SELF-LIMITING VIRAL VECTORS ENCODING NUCLEASES

Abstract

Disclosed herein are viral vectors for use in recombinant molecular biology techniques. In particular, the present disclosure relates to self-limiting viral vectors comprising genes encoding site-specific endonucleases as well as recognition sequences for site-specific endonucleases such that expression of the endonuclease in a cell cleaves the viral vector and limits its persistence time. In some embodiments, the viral vectors disclosed herein also carry directives to delete, insert, or change a target sequence.

Claims

1. A viral vector comprising: (a) a first nucleic acid sequence encoding a first engineered nuclease; (b) a first promoter operably linked to said first nucleic acid sequence, wherein said first promoter is positioned 5′ upstream of said first nucleic acid sequence and drives expression of said first engineered nuclease in a target cell; and (c) a first vector recognition sequence which is recognized and cleaved by said first engineered nuclease.

2. The viral vector of claim 1, wherein said viral vector further comprises a first polyA sequence positioned 3′ downstream of said first nucleic acid sequence.

3. The viral vector of claim 1 or claim 2, wherein cleavage of said first vector recognition sequence by said first engineered nuclease in said target cell causes said viral vector to have a lower persistence time in said target cell when compared to a viral vector which does not comprise a vector recognition sequence cleaved by said first engineered nuclease but which is otherwise identical.

4. The viral vector of any one of claims 1-3, wherein said first vector recognition sequence is identical to a first chromosomal recognition sequence present in the genome of said target cell.

5. The viral vector of any one of claims 1-4, wherein said first vector recognition sequence is a sub-optimal recognition sequence which is recognized and cleaved by said first engineered nuclease.

6. The viral vector of any one of claims 1-5, wherein said viral vector further comprises a transgene sequence, wherein said transgene sequence is flanked by sequences homologous to sequences flanking a region of interest in the genome of said target cell.

7. The viral vector of claim 6, wherein said transgene sequence is positioned 5′ upstream of said first promoter.

8. The viral vector of claim 6, wherein said transgene sequence is positioned 3′ downstream of said first nucleic acid sequence.

9. The viral vector of any one of claims 6-8, wherein said first chromosomal recognition sequence is positioned within said region of interest in the genome of said target cell.

10. The viral vector of any one of claims 1-5, wherein said viral vector further comprises a corrected gene sequence, wherein said corrected gene sequence does not comprise said first vector recognition sequence, and wherein said corrected gene sequence corresponds to a mutated gene sequence present in the genome of said target cell.

11. The viral vector of claim 10, wherein said mutated gene sequence differs from said corrected gene sequence by at least one nucleotide and comprises said first chromosomal recognition sequence.

12. The viral vector of claim 10 or claim 11, wherein said corrected gene sequence is positioned 5′ upstream of said first promoter.

13. The viral vector of claim 10 or claim 11, wherein said corrected gene sequence is positioned 3′ downstream of said first nucleic acid sequence.

14. The viral vector of any one of claims 1-5, wherein said viral vector further comprises a second nucleic acid sequence encoding a second engineered nuclease.

15. The viral vector of claim 14, wherein said viral vector further comprises a second promoter operably linked to said second nucleic acid sequence, wherein said second promoter is positioned 5′ upstream of said second nucleic acid sequence and drives expression of said second engineered nuclease in said target cell.

16. The viral vector of claim 14 or claim 15, wherein said second nucleic acid sequence is positioned 5′ upstream of said first promoter.

17. The viral vector of claim 14 or claim 15, wherein said second nucleic acid sequence is positioned 3′ downstream of said first nucleic acid sequence.

18. The viral vector of any one of claims 14-17, wherein said viral vector further comprises a second polyA sequence positioned 3′ downstream of said second nucleic acid sequence.

19. The viral vector of any one of claims 14-18, wherein said second engineered nuclease recognizes and cleaves a second chromosomal recognition sequence present in the genome of said target cell.

20. The viral vector of claim 19, wherein said first chromosomal recognition sequence and said second chromosomal recognition sequence are positioned on the same chromosome.

21. The viral vector of claim 19 or claim 20, wherein said first chromosomal recognition sequence and said second chromosomal recognition sequence flank a region of interest in the genome of said target cell.

22. The viral vector of claim 19, wherein said first chromosomal recognition sequence and said second chromosomal recognition sequence are positioned on different chromosomes.

23. The viral vector of any one of claims 1-22, wherein said first vector recognition sequence is positioned 5′ upstream of said first promoter.

24. The viral vector of any one of claims 1-22, wherein said first vector recognition sequence is positioned 3′ downstream of said first promoter and 5′ upstream of said first nucleic acid sequence.

25. The viral vector of any one of claims 1-22, wherein said first vector recognition sequence is positioned 3′ downstream of said first nucleic acid sequence.

26. The viral vector of any one of claims 1-22, wherein said first nucleic acid sequence comprises, from 5′ to 3′, a first exon, an intron, and a second exon.

27. The viral vector of claim 26, wherein said first vector recognition sequence is positioned within said intron of said first nucleic acid sequence.

28. The viral vector of any one of claims 2-22, wherein said first vector recognition sequence is positioned 3′ downstream of said first nucleic acid sequence and 5′ upstream of said first polyA sequence.

29. The viral vector of any one of claims 2-22, wherein said first vector recognition sequence is positioned 3′ downstream of said first polyA sequence.

30. The viral vector of any one of claims 6-9, wherein said first vector recognition sequence is positioned 5′ upstream of said transgene sequence.

31. The viral vector of any one of claims 6-9, wherein said first vector recognition sequence is positioned 3′ downstream of said transgene sequence.

32. The viral vector of any one of claims 10-13, wherein said first vector recognition sequence is positioned 5′ upstream of said corrected gene sequence.

33. The viral vector of any one of claims 10-13, wherein said first vector recognition sequence is positioned 3′ downstream of said corrected gene sequence.

34. The viral vector of any one of claims 14-22, wherein said first vector recognition sequence is positioned 5′ upstream of said second nucleic acid sequence.

35. The viral vector of any one of claims 15-22, wherein said first vector recognition sequence is positioned 3′ downstream of said second promoter and 5′ upstream of said second nucleic acid sequence.

36. The viral vector of any one of claims 14-22, wherein said first vector recognition sequence is positioned 3′ downstream of said second nucleic acid sequence.

37. The viral vector of any one of claims 14-22, wherein said second nucleic acid sequence comprises, from 5′ to 3′, a first exon, an intron, and a second exon.

38. The viral vector of claim 37, wherein said first vector recognition sequence is positioned within said intron of said second nucleic acid sequence.

39. The viral vector of any one of claims 18-22, wherein said first vector recognition sequence is positioned 3′ downstream of said second nucleic acid sequence and 5′ upstream of said second polyA sequence.

40. The viral vector of any one of claims 18-22, wherein said first vector recognition sequence is positioned 3′ downstream of said second polyA sequence.

41. The viral vector of any one of claims 1-40, wherein said viral vector is an adeno-associated virus (AAV) vector, a retroviral vector, a lentiviral vector, or an adenoviral vector.

42. The viral vector of any one of claims 1-41, wherein said viral vector is an AAV vector comprising a 5′ inverted terminal repeat and a 3′ inverted terminal repeat.

43. The viral vector of claim 42, wherein said AAV vector is a single-stranded AAV vector or a self-complementary AAV vector.

44. The viral vector of any one of claims 1-43, wherein said first promoter is a tissue-specific promoter, a species-specific promoter, or an inducible promoter.

45. The viral vector of any one of claims 1-44, wherein said engineered nuclease is an engineered meganuclease, a zinc finger nuclease (ZFN), a TALEN, a compact TALEN, or a CRISPR/Cas.

46. The viral vector of any one of claims 1-45, wherein said engineered nuclease is an engineered meganuclease.

47. The viral vector of any one of claims 1-46, wherein said first promoter comprises one or more binding sites for a transcription repressor that binds to and silences said first promoter.

48. The viral vector of claim 47, wherein said transcription repressor is a Tet repressor, a Lac repressor, a Cre repressor, or a Lambda repressor.

49. The viral vector of any one of claims 1-46, wherein said first promoter is an inducible promoter, and wherein said viral vector further comprises a nucleic acid sequence encoding a ligand-inducible transcription factor which regulates activation of said first promoter.

50. A recombinant DNA construct encoding said viral vector of any one of claims 1-49.

51. A recombinant DNA construct encoding said viral vector of claim 47 or claim 48, wherein said recombinant DNA construct further comprises a nucleic acid sequence encoding said transcription repressor.

52. The recombinant DNA construct of claim 51, wherein said nucleic acid sequence encoding said transcription repressor is positioned outside of the coding sequence of said viral vector.

53. A method for producing a viral vector, said method comprising transforming a packaging cell with said recombinant DNA construct of any one of claims 50-52, wherein said packaging cell produces said viral vector.

54. The method of claim 53, wherein said packaging cell is transformed with said recombinant DNA construct of claim 51 or claim 52.

55. The method of claim 54, wherein said recombinant DNA construct further comprises a nucleic acid sequence encoding said transcription repressor.

56. The method of claim 55, wherein said nucleic acid sequence encoding said transcription repressor is positioned outside of the coding sequence of said viral vector.

57. The method of claim 54, wherein said packaging cell is further transformed with a second recombinant DNA construct comprising a nucleic acid sequence encoding said transcription repressor.

58. The method of claim 54, wherein said packaging cell comprises in its genome a nucleic acid sequence encoding said transcription repressor, and wherein said packaging cell stably expresses said transcription repressor.

59. The method of claim 53, wherein said first promoter of said recombinant DNA construct is a tissue-specific promoter that is inactive in said packaging cell.

60. The method of claim 53, wherein said first promoter of said recombinant DNA construct is a species-specific promoter that is inactive in said packaging cell.

61. The method of claim 60, wherein said first promoter is a mammalian promoter and said packaging cell is a microbial cell, an insect cell, or a plant cell.

62. The method of claim 53, wherein said first promoter of said recombinant DNA construct is an inducible-promoter which is regulated by a ligand-inducible transcription factor, and wherein said recombinant DNA construct further comprises a nucleic acid sequence encoding said ligand-inducible transcription factor.

63. The method of claim 62, wherein said nucleic acid sequence encoding said ligand-inducible transcription factor is positioned within the coding sequence of said viral vector.

64. The method of any one of claims 53-63, wherein said packaging cell is an insect cell, and wherein said first nucleic acid sequence encoding said first engineered nuclease comprises an intron that prevents expression of said first engineered nuclease in said packaging cell.

65. The method of claim 64, wherein said intron is a human growth hormone intron (SEQ ID NO: 2) or an SV40 large T antigen intron (SEQ ID NO: 3).

66. The method of any one of claims 53-65, wherein said viral vector is an AAV vector, a retroviral vector, a lentiviral vector, or an adenoviral vector.

67. The method of any one of claims 53-66, wherein said viral vector is an AAV vector.

68. The method of claim 67, said method further comprising transforming said packaging cell with: (a) a second recombinant DNA construct comprising a cap gene and a rep gene; and (b) a third recombinant DNA construct comprising adenoviral helper components; wherein said packaging cell produces said AAV vector.

Description

BRIEF DESCRIPTION OF THE FIGURES

[0167] FIGS. 1A- 1D. Diagrams of example self-limiting rAAV vectors. The vector genome is shown with ITRs at the ends. Each vector encodes a site-specific endonuclease and a recognition site for the endonuclease in the genome. FIGS. 1A-1D show example embodiments of vector compositions wherein the recognition site is positioned in variable locations relative to the endonuclease gene and its associated promoter.

[0168] FIG. 2. General method for using a self-limiting rAAV vector to knock-out a gene. In this embodiment, a self-limiting viral vector is delivered to a cell or organism, the vector encoding a site-specific endonuclease that recognizes a target sequence in the coding sequence of a gene of interest within the cell. Following infection with the vector, the cell expresses the endonuclease. The endonuclease then cuts both the recognition site in the genome of the cell and the recognition site in the genome of the virus. The DNA break in the cell genome is repaired by non-homologous end-joining (NHEJ), which introduces mutations into the gene, thus disabling it. The cut virus is quickly degraded by exonucleases and ceases to persist in the cell or organism.

[0169] FIG. 3. General method for using a self-limiting rAAV to deliver a pair of endonucleases and excise a specific DNA fragment from the genome. In this embodiment, a self-limiting viral vector is delivered to a cell or organism, the vector encoding a pair of site-specific endonucleases that recognize different target sequences in a locus of interest. Following infection with the vector, the cell or organism expresses the endonucleases. The endonucleases then cut both of the recognition sites in the genome of the cell as well as a recognition site in the genome of the virus. The DNA breaks in the cell genome are repaired by deleting the fragment intervening the breaks, followed by subsequent re-ligation of the genomic ends. The cut virus is quickly degraded by exonucleases and ceases to persist in the cell or organism.

[0170] FIG. 4. General method for using a self-limiting rAAV to insert a transgene at a defined location within the genome of a cell. In this embodiment, a self-limiting viral vector is delivered to a cell or organism, the vector encoding a site-specific endonuclease that recognizes a target sequence in a locus of interest within the cell or organism’s genome. The self-limiting viral vector contains a transgene flanked by a DNA sequence homologous to the locus of interest. Following infection with the vector, the cell expresses the endonuclease. The endonucleases then cuts both the recognition site in the genome of the cell, as well as the recognition site in the genome of the virus. The DNA break in the cell genome is repaired by homologous recombination with the viral vector, resulting in the insertion of the transgene at the site of the DNA break. The cut virus is quickly degraded by exonucleases and ceases to persist in the cell or organism.

[0171] FIG. 5. General method for using a self-limiting rAAV to repair a mutation in the genome of a cell or organism. In this embodiment, a self-limiting viral vector is delivered to a cell or organism, the vector encoding a site-specific endonuclease that recognizes a target sequence in the genome of the cell near a mutation associated with disease. The self-limiting viral vector further comprises a partial “corrected” copy of the mutated gene. Following infection with the vector, the cell expresses the endonuclease. The endonucleases then cuts both the recognition site in the genome of the cell as well as the recognition site in the genome of the virus. The DNA break in the cell genome is repaired by homologous recombination with the viral vector, resulting in the “corrected” sequence being acquired by the genome of the cell. The cut virus is quickly degraded by exonucleases and ceases to persist in the cell or organism.

[0172] FIGS. 6A - 6B. FIG. 6A) The OLR plasmid DNA vector (SEQ ID NO: 4) is illustrated. The OLR vector comprises a coding sequence for an MDX ½ meganuclease operably-linked to a CMV promoter. The CMV promoter is modified to include three Lac operon sequences. The OLR vector further comprises a cassette including a LacI coding sequence for expression of a Lac repressor that binds to the Lac operons and suppresses expression of the nuclease gene. FIG. 6B) The 3xOi plasmid DNA vector (SEQ ID NO: 5) is illustrated. The 3xOi vector comprises the same elements as the OLR vector but lacks the cassette comprising the LacI coding sequence. Thus, no Lac repressor would be expressed and the nuclease gene would not be suppressed.

[0173] FIG. 7. Western blot for MDX ½ meganuclease expression. Experiments were conducted to determine whether nuclease protein expression was suppressed in viral packaging cells by using a Lac repressor. HEK293 cells were mock electroporated, or electroporated with 2 .Math.g of the OLR plasmid, the 3xOi plasmid, or a GFP (pMAX) RNA. At 1, 2, 4, 8, and 24 hours post-transformation, cell lysates were prepared and nuclease protein expression was determined by Western blot analysis.

[0174] FIG. 8. Vector map for the pDS GRK1 RHO½ L5-14 plasmid DNA vector (SEQ ID NO: 6). This vector comprises a RHO ½ meganuclease coding sequence that is operably-linked to a GRK1 promoter, which is a tissue-specific promoter that is specifically active in human retinal cells (i.e., rod cells). Thus, the meganuclease gene should not be expressed in viral packaging cells such as HEK293 cells.

[0175] FIGS. 9A - 9B. Plasmid DNA vectors comprising introns within a nuclease coding sequence. FIG. 9A) Vector map of the pDS CMV RHO ½ - HGH plasmid DNA vector (SEQ ID NO: 7). This vector comprises a RHO ½ meganuclease coding sequence which includes a human growth hormone intron 1 (SEQ ID NO: 2) within its sequence. FIG. 9B) Vector map of the pDS CMV RHO ½ - SV40LT plasmid DNA vector (SEQ ID NO: 8). This vector comprises a RHO ½ meganuclease coding sequence which includes an SV40 large T intron 1 (SEQ ID NO: 2) within its sequence.

[0176] FIGS. 10A - 10B. FIG. 10A) Vector map of the pDS CMV 3xOi RHO ½ L514 LacI plasmid DNA vector (SEQ ID NO: 9). FIG. 10B) Vector map of the pDS CMV 3xOi RHO ½ L514 plasmid DNA vector (SEQ ID NO: 10).

[0177] FIG. 11. Western blot analysis of RHO ½ meganuclease protein expression in transduced CHO cells. CHO cells were either mock transduced, or transduced with the pDS CMV 3xOi RHO ½ L514 LacI vector (a self-limiting vector comprising a RHO ½ binding site) or the pDS CMV 3xOi RHO ½ L514 vector (not self-limiting; no binding site). Protein was collected at time points of 2, 6, 12, 24, 48, and 72 hours and Western analysis was performed to detect RHO ½ meganuclease protein in cell lysates. The top panel shows detection of RHO ½ meganuclease protein in cell lysates at each time point. Lane 1 shows mock transduced cells. Lanes 2-7 show time points of 2, 6, 12, 24, 48, and 72 hours, respectively, for cells transduced with the pDS CMV 3xOi RHO ½ L514 vector. Lanes 8-13 show time points of 2, 6, 12, 24, 48, and 72 hours, respectively, for cells transduced with the self-limiting pDS CMV 3xOi RHO ½ L514 LacI vector. The arrow indicates the band associated with RHO ½ meganuclease protein. The bottom panel shows detection of a β-actin as a loading control.

[0178] FIG. 12. PCR analysis of viral vector cleavage. CHO cells were transduced with the self-limiting pDS CMV 3xOi RHO ½ L514 LacI vector and DNA was isolated at 2, 6, 12, 24, 48, and 72 hours post-transduction. An adapter molecule was designed having a 3′ overhang that matches the 3′ overhang generated in the viral genome by the RHO ½ meganuclease. PCR was then performed with adapter-ligated DNA and a pair of amplification primers, one matching the AAV sequence, and the other matching the adapter molecule sequence. The resulting PCR products were analyzed on gel. In case of AAV digestion by RHO ½ and ligation to adapter, a PCR band with size 585 bps was expected to be observed.

BRIEF DESCRIPTION OF THE SEQUENCES

[0179] SEQ ID NO: 1 sets forth the amino acid sequence of the wild-type I-CreI meganuclease.

[0180] SEQ ID NO: 2 sets forth the nucleic acid sequence of the human growth hormone intron 1.

[0181] SEQ ID NO: 3 sets forth the nucleic acid sequence of the SV40 large T antigen intron.

[0182] SEQ ID NO: 4 sets forth the nucleic acid sequence of the OLR DNA plasmid.

[0183] SEQ ID NO: 5 sets forth the nucleic acid sequence of the 3xOi plasmid.

[0184] SEQ ID NO: 6 sets forth the nucleic acid sequence of the pDS GRK1 RHO½ L5-14 plasmid.

[0185] SEQ ID NO: 7 sets forth the nucleic acid sequence of the pDS CMV RHO ½ -HGH plasmid.

[0186] SEQ ID NO: 8 sets forth the nucleic acid sequence of the pDS CMV RHO ½ -SV40LT plasmid.

[0187] SEQ ID NO: 9 sets forth the nucleic acid sequence of the pDS CMV 3xOi RHO ½ L514 LacI plasmid.

[0188] SEQ ID NO: 10 sets forth the nucleic acid sequence of the pDS CMV 3xOi RHO ½ L514 plasmid.

DETAILED DESCRIPTION OF THE INVENTION

1.1 References and Definitions

[0189] The patent and scientific literature referred to herein establishes knowledge that is available to those of skill in the art. The entire disclosures of the issued U.S. patents, pending applications, published foreign applications, and references, including GenBank database sequences, that are cited herein are hereby incorporated by reference to the same extent as if each was specifically and individually indicated to be incorporated by reference.

[0190] Reference will now be made in detail to the preferred embodiments of the self-limiting viral vector, examples of which are illustrated in the accompanying drawings.

[0191] As used herein, the term “cell” refers to a cell, whether it be part of a cell line, tissue, or organism. “Cell” may refer to microbial, plant, insect, or animalian (mammalian, reptilian, avian, or otherwise) type, and where necessary, is specified.

[0192] As used herein, the term “meganuclease” refers to an endonuclease that is derived from I-CreI. The term meganuclease, as used herein, refers to an engineered variant of I-CreI that has been modified relative to natural I-CreI with respect to, for example, DNA-binding specificity, DNA cleavage activity, DNA-binding affinity, or dimerization properties. Methods for producing such modified variants of I-Crel are known in the art (i.e. WO 2007/047859). A meganuclease may bind to double-stranded DNA as a homodimer, as is the case for wild-type I-CreI, or it may bind to DNA as a heterodimer. A meganuclease may also be a “single-chain meganuclease” in which a pair of DNA-binding domains derived from I-CreI are joined into a single polypeptide using a peptide linker.

[0193] As used herein, the term “single-chain meganuclease” refers to a polypeptide comprising a pair of meganuclease subunits joined by a linker. A single-chain meganuclease has the organization: N-terminal subunit - Linker - C-terminal subunit. The two meganuclease subunits, each of which is derived from I-CreI, will generally be non-identical in amino acid sequence and will recognize non-identical DNA sequences. Thus, single-chain meganucleases typically cleave pseudo-palindromic or non-palindromic recognition sequences. A single chain meganuclease may be referred to as a “single-chain heterodimer” or “single-chain heterodimeric meganuclease” although it is not, in fact, dimeric. For clarity, unless otherwise specified, the term “meganuclease” can refer to a dimeric or single-chain meganuclease.

[0194] As used herein, the term “site specific endonuclease” means a meganuclease, TALEN, Compact TALEN, Zinc-Finger Nuclease, or CRISPR.

[0195] As used herein, the term “Compact TALEN” refers to an endonuclease comprising a DNA-binding domain with 16-22 TAL domain repeats fused in any orientation to any portion of the I-TevI homing endonuclease.

[0196] As used herein, the term “Zinc-Finger Nuclease” refers to an endonuclease comprising a DNA-binding domain comprising 3-5 zinc-finger domains fused to any portion of the FokI nuclease domain.

[0197] As used herein, the term “TALEN” refers to an endonuclease comprising a DNA-binding domain comprising 16-22 TAL domain repeats fused to any portion of the FokI nuclease domain.

[0198] As used herein, the term “CRISPR” refers to a caspase-based endonuclease comprising a caspase, such as Cas9, and a guide RNA that directs DNA cleavage of the caspase by hybridizing to a recognition site in the genomic DNA.

[0199] As used herein, with respect to a protein, the term “recombinant” means having an altered amino acid sequence as a result of the application of genetic engineering techniques to nucleic acids which encode the protein, and cells or organisms which express the protein. With respect to a nucleic acid, the term “recombinant” means having an altered nucleic acid sequence as a result of the application of genetic engineering techniques. Genetic engineering techniques include, but are not limited to: PCR and DNA cloning technologies; transfection, transformation and other gene transfer technologies; homologous recombination; site-directed mutagenesis; and gene fusion. In accordance with this definition, a protein having an amino acid sequence identical to a naturally-occurring protein, but produced by cloning and expression in a heterologous host, is not considered recombinant. As used herein, the term “engineered” is synonymous with the term “recombinant.”

[0200] As used herein, the term “wild-type” refers to any naturally-occurring form of a meganuclease. The term “wild-type” is not intended to mean the most common allelic variant of the enzyme in nature but, rather, any allelic variant found in nature. Wild-type homing endonucleases are distinguished from recombinant or non-naturally-occurring meganucleases.

[0201] As used herein, the term “recognition sequence” refers to a DNA sequence that is bound and cleaved by an endonuclease. In the case of a meganuclease, a recognition sequence comprises a pair of inverted, 9 basepair “half sites” which are separated by four basepairs. In the case of a single-chain meganuclease, the N-terminal domain of the protein contacts a first half-site and the C-terminal domain of the protein contacts a second half-site. Cleavage by a meganuclease produces four basepair 3′ “overhangs”. “Overhangs”, or “sticky ends” are short, single-stranded DNA segments that can be produced by endonuclease cleavage of a double-stranded DNA sequence. In the case of meganucleases and single-chain meganucleases derived from I-CreI, the overhang comprises bases 10-13 of the 22 basepair recognition sequence. In the case of a Compact TALEN, the recognition sequence comprises a first CNNNGN sequence that is recognized by the I-TevI domain, followed by a nonspecific spacer 4-16 basepairs in length, followed by a second sequence 16-22 bp in length that is recognized by the TAL-effector domain (this sequence typically has a 5′ T base). Cleavage by a Compact TALEN produces two basepair 3′ overhangs. In the case of a CRISPR, the recognition sequence is the sequence, typically 16-24 basepairs, to which the guide RNA binds to direct Cas9 cleavage. Cleavage by a CRISPR produces blunt ends. In the case of a zinc finger, the DNA binding domains typically recognize an 18-bp recognition sequence comprising a pair of nine basepair “half-sites” separated by 2-10 basepairs and cleavage by the nuclease creates a blunt end or a 5′ overhang of variable length (frequently four basepairs).

[0202] As used herein, the term “target site” or “target sequence” refers to a region of the chromosomal DNA of a cell comprising a recognition sequence for a site specific endonuclease.

[0203] As used herein, the term “homologous recombination” or “HR” refers to the natural, cellular process in which a double-stranded DNA-break is repaired using a homologous DNA sequence as the repair template (see, e.g. Cahill et al. (2006) Front. Biosci. 11:1958-1976). The homologous DNA sequence may be an endogenous chromosomal sequence or an exogenous nucleic acid that was delivered to the cell. The term “homology” is used herein as equivalent to “sequence similarity” and is not intended to require identity by descent or phylogenetic relatedness.

[0204] As used herein, the term “non-homologous end-joining” or “NHEJ” refers to the natural, cellular process in which a double-stranded DNA-break is repaired by the direct joining of two non-homologous DNA segments (see, i.e. Cahill et al. (2006) Front. Biosci. 11:1958-1976). DNA repair by non-homologous end-joining is error-prone and frequently results in the untemplated addition or deletion of DNA sequences at the site of repair. The process of non-homologous end-joining occurs in both eukaryotes and prokaryotes such as bacteria.

[0205] As used herein, the term “re-ligation” refers to a process in which two DNA ends produced by a pair of double-strand DNA breaks are covalently attached to one another with the loss of the intervening DNA sequence but without the gain or loss of any additional DNA sequence. In the case of a pair of DNA breaks produced with single-strand overhangs, re-ligation can proceed via annealing of complementary overhangs followed by covalent attachment of 5′ and 3′ ends by a DNA ligase. Re-ligation is distinguished from NHEJ in that it does not result in the untemplated addition or removal of DNA from the site of repair.

[0206] As used herein, the term “concatamer” refers to long continuous DNA molecules that contain multiple copies of the same DNA sequence linked in series,

[0207] As used herein, the term “persistence” or “persist” refers to the viability of the self-limiting viral vector in the cell, tissue, or organism of interest. Attenuating persistence time refers to the degradation of the vector, and thus, viral genome.

[0208] As used herein, unless specifically indicated otherwise, the word “or” is used in the inclusive sense of “and/or” and not the exclusive sense of “either/or.”

2.1 Self-Limiting Viral Vectors

[0209] The present invention is based, in part, on the premise that a viral vector, such as a rAAV vector, will not persist in a cell after cleavage of the DNA by an endonuclease. rAAV is a preferred vector for delivery of genome editing endonucleases to cells and tissues, but its long persistence time in cells presents a problem. Genome editing applications using site-specific endonucleases generally do not require long-term expression of the endonuclease gene, and long-term expression may be harmful. Long-term expression of endonucleases may hinder cleavage specificity, thus introducing breakage in unintended sites, which may lead to detrimental consequences for cell health. Moreover, cell machinery is designed to detect and immunologically respond to the production of foreign proteins, such as endonucleases introduced by the rAAV vector. (Mingozzi F, and High K (2013) Blood 122(1):23-26). Thus, the invention provides vectors in which vector persistence time is “self-limited” through a recognition sequence for the genome editing endonuclease already incorporated into the vector.

[0210] The self-limiting viral vector is thus able to deliver the endonuclease gene to a cell or tissue such that the endonuclease is expressed and able to modify the genome of the cell. In addition, the same endonuclease will find its target site within the vector and will cut the genome of the virus, exposing free 5′ and 3′ ends and initiating degradation by exonucleases. It is taught herein that cleavage of the viral genome will prevent the virus from forming concatamers that can persist stably in the cell as episomes. Thus, the virus effectively “kills itself.”

[0211] The precise location of the endonuclease recognition sequence may vary, as exemplified in FIG. 1. Certain configurations are preferred when possible. One preferred configuration is shown in FIG. 1C where the endonuclease recognition sequence is positioned within an intron in the endonuclease gene. Intracellular cleavage of such a vector is expected to separate the two endonuclease exons such that the endonuclease gene can no longer be expressed. This leads to a more rapid attenuation of endonuclease expression.. Alternatively, it is possible to position the endonuclease recognition sequence between the endonuclease gene and its promoter (i.e. in the 5′ UTR), as shown in FIG. 1D. This configuration will also quickly attenuate expression of the endonuclease while not adding as much additional size to the gene. Also depicted in FIG. 1A, the endonuclease recognition sequence may be placed after the endonuclease gene sequence and poly A, or the endonuclease recognition site may be placed before the promoter in the 5′ position of the ITR as depicted in FIG. 1B. The endonuclease recognition site may be placed in various locations, as long as the site does not interfere with the proper expression of the endonuclease, and is accessible by the expressed nuclease.

[0212] The self-limiting viral vectors created can be used to infect cells, tissues, or organisms to achieve a multitude of therapeutic results. For instance, as exemplified in FIG. 2, self-limiting viral vectors can be used to disable (“knock-out”) a gene. ]. In infected cells, the expressed endonuclease within the cell recognizes a target sequence within a coding sequence of a gene of interest within the cell (that cell being part of a cell line, tissue, or organism) and cuts the DNA. The DNA break in the cell’s genome will then be repaired by non-homologous end-joining (NHEJ), such that mutations are introduced at the target site that disables the gene of interest’s function. Subsequently, the expressed endonuclease recognizes and cuts the self-limiting viral vector at the endonuclease recognition sequence. Once cut, the self-limiting viral vector cannot produce concameters that may otherwise form and persist within the episomes. The self-limiting viral vector will cease to persist within the cell.

[0213] In other embodiments, described in FIG. 3, the self-limiting viral vector comprises, starting at a 5′ position between the ITRs, a promoter, a first endonuclease coding sequence and poly A, an endonuclease recognitions site, a second promoter (which may be the same as the first), a second endonuclease with polyA followed by the 3′ ITR. Notably, this configuration may be altered, specifically the location of the endonuclease recognition site (as discussed above and exemplified in FIG. 1). The endonuclease recognition site may be recognized by any one of the endonucleases coded for within the self-limiting viral vector. FIG. 3 shows the endonuclease recognition site as being recognized by the first endonuclease. Moreover, it is contemplated that more than two endonucleases, each recognizing a unique site within a cell genome, may be housed within the self-limiting viral vector. FIG. 3 depicts a vector coding for two endonucleases, which when expressed within an infected cell, will each recognize their own target site, where the first endonuclease recognizes a “site 1” and the second endonuclease recognizes a “site 2.” The endonucleases cut the genome at each site, exposing the region of interest coded between each cut site. The region of interest fragment is excised and degraded by cell machinery, and the cell genome is repaired by re-ligation. As stated above, the ligation of the genome is achieved by cell processes that maintain the integrity of the sequence and does not introduce additional sequence to the genome. The endonuclease subsequently recognizes the endonuclease recognition site within the self-limiting viral vector and cuts the viral genome. Once cut, the self-limiting viral vector cannot produce concatamers that may otherwise form and persist within the episomes. The self-limiting viral vector will cease to persist within the cell.

[0214] The self-limiting viral vectors of the present invention may be employed to introduce a new transgene into the infected cell’s genome. In these embodiments, the self-limiting viral vector comprises from a 5′ position between the ITRs: a promoter, endonuclease coding sequence and poly A, an endonuclease recognition site, a homologous DNA sequence, the transgene, and another homologous sequence at the 3′ position within the ITRs. Notably, this configuration may be altered, specifically the location of the endonuclease recognition site (as discussed above and exemplified in FIG. 1). For example, the endonuclease site could be positioned on the 3′ end of the homologous DNA sequence of the transgene, or in an intron contained within the transgene sequence. After infection, the endonuclease is expressed within the cell, and recognizes a site within a region of interest. The endonuclease cleaves a site within the gene of interest, exposing 5′ and 3′ ends of the cell genome. The self-limiting viral vector contains matching homologous DNA for the exposed 5′ and 3′ ends of the cleaved cell genome. By homologous recombination, the homologous DNA regions flanking the 5′ and 3′ ends of the transgene recombine with the cleaved portion of the cell genome and the transgene of the self-limiting viral vector is inserted within the cell genome. The endonuclease subsequently recognizes the endonuclease recognition site within the self-limiting viral vector and cuts the viral genome. Once cut, the self-limiting viral vector cannot produce concameters that may otherwise form and persist within the episomes. The self-limiting viral vector will cease to persist within the cell.

[0215] As shown in FIG. 5, the self-limiting viral vectors of the present invention may be dispatched to alter a gene sequence within a cell genome (as previously defined, that cell being part of a cell line, tissue, or organism). In these embodiments, the self-limiting viral vector comprises at a 5′ position of the ITRs, a promoter, an endonuclease coding sequence with poly A, an endonuclease recognition site, a gene sequence and the 3′ position within the ITRs. The expressed endonuclease recognizes and cuts a site within the gene sequence in the infected cell’s genome. This cut exposes 5′ and 3′ ends of the infected cell’s genome that can recombine with the 5′ and 3′ ends of the gene sequence encoded within the self-limiting viral vector. The gene sequence is inserted into the infected cell’s genome through homologous recombination. The endonuclease subsequently recognizes the endonuclease recognition site within the self-limiting viral vector and cuts the viral genome. Once cut, the self-limiting viral vector cannot produce concameters that may otherwise form and persist within the episomes. The self-limiting viral vector will cease to persist within the cell

2.2 Kinetic Balancing

[0216] In some cases, it may be advantageous to modify the recognition sequence in the self-limiting viral vector to make it sub-optimal. The viral vector should not be cut before a sufficient concentration of endonuclease has been accumulated in the cell to modify the cell’s genome in the desired manner. Because the chromosomal target sequence of interest will be chromatainized, it is more difficult to access than an episomal vector sequence. Thus, higher concentrations of endonuclease are likely required to cut the chromosomal recognition site in the genome of the cell. If the transcribed endonuclease attacks the recognition sequence in the self-limiting viral vector before the appropriate amount of endonuclease is achieved, recognition of the target site within the cell may be unrealized. The use of sub-optimal recognition sequences in the viral vector is “kinetic balancing,” because it is done to coordinate the timing of DNA cleavage such that the genome of the cell is cut first, followed by the genome of the virus.

[0217] In general, sub-optimal recognition sequences can be generated by deviating from the sequence that the endonuclease was engineered to recognize. An engineered meganuclease, for example, recognizes a 22 bp sequence but will tolerate certain 1-2 basepair changes in its preferred sequence. These modified sequences are typically cut less efficiently than the preferred sequence and, so, are suitable for incorporation into self-limiting viral vectors. In selecting a sub-optimal recognition sequence for incorporation into self-limiting viral vectors, it is critical that the sub-optimal site is still cut by the nuclease, albeit less efficiently than the preferred sequence. For each of the engineered endonuclease types, regions of a recognition sequence may be able to tolerate changes. For example, engineered meganucleases tolerate single-base changes at bases 1, 10, 11, 12, 13, and 22 of the recognition sequence (Jurica MS, Monnat RJ Jr, Stoddard BL (1998) Mol. Cell. 2(4): 469-76).

[0218] Experimental methods to evaluate and quantify site-specific DNA cleavage may be performed, including in vitro DNA digests with purified endonuclease protein and cell-based reporter assays (Chevalier B, Turmel M, Lemieux C, Monnat RJ Jr, Stoddard BL (2003) J. Mol. Biol. 329(2): 253-69). These methods can be used to evaluate a variety of sub-optimal recognition sequences to determine the sequences that are cut less efficiently than the preferred recognition sequence in the genome of the cell.

2.3 Methods for Producing Self-Limiting Viruses

[0219] rAAV virus is typically produced in mammalian cell lines such as HEK-293. Because the viral cap and rep genes are removed from the vector to prevent its self-replication to make room for the therapeutic gene(s) to be delivered (e.g. the endonuclease gene), it is necessary to provide these in trans in the packaging cell line. In addition, it is necessary to provide the “helper” (e.g. adenoviral) components necessary to support replication (Cots D, Bosch A, Chillon M (2013) Curr. Gene Ther. 13(5): 370-81). Frequently, rAAV is produced using a triple-transfection in which a cell line is transfected with a first plasmid encoding the “helper” components, a second plasmid comprising the cap and rep genes, and a third plasmid comprising the viral ITRs containing the intervening DNA sequence to be packaged into the virus. Viral particles comprising a genome (ITRs and intervening gene(s) of interest) encased in a capsid are then isolated from cells by freeze-thaw cycles, sonication, detergent, or other means known in the art. Particles are then purified using cesium-chloride density gradient centrifugation or affinity chromatography and subsequently delivered to the gene(s) of interest to cells, tissues, or an organism such as a human patient.

[0220] Because rAAV particles are typically produced (manufactured) in cells, precautions must be taken in practicing the current invention to ensure that the site-specific endonuclease is NOT expressed in the packaging cells. Because the viral genomes of the invention comprise a recognition sequence for the endonuclease, any endonuclease expressed in the packaging cell line will be capable of cleaving the viral genome before it can be packaged into viral particles. This will result in reduced packaging efficiency and/or the packaging of fragmented genomes. Several approaches can be used to prevent endonuclease expression in the packaging cells, including:

[0221] 1. The endonuclease can be placed under the control of a tissue-specific promoter that is not active in the packaging cells. For example, if a self-limiting viral vector is developed for delivery of (an) endonuclease gene(s) to muscle tissue, a muscle-specific promoter can be used. Examples of muscle-specific promoters include C5-12 (Liu, et al. (2004) Hum Gene Ther. 15:783-92), the muscle-specific creatine kinase (MCK) promoter (Yuasa, et al. (2002) Gene Ther. 9: 1576-88), or the smooth muscle 22 (SM22) promoter (Haase, et al. (2013) BMC Biotechnol. 13:49-54). Examples of CNS (neuron)-specific promoters include the NSE, Synapsin, and MeCP2 promoters (Lentz, et al. (2012) Neurobiol Dis. 48:179-88). Examples of liver-specific promoters include albumin promoters ( such as Palb), human α1-antitrypsin (such as Pal AT), and hemopexin (such as Phpx) (Kramer, MG et al., (2003) Mol. Therapy 7:375-85). Examples of eye-specific promoters include opsin, and corneal epithelium-specific K12 promoters (Martin KRG, Klein RL, and Quigley HA (2002) Methods (28): 267-75) (Tong Y, et al., (2007) J Gene Med, 9:956-66). These promoters, or other tissue-specific promoters known in the art, are not highly-active in HEK-293 cells and, thus, will not expected to yield significant levels of endonuclease gene expression in packaging cells when incorporated into self-limiting viral vectors of the present invention. Similarly, the self-limiting viral vectors of the present invention contemplate the use of other cell lines with the use of incompatible tissue specific promoters (i.e., the HeLa cell line (human epithelial cell) and using the liver-specific hemopexin promoter). Other examples of tissue specific promoters include: synovial sarcomas PDZD4 (cerebellum), C6 (liver), ASB5 (muscle), PPP1R12B (heart), SLC5A12 (kidney), cholesterol regulation APOM (liver), ADPRHL1 (heart), and monogenic malformation syndromes TP73L (muscle). (Jacox E, et al., (2010) PLoS One v.5(8):e12274).

[0222] 2. Alternatively, the vector can be packaged in cells from a different species in which the endonuclease is not likely to be expressed. For example, viral particles can be produced in microbial, insect, or plant cells using mammalian promoters, such as the cytomegalovirus- or SV40 virus-early promoters, which are not active in the non-mammalian packaging cells. In a preferred embodiment, viral particles are produced in insect cells using the baculovirus system as described by Gao, et al. (Gao, H., et al. (2007) J. Biotechnol. 131(2):138-43). An endonuclease under the control of a mammalian promoter is unlikely to be expressed in these cells (Airenne, KJ, et al. (2013) Mol. Ther. 21(4):739-49). Moreover, insect cells utilize different mRNA splicing motifs than mammalian cells. Thus, it is possible to incorporate a mammalian intron, such as the human growth hormone (HGH) intron (SEQ ID NO: 2), or the SV40 large T antigen intron (SEQ ID NO:3), into the coding sequence of an endonuclease (see, for example, FIG. 1C). Because these introns are not spliced efficiently from pre-mRNA transcripts in insect cells, insect cells will not express a functional endonuclease and will package the full-length genome. In contrast, mammalian cells to which the resulting rAAV particles are delivered will properly splice the pre-mRNA and will express functional endonuclease protein. Haifeng Chen has reported the use of the HGH and SV40 large T antigen introns to attenuate expression of the toxic proteins barnase and diphtheria toxin fragment A in insect packaging cells, enabling the production of rAAV vectors carrying these toxin genes (Chen, H (2012) Mol Ther Nucleic Acids. 1(11): e57).

[0223] 3. The endonuclease gene can be operably linked to an inducible promoter such that a small-molecule inducer is required for endonuclease expression. Examples of inducible promoters include the Tet-On system (Clontech; Chen H., et al., (2015) BMC Biotechnol. 15(1):4)) and the RheoSwitch system (Intrexon; Sowa G., et al., (2011) Spine, 36(10): E623-8). Both systems, as well as similar systems known in the art, rely on ligand-inducible transcription factors (variants of the Tet Repressor and Ecdysone receptor, respectively) that activate transcription in response to a small-molecule activator (Doxycycline or Ecdysone, respectively). Practicing the current invention using such ligand-inducible transcription activators includes: 1) placing the endonuclease gene under the control of a promoter that responds to the corresponding transcription factor, the endonuclease gene having (a) binding site(s) for the transcription factor; and 2) including the gene encoding the transcription factor in the packaged viral genome. The latter step is necessary because the endonuclease will not be expressed in the target cells or tissues following rAAV delivery if the transcription activator is not also provided to the same cells. The transcription activator then induces endonuclease gene expression only in cells or tissues that are treated with the cognate small-molecule activator. This approach is advantageous because it enables endonuclease gene expression to be regulated in a spatio-temporal manner by selecting when and to which tissues the small-molecule inducer is delivered. However, the requirement to include the inducer in the viral genome, which has significantly limited carrying capacity, creates a drawback to this approach.

[0224] 4. In another preferred embodiment, rAAV particles are produced in a mammalian cell line that expresses a transcription repressor that prevents expression of the endonuclease. Transcription repressors are known in the art and include the Tet-Repressor, the Lac-Repressor, the Cro repressor, and the Lambda-repressor. Many nuclear hormone receptors such as the ecdysone receptor also act as transcription repressors in the absence of their cognate hormone ligand. To practice the current invention, packaging cells are transfected/transduced with a vector encoding a transcription repressor and the endonuclease gene in the viral genome (packaging vector) is operably linked to a promoter that is modified to comprise binding sites for the repressor such that the repressor silences the promoter. The gene encoding the transcription repressor can be placed in a variety of positions. It can be encoded on a separate vector; it can be incorporated into the packaging vector outside of the ITR sequences; it can be incorporated into the cap/rep vector or the adenoviral helper vector; or, most preferably, it can be stably integrated into the genome of the packaging cell such that it is expressed constitutively. Some methods to modify common mammalian promoters to incorporate transcription repressor sites have been disclosed in the art. For example, Chang and Roninson modified the strong, constitutive CMV and RSV promoters to comprise operators for the Lac repressor and showed that gene expression from the modified promoters was greatly attenuated in cells expressing the repressor (Chang BD, and Roninson IB (1996) Gene 183:137-42). The use of a non-human transcription repressor ensures that transcription of the endonuclease gene will be repressed only in the packaging cells expressing the repressor and not in target cells or tissues transduced with the resulting self-limiting rAAV vector.

2.4 Methods for Delivering Self-Limiting Viral Vectors to Human Patients and Animals

[0225] The self-limiting viral vectors of the invention, with their significant safety advantages relative to conventional gene-therapy vectors, will be used as therapeutic agents for the treatment of genetic disorders. For therapeutic applications, route of administration is an important consideration. These self-limiting viral vectors may be delivered systemically via intravenous injection, especially where the target tissues for the therapeutic are liver (e.g. hepatocytes) or vascular epithelium/endothelium. Alternatively, the self-limiting viral vectors of the invention may be injected directly into target tissues. For example, rAAV can be delivered to muscle cells via intramuscular injection (Maltzahn, et al. (2012) Proc Natl Acad Sci USA.109:20614-9), or hydrodynamic injection (Taniyama, et al. (2012) Curr Top Med Chem. 12:1630-7 and Hegge, et al. (2010) Hum Gene Ther. 21:829-42). Delivery to CNS can be accomplished by systemic delivery or intracranial injection (Weinberg, et al. (2013) Neuropharmacology. 69:82-8, Bourdenx, et al. (2014) Front MolNeurosci.7:50, and Ojala DS, et al. (2015) Neuroscientist. 21(1):84-98). Direct injection (e.g. subretinal injection) is the preferred route of administration for the eye (Willett K and Bennett J (2013) Front Immunol. 4:261 and Colella P and Auricchio A (2012) Hum Gene Ther. 23(8):796-807.)

2.5 Self-Limiting Adenoviral and Retroviral Vectors

[0226] While the preferred embodiments of the invention are self-limiting rAAV vectors, the same principles can be applied to adenoviral and lentiviral/retroviral vectors to limit the persistence times of these vectors in cells. These viral vectors have significantly larger genomes and, hence, larger “carrying capacities” than AAV which makes them preferable for the delivery of larger gene payloads to the cell. Indeed, for applications involving the use of a gene editing endonuclease to insert a transgene into the genome (as in FIG. 4), adenoviral or lentiviral/retroviral vectors are preferred when the transgene is larger than ~3.5 kb. For other applications (e.g. FIGS. 2, 3, and 5) adenoviral or lentiviral/retroviral vectors are preferred when the gene editing endonuclease is too large to be encoded by rAAV. This is particularly applicable when employing TALENs and most CRISPR/Cas9 endonucleases.

[0227] Adenovirus and lentiviruses/retroviruses naturally integrate into the genome of the host cell. To be useful for the present invention, the ability of the virus to integrate into the genome must be attenuated. For lentiviral/retroviral vectors, this is accomplished by mutating the int gene encoding the virus integrase. For example, Bobis-Wozowicz, et al. used an integration-deficient retroviral vector to deliver zinc-finger nucleases to human and mouse cells (Bobis-Wozowicz, et al (2014) Nature Scientific Reports 4:4656) (Qasim W, Vink CA, Thrasher AJ (2010) Mol. Ther. 18(7):1263-67), (Wanisch K, Yáñez-Muñoz RJ (2009) Mol. Ther. 17(8): 1316-32), (Nowrouzi A, et al. (2011) Viruses 3(5):429-55).

EXAMPLES

[0228] This invention is further illustrated by the following examples, which should not be construed as limiting. Those skilled in the art will recognize, or be able to ascertain, using no more than routine experimentation, numerous equivalents to the specific substances and procedures described herein. Such equivalents are intended to be encompassed in the scope of the claims that follow the examples below.

Example 1

Promoter Silencing in Viral Packaging Cells

1. Rationale

[0229] In one example of the self-limiting system described herein, a nuclease is expressed from its gene on a viral vector. The nuclease then recognizes and cleaves a recognition sequence integrated within the viral vector at any number of positions. In some examples, the recognition sequence can be positioned within an intron that is integrated into the nuclease gene sequence. As a result, the viral vector is cleaved and degraded by the cell in a self-limiting manner.

[0230] A major obstacle to utilizing this concept to produce a packaged virus, such an as AAV virus, is preventing the nuclease from being expressed in the packaging cell line during the production of the viral vector. If expressed in the packaging cell line, the nuclease could prematurely cut the viral vectors, as well as the plasmid DNA encoding the viral vectors, preventing packaging of whole, intact genomes that contain an intact meganuclease gene. Thus, one goal of the present studies was to determine strategies for turning off expression of the nuclease in the packaging cell line, but allowing the nuclease to be expressed in cells transfected with the self-limiting virus.

2. Recombinant DNA Plasmids Comprising a Lac Repressor

[0231] In one approach, recombinant DNA plasmids were produced which comprised a Lac operator-repressor system. As reported by Cronin et al., three Lac operators within a mammalian promoter can inhibit transcription by binding Lac repressor and inhibiting RNA polymerase from processing through (Cronin, C.A., Gluba, W., and Scrable, H. (2001) Genes Dev. 15(12): 1506 - 1517). It was reasoned that placing three Lac operators between a CMV promoter and a nuclease gene would allow similar inhibition of expression in the presence of a Lac repressor.

[0232] Thus, a DNA plasmid was produced which comprised a CMV promoter operably-linked to a nuclease gene encoding a meganuclease referred to as MDX ½. This plasmid, referred to herein as the OLR plasmid, is illustrated in FIG. 6A, and its nucleic acid sequence is set forth in SEQ ID NO: 4. As shown, the CMV promoter was modified to include three Lac operators. The naturally-occurring Lac operator sequences were substituted with ideal operator sequences because the Lac repressor binds more tightly to the ideal operator and, hence, should cause stronger resistance to the RNA polymerase and better repression. Further, a mammalian expression cassette was built for the Lac repressor consisting of a CMV promoter and SV40 poly A. The LacI gene was not codon-optimized for Lac repressor. The Lac repressor expression cassette was integrated into the plasmid backbone outside of the viral inverted terminal repeats (ITRs). This positioning was very important, as it allowed for expression of the Lac repressor in the packaging cell line to prevent expression of the meganuclease, but because the Lac repressor expression cassette is not packaged in the AAV virus, there should be no repression of the meganuclease in the target cells transfected with the AAV virus.

[0233] Additionally, a second DNA plasmid was produced which comprised a CMV promoter operably-linked to a nuclease gene encoding the MDX ½ meganuclease. This plasmid, referred to herein as the 3xOi plasmid, is illustrated in FIG. 6B, and its nucleic acid sequence is set forth in SEQ ID NO: 5. As shown, the CMV promoter in the 3xOi plasmid was also modified to include three Lac operators, but the 3xOi plasmid did not comprise the LacI cassette to express the Lac repressor. Thus, it was expected that there would be no suppression of meganuclease expression in the viral packaging cells.

3. Nuclease Protein Expression in HEK293 Cells

[0234] Experiments were conducted to determine whether nuclease protein expression was suppressed in viral packaging cells by using a Lac repressor. HEK293 cells were mock electroporated, or electroporated with 2 .Math.g of the OLR plasmid, the 3xOi plasmid, or a GFP (pMAX) RNA using a BioRad Gene Pulser Xcell according to the manufacturer’s instructions. At 1, 2, 4, 8, and 24 hours post-transformation, cell lysates were prepared by removing media, washing cells with phosphate buffered saline, adding 150 .Math.L of RIPA buffer, scraping cells from their wells, and freezing lysates at -80° C. Lysates from mock electroporated cells were obtained at 24 hours.

[0235] Nuclease protein expression was determined by Western blot analysis. Cell lysates were incubated at -80° C. for 15 minutes, thawed, re-frozen, re-thawed, and then centrifuged for 10 minutes at 16,000xg. Supernatants were collected and protein concentrations were determined by the BCA method in combination with a plate reader. 9 .Math.g total protein per sample was electrophoresed under reducing conditions on a 12-well 4-12% polyacrylamide gel. Duplicate gels were also run. Proteins were transferred to PVDF membranes and blocked for 3 hours in TBST (0.1%) and 5% milk.

[0236] To stain for the meganuclease, one membrane was incubated with a rabbit anti-I-CRE antibody (1:8000) in TBST (0.1%) and 5% milk overnight (~18 hours) at 4° C. The membrane was washed 6 times for 5 minutes in TBST (0.1%). The membrane was then incubated with a peroxidase-labeled goat anti-rabbit antibody at 1:40k in TBST (0.1%) with 5% milk for 60 minutes at room temperature. The membrane was then washed 6 times for 5 minutes in TBST (0.1%) and incubated for 5 minutes in Amersham’s ECL Prime Western Blotting Detection Reagent. The membrane was developed on Kodak’s BioMax XAR film.

[0237] As a control, the second membrane was stained for β-actin. The second membrane was incubated with a monoclonal anti β-actin antibody (1:15,000) in TBST (0.1%) and 5% milk overnight (~18 hrs) at 4° C. The membrane was washed 6 times for 5 minutes in TBST (0.1%). The membrane was then incubated with a peroxidase-labeled goat antimouse antibody at 1:40k in TBST (0.1%) with 5% milk for 60 minutes at room temperature. The membrane was then washed 6 times for 5 minutes in TBST (0.1%) and incubated for 5 minutes in Amersham’s ECL Prime Western Blotting Detection Reagent. The membrane was developed on Kodak’s BioMax XAR film.

[0238] The Western blot analysis showed that cells transformed with the 3xOi plasmid, which did not comprise the Lac repressor sequence, showed an increase in MDX ½ protein expression throughout the course of the experiment (FIG. 7). By contrast, expression of MDX ½ protein was dramatically suppressed over 24 hours in HEK293 cells transformed with the OLR plasmid encoding the Lac repressor. Indeed, even at 24 hours, only a very small fraction of the MDX ½ meganuclease produced by the 3xOi plasmid can be seen in cells transformed with the OLR plasmid.

4. Conclusion

[0239] It is clear from this study that the incorporation of a repressor sequence (such as the Lac repressor) into the DNA plasmid, as well as operators for the repressor in the promoter operably-linked to the nuclease gene, can effectively silence expression of a nuclease in a viral packaging cell line, such as HEK293.

Example 2

Suppression of Nuclease Expression in Viral Packaging Cells Using a Tissue-Specific Promoter

1. Rationale

[0240] In another example, nuclease expression can be suppressed in viral packaging cells by the use of a tissue-specific promoter that is operably-linked to the nuclease gene. In this approach, the tissue-specific promoter is not active in the viral packaging cell but is active in the target cell into which the viral vector is ultimately transduced.

2. Recombinant DNA Construct With Tissue-Specific Promoter

[0241] In this example, a DNA plasmid, referred to herein as pDS GRK1 RHO½ L5-14, was produced which has the nucleotide sequence of SEQ ID NO: 6 (see FIG. 8). This plasmid encodes a RHO ½ meganuclease. The RHO ½ meganuclease sequence is operably-linked to a GRK1 promoter, which is a tissue-specific promoter that is specifically active in human retinal cells (i.e., rod cells), but not in HEK293 cells used for packaging of viral vectors. Thus, the RHO ½ meganuclease will not be expressed in viral packaging cells but will be expressed in retinal cells transduced by the virus. Due to the presence of an intron comprising a recognition sequence for the RHO ½ meganuclease, the viral vector will be self-limiting in the retinal cells as the meganuclease is expressed and cleaves the viral genome.

Example 3

Suppression of Nuclease Expression in Insect Viral Packaging Cells Using a Mammalian Intron

1. Rationale

[0242] In another example, nuclease expression can be suppressed in insect viral packaging cells by the inclusion of a mammalian intron into the nuclease gene. In this approach, the insect packaging cell cannot splice the mammalian intron and, consequently, cannot express the nuclease during packaging of the viral vector. However, mammalian target cells transduced with the viral vectors are capable of splicing the intron and expressing the nuclease, resulting in the degradation of the viral vector in a self-limiting manner.

2, Recombinant DNA Construct

[0243] In this example, DNA plasmids were produced which are referred to herein as pDS CMV RHO ½-HGH (SEQ ID NO: 7; FIG. 9A) and pDS CMV RHO ½-SV40LT (SEQ ID NO: 8; FIG. 9B). Each of these DNA plasmids encodes a RHO ½ meganuclease comprising the mammalian human growth hormone intron (SEQ ID NO: 2), or an SV40 large T intron (SEQ ID NO: 3), respectively. Because insect cells utilize different mRNA splicing motifs than mammalian cells, these introns are not spliced efficiently from pre-mRNA transcripts in insect cells. Thus, insect cells will not express a functional nuclease and will package the full-length genome into a viral vector. Therefore, such DNA plasmids are useful for silencing nuclease expression in insect cell expression systems, such as a Baculovirus expression system, and allowing for the production of self-limiting viral vectors of the invention. In contrast, mammalian cells to which the resulting viral vectors are delivered will properly splice the pre-mRNA and will express functional nuclease protein.

Example 4

Promoter Silencing in Viral Packaging Cells Using a Repressor

1. Rationale

[0244] Experiments were conducted to further demonstrate that the self-limiting viral vectors of the invention could be successfully generated in viral packaging cells through the use of a transcription repressor or the use of a tissue-specific promoter. It was hypothesized that a higher titer of intact viral vectors could be achieved due to the suppression of nuclease activity and a subsequent lack of cleavage at the nuclease binding site in the viral genome.

2. Transfection of HEK293 Viral Packaging Cells

[0245] AAV vectors were produced in HEK293 cells using a standard triple transfection protocol. Briefly, the helper plasmid pXX680, the pRepCap2 plasmid encoding the rep and cap proteins, and a plasmid containing the intended vector genome flanked by AAV2 inverted terminal repeats were used for cell transfection according to standard protocols. A first group was transformed with the pDS CMV 3xOi RHO ½ L514 LacI plasmid DNA vector (SEQ ID NO: 9), illustrated in FIG. 10A, which comprises an intron containing a RHO ½ binding site, three Lac operators in the CMV promoter, and a LacI coding sequence for a Lac repressor. A second group was transformed with the pDS CMV 3xOi RHO ½ L514 plasmid DNA vector (SEQ ID NO: 10), illustrated in FIG. 10B, which comprises an intron containing a RHO ½ binding site, three Lac operators in the CMV promoter, but lacks a LacI coding sequence. A third group was transformed with the pDS GRK1 RHO½ L5-14 plasmid DNA vector (SEQ ID NO: 6), illustrated in FIG. 8, which comprises an intron containing a RHO ½ binding site and a tissue-specific GRK1 promoter that is specifically active in retinal cells (i.e., rod cells). Viral vectors were harvested from cell lysates after 72 hours in culture. Cesium chloride gradient centrifugation was used to purify AAV vectors from the lysate, which were then dialyzed in 1X PBS, aliquoted, and stored at -80° C.

3. AAV Vector Titers

[0246] Vector genome copy number (vg) produced in each group was determined by Southern dot blot analysis using standard protocols. Results are summarized in Table 1.

TABLE-US-00001 Virus Name Titer Value pDS CMV 3xOi RHO ½ L514 2.40E+07 pDS CMV 3xOi RHO ½ L514 LacI 1.10E+08 pDS GRK1 RHO½ L5-14 8.4E+0.7

[0247] As shown, the pDS CMV 3xOi RHO ½ L514 vector, which contained no mechanism for suppressing nuclease expression, had a viral titer of 2.4×10.sup.7 viral particles. By contrast, the pDS CMV 3xOi RHO ½ L514 LacI vector, which expressed a Lac repressor to suppress nuclease expression in the HEK293 packaging cells, had a viral titer of 1.1×10.sup.8 viral particles, an increase of approximately 450% compared to the pDS CMV 3xOi RHO ½ L5 vector. Further, it was observed that the pDS GRK1 RHO½ L5-14 vector having the tissue-specific GRK1 promoter had a viral titer of 8.4x107 viral particles, an increase of approximately 350% compared to the pDS CMV 3xOi RHO ½ L5 vector.

4. Conclusions

[0248] It is evident from these experiments that the inclusion of a mechanism to suppress nuclease expression (e.g., the use of a repressor system, a tissue-specific promoter, etc.) allows for a substantial increase in the titer of intact, self-limiting viral vectors of the invention.

Example 5

Transduction of CHO Cells With Self-Limiting Viral Vectors

1. Rationale

[0249] Experiments were conducted using the viral vectors prepared in Example 4 to demonstrate that they are self-limiting in a mammalian cell line. It was hypothesized that a control vector lacking the nuclease binding site would express and accumulate an encoded meganuclease, whereas the self-limiting viral vector would express and accumulate some meganuclease protein that would ultimately cleave the viral vectors and reduce further nuclease expression.

2. Transduction of Mammalian Cells

[0250] CHO cells were either mock transduced, or transduced with the pDS CMV 3xOi RHO ½ L514 LacI vector (a self-limiting vector comprising a RHO ½ binding site) or the pDS CMV 3xOi RHO ½ L514 vector (not self-limiting; no binding site). AAV vectors were incubated with CHO cells at 100,000 viral genomes/cells. Protein was collected at time points of 2, 6, 12, 24, 48, and 72 hours using M-Per reagents (Pierce) according to the manufacturer’s instructions. For Western analysis, 50 .Math.g of cell lysate was resolved on a 4-12% Bis-Tris gel (Invitrogen) according to the protocol previously described in Example 1 using the anti-I-Crel antibody at a dilution of 1:1000. A separate gel was stained for β-actin as a loading control. Signal detection was assessed by chemiluminescence.

3. Western Analysis

[0251] Western analysis is shown in FIG. 11. The top panel shows detection of RHO ½ meganuclease protein in cell lysates at each time point. Lane 1 shows mock transduced cells. Lanes 2-7 show time points of 2, 6, 12, 24, 48, and 72 hours, respectively, for cells transduced with the pDS CMV 3xOi RHO ½ L514 vector. Lanes 8-13 show time points of 2, 6, 12, 24, 48, and 72 hours, respectively, for cells transduced with the self-limiting pDS CMV 3xOi RHO ½ L514 LacI vector. The arrow indicates the band associated with RHO ½ meganuclease protein. As shown, the RHO ½ meganuclease is expressed and continues to accumulate in CHO cells transduced with the pDS CMV 3xOi RHO ½ L514 vector which is not self-limiting. By contrast, a low level of RHO ½ meganuclease expression is detectable by 12 hours in CHO cells transduced with the self-limiting pDS CMV 3xOi RHO ½ L514 LacI vector, but this expression level appears to plateau, presumably because the expressed nuclease recognized and cleaved the binding site in the viral genomes, causing degradation of the viral vectors and preventing further expression of the protein.

4. PCR Analysis of Viral Vector Cleavage

[0252] To confirm that the self-limiting viral vectors were cleaved in transduced CHO cells, a PCR protocol was developed that utilizes an adapter protein which ligates to the RHO ½ cleavage site of the viral genome.

[0253] Briefly, CHO cells were transduced with the self-limiting pDS CMV 3xOi RHO ½ L514 LacI vector as discussed above and DNA was isolated at 2, 6, 12, 24, 48, and 72 hours post-transduction as previously described. An adapter molecule was designed having a 3′ overhang that matches the 3′ overhang generated in the viral genome by the RHO ½ meganuclease. Thus, the adapter would specifically link to the viral genome at a cleaved RHO ½ recognition site. 800 ng of DNA was ligated with 2 pmol of adapter at 16° C. overnight. PCR was then performed with 200 ng ligated DNA and a pair of amplification primers, one matching the AAV sequence, and the other matching the adapter molecule sequence. The resulting PCR products were analyzed on gel. In case of AAV digestion by RHO ½ and ligation to adapter, a PCR band with size 585 bps was expected to be observed.

5. Results of PCR Analysis

[0254] The results of the PCR analysis are shown in FIG. 12 for time points of 2, 26, 12, 24, 48, and 72 hours post-transduction. Bands of ~585 bps corresponding to the correct PCR product are indicated by the arrow. As shown, band intensity significantly increases from the basal level (2 hours) over time, with a maximum signal observed at 24 hours. Band intensity then appears to be reduced at the 48 and 72 hour time points. These PCR results suggest that the self-limiting viral vectors are cleaved by the expressed RHO ½ meganuclease in transduced CHO cells.

6. Conclusions

[0255] These experiments demonstrated that the persistence time of a self-limiting viral vector of the invention, as measured by nuclease protein expression, is lower in a transduced mammalian cell line than the persistence time of a comparable viral vector that is not self-limiting and does not comprise a nuclease binding site. This is supported by the observation that self-limiting viral vectors are cleaved at the RHO ½ recognition sequence within the viral genome.