered base sequence, i.e., a change of C to T at
position 4 of the
U1 RNA transcript present in plasmid pHSD-4 (Manser, T. and Gesteland, R.,
Cell 22:257-
264 (1982), the contents of which are incorporated by reference). This U1 was
used to
form a chimeric molecules with each of three different antisense sequences,
each directed
18
CA 02596292 2007-08-23
against an HIV-1 target sequence. Replacement was done by replacement of a
portion of
the transcribed region of Ul (present in pHSD-4) with each antisense sequence.
Such chimeric molecules can be inserted into Heterologous Vectors such as
retroviruses to provide for delivery to and expression of such chimeric
antisense molecules
in a target cell. The absence of any vector promoter activity and the lack of
production of
any peptide by the virus vector sequences or by the Exogenous Nucleic Acid
thus produces
no non-native protein in a target cell, thus eliminating the possibility for
an immune
response.
Such immunogenically silent vectors could be especially useful for ex vivo
gene
transfer to such cells as hematopoietic stem cells. Treatment of virus
infections of these
cells could benefit from the use of these vectors for the delivery of
biologically active RNAs
such as antisense (including ribozymes) and sense RNAs directed against the
infecting
viruses. For example, treatment of diseases such as HIV-1 (and certain viral
leukemias)
could benefit from gene transfer of such sequences to hematopoietic stem cells
as a means
for providing a source of CD4+ cells with resistance to HIV-1 infection. Cells
for this
purpose could be derived from autologous sources such as the bone marrow or
the
circulating cells of the donor or from heterologous sources such as fetal cord
blood. Such
cells could be grown and transduced with such a vector according to procedures
such as
described by (Nolta et al. 1995 Blood $¾:101-110; Xu et al., Blood $¾:141-146
(1995);
Bertolini et at., Cancer Research x¾:2566-2572 (1996); and Wells et al., Gene
Therapy
2:512-520 (1995)).
These. procedures could utilize autologous sera and stroma. Cells so treated
could be administered to patients who had previously undergone partial or
complete
ablation.
Immunogenically silent Heterologous Vectors constituted as described above
could
also be utilized for in vivo gene delivery. Such tissues as liver, lung,
kidney, brain, muscle,
epithelial tissues and other tissues not easily amenable to ex vivo procedures
could be
targeted by the administration of such virus vectors to the bloodstream or by
direct
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CA 02596292 2007-08-23
injection into a tissue or organ. Such treatment procedures can be used in
combination
with other methods.
Virus Metamorphosis
The present invention provides compositions and methods of use for vectors or
viral
vectors that can, in an appropriately constructed packaging cell or in a
target cell,
propagate to a virus vector nucleic acid or virus vector which differ from the
original
vector in various elements as described herein, or even a second virus vector,
or produce a
virus vector genome of a different or even second virus vector or produce a
nucleic acid
that substantially resembles the genome of a different or second virus vector.
Such a
process of virus metamorphosis can be mediated by a virus vector modified in
its nucleic
acid sequence by the incorporation of one or more non-native sequences.
Introduction of
such a modified nucleic acid component or components into an appropriately
constructed
packaging cell can provide propagation of such second virus vectors from the
original
vector, or its introduction into a target cell can produce a nucleic acid of a
second virus
vector or virus vector nucleic acid which contains properties other than found
in the
original vector, including integration into the target cell genome.
Compositions are also
provided for packaging cells that can be modified to provide virus.
metamorphosis by the
incorporation of components non-native to said packaging cell. Compositions
for virus
metamorphosis can be useful for the production of defective virus vectors
wherein such
viruses can be propagated without the requirement for a helper virus and which
can also be
useful to provide properties for the integration of Exogenous Nucleic Acid
into the genome
of a target cell.
Whereas certain viruses possess useful properties for gene transfer, their use
is limited
by the requirement of a helper virus for virus vector production or by an
inability to provide
for stable transfer of Exogenous Nucleic Acid to a target cell or for
integration of
Exogenous Nucleic Acid at preferred sites of a target cell genome. For
example, certain
defective viruses can be propagated in packaging cells that provide the
required packaging
components but with the requirement for use of a helper virus. In order to
insure safe use
of such a virus vector preparation, however, the contaminating helper virus
must be
CA 02596292 2007-08-23
removed and the virus vector product must be extensively safety tested for the
presence of
any contaminating helper virus. The present invention overcomes these
limitations by
providing compositions for virus metamorphosis which can be used for
propagation of
second virus vectors without the requirement for a helper virus.
Among the novel and useful viral vectors of the present invention is one
comprising a
virus or viral portion having on a surface or an envelope thereof at least two
adsorbing
components, one component for adsorption to a packaging cell line for the
vector, and the
other component for adsorption to a target cell for delivery of the vector.
Both
aforementioned components can be native to the viral vector, or both can be
non-native to
the viral vector, or in some instances one component can be native and the
other
component can be non-native. When at least one component is native to the
viral vector,
one of the components can be ecotropic or amphotropic. Such non-native
components are
known in the art and can take a number of forms. These include, by way of
example, any
of the members selected or derived from the group consisting of Human
Immunodeficiency
Virus (HIV), Hepatitis B Virus (HBV), Hepatitis C Virus (HCV), Herpes Simplex
Virus
(HSV), and Vesticular Stomatis Virus (VSV), and a part or portion thereof, or
a
combination of any of the foregoing. In the case of HIV or its part or portion
thereof, the
non-native component can comprise gp120. In the case ofHBV or HCV, the non-
native
component comprises a surface antigen. One or the other or both components of
the viral
vector can be selected from any of the members of the group consisting of a
protein, an
oligo- or polypeptide, a glycoprotein, a fused peptide, a recombinant peptide,
a modified
protein, or a combination of any of the foregoing.
In preferred aspects, the above described viral vector comprises a retrovirus
such as a
murine retrovirus.
Vectors that can provide for vector metamorphosis can also be used to provide
integration properties to the vectors derived from the original vector. While
certain viruses
possess useful properties for gene delivery, their use is limited by an
inability to integrate
and/or to remain stably associated with a target cell, and such virus vectors
can thus only
provide for expression of Exogenous Nucleic Acid for a limited period.
Compositions for
virus metamorphosis can be used to provide for stable expression of Exogenous
Nucleic
21
CA 02596292 2007-08-23
Acid by providing properties for stable integration into a target cell genome
of the second
vector where the original vector lacks integration capability. Such properties
can be
provided to a vector or virus vector by components non-native to such a vector
or virus
vector wherein such properties can be derived from other viruses or from other
biological
systems or synthetically.
Virus metamorphosis can proceed in a packaging cell or in a target cell by the
introduction into said cell of the nucleic acid of an initiating vector (or
first virus vector)
wherein said nucleic acid is a component of a virus vector, is a virus vector
nucleic acid or,
is a nucleic acid construct or a component thereof. Propagation of said
nucleic acid in a
packaging cell or in a target cell can directly or indirectly yield a nucleic
acid with
properties native to a virus vector (second virus vector) that is unrelated to
the first virus
vector wherein the nucleic acid of the second virus vector differs from the
nucleic acid of
the first virus vector in i) complexity, wherein it can be shorter or longer,
ii) in chemical
nature wherein it can be either single or double stranded RNA or DNA or
partially single
stranded and partially double stranded RNA or DNA and iii) in the function of
promoters/enhancers, integration sequences and termination, processing
sequences, or the
difference lies in packaging surface component or components. The properties
of the
second vector nucleic acid could provide for the packaging of the.second
vector in a
packaging cell which is constructed to provide the required components for the
second
vector packaging. Alternatively, the nucleic acid of such an second virus
vector so
produced in a target cell could contain properties for its incorporation into
the genome of
said cell.
Virus vectors useful for the practice of this invention can be derived from
plant,
bacterial, animal and human viruses wherein these can be modified by
components non-
native to said initiating vector virus. Such components can normally be
derived from other
viruses but could also be derived from other biological systems or made
synthetically. Such
components include but are not necessarily limited to nucleic acid sequences
that provide
for virus propagation, integration function and gene expression for virus
components.
These include the LTR sequences of retroviruses, the integrase protein of
retroviruses, the
reverse transcriptase of retroviruses, the ITR sequences of AAV, the rep genes
of AAV,
22
CA 02596292 2007-08-23
the cap genes of AAV and other components that can provide useful functions.
The nucleic acid sequences of virus vectors used to initiate virus
metamorphosis, i.e.,
and first virus vector, can be conveniently constructed by the methods of
recombinant DNA
wherein the non-native vector components can be incorporated into a vector
nucleic acid
sequence.
Packaging cells for the practice of this invention can be prepared by the
introduction of
nucleic acid sequences normally derived from both the initiating vector and
the second
vector. Such nucleic acid sequences can provide for the synthesis of the
second vector
component(s) including packaging components, polymerases or other required
enzymes,
and for the synthesis of the second vector nucleic acid. Such nucleic acid
sequences can
present in such cells in either an integrated or in an episomal state.
Virus vectors that can be utilized for virus metamorphosis include
retroviruses like the
Moloney murine leukemia virus (MMLV). A retrovirus vector (vector, vector
nucleic acid,
or nucleic acid construct) can be modified to propagate an second virus
vector, such as the
AAV, by incorporating a sequence of the AAV ITR into the retroviral vector
nucleic acid
sequence. Two such sequences can be inserted into the retrovirus vector
nucleic acid.
Such vector can direct the synthesis of retrovirus vector RNA in a packaging
cell and the
packaging cell line can provide reverse transcriptase for synthesis of AAV
DNA.
Exogenous Nucleic Acid are present in the region flanked by the AAV ITRs. The
retroviral vector nucleic acid can be further modified by inactivation of the
ppt sequence
segment function (or others), thus eliminating synthesis of the second DNA
strand after
reverse transcription as a means of providing single stranded DNA copies of
the second
vector (for example, AAV). This can be accomplished by deletion of the ppt
sequence or
by the replacement of the retroviral ppt sequence with one of the AAV ITR
sequences or
with an AAV rep sequence by methods described elsewhere in this patent. AAV
rep and
cap nucleic acid sequences can be provided to packaging cells as part of the
retrovirus
nucleic acid component or such sequences can be provided separately on
plasmids or other
nucleic acid entities either inserted into a cell genome or present in the
packaging cell in an
episomal state or in a transient state.
This invention further provides a viral vector comprising a virus or viral
portion thereof
23
CA 02596292 2007-08-23
having on a surface or an envelope at least two components, the first
component being
native to the virus, and the second component characterized by three
characteristics. First,
it is non-native to said viral vector. Second, it is capable of adsorption to
a target cell of
interest. Third, the second component is incapable of adsorption to a cell
native for the
viral vector. In a preferred aspect, the viral vectors is a retrovirus.
Suitable or appropriate
retroviruses have been well characterized in the literature and can take a
number of diverse
forms. Merely by way of example, such retroviruses can be selected from any of
the
members of the group consisting of a murine leukemia virus, a human
immunodeficiency
virus, a human T cell leukemia virus and a Gibbon ape leukemia virus. or a
combination of
any of the foregoing.
The non-native component in the above-described viral vector can also take a
number
of forms, all of which are well described in the literature. These include any
or all of the
following members selected or derived from the group consisting of Human
Immunodeficiency Virus (HIV), Hepatitis B Virus (HBV), Hepatitis C Virus
(HCV),
Herpes Simplex Virus (HSV), and Vesticular Stomatis Virus (VSV), and a part or
portion
thereof, or a combination of any of the foregoing. In the case of HIV, the
derived member
can comprise gp120. In another instance, the non-native component can comprise
HBV or
HCV surface antigen.
The present invention contemplates a number of useful target cells, including
any of
the members selected from the group consisting of T cells, liver cells, bone
marrow cells
and epithelial cells, or a combination of any of the foregoing.
The present invention also provides a vector selected from the group
consisting of a (i)
viral vector, (ii) a viral nucleic acid, and (iii) a nucleic acid construct,
the vector comprising
a non-native nucleic acid sequence coding for a segment, the segment being
capable of
integration into a target cell's genome, and the vector being capable of
producing or
introducing a first nucleic acid in the target cell, the first nucleic acid
being capable of
producing a second nucleic acid that comprises a portion of the first nucleic
acid, the
second nucleic acid comprising the integration segment and being capable of
expressing an
exogenous gene or an exogenous nucleic acid sequence. In one aspect, this
vector can
comprise a viral vector and the integration segment can be non-native to the
viral vector.
24
CA 02596292 2007-08-23
The vector can also comprise a viral nucleic acid and the integration segment
can also be
non-native to the viral vector. In one preferred embodiment, the viral vector
comprises
adenovirus. In another, the first nucleic acid comprises a retrovirus and the
second nucleic
acid comprises adeno-associated virus (AAV). In yet another, the first nucleic
acid
comprises AAV and the second nucleic acid comprises a retrovirus. Still
further, the
second nucleic acid sequence comprises retroviral LTR or AAV.
This invention also provides a process for producing any of the viral vectors
or viral
vector nucleic acids as disclosed herein or claimed below. Such a process
typically
comprises the steps of providing such vector and introducing it into a
packaging cell under
conditions to produce the viral vector or said viral vector nucleic acid. In
one aspect, the
nucleic acid construct can be been modified in a promoter/enhancer region, in
a non-native
promoter. In other aspects of the just described process, the nucleic acid
construct is
capable of stable integration into the genome of said packaging cell line. It
should not be
overlooked that in the case where a nucleic acid construct is employed in such
process, the
construct can be modified by means of an episome or by means of transient
expression.
This invention also provides a packaging cell line for propagating a viral
vector
independent of a helper virus. The viral vector can comprise a nucleic acid
component and
a non-nucleic acid component. The sequence or sequences for the viral vector
nucleic acid
component can be stably integrated in the genome of the cell line, and the
sequence or
sequences for the non-nucleic acid component of the viral vector are
introduced into the
packaging cell line by a means selected from the group consisting of transient
expression,
episomal expression, stably integrated expression, or a combination of any of
the foregoing.
Packaging cells for this purpose can be prepared to contain retroviral reverse
transcriptase sequences in order to provide for reverse transcription of
transcripts produced
from the initiating vector (retrovirus).
An example of a virus vector that provides for production of an second vector
by virus
metamorphosis is presented in Examples 7, 8 and 9, and Figures 8, 9 and 10.
AAV ITRs
and sequences for AAV rep are inserted into an MMLV retrovirus vector sequence
contained in a vector construct. A packaging cell is prepared from mouse 3T3
cells by the
stable insertion into said cell of retrovirus reverse transcriptase sequences
in order to
CA 02596292 2007-08-23
provide for reverse transcription of retrovirus vector transcripts and
sequences for AAV
cap to provide for AAV virus vector packaging. Following introduction of the
initiating
retrovirus nucleic acid component (present on a plasmid) into a into such a
packaging cell,
reverse transcription of the retrovirus vector genome yields a single stranded
retrovirus
DNA containing two AAV ITR sequences that are separated by approximately 4.5
kb
wherein they flank an AAV rep gene and a sequence for Exogenous Nucleic Acid.
Such
DNA copies, by virtue of the AAV ITR sequences and the AAV rep function can be
replicated to produce AAV vector sequences which contain the AAV rep sequences
and
the Exogenous Nucleic Acid sequence. The presence of cap proteins and the AAV
packaging signal provide for packaging of such AAV vector viruses.
This invention also provides a packaging cell line for propagating any of the
viral
vectors of the present invention, as disclosed or claimed herein. Such
packaging cell line
can provide, for example, at least two packaging components for the surface or
envelope of
the viral vector. In the packaging cell line, the cell line can be native to
the viral vector.
The viral vector itself can comprise in preferred aspects a retrovirus. The
cell line for use in
the packaging line of this invention, can take on a number of forms known in
the art,
including, for example, any of the members selected from the group consisting
of NIH 3T3,
U937, H9 and 293, or a combination of any of the foregoing.
In other aspects, any sequences for both the surface or envelope components in
the
packaging cell line are stably integrated in a chromosome or chromosomes of
the packaging
cell line. Furthermore, a sequence of a surface or envelope component can be
stably
integrated in a chromosome or chromosomes of the packaging cell line, and a
sequence of
another surface or envelope component can be transiently expressed. Still yet
further, a
sequence of said envelope component can be stably integrated in a chromosome
or
chromosomes of said packaging cell line, and a sequence of the surface
component is
transiently expressed. In other aspects, any sequence for both the surface or
envelope
components in the packaging cell line can be transiently expressed.
This invention also provides a packaging cell line for propagating other viral
vectors as
disclosed or claimed herein. In such instances, the cell line can be non-
native to the viral
vector component or components but native to the viral vector nucleic acid.
The
26
CA 02596292 2007-08-23
packaging cell line expresses on its membrane or its surface a receptor or
receptors or
binding partner or partners for adsorption to the non-native component for the
vector.
Virus metamorphosis can also provide for integration of Exogenous Nucleic Acid
into
a cell genome. The ability of the second vector nucleic acid to integrate into
the host
genome provides distinct advantages for establishing stable expression of
Exogenous
Nucleic Acid in a target cell. However, some viruses lack this property but
possess other
useful properties for gene delivery, such as affinity for certain cell types,
stability in human
or animal tissues, efficient delivery of nucleic to target cells. The present
invention
provides compositions and methods of use for virus vectors that, through
compositions for
virus metamorphosis, can provide for the integration of Exogenous Nucleic Acid
into a
target cell genome. Such compositions can also provide for such integration to
occur at
preferred sites in the target cell genome.
Virus vectors .possessing integration properties can be constructed by the
incorporation
of non-native components into the virus vector genome. Such useful components
include
such entities as certain nucleic acid sequences such as those containing
integration signal
sequences and certain vector nucleic acid conformations such as secondary
structure. Non-
native components useful for these purposes include such nucleic acid
sequences such as
retrovirus LTRs, reverse transcriptase and integrase that can provide for
integration at
random sites in a target cell genome. Virus vectors can also be modified with
non-native
components that provide for integration at preferred sites in a target cell.
Such sequences
include ITR sequences and the rep genes derived from AAV. These can be
provided to a
variety of virus vectors, including retrovirus.
Virus vectors containing non-native components that provide integration at
preferred
sites can be constructed by the methods of recombinant DNA as described above.
Virus
vectors such as retroviruses vectors can be modified for this purpose by the
incorporation
into the retrovirus nucleic acid component of two such ITR sequences wherein,
following
reverse transcription of vector RNA in a cell, the ITR sequences will flank a
sequence or
sequences containing Exogenous Nucleic Acid. Sequences for AAV rep function
can also
be incorporated into such a retrovirus vector genome or these sequences can be
provided
on a separate entity such as a virus or a nucleic acid construct such as a
plasmid. The
27
CA 02596292 2007-08-23
presence of the AAV ITR sequences in the double stranded product of reverse
transcriptase
and the AAV rep function in the cell can provide the capability for site
specific integration
into the target cell genome. This process is illustrated in Figures 10, 11 and
12. The
process described above can also be performed through the production of a
single stranded
DNA product of the reverse transcriptase reaction. This can be achieved as
described
above by inactivation of the region of the retroviral genome involved in the
initiation of
second strand DNA synthesis, i.e., the ppi sequence (Figures 11 and 12).
Multitropic Virus Vectors
For gene delivery purposes, a virus vector can be developed from a virus that
is native
to a target cell or from a virus that is non native to a target cell. In
general it is desirable to
use a non-native virus vector rather than a native virus vector. While native
virus vectors
may possess a natural affinity for target cells, such viruses pose a greater
hazard since they
possess a potential for propagation in target cells. In this regard animal
virus vectors,
wherein they are not naturally designed for propagation in human cells, can be
useful for
gene delivery to human cells. In order to obtain sufficient yields of such
animal virus
vectors for use in gene delivery, however, it is necessary to carry out such
production in a
native animal packaging cell. However, virus vectors produced in this way
normally lack
any components either as part of the envelope or as part of the capsid that
can provide
tropism for human cells. For example, current practices for the production of
non-human
virus vectors, such as ecotropic mouse retroviruses like MMLV, are produced in
a mouse
packaging cell line. Although producing a high titter, this vector lacked
affinity for the
target human cell. Alternatively, amphitropic vectors could be used but the
titter could be
much lower.
This invention overcomes this limitation in the prior art by providing
compositions and
methods of use for novel virus vectors and for their production wherein such
vectors
contain at least two surface components that can confer tropism both for
target cells and
28
CA 02596292 2007-08-23
for packaging cells. The presence in these virus vectors of at least two such
components
can provide independent capabilities for the efficient propagation of said
vector viruses in
packaging cells and for the efficient gene delivery to target cells. Affinity
for the packaging
cell provides for propagation to high yields by the ability of propagated
vector viruses to
re-infect packaging cells and undergo repeated cycles of propagation.
A variety of compounds that can present themselves on the surface of a virus
can be
used for the purposes of this invention, and these can be derived from virus
envelope or
capsid proteins or from proteins derived from other biological systems that
have affinity for
animal, plant or human cells and that can be incorporated into a virus vector
surface. Such
compounds useful for this purpose include protein molecules that consist of
the natural
amino sequence of such a protein or of a portion thereof. Such proteins or
fragments can
be modified in whole or in part. Proteins that can present themselves on the
surface of a
multitropic virus vector can be chimeric molecules formed between a protein
native to the
vector virus or a fragment thereof and a protein non-native to said virus or a
fragment
thereof
The proteins of multitropic vector can be native or non-native to said virus
vector.
Useful native proteins include the retrovirus ecotropic and amphotropic,
polytropic or
xenotropic env proteins. Non-native proteins useful for gene delivery to human
cells
include all of the envelope proteins from human viruses, e.g., gp 120 derived
from HIV-1 or
HIV-2 that can provide tropism for CD4+ cells, env proteins of HTLV I and HTLV
II that
can provide tropism for T cells, the envelop proteins of hepatitis B virus
(HBV) that can
provide tropism for liver cells. Envelope proteins from influenza such as HA
that can
provide tropism to human cells can also be useful. Envelope protein from EBV
can also
provide tropism for human B cells.
Multitropic vectors can be conveniently produced in packaging cells that
provide for
the synthesis of such components. These components will incorporate into the
virus
envelope in such a packaging cell. Nucleic acid sequences that provide for the
synthesis of
such compounds can reside on one or more plasmids and such plasmids can be
introduced
into packaging cells. Such a nucleic acid construct can be present in an
episomal state or
can be integrated into the genome of the packaging cell or can be in a
combination of both
29
CA 02596292 2007-08-23
episomal and integrated states. Packaging can be carried out by the methods
and processes
as disclosed herein.
Multitropic vectors can be prepared from such viruses as retroviruses wherein
they
contain in the virus envelope two or more compounds that are native to said
virus such as
the ecotropic env protein of MMLV and the amphotropic, polytropic or
xenotropic env
proteins of MMLV. Packaging of such a multitropic vector can be carried out by
compositions described above. The presence of the ecotropic env protein in the
virus
envelope of the vectors can provide for efficient propagation of said virus
vector in
packaging cells derived from mouse cells, and the amphotropic, polytropic or
xenotropic
env protein can provide for delivery to human cells.
For example, a packaging cell that can produce multitropic retrovirus vectors
containing both the ecotropic env protein and an amphotropic, polytropic or
xenotropic env
protein can be made from a mouse packaging cell such as 3T3 cells. Such a
packaging cell
could be constructed by the introduction into the cell of one or more plasmids
containing
the sequences encoding the packaging components, i.e., gag and pol, and the
two envelope
proteins. A cell line that highly expresses the packaging components can be
selected and
cloned. The subsequent introduction of provirus vector DNA plasmid into such a
packaging cell line can initiate production of multitropic vectors...
Multitropic virus vectors can also be prepared wherein such viruses are
retroviruses
that contain in the virus envelope two or more compounds, at least one of
which is native
to said virus, such as the ecotropic env protein of MMLV, and at least one
compound that
is non-native to the virus vector but has affinity to the target cell. Such a
non-native
compound as that can be derived from another virus envelope and further
provides affinity
for the target cell. For example, a packaging cell that can produce
multitropic retrovirus
vectors containing both a native ecotropic env protein and a non-native
protein such as the
HIV-1 gp120 can be produced in a mouse packaging cell such as a modified 3T3
cell.
Such a multitropic virus vector can be produced as described above using
nucleic acid
sequences for production of gp 120 in place of nucleic acid sequences for the
amphotropic,
polytropic or xenotropic env protein. The presence of the ecotropic env
protein in the virus
envelope of the propagated multitropic vectors can provide for efficient
propagation of said
CA 02596292 2007-08-23
virus vector in packaging cells derived from mouse cells, and the gp 120
protein can provide
for delivery to CD4+ human cells. As described just above, the proteins of
multitropic
vector can be native or non-native to said virus vector. Useful native
proteins include the
retrovirus ecotropic and amphotropic, polytropic or xenotropic env proteins.
Non-native
proteins useful for gene delivery to human cells include all of the envelope
proteins from
human viruses, e.g., env proteins of HTLV I and HTLV II that can provide
tropism for T
cells, the envelop proteins of hepatitis B virus (HBV) that can provide
tropism for liver
cells. Envelope proteins from influenza such as HA that can provide tropism to
human
cells can also be useful. Envelope protein from EBV can also provide tropism
for human B
cells. All of the foregoing components could be propagated in a similar
manner.
The present invention also provides compositions and methods of use for virus
vectors
that contain in the virus envelope or in the virus capsid at least one
component that is non-
native to said virus but is native to a target cell. Such a component could be
a ligand for a
target cell receptor. Efficient propagation of such a virus vector (herein
designated as a
monotropic virus vector) can be attained by the use of a packaging cell that
is native to said
virus and that has been modified to contain on its cell surface a receptor for
the non-native
viral component.
Monotropic virus vectors thus possess the same advantages as multitropic
vectors for
the efficient delivery to a target cell. These vectors exhibit the efficient
adsorption similarly
to a native virus to its target cell. These vectors lack, however, the
undesirable risk to a
human subject posed by a native virus. Thus, vector viruses such as animal
retroviruses
like MMLV can provide the advantages of a native virus vector without its
dangers. Thus,
for example, monotropic properties can provide for animal viruses to be
utilized for gene
transfer to human cells by the incorporation into the virus envelope or onto
the virus
surface of any of a wide variety of compounds non-native to said virus wherein
such
compounds provide tropism for certain types of cells. Efficient propagation of
monotropic
viruses that lack a native compound for affinity to native packaging cells can
be attained by
modifications made to such packaging cells. Thus, a cognate cellular receptor
or receptors
corresponding to the non-native component which is present on the virus
surface or
associated with the virus envelope can be introduced onto the surface of a
packaging cell
31
CA 02596292 2007-08-23
native to the virus vector. As an alternative approach, human cells for
packaging of animal
virus can be developed by providing all sequences for packaging components
such as gag,
pol and env from HIV (gp 120).
A variety of compounds non-native to a virus vector that can present
themselves on
the surface of a virus or associate with the virus envelope can be used for
the preparation of
monotropic virus vectors, and these can be derived from envelope proteins or
from proteins
that provide affinity for animal, plant or human cells that can be derived
from viruses or
from other biological systems. Such compounds can include ligands derived from
viruses, .
protein ligands derived from cells and proteins or peptides that can provide
fusion with cell
membranes. Such compounds useful for this purpose include protein molecules
wherein
such proteins can consist of the entire amino sequence of such a protein or of
a portion
thereof or wherein such proteins or fragments thereof or contain partially
modified
sequences.
Propagation of monotropic virus vectors can be conveniently performed in
packaging
cells that are native to the virus vector or native to a ligand present in a
virus vector
wherein such cells have been modified by the introduction of one or more non-
native
components that can act as receptors for monotropic viruses. Thus, an
monotropic animal
virus vector could, for example, contain a non-native ligand that provides for
tropism to
human cells. Propagation of said vector could be realized by propagation in a
packaging
cell native to the virus vector that has been modified to contain on its
surface a receptor
corresponding to the non-native ligand present on the monotropic virus. Such
receptors
can be introduced into packaging cells. by the incorporation of nucleic acid
sequences that
provide for the synthesis of such receptors. Such nucleic acid sequences could
be present
in the cell either in an integrated (into the cell genome) or in an episomal
state. The
propagation of monotropic virus vectors can proceed by the introduction into
the cell
(native or non-native cell) of nucleic acid sequences for the virus vector
nucleic acid and for
the packaging components, including the non-native compound, wherein
expression can
proceed from these sequences present in an episomal state or in an integrated
state
A monotropic virus vector, such as, for example, a retrovirus vector such as
MMLV,
could be prepared to contain a non-native component (such as gp120) that
provides
32
CA 02596292 2010-02-01
tropism for specific types of human cells as well as for a modified mouse
packaging cell.
Such a vector will possess tropism for CD4+ human cells as well for modified
packaging
cell derived from mouse 3T3 cells that have been modified by the incorporation
of
nucleic acid sequences coding for CD4 and CCR-5 receptor proteins on the cell
surface
(Maddon, P.J., et at., Cell 47:33, 1986). Vector production could
be carried out, for example, by a reverse packaging process as describe
elsewhere in this
patent by the stable incorporation into the genome of said cell of nucleic
acid sequences
that code for vector nucleic acid sequence. Propagation can be initiated by
the introduction
into such cells of nucleic acid sequences that provide synthesis of the
packaging
components of said retrovirus wherein such nucleic acid sequences include
sequences for
gp120 but not for a native env protein, i.e., neither the ecotropic or the
amphotropic env
proteins native to MMLV. Such sequences can be present on plasmids that can'be
amplified such as described elsewhere in this patent to provide for maximum
synthesis of
packaging components.
Packaging Systems
In general, the propagation of a viral vector (without a helper virus)
proceeds in a
packaging cell in which a nucleic acid sequence for packaging components were
stably
integrated into the cellular genome and nucleic acid coding for viral nucleic
acid is
introduced in such a cell line. In such a system, the packaging components
availability is a
limiting element for packaging, which leads to low titter or loss of
continuous stability of
nucleic acid sequence related to packaging components, and could lead to a
packaging cell
incapable of viral production.
To overcome these limitations, the present invention provides methods and
compositions for novel reverse packaging systems that provide for efficient
synthesis of
packaging components without the use of helper virus and may further reduce or
eliminate
the probability for recombination events that can lead to the appearance of
recombination
competent virus by use of cDNA of a gene fragment or by any methods to
minimize
overlapping sequences of plasmids carrying sequences coding for packaging
components.
Such a composition provided by this invention comprises a packaging cell
wherein the
33
CA 02596292 2007-08-23
nucleic acid sequence coding for the production of a virus vector nucleic acid
components
is stably integrated into the cell's genome. The packaging cell further
provides all necessary
packaging components. The use of such a reverse packaging system can overcome
the
limitations of other packaging systems by providing for optimal synthesis of
packaging
components, which can be accomplished by amplified expression of packaging
components
following transfection or by compositions and the methods described in full
detail below.
Optimal expression of packaging components in the packaging cell where the
sequence
coding for vector nucleic acid is stably integrated into the cellular genome
is achieved by
introduction of a nucleic acid construct or constructs coding for packaging
components.
Such components could be native or non-native to the vector, or can be derived
from
genomic DNA or cDNA or any fragments thereof, or modification thereof. The
nucleic
acid construct coding for such packaging components could be present in
packaging cell
line in one or more copies.
Compositions for reverse packaging can provide optimal synthesis of virus
vector
packaging components by the use of nucleic acid amplification. Such
amplification can be
used in combination with highly efficient promoters for expression of
packaging
components as described above. Useful elements for the amplification of
nucleic sequences
for vector virus packaging components include the origin of replication for
SV40 virus
(SV40 ori) and the origin of replication for Epstein-Barr Virus (EBV ori).
These elements
can act to amplify a plasmid or other nucleic acid entity which contains
sequences for the
expression of vector components. Amplification of sequences by the use of
plasmids or
other nucleic acid entities whose replication is controlled by the SV40 on can
be
accomplished by the expression in a packaging cell of trans-acting T-antigen,
while
amplification by the use of plasmids or other nucleic acid entities whose
replication is
controlled by EBV on can be accomplished by the expression of EBNA. Cells with
properties for the packaging of vector virus through amplification can be
realized using
EBV on and EBNA.
For example, compositions for reverse packaging cells which utilize nucleic
acid
amplification can be prepared as described above for reverse packaging of
virus vectors but
wherein a packaging cell that efficiently and stably produces virus vector
nucleic acid is
34
CA 02596292 2007-08-23
transfected with one or more nucleic acid constructs containing SV40 on or EBV
on
wherein such nucleic acid constructs provide for the synthesis of packaging
components.
The trans acting T antigen or EBNA proteins can be produced from sequences
present in
the cell prior to transfection with said nucleic acid constructs or they can
be present on said
nucleic acid constructs.
Compositions and methods of use for reverse packaging systems can provide for
greatly reducing or eliminating the possibility of recombination events among
nucleic acid
segments that encode virus vector nucleic acids and packaging components
wherein such
recombination events could give rise to replication competent viruses. This
can be
accomplished by elimination of overlapping regions of virus genome between two
such
segments in packaging cells.
An example of a packaging system that markedly reduces or eliminates such
possibility
for recombination events and which can be used in combination with reverse
packaging
and/or amplification compositions as described above for the propagation of
retrovirus
vectors can be made by cloning of the retrovitus sequences for gag, pol and
env wherein
the sequences for LTR are not included. The gag, pol and env sequences can be
prepared
from cDNA preparations and cloned into a nucleic acid construct such as a
plasmid. All
such sequences can be cloned into the same plasmid wherein they can be
expressed from
one or more promoters, or such sequences can be cloned into two or more
plasmids
wherein two or more such plasmids are required to provide all of the required
sequences
for viral packaging components and wherein at least one promoter is required
for
expression in each plasmid.
A variety of non-native promoter/enhancer elements, along with polyadenylation
signal, can be used for driving cDNA expression. Promoters/enhancers which are
highly
efficient and either constitutive or inducible can be used. These include but
are not limited
to promoters derived from cellular genes, such as the metallothionen
promoter/enhancer
and the elongation factor (EF) promoter/enhancer, or promoters derived from
viruses such
as CMV early promoters/enhancers, including the promoter/enhancer for the CMV
Ela
gene, promoters derived from bacteriophages such as T3, T7 and SP6 when
expression of
cognate polymerases can be established in a packaging cell. The use of
CA 02596292 2007-08-23
promoters/enhancers such as the metallothionen promoter/enhancer can provide
for the
induction of expression of vector components in packaging cells.
Cells suitable for packaging retroviruses can be transfected with a plasmid
that
contains sequences for the expression of vector nucleic acid and a stably
transfected cell
line producing vector nucleic acid can be selected. Retrovirus vectors can be
produced by
transfection of this cell line with one or more nucleic acid constructs, such
as plasmids, that
provide for expression of packaging components. The propagation of retrovirus
vectors
can proceed from a transient transfection or from a stable transfection with
plasmids that
provide for packaging components.
Non-Viral Specific Nucleic Acid Complexes (NVS complexes)
The present invention provides compositions and methods of use for non-viral
specific
nucleic acid complexes (NVS complexes) that can offer significant advantages
for the use
of non-viral vectors in gene delivery. Such NVS complexes are composed of a
nucleic
acid component and one or more specific binding proteins that bind to one or
more specific
nucleic acid sequences in the nucleic acid construct. Previous compositions
for non-viral
nucleic acid complexes for gene delivery have relied on non-specific complexes
between
nucleic acid component and polypeptides or polycationic polymers lipids. A
wide variety of
such entities have been used wherein binding to the nucleic acid sequences is
non-specific
and/or ionic. It is recognized, however, that such non-specific binding to
nucleic acid can
interfere with function of such nucleic acid, such as transcription,
integration, transport into
the cell and/or into the nucleus and can have other interfering effects
including toxicity.
While non-viral nucleic acid complexes can provide significant advantages for
gene
delivery, these advantages have not or cannot be realized by the use of non-
specific nucleic
acid complexes that rely on non-sequence specific binding components. The
present
invention overcomes these limitations by providing for specific complex
formation between
specific nucleic acid sequence and protein components wherein the binding of
protein
molecules that provide useful properties for gene transfer can be localized to
defined
regions of the nucleic acid construct. Such localization of specific binding
proteins in the
nucleic acid construct can reduce or eliminate any interference with regions
of the nucleic
36
CA 02596292 2007-08-23
acid component that provide biological activity. The present invention also
provides for the
controlled displacement of such specific binding proteins from their cognate
binding sites
wherein such displacement can remove any possible interference with biological
function or
can release proteins that can provide useful function in the cell.
The present invention provides compositions and methods of use for non-viral
specific
nucleic acid complexes (NVS Complexes) that, upon introduction into a cell,
are capable of
biological function, i.e., gene expression, transcription, translation,
integration, intracellular
transport, production of a protein in a cell, production of a nucleic acid in
a cell or
interaction with a nucleic acid or protein in a cell. The present invention
can provide
significant advantages for non-viral vectors through the use of specific
binding proteins that
attach to cognate nucleic acid sequences in the vector nucleic acid component
and can
render the construct capable of one or more of the following properties: 1)
binding to a
target cell, 2) providing for introduction of the nucleic acid component into
cells, 3)
providing for localization to sites within a cell, 4) providing a signal for
integration into
cellular DNA, 5) providing enzymatic activity for replication and/or
expression of vector
nucleic acid within the cell 6) providing protection of the nucleic acid
component from
degradation both in vivo and in vitro. In the present invention one or more of
the above
properties can be provided without substantially interfering with biological
function of said
vector nucleic acid.
The present invention provides advantages over non-viral complexes that rely
on non-
specific or ionic binding between nucleic acid and polypeptides or lipids by
the use of
specific binding proteins that can recognize specific nucleic acid sequences
in the vector
nucleic acid component and thus provide the capability to segregate regions of
specific
protein binding from sequences in the nucleic acid component that provide
biological
function. Thus, one or more of the above properties can be provided without
substantially
interfering with biological function of the nucleic acid component. Such
specific sequences
are not an element or a part thereof of a gene expression cassette such as a
promoter
sequence, but if promoter sequences are used then they are not involved in
transcription but
only function to bind peptides. Transcription from such sequences can be
limited or
eliminated by the use of inverted nucleic segments or inverted nucleotides
immediately
37
CA 02596292 2007-12-18
downstream from such promoter sequences.
The specific binding proteins of NVS complexes can further attach through
fusion,
conjugation, or complexing either directly or indirectly to other moieties
including natural
or unnatural, modified or unmodified oligo- or polypeptides; polycations;
natural or
unnatural, modified or unmodified oligo- or polysaccharides; multimolecular
complexes;
inactivated viruses; lipids; and ligands. Such components can have enzymatic
activity such
as polymerase activity or protein with any biological function including
transport and
integration. The NVS complexes of the present invention can provide for the
delivery of
nucleic acid to eukaryotic cells including the cells of plants, humans and
other mammals
and to prokaryotic cells.
Specific binding protein molecules and their cognate nucleic acid sequences
useful to
the practice of this invention include:
the bacteriophage I repressor (SEQ ID NO.:1)
the bacteriophage 434 repressor (SEQ ID NO.:2)
the tryptophan repressor of E. coli (SEQ ID NO.:3)
the Met J repressor of E. coli, (SEQ ID NO.:4)
the lac repressor of E. coli, (SEQ ID NO.:5)
38
CA 02596292 2007-12-18
the Engrailed gene regulator protein of Drosophila, (SEQ ID NO.:6)
the MATa2 yeast repressor protein, (SEQ ID NO.:7)
the CAP gene activator of E. coli (SEQ ID NO.: 8)
the GAL4 yeast transcription activator, (SEQ ID NO.: 9)
the E2 papillomavirus transcription regulator, (SEQ ID NO.: l0)
the yeast GCN4 transcription regulator, (SEQ ID NO.:11)
the zif268 murine gene regulator, (SEQ ID NO.:12)
39
CA 02596292 2007-12-18
the glucocorticoid receptor transcription modulator, (SEQ ID NO.:13)
the TFIID transcription initiation factor, (SEQ ID NO.:14)
Cognate sequences can be part of a nucleic acid construct and can be present
at one or.
more sites in the nucleic acid construct wherein one or more such sequences
can be present
at any one site. Thus the number of such cognate nucleic acid sequences can be
so
arranged in order to achieve one or more objectives including nuclease
resistance.
Furthermore, the presence of multiple copies of such sequences in a repeated
array can
provide for a desired binding constant between the nucleic acid and a binding
protein. Two
or more such sequences can be present in a nucleic acid component to provide
for
association with two or more different kinds of specific binding proteins.
Useful properties can be provided to NVS complexes by protein/nucleic acid
interactions that can be dissociated in a controlled manner. Thus, for
example, as a means
of eliminating any interference of bound proteins with biological function of
the nucleic acid
component, a dissociable specific binding protein can be bound to its cognate
sequence in
the nucleic acid component and, following contact of the NVS complex with the
target cell
but prior to expression of biological function, said complex in the cell can
be exposed to a
molecule that induces dissociation. Such proteins as the lac repressor of E.
coil and its
cognate sequence are useful in this regard wherein dissociation can be
effected by an
inducer such as an appropriate saccharide or IPTG. It is preferred that when
such a
complex carrying another component that needs to bind to nucleic acid to
provide further
function, e.g., such proteins as RNA polymerase or reverse transcriptase
wherein such
induced release will further improve such function provided by the NVS vector.
CA 02596292 2007-08-23
Specific binding proteins can be modified by chemical modification or by
attachment to
a variety of ligands that can provide useful properties for nucleic acid
transfer to target
cells. Such ligands or chemical modifications, being any chemical moiety,
natural or
synthetic, that can be utilized in this invention include macromolecules
greater than 20,000
m.w. as well as small molecules less that 20,000 m.w. The ligand can include
both
macromolecules and small molecules. Macromolecules that can be utilized
include a
variety of natural and synthetic polymers including peptides and proteins,
nucleic acids,
polysaccharides, lipids, synthetic polymers including polycations, polyanions
and mixed
polymers. Small molecules include oligopeptides, oligonucleotides,
monosaccharides,
oligosaccharides and synthetic polymers including polyanions, polycations,
lipids and mixed
polymers. Small molecules can also include mononucleotides, oligonucleotides,
oligopeptides, oligosaccharides, monosaccharides, lipids, sugars and other
natural and
synthetic entities.
Ligands and chemical modifications can be utilized to provide for nucleic acid
transfer
to cells by providing such useful properties as 1) binding to a target cell,
2) providing for
introduction of the nucleic acid component into cells, 3) providing for
localization to sites
within the cell 4) providing a signal for integration into cellular DNA, 5)
providing
enzymatic activity for replication and/or expression of vector nucleic acid
within the cell by
such proteins as DNA polymerase, RNA polymerase, reverse transcriptase, DNA
ligase. 6)
Proteins that protect the nucleic acid component from degradation.
Cell targeting entities that can be utilized include:
antibodies to cellular surface components and epitopes
viruses, virus components of fragments of virus components that have affinity
for cellular
surface components. These include such proteins as the gp 120 protein of HIV-1
or HIV-2
that binds to the CD4+ receptor of T4 lymphocytes (Lever 1995 British Medical
Bulletin
51:149.
ligands that have affinity for cell surfaces. These include hormones, lectins,
peptides and
proteins, oligosaccharides and polysaccharides. Two such ligands that could be
used, for
example, are asialoorosomucoid that binds to the cellular asialoglycoprotein
receptor (Wu
41
CA 02596292 2010-02-01
et al. 1989 J. Biol Chem 269: 16985, and transferrin that binds to transferrin
cellular
receptors (Wagner et al. 1992 89: 6099).
polycations such as polylysine that bind non-specifically to cell surfaces (Wu
and Wu, US
Patent No. 5,166,320 wherein the function of a specific binding protein could
be
improved if the charge on the nucleic acid is neutralized.
e) matrix proteins such as fibronectin that bind to hematopoetic cells and
other cells
(Ruoslahti et al. 1981 J Biol Chem 256:7277 ).
Entities that facilitate cellular uptake include inactivated viruses such as
adenovirus (Crisitiano
et a1.1993 Proc Natl. Acad. Sci. USA 2Q:2122) Curiel et a1.1991 Proc Natl.
Acad. Sci
USA $$:8850): virus components such as the hemaglutinating protein of
influenza virus
and a peptide fragment derived from it, the hemagglutinin HA -2 N-terminal
fusogenic
peptide (Wagner et a! 1992 Proc Natl. Acad. Sci USA $2:7934).
Entities that confer cellular location include:
nuclear proteins such as histones
nucleic acid species such as the snRNAs Ul and U2 (which can be conjugated to
binding
proteins in accordance with known method, which associate with cytoplasmic
proteins
and localize in the nucleus (Zieve and Sautereauj, 1990, Biochemistry and
Molecular
Biology 25:1.
entities which facilitate incorporation into cellular nucleic acid include:
proteins that function in integration of nucleic acid into DNA. These include
integrase site
specific recombinases (Argos et al. 1986 EMBO Journ i:433).
42
CA 02596292 2007-08-23
and
5) Entities such as nucleic acid polymerases that act to replicate vector
nucleic acid
sequences. These include such enzymes as reverse transcriptase, RNA
polymerases such as
derived form E. coli, T7 bacteriophages, and other virus, prokaryotic and
eucaryotic
systems.
6) Entities such as that provide protection of the nucleic acid component from
degradation
both in vivo and in vitro. Chemical modifications or ligands can be fused,
attached or
conjugated directly or indirectly to specific binding proteins by covalent or
non-covalent
methods to provide such properties as described above. Thus a specific binding
protein or
a fragment thereof can be fused to a protein, such as a ligand, or a fragment
thereof,
wherein the fused protein is a chimeric molecule with properties provided by
both proteins.
Such a fused molecule can be prepared by the methods of recombinant DNA or by
chemical
synthesis. Such fused proteins can also be prepared wherein three or more
proteins, or
fragments thereof, can be fused to form a chimeric protein molecule. Such
proteins may
contain useful properties provided by each of the constituent protein
entities, or one or
more such sequences can act as a connector between polypeptide sequences that
provide
function. Covalent linkage of protein ligands to specific binding proteins by
direct linkages
can be by methods practiced in the art including direct or indirect chemical
attachment to
reactive sites in a specific binding protein. Such covalent attachment could
also be indirect
wherein a specific binding protein can be attached to a protein that is, in
turn, modified by
attachment to a compound or protein that provides useful function. Non-
covalent
methods that can be utilized include modification of the specific binding
protein to provide
for direct or indirect and/or specific or non-specific binding of useful
molecules including
antigen-antibody interactions, receptor-ligand interaction, by hydrophobic
interaction,
polyionic interaction. Thus a specific binding protein could contain native
properties for
binding to an antibody, or could be attached to contain a compound that can be
bound by
an antibody. Such an antibody could, in turn, be modified by attachment to a
protein or
other compound that provides useful function. Specific binding proteins could
also be
43
CA 02596292 2007-08-23
modified to contain ligands such as biotin that can provide binding to
proteins such as
avidin or streptavidin. Other useful ligands that can be used include lectins.
The nucleic acid component of an NVS complex can be DNA, RNA, a combination of
RNA and DNA, e.g., a DNA-RNA hybrid or a chimeric nucleic acid such as a DNA-
RNA
chimera. The nucleic acid components of a NVS complex can be single stranded,
double
stranded or triple stranded. The nucleic acid component be circular, linear or
branched and
may take the form of any DNA or RNA, and it can contain both double stranded
regions
and single regions. All or part of the nucleic acid component can be composed
of modified
nucleic acid or nucleic acid analogues. All or part of the nucleic acid
component can be
prepared by chemical or enzymatic methods.
Nucleic acid sequences recognized by specific binding proteins can be present
in the
nucleic acid component in one or more copies. More than one kind of such a
cognate
sequence can be present in a nucleic acid component in order to provide for
binding of two
or more different kinds of specific binding proteins. Multiple copies of
cognate sequences
can be present in close proximity one to another such as in one or more tandem
array or
such sequences can be present at sites throughout the nucleic acid component.
Regions of biological activity in the nucleic acid component ofNSV complexes
can
specify coding for RNA (such as antisense RNA or ribozymes) or for RNA that
can be
translated into protein. Regions of biological activity in NVS complexes can
contain
sequences for hybridization with intracellular nucleic acid sequences,
integration into
cellular DNA, termination sequences, primer sites and promoter sites.
A NVS complex can be prepared, for example, using a nucleic acid component
such as
a plasmid that contains nucleic acid sequences that can provide biological
function cell and
cognate nucleic acid sequences recognized by a specific binding protein such
as the lac
inducer region (Lac i) that can provide for the binding of lac repressor
protein. Sequences
for the lac inducer region can be included in multiple copies in order to
provide for binding
of multiple copies of lac repressor protein. In order to avoid any
interference of biological
activity by the lac repressor, the multiple copies of the lac inducer sequence
can be
localized to a region of the plasmid that is separate from sequences providing
biological
function. The lac repressor protein for these purposes can be modified to
provide to
44
CA 02596292 2007-08-23
provide useful properties for gene transfer. Thus, the lac repressor could be
modified to
provide for binding to a target cell by conjugating, fusing or complexing with
a protein that
provides affinity for targeted cells. Thus, such proteins as the gp 120
protein derived from
HIV-1 that has properties for attachment to CD4+ cells or the surface antigen
ofHBV that
provides affinity for liver cells could be used. Sattentau, Q.J. and Weiss,
R.A., Cell x:631-
633 (1988); Robinson, W.S: Hepandnavividae and their replication in Field, BN
(ed.),
Virology, Vol. 2, Second ed., 1989; pages 2137-2169.
An NVS complex can also contain more than one kind of specific binding protein
in
order to provide additional functions. A NVS complex could be constructed as
described
above wherein, in addition to the localized multiple copies of cognate
sequences for lac
repressor binding, additional regions of the nucleic acid component containing
multiple
copies of other specific binding proteins such as, for example, the
bacteriophage 434
repressor and the bacteriophage l repressor. These sequences can be also
included in the
nucleic acid component wherein they are present at sites separate from nucleic
acid
sequences providing biological function. The 434 repressor can be modified by
conjugation, fusion or complexing to a nuclear localizing entity such as Ul
RNA and the )
repressor can be modified by conjugation to an integrase in order to assist
integration into
the cell genome. Oraigie, R. et al., Cell ¾,2:829-837 (1990)
CA 02596292 2007-08-23
DESCRIPTION OF THE PREFERRED EMBODIMENTS
Example 1. Reconstitution of a cis effect that resulted from the inactivation
of the U3
promoter/enhancer in a Heterologous Vector (retrovirus vector) by the use of
irrelevant
sequence replacement
A Heterologous Vector (retrovirus vector) was prepared in which the LTR
promoter
and enhancer were inactivated wherein polyadenylation function was
reconstituted.
Replacements were made to a retroviral vector sequence (Figure 1) present in a
plasmid
(pENZI). A 188 base pair DNA fragment in the 3' LTR U3 enhancer was replaced
by 188
base pairs derived from the bacterial Neo gene (neomycin phosphotransferase)
sequence
through PCR strategy. Two regions of the promoter, one of 2 base pairs and one
of 6 base
pairs, were each replaced by restriction enzyme recognition sequences of the
same size
through oligonucleotide-mediated site directed mutagenesis. The removed native
sequences and the non-native replacement sequences are shown in Figure 2.
The replacements of the enhancer and promoter regions were confirmed by DNA
sequencing of these regions following manufacture's instruction (USB and ABI).
A complete Neo sequence was incorporated into this Heterologous Vector
sequence.
Heterologous Vector (retroviruses vector) were produced by transfection of a
packaging
cell he (PA 317 and GP+E-86) with the vector DNA construct. The propagated
Heterologous Vectors (retrovirus vectors) were assayed in a transducing titer
measuring
Neo transductants of 3T3 cells. A titer of up to 106 transducing particles per
ml was
obtained.
Exam. A retroviral vector with inactivated promoter/enhancer which contains a
non-
native polyadenylation signal (the mouse histone H2A614 gene).
The nucleic acid sequence of Heterologous Vector retrovirus present in a
plasmid that
contains a Neo gene in a region outside of the retrovirus vector nucleic acid
sequence can
46
CA 02596292 2007-08-23
be modified by (Figure 3) by replacement of a 188 base pair region of the 3'
enhancer with
188 base pairs derived from the bacterial Neo gene as described in Example 1.
By the same
methods, the promoter sequence can be replaced with sequences for a stem loop
processing
signal derived from mouse histone H2A614 gene. Retrovirus vectors containing
these
modifications can be produced by transfection of packaging cells with this
plasmid vector
and selection of a producer cell line. Such retrovirus vectors can be used for
delivery of an
Exogenous Nucleic Acid to a target cell wherein mRNA expressed from Exogenous
Nucleic Acid can be polyadenylated by using the downstream element of both the
non-
native mouse histone H2kA614 stem-loop processing signal and the retrovirus
AATAA
element.
Example 3. A retroviral vector with inactivated promoter/enhancer which
contains a non-
native polyadenylation signal (the human G-CSF gene with the AATAAA and mRNA
destabilization elements removed).
A Heterologous Vector (retrovirus vector) can be constructed in which the 3'
LTR
promoter and enhancer were inactivated wherein the endogenous retroviral
polyadenylation
site is used. Modifications to provide inactivation are made to a retroviral
vector nucleic
acid sequence present in a plasmid (pENZ-1). The region of the LTR containing
the
promoter/enhancer and the endogenous retroviral polyadenylation signal
upstream from the
AATAAA element was replaced with a portion of an efficient exogenous
polyadenylation
signal. In this way, vector mRNA can be polyadenylated by using the retroviral
downstream AATAAA element. Here, a polyadenylation processing signal from the
human
G-CSF gene with the AATAAA and mRNA destabilization elements removed can be
used
to replace a region of the 3' U3 that encompasses both the promoter and
enhancer
sequences (Figure 4). In the case, the retroviral AATAAA element is used.
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CA 02596292 2007-08-23
Example 4. Transcription of chimeric RNA from a Heterologous Vector retrovirus
using a
promoter/enhancer recognized by pol I.
A Heterologous Vector retrovirus can be constructed as described in Example 1
to
deliver an Exogenous Nucleic Acid sequence that transcribes a chimeric
molecule
composed of an antisense RNA and rRNA (Figure 5). A sequence such as Neo can
be
present residing outside of the Heterologous Vector sequence in the plasmid to
provide for
selection of producer cells. This vector construct is used to transfect
packaging cells to
produce Heterologous Vector retroviruses. The Heterologous Vector retroviruses
are
used to transduce a target cell. The polymerase I of the target cell provides
for synthesis of
the chimeric RNA from integrated Heterologous Vector DNA.
Example 5. Transcription of chimeric RNA from a Heterologous Vector retrovirus
using a
promoter/enhancer recognized by pol M.
A Heterologous Vector retrovirus can be constructed as described in Example 1
to
deliver an Exogenous Nucleic Acid sequence that transcribes a chimeric
molecule
composed of an antisense RNA and tRNA (Figure 6). A sequence such as Neo can
be
present in a region outside of the Heterologous Vector sequence in the plasmid
to provide
for selection of producer cells. This vector construct is used to transfect
packaging cells to
produce Heterologous Vector retroviruses. The Heterologous Vector retroviruses
are
used to transduce a target cell. The polymerase III of the target cell
provides for synthesis
of the chimeric RNA from integrated Heterologous Vector DNA.
E6. Transcription of chimeric RNA from a Heterologous Vector retrovirus using
a
promoter/enhancer recognized by pol II wherein the transcript is not
polyadenylated.
A Heterologous Vector retrovirus can be constructed as described in Example 1
to
deliver an Exogenous Nucleic Acid sequence that transcribes a chimeric
molecule
composed of an antisense RNA and the snRNA molecule Ul (Figure 7). A sequence
such
48
CA 02596292 2007-08-23
as Neo can reside in a region outside of the Heterologous Vector sequence in a
plasmid to
provide for selection of producer cells. This vector construct is used to
transfect packaging
cells to produce Heterologous Vector retroviruses. The Heterologous Vector
retroviruses
are used to transduce a target cell. The polymerase II of the target cell
provides for
synthesis of the chimeric RNA from integrated Heterologous Vector DNA.
Example 7. Propagation of AAV vector viruses from a Heterologous Vector
Retrovirus
containing Non-Native Vector Components derived from AAV.
A retroviral vector DNA construct can be constructed to contain two AAV ITR
sequences wherein one is inserted into a site immediately downstream from the
primer
binding site and the other is inserted into a site just upstream from the
retrovirus origin for
second strand DNA synthesis (ppt) such that following reverse transcription in
a cell the
ITR sequences will be separated by approximately 4.5 kb (Figure 8). An
Exogenous
Nucleic Acid can be inserted between the AAV ITR sequences.
The sequences for the AAV cap protein and for the retrovirus for reverse
transcriptase
function are inserted into a plasmid such as pBR322. The sequences are
expressed under
the control of the promoter/enhancer of a constitutive cellular gene such as
the elongation
factor (EF).
The retroviral vector DNA construct and the plasmid containing the cap and the
reverse transcriptase sequences are used to transfect a packaging cell.
Transcripts of
Heterologous Vector RNA are reverse transcribed to yield double stranded
retrovirus
vector DNA. The rep product can mediate synthesis of single stranded vector
DNA
wherein the rep sequences and the Exogenous Nucleic Acid are flanked by the
AAV ITR
sequences. The presence of cap protein provides for packaging of AAV virus
vectors.
Exam lam. Propagation of AAV vector viruses from a Heterologous Vector
Retrovirus
inactivated for ppt function and containing Non-Native Vector Components
derived from
AAV.
A retroviral vector DNA construct can be constructed to contain two AAV TTR
49
CA 02596292 2007-08-23
sequences wherein one is inserted into a site immediately downstream from the
primer
binding site and the other is inserted into a site from which the ppt
sequences were deleted.
The AAV rep sequences can be inserted into a site between the ITR sequences
(Figure 9).
An Exogenous Nucleic Acid can also be inserted between the AAV ITR sequences.
The sequences for the AAV cap protein and for the retrovirus reverse
transcriptase
function are inserted into a plasmid such as pBR322. The sequences are
expressed under
the control of the promoter/enhancer of a constitutive cellular gene, such as
the elongation
factor (EF).
The retroviral vector DNA construct and the plasmid containing the cap and
reverse
transcriptase sequences are used to cotransfect or sequentially transfect
cells. Transcripts
of Heterologous Vector RNA are reverse transcribed to yield Heterologous
Vector DNA
which is single stranded due to the lack of the ppt sequences. In the single
stranded DNA
product of reverse transcription the AAV ITRs are separated by approximately
4.5 kb and
they flank the rep sequence and the Exogenous Nucleic Acid. The rep products
can
mediate synthesis of single stranded vector DNA wherein the rep sequences and
the
Exogenous Nucleic Acid are flanked by the AAV ITR sequences. The presence of
cap
protein provides for packaging of AAV virus vectors.
Ems. Propagation of AAV vector viruses from a Heterologous Vector retrovirus
wherein ppt is deleted and AAV ITR sequences flank the PBS site.
A Heterologous Vector (retrovirus vector) DNA construct can be made to contain
two
AAV ITR sequences that flank the primer binding site (PBS) (Figure 10). The
ppt
sequences are removed and the AAV rep sequences are inserted in their place. A
Exogenous Nucleic Acid can be inserted between the inserted rep sequence and
the
downstream ITR sequence.
The sequences for the AAV cap protein and for the retrovirus reverse
transcriptase
function are inserted into a plasmid such as pBR322. These genes can be
expressed under
the control of the promoter/enhancer of a constitutive cellular gene such as
the elongation
factor (EF).
CA 02596292 2007-08-23
The retroviral vector DNA construct and the plasmid containing the sequences
for cap
and reverse transcriptase function are used to cotransfect or sequentially
transfect cells.
Transcripts of Heterologous Vector RNA are reverse transcribed to yield
Heterologous
Vector DNA which is single stranded due to the lack of the ppt sequences. The
rep
products can mediate synthesis of single stranded vector DNA wherein the rep
sequences
and the Exogenous Nucleic Acid are flanked by the AAV ITR sequences wherein
the AAV
ITR sequences are separated by approximately 4.5 kb. The presence of cap
protein
provides for packaging of AAV virus vectors.
Example 10. A Heterologous Vector (retrovirus vector) that provides for AAV-
directed
integration of Exogenous Nucleic Acid.
A Heterologous Vector (retrovirus vector) can be constructed to contain two
AAV
ITR sequences wherein one is inserted into a site immediately downstream from
the primer
binding site and the other is inserted into a site just upstream from the
retroviral origin for
second strand DNA synthesis (ppt) (Figure 11). The AAV rep sequences are
inserted at a
site between the two AAV ITR sequences. A Exogenous Nucleic Acid can be
inserted
between the ITR sequences. Heterologous Vector (retroviruses vector) are
produced in
retrovirus packaging cells such as the ones described in this patent. The
retrovirus vectors
are used to transduce target cells wherein the vector RNA undergoes reverse
transcription
to produce a double stranded DNA. The AAV ITRs and the rep product expressed
from
the Heterologous Vector can mediate synthesis of single stranded vector DNA
wherein the
rep sequences and the Exogenous Nucleic Acid are flanked by the AAV ITR
sequences.
The AAV rep also functions in integration with site specificity for the g13.4-
ter region of
chromosome 19 of a human target cell.
Example 11. A Heterologous Vector (retrovirus vector) with ppt deleted that
provides for
AAV-directed integration of Exogenous Nucleic Acid.
A Heterologous Vector (retrovirus vector) can be constructed to contain two
AAV
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CA 02596292 2007-08-23
ITR sequences wherein one is inserted into a site immediately downstream from
the primer
binding site and the other is used to replace the sequences for retroviral
origin for second
strand DNA synthesis (ppt) (Figure 12). The AAV rep sequences are inserted at
a site
between the two AAV ITR sequences. A Exogenous Nucleic Acid can be inserted
between the ITR sequences. Such Heterologous Vector (retroviruses vector) are
produced
in retrovirus packaging cells such as the ones described in this patent. The
retrovirus
vectors are used to transduce target cells wherein the vector RNA undergoes
reverse
transcription to produce single stranded Heterologous Vector DNA due to the
lack of the .
ppt sequences. The AAV ITRs and the rep product expressed from the
Heterologous
Vector can mediate synthesis of single stranded vector DNA wherein the rep
sequences and
the Exogenous Nucleic Acid are flanked by the AAV ITR sequences. The AAV rep
also
functions in integration with site specificity for the g13.4-ter region of
chromosome 19 of a
human target cell.
Example 12. A Heterologous Vector (retrovirus vector) that provides for AAV-
directed
integration of Exogenous Nucleic Acid wherein ppt is deleted and AAV ITR
sequences
flank the PBS site.
A Heterologous Vector (retrovirus vector) can be constructed to contain two
AAV
ITR sequences which flank the primer binding site (PBS) (Figure 13). The ppt
sequences
are removed and the AAV rep sequences are inserted in their place. A Exogenous
Nucleic
Acid can be inserted between the rep sequence and the downstream ITR sequence.
Such
Heterologous Vector(retrovirus vectors) are produced in retrovirus packaging
cells such as
the ones described in this patent. The retrovirus vectors are used to
transduce target cells
wherein the vector RNA undergoes reverse transcription to produce single
stranded
Heterologous Vector DNA due to the lack of the ppt sequences. In the single
stranded
DNA product of reverse transcription the AAV ITRs flank the rep sequence and
the
Exogenous Nucleic Acid. The AAV ITRs and the rep product expressed from the
Heterologous Vector can mediate synthesis of single stranded vector DNA. The
AAV rep
also functions in integration with site specificity for the q 13.4-ter region
of chromosome 19
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CA 02596292 2007-08-23
of a human target cell.
Example 13 Use of a Heterologous Vector for the delivery of chimeric antisense
RNA
directed against HIV-1 to CD34 cells in an ex vivo format.
A retrovirus vector can be prepared as described in Example 6 which contains a
sequence for a chimeric RNA composed of Ul snRNA and an antisense sequence
directed
against HIV-1. The promoter and enhancer regions of the LTR can be inactivated
as
described in Example 1. The vector can be constructed to contain no other
Heterologous
Nucleic Acid and thus cannot produce any protein.
Stromal cultures can be established from bone marrow collection from patients.
Cells
are plated at a concentration of 3-5 x 1 Os cells/ml in IMDM medium. After
generation of
the stromal layer, the stromal cells' are irradiated and plated at 5 x 10'
cells per T-25 vent-
cap flask in JMDM containing 10% autologous serum on the day before use.
After successful establishment of the stromal culture, leukapheresis of
patient blood
can begin. Patients undergo leukapheresis following priming with hematapoetic
growth
factor GCSF by conventional methods. Before leukapheresis, 300 nil of blood is
drawn and
sterile serum prepared by conventional methods, plasma is collected and white
blood cells
purified by standard ficoll separation methods. The leukapheresis collections
are further
purified by Ficoll-Hypaque density gradient centrifugation to separate the
PBMC from red
cells and neutrophils. The Baxter Isolex procedure can be used to enrich the
PBMC
fraction for cells expressing CD34+ antigen (stem cells). These cells are
eluted from the
Baxter column into a tissue culture bag. Cellular phenotype (presence of CD34+
markers)
is assessed by flow cytometry prior to expansion.
The cells from the column are expanded in a cell-free, factor-free growth
medium
supplemented with 10% autologous serum, using the autologous stromal cells as
a
supporting layer. Stroma is not used until the fourth passage. At this point
most
hematapoetic cells can be eradicated except for mature macrophages (Nolta,
J.A. et at.
1995, incorporated by reference herein). The autologous serum can be filter
sterilized and
determined to be free of mycoplasma, bacteria and fungi.
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CA 02596292 2007-08-23
The cells are grown in the tissue culture bag for 72 hours. The cells from
some patients
are grown in the absence of GCSF and the cells from the remaining patients are
grown in
the presence of GCSF. Before transduction, a sample of CD34+ enriched cells is
removed
for quantitative measurement of antisense DNA and RNA/cell using PCR and
RT/PCR.
The transducing vector can be produced as FDA certified material by
appropriate
contractors. Vectors consist of high titer (10' - 106 colony forming units per
ml)
supernatants of the packaging cell line, PA317. The supernatants. are free of
pathogens and
helper virus.
Cells are resuspended at a concentration of 105 per ml in a transduction
medium. The
cells are transduced with the MMLV construct (described above) with
inactivated 3' -
terminal LTR and a sequence for production of a chimeric Ul/HIV-1 antisense.
After
adsorption, fresh medium is added and the cells are grown for one week at 37
C. Aliquots
can be stored at all stages.
A sample of CD34+ enriched cells is removed at this time for quantitative
measurement of antisense DNA and RNA/cell using PCR and RT/PCR. The transduced
cells are grown for 1 week in culture at 37 C. The number of the transduced
cells are
determined at the end of one week. Samples are prepared for phenotypic
analysis.
Samples for Gram stain and microbiologic cultures for aerobic and anaerobic
bacteria and
fungus will be obtained prior to infusion.
The transduced cells are harvested, washed 3 times in normal saline and
resuspended in
normal saline. The final cell preparation is filtered through a platelet
filter and transferred
into a transfusion pack for infusion. Intravenous catheterization with
standard sterile
technique is performed. The infusion can be of not more than 5X10' cells/kg of
body
weight. Total volume of infused cells does not exceed 10 ml/kg of body weight.
After an
initial test infusion of 1-5% of the total volume, cells are infused over the
next 60-120
minutes. During infusion, the cell suspension is mixed gently approximately
every 5
minutes while the patient is being observed for acute and subacute toxicity.
Patients are monitored for the production of CD4+ cells expressing
Ul/antisense RNA
by RT-PCR as described (Liu, D. et al. 1997 J. Virol. in press. and for plasma
virus concentration and for CD4+ cell count.
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CA 02596292 2007-08-23
Many obvious variations will no doubt be suggested to those of ordinary skill
in the art
in light of the above detailed description and examples of the present
invention. All such
variations are fully embraced by the scope and spirit of the invention as more
particularly
defined by the claims that follow.
