U.S. patent application number 15/043377 was filed with the patent office on 2017-01-12 for combination anti-hiv vectors, targeting vectors, and methods of use.
This patent application is currently assigned to The Regents of the University of California. The applicant listed for this patent is The Regents of the University of California. Invention is credited to Joseph Anderson, Gerhard Bauer.
Application Number | 20170007721 15/043377 |
Document ID | / |
Family ID | 43032786 |
Filed Date | 2017-01-12 |
United States Patent
Application |
20170007721 |
Kind Code |
A1 |
Anderson; Joseph ; et
al. |
January 12, 2017 |
COMBINATION ANTI-HIV VECTORS, TARGETING VECTORS, AND METHODS OF
USE
Abstract
Recombinant lentiviral vectors containing at least: a lentiviral
backbone comprising essential lentiviral sequences for integration
into a target cell genome; a nucleic acid encoding a CCR5 RNAi; and
an expression control element that regulates expression of the
nucleic acid encoding the CCR5 RNAi element, are provided by this
invention. In an alternative aspect, the vector also contains
polynucleotides encoding TRIM5 alpha and HIV TAR decoy sequences
along with gene expression regulation elements such as promoters
operatively linked to the polynucleotides. The vectors are combined
with packaging plasmid and envelope plasmids and optionally
conjugated to cell-specific targeting antibodies. Diagnostic and
therapeutic methods for using the compositions are further provided
herein.
Inventors: |
Anderson; Joseph; (Davis,
CA) ; Bauer; Gerhard; (Davis, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
The Regents of the University of California |
Oakland |
CA |
US |
|
|
Assignee: |
The Regents of the University of
California
Oakland
CA
|
Family ID: |
43032786 |
Appl. No.: |
15/043377 |
Filed: |
February 12, 2016 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14254771 |
Apr 16, 2014 |
9309535 |
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15043377 |
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13266236 |
Dec 2, 2011 |
8728458 |
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PCT/US2010/033042 |
Apr 29, 2010 |
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14254771 |
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61174419 |
Apr 30, 2009 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61K 38/53 20130101;
C12N 7/00 20130101; C12N 15/1138 20130101; C12N 2310/531 20130101;
C12Y 603/02 20130101; A61K 31/7105 20130101; C12N 2310/141
20130101; C12N 2310/14 20130101; C12N 2320/32 20130101; C12N
2320/31 20130101; C12N 2740/16011 20130101; C12N 2740/16043
20130101; C07K 14/7158 20130101; A61K 48/0066 20130101; C12N 15/86
20130101; C12N 2740/16051 20130101; A61P 31/18 20180101 |
International
Class: |
A61K 48/00 20060101
A61K048/00; C12N 15/86 20060101 C12N015/86; A61K 38/53 20060101
A61K038/53; C12N 7/00 20060101 C12N007/00; C12N 15/113 20060101
C12N015/113; A61K 31/7105 20060101 A61K031/7105 |
Claims
1. A composition comprising a carrier and a recombinant nucleic
acid, the recombinant nucleic acid comprising: (a) a nucleic acid
encoding a CCR5 RNAi; (b) a nucleic acid encoding a TRIM5alpha; and
(c) a nucleic acid encoding an HIV TAR.
2. The composition of claim 1, wherein the recombinant nucleic acid
further comprises one or more expression control elements that
separately regulate expression of the nucleic acid encoding the
elements (a), (b) and (c).
3. The composition of claim 1 or 2, wherein the recombinant nucleic
acid further comprises a lentiviral backbone.
4. The composition of claim 1, comprising the recombinant nucleic
acid, wherein: the nucleic acid encoding a CCR5 RNAi, is selected
from the group consisting of a polynucleotide comprising
nucleotides 284-330 of SEQ ID NO: 11 or comprising SEQ ID NOS:
12-16, or a nucleic acid having at least 80% sequence identity to
each thereto; the nucleic acid encoding a TRIM5alpha is selected
from the group consisting of the TRIM5alpha polynucleotide
comprising SEQ ID NOs: 4 or 5 or a polynucleotide comprising
nucleotides 994 to 1032 of SEQ ID NO. 17, or a nucleic acid having
at least 80% sequence identity to each thereof; and the nucleic
acid encoding an HIV TAR is selected from the group consisting of
the HIV TAR comprising SEQ ID NOs: 1 to 3, or a polynucleotide
comprising nucleotides 284 to 415 of SEQ ID NO: 19, or a nucleic
acid having at least 80% sequence identity to each thereof.
5. The composition of claim 1, comprising the recombinant nucleic
acid, wherein at least one of the expression control elements is a
promoter.
6. The composition of claim 5, comprising the recombinant nucleic
acid, wherein the one or more promoters is a Polymerase-III
promoter or a Polymerase II promoter that regulates expression of
the CCR5 RNAi or the HIV TAR sequence.
7. The composition of claim 5, comprising the recombinant nucleic
acid, wherein the one or more expression promoters is a Polymerase
II promoter that regulates expression of the nucleic acid encoding
the TRIM5alpha sequence.
8. The composition of claim 6, comprising the recombinant nucleic
acid, wherein the Polymerase III promoter comprises a U6 promoter
sequence.
9. The composition of claim 6 or 7, comprising the recombinant
nucleic acid, wherein the Polymerase II promoter comprises the
MNDU3 Polymerase II promoter or an equivalent thereof.
10. The composition of claim 1, comprising the recombinant nucleic
acid, further comprising a nucleic acid encoding a reporter
marker.
11. An isolated cell comprising a recombinant nucleic acid, the
recombinant nucleic acid comprising: (a) a nucleic acid encoding a
CCR5 RNAi; (b) a nucleic acid encoding a TRIM5alpha; and (c) a
nucleic acid encoding an HIV TAR.
12. The isolated cell of claim 11, wherein the cell is a stem
cell.
13. A composition comprising the isolated cell of claim 11 or 12,
and a carrier.
14. A method to inhibit HIV replication in a subject in need
thereof comprising administering to the subject an effective amount
of the isolated cell of claim 11.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. application Ser.
No. 14/254,771, filed Apr. 16, 2014, which in turn is a
continuation of U.S. application Ser. No. 13/266,236, filed Dec. 2,
2011, now U.S. Pat. No. 8,728,458, issued May 20, 2014, which is a
national stage entry under 35 U.S.C. .sctn.371 of International
Application No. PCT/US2010/033042, filed Apr. 29, 2010, which
claims priority to U.S. Provisional Application No. 61/174,419,
filed Apr. 30, 2009, the disclosure of each of which is hereby
incorporated by reference in its entirety.
BACKGROUND
[0002] Throughout this disclosure, various publications, patents
and published patent specifications are referenced by an
identifying citation. The disclosures of these publications,
patents and published patent specifications are hereby incorporated
by reference into the present disclosure to more fully describe the
state of the art to which this invention pertains.
[0003] HIV infection continues to spread worldwide in both
developed and underdeveloped countries with no effective vaccine
available. Current antiretroviral drug therapies have been
successful in suppressing viral infection as long as the patient is
compliant with the prescribed regimen. However, with prolonged use,
these treatments can become toxic and drug resistant viral escape
mutants arise [1-5]. New and innovative therapies need to be
developed that overcome the limitations of current small drug
antiretrovirals. Gene therapy offers a promising alternative or
supplement to current treatments due to advantages which include
the possibility of a one-time treatment, controlled or constitutive
anti-HIV gene expression, and long-term viral inhibition
particularly if hematopoietic progenitor cells (HPCs) are targeted.
Many anti-HIV genes have been evaluated for their efficacy in
inhibiting viral infection including antisense RNAs, riboyzymes,
RNA decoys, siRNAs, intrabodies, transdominant proteins, and
restriction factors [8-23, 42-43]. These molecules have been
targeted to both viral genes and proteins and also cellular genes
critical for viral infection and replication. Several groups,
including ours, have been involved with human clinical trials using
a select number of these anti-HIV genes transferred into HPCs by
retroviral and lentiviral vectors [19-23]. However, improvements in
stem cell transduction efficiency and in the effectiveness of the
vector to interfere with different stages of the HIV life cycle are
still needed.
[0004] However, none of these prior art approaches have effectively
eliminated HIV entry and replication in vivo. This invention
satisfies this need and provides related advantages as well.
SUMMARY
[0005] HIV-1 gene therapy offers a promising alternative to small
molecule antiretroviral treatments and current vaccination
strategies by transferring, into HIV-1 susceptible cells, the
genetic ability to resist infection. The need for novel and
innovative strategies to prevent and treat HIV-1 infection is
critical due to devastating effects of the virus in developing
countries, high cost, toxicity, and generation of escape mutants
from antiretroviral therapies and the failure of past and current
vaccination efforts. To that end, applicants provide an HIV-1
susceptible cell-specific targeting vector to selectively transfer,
into CCR5 positive target cells, an anti-HIV CCR5-shRNA gene for
subsequent knockdown of CCR5 expression and protection from HIV-1
infection. Using a ZZ-domain/monoclonal antibody conjugated Sindbis
virus glycoprotein pseudotyped lentiviral vector, applicants
demonstrated the utility of this strategy for HIV-1 gene therapy by
specifically targeting HIV-1 susceptible cells and engineering
these cells to resist HIV-1 infection. CCR5 positive human cells
were successfully and specifically targeted and in vivo for
transduction by a lentiviral vector expressing a highly potent CCR5
shRNA which conferred resistance to HIV-1 infection.
[0006] This invention provides a lentiviral vector comprising, or
alternatively consisting essentially of, or yet further consisting
of: a lentiviral backbone comprising essential lentiviral sequences
for integration into a target cell genome; a nucleic acid encoding
a CCR5 RNAi that, in one aspect, inhibits integration of a human
immunodeficiency virus (HIV) into a mammalian cell; and an
expression control element that regulates expression of the nucleic
acid encoding the CCR5 RNAi element. In a further aspect, the
lentiviral vector also contains a nucleic acid encoding a
TRIM5alpha sequence and an HIV TAR decoy sequence.
[0007] The invention also provides a lentiviral vector as described
above and a packaging plasmid which contains the nucleoside, capsid
and matrix proteins. In a further aspect, the invention further
comprise an envelope plasmid and in a further aspect, a packaging
cell line is provided.
[0008] Also provided are pseudotyped lentiviral particles that are
optionally conjugated to cell-specific targeting antibodies. The
particles optionally can be conjugated to cells.
[0009] The vectors and particles are useful to inhibit, ex vivo and
in vivo, the replication of HIV in a cell system, such as a cell
culture, or in a subject in need thereof by administering an
effective amount of the vector, the particle or the cell conjugated
to the partice. In one aspect, the methods not only inhibit HIV
replication but also prevent replication in a subject infected with
the virus. Specific details of the various embodiments of this
invention are provided herein.
BRIEF DESCRIPTION OF THE DRAWINGS
[0010] FIG. 1 shows a CCR5 shRNA lentiviral vector: A third
generation lentiviral vector, CCLc-x-PGK-EGFP, containing an EGFP
reporter gene was used to generate the CCR5 shRNA construct. The
CCR5 shRNA was expressed under the control of the human
polymerase-III U6 small RNA promoter and was inserted upstream of
the EGFP reporter gene.
[0011] FIG. 2 shows CCR5-positive cell specific targeting of
Ghost-R5-X4-R3 cultured cells: a mixed culture of Ghost-R5-X4-R3
and HEK-293T cells was transduced with the CCR5 targeting vectors,
EGFP-ZZ and CCR5shRNA-ZZ. Seventy-two hours post-transduction, the
cells were stained with a PE-conjugated anti-human CD4 antibody.
Cells were analyzed by FACS for CD4 and EGFP expression.
[0012] FIGS. 3A-3C show down regulation of CCR5 protein and mRNA
levels in transduced Ghost-R5-X4-R3 cells: A mixed culture of
Ghost-R5-X4-R3 and HEK-293T cells was transduced with the CCR5
targeting vectors, EGFP-ZZ and CCR5shRNA-ZZ. (FIG. 3A) Seventy-two
hours post-transduction, the cells were stained with a
PE-conjugated anti-human CCR5 antibody and analyzed by FACS for
CCR5 and EGFP expression. (FIG. 3B) Cells were also analyzed by
QRT-PCR for intracellular CCR5 mRNA. (FIG. 3C) Human PBMCs were
transduced with the CCR5-targeting vectors, EGFP-ZZ and
CCR5shRNA-ZZ, and analyzed by FACS for CCR5 and EGFP
expression.
[0013] FIG. 4 shows CCR5-positive cell specific targeting of human
primary PBMCs: Freshly isolated peripheral blood mononuclear cells
were transduced with the CCR5 targeting vectors. Seventy-two hours
post-transduction, cells were stained with either an APC-conjugated
anti-human CD3 (T cells), PE-conjugated anti-human CD14
monocyte/macrophages), or a PE-conjugated anti-human CD19 (B cells)
antibody and analyzed by FACS.
[0014] FIGS. 5A-5D show HIV-1 challenge of CCR5 shRNA vector
transduced Ghost-R5-X4-R3 cells: Mixed culture
Ghost-R5-X4-R3/HEK-293T cells transduced with the EGFP-alone
(.diamond-solid.) or CCR5shRNA (.box-solid.) vector were challenged
with an R5-tropic BaL-1 strain of HIV-1. Cell culture supernatants
were sampled on various days post-infection and analyzed for p24
antigen by ELISA; (FIG. 5A) MOI and (FIG. 5B) MOI 0.05. Challenge
supernatants were also quantitated for infectious virus by a Ghost
cell assay; (FIG. 5C) MOI 0.01 and (FIG. 5D) MOI 0.05.
[0015] FIGS. 6A-6B show HIV-1 challenge of CCR5 shRNA vector
transduced PBMCs: PBMCs, nontransduced (.diamond-solid.),
EGFP-alone (.box-solid.), and CCR5shRNA (.tangle-solidup.) vector
transduced, were challenged with HIV-1 BaL-1 at an MOI of 0.01.
Cell culture supernatants were sampled on various days
post-infection and assayed for (FIG. 6A) p24 antigen by ELISA and
(FIG. 6B) quantitated for infectious virus by a Ghost cell
assay.
[0016] FIGS. 7A-7D show in vivo CCR5-positive cell specific
targeting: Adult NOD-SCID-IL2r-.gamma. knockout mice were injected
retro-orbitally with fresh PBMCs followed two weeks later by
injection with the CCR5 targeting vector. Cells from various
lymphoid organs were analyzed for cell transduction by staining for
(FIG. 7A) T cells, (FIG. 7B) CCR5, (FIG. 7C) B cells, (FIG. 7D)
macrophages and EGFP by FACS.
[0017] FIGS. 8A-8F show a combination anti-HIV lentiviral vector: a
third generation lentiviral vector, pCCLc-x-PGK-EGFP, which
contains an EGFP reporter gene was used to generate the combination
anti-HIV construct (FIG. 8A). The three transgenes, a chimeric
human/rhesus macaque TRIM5.alpha. driven by the MNDU3 promoter, a
CCR5 shRNA driven by the human polymerase-III small RNA U6
promoter, and a TAR decoy driven by the U6 promoter were inserted
upstream of the EGFP reporter gene to derive
pCCLc-Combination-PGK-EGFP (FIG. 8B). Ghost-R5-X4-R3 cells were
left nontransduced or were transduced with the EGFP alone or
combination lentiviral vectors. Total cellular RNA was extracted
and analyzed by quantitative real-time PCR for expression of (FIG.
8C) TRIM5.alpha., (FIG. 8D) the CCR5 shRNA, and (FIG. 8E) the TAR
decoy using gene-specific primers. (FIG. 8F) U6 snRNA was used as
an internal control. Experiments were performed in triplicate.
EGFP, enhanced green fluorescent protein; HIV, human
immunodeficiency virus; shRNA, short hairpin RNA; TAR,
transactivation response element.
[0018] FIGS. 9A-9B show down regulation of CCR5 surface expression
and mRNA levels in transduced cells: lentiviral vector transduced
Ghost-R5-X4-R3 cells were transduced with the EGFP-alone and
combination lentiviral vectors. (FIG. 9A) Seventy-two hours
post-transduction, the cells were analyzed for CCR5 expression by
FACS. (FIG. 9B) Cells were also analyzed by QRT-PCR for
intracellular CCR5 mRNA levels.
[0019] FIGS. 10A-10D show HIV-1 challenge of combination vector
transduced cultured cells: Ghost-R5-X4-R3 cells were transduced
with the EGFP-alone (.box-solid.) or the combination
(.tangle-solidup.) lentiviral vector. Nontransduced
(.diamond-solid.) and vector transduced cells were subsequently
challenged with the R5-tropic BaL-1 strain of HIV-1 at an MOI of
(FIG. 10A) 0.01 and (FIG. 10B) 0.05. Cells were also challenged
with the X4-tropic NL4-3 strain of HIV-1 at an MOI of (FIG. 10C)
0.01 and (FIG. 10D) 0.05. On various days post-infection, cell
culture supernatants were analyzed for HIV-1 p24 antigen by
ELISA.
[0020] FIGS. 11A-11D show HIV-1 challenge of combination vector
transduced CD34+ HPC derived macrophages: CD34+ hematopoietic
progenitor cells were transduced with the EGFP-alone (.box-solid.)
or the combination (.tangle-solidup.) lentiviral vector and
cultured in a macrophage differentiation medium. Upon development
of mature macrophages, nontransduced (.diamond-solid.) and vector
transduced cells were challenged with the R5-tropic BaL-1 strain of
HIV-1. Cell culture supernatants were sampled and analyzed for
HIV-1 p24 antigen by ELISA (FIG. 11A) (MOI 0.01) and (FIG. 11B)
(MOI 0.05). Challenge supernatants were also analyzed for
infectious virus by a Ghost cell assay (FIG. 11C) (MOI 0.01) and
(FIG. 11D) (MOI 0.05).
[0021] FIGS. 12A-12D show a generation of escape mutants after
long-term viral challenge: Naive nontransduced (.diamond-solid.),
EGFP-alone (.box-solid.), and combination (.tangle-solidup.) vector
transduced Ghost-R5-X4-R3 cells were challenged with the day 25
culture supernatants from their respective initial viral
challenges: (FIG. 12A) BaL-1 MOI 0.01, (FIG. 12B) BaL-1 MOI 0.05,
(FIG. 12C) NL4-3 MOI 0.01, and (FIG. 12D) NL4-3 MOI 0.05. Cell
culture supernatants were analyzed for infectious virus by a Ghost
cell assay.
[0022] FIGS. 13A-13B show a selective survival advantage of
combination vector transduced cells: Ghost-R5-X4-R3 cells were
transduced with the EGFP-alone or the combination lentiviral
vector. Transduced cells were mixed with nontransduced cells at a
ratio of 1:1 and 2:1 (transduced:nontransduced) and were challenged
with the (FIG. 13A) R5-tropic BaL-1 or (FIG. 13B) X4-tropic strain
of HIV-1 at an MOI of 0.01. Cells were analyzed by FACS for EGFP
expression pre-infection and on day 21 post-infection.
[0023] FIGS. 14A-14B show detection of integrated HIV-1 provirus:
Ghost-R5-X4-R3 nontransduced, EGFP-alone, and combination vector
transduced cells were challenged with the (FIG. 14A) R5-tropic
BaL-1 and (FIG. 14B) X4-tropic NL4-3 strain of HIV-1 at MOIs of
0.01 and 0.05. On day 25 post-infection, genomic DNA from virus
challenged cells was analyzed by QRT-PCR for integrated HIV-1
provirus using primers specific for the pol gene.
[0024] FIGS. 15A-15D depict analysis to rule out possible adverse
effects on progenitor cell proliferation and differentiation from
combination vector transduction and expression of the anti-HIV
transgenes: (FIG. 15A) CD34+ HPCs were transduced with the
EGFP-alone or combination lentiviral vector and differentiated into
mature macrophages. Cells were subsequently stained with the normal
macrophage cell surface markers CD14, CD4, and CD68 and analyzed by
FACS. (FIG. 15B) Peripheral blood mononuclear cells (PBMCs) were
transduced with the EGFP alone or combination vectors. On various
post-transduction, the transduced cells were analyzed for EGFP
expression by FACS or (FIG. 15C) total cell counts. (FIG. 15D)
Monocytes and dendritic cells from fresh PBMCs were left
unmanipulated or incubated with PHA, LPS, an 11-amino acid human
peptide, or a 13-aa rhesus macaque peptide. Lymphocytes were added
back to the culture and analyzed for various days for immune cell
activation by the absorbance (570 nm) spectrum of MTT crystals
formed from metabolically active cells.
[0025] FIGS. 16A-16E show gel pictures confirming stability of the
combination vector in transduced cells. Ghost-R5-X4-R3 cells were
left nontransduced or were transduced with the EGFP alone or
combination lentiviral vectors. Total genomic DNA was extracted and
analyzed by PCR with primers specific for the respective vector
transgenes. (FIG. 16A) MNDU3 (forward) and EGFP (reverse), (FIG.
16B) MNDU3 (forward) and TAR decoy (reverse), (FIG. 16C) MNDU3
(forward) and CCR5 shRNA (reverse), (FIG. 16D) TAR decoy (forward)
and EGFP (reverse), and (FIG. 16E) albumin (forward and reverse).
One kilobase DNA ladder (DLa), log DNA ladder (DLb), combination
transfer vector plasmid (lane 1), nontransduced cells (lane 2),
EGFP-alone vector transduced (lane 3), and combination vector
transduced (lane 4). A schematic of the PCR products is below the
panels. EGFP, enhanced green fluorescent protein; kb, kilobase;
TAR, transactivation response element.
[0026] FIGS. 17A-17G show a FACS analysis of cells isolated from
knock-out mice transplanted with CD34+ hematopoietic cells
transduced with combination anti-HIV lentiviral vectors.
BRIEF DESCRIPTION OF SELECTED SEQUENCE LISTINGS
[0027] SEQ ID NO: 11 is the nucleotide sequence of the CCR5
expression cassette. Nucleotides 1-283 corresponds to the
polymerase-III U6 promoter followed by the CCR5 shRNA sequence
(nucleotides 284-330) which is followed by a string of 6 thymidines
(nucleotides 331-336) which is the "transcriptional stop signal"
for the U6 promoter. Alternative CCR5 RNAi for use in this
invention are also shown in SEQ ID NOS: 12-15, as well as a full
length coding sequence for Human G-Protein Chemokine Receptor
(CCR5), SEQ ID NO: 16 that is reproduced from GenBank Accession No.
DM068065, last accessed on Apr. 29, 2009.
[0028] SEQ ID NO: 17 is a polynucleotide encoding a human/rhesus
macaque chimeric TRIM5alpha sequence. The first six nucleotides are
the Kozak sequence followed by the ATG start codon. The nucleotides
corresponding to the rhesus macaque 13 amino acids inserted into
the human TRIM5alpha sequence to make the chimeric protein
(994-1032). The last 39 nucleotides at the end of the sequence
(1492-1530) correspond to a hemmaglutinin tag which was put on the
end of the protein coding sequence for detection of expression.
These 39 nucleotides are followed by the TGA stop codon. The
chimeric TRIM5alpha protein was inserted just downstream from the
MNDU3 polymerase-II promoter in the CCLc-MNDU3-x-PGK-EGFP
lentiviral vector. Additional Polymerase-II promoters for use in
this invention include a) EF1-alpha; b) PGK (phosphoglycerate
kinase promoter); c) CMV (minimal cytomegalovirus promoter); and d)
LTRs from lentiviral and lentiviral vectors.
[0029] SEQ ID NO: 18 is the sequence of a lentiviral backbone of
this invention. The HIV genes were inserted into the EcoRI site
(e.g., at nucleotides 5208-5213). SEQ ID NO: 25 is a portion of the
lentiviral backbone sequence of SEQ ID NO: 18, without certain
promoter and reporter sequences from SEQ ID NO: 18.
[0030] SEQ ID NO: 19 is an HIV TAR decoy sequence for use in the
embodiments of this invention. The polymerase-III U6 promoter is
shown as nucleotides 1-283 followed by the TAR decoy sequence
(284-415). The TAR decoy sequence is followed by a string of 6
thymidines which is the "transcriptional stop signal" for the U6
promoter. Additional TAR sequences for use in this invention
include: a) 5'-cgacttaaaatcgctagccagatctgagcctgggagctctctggctag-3'
(SEQ ID NO: 1) or b)
5'-gggtctctctggttagaccagatttgagcctgggagctctctggctaactagggaaccc-3'
(SEQ ID NO: 2) or c) 5'-acgaagcttgatcccgtttgccggtcgatcgcttcga-3'
(SEQ ID NO: 3).
[0031] SEQ ID NO: 20 is the sequence of a packaging plasmid
sequence for use in this invention.
[0032] SEQ ID NO: 26 is an embodiment of polynucleotides encoding
the pSINDBIS-ZZ envelope plasmid and transcribed by the
polymerase-II CMV promoter into one messenger RNA. The pSINDBIS-ZZ
plasmid comprises the E3 gene (SEQ ID NO: 21), the E2 gene (SEQ ID
NO: 22) (the ZZ domain is between nucleotides 220 and 597), the 6K
gene (SEQ ID NO: 23) and the E1 gene (SEQ ID NO: 24).
MODES FOR CARRYING OUT THE INVENTION
Definitions
[0033] Unless defined otherwise, all technical and scientific terms
used herein have the same meanings as commonly understood by one of
ordinary skill in the art to which this invention belongs. Although
any methods and materials similar or equivalent to those described
herein can be used in the practice or testing of the present
invention, the preferred methods, devices, and materials are now
described. All technical and patent publications cited herein are
incorporated herein by reference in their entirety. Nothing herein
is to be construed as an admission that the invention is not
entitled to antedate such disclosure by virtue of prior
invention.
[0034] The practice of the present invention will employ, unless
otherwise indicated, conventional techniques of tissue culture,
immunology, molecular biology, microbiology, cell biology and
recombinant DNA, which are within the skill of the art. See, e.g.,
Sambrook and Russell eds. (2001) Molecular Cloning: A Laboratory
Manual, 3.sup.rd edition; the series Ausubel et al. eds. (2007)
Current Protocols in Molecular Biology; the series Methods in
Enzymology (Academic Press, Inc., N.Y.); MacPherson et al. (1991)
PCR 1: A Practical Approach (IRL Press at Oxford University Press);
MacPherson et al. (1995) PCR 2: A Practical Approach; Harlow and
Lane eds. (1999) Antibodies, A Laboratory Manual; Freshney (2005)
Culture of Animal Cells: A Manual of Basic Technique, 5.sup.th
edition; Gait ed. (1984) Oligonucleotide Synthesis; U.S. Pat. No.
4,683,195; Hames and Higgins eds. (1984) Nucleic Acid
Hybridization; Anderson (1999) Nucleic Acid Hybridization; Hames
and Higgins eds. (1984) Transcription and Translation; Immobilized
Cells and Enzymes (IRL Press (1986)); Perbal (1984) A Practical
Guide to Molecular Cloning; Miller and Calos eds. (1987) Gene
Transfer Vectors for Mammalian Cells (Cold Spring Harbor
Laboratory); Makrides ed. (2003) Gene Transfer and Expression in
Mammalian Cells; Mayer and Walker eds. (1987) Immunochemical
Methods in Cell and Molecular Biology (Academic Press, London);
Herzenberg et al. eds (1996) Weir's Handbook of Experimental
Immunology; Manipulating the Mouse Embryo: A Laboratory Manual,
3.sup.rd edition (Cold Spring Harbor Laboratory Press (2002));
Sohail (ed.) (2004) Gene Silencing by RNA Interference: Technology
and Application (CRC Press).
[0035] All numerical designations, e.g., pH, temperature, time,
concentration, and molecular weight, including ranges, are
approximations which are varied (+) or (-) by increments of 0.1 or
1.0, where appropriate. It is to be understood, although not always
explicitly stated that all numerical designations are preceded by
the term "about." It also is to be understood, although not always
explicitly stated, that the reagents described herein are merely
exemplary and that equivalents of such are known in the art.
[0036] As used in the specification and claims, the singular form
"a", "an" and "the" include plural references unless the context
clearly dictates otherwise. For example, the term "a cell" includes
a plurality of cells, including mixtures thereof.
[0037] As used herein, the term "comprising" or "comprises" is
intended to mean that the compositions and methods include the
recited elements, but not excluding others. "Consisting essentially
of" when used to define compositions and methods, shall mean
excluding other elements of any essential significance to the
combination for the stated purpose. Thus, a composition consisting
essentially of the elements as defined herein would not exclude
trace contaminants from the isolation and purification method and
pharmaceutically acceptable carriers, such as phosphate buffered
saline, preservatives and the like. "Consisting of" shall mean
excluding more than trace elements of other ingredients and
substantial method steps for administering the compositions of this
invention or process steps to produce a composition or achieve an
intended result. Embodiments defined by each of these transition
terms are within the scope of this invention.
[0038] The term "isolated" as used herein with respect to nucleic
acids, such as DNA or RNA, refers to molecules separated from other
DNAs or RNAs, respectively that are present in the natural source
of the macromolecule. The term "isolated nucleic acid" is meant to
include nucleic acid fragments which are not naturally occurring as
fragments and would not be found in the natural state. The term
"isolated" is also used herein to refer to polypeptides, proteins
and/or host cells that are isolated from other cellular proteins
and is meant to encompass both purified and recombinant
polypeptides. In other embodiments, the term "isolated" means
separated from constituents, cellular and otherwise, in which the
cell, tissue, polynucleotide, peptide, polypeptide, protein,
antibody or fragment(s) thereof, which are normally associated in
nature. For example, an isolated cell is a cell that is separated
form tissue or cells of dissimilar phenotype or genotype. As is
apparent to those of skill in the art, a non-naturally occurring
polynucleotide, peptide, polypeptide, protein, antibody or
fragment(s) thereof, does not require "isolation" to distinguish it
from its naturally occurring counterpart.
[0039] As is known to those of skill in the art, there are 6
classes of viruses. The DNA viruses constitute classes I and II.
The RNA viruses and retroviruses make up the remaining classes.
Class III viruses have a double-stranded RNA genome. Class IV
viruses have a positive single-stranded RNA genome, the genome
itself acting as mRNA Class V viruses have a negative
single-stranded RNA genome used as a template for mRNA synthesis.
Class VI viruses have a positive single-stranded RNA genome but
with a DNA intermediate not only in replication but also in mRNA
synthesis. Retroviruses carry their genetic information in the form
of RNA; however, once the virus infects a cell, the RNA is
reverse-transcribed into the DNA form which integrates into the
genomic DNA of the infected cell. The integrated DNA form is called
a provirus.
[0040] The terms "polynucleotide", "nucleic acid" and
"oligonucleotide" are used interchangeably and refer to a polymeric
form of nucleotides of any length, either deoxyribonucleotides or
ribonucleotides or analogs thereof. Polynucleotides can have any
three-dimensional structure and may perform any function, known or
unknown. The following are non-limiting examples of
polynucleotides: a gene or gene fragment (for example, a probe,
primer, EST or SAGE tag), exons, introns, messenger RNA (mRNA),
transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant
polynucleotides, branched polynucleotides, plasmids, vectors,
isolated DNA of any sequence, isolated RNA of any sequence, nucleic
acid probes and primers. A polynucleotide can comprise modified
nucleotides, such as methylated nucleotides and nucleotide analogs.
If present, modifications to the nucleotide structure can be
imparted before or after assembly of the polynucleotide. The
sequence of nucleotides can be interrupted by non-nucleotide
components. A polynucleotide can be further modified after
polymerization, such as by conjugation with a labeling component.
The term also refers to both double- and single-stranded molecules.
Unless otherwise specified or required, any embodiment of this
invention that is a polynucleotide encompasses both the
double-stranded form and each of two complementary single-stranded
forms known or predicted to make up the double-stranded form.
[0041] A polynucleotide is composed of a specific sequence of four
nucleotide bases: adenine (A); cytosine (C); guanine (G); thymine
(T); and uracil (U) for thymine when the polynucleotide is RNA.
Thus, the term "polynucleotide sequence" is the alphabetical
representation of a polynucleotide molecule. This alphabetical
representation can be input into databases in a computer having a
central processing unit and used for bioinformatics applications
such as functional genomics and homology searching.
[0042] "Homology" or "identity" or "similarity" refers to sequence
similarity between two peptides or between two nucleic acid
molecules. Homology can be determined by comparing a position in
each sequence which may be aligned for purposes of comparison. When
a position in the compared sequence is occupied by the same base or
amino acid, then the molecules are homologous at that position. A
degree of homology between sequences is a function of the number of
matching or homologous positions shared by the sequences. An
"unrelated" or "non-homologous" sequence shares less than 40%
identity, or alternatively less than 25% identity, with one of the
sequences of the present invention.
[0043] A polynucleotide or polynucleotide region (or a polypeptide
or polypeptide region) has a certain percentage (for example, 70%,
75%, 80%, 85%, 90%, 95%, 98% or 99%) of "sequence identity" to
another sequence means that, when aligned, that percentage of bases
(or amino acids) are the same in comparing the two sequences. This
alignment and the percent homology or sequence identity can be
determined using software programs known in the art, for example
those described in Ausubel et al. eds. (2007) Current Protocols in
Molecular Biology. Preferably, default parameters are used for
alignment. One alignment program is BLAST, using default
parameters. In particular, programs are BLASTN and BLASTP, using
the following default parameters: Genetic code=standard;
filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62;
Descriptions=50 sequences; sort by=HIGH SCORE;
Databases=non-redundant, GenBank+EMBL+DDBJ+PDB+GenBank CDS
translations+SwissProtein+SPupdate+PIR. Details of these programs
can be found at the following Internet address:
http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST.
[0044] An equivalent nucleic acid, polynucleotide or
oligonucleotide is one having at least 80% sequence identity, or
alternatively at least 85% sequence identity, or alternatively at
least 90% sequence identity, or alternatively at least 92% sequence
identity, or alternatively at least 95% sequence identity, or
alternatively at least 97% sequence identity, or alternatively at
least 98% sequence identity to the reference nucleic acid,
polynucleotide, or oligonucleotide.
[0045] The expression "amplification of polynucleotides" includes
methods such as PCR, ligation amplification (or ligase chain
reaction, LCR) and amplification methods. These methods are known
and widely practiced in the art. See, e.g., U.S. Pat. Nos.
4,683,195 and 4,683,202 and Innis et al., 1990 (for PCR); and Wu et
al. (1989) Genomics 4:560-569 (for LCR). In general, the PCR
procedure describes a method of gene amplification which is
comprised of (i) sequence-specific hybridization of primers to
specific genes within a DNA sample (or library), (ii) subsequent
amplification involving multiple rounds of annealing, elongation,
and denaturation using a DNA polymerase, and (iii) screening the
PCR products for a band of the correct size. The primers used are
oligonucleotides of sufficient length and appropriate sequence to
provide initiation of polymerization, i.e., each primer is
specifically designed to be complementary to each strand of the
genomic locus to be amplified.
[0046] Reagents and hardware for conducting PCR are commercially
available. Primers useful to amplify sequences from a particular
gene region are preferably complementary to, and hybridize
specifically to sequences in the target region or its flanking
regions. Nucleic acid sequences generated by amplification may be
sequenced directly. Alternatively the amplified sequence(s) may be
cloned prior to sequence analysis. A method for the direct cloning
and sequence analysis of enzymatically amplified genomic segments
is known in the art.
[0047] A "gene" refers to a polynucleotide containing at least one
open reading frame (ORF) that is capable of encoding a particular
polypeptide or protein after being transcribed and translated.
[0048] The term "express" refers to the production of a gene
product.
[0049] As used herein, "expression" refers to the process by which
polynucleotides are transcribed into mRNA and/or the process by
which the transcribed mRNA is subsequently being translated into
peptides, polypeptides, or proteins. If the polynucleotide is
derived from genomic DNA, expression may include splicing of the
mRNA in a eukaryotic cell.
[0050] A "gene product" or alternatively a "gene expression
product" refers to the amino acid (e.g., peptide or polypeptide)
generated when a gene is transcribed and translated.
[0051] "Under transcriptional control" is a term well understood in
the art and indicates that transcription of a polynucleotide
sequence, usually a DNA sequence, depends on its being operatively
linked to an element which contributes to the initiation of, or
promotes, transcription. "Operatively linked" intends the
polynucleotides are arranged in a manner that allows them to
function in a cell. In one aspect, this invention provides
promoters operatively linked to the downstream sequences, e.g., HIV
TAR, CCR5, siRNA and TRIM5alpha.
[0052] The term "encode" as it is applied to polynucleotides refers
to a polynucleotide which is said to "encode" a polypeptide if, in
its native state or when manipulated by methods well known to those
skilled in the art, it can be transcribed and/or translated to
produce the mRNA for the polypeptide and/or a fragment thereof. The
antisense strand is the complement of such a nucleic acid, and the
encoding sequence can be deduced therefrom.
[0053] A "probe" when used in the context of polynucleotide
manipulation refers to an oligonucleotide that is provided as a
reagent to detect a target potentially present in a sample of
interest by hybridizing with the target. Usually, a probe will
comprise a detectable label or a means by which a label can be
attached, either before or subsequent to the hybridization
reaction. Alternatively, a "probe" can be a biological compound
such as a polypeptide, antibody, or fragments thereof that is
capable of binding to the target potentially present in a sample of
interest.
[0054] "Detectable labels" or "markers" include, but are not
limited to radioisotopes, fluorochromes, chemiluminescent
compounds, dyes, and proteins, including enzymes. Detectable labels
can also be attached to a polynucleotide, polypeptide, antibody or
composition described herein.
[0055] A "primer" is a short polynucleotide, generally with a free
3' --OH group that binds to a target or "template" potentially
present in a sample of interest by hybridizing with the target, and
thereafter promoting polymerization of a polynucleotide
complementary to the target. A "polymerase chain reaction" ("PCR")
is a reaction in which replicate copies are made of a target
polynucleotide using a "pair of primers" or a "set of primers"
consisting of an "upstream" and a "downstream" primer, and a
catalyst of polymerization, such as a DNA polymerase, and typically
a thermally-stable polymerase enzyme. Methods for PCR are well
known in the art, and taught, for example in MacPherson et al.
(1991) PCR 1: A Practical Approach (IRL Press at Oxford University
Press). All processes of producing replicate copies of a
polynucleotide, such as PCR or gene cloning, are collectively
referred to herein as "replication." A primer can also be used as a
probe in hybridization reactions, such as Southern or Northern blot
analyses. Sambrook and Russell (2001), infra.
[0056] "Hybridization" refers to a reaction in which one or more
polynucleotides react to form a complex that is stabilized via
hydrogen bonding between the bases of the nucleotide residues. The
hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein
binding, or in any other sequence-specific manner. The complex may
comprise two strands forming a duplex structure, three or more
strands forming a multi-stranded complex, a single self-hybridizing
strand, or any combination of these. A hybridization reaction may
constitute a step in a more extensive process, such as the
initiation of a PCR reaction, or the enzymatic cleavage of a
polynucleotide by a ribozyme.
[0057] Hybridization reactions can be performed under conditions of
different "stringency". In general, a low stringency hybridization
reaction is carried out at about 40.degree. C. in 10.times.SSC or a
solution of equivalent ionic strength/temperature. A moderate
stringency hybridization is typically performed at about 50.degree.
C. in 6.times.SSC, and a high stringency hybridization reaction is
generally performed at about 60.degree. C. in 1.times.SSC.
Hybridization reactions can also be performed under "physiological
conditions" which is well known to one of skill in the art. A
non-limiting example of a physiological condition is the
temperature, ionic strength, pH and concentration of Mg.sup.2+
normally found in a cell.
[0058] When hybridization occurs in an antiparallel configuration
between two single-stranded polynucleotides, the reaction is called
"annealing" and those polynucleotides are described as
"complementary". A double-stranded polynucleotide can be
"complementary" or "homologous" to another polynucleotide, if
hybridization can occur between one of the strands of the first
polynucleotide and the second. "Complementarity" or "homology" (the
degree that one polynucleotide is complementary with another) is
quantifiable in terms of the proportion of bases in opposing
strands that are expected to form hydrogen bonding with each other,
according to generally accepted base-pairing rules.
[0059] The term "propagate" means to grow a cell or population of
cells. The term "growing" also refers to the proliferation of cells
in the presence of supporting media, nutrients, growth factors,
support cells, or any chemical or biological compound necessary for
obtaining the desired number of cells or cell type.
[0060] The term "culturing" refers to the in vitro propagation of
cells or organisms on or in media of various kinds. It is
understood that the descendants of a cell grown in culture may not
be completely identical (i.e., morphologically, genetically, or
phenotypically) to the parent cell.
[0061] A "viral vector" is defined as a recombinantly produced
virus or viral particle that comprises a polynucleotide to be
delivered into a host cell, either in vivo, ex vivo or in vitro.
Examples of viral vectors include retroviral vectors, lentiviral
vectors, adenovirus vectors, adeno-associated virus vectors,
alphavirus vectors and the like. Alphavirus vectors, such as
Semliki Forest virus-based vectors and Sindbis virus-based vectors,
have also been developed for use in gene therapy and immunotherapy.
See, Schlesinger and Dubensky (1999) Curr. Opin. Biotechnol.
5:434-439 and Ying, et al. (1999) Nat. Med. 5(7):823-827.
[0062] In aspects where gene transfer is mediated by a lentiviral
vector, a vector construct refers to the polynucleotide comprising
the lentiviral genome or part thereof, and a therapeutic gene. As
used herein, "lentiviral mediated gene transfer" or "lentiviral
transduction" carries the same meaning and refers to the process by
which a gene or nucleic acid sequences are stably transferred into
the host cell by virtue of the virus entering the cell and
integrating its genome into the host cell genome. The virus can
enter the host cell via its normal mechanism of infection or be
modified such that it binds to a different host cell surface
receptor or ligand to enter the cell. Retroviruses carry their
genetic information in the form of RNA; however, once the virus
infects a cell, the RNA is reverse-transcribed into the DNA form
which integrates into the genomic DNA of the infected cell. The
integrated DNA form is called a provirus. As used herein,
lentiviral vector refers to a viral particle capable of introducing
exogenous nucleic acid into a cell through a viral or viral-like
entry mechanism. A "lentiviral vector" is a type of retroviral
vector well-known in the art that has certain advantages in
transducing nondividing cells as compared to other retroviral
vectors. See, Trono D. (2002) Lentiviral vectors, New York:
Spring-Verlag Berlin Heidelberg.
[0063] The lentiviral vectors of this invention are based on or
derived from oncoretroviruses (the sub-group of retroviruses
containing MLV), and lentiviruses (the sub-group of retroviruses
containing HIV). Examples include ASLV, SNV and RSV all of which
have been split into packaging and vector components for lentiviral
vector particle production systems. The lentiviral vector particle
according to the invention may be based on a genetically or
otherwise (e.g. by specific choice of packaging cell system)
altered version of a particular retrovirus.
[0064] That the vector particle according to the invention is
"based on" a particular retrovirus means that the vector is derived
from that particular retrovirus. The genome of the vector particle
comprises components from that retrovirus as a backbone. The vector
particle contains essential vector components compatible with the
RNA genome, including reverse transcription and integration
systems. Usually these will include gag and pol proteins derived
from the particular retrovirus. Thus, the majority of the
structural components of the vector particle will normally be
derived from that retrovirus, although they may have been altered
genetically or otherwise so as to provide desired useful
properties. However, certain structural components and in
particular the env proteins, may originate from a different virus.
The vector host range and cell types infected or transduced can be
altered by using different env genes in the vector particle
production system to give the vector particle a different
specificity.
[0065] As used herein, "stem cell" defines a cell with the ability
to divide for indefinite periods in culture and give rise to
specialized cells. At this time and for convenience, stem cells are
categorized as somatic (adult) or embryonic. A somatic stem cell is
an undifferentiated cell found in a differentiated tissue that can
renew itself (clonal) and (with certain limitations) differentiate
to yield all the specialized cell types of the tissue from which it
originated. An embryonic stem cell is a primitive
(undifferentiated) cell from the embryo that has the potential to
become a wide variety of specialized cell types. An embryonic stem
cell is one that has been cultured under in vitro conditions that
allow proliferation without differentiation for months to years. A
clone is a line of cells that is genetically identical to the
originating cell; in this case, a stem cell.
[0066] As used herein, an "antibody" includes whole antibodies and
any antigen binding fragment or a single chain thereof. Thus the
term "antibody" includes any protein or peptide containing molecule
that comprises at least a portion of an immunoglobulin molecule.
Examples of such include, but are not limited to a complementarity
determining region (CDR) of a heavy or light chain or a ligand
binding portion thereof, a heavy chain or light chain variable
region, a heavy chain or light chain constant region, a framework
(FR) region, or any portion thereof, or at least one portion of a
binding protein, any of which can be incorporated into an antibody
of the present invention. The term "antibody" is further intended
to encompass digestion fragments, specified portions, derivatives
and variants thereof, including antibody mimetics or comprising
portions of antibodies that mimic the structure and/or function of
an antibody or specified fragment or portion thereof, including
single chain antibodies and fragments thereof. Examples of binding
fragments encompassed within the term "antigen binding portion" of
an antibody include a Fab fragment, a monovalent fragment
consisting of the V.sub.L, V.sub.H, C.sub.L and CH, domains; a
F(ab')2 fragment, a bivalent fragment comprising two Fab fragments
linked by a disulfide bridge at the hinge region; a Fd fragment
consisting of the V.sub.H and C.sub.H, domains; a Fv fragment
consisting of the V.sub.L and V.sub.H domains of a single arm of an
antibody, a dAb fragment (Ward et al. (1989) Nature 341:544-546),
which consists of a V.sub.H domain; and an isolated complementarity
determining region (CDR). Furthermore, although the two domains of
the Fv fragment, V.sub.L and V.sub.H, are coded for by separate
genes, they can be joined, using recombinant methods, by a
synthetic linker that enables them to be made as a single protein
chain in which the V.sub.L and V.sub.H regions pair to form
monovalent molecules (known as single chain Fv (scFv)). Bird et al.
(1988) Science 242:423-426 and Huston et al. (1988) Proc. Natl.
Acad Sci. USA 85:5879-5883. Single chain antibodies are also
intended to be encompassed within the term "fragment of an
antibody." Any of the above-noted antibody fragments are obtained
using conventional techniques known to those of skill in the art,
and the fragments are screened for binding specificity and
neutralization activity in the same manner as are intact
antibodies.
[0067] As used herein, an "antibody" includes whole antibodies and
any antigen binding fragment or a single chain thereof. Thus the
term "antibody" includes any protein or peptide containing molecule
that comprises at least a portion of an immunoglobulin molecule.
Examples of such include, but are not limited to a complementarity
determining region (CDR) of a heavy or light chain or a ligand
binding portion thereof, a heavy chain or light chain variable
region, a heavy chain or light chain constant region, a framework
(FR) region, or any portion thereof, or at least one portion of a
binding protein, any of which can be incorporated into an antibody
of the present invention. The term "antibody" is further intended
to encompass digestion fragments, specified portions, derivatives
and variants thereof, including antibody mimetics or comprising
portions of antibodies that mimic the structure and/or function of
an antibody or specified fragment or portion thereof, including
single chain antibodies and fragments thereof. It also includes in
some aspects, antibody variants, polyclonal antibodies, human
antibodies, humanized antibodies, chimeric antibodies, antibody
derivatives, a bispecific molecule, a multispecific molecule, a
heterospecific molecule, heteroantibodies and human monoclonal
antibodies.
[0068] Examples of binding fragments encompassed within the term
"antigen binding portion" of an antibody include a Fab fragment, a
monovalent fragment consisting of the V.sub.L, V.sub.H, C.sub.L and
CH, domains; a F(ab')2 fragment, a bivalent fragment comprising two
Fab fragments linked by a disulfide bridge at the hinge region; a
Fd fragment consisting of the V.sub.H and C.sub.H, domains; a Fv
fragment consisting of the V.sub.L and V.sub.H domains of a single
arm of an antibody, a dAb fragment (Ward et al. (1989) Nature
341:544-546), which consists of a V.sub.H domain; and an isolated
complementarity determining region (CDR). Furthermore, although the
two domains of the Fv fragment, V.sub.L and V.sub.H, are coded for
by separate genes, they can be joined, using recombinant methods,
by a synthetic linker that enables them to be made as a single
protein chain in which the V.sub.L and V.sub.H regions pair to form
monovalent molecules (known as single chain Fv (scFv)). Bird et al.
(1988) Science 242:423-426 and Huston et al. (1988) Proc. Natl.
Acad Sci. USA 85:5879-5883. Single chain antibodies are also
intended to be encompassed within the term "fragment of an
antibody." Any of the above-noted antibody fragments are obtained
using conventional techniques known to those of skill in the art,
and the fragments are screened for binding specificity and
neutralization activity in the same manner as are intact
antibodies.
[0069] The term "antibody variant" is intended to include
antibodies produced in a species other than a mouse. It also
includes antibodies containing post-translational modifications to
the linear polypeptide sequence of the antibody or fragment. It
further encompasses fully human antibodies.
[0070] The term "antibody derivative" is intended to encompass
molecules that bind an epitope as defined above and which are
modifications or derivatives of a native monoclonal antibody of
this invention. Derivatives include, but are not limited to, for
example, bispecific, multispecific, heterospecific, tri specific,
tetraspecific, multispecific antibodies, diabodies, chimeric,
recombinant and humanized.
[0071] The term "bispecific molecule" is intended to include any
agent, e.g., a protein, peptide, or protein or peptide complex,
which has two different binding specificities. The term
"multispecific molecule" or "heterospecific molecule" is intended
to include any agent, e.g. a protein, peptide, or protein or
peptide complex, which has more than two different binding
specificities.
[0072] The term "heteroantibodies" refers to two or more
antibodies, antibody binding fragments (e.g., Fab), derivatives
thereof, or antigen binding regions linked together, at least two
of which have different specificities.
[0073] The term "human antibody" as used herein, is intended to
include antibodies having variable and constant regions derived
from human germline immunoglobulin sequences. The human antibodies
of the invention may include amino acid residues not encoded by
human germline immunoglobulin sequences (e.g., mutations introduced
by random or site-specific mutagenesis in vitro or by somatic
mutation in vivo). However, the term "human antibody" as used
herein, is not intended to include antibodies in which CDR
sequences derived from the germline of another mammalian species,
such as a mouse, have been grafted onto human framework sequences.
Thus, as used herein, the term "human antibody" refers to an
antibody in which substantially every part of the protein (e.g.,
CDR, framework, C.sub.L, C.sub.H domains (e.g., C.sub.H1, C.sub.H2,
C.sub.H3), hinge, (VL, VH)) is substantially non-immunogenic in
humans, with only minor sequence changes or variations. Similarly,
antibodies designated primate (monkey, baboon, chimpanzee, etc.),
rodent (mouse, rat, rabbit, guinea pig, hamster, and the like) and
other mammals designate such species, sub-genus, genus, sub-family,
family specific antibodies. Further, chimeric antibodies include
any combination of the above. Such changes or variations optionally
and preferably retain or reduce the immunogenicity in humans or
other species relative to non-modified antibodies. Thus, a human
antibody is distinct from a chimeric or humanized antibody. It is
pointed out that a human antibody can be produced by a non-human
animal or prokaryotic or eukaryotic cell that is capable of
expressing functionally rearranged human immunoglobulin (e.g.,
heavy chain and/or light chain) genes. Further, when a human
antibody is a single chain antibody, it can comprise a linker
peptide that is not found in native human antibodies. For example,
an Fv can comprise a linker peptide, such as two to about eight
glycine or other amino acid residues, which connects the variable
region of the heavy chain and the variable region of the light
chain. Such linker peptides are considered to be of human
origin.
[0074] As used herein, a human antibody is "derived from" a
particular germline sequence if the antibody is obtained from a
system using human immunoglobulin sequences, e.g., by immunizing a
transgenic mouse carrying human immunoglobulin genes or by
screening a human immunoglobulin gene library. A human antibody
that is "derived from" a human germline immunoglobulin sequence can
be identified as such by comparing the amino acid sequence of the
human antibody to the amino acid sequence of human germline
immunoglobulins. A selected human antibody typically is at least
90% identical in amino acids sequence to an amino acid sequence
encoded by a human germline immunoglobulin gene and contains amino
acid residues that identify the human antibody as being human when
compared to the germline immunoglobulin amino acid sequences of
other species (e.g., murine germline sequences). In certain cases,
a human antibody may be at least 95%, or even at least 96%, 97%,
98%, or 99% identical in amino acid sequence to the amino acid
sequence encoded by the germline immunoglobulin gene. Typically, a
human antibody derived from a particular human germline sequence
will display no more than 10 amino acid differences from the amino
acid sequence encoded by the human germline immunoglobulin gene. In
certain cases, the human antibody may display no more than 5, or
even no more than 4, 3, 2, or 1 amino acid difference from the
amino acid sequence encoded by the germline immunoglobulin
gene.
[0075] The terms "monoclonal antibody" or "monoclonal antibody
composition" as used herein refer to a preparation of antibody
molecules of single molecular composition. A monoclonal antibody
composition displays a single binding specificity and affinity for
a particular epitope.
[0076] A "human monoclonal antibody" refers to antibodies
displaying a single binding specificity which have variable and
constant regions derived from human germline immunoglobulin
sequences.
[0077] The term "recombinant human antibody", as used herein,
includes all human antibodies that are prepared, expressed, created
or isolated by recombinant means, such as antibodies isolated from
an animal (e.g., a mouse) that is transgenic or transchromosomal
for human immunoglobulin genes or a hybridoma prepared therefrom,
antibodies isolated from a host cell transformed to express the
antibody, e.g., from a transfectoma, antibodies isolated from a
recombinant, combinatorial human antibody library, and antibodies
prepared, expressed, created or isolated by any other means that
involve splicing of human immunoglobulin gene sequences to other
DNA sequences. Such recombinant human antibodies have variable and
constant regions derived from human germline immunoglobulin
sequences. In certain embodiments, however, such recombinant human
antibodies can be subjected to in vitro mutagenesis (or, when an
animal transgenic for human Ig sequences is used, in vivo somatic
mutagenesis) and thus the amino acid sequences of the VH and VL
regions of the recombinant antibodies are sequences that, while
derived from and related to human germline VH and VL sequences, may
not naturally exist within the human antibody germline repertoire
in vivo.
[0078] "RNA interference" (RNAi) refers to sequence-specific or
gene specific suppression of gene expression (protein synthesis)
that is mediated by short interfering RNA (siRNA).
[0079] "Short interfering RNA" (siRNA) refers to double-stranded
RNA molecules (dsRNA), generally, from about 10 to about 30
nucleotides in length that are capable of mediating RNA
interference (RNAi), or 11 nucleotides in length, 12 nucleotides in
length, 13 nucleotides in length, 14 nucleotides in length, 15
nucleotides in length, 16 nucleotides in length, 17 nucleotides in
length, 18 nucleotides in length, 19 nucleotides in length, 20
nucleotides in length, 21 nucleotides in length, 22 nucleotides in
length, 23 nucleotides in length, 24 nucleotides in length, 25
nucleotides in length, 26 nucleotides in length, 27 nucleotides in
length, 28 nucleotides in length, or 29 nucleotides in length. As
used herein, the term siRNA includes short hairpin RNAs
(shRNAs).
[0080] "Double stranded RNA" (dsRNA) refer to double stranded RNA
molecules that may be of any length and may be cleaved
intracellularly into smaller RNA molecules, such as siRNA. In cells
that have a competent interferon response, longer dsRNA, such as
those longer than about 30 base pair in length, may trigger the
interferon response. In other cells that do not have a competent
interferon response, dsRNA may be used to trigger specific
RNAi.
[0081] The term siRNA includes short hairpin RNAs (shRNAs). shRNAs
comprise a single strand of RNA that forms a stem-loop structure,
where the stem consists of the complementary sense and antisense
strands that comprise a double-stranded siRNA, and the loop is a
linker of varying size. The stem structure of shRNAs generally is
from about 10 to about 30 nucleotides in length. For example, the
stem can be 10-30 nucleotides in length, or alternatively, 12-28
nucleotides in length, or alternatively, 15-25 nucleotides in
length, or alternatively, 19-23 nucleotides in length, or
alternatively, 21-23 nucleotides in length.
[0082] Tools to assist siRNA design are readily available to the
public. For example, a computer-based siRNA design tool is
available on the internet at www.dharmacon.com,
Ambion--www.ambion.com/jp/techlib/misc/siRNA_finder.html; Thermo
Scientific--Dharmacon--www.dharmacon.com/DesignCenter/DesignCenterPage.as-
px; Bioinformatics Research
Center--sysbio.kribb.re.kr:8080/AsiDesigner/menuDesigner.jsf; and
Invitrogen--rnaidesigner.invitrogen.com/rnaiexpress/.
[0083] Without being bound by theory, it is generally believed that
the primary cellular receptor for HIV entry is the CD4 receptor. In
addition to CD4 expression, CXCR4, and CCR5 are necessary
co-factors that allow HIV entry when co-expressed with CD4 on a
cell surface.
[0084] CXCR4, or fusin, is expressed on T cells (Feng et al. (1996)
Science 10:272(5263):872-7. Co-expression of CXCR4 and CD4 on a
cell allow T-tropic HIV isolates to fuse with and infect the cell.
HIV gp120 interacts with both CD4 and CXCR4 to adhere to the cell
and to effect conformational changes in the gp120/gp41 complex that
allow membrane fusion by gp41.
[0085] CCR5 is another co-receptor that is expressed on macrophages
and on some populations of T cells, can also function in concert
with CD4 to allow HIV membrane fusion (Deng et al. (1996) Nature,
June 20; 381(6584):661-6.
[0086] TRIM5alpha is 493 amino acid protein that is found in most
primate cells that appears to act to interfere with the replication
of retrovirus in infected cells. Human protein sequence is
published in GenBank (Accession number NP_149023) and the mRNA
sequence also has been published (NM_033034). Murine protein
sequence is available at NP_783608 and mRNA is available at
NM_175677. (All last accessed Apr. 29, 2009).
[0087] An "shRNA CCR5" is an interfering RNA that down regulates or
suppresses expression of the CCR5 polynucleotide, examples of which
are shown in SEQ ID NO: 11. CCR5 is also known as Human G-protein
Chemokine Receptor HDGNR10. Isolated polynucleotides encoding this
protein are known in the art and described, for example in U.S.
Pat. No. 7,501,123.
[0088] A "composition" is intended to mean a combination of active
polypeptide, polynucleotide or antibody and another compound or
composition, inert (e.g. a detectable label) or active (e.g. a gene
delivery vehicle).
[0089] A "pharmaceutical composition" is intended to include the
combination of an active polypeptide, polynucleotide or antibody
with a carrier, inert or active such as a solid support, making the
composition suitable for diagnostic or therapeutic use in vitro, in
vivo or ex vivo.
[0090] As used herein, the term "pharmaceutically acceptable
carrier" encompasses any of the standard pharmaceutical carriers,
such as a phosphate buffered saline solution, water, and emulsions,
such as an oil/water or water/oil emulsion, and various types of
wetting agents. The compositions also can include stabilizers and
preservatives. For examples of carriers, stabilizers and adjuvants,
see Martin (1975) Remington's Pharm. Sci., 15th Ed. (Mack Publ.
Co., Easton).
[0091] A "subject," "individual" or "patient" is used
interchangeably herein, and refers to a vertebrate, preferably a
mammal, more preferably a human. Mammals include, but are not
limited to, murines, rats, rabbit, simians, bovines, ovine,
porcine, canines, feline, farm animals, sport animals, pets,
equine, and primate, particularly human. Besides being useful for
human treatment, the present invention is also useful for
veterinary treatment of companion mammals, exotic animals and
domesticated animals, including mammals, rodents, and the like
which is susceptible to RNA and in particular, HIV viral infection.
In one embodiment, the mammals include horses, dogs, and cats. In
another embodiment of the present invention, the human is an
adolescent or infant under the age of eighteen years of age.
[0092] "Host cell" refers not only to the particular subject cell
but to the progeny or potential progeny of such a cell. Because
certain modifications may occur in succeeding generations due to
either mutation or environmental influences, such progeny may not,
in fact, be identical to the parent cell, but are still included
within the scope of the term as used herein.
[0093] The terms "disease," "disorder," and "condition" are used
inclusively and refer to any condition mediated at least in part by
infection by an RNA virus such as HIV.
[0094] "Treating" or "treatment" of a disease includes: (1)
preventing the disease, i.e., causing the clinical symptoms of the
disease not to develop in a patient that may be predisposed to the
disease but does not yet experience or display symptoms of the
disease; (2) inhibiting the disease, i.e., arresting or reducing
the development of the disease or its clinical symptoms; or (3)
relieving the disease, i.e., causing regression of the disease or
its clinical symptoms.
[0095] The term "suffering" as it related to the term "treatment"
refers to a patient or individual who has been diagnosed with or is
predisposed to infection or a disease incident to infection. A
patient may also be referred to being "at risk of suffering" from a
disease because of active or latent infection. This patient has not
yet developed characteristic disease pathology.
[0096] An "effective amount" is an amount sufficient to effect
beneficial or desired results. An effective amount can be
administered in one or more administrations, applications or
dosages. Such delivery is dependent on a number of variables
including the time period for which the individual dosage unit is
to be used, the bioavailability of the therapeutic agent, the route
of administration, etc. It is understood, however, that specific
dose levels of the therapeutic agents of the present invention for
any particular subject depends upon a variety of factors including
the activity of the specific compound employed, the age, body
weight, general health, sex, and diet of the subject, the time of
administration, the rate of excretion, the drug combination, and
the severity of the particular disorder being treated and form of
administration. Treatment dosages generally may be titrated to
optimize safety and efficacy. Typically, dosage-effect
relationships from in vitro and/or in vivo tests initially can
provide useful guidance on the proper doses for patient
administration. In general, one will desire to administer an amount
of the compound that is effective to achieve a serum level
commensurate with the concentrations found to be effective in
vitro. Determination of these parameters is well within the skill
of the art. These considerations, as well as effective formulations
and administration procedures are well known in the art and are
described in standard textbooks. Consistent with this definition,
as used herein, the term "therapeutically effective amount" is an
amount sufficient to inhibit RNA virus replication ex vivo, in
vitro or in vivo.
[0097] The term administration shall include without limitation,
administration by oral, parenteral (e.g., intramuscular,
intraperitoneal, intravenous, ICV, intracisternal injection or
infusion, subcutaneous injection, or implant), by inhalation spray
nasal, vaginal, rectal, sublingual, urethral (e.g., urethral
suppository) or topical routes of administration (e.g., gel,
ointment, cream, aerosol, etc.) and can be formulated, alone or
together, in suitable dosage unit formulations containing
conventional non-toxic pharmaceutically acceptable carriers,
adjuvants, excipients, and vehicles appropriate for each route of
administration. The invention is not limited by the route of
administration, the formulation or dosing schedule.
Descriptive Embodiments
Lentiviral Vectors
[0098] This invention provides a lentiviral vector comprising, or
alternatively consisting essentially of, or yet further consisting
of: a lentiviral backbone. In one aspect, the backbone contains
essential lentiviral sequences for integration into a target cell
genome. The vector also comprises, or alternatively consists
essentially of, or yet further consists of a nucleic acid encoding
a CCR5 RNAi and an expression control element that regulates
expression of the nucleic acid encoding the CCR5 RNAi element.
[0099] In one aspect, the term "lentiviral vector" intends a
recombinant vector that retains the ability to infect and transduce
non-dividing and/or slowly-dividing cells and integrate into the
target cell's genome. In several aspects, the lentiviral vector is
derived from or based on a wild-type lentivirus. Examples of such,
include without limitation, human immunodeficiency virus (HIV),
equine infectious anaemia virus (EIAV), simian immunodeficiency
virus (SIV) and feline immunodeficiency virus (Hy). Alternatively,
it is contemplated that other retrovirus can be used as a basis for
a vector backbone such murine leukemia virus (MLV). It will be
evident that a viral vector according to the invention need not be
confined to the components of a particular virus. The viral vector
may comprise components derived from two or more different viruses,
and may also comprise synthetic components. Vector components can
be manipulated to obtain desired characteristics, such as target
cell specificity.
[0100] The recombinant lentiviral vectors of this invention are
derived from primates and non-primates. Examples of primate
lentiviruses include the human immunodeficiency virus (HIV), the
causative agent of human acquired immunodeficiency syndrome (AIDS),
and the simian immunodeficiency virus (SIV). The non-primate
lentiviral group includes the prototype "slow virus" visna/maedi
virus (VMV), as well as the related caprine arthritis-encephalitis
virus (CAEV), equine infectious anaemia virus (EIAV) and the more
recently described feline immunodeficiency virus (FIV) and bovine
immunodeficiency virus (BIV). Prior art recombinant lentiviral
vectors are known in the art, e.g., see U.S. Pat. Nos. 6,924,123;
7,056,699; 7,07,993; 7,419,829 and 7,442,551, incorporated herein
by reference.
[0101] U.S. Pat. No. 6,924,123 discloses that certain retroviral
sequence facilitate integration into the target cell genome. This
patent teaches that each retroviral genome comprises genes called
gag, pol and env which code for virion proteins and enzymes. These
genes are flanked at both ends by regions called long terminal
repeats (LTRs). The LTRs are responsible for proviral integration,
and transcription. They also serve as enhancer-promoter sequences.
In other words, the LTRs can control the expression of the viral
genes. Encapsidation of the retroviral RNAs occurs by virtue of a
psi sequence located at the 5' end of the viral genome. The LTRs
themselves are identical sequences that can be divided into three
elements, which are called U3, R and U5. U3 is derived from the
sequence unique to the 3' end of the RNA. R is derived from a
sequence repeated at both ends of the RNA, and U5 is derived from
the sequence unique to the 5' end of the RNA. The sizes of the
three elements can vary considerably among different retroviruses.
For the viral genome. and the site of poly (A) addition
(termination) is at the boundary between R and U5 in the right hand
side LTR. U3 contains most of the transcriptional control elements
of the provirus, which include the promoter and multiple enhancer
sequences responsive to cellular and in some cases, viral
transcriptional activator proteins.
[0102] With regard to the structural genes gag, pol and env
themselves, gag encodes the internal structural protein of the
virus. Gag protein is proteolytically processed into the mature
proteins MA (matrix), CA (capsid) and NC (nucleocapsid). The pol
gene encodes the reverse transcriptase (RT), which contains DNA
polymerase, associated RNase H and integrase (IN), which mediate
replication of the genome.
[0103] For the production of lentiviral vector particles, the
vector RNA genome is expressed from a DNA construct encoding it, in
a host cell. The components of the particles not encoded by the
vector genome are provided in trans by additional nucleic acid
sequences (the "packaging system", which usually includes either or
both of the gag/pol and env genes) expressed in the host cell. The
set of sequences required for the production of the lentiviral
vector particles may be introduced into the host cell by transient
transfection, or they may be integrated into the host cell genome,
or they may be provided in a mixture of ways. The techniques
involved are known to those skilled in the art.
[0104] In one aspect, the lentiviral backbone comprises, or
alternatively consists essentially of, or yet further consists of,
the backbone sequence of SEQ ID NO: 18 or an equivalent thereof.
Alternative retroviral vectors for use in this invention include,
but are not limited to Invitrogen's pLenti series versions 4, 6,
and 6.2 "ViraPower" system. Manufactured by Lentigen Corp.;
pHIV-7-GFP, lab generated and used by the City of Hope Research
Institute; "Lenti-X" lentiviral vector, pLVX, manufactured by
Clontech; pLKO.1-puro, manufactured by Sigma-Aldrich; pLemiR,
manufactured by Open Biosystems; and pLV, lab generated and used by
Charite Medical School, Institute of Virology (CBF), Berlin,
Germany.
[0105] The lentiviral vector also comprises, or alternatively
consists essentially of, or yet further consists of, a nucleic acid
encoding a CCR5 RNAi. The RNAi may be any one or more of RNA
interfering molecules as described herein, e.g., shRNA, siRNA,
miRNA or dsRNA. In one particular aspect, the RNAi is one or more
of a shRNA or siRNA sequence shown in SEQ ID NO: 11 or a
polynucleotide having at least 80% sequence identity, or
alternatively at least 85% sequence identity, or alternatively at
least 90% sequence identity, or alternatively at least 92% sequence
identity, or alternatively at least 95% sequence identity, or
alternatively at least 97% sequence identity, or alternatively at
least 98% sequence identity. Alternate sequences for use in this
invention are available using the publicly available CCR5
polynucleotide sequence (see U.S. Pat. No. 7,501,123 or that
disclosed in SEQ ID NOS: 11-15) and a computer-based siRNA design
tool available on the internet at one or more of www.dharmacon.com,
Ambion--www.ambion.com/jp/techlib/misc/siRNA_finder.html; Thermo
Scientific--Dharmacon--www.dharmacon.com/DesignCenter/DesignCenterPage.as-
px; Bioinformatics Research
Center-sysbio.kribb.re.kr:8080/AsiDesigner/menuDesigner.jsf; and
Invitrogen--rnaidesigner.invitrogen.com/rnaiexpress/.
[0106] To produce RNAi for use in this invention, one can follow
conventional techniques as described in the art using published
sequences or that provided by the applications. dsRNA and siRNA can
be synthesized chemically or enzymatically in vitro using the
methods disclosed in Micura, R. (2002) Agnes Chem. Int. Ed. Emgl.
41: 2265-9; Betz, N. (2003) Promega Notes 85:15-18; Paddison, P. J.
and Hannon, G. J. (2002) Cancer Cell. 2:17-23. Chemical synthesis
can be performed via manual or automated methods, both of which are
well known in the art. Micura, R. (2002) Agnes Chem. Int. Ed. Emgl.
41: 2265-9. siRNA can also be endogenously expressed inside the
cells in the form of shRNAs. Yu, J-Y. et al. (2002) Proc. Natl.
Acad. Sci. USA 99: 6047-52; McManus, M. T. et al. (2002) RNA
8:842-50. Endogenous expression has been achieved using
plasmid-based expression systems using small nuclear RNA promoters,
such as RNA polymerase III U6 or H1, or RNA polymerase II U1.
Brummelkamp, T. R. et al. (2002) Science 296:550-3; Novarino, G. et
al. (2004) J. Neurosci. 24:5322-30.
[0107] In vitro enzymatic dsRNA and siRNA synthesis can be
performed using an RNA polymerase mediated process to produce
individual sense and antisense strands that are annealed in vitro
prior to delivery into the cells of choice. Fire A. et al. (1998)
Nature 391:806-811; Donze, O. and Picard, D. (2002) Nucl. Acids
Res. 30 (10):e46; Yu, J-Y. et al. (2002) Proc. Natl. Acad. Sci. USA
99:6047-52; Shim, E. Y. et al. (2002) J. Biol. Chem. 277:30413-6.
Several manufacturers (Promega Corp. (Madison, Wis.); Ambion, Inc.
(Austin, Tex.); New England Biolabs (Ipswich, Mass.); and Stragene
(La Jolla, Calif.) provide transcription kits useful in performing
the in vitro synthesis.
[0108] Alternatively, one can use a Polymerase-II promoter to
express CCR5 miRNA. For this embodiment, microRNAs are initially
transcribed from Pol-II promoters as long transcripts called
primary-miRNAs which are processed into small pre-miRNAs. These
pre-miRNAs are further processed intracellularly into miRNAs which
are the mediators of gene regulation. CCR5 shRNAs or siRNAs can be
converted to miRNAs by swapping in the exact CCR5 siRNA sequence in
place of the original miRNA sequence. Hence, the CCR5 siRNA can be
expressed via a Pol-II promoter in the context of a miRNA backbone
for efficient processing and regulation/knockdown of gene
expression. The original CCR5 siRNA sequence will be found within
the entire miRNA sequence but will be surrounded by the original
miRNA secondary structure generated from the extra nucleotides
found in the miRNA backbone. Alternative Polymerase II promoters
include, but are not limited to EF1-alpha; PGK (phosphoglycerate
kinase promoter); CMV (minimal cytomegalovirus promoter) and LTRs
from retroviral and lentiviral vectors.
[0109] In a further embodiment, the retroviral vector further
comprise, or alternatively consists essentially of, or yet further
consists of a nucleic acid encoding a TRIM5alpha polynucleotide and
a sequence the regulates expression of the TRIM5alpha sequence
operatively linked to it. For the purpose of illustration only, a
nucleic acid that encodes TRIM5alpha for use in this invention is
one that encodes either of the amino acid sequences for human
TRIM5.alpha. 11-amino acid patch (GARGTRYQTFV (SEQ ID NO: 4)) or
the rhesus macaque TRIM5.alpha. 13-amino acid patch (QAPGTLFTFPSLT
(SEQ ID NO: 5)) or equivalents to these sequences. A TRIM5
expression cassette having the TRIM5alpha sequence operatively
linked to a polymerase-III promoter is provided in SEQ ID NO: 17.
Alternative nucleic acids include, but are not limited to a
polynucleotide having at least 80% sequence identity, or
alternatively at least 85% sequence identity, or alternatively at
least 90% sequence identity, or alternatively at least 92% sequence
identity, or alternatively at least 95% sequence identity, or
alternatively at least 97% sequence identity, or alternatively at
least 98% sequence identity to the TRIM5alpha sequence shown in SEQ
ID NO: 17 as long as the 11 amino acid (human) or the 13 amino acid
sequence (rhesus macaque) remains.
[0110] In a yet further embodiment, the lentiviral vector further
comprise, or alternatively consists essentially of, or yet further
consists of a nucleic acid encoding an HIV TAR decoy
polynucleotide. For the purpose of illustration only, a nucleic
acid for use in this invention are provided in SEQ ID NO: 19 or an
equivalent thereof, along with the sequence of a suitable
regulation element such as polymerase-II promoter operatively
linked to the sequence. Alternative nucleic acids include, but are
not limited to a polynucleotide having at least 80% sequence
identity, or alternatively at least 85% sequence identity, or
alternatively at least 90% sequence identity, or alternatively at
least 92% sequence identity, or alternatively at least 95% sequence
identity, or alternatively at least 97% sequence identity, or
alternatively at least 98% sequence identity to the TAR decoy
sequence shown in SEQ ID NO: 19. Alternative sequences for use in
this invention are disclosed in U.S. Pat. Publication Nos.
2004/013167 and 2003/0013669 and U.S. Pat. Nos. 6,995,258;
5,994,108; and 5,693,508. HIV TAR mRNA sequences are also available
on the GenBank database, available under Accession Nos. NM_134324
(Homo sapiens TAR (HIV-1) RNA binding protein 2, transcript variant
2) and NM_004178 ((Homo sapiens TAR (HIV-1) RNA binding protein 2,
transcript variant 3), each last accessed on Apr. 29, 2009. These
sequences are incorporated by reference into this application.
Further additional sequences include: a)
5'-cgacttaaaatcgctagccagatctgagcctgggagctctctggctag-3' (SEQ ID NO:
1) or b)
5'-gggtctctctggttagaccagatttgagcctgggagctctctggctaactagggaaccc-3'
(SEQ ID NO: 2) or c) 5'-acgaagcttgatcccgtttgccggtcgatcgcttcga-3'
(SEQ ID NO: 3).
[0111] In a further aspect, the lentiviral vector further comprises
a marker or detectable label such as a gene encoding an enhanced
green fluorescent protein (EGFP), red fluorescence protein (RFP),
green fluorescent protein (GFP) and yellow fluorescent protein
(YFP) or the like. These are commercially available and described
in the technical art.
Packaging Systems
[0112] The invention also provides a lentiviral vector as described
above and a packaging plasmid which contains the nucleoside, capsid
and matrix proteins. As an example, SEQ ID NO: 20 provides the
sequence of a packaging plasmid that can be used in this invention.
Alternatives include, but are not limited to a polynucleotide
having at least 80% sequence identity, or alternatively at least
85% sequence identity, or alternatively at least 90% sequence
identity, or alternatively at least 92% sequence identity, or
alternatively at least 95% sequence identity, or alternatively at
least 97% sequence identity, or alternatively at least 98% sequence
identity to SEQ ID NO: 20. Alternatives are also described in the
patent literature, e.g., U.S. Pat. Nos. 7,262,049; 6,995,258;
7,252,991 and 5,710,037, incorporated herein by reference.
[0113] The system also contains a plasmid encoding a pseudotyped
envelope protein provided by an envelope plasmid. Pseudotyped
lentiviral vectors consist of vector particles bearing
glycoproteins derived from other enveloped viruses or alternatively
containing functional portions. See, for example U.S. Pat. No.
7,262,049, incorporated herein by reference. In a preferred aspect,
the envelope plasmid encodes an envelope protein that does not
cause the viral particle to unspecifically bind to a cell or
population of cells. The specificity of the viral particle is
conferred by the antibody binding domain that is inserted into the
particle. Examples of suitable envelope proteins include, but are
not limited to those containing the Staph. aureus ZZ domain, the
sequence of which is provided in SEQ ID NO: 26 or a polynucleotide
having at least 80% sequence identity, or alternatively at least
85% sequence identity, or alternatively at least 90% sequence
identity, or alternatively at least 92% sequence identity, or
alternatively at least 95% sequence identity, or alternatively at
least 97% sequence identity, or alternatively at least 98% sequence
identity to that shown in SEQ ID NO: 26. The choice of glycoprotein
for use in the envelope is determined in part, by the antibody to
which the particle may be conjugated.
[0114] This invention also provides the suitable packaging cell
line. In one aspect, the packaging cell line is the HEK-293 cell
line. Other suitable cell lines are known in the art, for example,
described in the patent literature within U.S. Pat. Nos. 7,070,994;
6,995,919; 6,475,786; 6,372,502; 6,365,150 and 5,591,624, each
incorporated herein by reference.
Pseudotyped Lentiviral Particles
[0115] This invention further provides a method for producing a
pseudotyped lentiviral particle, comprising, or alternatively
consisting essentially of, or yet further consisting of,
transducing a packaging cell line with the lentiviral system as
described above, under conditions suitable to package the
lentiviral vector. Such conditions are known in the art and briefly
described herein. The pseudotyped lentiviral particle can be
isolated from the cell supernatant, using methods known to those of
skill in the art, e.g., centrifugation. Such isolated particles are
further provided by this invention.
[0116] This invention further provides the isolated pseudotyped
lentiviral particle produced by this method. The pseudotyped
lentiviral particle comprises, or alternatively consists
essentially of, or yet further consists of a polynucleotide
encoding a CCR5 RNAi and envelope protein comprising the
pre-selected domain such as the ZZ S. aureus domain alone or in
combination with a TRIM5alpha sequence and an HIV TAR decoy
polynucleotide.
[0117] The isolated pseudotyped particles can be conjugate to one
or more of an antibody or an antibody fragment (e.g. an fragment
containing at least the Fc domain) that retains the ability to bind
a pre-selected cell receptor selected from the group consisting of
CCR5, CD4, CD34 and CXCR4. Such antibodies include anti-CCR5
antibody, an anti-CD4 antibody, an anti-CD34 antibody and a CXCR4
antibody. Anti-CCR5 antibodies are commercially available from
Invitrogen; abcam; ProSci Inc. and eptitomics, and described in the
patent literature within U.S. Pat. Nos. 7,122,185; 7,175,988;
7,160,546; and 6,930,174, each incorporated herein by reference.
Anti-CD34 antibodies are commercially available from R&D
Systems, Invitrogen; Biolegend; and Miltenyi Biotec, and described
in the patent literature within U.S. Pat. No. 4,965,204,
incorporated herein by reference. Anti-CD4 antibodies are
commercially available from R&D Systems, Invitrogen; Biolegend;
and Miltenyi Biotec, and described in the patent literature within
U.S. Pat. No. 4,965,204, incorporated herein by reference.
Anti-CXCR4 antibodies are commercially available from Leinco
Technologies, Capralogics and BioLegend, and described in the
patent literature within U.S. Pat. Nos. 7,521,045; 6,949,243 and
6,485,929, and U.S. Pat. Publication No. 2005/0271665, each
incorporated herein by reference.
[0118] The antibodies are not species specific. In other words, the
antibodies can be polyclonal or monoclonal and can be murine,
ovine, human or other species. In addition, they can be chimeric or
humanized.
[0119] When used in combination, the particles can be combination
of CD4/CCR5 or CD4/CXCR4 or CD4/CCR5/CXCR4 or CD4/CD34 or CD34/CCR5
or CD34/CXCR4 or CD4/CD34/CCR4/CXCR4, which target multiple
populations of HIV susceptible cells.
Methods to Produce the Pseudotyped Particles
[0120] This invention also provides methods to prepare a
pseudotyped lentiviral particle by transducing a packaging cell
line, as described herein with the vector, the envelope plasmid and
the packaging plasmid under conditions that facilitate packaging of
the vector into the envelope particle. In one aspect, the
pseudotyped lentiviral particle is a pseudotyped lentiviral
particle. In a further aspect, the particles are separated from the
cellular supernatant and conjugated to an antibody for
cell-specific targeting.
[0121] In one aspect, the complete vector particle is a lentiviral,
or alternatively a retroviral vector pseudotyped with a Sindbis
virus glycoprotein envelope containing the ZZ domain of Protein A
from Staphylococcus aureus.
[0122] The genetic information of the lentiviral vector particle is
RNA which contains, on the 5' and 3' ends, the minimal LTR regions
required for integration of the vector. In between the two LTR
regions is the psi region which is required for packaging of the
vector RNA into the particle. This region is followed by the RRE
and cPPT sequences which enhance vector production by transporting
the full length vector transcript out of the nucleus for efficient
packaging into the vector particle. Next is the polymerase-II
promoter MNDU3 which drives the expression of the chimeric
TRIM5alpha gene. The polymerase-III U6 promoter driven CCR5 shRNA
gene follows immediately downstream. Next is the polymerase-III U6
promoter driven TAR decoy gene. The last gene in the vector is an
EGFP gene (enhanced Green Fluorescent Protein) which is driven by
the polymerase-II PGK promoter. The EGFP gene is used as a reporter
gene to detect transduced cells. The above listed genetic elements
are transcribed into a full length RNA molecule which is packaged
into the vector particle and contains all of the genetic
information that will be integrated into the transduced cells.
[0123] The full length RNA transcript is packaged inside the capsid
of the vector particle which contains the nucleocapsid, capsid, and
matrix proteins which are generated from the packaging plasmid
delta-8.91. The reverse transcriptase polymerase which is generated
from the packaging plasmid delta-8.91 is also located within the
capsid with the RNA transcript. The capsid encases and protects the
full length RNA transcript.
[0124] Surrounding the capsid/RNA complex is the Sindbis-ZZ
glycoprotein envelope which is generated from the Sindbis-ZZ
plasmid. This envelope, when conjugated with a specific monoclonal
antibody, will direct the vector particle to specifically transduce
a cell of interest that expresses a cell surface receptor
recognized by the chosen monoclonal antibody.
[0125] The vector particle is generated by a transient transfection
protocol which includes a packaging cell line (HEK-293T cells), a
lipofection reagent (Transit-293T), and the three plasmids encoding
the parts of the vector particle (delta-8.91 (packaging plasmid),
CCLc-MNDU3-TRIM5alpha-U6-CCR5shRNA-U6-TARdecoy (lentiviral vector
plasmid), and Sindbis-ZZ (envelope plasmid).
[0126] HEK-293T cells are plated at 75% confluency in complete DMEM
media 24 hours prior to transfection. After at least 24 hours
post-plating of cells, the transfection mixture should be prepared.
Three milliliters of serum free media is incubated with 150 .mu.l
of the lipofection reagent for 20 minutes at room temperature. The
three plasmids are then added to the media/lipofection reagent
mixture at a ratio of 5:5:2 (packaging plasmid: lentiviral vector
plasmid: envelope plasmid) and incubated for 30 minutes. After this
final incubation period, the media/lipofection reagent/DNA mixture
is then added to the HEK-293T cells and left overnight for the
transfection to occur. The next day, the transfection media is
removed and fresh complete DMEM is added. Seventy-two hours later,
the cell culture supernatant is collected and concentrated by
ultracentrifugation at 20,000 rpm for 1.5 hours.
[0127] In one aspect, the 13-amino acid patch sequence required for
the TRIM5alpha molecule to inhibit HIV infection is N
terminal--QAPGTLFTFPSLT--C terminal. Thus, any TRIM5alpha
polynucleotide must encode this primary amino acid sequence.
[0128] To construct the ZZ domain containing Sindbis virus
glycoprotein, the ZZ domain from S. aureus was inserted in between
the amino acids #71-#74 of the E2 region of the Sindbis
glycoprotein gene. In the wild-type Sindbis glycoprotein E2 region,
this is where normal cell surface receptor recognition occurs. By
inserting the ZZ domain here, normal cell binding is abolished.
After the ZZ domain was inserted into the E2 region in a BsteII
restriction enzyme site, the entire E3-E2ZZ-6K-E1 glycoprotein gene
was PCR amplified and TOPO cloned into the pcDNA3.1 expression
plasmid. By inserting the glycoprotein genes into this expression
plasmid, the genes are under the control of the highly active
polymerase-II CMV promoter.
[0129] Once the vector particle buds from the packaging cells and
is released into the supernatant, this vector particle is
conjugated to an antibody as defined herein.
Isolated Host Cells
[0130] Yet further provided is an isolated cell or population of
cells, comprising, or alternatively consisting essentially of, or
yet further consisting of, a retroviral particle of this invention,
which in one aspect, is a lentiviral particle. In one aspect, the
isolated host cell is a packaging cell line.
[0131] In another aspect, the invention provides a pseudotyped
lentiviral particle conjugated to an antibody as described herein
which is further conjugated to a host cell expressing a receptor to
which the lentiviral particle as described herein. In one aspect,
the host cell is a cell expressing one or more of CD4, CD34, CXCR4
and/or CCR5. The cell can be any of a cell of a species of the
group of: murine, rats, rabbit, simians, bovines, ovine, porcine,
canines, feline, farm animals, sport animals, pets, equine, and
primate, and in particular a human cell. Cells that are known to
express such receptors include blood cell and in particular
lymphocyte cells such as peripheral blood lymphocytes and mobilized
blood lymphocytes. In another aspect, the host cell is an adult
stem cell such as an hematopoietic stem cell "HSC" (CD34.sup.+
and/or CD34.sup.+/Thy-1.sup.- HSC)
Compositions, Screens and Therapeutic Uses
[0132] Also provided by this invention is a composition or kit
comprising any one or more of the lentiviral vectors, packaging
system, pseudotyped lentiviral, lentiviral particle conjugated to
an antibody or fragment thereof which in turn may optionally be
conjugated to a cell and a carrier. In one aspect, the carrier is a
pharmaceutically acceptable carrier. These compositions can be used
diagnostically or therapeutically as described herein and can be
used in combination with other known anti-HIV therapies.
[0133] The compositions can be used in vitro to screen for small
molecules and other agents that may modify HIV infectivity and
replication by adding to the composition varying amounts of the
agent to be tested and comparing it to a companion system that does
not have the agent but which exhibits the desired therapeutic
effect. For example, if it is known that the lentiviral particle
inhibits HIV infection in a system, then the system can be used to
test alternative therapies to determine if it is a substitute to
the lentiviral particle. Alternatively, one can test agents in the
lentiviral particle system itself to determine if the agent acts
competitively, additively or synergistically with the lentiviral
particle system. After an in vitro screen, the test agent or
combination therapy can be assayed in an appropriate animal
model.
[0134] When the particles and/or antibody conjugated cells (to the
particles) are administered to an appropriate animal subject, the
animal subject can be used as an animal model to test alternative
therapies in the same manner as the in vitro screen. This invention
also provides a method to inhibit HIV replication in vivo or ex
vivo, comprising, or alternatively consisting essentially of, or
yet further consisting of administering to a subject in need
thereof an effective amount of the pseudotyped lentiviral particle
or the pseudotyped lentiviral particle conjugated to the antibody
as describe herein. In another aspect, a method to prevent HIV
replication in vivo or ex vivo is provided comprising, or
alternatively consisting essentially of, or yet further consisting
of administering to a subject in need thereof an effective amount
of the pseudotyped lentiviral particle or the pseudotyped
lentiviral particle conjugated to the antibody as describe herein.
The pseudotyped lentiviral particle or the pseudotyped lentiviral
particle conjugated to the antibody as describe herein can be
combined with other anti-lentiviral therapies that are known in the
art. When combined with other therapies, administration of the
therapies can be concurrent or sequential as determined by the
treating physician. In one aspect, bone marrow, mobilized bone
marrow cells or peripheral blood lymphocytes are removed from the
patient to be treated and cultured with the pseudotyped lentiviral
particle conjugated to the one or more antibodies. After an
appropriate amount of time to allow for the particle to bind to the
appropriate receptor, the cells are then re-administered to the
subject or patient to which they were isolated. As noted above,
this therapy can be combined with other anti-lentiviral therapies
or the like.
[0135] This invention also provides a method to treat a subject at
risk of developing an active infection or infected with HIV (AIDs)
by administering to the subject an effective amount of one of the
compositions as described herein. For the purpose of this aspect, a
subject is as described herein and therefore includes mammals,
animals and humans, for example. Additional effective therapies can
combined with this invention and/or added as necessary.
[0136] Further provided are methods to inhibit or prevent HIV
replication in a cell infected with HIV, by contacting the cell
with an effective amount of one or more of pseudotyped lentiviral
vector particle as described herein or the psuedotyped lentiviral
vector as described herein. In one aspect, the contacting is in
vitro. In another aspect it is in vivo.
[0137] This invention also provides the use of a compositions as
described herein to prevent or treat an HIV infection and/or AIDs
by administering to a subject an effective amount of one or more
compositions described herein. Further provided is the use of a
composition as described herein in the manufacture of a medicament
to treat or prevent HIV infection and/or AIDs. Additional effective
therapies can combined with this invention and/or added as
necessary.
[0138] Having been generally described herein, the follow examples
are provided to further illustrate this invention.
Experiment A
Specific Targeting of HIV Susceptible Cells
Background
[0139] More than 25 years after its discovery, the Human
Immunodeficiency Virus (HIV) continues to be a major public health
problem with more than 30 million people infected worldwide.
Current small molecule antiretroviral therapies have been
successful in suppressing viral replication and reducing morbidity
and mortality from HIV, however, after prolonged use, toxicity can
occur and viral escape mutants can arise from a continued low level
of viral replication [1-5]. Vaccine strategies including live
attenuated, whole inactivated virus, protein subunits, DNA
vaccines, and viral expression vectors encoding HIV proteins have
failed due to the broad diversity of HIV-1 strains and the ability
of the virus to evade immune responses [6]. Gene therapy provides
an alternative approach to current therapies and prophylactic
strategies by offering the potential of long-term and constitutive
protection from HIV infection and spread. Numerous anti-HIV RNA
molecules have been developed and used to inhibit HIV infection and
replication in gene therapy protocols including antisense RNAs, RNA
decoys, ribozymes, and small interfering RNAs (siRNAs) [7-18]. Many
of these anti-HIV genes have proven to be highly potent HIV
inhibitors both in vitro and in vivo with a select few proceeding
to clinical trials [19-23].
[0140] RNA-interference (RNAi) utilizes an innate cellular
mechanism to silence gene expression by degradation of mRNA [24].
RNAi is highly effective in targeted gene knockdown for both gene
discovery and the development of therapeutics by using 19-28 bp
siRNAs to seek out homologous mRNA for destruction [25]. In
numerous studies, this technology has been harnessed to inhibit
HIV-1 infection by targeting viral genes [10, 17-18, 22]. Cellular
genes necessary for HIV-1 attachment and fusion to target cells,
such as the major receptor CD4 and the two main coreceptors CCR5
and CXCR4, have also been previously targeted by siRNAs [11,
13-17]. By blocking the attachment and fusion of HIV with the
target cell membrane, viral entry and productive infection can be
inhibited. Due to a naturally occurring 32-base pair deletion in
the CCR5 gene, both homozygous and heterozygous individuals
harboring this mutant allele are highly resistant to HIV-1
infection [26-28]. Individuals harboring this deletion are
physiologically normal thus designating CCR5 as an excellent
candidate for knockdown by siRNA for HIV gene therapy. Recently,
long-term control of HIV-1 replication was observed in an infected
individual who received a stem cell transplant for acute myeloid
leukemia with donor stem cells from an individual homozygous for
the CCR5 .DELTA.32-bp mutant allele [29]. The results provided from
this study demonstrated the importance of developing anti-HIV
molecules to block the availability of CCR5, thus preventing HIV-1
infection.
[0141] Current gene therapy protocols rely on ex vivo transduction
of hematopoietic stem cells or peripheral blood mononuclear cells
(PBMCs) using retroviral or lentiviral vectors pseudotyped with
amphotropic or pantropic envelopes. These procedures require either
apheresis of PBMCs, mobilization of peripheral blood stem cells, or
bone marrow aspirations. Clinical grade methods to isolate the
target cells, tissue culture methods to introduce the vector, and
finally re-administration of the gene modified cells into the
patient are also required. The development of cell specific
targeting vectors capable of selectively transducing cells of
interest upon direct injection, in vivo, would greatly simplify and
enhance HIV gene therapy applications by bringing them to areas
where sophisticated laboratories and clinics are not available.
[0142] Several vector targeting approaches have focused on
generating chimeric proteins with receptor ligands or single chain
antibodies fused to membrane spanning molecules such as amphotropic
retroviral glycoproteins and the influenza hemagglutinin protein
[30-41]. Another novel method utilizes the ability of Sindbis virus
glycoproteins to pseudotype lentiviral vectors. By modifying the
Sindbis virus envelope through insertion of the ZZ-domain from the
Staphylococcus aureus Protein A into the receptor binding region of
the glycoprotein E2 gene, pseudotyped vectors acquired the ability
to bind purified antibodies [42-43]. The ZZ-domain encodes an
immunoglobulin binding domain allowing for a direct conjugation
between the selected monoclonal antibody and the vector particle.
These antibody-modified envelopes can then direct the lentiviral
vectors to specific cells of interest for targeted transduction.
These engineered vectors have been shown to transduce specific cell
types such as CD34+ cord blood stem cells, metastatic melanoma
cells, tumor cell lines, and cells expressing CD4 or the human
leukocyte antigen (HLA) [48-53].
[0143] For improved in vivo HIV gene therapy to prevent the spread
of viral infection and disease, innovative strategies need to be
evaluated to provide pre-exposure protection for patients in both
developed and developing countries. In this disclosure, applicants
evaluated the capacity of the Sindbis-ZZ envelope design to protect
HIV-1 susceptible cells in a gene therapy setting by delivering an
anti-HIV CCR5 shRNA specifically to cells expressing CCR5 on the
cell surface. Targeted transduction was achieved in mixed cell
populations with both cultured and primary cells. Potent knockdown
of CCR5 expression (>93%) was observed thus conferring HIV-1
resistance in CCR5 shRNA vector transduced cells.
Example No. 1
Lentiviral Vector Design and Production
[0144] A third generation HIV derived lentiviral vector containing
an EGFP reporter gene was used in this study, pCCLc-x-PGK-EGFP
(FIG. 1). The CCR5 shRNA gene driven by the human polymerase-III U6
small RNA promoter was generated, as described previously, and
inserted upstream of the PGK-EGFP reporter gene cassette [47].
Sequencing of clones was confirmed by Laragen Inc., Los Angeles,
Calif.
[0145] Lentiviral vectors were generated in HEK-293T cells by
lipofection with 25 .mu.g of the packaging construct, p.DELTA.8.9
(packaging plasmid containing the gag and pol genes), 25 .mu.g of
pCCLc-x-PGK-EGFP (control empty vector) or the CCR5 shRNA construct
pCCLc-CCR5shRNA-PGK-EGFP (transfer vector), and 12 .mu.g of
pSindbis-ZZ (envelope). Vector supernatants were collected at 72
hours post-transfection and concentrated by ultracentrifugation at
20,000 rpm.
[0146] Lentiviral vectors pseudotyped with the Sindbis-ZZ envelope
were incubated with a purified CCR5 monoclonal antibody (mAb) (BD
Biosciences, San Jose, Calif.) on ice for one hour. Vectors were
titered on Ghost-R5-X4-R3 cells which express CCR5 on the cell
surface. These cells were obtained from the AIDS Reference and
Reagent Program and cultured in complete DMEM with 10% FBS and
supplemented with hygromycin, puromycin, and G418 according to the
supplier's protocol. CCR5 targeting vectors were incubated on
Ghost-R5-X4-R3 cells for two hours at 37.degree. C. with 8 .mu.g/ml
protamine sulfate. Complete DMEM containing 10% FBS was then added
to the transduced cells. Forty-eight hours post-transduction, cells
were analyzed by FACS for EGFP expression. Vector titers
.about.1.0*10.sup.7 TU/ml were routinely achieved.
Example No. 2
Targeted Transduction of Mixed Cell Populations
[0147] A mixed population of cultured cells including HEK-293T and
Ghost-R5-X4-R3 cells were plated in complete DMEM including 10%
FBS. Cells were transduced with the CCR5 targeting vectors, either
EGFP-alone or the CCR5-shRNA vector (MOI 10) for two hours at
37.degree. C. with 8 .mu.g/ml protamine sulfate. Peripheral blood
mononuclear cells were isolated from whole blood by Ficoll-Paque
(GE Healthcare, Piscataway, N.J.). Total white blood cells were
cultured in complete RPMI media containing 10% FBS and supplemented
with 10 ng/ml IL-2. Cells were either left unstimulated or were
stimulated with 1 ug/ml PHA for four days prior to transduction.
Both unstimulated and stimulated PBMCs were transduced with the
CCR5 targeting vectors, either EGFP-alone or the CCR5-shRNA vector
(MOI 10) for two hours at 37.degree. C. with 8 .mu.g/ml protamine
sulfate. Four days post-transduction, both cultured cells and
primary human PBMCs were analyzed by flow cytometry for EGFP
expression and down regulation of CCR5 expression.
Example No. 3
Flow Cytometry Analysis and QRT-PCR
[0148] To determine the cell-specific targeted transduction and the
subsequent CCR5 down regulation conferred by the CCR5 shRNA,
transduced cell populations were analyzed by FACS. Four days
post-transduction, nontransduced, EGFP-alone, and CCR5-shRNA
lentiviral vector transduced cells, both cultured cells and PBMCs,
were analyzed by FACS for EGFP expression. Cultured
HEK-293T/Ghost-R5-X4-R3 mixed cells were stained with anti-human
PE-conjugated CD4 and CCR5 antibodies (BD Biosciences, San Jose,
Calif.) to determine the specificity of transduction and also the
down regulation of CCR5 expression in the CCR5-shRNA vector
transduced cells. PBMCs were stained with anti-human CD3-APC (T
cells), CD19-PE (B cells), CD14-PE (monocyte/macrophage), and
CCR5-PE (BD Biosciences, San Jose, Calif.) to determine cell
specific targeted transduction and CCR5 down regulation. All FACS
data was obtained on a Beckman Coulter Cytomics FC500 flow
cytometer and analyzed using CXP analysis software.
[0149] To more accurately quantitate the down regulation of CCR5 in
CCR5-shRNA transduced cells, quantitative real-time PCR (QRT-PCR)
was performed on total RNA extracted from transduced cells using
RNA-STAT-60 (Tel-Test, Friendswood, Tex.). First strand cDNA
synthesis was generated using the High Capacity cDNA Reverse
Transcription Kit (Applied Biosystems, Foster City, Calif.).
QRT-PCR was then performed using the SYBR Green PCR Master Mix Kit
(Applied Biosystems, Foster City, Calif.) using the primer set,
5'-ACTGCAAAAGGCTGAAGAGC-3' (SEQ ID NO: 6) and
5'-AGCATAGTGAGCCCAGAAGG-3' (SEQ ID NO: 7). GAPDH was used as an
internal control.
Example No. 4
HIV-1 Challenge of Transduced Cells
[0150] To determine whether the CCR5 targeted transduction and the
successive down regulation of CCR5 expression could confer HIV-1
resistance, transduced cells were challenged with BaL-1, an
R5-tropic strain of HIV-1. Transduced cells, both
HEK-293T/Ghost-R5-X4-R3 mixed cells (MOI 0.01 and 0.05) and PBMCs
(MOI 0.01), were challenged with BaL-1 for two hours at 37.degree.
C. with 8 .mu.g/ml polybrene. On various days post-infection, cell
culture supernatants were sampled for use in p24 antigen ELISA and
infectious virus assays. Supernatant aliquots were quantified for
p24 by ELISA according to the manufacturer's protocol (Zeptometrix
Corp., Buffalo, N.Y.). Challenged cell culture supernatants were
also analyzed for infectious virus by the Ghost Cell assay.
Briefly, 75 .mu.l of challenge culture supernatant was added to
uninfected Ghost-R5-X4-R3 cells (1.0*10.sup.6) with 8 .mu.g/ml
polybrene for two hours. Forty-eight hours post-infection, infected
Ghost-R5-X4-R3 cells were analyzed by flow cytometry for EGFP
expression to determine levels of infectious virus particles.
Example No. 5
In Vivo CCR5 Cell Specific Targeting
[0151] To determine the in vivo targeting ability of the CCR5 cell
specific vector, the immunodeficient NOD/SCID-IL2r-.gamma. knockout
mouse model was used to evaluate targeted transduction. Adult mice,
at least four months old were sublethally irradiated with 300 rads
total body irradiation. Freshly isolated primary human PBMCs were
injected retro-orbitally (RO) with 1*10.sup.7 cells. Cells were
allowed to engraft for two weeks and were followed by RO injection
with 1*10.sup.6TU of the EGFP-alone CCR5 targeting vector. Five
days post-injection of vector, single cell suspensions from mouse
organs were analyzed for cell specific transduction of engrafted
human cells using the PBMC antibody staining panel described above.
FACS data was collected on a Beckman Coulter Cytomics FC500 flow
cytometer and analyzed with CXP analysis software.
Experimental Results
CCR5 Cell Specific Transduction and CCR5 Down Regulation:
[0152] Lentiviral vectors, both the CCLc-EGFP alone and
CCLc-CCR5shRNA, were pseudotyped with the Sindbis virus envelope
containing the ZZ-domain from Protein A of S. aureus and were
evaluated for their ability to specifically transduce CCR5-positive
cells when conjugated with a CCR5 mAb. A mixed population of
cultured cells including HEK-293T cells (CD4 and CCR5 negative) and
Ghost-R5-X4-R3 cells (CD4 and CCR5 positive) were transduced with
the CCR5 targeting vectors. Cells were analyzed four days
post-transduction for EGFP expression to determine cell specific
targeted transduction. Ghost-R5-X4-R3 cells express CCR5 and should
be selectively transduced in the mixed cell culture. Another
surface molecule, CD4, expressed in the Ghost-R5-X4-R3 cells but
not HEK-293T cells, was used as an additional cell detector to
analyze targeting specificity using flow cytometry. Only cells
expressing CCR5 were transduced as displayed by the double positive
staining for CD4 and EGFP expression (FIG. 2). Ghost-R5-X4-R3 cells
were selectively transduced by both the EGFP-alone and CCR5-shRNA
CCR5 targeting vectors as compared to nontransduced cells in the
same cultures which were negative for CD4 and EGFP expression. The
transduced mixed cultures of Ghost-R5-X4-R3 and HEK-293T cells were
also stained for CCR5 cell surface expression and analyzed by flow
cytometry (FIG. 3A). The Ghost-R5-X4-R3 cells transduced with the
EGFP-ZZ vector were selectively transduced as displayed by double
positive staining for CCR5 and EGFP expression. The CCR5 positive
cells were also specifically transduced with the CCR5shRNA-ZZ
vector, however, due to the expression of the CCR5 shRNA, a
subsequent knock down of CCR5 expression was observed by negative
staining for CCR5 within the EGFP positive transduced population. A
knockdown level of >93% was observed as compared to
nontransduced and EGFP-alone vector transduced cells.
[0153] To further quantitate the level of CCR5 knockdown in shRNA
transduced Ghost-R5-X4-R3 cells, quantitative real-time PCR
(QRT-PCR) was performed to analyze the intracellular levels of CCR5
mRNA. Intracellular CCR5 mRNA levels were decreased in CCR5-shRNA
transduced cells, >93%, as compared to control nontransduced and
EGFP-alone transduced cells (FIG. 3B). These results correlated
with the CCR5 flow cytometry data (FIG. 3A). CCR5 downregulation,
91%, was also observed in primary PBMC cultures transduced with the
CCR5shRNA-ZZ vector (FIG. 3C). The above results established that
CCR5-expressing cells can be specifically targeted by the CCR5
antibody-conjugated vector and that these cells, when transduced
with the CCR5shRNAZZ vector, have decreased levels of CCR5
expression.
[0154] Primary PBMCs, both unstimulated and phytohemagglutinin
(PHA) stimulated, were transduced with the CCR5 targeting vector as
described above. Both T cell (CD3+) and monocyte/macrophage (CD14+)
cell populations were selectively transduced since these cell
populations express CCR5 in contrast to B cells (CD19+) which were
used as an internal negative control (FIG. 4). Targeted
transduction was observed for both the EGFP-ZZ and CCR5shRNA-ZZ
vectors as compared to cells transduced with Sindbis-ZZ pseudotyped
vector which was not conjugated to the CCR5 mAb. Both unstimulated
and stimulated PBMCs displayed similar transduction patterns in
both transduction efficiency and specificity (unstimulated cell
data not shown). These data confirm the ability of this vector to
specifically transduce CCR5 expressing cells and demonstrate that
these cells, after transduction with a CCR5-shRNA lentiviral
vector, displayed potent knockdown of CCR5 surface expression.
HIV-1 Inhibition of CCR5-shRNA Transduced Cells:
[0155] To determine whether CCR5 targeted CCR5-shRNA vector
transduced cells were capable of resisting HIV-1 infection upon
down regulation of cell surface CCR5 expression, cells were
challenged with BaL-1, an R5-tropic strain of HIV-1. Challenge
experiments were performed at two different multiplicities of
infection (MOI), 0.01 and 0.05 to evaluate the level of protection
afforded by the potent knockdown of cell surface CCR5. Strong
inhibition of viral infection was observed in cultured
Ghost-R5-X4-R3 cells transduced with the CCR5-shRNA vector (>1.5
log inhibition) as compared to EGFP-alone transduced cells as
measured by p24 antigen ELISA (FIGS. 5A and 5B) and quantitation of
infectious virus (FIGS. 5C and 5D). Upon challenge of CCR5 vector
targeted PBMCs (MOI 0.01), viral inhibition was observed in
CCR5-shRNA transduced cells as compared to nontransduced and
EGFP-alone vector transduced cells. Strong protection levels (>1
log) were observed at the peak of viral replication (day 14
post-infection) as measured by p24 antigen ELISA (FIG. 6A) and
quantitation of infectious virus (FIG. 6B). These data confirm that
targeted transduction of HIV-1 susceptible cells can confer
pre-exposure protection to HIV-1 infection by the selective down
regulation of CCR5 expression in successfully transduced CCR5
positive cells.
In Vivo Targeted Transduction of CCR5 Expressing Cells:
[0156] The above data confirmed the CCR5 targeting ability of this
vector system to selectively transduce cells that are positive for
CCR5 expression in vitro. To further evaluate the potential of this
targeting vector, the in vivo efficacy was assessed in a
NOD/SCID-IL2r-.gamma. knockout mouse model engrafted with freshly
isolated human PBMCs. Sublethally irradiated adult mice were
injected retro-orbitally (RO) with 1*10.sup.7 unstimulated PBMCs.
Two weeks after cell injection, to allow for human cell
engraftment, 1*10.sup.6 transducing units of the CCR5 targeting
vector were injected RO. Five days post-injection with the vector,
single cell suspensions from mouse peripheral blood and lymphoid
organs were analyzed by FACS to evaluate the in vivo targeted
transduction efficiency. Human T cells (CD3+) in the lymph node and
spleen (FIG. 7A) and macrophages (CD14+) in the bone marrow (FIG.
7D) were successfully transduced with the CCR5 targeting vector in
vivo as displayed by an increase in EGFP expression as compared to
engrafted mice not injected with vector. B cells (CD19+) in the
spleen and bone marrow (FIG. 7C), however, were not transduced
since they do not express CCR5. FACS analysis for CCR5 positive
cells was also performed to determine targeting efficiency. Only
those cells that were positive for CCR5 expression in the lymph
node and peripheral blood were successfully transduced in vivo
(FIG. 7B). These results confirm that this novel targeting vector
has predictable and reproducible efficacy to target and transduce
CCR5 expressing human cells in vivo.
Experimental Discussion
[0157] HIV gene therapy can be a very attractive and much needed
alternative approach to current small molecule antiretroviral
therapies and vaccination strategies for HIV-1 due to its potential
for a one-time treatment and long-term HIV-1 protection. Previous
and current HIV vaccination strategies including live attenuated,
whole inactivated virus, protein subunits, DNA vaccines, and viral
expression vectors encoding HIV proteins require a broad response
from cells of both the humoral and cytotoxic immune system [6].
However, due to the wide diversity of HIV-1 strains and their
ability to evade the host immune response, these techniques have
failed to provide effective protection.
[0158] Current ex vivo cellular transduction protocols for clinical
gene therapy which include bone marrow harvesting, apheresis of
PBMCs, and manipulation in a clean room setting, are not feasible
in developing countries where sophisticated laboratories and
equipment necessary to perform these procedures are unavailable.
Therefore, new and innovative ways to transduce and protect HIV-1
susceptible cells, in vivo, need to be developed. Cell specific
targeting vectors capable of selectively transducing a particular
population of cells of interest, after direct injection into the
body, have the potential to protect cells and can provide an "off
the shelf" therapy. Numerous strategies have been evaluated for
their ability to specifically target cells in vitro and in vivo
[30-41]. One approach utilizes the ability of the Sindbis virus
envelope to pseudotype lentiviral vectors. By inserting the
immunoglobulin binding ZZ-domain of Protein A from S. aureus into
the binding region of the Sindbis virus E2 glycoprotein, these
envelopes are then able to bind monoclonal antibodies [48-49]. This
strategy is simple yet ingenious since only one type of vector
needs to be manufactured in large scale, certified, and stored.
Depending on which cell population will be targeted, one specific,
well characterized monoclonal antibody can be selected and
conjugated to a small portion of the vector to render a
cell-specific vector preparation which is then suitable for in vivo
targeting and transduction.
[0159] Mainly R5-tropic strains of HIV-1 which utilize CCR5 as a
coreceptor are primarily responsible for viral transmission and
early stage infection [48]. These strains establish a primary
infection and viral reservoir in an infected individual. Targeting
CCR5 through therapeutic approaches utilizing either small molecule
HIV-1 entry inhibitors or gene silencing by siRNAs in a gene
therapy setting, offers a promising way to inhibit and possibly
prevent initial HIV-1 infection. As observed with the natural
.DELTA.32-bp deletion mutant allele occurring in individuals
resistant to HIV-1 infection, a targeted approach to knockdown
expression of CCR5 in the HIV susceptible population could provide
protection from HIV infection. The Sindbis-ZZ strategy was applied
to construct a CCR5 positive cell-specific targeting vector for
inhibition of initial HIV-1 infection by intracellular immunization
with a CCR5 shRNA.
[0160] Upon incubation with the CCR5 targeting vector, only those
cells expressing CCR5 were selectively transduced with a lentiviral
vector expressing a highly potent CCR5 shRNA capable of potent
knockdown of CCR5 gene expression. This approach was successful in
mixed cell populations of both cultured and primary human cells.
Transduction of freshly isolated PBMCs with the CCR5 targeting
vector demonstrated transduction of only T cells and
monocyte/macrophage populations which express CCR5 on the cell
surface and are the major cell types normally infected by HIV-1. B
cells in the culture remained nontransduced since they do not
express CCR5, demonstrating specificity. Transduction was also
shown to be dependent on vector conjugation with a monoclonal
antibody. When cells were incubated with vector not conjugated to
any antibody, no transduction was observed (FIG. 4). These data
confirm the necessity for a specific mAb for the vector to elicit
an effect, and also verify the lack of nonspecific transduction by
unconjugated vector particles. Also, PBMCs, both unstimulated and
stimulated with PHA displayed similar levels of transduction
efficiency with the EGFP-ZZ and CCR5shRNA-ZZ vectors. This suggests
that the targeting efficacy and transduction ability of the CCR5
targeting vector is independent of cell stimulation. Targeted
transduction of CCR5 expressing cells with the CCR5 shRNA vector
conferred to HIV-1 target cells a potent ability to down regulate
the expression of CCR5 and to be protected from HIV-1 infection as
measured by p24 antigen ELISA and by quantitating infectious virus
(FIGS. 5A-5D, 6A-6B). A slight rise in viral replication was
observed in the CCR5 shRNA transduced population due to infected
nontransduced cells, however, a subsequent decrease in detection of
virus followed after the infected cells were killed. This
observation highlights the selective survival advantage of CCR5
shRNA transduced cells which were able to resist infection during
the course of the virus challenge and to eventually take over the
culture.
[0161] The efficacy of this targeting strategy was further
evaluated, in vivo, in a NOD/SCID-IL2r-.gamma. knockout mouse model
engrafted with freshly isolated human PBMCs. Upon irradiation,
injection of cells, and engraftment of the PBMCs, the mice were
injected with the CCR5 targeting lentiviral vector. Cell specific
transduction was observed in both the T cell and
monocyte/macrophage cell populations in a similar manner as seen in
the in vitro PBMC transductions. Specific cell targeting could be
demonstrated in vivo by the fact that none of the human B cells
were transduced, as measured by EGFP expression (FIG. 7C). This
lack of B cell transduction could also be observed in the in vitro
experiments, and is due to the absence of the CCR5 receptor on B
cells. Upon retro-orbital injection, the CCR5 targeting vector will
first drain into the lymphatics and selectively transduce cells in
the lymph nodes followed by transduction of cells in other lymphoid
organs and in the peripheral blood. The flow of vector particles
from the retro-orbital capillary beds to the lymphatics was
confirmed by the high T cell transduction efficiency observed in
the lymph nodes (FIG. 7A).
[0162] The results presented here offer an encouraging and
alternative method to provide pre-exposure prophylaxis for HIV-1
infection by utilizing an HIV-1 susceptible cell-specific targeting
strategy via direct injection of vector particles. This innovative
strategy could potentially be applied as a pre-exposure protection
for highly susceptible human populations, even in areas where
sophisticated laboratories are not available. Upon injection with
the CCR5 cell-specific targeting vector and after transduction of a
sufficient number of CCR5 expressing cells, individuals coming in
contact with HIV could potentially resist the initial infection due
to expression of the CCR5 shRNA to silence CCR5 and thus block
HIV-1 entry. Gene therapy could therefore aid in transferring the
genetic ability to resist HIV-1 infection to susceptible
individuals by silencing the expression of CCR5, mimicking the
natural ability of individuals harboring the .DELTA.32-bp mutant
allele to resist infection.
Experiment B
From Pre-Integration HIV-1 Inhibition
Background
[0163] Pre-entry and pre-integration inhibition of infection is an
ideal method to elicit resistance to HIV-1 infection. Therapies
aimed at blocking HIV-1 integration will combat the generation of
provirus and the further establishment of a viral reservoir which
is the main reason for the failure to cure an HIV infected
individual. A number of pre-integration anti-HIV transgenes have
been previously tested as individual constructs and have displayed
strong resistance to HIV-1 infection [5, 9, 11, 14, 15, 16, 43]. By
combining multiple anti-HIV genes in a single vector, a novel
anti-HIV vector could be produced which not only provides strong
inhibition of HIV-1 infection but would also provide a block to the
generation of escape mutants by creating a difficult environment
for HIV to mutate around the multiple anti-HIV molecules.
[0164] In the initial stages of HIV-1 infection, attachment and
fusion to target cells occurs via interaction of the viral envelope
gp120 and gp41 glycoproteins with the cellular major receptor CD4
and a minor coreceptor, two of these being CCR5 and CXCR4 which are
members of the chemokine receptor family. CCR5 is utilized by
R5-tropic strains of HIV-1 primarily during the initial stages of
infection, followed by a switch in tropism to X4-tropic HIV-1 which
is mainly detected during late stage infection [44]. In a small
percentage of the human population, a mutant allele of the CCR5
gene, containing a 32-base pair deletion, renders the protein
defective and therefore the receptor is absent from the cell
surface. Homozygous and heterozygous individuals harboring this
allele have been reported to be resistant to HIV-1 infection and
remain physiologically normal due to receptor redundancy in the
chemokine system [26-28]. Recently, long term control of viral
replication was observed in an HIV-1 infected individual who
received a stem cell transplant for acute myeloid leukemia [29].
The transplanted allogeneic stem cells were from an individual who
was homozygous for the CCR5 .DELTA.32-bp deletion. The results
provided from this study demonstrate the importance in developing
anti-HIV molecules which block the use of CCR5 during HIV-1
infection. Based on this natural phenotype of CCR5 null, CCR5
knockdown for HIV gene therapy offers a promising approach to
inhibit viral infection at the level of viral entry.
[0165] The mechanism of RNA interference using small interfering
RNAs is a highly potent method to silence gene expression and
offers an ideal approach to knock down expression of CCR5 [24].
Numerous reports have evaluated the efficacy of CCR5 gene knockdown
using small interfering RNAs (siRNAs) and have demonstrated
protection from HIV-1 infection [11, 14-16]. However, the silencing
of CCR5 gene expression, alone, will not be sufficient to
completely inhibit HIV infection and also would not inhibit
infection from X4-tropic or dual-tropic viral strains. Other
anti-HIV strategies added to the CCR5 knockdown would therefore
greatly enhance viral protection.
[0166] Another naturally occurring molecule, TRIM5.alpha., has been
shown to inhibit HIV-1 infection at the post-entry/pre-integration
stage by disrupting the uncoating of the viral capsid upon entering
the cytoplasm [45]. Certain isoforms of TRIM5.alpha. found in Old
World monkeys are capable of strongly restricting HIV-1 infection.
Humans also naturally express a distinct isoform of TRIM5.alpha.
but it does not afford protection from HIV-1 infection. A recently
developed human/rhesus macaque chimeric TRIM5.alpha. isoform,
incorporating a small number of key HIV-restrictive amino acids,
was demonstrated to inhibit HIV-1 infection in a hematopoietic stem
cell gene therapy setting [43, 46]. If used in a clinical
application, the design of this chimeric TRIM5.alpha. molecule,
which consists of mainly human amino acid sequences, will help to
avoid immune rejection which would occur with the use of wild-type
rhesus macaque TRIM5.alpha.. A third molecule, a TAR decoy, has
been previously described to inhibit transactivation of proviral
transcription [12]. By mimicking the structure of the viral
transcriptional responsive element (TAR), the TAR decoy is able to
bind the viral Tat protein and sequester it away from its normal
action of aiding efficient proviral HIV transcription.
[0167] In the present study, applicants describe the construction
and pre-clinical evaluation of a triple combination anti-HIV
lentiviral vector that focuses on the pre-integration block of
HIV-1 infection to minimize the formation of integrated provirus
and the generation of escape mutants. The three highly potent
anti-HIV transgenes, a chimeric TRIM5.alpha. molecule, a CCR5 shRNA
capable of almost complete knockdown of CCR5 expression, and a TAR
decoy, combined in a single vector, displayed complete protection
from productive viral infection and integration of multiple strains
of HIV-1 upon transduction into HIV target cells. These results
establish the future application of this vector for use in a
clinical setting.
[0168] HIV infection continues to spread worldwide in both
developed and underdeveloped countries with no effective vaccine
available. Current antiretroviral drug therapies have been
successful in suppressing viral infection as long as the patient is
compliant with the prescribed regimen. However, with prolonged use,
these treatments can become toxic and drug resistant viral escape
mutants arise [1-5]. New and innovative therapies need to be
developed that overcome the limitations of current small drug
antiretrovirals. Gene therapy offers a promising alternative or
supplement to current treatments due to advantages which include
the possibility of a one-time treatment, controlled or constitutive
anti-HIV gene expression, and long-term viral inhibition
particularly if hematopoietic progenitor cells (HPCs) are targeted.
Many anti-HIV genes have been evaluated for their efficacy in
inhibiting viral infection including antisense RNAs, riboyzymes,
RNA decoys, siRNAs, intrabodies, transdominant proteins, and
restriction factors [8-23, 42, 43]. These molecules have been
targeted to both viral genes and proteins and also cellular genes
critical for viral infection and replication. Several groups, have
been involved with human clinical trials using a select number of
these anti-HIV genes transferred into HPCs by retroviral and
lentiviral vectors [19-23]. However, improvements in stem cell
transduction efficiency and in the effectiveness of the vector to
interfere with different stages of the HIV life cycle are still
needed.
[0169] Pre-entry and pre-integration inhibition of infection is an
ideal method to elicit resistance to HIV-1 infection. Therapies
aimed at blocking HIV-1 integration will combat the generation of
provirus and the further establishment of a viral reservoir which
is the main reason for the failure to cure an HIV infected
individual. A number of pre-integration anti-HIV transgenes have
been previously tested as individual constructs and have displayed
strong resistance to HIV-1 infection [5, 9, 11, 14, 15, 16, 43]. By
combining multiple anti-HIV genes in a single vector, a novel
anti-HIV vector could be produced which not only provides strong
inhibition of HIV-1 infection but would also provide a block to the
generation of escape mutants by creating a difficult environment
for HIV to mutate around the multiple anti-HIV molecules.
[0170] In the initial stages of HIV-1 infection, attachment and
fusion to target cells occurs via interaction of the viral envelope
gp120 and gp41 glycoproteins with the cellular major receptor CD4
and a minor coreceptor, two of these being CCR5 and CXCR4 which are
members of the chemokine receptor family. CCR5 is utilized by
R5-tropic strains of HIV-1 primarily during the initial stages of
infection, followed by a switch in tropism to X4-tropic HIV-1 which
is mainly detected during late stage infection [44]. In a small
percentage of the human population, a mutant allele of the CCR5
gene, containing a 32-base pair deletion, renders the protein
defective and therefore the receptor is absent from the cell
surface. Homozygous and heterozygous individuals harboring this
allele have been reported to be resistant to HIV-1 infection and
remain physiologically normal due to receptor redundancy in the
chemokine system [26-28]. Recently, long term control of viral
replication was observed in an HIV-1 infected individual who
received a stem cell transplant for acute myeloid leukemia [29].
The transplanted allogeneic stem cells were from an individual who
was homozygous for the CCR5 .DELTA.32-bp deletion. The results
provided from this study demonstrate the importance in developing
anti-HIV molecules which block the use of CCR5 during HIV-1
infection. Based on this natural phenotype of CCR5 null, CCR5
knockdown for HIV gene therapy offers a promising approach to
inhibit viral infection at the level of viral entry.
[0171] The mechanism of RNA interference using small interfering
RNAs is a highly potent method to silence gene expression and
offers an ideal approach to knock down expression of CCR5 [24].
Numerous reports have evaluated the efficacy of CCR5 gene knockdown
using small interfering RNAs (siRNAs) and have demonstrated
protection from HIV-1 infection [11, 14-16]. However, the silencing
of CCR5 gene expression, alone, will not be sufficient to
completely inhibit HIV infection and also would not inhibit
infection from X4-tropic or dual-tropic viral strains. Other
anti-HIV strategies added to the CCR5 knockdown would therefore
greatly enhance viral protection.
[0172] Another naturally occurring molecule, TRIM5.alpha., has been
shown to inhibit HIV-1 infection at the post-entry/pre-integration
stage by disrupting the uncoating of the viral capsid upon entering
the cytoplasm [45]. Certain isoforms of TRIM5.alpha. found in Old
World monkeys are capable of strongly restricting HIV-1 infection.
Humans also naturally express a distinct isoform of TRIM5.alpha.
but it does not afford protection from HIV-1 infection. A recently
developed human/rhesus macaque chimeric TRIM5.alpha. isoform,
incorporating a small number of key HIV-restrictive amino acids,
was demonstrated to inhibit HIV-1 infection in a hematopoietic stem
cell gene therapy setting [43, 46]. If used in a clinical
application, the design of this chimeric TRIM5.alpha. molecule,
which consists of mainly human amino acid sequences, will help to
avoid immune rejection which would occur with the use of wild-type
rhesus macaque TRIM5.alpha.. A third molecule, a TAR decoy, has
been previously described to inhibit transactivation of proviral
transcription [12]. By mimicking the structure of the viral
transcriptional responsive element (TAR), the TAR decoy is able to
bind the viral Tat protein and sequester it away from its normal
action of aiding efficient proviral HIV transcription.
[0173] In the present study, the construction and pre-clinical
evaluation of a triple combination anti-HIV lentiviral vector is
described that focuses on the pre-integration block of HIV-1
infection to minimize the formation of integrated provirus and the
generation of escape mutants. The three highly potent anti-HIV
transgenes, a chimeric TRIM5.alpha. molecule, a CCR5 shRNA capable
of almost complete knockdown of CCR5 expression, and a TAR decoy,
combined in a single vector, displayed complete protection from
productive viral infection and integration of multiple strains of
HIV-1 upon transduction into HIV target cells. Our results
establish the future application of this vector for use in a
clinical setting.
Example No. 6
Lentiviral Vector Design and Production
[0174] A third-generation HIV-derived lentiviral vector containing
an EGFP reporter gene was used in this study,
pCCLc-MNDU3-x-PGK-EGFP (FIG. 8A). A chimeric human/rhesus macaque
TRIM5.alpha. gene was inserted into the lentiviral vector under the
control of the MNDU3 promoter. The human polymerase-III U6 promoter
driven CCR5 shRNA expression cassette was generated, as described
previously, and inserted directly downstream of the
MNDU3-TRIM5.alpha. gene [47]. The TAR decoy expression cassette was
generated in a similar way to the CCR5 shRNA cassette and inserted
directly downstream from the CCR5 shRNA gene. All three of these
anti-HIV expression cassettes were inserted upstream of the EGFP
reporter gene to derive pCCLc-Combination-PGK-EGFP (FIG. 8B).
Sequencing of clones was confirmed by Laragen Inc., Los Angeles,
Calif.
[0175] Lentiviral vectors were generated in HEK-293T cells.
Twenty-five micrograms of the packaging construct, p.DELTA.8.9
(packaging plasmid containing the gag and pol genes), 25 .mu.g of
pCCLc-MNDU3-x-PGK-EGFP (control empty vector) or the combination
vector, pCCLc-MNDU3-TRIM5.alpha.-U6-CCR5shRNA-U6-TARdecoy-PGK-EGFP
(transfer vector), and 5 .mu.g of VSVG (envelope). DNA plasmids
were transfected into cells in T225 flasks by lipofection. Vector
supernatants were collected at 48 hours post-transfection and
concentrated by ultrafiltration.
Example No. 7
Transduction of Cultured Cells and Primary CD34+ HPCs
[0176] Ghost-R5-X4-R3 cultured cells obtained from the AIDS
Reference and Reagent Program were cultured in complete DMEM
including 10% FBS supplemented with hygromycin, puromycin, and G418
according to the supplier's protocol. Cells were transduced with
the lentiviral vectors, either EGFP-alone or the combination vector
(MOI 10) for two hours at 37.degree. C. with 8 .mu.g/ml protamine
sulfate. Complete medium was then added to the cells.
[0177] CD34+ hematopoietic progenitor cells (HPCs) were isolated
from umbilical cord blood (NDRI, Philadelphia, Pa.) by Ficoll-Paque
(GE Healthcare, Piscataway, N.J.) and purified by magnetic bead
column separation (Miltenyi Biotec, Auburn, Calif.). CD34+ cell
isolation purity (>93%) was routinely obtained. Total CD34+
cells were cultured in complete IMDM media containing 10% FBS and
supplemented with 50 ng/ml SCF, Flt-3 ligand, and TPO. Cells were
transduced with the lentiviral vectors EGFP-alone or the
combination vector (MOI 10) for three hours at 37.degree. C. with
Bug/ml protamine sulfate. Two days post-transduction, cells were
sorted based on EGFP expression and cultured in semi-solid
methylcellulose medium with growth factors (Stem Cell Technologies,
Vancouver, BC, Canada) for 12 days to derive mature macrophages.
After differentiation, cells were removed from the methylcellulose
medium and plated in 6-well plates in complete DMEM medium with 10%
FBS supplemented with 10 ng/ml of GM-CSF and M-CSF. Media was
changed every two days for four days to derive mature macrophages.
Both nontransduced and lentiviral vector transduced cultured and
primary CD34+ cell derived macrophages were used for subsequent
experiments.
Example No. 8
Flow Cytometry and QRT-PCR
[0178] To determine if cells transduced with the combination
lentiviral vector had decreased levels of CCR5 due to the
expression of the CCR5 shRNA, cells were analyzed by FACS.
Seventy-two hours post-transduction, transduced Ghost-R5-X4-R3
cells were stained with a PE-conjugated anti-human CCR5 antibody
(BD Biosciences, San Jose, Calif.). CD34+ cell derived macrophages,
nontransduced, EGFP-alone transduced, and combination vector
transduced cells, were stained with antibodies to detect normal
macrophage cell surface markers including, CD14-PE, CD4-PE, and
CD68-PE (BD Biosciences, San Jose, Calif.). All FACS data was
obtained on a Beckman Coulter Cytomics FC500 flow cytometer and
analyzed on CXP analysis software.
[0179] To further quantitate the levels of CCR5 knockdown in
combination lentiviral vector transduced cells, quantitative
real-time PCR (QRT-PCR) was performed on transduced cell RNA. Total
RNA was extracted from Ghost-R5-X4-R3 cells using RNA-STAT-60
(Tel-Test Inc., Friendswood, Tex.). First strand cDNA synthesis was
performed using the High Capacity cDNA Reverse Transcription Kit
(Applied Biosystems, Foster City, Calif.). QRT-PCR was then
performed using the SYBR Green PCR Master Mix Kit (Applied
Biosystems, Foster City, Calif.) with primers:
5'-ACTGCAAAAGGCTGAAGAGC-3' (SEQ ID NO: 6) and
5'-AGCATAGTGAGCCCAGAAGG-3' (SEQ ID NO: 7). GAPDH was used as an
internal control.
[0180] To quantitate the levels of integrated HIV-1 provirus
following viral challenge of transduced cells, QRT-PCR was
performed on the cell's genomic DNA. Total genomic DNA was isolated
from challenged cells using the Wizard Genomic DNA Isolation System
(Promega, Madison, Wis.). QRT-PCR was performed using the Taqman
PCR Core Reagents Kit (Applied Biosystems, Foster City, Calif.)
using the primers 5'-CTGGCTACTATTTCTTTTGCTA-3' (SEQ ID NO: 8) and
5'-TGGCATGGGTACCAGCACA-3' (SEQ ID NO: 9) and probe
5'-TTTATCTACTTGTTCATTTCCTCCAATTCCTT-3' (SEQ ID NO: 10) (IDT DNA
Technologies, Coralville, Iowa). The single copy albumin gene was
used as an internal control.
Example No. 9
HIV-1 Challenge of Vector Transduced Cells
[0181] To determine whether the expression of the triple
combination of anti-HIV genes conferred resistance to HIV-1
infection, transduced cells were challenged with R5, X4, and
dual-tropic strains of HIV-1, BaL-1, NL4-3, and 89.6, respectively.
Ghost-R5-X4-R3 cells, nontransduced, EGFP-alone, and combination
vector transduced, were incubated with R5-tropic BaL-1 and
X4-tropic NL4-3 strains of HIV-1, MOI 0.01 and 0.05, for two hours
at 37.degree. C. with 8 .mu.g/ml polybrene. On various days
post-infection, challenge supernatants were sampled for use in an
HIV-1 p24 antigen ELISA and infectious virus assays. Nontransduced
and transduced CD34+ cell derived macrophages were similarly
challenged with BaL-1 at MOIs of 0.01 and 0.05. On various days
post-infection, challenge supernatants were sampled for use in an
HIV-1 p24 antigen ELISA (Zeptometrix Corp., Buffalo, N.Y.) and
infectious virus assays.
[0182] Viral escape mutants can be generated after prolonged use
with current anti-retroviral therapies. To determine if escape
mutants were generated upon challenge of combination transduced
cells, subsequent challenges were performed with culture
supernatants from the initial HIV-1 challenge experiments. Naive
Ghost-R5-X4-R3 cells, nontransduced, EGFP-alone, and combination
vector transduced, were challenged with culture supernatants from
their respective day 25 HIV-1 challenge supernatants from the
initial challenge experiment. On various days post-infection,
culture supernatants were sampled for infectious virus. Briefly,
supernatants (75 ul) from viral challenges were incubated on naive
nontransduced Ghost-R5-X4-R3 cells for 2 hours at 37.degree. C.
with 8 .mu.g/ml polybrene. Complete cell culture media was added.
Forty-eight hours post-infection, cells were analyzed by FACS for
EGFP expression to quantitate the levels of infectious virus.
Example No. 10
Selective Survival Advantage of Combination Vector Transduced
Cells
[0183] To evaluate whether combination vector transduced cells have
a selective survival advantage over nontransduced cells, a mixed
culture of both cell types was challenged with HIV-1. Mixed
populations of cells, with ratios of 1:1 and 2:1, transduced cells
(either EGFP-alone or combination vector transduced) to
nontransduced cells, were challenged with R5 and X4-tropic strains
of HIV-1, BaL-1 and NL4-3, respectively, at an MOI of 0.01. Cells
were analyzed by FACS for EGFP expression on day 0 (pre-infection)
and on day 21 post-infection to evaluate the survival advantage of
the transduced cell populations.
Example No. 11
Immune Cell Activation Assay
[0184] The insertion of the rhesus macaque TRIM5.alpha. 13-aa patch
into the C-terminal region of the human TRIM5.alpha. isoform may
result in immune activation and rejection of cells expressing the
chimeric TRIM5.alpha. molecule. To determine if immune system cells
were capable of responding to the presentation of the 13-aa patch,
an MTT cell activation assay was performed. Fresh PBMCs were
isolated by Ficoll-Paque and plated in 96-well plates in complete
RPMI with 10% FBS and supplemented with 10 ng/ml IL-2. Monocytes
and dendritic cells were allowed to attach to the bottom of the
wells. Lymphocytes were removed and plated in separate wells.
Monocytes/dendritic cells were pulsed overnight with small peptides
corresponding to either a human TRIM5.alpha. 11-aa patch
(GARGTRYQTFV (SEQ ID NO: 4)) or the rhesus macaque TRIM5.alpha.
13-aa patch (QAPGTLFTFPSLT (SEQ ID NO: 5)) which was used to
generate the chimeric TRIM5.alpha. isoform. Peptides were
synthesized by Genscript (Piscataway, N.J.). A separate set of
monocytes/dendritic cells were pulsed with LPS as a positive
control. A fourth set of monocytes/dendritic cells were incubated
with PHA 1 ug/ml to act as a positive T cell activation control.
The fifth set of monocytes/dendritic cells were left unmanipulated
to serve as a negative nonactivated control. Lymphocytes were added
back to the cultures the following day. On various days
post-addition of the lymphocytes, the MTT cell activation assay was
performed on the cells according to the manufacturer's protocol
(Roche Applied Science, Indianapolis, Ind.).
Experimental Results
[0185] High Titer Vector Production and Transduction with
Lentiviral Vectors:
[0186] A third generation lentiviral vector, CCLC-MNDU3-X-PGK-EGFP,
was utilized to construct the triple combination anti-HIV vector
(FIG. 8A). The three genes inserted into this vector include a
human/rhesus macaque TRIM5.alpha. isoform, a CCR5 shRNA, and a TAR
decoy (FIG. 8B). By combining these three genes, a potent
pre-integration block to HIV-1 infection could be established due
to the pre-entry block by the knockdown of CCR5 expression and the
post-entry/pre-integration block by the chimeric TRIM5.alpha.. If
infectious virus is able to circumvent the potent inhibition
established by the first two anti-HIV molecules, the TAR decoy will
prevent upregulation of HIV-1 transcription.
[0187] With the incorporation of three anti-HIV genes into a single
gene therapy vector which is based on HIV, detrimental effects on
the quantity of vector production and titer due to the increased
size of the vector payload and also the anti-HIV effects of the
vector transgenes could be possible. Therefore, combination vector
titers were compared to control EGFP-alone titers on HEK-293T
cells. Combination vector titers, upon 100-fold concentration, were
found to be, on average, .about.5*10.sup.9TU/ml compared to
EGFP-alone vector titers which generated .about.3.5*10.sup.9TU/ml
(data not shown). This excludes any negative effects on vector
titer using our combination vector construct and packaging
system.
[0188] Due to the complexity of this combination vector containing
three anti-HIV expression cassettes and a fourth EGFP reporter
gene, expression levels of the downstream transcripts, including
the two polymerase (pol)-III transcription units, may be affected.
Expression of all three anti-HIV genes was confirmed by
quantitative real-time PCR (QRT-PCR). The expression levels of the
chimeric TRIM5.alpha. (FIG. 8C), CCR5 shRNA (FIG. 8D), and TAR
decoy (FIG. 8E) were 4,535-, 824-, and 34-fold higher,
respectively, compared to control cells that do not express any of
the anti-HIV genes. The levels of the internal control U6 snRNA
were consistent among all cell types (FIG. 8F).
[0189] The stability of the vector in transduced cells is also a
concern due to its complexity. To evaluate any vector deletions or
rearrangements that may have occurred, genomic PCR was performed
with vector transgene specific primers: FIG. 17A shows MNDU3
forward and EGFP reverse [.about.3 kilobases (kb)], FIG. 16B shows
MNDU3 forward and TAR decoy reverse (.about.2.5 kb), FIG. 16C shows
MNDU3 forward and CCR5 shRNA reverse (.about.2 kb), FIG. 16D shows
TAR decoy forward and EGFP reverse (.about.0.7 kb), and FIG. 16E
shows albumin forward and reverse (.about.0.1 kb). As displayed in
FIGS. 16A-16E, no deletions or rearrangements were detected, as PCR
bands from genomic DNA from combination transduced Ghost-R5-X4-R3
cells (lane 4) corresponded to PCR bands amplified from the
combination transfer vector plasmid (lane 1) used in vector
preparations. This was in contrast to nontransduced (lane 2) and
EGFP-alone-transduced cells (lane 3) that did not amplify the
correct PCR products and only displayed background bands. A
schematic of the theoretical PCR products is displayed below the
panels.
[0190] Due to the insertion of the three anti-HIV genes,
transduction efficiencies obtained with the combination vector
could also be negatively affected. In order to determine if there
was such an effect, both cultured Ghost-R5-X4-R3 cells and primary
CD34+ hematopoietic progenitor cells (HPCs), were transduced with
the control EGFP-alone vector and the anti-HIV gene combination
vector. Transduction efficiencies were not affected by use of the
combination vector, regardless of the MOI chosen, as observed by
EGFP expression during FACS analysis. Transduction efficiencies in
cultured Ghost-R5-X4-R3 cells and primary CD34+ HPCs at an MOI of
10 were greater than 95% and 50%, respectively, for each vector
transduction (data not shown).
CCR5 Down-Regulation in Combination Vector Transduced Cells:
[0191] To determine if successful transduction of cells with the
combination anti-HIV lentiviral vector conferred knockdown of CCR5
expression, transduced cells were analyzed by FACS for CCR5 surface
expression. As seen in FIG. 9A, the combination vector transduced
Ghost-R5-X4-R3 cells displayed dramatic knockdown of CCR5
expression (>92%) as compared to nontransduced and EGFP-alone
transduced cells. To further quantitate the levels of CCR5 gene
silencing in combination vector transduced cells, quantitative
real-time PCR (QRT-PCR) was performed. Cells expressing the CCR5
shRNA displayed high levels of knockdown of CCR5 expression
(>91%) as compared to nontransduced and EGFP-alone transduced
cells (FIG. 9B). These data confirm a potent knockdown of CCR5 gene
expression in cells transduced with the combination lentiviral
vector.
HIV-1 Challenge of Combination Vector Transduced Cells:
[0192] Cultured Ghost-R5-X4-R3 cells and primary macrophages are
susceptible to infection from R5 and X4-tropic strains of HIV-1.
However, upon transduction with the combination anti-HIV lentiviral
vector, transduced cells should be resistant to HIV-1 infection. To
determine if transduction and expression of the three anti-HIV
genes conferred viral resistance, cells were challenged with
various strains of HIV-1. Combination vector transduced
Ghost-R5-X4-R3 cells displayed strong HIV-1 resistance and
inhibition of viral replication (>1.5 log) after challenge with
both R5 (BaL-1) (FIGS. 10A, 10B) and X4-tropic (NL4-3) (FIGS. 10C,
10D) strains of HIV-1 at multiple MOIs (0.01 and 0.05) as compared
to nontransduced and EGFP-alone vector transduced cells as measured
by p24 antigen ELISA. CD34+ HPC derived macrophages transduced with
the combination vector also displayed strong inhibition of
R5-tropic BaL-1 HIV-1 infection (>1.5 log) at multiple MOIs
compared to control nontransduced and EGFP-alone transduced cells.
Inhibition was observed by p24 antigen ELISA (FIGS. 11A, 11B) and
by quantitating total infectious virus using a Ghost cell assay
(FIGS. 11C, 11D).
[0193] To evaluate the possible generation of escape mutants
arising in long-term HIV-1 challenged combination vector transduced
cells, a secondary challenge experiment was performed. Naive cells,
nontransduced, EGFP-alone, and combination vector transduced cells
were challenged using the respective viral supernatant from the
last time point (day 25) of the initial challenge experiment. Cell
culture supernatants were monitored for three weeks to identify any
virus replication resulting from the generation of escape mutants.
As seen in FIGS. 12A-12D, no viral replication was detected in
challenged cells transduced with the combination lentiviral vector:
BaL-1 MOI 0.01 (FIG. 12A), BaL-1 MOI 0.05 (FIG. 12B), NL4-3 MOI
0.01 (FIG. 12C), and NL4-3 MOI 0.05 (FIG. 12D). In contrast,
control nontransduced and EGFP-alone vector transduced cells were
successfully infected initially which resulted in detection of
infectious virus. The levels of infectious virus then started to
decrease after day 15 post-infection due to killing of infected
cells within the cultures. The results from the secondary challenge
experiments confirmed that no viral escape mutants could be
detected in culture supernatants from combination vector transduced
cells challenged long-term with HIV-1.
[0194] It is expected that in a human clinical HIV gene therapy
application, not all of an individual's HIV susceptible cells will
be transduced with anti-HIV gene therapy vectors and will be
capable of resisting viral infection and replication. Therefore, to
evaluate the selective survival advantage of anti-HIV gene
transduced cells, a mixed population of nontransduced and
transduced cells, either EGFP-alone or combination vector
transduced, were challenged with HIV-1, both BaL-1 and NL4-3. As
seen in FIGS. 13A-13B, a selective survival advantage was conferred
and maintained in cultures containing the combination vector
transduced cells demonstrated by an increase of the total percent
EGFP positive cells by the end of the viral challenge. In cultures
containing a 1:1 and 2:1 ratio of combination vector transduced
cells to nontransduced cells, the pre-infection EGFP percentage
being, .about.46% and .about.73% respectively, increased to >84%
EGFP positive cells by day 21 post-infection for both BaL-1 (FIG.
13A) and NL4-3 (FIG. 13B). These results are in contrast to
cultures containing EGFP-alone vector transduced cells where the
EGFP percent positive cell population remained relatively constant
on day 21 post-infection (.about.42% and .about.72% for ratios of
1:1 and 2:1, respectively) compared to the pre-infection EGFP
percentages of 46% and 70%. These results establish that the
anti-HIV combination vector transduced cells were able to survive
and increase in number during the course of the HIV-1
infection.
Inhibition of HIV-1 Proviral Formation:
[0195] Viral reservoirs which are maintained in an HIV infected
individual continue to be a major barrier for HIV eradication and
curing patients with an established infection. To better eradicate
the virus from infected individuals, the combination anti-HIV
vector was designed to inhibit HIV-1 prior to integration, thus
avoiding any provirus formation. To determine if viral inhibition
was occurring at the stages of pre-entry (due to the CCR5 shRNA)
and post-entry/pre-integration (due to TRIM5.alpha.), cells
challenged with both BaL-1 and NL4-3 were further analyzed by
QRT-PCR for genomic HIV-1 provirus. As seen in FIGS. 14A-14B, a
highly potent block of HIV-1 provirus formation could be
demonstrated when genomic DNA from challenged cells (day 25
post-infection) was analyzed by QRT-PCR with primers specific for
the HIV-1 pol gene. Combination vector transduced cells contained
undetectable levels, similar to background levels in uninfected
cells, of HIV-1 provirus as compared to control nontransduced and
EGFP-alone vector transduced infected cells at MOIs of 0.01 and
0.05 for BaL-1 (FIG. 14A) and NL4-3 (FIG. 14B) strains of HIV-1.
These data confirm that the combination vector, indeed, conferred a
strong block to HIV-1 integration, therefore preventing HIV
proviral DNA formation.
Phenotypic Analysis of Transduced CD34+ HPC Derived
Macrophages:
[0196] The introduction of foreign genes into cells has the
potential to cause detrimental effects on their development. To
evaluate whether lentiviral vector transduction of target cells and
expression of the combination vector anti-HIV transgenes affected
the differentiation of CD34+ HPCs into mature macrophages, cells
were analyzed by FACS for macrophage specific cell surface markers.
Combination vector transduced macrophages displayed normal levels
of the surface markers CD14 (>93%), CD4 (>93%), and CD68 (an
activation marker) (.about.2%) as compared to nontransduced and
EGFP-alone transduced cells (FIG. 15A). Phenotypic analysis of
these cells confirmed that normal differentiation had occurred from
transduced CD34+ HPCs to mature macrophages and that transduced
cells were indistinguishable from nontransduced cells.
Toxicity Studies of Vector-Transduced Cells:
[0197] A previous report demonstrated that CCR5 shRNAs expressed by
the U6 pol-III promoter were toxic to cells as compared to
expression from the less robust H1 pol-III promoter.32 To evaluate
the toxicity of the combination anti-HIV vector that contains a
U6-expressed CCR5 shRNA, phytohemagglutinin-stimulated peripheral
blood mononuclear cells (PBMCs) were either left nontransduced or
transduced with the EGFP-alone or combination vectors. Cells were
monitored on days 0, 4, 7, and 12 for both EGFP expression and
total cell counts. Constant EGFP expression was observed for both
the EGFP-alone and combination vector-transduced PBMCs throughout
the experiment (FIG. 15B). Also, total cell counts were comparable
between nontransduced, EGFP-alone-transduced, and combination
vector-transduced PBMCs (FIG. 15C).
Detection of Immune Activation by the Chimeric TRIM5.alpha. Rhesus
Macaque Amino Acid Sequence:
[0198] The expression of the chimeric TRIM5.alpha. isoform has the
possibility of invoking an immune response due to the 13-aa patch
from the rhesus macaque isoform which was inserted into the human
isoform. To detect immune activation in response to presentation of
the rhesus macaque 13-aa patch, an immune cell activation assay was
performed. As displayed in FIG. 15D, no activation of immune cells
had occurred in the samples which were pulsed with the rhesus
macaque 13-aa peptide. The metabolic activity of the immune cells
was similar to those observed in unmanipulated cells (day 6 P
value=0.951 and day 8 P value=0.993) and the cell samples pulsed
with the human 11-aa peptide (day 6 P value=0.938 and day 8 P
value=0.419). However, activation of cells was observed in PHA and
LPS stimulated cell samples as displayed by the decrease in total
cell numbers. These results confirm that the rhesus macaque 13-aa
patch located in the human/rhesus macaque chimeric TRIM5.alpha.
isoform does not invoke immune cell activation when tested in a
monocytes/dendritic cell culture system.
Experiment C
In Vivo Safety Data of a Combination Anti-HIV Lentiviral Vector
[0199] Human cord blood CD34+ hematopoietic progenitor cells were
transduced with the combination anti-HIV lentiviral vector and
transplanted into the humanized NOD/SCID-IL2 gamma receptor (NSG)
knockout mouse model. After allowing 16 weeks for the mice and
human cells to develop, the peripheral blood and lymphoid organs
were analyzed by FACS for engraftment (EGFP+) of the anti-HIV gene
modified human cells. EGFP+ cells=anti-HIV gene modified cells. The
data displayed in FIGS. 17A-17G demonstrates the in vivo safety of
the combination anti-HIV lentiviral vector in an HIV stem cell gene
therapy setting. Stem cells transduced with the vector were able to
develop into mature human immune system cells and undergo normal
distribution in the NSG mice.
[0200] It is to be understood that while the invention has been
described in conjunction with the above embodiments, that the
foregoing description and examples are intended to illustrate and
not limit the scope of the invention. Other aspects, advantages and
modifications within the scope of the invention will be apparent to
those skilled in the art to which the invention pertains.
REFERENCES
[0201] 1. Bacheler, L. T. et al. Human immunodeficiency virus type
1 mutations selected in patients failing efavirenz combination
therapy. Antimicrob. Agents Chemother. 44, 2475-2484 (2000). [0202]
2. Martinez-Picado, J. et al. Antiretroviral resistance during
successful therapy of HIV type 1 infection. Proc. Natl. Acad. Sci.
USA. 97, 10948-10953 (2000). [0203] 3. Winters, M. A. et al.
Frequency of antiretroviral drug resistance mutations in HIV-1
strains from patients failing triple drug regimens. The Terry Beirn
Community Programs for Clinical Research on AIDS. Antivir. Ther. 5,
57-63 (2000). [0204] 4. Lafeuillade, A., Poggi, C., Hittinger, G.
& Chadapaud, S. Phenotypic and genotypic resistance to
nucleoside reverse transcriptase inhibitors in HIV-1 clinical
isolates. HIV Med. 2, 231-235 (2002). [0205] 5. Marks, K. &
Gulick, R. M. New antiretroviral agents for the treatment of HIV
infection. Curr. HIV/AIDS Rep. 1, 82-88 (2004). [0206] 6. Barouch,
D. H. Challenges in the development of an HIV-1 vaccine. Nature.
455, 613-619 (2008). [0207] 7. Rossi, J. J. The application of
ribozymes to HIV infection. Curr. Opin. Mol. Ther. 1, 316-322
(1999). [0208] 8. Bai, J. et al. Characterization of Anti-CCR5
Ribozyme-Transduced CD34+ Hematopoietic Progenitor Cells in Vitro
and in a SCID-hu Mouse Model in Vivo. Mol. Ther. 1, 244-254 (2002).
[0209] 9. Ding, S. F., Lombardi, R., Nazari, R. & Joshi, S. A
combination anti-HIV-1 gene therapy approach using a single
transcription unit that expresses antisense, decoy, and sense RNAs,
and transdominant negative mutant Gag and Env proteins. Front.
Biosci. 7, a15-28 (2002). [0210] 10. Lee, N. S. et al. Expression
of small interfering RNAs targeted against HIV-1 rev transcripts in
human cells. Nat. Biotechnol. 20, 500-505 (2002). [0211] 11.
Martinez, M. A. et al. Suppression of chemokine receptor expression
by RNA interference allows for inhibition of HIV-1 replication.
AIDS 16, 2385-2390 (2002). [0212] 12. Michienzi, A., Li, S., Zaia,
J. A. & Rossi, J. J. A nucleolar TAR decoy inhibitor of HIV-1
replication. Proc. Natl. Acad. Sci. USA. 99, 14047-52 (2002).
[0213] 13. Novina, C. D. et al. siRNA-directed inhibition of HIV-1
infection. Nat. Med. 8, 681-686 (2002). [0214] 14. Cordelier, P.,
Morse, B. & Strayer, D. S. Targeting CCR5 with siRNAs: using
recombinant SV40-derived vectors to protect macrophages and
microglia from R5-tropic HIV. Oligonucleotides 13, 281-294 (2003).
[0215] 15. An, D. S. et al. Stable reduction of CCR5 by RNAi
through hematopoietic stem cell transplant in non-human primates.
Proc. Natl. Acad. Sci. USA. 104, 13110-13115 (2007). [0216] 16.
Anderson, J. & Akkina, R. Complete knockdown of CCR5 by
lentiviral vector-expressed siRNAs and protection of transgenic
macrophages against HIV-1 infection. Gene Ther. 14, 1287-1297
(2007). [0217] 17. Kumar, P. et al. T cell-specific siRNA delivery
suppresses HIV-1 infection in humanized mice. Cell 134, 577-586
(2008). [0218] 18. ter Brake, O. et al. Evaluation of safety and
efficacy of RNAi against HIV-1 in the human immune system
(Rag-2(-/-)gammac(-/-)) mouse model. Gene Ther. 16, 148-153 (2009).
[0219] 19. Kohn, D. B. et al. A clinical trial of
retroviral-mediated transfer of a Rev-responsive element decoy gene
into CD34+ cells from the bone marrow of human immunodeficiency
virus-1-infected children. Blood 94, 368-371 (1999). [0220] 20.
Bauer, G. et al. Gene therapy for pediatric AIDS. Ann. NY Acad.
Sci. 918, 318-329 (2000). [0221] 21. Humeau, L. M. et al. Efficient
lentiviral vector-mediated control of HIV-1 replication in CD4
lymphocytes from diverse HIV+ infected patients grouped according
to CD4 count and viral load. Mol. Ther. 9, 902-13 (2004). [0222]
22. Anderson, J. et al. Safety and efficacy of a lentiviral vector
containing three anti-HIV genes-CCR5 ribozyme, tat-rev siRNA, and
TAR decoy-in SCID-hu mouse-derived T cells. Mol. Ther. 15,
1182-1188 (2007). [0223] 23. Mitsuyasu, R. T. et al. Phase 2 gene
therapy trial of an anti-HIV ribozyme in autologous CD34+ cells.
Nat. Med. 5, 285-292 (2009). [0224] 24. Fire, A. et al. Potent and
specific genetic interference by double-stranded RNA in
Caenorhabditis elegans. Nature 391, 806-811 (1998). [0225] 25.
Elbashir, S. M. et al. Duplexes of 21-nucleotide RNAs mediate RNA
interference in cultured mammalian cells. Nature 411, 494-498
(2001). [0226] 26. Huang, Y. et al. The role of a mutant CCR5
allele in HIV-1 transmission and disease progression. Nat. Med. 2,
1240-1243 (1996). [0227] 27. Liu, R. et al. Homozygous defect in
HIV-1 coreceptor accounts for resistance of some multiply exposed
individuals to HIV-1 infection. Cell 86, 267-377 (1996). [0228] 28.
Naif, H. M. et al. A human immunodeficiency virus type 1 isolate
from an infected person homozygous for CCR5.DELTA.32 exhibits dual
tropism by infecting macrophages and MT2 cells via CXCR4. J. Virol.
76, 3114-3124 (2002). [0229] 29. Hutter, G. et al. Long-Term
Control of HIV by CCR5 Delta32/Delta32 Stem-Cell Transplantation.
N. Engl. J. Med. 360, 692-698 (2009). [0230] 30. Hatziioannou, T.,
Delahaye, E., Martin, F., Russell, S. J. & Cosset, F-L.
Retroviral Display of Functional Binding Domains Fused to the Amino
Terminus of Influenza Hemagglutinin. Hum. Gene Ther. 10, 1533-1544
(1999). [0231] 31. Jiang, A. & Dornburg, R. In vivo cell
type-specific gene delivery with retroviral vectors that display
single chain antibodies. Gene Ther. 6, 1982-1987 (1999). [0232] 32.
Engelstadter, M. et al. Targeted gene transfer to lymphocytes using
murine leukaemia virus vectors pseudotyped with spleen necrosis
virus envelope proteins. Gene Ther. 8, 1202-1206 (2001). [0233] 33.
Lavillette, D., Russell, S. J. & Cosset, F-L. Retargeting gene
delivery using surface-engineered retroviral vector particles.
Curr. Opin. Biotechnol. 12, 461-466 (2001). [0234] 34. Lin, A. H.
et al. Receptor-Specific Targeting Mediated by the Coexpression of
a Targeted Murine Leukemia Virus Envelope Protein and a
Binding-Defective Influenza Hemagglutinin Protein. Hum. Gene Ther.
12, 323-332 (2001). [0235] 35. Zhong, Q. et al. Efficient c-kit
Receptor-Targeted Gene Transfer to Primary Human CD34-Selected
Hematopoietic Stem Cells. J. Virol. 75, 10393-10400 (2001). [0236]
36. Maurice, M. et al. Efficient gene transfer into human primary
blood lymphocytes by surface-engineered lentiviral vectors that
display a T cell-activating polypeptide. Blood 99, 2342-2350
(2002). [0237] 37. Chandrashekran, A., Gordon, M. Y. & Casimir,
C. Targeted retroviral transduction of c-kit.sup.+ hematopoietic
cells using novel ligand display technology. Blood 104, 2697-2703
(2004). [0238] 38. Verhoeyen, E. et al. Novel lentiviral vectors
displaying "early-acting cytokines" selectively promote survival
and transduction of NOD/SCID repopulating human hematopoietic stem
cells. Blood 106, 3386-3395 (2005). [0239] 39. Yang, L., Bailey,
L., Baltimore, D. & Wang, P. Targeting lentiviral vectors to
specific cell types in vivo. Proc. Natl. Acad. Sci. USA. 103,
11479-11484 (2006). [0240] 40. Yang, L. et al. Engineered
lentivector targeting of dendritic cells for in vivo immunization.
Nat. Biotechnol. 26, 326-334 (2008). [0241] 41. Silva, F. A. D.,
Costa, M. J. L., Corte-Real, S. & Goncalves, J.
Celltype-specific targeting with Sindbis pseudotyped lentiviral
vectors displaying anti-CCR5 single-chain antibodies. Hum. Gene
Ther. 16, 223-234 (2005). [0242] 42. Bonyhadi M, Moss K, Voytovich
A, Auten J, Kalfoglou C, Plavec I, et al. (1997). RevM10-expressing
T cells derived in vivo from transduced human hematopoietic
stem-progenitor cells inhibit human immunodeficiency virus
replication. J Virol; 71: 4707-4716. [0243] 43. Anderson J, Akkina
R (2008). Human immunodeficiency virus type 1 restriction by
human-rhesus chimeric tripartite motif 5alpha (TRIM 5alpha) in
CD34+(+) cell-derived macrophages in vitro and in T cells in vivo
in severe combined immunodeficient (SCID-hu) mice transplanted with
human fetal tissue. Hum Gene Ther; 19: 217-228. [0244] 44. Berger E
A, Murphy P M, Farber J M (1999). Chemokine receptors as
HIV-lcoreceptors: roles in viral entry, tropism, and disease. Annu
Rev Immunol; 17: 657-700. [0245] 45. Stremlau M, Owens C M, Perron
M J, Kiessling M, Autissier P, Sodroski J (2004). The cytoplasmic
body component TRIM5alpha restricts HIV-1 infection in Old World
monkeys. Nature; 427: 848-853. [0246] 46. Sawyer S L, Wu L I,
Emerman M, Malik H S (2005). Positive selection of primate
TRIM5alpha identifies a critical species-specific retroviral
restriction domain. Proc Natl Acad Sci USA; 102: 2832-2837. [0247]
47. Castanotto D, Li H, Rossi J (2002). Functional siRNA expression
from transfected PCR products. RNA; 8: 1454-1460. [0248] 48. Ohno,
K., Sawai, K., lijima, Y., Levin, B. & Meruelo, D.
Cell-specific targeting of Sindbis virus vectors displaying
IgG-binding domains of protein A. Nat. Biotechnol. 15, 763-767
(1997). [0249] 49. Morizono, K., Bristol, G., Xie, Y. M., Kung, S.
K. & Chen, I. S. Antibody-directed targeting of retroviral
vectors via cell surface antigens. J. Virol. 75, 8016-8020 (2001).
[0250] 50. Iijima, Y. et al. Cell-specific targeting of a thymidine
kinase/gancyclovir gene therapy system using a recombinant Sindbis
virus vector. Int. J. Cancer. 80, 110-118 (1999). [0251] 51.
Morizono, K. et al. Lentiviral vector retargeting to P-glycoprotein
on metastatic melanoma through intravenous injection. Nat. Med. 11,
346-352 (2005). [0252] 52. Morizono, K. & Chen, I. S. Targeted
gene delivery by intravenous injection of retroviral vectors. Cell
Cycle 4, 854-856 (2005). [0253] 53. Liang, M., Pariente, N.,
Morizono, K. & Chen, I. S. Targeted transduction of CD34+
hematopoietic progenitor cells in nonpurified human mobilized
peripheral blood mononuclear cells. J. Gene Med. 11, 185-196
(2009).
Sequence CWU 1
1
26148DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 1cgacttaaaa tcgctagcca gatctgagcc
tgggagctct ctggctag 48259DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 2gggtctctct
ggttagacca gatttgagcc tgggagctct ctggctaact agggaaccc
59337DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 3acgaagcttg atcccgtttg ccggtcgatc gcttcga
37411PRTHomo sapiens 4Gly Ala Arg Gly Thr Arg Tyr Gln Thr Phe Val 1
5 10 513PRTMacaca mulatta 5Gln Ala Pro Gly Thr Leu Phe Thr Phe Pro
Ser Leu Thr 1 5 10 620DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 6actgcaaaag gctgaagagc
20720DNAArtificial SequenceDescription of Artificial Sequence
Synthetic primer 7agcatagtga gcccagaagg 20822DNAArtificial
SequenceDescription of Artificial Sequence Synthetic primer
8ctggctacta tttcttttgc ta 22919DNAArtificial SequenceDescription of
Artificial Sequence Synthetic primer 9tggcatgggt accagcaca
191032DNAArtificial SequenceDescription of Artificial Sequence
Synthetic probe 10tttatctact tgttcatttc ctccaattcc tt
3211336DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 11agatccagtt tggggatcca aggtcgggca
ggaagagggc ctatttccca tgattccttc 60atatttgcat atacgataca aggctgttag
agagataatt agaattaatt tgactgtaaa 120cacaaagata ttagtacaaa
atacgtgacg tagaaagtaa taatttcttg ggtagtttgc 180agttttaaaa
ttatgtttta aaatggacta tcatatgctt accgtaactt gaaagtattt
240cgatttcttg gctttatata tcttgtggaa aggacgaaac accgagcatg
actgacatct 300acttcaagag agtagatgtc agtcatgctc tttttt
3361263DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 12gtgtcaagtc caatctatga catcaattat
atgtgaattg atgtcataga ttggacttga 60cac 631345DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 13gttcagaaac tacctcttaa tatgtgtaag aggtagtttc tgaac
451463DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 14gttcagaaac tacctcttag tcttcttcat
atgtggaaga agactaagag gtagtttctg 60aac 631563DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 15gagcatgact gacatctacc tgctcaacat atgtggttga
gcaggtagat gtcagtcatg 60ctc 6316324DNAHomo sapiens 16gacatccaga
tgacccagtc tccatcctcc ctgtctgcat ctgtaggaga cagagtcacc 60atcacttgcc
aggcgagtca gggcattcgc aaatatttaa attggtatca gcaaaaacca
120gggaaagtcc ctaagctcct gatctacgat gcatccaatt tggaaacagg
ggtcccatca 180aggttcagtg gaagtggatc agggacagat tttactttcg
ccatcagcag cctgcagccg 240gaagatactg caacatatta ctgtcaacaa
tatgatgatt tccccttcac cttcggccag 300gggacacgac tggagattaa acgt
324171533DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 17gctactatgg cttctggaat cctggttaat
gtaaaggagg aggtgacctg ccccatctgc 60ctggaactcc tgacacaacc cctgagcctg
gactgcggcc acagcttctg ccaagcatgc 120ctcactgcaa accacaagaa
gtccatgcta gacaaaggag agagtagctg ccctgtgtgc 180cggatcagtt
accagcctga gaacatacgg cctaatcggc atgtagccaa catagtggag
240aagctcaggg aggtcaagtt gagcccagag gggcagaaag ttgatcattg
tgcacgccat 300ggagagaaac ttctactctt ctgtcaggag gacgggaagg
tcatttgctg gctttgtgag 360cggtctcagg agcaccgtgg tcaccacacg
ttcctcacag aggaggttgc ccgggagtac 420caagtgaagc tccaggcagc
tctggagatg ctgaggcaga agcagcagga agctgaagag 480ttagaagctg
acatcagaga agagaaagct tcctggaaga ctcaaataca gtatgacaaa
540accaacgtct tggcagattt tgagcaactg agagacatcc tggactggga
ggagagcaat 600gagctgcaaa acctggagaa ggaggaggaa gacattctga
aaagccttac gaactctgaa 660actgagatgg tgcagcagac ccagtccctg
agagagctca tctcagatct ggagcatcgg 720ctgcaggggt cagtgatgga
gctgcttcag ggtgtggatg gcgtcataaa aaggacggag 780aacgtgacct
tgaagaagcc agaaactttt ccaaaaaatc aaaggagagt gtttcgagct
840cctgatctga aaggaatgct agaagtgttt agagagctga cagatgtccg
acgctactgg 900gttgatgtga cagtggctcc aaacaacatt tcatgtgctg
tcatttctga agataagaga 960caagtgagct ctccgaaacc acagataata
tatcaggcac cagggacatt atttacgttt 1020ccgtcactca cgaatttcaa
ttattgtact ggcatcctgg gctctcaaag tatcacatca 1080gggaaacatt
actgggaggt agacgtgtcc aagaaaactg cttggatcct gggggtatgt
1140gctggcttcc aacctgatgc aatgtgtaat attgaaaaaa atgaaaatta
tcaacctaaa 1200tacggctact gggttatagg gttagaggaa ggagttaaat
gtagtgcttt ccaggatagt 1260tccttccata ctccttctgt tcctttcatt
gtgcccctct ctgtgattat ttgtcctgat 1320cgtgttggag ttttcctaga
ctatgaggct tgcactgtct cattcttcaa tatcacaaac 1380catggatttc
tcatctataa gttttctcac tgttcttttt ctcagcctgt atttccatat
1440ttaaatccta gaaaatgtgg agtccccatg actctgtgct caccaagctc
tggcggctac 1500ccatacgacg tcccagacta cgcttgagcc tga
1533187865DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 18caggtggcac ttttcgggga aatgtgcgcg
gaacccctat ttgtttattt ttctaaatac 60attcaaatat gtatccgctc atgagacaat
aaccctgata aatgcttcaa taatattgaa 120aaaggaagag tatgagtatt
caacatttcc gtgtcgccct tattcccttt tttgcggcat 180tttgccttcc
tgtttttgct cacccagaaa cgctggtgaa agtaaaagat gctgaagatc
240agttgggtgc acgagtgggt tacatcgaac tggatctcaa cagcggtaag
atccttgaga 300gttttcgccc cgaagaacgt tttccaatga tgagcacttt
taaagttctg ctatgtggcg 360cggtattatc ccgtattgac gccgggcaag
agcaactcgg tcgccgcata cactattctc 420agaatgactt ggttgagtac
tcaccagtca cagaaaagca tcttacggat ggcatgacag 480taagagaatt
atgcagtgct gccataacca tgagtgataa cactgcggcc aacttacttc
540tgacaacgat cggaggaccg aaggagctaa ccgctttttt gcacaacatg
ggggatcatg 600taactcgcct tgatcgttgg gaaccggagc tgaatgaagc
cataccaaac gacgagcgtg 660acaccacgat gcctgtagca atggcaacaa
cgttgcgcaa actattaact ggcgaactac 720ttactctagc ttcccggcaa
caattaatag actggatgga ggcggataaa gttgcaggac 780cacttctgcg
ctcggccctt ccggctggct ggtttattgc tgataaatct ggagccggtg
840agcgtgggtc tcgcggtatc attgcagcac tggggccaga tggtaagccc
tcccgtatcg 900tagttatcta cacgacgggg agtcaggcaa ctatggatga
acgaaataga cagatcgctg 960agataggtgc ctcactgatt aagcattggt
aactgtcaga ccaagtttac tcatatatac 1020tttagattga tttaaaactt
catttttaat ttaaaaggat ctaggtgaag atcctttttg 1080ataatctcat
gaccaaaatc ccttaacgtg agttttcgtt ccactgagcg tcagaccccg
1140tagaaaagat caaaggatct tcttgagatc ctttttttct gcgcgtaatc
tgctgcttgc 1200aaacaaaaaa accaccgcta ccagcggtgg tttgtttgcc
ggatcaagag ctaccaactc 1260tttttccgaa ggtaactggc ttcagcagag
cgcagatacc aaatactgtc cttctagtgt 1320agccgtagtt aggccaccac
ttcaagaact ctgtagcacc gcctacatac ctcgctctgc 1380taatcctgtt
accagtggct gctgccagtg gcgataagtc gtgtcttacc gggttggact
1440caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt
tcgtgcacac 1500agcccagctt ggagcgaacg acctacaccg aactgagata
cctacagcgt gagctatgag 1560aaagcgccac gcttcccgaa gggagaaagg
cggacaggta tccggtaagc ggcagggtcg 1620gaacaggaga gcgcacgagg
gagcttccag ggggaaacgc ctggtatctt tatagtcctg 1680tcgggtttcg
ccacctctga cttgagcgtc gatttttgtg atgctcgtca ggggggcgga
1740gcctatggaa aaacgccagc aacgcggcct ttttacggtt cctggccttt
tgctggcctt 1800ttgctcacat gttctttcct gcgttatccc ctgattctgt
ggataaccgt attaccgcct 1860ttgagtgagc tgataccgct cgccgcagcc
gaacgaccga gcgcagcgag tcagtgagcg 1920aggaagcgga agagcgccca
atacgcaaac cgcctctccc cgcgcgttgg ccgattcatt 1980aatgcagctg
gcacgacagg tttcccgact ggaaagcggg cagtgagcgc aacgcaatta
2040atgtgagtta gctcactcat taggcacccc aggctttaca ctttatgctt
ccggctcgta 2100tgttgtgtgg aattgtgagc ggataacaat ttcacacagg
aaacagctat gaccatgatt 2160acgccaagcg cgcaattaac cctcactaaa
gggaacaaaa gctggagctg caagcttggc 2220cattgcatac gttgtatcca
tatcataata tgtacattta tattggctca tgtccaacat 2280taccgccatg
ttgacattga ttattgacta gttattaata gtaatcaatt acggggtcat
2340tagttcatag cccatatatg gagttccgcg ttacataact tacggtaaat
ggcccgcctg 2400gctgaccgcc caacgacccc cgcccattga cgtcaataat
gacgtatgtt cccatagtaa 2460cgccaatagg gactttccat tgacgtcaat
gggtggagta tttacggtaa actgcccact 2520tggcagtaca tcaagtgtat
catatgccaa gtacgccccc tattgacgtc aatgacggta 2580aatggcccgc
ctggcattat gcccagtaca tgaccttatg ggactttcct acttggcagt
2640acatctacgt attagtcatc gctattacca tggtgatgcg gttttggcag
tacatcaatg 2700ggcgtggata gcggtttgac tcacggggat ttccaagtct
ccaccccatt gacgtcaatg 2760ggagtttgtt ttggcaccaa aatcaacggg
actttccaaa atgtcgtaac aactccgccc 2820cattgacgca aatgggcggt
aggcgtgtac ggtgggaggt ctatataagc agagctcgtt 2880tagtgaaccg
gggtctctct ggttagacca gatctgagcc tgggagctct ctggctaact
2940agggaaccca ctgcttaagc ctcaataaag cttgccttga gtgcttcaag
tagtgtgtgc 3000ccgtctgttg tgtgactctg gtaactagag atccctcaga
cccttttagt cagtgtggaa 3060aatctctagc agtggcgccc gaacagggac
ctgaaagcga aagggaaacc agaggagctc 3120tctcgacgca ggactcggct
tgctgaagcg cgcacggcaa gaggcgaggg gcggcgactg 3180gtgagtacgc
caaaaatttt gactagcgga ggctagaagg agagagatgg gtgcgagagc
3240gtcagtatta agcgggggag aattagatcg cgatgggaaa aaattcggtt
aaggccaggg 3300ggaaagaaaa aatataaatt aaaacatata gtatgggcaa
gcagggagct agaacgattc 3360gcagttaatc ctggcctgtt agaaacatca
gaaggctgta gacaaatact gggacagcta 3420caaccatccc ttcagacagg
atcagaagaa cttagatcat tatataatac agtagcaacc 3480ctctattgtg
tgcatcaaag gatagagata aaagacacca aggaagcttt agacaagata
3540gaggaagagc aaaacaaaag taagaccacc gcacagcaag cggccgctga
tcttcagacc 3600tggaggagga gatatgaggg acaattggag aagtgaatta
tataaatata aagtagtaaa 3660aattgaacca ttaggagtag cacccaccaa
ggcaaagaga agagtggtgc agagagaaaa 3720aagagcagtg ggaataggag
ctttgttcct tgggttcttg ggagcagcag gaagcactat 3780gggcgcagcc
tcaatgacgc tgacggtaca ggccagacaa ttattgtctg gtatagtgca
3840gcagcagaac aatttgctga gggctattga ggcgcaacag catctgttgc
aactcacagt 3900ctggggcatc aagcagctcc aggcaagaat cctggctgtg
gaaagatacc taaaggatca 3960acagctcctg gggatttggg gttgctctgg
aaaactcatt tgcaccactg ctgtgccttg 4020gaatgctagt tggagtaata
aatctctgga acagattgga atcacacgac ctggatggag 4080tgggacagag
aaattaacaa ttacacaagc ttaatacact ccttaattga agaatcgcaa
4140aaccagcaag aaaagaatga acaagaatta ttggaattag ataaatgggc
aagtttgtgg 4200aattggttta acataacaaa ttggctgtgg tatataaaat
tattcataat gatagtagga 4260ggcttggtag gtttaagaat agtttttgct
gtactttcta tagtgaatag agttaggcag 4320ggatattcac cattatcgtt
tcagacccac ctcccaaccc cgaggggacc cgacaggccc 4380gaaggaatag
aagaagaagg tggagagaga gacagagaca gatccattcg attagtgaac
4440ggatctcgac ggtatcgata agctaattca caaatggcag tattcatcca
caattttaaa 4500agaaaagggg ggattggggg gtacagtgca ggggaaagaa
tagtagacat aatagcaaca 4560gacatacaaa ctaaagaatt acaaaaacaa
attacaaaaa ttcaaaattt tcgggtttat 4620tacagggaca gcagagatcc
agtttgggaa ttagcttgat cgattagtcc aatttgttaa 4680agacaggata
tcagtggtcc aggctctagt tttgactcaa caatatcacc agctgaagcc
4740tatagagtac gagccataga tagaataaaa gattttattt agtctccaga
aaaagggggg 4800aatgaaagac cccacctgta ggtttggcaa gctaggatca
aggttaggaa cagagagaca 4860gcagaatatg ggccaaacag gatatctgtg
gtaagcagtt cctgccccgg ctcagggcca 4920agaacagttg gaacagcaga
atatgggcca aacaggatat ctgtggtaag cagttcctgc 4980cccggctcag
ggccaagaac agatggtccc cagatgcggt cccgccctca gcagtttcta
5040gagaaccatc agatgtttcc agggtgcccc aaggacctga aatgaccctg
tgccttattt 5100gaactaacca atcagttcgc ttctcgcttc tgttcgcgcg
cttctgctcc ccgagctcaa 5160taaaagagcc cacaacccct cactcggcgc
gatctagatc tcgaatcgaa ttctaccggg 5220taggggaggc gcttttccca
aggcagtctg gagcatgcgc tttagcagcc ccgctggcac 5280ttggcgctac
acaagtggcc tctggcctcg cacacattcc acatccaccg gtaggcgcca
5340accggctccg ttctttggtg gccccttcgc gccaccttct actcctcccc
tagtcaggaa 5400gttccccccc gccccgcagc tcgcgtcgtg caggacgtga
caaatggaag tagcacgtct 5460cactagtctc gtgcagatgg acagcaccgc
tgagcaatgg aagcgggtag gcctttgggg 5520cagcggccaa tagcagcttt
gctccttcgc tttctgggct cagaggctgg gaaggggtgg 5580gtccgggggc
gggctcaggg gcgggctcag gggcggggcg ggcgcccgaa ggtcctccgg
5640aggcccggca ttctcgcacg cttcaaaagc gcacgtctgc cgcgctgttc
tcctcttcct 5700catctccggg cctttcgacc atctagatcc accggtcgcc
accatggtga gcaagggcga 5760ggagctgttc accggggtgg tgcccatcct
ggtcgagctg gacggcgacg taaacggcca 5820caagttcagc gtgtccggcg
agggcgaggg cgatgccacc tacggcaagc tgaccctgaa 5880gttcatctgc
accaccggca agctgcccgt gccctggccc accctcgtga ccaccctgac
5940ctacggcgtg cagtgcttca gccgctaccc cgaccacatg aagcagcacg
acttcttcaa 6000gtccgccatg cccgaaggct acgtccagga gcgcaccatc
ttcttcaagg acgacggcaa 6060ctacaagacc cgcgccgagg tgaagttcga
gggcgacacc ctggtgaacc gcatcgagct 6120gaagggcatc gacttcaagg
aggacggcaa catcctgggg cacaagctgg agtacaacta 6180caacagccac
aacgtctata tcatggccga caagcagaag aacggcatca aggtgaactt
6240caagatccgc cacaacatcg aggacggcag cgtgcagctc gccgaccact
accagcagaa 6300cacccccatc ggcgacggcc ccgtgctgct gcccgacaac
cactacctga gcacccagtc 6360cgccctgagc aaagacccca acgagaagcg
cgatcacatg gtcctgctgg agttcgtgac 6420cgccgccggg atcactctcg
gcatggacga gctgtacaag taaagcggcc aactcgaggg 6480atcccccggg
gtcgactgat caaattcgag ctcggtacct ttaagaccaa tgacttacaa
6540ggcagctgta gatcttagcc actttttaaa agaaaagggg ggactggaag
ggctaattca 6600ctcccaacga agacaagatc tgctttttgc ttgtactggg
tctctctggt tagaccagat 6660ctgagcctgg gagctctctg gctaactagg
gaacccactg cttaagcctc aataaagctt 6720gccttgagtg cttcaagtag
tgtgtgcccg tctgttgtgt gactctggta actagagatc 6780cctcagaccc
ttttagtcag tgtggaaaat ctctagcagt agtagttcat gtcatcttat
6840tattcagtat ttataacttg caaagaaatg aatatcagag agtgagagga
acttgtttat 6900tgcagcttat aatggttaca aataaagcaa tagcatcaca
aatttcacaa ataaagcatt 6960tttttcactg cattctagtt gtggtttgtc
caaactcatc aatgtatctt atcatgtctg 7020gctctagcta tcccgcccct
aactccgccc atcccgcccc taactccgcc cagttccgcc 7080cattctccgc
cccatggctg actaattttt tttatttatg cagaggccga ggccgcctcg
7140gcctctgagc tattccagaa gtagtgagga ggcttttttg gaggcctagg
cttttgcgtc 7200gagacgtacc caattcgccc tatagtgagt cgtattacgc
gcgctcactg gccgtcgttt 7260tacaacgtcg tgactgggaa aaccctggcg
ttacccaact taatcgcctt gcagcacatc 7320cccctttcgc cagctggcgt
aatagcgaag aggcccgcac cgatcgccct tcccaacagt 7380tgcgcagcct
gaatggcgaa tggcgcgacg cgccctgtag cggcgcatta agcgcggcgg
7440gtgtggtggt tacgcgcagc gtgaccgcta cacttgccag cgccctagcg
cccgctcctt 7500tcgctttctt cccttccttt ctcgccacgt tcgccggctt
tccccgtcaa gctctaaatc 7560gggggctccc tttagggttc cgatttagtg
ctttacggca cctcgacccc aaaaaacttg 7620attagggtga tggttcacgt
agtgggccat cgccctgata gacggttttt cgccctttga 7680cgttggagtc
cacgttcttt aatagtggac tcttgttcca aactggaaca acactcaacc
7740ctatctcggt ctattctttt gatttataag ggattttgcc gatttcggcc
tattggttaa 7800aaaatgagct gatttaacaa aaatttaacg cgaattttaa
caaaatatta acgtttacaa 7860tttcc 786519421DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
19agatccagtt tggggatcca aggtcgggca ggaagagggc ctatttccca tgattccttc
60atatttgcat atacgataca aggctgttag agagataatt agaattaatt tgactgtaaa
120cacaaagata ttagtacaaa atacgtgacg tagaaagtaa taatttcttg
ggtagtttgc 180agttttaaaa ttatgtttta aaatggacta tcatatgctt
accgtaactt gaaagtattt 240cgatttcttg gctttatata tcttgtggaa
aggacgaaac accgtcgacc ttgcaatgat 300gtcgtaattt gcgtcttact
ctgttctcag cgacagccag atctgagcct gggagctctc 360tggctgtcag
taagctggta cagaaggttg acgaaaattc ttactgagca agaaattttt 420t
4212012061DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 20taattcgagc tcgcccgaca ttgattattg
actagttatt aatagtaatc aattacgggg 60tcattagttc atagcccata tatggagttc
cgcgttacat aacttacggt aaatggcccg 120cctggctgac cgcccaacga
cccccgccca ttgacgtcaa taatgacgta tgttcccata 180gtaacgccaa
tagggacttt ccattgacgt caatgggtgg agtatttacg gtaaactgcc
240cacttggcag tacatcaagt gtatcatatg ccaagtacgc cccctattga
cgtcaatgac 300ggtaaatggc ccgcctggca ttatgcccag tacatgacct
tatgggactt tcctacttgg 360cagtacatct acgtattagt catcgctatt
accatggtga tgcggttttg gcagtacatc 420aatgggcgtg gatagcggtt
tgactcacgg ggattccaag tctcacccca ttgacgtcaa 480tgggagtttg
ttttggcacc aaaatcaacg ggactttcca aaatgtcgta acaactccgc
540cccattgacg caaatgggcg gtaggcgtgt acggtgggag gtctatataa
gcagagctcg 600tttagtgaac cgtcagatcg cctggagacg ccatccacgc
tgttttgacc tccatagaag 660acaccgggac cgatcctagc ctccgcggcc
gggaacggtg cattggaacg cggattcccc 720gtgccaagag tgacgtaagt
accgcctata gagtctatag gcccaccccc ttggcttctt 780atgcgacgga
tcgatcccgt aataagcttc gaggtccgcg gccggccgcg ttgacgcgca
840cggcagaggc gatggggctg gcgactggtg agagatgggt gcgagagcgt
cagtattaag 900cgggggagaa ttagatcgat gggaaaaaat tcggttaagg
ccagggggaa agaaaaaata 960taaattaaaa catatagtat gggcaagcag
ggagctagaa cgattcgcag ttaatcctgg 1020cctgttagaa acatcagaag
gctgtagaca aatactggga cagctacaac catcccttca 1080gacaggatca
gaagaactta gatcattata taatacagta gcaaccctct attgtgtgca
1140tcaaaggata gagataaaag acaccaagga agctttagac aagatagagg
aagagcaaaa 1200caaaagtaag aaaaaagcac agcaagcagc agctgacaca
ggacacagca atcaggtcag 1260ccaaaattac cctatagtgc agaacatcca
ggggcaaatg gtacatcagg ccatatcacc 1320tagaacttta aatgcatggg
taaaagtagt agaagagaag gctttcagcc cagaagtgat 1380acccatgttt
tcagcattat cagaaggagc caccccacaa gatttaaaca ccatgctaac
1440acagtggggg gacatcaagc agccatgcaa atgttaaaag agaccatcaa
tgaggaagct 1500gcagaatggg atagagtgca tccagtgcat gcagggccta
ttgcaccagg ccagatgaga 1560gaaccaaggg gaagtgacat agcaggaact
actagtaccc ttcaggaaca aataggatgg 1620atgacacata atccacctat
cccagtagga gaaatctata aaagatggat aatcctggga 1680ttaaataaaa
tagtaagaat gtatagccct accagcattc tggacataag acaaggacca
1740aaggaaccct ttagagacta tgtagaccga ttctataaaa ctctaagagc
cgagcaagct 1800tcacaagagg taaaaaattg gatgacagaa accttgttgg
tccaaaatgc gaacccagat 1860tgtaagacta ttttaaaagc attgggacca
ggagcgacac tagaagaaat gatgacagca
1920tgtcagggag tggggggacc cggccataaa gcaagagttt tggctgaagc
aatgagccaa 1980gtaacaaatc cagctaccat aatgatacag aaaggcaatt
ttaggaacca aagaaagact 2040gttaagtgtt tcaattgtgg caaagaaggg
cacatagcca aaaattgcag ggcccctagg 2100aaaagggctg ttggaaatgt
ggaaaggaag gacacccaat gaaagattgt actgagagac 2160aggctatttt
ttagggaaga tctggccttc cacagggaag gccagggaat tttcttcaga
2220gcagaccaga gccaacagcc ccaccagaag agagcttcag gtttggggaa
gagacaacaa 2280ctccctctca gaagcaggag ccgatagaca aggaactgtg
tcctttagct tccctcagat 2340cactctttgg cagcgacccc tcgtcacaat
aaagataggg gggcaattaa aggaagctct 2400attagataca ggagcagatg
atacagtatt agaagaaatg aatttgccag gaagatggaa 2460accaaaaatg
atagggggaa ttggaggttt tatcaaagta ggacagtatg atcagatact
2520catagaaatc tgcggacata aagctatagg tacagtatta gtaggaccta
cacctgtcaa 2580cataattgga agaaatctgt tgactcagat tggctgcact
ttaaattttc ccattagtcc 2640tattgagact gtaccagtaa aattaaagcc
aggaatggat ggcccaaaag ttaaacaatg 2700gccattgaca gaagaaaaaa
taaaagcatt agtagaaatt tgtacagaaa tggaaaagga 2760aggaaaaatt
tcaaaaattg ggcctgaaaa tccatacaat actccagtat ttgccataaa
2820gaaaaaagac agtactaaat ggagaaaatt agtagatttc agagaactta
ataagagaac 2880tcaagatttc tgggaagttc aattaggaat accacatcct
gcagggttaa aacagaaaaa 2940atcagtaaca gtactggatg tgggcgatgc
atatttttca gttcccttag ataaagactt 3000caggaagtat actgcattta
ccatacctag tataaacaat gagnacacca gggnattagn 3060atatcagtac
aatgtgcttc cacagggnat ggaaaggatc accagcaata ttccagtgta
3120gcatgacaaa aatcttagag ccttttagaa aacaaaatcc agacatagtc
atctatcaat 3180acatggatga tttgtatgta ggatctgact tagaaatagg
gcagcataga acaaaaatag 3240aggaactgag acaacatctg ttgaggtggg
gatttaccac accagacaaa aaacatcaga 3300aagaacctcc attcctttgg
atgggttatg aactccatcc tgataaatgg acagtacagc 3360ctatagtgct
gccagaaaag gacagctgga ctgtcaatga catacagaaa ttagtgggaa
3420aattgaattg ggcaagtcag atttatgcag ggattaaagt aaggcaatta
tgtaaacttc 3480ttaggggaac caaagcacta acagaagtag taccactaac
agaagaagca gagctagaac 3540tggcagaaaa cagggagatt ctaaaagaac
cggtacatgg agtgtattat gacccatcaa 3600aagacttaat agcagaaata
cagaagcagg ggcaaggcca atggacatat caaatttatc 3660aagagccatt
taaaaatctg aaaacaggaa aatatgcaag aatgaagggt gcccacacta
3720atgatgtgaa acaattaaca gaggcagtac aaaaaatagc cacagaaagc
atagtaatat 3780ggggaaagac tcctaaattt aaattaccca tacaaaagga
aacatgggaa gcatggtgga 3840cagagtattg gcaagccacc tggattcctg
agtgggagtt tgtcaatacc cctcccttag 3900tgaagttatg gtaccagtta
gagaaagaac ccataatagg agcagaaact ttctatgtag 3960atggggcagc
caatagggaa actaaattag gaaaagcagg atatgtaact gacagaggaa
4020gacaaaaagt tgtcccccta acggacacaa caaatcagaa gactgagtta
caagcaattc 4080atctagcttt gcaggattcg ggattagaag taaacatagt
gacagactca caatatgcat 4140tgggaatcat tcaagcacaa ccagataaga
gtgaatcaga gttagtcagt caaataatag 4200agcagttaat aanaaaagga
aaaagtctac ctggcatggg taccagcaca caaaggaatt 4260ggaggaaatg
aacagtagat aaattggtca gtgctggaat caggaaagta ctatttttag
4320atggaataga taaggcccaa gaagaacatg agaaatatca cagtaattgg
agagcaatgg 4380ctagtgattt taacctacca cctgtagtag caaaagaaat
agtagccagc tgtgataaat 4440gtcagctaaa aggggaagcc atgcatggac
aagtagactg tagcccagga atatggcagc 4500tagattgtac acatttagaa
ggaaaagtta tcttggtagc agttcatgta gccagtggat 4560atatagaagc
agaagtaatt ccagcagaga cagggcaaga aacagcatac ttcctcttaa
4620aattagcagg aagatggcca gtaaaaacag tacatacaga caatggcagc
aatttcacca 4680gtactacagt taaggccgcc tgttggtggg cggggatcag
caggaatttg gcattcccta 4740caatccccaa agtcaaggag taatagaatc
tatgaataaa gaattaaaga aaattatagg 4800acaggtaaga gatcaggctg
aacatcttaa gacagcagta caaatggcag tattcatcca 4860caattttaaa
agaaaagggg ggattggggg gtacagtgca ggggaaagaa tagtagacat
4920aatagcaaca gacatacaaa ctaaagaatt acaaaaacaa attacaaaaa
ttcaaaattt 4980tcgggtttat tacagggaca gcagagatcc agtttggaaa
ggaccagcaa agctcctctg 5040gaaaggtgaa ggggcagtag taatacaaga
taatagtgac ataaaagtag tgccaagaag 5100aaaagcaaag atcatcaggg
attatggaaa acagatggca ggtgatgatt gtgtggcaag 5160tagacaggat
gaggattaac acatggaatt ctgcaacaac tgctgtttat ccatttcaga
5220attgggtgtc gacatagcag aataggcgtt actcgacaga ggagagcaag
aaatggagcc 5280agtagatcct agactagagc cctggaagca tccaggaagt
cagcctaaaa ctgcttgtac 5340caattgctat tgtaaaaagt gttgctttca
ttgccaagtt tgtttcatga caaaagcctt 5400aggcatctcc tatggcagga
agaagcggag acagcgacga agagctcatc agaacagtca 5460gactcatcaa
gcttctctat caaagcagta agtagtacat gtaatgcaac ctataatagt
5520agcaatagta gcattagtag tagcaataat aatagcaata gttgtgtggt
ccatagtaat 5580catagaatat aggaaaatgg ccgctgatct tcagacctgg
aggaggagat atgagggaca 5640attggagaag tgaattatat aaatataaag
tagtaaaaat tgaaccatta ggagtagcac 5700ccaccaaggc aaagagaaga
gtggtgcaga gagaaaaaag agcagtggga ataggagctt 5760tgttccttgg
gttcttggga gcagcaggaa gcactatggg cgcagcgtca atgacgctga
5820cggtacaggc cagacaatta ttgtctggtn tagtgcagca gcagaacaat
ttgctgaggg 5880ctattgaggc gcaacagcat ctgttgcaac tcacagtctg
gggcatcaag cagctccagg 5940caagaatcct ggctgtggaa agatacctaa
aggatcaaca gctcctgggg atttggggtt 6000gctctggaaa actcatttgc
accactgctg tgccttggaa tgctagttgg agtaataaat 6060ctctggaaca
gatttggaat cacacgacct ggatggagtg ggacagagaa attaacaatt
6120acacaagctt aatacactcc ttaattgaag aatcgcaaaa ccagcaagaa
aagaatgaac 6180aagaattatt ggaattagat gaatgggcaa gtttgtggaa
ttggtttaac ataacaaatt 6240ggctgtggta tataaaatta ttcataatga
tagtaggagg cttggtaggt ttaagaatag 6300tttttgctgt actttctata
gtgaatagag ttaggcaggg atattcacca ttatcgtttc 6360agacccacct
cccaaccccg aggggacccg acaggcccga aggaatagaa gaagaaggtg
6420gagagagaga cagagacaga tccattcgat tagtgaacgg atccttggca
cttatctggg 6480acgatctgcg gagcctgtgc ctcttcagct accaccgctt
gagagactta ctcttgattg 6540taacgaggat tgtggaactt ctgggacgca
gggggtggga agccctcaaa tattggtgga 6600atctcctaca atattggagt
caggagctaa agaatagtgc tgttagcttg ctcaatgcca 6660cagccatagc
agtagctgag gggacagata gggttataga agtagtacaa ggagcttgta
6720gagctattcg ccacatacct agaagaataa gacagggctt ggaaaggatt
ttgctataag 6780ctcgaggccg ccccggtgac cttcagacct tggcactgga
ggtggcccgg cagaagcgcg 6840gcatcgtgga tcagtgctgc accagcatct
gctctctcta ccaactggag aactactgca 6900actaggccca ccactaccct
gtccacccct ctgcaatgaa taaaaccttt gaaagagcac 6960tacaagttgt
gtgtacatgc gtgcatgtgc atatgtggtg cggggggaac atgagtgggg
7020ctggctggag tggcgatgat aagctgtcaa acatgagaat taattcttga
agacgaaagg 7080gcctcgtgat acgcctattt ttataggtta atgtcatgat
aataatggtt tcttagtcta 7140gaattaattc cgtgtattct atagtgncac
ctaaatcgta tgtgtatgat acataaggtt 7200atgtattaat tgtagccgcg
ttctaacgac aatatgtaca agcctaattg tgtagcatct 7260ggcttactga
agcagaccct atcatctctc tcgtaaactg ccgtcagagt cggtttggtt
7320ggacgaacct tctgagtttc tggtaacgcc gtcccgcacc cgcacccggn
aaatggtcag 7380cgaaccaatc agcagggtca tcgctagcca gatcctctac
gccggacgca tcgtggccgg 7440catcaccggc gccacaggtg cggttgcatg
gcgcctatat cgccgacatc accgatgggg 7500aagatcgggc tcgccacttc
gggctcatga gcgcttgttt cggcgtgggt atggtggcag 7560gccccgtggc
cgggggactg ttgggcgcca tctccttgca tgcaccattc cttgcggcgg
7620cggtgctcaa cggcctcaac ctactactgg gctgcttcct aatgcaggag
tcgcataagg 7680gagagcgtcg aatggtgcac tctcagtaca atctgctctg
atgccgcata gttaagccag 7740ccccgacacc cgccaacacc cgctgacgcg
ccctgacggg cttgtctgct cccggcatcc 7800gcttacagac aagctgtgac
cgtctccggg agctgcatgt gtcagaggtn ntcaccgtca 7860tcaccgaaac
gcgcgagacg aaagggcctc gtgatacgcc tatttttata ggttaatgtc
7920atgataataa tggtttctta gacgtcaggt ggcacttttc ggggaaatgt
gcgcggaacc 7980cctatttgtt tatttttcta aatacattca aatatgtatc
cgctcatgag acaataaccc 8040tgataaatgc ttcaataata ttgaaaaagg
aagagtatga gtattcaaca tttccgtgtc 8100gcccttattc ccttttttgc
ggcattttgc cttcctgttt ttgctcaccc agaaacgctg 8160gtgaaagtaa
aagatgctga agatcagttg ggtgcacgag tgggttacat cgaactggat
8220ctcaacagcg gtaagatcct tgagagtttt cgccccgaag aacgttttcc
aatgatgagc 8280acttttaaag ttctgctatg tggcgcggta ttatcccgta
ttgacgccgg gcaagagcaa 8340ctcggtcgcc gcatacacta ttctcagaat
gacttggttg agtactcacc agtcacagaa 8400aagcatctta cggatggcat
gacagtaaga gaattatgca gtgctgccat aaccatgagt 8460gataacactg
cggccaactt acttctgaca acgatcggag gaccgaagga gctaaccgct
8520tttttgcaca acatggggga tcatgtaact cgccttgatc gttgggaacc
ggagctgaat 8580gaagccatac caaacgacga gcgtgacacc acgatgcctg
tagcaatggc aacaacgttg 8640cgcaaactat taactggcga actacttact
ctagcttccc ggcaacaatt aatagactgg 8700atggaggcgg ataaagttgc
aggaccactt ctgcgctcgg cccttccggc tggctggttt 8760attgctgata
aatctggagc cggtgagcgt gggtctcgcg gtatcattgc agcactgggg
8820ccagatggta agccctcccg tatcgtagtt atctacacga cggggagtca
ggcaactatg 8880gatgaacgaa atagacagat cgctgagata ggtgcctcac
tgattaagca ttggtaactg 8940tcagaccaag tttactcata tatactttag
attgatttaa aacttcattt ttaatttaaa 9000aggatctagg tgaagatcct
ttttgataat ctcatgacca aaatccctta acgtgagttt 9060tcgttccact
gagcgtcaga ccccgtagaa aagatcaaag gatcttcttg agatcctttt
9120tttctgcgcg taatctgctg cttgcaaaca aaaaaaccac cgctaccagc
ggtggtttgt 9180ttgccggatc aagagctacc aactcttttt ccgaaggtaa
ctggcttcag cagagcgcag 9240ataccaaata ctgtccttct agtgtagccg
tagttaggcc accacttcaa gaactctgta 9300gcaccgccta catacctcgc
tctgctaatc ctgttaccag tggctgctgc cagtggcgat 9360aagtcgtgtc
ttaccgggtt ggactcaaga cgatagttac cggataaggc gcagcggtcg
9420ggctgaacgg ggggttcgtg cacacagccc agcttggagc gaacgaccta
caccgaactg 9480agatacctac agcgtgagca ttgagaaagc gccacgcttc
ccgaagggag aaaggcggac 9540aggtatccgg taagcggcag ggtcggaaca
ggagagcgca cgagggagct tccaggggga 9600aacgcctggt atctttatag
tcctgtcggg tttcgccacc tctgacttga gcgtcgattt 9660ttgtgatgct
cgtcaggggg gcggagccta tggaaaaacg ccagcaacgc ggccttttta
9720cggttcctgg ccttttgctg gccttttgct cacatgttct ttcctgcgtt
atcccctgat 9780tctgtggata accgtattac cgcctttgag tgagctgata
ccgctcgccg cagccgaacg 9840accgagcgca gcgagtcagt gagcgaggaa
gcggaagagc gcccaatacg caaaccgcct 9900ctccccgcgc gttggccgat
tcattaatgc agctgtggaa tgtgtgtcag ttagggtgtg 9960gaaagtcccc
aggctcccca gcaggcagaa gtatgcaaag catgcatctc aattagtcag
10020caaccaggtg tggaaagtcc ccaggctccc cagcaggcag aagtatgcaa
agcatgcatc 10080tcaattagtc agcaaccata gtcccgcccc taactccgcc
catcccgccc ctaactccgc 10140ccagttccgc ccattctccg ccccatggct
gactaatttt ttttatttat gcagaggccg 10200aggccgcctc ggcctctgag
ctattccaga agtagtgagg aggctttttt ggaggcctag 10260gcttttgcaa
aaagcttgga cacaagacag gcttgcgaga tatgtttgag aataccactt
10320tatcccgcgt cagggagagg cagtgcgtaa aaagacgcgg actcatgtga
aatactggtt 10380tttagtgcgc cagatctcta taatctcgcg caacctattt
tcccctcgaa cactttttaa 10440gccgtagata aacaggctgg gacacttcac
atgagcgaaa aatacatcgt cacctgggac 10500atgttgcaga tccatgcacg
taaactcgca agccgactga tgccttctga acaatggaaa 10560ggcattattg
ccgtaagccg tggcggtctg taccgggtgc gttactggcg cgtgaactgg
10620gtattcgtca tgtcgatacc gtttgtattt ccagctacga tcacgacaac
cagcgcgagc 10680ttaaagtgct gaaacgcgca gaaggcgatg gcgaaggctt
catcgttatt gatgacctgg 10740tggataccgg tggtactgcg gttgcgattc
gtgaaatgta tccaaaagcg cactttgtca 10800ccatcttcgc aaaaccggct
ggtcgtccgc tggttgatga ctatgttgtt gatatcccgc 10860aagatacctg
gattgaacag ccgtgggata tgggcgtcgt attcgtcccg ccaatctccg
10920gtcgctaatc ttttcaacgc ctggcactgc cgggcgttgt tctttttaac
ttcaggcggg 10980ttacaatagt ttccagtaag tattctggag gctgcatcca
tgacacaggc aaacctgagc 11040gaaaccctgt tcaaaccccg ctttaaacat
cctgaaacct cgacgctagt ccgccgcttt 11100aatcacggcg cacaaccgcc
tgtgcagtcg gcccttgatg gtaaaaccat ccctcactgg 11160tatcgcatga
ttaaccgtct gatgtggatc tggcgcggca ttgacccacg cgaaatcctc
11220gacgtccagg cacgtattgt gatgagcgat gccgaacgta ccgacgatga
tttatacgat 11280acggtgattg gctaccgtgg cggcaactgg atttatgagt
gggccccgga tctttgtgaa 11340ggaaccttac ttctgtggtg tgacataatt
ggacaaacta cctacagaga tttaaagctc 11400taaggtaaat ataaaatttt
taagtgtata atgtgttaaa ctactgattc taattgtttg 11460tgtattttag
attccaacct atggaactga tgaatgggag cagtggtgga atgcctttaa
11520tgaggaaaac ctgttttgct cagaagaaat gccatctagt gatgatgagg
ctactgctga 11580ctctcaacat tctactcctc caaaaaagaa gagaaaggta
gaagacccca aggactttcc 11640ttcagaattg ctaagttttt tgagtcatgc
tgtgtttagt aatagaactc ttgcttgctt 11700tgctatttac accacaaagg
aaaaagctgc actgctatac aagaaaatta tggaaaaata 11760ttctgtaacc
tttataagta ggcataacag ttataatcat aacatactgt tttttcttac
11820tccacacagg catagagtgt ctgctattaa taactatgct caaaaattgt
gtacctttag 11880ctttttaatt tgtaaagggg ttaataagga atatttgatg
tatagtgcct tgactagaga 11940tcataatcag ccataccaca tttgtagagg
ttttacttgc tttaaaaaac ctccccacac 12000ctccccctga acctgaaaca
taaaatgaat gcaattgttg ttgttgggct gcagtatgaa 12060t
1206121195DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 21atgtccgcag caccactggt cacggcaatg
tgtttgctcg gaaatgtgag cttcccatgc 60gaccgcccgc ccacatgcta tacccgcgaa
ccttccagag ccctcgacat ccttgaagag 120aacgtgaacc atgaggccta
cgataccctg ctcaatgcca tattgcggtg cggatcgtct 180ggcagaagca aaaga
195221653DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 22agcgtcactg acgactttac cctgaccagc
ccctacttgg gcacatgctc gtactgccac 60catactgaac cgtgcttcag ccctgttaag
atcgagcagg tctgggacga agcggacgat 120aacaccatac gcatacagac
ttccgcccag tttggatacg accatagcgg agcagcaagc 180gcaaacaagt
accgctacat gtcgcttaag caggtaacca acgtagacaa caaattcaac
240aaagaacaac aaaacgcgtt ctatgagatc ttacatttac ctaacttaaa
cgaagaacaa 300cgaaacgcct tcatccaaag tttaaaagat gacccaagcc
aaagcgctaa ccttttagca 360gaagctaaaa agctaaatga tgctcaggcg
ccgaaagtag acaacaaatt caacaaagaa 420caacaaaacg cgttctatga
gatcttacat ttacctaact taaacgaaga acaacgaaac 480gccttcatcc
aaagtttaaa agatgaccca agccaaagcg ctaacctttt agcagaagct
540aaaaagctaa atgatgctca ggcgccgaaa gtagacgcga attcgagctc
ggtacccgta 600accaccgtta aagaaggcac catggatgac atcaagatta
gcacctcagg accgtgtaga 660aggcttagct acaaaggata ctttctcctc
gcaaaatgcc ctccagggga cagcgtaacg 720gttagcatag tgagtagcaa
ctcagcaacg tcatgtacac tggcccgcaa gataaaacca 780aaattcgtgg
gacgggaaaa atatgatcta cctcccgttc acggtaaaaa aattccttgc
840acagtgtacg accgtctgaa agaaacaact gcaggctaca tcactatgca
caggccggga 900ccgcacgctt atacatccta cctggaagaa tcatcaggga
aagtttacgc aaagccgcca 960tctgggaaga acattacgta tgagtgcaag
tgcggcgact acaagaccgg aaccgtttcg 1020acccgcaccg aaatcactgg
ttgcaccgcc atcaagcagt gcgtcgccta taagagcgac 1080caaacgaagt
gggtcttcaa ctcaccggac ttgatcagac atgacgacca cacggcccaa
1140gggaaattgc atttgccttt caagttgatc ccgagtacct gcatggtccc
tgttgcccac 1200gcgccgaatg taatacatgg ctttaaacac atcagcctcc
aattagatac agaccacttg 1260acattgctca ccaccaggag actaggggca
aacccggaac caaccactga atggatcgtc 1320ggaaagacgg tcagaaactt
caccgtcgac cgagatggcc tggaatacat atggggaaat 1380catgagccag
tgagggtcta tgcccaagag tcagcaccag gagaccctca cggatggcca
1440cacgaaatag tacagcatta ctaccatcgc catcctgtgt acaccatctt
agccgtcgca 1500tcagctaccg tggcgatgat gattggcgta actgttgcag
tgttatgtgc ctgtaaagcg 1560cgccgtgagt gcctgacgcc atacgccctg
gccccaaacg ccgtaatccc aacttcgctg 1620gcactcttgt gctgcgttag
gtcggccaat gct 165323165DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 23gaaacgttca
ccgagaccat gagttacttg tggtcgaaca gtcagccgtt cttctgggtc 60cagttgtgca
tacctttggc cgctttcatc gttctaatgc gctgctgctc ctgctgcctg
120ccttttttag tggttgccgg cgcctacctg gcgaaggtag acgcc
165241320DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 24tacgaacatg cgaccactgt tccaaatgtg
ccacagatac cgtataaggc acttgttgaa 60agggcagggt atgccccgct caatttggag
atcactgtca tgtcctcgga ggttttgcct 120tccaccaacc aagagtacat
tacctgcaaa ttcaccactg tggtcccctc cccaaaaatc 180aaatgctgcg
gctccttgga atgtcagccg gccgctcatg cagactatac ctgcaaggtc
240ttcggagggg tctacccctt tatgtgggga ggagcgcaat gtttttgcga
cagtgagaac 300agccagatga gtgaggcgta cgtcgaattg tcagcagatt
gcgcgtctga ccacgcgcag 360gcgattaagg tgcacactgc cgcgatgaaa
gtaggactgc gtatagtgta cgggaacact 420accagtttcc tagatgtgta
cgtgaacgga gtcacaccag gaacgtctaa agacttgaaa 480gtcatagctg
gaccaatttc agcatcattt acgccattcg atcataaggt cgttatccat
540cgcggcctgg tgtacaacta tgacttcccg gaatatggag cgatgaaacc
aggagcgttt 600ggagacattc aagctacctc cttgactagc aaggatctca
tcgccagcac agacattagg 660ctactcaagc cttccgccaa gaatgtgcat
gtcccgtaca cgcaggccgc atcaggattt 720gagatgtgga aaaacaactc
aggccgccca ttgcaggaaa ccgcaccttt cgggtgtaag 780attgcagtaa
atccgctccg agcggtggac tgttcatacg ggaacattcc catttctatt
840gacatcccga acgctgcctt tatcaggaca tcagatgcac cactggtctc
aacagtcaaa 900tgtgaagtca gtgagtgcac ttattcagca gacttcgacg
ggatggccac cctgcagtat 960gtatccgacc gcgaaggtca atgccccgta
cattcgcatt cgagcacagc aactctccaa 1020gagtcgacag tacatgtcct
ggagaaagga gcggtgacag tacactttag caccgcgagt 1080ccacaggcga
actttatcgt atcgctgtgt gggaagaaga caacatgcaa tgcagaatgt
1140aaaccaccag ctgaccatat cgtgagcacc ccgcacaaaa atgaccaaga
atttcaagcc 1200gccatctcaa aaacatcatg gagttggctg tttgcccttt
tcggcggcgc ctcgtcgcta 1260ttaattatag gacttatgat ttttgcttgc
agcatgatgc tgactagcac acgaagatga 1320256612DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
25caggtggcac ttttcgggga aatgtgcgcg gaacccctat ttgtttattt ttctaaatac
60attcaaatat gtatccgctc atgagacaat aaccctgata aatgcttcaa taatattgaa
120aaaggaagag tatgagtatt caacatttcc gtgtcgccct tattcccttt
tttgcggcat 180tttgccttcc tgtttttgct cacccagaaa cgctggtgaa
agtaaaagat gctgaagatc 240agttgggtgc acgagtgggt tacatcgaac
tggatctcaa cagcggtaag atccttgaga 300gttttcgccc cgaagaacgt
tttccaatga tgagcacttt taaagttctg ctatgtggcg 360cggtattatc
ccgtattgac gccgggcaag agcaactcgg tcgccgcata cactattctc
420agaatgactt ggttgagtac tcaccagtca cagaaaagca tcttacggat
ggcatgacag 480taagagaatt atgcagtgct gccataacca tgagtgataa
cactgcggcc aacttacttc 540tgacaacgat cggaggaccg aaggagctaa
ccgctttttt gcacaacatg ggggatcatg 600taactcgcct tgatcgttgg
gaaccggagc tgaatgaagc cataccaaac gacgagcgtg 660acaccacgat
gcctgtagca atggcaacaa cgttgcgcaa actattaact ggcgaactac
720ttactctagc ttcccggcaa caattaatag actggatgga ggcggataaa
gttgcaggac 780cacttctgcg ctcggccctt ccggctggct ggtttattgc
tgataaatct ggagccggtg 840agcgtgggtc tcgcggtatc attgcagcac
tggggccaga tggtaagccc tcccgtatcg 900tagttatcta cacgacgggg
agtcaggcaa ctatggatga acgaaataga cagatcgctg 960agataggtgc
ctcactgatt aagcattggt
aactgtcaga ccaagtttac tcatatatac 1020tttagattga tttaaaactt
catttttaat ttaaaaggat ctaggtgaag atcctttttg 1080ataatctcat
gaccaaaatc ccttaacgtg agttttcgtt ccactgagcg tcagaccccg
1140tagaaaagat caaaggatct tcttgagatc ctttttttct gcgcgtaatc
tgctgcttgc 1200aaacaaaaaa accaccgcta ccagcggtgg tttgtttgcc
ggatcaagag ctaccaactc 1260tttttccgaa ggtaactggc ttcagcagag
cgcagatacc aaatactgtc cttctagtgt 1320agccgtagtt aggccaccac
ttcaagaact ctgtagcacc gcctacatac ctcgctctgc 1380taatcctgtt
accagtggct gctgccagtg gcgataagtc gtgtcttacc gggttggact
1440caagacgata gttaccggat aaggcgcagc ggtcgggctg aacggggggt
tcgtgcacac 1500agcccagctt ggagcgaacg acctacaccg aactgagata
cctacagcgt gagctatgag 1560aaagcgccac gcttcccgaa gggagaaagg
cggacaggta tccggtaagc ggcagggtcg 1620gaacaggaga gcgcacgagg
gagcttccag ggggaaacgc ctggtatctt tatagtcctg 1680tcgggtttcg
ccacctctga cttgagcgtc gatttttgtg atgctcgtca ggggggcgga
1740gcctatggaa aaacgccagc aacgcggcct ttttacggtt cctggccttt
tgctggcctt 1800ttgctcacat gttctttcct gcgttatccc ctgattctgt
ggataaccgt attaccgcct 1860ttgagtgagc tgataccgct cgccgcagcc
gaacgaccga gcgcagcgag tcagtgagcg 1920aggaagcgga agagcgccca
atacgcaaac cgcctctccc cgcgcgttgg ccgattcatt 1980aatgcagctg
gcacgacagg tttcccgact ggaaagcggg cagtgagcgc aacgcaatta
2040atgtgagtta gctcactcat taggcacccc aggctttaca ctttatgctt
ccggctcgta 2100tgttgtgtgg aattgtgagc ggataacaat ttcacacagg
aaacagctat gaccatgatt 2160acgccaagcg cgcaattaac cctcactaaa
gggaacaaaa gctggagctg caagcttggc 2220cattgcatac gttgtatcca
tatcataata tgtacattta tattggctca tgtccaacat 2280taccgccatg
ttgacattga ttattgacta gttattaata gtaatcaatt acggggtcat
2340tagttcatag cccatatatg gagttccgcg ttacataact tacggtaaat
ggcccgcctg 2400gctgaccgcc caacgacccc cgcccattga cgtcaataat
gacgtatgtt cccatagtaa 2460cgccaatagg gactttccat tgacgtcaat
gggtggagta tttacggtaa actgcccact 2520tggcagtaca tcaagtgtat
catatgccaa gtacgccccc tattgacgtc aatgacggta 2580aatggcccgc
ctggcattat gcccagtaca tgaccttatg ggactttcct acttggcagt
2640acatctacgt attagtcatc gctattacca tggtgatgcg gttttggcag
tacatcaatg 2700ggcgtggata gcggtttgac tcacggggat ttccaagtct
ccaccccatt gacgtcaatg 2760ggagtttgtt ttggcaccaa aatcaacggg
actttccaaa atgtcgtaac aactccgccc 2820cattgacgca aatgggcggt
aggcgtgtac ggtgggaggt ctatataagc agagctcgtt 2880tagtgaaccg
gggtctctct ggttagacca gatctgagcc tgggagctct ctggctaact
2940agggaaccca ctgcttaagc ctcaataaag cttgccttga gtgcttcaag
tagtgtgtgc 3000ccgtctgttg tgtgactctg gtaactagag atccctcaga
cccttttagt cagtgtggaa 3060aatctctagc agtggcgccc gaacagggac
ctgaaagcga aagggaaacc agaggagctc 3120tctcgacgca ggactcggct
tgctgaagcg cgcacggcaa gaggcgaggg gcggcgactg 3180gtgagtacgc
caaaaatttt gactagcgga ggctagaagg agagagatgg gtgcgagagc
3240gtcagtatta agcgggggag aattagatcg cgatgggaaa aaattcggtt
aaggccaggg 3300ggaaagaaaa aatataaatt aaaacatata gtatgggcaa
gcagggagct agaacgattc 3360gcagttaatc ctggcctgtt agaaacatca
gaaggctgta gacaaatact gggacagcta 3420caaccatccc ttcagacagg
atcagaagaa cttagatcat tatataatac agtagcaacc 3480ctctattgtg
tgcatcaaag gatagagata aaagacacca aggaagcttt agacaagata
3540gaggaagagc aaaacaaaag taagaccacc gcacagcaag cggccgctga
tcttcagacc 3600tggaggagga gatatgaggg acaattggag aagtgaatta
tataaatata aagtagtaaa 3660aattgaacca ttaggagtag cacccaccaa
ggcaaagaga agagtggtgc agagagaaaa 3720aagagcagtg ggaataggag
ctttgttcct tgggttcttg ggagcagcag gaagcactat 3780gggcgcagcc
tcaatgacgc tgacggtaca ggccagacaa ttattgtctg gtatagtgca
3840gcagcagaac aatttgctga gggctattga ggcgcaacag catctgttgc
aactcacagt 3900ctggggcatc aagcagctcc aggcaagaat cctggctgtg
gaaagatacc taaaggatca 3960acagctcctg gggatttggg gttgctctgg
aaaactcatt tgcaccactg ctgtgccttg 4020gaatgctagt tggagtaata
aatctctgga acagattgga atcacacgac ctggatggag 4080tgggacagag
aaattaacaa ttacacaagc ttaatacact ccttaattga agaatcgcaa
4140aaccagcaag aaaagaatga acaagaatta ttggaattag ataaatgggc
aagtttgtgg 4200aattggttta acataacaaa ttggctgtgg tatataaaat
tattcataat gatagtagga 4260ggcttggtag gtttaagaat agtttttgct
gtactttcta tagtgaatag agttaggcag 4320ggatattcac cattatcgtt
tcagacccac ctcccaaccc cgaggggacc cgacaggccc 4380gaaggaatag
aagaagaagg tggagagaga gacagagaca gatccattcg attagtgaac
4440ggatctcgac ggtatcgata agctaattca caaatggcag tattcatcca
caattttaaa 4500agaaaagggg ggattggggg gtacagtgca ggggaaagaa
tagtagacat aatagcaaca 4560gacatacaaa ctaaagaatt acaaaaacaa
attacaaaaa ttcaaaattt tcgggtttat 4620tacagggaca gcagagatcc
agtttgggaa ttagcttgat cgattagtcc aatttgttaa 4680agacaggata
tcagtggtcc aggctctagt tttgactcaa caatatcacc agctgaagcc
4740tatagagtac gagccataga tagaataaaa gattttattt agtctccaga
aaaagggggg 4800aatgaaagac cccacctgta ggtttggcaa gctaggatca
aggttaggaa cagagagaca 4860gcagaatatg ggccaaacag gatatctgtg
gtaagcagtt cctgccccgg ctcagggcca 4920agaacagttg gaacagcaga
atatgggcca aacaggatat ctgtggtaag cagttcctgc 4980cccggctcag
ggccaagaac agatggtccc cagatgcggt cccgccctca gcagtttcta
5040gagaaccatc agatgtttcc agggtgcccc aaggacctga aatgaccctg
tgccttattt 5100gaactaacca atcagttcgc ttctcgcttc tgttcgcgcg
cttctgctcc ccgagctcaa 5160taaaagagcc cacaacccct cactcggcgc
gatctagatc tcgaatcgaa ttcgttaacc 5220tcgagggatc ccccggggtc
gactgatcaa attcgagctc ggtaccttta agaccaatga 5280cttacaaggc
agctgtagat cttagccact ttttaaaaga aaagggggga ctggaagggc
5340taattcactc ccaacgaaga caagatctgc tttttgcttg tactgggtct
ctctggttag 5400accagatctg agcctgggag ctctctggct aactagggaa
cccactgctt aagcctcaat 5460aaagcttgcc ttgagtgctt caagtagtgt
gtgcccgtct gttgtgtgac tctggtaact 5520agagatccct cagacccttt
tagtcagtgt ggaaaatctc tagcagtagt agttcatgtc 5580atcttattat
tcagtattta taacttgcaa agaaatgaat atcagagagt gagaggaact
5640tgtttattgc agcttataat ggttacaaat aaagcaatag catcacaaat
ttcacaaata 5700aagcattttt ttcactgcat tctagttgtg gtttgtccaa
actcatcaat gtatcttatc 5760atgtctggct ctagctatcc cgcccctaac
tccgcccatc ccgcccctaa ctccgcccag 5820ttccgcccat tctccgcccc
atggctgact aatttttttt atttatgcag aggccgaggc 5880cgcctcggcc
tctgagctat tccagaagta gtgaggaggc ttttttggag gcctaggctt
5940ttgcgtcgag acgtacccaa ttcgccctat agtgagtcgt attacgcgcg
ctcactggcc 6000gtcgttttac aacgtcgtga ctgggaaaac cctggcgtta
cccaacttaa tcgccttgca 6060gcacatcccc ctttcgccag ctggcgtaat
agcgaagagg cccgcaccga tcgcccttcc 6120caacagttgc gcagcctgaa
tggcgaatgg cgcgacgcgc cctgtagcgg cgcattaagc 6180gcggcgggtg
tggtggttac gcgcagcgtg accgctacac ttgccagcgc cctagcgccc
6240gctcctttcg ctttcttccc ttcctttctc gccacgttcg ccggctttcc
ccgtcaagct 6300ctaaatcggg ggctcccttt agggttccga tttagtgctt
tacggcacct cgaccccaaa 6360aaacttgatt agggtgatgg ttcacgtagt
gggccatcgc cctgatagac ggtttttcgc 6420cctttgacgt tggagtccac
gttctttaat agtggactct tgttccaaac tggaacaaca 6480ctcaacccta
tctcggtcta ttcttttgat ttataaggga ttttgccgat ttcggcctat
6540tggttaaaaa atgagctgat ttaacaaaaa tttaacgcga attttaacaa
aatattaacg 6600tttacaattt cc 6612269061DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
26catggccaag ttgaccagtg ccgttccggt gctcaccgcg cgcgacgtcg ccggagcggt
60cgagttctgg accgaccggc tcgggttctc ccgggacttc gtggaggacg acttcgccgg
120tgtggtccgg gacgacgtga ccctgttcat cagcgcggtc caggaccagg
tggtgccgga 180caacaccctg gcctgggtgt gggtgcgcgg cctggacgag
ctgtacgccg agtggtcgga 240ggtcgtgtcc acgaacttcc gggacgcctc
cgggccggcc atgaccgaga tcggcgagca 300gccgtggggg cgggagttcg
ccctgcgcga cccggccggc aactgcgtgc acttcgtggc 360cgaggagcag
gactgacacg tgctacgaga tttcgattcc accgccgcct tctatgaaag
420gttgggcttc ggaatcgttt tccgggacgc cggctggatg atcctccagc
gcggggatct 480catgctggag ttcttcgccc accccaactt gtttattgca
gcttataatg gttacaaata 540aagcaatagc atcacaaatt tcacaaataa
agcatttttt tcactgcatt ctagttgtgg 600tttgtccaaa ctcatcaatg
tatcttatca tgtctgtata ccgtcgacct ctagctagag 660cttggcgtaa
tcatggtcat agctgtttcc tgtgtgaaat tgttatccgc tcacaattcc
720acacaacata cgagccggaa gcataaagtg taaagcctgg ggtgcctaat
gagtgagcta 780actcacatta attgcgttgc gctcactgcc cgctttccag
tcgggaaacc tgtcgtgcca 840gctgcattaa tgaatcggcc aacgcgcggg
gagaggcggt ttgcgtattg ggcgctcttc 900cgcttcctcg ctcactgact
cgctgcgctc ggtcgttcgg ctgcggcgag cggtatcagc 960tcactcaaag
gcggtaatac ggttatccac agaatcaggg gataacgcag gaaagaacat
1020gtgagcaaaa ggccagcaaa aggccaggaa ccgtaaaaag gccgcgttgc
tggcgttttt 1080ccataggctc cgcccccctg acgagcatca caaaaatcga
cgctcaagtc agaggtggcg 1140aaacccgaca ggactataaa gataccaggc
gtttccccct ggaagctccc tcgtgcgctc 1200tcctgttccg accctgccgc
ttaccggata cctgtccgcc tttctccctt cgggaagcgt 1260ggcgctttct
caatgctcac gctgtaggta tctcagttcg gtgtaggtcg ttcgctccaa
1320gctgggctgt gtgcacgaac cccccgttca gcccgaccgc tgcgccttat
ccggtaacta 1380tcgtcttgag tccaacccgg taagacacga cttatcgcca
ctggcagcag ccactggtaa 1440caggattagc agagcgaggt atgtaggcgg
tgctacagag ttcttgaagt ggtggcctaa 1500ctacggctac actagaagga
cagtatttgg tatctgcgct ctgctgaagc cagttacctt 1560cggaaaaaga
gttggtagct cttgatccgg caaacaaacc accgctggta gcggtggttt
1620ttttgtttgc aagcagcaga ttacgcgcag aaaaaaagga tctcaagaag
atcctttgat 1680cttttctacg gggtctgacg ctcagtggaa cgaaaactca
cgttaaggga ttttggtcat 1740gagattatca aaaaggatct tcacctagat
ccttttaaat taaaaatgaa gttttaaatc 1800aatctaaagt atatatgagt
aaacttggtc tgacagttac caatgcttaa tcagtgaggc 1860acctatctca
gcgatctgtc tatttcgttc atccatagtt gcctgactcc ccgtcgtgta
1920gataactacg atacgggagg gcttaccatc tggccccagt gctgcaatga
taccgcgaga 1980cccacgctca ccggctccag atttatcagc aataaaccag
ccagccggaa gggccgagcg 2040cagaagtggt cctgcaactt tatccgcctc
catccagtct attaattgtt gccgggaagc 2100tagagtaagt agttcgccag
ttaatagttt gcgcaacgtt gttgccattg ctacaggcat 2160cgtggtgtca
cgctcgtcgt ttggtatggc ttcattcagc tccggttccc aacgatcaag
2220gcgagttaca tgatccccca tgttgtgcaa aaaagcggtt agctccttcg
gtcctccgat 2280cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg
gttatggcag cactgcataa 2340ttctcttact gtcatgccat ccgtaagatg
cttttctgtg actggtgagt actcaaccaa 2400gtcattctga gaatagtgta
tgcggcgacc gagttgctct tgcccggcgt caatacggga 2460taataccgcg
ccacatagca gaactttaaa agtgctcatc attggaaaac gttcttcggg
2520gcgaaaactc tcaaggatct taccgctgtt gagatccagt tcgatgtaac
ccactcgtgc 2580acccaactga tcttcagcat cttttacttt caccagcgtt
tctgggtgag caaaaacagg 2640aaggcaaaat gccgcaaaaa agggaataag
ggcgacacgg aaatgttgaa tactcatact 2700cttccttttt caatattatt
gaagcattta tcagggttat tgtctcatga gcggatacat 2760atttgaatgt
atttagaaaa ataaacaaat aggggttccg cgcacatttc cccgaaaagt
2820gccacctgac gtcgacggat cgggagatct cccgatcccc tatggtcgac
tctcagtaca 2880atctgctctg atgccgcata gttaagccag tatctgctcc
ctgcttgtgt gttggaggtc 2940gctgagtagt gcgcgagcaa aatttaagct
acaacaaggc aaggcttgac cgacaattgc 3000atgaagaatc tgcttagggt
taggcgtttt gcgctgcttc gcgatgtacg ggccagatat 3060acgcgttgac
attgattatt gactagttat taatagtaat caattacggg gtcattagtt
3120catagcccat atatggagtt ccgcgttaca taacttacgg taaatggccc
gcctggctga 3180ccgcccaacg acccccgccc attgacgtca ataatgacgt
atgttcccat agtaacgcca 3240atagggactt tccattgacg tcaatgggtg
gactatttac ggtaaactgc ccacttggca 3300gtacatcaag tgtatcatat
gccaagtacg ccccctattg acgtcaatga cggtaaatgg 3360cccgcctggc
attatgccca gtacatgacc ttatgggact ttcctacttg gcagtacatc
3420tacgtattag tcatcgctat taccatggtg atgcggtttt ggcagtacat
caatgggcgt 3480ggatagcggt ttgactcacg gggatttcca agtctccacc
ccattgacgt caatgggagt 3540ttgttttggc accaaaatca acgggacttt
ccaaaatgtc gtaacaactc cgccccattg 3600acgcaaatgg gcggtaggcg
tgtacggtgg gaggtctata taagcagagc tctctggcta 3660actagagaac
ccactgctta ctggcttatc gaaattaata cgactcacta tagggagacc
3720caagctggct agcgtttaaa cttaagctta tgaatagagg attctttaac
atgctcggcc 3780gccgcccctt cccggccccc actgccatgt ggaggccgcg
gagaaggagg caggcggccc 3840cgatgcctgc ccgcaacggg ctggcttctc
aaatccagca actgaccaca gccgtcagtg 3900ccctagtcat tggacaggca
actagacctc aacccccacg tccacgcccg ccaccgcgcc 3960agaagaagca
ggcgcccaag caaccaccga agccgaagaa accaaaaacg caggagaaga
4020agaagaagca acctgcaaaa cccaaacccg gaaagagaca gcgcatggca
cttaagttgg 4080aggccgacag attgttcgac gtcaagaacg aggacggaga
tgtcatcggg cacgcactgg 4140ccatggaagg aaaggtaatg aaacctctgc
acgtgaaagg aaccatcgac caccctgtgc 4200tatcaaagct caaatttacc
aagtcgtcag catacgacat ggagttcgca cagttgccag 4260tcaacatgag
aagtgaggca ttcacctaca ccagtgaaca ccccgaagga ttctataact
4320ggcaccacgg agcggtgcag tatagtggag gtagatttac catccctcgc
ggagtaggag 4380gcagaggaga cagcggtcgt ccgatcatgg ataactccgg
tcgggttgtc gcgatagtcc 4440tcggtggagc tgatgaagga acacgaactg
ccctttcggt cgtcacctgg aatagtaaag 4500ggaagacaat taagacgacc
ccggaaggga cagaagagtg gtccgcagca ccactggtca 4560cggcaatgtg
tttgctcgga aatgtgagct tcccatgcga ccgcccgccc acatgctata
4620cccgcgaacc ttccagagcc ctcgacatcc ttgaagagaa cgtgaaccat
gaggcctacg 4680ataccctgct caatgccata ttgcggtgcg gatcgtctgg
cagaagcaaa agaagcgtca 4740ctgacgactt taccctgacc agcccctact
tgggcacatg ctcgtactgc caccatactg 4800aaccgtgctt cagccctgtt
aagatcgagc aggtctggga cgaagcggac gataacacca 4860tacgcataca
gacttccgcc cagtttggat acgaccatag cggagcagca agcgcaaaca
4920agtaccgcta catgtcgctt aagcaggtaa ccgacaacaa attcaacaaa
gaacaacaaa 4980acgcgttcta tgagatctta catttaccta acttaaacga
agaacaacga aacgccttca 5040tccaaagttt aaaagatgac ccaagccaaa
gcgctaacct tttagcagaa gctaaaaagc 5100taaatgatgc tcaggcgccg
aaagtagaca acaaattcaa caaagaacaa caaaacgcgt 5160tctatgagat
cttacattta cctaacttaa acgaagaaca acgaaacgcc ttcatccaaa
5220gtttaaaaga tgacccaagc caaagcgcta accttttagc agaagctaaa
aagctaaatg 5280atgctcaggc gccgaaagta gacgcgaatt cgagctcggt
acccggggat ccggtaacca 5340ccgttaaaga aggcaccatg gatgacatca
agattagcac ctcaggaccg tgtagaaggc 5400ttagctacaa aggatacttt
ctcctcgcaa aatgccctcc aggggacagc gtaacggtta 5460gcatagtgag
tagcaactca gcaacgtcat gtacactggc ccgcaagata aaaccaaaat
5520tcgtgggacg ggaaaaatat gatctacctc ccgttcacgg taaaaaaatt
ccttgcacag 5580tgtacgaccg tctgaaagaa acaactgcag gctacatcac
tatgcacagg ccgggaccgc 5640acgcttatac atcctacctg gaagaatcat
cagggaaagt ttacgcaaag ccgccatctg 5700ggaagaacat tacgtatgag
tgcaagtgcg gcgactacaa gaccggaacc gtttcgaccc 5760gcaccgaaat
cactggttgc accgccatca agcagtgcgt cgcctataag agcgaccaaa
5820cgaagtgggt cttcaactca ccggacttga tcagacatga cgaccacacg
gcccaaggga 5880aattgcattt gcctttcaag ttgatcccga gtacctgcat
ggtccctgtt gcccacgcgc 5940cgaatgtaat acatggcttt aaacacatca
gcctccaatt agatacagac cacttgacat 6000tgctcaccac caggagacta
ggggcaaacc cggaaccaac cactgaatgg atcgtcggaa 6060agacggtcag
aaacttcacc gtcgaccgag atggcctgga atacatatgg ggaaatcatg
6120agccagtgag ggtctatgcc caagagtcag caccaggaga ccctcacgga
tggccacacg 6180aaatagtaca gcattactac catcgccatc ctgtgtacac
catcttagcc gtcgcatcag 6240ctaccgtggc gatgatgatt ggcgtaactg
ttgcagtgtt atgtgcctgt aaagcgcgcc 6300gtgagtgcct gacgccatac
gccctggccc caaacgccgt aatcccaact tcgctggcac 6360tcttgtgctg
cgttaggtcg gccaatgctg aaacgttcac cgagaccatg agttacttgt
6420ggtcgaacag tcagccgttc ttctgggtcc agttgtgcat acctttggcc
gctttcatcg 6480ttctaatgcg ctgctgctcc tgctgcctgc cttttttagt
ggttgccggc gcctacctgg 6540cgaaggtaga cgcctacgaa catgcgacca
ctgttccaaa tgtgccacag ataccgtata 6600aggcacttgt tgaaagggca
gggtatgccc cgctcaattt ggagatcact gtcatgtcct 6660cggaggtttt
gccttccacc aaccaagagt acattacctg caaattcacc actgtggtcc
6720cctccccaaa aatcaaatgc tgcggctcct tggaatgtca gccggccgct
catgcagact 6780atacctgcaa ggtcttcgga ggggtctacc cctttatgtg
gggaggagcg caatgttttt 6840gcgacagtga gaacagccag atgagtgagg
cgtacgtcga attgtcagca gattgcgcgt 6900ctgaccacgc gcaggcgatt
aaggtgcaca ctgccgcgat gaaagtagga ctgcgtatag 6960tgtacgggaa
cactaccagt ttcctagatg tgtacgtgaa cggagtcaca ccaggaacgt
7020ctaaagactt gaaagtcata gctggaccaa tttcagcatc atttacgcca
ttcgatcata 7080aggtcgttat ccatcgcggc ctggtgtaca actatgactt
cccggaatat ggagcgatga 7140aaccaggagc gtttggagac attcaagcta
cctccttgac tagcaaggat ctcatcgcca 7200gcacagacat taggctactc
aagccttccg ccaagaatgt gcatgtcccg tacacgcagg 7260ccgcatcagg
atttgagatg tggaaaaaca actcaggccg cccattgcag gaaaccgcac
7320ctttcgggtg taagattgca gtaaatccgc tccgagcggt ggactgttca
tacgggaaca 7380ttcccatttc tattgacatc ccgaacgctg cctttatcag
gacatcagat gcaccactgg 7440tctcaacagt caaatgtgaa gtcagtgagt
gcacttattc agcagacttc gacgggatgg 7500ccaccctgca gtatgtatcc
gaccgcgaag gtcaatgccc cgtacattcg cattcgagca 7560cagcaactct
ccaagagtcg acagtacatg tcctggagaa aggagcggtg acagtacact
7620ttagcaccgc gagtccacag gcgaacttta tcgtatcgct gtgtgggaag
aagacaacat 7680gcaatgcaga atgtaaacca ccagctgacc atatcgtgag
caccccgcac aaaaatgacc 7740aagaatttca agccgccatc tcaaaaacat
catggagttg gctgtttgcc cttttcggcg 7800gcgcctcgtc gctattaatt
ataggactta tgatttttgc ttgcagcatg atgctgacta 7860gcacacgaag
atgacgggcc cgtttaaacc cgctgatcag cctcgactgt gccttctagt
7920tgccagccat ctgttgtttg cccctccccc gtgccttcct tgaccctgga
aggtgccact 7980cccactgtcc tttcctaata aaatgaggaa attgcatcgc
attgtctgag taggtgtcat 8040tctattctgg ggggtggggt ggggcaggac
agcaaggggg aggattggga agacaatagc 8100aggcatgctg gggatgcggt
gggctctatg gcttctgagg cggaaagaac cagctggggc 8160tctagggggt
atccccacgc gccctgtagc ggcgcattaa gcgcggcggg tgtggtggtt
8220acgcgcagcg tgaccgctac acttgccagc gccctagcgc ccgctccttt
cgctttcttc 8280ccttcctttc tcgccacgtt cgccggcttt ccccgtcaag
ctctaaatcg gggcatccct 8340ttagggttcc gatttagtgc tttacggcac
ctcgacccca aaaaacttga ttagggtgat 8400ggttcacgta gtgggccatc
gccctgatag acggtttttc gccctttgac gttggagtcc 8460acgttcttta
atagtggact cttgttccaa actggaacaa cactcaaccc tatctcggtc
8520tattcttttg atttataagg gattttgggg atttcggcct attggttaaa
aaatgagctg 8580atttaacaaa aatttaacgc gaattaattc tgtggaatgt
gtgtcagtta gggtgtggaa 8640agtccccagg ctccccaggc aggcagaagt
atgcaaagca tgcatctcaa ttagtcagca 8700accaggtgtg gaaagtcccc
aggctcccca gcaggcagaa gtatgcaaag catgcatctc 8760aattagtcag
caaccatagt cccgccccta actccgccca tcccgcccct aactccgccc
8820agttccgccc attctccgcc ccatggctga ctaatttttt ttatttatgc
agaggccgag 8880gccgcctctg cctctgagct attccagaag tagtgaggag
gcttttttgg aggcctaggc 8940ttttgcaaaa agctcccggg agcttgtata
tccattttcg gatctgatca gcacgtgttg 9000acaattaatc atcggcatag
tatatcggca tagtataata cgacaaggtg aggaactaaa 9060c 9061
* * * * *
References