WO2012170431A2 - Systèmes perfectionnés de commutation génique - Google Patents

Systèmes perfectionnés de commutation génique Download PDF

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WO2012170431A2
WO2012170431A2 PCT/US2012/040932 US2012040932W WO2012170431A2 WO 2012170431 A2 WO2012170431 A2 WO 2012170431A2 US 2012040932 W US2012040932 W US 2012040932W WO 2012170431 A2 WO2012170431 A2 WO 2012170431A2
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virus
promoter
cell
vector
mammalian
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WO2012170431A3 (fr
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Robert H. KUTNER
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Bluebird Bio Inc
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Bluebird Bio Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2740/00—Reverse transcribing RNA viruses
    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/10051—Methods of production or purification of viral material
    • C12N2740/10052—Methods of production or purification of viral material relating to complementing cells and packaging systems for producing virus or viral particles
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2740/00—Reverse transcribing RNA viruses
    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/15011—Lentivirus, not HIV, e.g. FIV, SIV
    • C12N2740/15041—Use of virus, viral particle or viral elements as a vector
    • C12N2740/15043—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2740/00—Reverse transcribing RNA viruses
    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/15011—Lentivirus, not HIV, e.g. FIV, SIV
    • C12N2740/15051—Methods of production or purification of viral material
    • C12N2740/15052—Methods of production or purification of viral material relating to complementing cells and packaging systems for producing virus or viral particles
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/36011—Togaviridae
    • C12N2770/36111—Alphavirus, e.g. Sindbis virus, VEE, EEE, WEE, Semliki
    • C12N2770/36122—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes

Definitions

  • the present invention generally relates to improved molecular switch systems and improved retroviral packaging cells and viral particle production.
  • the present invention comprises retroviral vectors that have increased control over gene expression.
  • Neurologix, Inc. announced positive results in a Phase 2 trial of its investigational gene therapy for advanced Parkinson's disease (PD), NLX-P101. Study participants who received NLX-P101 experienced statistically significant and clinically meaningful improvements in off-medication motor scores compared to control subjects who received sham surgery. In the trial, this benefit was seen at one month and continued virtually unchanged throughout the six month blinded study period. The results also demonstrated a positive safety profile for NLX-P101, with no serious adverse events related to the gene therapy or surgical procedure reported.
  • PD Parkinson's disease
  • the therapeutic DNA introduced into target cells must remain functional and the cells containing the therapeutic DNA must be long-lived and stable. Problems with integrating therapeutic DNA into the genome and the rapidly dividing nature of many cells prevent gene therapy from many times achieving any long-term benefits. Patients will have to undergo multiple rounds of gene therapy. Anytime a foreign object is introduced into human tissues, the immune system is designed to attack the invader. The risk of stimulating the immune system in a way that reduces gene therapy effectiveness is always a potential risk. Furthermore, the immune system's enhanced response to invaders it has seen before makes it difficult for gene therapy to be repeated in patients.
  • the present invention provides a mammalian packaging cell comprising a cell having a first polynucleotide comprising a first promoter operable in mammalian cells operably linked to the reverse complement of one or more viral structural genes selected from the group consisting of gag, pol, and env; operably linked to an RNA dependent RNA polymerase (RDRP) promoter.
  • RDRP RNA dependent RNA polymerase
  • the single stranded RNA virus is a minus-strand single stranded RNA virus.
  • the first polynucleotide is stably integrated into the cell genome.
  • the single stranded RNA virus is a plus- strand single stranded RNA virus.
  • the present invention provides a mammalian packaging cell comprising a cell having a first polynucleotide comprising a first promoter operable in mammalian cells operably linked to an RNA dependent RNA polymerase promoter of a single stranded RNA virus operably linked to one or more viral structural genes selected from the group consisting of gag, pol, and env; and an RNA polymerase recognition site (CSE).
  • the single stranded RNA virus is a plus-strand single stranded RNA virus.
  • the plus-strand single stranded RNA virus is a narnavirus or an alphavirus.
  • the first polynucleotide is stably integrated into the cell genome.
  • the alphavirus is selected from the group consisting of: Aura virus, Bebaru virus, Cabassou virus, Chikungunya virus, Eastern equine encephalomyelitis virus, Fort Morgan virus, Getah virus, Kyzylagach virus, Mayaro virus, Middleburg virus, Mucambo virus, Ndumu virus, Pixuna virus, Ross River virus, Semliki Forest virus, Sindbis virus, Tonate virus, Triniti virus, Una virus, Venezuelan equine encephalomyelitis virus, Western equine encephalomyelitis virus, Whataroa virus, and Y-62-33 virus.
  • the first polynucleotide comprises any one of a gag gene, a pol gene, or an env gene.
  • the first polynucleotide comprises any two of a gag gene, a pol gene, or an env gene.
  • the first polynucleotide comprises a gag gene, a pol gene, and an env gene.
  • the cell comprises a second polynucleotide comprising a second promoter operably linked to a viral RNA dependent RNA polymerase promoter operably linked to a viral structural gene not encoded by the first polynucleotide and a CSE.
  • the mammalian packaging cell comprises a second polynucleotide comprising a second promoter operably linked to the reverse complement of a viral structural gene not encoded by the first polynucleotide; operably linked to a viral RNA dependent RNA polymerase promoter.
  • the mammalian packaging cell comprises a third polynucleotide comprising a third promoter operably linked to a viral RNA dependent RNA polymerase promoter operably linked to a viral structural gene not encoded by the first or second polynucleotides and a CSE.
  • the mammalian packaging cell comprises a third polynucleotide comprising a third promoter operably linked to the reverse complement of a viral structural gene not encoded by the first or second polynucleotides; operably linked to a viral RNA dependent RNA polymerase promoter.
  • the first, second, third, and fourth promoters are independently selected from the group consisting of: an constitutive promoter and an inducible promoter.
  • the first promoter is an inducible promoter and one or more of the second, third, and fourth promoters are the same inducible promoter or a different inducible promoter.
  • the first promoter is an constitutive promoter and one or more of the second, third, and fourth promoters are the same constitutive promoter or a different constitutive promoter.
  • the cell further comprises a polynucleotide comprising a constitutive or inducible promoter operably linked to one or more isolated non-structural protein genes of the single-stranded RNA virus.
  • the constitutive promoter is selected from the group consisting of: a cytomegalovirus immediate early gene promoter (CMV), an elongation factor 1 alpha promoter (EFl-a), a phosphoglycerate kinase- 1 promoter (PGK), a ubiquitin-C promoter (UBQ-C), a cytomegalovirus enhancer/chicken beta- actin promoter (CAG), polyoma enhancer/herpes simplex thymidine kinase promoter (MCI), a beta actin promoter ( ⁇ -ACT), and a simian virus 40 promoter (SV40).
  • CMV cytomegalovirus immediate early gene promoter
  • EFl-a an elongation factor 1 alpha promoter
  • PGK phosphoglycerate kinase- 1 promoter
  • UQ-C ubiquitin-C promoter
  • CAG cytomegalovirus enhancer/chicken beta- actin promoter
  • the inducible promoter is selected from the group consisting of: a tetracycline responsive promoter, an ecdysone responsive promoter, a cumate responsive promoter, a glucocorticoid responsive promoter, and estrogen responsive promoter, and an RU-486 responsive promoter.
  • the cell is contacted with a composition comprising one or more isolated non-structural protein polypeptides of the single-stranded RNA virus.
  • the one or more non-structural protein polypeptides comprise a cell permeable peptide domain.
  • the cell permeable peptide domain is selected from the group consisting of: RKKRRQRRR, KKRRQRRR, RKKRRQRR, RRRRRRR, KKKK KKK , RQIKIWFQNRRMKWK , RQIKIWFQNRRMKSKK, RQIKIWFQNKRAKIKK, RQIKIWFQNRRMKWKK, and
  • the one or more viral structural genes are independently isolated from a virus selected from the group consisting of: human immunodeficiency virus type 1 (HIV-1), human immunodeficiency virus type 2 (HIV-
  • visna virus a virus that has a visna virus, caprine arthritis-encephalitis virus (CAEV), equine infectious anemia virus (EIAV), feline immunodeficiency virus (FIV), bovine immune deficiency virus
  • CAEV caprine arthritis-encephalitis virus
  • EIAV equine infectious anemia virus
  • FV feline immunodeficiency virus
  • the gag and pol viral structural genes are independently selected from the group consisting of: human immunodeficiency virus type 1 (HIV-1), human immunodeficiency virus type 2 (HIV-2), visna virus, caprine arthritis-encephalitis virus (CAEV), equine infectious anemia virus (EIAV), feline immunodeficiency virus (FIV), bovine immune deficiency virus (BIV), and simian immunodeficiency virus (SIV).
  • the wherein the pol viral structural gene is isolated from the caprine arthritis-encephalitis virus (CAEV).
  • CAEV caprine arthritis-encephalitis virus
  • the wherein the env viral structural gene encodes an envelope polypeptide selected from group consisting of FIV, HIV,
  • VSV VSV
  • MoMLV MoMLV
  • GALV GALV
  • JSRV LCMV
  • Marburg virus Mokola virus
  • Ebola virus Rabies virus
  • Ross River Virus Sendai virus
  • foul plague virus influenza virus
  • influenza virus and
  • the cell is selected from the group consisting of: CHO, BHK, MDCK, 10T1/2, WEHI cells, COS, BSC 1, BSC 40, BMT 10, VERO, W138, MRC5, A549, HT1080, 293, 293T, B-50, 3T3, NIH3T3, HepG2, Saos-2, Huh7, HeLa cells W163, HeLa, Vera, 211, and 211A.
  • the present invention provides a mammalian packaging cell comprising:
  • the present invention provides a mammalian packaging cell comprising a cell having a first polynucleotide comprising a first promoter operable in mammalian cells operably linked to the reverse complement one or more viral structural genes selected from the group consisting of gag, pol, and env; operably linked to an alphavirus 26S subgenomic promoter.
  • the cell further comprises a polynucleotide comprising a constitutive or inducible promoter operably linked to one or more alphavirus non-structural protein genes.
  • the cell is contacted with a composition comprising one or more alphavirus non- structural protein polypeptides.
  • the one or more non-structural protein polypeptides comprise a cell permeable peptide domain.
  • the cell permeable peptide domain is selected from the group consisting of: RKKRRQRRR, KKRRQRRR, RKKRRQRR, RRRRRRRRR, KKKK KKK , RQIKIWFQNRRMKWKK,
  • RQIKIWFQNRRMKSKK RQIKIWFQNKRAKIKK, RQIKIWFQNRRMKWKK, and RVIRVWFQNKRCKDKK.
  • the one or more non-structural proteins is selected from the group consisting of: NSP1, NSP2, NSP3, and NSP4.
  • the one or more non-structural proteins are NSP2 and NSP4.
  • the non- structural protein is NSP4.
  • the present invention provides a producer cell comprising a mammalian packaging cell according to any of the preceding packaging cells, wherein the cell is contacted with a composition comprising one or more nonstructural proteins of the single-stranded RNA virus or, wherein the cell comprises a polynucleotide comprising a constitutive or inducible promoter operably linked to one or more non-structural genes isolated from the single-stranded RNA virus; and a transfer vector comprising a replication defective lentiviral genome, a packaging signal, and a mammalian promoter operably linked to a mammalian polypeptide; wherein the mammalian cell is cultured for a time sufficient to package the lentiviral genome and produce lentiviral particles.
  • the present invention provides a producer cell comprising the mammalian packaging cell according to any of the preceding packaging cells, wherein the cell is contacted with a composition comprising one or more nonstructural proteins of the alphavirus or, wherein the cell comprises a polynucleotide comprising a constitutive or inducible promoter operably linked to one or more nonstructural genes isolated from the alphavirus; and a transfer vector comprising a replication defective lentiviral genome, a packaging signal, and a mammalian promoter operably linked to a mammalian polypeptide; wherein the mammalian cell is cultured for a time sufficient to package the lentiviral genome and produce lentiviral particles.
  • the present invention provides a method of producing a lentiviral particle comprising culturing a mammalian cell that expresses lentiviral gag and pol genes, a heterologous envelope gene, wherein expression of one or more of the gag, pol, and env genes is dependent upon expression of one or more non-structural proteins of a single stranded R A virus in the cell; introducing a polynucleotide into the mammalian cell, the polynucleotide comprising a replication defective lentiviral genome; and culturing the mammalian cell for a time sufficient to package the lentiviral genome and produce lentiviral particles.
  • the present invention provides a lentiviral vector comprising: a 5' LTR; a packaging signal, a promoter operative in mammalian cells; an RNA dependent RNA polymerase promoter of a single stranded RNA virus operably linked to a polynucleotide encoding a mammalian polypeptide; and a 3' LTR.
  • the present invention provides a lentiviral vector comprising a 5' LTR; packaging signal; a mammalian promoter; the reverse complement sequence of a polynucleotide encoding a mammalian polypeptide operably linked to an RNA dependent RNA polymerase promoter of a single stranded RNA virus; and a 3' LTR.
  • the single stranded RNA virus is a plus-strandor minus-strand single stranded RNA virus.
  • the present invention provides a lentiviral vector comprising a 5' LTR; packaging signal; a mammalian promoter; an RNA dependent RNA polymerase promoter of a single stranded RNA virus operably linked to a polynucleotide encoding a mammalian polypeptide; an RNA polymerase recognition site (CSE); and
  • the single stranded RNA virus is a plus- strand single stranded RNA virus.
  • the RNA dependent RNA polymerase promoter comprises the alphavirus 26S subgenomic promoter.
  • the U3 region of the 5' LTR comprises a heterologous transcriptional regulatory element.
  • the heterologous transcriptional regulatory element is selected from the group consisting of: a cytomegalovirus enhancer, a cytomegalovirus promoter, a cytomegalovirus enhancer and promoter, a Rous sarcoma virus enhancer, a Rous sarcoma virus promoter, and a Rous sarcoma virus enhancer and promoter.
  • the promoter operative in mammalian cells is selected from the group consisting of: a ubiquitous promoter, a tissue specific promoter, and an inducible promoter.
  • the ubiquitous promoter is selected from the group consisting of: a cytomegalovirus immediate early gene promoter (CMV), an elongation factor 1 alpha promoter (EFl-a), a phosphoglycerate kinase- 1 promoter (PGK), a ubiquitin-C promoter (UBQ-C), a cytomegalovirus enhancer/chicken beta- actin promoter (CAG), polyoma enhancer/herpes simplex thymidine kinase promoter (MCI), a beta actin promoter ( ⁇ -ACT), and a simian virus 40 promoter (SV40).
  • CMV cytomegalovirus immediate early gene promoter
  • EFl-a an elongation factor 1 alpha promoter
  • PGK phosphoglycerate kinase- 1 promoter
  • UQ-C ubiquitin-C promoter
  • CAG cytomegalovirus enhancer/chicken beta- actin promoter
  • MCI
  • the tissue specific promoter expresses the polynucleotide encoding the mammalian polypeptide in ectodermal cells, endodermal cells, mesodermal cells, or mesenchymal cells.
  • the inducible promoter is selected from the group consisting of: a tetracycline responsive promoter, an ecdysone responsive promoter, a cumate responsive promoter, a glucocorticoid responsive promoter, and estrogen responsive promoter, and an RU-486 promoter.
  • the lentivirus is selected from the group consisting of: human immunodeficiency virus type 1 (HIV-1), human
  • HIV-2 immunodeficiency virus type 2
  • CAEV caprine arthritis-encephalitis virus
  • EIAV equine infectious anemia virus
  • FV feline immunodeficiency virus
  • BIV bovine immune deficiency virus
  • SIV simian immunodeficiency virus
  • the alphavirus is selected from the group consisting of: Aura virus, Bebaru virus, Cabassou virus, Chikungunya virus, Eastern equine encephalomyelitis virus, Fort Morgan virus, Getah virus, Kyzylagach virus, Mayaro virus, Middleburg virus, Mucambo virus, Ndumu virus, Pixuna virus, Ross River virus, Semliki Forest virus, Sindbis virus, Tonate virus, Triniti virus, Una virus, Venezuelan equine encephalomyelitis virus, Western equine encephalomyelitis virus, Whataroa virus, and Y-62-33 virus.
  • the mammalian polypeptide is the mammalian polypeptide is adrenoleukodystrophy protein (ABCD1). In other particular embodiments, the mammalian polypeptide is ⁇ -globin.
  • one or more nucleotides of the U3 region of the 3 * LTR are deleted.
  • a vector comprises one or more vector sequences selected from the group consisting of: a central polypurine tract and the central termination sequence (cPPT/CTS), a woodchuck hepatitis virus
  • WPRE posttranscriptional regulatory element
  • HPRE hepatitis B virus posttranscriptional regulatory element
  • mammalian polyadenylation sequence 3' of the 3' R region WPRE
  • WPRE posttranscriptional regulatory element
  • HPRE hepatitis B virus posttranscriptional regulatory element
  • a vector comprises one or more recombinase recognition sites selected from the group consisting of: LoxP, Lox511 , Lox5171,
  • the present invention contemplates, in part, inventive retroviral vector systems that are useful in developing improved gene switches and regulatable viral particle packaging cell lines that produce high viral titers. Retroviral transfer vectors and transfer vector systems that provide increased control and/or amplification of gene expression in transduced mammalian cells are also provided. Further, the present invention contemplates, in part, single transfer vector constructs, binary retroviral transfer vector systems, and polypeptide compositions used in combination with transfer vectors. Improved methods of gene therapy are also provided.
  • the term "about” or “approximately” refers to a quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length that varies by as much as 15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1% to a reference quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length.
  • the term "about” or “approximately” refers a range of quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length ⁇ 15%, ⁇ 10%, ⁇ 9%, ⁇ 8%, ⁇ 7%, ⁇ 6%, ⁇ 5%, ⁇ 4%, ⁇ 3%, ⁇ 2%>, or ⁇ 1%) about a reference quantity, level, value, number, frequency, percentage, dimension, size, amount, weight or length.
  • polynucleotide or “nucleic acid” refers to messenger RNA (mR A), R A, genomic RNA (gRNA), plus strand RNA (RNA(+)), minus strand RNA
  • RNA(-) genomic DNA
  • cDNA complementary DNA
  • Polynucleotides refer to polymeric form of nucleotides of at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 40, at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, at least 1000, at least 5000, at least 10000, or at least 15000 or more nucleotides in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide.
  • Polynucleotides include single and double stranded polynucleotides.
  • polynucleotides of the invention include polynucleotides or variants having at least about 65%, 70%, 75%>, 85%>, 90%>, 95%>, 98%o, or 99%o nucleotide identity thereto.
  • polynucleotide variant and “variant” and the like refer to polynucleotides displaying substantial sequence identity with a reference polynucleotide sequence or polynucleotides that hybridize with a reference sequence under stringent conditions that are defined hereinafter. These terms also encompass polynucleotides that are distinguished from a reference polynucleotide by the addition, deletion or substitution of at least one nucleotide. Accordingly, the terms
  • polynucleotide variant and “variant” include polynucleotides in which one or more nucleotides have been added or deleted, or replaced with different nucleotides.
  • certain alterations inclusive of mutations, additions, deletions and substitutions can be made to a reference polynucleotide whereby the altered polynucleotide retains the biological function or activity of the reference polynucleotide.
  • sequence identity or, for example, comprising a “sequence 50%> identical to,” as used herein, refer to the extent that sequences are identical on a nucleotide-by-nucleotide basis or an amino acid-by-amino acid basis over a window of comparison.
  • a "percentage of sequence identity” may be calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g., A, T, C, G, I) or the identical amino acid residue (e.g., Ala, Pro, Ser, Thr, Gly, Val, Leu, He, Phe, Tyr, Trp, Lys, Arg, His, Asp, Glu, Asn, Gin, Cys and Met) occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison (i.e., the window size), and multiplying the result by 100 to yield the percentage of sequence identity.
  • the identical nucleic acid base e.g., A, T, C, G, I
  • the identical amino acid residue e.g., Ala, Pro, Ser, Thr, Gly, Val, Leu, He, Phe, Tyr, Trp, Lys, Arg,
  • nucleotides and polypeptides having at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to any of the reference sequences described herein, typically where the polypeptide variant maintains at least one biological activity of the reference polypeptide.
  • references to describe sequence relationships between two or more polynucleotides or polypeptides include “reference sequence,” “comparison window,” “sequence identity,” “percentage of sequence identity,” and “substantial identity”.
  • a “reference sequence” is at least 12 but frequently 15 to 18 and often at least 25 monomer units, inclusive of nucleotides and amino acid residues, in length.
  • two polynucleotides may each comprise (1) a sequence (i.e., only a portion of the complete polynucleotide sequence) that is similar between the two polynucleotides, and (2) a sequence that is divergent between the two polynucleotides
  • sequence comparisons between two (or more) polynucleotides are typically performed by comparing sequences of the two polynucleotides over a "comparison window" to identify and compare local regions of sequence similarity.
  • a “comparison window” refers to a conceptual segment of at least 6 contiguous positions, usually about 50 to about 100, more usually about 100 to about 150 in which a sequence is compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
  • the comparison window may comprise additions or deletions (i.e., gaps) of about 20%> or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences.
  • Optimal alignment of sequences for aligning a comparison window may be conducted by computerized implementations of algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Drive Madison, WI, USA) or by inspection and the best alignment (i.e., resulting in the highest percentage homology over the comparison window) generated by any of the various methods selected.
  • GAP Garnier et al.
  • BESTFIT Pearson FASTA
  • FASTA Pearson's Alignment of sequences
  • TFASTA Pearson's Alignin
  • isolated means material that is substantially or essentially free from components that normally accompany it in its native state.
  • isolated polynucleotide refers to a polynucleotide that has been purified from the sequences which flank it in a naturally-occurring state, e.g., a DNA fragment that has been removed from the sequences that are normally adjacent to the fragment.
  • Polynucleotide sequences can be annotated in the 5' to 3' orientation or the 3' to 5' orientation.
  • the 5' to 3' strand is designated the “sense,” “plus,” or “coding” strand because its sequence is identical to the sequence of the premessenger (premRNA) [except for uracil (U) in RNA, instead of thymine (T) in DNA].
  • premRNA premessenger
  • the complementary 3' to 5' strand which is the strand transcribed by the RNA polymerase is designated as "template,” “antisense,” “minus,” or “non-coding” strand.
  • reverse orientation refers to a 5' to 3' sequence written in the 3' to 5' orientation or a 3' to 5' sequence written in the 5' to 3' orientation.
  • reverse orientation of a minus-strand RDRP promoter is the 3' to 5' sequence of the promoter on the minus-strand written in the 5' to 3' orientation on the plus-strand.
  • a transcribed mRNA may comprise a non- functional or inoperable RDRP promoter or subgenomic promoter in the 5' to 3' orientation because it is in the reverse orientation; but the same mRNA can also be used as a minus-strand template because the RDRP or subgenomic promoter is operable or functional in the 3' to 5' orientation.
  • RNA virus In virology, the genome of an RNA virus can be said to be either positive-sense, also known as a "plus-strand,” or negative-sense, also known as a "minus-strand.” In this context, the terms sense and strand can be used
  • Positive-sense (5' to 3') viral RNA signifies that a particular viral RNA sequence may be directly translated into the desired viral proteins. Therefore, in positive-sense RNA viruses, the viral RNA genome can be considered viral mRNA, and can be immediately translated by the host cell. Unlike negative-sense RNA, positive-sense RNA is of the same sense as mRNA. Negative-sense (3' to 5') viral RNA is complementary to the viral mRNA and thus must be converted to positive- sense RNA by an RNA dependent RNA polymerase prior to translation.
  • Negative- sense RNA (like DNA) has a polynucleotide sequence complementary to the mRNA that it encodes. Like DNA, this RNA is not translated into protein directly. Instead, it must first be transcribed into a positive-sense RNA that acts as an mRNA.
  • complementary and complementarity refer to polynucleotides (i.e., a sequence of nucleotides) related by the base-pairing rules.
  • a strand is complementary to another in that the base pairs between them are non- covalently connected via two or three hydrogen bonds.
  • adenine (A) bases complement thymine (T) bases and vice versa
  • guanine (G) bases complement cytosine (C) bases and vice versa.
  • RNA it is the same except that adenine (A) bases complement uracil (U) bases instead of thymine (T) bases.
  • Complementarity can be "partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules. Or, there can be “complete” or “total” complementarity between the nucleic acids.
  • the degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands.
  • the complementary strand of the DNA sequence 5' A G T C A T G 3' is 3' T C A G T A C 5'.
  • the latter sequence is often written as the reverse complement with the 5' end on the left and the 3' end on the right, 5' C A T G A C T 3'.
  • a sequence that is equal to its reverse complement is said to be a palindromic sequence.
  • polynucleotides are provided by this invention that encode at least about 5, 10, 25, 50, 100, 150, 200, 250, 300, 350, 400, 500, 1000 or more contiguous amino acid residues of a polypeptide of the invention, as well as all intermediate lengths.
  • intermediate lengths means any length between the quoted values, such as 6, 7, 8, 9, etc., 101, 102, 103, etc.; 151, 152, 153, etc.; 201, 202, 203, etc.
  • Polynucleotides include a polynucleotide-of-interest.
  • polynucleotide-of-interest refers to the polynucleotide, e.g., a polynucleotide encoding a polypeptide ⁇ i.e., a polypeptide-of-interest), inserted into an expression vector that is desired to be expressed.
  • the polynucleotide-of- interest encodes a polypeptide that provides a therapeutic effect in the treatment or prevention of a disease or disorder, which may be referred to as a "therapeutic polypeptide.”
  • Polynucleotides-of-interest, and polypeptides encoded therefrom include both polynucleotides that encode wild-type polypeptides, as well as functional variants and fragments thereof.
  • a functional variant has at least 80%, at least 90%>, at least 95%>, or at least 99%> identity to a corresponding wild-type reference polynucleotide or polypeptide sequence.
  • a functional variant or fragment has at least 50%, at least 60%, at least 70%, at least 80%, or at least 90%) of a biological activity of a corresponding wild-type polypeptide.
  • the polynucleotide-of-interest encodes a polypeptide which provides a therapeutic function for the treatment of a hemoglobinopathy.
  • nucleotide sequences that encode a polypeptide, or fragment of variant thereof, as described herein. Some of these polynucleotides bear minimal homology to the nucleotide sequence of any native gene. Nonetheless, polynucleotides that vary due to differences in codon usage are specifically contemplated by the present invention, for example polynucleotides that are optimized for human and/or primate codon selection. Further, alleles of the genes comprising the polynucleotide sequences provided herein may also be used. Alleles are endogenous genes that are altered as a result of one or more mutations, such as deletions, additions and/or substitutions of nucleotides.
  • the polynucleotide-of-interest comprises an inhibitory nucleic acid sequence including, but not limited to: an siRNA, an miR A, an shRNA, and a ribozyme.
  • RNA short interfering RNA
  • siRNA short polynucleotide sequence that mediates a process of sequence-specific post- transcriptional gene silencing, translational inhibition, transcriptional inhibition, or epigenetic RNAi in animals (Zamore et ah, 2000, Cell, 101, 25-33; Fire et ah, 1998, Nature, 391, 806; Hamilton et al, 1999, Science, 286, 950-951; Lin et al, 1999, Nature, 402, 128-129; Sharp, 1999, Genes & Dev., 13, 139-141; and Strauss, 1999, Science, 286, 886).
  • a repressor, or RNAi oligonucleotide is single stranded. In other embodiments, the repressor, or RNAi oligonucleotide, is double stranded. Certain embodiments may also employ short-interfering RNAs (siRNA). In certain embodiments, the first strand of the double-stranded
  • oligonucleotide contains two more nucleoside residues than the second strand.
  • the first strand and the second strand have the same number of nucleosides; however, the first and second strands are offset such that the two terminal nucleosides on the first and second strands are not paired with a residue on the complimentary strand.
  • the two nucleosides that are not paired are thymidine resides.
  • the siRNA should include a region of sufficient homology to the target gene, and be of sufficient length in terms of nucleotides, such that the siRNA, or a fragment thereof, can mediate down regulation of the target gene.
  • an siRNA includes a region which is at least partially complementary to the target RNA.
  • the mismatches are most tolerated in the terminal regions, and if present are preferably in a terminal region or regions, e.g., within 6, 5, 4, or 3 nucleotides of the 5' and/or 3' terminus.
  • the sense strand need only be sufficiently complementary with the antisense strand to maintain the overall double-strand character of the molecule.
  • an siRNA may be modified or include nucleoside analogs.
  • Single stranded regions of an siRNA may be modified or include nucleoside analogs, e.g., the unpaired region or regions of a hairpin structure, e.g., a region which links two complementary regions, can have modifications or nucleoside analogs.
  • Modification to stabilize one or more 3'- or 5'-terminus of an siRNA, e.g., against exonucleases, or to favor the antisense siRNA agent to enter into RISC are also useful.
  • Modifications can include C3 (or C6, C7, CI 2) amino linkers, thiol linkers, carboxyl linkers, non- nucleotidic spacers (C3, C6, C9, CI 2, abasic, triethylene glycol, hexaethylene glycol), special biotin or fluorescein reagents that come as phosphoramidites and that have another DMT-protected hydroxyl group, allowing multiple couplings during RNA synthesis.
  • Each strand of an siRNA can be equal to or less than 30, 25, 24, 23, 22, 21, or 20 nucleotides in length.
  • the strand is preferably at least 19 nucleotides in length.
  • each strand can be between 21 and 25 nucleotides in length.
  • Preferred siRNAs have a duplex region of 17, 18, 19, 29, 21, 22, 23, 24, or 25 nucleotide pairs, and one or more overhangs of 2-3 nucleotides, preferably one or two 3' overhangs, of 2- 3 nucleotides.
  • miRNA refers to small non-coding RNAs of 20-22 nucleotides, typically excised from -70 nucleotide foldback RNA precursor structures known as pre-miRNAs. miRNAs negatively regulate their targets in one of two ways depending on the degree of complementarity between the miRNA and the target. First, miRNAs that bind with perfect or nearly perfect complementarity to protein-coding mRNA sequences induce the RNA-mediated interference (RNAi) pathway.
  • RNAi RNA-mediated interference
  • miRNAs that exert their regulatory effects by binding to imperfect complementary sites within the 3' untranslated regions (UTRs) of their mRNA targets, repress target-gene expression post-transcriptionally, apparently at the level of translation, through a RISC complex that is similar to, or possibly identical with, the one that is used for the RNAi pathway. Consistent with translational control, miRNAs that use this mechanism reduce the protein levels of their target genes, but the mRNA levels of these genes are only minimally affected. miRNAs encompass both naturally occurring miRNAs as well as artificially designed miRNAs that can specifically target any mRNA sequence. For example, in one embodiment, the skilled artisan can design short hairpin RNA constructs expressed as human miRNA (e.g.
  • the hairpin stem consists of 22-nt of dsRNA ⁇ e.g., antisense has perfect complementarity to desired target) and a 15-19-nt loop from a human miR. Adding the miR loop and miR30 flanking sequences on either or both sides of the hairpin results in greater than 10-fold increase in Drosha and Dicer processing of the expressed hairpins when compared with conventional shRNA designs without microRNA. Increased Drosha and Dicer processing translates into greater
  • siRNA/miRNA production and greater potency for expressed hairpins are desirable.
  • RNA short hairpin RNA
  • shRNA refers to double-stranded structure that is formed by a single self-complementary RNA strand.
  • ⁇ shRNA constructs containing a nucleotide sequence identical to a portion, of either coding or non-coding sequence, of the target gene are preferred for inhibition.
  • RNA sequences with insertions, deletions, and single point mutations relative to the target sequence have also been found to be effective for inhibition. Greater than 90% sequence identity, or even 100%) sequence identity, between the inhibitory RNA and the portion of the target gene is preferred.
  • the length of the duplex-forming portion of an shRNA is at least 20, 21 or 22 nucleotides in length, e.g., corresponding in size to RNA products produced by Dicer-dependent cleavage.
  • the shRNA construct is at least 25, 50, 100, 200, 300 or 400 bases in length.
  • the shRNA construct is 400-800 bases in length. shRNA constructs are highly tolerant of variation in loop sequence and loop size.
  • ribozyme refers to a catalytically active RNA molecule capable of site-specific cleavage of target mRNA.
  • RNA molecules capable of site-specific cleavage of target mRNA.
  • subtypes e.g., hammerhead and hairpin ribozymes.
  • Ribozyme catalytic activity and stability can be improved by substituting deoxyribonucleotides for ribonucleotides at noncatalytic bases. While ribozymes that cleave mRNA at site-specific recognition sequences can be used to destroy particular mRNAs, the use of hammerhead ribozymes is preferred.
  • Hammerhead ribozymes cleave mRNAs at locations dictated by flanking regions that form complementary base pairs with the target mRNA.
  • the sole requirement is that the target mRNA has the following sequence of two bases: 5'-UG-3'.
  • the construction and production of hammerhead ribozymes is well known in the art.
  • a preferred method of delivery of a polynucleotide-of-interest that comprises an siRNA, an miRNA, an shRNA, or a ribozyme comprises one or more regulatory sequences, such as, for example, a strong constitutive pol III, e.g., human U6 snRNA promoter, the mouse U6 snRNA promoter, the human and mouse HI RNA promoter and the human tRNA-val promoter, or a strong constitutive pol II promoter, as described elsewhere herein.
  • a strong constitutive pol III e.g., human U6 snRNA promoter, the mouse U6 snRNA promoter, the human and mouse HI RNA promoter and the human tRNA-val promoter, or a strong constitutive pol II promoter, as described elsewhere herein.
  • polynucleotides of the present invention may be combined with other DNA sequences, such as promoters, untranslated regions (UTRs), Kozak sequences, polyadenylation signals, additional restriction enzyme sites, multiple cloning sites, internal ribosomal entry sites (IRES), recombinase recognition sites ⁇ e.g., LoxP, FRT, and Att sites), termination codons, transcriptional termination signals, and polynucleotides encoding self-cleaving polypeptides, epitope tags, as disclosed elsewhere herein, such that their overall length may vary considerably. It is therefore contemplated that a polynucleotide fragment of almost any length may be employed, with the total length preferably being limited by the ease of preparation and use in the intended recombinant DNA protocol.
  • Polynucleotides can be prepared, manipulated and/or expressed using any of a variety of well established techniques known and available in the art.
  • a nucleotide sequence encoding the polypeptide can be inserted into appropriate vector.
  • vector includes viral vectors as disclosed elsewhere herein and "expression vectors" ⁇ e.g., a plasmid, cosmid or phage
  • viral vectors are expression vectors.
  • the "control elements” or “regulatory sequences” present in an expression vector are those non-translated regions of the vector— origin of replication, selection cassettes, promoters, enhancers, translation initiation signals (Shine Dalgarno sequence or Kozak sequence) introns, a polyadenylation sequence, 5' and 3' untranslated regions— which interact with host cellular proteins to carry out transcription and translation.
  • Such elements may vary in their strength and specificity.
  • any number of suitable transcription and translation elements including ubiquitous promoters and inducible promoters may be used.
  • a vector for use in practicing the invention including, but not limited to expression vectors and viral vectors, will include exogenous, endogenous, or heterologous control sequences such as promoters and/or enhancers.
  • promoter refers to a recognition site of a polynucleotide (DNA or RNA) to which an R A polymerase binds. An R A polymerase initiates and transcribes polynucleotides operably linked to the promoter.
  • promoters operative in mammalian cells comprise an AT- rich region located approximately 25 to 30 bases upstream from the site where transcription is initiated and/or another sequence found 70 to 80 bases upstream from the start of transcription, a CNCAAT region where N may be any nucleotide.
  • the term "enhancer” refers to a segment of DNA which contains sequences capable of providing enhanced transcription and in some instances can function independent of their orientation relative to another control sequence. An enhancer can function
  • promoter/enhancer refers to a segment of DNA which contains sequences capable of providing both promoter and enhancer functions.
  • An "endogenous" control sequence is one which is naturally linked with a given gene in the genome.
  • An “exogenous” control sequence is one which is placed in juxtaposition to a gene by means of genetic manipulation (i.e., molecular biological techniques) such that transcription of that gene is directed by the linked
  • a "heterologous" control sequence is an exogenous sequence that is from a different species than the cell being genetically manipulated.
  • the term “operably linked” refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner. In one embodiment, the term refers to a functional linkage between a nucleic acid expression control sequence (such as a promoter, and/or enhancer) and a second polynucleotide sequence, e.g., a polynucleotide-of-interest, wherein the expression control sequence directs transcription of the nucleic acid corresponding to the second sequence.
  • a nucleic acid expression control sequence such as a promoter, and/or enhancer
  • an operable linkage may be operable on the sense or plus strand or on the non-sense or minus strand.
  • a reverse complement of a polynucleotide encoding a polypeptide of interest is operably linked to an RDRP promoter or subgenomic promoter in the reverse orientation. This means that the linkage is operable in the 3' to 5' orientation but not in the 5' to 3' orientation.
  • an operable linkage may be operable on both strands (independent of directionality).
  • a polynucleotide of the invention comprises a constitutive promoter.
  • constitutive promoter refers to a promoter that continually or continuously allows for transcription of an operably linked sequence.
  • Constitutive promoters may be a "ubiquitous promoter” that allows expression in a wide variety of cell and tissue types or a "tissue-specific promoter” that allows expression in a restricted variety of cell and tissue types.
  • Ubiquitous promoters can be selected based on strength of ubiquitous promoter activity, specificity for target tissue or other factors relating to desired control over expression, as is understood in the art.
  • the sequences of these and numerous additional ubiquitous promoters are known in the art. The relevant sequences may be readily obtained from public databases and incorporated into vectors for use in practicing the present invention.
  • Illustrative ubiquitous promoters include, but are not limited to, a cytomegalovirus (CMV) immediate early promoter, a viral simian virus 40 (SV40) ⁇ e.g., early or late), a Moloney murine leukemia virus (MoMLV) LTR promoter, a Rous sarcoma virus (RSV) LTR, a herpes simplex virus (HSV) (thymidine kinase) promoter, H5, P7.5, and PI 1 promoters from vaccinia virus, an elongation factor 1-alpha (EFla) promoter, early growth response 1 (EGR1), ferritin H (FerH), ferritin L (FerL), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), eukaryotic translation initiation factor 4A1 (EIF4A1), heat shock 70kDa protein 5 (HSPA5), heat shock protein 90kDa beta, member 1 (HSP90B
  • tissue-specific promoter it may be desirable to use a tissue-specific promoter to achieve cell type specific, lineage specific, or tissue-specific expression of a desired polynucleotide sequence ⁇ e.g. , to express a particular nucleic acid encoding a polypeptide in only a subset of cell types or tissues or during specific stages of development).
  • a vector of the present invention comprises a tissue specific promoter and/or enhancer that expresses a desired polypeptide.
  • tissue specific promoters include, but are not limited to: an B29 promoter (B cell expression), a runt transcription factor (CBFa2) promoter (stem cell specific expression), an CD 14 promoter (monocytic cell expression), an CD43 promoter
  • an CD45 promoter hematopoietic cell expression
  • an CD68 promoter macrophage expression
  • a CYP450 3A4 promoter hepatocyte expression
  • an desmin promoter muscle expression
  • pancreatic acinar cell expression an endoglin promoter (endothelial cell expression), a fibroblast specific protein 1 promoter (FSP1) promoter (fibroblast cell expression), a fibronectin promoter (fibroblast cell expression), a fms-related tyrosine kinase 1 (FLT1) promoter (endothelial cell expression), a glial fibrillary acidic protein (GFAP) promoter (astrocyte expression), an insulin promoter (pancreatic beta cell expression), an integrin, alpha 2b (ITGA2B) promoter (megakaryocytes), an intracellular adhesion molecule 2 (ICAM-2) promoter (endothelial cells), an interferon beta (IFN- ⁇ ) promoter (hematopoietic cells), a keratin 5 promoter (keratinocyte expression), a myoglobin (MB) promoter (muscle expression), a myogenic differentiation 1 (MYOD1) promoter (muscle expression), a fibro
  • a cell type specific promoter is specific for cell types found in the brain (e.g., neurons, glial cells), liver (e.g., hepatocytes), pancreas, skeletal muscle (e.g., myocytes), immune system (e.g., T cells, B cells, macrophages), heart (e.g., cardiac myocytes), retina, skin (e.g., keratinocytes), bone (e.g., osteoblasts or osteoclasts), etc.
  • the brain e.g., neurons, glial cells
  • liver e.g., hepatocytes
  • pancreas e.g., myocytes
  • immune system e.g., T cells, B cells, macrophages
  • heart e.g., cardiac myocytes
  • retina e.g., skin
  • skin e.g., keratinocytes
  • bone e.g., osteoblasts or osteoclasts
  • tissue specific promoters Numerous cell type or tissue-specific promoters are known, and one of ordinary skill in the art will readily be able to identify tissue specific promoters (or to determine whether any particular promoter is a tissue specific promoter) from the literature or by performing experiments such as Northern blots, immunoblots, etc. in which expression of either an endogenous gene or a reporter gene operably linked to the promoter is compared in different cell or tissue types).
  • a lineage specific promoter directs transcription in cells of a particular lineage and not in fully differentiated cells of most or all other lineages.
  • the promoter may direct transcription in cells types of the B cell lineage, T cell lineage, macrophage lineage, etc.
  • Erythrocyte- specific expression can be achieved by using the human ⁇ -globin promoter region and locus control region (LCR).
  • the invention therefore provides polynucleotides as described elsewhere herein, supra and infra, including but not limited to expression and viral vectors, comprising a cell type or tissue-specific promoter and methods of using the vectors and/or viral particles derived therefrom to achieve cell type or tissue specific expression of genes, e.g., a polynucleotide-of-interest.
  • conditional expression of a polynucleotide-of-interest e.g., expression is controlled by subjecting a cell, tissue, organism, etc., to a treatment or condition that causes the polynucleotide to be expressed or that causes an increase or decrease in expression of the polynucleotide encoded by the polynucleotide-of-interest.
  • conditional expression may refer to any type of conditional expression including, but not limited to, inducible expression; repressible expression; expression in cells or tissues having a particular physiological, biological, or disease state, etc. This definition is not intended to exclude cell type or tissue-specific expression.
  • inducible promoter refers to a control element ⁇ e.g., a promoter, enhancer, promoter/enhancer, or portion thereof) whose transcriptional activity may be regulated by exposing a cell or tissue comprising a nucleic acid sequence operably linked to the promoter to a treatment or condition that alters the transcriptional activity of the promoter, resulting in increased transcription of the nucleic acid sequence.
  • inducible promoter also includes repressible promoters, i.e., promoters whose transcriptional activity may be regulated by exposing a cell or tissue comprising a nucleic acid sequence operably linked to the promoter to a treatment or condition that alters the transcriptional activity of the promoter, resulting in decreased transcription of the nucleic acid sequence.
  • Typical inducible promoters are active in mammalian cells.
  • Inducible promoters/sy stems include, but are not limited to, steroid-inducible promoters such as promoters for genes encoding glucocorticoid or estrogen receptors (inducible by treatment with the corresponding hormone), metallothionine promoter (inducible by treatment with various heavy metals), MX-1 promoter (inducible by interferon), the "GeneSwitch” mifepristone-regulatable system (Sirin et ah, 2003, Gene, 323:67), the cumate inducible gene switch (WO 2002/088346), tetracycline-dependent regulatory systems, etc.
  • steroid-inducible promoters such as promoters for genes encoding glucocorticoid or estrogen receptors (inducible by treatment with the corresponding hormone), metallothionine promoter (inducible by treatment with various heavy metals), MX-1 promoter (inducible by interferon), the "GeneSwitch
  • the effector is a fusion of sequences that encode the VP 16 transactivation domain and the Escherichia coli tetracycline repressor (TetR) protein, which specifically binds both tetracycline and the 19-bp operator sequences (tetO) of the tet operon in the target transgene, resulting in its transcription.
  • TetR Escherichia coli tetracycline repressor
  • tTA tetracycline-controlled transactivator
  • rtTA reverse tTA
  • the invention therefore provides polynucleotides comprising a tetracycline-controlled transactivator or reverse tetracycline-controlled transactivator, vectors comprising operator sequences of the tet operon to which the tetracycline-controlled transactivator or reverse tetracycline-controlled transactivator specifically bind, and methods of using the polynucleotides and/or viral particles derived therefrom to achieve conditional expression.
  • Conditional expression can also be achieved by using a site-specific DNA recombinase.
  • the vector comprises at least one (typically two) site(s) for recombination mediated by a site- specific recombinase.
  • site-specific recombinase include excisive or integrative proteins, enzymes, co-factors or associated proteins that are involved in recombination reactions involving one or more
  • recombination sites e.g., two, three, four, five, seven, ten, twelve, fifteen, twenty, thirty, fifty, etc.
  • wild-type proteins see Landy, Current Opinion in Biotechnology 3:699-707 (1993)
  • mutants, derivatives e.g., fusion proteins containing the recombination protein sequences or fragments thereof
  • fragments and variants thereof.
  • Illustrative examples of recombinases suitable for use in particular embodiments of the present invention include, but are not limited to: Cre, Int, IHF, Xis, Flp, Fis, Hin, Gin, OC31, Cin, Tn3 resolvase, TndX, XerC, XerD, TnpX, Hjc, Gin, SpCCEl. and ParA.
  • the vectors may comprise one or more recombination sites for any of a wide variety of site-specific recombinases. It is to be understood that the target site for a site-specific recombinase is in addition to any site(s) required for integration of a vector, e.g., a retroviral vector or lentiviral vector. As used herein, the terms
  • recombination sequence refers to a particular nucleic acid sequence to which a recombinase recognizes and binds.
  • loxP which is a 34 base pair sequence comprising two 13 base pair inverted repeats (serving as the recombinase binding sites) flanking an 8 base pair core sequence (see FIG. 1 of Sauer, B., Current Opinion in Biotechnology 5:521-527 (1994)).
  • exemplary loxP sites include, but are not limited to: lox511 (Hoess et ah, 1996; Bethke and Sauer, 1997), 1 ⁇ 5171 (Lee and Saito, 1998), lox2272 (Lee and Saito, 1998), m2 (Langer et al, 2002), lox71 (Albert et al, 1995), and lox66 (Albert et al, 1995).
  • Suitable recognition sites for the FLP recombinase include, but are not limited to: FRT (McLeod, et al, 1996), Fi, F 2 , F 3 (Schlake and Bode, 1994), F 4 , F 5 (Schlake and Bode, 1994), FRT(LE) (Senecoff et al, 1988), FRT(RE) (Senecoff ei al, 1988).
  • recognition sequences are the attB, attP, attL, and attR sequences, which are recognized by the recombinase enzyme ⁇ Integrase, e.g, phi- c31.
  • the ⁇ C31 SSR mediates recombination only between the heterotypic sites attB (34 bp in length) and attP (39 bp in length) (Groth et al, 2000).
  • attB and attP named for the attachment sites for the phage integrase on the bacterial and phage genomes, respectively, both contain imperfect inverted repeats that are likely bound by ⁇ C31 homodimers (Groth et al, 2000).
  • conditional expression of a polynucleotide sequence e.g., a polynucleotide-of-interest operably linked to a promoter element, a promoter element or both
  • a polynucleotide sequence e.g., a polynucleotide-of-interest operably linked to a promoter element, a promoter element or both
  • conditional expression of a polynucleotide sequence e.g., a polynucleotide-of-interest operably linked to a promoter element, a promoter element or both
  • recombinase recognition sites e.g., Ventura et al., 2004. Proc Natl Acad Sci USA. 101(28): 10380-5.
  • polynucleotide sequence is excised, thus preventing further transcription and/or expression of a polynucleotide-of-interest and effectively eliminating expression of the sequence.
  • This system has a number of applications including recombinase-mediated gene activation and inactivation.
  • Recombinase expression may be induced in any of a variety of ways.
  • the recombinase may be present in the cells under control of an inducible promoter, and recombinase expression may be induced by activating the promoter.
  • recombinase expression may be induced by introducing an expression vector that directs expression of recombinase into the cell.
  • Any suitable expression vector can be used, including, but not limited to, viral vectors such as lenti viral or retroviral vectors.
  • Vectors comprising two recombinase recognition sites are useful in any applications for which standard vectors comprising two recombinase recognition sites can be used.
  • selectable markers may be placed between the recombinase recognition sites. This allows for sequential and repeated targeting of multiple genes to a single cell (or its progeny).
  • stable transfectants may be selected after introduction of a vector comprising a floxed polynucleotide into a cell. After introduction of a vector comprising a floxed polynucleotide into a cell. After introduction of a vector comprising a floxed polynucleotide into a cell, stable transfectants may be selected. After isolation of a stable transfectant, the polynucleotide can be excised by induction of Cre or replaced by another polynucleotide sequence harboring a different selectable marker. The orientation of the recombinase recognition sites dictates whether excision or replacement occurs.
  • the vectors contemplated by the invention include one or more polynucleotides-of-interest that encode one or more polypeptides.
  • the vectors contemplated by the invention include one or more polynucleotides-of-interest that encode one or more polypeptides.
  • polynucleotide sequences can be separated by one or more IRES sequences or polynucleotide sequences encoding self-cleaving polypeptides.
  • an "internal ribosome entry site” or “IRES” refers to an element that promotes direct internal ribosome entry to the initiation codon, such as ATG, of a cistron (a protein encoding region), thereby leading to the cap-independent translation of the gene. See, e.g., Jackson et al, 1990. Trends Biochem Sci 15(12):477-83) and Jackson and
  • RNA 1(10):985-1000 Examples of IRES generally employed by those of skill in the art include those described in U.S. Pat. No. 6,692,736. Examples of "IRES" known in the art include, but are not limited to IRES obtainable from
  • picornavirus (Jackson et al, 1990) and IRES obtainable from viral or cellular mRNA sources, such as for example, immunoglobulin heavy-chain binding protein (BiP), the vascular endothelial growth factor (VEGF) (Huez et al. 1998. Mol. Cell. Biol.
  • IRES obtainable from viral or cellular mRNA sources, such as for example, immunoglobulin heavy-chain binding protein (BiP), the vascular endothelial growth factor (VEGF) (Huez et al. 1998. Mol. Cell. Biol.
  • fibroblast growth factor 2 FGF-2
  • insulin-like growth factor IGFII
  • eIF4G translational initiation factor 4G and yeast transcription factors TFIID and HAP4
  • EMCV encephelomycarditis virus
  • IRES Huez et al, 1998. Mol Cell Biol 18(11):6178-90
  • IRES have also been reported in different viruses such as cardiovirus, rhinovirus, aphthovirus, HCV, Friend murine leukemia virus (FrMLV) and Moloney murine leukemia virus (MoMLV).
  • IRES encompasses functional variations of IRES sequences as long as the variation is able to promote direct internal ribosome entry to the initiation codon of a cistron.
  • An IRES may be mammalian, viral or protozoan.
  • Under translational control of an IRES as used herein means that translation is associated with the IRES and proceeds in a cap-independent manner.
  • polynucleotides encoding a polypeptide of the invention comprise a short recognition sequence, i.e., a Kozak sequence, that greatly facilitates the initial binding of mRNA to the small subunit of the ribosome and increases translation.
  • the consensus Kozak sequence is (GCC)RCCATGG, where R is a purine (A or G) (Kozak, 1986. Cell. 44(2):283-92, and Kozak, 1987 Nucleic Acids Res. 15(20):8125-48).
  • vectors comprise a polyadenylation sequence
  • Polyadenylation sequences can promote mR A stability by addition of a polyA tail to the 3' end of the coding sequence and thus, contribute to increased translational efficiency. Recognized polyadenylation sites include an ideal polyA sequence (e.g., AATAAA, ATTAAA AGTAAA), an SV40 polyA sequence, a bovine growth hormone polyA sequence (BGHpA), a rabbit ⁇ -globin polyA sequence (rPgpA), or another suitable heterologous or endogenous polyA sequence known in the art.
  • an ideal polyA sequence e.g., AATAAA, ATTAAA AGTAAA
  • BGHpA bovine growth hormone polyA sequence
  • rPgpA rabbit ⁇ -globin polyA sequence
  • vectors comprise a selection gene, also termed a selectable marker.
  • selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, hygromycin, methotrexate, Zeocin, Blastocidin, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D- alanine racemase for Bacilli. Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase (Wigler et ah, 1977. Cell 11 :223-232) and adenine
  • phosphoribosyltransferase (Lowy et ah, 1990. Cell 22:817-823) genes which can be employed in tk- or aprt- cells, respectively.
  • antimetabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dhfr which confers resistance to methotrexate (Wigler et ah, 1980. Proc. Natl. Acad. Sci. U.S.A. 77:3567- 70); npt, which confers resistance to the aminoglycosides, neomycin and G-418 (Colbere-Garapin et al., 1981. J. Mol. Biol. 150: 1-14); and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively.
  • Trpl and/or Leu2 deficient yeast strains provide a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan (e.g., ATCC No. 44076 or PEP4-1) or leucine (e.g., ATCC 20,622 or 38,626).
  • host cell includes an isolated primary cell or a cell in culture which can be or has been a recipient of any recombinant vector(s) or isolated polynucleotide of the invention.
  • Host cells include eukaryotic cells and prokaryotic cells.
  • eukaryotic cells include, plant cells (e.g., Arabidopsis), yeast cells (e.g., Pichia Saccharomyces, and Schizosaccharomyces), insect cells (e.g., Drosophila), and mammalian cells (e.g., murine and human).
  • Exemplary prokaryotic cells include Escherichia coli, among others.
  • Host cells include progeny of a single host cell, and the progeny may not necessarily be completely identical (in morphology or in total DNA complement) to the original parent cell due to natural, accidental, or deliberate mutation and/or genetic change.
  • a host cell includes cells transfected or infected in vivo or in vitro with a recombinant vector or a polynucleotide of the invention.
  • transfection refers to the introduction of foreign DNA into eukaryotic cells.
  • Transfection may be accomplished by a variety of means known in the art including but not limited to calcium phosphate-DNA co-precipitation, DEAE- dextran-mediated transfection, polybrene-mediated transfection, electroporation, microinjection, liposome fusion, lipofection, protoplast fusion, retroviral infection, and biolistics.
  • a host cell which comprises a recombinant vector of the invention is a recombinant host cell.
  • a host cell also includes cells transduced in vivo or in vitro with a recombinant polypeptide or polypeptide fusion protein of the invention, as described elsewhere herein.
  • compositions comprising polypeptides and vectors that express polypeptides.
  • Polypeptide polypeptide
  • polypeptide fragment polypeptide
  • protein protein
  • Polypeptides are not limited to a specific length, e.g., they may comprise a full length protein sequence or a fragment of a full length protein, and may include post- translational modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like, as well as other modifications known in the art, both naturally occurring and non-naturally occurring.
  • Polypeptides can be prepared using any of a variety of well known recombinant and/or synthetic techniques.
  • An "isolated peptide” or an “isolated polypeptide” and the like, as used herein, refer to in vitro isolation and/or purification of a peptide or polypeptide molecule from a cellular environment, and from association with other components of the cell, i.e., it is not significantly associated with in vivo substances.
  • an "isolated cell” refers to a cell that has been obtained from an in vivo tissue or organ and is substantially free of extracellular matrix.
  • Polypeptides include polypeptide variants.
  • Polypeptide variants may differ from a naturally occurring polypeptide in one or more substitutions, deletions, additions and/or insertions. Such variants may be naturally occurring or may be synthetically generated, for example, by modifying one or more of the above polypeptide sequences used in the methods of the invention and evaluating their effects using any of a number of techniques well known in the art.
  • polypeptides of the invention include polypeptides having at least about 65%, 70%, 75%, 85%, 90%, 95%, 98%, or 99% amino acid identity thereto.
  • a variant will contain conservative substitutions.
  • a "conservative substitution” is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged. Modifications may be made in the structure of the polynucleotides and polypeptides of the present invention and still obtain a functional molecule that encodes a variant or derivative polypeptide with desirable characteristics.
  • amino acid changes in the protein variants disclosed herein are conservative amino acid changes, i.e., substitutions of similarly charged or uncharged amino acids.
  • a conservative amino acid change involves substitution of one of a family of amino acids which are related in their side chains.
  • Naturally occurring amino acids are generally divided into four families: acidic (aspartate, glutamate), basic (lysine, arginine, histidine), non-polar (alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), and uncharged polar (glycine, asparagine, glutamine, cystine, serine, threonine, tyrosine) amino acids. Phenylalanine, tryptophan, and tyrosine are sometimes classified jointly as aromatic amino acids. In a peptide or protein, suitable conservative substitutions of amino acids are known to those of skill in this art and generally can be made without altering a biological activity of a resulting molecule.
  • hydropathic index of amino acids may be considered.
  • the importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte and Doolittle, 1982, incorporated herein by reference). Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics (Kyte and Doolittle, 1982). These values are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8);
  • glycine (-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (-3.5); asparagine (-3.5); lysine (-3.9); and arginine (-4.5).
  • amino acid substitutions may be based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like.
  • Polypeptide variants further include glycosylated forms, aggregative conjugates with other molecules, and covalent conjugates with unrelated chemical moieties (e.g., pegylated molecules).
  • Covalent variants can be prepared by linking functionalities to groups which are found in the amino acid chain or at the N- or C- terminal residue, as is known in the art.
  • Variants also include allelic variants, species variants, and muteins. Truncations or deletions of regions which do not affect functional activity of the proteins are also variants.
  • polypeptide sequences encoding them can be separated by and IRES sequence as discussed elsewhere herein.
  • two or more polypeptides can be expressed as a fusion protein that comprises one or more self- cleaving polypeptide sequences.
  • Polypeptides of the present invention include fusion polypeptides.
  • fusion polypeptides and polynucleotides encoding fusion polypeptides are provided.
  • Fusion polypeptides and fusion proteins refer to a polypeptide having at least two, three, four, five, six, seven, eight, nine, or ten polypeptide segments.
  • Fusion polypeptides can comprise one or more polypeptide domains or segments including, but are not limited to cell permeable peptide domains (CPP), epitope tags (e.g., maltose binding protein ("MBP"), glutathione S transferase (GST), HIS6, MYC, FLAG, V5, VSV-G, and HA), polypeptide linkers, and polypeptide cleavage signals.
  • CPP cell permeable peptide domains
  • epitope tags e.g., maltose binding protein (“MBP"), glutathione S transferase (GST), HIS6, MYC, FLAG, V5, VSV-G, and HA
  • Fusion polypeptides are typically linked C-terminus to N-terminus, although they can also be linked C-terminus to C-terminus, N-terminus to N-terminus, or N-terminus to C-terminus.
  • the polypeptides of the fusion protein can be in any order.
  • Fusion polypeptides or fusion proteins can also include conservatively modified variants, polymorphic variants, alleles, mutants, subsequences, and interspecies homologs, so long as the desired transcriptional activity of the fusion polypeptide is preserved. Fusion polypeptides may be produced by chemical synthetic methods or by chemical linkage between the two moieties or may generally be prepared using other standard techniques. Ligated DNA sequences comprising the fusion polypeptide are operably linked to suitable transcriptional or translational control elements as discussed elsewhere herein.
  • a fusion partner comprises a sequence that assists in expressing the protein (an expression enhancer) at higher yields than the native recombinant protein.
  • Other fusion partners may be selected so as to increase the solubility of the protein or to enable the protein to be targeted to desired intracellular compartments or to facilitate transport of the fusion protein through the cell membrane.
  • fusion polypeptides comprise one or more CPPs.
  • An important factor in the administration of polypeptide compounds is ensuring that the polypeptide has the ability to traverse the plasma membrane of a cell, or the membrane of an intra-cellular compartment such as the nucleus.
  • Cellular membranes are composed of lipid-protein bilayers that are freely permeable to small, nonionic lipophilic compounds and are inherently impermeable to polar compounds,
  • proteins, lipids and other compounds which have the ability to translocate polypeptides across a cell membrane, have been described.
  • peptide sequences which can facilitate protein uptake into cells include, but are not limited to: HIV TAT polypeptides; a 20 residue peptide sequence which corresponds to amino acids 84-103 of the pl6 protein (see Fahraeus et al., 1996. Curr. Biol. 6:84); the third helix of the 60-amino acid long homeodomain of Antennapedia (Derossi et al, 1994. J. Biol. Chem. 269: 10444); the h region of a signal peptide, such as the Kaposi fibroblast growth factor (K-FGF) h region; and the VP22 translocation domain from HSV (Elliot et al, 1997. Cell 88:223-233).
  • K-FGF Kaposi fibroblast growth factor
  • Clostridium perfringens iota toxin diphtheria toxin (DT), Pseudomonas exotoxin A (PE), Bordetella pertussis toxin (PT), Bacillus anthracis toxin, and Bordetella pertussis adenylate cyclase (CYA)
  • DT diphtheria toxin
  • PE Pseudomonas exotoxin A
  • PT Bordetella pertussis toxin
  • Bacillus anthracis toxin Bacillus anthracis toxin
  • Bordetella pertussis adenylate cyclase CYA
  • CPP amino acid sequences include, but are not limited to: RKKRRQRRR (SEQ ID NO: 1), KKRRQRRR (SEQ ID NO: 2), and RKKRRQRR (SEQ ID NO: 3) (derived from HIV TAT protein); RRRRRRRRR (SEQ ID NO: 4); KKKKKKKKK (SEQ ID NO: 5); RQIKIWFQNRRMKWKK (SEQ ID NO: 6) (from Drosophila Antp protein); RQIKIWFQNRRMKSKK (SEQ ID NO: 7) (from
  • Drosophila Ftz protein Drosophila Ftz protein
  • RQIKIWFQNKRAKIKK SEQ ID NO: 8
  • RQIKIWFQNRRMKWKK SEQ ID NO: 9
  • RVIRVWFQNKRCKDKK from human Isl-I protein.
  • Such subsequences can be used to facilitate polypeptide translocation, including the fusion polypeptides contemplated herein, across a cell membrane.
  • Fusion polypeptides may optionally comprises a linker that can be used to link the one or more polypeptides.
  • a peptide linker sequence may be employed to separate any two or more polypeptide components by a distance sufficient to ensure that each polypeptide folds into its appropriate secondary and tertiary structures so as to allow the polypeptide domains to exert their desired functions.
  • Such a peptide linker sequence is incorporated into the fusion polypeptide using standard techniques in the art.
  • Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes.
  • Preferred peptide linker sequences contain Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala may also be used in the linker sequence.
  • Amino acid sequences which may be usefully employed as linkers include those disclosed in Maratea et al, Gene 40:39-46, 1985; Murphy et al, Proc. Natl. Acad. Sci.
  • Linker sequences are not required when a particular fusion polypeptide segment contains non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.
  • Preferred linkers are typically flexible amino acid subsequences which are synthesized as part of a recombinant fusion protein.
  • Linker polypeptides can be between 1 and 200 amino acids in length, between 1 and 100 amino acids in length, or between 1 and 50 amino acids in length, including all integer values in between.
  • linkers include, but are not limited to the following amino acid sequences: DGGGS (SEQ ID NO: 11); TGEKP (SEQ ID NO: 12) (see, e.g., Liu et al, PNAS 5525-5530 (1997)); GGRR (SEQ ID NO: 13) (Pomerantz et al. 1995, supra); (GGGGS) n (SEQ ID NO: 14) (Kim et al, PNAS 93, 1156-1160 (1996.);
  • EGKSSGSGSESKVD (SEQ ID NO: 15) (Chaudhary et al., 1990, Proc. Natl. Acad. Sci. U.S.A. 87:1066-1070); KESGSVSSEQLAQFRSLD (SEQ ID NO: 16) (Bird et al, 1988, Science 242:423-426), GGRRGGGS (SEQ ID NO: 17); LRQRDGERP (SEQ ID NO: 18); LRQKDGGGSERP (SEQ ID NO: 19); LRQKD(GGGS) 2 ERP (SEQ ID NO: 20).
  • flexible linkers can be rationally designed using a computer program capable of modeling both DNA-binding sites and the peptides themselves (Desjarlais & Berg, PNAS 90:2256-2260 (1993), PNAS 91 :11099-11103 (1994) or by phage display methods.
  • Fusion polypeptides may further comprise a polypeptide cleavage signal between each of the polypeptide domains described herein.
  • polypeptide site can be put into any linker peptide sequence.
  • Exemplary polypeptide cleavage signals include polypeptide cleavage recognition sites such as protease cleavage sites, nuclease cleavage sites ⁇ e.g., rare restriction enzyme recognition sites, self-cleaving ribozyme recognition sites), and self-cleaving viral oligopeptides (see deFelipe and Ryan, 2004. Traffic, 5(8); 616-26).
  • Suitable protease cleavages sites and self-cleaving peptides are known to the skilled person ⁇ see, e.g., in Ryan et al, 1997. J. Gener. Virol. 78, 699-722;
  • Exemplary protease cleavage sites include, but are not limited to the cleavage sites of potyvirus NIa proteases ⁇ e.g., tobacco etch virus protease), potyvirus HC proteases, potyvirus PI (P35) proteases, byovirus NIa proteases, byovirus RNA-2-encoded proteases, aphthovirus L proteases, enterovirus 2A proteases, rhinovirus 2A proteases, picorna 3C proteases, comovirus 24K proteases, nepovirus 24K proteases, RTSV (rice tungro spherical virus) 3C-like protease, PYVF (parsnip yellow fleck virus) 3C-like protease, heparin, thrombin, factor Xa and enterokinase.
  • potyvirus NIa proteases ⁇ e.g., tobacco etch virus protease
  • potyvirus HC proteases pot
  • TEV tobacco etch virus protease cleavage sites
  • EXXYXQ(G/S) SEQ ID NO: 21
  • ENLYFQG SEQ ID NO: 22
  • ENLYFQS SEQ ID NO: 23
  • self-cleaving peptides include those polypeptide sequences obtained from potyvirus and cardiovirus 2A peptides, FMDV (foot-and-mouth disease virus), equine rhinitis A virus, Thosea asigna virus and porcine tescho virus.
  • the self-cleaving polypeptide site comprises a 2A or 2A-like site, sequence or domain (Donnelly et al, 2001. J. Gen. Virol. 82: 1027- 1041).
  • Exemplary 2 A sites include the following sequences:
  • the present invention contemplates, in part, engineering effective therapeutic viral vector systems by taking advantage of the desirable features of various types of viruses.
  • retroviral, or optionally lentiviral genomes are used as the transfer vector backbone and heterologous RNA dependent RNA polymerase systems, e.g., of alphavirus or narnavirus, are used to control and amplify transcription of one or more
  • a therapeutic vector system comprises at least two vectors.
  • at least one of the vectors encodes the RNA dependent RNA polymerase, e.g., from alphavirus or narnavirus, either from an expression vector or a retroviral, e.g., lentiviral vector, and at least one of the vectors is a retroviral or lentiviral vector comprising a RNA dependent RNA polymerase promoter operably linked to one or more polynucleotides-of-interest.
  • Retroviral vectors are a common tool for gene delivery (Miller, 2000, Nature. 357: 455-460).
  • retrovirus refers an RNA virus that utilizes reverse transcriptase during its replication cycle.
  • retroviruses include, but are not limited to: type c retroviruses, such as Moloney murine sarcoma virus (MoMSV), Harvey murine sarcoma virus (HaMuSV), murine mammary tumor virus (MuMTV), gibbon ape leukemia virus (GaLV), feline leukemia virus (FLV), spumavirus, Friend, Murine Stem Cell Virus (MSCV) and Rous Sarcoma Virus (RSV)).
  • MoMSV Moloney murine sarcoma virus
  • HaMuSV Harvey murine sarcoma virus
  • MuMTV murine mammary tumor virus
  • GaLV gibbon ape leukemia virus
  • FLV feline leukemia virus
  • RSV Rous Sarcoma
  • Retroviruses of the invention also include human T cell leukemia viruses, HTLV-1 and HTLV-2, and the lentiviral family of retroviruses.
  • the core sequence of the retroviral vectors of the present invention may be readily derived from a wide variety of retroviruses, including for example, B, C, and D type retroviruses as well as
  • RNA Tumor Viruses Second Edition, Cold Spring Harbor Laboratory, 1985.
  • An example of a retrovirus suitable for use in the compositions and methods of the present invention includes, but is not limited to, a lentivirus.
  • Other retroviruses suitable for use in the compositions and methods of the present invention include, but are not limited to, Avian Leukosis Virus, Bovine Leukemia Virus, Murine Leukemia Virus, Mink-Cell Focus-Inducing Virus, Murine Sarcoma Virus, Reticuloendotheliosis virus and Rous Sarcoma Virus.
  • Preferred Murine Leukemia Viruses include 4070A and 1504A (Hartley and Rowe, 1976. J.
  • Retroviruses may be readily obtained from depositories or collections such as the American Type Culture Collection ("ATCC"; Rockville, Md.), or isolated from known sources using commonly available techniques .
  • Retroviral vectors and more particularly lentiviral vectors may be used in practicing the present invention. Accordingly, the term “retrovirus” or “retroviral vector”, as used herein is meant to include “lentivirus” and “lentiviral vectors” respectively. As used herein, the term “lentivirus” refers to a group (or genus) of retroviruses that give rise to slowly developing disease.
  • HIV human immunodeficiency virus
  • HIV type 1 HIV type 2
  • HIV type 2 HIV type 2
  • AIDS human immunodeficiency syndrome
  • visna-maedi which causes encephalitis (visna) or pneumonia (maedi) in sheep (VMV) virus
  • CAEV caprine arthritis-encephalitis virus
  • immune deficiency, arthritis, and encephalopathy in goats HIV infectious anemia virus
  • EIAV feline immunodeficiency virus
  • FIV bovine immune deficiency virus
  • SIV simian immunodeficiency virus
  • Retroviral vectors have been tested and found to be suitable delivery vehicles for the stable introduction of genes of interest into the genome of a broad range of target cells.
  • vector is used herein to refer to a nucleic acid molecule capable transferring or transporting another nucleic acid molecule.
  • the transferred nucleic acid is generally linked to, e.g., inserted into, the vector nucleic acid molecule.
  • a vector may include sequences that direct autonomous replication in a cell, or may include sequences sufficient to allow integration into host cell DNA.
  • Useful vectors include, for example, plasmids (e.g., DNA plasmids or RNA plasmids), cosmids, bacterial artificial chromosomes, and viral vectors.
  • Useful viral vectors include, e.g., replication defective retroviruses and lentiviruses.
  • viral vector refers either to a nucleic acid molecule (e.g., a transfer plasmid) that includes virus-derived nucleic acid elements that typically facilitate transfer of the nucleic acid molecule or integration into the genome of a cell or to a viral particle that mediates nucleic acid transfer.
  • Viral particles will typically include various viral components and sometimes also host cell components in addition to nucleic acid(s).
  • viral vector may refer either to a virus or viral particle capable of transferring a nucleic acid into a cell or to the transferred nucleic acid itself.
  • Viral vectors and transfer plasmids contain structural and/or functional genetic elements that are primarily derived from a virus.
  • the term "retroviral vector” refers to a viral vector or plasmid containing structural and functional genetic elements that are primarily derived from a retrovirus.
  • the term “lentiviral vector” refers to a viral vector or plasmid containing structural and functional genetic elements, including LTRs that are primarily derived from a lenti virus.
  • hybrid refers to a vector, LTR or other nucleic acid containing both retroviral, e.g.
  • a hybrid vector refers to a vector or transfers plasmid comprising retroviral e.g., lentiviral, sequences for reverse transcription, replication, integration and/or packaging and alphavirus subgenomic promoter sequences, non-structural proteins, and/or polymerase recognition sites.
  • lentiviral vector may be used to refer to lentiviral transfer plasmids and/or infectious lentiviral particles.
  • elements such as cloning sites, promoters, regulatory elements, heterologous nucleic acids, etc., it is to be understood that the sequences of these elements are present in RNA form in the lentiviral particles of the invention and are present in DNA form in the DNA plasmids of the invention.
  • retroviral vectors are transduced into a cell through infection and provirus integration.
  • a cell is "transduced” if it comprises a gene or other polynucleotide sequence delivered to the cell by infection using a viral or retroviral vector.
  • a transduced cell comprises the gene or other polynucleotide sequence delivered to by a viral or retroviral vector in its cellular genome.
  • the provirus serves as a template for RNA polymerase II and directs the expression of RNA molecules which encode the structural proteins and enzymes needed to produce new viral particles.
  • LTRs Long terminal repeats
  • LTRs generally provide functions fundamental to the expression of retroviral genes (e.g., promotion, initiation and polyadenylation of gene transcripts) and to viral replication.
  • the LTR contains numerous regulatory signals including transcriptional control elements, polyadenylation signals and sequences needed for replication and integration of the viral genome.
  • the viral LTR is divided into three regions called U3, R and U5.
  • the U3 region contains the enhancer and promoter elements.
  • the U5 region is the sequence between the primer binding site and the R region and contains the polyadenylation sequence.
  • the R (repeat) region is flanked by the U3 and U5 regions.
  • the 5' LTR and/or 3' LTR is modified.
  • Modifications of the 3' LTR are often made to improve the safety of lentiviral or retroviral systems by rendering viruses replication-defective.
  • replication-defective refers to virus that is not capable of complete, effective replication such that infective virions are not produced (e.g., replication-defective lentiviral progeny).
  • replication-competent refers to wild-type virus or mutant virus that is capable of replication, such that viral replication of the virus is capable of producing infective virions (e.g., replication-competent lentiviral progeny).
  • “Self-inactivating" (SIN) vectors refers to replication-defective vectors, e.g., retroviral or lentiviral vectors, in which the right (3') LTR enhancer-promoter region, known as the U3 region, has been modified (e.g., by deletion or substitution) to prevent viral transcription beyond the first round of viral replication. Consequently, the vectors are capable of infecting and then integrating into the host genome only once, and cannot be passed further. This is because the right (3') LTR U3 region is used as a template for the left (5') LTR U3 region during viral replication and, thus, the viral transcript cannot be made without the U3 enhancer-promoter. If the viral transcript is not made, it cannot be processed or packaged into virions, hence the life cycle of the virus ends.
  • the right (3') LTR enhancer-promoter region known as the U3 region
  • SIN vectors greatly reduce risk of creating unwanted replication- competent virus since the right (3') LTR U3 region has been modified to prevent viral transcription beyond the first round of replication, hence eliminating the ability of the virus to be passed.
  • the 3' LTR is modified such that the U5 region is replaced, for example, with an ideal poly(A) sequence. It should be noted that modifications to the LTRs such as modifications to the 3' LTR, the 5' LTR, or both 3' and 5' LTRs, are also included in the invention.
  • heterologous promoters which can be used include, for example, viral simian virus 40 (SV40) (e.g., early or late),
  • CMV cytomegalovirus
  • MoMLV Rous sarcoma virus
  • RSV Rous sarcoma virus
  • HSV herpes simplex virus
  • Typical promoters are able to drive high levels of transcription in a Tat-independent manner. This replacement reduces the possibility of recombination to generate replication-competent virus because there is no complete U3 sequence in the virus production system.
  • viral vectors comprise a TAR element.
  • TAR refers to the "trans-activation response” genetic element located in the R region of lentiviral (e.g., HIV) LTRs. This element interacts with the lentiviral trans-activator (tat) genetic element to enhance viral replication.
  • lentiviral e.g., HIV
  • tat lentiviral trans-activator
  • the "R region” refers to the region within retroviral LTRs beginning at the start of the capping group (i.e., the start of transcription) and ending immediately prior to the start of the poly A tract.
  • the R region is also defined as being flanked by the U3 and U5 regions. The R region plays a role during reverse transcription in permitting the transfer of nascent DNA from one end of the genome to the other.
  • the retroviral or lentiviral vector backbones comprise one or more FLAP elements upstream or downstream of the heterologous genes of interest in the vectors.
  • a transfer plasmid includes a FLAP element.
  • FLAP element refers to a nucleic acid whose sequence includes the central polypurine tract and central termination sequences (cPPT and CTS) of a retrovirus.
  • the retrovirus is a lentivirus, e.g., HIV-1 or HIV-2.
  • Suitable FLAP elements are described in U.S. Pat. No. 6,682,907 and in Zennou, et al, (2000, Cell, 101 : 173).
  • the DNA flap may act as a cis-active determinant of lentiviral genome nuclear import and/or may increase the titer of the virus.
  • retroviral or lentiviral transfer vectors comprise one or more export elements.
  • export element refers to a cis-acting posttranscriptional regulatory element which regulates the transport of an RNA transcript from the nucleus to the cytoplasm of a cell.
  • RNA export elements include, but are not limited to, the human immunodeficiency virus (HIV) rev response element (RRE) (see e.g., Cullen et al, 1991. J. Virol. 65: 1053; and Cullen et al, 1991. Cell 58: 423), and the hepatitis B virus post-transcriptional regulatory element (HPRE).
  • HCV human immunodeficiency virus
  • RRE hepatitis B virus post-transcriptional regulatory element
  • the RNA export element is placed within the 3' UTR of a gene, and can be inserted as one or multiple copies.
  • expression of heterologous sequences in viral vectors is increased by incorporating posttranscriptional regulatory elements, and efficient polyadenylation sites and optionally, transcription termination signals into the vectors.
  • posttranscriptional regulatory elements can increase expression of a heterologous nucleic acid at the protein level.
  • PRE posttranscriptional regulatory element
  • WPRE woodchuck hepatitis virus posttranscriptional regulatory element
  • Other posttranscriptional regulatory elements include the
  • posttranscriptional processing element present within the genome of various viruses such as that present within the thymidine kinase gene of herpes simplex virus (Liu et al, 1995, Genes Dev., 9: 1766), and the posttranscriptional regulatory element present in hepatitis B virus (HPRE) (Huang et al, Mol. Cell. Biol, 5:3864).
  • HPRE hepatitis B virus
  • posttranscriptional regulatory element is positioned at the 3' end the heterologous nucleic acid sequence. This configuration results in synthesis of a transcript whose 5' portion comprises the heterologous nucleic acid coding sequences and whose 3' portion comprises the posttranscriptional regulatory element sequence.
  • polyA site or "polyA sequence” as used herein denotes a DNA sequence which directs both the termination and polyadenylation of the nascent R A transcript by R A polymerase II. Efficient polyadenylation of the recombinant transcript is desirable as transcripts lacking a poly A tail are unstable and are rapidly degraded.
  • the polyA signal utilized in an expression vector may be heterologous or endogenous polyA signal.
  • Retroviruses have a different distribution of favored integration sites in the human genome than is seen with lentiviruses. Lentiviruses favor integration within active transcription units, while retroviruses favor integration near transcription start sites and associated features such as CpG islands and DNAsel cleavage sites. The association of retroviral integration with gene 5 '-ends may be part of the reason insertional activation is seen with these vectors. However, both retroviruses and lentiviruses may be subject to position effects of surrounding gene expression elements, depending on where the pro viral integration site is in the genome. Accordingly, in certain embodiments, a retroviral or lentiviral vector further comprises an insulator element.
  • Insulator elements act to preserve the independent function of genes or transcription units embedded in a genome or genetic context in which their expression may otherwise be influenced by regulatory signals within the genome or genetic context (i.e., position effect; see, e.g., Burgess-Beusse et al., 2002, Proc. Natl. Acad. Sci., USA, 99: 16433; and Zhan et ah, 2001, Hum. Genet., 109:471).
  • insulators may contribute to protecting lentivirus-expressed sequences from integration site effects, which may be mediated by cis-acting elements present in genomic DNA and lead to deregulated expression of transferred sequences.
  • transfer vectors comprise an insulator element in one or both LTRs or elsewhere in the region of the vector that integrates into the cellular genome.
  • Suitable insulators for use in the invention include, but are not limited to, the chicken ⁇ -Globin insulator (see Chung et al, 1993. Cell 74:505; Chung et al, 1997. PNAS 94:575; and Bell et al, 1999. Cell 98:387, incorporated by reference herein).
  • Examples of insulator elements include, but are not limited to, an insulator from an ⁇ -globin locus, such as chicken HS4.
  • most or all of the viral vector backbone sequences are derived from a lentivirus, e.g., HIV-1.
  • lentiviral vectors are known in the art, see Naldini et al, (1996a, 1996b, and 1998); Zufferey et al, (1997); Dull et al, 1998, U.S. Pat. Nos. 6,013,516; and 5,994,136, any of which may be adapted to produce a transfer vector of the present invention.
  • the present invention provides improved gene switches that solve the problems associated with poorly controlled or regulatable gene expression systems.
  • the invention provides systems that are not leaky, in contrast to other inducible gene expression systems such a cumate or tetracycline inducible gene expression systems, which are very leaky. Accordingly, the gene switches of the present invention are superior to and provide numerous advantages over existing gene expression systems in the art.
  • Temporal control of gene expression, as well as control of the amplitude of gene expression, are both important considerations in many viral-based methods of gene therapy. For example, tight regulation of cell-toxic viral packaging genes is important to preserve the safety, longevity, and fitness of packaging and producer cell lines.
  • Illustrative embodiments of the present invention provide state-of-the-art packaging and producer cell lines that provide for maximum safety, longevity, and health of cell lines. This results in maximum scalable production of safe virus at increased viral titers compared to existing methods in the art.
  • embodiments of the present invention provide robust systems for controlling the temporal expression and amplitude of gene expression in vivo, in methods of gene therapy. Tight control of therapeutic gene expression in vivo is extremely important due to the fact that insertion of viral vectors comprising the therapeutic genes in the genome is semi-random. Thus, in situations where insertion results in abnormal or dangerous levels of therapeutic gene expression, embodiments of the present invention advantageously provide mechanisms for damping gene expression to safe therapeutic levels and/or eliminating gene expression all together. Accordingly, illustrative embodiments of the invention provide for the maximum therapeutic efficacy while preserving maximum safety for the patient.
  • RNA dependent RNA polymerase refers to any RNA-based virus protein that uses RNA as a template for replication of RNA sequences.
  • suitable RNA viruses for use in RDRP systems of the invention include, but are not limited to plus-strand single stranded RNA viruses (i.e., plus single stranded RNA viruses, plus or positive sense ssRNA viruses, or (+) ssRNA viruses) and minus-strand single stranded RNA viruses (i.e., minus single stranded RNA viruses, minus or negative sense ssRNA viruses, or (-) ssRNA viruses).
  • Plus single stranded RNA viruses have their genome directly utilized as if it were mRNA, producing one or more proteins or polyprotein which are modified by host and viral proteins to form the various proteins needed for replication.
  • One of these proteins, RDRP catalyzes the synthesis of large numbers of "antisense" replicative intermediates. These intermediates serve as templates for the synthesis of large numbers of mRNA molecules that are translated by the host cell machinery into the proteins needed to make fresh virions.
  • the templates for amplification are minus-strand RNAs comprising minus-strand RDRP promoters, e.g., junctional or subgenomic promoters.
  • the minus-strand subgenomic promoters are operable or functional on the minus-strand, but not on the plus-strand.
  • the plus-strand mRNAs comprise the minus- RDRP promoters in the reverse orientation, which allows the RDRP to use the plus- strand like a minus-strand template (i.e., transcribe RNAs in the 3' to 5' direction), thus, amplifying the pool of translatable RNAs.
  • Minus single stranded RNA viruses must have their genome copied by an RNA polymerase to form positive-sense RNA. This means that the virus comprises an RNA-dependent RNA polymerase enzyme along with its genomic RNA.
  • the positive-sense RNA molecule then acts as viral mRNA, which is translated into proteins by the host ribosomes.
  • the resultant protein goes on to direct the synthesis of new virions, such as capsid proteins and RNA replicase, which is used to produce new negative-sense RNA molecules.
  • Exemplary plus single stranded RNA viruses suitable for use in the RDRP systems of the present invention are present in Table 3.
  • Betacoronavirus Human SARS coronavirus NC_004718.3
  • Flaviridae Flavirus (Infectious flacherie virus (IFV)) NC_003781.1
  • Picornaviridae Aphthovirus (Foot-and-mouth disease virus 0 NC_004004.1
  • Cardiovirus (Encephalomyocarditis virus (EMCV)) NC_001479.1
  • Erbo virus (Equine rhinitis B virus 1 (ERBV-1)) NC_003983.1
  • Hepatovirus Hepatitis A virus (HAV) NC_001489.1
  • Parechovirus Human parechovirus 2 (HPeV-2)) NC_001897.1
  • Senecavirus (Seneca Valley virus (SW)) NC_011349.1
  • Tescho virus (Porcine tescho virus 1 (PTV-1)) NC_003985.1
  • Tremovirus (Avian encephalomyelitis virus (AEV)) NC_003990.1
  • Torradovirus Tomato torrado virus (ToTV) NC_009013.1
  • Waikivirus (Rice tungro spherical virus (RTSV)) NC_001632.1 Comovirinae Comovirus (Cowpea mosaic virus (CPMV)) NC_003549.1
  • Fabavirus Broad bean wilt virus 1 (BBWV-1)) NC_005289.1
  • Nepovirus Tomatop ringspot virus NC_003840.1
  • Astroviridae Avastro virus (Turkey astro virus 1 (TAstV-1)) Y15936.2
  • Alfamovirus Alfamovirus (Alfalfa mosaic virus (AMV)) NC_001495.1
  • Anulavirus (Pelargonium zonate spot virus (PZSV)) NC_003649.1
  • Cucumovirus (Cucumber mosaic virus (strain FNY)) NC_002034.1
  • Oleavirus (Olive latent virus 2 (OLV-2)) NC_003673.1
  • Nebo virus (Newbury- 1 virus) NC_007916.1
  • Vesivirus (Vesicular exanthema of swine virus NC_002551.1 (VESV))
  • Closteroviridae Ampelovirus (Grapevine leafroll-associated virus 3 NC_004667.1
  • Closterovirus (Beet yellows virus (BYV)) NC_001598.1
  • Hepacivirus Hepatitis C virus (HCV) NC_004102.1
  • Pestivirus Bovine diarrhea virus 1 (BVDV-1) NC_001461.1
  • Hepeviridae Hepevirus (Hepatitis E virus (HEV)) NC_001434.1
  • Luteoviridae Enamovirus (Pea enation mosaic virus-1 (PEMV-1)) NC_003629.1
  • Mito virus (Cryphonectria parasitica mito virus 1- NC_004046.1 NB631)
  • Betanodavirus Striped jack nervous necrosis vims NC_003448.1 (SJNNV)
  • Macluravirus (Maclura mosaic vims (MacMV)) Not yet
  • Tritimovirus (Brome streak vims) NC_003501.1
  • Virgaviridae Furovirus Soil-bome wheat mosaic vims (SBWMV)) NC_002041.1 Hordeivirus (Barley stripe mosaic virus (BSMV)) NC_003469.1
  • Pecluvirus Peanutt clump virus (PCV)
  • Pomovirus Potato mop-top virus (PMTV) NC_003723.1
  • Cilevirus (Citrus leprosis virus C (CiLV-C)) NC_008169.1
  • Ourmiavirus (Ourmia melon virus (OuMV)) NC_011068.1
  • Sobemovirus (Southern bean mosaic virus (SBMV)) NC_004060.1
  • Umbravirus (Groundnut rosette virus (GRV)) NC_003603.1
  • Exemplary minus single stranded RNA viruses suitable for use in the RDRP systems of the present invention are present in Table 4.
  • Morbillivirus (Measles virus (MeV)) NC_001498.1
  • Arenaviridae Arenavirus (Lymphocytic choriomeningitis virus NC_004291.1
  • Tospovirus Tomato spotted wilt virus (TSWV)
  • TSWV tomato spotted wilt virus NC_002052.1
  • Ophioviridae Ophiovirus (Citrus psorosis virus (CPsV)) NC_006314.1
  • H5N1 Influenza A virus A/Goose/Guangdong/1/96 NC_007357.1 H5N1 (FLUAV)
  • Influenzavirus B Influenza B/Lee/1940 (FLUBV)) NC_002204.1
  • Influenzavirus C Influenza C virus (C/Ann NC_006307.1 Arbor/ 1/50)
  • Isavirus Infectious salmon anemia virus (ISAV) NC_006505.1
  • Emaravirus European mountain ash ringspot-associated NC_013106.1 virus
  • Alphaviruses comprise a set of genetically, structurally, and serologically related arthropod-borne viruses of the Togaviridae family. These viruses are distributed worldwide, and persist in nature through a mosquito to vertebrate cycle. Birds, rodents, horses, primates, and humans are among the defined alphavirus vertebrate reservoir/hosts. Twenty- six known viruses and virus subtypes have been classified within the alphavirus genus utilizing the hemagglutination inhibition (HI) assay. Sequences encoding wild-type alphaviruses suitable for use in preparing the vectors disclosed herein can be readily obtained from naturally-occurring sources, or from depositories ⁇ e.g., the American Type Culture Collection, Rockville, Md.).
  • alphaviruses include Aura virus (ATCC VR-368), Bebaru virus (ATCC VR-600, ATCC VR-1240), Cabassou virus (ATCC VR-922), Chikungunya virus (ATCC VR-64, ATCC VR-1241), Eastern equine encephalomyelitis virus (ATCC VR-65, ATCC VR-1242), Fort Morgan virus (ATCC VR-924), Getah virus (ATCC VR-369, ATCC VR- 1243), Kyzylagach virus (ATCC VR-927), Mayaro virus (ATCC VR-66, ATCC VR-1277), Middleburg virus (ATCC VR-370), Mucambo virus (ATCC VR-580, ATCC VR-1244), Ndumu virus (ATCC VR-371), Pixuna virus (ATCC VR-372, ATCC VR-1245), Ross River virus (ATCC VR-373, ATCC VR-1246), Semliki Forest virus (ATCC VR-67, ATCC VR-1247), Sindbis virus (ATCC VR-68,
  • Venezuelan equine encephalomyelitis virus (ATCC VR-69, ATCC VR-923, ATCC VR-1250 ATCC VR-1249, ATCC VR-532), Western equine encephalomyelitis virus (ATCC VR-70, ATCC VR-1251, ATCC VR-622, ATCC VR-1252), Whataroa virus (ATCC VR-926), and Y-62-33 virus (ATCC VR-375).
  • the genome of an alphavirus is an approximately 12 kb single-stranded positive-sense RNA molecule which is capped and polyadenylated, and contained within a virus-encoded capsid protein shell.
  • the replicative process is initiated by translation of four nonstructural proteins (NSP1-NSP4) from the 5' two-thirds of the viral genome that participate in the RNA replicative process, which includes binding to the conserved nucleotide sequence elements (CSEs) present at the 5' and 3' ends, and a junction region subgenomic promoter (i.e., a 26S subgenomic promoter) located internally in the genome.
  • NSP1-NSP4 nonstructural proteins from the 5' two-thirds of the viral genome that participate in the RNA replicative process, which includes binding to the conserved nucleotide sequence elements (CSEs) present at the 5' and 3' ends, and a junction region subgenomic promoter (i.e., a 26S subgenomic promoter) located internally in the genome.
  • CSEs conserved nucleotide sequence elements
  • the positive strand genomic RNA i.e., the sense strand
  • the positive strand genomic RNA serves as template for the NSP-catalyzed synthesis of a full-length complementary negative strand, i.e., the non-sense or antisense strand.
  • Synthesis of a complementary negative strand is catalyzed by NSPs binding to the 3' terminal CSE of the positive strand genomic RNA.
  • the negative strand serves as template for the synthesis of additional positive strand genomic RNA and an abundantly expressed 26S subgenomic RNA, initiated internally at the junction region promoter.
  • the 5' end CSE and junction region promoter are functional only after they are transcribed into the negative strand, i.e., the complement of the positive strand genomic RNA (i.e., the 5' end CSE is functional when it is the 3' end of the genomic negative stranded complement).
  • alphavirus nonstructural proteins may be utilized in the present invention, and are therefore deemed to fall within the scope of the phrase "alphavirus nonstructural proteins.” For example, due to the degeneracy of the genetic code, more than one codon may code for a given amino acid. Therefore, a wide variety of nucleic acid sequences which encode alphavirus nonstructural proteins may be generated.
  • amino acid substitutions, additions, or deletions at any of numerous positions may still provide functional or biologically active nonstructural proteins. Methods for making such derivatives are readily accomplished by one of ordinary skill in the art given the disclosure provided herein.
  • retroviral or lentiviral transfer vectors may comprise polynucleotide sequences encoding one, two, three, or all four of the nonstructural proteins of an alphavirus.
  • retroviral or lentiviral transfer vectors comprise a polynucleotide-of-interest operably linked to a 26S promoter.
  • NSP1 can play a role in the initiation of (or continuation of) minus- strand RNA synthesis and capping of the 5' terminus of genomic and subgenomic alphavirus RNAs during transcription.
  • NSP1 has both methyltransferase (Mi and Stollar, 1991. Vir. 184:423-427) and guanyltransferase activity (Strauss and Strauss, 1994. Microbiol. Rev. 58(3):491-562).
  • NSP1 also modulates the proteinase activity of NSP2, as polyproteins containing NSP1 inefficiently cleave between NSP2 and NSP3 (de Groot et al, 1990. EMBO J. 9:2631-2638).
  • NSP2 is a multifunctional protein, involved in the replication of the viral
  • RNA and processing of the nonstructural polyprotein can act as a helicase, which is active in duplex unwinding during RNA replication and transcription.
  • the N-terminal domain of the protein (spanning about the first 460 amino acids) can act as a helicase, which is active in duplex unwinding during RNA replication and transcription.
  • Synthesis of RNA operably linked to the 26S subgenomic promoter and encoding the gene(s) of interest requires functional NSP2.
  • a number of mutations in the proteinase domain of NSP2 have been found to render the synthesis of 26S RNA temperature sensitive (Hahn et al. 1989. J. Virol. 63:3142-3150; Sawicki and Sawicki. 1985. Virology 144:20-34; Sawicki and Sawicki. 1993. J. Virol. 67:3605-3610).
  • NSP3 contains two distinct domains.
  • the N-terminal domain ranges in length from 322 to 329 residues in different alphaviruses and exhibits a minimum of 51% amino acid sequence identity among any two alphaviruses.
  • the C-terminal domain is not conserved among known alphaviruses in length or in sequence, and multiple changes are tolerated (Li et ah, 1990. Virology, 179:416-427).
  • NSP3 play a role in minus-strand viral RNA synthesis.
  • NSP4 is the virus-encoded RNA polymerase and contains the GDD motif characteristic of such enzymes (Karner and Argos, 1984. Nucleic Acids Res.
  • NSP4 plays a role in alphavirus RNA replication, positive strand genomic RNA synthesis from the 5 'CSE, and abundant expression of 26S subgenomic RNA from the 26S promoter. Additionally, NSP4 can be metabolically unstable, through degradation by the N-end rule pathway (Gonda et al, 1989. J. Biol. Chem. 264: 16700-16712). However, NSP4 is stabilized through its association with replication complexes which conceal degradation signals. Further stabilization of the enzyme may be achieved by altering the amino terminal residue of NSP4. Stabilizing amino terminal residues include methionine, alanine, and tyrosine.
  • retroviral or lentiviral transfer vectors may comprise polynucleotide sequences encoding one, two, three, or more junction region promoters (26S promoters).
  • retroviral or lentiviral transfer vectors comprise a 26S subgenomic promoter operably linked to one or more heterologous polynucleotide(s)-of-interest ⁇ e.g., gene encoding a therapeutic
  • the alphavirus viral junction region normally controls transcription initiation of the subgenomic mRNA; thus, this element is also referred to as the subgenomic mRNA promoter.
  • the following table contains an exemplary list of junctional region promoter (26S promoter) sequences for the following alphaviruses: Sindbis virus (SIN), Aura virus (AURA), Eastern equine encephalomyelitis virus (EEE), Middleburg virus (MBV), Ross River virus (RRV), Semliki Forest virus (SFV, SFVl), O'Nyong-Nyong virus (ONN, ONN*), Whataroa virus (WHA), Western equine encephalomyelitis virus (WEE), Venezuelan equine encephalomyelitis virus (VEE, VEE*) and Mayaro virus (MAY); and the Rubella virus (RUB), which is not an alphavirus but has a sequence that resembles the minimal junction region.
  • Table 5 Joint region promoter sequences.
  • vectors of the invention comprise variants or optimal 26S promoter sequences that increase RNA levels compared to unmodified 26S promoter sequences.
  • vectors of the invention that comprise a 26S promoter sequence also include an alphavirus RNA polymerase recognition sequence (also termed "alphavirus replicase recognition sequence", "3' terminal CSE,” or "3' cis replication sequence”).
  • alphavirus RNA polymerase recognition sequence also termed "alphavirus replicase recognition sequence", "3' terminal CSE,” or "3' cis replication sequence”
  • the alphavirus RNA polymerase recognition sequence which is located at the 3' end region of positive stranded genomic RNA, provides a recognition site at which the virus begins replication by synthesis of the negative strand.
  • a wide variety of sequences may be utilized as an alphavirus RNA polymerase recognition sequence.
  • virus vector constructs in which the polymerase recognition is truncated to the smallest region that can still function as a recognition sequence can be utilized.
  • 20S and 23 S RNAs are positive strand RNA viruses found in Saccharomyces cerevisiae and belong to the genus Narnavirus.
  • the 20S and 23 S RNA genomes are small (2514 and 2891 nucleotides, respectively), and each RNA encodes only a single protein: a 91-kDa protein (p91) and a 104-kDa (pi 04), respectively. Both proteins contain four amino acid motifs well conserved among RNA-dependent RNA polymerases.
  • the cis-acting signals for replication in 23S RNA and 20S have been determined (Fujimura and Esteban. J Biol Chem. 282(26): 1901 1-9 (2007), Esteban et al. , JBiol Chem. 280(40):33725-34 (2005), and Esteban and Fujimura. PNAS.
  • the positive strand genomic RNA i.e., the sense strand
  • Synthesis of a complementary negative strand is catalyzed by RDRP binding to the 3' terminal cis- acting sequence of the positive strand genomic RNA.
  • the negative strand serves as template for the synthesis of additional positive strand genomic RNA catalyzed by RDRP binding to the 5' terminal cis-acting sequence.
  • the 5' end cis- acting sequence is functional only after it transcribed into the negative strand, i.e., the complement of the positive strand genomic RNA (i.e., the 5' end cis-acting sequence is functional when it is the 3' end of the genomic negative stranded complement).
  • RNA genomes share five-nucleotide inverted repeats at the 5' and 3' termini (5'-GGGGC... GCCCC-OH). Id.
  • the RNA genomes contain a bipartite cis-signal in the 3 '-region that consists of the cluster of the terminal four Cs and a mismatched pair of purines present in a stem structure adjacent to the 3 '-end.
  • the 3 '-terminal and penultimate Cs are dispensable for launching 20S or 23 S RNA virus, the generated viruses recover these Cs. This indicates that the virus has an efficient 3 '-terminal repair mechanism(s).
  • the bipartite 3 '-cis-signal for replication is also essential for formation of ribonucleoprotein complexes in vivo with its RNA-dependent RNA polymerase, i.e., p91 or pl04.
  • RNA-dependent RNA polymerase i.e., p91 or pl04.
  • the narnavirus RNA 3' cis-acting sequence that binds the RDRP is located at the 3' end region of positive stranded genomic RNA and provides a recognition site at which the virus begins replication by synthesis of the negative strand.
  • RDRP binds to the 5' cis-acting sequence (5'-GGGGC... GCCCC-OH; at the 3' end of the negative genomic RNA) and transcribes the positive strand RNA encoding the RDRP.
  • retroviral or lentiviral transfer vectors may comprise polynucleotide sequences encoding the RDRP of the 23 S RNA narnavirus, pi 04 or an active fragment or variant thereof.
  • retroviral or lentiviral transfer vectors comprise a polynucleotide-of-interest operably linked to the 5' cis-acting sequence that binds pi 04.
  • retroviral or lentiviral transfer vectors comprise a 5' cis-acting sequence that binds pi 04 operably linked to one or more heterologous gene(s)-of-interest.
  • vectors of the invention that comprise a 5' cis-acting sequence that binds pi 04 also include a 3' cis-acting sequence that binds pl04.
  • retroviral or lentiviral transfer vectors may comprise polynucleotide sequences encoding the RDRP of the 20S RNA narnavirus, p91 or an active fragment or variant thereof.
  • retroviral or lentiviral transfer vectors comprise a polynucleotide-of-interest operably linked to the 5' cis-acting sequence that binds p91.
  • retroviral or lentiviral transfer vectors comprise a 5' cis-acting sequence that binds p91 operably linked to one or more heterologous gene(s)-of-interest.
  • vectors of the invention that comprise a 5' cis-acting sequence that binds p91 also include a 3' cis-acting sequence that binds p91.
  • vectors of the invention may be used to achieve ubiquitous, conditional, reversible, or tissue-specific expression or one or more polypeptides, e.g., therapeutic polypeptide or polypeptide-of-interest, in cells, tissues, or organisms.
  • Vectors, including lentiviral vectors and transfer plasmids of the invention may comprise a polynucleotide-of-interest, including, for example, polynucleotide sequences that express a polypeptide of interest or a therapeutic polypeptide.
  • a therapeutic polypeptide is provided to a patient in whom said polypeptide is expressed at a reduced level or in a mutated, less functional form.
  • a polynucleotide-of-interest and its expressed polypeptide includes, but is not limited to, any gene, for which a deficiency results in, or contributes to a disease, disorder, or condition or another disease, e.g., ATP-binding cassette, subfamily D (ALD), member 1 (ABCD1) in adrenoleukodystrophy and
  • Transfer vectors including lentiviral vectors, optionally in combination with polypeptide compositions of the invention can be used in gene therapy, including for the treatment of various diseases, disorders, and conditions.
  • the invention also includes host cells comprising, e.g., transfected with, the vectors of the invention.
  • the host cell is an embryonic stem cell, a somatic stem cell, or a progenitor cell.
  • the present invention contemplates, in part, engineering effective therapeutic viral vector systems by using lentiviral genomes as the transfer vector backbone and heterologous RNA dependent RNA polymerase (RDRP) systems, e.g., of plus-strand or minus-strand ssRNA viruses, to control and amplify transcription of one or more polynucleotides-of-interest.
  • RDRP heterologous RNA dependent RNA polymerase
  • the present invention contemplates several single vector strategies to amplify and control gene expression.
  • the DNA sense strand of an integrated transfer vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the plus strand sequence of a plus-strand ssRNA virus RDRP promoter, e.g., 5' cis-acting sequence and/or subgenomic promoter, operably linked to the sense strand of a polynucleotide- of-interest and a plus strand sequence of a 3' cis-acting sequence.
  • the ubiquitous, tissue specific, or inducible promoter transcribes a sense (plus-strand) mRNA that encodes the polypeptide-of-interest and that can be translated by the ribosome to produce the polypeptide of interest.
  • this arrangement allows for controlled amplification of gene expression.
  • an RDRP binds to the 3' cis-acting sequence at the 3' end of the plus-stranded RNA and using the plus strand as a template, polymerize a non-sense (minus-strand) RNA.
  • the RDRP binds to the subgenomic promoter and/or 5' cis- acting sequence and amplifies sense (plus-strand) RNA copies using the minus strand as a template. These amplified sense (plus-strand) RNA copies of the polypeptide of interest are then translated by the ribosome. Accordingly, this design allows for expression of a translatable RNA from both the ubiquitous, tissue specific, or inducible promoter and the subgenomic promoter, albeit using different RNA templates. In this manner, gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the present invention contemplates several single vector strategies to amplify and control gene expression.
  • the DNA sense strand of an integrated transfer vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the plus strand sequence of a plus-strand ssRNA virus RDRP promoter, e.g., a subgenomic promoter, operably linked to the sense strand of a polynucleotide -of- interest and a plus strand sequence of a 3' cis-acting sequence.
  • the ubiquitous, tissue specific, or inducible promoter transcribes a sense (plus-strand) mRNA that encodes the polypeptide-of-interest and that can be translated by the ribosome to produce the polypeptide of interest.
  • this arrangement allows for controlled amplification of gene expression.
  • an RDRP binds to the 3' cis-acting sequence at the 3' end of the plus-stranded RNA and using the plus strand as a template, polymerize a non-sense (minus-strand) RNA. Once the minus strand RNA has been formed, the RDRP binds to the subgenomic promoter and amplifies sense (plus-strand) RNA copies using the minus strand as a template.
  • RNA copies of the polypeptide of interest are then translated by the ribosome. Accordingly, this design allows for expression of a translatable RNA from both the ubiquitous, tissue specific, or inducible promoter and the subgenomic promoter, albeit using different RNA templates. In this manner, gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the present invention contemplates several single vector strategies to amplify and control gene expression.
  • the DNA sense strand of an integrated transfer vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the plus strand sequence of an alphavirus subgenomic promoter, e.g., 26S
  • the ubiquitous, tissue specific, or inducible promoter transcribes a sense (plus-strand) m NA that encodes the polypeptide-of-interest and that can be translated by the ribosome to produce the polypeptide of interest.
  • this arrangement allows for controlled
  • one or more NSPs bind to the CSE at the 3' end of the plus-stranded RNA and using the plus strand as a template, polymerize a non-sense (minus-strand) RNA. Once the minus strand RNA has been formed, one or more NSPs bind to the alphavirus subgenomic promoter and amplify sense (plus-strand) RNA copies using the minus strand as a template. These amplified sense (plus-strand) RNA copies of the polypeptide of interest are then translated by the ribosome.
  • this design allows for expression of a translatable RNA from both the ubiquitous, tissue specific, or inducible promoter and the subgenomic promoter, albeit using different RNA templates.
  • gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the DNA sense strand of an integrated vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide of interest, which is operably linked to a plus-strand or minus-strand ssRNA virus RDRP promoter in the reverse orientation, e.g., 5' cis-acting sequence and/or subgenomic promoter.
  • RDRP plus-strand or minus-strand ssRNA virus
  • the ubiquitous, tissue specific, or inducible promoter transcribes a reverse complement of the mRNA that encodes the polypeptide of interest and an RDRP promoter in the reverse orientation: the reverse complement sequence encoding a polypeptide of interest cannot be directly translated into the polypeptide of interest.
  • the transcribed mRNA can be used as a minus strand RNA template because it comprises an RDRP promoter in an operable orientation.
  • the RDRP binds to the RDRP promoter sequence (now in the proper orientation) on the transcribed strand and amplifies translatable RNA copies using the transcribed strand as a template in the 3' to 5' orientation.
  • These amplified sense (plus-strand) RNA copies of the polypeptide of interest are now in the proper orientation and are then translated by the ribosome.
  • the 3' cis-acting sequence (CSE) is not needed to generate a minus strand because the RDRP can use the plus-strand RNA in the 3' to 5' orientation as a minus-strand template.
  • CSE 3' cis-acting sequence
  • the DNA sense strand of an integrated vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide of interest, which is operably linked to a plus-strand or minus-strand ssRNA virus RDRP promoter in the reverse orientation, e.g., a subgenomic promoter.
  • a ubiquitous, tissue specific, or inducible promoter transcribes a reverse complement of the mRNA that encodes the polypeptide of interest and the subgenomic promoter in the reverse orientation: the reverse complement sequence encoding the polypeptide of interest cannot be directly translated into the polypeptide of interest.
  • the transcribed mRNA can be used as a minus strand RNA template.
  • RDRP binds to the subgenomic promoter sequence, which is operable in the 3' to 5' orientation on the transcribed mRNA, and amplifies translatable RNA copies using the transcribed strand as a template in the 3' to 5' orientation.
  • These amplified sense (plus-strand) RNA copies of the polypeptide of interest are now in the proper orientation and are then translated by the ribosome. Accordingly, the CSE is not needed to generate a minus strand because the RDRP can use the plus-strand RNA in the 3 ' to 5 ' orientation as a minus-strand template. In this manner, gene expression of the one or more
  • polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the DNA sense strand of an integrated vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide of interest, which is operably linked to an alphavirus subgenomic promoter in the reverse orientation, e.g., 26S subgenomic promoter.
  • the ubiquitous, tissue specific, or inducible promoter transcribes a reverse complement of the mRNA that encodes the polypeptide of interest and an alphavirus subgenomic promoter in reverse orienation: the reverse complement encoding the polypeptide of interest cannot be directly translated into the polypeptide of interest.
  • the transcribed mRNA can be used as a minus strand RNA template in the 3' to 5' orientation.
  • one or more NSPs bind to the alphavirus subgenomic promoter sequence on the transcribed strand and amplify translatable RNA copies using the transcribed strand as a template.
  • These amplified sense (plus-strand) RNA copies of the polypeptide of interest are now in the proper orientation and are then translated by the ribosome. Accordingly, the CSE is not needed to generate a minus strand because the RDRP can use the plus-strand RNA in the 3' to 5' orientation as a minus-strand template..
  • gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the DNA sense strand of an integrated vector comprises: 1) a ubiquitous, tissue specific, or inducible promoter operably linked to the sense strand of a polynucleotide of interest and 2) the reverse complement sequence of a polynucleotide of interest, which is operably linked to a plus-strand single strand ssRNA virus RDRP promoter in the reverse orientation, e.g., 5' cis-acting sequence or subgenomic promoter ⁇ e.g., 26S subgenomic promoter).
  • the ubiquitous, tissue specific, or inducible promoter transcribes a sense (plus-strand) mRNA that encodes the polypeptide of interest and that can be translated by the ribosome to produce the polypeptide of interest.
  • the mRNA comprises a reverse complement of the mRNA that encodes the polypeptide of interest and an RDRP promoter in the reverse orientation.
  • either one or both of the sequences can be codon optimized so that the identity between the sequences is neglible. Accordingly, this design allows for expression of a translatable RNA from both the ubiquitous, tissue specific, or inducible promoter and the RDRP promoter. In this manner, gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • RDRP RNA dependent RNA polymerase
  • an RDRP promoter e.g. 5' cis-acting sequence or subgenomic promoter
  • the RNA dependent RDRP and RDRP promoter can be selected from any plus-strand ssRNA virus.
  • the plus-strand ssRNA virus is an alphavirus or narnavirus.
  • a vector, e.g., viral vector or transfer plasmid, of the invention comprises a left (5') retroviral LTR; a promoter operably linked to one or more polynucleotides encoding an RDRP, the reverse complement sequence of a polynucleotide encoding a mammalian polypeptide operably linked to an RDRP promoter in the reverse orientation (e.g. 5' cis-acting sequence or subgenomic promoter); and a right (3') retroviral LTR.
  • the RDRP and RDRP promoter can be selected from any minus-strand or plus-strand ssRNA virus.
  • the plus-strand ssRNA virus is an alphavirus or narnavirus.
  • a vector, e.g., viral vector or transfer plasmid, of the invention comprises a left (5') retroviral LTR; a promoter operably linked to one or more polynucleotides encoding an RDRP, a polynucleotide encoding a mammalian polypeptide, the reverse complement of a polynucleotide encoding the mammalian polypeptide operably linked to the an RDRP promoter in the reverse orientation; and a right (3') retroviral LTR, wherein one or both polynucleotide sequences of the mammalian therapeutic polypeptide are codon optimized.
  • the RDRP and RDRP promoter can be selected from any minus-strand or plus-strand ssRNA virus.
  • the plus-strand ssRNA virus is an alphavirus or narnavirus.
  • a vector of the invention comprises: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding one or more alphavirus non-structural proteins (NSP1-NSP4), an alphavirus subgenomic promoter, e.g., a 26S subgenomic promoter, at least one polynucleotide encoding a mammalian therapeutic polypeptide, and a CSE for production of a minus strand RNA.
  • a heterologous promoter e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion
  • one, two, three, or all four NSPs are operably linked to a ubiquitous, tissue specific, or inducible promoter.
  • the polynucleotide sequences encoding NSPs can be contiguous or they can be separated by one or more IRES sequences and or polynucleotide sequences that include self-cleaving polypeptide sites, e.g., a 2A or 2A polypeptides as disclosed elsewhere herein.
  • NSPs can be expressed as a polyprotein that undergoes self-cleaving or, a polyprotein comprising individual NSP/self-cleaving 2A peptide fusion polypeptides.
  • a ubiquitous, tissue specific, or inducible promoter is operably linked to an NSP2-2A-NSP4 fusion polypeptide.
  • a ubiquitous, tissue specific, or inducible promoter is operably linked to NSP4.
  • a vector of the invention comprises: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; and a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding one or more alphavirus non-structural proteins (NSP1-NSP4), the reverse complement of a polynucleotide encoding a mammalian therapeutic polypeptide operably linked to an alphavirus 26S subgenomic promoter in the reverse orientation.
  • a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding one or more alphavirus non-structural proteins
  • a vector of the invention comprises: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; and a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding one or more alphavirus non-structural proteins (NSP1-NSP4), a polynucleotide encoding a mammalian therapeutic polypeptide, the reverse complement of a polynucleotide encoding the mammalian therapeutic polypeptide operably linked ton alphavirus 26S subgenomic promoter in the reverse orientation, wherein one or both polynucleotide sequences of the mammalian therapeutic polypeptide are codon optimized.
  • a ubiquitous, tissue specific, or inducible promoter oper
  • a vector of the invention comprises: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding NSP4 or NSP2 and NSP4, optionally encoded as a fusion polypeptide, e.g.,NSP2-2A-NSP4; and another ubiquitous, tissue specific, or inducible promoter operably linked to an alphavirus 26S subgenomic promoter and at least one polynucleotide encoding a mammalian therapeutic polypeptide, e.g., a globin polypeptide or variant thereof, and a CSE for production of a minus strand RNA.
  • a vector of the invention comprises: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding NSP4 or NSP2 and NSP4, optionally encoded as a fusion polypeptide, e.g.,NSP2-2A-NSP4; and another ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement of a polynucleotide encoding a mammalian therapeutic polypeptide, e.g., a globin polypeptide or variant thereof operably linked to an alphavirus 26S subgenomic promoter in the reverse orientation.
  • a vector of the invention comprises: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding NSP4 or NSP2 and NSP4, optionally encoded as a fusion polypeptide, e.g.,NSP2-2A-NSP4; and another ubiquitous, tissue specific, or inducible promoter operably linked a polynucleotide encoding a mammalian therapeutic polypeptide, e.g., a globin polypeptide or variant thereof, the reverse complement of a polynucleotide encoding a mammalian therapeutic polypeptide operably linked to an alphavirus
  • the foregoing vectors may further comprise one or more of each of the following: packaging sequences, posttranscriptional recognition elements ⁇ e.g., WPRE, HPRE), insulator elements, cPPT/FLAP sequences, selectable markers, a retroviral export element, e.g., a lentiviral REV response element (RRE), and other lentiviral vector features as disclosed elsewhere herein.
  • packaging sequences posttranscriptional recognition elements ⁇ e.g., WPRE, HPRE
  • insulator elements e.g., insulator elements
  • cPPT/FLAP sequences e.g., selectable markers
  • a retroviral export element e.g., a lentiviral REV response element (RRE)
  • RRE lentiviral REV response element
  • the present invention contemplates, in part, engineering effective therapeutic vector systems by using at least two vectors: at least one of the vectors encoding the RDRP either from an expression vector or a retroviral vector, e.g., lentiviral vector, and at least one retroviral or lentiviral vector comprising a RDRP promoter operably linked to one or more polynucleotides-of-interest.
  • a retroviral vector e.g., lentiviral vector
  • retroviral or lentiviral vector comprising a RDRP promoter operably linked to one or more polynucleotides-of-interest.
  • the present invention contemplates, in part, engineering effective therapeutic vector systems by using a vector that encodes a heterologous RDRP and a lentiviral vector comprising a RDRP promoter sequence, e.g., 5' cis-acting sequence or subgenomic promoter ⁇ e.g., 26S subgenomic promoter) operably linked to one or more polynucleotides-of-interest.
  • a RDRP promoter sequence e.g., 5' cis-acting sequence or subgenomic promoter ⁇ e.g., 26S subgenomic promoter
  • the second vector has integrated as provirus into a cell and the first vector is also present in the same cell, either as an expression plasmid or integrated viral vector
  • the RDRP controls and/or amplifies transcription of the one or more polynucleotides-of-interest.
  • expression is tightly controlled by using the RDRP expression as a gene switch.
  • the gene expression system is "off and in
  • a first vector either an expression vector or viral vector (e.g., retroviral or lentiviral vector) comprises a ubiquitous, tissue specific, or inducible promoter operably linked to a polynucleotide encoding an RDRP or RDRP complex.
  • the first vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to one, two, three, or four members of an RDRP complex.
  • polynucleotide sequences encoding members of the RDRP complex can be contiguous or they can be separated by one or more IRES sequences and or polynucleotide sequences that include self-cleaving polypeptide sites, e.g., a 2A or 2A polypeptides as disclosed elsewhere herein
  • a first vector either an expression vector or viral vector (e.g., retroviral or lentiviral vector) comprises a ubiquitous, tissue specific, or inducible promoter operably linked to a polynucleotide encoding an RNA dependent RNA polymerase or polymerase complex.
  • the first vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to a polynucleotide encoding one or more alphavirus nonstructural proteins (NSP1-NSP4).
  • the first vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to one, two, three, or four NSPs.
  • the first vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to NSP4 or NSP2 and NSP4.
  • the polynucleotide sequences encoding NSPs can be contiguous or they can be separated by one or more IRES sequences and or
  • NSPs can be expressed as a polyprotein that undergoes self-cleaving or, a polyprotein comprising individual NSP/self-cleaving 2A peptide fusion polypeptides.
  • a ubiquitous, tissue specific, or inducible promoter is operably linked to NSP4 or an NSP2-2A-NSP4 fusion polypeptide.
  • the second vector of the binary vector strategy is a lentiviral or retroviral vector comprising a RDRP promoter sequence operably linked to one or more polynucleotides-of-interest.
  • the DNA sense strand of an integrated second vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the plus strand sequence of a plus-strand ssRNA virus RDRP promoter, e.g., 5' cis-acting sequence and/or subgenomic promoter, operably linked to the sense strand of a polynucleotide -of-interest and a plus strand sequence of a 3' cis- acting sequence.
  • the ubiquitous, tissue specific, or inducible promoter transcribes a sense (plus-strand) mRNA that encodes the polypeptide-of- interest and that can be translated by the ribosome to produce the polypeptide of interest.
  • an RDRP binds to the 3' cis-acting sequence at the 3' end of the plus-stranded RNA and using the plus strand as a template, polymerize a non-sense (minus-strand) RNA. Once the minus strand RNA has been formed, the RDRP binds to the subgenomic promoter and/or 5' cis-acting sequence and amplifies sense (plus- strand) RNA copies using the minus strand as a template. These amplified sense (plus- strand) RNA copies of the polypeptide of interest are then translated by the ribosome.
  • this design allows for expression of a translatable RNA from both the ubiquitous, tissue specific, or inducible promoter and the subgenomic promoter, albeit using different RNA templates.
  • gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the DNA sense strand of an integrated second vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the plus strand sequence of a plus-strand ssRNA virus RDRP promoter, e.g., a subgenomic promoter, operably linked to the sense strand of a polynucleotide-of-interest and a plus strand sequence of a 3' cis-acting sequence.
  • the ubiquitous, tissue specific, or inducible promoter transcribes a sense (plus-strand) mRNA that encodes the polypeptide -of-interest and that can be translated by the ribosome to produce the polypeptide of interest.
  • an RDRP binds to the 3' cis-acting sequence at the 3' end of the plus-stranded RNA and using the plus strand as a template, polymerize a non-sense (minus-strand) RNA. Once the minus strand RNA has been formed, the RDRP binds to the subgenomic promoter and amplifies sense (plus-strand) RNA copies using the minus strand as a template. These amplified sense (plus-strand) RNA copies of the polypeptide of interest are then translated by the ribosome.
  • this design allows for expression of a translatable RNA from both the ubiquitous, tissue specific, or inducible promoter and the subgenomic promoter, albeit using different RNA templates.
  • gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the DNA sense strand of an integrated second vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the plus strand sequence of an alphavirus subgenomic promoter, e.g., 26S subgenomic promoter, operably linked to the sense strand of a polynucleotide-of-interest and a plus strand sequence of a CSE.
  • an alphavirus subgenomic promoter e.g., 26S subgenomic promoter
  • the ubiquitous, tissue specific, or inducible promoter transcribes a sense (plus-strand) mRNA that encodes the polypeptide-of-interest and that can be translated by the ribosome to produce the polypeptide of interest.
  • this arrangement allows for controlled amplification of gene expression.
  • one or more NSPs When, present, one or more NSPs bind to the CSE at the 3' end of the plus-stranded RNA and using the plus strand as a template, polymerize a non-sense (minus-strand) RNA. Once the minus strand RNA has been formed, one or more NSPs bind to the alphavirus subgenomic promoter and amplify sense (plus-strand) RNA copies using the minus strand as a template.
  • RNA copies of the polypeptide of interest are then translated by the ribosome. Accordingly, this design allows for expression of a translatable RNA from both the ubiquitous, tissue specific, or inducible promoter and the subgenomic promoter, albeit using different RNA templates. In this manner, gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the DNA sense strand of an integrated second vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide of interest, which is operably linked to the a plus-strand or minus-strand ssRNA virus RDRP promoter in the reverse orientation, e.g., 5' cis-acting sequence and/or subgenomic promoter.
  • the ubiquitous, tissue specific, or inducible promoter transcribes a reverse complement of the mRNA that encodes the polypeptide of interest and an RDRP promoter in the reverse orientation: the reverse complement encoding the polypeptide of interest cannot be directly translated into the polypeptide of interest.
  • the transcribed mRNA can be used as a minus strand RNA template in the 3' to 5' orientation.
  • the RDRP binds to the RDRP promoter sequence on the transcribed strand and amplifies translatableRNA copies using the transcribed strand as a template.
  • These amplified sense (plus-strand) RNA copies of the polypeptide of interest are now in the proper orientation and are then translated by the ribosome.
  • the 3' cis-acting sequence (CSE) is not needed to generate a minus strand because the RDRP can use the plus-strand RNA in the 3' to 5' orientation as a minus-strand template.
  • gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the DNA sense strand of an integrated second vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide of interest, which is operably linked to a plus-strand or minus-strand ssRNA virus RDRP promoter in the reverse orientation, e.g., a subgenomic promoter.
  • a ubiquitous, tissue specific, or inducible promoter transcribes a reverse complement of the mRNA that encodes the polypeptide of interest and a subgenomic promoter in the reverse orientation: the reverse complement encoding the polypeptide of interest cannot be directly translated into the polypeptide of interest.
  • the transcribed mRNA can be used as a minus strand RNA template in the 3' to 5 ' orientation.
  • RDRP binds to the subgenomic promoter sequence on the transcribed strand and amplifies translatable RNA copies using the minus strand as a template.
  • These amplified sense (plus-strand) RNA copies of the polypeptide of interest are now in the proper orientation and are then translated by the ribosome.
  • the CSE is not needed to generate a minus strand because RDRP can use the plus-strand RNA in the 3' to 5' orientation as a minus-strand template.
  • gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the DNA sense strand of an integrated second vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide of interest, which is operably linked to the an alphavirus subgenomic promoter in the reverse orientation, e.g., 26S subgenomic promoter.
  • the ubiquitous, tissue specific, or inducible promoter transcribes a reverse complement of the mRNA that encodes the polypeptide of interest and an alphavirus subgenomic promoter in the reverse orientation: the reverse complement encoding the polypeptide of interest cannot be directly translated into the polypeptide of interest.
  • the transcribed mRNA can be used as a minus strand RNA template in the 3' to 5' orientation.
  • one or more NSPs bind to the alphavirus subgenomic promoter sequence on the transcribed strand and amplify translatable RNA copies using the transcribed strand as a template.
  • These amplified sense (plus-strand) RNA copies of the polypeptide of interest are now in the proper orientation and are then translated by the ribosome. Accordingly, the CSE is not needed to generate a minus strand because RDRP can use the plus-strand RNA in the 3' to 5' orientation as a minus-strand template.
  • gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the DNA sense strand of an integrated second vector comprises: 1) a ubiquitous, tissue specific, or inducible promoter operably linked to the sense strand of a polynucleotide of interest and 2) the reverse complement sequence of a polynucleotide of interest, which is operably linked to a plus-strand single strand ssRNA virus RDRP promoter in the reverse orientation, e.g., 5' cis-acting sequence or subgenomic promoter ⁇ e.g., 26S subgenomic promoter).
  • the ubiquitous, tissue specific, or inducible promoter transcribes a sense (plus-strand) mRNA that encodes the polypeptide of interest and that can be translated by the ribosome to produce the polypeptide of interest.
  • the mRNA comprises a reverse complement of the mRNA that encodes the polypeptide of interest and an RDRP promoter in the reverse orientation.
  • either one or both of the sequences can be codon optimized so that the identity between the sequences is neglible. Accordingly, this design allows for expression of a translatable RNA from both the ubiquitous, tissue specific, or inducible promoter and the RDRP promoter. In this manner, gene expression of the one or more polypeptides of interest can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • a binary vector system comprises a first vector, either an expression vector or viral vector ⁇ e.g., retroviral or lentiviral vector) comprising a ubiquitous, tissue specific, or inducible promoter operably linked to a polynucleotide encoding an RDRP or RDRP complex; and a second vector comprising a left (5') retroviral LTR; a promoter operably linked to an RDRP promoter operably linked to at least one polynucleotide encoding a mammalian polypeptide, and a CSE for production of a minus strand RNA; and a right (3') retroviral LTR.
  • an expression vector or viral vector ⁇ e.g., retroviral or lentiviral vector
  • a ubiquitous, tissue specific, or inducible promoter operably linked to a polynucleotide encoding an RDRP or RDRP complex
  • a second vector comprising a left (5') retroviral LTR
  • the RNA dependent RDRP and RDRP promoter can be selected from any plus-strand ssRNA virus.
  • the plus-strand ssRNA virus is an alphavirus or narnavirus.
  • a binary vector system comprises a first vector, either an expression vector or viral vector ⁇ e.g., retroviral or lentiviral vector) comprising a ubiquitous, tissue specific, or inducible promoter operably linked to a polynucleotide encoding an RDRP or RDRP complex; and a second vector comprising a left (5') retroviral LTR; a promoter operably linked to the reverse complement sequence of a polynucleotide encoding a mammalian polypeptide operably linked to an RDRP promoter in the reverse orientation; and a right (3') retroviral LTR.
  • the RDRP and RDRP promoter can be selected from any minus-strand or plus-strand ssRNA virus.
  • the plus-strand ssRNA virus is an alphavirus or narnavirus.
  • a binary vector system comprises a first vector, either an expression vector or viral vector (e.g., retroviral or lentiviral vector) comprising a ubiquitous, tissue specific, or inducible promoter operably linked to a polynucleotide encoding an RDRP or RDRP complex; and a second vector comprising a left (5') retroviral LTR; a promoter operably linked to a polynucleotide encoding a mammalian polypeptide, the reverse complement of a polynucleotide encoding the mammalian polypeptide operably linked to an RDRP promoter in the reverse orientation; and a right (3') retroviral LTR, wherein one or both polynucleotide sequences of the mammalian therapeutic polypeptide are codon optimized.
  • the RDRP and RDRP promoter can be selected from any minus-strand or plus-strand ssRNA virus.
  • the plus-strand ss can be selected from any minus-strand
  • a binary vector system comprises a first vector, either an expression vector or viral vector (e.g., retroviral or lentiviral vector) comprising a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding one or more alphavirus non-structural proteins (NSP1-NSP4); and a second vector comprising: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; a ubiquitous, tissue specific, or inducible promoter operably linked to an alphavirus 26S subgenomic promoter, at least one polynucleotide encoding a mammalian therapeutic polypeptide, and a CSE for production of a minus strand RNA.
  • an expression vector or viral vector
  • a binary vector system comprises a first vector, either an expression vector or viral vector (e.g., retroviral or lentiviral vector) comprising a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding one or more alphavirus non-structural proteins (NSP1- NSP4); and a second vector comprising: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; and a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement of a polynucleotide encoding a mammalian therapeutic polypeptide operably linked to an alphavirus 26S subgenomic promoter in the reverse orientation.
  • an expression vector or viral vector e.g.,
  • a binary vector system comprises a first vector, either an expression vector or viral vector (e.g., retroviral or lentiviral vector) comprising a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding one or more alphavirus non-structural proteins (NSP1-
  • a second vector comprising: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; and a ubiquitous, tissue specific, or inducible promoter operably linked to a polynucleotide encoding a mammalian therapeutic polypeptide, the reverse complement of a polynucleotide encoding the mammalian therapeutic polypeptide operably linked to an alphavirus 26S subgenomic promoter in the reverse orientation, wherein one or both polynucleotide sequences of the mammalian therapeutic polypeptide are codon optimized.
  • a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and
  • a binary vector system comprises a first vector, either an expression vector or viral vector (e.g., retroviral or lentiviral vector) comprising a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding NSP4 or NSP2 and NSP4, optionally encoded as a fusion polypeptide, e.g.,NSP2-2A-NSP4; and a second vector comprising: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; a ubiquitous, tissue specific, or inducible promoter operably linked to an alphavirus 26S subgenomic promoter and at least one polynucleotide encoding a mammalian therapeutic polypeptide,
  • a binary vector system comprises a first vector, either an expression vector or viral vector ⁇ e.g., retroviral or lentiviral vector) comprising a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding NSP4 or NSP2 and NSP4, optionally encoded as a fusion polypeptide, e.g.,NSP2-2A-NSP4; and a second vector comprising: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement of a polynucleotide encoding a mammalian therapeutic polypeptide, e.g., a globin poly
  • a binary vector system comprises a first vector, either an expression vector or viral vector ⁇ e.g., retroviral or lentiviral vector) comprising a ubiquitous, tissue specific, or inducible promoter operably linked to polynucleotides encoding NSP4 or NSP2 and NSP4, optionally encoded as a fusion polypeptide, e.g.,NSP2-2A-NSP4; and a second vector comprising: a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence; a ubiquitous, tissue specific, or inducible promoter operably linked to a polynucleotide encoding a mammalian therapeutic polypeptide, e.g., a globin polypeptide
  • posttranscriptional recognition elements ⁇ e.g., WPRE, HPRE
  • insulator elements e.g., insulator elements, cPPT/FLAP sequences, selectable markers, a retroviral export element, e.g., a lentiviral REV response element (RRE), and other lentiviral vector features as disclosed elsewhere herein.
  • RRE lentiviral REV response element
  • the present invention contemplates, in part, engineering effective therapeutic vector systems that are used in combination with a polypeptide composition.
  • the present invention contemplates, in part, engineering effective therapeutic vector systems comprising: a composition comprising an RDRP or RDRP complex and a lentiviral vector comprising a RDRP promoter sequence operably linked to one or more polynucleotides-of-interest.
  • a composition comprising an RDRP or RDRP complex and a lentiviral vector comprising a RDRP promoter sequence operably linked to one or more polynucleotides-of-interest.
  • the composition and integrated viral vector are present in the same cell, the RDRP or RDRP complex controls and/or amplifies transcription of the one or more
  • the vector component can be identical to the second vector disclosed in the binary vector system, see supra.
  • the cell can be contacted with a composition comprising an RDRP or RDRP complex.
  • the RDRP, polypeptides of the RDRP complex, and/or one or more RDRP polypeptides are fusion polypeptides comprising one or more cell permeable peptides (CPP), as discussed elsewhere herein, to facilitate entry of the polypeptides into the transduced cell.
  • CPP cell permeable peptides
  • a composition comprising an RDRP or RDRP complex contacts a cell transduced with a vector comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the plus strand sequence of a plus- strand ssRNA virus RDRP promoter operably linked to the sense strand of a polynucleotide of interest and the plus strand of a 3' cis-acting element.
  • a composition comprising an RDRP or RDRP complex contacts a cell transduced with a vector comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the plus strand sequence of an alphavirus 26S subgenomic promoter operably linked to the sense strand of a polynucleotide of interest and a CSE.
  • a composition comprising one or more alphavirus comprising one or more alphavirus
  • nonstructural proteins contacts a cell transduced with a vector comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the plus strand sequence of an alphavirus 26S subgenomic promoter operably linked to the sense strand of a polynucleotide of interest and a CSE.
  • a composition comprising NSP4 or NSP2 and NSP4 contacts a cell transduced with a vector comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the plus strand sequence of an alphavirus 26S subgenomic promoter operably linked to the sense strand of a polynucleotide of interest and a CSE.
  • a composition comprising an RNA dependent RNA polymerase or polymerase complex vector strategies contacts a cell transduced with a vector comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide of interest, which is operably linked to a plus-strand or minus-strand ssRNA virus RDRP promoter in the reverse orientation.
  • a composition comprising an RDRP or RDRP complex vector strategies contacts a cell transduced with a vector comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide of interest, which is operably linked to an alphavirus 26S subgenomic promoter in the reverse orientation.
  • a composition comprising one or more alphavirus nonstructural proteins contacts a cell transduced with a vector comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide of interest, which is operably linked to an alphavirus 26S subgenomic promoter in the reverse orientation.
  • composition comprising NSP4 or NSP2 and NSP4 contacts a cell transduced with a vector comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide of interest, which is operably linked to an alphavirus 26S subgenomic promoter in the reverse orientation.
  • composition comprising an RDRP or RDRP complex vector strategies contacts a cell transduced with a vector comprising: 1) a ubiquitous, tissue specific, or inducible promoter operably linked to the sense strand of a polynucleotide of interest and 2) the reverse complement sequence of a
  • a composition comprising an RDRP or RDRP complex contacts a cell transduced with a vector comprising: 1) a ubiquitous, tissue specific, or inducible promoter operably linked to the sense strand of a polynucleotide of interest and 2) the reverse complement sequence of a polynucleotide of interest, which is operably linked to the an alphavirus 26S subgenomic promoter in the reverse orientation.
  • a composition comprising one or more alphavirus nonstructural proteins contacts a cell transduced with a vector comprising: 1) a ubiquitous, tissue specific, or inducible promoter operably linked to the sense strand of a polynucleotide of interest and 2) the reverse complement sequence of a polynucleotide of interest, which is operably linked to an alphavirus 26S subgenomic promoter in the reverse orientation.
  • a composition comprising NSP4 or NSP2 and NSP4 contacts a cell transduced with a vector comprising: 1) a ubiquitous, tissue specific, or inducible promoter operably linked to the sense strand of a polynucleotide of interest and 2) the reverse complement sequence of a polynucleotide of interest, which is operably linked to an alphavirus 26S subgenomic promoter in the reverse orientation.
  • a vector comprises a left (5') retroviral LTR; a promoter operably linked to an RDRP promoter operably linked to at least one polynucleotide encoding a mammalian polypeptide, and a CSE for production of a minus strand RNA; and a right (3') retroviral LTR.
  • a vector comprises a left (5') retroviral LTR; a promoter operably linked to the reverse complement sequence of a polynucleotide encoding a mammalian polypeptide operably linked to a plus-strand or minus-strand ssRNA virus RDRP promoter in the reverse orientation; and a right (3') retroviral LTR.
  • a vector comprises a left (5') retroviral LTR; a promoter operably linked to a polynucleotide encoding a mammalian polypeptide, the reverse complement of a polynucleotide encoding the mammalian polypeptide operably linked to a plus-strand or minus-strand ssRNA virus RDRP promoter in the reverse orientation; and a right (3') retroviral LTR, wherein one or both polynucleotide sequences of the mammalian therapeutic polypeptide are codon optimized.
  • a vector comprises a left (5') retroviral LTR; a promoter operably linked to an RDRP promoter, e.g., an alphavirus 26S subgenomic promoter, operably linked to at least one polynucleotide encoding a mammalian polypeptide, and a CSE for production of a minus strand RNA; and a right (3') retroviral LTR.
  • an RDRP promoter e.g., an alphavirus 26S subgenomic promoter, operably linked to at least one polynucleotide encoding a mammalian polypeptide, and a CSE for production of a minus strand RNA
  • RDRP promoter e.g., an alphavirus 26S subgenomic promoter
  • a vector comprises a left (5') retroviral LTR; a promoter operably linked to the reverse complement sequence of a polynucleotide encoding a mammalian polypeptide operably linked to an RDRP promoter in the reverse orientation, e.g., an alphavirus 26S subgenomic promoter; and a right (3') retroviral LTR.
  • a vector comprises a left (5') retroviral LTR; a promoter operably linked to a polynucleotide encoding a mammalian
  • polypeptide the reverse complement of a polynucleotide encoding the mammalian polypeptide operably linked to an RDRP in the reverse orientation, e.g., an alphavirus 26S subgenomic promoter; and a right (3') retroviral LTR, wherein one or both polynucleotide sequences of the mammalian therapeutic polypeptide are codon optimized.
  • the vectors comprise a modified left (5') retroviral LTR comprising a deletion in U3 and a heterologous promoter, e.g., CMV, RSV, MoMLV and/or a modified right (3') retroviral LTR comprising a U3 deletion and/or U5 deletion and a heterologous polyA tail addition sequence.
  • the transfer vectors comprise a mammalian therapeutic polypeptide, such as, for example, a globin polypeptide or variant thereof.
  • the vectors e.g., retroviral or lentiviral transfer vectors may further comprise one or more of each of the following: packaging sequences, posttranscriptional recognition elements ⁇ e.g., WPRE, HPRE), insulator elements, cPPT/FLAP sequences, selectable markers, and other lentiviral vector features as disclosed elsewhere herein.
  • packaging sequences e.g., WPRE, HPRE
  • insulator elements e.g., WPRE, HPRE
  • cPPT/FLAP sequences e.g., cPPT/FLAP sequences
  • selectable markers e.g., selectable markers
  • other lentiviral vector features as disclosed elsewhere herein.
  • compositions of the invention may comprise one or more polypeptides, polynucleotides, vectors comprising same, etc., as described herein, formulated in pharmaceutically-acceptable or physiologically-acceptable solutions for administration to a cell or an animal, either alone, or in combination with one or more other modalities of therapy. It will also be understood that, if desired, the compositions of the invention may be administered in combination with other agents as well, such as, e.g., other proteins, polypeptides, small molecules or various pharmaceutically-active agents. There is virtually no limit to other components that may also be included in the compositions, provided that the additional agents do not adversely affect the ability of the composition to deliver the intended gene therapy.
  • compositions of the invention formulation of pharmaceutically-acceptable excipients and carrier solutions is well-known to those of skill in the art, as is the development of suitable dosing and treatment regimens for using the particular compositions described herein in a variety of treatment regimens, including e.g., oral, parenteral, intravenous, intranasal, and intramuscular administration and formulation.
  • compositions disclosed herein may be delivered via oral administration to a subject.
  • these compositions may be formulated with an inert diluent or with an assimilable edible carrier, or they may be enclosed in hard- or soft-shell gelatin capsule, or they may be compressed into tablets, or they may be incorporated directly with the food of the diet.
  • Solutions of the active compounds as free base or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as
  • Dispersions may also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms .
  • the pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions (U.S. Pat. No. 5,466,468, specifically incorporated herein by reference in its entirety).
  • the form should be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and should be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils.
  • polyol e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like
  • suitable mixtures thereof e.g., vegetable oils
  • vegetable oils e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like
  • suitable mixtures thereof e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like
  • vegetable oils e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like
  • Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion
  • isotonic agents for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
  • the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose.
  • a sterile aqueous medium that can be employed will be known to those of skill in the art in light of the present disclosure.
  • one dosage may be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion (see, e.g.,
  • Sterile injectable solutions can be prepared by incorporating the active compounds in the required amount in the appropriate solvent with the various other ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above.
  • the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • compositions disclosed herein may be formulated in a neutral or salt form.
  • Pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like.
  • solutions Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective.
  • the formulations are easily administered in a variety of dosage forms such as injectable solutions, drug-release capsules, and the like.
  • carrier includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like.
  • carrier includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like.
  • the use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.
  • phrases "pharmaceutically-acceptable" refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human.
  • the preparation of an aqueous composition that contains a protein as an active ingredient is well understood in the art. Typically, such
  • compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection can also be prepared.
  • the preparation can also be emulsified.
  • the compositions may be delivered by intranasal sprays, inhalation, and/or other aerosol delivery vehicles.
  • Methods for delivering genes, polynucleotides, and peptide compositions directly to the lungs via nasal aerosol sprays has been described e.g., in U.S. Pat. No. 5,756,353 and U.S. Pat. No. 5,804,212 (each specifically incorporated herein by reference in its entirety).
  • the delivery of drugs using intranasal microparticle resins Takenaga et ah, 1998) and lysophosphatidyl-glycerol compounds (U.S. Pat. No. 5,725,871, specifically
  • transmucosal drug delivery in the form of a
  • the delivery may occur by use of liposomes, nanocapsules, microparticles, microspheres, lipid particles, vesicles, optionally mixing with CPP polypeptides, and the like, for the introduction of the compositions of the present invention into suitable host cells.
  • the compositions of the present invention may be formulated for delivery either encapsulated in a lipid particle, a liposome, a vesicle, a nanosphere, a nanoparticle or the like.
  • the formulation and use of such delivery vehicles can be carried out using known and conventional techniques.
  • the formulations and compositions of the invention may comprise one or more repressors and/or activators comprised of a combination of any number of polypeptides, polynucleotides, and small molecules, as described herein, formulated in
  • compositions of the invention may be administered in combination with other agents as well, such as, e.g., cells, other proteins or polypeptides or various pharmaceutically- active agents.
  • a formulation or composition according to the present invention comprises a cell contacted with a combination of any number of polypeptides, polynucleotides, and small molecules, as described herein.
  • the present invention provides formulations or compositions suitable for the delivery of viral vector systems (i.e., viral-mediated transduction) including, but not limited to, retroviral (e.g., lentiviral) vectors.
  • viral vector systems i.e., viral-mediated transduction
  • retroviral vectors e.g., lentiviral
  • Exemplary formulations for ex vivo delivery may also include the use of various transfection agents known in the art, such as calcium phosphate, electoporation, heat shock and various liposome formulations (i.e., lipid-mediated transfection).
  • various transfection agents known in the art, such as calcium phosphate, electoporation, heat shock and various liposome formulations (i.e., lipid-mediated transfection).
  • Liposomes are lipid bilayers entrapping a fraction of aqueous fluid. DNA spontaneously associates to the external surface of cationic liposomes (by virtue of its charge) and these liposomes will interact with the cell membrane.
  • the present invention provides pharmaceutically acceptable compositions which comprise a therapeutically-effective amount of one or more polynucleotides or polypeptides, as described herein, formulated together with one or more pharmaceutically acceptable carriers (additives) and/or diluents (e.g., pharmaceutically acceptable cell culture medium).
  • cells are contacted with a composition comprising an PvDRP polymerase, polypeptides of an RDRP complex, or one or more NSP polypeptides (NSP1-NSP4), or polynucleotides encoding the same.
  • cells are contacted with a fusion polypeptide comprising one or more cell permeable peptides (CPP) fused to an RDRP, polypeptides of an RDRP complex, or one or more NSP polypeptides. It is contemplated that the cells of the invention may be contacted in vitro, ex vivo, or in vivo with compositions of the present invention.
  • compositions of the invention can be administered
  • compositions directly to the subject or delivered ex vivo, to cells derived from the subject (e.g., as in ex vivo gene therapy).
  • Direct in vivo delivery of the compositions will generally be accomplished by parenteral injection, e.g.,
  • Dosage treatment can be a single dose schedule or a multiple dose schedule.
  • nucleic acids for both ex vivo and in vitro applications can be accomplished by, for example, dextran-mediated transfection, calcium phosphate precipitation, polybrene mediated transfection, transduction, protoplast fusion, electroporation, encapsulation of the polynucleotide(s) in liposomes, direct microinjection of the DNA into nuclei, by iontophoresis, or by incorporation into other vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres.
  • nucleic acid and polypeptide delivery are further discussed below.
  • a viral vector e.g., a retroviral vector or an expression vector, or other in vivo polynucleotide delivery technique.
  • the viral vector is a lentiviral vector. This may be achieved using any of a variety or well-known approaches.
  • the retroviruses are a group of single-stranded R A viruses characterized by an ability to convert their RNA to double-stranded DNA that stably integrates into cellular chromosomes as a provirus and directs synthesis of viral proteins. Most retrovirus will only infect actively dividing cells; thus, limiting their utility. However, another class of retrovirus, the lentivirus, is able to infect dividing as well as non-dividing cells; thus making lentivirus the vector of choice in virally mediated transgenesis.
  • Exemplary lentiviral vectors include, but are not limited to HIV-1, HIV- 2, VMV, CAEV, EIAV, FIV, BIV, and SIV.
  • HIV-1 has long been known to form pseudotypes by the incorporation of heterologous glycoproteins (GPs) through phenotypic mixing, and thus, broadening the tropism of the virus.
  • Exemplary pseudotyping glycoproteins include, but are not limited to glycoproteins derived from the following viruses: Ebola, GALV, JSRV, LCMV, Marburg, Mokola, Rabies, RD114, RRV, SeV F, and VSV (Cronin et al, 2006). Recent advances have provided episomal forms of retroviral vectors based on lentiviruses.
  • the nonintegrating lentiviral vectors retain the high transduction efficiency and broad tropism of conventional lentiviruses but avoid the potential problems associated with the nonspecific integration of a transgene. In this respect they are particularly useful from a safety standpoint, and in certain embodiments, are preferred.
  • cells are contacted with a fusion polypeptide comprising an RDRP, polypeptides of an RDRP complex, or one or more NSP polypeptides and one or more cell permeable peptides (CPP) are incubated in growth medium with cells that will be used to provide a cell-based gene therapy.
  • the incubation step can be repeated one, two, three, four, or five or more times in order to provide a continuous supply of the polypeptides to the cell.
  • a polynucleotide may be administered directly to a cell via microinjection.
  • Dubensky et ah, (1984) successfully injected polyomavirus DNA in the form of calcium phosphate precipitates into liver and spleen of adult and newborn mice demonstrating active viral replication and acute infection.
  • Benvenisty & Reshef (1986) also demonstrated that direct intraperitoneal injection of calcium phosphate-precipitated plasmids results in expression of the transfected genes. It is envisioned that polynucleotides encoding an RDRP, polypeptides of an RDRP complex, or one or more NSP polypeptides may also be transferred in a similar manner in vivo and express the gene product.
  • Another embodiment of the invention for transferring a naked DNA expression construct into cells may involve particle bombardment. This method depends on the ability to accelerate DNA-coated microprojectiles to a high velocity allowing them to pierce cell membranes and enter cells without killing them (Klein et ah, 1987).
  • Several devices for accelerating small particles have been developed. One such device relies on a high voltage discharge to generate an electrical current, which in turn provides the motive force (Yang et ah, 1990).
  • the microprojectiles used have consisted of biologically inert substances such as tungsten or gold beads.
  • polynucleotides are administered to cells via electroporation.
  • liposomes act as gene and or polypeptide delivery vehicles and are described in U.S. Patent No. 5,422,120; WO 95/13796; WO 94/23697; WO 91/14445; and EP 0524968. Additional approaches are described in Philip, Mol. Cell Biol. 14:2411 (1994), and in Woffendin, Proc. Natl. Acad. Sci. (1994) 91 : 11581-11585.
  • the liposome fuses with the plasma membrane, thereby releasing the compound into the cytosol.
  • the liposome is phagocytosed or taken up by the cell in a transport vesicle. Once in the endosome or phagosome, the liposome is either degraded or it fuses with the membrane of the transport vesicle and releases its contents.
  • liposomes typically comprise a polypeptide or fusion polypeptide as disclosed herein, a lipid component, e.g., a neutral and/or cationic lipid, and optionally include a receptor- recognition molecule such as an antibody that binds to a predetermined cell surface receptor or ligand ⁇ e.g., an antigen).
  • a receptor- recognition molecule such as an antibody that binds to a predetermined cell surface receptor or ligand ⁇ e.g., an antigen.
  • Liposomes from Physics to Applications (1993). Suitable methods include, for example, sonication, extrusion, high pressure/homogenization, microfluidization, detergent dialysis, calcium-induced fusion of small liposome vesicles and ether-fusion methods, all of which are well known in the art.
  • targeting moieties e.g., ligands, receptors, and monoclonal antibodies
  • Standard methods for coupling targeting agents to liposomes are used. These methods generally involve the incorporation into liposomes of lipid components, e.g., phosphatidylethanolamme, which can be activated for attachment of targeting agents, or incorporation of derivatized lipophilic compounds, such as lipid derivatized bleomycin.
  • Antibody targeted liposomes can be constructed using, for instance, liposomes which incorporate protein A. See Renneisen et al. (1990) J. Biol. Chem. 265:16337-16342 and Leonetti et al. (1990) Proc. Natl. Acad. Sci. USA 87:2448- 2451.
  • Retroviral vector safety has been the impetus underlying the progress in packaging cell line development.
  • the prospects of generating replication-competent retroviruses and the potential for vector mobilization continue to be the driving force for the advancement of packaging cell lines.
  • the advent of stable packaging cell lines has provided an avenue by which to generate vector in a safe and reproducible manner for gene delivery in animal models, as well as clinical applications.
  • packaging cell lines suffer from the cytotoxic expression of viral packaging genes, such as gag, pol, and env.
  • the art has evolved to include inducible expression systems to increase packaging cell line viability, but inducible cell lines using tetracycline, hormone (dexamethasone), or cumate gene switches are leaky and do not provide the requisite control of gene expression for optimum viral packaging. The end result is poor efficiency in generating high titer virus.
  • the present invention provides improved gene switches that solve the problems associated with poorly controlled or regulatable gene expression systems.
  • the invention provides systems that are not leaky compared to existing inducible gene expression systems. Accordingly, the gene switches of the present invention are superior to and provide numerous advantages over existing gene expression systems in the art.
  • Temporal control of gene expression, as well as control of the amplitude of gene expression, are both important considerations in packaging viral particles. For example, tight regulation of cell-toxic viral packaging genes is important to preserve the safety, longevity, and fitness of packaging and producer cell lines.
  • Illustrative embodiments of the present invention provide state-of-the-art packaging and producer cell lines that provide for maximum safety, longevity, and health of cell lines. This results in maximum scalable production of safe virus at increased viral titers compared to existing methods in the art.
  • First generation lentiviral vector packaging systems provide separate packaging constructs for gag/pol and env, and typically employ a heterologous or functionally modified envelope protein for safety reasons. See e.g., Miller and
  • the accessory genes, vif, vpr, vpu and nef are deleted or inactivated and the packaging functions are divided into two genomes: one genome expresses the gag and pol gene products, and the other genome expresses the env gene product ⁇ see e.g., Bosselman et al, 1987. Molec. Cell. Biol. 7(5): 1797-1806; Markowitz et al, 1988. J. Virol. 62(4): 1120-1124; Danos and Mulligan, 1988. Proc. Natl Acad. Sci. (USA) 85:6460-6464).
  • Third generation lentiviral vector systems include those from which the tat gene has been deleted or otherwise inactivated ⁇ e.g., via mutation). Compensation for the regulation of transcription normally provided by tat can be provided by the use of a strong ubiquitous promoter, such as the human cytomegalovirus immediate early (HCMV-IE) enhancer/promoter.
  • the gene encoding rev is preferably provided on a separate expression construct, such that a typical third generation lentiviral vector system will involve four plasmids: one each for gagpol, rev, envelope and the transfer vector.
  • retroviral packaging cell lines are inefficient and/or expression of the viral proteins required for packaging retrovirus are toxic to the packaging cells.
  • Another contributing factor to inefficient viral particle production or low viral titers is the absence of full length retroviral genomic transcripts produced by transfer plasmids (vectors).
  • the present invention contemplates, in part, safer and more efficient retroviral packaging and producer cell lines that provide solutions to these and other problems that exist in the art with regard to retroviral packaging and producer cells.
  • the term “packaging” refers to the process of sequestering (or packaging) a viral genome inside a protein capsid, whereby a virion or viral particle is formed. This process is also known as encapsidation.
  • the term “packaging signal” or “packaging sequence” refers to sequences located within the retroviral genome which are required for insertion of the viral RNA into the viral capsid or particle, see e.g., Clever et ah, 1995. J. of Virology, Vol. 69, No. 4; pp. 2101- 2109.
  • retroviral vectors use the minimal packaging signal (also referred to as the psi [ ⁇ ] sequence) needed for encapsidation of the viral genome.
  • the terms "packaging sequence,” “packaging signal,” “psi” and the symbol “ ⁇ ,” are used in reference to the non-coding sequence required for encapsidation of retroviral RNA strands during viral particle formation.
  • packaging vector refers to an expression vector or viral vector that lacks a packaging signal and comprises a polynucleotide encoding one, two, three, four or more gag, pol, env, tat , rev, vif, vpr, vpu, vpx, or nef genes or other retroviral genes.
  • packaging cell lines is used in reference to cell lines that do not contain a packaging signal, but do stably or transiently express viral structural proteins and replication enzymes ⁇ e.g., gag, pol and env) which are necessary for the correct packaging of viral particles.
  • the retroviral gag gene encodes structural proteins CA (p24), MA (pi 7) and NC (p7-l 1; and the pol gene encodes reverse transcriptase (RT), protease (PR) and integrase (IN). HIV-1 and HIV-2 contain accessory and other proteins involved in regulation of synthesis and processing virus RNA and other replicative functions.
  • packaging cell lines of the invention also encode viral envelope proteins (env) which determine the range of host cells which can ultimately be infected and transformed by recombinant retroviruses generated from the cell lines.
  • the env proteins include gp41 and gpl20.
  • the viral env proteins expressed by packaging cells of the invention are encoded on a separate vector from the viral gag and pol genes, as has been previously described.
  • Integration-incompetent lentiviral vectors are obtained by modifying the pol gene encoding the Integrase, resulting in a mutated pol gene encoding an integrative deficient integrase, said modified pol gene being contained in the encapsidation plasmid.
  • Such integration-incompetent lentiviral vectors have been described in patent application WO 2006/010834.
  • the integrase capacity of the protein is altered whereas the correct expression from the encapsidation plasmid of the GAG, PRO and POL proteins and/or the formation of the capsid and hence of the vector particles, as well as other steps of the viral cycle, preceding or subsequent to the integration step, such as the reverse transcription, the nuclear import, stay intact.
  • An integrase is said defective when the integration that it should enable is altered in a way that an integration step takes place less than 1 over 1000, preferably less than 1 over 10000, when compared to a lentiviral vector containing a corresponding wild-type integrase.
  • a defective integrase results from a mutation of class 1 , preferably amino acid substitutions (one- amino acid substitution) or short deletions fulfilling the requirements of the expression of a defective integrase.
  • the mutation is carried out within the pol gene.
  • These vectors may carry a defective integrase with the mutation D64V in the catalytic domain of the enzyme, which specifically blocks the DNA cleaving and joining reactions of the integration step.
  • the D64V mutation decreases integration of pseudotyped HIV-1 up to 1/10,000 of wild type, but keep their ability to transduce non dividing cells, allowing efficient transgene expression.
  • mutation in the pol gene is performed at either of the following positions D64, Dl 16 or El 52, or at several of these positions which are in the catalytic site of the protein. Any substitution at these positions is suitable, including those described above. Another proposed substitution is the replacement of the amino acids residues RRK (positions 262 to 264) by the amino acids residues AAH.
  • the lentiviral vector is integration-incompetent.
  • the lentiviral genome further comprises an origin of replication (ori), whose sequence is dependent on the nature of cells where the lentiviral genome has to be expressed. Said origin of replication may be from eukaryotic origin, preferably of mammalian origin, most preferably of human origin.
  • retroviral-derived env genes which can be employed in the invention include, but are not limited to type C retroviral envelope proteins, such as those from Moloney murine leukemia virus (MoMuLV), Harvey murine sarcoma virus (HaMuSV), murine mammary tumor virus (MuMTV), gibbon ape leukemia virus (GaLV), and Rous Sarcoma Virus (RSV).
  • Other viral env genes which can be used include, for example, env genes from immunodeficiency viruses (HIV-1 , HIV-2, FIV, SIV and EIV), human T cell leukemia viruses (HTLV-1 and HTLV-3), and Vesicular stomatitis virus (VSV) (Protein G).
  • the wild-type retroviral (e.g., lentiviral) env gene can be used, or can be substituted with any other viral env gene, such those listed above.
  • Methods of pseudotyping recombinant viruses with envelope proteins from other viruses in this manner are well known in the art.
  • a "pseudotype envelope" is an envelope protein other than the one that naturally occurs with the retroviral core virion, which encapsidates the retroviral core virion (resulting in a phenotypically mixed virus).
  • Additional exemplary envelope proteins that may be used include ecotropic or amphotropic MLV envelopes, 10A1 envelope, BAEV, FeLV-B, RD1 14, SSAV, Ebola, Sendai, FPV (Fowl plague virus), and influenza virus envelopes.
  • RNA viruses e.g., RNA virus families of Picornaviridae, Calciviridae, Astroviridae, Togaviridae, Flaviviridae, Coronaviridae, Paramyxoviridae, Rhabdoviridae, Filoviridae, Orthomyxoviridae, Bunyaviridae, Arenaviridae, Reoviridae, Birnaviridae, Retroviridae) as well as from the DNA viruses (families of Hepadnaviridae, Circoviridae, Parvoviridae, Papovaviridae, Adenoviridae, Herpesviridae, Poxyiridae, and Iridoviridae) may be utilized.
  • RNA viruses e.g., RNA virus families of Picornaviridae, Calciviridae, Astroviridae, Togaviridae, Flaviviridae, Coronaviridae, Paramyxoviridae
  • Representative examples include , FeLV, VEE, HFVW, WDSV, SFV, Rabies, ALV, BIV, BLV, EBV, CAEV, SNV, ChTLV, STLV, MPMV, SMRV, RAV, FuSV, MH2, AEV, AMV, CT10, EIAV.
  • envelope proteins for pseudotyping a virus of present invention include, but are not limited to any of the following virus: Influenza A such as H1N1 , H1N2, H3N2 and H5N1 (bird flu), Influenza B, Influenza C virus, Hepatitis A virus, Hepatitis B virus, Hepatitis C virus, Hepatitis D virus, Hepatitis E virus, Rotavirus, any virus of the Norwalk virus group, enteric adenoviruses, parvovirus, Dengue fever virus, Monkey pox, Mononegavirales, Lyssavirus such as rabies virus, Lagos bat virus, Mokola virus, Duvenhage virus, European bat virus 1 & 2 and Australian bat virus, Ephemera virus, Vesiculovirus, Vesicular Stomatitis Virus (VSV), Herpesviruses such as Herpes simplex virus types 1 and 2, varicella zoster, cytomegalovirus, Epstein-Bar virus (EBV), human herpe
  • Venezuelan hemorrhagic fever virus Lassa fever virus, Machupo virus, Lymphocytic choriomeningitis virus (LCMV), Bunyaviridiae such as Crimean-Congo hemorrhagic fever virus, Hantavirus, hemorrhagic fever with renal syndrome causing virus, Rift Valley fever virus, Filoviridae (filovirus) including Ebola hemorrhagic fever and Marburg hemorrhagic fever, Flaviviridae including Kaysanur Forest disease virus, Omsk hemorrhagic fever virus, Tick-borne encephalitis causing virus and
  • Paramyxoviridae such as Hendra virus and Nipah virus, variola major and variola minor (smallpox), alphaviruses such as Venezuelan equine encephalitis virus, eastern equine encephalitis virus, western equine encephalitis virus, SARS-associated coronavirus (SARS-CoV), West Nile virus, any encephaliltis causing virus.
  • the invention provides packaging cells which produce recombinant retrovirus, e.g., lentivirus, pseudotyped with the VSV-G glycoprotein.
  • stably or transiently expressing a functional tat gene, rev gene, and/or one or functional viral accessory genes may increase the efficiency of the packaging cell.
  • the term "producer cell line” refers to a cell line which is capable of producing recombinant retroviral particles, comprising a packaging cell line and a transfer vector construct comprising a packaging signal.
  • any suitable cell line can be employed to prepare packaging cells of the invention.
  • the cells are mammalian cells.
  • the cells used to produce the packaging cell line are human cells.
  • Suitable cell lines which can be used include, for example, CHO cells, BHK cells, MDCK cells, C3H 10T1/2 cells, FLY cells, Psi-2 cells, BOSC 23 cells, PA317 cells, WEHI cells, COS cells, BSC 1 cells, BSC 40 cells, BMT 10 cells, VERO cells, W138 cells, MRC5 cells, A549 cells, HT1080 cells, 293 cells, 293T cells, B-50 cells, 3T3 cells, NIH3T3 cells, HepG2 cells, Saos-2 cells, Huh7 cells, HeLa cells, W163 cells, 211 cells, and 211A cells.
  • the packaging cells are 293 cells, 293T cells, or A549 cells.
  • the cells are A549 cells.
  • the packaging vectors are included in a packaging cell, and are introduced into the cell via transfection, transduction or infection. Methods for transfection, transduction or infection are well known by those of skill in the art.
  • a retroviral/lentiviral transfer vector of the present invention can be introduced into a packaging cell line, via transfection, transduction or infection, to generate a producer cell or cell line.
  • the packaging vectors of the present invention can be introduced into human cells or cell lines by standard methods including, e.g., calcium phosphate transfection, lipofection or electroporation.
  • the packaging vectors are introduced into the cells together with a dominant selectable marker, such as neomycin, hygromycin, puromycin, blastocidin, zeocin, thymidine kinase, DHFR, Gin synthetase or ADA, followed by selection in the presence of the appropriate drug and isolation of clones.
  • a selectable marker gene can be linked physically to genes encoding by the packaging vector, e.g., by IRES or self cleaving viral peptides.
  • the packaging system used to generate retroviral vectors of the invention comprises at least two packaging vectors, a first packaging vector which comprises a first nucleotide sequence comprising a ubiquitous, tissue specific, or inducible promoter operably linked to an RDRP of a plus-strand or minus strand ssRNA virus; and a second packaging vector comprising a second polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to a plus-strand ssRNA virus RDRP promoter operably linked to a polynucleotide encoding one or more of the viral structural genes gag, pol, and env, and a CSE for production of a minus strand RNA.
  • the second packaging vector comprises a second polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide encoding one or more of the viral structural genes gag, pol, and env, operably linked to a plus-strand or minus-strand ssRNA virus RDRP promoter in the reverse orientation.
  • the packaging system used to generate retroviral vectors of the invention comprises at least two packaging vectors, a first packaging vector which comprises a first nucleotide sequence comprising a ubiquitous, tissue specific, or inducible promoter operably linked to one or more alphavirus nonstructural proteins (NSP1-NSP4).
  • the first packaging vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to one, two, three, or four NSPs.
  • the first packaging vector comprises a ubiquitous, tissue specific, or inducible promoter operably linked to NSP4 or NSP2 and NSP4.
  • the polynucleotide sequences encoding NSPs can be contiguous or they can be separated by one or more IRES sequences and or polynucleotide sequences that include self-cleaving polypeptide sites, e.g., a 2A or 2A polypeptides as disclosed elsewhere herein.
  • the first packaging vector comprises an inducible promoter, e.g., a tetracyline or cumate inducible promoter.
  • second packaging vector comprises a second polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked an RDRP promoter operably linked to a polynucleotide encoding one or more of the viral structural genes gag, pol, and env, and a CSE for production of a minus strand R A.
  • the second packaging vector comprises a second
  • polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement sequence of a polynucleotide encoding one or more of the viral structural genes gag, pol, and env, operably linked to an RDRP promoter in the reverse orientation, e.g., alphavirus 26S promoter.
  • the packaging system used to generate retroviral vectors of the invention comprises at least three packaging vectors, a first packaging vector which comprises a first nucleotide sequence comprising a ubiquitous, tissue specific, or inducible promoter operably linked to an RDRP; one, two, three, or four NSPs; NSP2 and NSP4; or NSP4.
  • the first packaging vector comprises an inducible promoter, e.g., a tetracyline or cumate inducible promoter.
  • the second packaging vector comprises a second polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to an RDRP promoter, e.g., alphavirus 26S promoter, operably linked to a polynucleotide encoding gag, pol, or env, and a CSE for production of a minus strand RNA
  • the third packaging vector comprises a third polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to an RDRP promoter, e.g., alphavirus 26S promoter, operably linked to a polynucleotide encoding the two viral structural genes not encoded by the second packaging construct, e.g., gag and pol, pol and env, or env and gag, and a CSE for production of a minus strand RNA.
  • the second packaging vector comprises a second polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement of a polynucleotide encoding gag, pol, or env, operably linked to an RDRP promoter in the reverse orientation, e.g., a plus-strand or minus-strand ssRNA virus RDRP promoter; and the third packaging vector comprises a third polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement of a polynucleotide encoding the two viral structural genes not encoded by the second packaging construct, e.g., gag and pol, pol and env, or env and gag, operably linked to an RNA dependent RNA polymerase promoter in the reverse orientation, e.g., a plus-strand or minus-strand ssR A virus RDRP promoter.
  • the packaging system used to generate retroviral vectors of the invention comprises at least four packaging vectors, a first packaging vector which comprises a first nucleotide sequence comprising a ubiquitous, tissue specific, or inducible promoter operably linked to an RDRP; one, two, three, or four NSPs; NSP2 and NSP4; or NSP4.
  • the first packaging vector comprises an inducible promoter, e.g., a tetracyline or cumate inducible promoter.
  • the second packaging vector comprises a second polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to an RDRP promoter, e.g., alphavirus 26S promoter, operably linked to a polynucleotide encoding gag and a CSE for production of a minus strand RNA;
  • the third packaging vector comprises a third polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to an RDRP promoter, e.g., alphavirus 26S promoter, operably linked to a polynucleotide encoding pol, and a CSE for production of a minus strand RNA;
  • the fourth packaging vector comprises a fourth polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to an RDRP promoter, e.g., alphavirus 26S promoter, operably linked to a polynucleotide
  • the second packaging vector comprises a second polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement of a polynucleotide encoding gag, operably linked to an RDRP promoter in the reverse orientation, e.g., a plus-strand or minus- strand ssRNA virus RDRP promoter;
  • the third packaging vector comprises a third polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement of a polynucleotide encoding pol, operably linked to an RDRP promoter in the reverse orientation, e.g., a plus-strand or minus-strand ssRNA virus RDRP promoter;
  • the fourth packaging vector comprises a fourth
  • polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement of a polynucleotide encoding env, operably linked to an RDRP promoter in the reverse orientation, e.g., a plus-strand or minus-strand ssR A virus RDRP promoter.
  • the present invention further contemplates, packaging cell lines comprising at least 5, at least 6, at least 7, at least 8, at least 9, or at least 10 or more packaging vectors.
  • 5, 6, 7, 8, 9, or 10 packaging vector cell lines comprise a 5 th , 6 th , 7 th , 8 th , 9 th , or 10 th polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to an RDRP promoter, e.g., alphavirus 26S promoter, operably linked to a polynucleotide encoding a viral gene selected from the group consisting of tat, rev, vif, vpr, vpu, vpx, and nef, and a CSE for production of a minus strand RNA.
  • RDRP promoter e.g., alphavirus 26S promoter
  • 5, 6, 7, 8, 9, or 10 packaging vector cell lines comprise a 5 th , 6 th , 7 th , 8 th , 9 th , or 10 th polynucleotide comprising a ubiquitous, tissue specific, or inducible promoter operably linked to the reverse complement of a polynucleotide encoding a viral gene selected from the group consisting of tat, rev, vif, vpr, vpu, vpx, and nef, operably linked to an RDRP promoter in the reverse orientation, e.g., a plus-strand or minus-strand ssRNA virus RDRP promoter.
  • the present invention contemplates that any number or, or all of the 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 packaging vectors can be expression vectors, e.g., commercial plasmid expression vectors, or retroviral vectors. Accordingly, the invention contemplates providing packaging cell lines by both transient transfection and viral transduction.
  • the packaging vectors are viral vectors, e.g., retroviral or lentiviral transfer vectors
  • the vectors may comprise one or more of each of the following: 5' and 3' LTRs, optionally modified as discussed elsewhere herein, packaging sequences, posttranscriptional recognition elements (e.g., WPRE, HPRE), insulator elements, cPPT/FLAP sequences, selectable markers, a retroviral export element, e.g., a lentiviral REV response element (RRE), and other lentiviral vector features as disclosed elsewhere herein.
  • posttranscriptional recognition elements e.g., WPRE, HPRE
  • insulator elements e.g., insulator elements
  • cPPT/FLAP sequences e.g., selectable markers
  • a retroviral export element e.g., a lentiviral REV response element (RRE)
  • RRE lentiviral REV response element
  • the present invention contemplates a producer cell comprising a packaging cell and one or more viral transfer vectors (e.g., plasmid) each comprising viral packaging sequences (*Fs) and LTRs and one or more polynucleotides.
  • viral transfer vectors e.g., plasmid
  • a transfer vector (e.g. plasmid) comprises a ubiquitous, tissue specific, or inducible promoter operably linked to a plus-strand ssRNA virus RDRP promoter sequence, e.g., an alphavirus subgenomic promoter, operably linked to a left (3') retroviral LTR; a packaging sequence ( ⁇ ), another ubiquitous, tissue specific, or inducible promoter operably linked operably to a polynucleotide of interest; a right (3') retroviral LTR; and a CSE for generation of a minus strand RNA.
  • RDRP promoter sequence e.g., an alphavirus subgenomic promoter, operably linked to a left (3') retroviral LTR
  • ⁇ packaging sequence
  • another ubiquitous, tissue specific, or inducible promoter operably linked operably to a polynucleotide of interest
  • a right (3') retroviral LTR e.g., a right retroviral LTR
  • the ubiquitous, tissue specific, or inducible promoter transcribes a sense (plus- strand) mRNA comprising the entire retroviral genome ready for packaging.
  • this arrangement allows for controlled amplification of the retroviral genome of the transfer plasmid that will be packaged.
  • the RDRP binds to the 3' cis-acting sequence, e.g., CSE, at the 3' end of the plus-stranded RNA and using the plus strand as a template, polymerizes a non-sense (minus-strand) RNA.
  • the RDRP binds 5' cis-acting sequence or subgenomic promoter and amplifies sense (plus-strand) RNA copies using the minus strand as a template.
  • These amplified sense (plus-strand) RNA copies comprise the entire retroviral genome that will be packaged. Accordingly, this design allows for packaging of genomic RNA from both the ubiquitous, tissue specific, or inducible promoter and the 5' cis-acting sequence or subgenomic promoter, albeit using different RNA templates.
  • the retroviral genomic RNA can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an
  • RDRP/promoter system Furthermore, this system provides advantages in that it increases the amount full-length retroviral genomic RNA, thereby increasing viral titer 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • a transfer vector (e.g. plasmid) comprises a ubiquitous, tissue specific, or inducible promoter operably linked to an RNA dependent RNA polymerase promoter sequence, e.g., the alphavirus 26S subgenomic promoter, operably linked to a left (3') retroviral LTR; a packaging sequence ( ⁇ ), another ubiquitous, tissue specific, or inducible promoter operably linked operably to a polynucleotide of interest; a right (3') retroviral LTR; and a CSE for generation of a minus strand RNA.
  • an RNA dependent RNA polymerase promoter sequence e.g., the alphavirus 26S subgenomic promoter
  • ⁇ ubiquitous, tissue specific, or inducible promoter operably linked operably to a polynucleotide of interest
  • a right (3') retroviral LTR e.g., a right (3') retroviral LTR
  • CSE for generation of a minus strand
  • the ubiquitous, tissue specific, or inducible promoter transcribes a sense (plus- strand) mRNA comprising the entire retroviral genome ready for packaging.
  • this arrangement allows for controlled amplification of the retroviral genome of the transfer plasmid that will be packaged.
  • one or more NSPs bind to the CSE at the 3' end of the plus-stranded RNA and using the plus strand as a template, polymerize a non-sense (minus-strand) RNA.
  • one or more NSPs bind to the alphavirus 26S subgenomic promoter and amplify sense (plus-strand) RNA copies using the minus strand as a template.
  • These amplified sense (plus-strand) RNA copies comprise the entire retroviral genome that will be packaged. Accordingly, this design allows for packaging of genomic RNA from both the ubiquitous, tissue specific, or inducible promoter and the 26S promoter, albeit using different RNA templates.
  • the retroviral genomic RNA can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • this system provides advantages in that it increases the amount full-length retroviral genomic RNA, thereby increasing viral titer 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • a transfer vector (e.g. plasmid) comprises a constitutive, e.g., ubiquitous or tissue specific, or an inducible promoter operably linked to the reverse complement of: a right (3') retroviral LTR; a polynucleotide of interest operably linked to another ubiquitous, tissue specific, or inducible promoter; a packaging sequence ( ⁇ ); a left (3') retroviral LTR; and a plus-strand or minus-strand ssRNA virus RDRP promoter sequence in the reverse orientation.
  • a constitutive e.g., ubiquitous or tissue specific, or an inducible promoter operably linked to the reverse complement of: a right (3') retroviral LTR; a polynucleotide of interest operably linked to another ubiquitous, tissue specific, or inducible promoter; a packaging sequence ( ⁇ ); a left (3') retroviral LTR; and a plus-strand or minus-strand ssRNA virus RDRP promoter sequence in the reverse orientation.
  • the ubiquitous, tissue specific, or inducible promoter transcribes a reverse complement of the mRNA that encodes the entire retroviral genome that will be packaged the polypeptide of interest and an RDRP 5' cis-acting sequence or subgenomic promoter in the reverse orientation: the reverse complement of the viral vector cannot be directly packaged into the retroviral particle.
  • the transcribed RNA can be used a minus strand RNA template in the 3' to 5' orientation.
  • the RDRP binds to the 5' cis-acting sequence or subgenomic promoter sequence on the transcribed strand and amplifies translatable RNA copies using the transcribed strand as a template.
  • amplified sense (plus-strand) RNA comprise the entire retroviral genome that will be packaged. Accordingly, the CSE is not needed to generate a minus strand because the RDRP can use the plus-strand RNA in the 3' to 5' orientation as a minus- strand template. In this manner, the retroviral genomic RNA can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an
  • RDRP/promoter system Furthermore, this system provides advantages in that it increases the amount full-length retroviral genomic RNA, thereby increasing viral titer 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • the transfer vector (e.g. plasmid) comprises a constitutive, e.g., ubiquitous or tissue specific, or an inducible promoter operably linked to the reverse complement of: a right (3') retroviral LTR; a polynucleotide of interest operably linked to another ubiquitous, tissue specific, or inducible promoter; a packaging sequence ( ⁇ ); a left (3') retroviral LTR; and an RNA dependent RNA polymerase promoter sequence in the reverse orientation, e.g., the alphavirus 26S subgenomic promoter.
  • a constitutive e.g., ubiquitous or tissue specific, or an inducible promoter operably linked to the reverse complement of: a right (3') retroviral LTR; a polynucleotide of interest operably linked to another ubiquitous, tissue specific, or inducible promoter; a packaging sequence ( ⁇ ); a left (3') retroviral LTR; and an RNA dependent RNA polymerase promoter sequence in the reverse orientation, e
  • the ubiquitous, tissue specific, or inducible promoter transcribes a reverse complement of the mRNA that encodes the entire retroviral genome that will be packaged, the polypeptide of interest, and the alphavirus 26S subgenomic promoter in reverse orientation: the reverse complement cannot be directly packaged into the retroviral particle.
  • thetranscribed RNA can be used a minus strand RNA template in the 3' to 5' orientation.
  • one or more NSPs bind to the alphavirus 26S subgenomic promoter sequence on the transcribed strand and amplify translatable RNA copies using the minus strand as a template.
  • These amplified sense (plus-strand) RNA comprise the entire retroviral genome that will be packaged.
  • the CSE is not needed to generate a minus strand because the RDRP can use the plus-strand RNA in the 3 ' to 5 ' orientation as a minus-strand template.
  • the retroviral genomic RNA can be amplified 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • this system provides advantages in that it increases the amount full-length retroviral genomic RNA, thereby increasing viral titer 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 fold or more compared to a system that lacks an RDRP/promoter system.
  • each of the foregoing transfer vectors may further comprise recombinase recognition sites that flank the retroviral genome to be packaged, and optionally a selectable marker.
  • transfer vector bearing the recombinase recognition sites has integrated into the packaging cell genome, other transfer vectors comprising recombinase recognition sites compatible to those flanking the retroviral genome of the integrated transfer vector can be exchanged with the integrated transfer vector in the presence of a suitable recombinase.
  • RMCE Recombinase Mediated Cassette Exchange
  • the recombinase activity is introduced transiently in the producer cell for a time and duration effective to mediate the cassette exchange.
  • the recombinase can be introduced into the packaging cell transiently or permanently and under the control of a ubiquitous, tissue specific, or inducible promoter.
  • Recombinase mediated cassette exchange is a process in which site-specific recombinases exchange one gene cassette flanked by a pair of incompatible target sites for another cassette flanked by an identical pair of sites.
  • one cassette is present in the host genome, e.g., the packaging cell, whereas the other gene cassette is introduced into the host cell by chemical or biological means, e.g., on a transfer plasmid.
  • successful RMCE can be accomplished using a retroviral vector carrying both the transgene cassette to be inserted and the recombinase coding region.
  • RMCE proceeds efficiently in cells in which the vector is able to replicate. Additional transfection of the transgene cassette significantly enhances the RMCE frequency. This demonstrates that an RMCE system in the context of a viral vector allows the site directed insertion of a transgene into a defined genomic site.
  • packaging/producer cells are contacted with a polynucleotide encoding an expressible RDRP or an RDRP polypeptide capable of entering the cell.
  • a polynucleotide encoding an expressible RDRP or an RDRP polypeptide capable of entering the cell.
  • the packaging vectors are transfer vectors, e.g., retroviral or lentiviral transfer vectors ⁇ e.g., plasmids
  • the vectors may comprise one or more of each of the following: 5' and 3' LTRs, optionally modified as discussed elsewhere herein, packaging sequences, posttranscriptional recognition elements ⁇ e.g., WPRE, HPRE), insulator elements, cPPT/FLAP sequences, selectable markers, a retroviral export element, e.g., a lentiviral REV response element (RRE), and other lentiviral vector features as disclosed elsewhere herein.
  • the preceding transfer vectors recite an ordered list of features, one having ordinary skill in the art would appreciate that other orders of the features are possible and in some cases preferred.
  • the invention employs an inducible promoter within the retroviral vectors, so that transcription of selected genes can be turned on and off. This minimizes cellular toxicity caused by expression of cytotoxic viral proteins, increasing the stability of the packaging cells containing the vectors.
  • VSV-G envelope protein
  • Vpr can be cytotoxic (Yee, J. - K., et al., 1994. Proc. Natl. Acad. Sci., 91 :9654-9568) and, therefore, expression of these proteins in packaging cells of the invention can be controlled by an inducible promoter systems as discussed elsewhere herein.
  • Viruses may be used to infect cells in vivo, ex vivo, or in vitro using techniques well known in the art
  • the vector particles may be incubated with the cells using a dose generally in the order of between 1 to 50 multiplicities of infection (MOI) which also corresponds to lxlO 5 to 50xl0 5 transducing units of the viral vector per 10 5 cells.
  • MOI multiplicities of infection
  • This includes amount of vector corresponding to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, and 50 MOI.
  • Viruses may also be delivered to a subject in vivo, by direct injection to the cell, tissue, or organ in need of therapy.
  • Direct injection requires on the order of between 1 to 50 multiplicities of infection (MOI) which also corresponds to lxlO 5 to 50xl0 5 transducing units of the viral vector per 10 5 cells.
  • MOI multiplicities of infection
  • Viruses may also be delivered according to viral titer (TU/mL), which can be measured, for example, by using a commercially available p24 titer assay, which is an ELISA against the p24 viral coat protein.
  • VSV-G pseudotyped lentiviral vector will have an infectivity index in the range of 1 TU per 1000 physical particles (PP) to 1 TU per 100 PP (or less). Thus, the range is approximately 10 to 100 TU/pg of p24. It is through this conversion that TU/mL is obtained.
  • the amount of lentivirus directly injected is determined by total TU and can vary based on both the volume that could be feasibly injected to the site and the type of tissue to be injected.
  • a brain injection site may only allow for a very small volume of virus to be injected, so a high titer prep would be preferred, a TU of about 1 x 10 6 to 1 x 10 7 , about 1 x 10 6 to 1 x 10 8 , 1 x 10 6 to 1 x 10 9 , about 1 x 10 7 to 1 x 10 10 , 1 x 10 8 to 1 x 10 11 , about 1 x 10 8 to 1 x 10 12 , or about 1 x 10 10 to 1 x 10 12 or more per injection could be used.
  • a systemic delivery could accommodate a much larger TU, a load of 1 x 10 8 , 1 x 10 9 , 1 x 10 10 , 1 x 10 11 , 1 x 10 12 , 1 x 10 13 , 1 x 10 14 , or 1 x 10 15 , could be delivered.
  • the retroviral vector geneswitch expression systems of the invention provide improved viral titers and highly controlled strategies for amplification of one or more mammalian polypeptides, e.g., therapeutic polypeptides, in a transduced cell.
  • the viruses and transduced cells herein are suitable for gene therapy applications.
  • gene therapy refers to the introduction of a gene into a cell's genome.
  • the virus can infect and transduce the cell in vivo, ex vivo, or in vitro.
  • the transduced cells can then be administered to a subject in need of therapy.
  • the present invention contemplates that the vector systems, viral particles, and transduced cells of the invention are broadly applicable to any disease, disorder, or condition.
  • the gene therapy systems of the invention are broadly applicable to treat, prevent, and/or ameliorate monogenic diseases, disorders, or conditions.
  • the retroviral vectors are administered by direct injection to a cell, tissue, or organ of a subject in need of gene therapy, in vivo.
  • cells are transduced in vitro or ex vivo with one or more retroviral, e.g., lentiviral, vectors of the invention depending on whether the single vector system, the binary vector system, or the polypeptide composition/ vector system is used. The transduced cells are then administered to a subject in need of gene therapy.
  • the virus of the first or second vectors may be directly administered to the subject to transduced the desired cells, in any order or together, or the cells may be transduced ex vivo or in vitro, with either one of, or both of, the viruses from the first and second vectors, and administered to the subject. If the cells is transduced with only one of the vectors, the cells can be administered to the subject and the second vector can be administered as a virus or expression vector to the transduced cells of the subject to control and/or amplify therapeutic polypeptide expression.
  • the virus may be directly administered to the subject to transduce the desired cells or the cells may be transduced ex vivo or in vitro and administered to the subject.
  • a composition comprising RDRP or polynucleotides encoding an expressible RDRP, e.g., NSP1-NSP4, NSP2-2A-NSP4, or NSP4, can be administered to the subject to control and/or amplify therapeutic polypeptide expression.
  • Cells suitable for transduction and administration in the gene therapy methods of the invention include, but are not limited to stem cells, progenitor cells, and differentiated cells.
  • stem cell refers to a cell which is an undifferentiated cell capable of (1) long term self -renewal, or the ability to generate at least one identical copy of the original cell, (2) differentiation at the single cell level into multiple, and in some instance only one, specialized cell type and (3) of in vivo functional regeneration of tissues.
  • Stem cells are subclassified according to their developmental potential as totipotent, pluripotent, multipotent and oligo/unipotent.
  • Self-renewal refers a cell with a unique capacity to produce unaltered daughter cells and to generate specialized cell types (potency).
  • Asymmetric cell division produces one daughter cell that is identical to the parental cell and one daughter cell that is different from the parental cell and is a progenitor or differentiated cell. Asymmetric cell division does not increase the number of cells. Symmetric cell division produces two identical daughter cells.
  • Proliferation or “expansion” of cells refers to symmetrically dividing cells.
  • the term “totipotent” means the ability of a cell to form all cell lineages of an organism. For example, in mammals, only the zygote and the first cleavage stage blastomeres are totipotent.
  • the term “pluripotent” means the ability of a cell to form all lineages of the body or soma (i.e., the embryo proper).
  • embryonic stem cells are a type of pluripotent stem cells that are able to form cells from each of the three germs layers, the ectoderm, the mesoderm, and the endoderm.
  • the term “multipotent” refers to the ability of an adult stem cell to form multiple cell types of one lineage.
  • hematopoietic stem cells are capable of forming all cells of the blood cell lineage, e.g., lymphoid and myeloid cells.
  • oligopotent refers to the ability of an adult stem cell to differentiate into only a few different cell types.
  • lymphoid or myeloid stem cells are capable of forming cells of either the lymphoid or myeloid lineages, respectively.
  • unipotent means the ability of a cell to form a single cell type.
  • spermatogonial stem cells are only capable of forming sperm cells.
  • progenitor or “progenitor cells” refers to cells have the capacity to self-renew and to differentiate into more mature cells. Many progenitor cells differentiate along a single lineage, but may have quite extensive proliferative capacity.
  • the population or source of cells used in the methods contemplated herein comprises mesenchymal stem and/or progenitor cells, mesodermal stem and/or progenitor cells, endodermal stem and/or progenitor cells, or ectodermal stem and/or progenitor cells.
  • the population or source of cells used in the methods contemplated herein comprises bone marrow stem cells, umbilical cord blood stem and/or progenitor cells, bone stem and/or progenitor cells ⁇ muscle stem and/or progenitor cells, hematopoietic stem and/or progenitor cells, fat stem and/or progenitor cells, cartilage stem and/or progenitor cells, neural stem and/or progenitor cells, skin stem and/or progenitor cells, liver stem and/or progenitor cells, pancreas stem and/or progenitor cells, kidney stem and/or progenitor cells, gastric stem and/or progenitor cells, and intestinal stem and/or progenitor cells.
  • Hematopoietic stem cells give rise to committed hematopoietic progenitor cells (HPCs) that are capable of generating the entire repertoire of mature blood cells over the lifetime of an organism.
  • HPC hematopoietic stem cell
  • myeloid e.g., monocytes and macrophages, neutrophils, basophils, eosinophils, erythrocytes, megakaryocytes/platelets, dendritic cells
  • lymphoid lineages e.g., T-cells, B-cells, NK-cells
  • hematopoietic stem and progenitor cells When transplanted into lethally irradiated animals or humans, hematopoietic stem and progenitor cells can repopulate the erythroid, neutrophil-macrophage, megakaryocyte and lymphoid hematopoietic cell pool.
  • Cells of the invention can be autologous/autogeneic ("self) or non- autologous ("non-self,” e.g., allogeneic, syngeneic or xenogeneic).
  • autologous refers to cells from the same subject.
  • Allogeneic refers to cells of the same species that differ genetically to the cell in comparison.
  • “Syngeneic,” as used herein, refers to cells of a different subject that are genetically identical to the cell in comparison.
  • "Xenogeneic,” as used herein, refers to cells of a different species to the cell in comparison. In preferred embodiments, the cells of the invention are allogeneic.
  • a "subject,” as used herein, includes any animal that exhibits a symptom that can be treated with the gene therapy vectors, cell-based therapeutics, and methods disclosed elsewhere herein.
  • Suitable subjects include laboratory animals (such as mouse, rat, rabbit, or guinea pig), farm animals, and domestic animals or pets (such as a cat or dog).
  • Non-human primates and, preferably, human patients, are included.
  • Typical subjects include animals that exhibit aberrant amounts (lower or higher amounts than a "normal” or "healthy” subject) of one or more physiological activities that can be modulated by gene therapy.
  • treatment includes any beneficial or desirable effect on the symptoms or pathology of a disease or pathological condition, and may include even minimal reductions in one or more measurable markers of the disease or condition being treated. Treatment can involve optionally either the reduction or amelioration of symptoms of the disease or condition, or the delaying of the progression of the disease or condition. “Treatment” does not necessarily indicate complete eradication or cure of the disease or condition, or associated symptoms thereof.
  • prevention and similar words such as “prevented,” “preventing” etc., indicate an approach for preventing, inhibiting, or reducing the likelihood of the occurrence or recurrence of, a disease or condition. It also refers to delaying the onset or recurrence of a disease or condition or delaying the occurrence or recurrence of the symptoms of a disease or condition. As used herein, “prevention” and similar words also includes reducing the intensity, effect, symptoms and/or burden of a disease or condition prior to onset or recurrence of the disease or condition.
  • the term “amount” refers to "an amount effective” or “an effective amount” of a virus or transduced therapeutic cell to achieve a beneficial or desired prophylactic or therapeutic result, including clinical results.
  • a “prophylactically effective amount” refers to an amount of a virus or transduced therapeutic cell effective to achieve the desired prophylactic result.
  • the prophylactically effective amount is less than the therapeutically effective amount.
  • a “therapeutically effective amount” of a virus or transduced therapeutic cell may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the stem and progenitor cells to elicit a desired response in the individual.
  • a therapeutically effective amount is also one in which any toxic or detrimental effects of the virus or transduced therapeutic cells are outweighed by the therapeutically beneficial effects.
  • the term “therapeutically effective amount” includes an amount that is effective to "treat" a subject ⁇ e.g., a patient).
  • Viral vectors of the present invention may be used to control the expression of one or more mammalian polypeptides useful in the treatment of a disease, disorder, or condition that is amenable to treatment with gene therapy, including, but not limited to monogenic diseases, disorders, and conditions. 1. Monogenic Diseases
  • monogenic disease refers to a disease in which modifications of a single gene is associated with a disorder, disease, or condition in a subject. Though relatively rare, monogenic diseases affect millions of people worldwide. scientistss currently estimate that over 10,000 human diseases are known to be monogenic. Pure genetic diseases are caused by a single error in a single gene in the human DNA. The nature of disease depends on the functions performed by the modified gene. The single-gene or monogenic diseases can be classified into three main categories: Dominant, Recessive, and X- linked. All human beings have two sets or copies of each gene called "allele"; one copy on each side of the chromosome pair. Recessive diseases are monogenic disorders that occur due to damages in both copies or allele.
  • Dominant diseases are monogenic disorders that involve damage to only one gene copy.
  • X linked diseases are monogenic disorders that are linked to defective genes on the X chromosome which is the sex chromosome.
  • the X linked alleles can also be dominant or recessive. These alleles are expressed equally in men and women, more so in men as they carry only one copy of X chromosome (XY) whereas women carry two (XX).
  • Monogenic diseases are responsible for a heavy loss of life. The global prevalence of all single gene diseases at birth is approximately 1/100. In Canada, it has been estimated that taken together, monogenic diseases may account for up to 40% of the work of hospital based pediatric practice (Scriver, 1995).
  • Illustrative embodiments of monogenic disorders, diseases, and conditions that can be treated, prevented, or ameliorated with compositions and methods of the present invention include, but are not limited to: 11 -hydroxylase deficiency; 17,20-desmolase deficiency; 17-hydroxylase deficiency; 3- hydroxyisobutyrate aciduria; 3 -hydroxy steroid dehydrogenase deficiency; 46,XY gonadal dysgenesis; AAA syndrome; ABCA3 deficiency; ABCC8-associated hyperinsulinism; aceruloplasminemia; achondrogenesis type 2; acral peeling skin syndrome; acrodermatitis enteropathica; adrenocortical micronodular hyperplasia; adrenoleukodystrophies; adrenomyeloneuropathies; Aicardi-Goutieres syndrome;
  • Alagille disease Alpers syndrome; alpha-mannosidosis; Alstrom syndrome; Alzheimer disease; amelogenesis imperfecta; amish type microcephaly; amyotrophic lateral sclerosis; anauxetic dysplasia; androgen insentivity syndrome; Antley-Bixler syndrome; APECED, Apert syndrome, aplasia of lacrimal and salivary glands, argininemia, arrhythmogenic right ventricular dysplasia, Arts syndrome, ARVD2, arylsulfatase deficiency type metachromatic leokodystrophy, ataxia telangiectasia, autoimmune lymphoproliferative syndrome; autoimmune polyglandular syndrome type 1 ; autosomal dominant anhidrotic ectodermal dysplasia; autosomal dominant polycystic kidney disease; autosomal recessive microtia; autosomal recessive renal glucosuria; autosomal visceral heterotaxy; Bardet-Biedl
  • centronuclear myopathy cerebral capillary malformation; cerebrooculofacioskeletal syndrome type 4; cerebrooculogacioskeletal syndrome; cerebrotendinous
  • xanthomatosis CHARGE association; cherubism; CHILD syndrome; chronic granulomatous disease; chronic recurrent multifocal osteomyelitis; citrin deficiency; classic hemochromatosis; CNPPB syndrome; cobalamin C disease; Cockayne syndrome; coenzyme Q10 deficiency; Coffin-Lowry syndrome; Cohen syndrome; combined deficiency of coagulation factors V; common variable immune deficiency; complete androgen insentivity; cone rod dystrophies; conformational diseases;
  • congenital bile adid synthesis defect type 1 congenital bile adid synthesis defect type 2; congenital defect in bile acid synthesis type; congenital erythropoietic porphyria;
  • hypoglycemia facioscapulohumeral muscular dystrophy; Faisalabad histiocytosis; familial atypical mycobacteriosis; familial capillary malformation-arteriovenous;
  • familial esophageal achalasia familial glomuvenous malformation; familial hemophagocytic lymphohistiocytosis; familial mediterranean fever; familial megacalyces; familial schwannomatosisl; familial spina bifida; familial splenic asplenia/hypoplasia; familial thrombotic thrombocytopenic purpura; Fanconi disease; Feingold syndrome; FENIB; fibrodysplasia ossificans progressiva; FKTN; Francois- Neetens fleck corneal dystrophy; Frasier syndrome; Friedreich ataxia; FTDP-17;
  • fucosidosis G6PD deficiency; galactosialidosis; Galloway syndrome; Gardner syndrome; Gaucher disease; Gitelman syndrome; GLUT1 deficiency; glycogen storage disease type lb; glycogen storage disease type 2; glycogen storage disease type 3; glycogen storage disease type 4; glycogen storage disease type 9a; glycogen storage diseases; GM1 -gangliosidosis; Greenberg syndrome; Greig cephalopolysyndactyly syndrome; hair genetic diseases; HANAC syndrome; harlequin type ichtyosis congenita; HDR syndrome; hemochromatosis type 3; hemochromatosis type 4;
  • hemophilia A hereditary angioedema type 3; hereditary angioedemas; hereditary hemorrhagic telangiectasia; hereditary hypofibrinogenemia; hereditary intraosseous vascular malformation; hereditary leiomyomatosis and renal cell cancer; hereditary neuralgic amyotrophy; hereditary sensory and autonomic neuropathy type; Hermansky- Pudlak disease; HHH syndrome; HHT2; hidrotic ectodermal dysplasia type 1; hidrotic ectodermal dysplasias; HNF4A-associated hyperinsulinism; HNPCC; human immunodeficiency with microcephaly; Huntington disease; hyper-IgD syndrome; hyperinsulinism-hyperammonemia syndrome; hypertrophy of the retinal pigment epithelium; hypochondrogenesis; hypohidrotic ectodermal dysplasia; ICF syndrome; idiopathic congenital intestinal pseudo-obstruction; immuno
  • phospholipid-associated cholelithiasis phospholipid-associated cholelithiasis; lysinuric protein intolerance; Maffucci syndrome; Majeed syndrome; mannose-binding protein deficiency; Marfan disease; Marshall syndrome; MASA syndrome; MCAD deficiency; McCune-Albright syndrome; MCKD2; Meckel syndrome; Meesmann corneal dystrophy; megacystis- microcolon-intestinal hypoperistalsis; megaloblastic anemia type 1; MEHMO; MELAS; Melnick-Needles syndrome; MEN2s; Menkes disease; metachromatic
  • neurogastrointestinal encephalomyopathy monilethrix; monosomy X; mosaic trisomy 9 syndrome; Mowat- Wilson syndrome; mucolipidosis type 2; mucolipidosis type Ilia; mucolipidosis type IV; mucopolysaccharidoses; mucopolysaccharidosis type 3A;
  • mucopolysaccharidosis type 3C mucopolysaccharidosis type 4B; multiminicore disease; multiple acyl-CoA dehydrogenation deficiency; multiple cutaneous and mucosal venous malformations; multiple endocrine neoplasia type 1 ; multiple sulfatase deficiency; NAIC; nail-patella syndrome; nemaline myopathies; neonatal diabetes mellitus; neonatal surfactant deficiency; nephronophtisis; Netherton disease; neurofibromatoses; neurofibromatosis type 1 ; Niemann-Pick disease type A; Niemann- Pick disease type B; Niemann-Pick disease type C; NKX2E; Noonan syndrome; North American Indian childhood cirrhosis; NROB1 duplication-associated DSD; ocular genetic diseases; oculo-auricular syndrome; OLEDAID; oligomeganephronia;
  • oligomeganephronic renal hypolasia Oilier disease; Opitz-Kaveggia syndrome;
  • orofaciodigital syndrome type 1 orofaciodigital syndrome type 2; osseous Paget disease; otopalatodigital syndrome type 2; OXPHOS diseases; palmoplantar hyperkeratosis; panlobar nephroblastomatosis; Parkes- Weber syndrome; Parkinson disease; partial deletion of 21q22.2-q22.3; Pearson syndrome; Pelizaeus-Merzbacher disease; Pendred syndrome; pentalogy of Cantrell; peroxisomal acyl-CoA-oxidase deficiency; Peutz-Jeghers syndrome; Pfeiffer syndrome; Pierson syndrome; pigmented nodular adrenocortical disease; pipecolic acidemia; Pitt-Hopkins syndrome;
  • plasmalogens deficiency pleuropulmonary blastoma and cystic nephroma; polycystic lipomembranous osteodysplasia; porphyrias; premature ovarian failure; primary erythermalgia; primary hemochromatoses; primary hyperoxaluria; progressive familial intrahepatic cholestasis; propionic acidemia; pyruvate decarboxylase deficiency;
  • RAPADILINO syndrome renal cystinosis; rhabdoid tumor predisposition syndrome; Rieger syndrome; ring chromosome 4; Roberts syndrome; Robinow-Sorauf syndrome; Rothmund-Thomson syndrome; SCID; Saethre-Chotzen syndrome; Sandhoff disease; SC phocomelia syndrome; SCA5; Schinzel phocomelia syndrome; short rib-polydactyly syndrome type 1; short rib-polydactyly syndrome type 4; short-rib Polydactyly syndrome type 2; short-rib Polydactyly syndrome type 3; Shwachman disease;
  • Shwachman-Diamond disease sickle cell anemia; Silver-Russell syndrome; Simpson- Golabi-Behmel syndrome; Smith-Lemli-Opitz syndrome; SPG7-associated hereditary spastic paraplegia; spherocytosis; split-hand/foot malformation with long bone deficiencies; spondylocostal dysostosis; sporadic visceral myopathy with inclusion bodies; storage diseases; STRA6-associated syndrome; Tay-Sachs disease;
  • transthyretin-associated amyloidosis trisomy 13; trisomy 22; trisomy 2p syndrome; tuberous sclerosis; tufting enteropathy; urea cycle diseases; Van Den Ende-Gupta syndrome; Van der Woude syndrome; variegated mosaic aneuploidy syndrome; VLCAD deficiency; von Hippel-Lindau disease; Waardenburg syndrome; WAGR syndrome; Walker- Warburg syndrome; Werner syndrome; Wilson disease; Wolcott- Rallison syndrome; Wolfram syndrome; X-linked agammaglobulinemia; X-linked chronic idiopathic intestinal pseudo-obstruction; X-linked cleft palate with ankyloglossia; X-linked dominant chondrodysplasia punctata ; X-linked ectodermal dysplasia; X-linked Emery-Dreifuss muscular dystrophy; X-linked lissencephaly; X- linked lymphoproliferative disease;
  • inhibitory effects against a cellular and/or humoral immune response including a response not associated with inflammation; inhibit the ability of macrophages and T cells to adhere to extracellular matrix components and fibronectin, as well as up- regulated fas receptor expression in T cells; inhibit unwanted immune reaction and inflammation including arthritis, including rheumatoid arthritis, inflammation associated with hypersensitivity, allergic reactions, asthma, systemic lupus erythematosus, collagen diseases and other autoimmune diseases, inflammation associated with atherosclerosis, arteriosclerosis, atherosclerotic heart disease, reperfusion injury, cardiac arrest, myocardial infarction, vascular inflammatory disorders, respiratory distress syndrome or other cardiopulmonary diseases, inflammation associated with peptic ulcer, ulcerative colitis and other diseases of the gastrointestinal tract, hepatic fibrosis, liver cirrhosis or other hepatic diseases, thyroiditis or other glandular diseases, glomerulonephritis or other renal and urologic diseases, otitis or other oto-rhino
  • retinitis or cystoid macular oedema retinitis or cystoid macular oedema, sympathetic ophthalmia, scleritis, retinitis pigmentosa, immune and inflammatory components of degenerative fondus disease, inflammatory components of ocular trauma, ocular inflammation caused by infection, proliferative vitreo-retinopathies, acute ischaemic optic neuropathy, excessive scarring, e.g.
  • autoimmune diseases or conditions or disorders where, both in the central nervous system (CNS) or in any other organ, immune and/or inflammation suppression would be beneficial, Parkinson's disease, complication and/or side effects from treatment of Parkinson's disease, AIDS-related dementia complex HIV-related encephalopathy, Devic's disease, Sydenham chorea, Alzheimer's disease and other degenerative diseases, conditions or disorders of the CNS, inflammatory components of strokes, post-polio syndrome, immune and inflammatory components of psychiatric disorders, myelitis, encephalitis, subacute sclerosing pan-encephalitis, encephalomyelitis, acute neuropathy, subacute neuropathy, chronic neuropathy, Guillaim-Barre syndrome, Sydenham chora, myasthenia gravis, pseudo-tumour cerebri, Down's Syndrome, Huntington's disease, amyo
  • the invention provides improved viral vector systems optimized to express high levels of one or more therapeutic proteins in erythroid cells or erythroid precursor cells.
  • Retroviral vectors including lentiviral vectors, of the invention further comprise a polynucleotide-of-interest, including, for example, a globin gene or a gene which encodes an antisickling protein.
  • the globin gene expressed in the retroviral vector of the invention is ⁇ - globin, ⁇ -globin, or ⁇ -globin.
  • the human ⁇ -globin gene is the wild type human ⁇ -globin gene or human p A -globin gene.
  • the human ⁇ -globin gene comprises one or more deletions of intron sequences or is a mutated human ⁇ -globin gene encoding at least one antisickling amino acid residue.
  • Antisickling amino acids can be derived from human ⁇ -globin or human ⁇ -globin.
  • the mutated human ⁇ -globin gene encodes a threonine to glutamine mutation at codon 87 ( ⁇ - ⁇ 87(3 ⁇ 4.
  • Retroviral vectors, including lentiviral vectors, of the invention can be used in gene therapy, including for the treatment of hemoglobinopathies.
  • the invention provides methods for using the foregoing vectors to achieve stable, high levels of gene expression in erythroid cells, e.g., in order to treat erythroid- specific diseases.
  • the gene therapy vectors are used to treat hemoglobinopathies, including, for example, sickle cell disease (SCD).
  • the gene therapy vectors are used for treatment of thalassemias, including, but not limited to, ⁇ -thalassemia.
  • vectors of the invention comprise an ABCD1 gene for treatment of adrenoleukodystropies and/or adrenomyeloneuropathies.

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Abstract

La présente invention concerne des systèmes perfectionnés d'expression génique à commutation moléculaire et une production perfectionnée de cellules d'encapsidation de rétrovirus et de particules virales. Dans divers modes de réalisation, la présente invention concerne également des vecteurs rétroviraux qui ont un contrôle accru vis-à-vis de l'expression génique. La présente invention concerne en outre des systèmes de vecteurs qui sont utiles dans des méthodes de thérapie génique.
PCT/US2012/040932 2011-06-06 2012-06-05 Systèmes perfectionnés de commutation génique Ceased WO2012170431A2 (fr)

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WO2016107958A1 (fr) * 2015-01-02 2016-07-07 Instituto De Salud Carlos Iii Vecteur lentiviral à expression auto-limitée
WO2017144893A1 (fr) * 2016-02-26 2017-08-31 Ucl Business Plc Cellule d'encapsidation de rétrovirus
US9913914B2 (en) 2013-10-28 2018-03-13 Cupid Peptide Company Limited Cell transport
CN109402178A (zh) * 2018-11-16 2019-03-01 佛山科学技术学院 一种小鼠精原干细胞高效重编程的方法及应用
EP3489353A1 (fr) * 2015-11-24 2019-05-29 GlaxoSmithKline Intellectual Property Development Limited Lignées cellulaires stables pour la production de rétrovirus
US10450574B2 (en) 2015-11-24 2019-10-22 Glaxosmithkline Intellectual Property Development Limited Transient transfection method for retroviral production
WO2020041647A1 (fr) 2018-08-24 2020-02-27 Calimmune, Inc. Production de vecteur dans un milieu sans sérum
EP3475416A4 (fr) * 2016-06-22 2020-04-29 Icahn School of Medicine at Mount Sinai Administration virale d'arn à l'aide de ribozymes à auto-clivage et applications basées sur crispr
CN112143754A (zh) * 2020-09-30 2020-12-29 扬州大学 猪盖塔病毒感染性克隆及其建构方法及应用
CN112941036A (zh) * 2021-02-08 2021-06-11 吉林迈丰生物药业有限公司 一种提高狂犬病毒在人二倍体细胞中复制水平的方法
CN113322282A (zh) * 2021-04-20 2021-08-31 华南农业大学 稳定表达NS1蛋白的犬肾细胞系MDCK-pCDH-NS1及其构建方法和应用
US20220202958A1 (en) * 2015-01-21 2022-06-30 Cornell University Viral Vectors for Prophylaxis and Therapy of Hemoglobinopathies
CN114761566A (zh) * 2019-08-29 2022-07-15 G科技生物有限责任公司 用于治疗病毒感染的组合物和方法
EP4035659A1 (fr) 2016-11-29 2022-08-03 PureTech LYT, Inc. Exosomes destinés à l'administration d'agents thérapeutiques
CN117304276A (zh) * 2023-11-30 2023-12-29 江门海关技术中心 含口蹄疫病毒o型和塞内卡病毒核酸的病毒样颗粒
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WO2003064621A2 (fr) * 2002-02-01 2003-08-07 Ambion, Inc. Courts fragments d'arn interferant haute activite visant a reduire l'expression de genes cibles
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WO2016107958A1 (fr) * 2015-01-02 2016-07-07 Instituto De Salud Carlos Iii Vecteur lentiviral à expression auto-limitée
US20220202958A1 (en) * 2015-01-21 2022-06-30 Cornell University Viral Vectors for Prophylaxis and Therapy of Hemoglobinopathies
EP3489353A1 (fr) * 2015-11-24 2019-05-29 GlaxoSmithKline Intellectual Property Development Limited Lignées cellulaires stables pour la production de rétrovirus
US10450574B2 (en) 2015-11-24 2019-10-22 Glaxosmithkline Intellectual Property Development Limited Transient transfection method for retroviral production
US10704032B2 (en) 2016-02-26 2020-07-07 Ucl Business Ltd Retrovirus packaging cell
WO2017144893A1 (fr) * 2016-02-26 2017-08-31 Ucl Business Plc Cellule d'encapsidation de rétrovirus
US10988779B2 (en) 2016-06-22 2021-04-27 Icahn School Of Medicine At Mount Sinai Viral delivery of RNA utilizing self-cleaving ribozymes and CRISPR-based applications thereof
EP3475416A4 (fr) * 2016-06-22 2020-04-29 Icahn School of Medicine at Mount Sinai Administration virale d'arn à l'aide de ribozymes à auto-clivage et applications basées sur crispr
EP4035659A1 (fr) 2016-11-29 2022-08-03 PureTech LYT, Inc. Exosomes destinés à l'administration d'agents thérapeutiques
WO2020041647A1 (fr) 2018-08-24 2020-02-27 Calimmune, Inc. Production de vecteur dans un milieu sans sérum
CN109402178A (zh) * 2018-11-16 2019-03-01 佛山科学技术学院 一种小鼠精原干细胞高效重编程的方法及应用
CN114761566A (zh) * 2019-08-29 2022-07-15 G科技生物有限责任公司 用于治疗病毒感染的组合物和方法
EP4117720A4 (fr) * 2020-03-09 2024-04-24 Arcturus Therapeutics, Inc. Compositions et méthodes pour l'induction de réponses immunitaires
US12390524B2 (en) 2020-03-09 2025-08-19 Arcturus Therapeutics, Inc. Compositions and methods for inducing immune responses
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CN112143754B (zh) * 2020-09-30 2021-05-18 扬州大学 猪盖塔病毒感染性克隆及其建构方法及应用
CN112143754A (zh) * 2020-09-30 2020-12-29 扬州大学 猪盖塔病毒感染性克隆及其建构方法及应用
CN112941036A (zh) * 2021-02-08 2021-06-11 吉林迈丰生物药业有限公司 一种提高狂犬病毒在人二倍体细胞中复制水平的方法
CN113322282A (zh) * 2021-04-20 2021-08-31 华南农业大学 稳定表达NS1蛋白的犬肾细胞系MDCK-pCDH-NS1及其构建方法和应用
CN117304276B (zh) * 2023-11-30 2024-04-12 江门海关技术中心 含口蹄疫病毒o型和塞内卡病毒核酸的病毒样颗粒
CN117304276A (zh) * 2023-11-30 2023-12-29 江门海关技术中心 含口蹄疫病毒o型和塞内卡病毒核酸的病毒样颗粒

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