US20060153826A1 - Use of meganucleases for inducing homologous recombination ex vivo and in toto in vertebrate somatic tissues and application thereof - Google Patents

Use of meganucleases for inducing homologous recombination ex vivo and in toto in vertebrate somatic tissues and application thereof Download PDF

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US20060153826A1
US20060153826A1 US10/543,557 US54355704A US2006153826A1 US 20060153826 A1 US20060153826 A1 US 20060153826A1 US 54355704 A US54355704 A US 54355704A US 2006153826 A1 US2006153826 A1 US 2006153826A1
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meganuclease
dna
gene
site
cells
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Sylvain Arnould
Sylvia Bruneau
Jean-Pierre Cabaniols
Patrick Chames
Andre Choulika
Philippe Duchateau
Jean-Charles Epinat
Agnes Gouble
Emmanuel Lacroix
Frederic Paques
Christophe Perez-Michaut
Julianne Smith
David Sourdive
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Cellectis SA
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Cellectis SA
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First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=32829807&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=US20060153826(A1) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Priority to US10/543,557 priority Critical patent/US20060153826A1/en
Application filed by Cellectis SA filed Critical Cellectis SA
Assigned to CELLECTIS reassignment CELLECTIS ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: ARNOULD, SYLVAIN, BRUNEAU, SYLVIA, CABANIOLS, JEAN-PIERRE, CHAMES, PATRICK, CHOULIKA, ANDRE, DUCHATEAU, PHILIPPE, EPINAT, JEAN-CHARLES, GOUBLE, AGNES, LACROIX, EMMANUEL, PAQUES, FREDERIC, PEREZ-MICHAUT, CHRISTOPHE, SMITH, JULIANNE, SOURDIVE, DAVID
Publication of US20060153826A1 publication Critical patent/US20060153826A1/en
Priority to US12/710,969 priority patent/US7842489B2/en
Priority to US13/021,473 priority patent/US20110151539A1/en
Priority to US13/152,961 priority patent/US8530214B2/en
Priority to US13/485,486 priority patent/US20120331574A1/en
Priority to US13/485,469 priority patent/US8624000B2/en
Priority to US13/485,561 priority patent/US20120304321A1/en
Priority to US13/524,995 priority patent/US20120322689A1/en
Priority to US13/556,209 priority patent/US20120288943A1/en
Priority to US13/556,206 priority patent/US8697395B2/en
Priority to US13/556,208 priority patent/US20120288942A1/en
Priority to US13/649,093 priority patent/US20130203840A1/en
Priority to US15/080,232 priority patent/US20160273003A1/en
Abandoned legal-status Critical Current

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Definitions

  • the present invention relates to the use of meganucleases for inducing homologous recombination ex vivo and in toto in vertebrate somatic tissues and to its application for genome engineering and gene therapy.
  • Homologous gene targeting has been widely used in the past to obtain site-specific and precise genome surgery (Thomas and Capecchi, 1986, Nature, 324, 34-8; Thomas et al., 1986, Cell, 44, 419-28; Thomas and Capecchi, 1986, Cold Spring Harb Symp Quant Biol, 51 Pt 2, 1101-13; Doetschman et al., 1988, PNAS, 85, 8583-7).
  • Homologous gene targeting relies on the homologous recombination machinery, one of the endogenous maintenance systems of the cell. Since this system has been well conserved throughout evolution, gene targeting could be used in organisms as different as bacteria, yeast, filamentous fungi, mammals, insects, and plants.
  • gene expression often depends on very long tracts of surrounding sequences. In higher eukaryotes, these sequences can span over several hundreds of kbs, and are necessary for the precise tuning of gene expression during the cell cycle, development, or in response to physiological signals. Even though transgenic sequences involve most of the time a few kbs, there is no way they can restore a fully wild type phenotype. This problem can however be alleviated by transformation with very large sequences (BAC), but it requires additional skills.
  • BAC very large sequences
  • random transgenesis results in insertions anywhere in the genome, with a non-nul probability of a deleterious effect: insertion in a gene will disrupt the gene or its proper regulation.
  • homologous recombination allows the precise modification of a chromosomal locus: it can result in gene deletion, gene insertion, or gene replacement, depending on the targeting vector.
  • subtle changes can be introduced in a specific locus, including the modification of coding and regulatory sequences (EP 419621; U.S. Pat. Nos. 6,528,313; 6,528,314; 5,272,071; 5,641,670; 6,063,630).
  • homologous gene targeting a universal tool for genome engineering, and the only safe methodology for gene therapy.
  • the use of homologous recombination is limited by its poor efficiency in most cells.
  • homologous gene targeting is extremely efficient in the yeast Saccharomyces cerevisiae (Paques and Haber, 1999, Microbiol Mol Biol Rev, 63, 349-404), the moss Physcomitrella patens (Schaefer and Zryd, 1997, Plant J, 11, 1195-206), certain mutant Escherichia coli strains (Murphy, 1998, J.
  • the introduction of the double-strand break is accompanied by the introduction of a targeting segment of DNA homologous to the region surrounding the cleavage site, which results in the efficient introduction of the targeting sequences into the locus (either to repair a genetic lesion or to alter the chromosomal DNA in some specific way).
  • the induction of a double-strand break at a site of interest is employed to obtain correction of a genetic lesion via a gene conversion event in which the homologous chromosomal DNA sequences from an other copy of the gene donates sequences to the sequences where the double-strand break was induced.
  • site-specific DSBs proved to be another challenge. It requires the use of site-specific endonucleases recognizing large sequences. Such very rare-cutting endonucleases recognizing sequences larger than 12 base pairs are called meganucleases. Ideally, one would like to use endonucleases cutting only once in the genome of interest, the cleavage being limited to the locus of interest.
  • endonucleases are essentially represented by homing endonucleases (Chevalier and Stoddard, 2001, N.A.R., 29, 3757-74). Homing endonucleases are found in fungi, algae, eubacteria and archae, and are often encoded in mobile genetic elements. Their cleavage activities initiate the spreading of these mobile elements by homologous recombination.
  • HO and I-SceI have been used to induce homologous gene targeting in yeast (Haber, 1995, precited; Fairhead and Dujon, 1993, precited; Plessis et al., 1992, precited; U.S. Pat. Nos. 5,792,632 and 6,238,924), in cultured mammalian cells (Donoho et al.; Rouet et al.; Choulika et al.; Cohen-Tannoudji et al., precited; U.S. Pat. Nos. 5,792,632; 5,830,729 and 6,238,924) and plants (Puchta et al., 1996, PNAS, 93, 5055-60; U.S. Pat. Nos.
  • Group II introns proteins can also be used as meganucleases.
  • the biology of these proteins is much more complex than the biology of homing endonucleases encoded by group I introns and inteins (Chevalier and Stoddard, precited).
  • the protein is involved in intron splicing, and forms a ribonucleic particle with the spliced RNA molecule.
  • This complex displays different activities including reverse splicing (of the RNA intron in a DNA strand from the target gene), nicking (of the second DNA strand in the novel gene) and reverse transcriptase (which copies the inserted RNA into a DNA strand).
  • the final insertion of the intron into the target gene depends on all these activities.
  • These proteins seem to induce homologous recombination, with a DSB intermediate, when the reverse transcriptase activity is mutated (Karberg et al., 2001, Nat. Biotechnol, 19, 1162-7).
  • Zinc-finger nucleases have been used to induce tandem repeat recombination in Xenopus oocytes (Bibikova et al., 2001, Mol Cell Biol, 21, 289-97), and homologous gene targeting in cultured mammalian cell lines (Porteus and Baltimore, precited) and Drosophila (Bibikova et al., precited).
  • Chevalier et al. (2002, Molecular Cell, 10, 895-905) have also generated an artificial highly specific endonuclease by fusing domains of homing endonucleases I-Dmo I and I-Cre I.
  • the resulting enzyme binds a long chimeric DNA target site and cleaves it precisely at a rate equivalent to its natural parents.
  • this experiment leads to one endonuclease with a new specificity but it is not applicable to find an endonuclease that recognizes and cleaves any desired polynucleotide sequence.
  • Fusions between nucleic acids and chemical compounds are another class of artificial meganucleases, wherein DNA binding and specificity rely on an oligonucleotide and cleavage on a chemical compound tethered to the oligonucleotide.
  • the chemical compounds can have an endogenous cleavage activity, or cleave when complexed with topoisomerases (Arimondo et al., 2001, Angew Chem Int Ed Engl, 40, 3045-3048; Arimondo and Helene, 2001, Curr Med Chem Anti-Canc Agents, 1, 219-35).
  • meganuclease-induced recombination appears to be an extremely powerful tool for introducing targeted modifications in genomes.
  • the development of new meganucleases able to cleave DNA at the position where the recombinational event is desired would allow targeting at any given locus at will and with a reasonable efficiency.
  • DSBs between two tandem repeats induce very high levels of homologous recombination resulting in deletion of one repeat together with all the intervening sequences (Paques and Haber, 1999, Microbiol Mol Biol Rev, 63, 349-404), and this can easily be used for the removal of any transgene with an appropriate design.
  • cells in a living organism do not necessarily behave as cultured cells or germinal cells.
  • Cultured cells and early (and sometimes late) germ cells are dividing cells, going through G1, S, G2, and M phases.
  • most cells in an adult animal are differentiated cells, stuck in a G0 phase.
  • Many results indicate and/or suggest that homologous recombination does not have the same efficiency in all phases of the cell cycle (Takata et al., 1998, Embo J, 17, 5497-508; Kadyk and Hartwell, 1992, Genetics, 132, 387-402; Gasior et al., 2001, PNAS, 98, 8411-8; Essers et al., 1997, Cell, 89,195-204).
  • meganucleases are indeed able to induce targeted homologous recombination ex vivo and in toto, in vertebrate somatic tissues.
  • meganucleases can be used for repairing a specific sequence, modifying a specific sequence, for attenuating or activating an endogenous gene of interest, for inactivating or deleting an endogenous gene of interest or part thereof, for introducing a mutation into a site of interest or for introducing an exogenous gene or part thereof, in vertebrate somatic tissues.
  • the purpose of the present invention is to use meganucleases for inducing homologous recombination ex vivo and in toto in vertebrate somatic tissues.
  • the present invention relates to the use of at least one meganuclease for the preparation of a medicament for preventing, improving or curing a genetic disease in a vertebrate in need thereof; said medicament being administered by any means to said vertebrate.
  • the invention also concerns the use of at least one meganuclease for the preparation of a medicament for preventing, improving or curing a disease caused by an infectious agent that presents a DNA intermediate, in a vertebrate in need thereof; said medicament being administered by any means to said vertebrate.
  • said infectious agent is a virus.
  • Another object of the present invention is the use of at least one meganuclease for genome engineering of non-human vertebrate somatic tissues, for non-therapeutic purpose, by introducing said meganuclease into the body of said non-human vertebrate.
  • meganuclease is intended a double-stranded endonuclease having a large polynucleotide recognition site, at least 12 bp, preferably from 12 bp to 60 bp.
  • Said meganuclease is also called rare-cutting or very rare-cutting endonuclease.
  • Said meganuclease is either monomeric or dimeric.
  • any natural meganuclease such as a homing endonuclease, but also any artificial or man-made meganuclease endowed with such high specificity, either derived from homing endonucleases of group I introns and inteins, or other proteins such as Zinc-Finger proteins or group II intron proteins, or compounds such as nucleic acid fused with chemical compounds.
  • artificial meganucleases include the so-called “custom-made meganuclease” which is a meganuclease derived from any initial meganuclease, either natural or not, presenting a recognition and cleavage site different from the site of the initial one; zinc-finger nucleases may also be considered as custom-made meganucleases.
  • custom-made meganuclease cleaves the novel site with an efficacy at least 10 fold more than the natural meganuclease, preferably at least 50 fold, more preferably at least 100 fold.
  • Natural refers to the fact that an object can be found in nature. For example, a meganuclease that is present in an organism, that can be isolated from a source in nature and which has not been intentionally modified by man in the laboratory is natural.
  • ex vivo is intended that the homologous recombination event induced by the meganuclease takes place in somatic cells removed from the body of a vertebrate; said meganuclease is introduced (ex vivo) into the cells of said vertebrate by any convenient mean and the modified cells are then returned into the body of said vetebrate.
  • tissue is intended any tissue within the body of an organism including any type of cells from the precursor cells (stem cells) to the fully differentiated cells, with the exception of the germ line cells.
  • Identity refers to sequence identity between two nucleic acid molecules or polypeptides. Identity can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base, then the molecules are identical at that position. A degree of similarity or identity between nucleic acid or amino acid sequences is a function of the number of identical or matching nucleotides at positions shared by the nucleic acid sequences. Various alignment algorithms and/or programs may be used to calculate the identity between two sequences, including FASTA, or BLAST which are available as a part of the GCG sequence analysis package (University of Wisconsin, Madison, Wis.), and can be used with, e.g., default settings.
  • homologous is intended a sequence with enough identity to another one to lead to a homologous recombination between sequences, more particularly having at least 95% identity, preferably 97%, and more preferably 99%.
  • site of interest refers to a distinct DNA location, preferably a chromosomal location, at which a double stranded break (cleavage) is to be induced by the meganuclease.
  • the term “individual” includes mammals, as well as other vertebrates (e.g., birds, fish and reptiles).
  • mammals e.g., birds, fish and reptiles.
  • Examples of mammalian species include humans and other primates (e.g., monkeys, chimpanzees), rodents (e.g., rats, mice, guinea pigs) and ruminants (e.g., cows, pigs, horses).
  • genetic disease is intended any disease, partially or completely, directly or indirectly, due to an abnormality in one or several genes.
  • Said abnormality can be a mutation, an insertion or a deletion.
  • Said mutation can be a punctual mutation.
  • Said abnormality can affect the coding sequence of the gene or its regulatory sequence.
  • Said abnormality can affect the structure of the genomic sequence or the structure or stability of the encoded mRNA.
  • Said genetic disease can be recessive or dominant.
  • vector refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
  • said meganuclease is selected from the group consisting of a homing endonuclease, a zinc-finger nuclease or a meganuclease variant.
  • homing endonuclease are as described in Chevalier and Stoddard, precited.
  • the meganuclease is a heterodimer of two fusion protein.
  • Each fusion protein includes a DNA-binding domain derived from Zif268 (or other zinc-finger proteins), tethered to a nuclease domain (derived from the FokI endonuclease or other endonucleases) through a linker.
  • the DNA target site includes two external regions of 9 bp, bound by the DNA binding domains, and a central spacer region of 0-15 bp.
  • the DNA binding Zinc-Finger domain has been selected to bind one of the 9 bp external regions, as described by Isalan and Choo (2001, Methods Mol Biol, 148,417-29), Isalan et al. (2001, Nat. Biotechnol, 19, 656-60) and Isalan and Choo (2001, Methods Enzymol, 340,593-609). Selection can be made by phage display, as described by the authors, but other methods such as screening in yeast or with a bacterial two-hybrid system can also be used, as described by Young et al. (2000, PNAS, 97, 7382-7) and Bae et al.
  • DNA binding domains encompassing 6 Zinc Finger motifs can be used, as described by Klug and collaborators (Moore et al., 2001, PNAS, 98, 1432-6; Papworth et al., 2003, PNAS, 100, 1621-6; Reynolds et al., 2003, PNAS, 100, 1615-20; Moore et al., 2001, PNAS, 98, 1437-41).
  • each FokI catalytic domain cleaving only one strand, it takes two such domains to obtain a double-strand cleavage.
  • Custom-made meganuclease is defined as a meganuclease able to cleave a targeted DNA sequence.
  • This definition includes any meganuclease variant produced by a method comprising the steps of preparing a library of meganuclease variants and isolating, by selection and/or screening, the variants able to cleave the targeted DNA sequence.
  • Said custom-made meganuclease which is derived from any initial meganuclease by introduction of diversity, presents a recognition and cleavage site different from the site of the initial one.
  • the diversity could be introduced in the meganuclease by any method available for the man skilled in the art.
  • the diversity is introduced by targeted mutagenesis (i.e. cassette mutagenesis, oligonucleotide directed codon mutagenesis, targeted random mutagenesis), by random mutagenesis (i.e. mutator strains, Neurospora crassa system (U.S. Pat. No. 6,232,112; WO01/70946, error-prone PCR), by DNA shuffling, by directed mutation or a combination of these technologies (See Current Protocols in Molecular Biology, Chapter 8 “Mutagenesis in cloned DNA”, Eds Ausubel et al., John Wiley and Sons).
  • the meganuclease variants are preferably prepared by the targeted mutagenesis of the initial meganuclease.
  • the diversity is introduced at positions of the residues contacting the DNA target or interacting (directly or indirectly) with the DNA target.
  • the diversity is preferably introduced in regions interacting with the DNA target, and more preferably introduced at the positions of the interacting amino acids.
  • the 20 amino acids can be introduced at the chosen variable positions.
  • the amino acids present at the variable positions are the amino acids well-known to be generally involved in protein-DNA interaction. More particularly, these amino acids are generally the hydrophilic amino acids.
  • the amino acids present at the variable positions comprise D, E, H, K, N, Q, R, S, T, Y.
  • the amino acids present at the variable positions are selected from the group consisting of D, E, H, K, N, Q, R, S, T, Y. Synthetic or modified amino acids may also be used.
  • a degenerated codon N N K leads to 32 different codons encoding the 20 amino acids and one stop.
  • a degenerated codon N V K leads to 24 different codons encoding the 15 amino acids and one stop.
  • a degenerated codon V V K leads to 18 different codons encoding the 12 amino acids (A, D, E, G, H, K, N, P, Q, R, S, T) and no stop.
  • a degenerated codon R V K leads to 12 different codons encoding the 9 amino acids (A, D, E, G, K, N, R, S, T).
  • a degenerated codon V V K leading to 18 different codons encoding the 12 amino acids (A, D, E, G, H, K, N, P, Q, R, S, T) is used for generating the library.
  • the V V K degenerated codon does not contain any stop codon and comprises all the hydrophilic amino acids.
  • a directed library knowledge on amino acids interacting with the DNA target is useful. This knowledge could be provided, for example, by X-ray cristallography, Alanine scanning, or cross-linking experiments.
  • the amino acids interacting with the DNA target can also be deduced by sequence alignment with a homologous protein.
  • the custom-made meganuclease is derived from any initial meganuclease.
  • the initial meganuclease is selected so as its natural recognition and cleavage site is the closest to the targeted DNA site.
  • the initial meganuclease is a homing endonuclease, as specified, in the here above definitions. Homing endonucleases fall into 4 separated families on the basis of well conserved amino acids motifs, namely the LAGLIDADG family, the GIY-YIG family, the His-Cys box family, and the HNH family (Chevalier et al., 2001, N.A.R, 29, 3757-3774).
  • E-Dre I The detailed three-dimensional structures of several homing endonucleases are known, namely I-Dmo I, PI-Sce I, PI-Pfu I, I-Cre I, I-Ppo I, and a hybrid homing endonuclease I-Dmo I/I-Cre I called E-Dre I (Chevalier et al., 2001, Nat Struct Biol, 8, 312-316; Duan et al., 1997, Cell, 89, 555-564; Heath et al., 1997, Nat Struct Biol, 4, 468-476; Hu et al., 2000, J Biol Chem, 275, 2705-2712; Ichiyanagi et al., 2000, J Mol Biol, 300, 889-901; Jurica et al., 1998, Mol Cell, 2, 469-476; Poland et al., 2000, J Biol Chem, 275, 16408-16413;
  • the LAGLIDADG family is the largest family of proteins clustered by their most general conserved sequence motif: one or two copies of a twelve-residue sequence: the di-dodecapeptide, also called LAGLIDADG motif.
  • Homing endonucleases with one dodecapeptide (D) are around 20 kDa in molecular mass and act as homodimer.
  • Those with two copies (DD) range from 25 kDa (230 AA) to 50 kDa (HO, 545 AA) with 70 to 150 residues between each motif and act as monomer.
  • Cleavage is inside the recognition site, leaving 4 nt staggered cut with 3′OH overhangs.
  • I-Ceu I, and I-Cre I illustrate the homodimeric homing endonucleases with one Dodecapeptide motif (mono-dodecapeptide).
  • I-Dmo I, I-Sce I, PI-Pfu I and PI-Sce I illustrate monomeric homing endonucleases with two Dodecapeptide motifs.
  • the initial LAGLIDADG homing endonuclease can be selected from the group consisting of: I-See I, I-Chu I, I-Dmo I, I-Cre I, I-Csm I, PI-Sce I, PI-Tli I, PI-Mtu I, I-Ceu I, I-Sce II, I-Sce III, HO, PI-Civ I, PI-Ctr I, PI-Aae I, PI-Bsu I, PI-Dha I, PI-Dra I, PI-Mav I, PI-Mch I, PI-Mfu I, PI-Mfl I, PI-Mga I, PI-Mgo I, PI-Min I, PI-Mka I, PI-Mle I, PI-Mma I, PI-Msh I, PI-Msm I, PI-Mth I, PI-Mtu I,
  • LAGLIDADG homing endonucleases reveal the functional significance of the LAGIDADG motif, and the nature of the DNA-binding interface.
  • the core ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ ⁇ fold of the homodimer homing endonuclease is repeated twice in the monomer homing endonuclease and confers upon the monomer a pseudo-dimeric structure.
  • the first ⁇ -helix of each domain or subunit contains the defining LAGLIDADG motif.
  • the two LAGLIDADG helices of each protein form a tightly packed dimer or domain interface.
  • the DNA binding interface is formed by the four ⁇ -strands of each domain or subunit that fold into an antiparallel ⁇ -sheet.
  • a minimal DNA binding moiety could be defined in the LAGLIDADG homing endonucleases as a ⁇ -hairpin (2 ⁇ -strands connected by a loop or turn), two such ⁇ -hairpins being connected into the 4-stranded ⁇ -sheet.
  • Each domain or subunit interacts with a half recognition site.
  • the external quarter recognition site can be defined by its interaction with only one of the 2 ⁇ -hairpins of each domain or subunit.
  • meganuclease variants derived from LAGLIDADG homing endonuclease can be fragmented in several directed libraries. This fragmented approach for the evolution of an initial meganuclease allows the introduction of a greater diversity (more amino acids at a position and/or more diversificated positions).
  • the diversity is introduced only in the region involved in the interaction with a half or a quarter recognition site, the targeted DNA being modified only for the part interacting with the region comprising the introduced diversity. More particularly, if a new half site is searched for, then the diversity is preferably introduced in the 4-stranded ⁇ -sheet of one domain or subunit, more preferably at the positions of the DNA interacting amino acids in this structure. If a new quarter site is searched for, then the diversity is introduced in the corresponding ⁇ -hairpin, more preferably at the positions of the DNA interacting amino acids of this structure.
  • a set of libraries covers the entire targeted DNA site.
  • the libraries comprise diversity only in the region interacting with a half-site, at least two libraries, preferably two, are necessary.
  • the initial meganuclease is a dimer, one library is enough with a half-site approach.
  • the libraries comprise diversity only in the region interacting with a quarter site, at least four libraries, preferably four, are necessary. If the initial meganuclease is a dimer, two libraries can be enough with a quarter site approach.
  • the selected elements from the primary libraries are fused or combined in a subsequent library for a new cycle of selection.
  • two libraries can be fused by shuffling.
  • a new cycle of selection could be then done on the whole targeted DNA site.
  • the new cycle of selection can be done on a half targeted DNA site if the first libraries are based on a quarter site.
  • the results of the selection and/or screening of the half site are combined to give a final library which can be screened for the whole targeted DNA site.
  • the best elements from each libraries are joined together in order to obtain a meganuclease able to bind and cleave the targeted DNA site.
  • a library with diversity located only in the region involved in the interaction with a half or a quarter recognition site is prepared. Then, after selection or screening of this library, the selected elements from the library are modified such as to introduce diversity in another region involved in the interaction with recognition site, leading to a subsequent library. Libraries are generated until the complete targeted DNA site is bound and cleaved by the selected meganuclease.
  • a library can be generated by introducing diversity only in the region interacting with a half-site, a half site corresponding to one monomer of the initial homing endonuclease.
  • This library can be used for selection and/or screening on each half sites of the target DNA sequence.
  • positive elements from the library have been selected for each half sites, a variant for the first half site and a variant for the other half site are brought together for binding and cleaving the whole target DNA sequence.
  • the positive variants can be introduced in a single chain meganuclease structure.
  • a single chain meganuclease is an enzyme in which the two monomers of the initial dimeric homing endonuclease are covalently bound by a linker.
  • an approach by a quarter site is chosen from an initial dimer homing endonuclease, at least two libraries are generated by introducing diversity only in the region involved in the interaction with each quarter recognition sites.
  • the selected variants from the primary libraries are fused in a subsequent library for a new cycle of selection on the half site.
  • the best elements from each libraries are joined together to obtain a monomer able to bind the half site.
  • a library with diversity only in the region involved in the interaction with a quarter recognition site is prepared. Then, after selection or screening of this library, the selected elements from the library are modified such as to introduce diversity in the region involved in the interaction with the other quarter site, leading to a subsequent library.
  • this second library lead to the variants monomer able to bind the half site.
  • a variant for the first half site and a variant for the other half site are brought together for binding and cleaving the target DNA sequence.
  • the positive variants can be introduced in a single chain meganuclease structure.
  • the custom-made meganuclease which recognizes and cleaves a desired polynucleotide target is derived from the directed evolution of the homing endonuclease I-Cre I.
  • the homing endonuclease is a homodimer, the approach in this case is based either on the half recognition site or on the quarter site.
  • the directed evolution is based on a library of I-Cre I variants. These I-Cre I variants present a diversity of amino acids at several positions predicted to interact with the polynucleotide target.
  • a set of I-Cre I variants is prepared by introducing amino acid diversity in positions selected from the group consisting of: Q26, K28, N30, S32, Y33, Q38, Q44, R68, R70 and T140.
  • a set of I-Cre I variants is prepared by introducing diversity in positions: a) Q26, K28, N30, Y33, Q38, Q44, R68, R70, T140; b) Q26, K28, N30, Y33, Q38, Q44, R68, R70; c) Q26, K28, N30, Y33, Q44, R68, R70; or d) Q26, K28, Y33, Q38, Q44, R68, R70.
  • a set of I-Cre I variants is prepared by introducing diversity in positions Q26, K28, N30, Y33, Q38, Q44, R68, and R70.
  • the residue D75 of 1-Cre I could be mutated in an uncharged amino acid such as N.
  • this amino acid has an interaction with 2 residues which are preferably modified in the library. As this charge is present in the core of the structure, it could be preferable to abolish this charge.
  • residues interacting directly with DNA should be modified: I24, Q26, K28, N30, S32, Y33, Q38, S40 and T42.
  • the turn at the middle of the ⁇ -hairpin, which interacts with the very end of the 24 bp-long DNA target may be replaced by a short and flexible loop that would be tolerant to DNA bases substitution.
  • residues 30 to 36 could be replaced by 2, 3, 4, 5 or 6 glycine residues.
  • the second hairpin could be replaced similarly as a single unit (from residue Y66 to I77). However, while this hairpin interacts predominantly with the internal quarter site (bases ⁇ 6 to ⁇ 1 or +1 to +6), other residues (i.e. S22, Q44 and T46) separated from the hairpin may play a role in directing the specificity of interaction.
  • a library could be created by replacing residues Y66, R68, R70, V73, D75 and I77.
  • S22, Q44 and T46 may either be left untouched, replaced by small polar amino acids (G, S or T; more preferably S or T), or randomized to contribute to the library.
  • Mutants selected from separate library can be combined together by standard DNA shuffling methods based on recombination at homologous DNA regions (i.e. the DNA coding for the region between residue 43 and residue 65 is strictly conserved).
  • the second library includes mutations of residues S22, Q44 and T46, recombination becomes impractical, and more classical DNA/protein engineering is required.
  • a library of I-Cre I variants is prepared by introducing diversity in positions selected from the group consisting of: a) I24, Q26, K28, N30, S32, Y33, Q38, S40 and T42; or b) Y66, R68, R70, V73, D75, and I77.
  • the diversity could be also introduced in positions selected from the group consisting of: S22, Q44, and T46.
  • a custom-made meganuclease which recognizes and cleaves a desired polynucleotide target could be prepared by the directed evolution of single chain I-Cre I endonuclease.
  • a set of single-chain I-Cre I variants is prepared by introducing amino acid diversity in positions selected from the group consisting of: Q26, K28, N30, S32, Y33, Q38, Q44, R68, R70, Q123, K125, N127, S129, Y130, Q135, Q141, R165, R167.
  • Two properties of the meganuclease can be used for the steps of selection and/or screening, namely the capacity to bind the targeted DNA sequence and the ability to cleave it.
  • the meganuclease variants can be selected and screened, or only screened.
  • the selection and/or screening can be done directly for the ability of the meganuclease to cleave the targeted DNA sequence.
  • the selection and/or screening can be done for the binding capacity on the targeted DNA sequence, and then for ability of the meganuclease to cleave it.
  • the method to prepare custom-made meganuclease comprises or consists of the following steps:
  • the method to prepare a custom-made meganuclease comprises or consists of the following steps: a selection step for the binding ability, a selection for the cleavage activity, and a screening step for the cleavage activity.
  • a screening assay for the binding ability after a selection step based on the binding capacity can be done in order to estimate the enrichment of the library for meganuclease variants presenting a binding capacity.
  • the selection and screening assays are performed on the DNA region in which a double stranded cleavage has to be introduced or a fragment thereof.
  • the targeted sequences comprise at least 15 nucleotides, preferably 18 to 40, more preferably 18 to 30 nucleotides.
  • the targeted DNA polynucleotide can be reduced to at least 8 nucleotides for binding only.
  • the targeted DNA polynucleotide length is less than 10 kb, preferably less than 3 kb, more preferably less than 1 kb.
  • the targeted DNA polynucleotide length is preferably less than 500 bp, more preferably less than 200 bp.
  • any targeted sequence can be used to generate a custom-made meganuclease able to cleave it according.
  • the targeted sequence is chosen such as to present the most identity with the original recognition and cleavage site of the initial meganuclease. Therefore, the DNA region in which a double stranded break has to be introduced is analyzed to choose at least 1, 2, 3 or 5 sequences of at least 15 nucleotides length, preferably 18 to 40, more preferably 18 to 30 nucleotides, having at least 25% identity, preferably 50% identity and more preferably 75% identity with the original recognition and cleavage site of the initial meganuclease.
  • the targeted DNA sequence is adapted to the type of meganuclease variants library. If the library is based on a half site approach, the targeted DNA sequence used for the selection/screening comprises one half original site and one half site of the desired DNA sequence. If the library is based on a quarter site approach, the targeted DNA sequence used for the selection/screening comprises three quarters of the original site and one quarter site of the desired DNA sequence.
  • the meganuclease variants resulting from the selection and/or screening steps could optionally be an input for another cycle of diversity introduction.
  • the positive meganuclease variants selected by the selection and/or screening steps are validated by in vitro and/or ex vivo cleavage assay.
  • the selection and screening of meganuclease variants based on the binding capacity has to be made in conditions that are not compatible with the cleavage activity. For example, most of homing endonucleases need manganese or magnesium for their cleavage activity. Therefore, the binding assays on this type of homing endonuclease variants are done without manganese or magnesium, preferably replaced by calcium.
  • the binding selection assay is based on the enrichment of the meganuclease variants able to bind the targeted DNA polynucleotide. Therefore, the meganuclease variants encoded by the library are incubated with an immobilized targeted DNA polynucleotide so that meganuclease variants that bind to the immobilized targeted DNA polynucleotide can be differentially partitioned from those that do not present any binding capacity. The meganuclease variants which are bound to the immobilized targeted DNA polynucleotide are then recovered and amplified for a subsequent round of affinity enrichment and amplification. After several rounds of affinity enrichment and amplification, the library members that are thus selected can be isolated. Optionally, the nucleotide sequences encoding the selected meganuclease variants are determined, thereby identifying of the meganuclease variants able to bind the targeted DNA sequence.
  • meganuclease variants require a system linking genotype and phenotype such as phage display (WO91/17271, WO91/18980, and WO91/19818 and WO93/08278; the disclosures of which are incorporated herein by reference), ribosome display (Hanes & Plückthun, PNAS, 1997, vol. 94, 4937-4942; He & Taussig, Nucl. Acids Res. (1997) vol. 25, p 5132-5143) and mRNA-protein fusion (WO00/47775; U.S. Pat. No. 5,843,701; Tabuchi et al FEBS Letters 508 (2001) 309-312; the disclosures of which are incorporated herein by reference).
  • phage display WO91/17271, WO91/18980, and WO91/19818 and WO93/08278; the disclosures of which are incorporated herein by reference
  • ribosome display He & Plückth
  • Phage display involves the presentation of a meganuclease variant on the surface of a filamentous bacteriophage, typically as a fusion with a bacteriophage coat protein.
  • the library of meganuclease variants is introduced into a phage chromosome or phagemid so as to obtain a protein fusion with a bacteriophage coat protein, preferably with the pill protein. If the initial meganuclease is a homodimer, the monomer variants of the meganuclease are introduced so as to be displayed and the constant monomer can be introduced so as to be produced in the periplasm.
  • the bacteriophage library can be incubated with an immobilized targeted DNA sequence so that elements able to bind the DNA are selected.
  • mRNA-protein fusion system opens the possibility to select among 10 13 different meganuclease variants.
  • This system consists in the creation of a link between the mRNA and the encoded protein via a puromycin at the 3′ end of the mRNA which leads to a covalent mRNA-protein fusion at the end of the translation.
  • a double-stranded DNA library comprising the coding sequence for the meganuclease variants is used regenerate mRNA templates for translation that contain 3′ puromycin.
  • the mRNA-puromycin conjugates are translated in vitro to generate the mRNA-meganuclease fusions.
  • the fusions are tested for the ability to bind the immobilized targeted DNA polynucleotide.
  • a PCR is then used to generate double-stranded DNA enriched in meganuclease variants presenting the binding capacity. If the initial meganuclease is a homodimer, the constant monomer can be introduced either as DNA or mRNA encoding this monomer or as a monomer protein. In this case, an approach with the single chain meganuclease will be preferably used.
  • Ribosome display involves a double-stranded DNA library comprising the coding sequence for the meganuclease variants that is used to generate mRNA templates for translation. After a brief incubation, translation is halted by addition of Mg 2+ and incubation al low temperature or addition of translation inhibitor. The ribosome complexes are then tested for the ability to bind immobilized targeted DNA polynucleotide. The selected mRNA is used to construct cDNA and a PCR generates double-stranded DNA enriched in meganuclease variants presenting the binding capacity.
  • the constant monomer is introduced either as DNA or mRNA encoding this monomer or as a monomer protein. In this case, an approach with the single chain meganuclease will be preferably used.
  • the targeted DNA sequence can be immobilized on a solid support.
  • Said solid support could be a column, paramagnetic beads or a well of a microplate.
  • the polynucleotides comprising the targeted DNA sequence present a ligand (such as a biotin) at one end, said ligand allowing the immobilization on a solid support bearing the target of the ligand (for example, streptavidin if biotin is used).
  • the selection of the meganuclease variants may usually be monitored by a screening assay based on the binding or cleavage capacity of these meganucleases.
  • the selected meganuclease variants can be also directly introduced in a selection step based on the cleavage capacity.
  • the selected meganuclease variants need to be cloned. If the selection was done with the phage display system, the clone encoding each meganuclease variants can be easily isolated. If the selection was done by mRNA-protein fusion or ribosome display, the selected meganuclease variants have to be subcloned in expression vector.
  • the screening assays are preferably performed in microplates (96, 384 or 1536 wells) in which the targeted DNA polynucleotides are immobilized. After expression of the meganuclease variants, these variants are incubated with the immobilized targeted DNA polynucleotides.
  • the meganuclease variants expression can be performed either in vivo or in vitro, preferably by in vitro expression system.
  • the meganuclease variants are purified prior to the incubation with the targeted polynucleotide. The retained meganuclease variants are then detected. The detection could be done by several means well known by the man skilled in the art.
  • the detection can be done with antibodies against phages (ELISA). Otherwise, the expression could be done in presence of S35 amino acids in order to obtain radioactive meganucleases. Thus, the binding is estimated by a radio-activity measurement.
  • the invention also considers the others means of detection of DNA binding by meganuclease available to the man skilled in the art.
  • the nucleotide sequences encoding the positively screened meganuclease variants are determined, thereby identifying of the meganuclease variants able to bind the targeted DNA sequence.
  • the positively screened meganuclease variants have to be tested for their cleavage capacity. Therefore, said meganuclease variants are incorporated in a cleavage selection and/or screening experiment, preferably an in vivo cleavage screening assay. Optionally, said meganuclease variants can be tested by an in vitro cleavage assay.
  • the screening assay can also be used only for estimate the enrichment in meganuclease variants presenting the binding capacity. This estimation helps to decide if a new round of selection based on the binding capacity is necessary or if the selected library can be submitted to a cleavage selection and/or screening, preferably an in vivo cleavage selection and/or screening.
  • the selection and screening of meganuclease variants based on the cleavage capacity has to be made in conditions compatible with the cleavage activity.
  • the meganuclease variants used in the selection and/or screening based on cleavage capacity may be either the initial library of meganuclease variants or the meganuclease variants selected and/or screened for the binding activity.
  • the selected and/or screened meganuclease variants are subcloned in an appropriate expression vector for the in vitro and in vivo cleavage assay.
  • Such subcloning step can be performed in batch or individually. More particularly, if the initial meganuclease is a dimer, the subcloning step allows the introduction of the selected library(ies) in a single chain meganuclease structure. If two libraries have been selected and/or screened for two half recognition and cleavage sites, the subcloning step allows to bring together the two selected libraries in a single chain meganuclease structure.
  • the general principle of an in vivo selection of the meganuclease variants based on their cleavage capacity is that the double-strand break leads to the activation of a positive selection marker or the inactivation of a negative selection marker.
  • the method involves the use of cell containing an expression vector comprising the coding sequence for a negative selection marker and the targeted DNA sequence for the desired meganuclease and an expression vector comprising the library of meganuclease variants.
  • said expression vector is a plasmid.
  • said targeted DNA sequence is located either near the negative selection gene or in the negative selection gene, preferably between the promoter driving the expression of the negative selection and the ORF.
  • the expression of the negative selection marker has to be conditional in order to keep the cell alive until the meganuclease variants have the opportunity to cleave. Such a conditional expression can be easily done with a conditional promoter.
  • the meganuclease variants are introduced in an expression cassette.
  • the meganuclease encoding sequence can be operably linked to an inducible promoter or to a constitutive promoter.
  • the promoter is compatible with the cell used in the assay. If the meganuclease variant has the capacity to cleave the targeted DNA, then the negative selection marker is inactivated, either by deleting the whole negative marker gene or a part thereof (coding sequence or promoter) or by degrading the vector.
  • a culture in a negative selection condition allows the selection of the cell containing the meganuclease variants able to cleave the targeted DNA sequence.
  • the vector comprising the negative selection marker is preferably transfected before the introduction of the vector encoding the meganuclease variants.
  • the vector comprising the negative selection marker can be conserved in the cell in an episomal form.
  • the vector comprising the negative selection marker and the vector encoding the meganuclease variants can be cotransfected into the cell.
  • the cell can be prokaryotic or eukaryotic.
  • the prokaryotic cell is E. coli .
  • the eukaryotic cell is a yeast cell.
  • the negative selection marker is a protein directly or indirectly toxic for the cell.
  • the negative selection marker can be selected from the group consisting of toxins, translation inhibitors, barnase, and antibiotic for bacteria, URA3 with 5FOA (5-fluoro-orotic acid) medium and LYS2 with a ⁇ -AA medium (alpha-adipic acid) for yeast, and thymidine kinase for superior eukaryotic cells.
  • toxins toxins, translation inhibitors, barnase, and antibiotic for bacteria
  • URA3 with 5FOA (5-fluoro-orotic acid) medium and LYS2 with a ⁇ -AA medium (alpha-adipic acid) for yeast
  • thymidine kinase for superior eukaryotic cells.
  • the method involves the use of cell containing an expression vector comprising an inactive positive selection marker and the targeted DNA sequence for the desired meganuclease and an expression vector comprising the library of meganuclease variants.
  • the inactive positive selection marker, the targeted DNA sequence and the library of meganuclease variants can be on the same vector (See WO 02/44409).
  • said expression vector is a plasmid.
  • the meganuclease variants are introduced in an expression cassette.
  • the meganuclease encoding sequence can be operably linked to an inducible promoter or to a constitutive promoter.
  • the promoter is compatible with the cell used in the assay.
  • the positive selection marker can be an antibiotic resistance (e.g. tetracycline, rifampicin and ampicillin resistance) or an auxotrophy marker for bacteria, TRP1, URA3, or an auxotrophy marker for yeast, and neomycine et puromycine for superior eukaryotic cell.
  • the positive selection marker can be an auxotrophy marker compatible with both bacteria and yeast (e.g. URA3, LYS2, TRP1 and LEU2).
  • the inactive positive selection marker gene and the targeted DNA sequence have to be arranged so that the double-strand break leads to a rearrangement of the marker in an active positive marker.
  • Two kinds of repair processes can lead to an active positive selection marker, namely single-strand annealing (SSA) or gene conversion (GC).
  • SSA Single-strand annealing recombination test
  • an in vivo assay based on SSA in a cell preferably a bacterial or yeast cell
  • the method uses a yeast cell. This organism has the advantage that it recombines naturally its DNA via homologous recombination with a high frequency.
  • This in vivo test is based on the reparation by SSA of a positive selection marker induced by double-strand break generated by an active meganuclease variant.
  • the target consists of a modified positive selection gene with an internal duplication separated by a intervening sequence comprising the targeted DNA sequence.
  • the internal duplication should contain at least 50 bp, preferably at least 200 bp.
  • the efficiency of the SSA test will be increased by the size of the internal duplication.
  • the intervening sequences are at least the targeted DNA sequence.
  • the intervening sequence can optionally comprise a selection marker, this marker allowing checking that the cell has not repaired the positive selection marker by a spontaneous recombination event.
  • the positive selection marker gene is preferably operably linked to a constitutive promoter relating to the cell used in the assay. According to said assay method, the cell will be selected only if a SSA event occurs following the double-strand break introduced by an active meganuclease variant.
  • each vector can comprise a selectable marker to ensure the presence of the plasmid in the cell.
  • the presence of this selectable marker is preferable for the assay performed in yeast cell.
  • a first construct comprising the target gene can comprise a Leu2 selectable marker allowing transformed yeast to grow on a synthetic medium that does not contain any Leucine and a second construct can comprise the Trp1 selectable marker allowing transformed yeast to grow on a synthetic medium that does not contain any tryptophane.
  • the vector comprising the positive selection marker is preferably transfected before the introduction of the vector encoding the meganuclease variants.
  • the vector comprising the positive selection marker can be conserved in the cell in an episomal form.
  • the vector comprising the positive selection marker and the vector encoding the meganuclease variants can be cotransfected into the cell.
  • the in vivo selection of the meganuclease variants can also be performed with a gene conversion assay.
  • the selection vector comprises a first modified positive selection gene with a deletion or a mutation and an insertion of the targeted DNA sequence for the meganuclease at the place of the deletion.
  • the positive selection gene can also be inactivated by the interruption of the gene by an insert comprising the targeted DNA sequence.
  • the selection construct further comprises the segment of the positive selection marker gene which has been deleted flanked at each side by the positive selection marker gene sequences bordering the deletion.
  • the bordering sequences comprise at least 100 bp of homology with the positive selection marker gene at each side, preferably at least 300 pb.
  • the double-stand break generated by an active meganuclease variant in the targeted DNA sequence triggers on a gene conversion event resulting in a functional positive selection marker gene.
  • This kind of assay is documented in the following articles: Rudin et al (Genetics 1989, 122, 519-534), Fishman-Lobell & Haber (Science 1992, 258, 480-4), Paques & Haber (Mol. Cell. Biol., 1997, 17, 6765-6771), the disclosures of which are incorporated herein by reference.
  • the in vivo selection of the meganuclease variants can be performed through a recombination assay on chromosomic target.
  • the recombination can be based on SSA or gene conversion mechanisms.
  • a first example based on SSA is the following.
  • a modified positive selection gene with an internal duplication separated by an intervening sequence comprising the targeted DNA sequence for the desired meganuclease variant is introduced into the chromosome of the cell.
  • the internal duplication should contain at least 50 bp, preferably at least 200 bp.
  • the efficiency of the SSA test will be increased by the size of the internal duplication.
  • the intervening sequence is at least the targeted DNA sequence.
  • a mutated non-functional positive selection marker gene comprising the targeted DNA sequence for the desired meganuclease variant is introduced into the chromosome of the cell.
  • Said targeted DNA sequence has to be in the vicinity of the mutation, preferably at less than 1 kb from the mutation, more preferably at less than 500 bp, 200 bp, or 100 pb surrounding the mutation.
  • the fragment of the functional positive selection marker allowing the repair can be integrated on the chromosome.
  • This kind of assay is documented in the following articles: Rouet et al (Mol. Cell. Biol., 1994, 14, 8096-8106); Choulika et al (Mol. Cell. Biol., 1995, 15, 1968-1973); Donoho et al (Mol. Cell. Biol., 1998, 18, 4070-4078); the disclosures of which are incorporated herein by reference.
  • the selected clones comprise a meganuclease variant presenting the capacity to cleave the targeted DNA sequence. It is preferable to validate the selection by a screening assay.
  • This screening assay can be performed in vivo or in vitro, preferably in vivo.
  • nucleotide sequences encoding the positively screened meganuclease variants are determined, thereby identifying the meganuclease variants able to cleave the targeted DNA sequence.
  • the selected meganuclease variants need to be cloned and the cleavage assay need to be performed individually for each clone.
  • the in vivo cleavage assay for the screening is similar to those used for the selection step. It can be based on the inactivation of either a negative selection marker or a reporter gene, or on the activation of either a positive selection marker or a reporter gene.
  • reporter gene any nucleic acid encoding a product easily assayed, for example ⁇ -galactosidase, luciferase, alkaline phosphatase, green fluorescent protein, tyrosinase, DsRed proteins.
  • the reporter gene is preferably operably linked to a constitutive promoter relating to the cell used in the assay (for example CMV promoter).
  • Cells used for this screening assay can be prokaryotic, preferably E. coli , or eukaryotic, preferably a yeast cell or a mammalian cell. More particularly, it could be interesting to use mammalian cells for a validation of a positive meganuclease variant by an ex vivo cleavage assay.
  • the recognition and cleavage of the targeted DNA sequence or a part thereof by the meganuclease variants can be assayed by any method known by the man skilled in the art.
  • One way to test the activity of the meganuclease variants is to use an in vitro cleavage assay on a polynucleotide substrate comprising the targeted DNA sequence or a part thereof.
  • Said polynucleotide substrate could be a synthetic target site corresponding to:
  • Said polynucleotide substrate can be linear or circular and comprises preferably only one cleavage site.
  • the assayed meganuclease variant is incubated with the polynucleotide substrate in appropriate conditions.
  • the resulting polynucleotides are analyzed by any known method, for example by electrophoresis on agarose or by chromatography. If the polynucleotide substrate is a linearized plasmid, the meganuclease activity is detected by the apparition of two bands (products) and the disappearance of the initial full-length substrate band.
  • such in vitro cleavage assay can be performed with polynucleotide substrates linked to fluorophores, such substrates comprising the targeted DNA sequence.
  • polynucleotide substrates are immobilized on a solid support.
  • Said solid support is preferably a microplate (96, 384 or 1536 wells).
  • the polynucleotides comprising the targeted DNA sequence present a ligand (such as a biotin) at one end, said ligand allowing the immobilization on a solid support bearing the target of the ligand (for example, streptavidin if biotin is used).
  • the end opposite to the immobilized end is linked to a fluorophore. Cleavage leads to loss of fluorescence by release of the fluorochrome from the solid support.
  • chromosomal DNA can be any other sequence used to alter the chromosomal DNA in some specific way including a sequence used to modify of a specific sequence, to attenuate or activate an endogenous gene of interest, to inactivate or delete an endogenous gene of interest or part thereof, to introduce a mutation into a site of interest or to introduce an exogenous gene or part thereof.
  • chromosomal DNA alterations are used for genome engineering (animal models, protein production) or for antiviral therapy.
  • the meganuclease can be used either as a polypeptide or as a polynucleotide construct encoding said polypeptide under the control of appropriate transcription regulatory elements including a promoter, for example a tissue specific and/or inducible promoter.
  • a promoter for example a tissue specific and/or inducible promoter.
  • inducible promoters are: eukaryotic metallothionine promoter which is induced by increased levels of heavy metals, prokaryotic lacZ promoter which is induced in response to isopropyl- ⁇ -D-thiogalactopyranoside (IPTG) and eukaryotic heat shock promoter which is induced by increased temperature.
  • the meganuclease (polypeptide) is associated with:
  • liposomes polyethyleneimine (PEI); in such a case said association is administered and therefore introduced into somatic cells target.
  • PEI polyethyleneimine
  • Meganucleases can also be introduced into somatic tissue(s) from an individual according to methods generally known in the art which are appropriate for the particular meganuclease and cell type.
  • the meganuclease (polynucleotide encoding said meganuclease) and/or the targeting DNA is inserted in a vector.
  • Vectors comprising targeting DNA and/or nucleic acid encoding a meganuclease can be introduced into a cell by a variety of methods (e.g., injection, direct uptake, projectile bombardment, liposomes).
  • Meganucleases can be stably or transiently expressed into cells using expression vectors. Techniques of expression in eukaryotic cells are well known to those in the art.
  • sequence encoding the meganuclease and the targeting DNA are inserted in the same vector.
  • a vector which can be used in the present invention includes, but is not limited to, a viral vector, a plasmid, a RNA vector or a linear or circular DNA or RNA molecule which may consists of a chromosomal, non chromosomal, semisynthetic or synthetic DNA.
  • Preferred vectors are those capable of autonomous replication (episomal vector) and/or expression of nucleic acids to which they are linked (expression vectors). Large numbers of suitable vectors are known to those of skill in the art and commercially available.
  • RNA viruses such as picornavirus and alphavirus
  • double stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, fowlpox and canarypox).
  • herpesvirus e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus
  • poxvirus e.g., vaccinia, fowlpox and canarypox
  • Other viruses include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus, for example.
  • retroviruses examples include: avian leukosis-sarcoma, mammalian C-type, B-type viruses, Dtype viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields, et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996).
  • murine leukemia viruses include murine leukemia viruses, murine sarcoma viruses, mouse mammary tumor virus, bovine leukemia virus, feline leukemia virus, feline sarcoma virus, avian leukemia virus, human T-cell leukemia virus, baboon endogenous virus, Gibbon ape leukemia virus, Mason Pfizer monkey virus, simian immunodeficiency virus, simian sarcoma virus, Rous sarcoma virus and lentiviruses.
  • vectors are described, for example, in McVey et al., U.S. Pat. No. 5,801,030, the teachings of which are incorporated herein by reference.
  • Vectors can also comprise selectable markers (for example, neomycin phosphotransferase, histidinol dehydrogenase, dihydrofolate reductase, hygromycin phosphotransferase, herpes simplex virus thymidine kinase, adenosine deaminase, glutamine synthetase, and hypoxanthine-guanine phosphoribosyl transferase for eukaryotic cell culture; TRP1 for S. cerevisiae ; tetracycline, rifampicin or ampicillin resistance in E. coli ; etc. . . . ).
  • selectable markers for example, neomycin phosphotransferase, histidinol dehydrogenase, dihydrofolate reductase, hygromycin phosphotransferase, herpes simplex virus thymidine kinase,
  • the meganuclease and if present, the vector comprising targeting DNA and/or nucleic acid encoding a meganuclease are imported or translocated by the cell from the cytoplasm to the site of action in the nucleus.
  • Meganucleases and vectors which comprise targeting DNA homologous to the region surrounding the cleavage site and/or nucleic acid encoding a custom-made meganuclease can be introduced into an individual using routes of administration generally known in the art.
  • Administration may be topical or internal, or by any other suitable avenue for introducing a therapeutic agent to a patient.
  • Topical administration may be by application to the skin, or to the eyes, ears, or nose.
  • Internal administration may proceed intradermally, subcutaneously, intramuscularly, intraperitoneally, intraarterially or intravenously, or by any other suitable route. It also may in some cases be advantageous to administer a composition of the invention by oral ingestion, by respiration, rectally, or vaginally.
  • the meganucleases and vectors can be administered in a pharmaceutically acceptable carrier, such as saline, sterile water, Ringer's solution, and isotonic sodium chloride solution.
  • a pharmaceutically acceptable carrier such as saline, sterile water, Ringer's solution, and isotonic sodium chloride solution.
  • the meganucleases will be combined with a pharmaceutically acceptable vehicle appropriate to a planned route of administration.
  • a pharmaceutically acceptable vehicles are well known, from which those that are effective for delivering meganucleases to a site of infection may be selected.
  • the HANDBOOK OF PHARMACEUTICAL EXCIPIENTS published by the American Pharmaceutical Association is one useful guide to appropriate vehicles for use in the invention.
  • a composition is said to be a “pharmaceutically acceptable vehicle” if its administration can be tolerated by the recipient.
  • Sterile phosphate-buffered saline is one example of a pharmaceutically acceptable vehicle that is appropriate for intravenous administration.
  • the dosage of meganuclease or vector according to the present invention administered to an individual, including frequency of administration, will vary depending upon a variety of factors, including mode and route of administration: size, age, sex, health, body weight and diet of the recipient; nature and extent of symptoms of the disease or disorder being treated; kind of concurrent treatment, frequency of treatment, and the effect desired.
  • mode and route of administration size, age, sex, health, body weight and diet of the recipient; nature and extent of symptoms of the disease or disorder being treated; kind of concurrent treatment, frequency of treatment, and the effect desired.
  • the meganucleases and a pharmaceutically acceptable excipient are administered in a therapeutically effective amount.
  • Such a combination is said to be administered in a “therapeutically effective amount” if the amount administered is physiologically significant.
  • An agent is physiologically significant if its presence results in a detectable change in the physiology of the recipient.
  • an agent is physiologically significant if its presence results: in a decrease in the severity of one or more symptoms of the targeted disease, in a genome correction of the lesion or abnormality, or in inhibition of viral infection.
  • the meganuclease is substantially non-immunogenic, i.e., engender little or no adverse immunological response.
  • a variety of methods for ameliorating or eliminating deleterious immunological reactions of this sort can be used in accordance with the invention.
  • the meganuclease is substantially free of N-formyl methionine.
  • Another way to avoid unwanted immunological reactions is to conjugate meganucleases to polyethylene glycol (“PEG”) or polypropylene glycol (“PPG”) (preferably of 500 to 20,000 daltons average molecular weight (MW)). Conjugation with PEG or PPG, as described by Davis et al., (U.S. Pat. No.
  • 4,179,337) for example, can provide non-immunogenic, physiologically active, water soluble endonuclease conjugates with anti-viral activity.
  • Similar methods also using a polyethylene-polypropylene glycol copolymer are described in Saifer et al. (U.S. Pat. No. 5,006,333).
  • meganucleases for gene therapy according to the present invention varies depending on the type of genetic disease (monogenic recessive disease, trinucleotide repeats diseases or diseases caused by dominant and compound heterozygous mutations).
  • the meganuclease is used in association with a targeting DNA as defined above, comprising a sequence to repair the site of interest, for preventing, improving or curing a monogenetic recessive disease.
  • the use of the meganuclease comprises at least the step of (a) inducing in somatic tissue(s) of the individual a double stranded cleavage at a site of interest comprising at least one recognition and cleavage site of said region surrounding the site of cleavage to be deleted into the site of interest and repair of the site of interest (intrachromosomal homologous recombination).
  • Trinucleotide repeats diseases include with no limitations, diseases affecting the genes as follows:
  • Fragile X syndrome CGG repeat, FMR1 gene
  • Fragile XE syndrome CCG repeat, FMR2 gene
  • Myotonic dystrophy CAG repeat, DMPK gene
  • Haw river syndrome GAA repeat, DRPLA gene.
  • the meganuclease is used alone or in association with a targeting DNA as defined above and/or with at least one appropriate vehicle and/or carrier for preventing, improving or curing genetic diseases caused by dominant or compound heterozygous mutations.
  • Meganuclease used alone the double-strand break at the site of the mutation is employed to obtain correction of a genetic lesion via a gene conversion event in which the homologous chromosomal DNA sequences from another copy of the gene donates sequences to the sequences where the double-stranded break was induced (interchromosomal homologous recombination).
  • the use of the meganuclease comprises: inducing in somatic tissue(s) of the individual a double stranded break at a site of interest comprising at least one recognition and cleavage site of said meganuclease under conditions appropriate for chromosomal DNA homologous to the region surrounding the site of cleavage to be introduced into the site of interest and repair of the site of interest.
  • the use of the meganuclease comprises at least the step of (a) inducing in somatic tissue(s) of the individual a double stranded cleavage at a site of interest comprising at least one recognition and cleavage site of said meganuclease, and (b) introducing into the individual a targeting DNA, wherein said targeting DNA comprises (1) DNA sharing homologies to the region surrounding the cleavage site and (2) DNA which repairs the meganuclease, and (b) introducing into the individual a targeting DNA, wherein said targeting DNA comprises (1) DNA sharing homologies to the region surrounding the cleavage site and (2) DNA which repairs the site of interest upon recombination between the targeting DNA and the chromosomal DNA.
  • the targeting DNA is introduced into the individual under conditions appropriate for introduction of the targeting DNA into the site of interest.
  • Monogenetic recessive diseases include with no limitations diseases affecting the following genes in the corresponding somatic tissues:
  • liver apolipoprotein deficiencies (apoA-I or apoB genes); familial hypercholesterolemia (FH; LDL receptor gene); Wilson's disease (WND gene); Sickle cell anemia (hemoglobin beta gene (HBB)); alpha-1 antitrypsin deficiency (alpha-1 antitrypsin gene); Hereditary hemochromatosis (HFE gene); Hemophilia A or B (Factor IX or X genes); Aminoacidopathies (tyrosinemia (fumarylacetoacetate hydrolase gene (FAH)), phenylketonurea (phenylalanine hydroxylase gene (PAH)), . . . ).
  • apoA-I or apoB genes familial hypercholesterolemia
  • FH familial hypercholesterolemia
  • WND gene Wilson's disease
  • Sickle cell anemia hemoglobin beta gene (HBB)
  • alpha-1 antitrypsin deficiency alpha-1 antitryps
  • Muscle Limb-girdle Muscular Dystrophies ( ⁇ , ⁇ , ⁇ or ⁇ -sarcoglycan genes)
  • Kidney Polycystic Kidney Disease (PKHDI)
  • Retina Retinitis pigmentosa (Rhodopsin gene
  • Central Nervous system Tay-Sachs disease; Lese-Nyhan syndrome (HPRT gene).
  • the meganuclease is used alone or in association with at least one appropriate vehicle and/or carrier for preventing, improving or curing a trinucleotide repeats disease.
  • the trinucleotide repeats ((CGG)n, (CAG)n, or (GAA)n) flanking the meganuclease recognition and cleavage site are deleted by intrachromosomal homologous recombination.
  • the use of the meganuclease comprises: inducing in somatic tissue(s) of the individual a double stranded break at a site of interest comprising at least one recognition and cleavage site of said meganuclease under conditions appropriate for chromosomal DNA homologous to the site of interest upon recombination between the targeting DNA and the chromosomal DNA.
  • the targeting DNA is introduced into the individual under conditions appropriate for introduction of the targeting DNA into the site of interest.
  • the sequence encoding the meganuclease and the sequence encoding the targeting DNA may be carried by the same vector.
  • said double-stranded cleavage is induced, either in toto by administration of said meganuclease to an individual, or ex vivo by introduction of said meganuclease into somatic cells removed from an individual and returned into the individual after modification.
  • Genetic diseases caused by dominant or compound heterozygous mutations include with no limitations: Huntington disease, familial hypercholesterolaemia, familial hyperlipidaemia, oro-facio-digital syndrome type 1, dominant otosclerosis, the Bannayan syndrome, hailey-hailey disease, achondroplasia.
  • meganucleases are used as therapeutics in the treatment of viral diseases caused by viruses or retroviruses that present a DNA intermediate. Indeed, many viruses which infect eukaryotic cells possess, during at least one part of their life cycle, genomes that consist of double stranded DNA which can be cleaved readily by a meganuclease.
  • This strategy involves identification of DNA sequences within the viral genome that are viral-specific, i.e., they are not present within the human genome. Once identified, meganucleases that specifically bind and cleave such sequences with high affinity and specificity can be designed using the method for preparing custom-made meganucleases as described in the present invention. Then the designed meganucleases are used for the treatment of viral infection.
  • Meganucleases or expression vector encoding said meganucleases are introduced into the individual by any convenient mean.
  • the custom-made meganucleases are introduced or expressed into the infected cells, the virus is inactivated and/or deleted.
  • the meganuclease treatment has no functional impact on healthy cells.
  • such antiviral therapy based on the use of at least one meganuclease could be used to treat organs of an animal dedicated to xenotransplantation.
  • Any virus that contains a double stranded DNA stage in its life cycle can be targeted for deletion or inactivation by creating a meganuclease that recognizes DNA sequences specific of the viral genome.
  • These viruses could be in replicative or latent form. They could stay either episomal or integrated in the host's genome.
  • the double stranded DNA genome viruses are well appropriate to be treated by using meganuclases as defined in the present invention.
  • the adenoviruses include herpes simplex virus (HSV), varicella virus (VZV), Epstein-Barr virus (EBV), cytomegalo virus (CMV), herpes virus 6, 7 and 8.
  • HSV herpes simplex virus
  • VZV varicella virus
  • EBV Epstein-Barr virus
  • CMV cytomegalo virus
  • HBV herpes simplex virus
  • VZV varicella virus
  • EBV Epstein-Barr virus
  • CMV cytomegalo virus
  • the hepadnaviruses are found the human hepatitis B virus (HBV).
  • the papovariruses are found papillomavirus (HPV) (i.e. HPV16 or HPV18) and polyoma virus.
  • the retroviruses are also well appropriate to be treated by using meganucleases according to the present invention. Although they are RNA viruses, they are integrated in the host genome as double-stranded DNA form. Among the retroviruses are found the human immunodeficiency virus (HIV) and the human T lymphoma virus (HTLV) (i.e. HTLV1).
  • HIV human immunodeficiency virus
  • HTLV human T lymphoma virus
  • said virus is selected from HIV, HBV, HTLV, HPV and HSV.
  • EBV in Burkitt's lymphoma, other lymphoproliferative disease and nasopharyngeal carcinoma
  • herpes virus 8 in Kaposi sarcoma
  • HBV in hepatocellular carcinoma
  • HPV in genital cancer
  • HTLV-1 in T-cell leukemia.
  • episomal viruses For episomal viruses, a double-strand break introduced in its genome leads to the linearisation of the genome and its degradation. Examples of episomal viruses are HSV-1, EBV, and HPV.
  • a double strand break introduced in or near the integrated viral sequence leads to partial or complete deletion of the integrated viral sequence.
  • integrated viruses are HPV, HTLV, HBV, and HIV.
  • a double-strand break in a chromosome induces a gene conversion with the homologous chromosome, therefore leading to viral sequence deletion.
  • the break could also be repaired by SSA (single strand annealing) leading to partial or complete viral deletion.
  • SSA single strand annealing
  • the chromosome could also be repaired by end joining leading to partial or complete deletion of the virus, depending on the positions of the double-strand breaks. See Example 5 in U.S. Pat. No. 5,948,678, the disclosure of which is incorporated herein by reference.
  • DNA target sequences should be at least 15 nucleotides in length and preferably at least 18 nucleotides in length.
  • the homing endonuclease present a recognition sequence spanning to 12-40 bp, this condition is fulfilled with the custom-made meganucleases as defined in the present invention. More particularly, I-Cre I homing endonuclease has a 22 bp recognition sequence.
  • Any DNA sequence of viral genomes can be targeted for cleavage by meganucleases as defined in the present invention.
  • Preferred target sites include those sequences that are conserved between strains of virus and/or which genes are essential for virus propagation or infectivity. These positions are preferable for at least two reasons. First, essential parts of viruses are less mutated than others. Secondly, it is preferably to target an essential region of the virus to maximize the inactivation of the virus.
  • a good target for the custom-made meganuclease could be the viral origin of replication (ori) and/or the viral gene encoding an ori binding protein.
  • ori binding proteins include the HSV-1 UL9 gene product, the VZV gene 51 product, the human herpesvirus 6B CH6R gene product, the EBV EBNA-1 gene product and the HPV E1 and E2 gene products.
  • Other interesting targets for HPV are the genes E6 and E7 as products of which are involved in the initiation and maintenance of the proliferative and malignant phenotype.
  • a preferred target is the highly conserved 62 nucleotides sequence in the pre-core/core region of HPV (E6, E7).
  • Examples of interesting targets for EBV are the genes EBNA and LMP.
  • an interesting target could be the X gene as the X protein interacts with elements of the DNA repair system and may increase the mutation rate of p53.
  • a preferred target is within TAT, REV, or TAR genes.
  • the viral targets are not limited to the above-mentioned examples.
  • the target DNA could be located in the viral repeated sequences such as ITR (Inverted Terminal Repeat) and LTR (Long Terminal Repeat).
  • At least two different targeted sites are used.
  • the main protection of the viruses is their ability to mutate. Therefore, two targeted sites avoid the virus to escape the treatment by using the custom-made meganucleases, according to the present invention.
  • the successive use of different custom-made meganucleases may avoid the adverse immunologic response.
  • Said different custom-made meganuclease can present different initial meganucleases, therefore different immunogenicities.
  • the effectiveness of a meganuclease to inhibit viral propagation and infection is preferably assessed by in vitro and in vivo assays of infection.
  • assays can be carried out first in cell culture to establish the potential of different meganucleases to cleave a viral DNA in a way that deleteriously affects viral propagation. Preliminary studies of this type are followed by studies in appropriate animal models. Finally, clinical studies will be carried out.
  • viruses require different assay systems, since hosts and culture conditions suitable to different viruses vary greatly. However, such appropriate conditions have been described for culturing many viruses and these conditions can be used to test the effect of exposing virus and/or host to meganucleases to determine the ability of the endonuclease to inhibit viral infection.
  • culture conditions for specific viruses see Chapter 17 in Fields and Knipe, Eds., FIELDS VIROLOGY, 2nd Ed., Raven Press, N.Y. (1990).
  • a host and/or virus can be exposed at various times during a course of infection, under varying conditions, in several amounts, and in a variety of vehicles, to mention just a few relevant parameters that can be varied, to assess the potential of meganuclease to achieve a potentially therapeutic effect.
  • potential therapeutical meganuclease can be tested in animal models to assess prophylactic, ameliorative, therapeutic and/or curative potential, either alone or in conjunction with other therapeutic agents.
  • different animal models will be appropriate to different viruses. Any animal model, however, can be used to assess the therapeutic potential of a meganuclease.
  • a potentially effective dose of the assayed meganucleases may be administered to a suitable population of animals, and the effect of the meganucleases on the course of a viral infection may be assessed by comparison with an appropriate control.
  • Such methods for assessing pharmacological effect are well known in the art and can readily be adapted to determining the therapeutic profile of the meganucleases.
  • Genome engineering is the set of methods used to induce a change in the genetic program of a living cell and/or organism.
  • the meganucleases obtained by the method of the present invention allows rational site directed modifications of cell genomes. The purpose of these techniques is to rewrite chromosomes precisely where they should be modified leaving the rest of the genome intact.
  • Fields of applications of the genome engineering are multiple: animal models generation (knock-in or knock-out), protein production (engineering of production strains, protein production in plant and animals for protein production in milks), agricultural biotechnology (addition or removal of a trait, marker excision), modification and study of metabolic pathway.
  • a double-strand break at the genomic locus comprising at least one recognition and cleavage site of said meganuclease; 2) providing a targeting DNA construct comprising the sequence to be introduced flanked by sequences sharing homologies to the targeted locus. Indeed, shared DNA homologies are located in regions flanking upstream and downstream the site of the break in the targeting DNA construct and the DNA that might be introduced should be located between the two arms.
  • Said meganuclease can be provided directly to the cell or through an expression vector comprising the polynucleotide sequence encoding said meganuclease and suitable for its expression in the used cell. This strategy is used to introduce a DNA sequence at the target site, for example to generate knock-in animal models or cell lines that can be used for drug testing or the production of proteins.
  • the use according to the present invention comprises at least the following steps: 1) introducing a double-strand break at the genomic locus comprising at least one recognition and cleavage site of said meganuclease; 2) maintaining under conditions appropriate for homologous recombination with the chromosomal DNA homologous to the region surrounding the cleavage site.
  • This strategy is used to delete a DNA sequence at the target site, for example to generate knock-out animal models for functional genomic studies or for the generation of appropriate animal models for drug testing.
  • knock-outs can be used for the improvement or optimization of cell lines including the modification of metabolic pathways or the generation of cell lines for drug testing.
  • FIG. 1 discloses the amino acid sequence of a single chain I-Cre I meganuclease and one polynucleotide encoding said single chain meganuclease.
  • the two first N-terminal residues are methionine and alanine (MA), and the three C-terminal residues alanine, alanine and aspartic acid (AAD).
  • MA methionine and alanine
  • AAD aspartic acid
  • FIG. 2 discloses polynucleotide sequences.
  • FIG. 2A discloses a polynucleotide called “Natural” encoding the I-Cre I homing endonuclease.
  • FIG. 2B discloses a polynucleotide sequence called “Non homologous” encoding the I-Cre I homing endonuclease.
  • FIG. 2C discloses a polynucleotide sequence called “Template” encoding the I-Cre I homing endonuclease comprising the mutation D75NJ.
  • Each I-Cre I homing endonuclease has two additional amino acids (MA) at the N terminal end and three additional amino acids (AAD) at the C-terminal ends.
  • FIG. 2D discloses the polynucleotide sequences of the primers, called UlibIfor, UlibIrev, UlibIIfor, and UlibIIrev, used for the generation of the libraries UlibI and UlibII.
  • FIG. 3 is a schematic representation of the polynucleotide sequence called “Template” encoding the I-Cre I homing endonuclease comprising the mutation D75N.
  • the dark arrows indicate the position of the primers UlibIfor, UlibIrev, UlibIIfor, and UlibIIrev used to generate the two libraries UlibI and UliblII.
  • D-Helix refers to the LAGLIDADG helix.
  • N75 refers to the mutation D75N.
  • FIG. 4 is a schematic representation of the strategy for the library construction.
  • pET24C-T is a plasmid comprising a polynucleotide Template .
  • Two PCR amplifications, PCR ulib1 and ulib2 are done with either UlibIfor and UlibIIrev, or UliblIfor and UliblIIrev.
  • the PCR ulib1 products are cloned in a phagemid pCes4 NHT.
  • the PCR ulib2 products are cloned in a plasmid pET24C-T.
  • Step 2 Subcloning a fragment of Ulib2 vector (pET45C-Ulib2) into the Ulib1 phagemid (pCes4-Ulib1).
  • FIG. 5 COS cells monolayers were transfected with vector expressing I Sce-I (B) or with control plasmid (A). Fourty eight (48) hours after transfection cells were infected with rHSV-1 (30 PFU). Two days later monolayer was fixed and stained (X-Gal). Infected cells appeared in blue.
  • FIG. 6 FIG. 6A : cells monolayer was infected with 30 PFU. HSV-1 growth was quantified by ⁇ -galactosidase activity in cell lysate.
  • FIG. 6B cell monolayer was infected with 300 PFU. Cell survival was measured by protein determination in cell lysate.
  • I-Sce I refers to vector expressing I-Sce I;
  • I-Sce I( ⁇ ) refers to a vector in which ORF of I Sce-I was inserted in reverse orientation; negative control refers to control plasmid.
  • FIG. 7A is a schematic representation of recombinant HSV-1 genomic DNA.
  • Cassette containing CMV promoter driving Lac gene was inserted in the major LAT transcript.
  • I-Sce I restriction site was cloned between promoter and reporter gene.
  • a and b represent primers used for the semi-quantitative PCR.
  • COS-7 monolayers were transfected with vector expressing I-Sce I or with control plasmids. Fourty eight hours after transfection cells were infected with rHSV-1 (30 PFU). DNA was extracted 1, 2 or 3 days after infection. PCR was carried out as described in experimental procedures .
  • Std refers to Internal standard; Lac refers to an amplicon of the rHSV-1 Lac gene.
  • I-Sce I refers to vector expressing I-Sce I
  • I-Sce I( ⁇ ) refers to a vector in which ORF of I-Sce I was inserted in reverse orientation
  • negative control refers to control plasmid.
  • FIG. 7B PCR quantification of the viral thymidine kinase (TK) gene. PCR was carried out at 2 DNA concentrations.
  • I-SceI refers to vector expressing I-Sce I; I-Sce I( ⁇ ) refers to a vector in which ORF of I-SceI was inserted in reverse orientation; negative control refers to control plasmid.
  • FIG. 8 illustrates the titration of the virus released in the medium after infection of the transfected cells. Every day, medium was collected and fresh medium was added. Viruses were measured by standard plaque assay.
  • I-Sce I refers to vector expressing I-SceI;
  • I-Sce I( ⁇ ) refers to a vector in which ORF of I-Sce I was inserted in reverse orientation;
  • negative control refers to control plasmid.
  • FIG. 9 represents the I-CreI DNA target and five related targets. Conserved positions are in grey boxes.
  • FIG. 10 illustrates four binding patterns obtained after screening of the Lib2 library with six targets. Positives were identified in a first screen and confirmed in a second one during which they were assayed eight times (corresponding to the eight solid bars) on each of the targets (C1234, C1221, C4334, H1234, H1221 and H4334). Histograms are shown for one clone from each class. Targets are described in FIG. 9 .
  • FIG. 11 illustrates the schematic representation of the target vectors.
  • the CpG depleted LacZ gene (LagoZ) is driven by the human elongation factor 1 alpha promoter.
  • the LagoZ gene is inactivated by the insertion of I-SceI cleavage site. Flanking repeats are represented by open arrows. The length of the homologous sequences are indicated in bold.
  • FIG. 12 illustrates the effect of the length of homology on single strand annealing (SSA) efficiency.
  • SSA single strand annealing
  • FIG. 13 Cell monolayers were cotransfected with a vector expressing (+)I-SceI or with a control plasmid ( ⁇ )I-SceI. Seventy-two hours after transfection cells were fixed and stained (X-Gal).
  • FIG. 13A cells where gene repair took place appeared in dark.
  • FIG. 13B frequency of I-SceI induced recombination on 70 and 220 bp duplication target vectors. The frequency is calculated by the ratio of blue cells/transfected cells.
  • FIG. 14A X-Gal staining of liver from mice injected with a mixture of the target LagoZ gene (30 ⁇ g) and an I-SceI expression vector (10 ⁇ g).
  • FIG. 14B X-Gal staining of liver from mice injected with a mixture of the target LagoZ gene (30 ⁇ g) and an expression vector where the ORF of 1-SceI was inserted in the reverse orientation (10 ⁇ g).
  • FIG. 15 X-Gal staining of the liver of hemizygote transgenic mice of two independent strains infected with the Ad.I-SceI adenovirus by IV.
  • B. and C X-Gal staining of the livers of Ad.control -infected hemizygote or un-infected 58A littermates (data not shown).
  • ⁇ -galactosidase activity is detected in multiple cells of the entire liver of 10 9 infectious units infected mouse (B) and 10 10 infectious units infected mouse (C). Stronger signal is detected in C compared to B, probably because of the bigger number of cells that were infected with the Ad.I-SceI . In contrast, no ⁇ 3-galactosidase activity could be detected by X-Gal staining of the livers of un-infected 361 littermates (data not shown).
  • FIG. 16 Fluorescent ⁇ -galactosidase assay on liver extract.
  • Two independent strains of transgenic mice (58 A and 361) were injected with 10 9 or 10 10 PFU of adenovirus expressing I-SceI (Ad.I-SceI) or control virus (Ad.control).
  • Mice were sacrified 5 or 14 days post injection, liver was dissected and protein were extracted. 30 ⁇ l of liver protein extract were incubated at 37° C. in presence of Fluorescein digalactoside (FDG). Bars represent the standard deviation of the assay (two measure experiments with samples of the same extracts).
  • NI non injected mice
  • Ad.I-SceI mice injected with adenovirus expressing I-SceI
  • Ad.control mice injected with control adenovirus.
  • FIG. 17 represents the transgene, the DNA repair matrix and the sequences of the primers used in example 7.
  • FIG. 18 illustrates the RT-PCR analysis of I-SceI-hApo A-I transgene repair by I-SceI induced gene conversion in mice.
  • Hydrodynamic tail vein injection of naked DNA I-SceI expression vector and DNA repair matrix
  • A 2 kbp DNA repair matrix (RM)
  • B 1.5 kbp RM.
  • I-SceI induced gene conversion on I-SceI-hApo A-I transgene in CHO cells was used as PCR positive control.
  • LAGLIDADG homing endonucleases are active as homodimer. Each monomer mainly dimerizes through their dodecapeptide motifs.
  • a single-chain meganuclease can be engineered by covalently binding two monomers modified such as to introduce a covalent link between the two sub-units of this enzyme. Preferably, the covalent link is introduced by creating a peptide bond between the two monomers. However, other convenient covalent links are also contemplated.
  • the single-chain meganuclease preferably comprises two subunits from the same homing endonuclease such as single-chain I-Cre I and single-chain I-Ceu I.
  • a single-chain meganuclease has multiple advantages.
  • a single-chain meganuclease is easier to manipulate.
  • the single-chain meganuclease is thermodynamically favored, for example for the recognition of the target sequence, compared to a dimer formation.
  • the single-chain meganuclease allows the control of the oligomerisation.
  • scI-CreI A single chain version of I-CreI (scI-CreI) was modeled and engineered. scI-CreI cleaves its cognate DNA substrate in vitro and induces homologous recombination both in yeast and mammalian cells.
  • I-CreI from Chlamydomonas reinhardtii is a small LAGLIDADG homing endonuclease that dimerizes into a structure similar to that of larger monomer LAGLIDADG homing endonuclease.
  • scI-CreI single chain version of I-CreI
  • two I-CreI copies were fused. This required placing a linker region between the two domains, and a significant part of the I-CreI protein had to be removed at the end of the domain preceding the linker.
  • I-DmoI The three-dimensional structure of I-DmoI is comparable to that of I-CreI, with the exception that I-DmoI comprises a linker region that leads from one apparent domain to the other. The boundary of that linker finely matches related main chain atoms of the I-CreI dimer. In the first domain, residues 93 to 95 from the third ⁇ -helices of I-CreI and I-DmoI (prior to the linker) are structurally equivalent. At the beginning of the second LAGLIDADG ⁇ -helix (second domain), I-DmoI residues 104 to 106 correspond to I-CreI residues 7 to 9.
  • I-DmoI residue Arg104 aligns with another basic residue in I-CreI (Lys7).
  • scI-CreI single chain I-CreI
  • His-tagged proteins were over-expressed in E. coli BL21 (DE3) cells using pET-24d (+) vectors (Novagen). Induction with IPTG (1 mM), was performed at 25° C. Cells were sonicated in a solution of 25 mM HEPES (pH 8) containing protease inhibitors (Complete EDTA-free tablets, Roche) and 5% (v/v) glycerol. Cell lysates were centrifuged twice (15 000 g for 30 min). His-tagged proteins were then affinity-purified, using 5 ml Hi-Trap chelating columns (Amersham) loaded with cobalt.
  • pGEM plasmids with single meganuclease DNA target cut sites were first linearized with XmnI. Cleavage assays were performed at 37° C. or 65° C. in 12.5 mM HEPES (pH 8), 2.5% (v/v) glycerol and 10 mM MgCl2. Reactions were stopped by addition of 0.1 volume of 0.1 M Tris-HCl (pH 7.5), 0.25 M EDTA, 5% (w/v) SDS, and 0.5 mg/ml proteinase K and incubation at 37° C. for 20 minutes. Reaction products were examined following separation by electrophoresis in 1% agarose gels.
  • the yeast transformation method has been adapted from previous protocols.
  • a classic qualitative X-Gal Agarose Overlay Assay was used for staining. Each plate was covered with 2.5 ml of 1% agarose in 0.1 M Sodium Phosphate buffer, pH 7.0, 0.2% SDS, 12% Dimethyl Formamide (DMF), 14 mM ⁇ -mercaptoethanol, 0.4% X-Gal, at 60°. Plates were incubated at 37° C.
  • COS cells were transfected with Superfect transfection reagent accordingly to the supplier (Qiagen) protocol. 72 hours after transfection, cells were rinsed twice with PBS1 ⁇ and incubated in lysis buffer (Tris-HCl 10 mM pH7.5, NaCl 150 mM, Triton X100 0.1%, BSA 0.1 mg/ml, protease inhibitors). Lysate was centrifuged and the supernatant used for protein concentration determination and ⁇ -galactosidase liquid assay.
  • lysis buffer Tris-HCl 10 mM pH7.5, NaCl 150 mM, Triton X100 0.1%, BSA 0.1 mg/ml, protease inhibitors
  • a synthetic gene corresponding to the new enzyme was engineered and the scI-CreI protein over-expressed in E. coli .
  • the ability of purified scI-CreI to cleave DNA substrates in vitro was tested, using linearized plasmids bearing a copy of the I-CreI homing site.
  • the novel enzyme cleaves an I-CreI target site at 37° C.
  • SSA reporter vector with two truncated, non-functional copies of the bacterial LacZ gene and an I-CreI cut site within the intervening sequence was constructed in a yeast replicative plasmid. Cleavage of the cut site should result in a unique, functional LacZ copy that can be easily detected by X-gal staining.
  • the reporter vector was used to transform yeast cells. A small fraction of cells appeared to express functional LacZ, probably due to recombination events during transformation. Co-transformation with plasmids expressing either I-CreI or scI-CreI, in contrast, resulted in blue staining for all plated cells. Even in non-induced conditions (glucose), the residual level of protein was enough to induce SSA, suggesting that scI-CreI, as much as I-CreI, is highly efficient in yeast cells. Furthermore, SSA induction was truly dependent on cleavage of the target cut site by I-CreI proteins, as vectors devoid of that site display no increase in ⁇ -galactosidase activity compared to background levels.
  • the SSA assay was modified for tests in mammalian cells.
  • the promoter and termination sequences of the reporter and meganuclease expression plasmid were changed, and plasmid recombination was evaluated in a transient transfection assay. Similar levels of induced recombination (2 to 3-fold increase) were observed with either scI-CreI or I-CreI. As in the yeast experiment, recombination depends on an I-CreI cut site between the repeats, for no increase of the ⁇ -galactosidase was observed in the absence of this site.
  • a combinatorial library was constructed by mutagenesis of the I-Cre I homing endonuclease replacing DNA binding residues. Selection and screening applications then enabled to find those variants that were able to bind a particular, chosen DNA target.
  • phage display as I-Cre I is a homodimer, a phagemid vector was required that encoded two separate I-Cre I proteins. Only one of the two I-Cre I copies, which was fused to the phage coat protein p3, was mutated. The resulting protein library, in phage display format, comprised thus I-Cre I wild-type/mutant heterodimers.
  • residue D75 which is shielded from solvent by R68 and R70, was mutated to N (Asn) in order to remove the likely energetic strain caused by replacements of those two basic residues in the library.
  • Homodimers of mutant D75N purified from E. coli cells wherein it was over-expressed using a pET expression vector
  • a phagemid vector was then engineered that encodes wild-type I-CreI (FIGS. 2 A and 2 B: Natural or Non homologous ) and the D75N mutant ( FIG. 2C : Template ) fused to the phage coat protein p3 and phage-displayed wild-type/D75N heterodimers were shown to bind that target DNA.
  • Lib1 (residues 26, 28, 30, 33 and 38 mutated; theoretical diversity 12 5 or 2.48 ⁇ 10 5 ) and Lib2 (residues 44, 68 and 70 mutated; theoretical diversity 12 3 or 1.7 ⁇ 10 3 ).
  • DNA fragments carrying combinations of the desired mutations were obtained by PCR (several reactions in 50 ⁇ l), using degenerated primers ( FIG. 2D : Uliblfor, Uliblrev, Ulibllfor, Ulibllrev) and as DNA template, the D75N gene.
  • Lib1 and Lib2 were constructed by ligation of the corresponding PCR products, digested with specific restriction enzymes, into the D75N mutant gene, within the phagemid vector and within the pET expression vector, respectively. Digestions of vectors and inserts DNA were conducted in two steps (single enzyme digestions) between which the DNA sample was extracted (phenol:chloroform:isoamylalcohol) and EtOH-precipitated. 10 ⁇ g of digested vector DNA were used for ligations, with a 5:1 excess of insert DNA. E. coli TG1 cells were transformed with the resulting vectors by electroporation.
  • Lib1 and Lib2 bacterial clones were scraped from plates and the corresponding plasmid vectors were extracted and purified.
  • the complete library was then obtained by sub-cloning a fragment of the Lib2 vector into the Lib1 phagemid vector (see FIG. 4 for a schematic diagram of the library construction).
  • Several rounds of DNA 2-step digestions, dephosphorylation, purification, quantification, ligation and electroporation were performed. After 4 rounds of 150 electroporation shots (which corresponds to 12 ligations of 1.4 ⁇ g vector with 0.4 ⁇ g insert), 5.5 ⁇ 10 7 bacterial clones were obtained (after correction for background).
  • Bacteria were scraped and stored as a glycerol stock. In addition, an aliquot of this glycerol stock was used to inoculate a 200 ml culture and the library vector was extracted and purified from this culture for storage or potential subcloning.
  • pGEM plasmids with single meganuclease DNA target cut sites were first linearized with XmnI. Cleavage assays were performed at 37° C. in 12.5 mM HEPES (pH 8), 2.5% (v/v) glycerol and 10 mM MgCl 2 . Reactions were stopped by addition of 0.1 volume of 0.1 M Tris-HCl (pH 7.5), 0.25 M EDTA, 5% (w/v) SDS, and 0.5 mg/ml proteinase K and incubation at 37° C. for 20 minutes. Reaction products were examined following separation by electrophoresis in 1% agarose gels.
  • Phage Display of I-Cre I/D75N heterodimer was obtained by using a phagemid harboring two different ORFs as a bicistron, under the control of promoter pLac. The first one yields a soluble protein fused to a N-terminal signal sequence directing the product into the periplasmic space of E. coli Gene 1-Cre I WT was cloned into this ORF using restriction enzymes ApaLI and AscI. The D75N domain was cloned into the second ORF using Nco I and Eag I restriction enzyme, leading to a fusion with the phage coat protein p3 via a hexahis tag, a C-Myc tag and an amber stop codon.
  • This final phagemid was called pCes1CreT.
  • a suppressive strain like TG1 or XL1blue
  • a helper phage e.g. M13K07
  • D75N-p3 fusions are incorporated in the phage coat and the soluble I-CreI mononers produced in the same compartment will either dimerize or interact with the displayed D75N domain, thereby producing particles displaying I-CreI WT/D75N heterodimer.
  • a 5 mL culture of 2 ⁇ TY containing 100 ⁇ g/ml of ampicillin and 2% glucose was inoculated with a 1/100 dilution of an overnight culture of bacteria containing phagemid pCes1CreT and agitated at 37° C.
  • phage helper M13K07 (Pharmacia) was added at a ratio phage:bacteria of 20:1. After 30 min at 37° C.
  • the culture was centrifuged for 10 min at 4000 rpm and the pellet was resuspended in 25 ml of 2 ⁇ TY containing 100 ⁇ g/mL Ampicillin and 25 ⁇ g/mL Kanamycin, and agitated overnight at 30° C. Culture were centrifuged and supernatant were used as such in phage ELISA.
  • Microtiter plates were coated for 1 h at 37° C. with 100 ⁇ l/well of biotinylated BSA at 2 ⁇ g/mL in PBS. After several washes in PBS containing 0.1% Tween20 (PBST), wells were incubated with 100 ⁇ l/well of streptavidin at 10 ⁇ g/mL in PBS and incubated for 1 h at RT. Plates were further washed and incubated with biotinylated PCR fragments harboring the target site, at 250 pM in PBS. After 1 h incubation at RT and washing, plates were saturated with 200 ⁇ l/well of PBS containing 3% powder milk and 25 mM CaCl 2 (PMC).
  • PMC CaCl 2
  • PMC was discarded and plates were filled with 80 ⁇ l of PMC and 20 ⁇ l/well of culture supernatant containing the phage particles.
  • plates were extensively washed with PBST and incubated with 100 ⁇ l/well of anti 25 M13-HRP conjugated antibody (Pharmacia) diluted 1/5000 in PMC. Plates were incubated for 1 h at RT, washed and incubated with TMB solution (Sigma). The reaction was blocked with 50 ⁇ l/well of 1M H 2 SO 4 . Plates were read at 450 nm. A signal higher than 3 ⁇ the background (irrelevant target) can be considered as positive.
  • Plasmid pET24-T45 containing the gene I-CreI D75N was diluted at 1 ng/ ⁇ l to be used as template for PCR.
  • Degenerated oligonucleotides encoding the desired randomizations were used to amplify PCR fragments Lib1 and Lib2 in 4 ⁇ 50 ⁇ l PCR reactions per inserts.
  • PCR products were pooled, EtOH precipitated and resuspended in 50 ⁇ l 10 mM Tris.
  • the goal of this project was to obtain a meganuclease capable of cutting a sequence found in the genome of HIV2 (GGAAGAAGCCTTAAGACATTTTGA).
  • the homing endonuclease I-Cre I was used as a scaffold to build a library of 10 8 variants by randomizing 8 residues located at the DNA-binding interface of one I-Cre I monomer (see previous section).
  • This library was enriched for binders by several rounds of selection/amplification using biotinylated DNA fragments harboring the HIV2 derived target (H1V6335). The selected targets were subsequently screened for binding using a phage ELISA.
  • a phagemid based on pCesl (pCLS346) was chosen. This plasmid harbored two different ORFs as a bicistron, under the control of promoter pLac. The first one yielded a soluble protein fused to a N-terminal signal sequence directing the product into the periplasmic space of E. coli . In our case, this first product was a wild-type monomer of I-CreI. The second ORF encoded an I-CreI monomer that was fused to the phage coat protein p3 via a hexahis tag, a C-Myc tag and an amber stop codon.
  • helper phage e.g. M13K07
  • bacteria harboring this phagemid produces phage particles and around 1-10% of them displays the recombinant protein on their surface.
  • the monomer fused to p3 and randomized on the DNA-binding interface was incorporated in the phage coat and the soluble I-CreI monomers produced in the same compartment either dimerize or interact with the displayed monomer, thereby producing particles displaying I-CreI homodimers (or heterodimers if the monomer fused to p3 was mutated).
  • Two complementary primers encoding the desired sequences but harboring an extra adenosine in 3′ were annealed and ligated into pGEM-t Easy (Promega). After sequencing, a correct clone was chosen as template to PCR amplify a biotinylated 200 pb fragment using the kit KOD (Novagen) and primers SP6 (TTTAGGTGACACTATAGAATAC) and biotT7 (biot-TAATACGACTCACTATAGG). The PCR product concentration was estimated on gel and the fragment was used as such in ELISA or selection procedures.
  • a representative aliquot of the library (at least 10 ⁇ more bacteria than the library size) was used to inoculate 50 ml of 2 ⁇ TY containing 100 ⁇ g/ml ampicillin and 2% glucose (2TYAG) and the culture was agitated at 37° C. At an OD 600 of 0.5, 5 ml of this culture was infected with helper phage K07 at a ratio phage:bacteria of 20:1 and incubated without agitation for 30 min at 37° C.
  • the pellet was resuspended in 25 ml of 2 ⁇ TY containing 100 ⁇ g/ml ampicillin and 25 ⁇ g/ml kanamycin (2TYAK) and agitated overnight at 30° C.
  • the culture was centrifuged at 4000 rpm for 20 min at 4° C. and phage particles were precipitated by the addition of 0.2 volume of 20% PEG6000/2.5M NaCl for 1 h on ice.
  • the phage pellet was resuspended in 1 ml of PBS and centrifuged at 10 00 rpm for 5 min. 0.2 volume of 20% PEG6000/2.5M NaCl was added to the supernatant and the mix was centrifuged at 10 000 rpm to pellet the phage particles. Particles were finally resuspended in 250 ⁇ l PBS.
  • Phage particles were diluted in 1 ml of PBS containing 3% dry milk and 25 mM CaC1 (PMC) and incubated for 1 h at RT.
  • 100 pI Streptavidin beads (Dynal, 200 ⁇ l for the first round) were washed 3 ⁇ in PMC and blocked for 1 h in the same buffer.
  • the biotinylated targets were added to the phage at the indicated concentration and the mix was agitated at RT for 1 h. Beads were added to the mix and incubated at RT for 15 min. Beads were collected on the vial wall using a magnet and washed 10 ⁇ in PMC containing 0.1% tween.
  • Isolated colonies from selection outputs were toothpicked into 100 ⁇ l of 2TYAG in 96 well plates, and agitated overnight at 37° C.
  • a fresh plate containing 100 ⁇ l 2TYAG was isolated using a transfer device. 50 ⁇ l of sterile 60% glycerol was added to the overnight plate and this masterplate was stored at ⁇ 80° C.
  • the fresh plate was agitated at 37° C. for 2.5 h, rescued by the addition of 2TYAG containing 2 ⁇ 10 9 pfu of helper phage M13K07, incubated for 30 min at 30° C., spun at 1700 rpm for 15 min. Cells pellets were resuspended in 150 ⁇ l 2TYAK and agitated overnight at 30° C. After centrifugation, 20 ⁇ l of supernatant was used as described in the previous section.
  • Phage particles displaying I-Cre I variants were produced by infecting bacteria harboring the phagemid library with helper phage M13KO7. Phage particles were purified by PEG precipitation and incubated with a biotinylated PCR fragment harboring HIV6335 target. After 1 h of incubation at room temperature, streptavidin-coated magnetic beads were added to the solution to retrieve the biotinylated DMA and bound phages. The beads were extensively washed and the bound phages were eluted by pH shock. Bacteria were infected with the eluted phages and plated on large 2 ⁇ TY plates containing ampicillin and 2% glucose. Serial dilutions of an aliquot of the eluted phages were used to infect bacteria to calculate the number of phage particle and obtain isolated colonies.
  • the stringency of the selections was increased after each round.
  • the first selection was done using 110 nM of biotinylated target.
  • the second was done with 400 pM and the washing steps were extended.
  • the third round was done using 250 pM and washed more extensively.
  • E. coli provided by Stratagene following standard procedures.
  • S. cerevisiae Experiments in S. cerevisiae are done in the following strains:
  • FYC2-6A alpha, trp1 ⁇ 63, leu2 ⁇ 1, his3 ⁇ 200
  • FYBL2-7B a, ura3 ⁇ 851, trp1 ⁇ 63, leu2 ⁇ 1, lys2 ⁇ 202
  • YASP3 (derived from FYC2-6A): alpha, ura3::SSA-ura3-HIV2-KanR, ade2::SSA-ade2-HIV2-TRP1, trp1 ⁇ 63, leu2 ⁇ , his3 ⁇ 200
  • pCLS0279 ADH1 promoter, TRP1 selectable marker and ARS-CEN origin of replication, ⁇ -galactosidase SSA target, HIV2 6335 cleavage site.
  • pCLS0569 kanamycin resistance cassette, HIV2 6335, internal fragment of the URA3 gene.
  • pCLS0570 kanamycin resistance cassette, HIV2 6335, internal fragment of the LYS2 gene.
  • pCLS0576 TRP1 selectable marker, HIV2 6335, internal fragment of the ADE2 gene.
  • pCLS0047 Galactose inducible promoter, LEU2 selectable marker and 2 micron origin of replication.
  • a library of mutated I-CreI meganucleases has been first selected by a phage display procedure, resulting in a sub-library enriched for variants of interest, able to bind the HIV2 6335 target.
  • the inserts from this enriched sub-library are subcloned into pCLS0047 under the control of a galactose-inducible promoter, for further selection in yeast.
  • YASP3 Single Strand Annealing
  • the URA3 SSA target was a modified ura3 gene with 2 direct repeats of 600 base pairs separated by 4.3 kb (containing a kanamycin resistance cassette and the HIV2 6335 cleavage site).
  • the strain was unable to grow on a minimal medium lacking uracile but was resistant to G418.
  • this target was cleaved and recombined properly, the yeast was able to grow on media without uracil and was sensitive to G418.
  • the ADE2 SSA target was a modified ade2 gene with 2 direct repeats of 1.1 kb separated by 3.6 kb (containing a tryptophan selectable marker and the HIV2 6335 cleavage site). Because of this mutated ade2 gene, the yeast strain was unable to grow on a minimal medium lacking adenine, but harbored a red color on a medium with a low adenine content. Because of the tryptophan selectable marker, it was able to grow on minimal media without tryptophan. When this target was cleaved and recombined properly, the yeast was white, able to grow on media without adenine and unable to grow on a minimal medium lacking tryptophan.
  • the recipient yeast strain was red (on low adenine medium), G418 resistant, tryptophan prototroph and auxotroph for uracile and adenine. If a specific meganuclease is expressed in this strain and cleaves its target sites, the resulting yeast clone is white, G418 sensitive, prototroph for tryptophan and auxotroph for uracile and adenine.
  • the YASP3 strain was validated by determining the level of spontaneous recombination of each target alone and of both targets taken together.
  • the URA3 SSA 10 target recombined spontaneously as an uracile prototrophe, G418 sensitive at an approximate 6 10 ⁇ 4 rate.
  • the ADE2 SSA target recombined spontaneously as an adenine prototrophe at an approximate 2.7 10 ⁇ 3 rate. Recombination of both markers occurred spontaneously (resulting in uracile/adenin rototrophes) at an approximate 10 ⁇ 6 rate.
  • a pilot experiment with 1.5 ⁇ 10 in transformants showed no background level of uracileladenine prototrophes means that the number of false positive clones should be less than 10 after a transformation experiment with a library that would yield about a million of independent clones.
  • the library is used to transform YASP3.
  • a classical chemical/heat chock protocol that routinely gives 10 6 independent transformants per pg of DNA was used (Gietz, R. D. and Woods, R. A., 2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method (Methods Enzymol, 350, 87-96).
  • Transformation of the strain with the library gives more than 10 6 independent yeast transformants from which a number of clones are able to grow on a selective medium whithout uracile, leucine and containing galactose as a carbone source and a low amount of adenine.
  • those clones the interesting ones are white indicating that they contain a LEU2 vector allowing the expression of a meganuclease specific for HIV2 6335 site and that the enzyme is able to cut both URA3 and ADE2 reporters.
  • the positive clones are isolated and screened for their ability to induce the specific recombination of a plasmidic SSA ⁇ -galactosidase target (pCLSO279).
  • This plasmidic reporter was a modified LacZ gene with 2 direct repeats of 825 base pairs separated by 1.3 kb (containing a URA3 selectable marker and the HIV2 6335 cleavage site).
  • the vector (which can be selected on a medium without tryptophan) is used to transform a yeast strain (FYBL2-7B) and clones are maintained on minimal media 35 lacking uracile to maintain the unrecombined LacZ target.
  • Yeast clones resulting from the selection experiment are mated with the yeast strain containing the SSA ⁇ -galactosidase target. Diploids are selected and assayed for induced ⁇ -galactosidase activity. A number of clones are expected to behave as false positives at this step. They correspond to the background level of spontaneous recombination of the URA3 and ADE2 SSA targets. All remaining clones (uracile and adenine auxotrophes able to induce recombination of the SSA-LacZ target) are true positives expressing a meganuclease cleaving the HIV2 6335 target in vivo. Also, other experiments, based on the ones described above, can be used to determine more precisely the activity of such novel enzymes.
  • COS-7 cell lines from the american Type culture collection were cultured in DMEM plus 10% fetal bovine serum.
  • PC-12 cells from ATCC were grown in RPMI1640 supplemented with 10% heat-inactivated horse serum and 5% heat-inactivated fetal bovine serum.
  • PC-12 cells were differentiated as previously described (Su et al., 1999, Journal of Virology, 4171-4180). Briefly, cells were seeded on 6 well-plate at 5 10 4 cells per well. The following day, cells were incubated in PC-12 medium containing 100 ng/ml of 2,5S NGF (Invitrogen). Medium was changed every three days. After 7 days of incubation, undifferentiated cells were eliminated by adding 21M of fluorodeoxyuridine (FdUrd).
  • HSV-1 was purchased from ATCC. Viruses were propagated on COS-7 cells at low MOI (0.01 PFU/cell). Recombinant virus (rHSV-1) were generated as previously described (Lachmann, R. H., Efstathiou, S., 1997, Journal of Virology, 3197-3207). A 4.6 Kb pstI-bamHI viral genomic DNA fragment was cloned in pUC 19. Based on HSV-1 sequence from data base (ID: NC 001806), this region represents nucleotides 118867 to 123460. A cassette consisting of a CMV promoter driving Lac gene expression was introduced into a 168 bp HpaI deletion. This region is located within the major LAT locus of HSV-1.
  • I-Sce I cleavage site was finally cloned directly after the CMV promoter. This construct was used to generate recombinant viruses. Plasmid was linearized by XmnI digestion, and 2 ⁇ g of this plasmid DNA was contransfected with 15 ⁇ g of HSV-1 genomic DNA prepared from COS-7 infected cells by CaCl 2 method. After 3 or 4 days, infected cells were harvested and sonicated. Aliquot of the lysed cells were used to infect COS monolayer.
  • Virus recombinant were selected by overlaying COS monolayer with 1% agarose in medium containing 300 ⁇ g/ml of X-Gal (5-bromo-4-chloro-3-indolyl- ⁇ -D-galactopyranoside). Blue clones were picked and further subjected to three round of plaque purification. Presence of the I-Sce I site was confirmed by PCR and in vitro I Sce-I enzymatic digestion.
  • Cell monolayer was fixed in 0.5% glutaraldehyde in 100 mM PBS containing 1 mM MgCl 2 at 4° for 10 minutes. After one wash with detergent solution (100 mM PBS, 1 mM MgCl 2 , 0.02% Nonidet p-40) cells were incubated at 37° in X-Gal stain solution (10 mM PBS, 1 mM MgCl 2 , 150 mM NaCl, 33 mM K 4 Fe(CN) 6 .3H 2 O, 33 mM K 3 Fe(CN) 6 , 0.1% X-Gal) until color development.
  • X-Gal stain solution 10 mM PBS, 1 mM MgCl 2 , 150 mM NaCl, 33 mM K 4 Fe(CN) 6 .3H 2 O, 33 mM K 3 Fe(CN) 6 , 0.1% X-Gal
  • Beta-galactosidase activity was also measured on cell extract with o-nitrophenyl- ⁇ -D-galactopyrannoside (ONPG) as substrate.
  • Cell monolayer was washed once with PBS.
  • Cells were then lysed with 10 mM Tris ph 7.5, 150 mM NaCl, 1% Triton X-100, protease inhibitors. After 30 minutes incubation on ice cell lysate was centrifuged and 3-galactosidase was assayed.
  • reaction buffer 10 mM PBS; ph 7.5, 1 mM MgCl 2 , 0.3% 3-mercaptoethanol
  • the reaction was carried out at 37° and stopped with 0.5 ml of 1M NaCO 3 .
  • Optical density was measured at 415 nm.
  • Beta-galactosidase activity is calculated as relative unit normalized for protein concentration and incubation time.
  • oligonucleotides were designed to amplify a 217 bp fragment from Lac gene.
  • the standard DNA used in this assay was generated by cloning this fragment in a Bluescript plasmid, and by inserting a 50 bp fragment downstream to the 5′ oligonucleotide.
  • PCR of the standard produced 267 bp amplicon.
  • Series of PCR (not shown) were carried out to fix the amount of standard and DNA sample, and the number of cycles to achieve linear response of the amplification.
  • the basic semi-quantitative PCR were carried out in a total volume of 30 ⁇ l, using the READYMIXTM TAQ (Sigma) with 20 pmols of each primers and 180 pg of DNA.
  • the tubes were heated for 4 min at 94° and subjected to 22 cycles: 94° for 1 min, 62° for 50 sec, 72° for 2 min, and 72° for 7 min.
  • the culture medium was collected every day at days 1, 2, 3, and 4, and fresh medium was added. In the other, the medium was not changed during experiment and aliquots were collected every day. To monitor for the release of HSV-1 progeny, aliquot of medium were titred on COS-7 cells by standard plaque assay.
  • I-Sce I The effect of I-Sce I on viral replication was examined using a recombinant Herpes simplex virus carrying a I-Sce I restriction site (rHSV-1).
  • rHSV-1 was build with a cassette containing CMV promoter driving the Lac gene.
  • I-Sce I site was inserted at the junction of the CMV promoter and Lac gene.
  • the expression cassette was cloned by homologous recombination in the major LAT locus which allowed Beta-galactosidase ( ⁇ -gal) expression during lytic infection in COS-7 cell monolayer. Strinkingly transfection of I-Sce I expression vector before viral infection virtually completely inhibited HSV-1 plaque formation in COS cells ( FIG. 5 ) as shown by X-Gal coloration.
  • the cells were checked for I-Sce I expression. All the lysis plaques formed in cells monolayer transfected with I-Sce I expression vector represented cells which did not expressed I-Sce I (the transient transfection is about 70% efficient). However, cells expressing I-Sce I surrounding the lysis plaque inhibited the viral propagation. The I-Sce I effect was confirmed by measuring the ⁇ -galactosidase activity in a cell lysate.
  • FIG. 6A shows a drastic decrease of the ⁇ -galactosidase activity reflecting the inhibition of rHSV-1 replication.
  • the protective effect of I-Sce I over a time course of rHSV-1 infection was evaluated next.
  • cells transfected with I-Sce I expressing vector shown no sign of cytopathic effect whereas control cultures were completely lysed as shown in FIG. 6B .
  • TK Thymidine Kinase
  • COS-7 cells expressing active I-Sce I or I-Sce I ORF in the reverse orientation were infected with rHSV-1 and the concentration of virus released in the medium at different time points was measured by plaque assay ( FIG. 8 ).
  • Viruses were quantified in a rough array at day one when I-Sce I was produced. Viruses production was still markly decreased two days after the infection when compared with cells which did not expressed I-Sce I showing that I-Sce I effectively inhibited viral replication. This effect was still observed at day three although in a lesser extent. Probably the high mutation rate occuring during viral replication allowed emergence of mutant HSV-1 which were able to escape the I-Sce I activity.
  • the purpose of this experiment was to obtain novel meganucleases binding target sites close to the I-CreI natural target site.
  • a series of 6 targets were used ( FIG. 9 ), including the wild-type natural I-CreI target (named C1234), the HIV2 target described in example 2 (named here H1234), and four additional targets. These four additional targets are 24 bp palindromes corresponding to inverted repeats of a 12 bp half I-CreI or HIV2 target site: C1221 and C4334 are inverted repeats of the first half and second half, respectively, of the C1234 target; H1221 and H4334 are inverted repeats of the first half and second half, respectively, of the H1234 target.
  • the method used here did not involve any selection step, but was based on the extensive screening of the Lib2 library (see example 2). Three residues (Q44, R68 and R70) capable of base specific interactions with the DNA target were selected.
  • the combinatorial library was obtained by replacing the three corresponding codons with a unique degenerated VVK codon.
  • mutants in the protein library corresponded to independant combinations of any of the 12 amino acids encoded by the VVK codon (ADEGHKNPQRST) at three residue positions.
  • the maximal (theoretical) diversity of the protein library was 12 3 or 1728.
  • residue D75 which is shielded from solvent by R68 and R70, was mutated to N (Asn) in order to remove the likely energetic strain caused by replacements of those two basic residues in the library.
  • Homodimers of mutant D75N purified from E. coli cells wherein it was over-expressed using a pET expression vector
  • a phagemid vector was then engineered that encodes the D75N mutant ( FIG. 2C : Template ) fused to the phage coat protein p3 and phage-displayed D75N monomers were shown to bind the I-CreI natural DNA target (C1234 on FIG. 9 ).
  • DNA fragments carrying combinations of the desired mutations were obtained by PCR (several reactions in 50 ⁇ l), using degenerated primers ( FIG. 2D : UlibIIfor, UlibIIrev) and as DNA template, the D75N gene.
  • Lib2 was constructed by ligation of the corresponding PCR products, digested with specific restriction enzymes, into the D75N mutant gene, within the phagemid vector, as described in example 2.
  • FIG. 10 features one representative example for each one.
  • the first class (Class I) corresponds to a strong binding of C1234, C1221, C4334 and H4334.
  • the wild-type protein (QRR) was recovered in this class, showing that Class I profile is the regular binding profile of the original scaffold. Two variants were also shown to display such binding (QRK and another yet not completely identified mutant).
  • Variants from the second class have lowered their affinity for all targets, but H4334, since no binding was observed with C1234, C1221 and C4334.
  • Eight different proteins were found to belong to this class, plus a protein which sequence could not be determined.
  • sequence variants of Class II five retain the Q44 amino acid from the wild-type sequence, and one of the two arginines in position 68 or 70.
  • DSH one mutant
  • none of the amino acids from position 44, 68 and 70 has been retained.
  • Class III (4 different proteins) has a more complex pattern, as it retains apparent binding for the C1221 and H4334 target.
  • one protein (Class IV) retains only a slight binding for target C1221 as none of the other targets are bound anymore.
  • the target vectors are based on a LagoZ expression vector driven by promoter of the human EF1-alpha gene.
  • This promoter has been shown previously to have wide expression spectrum in vivo (Kim, D. W., Uetsuki, T., Kaziro, Y., Yamaguchi, N., Sugano, S, 1990, Gene, 91, 217-223).
  • the promoter region includes splice donor and acceptor sites in the 5′ untranslated region of the h-EF1-alpha gene-LagoZ is a CpG island depleted LacZ gene designed to abolish gene silencing in transgenic mice (Henry I, Forlani S, Vaillant S, Muschler J, Choulika A, Nicolas J F, 1999, C R Acad Sci III. 322, 1061-70).
  • the 3′ fragment of the LagoZ gene was first deleted (about 2000 bp) and replaced by the I-Sce I cleavage site. The 3′ fragments of different lengths were generated by digestion of the parental plasmid.
  • COS-7 and CHO-K1 cell lines from the American Type Culture Collection (ATCC) were cultured in DMEM or Ham's F12K medium respectively plus 10% fetal bovine serum.
  • ATCC American Type Culture Collection
  • DMEM fetal bovine serum
  • SSA Single Strand annealing
  • cells were seeded in 12 well-plates at a 15.10 3 cells per well one day prior transfection. Transient transfection was carried out the following day with 500 ng of DNA using the EFFECTENE transfection kit (Qiagen). Equimolar amounts of target plasmid and I-SceI expression vector were used. The next day, medium was replaced and cells were incubated for an other 72 hours.
  • Cell monolayers were fixed in 0.5% glutaraldehyde in 100 mM PBS containing 1 mM MgCl 2 at 4° for 10 minutes. After one wash with detergent solution (100 mM PBS, 1 mM MgCl 2 , 0.02% Nonidet p-40) cells were incubated at 37° in X-Gal stain solution (10 mM PBS, 1 mM MgCl 2 , 150 mM NaCl, 33 mM K 4 Fe(CN) 6 .3H 2 O, 33 mM K 3 Fe(CN) 6 , 0.1% X-Gal) until color development.
  • X-Gal stain solution 10 mM PBS, 1 mM MgCl 2 , 150 mM NaCl, 33 mM K 4 Fe(CN) 6 .3H 2 O, 33 mM K 3 Fe(CN) 6 , 0.1% X-Gal
  • Beta-galactosidase activity was also measured in cell extracts with o-nitrophenyl- ⁇ -D-galactopyrannoside (ONPG) as a substrate.
  • Cell monolayers were washed once with PBS.
  • Cells were then lysed with 10 mM Tris pH 7.5, 150 mM NaCl, 1% Triton X-100, protease inhibitors. After 30 minutes incubation on ice, cells lysates were centrifuged and ⁇ -galactosidase was assayed.
  • ONPG o-nitrophenyl- ⁇ -D-galactopyrannoside
  • reaction buffer 10 mM PBS; pH 7.5, 1 mM MgCl 2 , 0.3% ⁇ -mercaptoethanol
  • reaction buffer 10 mM PBS; pH 7.5, 1 mM MgCl 2 , 0.3% ⁇ -mercaptoethanol
  • the reaction was carried out at 37° and stopped with 0,5 ml of 1M NaCO 3 .
  • Optical density was measured at 415 nm.
  • Beta-galactosidase activity is calculated as relative unit normalized for protein concentration and incubation time.
  • SSA single-strand annealing
  • LagoZ codes for the ⁇ -galactosidase enzyme which can be detected by colorimetry.
  • Transient transfection with equimolar amounts of target vector and I-SceI expression vector or expression vector that doesn't express the meganuclease were carried out in CHO or COS-7 cells. The results obtained with the different constructs are presented in FIG. 12 . I-SceI induced DSBs clearly stimulate the SSA repair mechanism.
  • homology of 70 bp was sufficient to achieve nearly maximum efficiencies of induced SSA, while the level of spontaneous recombination (without I-SceI induced DSB) was minimal. With duplication of 220 bp maximum efficiency was achieved while no additional gains in SSA efficiency were observed with longer duplications. Similar results were obtained with COS-7 cells (data not shown). 70 and 220 bp of homology gave the best ratio of activity vs background. Because ⁇ -galactosidase is assayed in cell lysates and one single cell can contain several copies of the target plasmid, it is impossible to evaluate the absolute SSA efficiency by this method. Therefore direct coloration of the cellular monolayer was performed 72 hours post-transfection ( FIG. 13 ).
  • FIG. 13A Virtually no blue cells were detected in the absence of the meganuclease ( FIG. 13A ). In contrast, many ⁇ -galactosidase-positive cells are present when I-SceI is cotransfected with the target vector, demonstrating the stimulation of homologous recombination by meganuclease induced DSB. The efficiency of I-SceI induced SSA was calculated by counting the blue cells (cells where recombination has taken place) and comparing it with the number of transfected cells (cells that effectively received DNA). FIG.
  • 13B shows that 50 to 60% of the cells undergo homologous recombination when I-SceI is present along with the target vector carrying 70 or 220 bp duplications while spontaneous recombination represents less than 0.1% of the events.
  • the construct with the 70 bp and 220 bp of homology as well as the transgene were selected for the animal study.
  • Transduction of the mouse liver cells was performed by hydrodynamic tail vein injections as previously described (Zhang, G., Budker, V., Wolff, A., 1999, Human Gene Therapy, 10, 1735-1737; Liu, F., Song, Y. K., Liu, D., 1999, Gene Therapy, 6, 1258-1266).
  • This method allows efficient transduction and expression of exogenous genes in animals by administration of plasmid DNA by tail vein injection. Briefly, DNA is mixed in 1.5 to 2 ml of PBS, which represents 10% of the animal's weight. Tail vein injections are subsequently performed with a 26-gauge needle over a 5-10 sec period using sterile materials and working conditions.
  • the I-SceI expressing vector used is the pCLS 197 corresponding to the I-SceI-coding sequences (patent U.S. Pat. No. 5,474,896) under the control of the CMV promoter in a pUC backbone and is 5737 bp long.
  • OF1 mice weighing fifteen to twenty grams were obtained from Charles River Laboratories, France. A total of twenty micrograms of DNA, containing equal amounts of target vector and either an I-SceI expression or control vector, was injected into mouse tail veins.
  • the target vector contains the LagoZ gene interrupted by an I-SceI cleavage site flanked by direct repeat sequences containing 70 bp of homology.
  • Control mice were injected with a mixture of the target vector and a plasmid that does not express I-SceI.
  • mice were euthanized by cervical dislocation and X-Gal stainings of their livers were performed. Livers were dissected out of the animals in cold 1 ⁇ PBS and the lobes were cut in pieces of about one fourth a centimeter in order to allow a better access of the X-Gal in the tissue. Then liver pieces were placed in fresh cold PBS 1 ⁇ in a 12-well cell culture plate kept on ice, and fixed in 4% paraformaldehyde for 1 hour under agitation at 4° C.
  • FIG. 14 shows a magnified picture of liver collected and stained 3 days after injection. Blue dots represent cells where a defective LagoZ gene, bearing an I-SceI site flanked by a 70 bp duplication, was repaired.
  • the SSA pathway results in the deletion of one repeat and reconstitution of a functional gene. Active 3-galactosidase encoded by the LagoZ gene can then be detected by X-Gal stainings. Furthermore, no gene correction was detected in the absence of the meganuclease expression vector
  • the transgene used for the generation of transgenic founders was a BglII/NotI fragment of 5919 bp carrying the defective LagoZ gene, inactivated by a LagoZ duplication of 70 bp or 220 bp and the I-SceI cleavage site, under the control of the human elongation factor 1 alpha promoter (See FIG. 11 ).
  • Transgenic founder were generated by classical transgenesis, i.e. by microinjecting the linear and purified BglII/NotI fragment described above at 500 copies/picolitres into the male pronuclei of fertilized ova at the one-cell stage derived from the mating of B6D2 ⁇ l males and females purchased from Elevage Janvier. Microinjections were performed under a Nikon TE2000 microscope with Normarski DIC with eppendorf transferMan NK2 micromanipulators and eppendorf Femtojet 5247 micro-injector. After injections, ova were transferred to surrogate pseudopregnant B6CBAF1/J females (Elevage Janvier) for development and delivery. Transgenic mice generated by this procedure were identified by PCR and Southern Blot analysis on genomic DNA extracted from tail biopsies of F0 mice. The molecular characterization of the transgene integration was done by PCR and Southern Blot analysis.
  • the founder were mated to B6D2F1 mice in order to obtain hemizygote transgenic F1 animal.
  • Expression of the transgene was tested by performing an RT-PCR experiment on RNAs extracted from a tail biopsie from a transgenic F1 animal using Qiagen RNeasy kit (cat N o 74124). Hemizygote F1 mice were then mated to B6D2F1 mice in order to establish an F2 hemizygote transgenic strain.
  • strain 361 and 58A Two independent strains were used bearing either 220 bp or 70 bp long lagoZ gene repeated sequences. These transgenic strains are referred as strain 361 and 58A , respectively.
  • the molecular characterization of the transgene integration showed that the integration is about 5 direct repeats of the BglII/NotI transgene in 361 and 2 inverted repeats plus 5 direct repeats in 58A .
  • Hemizygote mice were identified by tail biopsies, genomic DNA extraction and PCR analysis. 361 and 58A hemizygote mice were then used for in toto I-SceI mediated-lagoZ gene repair and transgenic littermates were used as negative controls.
  • Recombinant type V adenovirus bearing the I-SceI meganuclease coding region under the control of a CMV promoter Ad.I-SceI was provided by Q BIO gene company at 1.58 10 11 infectious units concentration scored by the TCID 50 method.
  • the negative adenovirus control Ad.control was as well provided by Q BIO gene company at 3.76 10 11 infectious units concentration.
  • Recombinant type V adenovirus infections were performed by intraveinous (IV) injections in transgenic mice tail veins. Transgenic mice were weighed and anesthetized before infections by intraperitoneal injection of a mixture of Xylasin (100 mg/kg) and Ketamine (10 mg/kg).
  • IV infections were performed with 10 10 infectious units/animal in a volume of 400 ⁇ l. Infections were performed in 4 to 7 weeks-old transgenic mice. Adenovirus-infected mice and uninfected control littermates were bred in isolator untill sacrificed for ⁇ -galactosidase assays.
  • mice were sacrificed by CO 2 inhalation from 5 to 14 days-post-infections (dpi) and their organs were processed for ⁇ -galactosidase assays. About 10% of the liver (8 mm 3 ) was employed for protein extraction and the remaining 90% was used for ⁇ -galactosidase in toto X-gal assays (protocol described previously).
  • Fluorescent ⁇ -galactosidase assays were incubated at 37° C. in 96 well plate. The assays were performed in a total volume of 100 ⁇ l containing 30 ⁇ l of protein extract, 1 ⁇ M Fluorescein digalactoside (FDG, Sigma), 0.1% ⁇ -mercaptoethanol, 1 mM MgCl 2 , and 100 mM Phosphate buffer, pH 7.0. The plates were scanned on the Fuoroskan Ascent (Labsystem) at 5-minutes intervals. The ⁇ -galactosidase activity is calculated as relative unit normalized for protein concentration and incubation time.
  • mice Two 58A transgenic mice were IV-injected with 10 10 infectious units of Ad.I-SceI adenovirus in order to target a DSB in-between the 70 bp duplicated lagoZ sequences and induce the repair of the reporter gene.
  • the mice were sacrificed and several organs were dissected and analyzed by in toto X-gal assays. Blue staining was detected as dispersed cells over the entire liver of infected mouse euthanized at 5 dpi ( FIG. 15A ). No staining could be detected in the other organs tested, i.e. kidneys, spleen, heart and lungs.
  • the IV-injected mouse with 10 10 infectious units of Ad.1-SceI adenovirus exhibited more stained liver cells and more ⁇ -galactosidase activity than the IV-injected mouse with 10 9 infectious units of Ad.1-SceI adenovirus.
  • I-SceI-induced recombination could be dose dependent and that a better yield of I-SceI induced recombination could be obtained by increasing the injected-adenovirus titer.
  • the detection of I-SceI-induced genome surgery in other organs reported to be less sensitive to type V adenovirus infection should be feasible.
  • Gene correction would be the safest methodology of gene therapy. Indeed homologous recombination allows precise modification of chromosomal locus and has been widely used in cell culture. Unfortunately its efficiency is extremely low and cannot be envisioned, as it is, as a therapeutic tool. However this mechanism has been shown to be enhanced by double strand break (DSB) in the genomic target. So far, in vertebrates, the use of this technology has been limited to cell applications. This is the report for the first time of the use of DSB induced gene conversion in mammal in toto by direct injection of a mixture of meganuclease expression cassette and DNA repair matrix in the blood stream.
  • DSB double strand break
  • the system is based on the repair of a human Apo A-I transgene in mice in toto.
  • the apolipoprotein A-I (APO A-I) is the main protein constituent of high density lipoprotein (HDL) and plays an important role in HDL metabolism. High density lipoproteins have a major cardio-protective role as the principal mediator of the reverse cholesterol transport.
  • the Apo A-I gene is expressed in the liver and the protein is secreted in the blood.
  • Apo A-I deficiency in human leads to premature coronary heart disease. All together, these criteria make Apo A-I gene a good candidate for the study of meganuclease-induced gene correction.
  • the genomic sequence coding for the human Apo A-I gene was used to construct the transgene. Expression of the Apo A-I gene is driven by its own minimal promotor (328 bp) that has been shown to be sufficient to promote transgene expression in the liver (Walsh et al., J. Biol. Chem., 1989, 264, 6488-6494). Briefly, human Apo A-I gene was obtained by PCR on human liver genomic DNA (Clontech) and cloned in plasmide pUC19. The I-SceI site, containing two stop codons, was inserted by PCR at the beginning of exon 4 ( FIG. 17 ).
  • the resulting mutated gene (I-SceI-hApo A-I) encodes a truncated form of the native human APO A-I (80 residues vs. 267 amino-acids for the wild type APO A-I). All the constructs were sequenced and checked against the human Apo A-I gene sequence.
  • the EcoRI/XbaI genomic DNA fragment carrying the mutated human Apo A-I gene was used for the generation of transgenic founders. Microinjections were done into fertilized oocytes from breeding of knock out males for the mouse apo a-I gene (WT KO mice) (The Jackson Laboratory, #002055) and B6SJLF1 females (Janvier). Transgenic founder mice (F0) were identified by PCR and Southern blot analysis on genomic DNA extracted from tail. F0 were then mated to WT KO mice in order to derive I-SceI-hApo A-I transgenic lines in knock out genetic background for the endogenous murine apo a-I gene. A total of seven independent transgenic lines were studied. The molecular characterization of transgene integration was done by Southern blot experiments.
  • transgene expression in each transgenic line was performed by RT-PCR on total RNA extracted from the liver (Trizol Reagent, Invitrogen).
  • primers specific for the human transgenic I-SceI-hApo A-I cDNA oligonucleotides E and F, FIG. 17 . Actin primers were used as an internal control.
  • Transduction of transgenic mouse liver cells in toto was performed by hydrodynamic tail vein injection as previously described (Zhang et al., 1999, Human Gene Therapy, 10, 1735-1737). 10 to 20 g animals were injected with circular plasmid DNA in a volume of one tenth their weight in PBS in less than 10 seconds.
  • a mixture of 20 or 50 ⁇ g of a plasmid coding for I-SceI under the control of the CMV promoter and the same amount of a plasmid carrying the DNA repair matrix (2 kbp or 1.5 kbp as depicted in FIG. 17 ).
  • the correction of the transgene in mice after injection of the I-SceI expression cassette and DNA repair matrix was analyzed by nested PCR on total liver RNA reverse transcribed using random hexamers.
  • primers sets that specifically amplified the repaired transgene. The specificity was achieved by using reverse oligonucleotides spanning the I-SceI site, forward being located outside the repair matrix (oligonucleotides G and H in the first PCR and E and I in the nested one, FIG. 17 ). Actin primers were used as an internal control.
  • mice were injected with either a mixture of 1-SceI-expressing vector and DNA repair matrix or with a vector carrying both I-SceI-expressing cassette and the DNA repair matrix.
  • the repair of the mutated human Apo A-I gene was monitored by RT-PCR on total liver RNA ( FIG. 18 ) using primers specifically designed to pair only with the corrected human Apo A-I gene ( FIG. 17 ).
  • RT-PCR was performed on non- or injected transgenic mice or injected with I-SceI expressing vector alone or the DNA repair matrix alone. No gene correction could be detected with these experimental conditions.
  • mice injected with either a mixture of I-SceI-expressing vector and DNA repair matrix or with a vector carrying both I-SceI-expressing cassette and the DNA repair matrix did not reveal any PCR-amplified DNA fragment.
  • PCR fragments were specifically visualized in transgenic mice where I-SceI-expressing cassette and the DNA repair matrix were injected ( FIG. 18 ).
  • the gene correction was detectable in all the transgenic lines tested containing one or several copies of the transgene (Table 5).
  • NI non-injected mice
  • WT wild type mice
  • I-SceI vector carrying the I-SceI expression cassette
  • RM A vector containing the 2 kbp repair matrix
  • RM B vector containing the 1.5 kbp repair matrix
  • I-SceI-RM A I-SceI expression cassette and the 2 kbp repair matrix in the same vector.
  • I-SceI- ISceI RM A RM B Line I-SceI/RM A I-SceI/RM B RM A Total alone alone alone NI 14A 3/3 2/2 6/6 11/11 0/2 0/1 0/2 0/6 100% 14B 4/4 0/1 1/3 5/8 0/1 0/3 62% 21 2/6 1/1 0/1 3/8 0/2 0/2 0/1 0/6 37% 66 2/2 2/2 0/1 100% 95 0/3 1/4 1/7 0/4 14% Total 22/36 61% WT 0/6 0/1 0/8 0/4 0/1

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US13/021,473 US20110151539A1 (en) 2003-01-28 2011-02-04 Use of meganucleases for inducing homologous recombination ex vivo and in toto in vertebrate somatic tissues and application thereof
US13/152,961 US8530214B2 (en) 2003-01-28 2011-06-03 Use of meganucleases for inducing homologous recombination ex vivo and in toto in vertebrate somatic tissues and application thereof
US13/485,486 US20120331574A1 (en) 2003-01-28 2012-05-31 Use of meganucleases for inducing homologous recombination ex vivo and in toto in vertebrate somatic tissues and application thereof
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