# Patent

## Title
Methods and compositions for gene correction

## Abstract

Disclosed herein are methods and compositions for correction and/or mutation of genes associated with Parkinson's Disease as well as clones and animals derived therefrom.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
The present application claims the benefit of U.S. Provisional Application Nos. 61/460,686, filed Jan. 5, 2011 and 61/517,478, filed Apr. 20, 2011, the disclosures of which are hereby incorporated by reference in their entireties.


TECHNICAL FIELD
The present disclosure is in the fields of genome editing.
BACKGROUND
Parkinson's disease (PD) is a neurodegenerative disease that afflicts approximately 4-6 million people worldwide. In the United States, approximately one to two hundred people per 100,000 have PD. Interestingly, the prevalence among Amish people is approximately 970 per 100,000 although the basis for this high rate, be it genetic or environmental, is not known. The prevalence of PD increases in the older population, with approximately 4% of people over the age of 80 suffering from this disease (Davie (2008) Brit Med Bull 86(1) p. 109), although 10% of patients are under 40 years of age (Kumari (2009) FEBS J 276(22) p. 6455).
Typically a patient diagnosed with PD is identified by several hallmark physical behaviors: bradykinesia, rigidity and rest tremor. Often these physical symptoms are asymmetric. Within the brain, PD is characterized by a progressive and profound loss of neuromelanin-containing dopaminergic neurons in the substantia nigra pars compacta with the presence of eosinophillic, intracytoplasmic and proteinaceous inclusions termed Lewy bodies in the surviving neurons (Davie, ibid and Kumari, ibid). By the time of death, this region will have lost 50-70% of its neurons as compared to an individual without PD.
Lewy bodies are α-synuclein reactive inclusions that are made up of made of several neurofilament proteins combined with proteolytic enzymes. Lewy bodies are found in PD, and a variant of dementia called Dementia with Lewy Bodies, but are not observed in any other neurological diseases.
It appears to have many factors can play a role in disease onset and/or progression of PD. In particular, genes including α-synuclein (PARK1/PARK4, SCNA), parkin (PARK 2), PARK 3, ubiquitin carboxy-terminal hydrolyase L1 (PARK5) etc.) and environmental factors such as exposure to heavy metals and certain pesticides are believed to contribute to PD.
Additionally, genetic mutations in the leucine rich repeat kinase 2 gene (LRRK2, also known as PARK8) has been identified to be involved in both familial and sporatic forms of PD. In fact, studies suggest that LRRK2 mutations may be responsible for between 5 and 13% of familial PD, and from 1 to 5% of sporadic PD. The protein itself is a large (>280 kD) multidomain protein containing the following known domains: armadillo (ARM), ankryn (ANK), LRR, Ras of complex proteins (ROC), C-terminal of ROC (COR), mitogen-activated protein kinase kinase kinase and WD40. Thus, LRRK2 contains several protein-protein interactive domains (ARM/ANK, LRR and WD40) suggesting that LRRK2 plays a role in protein complex formation (Kumari, ibid). Several clusters of mutations have been identified which fall across its length of the gene, with the majority of pathological mutations clustering in the enzymatic domains of the protein.
Specifically, the LRRK2 mutation G2019S has been suggested to play an important role in PD in some ethnicities. Although prevalence among Asians, South Africans and some Europeans (of Polish, Greek and German descent) is quite low, among Ashkenazi Jews and North African Arabs, the prevalence is from 37-40%. In the US and the rest of Europe, G2019S accounts for approximately 1-7% of familial PD and 1-3% of sporadic PD in Caucasians (Kumari, ibid). The mutation is autosomal dominant and the lifetime penetrance for the mutation has been estimated at 31.8%. The SNP responsible for this missense mutation in patients is annotated as rs34637584 in the human genome, and is a G to A substitution at the genomic level (6055G>A). The G2019S mutation has been shown to increase LRRK2 kinase activity, and is found in the within the activation domain of the protein (Luzon-Toro, (2007) Hum Mol Genet 16(17) p. 2031).
The α-synuclein protein is an 140 amino acid protein comprising three domains: an N-terminal amphipathic domain comprising repeats of KTKEGV (SEQ ID NO: 51), a central hydrophobic, non-amyloid domain, and an acidic C-terminal domain. Increased gene dosage of α-synuclein has been shown to be in and of itself, a toxic event that leads to PD. Gene duplications of α-synuclein, which lead to increased gene expression, causes rare cases Of autosomal dominant PD. The function of the α-synuclein gene (SNCA) in a wild type setting is still unclear, but it appears that it plays a role in the regulation of autophagy (Winslow and Rubensztein (2010, online publication) Autophagy 7:4, p 1-3). It appears that overexpression of the protein inhibits the secretory pathway by a loss of function of the Rabla protein which is involved in autophagasome formation at a very early stage of the autophagy process. This in turn may lead to the cellular pathologies observed in PD: abnormal protein aggregation, mitochondrial abnormalities, increased levels of reactive oxygen species and increased sensitivity to cell death (Winslow and Rubensztein ibid).
In addition to increased gene dosage of the wild type SCNA gene, three mutations have been found which are also associated with PD. The three mutations, A53T, A30P, and E46K are all localized in the N-terminal domain of the protein, and appear to exacerbate toxic fibril formation (Perkevi et al (2009) The Anatomical Record 292 (12): 1893). However, cellular and transgenic animal models expressing such mutants only partially recapitulate PD pathology. See, Dawson et al. (2010) Neuron 66(5):646-61. Individuals with PD caused by α-synuclein mutation have similar clinical and pathological features of their PD as patients with idiopathic PD, however the onset of symptoms occurs significantly than typically seen with other PD patients (Pankratz and Foroud (2004) Am Soc Exp Neu Ther 1:235-242).
Thus, there remains a need for the development of novel anti-PD strategies to model and treat PD based on investigation of LRRK2 and SCNA mutations.
SUMMARY
Disclosed herein are methods and compositions for generating models for studying the function of PD-related genes, models for PD drug discovery and for treating PD. In particular, methods and compositions for altering PD related genetic loci such as SCNA and LRRK2 are described. The compositions and methods described herein can be used for genome editing, including, but not limited to: cleaving of one or more genes in an animal cell resulting in targeted alteration (insertion, deletion and/or substitution mutations) in one or more genes, including the incorporation of these targeted alterations into the germline; targeted introduction of non-endogenous nucleic acid sequences, the partial or complete inactivation of one or more genes in an animal; methods of inducing homology-directed repair; and generation of transgenic animals (e.g., rodents and non-human primates).
In one aspect, described herein is a zinc-finger protein (ZFP) that binds to target site in a LRRK2 or SCNA gene in a genome, wherein the ZFP comprises one or more engineered zinc-finger binding domains. In one embodiment, the ZFP is a zinc-finger nuclease (ZFN) that cleaves a target genomic region of interest, wherein the ZFN comprises one or more engineered zinc-finger binding domains and a nuclease cleavage domain or cleavage half-domain. Cleavage domains and cleavage half domains can be obtained, for example, from various restriction endonucleases and/or homing endonucleases. In one embodiment, the cleavage half-domains are derived from a Type IIS restriction endonuclease (e.g., Fok I). In certain embodiments, the zinc finger domain recognizes a target site in a LRRK2 or SCNA gene.
The ZFN may bind to and/or cleave a LRRK2 or SCNA gene within the coding region of the gene or in a non-coding sequence within or adjacent to the gene, such as, for example, a leader sequence, trailer sequence or intron, or within a non-transcribed region, either upstream or downstream of the coding region.
In another aspect, described herein is a TALE protein (Transcription activator like) that binds to target site in a LRRK2 or SCNA gene in a genome, wherein the TALE comprises one or more engineered TALE binding domains. In one embodiment, the TALE is a nuclease (TALEN) that cleaves a target genomic region of interest, wherein the TALEN comprises one or more engineered TALE DNA binding domains and a nuclease cleavage domain or cleavage half-domain. Cleavage domains and cleavage half domains can be obtained, for example, from various restriction endonucleases and/or homing endonucleases. In one embodiment, the cleavage half-domains are derived from a Type IIS restriction endonuclease (e.g., Fok I). In certain embodiments, the TALE DNA binding domain recognizes a target site in a LRRK2 or SCNA gene.
The TALEN may bind to and/or cleave a LRRK2 or SCNA gene within the coding region of the gene or in a non-coding sequence within or adjacent to the gene, such as, for example, a leader sequence, trailer sequence or intron, or within a non-transcribed region, either upstream or downstream of the coding region.
In another aspect, described herein are compositions comprising one or more of the zinc-finger or TALE nucleases described herein. In certain embodiments, the composition comprises one or more zinc-finger or TALE nucleases in combination with a pharmaceutically acceptable excipient.
In another aspect, described herein is a polynucleotide encoding one or more ZFNs or TALENs described herein. The polynucleotide may be, for example, mRNA.
In another aspect, described herein is a ZFN or TALEN expression vector comprising a polynucleotide, encoding one or more ZFNs or TALENs described herein, operably linked to a promoter.
In another aspect, described herein is a host cell comprising one or more ZFN or TALEN expression vectors. The host cell may be stably transformed or transiently transfected or a combination thereof with one or more ZFP or TALEN expression vectors. In one embodiment, the host cell is an embryonic stem cell. In other embodiments, the one or more ZFP or TALEN expression vectors express one or more ZFNs or TALENs in the host cell. In another embodiment, the host cell may further comprise an exogenous polynucleotide donor sequence. In any of the embodiments, described herein, the host cell can comprise an embryo cell, for example a one or more mouse, rat, rabbit or other mammal cell embryo (e.g., a non-human primate).
In another aspect, described herein is a method for cleaving one or more LRRK2 or SCNA genes in a cell, the method comprising: (a) introducing, into the cell, one or more polynucleotides encoding one or more ZFNs or TALENs that bind to a target site in the one or more genes under conditions such that the ZFN(s) is (are) or TALENs is (are) expressed and the one or more genes are cleaved.
In another embodiment, described herein is a method for modifying one or more LRRK2 or SCNA gene sequence(s) in the genome of cell, the method comprising (a) providing a cell comprising one or more LRRK2 or SCNA sequences; and (b) expressing first and second zinc-finger nucleases (ZFNs) or TALENs in the cell, wherein the first ZFN or TALEN cleaves at a first cleavage site and the second ZFN or TALEN cleaves at a second cleavage site, wherein the gene sequence is located between the first cleavage site and the second cleavage site, wherein cleavage of the first and second cleavage sites results in modification of the gene sequence by non-homologous end joining and/or homology directed repair. Optionally, the cleavage results in insertion of an exogenous sequence (transgene) which also has been introduced into the cell. In certain embodiments, the exogenous sequence comprises a marker, for example a selectable marker (e.g., antibiotic resistance) and/or a recombinase site (e.g., a Cre-recombinase site such as loxP). In other embodiments, the exogenous sequence does not include a reporter (e.g., selection marker). In still other embodiments, non-homologous end joining results in a deletion between the first and second cleavage sites. The size of the deletion in the gene sequence is determined by the distance between the first and second cleavage sites. Accordingly, deletions of any size, in any genomic region of interest, can be obtained. Deletions of 1, 5, 10, 25, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1,000 nucleotide pairs, or any integral value of nucleotide pairs within this range, can be obtained. In addition deletions of a sequence of any integral value of nucleotide pairs greater than 1,000 nucleotide pairs can be obtained using the methods and compositions disclosed herein. Using these methods and compositions, constructs encoding mutant LRRK2 or SCNA proteins may be developed that lack one or more of the known domains. These constructs can then be used to study the function of the protein within a cell and/or animal.
In another aspect, specific mutations associated with PD can be corrected to understand the function of the gene that harbors the mutation, and/or to discover phenotypes associated with the correction of the mutant gene. Such an understanding then can be used to design cells, cell lines and transgenic animals for use in drug screening and drug discovery.
In another aspect, site specific mutations in a gene associated with PD can be constructed to model known or novel mutations. For example, the A53T, A30P, and E46K mutations in SCNA can be constructed to develop a cell, cell line, primary cell, or transgenic animal bearing these mutations, either as single mutations or in combination. The G2019S mutation in LRRK2 can be similarly constructed in a cell, cell line, primary cell or transgenic animal. In one embodiment, a cell, cell line or transgenic animal carrying a heterozygous genotype for the selected gene is constructed, while in another embodiment, a homozygous cell, cell line or transgenic animal is made carrying two mutant copies in both alleles of a desired locus. The sequences encoding the PD-related mutation(s) may be integrated into any wild-type gene (e.g., the wild-type gene corresponding to the mutant sequence such as a mutant SCNA into a wild-type SCNA gene) or into any mutant gene. In a further embodiment, a cell, cell line or transgenic animal is made comprising two or more mutations in genes associated with PD at separate loci, (e.g. LRRK2 and SCNA) and these cells, cell lines or transgenic animals may be heterozygous for a mutation in each loci, homozygous and all combinations thereof.
In another aspect, described herein are methods of inactivating a LRRK2 or SCNA gene in a cell by introducing one or more proteins, polynucleotides and/or vectors into the cell as described herein. In any of the methods described herein the ZFNs or TALENs may induce targeted mutagenesis, targeted deletions of cellular DNA sequences, and/or facilitate targeted recombination at a predetermined chromosomal locus. Thus, in certain embodiments, the ZFNs or TALENs delete or insert one or more nucleotides of the target gene. In some embodiments the LRRK2 or SCNA gene is inactivated by ZFN or TALEN cleavage followed by non-homologous end joining (NHEJ). In other embodiments, a genomic sequence in the target gene is replaced, for example using a ZFN or TALEN (or vector encoding said ZFN or TALEN) as described herein and a “donor” sequence that is inserted into the gene following targeted cleavage with the ZFN or TALEN. Thus, also provided by the invention is a donor nucleic acid, which can comprise a transgene or sections thereof, or regions of homology with genome flanking the nuclease cleavage site, or nucleic acid sequences relating to gene elements such as promoter sequences and the like. The donor sequence may be present in the ZFN or TALEN vector, present in a separate vector (e.g., Ad or LV vector) or, alternatively, may be introduced into the cell using a different nucleic acid delivery mechanism. In one aspect, the donor sequence causes a known mutation, e.g., A53T, A30P, and E46K alterations in the SCNA protein or the G2019S mutation in the LRRK2 protein. In other aspects, other well known LRRK2 mutation proteins can be constructed through gene modification (e.g. G2385R, R1441C, R1628P and others known in the art).
In another aspect, described herein are methods of correcting a LRRK2 or SCNA gene in a cell by introducing one or more proteins, polynucleotides and/or vectors into the cell as described herein. In any of the methods described herein the ZFNs or TALENs may induce targeted mutagenesis, targeted deletions of cellular DNA sequences, and/or facilitate targeted recombination at a predetermined chromosomal locus. Thus, in certain embodiments, the ZFNs or TALENs delete or insert one or more nucleotides of the target gene. In some embodiments the SCNA gene is corrected by ZFN or TALEN cleavage followed by non-homologous end joining (NHEJ). In other embodiments, a genomic sequence in the target gene is replaced, for example using a ZFN or TALEN (or vector encoding said ZFN or TALEN) as described herein and a “donor” sequence that is integrated into the gene following targeted cleavage with the ZFN or TALEN correcting the sequence of the LRRK2 or SCNA gene. The donor sequence may be present in the ZFN or TALEN vector, present in a separate vector (e.g., Ad or LV vector) or, alternatively, may be introduced into the cell using a different nucleic acid delivery mechanism. In one aspect, the donor sequence corrects a known mutation, e.g., A53T, A30P, and E46K alterations in the SCNA protein or the alteration of an adenine or ‘A’ guanine to ‘G’ at position 6055 in a mutant LRRK2 gene to cause the correction of the G2019S mutation. In other aspects, other well known LRRK2 mutation proteins can be corrected through gene modification (e.g. G2385R, R1441C, R1628P and others known in the art).
In some aspects, the cell is a stem cell. Specific stem cell types that may used with the methods and compositions of the invention include embryonic stem cells (ESC), hematopoietic stem cells, nerve stem cells, skin stem cells, muscle stem cells and induced pluripotent stem cells (iPSCs). To investigate the multi-gene aspect of PD, the methods and compositions of the invention can be used in stem cells, e.g. ESC, derived from a variety of differing host cell genetic backgrounds (e.g. differing ethnicities, etc). iPSCs can be derived from patient samples and from normal controls wherein the patient derived iPSCs can be mutated to normal gene sequence at the gene of interest, or normal cells can be altered to the known disease allele at the gene of interest. Panels of these iPSCs can be used to create isogenic cells with both patient and normal cells carrying one or more mutations at their endogenous loci. These cells can be used to create cell lines and/or transgenic animals bearing several mutations of interest to study multigene affects of disease severity and possible therapeutic treatments. Other cell types that may be used for these studies are patient derived fibroblasts.
In yet another aspect, described herein is a method for germline disruption of one or more target LRRK2 or SCNA genes, the method comprising modifying one or more LRRK2 or SCNA sequences in the genome of one or more cells of an embryo by any of the methods described herein and allowing the embryo to develop, wherein that the modified gene sequences are present in at least a portion of gametes of the sexually mature animal. In certain embodiments, the animal is a small mammal, such as a rodent or rabbit. In some embodiments, the animal is a non-human primate.
In another aspect, described herein is a method of creating one or more heritable mutant alleles in at least one LRRK2 or SCNA locus of interest, the method comprising modifying one or more LRRK2 or SCNA loci in the genome of one or more cells of an animal embryo by any of the methods described herein; raising the embryo to sexual maturity; and allowing the sexually mature animal to produce offspring; wherein at least some of the offspring comprise the mutant alleles. In certain embodiments, the animal is a small mammal, for example a rabbit or a rodent such as rat, a mouse or a guinea pig. In other embodiments, the animal is a non-human primate.
In any of the methods described herein, the polynucleotide encoding the zinc finger nuclease(s) or TALEN(s) can comprise DNA, RNA or combinations thereof. In certain embodiments, the polynucleotide comprises a plasmid. In other embodiments, the polynucleotide encoding the nuclease comprises mRNA.
In a still further aspect, provided herein is a method for site specific integration of a nucleic acid sequence into a LRRK2 or SCNA locus of a chromosome. In certain embodiments, the method comprises: (a) injecting an embryo with (i) at least one DNA vector, wherein the DNA vector comprises an upstream sequence and a downstream sequence flanking the nucleic acid sequence to be integrated, and (ii) at least one RNA molecule encoding a zinc finger or TALE nuclease that recognizes the site of integration in the LRRK2 or SCNA locus, and (b) culturing the embryo to allow expression of the zinc finger or TALE nuclease, wherein a double stranded break introduced into the site of integration by the zinc finger nuclease or TALEN is repaired, via homologous recombination with the DNA vector, so as to integrate the nucleic acid sequence into the chromosome.
Suitable embryos may be derived from several different vertebrate species, including mammalian, bird, reptile, amphibian, and fish species. Generally speaking, a suitable embryo is an embryo that may be collected, injected, and cultured to allow the expression of a zinc finger or TALE nuclease. In some embodiments, suitable embryos may include embryos from small mammals (e.g., rodents, rabbits, etc.), companion animals, livestock, and primates. Non-limiting examples of rodents may include mice, rats, hamsters, gerbils, and guinea pigs. Non-limiting examples of companion animals may include cats, dogs, rabbits, hedgehogs, and ferrets. Non-limiting examples of livestock may include horses, goats, sheep, swine, llamas, alpacas, and cattle. Non-limiting examples of primates may include capuchin monkeys, chimpanzees, lemurs, macaques, marmosets, tamarins, spider monkeys, squirrel monkeys, and vervet monkeys. In other embodiments, suitable embryos may include embryos from fish, reptiles, amphibians, or birds. Alternatively, suitable embryos may be insect embryos, for instance, a Drosophila embryo or a mosquito embryo.
Also provided is an embryo comprising at least one DNA vector, wherein the DNA vector comprises an upstream sequence and a downstream sequence flanking the nucleic acid sequence to be integrated, and at least one RNA molecule encoding a zinc finger nuclease that recognizes the chromosomal site of integration. Organisms derived from any of the embryos as described herein are also provided.
In another aspect provided by the methods and compositions of the invention is the use of cells, cell lines and transgenic animals in the screening of drug libraries and/or other therapeutic compositions (i.e., antibodies, structural RNAs, etc.) for use in treatment of an animal afflicted with PD. Such screens can begin at the cellular level with manipulated cell lines or primary cells, and can progress up to the level of treatment of a whole animal.
A kit, comprising the ZFPs or TALENs of the invention, is also provided. The kit may comprise nucleic acids encoding the ZFPs or TALENs, (e.g. RNA molecules or ZFP or TALEN encoding genes contained in a suitable expression vector), donor molecules, suitable host cell lines, instructions for performing the methods of the invention, and the like.
These and other aspects will be readily apparent to the skilled artisan in light of disclosure as a whole.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 depicts a gel showing the results of a Cel-I mismatch assay on K562 cells treated with ZFNs targeting the LRRK2 gene. All samples were ZFN pairs where one member of the pair is always the ZFN SBS 27870. The lanes show the results where the other member of the ZFN pair was varied. The Cel-I assay (SurveyorTM, Transgenomic) identifies mismatches in a DNA sequence that occur as a result of cleavage followed by repair of the DSB by the NHEJ cellular machinery. In the NHEJ process, small insertions and deletions are often observed (indels), and these create the mismatches identified in the Cel-I assay. At the bottom of each lane is shown the percent of the sequences that display some amount of NHEJ-caused indels at the targeted location. The arrow indicates the band observed from the cleavage by the SurveyorTM enzyme of the mismatch bubble.
FIG. 2 shows a gel wherein screening of ZFNs directed against nucleotide base 209 in exon 3 of human alpha-synuclein (SNCA) was performed. The indicated ZFN pairs were transiently transfected into K562 cells, genomic DNA was isolated 48 hrs later, and the frequency of target locus disruption was measured by the Surveyor/Cel-1 assay. The frequency of gene disruption of the most efficient ZFN pairs is indicated below each lane.
FIG. 3 shows a gel depicting results of an experiment designed to knock in the 6055G>A mutation to create the G2019S allele in the LRRK2 gene. In this experiment, ZFNs and donor plasmid containing the sequence for the mutated allele were nucleofected into K562 cells. The DNA was isolated, and a PCR reaction was performed to amplify the region around the mutant locus. The product was then digested with SfcI, and run on a gel. The presence of the mutation results in a faster migrating band as described above. The faster migrating band is indicated with an arrow while the wild type band is indicated with an open triangle.
FIG. 4, panels A and B, are gels depicting the results of an experiment designed to knock in the synuclein G209A mutation (encoding the PD-associated A53T mutation in the SCNA protein) in K562 cells. FIG. 4A shows a gel containing the results of a Tsp45I digest. The introduction of the G209G mutation in the DNA creates a Tsp45I restriction site. In the gel, in the presence of both donor and ZFNs, incorporation of the mutation sequence does occur as demonstrated by the percent of alleles that are now sensitive to the Tsp45I enzyme. FIG. 4B depicts the results of a Cel-I assay (described above) performed on these same samples and demonstrates that the ZFN pair was active because indels are observed in all samples tested that were treated with ZFNs.
FIG. 5 is a schematic depicting the genomic α-synuclein locus (SNCA) and the targeting strategy showing exons (blue boxes), restriction sites and location of external and internal southern blot probes (red bars). Enlarged sequence (SEQ ID NO: 52) indicates ZFNs induced cut site at base 209 in exon 3 of α-synuclein (red base pair) and insertion site of loxP-site-flanked pGK-puro selection cassette (red box). Shown below is a schematic of the donor plasmid design for either normal selection (Syn-A53T-loxP-pGK-puro-loxP) or positive-negative selection (Syn-A53T-loxP-pGK-puro-loxP-HSV-TK-DT-A) and targeted genomic locus before and after Cre-excision of the selection cassette. The donor plasmids comprise  ̃600 bp homology on each side of the ZFN cut. pGK-promoter, phosphoglycerol kinase promoter; puro, puromycin resistance gene; pGKpolyA, polyadenylation sequence; HSV-TK, herpes simplex virus thymidine kinase; pGK-DT-A-pA, diphteria toxin A-chain.
FIG. 6 is a schematic depicting the genomic α-synuclein (SNCA) locus and the targeting strategy showing exons (blue boxes), restriction sites and location of internal southern blot probe (red bars). Enlarged sequence (SEQ ID NO: 52) indicates ZFNs induced cut site at base 209 in exon3 of α-synuclein (red base pair). Shown below is a schematic of donor plasmid design and targeted genomic locus for either insertion (Donor-A53T) or correction (wild-type Donor) of A53T (G209A) α-synuclein mutation. The donor plasmids contain  ̃1 kb homology to the targeting site.
FIG. 7, panels A and B, depict the results of a SELEX assay designed to demonstrate the target sequence binding preference for a given zinc finger protein. In these diagrams, the binding results for each base of the expected target sequence is shown above the horizontal line, while the binding results for each position to other bases is shown below the line. The larger the block of each base type (A, C, G or T), the greater the preference for that base. FIG. 7A depicts the results using the 27870 ZFN and FIG. 7B depicts the results using the 30888 ZFN. The nucleotide base in both panels indicated by the arrows is position 6055, and the data demonstrates that the 27870 ZFN prefers binding to G at this position while 30888 prefers to bind to A.
FIG. 8 depicts gels demonstrating the percent of gene modification in K562 cells by the Cel I assay described above using the 30885/88 or the 27866/70 ZFN pairs. Both pairs are able to elicit gene modification at the target in the range of 14-28 percent (“% NHEJ). This assay was carried out in both the standard (37°) and transient hypothermic (30°) conditions.



DETAILED DESCRIPTION
Disclosed herein are compositions and methods for treating and/or developing models useful in the treatment of PD. In particular, nuclease-mediated cleavage and integration is used to create or repair known mutations in the LRRK2 or SCNA gene. These compositions and methods can be used to correct or create specific LRRK2 or SCNA mutations in any selected genetic background to allow for study of multifactorial interaction in PD. The invention can be used to create isogenic panels of a set of mutations in LRRK2 or SCNA to allow for controlled study of these mutations, to investigate the link between a certain mutation and cellular dysfunction and to identify phenotypes associated with the mutation or with the correction of the mutation. In addition, any LRRK2 or SCNA mutation can be introduced into patient derived cells, e.g. patient derived induced pluripotent stem cells, to investigate the affects of a certain mutation in a patient cell background. In addition, creation of LRRK2 or SCNA mutants with in-frame alterations is also part of the invention described herein, to allow for fine tuned analysis of the functional domains of this protein. In addition, LRRK2 or SCNA mutations associated with PD can be created within the native gene in model animals (rat, non-human primate, etc.) to generate PD models. These animals may contain one or more inserted LRRK2 or SCNA mutations.
Also described herein are methods and compositions for altering specific LRRK2 or SCNA defects in patient cells. For example, mutated LRRK2 or SCNA genes may be knocked out by use of specific nucleases that will only act on mutant alleles and not act on a wild type gene sequence. Knock out of a specific gene may be a result of cleavage followed by NHEJ, or by cleavage at two loci within the gene to delete a large portion of the gene, or by cleavage followed by targeted integration of an oligonucleotide or larger donor DNA. Alternatively, specific LRRK2 or SCNA mutations in patient cells may be corrected using the methods and compositions of the invention. These corrected cells may then be re-introduced into the patient for treatment of the disease.
General
Practice of the methods, as well as preparation and use of the compositions disclosed herein employ, unless otherwise indicated, conventional techniques in molecular biology, biochemistry, chromatin structure and analysis, computational chemistry, cell culture, recombinant DNA and related fields as are within the skill of the art. These techniques are fully explained in the literature. See, for example, Sambrook et al. MOLECULAR CLONING: A LABORATORY MANUAL, Second edition, Cold Spring Harbor Laboratory Press, 1989 and Third edition, 2001; Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, 1987 and periodic updates; the series METHODS IN ENZYMOLOGY, Academic Press, San Diego; Wolfe, CHROMATIN STRUCTURE AND FUNCTION, Third edition, Academic Press, San Diego, 1998; METHODS IN ENZYMOLOGY, Vol. 304, “Chromatin” (P. M. Wassarman and A. P. Wolffe, eds.), Academic Press, San Diego, 1999; and METHODS IN MOLECULAR BIOLOGY, Vol. 119, “Chromatin Protocols” (P. B. Becker, ed.) Humana Press, Totowa, 1999.
DEFINITIONS
The terms “nucleic acid,” “polynucleotide,” and “oligonucleotide” are used interchangeably and refer to a deoxyribonucleotide or ribonucleotide polymer, in linear or circular conformation, and in either single- or double-stranded form. For the purposes of the present disclosure, these terms are not to be construed as limiting with respect to the length of a polymer. The terms can encompass known analogues of natural nucleotides, as well as nucleotides that are modified in the base, sugar and/or phosphate moieties (e.g., phosphorothioate backbones). In general, an analogue of a particular nucleotide has the same base-pairing specificity; i.e., an analogue of A will base-pair with T.
The terms “polypeptide,” “peptide” and “protein” are used interchangeably to refer to a polymer of amino acid residues. The term also applies to amino acid polymers in which one or more amino acids are chemical analogues or modified derivatives of corresponding naturally-occurring amino acids.
“Binding” refers to a sequence-specific, non-covalent interaction between macromolecules (e.g., between a protein and a nucleic acid). Not all components of a binding interaction need be sequence-specific (e.g., contacts with phosphate residues in a DNA backbone), as long as the interaction as a whole is sequence-specific. Such interactions are generally characterized by a dissociation constant Kd) of 10−6 M−1 or lower. “Affinity” refers to the strength of binding: increased binding affinity being correlated with a lower Kd.
A “binding protein” is a protein that is able to bind non-covalently to another molecule. A binding protein can bind to, for example, a DNA molecule (a DNA-binding protein), an RNA molecule (an RNA-binding protein) and/or a protein molecule (a protein-binding protein). In the case of a protein-binding protein, it can bind to itself (to form homodimers, homotrimers, etc.) and/or it can bind to one or more molecules of a different protein or proteins. A binding protein can have more than one type of binding activity. For example, zinc finger proteins have DNA-binding, RNA-binding and protein-binding activity.
A “zinc finger DNA binding protein” (or binding domain) is a protein, or a domain within a larger protein, that binds DNA in a sequence-specific manner through one or more zinc fingers, which are regions of amino acid sequence within the binding domain whose structure is stabilized through coordination of a zinc ion. The term zinc finger DNA binding protein is often abbreviated as zinc finger protein or ZFP.
Zinc finger binding domains or TALEN can be “engineered” to bind to a predetermined nucleotide sequence, for example via engineering (altering one or more amino acids) of the recognition helix region of a naturally occurring zinc finger or by engineering the RVDs of a TALEN protein. Therefore, engineered zinc finger proteins or TALENs are proteins that are non-naturally occurring. Non-limiting examples of methods for engineering zinc finger or TALEN proteins are design and selection. A designed zinc finger or TALEN protein is a protein not occurring in nature whose design/composition results principally from rational criteria. Rational criteria for design include application of substitution rules and computerized algorithms for processing information in a database storing information of existing ZFP designs and binding data. See, for example, U.S. Pat. Nos. 6,140,081; 6,453,242; and 6,534,261; see also WO 98/53058; WO 98/53059; WO 98/53060; WO 02/016536 and WO 03/016496.
A “selected” zinc finger or TALEN protein is a protein not found in nature whose production results primarily from an empirical process such as phage display, interaction trap or hybrid selection. See e.g., U.S. Pat. No. 5,789,538; U.S. Pat. No. 5,925,523; U.S. Pat. No. 6,007,988; U.S. Pat. No. 6,013,453; U.S. Pat. No. 6,200,759; WO 95/19431; WO 96/06166; WO 98/53057; WO 98/54311; WO 00/27878; WO 01/60970 WO 01/88197 and WO 02/099084.
“Recombination” refers to a process of exchange of genetic information between two polynucleotides. For the purposes of this disclosure, “homologous recombination (HR)” refers to the specialized form of such exchange that takes place, for example, during repair of double-strand breaks in cells via homology-directed repair mechanisms. This process requires nucleotide sequence homology, uses a “donor” molecule to template repair of a “target” molecule (i.e., the one that experienced the double-strand break), and is variously known as “non-crossover gene conversion” or “short tract gene conversion,” because it leads to the transfer of genetic information from the donor to the target. Without wishing to be bound by any particular theory, such transfer can involve mismatch correction of heteroduplex DNA that forms between the broken target and the donor, and/or “synthesis-dependent strand annealing,” in which the donor is used to re-synthesize genetic information that will become part of the target, and/or related processes. Such specialized HR often results in an alteration of the sequence of the target molecule such that part or all of the sequence of the donor polynucleotide is incorporated into the target polynucleotide.
In the methods of the disclosure, one or more targeted nucleases as described herein create a double-stranded break in the target sequence (e.g., cellular chromatin) at a predetermined site, and a “donor” polynucleotide, having homology to the nucleotide sequence in the region of the break, can be introduced into the cell. The presence of the double-stranded break has been shown to facilitate integration of the donor sequence. The donor sequence may be physically integrated or, alternatively, the donor polynucleotide is used as a template for repair of the break via homologous recombination, resulting in the introduction of all or part of the nucleotide sequence as in the donor into the cellular chromatin. Thus, a first sequence in cellular chromatin can be altered and, in certain embodiments, can be converted into a sequence present in a donor polynucleotide. Thus, the use of the terms “replace” or “replacement” can be understood to represent replacement of one nucleotide sequence by another, (i.e., replacement of a sequence in the informational sense), and does not necessarily require physical or chemical replacement of one polynucleotide by another.
In any of the methods described herein, additional pairs of zinc-finger or TALEN proteins can be used for additional double-stranded cleavage of additional target sites within the cell.
In certain embodiments of methods for targeted recombination and/or replacement and/or alteration of a sequence in a region of interest in cellular chromatin, a chromosomal sequence is altered by homologous recombination with an exogenous “donor” nucleotide sequence. Such homologous recombination is stimulated by the presence of a double-stranded break in cellular chromatin, if sequences homologous to the region of the break are present.
In any of the methods described herein, the first nucleotide sequence (the “donor sequence”) can contain sequences that are homologous, but not identical, to genomic sequences in the region of interest, thereby stimulating homologous recombination to insert a non-identical sequence in the region of interest. Thus, in certain embodiments, portions of the donor sequence that are homologous to sequences in the region of interest exhibit between about 80 to 99% (or any integer therebetween) sequence identity to the genomic sequence that is replaced. In other embodiments, the homology between the donor and genomic sequence is higher than 99%, for example if only 1 nucleotide differs as between donor and genomic sequences of over 100 contiguous base pairs. In certain cases, a non-homologous portion of the donor sequence can contain sequences not present in the region of interest, such that new sequences are introduced into the region of interest. In these instances, the non-homologous sequence is generally flanked by sequences of 50-1,000 base pairs (or any integral value therebetween) or any number of base pairs greater than 1,000, that are homologous or identical to sequences in the region of interest. In other embodiments, the donor sequence is non-homologous to the first sequence, and is inserted into the genome by non-homologous recombination mechanisms.
Any of the methods described herein can be used for partial or complete inactivation of one or more target sequences in a cell by targeted integration of donor sequence that disrupts expression of the gene(s) of interest. Cell lines with partially or completely inactivated genes are also provided.
Furthermore, the methods of targeted integration as described herein can also be used to integrate one or more exogenous sequences. The exogenous nucleic acid sequence can comprise, for example, one or more genes or cDNA molecules, or any type of coding or non-coding sequence, as well as one or more control elements (e.g., promoters). In addition, the exogenous nucleic acid sequence may produce one or more RNA molecules (e.g., small hairpin RNAs (shRNAs), inhibitory RNAs (RNAis), microRNAs (miRNAs), etc.).
“Cleavage” refers to the breakage of the covalent backbone of a DNA molecule. Cleavage can be initiated by a variety of methods including, but not limited to, enzymatic or chemical hydrolysis of a phosphodiester bond. Both single-stranded cleavage and double-stranded cleavage are possible, and double-stranded cleavage can occur as a result of two distinct single-stranded cleavage events. DNA cleavage can result in the production of either blunt ends or staggered ends. In certain embodiments, fusion polypeptides are used for targeted double-stranded DNA cleavage.
A “cleavage half-domain” is a polypeptide sequence which, in conjunction with a second polypeptide (either identical or different) forms a complex having cleavage activity (preferably double-strand cleavage activity). The terms “first and second cleavage half-domains;” “+ and − cleavage half-domains” and “right and left cleavage half-domains” are used interchangeably to refer to pairs of cleavage half-domains that dimerize.
An “engineered cleavage half-domain” is a cleavage half-domain that has been modified so as to form obligate heterodimers with another cleavage half-domain (e.g., another engineered cleavage half-domain). See, also, U.S. Patent Publication Nos. 2005/0064474, 20070218528, 2008/0131962 and 2011/0201055, incorporated herein by reference in their entireties.
The term “sequence” refers to a nucleotide sequence of any length, which can be DNA or RNA; can be linear, circular or branched and can be either single-stranded or double stranded. The term “donor sequence” refers to a nucleotide sequence that is inserted into a genome. A donor sequence can be of any length, for example between 2 and 10,000 nucleotides in length (or any integer value therebetween or thereabove), preferably between about 100 and 1,000 nucleotides in length (or any integer therebetween), more preferably between about 200 and 500 nucleotides in length.
“Chromatin” is the nucleoprotein structure comprising the cellular genome. Cellular chromatin comprises nucleic acid, primarily DNA, and protein, including histones and non-histone chromosomal proteins. The majority of eukaryotic cellular chromatin exists in the form of nucleosomes, wherein a nucleosome core comprises approximately 150 base pairs of DNA associated with an octamer comprising two each of histones H2A, H2B, H3 and H4; and linker DNA (of variable length depending on the organism) extends between nucleosome cores. A molecule of histone H1 is generally associated with the linker DNA. For the purposes of the present disclosure, the term “chromatin” is meant to encompass all types of cellular nucleoprotein, both prokaryotic and eukaryotic. Cellular chromatin includes both chromosomal and episomal chromatin.
A “chromosome,” is a chromatin complex comprising all or a portion of the genome of a cell. The genome of a cell is often characterized by its karyotype, which is the collection of all the chromosomes that comprise the genome of the cell. The genome of a cell can comprise one or more chromosomes.
An “episome” is a replicating nucleic acid, nucleoprotein complex or other structure comprising a nucleic acid that is not part of the chromosomal karyotype of a cell. Examples of episomes include plasmids and certain viral genomes.
A “target site” or “target sequence” is a nucleic acid sequence that defines a portion of a nucleic acid to which a binding molecule will bind, provided sufficient conditions for binding exist.
An “exogenous” molecule is a molecule that is not normally present in a cell, but can be introduced into a cell by one or more genetic, biochemical or other methods. “Normal presence in the cell” is determined with respect to the particular developmental stage and environmental conditions of the cell. Thus, for example, a molecule that is present only during embryonic development of muscle is an exogenous molecule with respect to an adult muscle cell. Similarly, a molecule induced by heat shock is an exogenous molecule with respect to a non-heat-shocked cell. An exogenous molecule can comprise, for example, a functioning version of a malfunctioning endogenous molecule or a malfunctioning version of a normally-functioning endogenous molecule.
An exogenous molecule can be, among other things, a small molecule, such as is generated by a combinatorial chemistry process, or a macromolecule such as a protein, nucleic acid, carbohydrate, lipid, glycoprotein, lipoprotein, polysaccharide, any modified derivative of the above molecules, or any complex comprising one or more of the above molecules. Nucleic acids include DNA and RNA, can be single- or double-stranded; can be linear, branched or circular; and can be of any length. Nucleic acids include those capable of forming duplexes, as well as triplex-forming nucleic acids. See, for example, U.S. Pat. Nos. 5,176,996 and 5,422,251. Proteins include, but are not limited to, DNA-binding proteins, transcription factors, chromatin remodeling factors, methylated DNA binding proteins, polymerases, methylases, demethylases, acetylases, deacetylases, kinases, phosphatases, integrases, recombinases, ligases, topoisomerases, gyrases and helicases.
An exogenous molecule can be the same type of molecule as an endogenous molecule, e.g., an exogenous protein or nucleic acid. For example, an exogenous nucleic acid can comprise an infecting viral genome, a plasmid or episome introduced into a cell, or a chromosome that is not normally present in the cell. Methods for the introduction of exogenous molecules into cells are known to those of skill in the art and include, but are not limited to, lipid-mediated transfer (i.e., liposomes, including neutral and cationic lipids), electroporation, direct injection, cell fusion, particle bombardment, calcium phosphate co-precipitation, DEAE-dextran-mediated transfer and viral vector-mediated transfer. An exogenous molecule can also be the same type of molecule as an endogenous molecule but derived from a different species than the cell is derived from. For example, a human nucleic acid sequence may be introduced into a cell line originally derived from a mouse or hamster.
By contrast, an “endogenous” molecule is one that is normally present in a particular cell at a particular developmental stage under particular environmental conditions. For example, an endogenous nucleic acid can comprise a chromosome, the genome of a mitochondrion, chloroplast or other organelle, or a naturally-occurring episomal nucleic acid. Additional endogenous molecules can include proteins, for example, transcription factors and enzymes.
A “fusion” molecule is a molecule in which two or more subunit molecules are linked, preferably covalently. The subunit molecules can be the same chemical type of molecule, or can be different chemical types of molecules. Examples of the first type of fusion molecule include, but are not limited to, fusion proteins (for example, a fusion between a ZFP or TALE DNA-binding domain and one or more activation domains) and fusion nucleic acids (for example, a nucleic acid encoding the fusion protein described supra). Examples of the second type of fusion molecule include, but are not limited to, a fusion between a triplex-forming nucleic acid and a polypeptide, and a fusion between a minor groove binder and a nucleic acid.
Expression of a fusion protein in a cell can result from delivery of the fusion protein to the cell or by delivery of a polynucleotide encoding the fusion protein to a cell, wherein the polynucleotide is transcribed, and the transcript is translated, to generate the fusion protein. Trans-splicing, polypeptide cleavage and polypeptide ligation can also be involved in expression of a protein in a cell. Methods for polynucleotide and polypeptide delivery to cells are presented elsewhere in this disclosure.
A “gene,” for the purposes of the present disclosure, includes a DNA region encoding a gene product (see infra), as well as all DNA regions which regulate the production of the gene product, whether or not such regulatory sequences are adjacent to coding and/or transcribed sequences. Accordingly, a gene includes, but is not necessarily limited to, promoter sequences, terminators, translational regulatory sequences such as ribosome binding sites and internal ribosome entry sites, enhancers, silencers, insulators, boundary elements, replication origins, matrix attachment sites and locus control regions.
“Gene expression” refers to the conversion of the information, contained in a gene, into a gene product. A gene product can be the direct transcriptional product of a gene (e.g., mRNA, tRNA, rRNA, antisense RNA, ribozyme, structural RNA or any other type of RNA) or a protein produced by translation of an mRNA. Gene products also include RNAs which are modified, by processes such as capping, polyadenylation, methylation, and editing, and proteins modified by, for example, methylation, acetylation, phosphorylation, ubiquitination, ADP-ribosylation, myristilation, and glycosylation.
“Modulation” of gene expression refers to a change in the activity of a gene. Modulation of expression can include, but is not limited to, gene activation and gene repression. Genome editing (e.g., cleavage, alteration, inactivation, random mutation) can be used to modulate expression. Gene inactivation refers to any reduction in gene expression as compared to a cell that does not include a ZFP or TALEN as described herein. Thus, gene inactivation may be partial or complete.
A “region of interest” is any region of cellular chromatin, such as, for example, a gene or a non-coding sequence within or adjacent to a gene, in which it is desirable to bind an exogenous molecule. Binding can be for the purposes of targeted DNA cleavage and/or targeted recombination. A region of interest can be present in a chromosome, an episome, an organellar genome (e.g., mitochondrial, chloroplast), or an infecting viral genome, for example. A region of interest can be within the coding region of a gene, within transcribed non-coding regions such as, for example, leader sequences, trailer sequences or introns, or within non-transcribed regions, either upstream or downstream of the coding region. A region of interest can be as small as a single nucleotide pair or up to 2,000 nucleotide pairs in length, or any integral value of nucleotide pairs.
“Eukaryotic” cells include, but are not limited to, fungal cells (such as yeast), plant cells, animal cells, mammalian cells and human cells (e.g., T-cells).
The terms “operative linkage” and “operatively linked” (or “operably linked”) are used interchangeably with reference to a juxtaposition of two or more components (such as sequence elements), in which the components are arranged such that both components function normally and allow the possibility that at least one of the components can mediate a function that is exerted upon at least one of the other components. By way of illustration, a transcriptional regulatory sequence, such as a promoter, is operatively linked to a coding sequence if the transcriptional regulatory sequence controls the level of transcription of the coding sequence in response to the presence or absence of one or more transcriptional regulatory factors. A transcriptional regulatory sequence is generally operatively linked in cis with a coding sequence, but need not be directly adjacent to it. For example, an enhancer is a transcriptional regulatory sequence that is operatively linked to a coding sequence, even though they are not contiguous.
With respect to fusion polypeptides, the term “operatively linked” can refer to the fact that each of the components performs the same function in linkage to the other component as it would if it were not so linked. For example, with respect to a fusion polypeptide in which a ZFP or TALE DNA-binding domain is fused to an activation domain, the ZFP or TALE DNA-binding domain and the activation domain are in operative linkage if, in the fusion polypeptide, the ZFP or TALE DNA-binding domain portion is able to bind its target site and/or its binding site, while the activation domain is able to up-regulate gene expression. When a fusion polypeptide in which a ZFP or TALE DNA-binding domain is fused to a cleavage domain, the ZFP or TALE DNA-binding domain and the cleavage domain are in operative linkage if, in the fusion polypeptide, the ZFP or TALE DNA-binding domain portion is able to bind its target site and/or its binding site, while the cleavage domain is able to cleave DNA in the vicinity of the target site.
A “functional fragment” of a protein, polypeptide or nucleic acid is a protein, polypeptide or nucleic acid whose sequence is not identical to the full-length protein, polypeptide or nucleic acid, yet retains the same function as the full-length protein, polypeptide or nucleic acid. A functional fragment can possess more, fewer, or the same number of residues as the corresponding native molecule, and/or can contain one or more amino acid or nucleotide substitutions. Methods for determining the function of a nucleic acid (e.g., coding function, ability to hybridize to another nucleic acid) are well-known in the art. Similarly, methods for determining protein function are well-known. For example, the DNA-binding function of a polypeptide can be determined, for example, by filter-binding, electrophoretic mobility-shift, or immunoprecipitation assays. DNA cleavage can be assayed by gel electrophoresis. See Ausubel et al., supra. The ability of a protein to interact with another protein can be determined, for example, by co-immunoprecipitation, two-hybrid assays or complementation, both genetic and biochemical. See, for example, Fields et al. (1989) Nature 340:245-246; U.S. Pat. No. 5,585,245 and PCT WO 98/44350.
A “vector” is capable of transferring gene sequences to target cells. Typically, “vector construct,” “expression vector,” and “gene transfer vector,” mean any nucleic acid construct capable of directing the expression of a gene of interest and which can transfer gene sequences to target cells. Thus, the term includes cloning, and expression vehicles, as well as integrating vectors.
A “reporter gene,” “reporter sequence,” “marker gene” or “marker sequence” refers to any sequence that produces a protein product that is easily measured, preferably although not necessarily in a routine assay. Suitable reporter/marker genes include, but are not limited to, sequences encoding proteins that mediate antibiotic resistance (e.g., ampicillin resistance, neomycin resistance, G418 resistance, puromycin resistance), sequences encoding colored or fluorescent or luminescent proteins (e.g., green fluorescent protein, enhanced green fluorescent protein, red fluorescent protein, luciferase), and proteins which mediate enhanced cell growth and/or gene amplification (e.g., dihydrofolate reductase). Epitope tags include, for example, one or more copies of FLAG, His, myc, Tap, HA or any detectable amino acid sequence. “Expression tags” include sequences that encode reporters that may be operably linked to a desired gene sequence in order to monitor expression of the gene of interest.
Nucleases
Described herein are compositions, particularly nucleases, which are useful in integration of a peptide fusion inhibitor into a cell surface receptor (e.g., viral receptor) or disruption of the cell surface receptor to inhibit entry of macromolecules that bind to the cell surface receptor. In certain embodiments, the nuclease is naturally occurring. In other embodiments, the nuclease is non-naturally occurring, i.e., engineered in the DNA-binding domain and/or cleavage domain. For example, the DNA-binding domain of a naturally-occurring nuclease may be altered to bind to a selected target site (e.g., a meganuclease that has been engineered to bind to site different than the cognate binding site). In other embodiments, the nuclease comprises heterologous DNA-binding and cleavage domains (e.g., zinc finger nucleases; TAL-effector nucleases; meganuclease DNA-binding domains with heterologous cleavage domains).
A. DNA-Binding Domains
In certain embodiments, the nuclease is a meganuclease (homing endonuclease). Naturally-occurring meganucleases recognize 15-40 base-pair cleavage sites and are commonly grouped into four families: the LAGLIDADG family, the GIY-YIG family, the His-Cyst box family and the HNH family. Exemplary homing endonucleases include I-SceI, I-CeuI, PI-PspI, PI-Sce, I-SceIV, I-CsmI, I-PanI, I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI, I-TevII and I-TevIII. Their recognition sequences are known. See also U.S. Pat. No. 5,420,032; U.S. Pat. No. 6,833,252; Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388; Dujon et al. (1989) Gene 82:115-118; Perler et al. (1994) Nucleic Acids Res. 22, 1125-1127; Jasin (1996) Trends Genet. 12:224-228; Gimble et al. (1996) J. Mol. Biol. 263:163-180; Argast et al. (1998) J. Mol. Biol. 280:345-353 and the New England Biolabs catalogue.
In certain embodiments, the nuclease comprises an engineered (non-naturally occurring) homing endonuclease (meganuclease). The recognition sequences of homing endonucleases and meganucleases such as I-SceI, I-CeuI, PI-PspI, PI-Sce, I-SceIV, I-CsmI, IPanI, I-SceII, I-PpoI, I-SceIII, I-CreI, I-TevI, I-TevII and I-TevIII are known. See also U.S. Pat. No. 5,420,032; U.S. Pat. No. 6,833,252; Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388; Dujon et al. (1989) Gene 82:115-118; Perler et al. (1994) Nucleic Acids Res. 22, 1125-1127; Jasin (1996) Trends Genet. 12:224-228; Gimble et al. (1996) J. Mol. Biol. 263:163-180; Argast et al. (1998) J. Mol. Biol. 280:345-353 and the New England Biolabs catalogue. In addition, the DNA-binding specificity of homing endonucleases and meganucleases can be engineered to bind non-natural target sites. See, for example, Chevalier et al. (2002) Molec. Cell 10:895-905; Epinat et al. (2003) Nucleic Acids Res. 31:2952-2962; Ashworth et al. (2006) Nature 441:656-659; Paques et al. (2007) Current Gene Therapy 7:49-66; U.S. Patent Publication No. 20070117128. The DNA-binding domains of the homing endonucleases and meganucleases may be altered in the context of the nuclease as a whole (i.e., such that the nuclease includes the cognate cleavage domain) or may be fused to a heterologous cleavage domain.
In other embodiments, the DNA-binding domain comprises a naturally occurring or engineered (non-naturally occurring) TAL effector DNA binding domain. The plant pathogenic bacteria of the genus Xanthomonas are known to cause many diseases in important crop plants. Pathogenicity of Xanthomonas depends on a conserved type III secretion (T3S) system which injects more than 25 different effector proteins into the plant cell. Among these injected proteins are transcription activator-like effectors (TALE) which mimic plant transcriptional activators and manipulate the plant transcriptome (see Kay et al (2007) Science 318:648-651). These proteins contain a DNA binding domain and a transcriptional activation domain. One of the most well characterized TALEs is AvrBs3 from Xanthomonas campestgris pv. Vesicatoria (see Bonas et al (1989) Mol Gen Genet 218: 127-136 and WO2010079430). TALEs contain a centralized domain of tandem repeats, each repeat containing approximately 34 amino acids, which are key to the DNA binding specificity of these proteins. In addition, they contain a nuclear localization sequence and an acidic transcriptional activation domain (for a review see Schornack S, et al (2006) J Plant Physiol 163(3): 256-272). In addition, in the phytopathogenic bacteria Ralstonia solanacearum two genes, designated brg11 and hpx17 have been found that are homologous to the AvrBs3 family of Xanthomonas in the R. solanacearum biovar 1 strain GMI1000 and in the biovar 4 strain RS1000 (See Heuer et al (2007) Appl and Envir Micro 73(13): 4379-4384). These genes are 98.9% identical in nucleotide sequence to each other but differ by a deletion of 1,575 bp in the repeat domain of hpx17. However, both gene products have less than 40% sequence identity with AvrBs3 family proteins of Xanthomonas. 
Specificity of these TALEs depends on the sequences found in the tandem repeats. The repeated sequence comprises approximately 102 bp and the repeats are typically 91-100% homologous with each other (Bonas et al, ibid). Polymorphism of the repeats is usually located at positions 12 and 13 and there appears to be a one-to-one correspondence between the identity of the hypervariable diresidues at positions 12 and 13 with the identity of the contiguous nucleotides in the TALE's target sequence (see Moscou and Bogdanove, (2009) Science 326:1501 and Boch et al (2009) Science 326:1509-1512). Experimentally, the code for DNA recognition of these TALEs has been determined such that an HD sequence at positions 12 and 13 leads to a binding to cytosine (C), NG binds to T, NI to A, C, G or T, NN binds to A or G, and IG binds to T. These DNA binding repeats have been assembled into proteins with new combinations and numbers of repeats, to make artificial transcription factors that are able to interact with new sequences and activate the expression of a non-endogenous reporter gene in plant cells (Boch et al, ibid). Engineered TAL proteins have been linked to a FokI cleavage half domain to yield a TAL effector domain nuclease fusion (TALEN) exhibiting activity in a yeast reporter assay (plasmid based target). Christian et al ((2010)<Genetics epub 10.1534/genetics.110.120717). See, also, U.S. Patent Publication No. 20110301073, incorporated by reference in its entirety herein.
In certain embodiments, the DNA binding domain comprises a zinc finger protein. Preferably, the zinc finger protein is non-naturally occurring in that it is engineered to bind to a target site of choice. See, for example, See, for example, Beerli et al. (2002) Nature Biotechnol. 20:135-141; Pabo et al. (2001) Ann. Rev. Biochem. 70:313-340; Isalan et al. (2001) Nature Biotechnol. 19:656-660; Segal et al. (2001) Curr. Opin. Biotechnol. 12:632-637; Choo et al. (2000) Curr. Opin. Struct. Biol. 10:411-416; U.S. Pat. Nos. 6,453,242; 6,534,261; 6,599,692; 6,503,717; 6,689,558; 7,030,215; 6,794,136; 7,067,317; 7,262,054; 7,070,934; 7,361,635; 7,253,273; and U.S. Patent Publication Nos. 2005/0064474; 2007/0218528; 2005/0267061, all incorporated herein by reference in their entireties.
An engineered zinc finger binding domain can have a novel binding specificity, compared to a naturally-occurring zinc finger protein. Engineering methods include, but are not limited to, rational design and various types of selection. Rational design includes, for example, using databases comprising triplet (or quadruplet) nucleotide sequences and individual zinc finger amino acid sequences, in which each triplet or quadruplet nucleotide sequence is associated with one or more amino acid sequences of zinc fingers which bind the particular triplet or quadruplet sequence. See, for example, co-owned U.S. Pat. Nos. 6,453,242 and 6,534,261, incorporated by reference herein in their entireties.
Exemplary selection methods, including phage display and two-hybrid systems, are disclosed in U.S. Pat. Nos. 5,789,538; 5,925,523; 6,007,988; 6,013,453; 6,410,248; 6,140,466; 6,200,759; and 6,242,568; as well as WO 98/37186; WO 98/53057; WO 00/27878; WO 01/88197 and GB 2,338,237. In addition, enhancement of binding specificity for zinc finger binding domains has been described, for example, in co-owned WO 02/077227.
In addition, as disclosed in these and other references, DNA domains (e.g., multi-fingered zinc finger proteins) may be linked together using any suitable linker sequences, including for example, linkers of 5 or more amino acids in length. See, also, U.S. Pat. Nos. 6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 or more amino acids in length. The zinc finger proteins described herein may include any combination of suitable linkers between the individual zinc fingers of the protein. In addition, enhancement of binding specificity for zinc finger binding domains has been described, for example, in co-owned WO 02/077227.
Selection of target sites; ZFPs and methods for design and construction of fusion proteins (and polynucleotides encoding same) are known to those of skill in the art and described in detail in U.S. Pat. Nos. 6,140,081; 5,789,538; 6,453,242; 6,534,261; 5,925,523; 6,007,988; 6,013,453; 6,200,759; WO 95/19431; WO 96/06166; WO 98/53057; WO 98/54311; WO 00/27878; WO 01/60970 WO 01/88197; WO 02/099084; WO 98/53058; WO 98/53059; WO 98/53060; WO 02/016536 and WO 03/016496.
In addition, as disclosed in these and other references, zinc finger domains and/or multi-fingered zinc finger proteins may be linked together using any suitable linker sequences, including for example, linkers of 5 or more amino acids in length. See, also, U.S. Pat. Nos. 6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 or more amino acids in length. The proteins described herein may include any combination of suitable linkers between the individual zinc fingers of the protein.
B. Cleavage Domains
Any suitable cleavage domain can be operatively linked to a DNA-binding domain to form a nuclease. For example, ZFP DNA-binding domains have been fused to nuclease domains to create ZFNs—a functional entity that is able to recognize its intended nucleic acid target through its engineered (ZFP) DNA binding domain and cause the DNA to be cut near the ZFP binding site via the nuclease activity. See, e.g., Kim et al. (1996) Proc Nat'l Acad Sci USA 93(3):1156-1160. More recently, ZFNs have been used for genome modification in a variety of organisms. See, for example, United States Patent Publications 20030232410; 20050208489; 20050026157; 20050064474; 20060188987; 20060063231; and International Publication WO 07/014,275.
As noted above, the cleavage domain may be heterologous to the DNA-binding domain, for example a zinc finger DNA-binding domain and a cleavage domain from a nuclease or a TALEN DNA-binding domain and a cleavage domain, or meganuclease DNA-binding domain and cleavage domain from a different nuclease. Heterologous cleavage domains can be obtained from any endonuclease or exonuclease. Exemplary endonucleases from which a cleavage domain can be derived include, but are not limited to, restriction endonucleases and homing endonucleases. See, for example, 2002-2003 Catalogue, New England Biolabs, Beverly, Mass.; and Belfort et al. (1997) Nucleic Acids Res. 25:3379-3388. Additional enzymes which cleave DNA are known (e.g., S1 Nuclease; mung bean nuclease; pancreatic DNase I; micrococcal nuclease; yeast HO endonuclease; see also Linn et al. (eds.) Nucleases, Cold Spring Harbor Laboratory Press, 1993). One or more of these enzymes (or functional fragments thereof) can be used as a source of cleavage domains and cleavage half-domains.
Similarly, a cleavage half-domain can be derived from any nuclease or portion thereof, as set forth above, that requires dimerization for cleavage activity. In general, two fusion proteins are required for cleavage if the fusion proteins comprise cleavage half-domains. Alternatively, a single protein comprising two cleavage half-domains can be used. The two cleavage half-domains can be derived from the same endonuclease (or functional fragments thereof), or each cleavage half-domain can be derived from a different endonuclease (or functional fragments thereof). In addition, the target sites for the two fusion proteins are preferably disposed, with respect to each other, such that binding of the two fusion proteins to their respective target sites places the cleavage half-domains in a spatial orientation to each other that allows the cleavage half-domains to form a functional cleavage domain, e.g., by dimerizing. Thus, in certain embodiments, the near edges of the target sites are separated by 5-8 nucleotides or by 15-18 nucleotides. However any integral number of nucleotides or nucleotide pairs can intervene between two target sites (e.g., from 2 to 50 nucleotide pairs or more). In general, the site of cleavage lies between the target sites.
Restriction endonucleases (restriction enzymes) are present in many species and are capable of sequence-specific binding to DNA (at a recognition site), and cleaving DNA at or near the site of binding. Certain restriction enzymes (e.g., Type IIS) cleave DNA at sites removed from the recognition site and have separable binding and cleavage domains. For example, the Type IIS enzyme Fok I catalyzes double-stranded cleavage of DNA, at 9 nucleotides from its recognition site on one strand and 13 nucleotides from its recognition site on the other. See, for example, U.S. Pat. Nos. 5,356,802; 5,436,150 and 5,487,994; as well as Li et al. (1992) Proc. Natl. Acad. Sci. USA 89:4275-4279; Li et al. (1993) Proc. Natl. Acad. Sci. USA 90:2764-2768; Kim et al. (1994a) Proc. Natl. Acad. Sci. USA 91:883-887; Kim et al. (1994b) J. Biol. Chem. 269:31,978-31,982. Thus, in one embodiment, fusion proteins comprise the cleavage domain (or cleavage half-domain) from at least one Type IIS restriction enzyme and one or more zinc finger binding domains, which may or may not be engineered.
An exemplary Type IIS restriction enzyme, whose cleavage domain is separable from the binding domain, is Fok I. This particular enzyme is active as a dimer. Bitinaite et al. (1998) Proc. Natl. Acad. Sci. USA 95: 10,570-10,575. Accordingly, for the purposes of the present disclosure, the portion of the Fok I enzyme used in the disclosed fusion proteins is considered a cleavage half-domain. Thus, for targeted double-stranded cleavage and/or targeted replacement of cellular sequences using zinc finger-Fok I fusions, two fusion proteins, each comprising a FokI cleavage half-domain, can be used to reconstitute a catalytically active cleavage domain. Alternatively, a single polypeptide molecule containing a DNA binding domain and two Fok I cleavage half-domains can also be used.
A cleavage domain or cleavage half-domain can be any portion of a protein that retains cleavage activity, or that retains the ability to multimerize (e.g., dimerize) to form a functional cleavage domain.
Exemplary Type IIS restriction enzymes are described in International Publication WO 07/014,275, incorporated herein in its entirety. Additional restriction enzymes also contain separable binding and cleavage domains, and these are contemplated by the present disclosure. See, for example, Roberts et al. (2003) Nucleic Acids Res. 31:418-420.
In certain embodiments, the cleavage domain comprises one or more engineered cleavage half-domain (also referred to as dimerization domain mutants) that minimize or prevent homodimerization, as described, for example, in U.S. Patent Publication Nos. 20050064474; 20060188987 and 2008/0131962, the disclosures of all of which are incorporated by reference in their entireties herein. Amino acid residues at positions 446, 447, 479, 483, 484, 486, 487, 490, 491, 496, 498, 499, 500, 531, 534, 537, and 538 of Fok I are all targets for influencing dimerization of the Fok I cleavage half-domains.
Exemplary engineered cleavage half-domains of Fok I that form obligate heterodimers include a pair in which a first cleavage half-domain includes mutations at amino acid residues at positions 490 and 538 of Fok I and a second cleavage half-domain includes mutations at amino acid residues 486 and 499.
Thus, in one embodiment, a mutation at 490 replaces Glu (E) with Lys (K); the mutation at 538 replaces Iso (I) with Lys (K); the mutation at 486 replaced Gln (Q) with Glu (E); and the mutation at position 499 replaces Iso (I) with Lys (K). Specifically, the engineered cleavage half-domains described herein were prepared by mutating positions 490 (E→K) and 538 (I→K) in one cleavage half-domain to produce an engineered cleavage half-domain designated “E490K:I538K” and by mutating positions 486 (Q→E) and 499 (I→L) in another cleavage half-domain to produce an engineered cleavage half-domain designated “Q486E:I499L”. The engineered cleavage half-domains described herein are obligate heterodimer mutants in which aberrant cleavage is minimized or abolished. See, e.g., U.S. Patent Publication No. 2008/0131962, the disclosure of which is incorporated by reference in its entirety for all purposes. In certain embodiments, the engineered cleavage half-domain comprises mutations at positions 486, 499 and 496 (numbered relative to wild-type FokI), for instance mutations that replace the wild type Gln (Q) residue at position 486 with a Glu (E) residue, the wild type Iso (I) residue at position 499 with a Leu (L) residue and the wild-type Asn (N) residue at position 496 with an Asp (D) or Glu (E) residue (also referred to as a “ELD” and “ELE” domains, respectively). In other embodiments, the engineered cleavage half-domain comprises mutations at positions 490, 538 and 537 (numbered relative to wild-type FokI), for instance mutations that replace the wild type Glu (E) residue at position 490 with a Lys (K) residue, the wild type Iso (I) residue at position 538 with a Lys (K) residue, and the wild-type His (H) residue at position 537 with a Lys (K) residue or a Arg (R) residue (also referred to as “KKK” and “KKR” domains, respectively). In other embodiments, the engineered cleavage half-domain comprises mutations at positions 490 and 537 (numbered relative to wild-type Fold), for instance mutations that replace the wild type Glu (E) residue at position 490 with a Lys (K) residue and the wild-type His (H) residue at position 537 with a Lys (K) residue or a Arg (R) residue (also referred to as “KIK” and “KIR” domains, respectively). (See US U.S. Patent Publication No. 2011/0201055).
Engineered cleavage half-domains described herein can be prepared using any suitable method, for example, by site-directed mutagenesis of wild-type cleavage half-domains (Fok I) as described in U.S. Patent Publication Nos. 20050064474 and 20080131962.
Alternatively, nucleases may be assembled in vivo at the nucleic acid target site using so-called “split-enzyme” technology (see e.g. U.S. Patent Publication No. 20090068164). Components of such split enzymes may be expressed either on separate expression constructs, or can be linked in one open reading frame where the individual components are separated, for example, by a self-cleaving 2A peptide or IBES sequence. Components may be individual zinc finger binding domains or domains of a meganuclease nucleic acid binding domain.
Nucleases can be screened for activity prior to use, for example in a yeast-based chromosomal system as described in WO 2009/042163 and U.S. Publication No. 20090068164. Nuclease expression constructs can be readily designed using methods known in the art. See, e.g., United States Patent Publications 20030232410; 20050208489; 20050026157; 20050064474; 20060188987; 20060063231; and International Publication WO 07/014275. Expression of the nuclease may be under the control of a constitutive promoter or an inducible promoter, for example the galactokinase promoter which is activated (de-repressed) in the presence of raffinose and/or galactose and repressed in presence of glucose.
Target Sites
As described in detail above, DNA domains can be engineered to bind to any sequence of choice. An engineered DNA-binding domain can have a novel binding specificity, compared to a naturally-occurring DNA-binding domain. Engineering methods include, but are not limited to, rational design and various types of selection. Rational design includes, for example, using databases comprising triplet (or quadruplet) nucleotide sequences and individual (e.g., zinc finger) amino acid sequences, in which each triplet or quadruplet nucleotide sequence is associated with one or more amino acid sequences of DNA binding domain which bind the particular triplet or quadruplet sequence. See, for example, co-owned U.S. Pat. Nos. 6,453,242 and 6,534,261, incorporated by reference herein in their entireties. Rational design of TAL-effector domains can also be performed. See, e.g., U.S. Patent Publication No. 20110301073, incorporated by reference in its entirety herein.
Exemplary selection methods applicable to DNA-binding domains, including phage display and two-hybrid systems, are disclosed in U.S. Pat. Nos. 5,789,538; 5,925,523; 6,007,988; 6,013,453; 6,410,248; 6,140,466; 6,200,759; and 6,242,568; as well as WO 98/37186; WO 98/53057; WO 00/27878; WO 01/88197 and GB 2,338,237.
Selection of target sites; nucleases and methods for design and construction of fusion proteins (and polynucleotides encoding same) are known to those of skill in the art and described in detail in U.S. Patent Application Publication Nos. 20050064474 and 20060188987, incorporated by reference in their entireties herein.
In addition, as disclosed in these and other references, DNA-binding domains (e.g., multi-fingered zinc finger proteins) may be linked together using any suitable linker sequences, including for example, linkers of 5 or more amino acids. See, e.g., U.S. Pat. Nos. 6,479,626; 6,903,185; and 7,153,949 for exemplary linker sequences 6 or more amino acids in length. The proteins described herein may include any combination of suitable linkers between the individual DNA-binding domains of the protein. See, also, U.S. Patent Application No. 20110287512.
Donors
It will be readily apparent that the donor sequence is typically not identical to the genomic sequence that it replaces. For example, the sequence of the donor polynucleotide can contain one or more single base changes, insertions, deletions, inversions or rearrangements with respect to the genomic sequence, so long as sufficient homology with chromosomal sequences is present. Alternatively, a donor sequence can contain a non-homologous sequence flanked by two regions of homology. Additionally, donor sequences can comprise a vector molecule containing sequences that are not homologous to the region of interest in cellular chromatin. A donor molecule can contain several, discontinuous regions of homology to cellular chromatin. For example, for targeted insertion of sequences not normally present in a region of interest, said sequences can be present in a donor nucleic acid molecule and flanked by regions of homology to sequence in the region of interest.
The donor polynucleotide can be DNA or RNA, single-stranded or double-stranded and can be introduced into a cell in linear or circular form. If introduced in linear form, the ends of the donor sequence can be protected (e.g., from exonucleolytic degradation) by methods known to those of skill in the art. For example, one or more dideoxynucleotide residues are added to the 3′ terminus of a linear molecule and/or self-complementary oligonucleotides are ligated to one or both ends. See, for example, Chang et al. (1987) Proc. Natl. Acad. Sci. USA 84:4959-4963; Nehls et al. (1996) Science 272:886-889. Additional methods for protecting exogenous polynucleotides from degradation include, but are not limited to, addition of terminal amino group(s) and the use of modified internucleotide linkages such as, for example, phosphorothioates, phosphoramidates, and O-methyl ribose or deoxyribose residues.
A polynucleotide can be introduced into a cell as part of a vector molecule having additional sequences such as, for example, replication origins, promoters and genes encoding antibiotic resistance. Moreover, donor polynucleotides can be introduced as naked nucleic acid, as nucleic acid complexed with an agent such as a liposome or poloxamer, or can be delivered by viruses (e.g., adenovirus, AAV, herpesvirus, retrovirus, lentivirus and integrase defective lentivirus (IDLV)).
The donor is generally inserted so that its expression is driven by the endogenous promoter at the integration site, namely the promoter that drives expression of the cell surface receptor with which the peptide fusion inhibitor is expressed. However, it will be apparent that the donor may comprise a promoter and/or enhancer, for example a constitutive promoter or an inducible or tissue specific promoter that drives expression of the function peptide fusion inhibitor upon integration.
Furthermore, although not required for expression, exogenous sequences may also be transcriptional or translational regulatory sequences, for example, promoters, enhancers, insulators, internal ribosome entry sites, sequences encoding 2A peptides and/or polyadenylation signals.
Delivery
The nucleases, polynucleotides encoding these nucleases, donor polynucleotides and compositions comprising the proteins and/or polynucleotides described herein may be delivered in vivo or ex vivo by any suitable means.
Methods of delivering nucleases as described herein are described, for example, in U.S. Pat. Nos. 6,453,242; 6,503,717; 6,534,261; 6,599,692; 6,607,882; 6,689,558; 6,824,978; 6,933,113; 6,979,539; 7,013,219; and 7,163,824, the disclosures of all of which are incorporated by reference herein in their entireties.
Nucleases and/or donor constructs as described herein may also be delivered using vectors containing sequences encoding one or more of the zinc finger or TALEN protein(s). Any vector systems may be used including, but not limited to, plasmid vectors, retroviral vectors, lentiviral vectors, adenovirus vectors, poxvirus vectors; herpesvirus vectors and adeno-associated virus vectors, etc. See, also, U.S. Pat. Nos. 6,534,261; 6,607,882; 6,824,978; 6,933,113; 6,979,539; 7,013,219; and 7,163,824, incorporated by reference herein in their entireties. Furthermore, it will be apparent that any of these vectors may comprise one or more of the sequences needed for treatment. Thus, when one or more nucleases and a donor construct are introduced into the cell, the nucleases and/or donor polynucleotide may be carried on the same vector or on different vectors. When multiple vectors are used, each vector may comprise a sequence encoding one or multiple nucleases and/or donor constructs.
Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids encoding nucleases and donor constructs in cells (e.g., mammalian cells) and target tissues. Non-viral vector delivery systems include DNA plasmids, naked nucleic acid, and nucleic acid complexed with a delivery vehicle such as a liposome or poloxamer. Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell. For a review of gene therapy procedures, see Anderson, Science 256:808-813 (1992); Nabel & Felgner, TIBTECH 11:211-217 (1993); Mitani & Caskey, TIBTECH 11:162-166 (1993); Dillon, TIBTECH 11:167-175 (1993); Miller, Nature 357:455-460 (1992); Van Brunt, Biotechnology 6(10):1149-1154 (1988); Vigne, Restorative Neurology and Neuroscience 8:35-36 (1995); Kremer & Perricaudet, British Medical Bulletin 51(1):31-44 (1995); Haddada et al., in Current Topics in Microbiology and Immunology Doerfler and Böhm (eds.) (1995); and Yu et al., Gene Therapy 1:13-26 (1994).
Methods of non-viral delivery of nucleic acids include electroporation, lipofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipid:nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA. Sonoporation using, e.g., the Sonitron 2000 system (Rich-Mar) can also be used for delivery of nucleic acids.
Additional exemplary nucleic acid delivery systems include those provided by Amaxa Biosystems (Cologne, Germany), Maxcyte, Inc. (Rockville, Md.), BTX Molecular Delivery Systems (Holliston, Mass.) and Copernicus Therapeutics Inc, (see for example U.S. Pat. No. 6,008,336). Lipofection is described in e.g., U.S. Pat. Nos. 5,049,386; 4,946,787; and 4,897,355) and lipofection reagents are sold commercially (e.g., TransfectamTM and LipofectinTM). Cationic and neutral lipids that are suitable for efficient receptor-recognition lipofection of polynucleotides include those of Feigner, WO 91/17424, WO 91/16024.
The preparation of lipid:nucleic acid complexes, including targeted liposomes such as immunolipid complexes, is well known to one of skill in the art (see, e.g., Crystal, Science 270:404-410 (1995); Blaese et al., Cancer Gene Ther. 2:291-297 (1995); Behr et al., Bioconjugate Chem. 5:382-389 (1994); Remy et al., Bioconjugate Chem. 5:647-654 (1994); Gao et al., Gene Therapy 2:710-722 (1995); Ahmad et al., Cancer Res. 52:4817-4820 (1992); U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, and 4,946,787).
Additional methods of delivery include the use of packaging the nucleic acids to be delivered into EnGeneIC delivery vehicles (EDVs). These EDVs are specifically delivered to target tissues using bispecific antibodies where one arm of the antibody has specificity for the target tissue and the other has specificity for the EDV. The antibody brings the EDVs to the target cell surface and then the EDV is brought into the cell by endocytosis. Once in the cell, the contents are released (see MacDiarmid et al (2009) Nature Biotechnology 27(7):643).
The use of RNA or DNA viral based systems for the delivery of nucleic acids encoding engineered ZFPs take advantage of highly evolved processes for targeting a virus to specific cells in the body and trafficking the viral payload to the nucleus. Viral vectors can be administered directly to patients (in vivo) or they can be used to treat cells in vitro and the modified cells are administered to patients (ex vivo). Conventional viral based systems for the delivery of ZFPs include, but are not limited to, retroviral, lentivirus, adenoviral, adeno-associated, vaccinia and herpes simplex virus vectors for gene transfer. Integration in the host genome is possible with the retrovirus, lentivirus, and adeno-associated virus gene transfer methods, often resulting in long term expression of the inserted transgene. Additionally, high transduction efficiencies have been observed in many different cell types and target tissues.
The tropism of a retrovirus can be altered by incorporating foreign envelope proteins, expanding the potential target population of target cells. Lentiviral vectors are retroviral vectors that are able to transduce or infect non-dividing cells and typically produce high viral titers. Selection of a retroviral gene transfer system depends on the target tissue. Retroviral vectors are comprised of cis-acting long terminal repeats with packaging capacity for up to 6-10 kb of foreign sequence. The minimum cis-acting LTRs are sufficient for replication and packaging of the vectors, which are then used to integrate the therapeutic gene into the target cell to provide permanent transgene expression. Widely used retroviral vectors include those based upon murine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), Simian Immunodeficiency virus (SIV), human immunodeficiency virus (HIV), and combinations thereof (see, e.g., Buchscher et al., J. Virol. 66:2731-2739 (1992); Johann et al., J. Virol. 66:1635-1640 (1992); Sommerfelt et al., Virol. 176:58-59 (1990); Wilson et al., J. Virol. 63:2374-2378 (1989); Miller et al., J. Virol. 65:2220-2224 (1991); PCT/US94/05700).
In applications in which transient expression is preferred, adenoviral based systems can be used. Adenoviral based vectors are capable of very high transduction efficiency in many cell types and do not require cell division. With such vectors, high titer and high levels of expression have been obtained. This vector can be produced in large quantities in a relatively simple system. Adeno-associated virus (“AAV”) vectors are also used to transduce cells with target nucleic acids, e.g., in the in vitro production of nucleic acids and peptides, and for in vivo and ex vivo gene therapy procedures (see, e.g., West et al., Virology 160:38-47 (1987); U.S. Pat. No. 4,797,368; WO 93/24641; Kotin, Human Gene Therapy 5:793-801 (1994); Muzyczka, J. Clin. Invest. 94:1351 (1994). Construction of recombinant AAV vectors are described in a number of publications, including U.S. Pat. No. 5,173,414; Tratschin et al., Mol. Cell. Biol. 5:3251-3260 (1985); Tratschin, et al., Mol. Cell. Biol. 4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466-6470 (1984); and Samulski et al., J. Virol. 63:03822-3828 (1989).
At least six viral vector approaches are currently available for gene transfer in clinical trials, which utilize approaches that involve complementation of defective vectors by genes inserted into helper cell lines to generate the transducing agent.
pLASN and MFG-S are examples of retroviral vectors that have been used in clinical trials (Dunbar et al., Blood 85:3048-305 (1995); Kohn et al., Nat. Med. 1:1017-102 (1995); Malech et al., PNAS 94:22 12133-12138 (1997)). PA317/pLASN was the first therapeutic vector used in a gene therapy trial. (Blaese et al., Science 270:475-480 (1995)). Transduction efficiencies of 50% or greater have been observed for MFG-S packaged vectors. (Ellem et al., Immunol Immunother. 44(1):10-20 (1997); Dranoff et al., Hum. Gene Ther. 1:111-2 (1997).
Recombinant adeno-associated virus vectors (rAAV) are a promising alternative gene delivery systems based on the defective and nonpathogenic parvovirus adeno-associated type 2 virus. All vectors are derived from a plasmid that retains only the AAV 145 bp inverted terminal repeats flanking the transgene expression cassette. Efficient gene transfer and stable transgene delivery due to integration into the genomes of the transduced cell are key features for this vector system. (Wagner et al., Lancet 351:9117 1702-3 (1998), Kearns et al., Gene Ther. 9:748-55 (1996)). Other AAV serotypes, including AAV1, AAV3, AAV4, AAV5, AAV6 and AAV8, can also be used in accordance with the present invention.
Replication-deficient recombinant adenoviral vectors (Ad) can be produced at high titer and readily infect a number of different cell types. Most adenovirus vectors are engineered such that a transgene replaces the Ad E1a, E1b, and/or E3 genes; subsequently the replication defective vector is propagated in human 293 cells that supply deleted gene function in trans. Ad vectors can transduce multiple types of tissues in vivo, including non-dividing, differentiated cells such as those found in liver, kidney and muscle. Conventional Ad vectors have a large carrying capacity. An example of the use of an Ad vector in a clinical trial involved polynucleotide therapy for anti-tumor immunization with intramuscular injection (Sterman et al., Hum. Gene Ther. 7:1083-9 (1998)). Additional examples of the use of adenovirus vectors for gene transfer in clinical trials include Rosenecker et al., Infection 24:1 5-10 (1996); Sterman et al., Hum. Gene Ther. 9:7 1083-1089 (1998); Welsh et al., Hum. Gene Ther. 2:205-18 (1995); Alvarez et al., Hum. Gene Ther. 5:597-613 (1997); Topf et al., Gene Ther. 5:507-513 (1998); Sterman et al., Hum. Gene Ther. 7:1083-1089 (1998).
Packaging cells are used to form virus particles that are capable of infecting a host cell. Such cells include 293 cells, which package adenovirus, and ψ2 cells or PA317 cells, which package retrovirus. Viral vectors used in gene therapy are usually generated by a producer cell line that packages a nucleic acid vector into a viral particle. The vectors typically contain the minimal viral sequences required for packaging and subsequent integration into a host (if applicable), other viral sequences being replaced by an expression cassette encoding the protein to be expressed. The missing viral functions are supplied in trans by the packaging cell line. For example, AAV vectors used in gene therapy typically only possess inverted terminal repeat (ITR) sequences from the AAV genome which are required for packaging and integration into the host genome. Viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences. The cell line is also infected with adenovirus as a helper. The helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV.
In many gene therapy applications, it is desirable that the gene therapy vector be delivered with a high degree of specificity to a particular tissue type. Accordingly, a viral vector can be modified to have specificity for a given cell type by expressing a ligand as a fusion protein with a viral coat protein on the outer surface of the virus. The ligand is chosen to have affinity for a receptor known to be present on the cell type of interest. For example, Han et al., Proc. Natl. Acad. Sci. USA 92:9747-9751 (1995), reported that Moloney murine leukemia virus can be modified to express human heregulin fused to gp70, and the recombinant virus infects certain human breast cancer cells expressing human epidermal growth factor receptor. This principle can be extended to other virus-target cell pairs, in which the target cell expresses a receptor and the virus expresses a fusion protein comprising a ligand for the cell-surface receptor. For example, filamentous phage can be engineered to display antibody fragments (e.g., FAB or Fv) having specific binding affinity for virtually any chosen cellular receptor. Although the above description applies primarily to viral vectors, the same principles can be applied to nonviral vectors. Such vectors can be engineered to contain specific uptake sequences which favor uptake by specific target cells.
Gene therapy vectors can be delivered in vivo by administration to an individual patient, typically by systemic administration (e.g., intravenous, intraperitoneal, intramuscular, subdermal, or intracranial infusion) or topical application, as described below. Alternatively, vectors can be delivered to cells ex vivo, such as cells explanted from an individual patient (e.g., lymphocytes, bone marrow aspirates, tissue biopsy) or universal donor hematopoietic stem cells, followed by reimplantation of the cells into a patient, usually after selection for cells which have incorporated the vector.
Vectors (e.g., retroviruses, adenoviruses, liposomes, etc.) containing nucleases and/or donor constructs can also be administered directly to an organism for transduction of cells in vivo. Alternatively, naked DNA can be administered. Administration is by any of the routes normally used for introducing a molecule into ultimate contact with blood or tissue cells including, but not limited to, injection, infusion, topical application and electroporation. Suitable methods of administering such nucleic acids are available and well known to those of skill in the art, and, although more than one route can be used to administer a particular composition, a particular route can often provide a more immediate and more effective reaction than another route.
Vectors suitable for introduction of polynucleotides (nuclease-encoding and/or peptide fusion inhibitor-encoding) described herein include non-integrating lentivirus vectors (IDLV). See, for example, Ory et al. (1996) Proc. Natl. Acad. Sci. USA 93:11382-11388; Dull et al. (1998) J. Virol. 72:8463-8471; Zuffery et al. (1998) J. Virol. 72:9873-9880; Follenzi et al. (2000) Nature Genetics 25:217-222; U.S. Patent Publication No 2009/054985.
Pharmaceutically acceptable carriers are determined in part by the particular composition being administered, as well as by the particular method used to administer the composition. Accordingly, there is a wide variety of suitable formulations of pharmaceutical compositions available, as described below (see, e.g., Remington's Pharmaceutical Sciences, 17th ed., 1989).
It will be apparent that the nuclease-encoding sequences and donor constructs can be delivered using the same or different systems. For example, a donor polynucleotide can be carried by a plasmid, while the one or more nucleases can be carried by a AAV vector. Furthermore, the different vectors can be administered by the same or different routes (intramuscular injection, tail vein injection, other intravenous injection, intraperitoneal administration and/or intramuscular injection. The vectors can be delivered simultaneously or in any sequential order.
Formulations for both ex vivo and in vivo administrations include suspensions in liquid or emulsified liquids. The active ingredients often are mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients include, for example, water, saline, dextrose, glycerol, ethanol or the like, and combinations thereof. In addition, the composition may contain minor amounts of auxiliary substances, such as, wetting or emulsifying agents, pH buffering agents, stabilizing agents or other reagents that enhance the effectiveness of the pharmaceutical composition.
Parkinson's Disease and Genetic Mutations
As described above, mutations in several genes are found in both familial and sporadic cases of PD. The instant invention describes methods and compositions that can be used to introduce or repair such mutations. Shown below is a table of exemplary genes and loci that have been associated with PD in some manner.







TABLE 1







Exemplary genes and loci linked with PD










Locus
Gene
Chromosome
Inheritance/clinical phenotype





PARK1/
α-
4q21
AD and sporadic/early 


PARK4/
synuclein

onset PD


SCNA





PARK2
Parkin
6q25.2-q27
AR and sporadic/early 





onset PD


PARK3
unknown
2p13
AD/late onset PD, no 





caustative gene identified


PARK5
UCH-L1
4p14
AD/late onset PD, reported 





in a PD sibling pair


PARK7
DJ-1
1p36
AR/early onset PD


PARK8
LRRK2
12p11.2-
AD and sporadic/late 




q13.1
onset PD


PARK9
ATP13A2
1P36
AR/early onset PD


PARK10
unknown
Xq21-q25
Unknown, no causative 





gene identified


PARK11
GIGYF2
2q36-q37
AD/late onset PD, 





pathogenicity unknown


PARK12
unknown
Xq21-q25
Unknown, no causitive 





gene identified


PARK13
HTRA2
2p13
Unknown, no causitive 





gene identified


PARK14
PLA2G6
22q12-q13
AR/L-dopa responsive dystonia-





parkinsonism


PARK15
FBX07
22q12-q13
AR/parkinsonism-pyramidal 





syndrome





Notes:


AD, autosomal dominant; AR, autosomal recessive, UCHL1, ubiquitin carboxy-terminal hydroplast L1; PINK1, PTEN-induced kinase 1; ATP13A2, ATPase type 13A2; GIGYF2, GRB10-interacting GYF protein 2; HTRA2, HtrA serine peptidase 2; PLA2G6, group VI phospolipase A2; FBX07, F-box protein 7






In particular, specific mutations at the LRRK2 gene that have been proven shown to be pathogenic in the development of PD include Y1699C, R1441C, R1441H, R1441H, 11371V, Y1699G, G2019S, 12020T, and G2385R. Mutations within LRRK2 that are potentially pathogenic include E334K, Q1111H, I1192V, I1122V, S1228T, A1442P, L1719F, and T2356I. Those mutations that are associated with an increased risk of developing PR are R1628P and G2385R (see Kumari, ibid). Specific mutations at the SCNA gene that have been shown to be pathogenic in the development of PD include A53T, A30P, and E46K. Thus, the methods and compositions of the instant invention are useful for repairing such mutations in LRRK2 or SCNA or other genes associated with PD, and are useful for developing cell and transgenic animal models to study the intracellular pathology associated with the various mutations and for studying the whole organism consequences of these mutations.
Additionally, cells, cell lines and transgenic animals are useful for drug development. Such cells and animals may reveal phenotypes associated with a particular mutation (e.g. LRRKs G2019S or SCNA A53T, A30P, and E46K alterations) or with its correction, and may be used to screen drugs that will interact either specifically with the mutation(s) in question, or that are useful for treatment of the disease in an afflicted animal. Therapeutically, iPSCs can be derived ex vivo from a patient afflicted with a known genetic mutation associated with PD, and this mutation can be corrected using ZFN- or TALEN-mediated gene correction. The corrected iPSCs can then be differentiated into dopaminergic neurons and reimplanted into the patient.
The following Examples relate to exemplary embodiments of the present disclosure in which the nuclease comprises a zinc finger nuclease (ZFN). It will be appreciated that this is for purposes of exemplification only and that other nucleases can be used, for instance homing endonucleases (meganucleases) with engineered DNA-binding domains and/or fusions of naturally occurring of engineered homing endonucleases (meganucleases) DNA-binding domains and heterologous cleavage domains or TALENs.
EXAMPLES
Example 1
Nucleases Specific for LRRK2 and SCNA
ZFN pairs targeting the human LRRK2 gene in proximity of the rs34637584 SNP were used to test the ability of these ZFNs to induce DSBs at a specific target site. The amino acid sequence of the recognition helix region of the indicated ZFNs are shown below in Tables 2 and 4 and their target sites shown in Tables 3 and 5 ((DNA target sites indicated in uppercase letters; non-contacted nucleotides indicated in lowercase). The Cel-I assay (SurveyorTM, Transgenomics. Perez et al. (2008) Nat. Biotechnol. 26: 808-816 and Guschin et al. (2010) Methods Mol Biol. 649:247-56), was used where PCR-amplification of the target site was followed by quantification of insertions and deletions (indels) using the mismatch detecting enzyme Cel-I (Yang et al. (2000) Biochemistry 39, 3533-3541) which provides a lower-limit estimate of DSB frequency. Two days following transfection of the ZFN expression vector, genomic DNA was isolated from K562 cells using the DNeasy kit (Qiagen). In these experiments, all ZFN pairs were ELD/KKR FokI mutation pairs (described above).
Results from the Cel-I assay are shown in FIG. 1, and demonstrate that the ZFNs shown below are capable of inducing cleavage at their respective target sites.







TABLE 2







LRRK2-specific ZFNs













ZFN name
F1
F2
F3
F4
F5
F6





SBS 27870
QSGDLTR
RNDILAS
DRSNLSR
LRQDLKR
TSGNLTR
QSNQLRQ



(SEQ ID NO: 1)
(SEQ ID NO: 2)
(SEQ ID NO: 3)
(SEQ ID NO :4)
(SEQ ID NO: 5)
(SEQ ID NO: 6)


 


SBS 27865
QSGHLSR
RSDSLSV
QSSDLRR
QSGDLTR
RKDPLKE
N/A



(SEQ ID NO: 7)
(SEQ ID NO: 8)
(SEQ ID NO: 9)
(SEQ ID NO: 1)
(SEQ ID NO: 10)



 


SBS 27866
QSGHLSR
RSDSLSV
QSSDLRR
QSGDLTR
RRDPLIN
N/A



(SEQ ID NO: 7)
(SEQ ID NO: 8)
(SEQ ID NO: 9)
(SEQ ID NO: 1)
(SEQ ID NO: 11)



 


SBS 27867
QSGHLAR
RKWTLQG
QSSDLSR
QWSTRKR
RSDALTQ
N/A



(SEQ ID NO: 12)
(SEQ ID NO: 13)
(SEQ ID NO: 14)
(SEQ ID NO: 15)
(SEQ ID NO: 16)



 


SBS 27868
QSGHLAR
RKWTLQG
QSGDLTR 
QSGDLTR
RKDPLKE
N/A



(SEQ ID NO: 12)
(SEQ ID NO: 13)
(SEQ ID NO: 1)
(SEQ ID NO: 1)
(SEQ ID NO: 10)



 


SBS 30886
QSGHLSR
RSDSLSA
QSGDLTR
QSGDLTR
RKDPLKE
N/A



(SEQ ID NO: 7)
(SEQ ID NO: 44)
(SEQ ID NO: 1)
(SEQ ID NO: 1)
(SEQ ID NO: 10)



 


SBS 30888
QSGDLTR
QWGTRYR
DRSNLSR
LRQDLKR
TSGNLTR
QSNQLRQ



(SEQ ID NO: 1)
(SEQ ID NO: 45)
(SEQ ID NO: 3)
(SEQ ID NO: 4)
(SEQ ID NO: 5)
(SEQ ID NO: 6)
















TABLE 3







Target sites for LRRK2-specific ZFNs










ZFN Name
Target Site







SBS 27870
gcAAAGATtGCTGACtACGGCAttgctc




(SEQ ID NO: 17)



 



SBS 27865
tgATGGCAGCATTGGGAtacagtgtgaa




(SEQ ID NO: 18)



 



SBS 27866
tgATGGCAGCATTGGGAtacagtgtgaa




(SEQ ID NO: 18)



 



SBS 27867
tgATGGCAGCATTGGGAtacagtgtgaa




(SEQ ID NO: 18)



 



SBS 27868
tgATGGCAGCATTGGGAtacagtgtgaa




(SEQ ID NO: 18)



 



SBS 30886
tgATGGCAGCATTGGGAtacagtgtgaa




(SEQ ID NO: 18)



 



SBS 30888
gcAAAGATtGCTGACtACAGCAttgctc




(SEQ ID NO: 46)










ZFN pairs targeting the position nucleotide position 209 of exon 3 in the human SCNA gene were used to test the ability of these ZFNs to induce DSBs at the specific target site in K562 cells as described above. The ZFNS and their target sites are shown below in Tables 4 and 5.
Samples of the nucleofected cell pools were used to PCR amplify the region around the DSB, and then subjected to the Cel-I assay. The data are presented in FIG. 2 and demonstrate that these ZFNs pairs were capable of inducing DSBs at the target sequence. All ZFN pairs contained ELD/KKR FokI pairs (see above).







TABLE 4







SCNA-specific ZFNs













ZFN Name
F1
F2
F3
F4
F5
F6





SBS 26343
IRDYLIK
RPYTLRL
QSGDLTR
HRSDRTR
QSGALAR
RSDNLRE


(“43”)
(SEQ ID NO: 19)
(SEQ ID NO: 20)
(SEQ ID NO: 1)
(SEQ ID NO: 21)
(SEQ ID NO: 22)
(SEQ ID NO: 23)


 


SBS 26344
QKRNRTK
RPYTLRL
QSGDLTR
HRSDRTR
QSGALAR
RSDNLRE


(“44”)
(SEQ ID NO: 24)
(SEQ ID NO: 20)
(SEQ ID NO: 1)
(SEQ ID NO: 21)
(SEQ ID NO: 22)
(SEQ ID NO: 23)


 


SBS 26323
DSSDRKK
DQSNLRA
QSGDLTR
ASHNLRT
DQSNLRA
N/A


(“23”)
(SEQ ID NO: 25)
(SEQ ID NO: 26)
(SEQ ID NO: 1)
(SEQ ID NO: 27)
(SEQ ID NO: 26)



 


SBS 26327
DSSDRKK
DQSNLRA
QSGDLTR
TSHNRNA
DQSNLRA
N/A


(“27”)
(SEQ ID NO: 25)
(SEQ ID NO: 26)
(SEQ ID NO: 1)
(SEQ ID NO: 28)
(SEQ ID NO: 26)



 


SBS 26326
DRSYRNT
QSNDLNS
QSGDLTR
TSHNRNA
DQSNLRA
N/A


(“26”)
(SEQ ID NO: 29)
(SEQ ID NO: 30)
(SEQ ID NO: 1)
(SEQ ID NO: 28)
(SEQ ID NO: 26)



 


SBS 25356
DQSNLRA
QSGDLTR
ASHNLRT
DQSNLRA
N/A
N/A


(“56”)
(SEQ ID NO: 26)
(SEQ ID NO: 1)
(SEQ ID NO: 27)
(SEQ ID NO: 26)




 


SBS 25358
TSGSLSR
WRSSLTA
GRDSLIE
RSSDLSR 
QSGALAR
RSDNLRE


(“58”)
(SEQ ID NO: 31)
(SEQ ID NO: 32)
(SEQ ID NO: 33)
(SEQ ID NO: 34)
(SEQ ID NO: 22)
(SEQ ID NO: 23)


 


SBS 26329
DQSNLRA
QSGDLTR
TSHNRNA
DRSNRKT
N/A
N/A


(“29”)
(SEQ ID NO: 26)
(SEQ ID NO: 1)
(SEQ ID NO: 28)
(SEQ ID NO: 35)




 


SBS 26334
TSGSLSR
WRSSLTA
QSGDLTR
HRSDRTR
QSGALAR
RSDNLRE


(“34”)
(SEQ ID NO: 31)
(SEQ ID NO: 32)
(SEQ ID NO: 1)
(SEQ ID NO: 21)
(SEQ ID NO: 22)
(SEQ ID NO: 23)


 


SBS 26331
DSSDRKK
DQSNLRA
QSGDLTR
TSHNRNA
DRSNRKT
N/A


(“31”)
(SEQ ID NO: 25)
(SEQ ID NO: 26)
(SEQ ID NO: 1)
(SEQ ID NO: 28)
(SEQ ID NO: 35)
















TABLE 5







Target sites of SCNA-specific ZFNs










ZFN Name
Target Site







SBS 26343
aaCAGGTAaGCTCCATTGTGCttatatc



(“43”)
(SEQ ID NO: 36)



 



SBS 26344
aaCAGGTAaGCTCCATTGTGCttatatc



(“44”)
(SEQ ID NO: 36)



 



SBS 26323
caCACCATGCAcCACTCCctccttggtt



(“23”)
(SEQ ID NO: 37)



 



SBS 26327
caCACCATGCAcCACTCCctccttggtt



(“27”)
(SEQ ID NO: 37)



 



SBS 26326
caCACCATGCACCACTCcctccttggtt



(“26”)
(SEQ ID NO: 37)



 



SBS 25356
caCACCATGCAcCACtccctccttggtt



(“56”)
(SEQ ID NO: 37)



 



SBS 25358
aaCAGGTAaGCTCCAtTGTGCTtatatc



(“58”)
(SEQ ID NO: 36)



 



SBS 26329
caCACCATGCAcCACtccctccttggtt



(“29”)
(SEQ ID NO: 37)



 



SBS 26334
aaCAGGTAaGCTCCAtTGTGCTtatatc_



(“34”)
(SEQ ID NO: 36)



 



SBS 26331
caCACCATGCAcCACTCCctccttggtt



(“31”)
(SEQ ID NO: 37)










Example 3
Insertion of a 6055G>A Mutation into a Wild Type LRRK2 Allele
It would be advantageous to be able to create a mutant allele in the LRRK2 in any desired cell type to allow for study of the mutation in a variety of genotypic backgrounds.
Accordingly, the LRRK2-specific ZFNs were used to induce targeted integration of the sequences encoding this mutation within wild type cells using a donor DNA including the mutation. For donor, 1000 bp of a PCR product generated by performing a PCR reaction on patient DNA carrying the mutation was used, and is shown below, where the mutation is indicated in bold and underlined font:







(SEQ ID NO: 38)


5′ AGCTGAGCTAAACCTCTATGTGGTTTTAGGAAAATCAAAACTATTA


 


AATAAATGGCAAGTACAACAAAATCCCATCAATTCTTATTTAACATACT


 


TACATTTTGAAATAGTTAAAATATTCATATGATCATTGAGAGAATTCAG


 


AATTGCCTTTAAGTAATTGTTCACATATACAAAAGAAAAGTCTCCAAAA


 


ATTGGGTCTTTGCCTGAGATAGATTTGTCTTAAAATTGAAATCATTCAC


 


TTATCAGATTTGACCCTTTTTTAAAGCATAACTTTGCTGTGTAATATTA


 


GACTTATATGTTTTGATTTCCTTCTACAATATCTCTTAACTTTAAGGGA


 


CAAAGTGAGCACAGAATTTTTGATGCTTGACATAGTGGACATTTATATT


 


TAAGGAAATTAGGACAAAAATTATTATAATGTAATCACATTTGAATAAG


 


ATTTCCTGTGCATTTTCTGGCAGATACCTCCACTCAGCCATGATTATAT


 


ACCGAGACCTGAAACCCCACAATGTGCTGCTTTTCACACTGTATCCCAA


 


TGCTGCCATCATTGCAAAGATTGCTGACTACAGCATTGCTCAGTACTGC


 


TGTAGAATGGGGATAAAAACATCAGAGGGCACACCAGGTAGGTGATCAG


 


GTCTGTCTCATAATTCTATCTTCAGGATGGATAACCACTGACCTCAGAT


 


GTGAGTTCAGAAGAGTCAAAAGGAAAACAGAGTCTATCACATTGTGAAC


 


AGAGGTTTATTTTGTGAAAAAATGCAAGCATCACATTGTGATTTTTATC


 


TTGTATTTTGTAGGAAAAAAACAATTGATGTAATTTTTCAGGGCAAAAA


 


ACTGAATAAAAAGAAGAGAATGTTTGATATCAAGTTATATGTTTTAAAG


 


TTAGATTTGTAGATTCTTTAGATACTCTAGAGGTCATAAAAAGTAACAG


 


ACAAAACTTTAGTCTAGGTATTGTTGGCACTTGTGAGGCAAATCAAATT


 


CAGGTCCACAAATTCTTTTTC 3′






The LRRK2-specific ZFNs were nucleofected into K562 cells along with varying amounts of donor (from 0.5 μg-2.0 μg) according to standard protocol as described above. DNA was then isolated from the transfectants and used for a PCR reaction where a first PCR reaction was done to isolate the genomic DNA. This reaction was then diluted and subjected to another PCR yielding an approximately 320 bp product that was then subjected to SfcI digestion which exclusively recognizes the mutant sequence and creates a faster moving product on a gel.
The results are depicted in FIG. 3. Controls included nucleofection with the ZFNs only (lanes 2 and 6) and nucleofection with a plasmid encoding GFP (lane 10). The mutant digestion bands are evident in lanes 3, 4 and 7, (indicated with an arrow) demonstrating that these clones now carry the 6055 G> A mutation associated with the G2019S LRRK2 mutant allele. The band from the wild type gene is indicated with an open triangle.
ZFNs specific for either the wild type LRRK2 target sequence or the mutant target sequence were developed. As shown below, the 6055 G> A mutation in LRRK2 results in the expression of the mutant G2019S protein. Thus, it is of interest to develop ZFNs which are capable of enhanced cleavage on the mutant 6055 locus in comparison with the wild type 6055 locus. The two sequences are shown below, where the “Wildtype” sequence additionally has a silent mutation resulting in the creation of an AciI restriction site inserted:








(SEQ ID NO: 47)










 


(SEQ ID NO: 48)










 


(SEQ ID NO: 49)










 


(SEQ ID NO: 50)














ZFNs were developed with an increased affinity for the mutant sequence that ZFN 27870 binds to in the wild type LRRK2 gene. The new ZFP demonstrated specificity in a SELEX assay (as described in Perez et al (2008) supra) for A in the 6055 location rather than the wild type G (see, FIG. 7). These ZFNs were then used to test DNA cutting in vitro in K562 cells and were found to cut the LRRK2 locus using the Cel I assay as described above, where the assay was also conducted using a transient hypothermic shock (see co-owned US Patent publication 20110129898). The 30886/30888 pair has an enhanced affinity for the mutant 6055 locus but is still able to cleave the wild type gene in these conditions (see, FIG. 8).
Example 4
Insertion of a Mutation into a Wild Type SNCA Allele
For the development of model systems, it would be advantageous to insert a mutation into a PD-associated gene in any cell of interest. Accordingly, K562 cells were nucleofected as described above with 0.4 ug of each plasmid encoding ZFNs 26323/26334 (ELD/KKR) targeting the SNCA locus, along with increasing amounts of donor DNA. The donor used comprised approximately 1000 bp homology with the SNCA locus and contained the G209A mutation encoding the A53T SNCA mutation. The donor sequence is shown below where the G2019A mutation is indicated in bold/underline.







(SEQ ID NO: 39)


CTCGTGATCTGCCCACCTCGGCCTCCCAAATTGCTGGGATTACAGGCAT


 


GAGCCACTGCGCCCAGCCTAAAATGTTTTTTTTACATAATGGGTGTTCA


 


GCACATGTTAAAGCCTTCTCTCCATCCTTCTTCCCTTTTGTTTCATGGG


 


TTGACTGATCTGTCTCTAGTGCTGTACTTTTAAAGCTTCTACAGTTCTG


 


AATTCAAAATTATCTTCTCACTGGGCCCCGGTGTTATCTCATTCTTTTT


 


TCTCCTCTGTAAGTTGACATGTGATGTGGGAACAAAGGGGATAAAGTCA


 


TTATTTTGTGCTAAAATCGTAATTGGAGAGGACCTCCTGTTAGCTGGGC


 


TTTCTTCTATTTATTGTGGTGGTTACTGGAGTTCCTTCTTCTAGTTTTA


 


GGATATATATATATATTTTTTTCTTTCCCTGAAGATATAATAATATATA


 


TACTTCTGAAGATTGAGATTTTTAAATTAGTTGTATTGAAAACTAGCTA


 


ATCAGCAATTTAAGGCTAGCTTGAGACTTATGTCTTGAATTTGTTTTTG


 


TAGGCTCCAAAACCAAGGAGGGAGTGGTGCATGGTGTGACAACAGGTAA


 


GCTCCATTGTGCTTATATCCAAAGATGATATTTAAAGTATCTAGTGATT


 


GTGTGGCCCAGTATTCAAGATTCCTATGAAATTGTAAAACAATCACTGA


 


GCATTCTAAGAACATATCAGTCTTATTGAAACTGAATTCTTTATAAAGT


 


ATTTTTAAATAGGTAAATATTGATTATAAATAAAAAATATACTTGCCAA


 


GAATAATGAGGGCTTTGAATTGATAAGCTATGTTTAATTTATAGTAAGT


 


GGGCATTTAAATATTCTGACCAAAAATGTATTGACAAACTGCTGACAAA


 


AATAAAATGTGAATATTGCCATAATTTTAAAAAAAGTAAAATTTCTGTT


 


GATTACAGTAAAATATTTTGACCTTAAATTATGTTGATTACAATATTCC


 


TTTGATAATTCAGAGTGCATTTCAGGAAACACCCTTGGACAG






PCR was performed on the genomic DNA following nucleofection using the primer pairs described below that have homology to regions outside the target domain (making sure not to amplify the donor DNA that may be unintegrated). The primers were as shown below and amplified a 1929 bp sequence:









(SEQ ID NO: 40)



F: AAG ATT CCC ATA TCA TTG TCC TC



 



(SEQ ID NO: 41)



R: GGT TTG GAA GAA ATT CTG ATC CTG






The introduction of the G209A mutation results in generation of a Tsp45I restriction site, thus successful incorporation of the donor will result in a Tsp45I sensitive PCR product. Thus, the PCR product was digested with the Tsp45I restriction enzyme, and the product ran on a 1% agarose gel. The expected band sizes of the digestion products are 1018 and 912 bp. In a parallel experiment, the PCR product was diluted, and used as a template for the Cel-1 assay as described previously, using the Cel-I primers shown below.









(SEQ ID NO: 42)



F: AAA CTA GCT AAT CAG CAA TTT AAG GC



 



(SEQ ID NO: 43)



R: AGC CCT CAT TAT TCT TGG CA






The results of these experiments are shown in FIG. 4. FIG. 4A shows the results of the Tsp451 digest on samples that were nucleofected with either donor+ZFN, or donor alone. The results demonstrated that up to 13.5% of the SCNA alleles were mutated in the presence of the donor DNA. FIG. 4B shows the results of the Cel-I assay performed on these same samples. These data demonstrate that the ZFNs were active in these samples (e.g., up to 45% indels present in the absence of donor). Thus, the PD associated A53T mutation in SCNA was successfully introduced into these cells.
Example 5
Insertion of Disease-Causing A53T (G209) α-Synuclein Mutation into hESCs
A loxP site flanked puromycin resistance gene was inserted in the adjacent intron 23 bases downstream of position 209 in the wild type α-synuclein gene (the site corresponding to the A53T mutation) and the DSB (see, FIG. 5). For this gene editing strategy, a correct targeting event followed by Cre-recombinase mediated excision of the selection cassette is expected to result in a single base pair change that creates the A53T (G209A) mutation in exon 3 of α-synuclein, with a remaining single loxP site in the following intron (FIG. 5).
The targeting donor construct (Syn-A53T-loxP-pGK-puro-loxP) comprising approximately 600 bp homology on each side of the ZFN targeted site carrying the A53T (G209A) mutation (FIG. 5), together with 4 distinct ZFN pairs were electroporated into two different hESC lines (BGO1 and WIBR3).
Southern blot analysis of individual single-cell-derived puromycin-resistant clones using Southern blot probes 5′ and 3′ external to the donor homology region demonstrated the disruption of the genomic locus and integration of the targeting donor vector with a frequency of at least 25%. Further analysis using an internal probe against the 3′ targeting arm of the donor vector and against the ampicillin resistance gene revealed integrations of additional donor-derived vector sequences into the target locus in some clones, presumably via a hybrid homology directed repair (HDR)-end joining based process.
Three out of 336 puromycin resistant clones showed the correct modification of the targeted genomic locus by Southern blot, which was further confirmed by sequencing after Cre-mediated excision of the selection cassette. Two out of the three clones carried a small deletion in the second allele as a result of ZFN mediated gene disruption. The remaining correctly targeted clone with a non-disrupted wild-type allele (WIBR3-SNCAA53T/WT) displayed a normal karyotype and maintained a pluripotent state as indicated by the uniform expression of the pluripotency markers OCT4, NANOG, SOX2, Tra-1-60, Tra-1-81 and SSEA4 and the ability to form teratomas comprised of cell types originating from all three developmental germ layers. The stable integration of the transiently transfected ZFNs or the Cre recombinase expressing plasmid was excluded by Southern blot analysis. Furthermore, using an embryoid body (EB) based protocol to induce neural differentiation, we were able to derive efficiently dopaminergic thyrosine hydroxylase (TH) expressing neurons from the targeted WIBR3-SNCAA53T/WT hESC.
It is well established that increased α-synuclein expression levels in patients with genomic α-synuclein duplications and triplications are sufficient to cause PD (see, e.g. Singleton (2003) Science 302(5646):841). In order to verify that the loxP site remaining after Cre-mediated excision of the selection cassette does not interfere with the splicing or gene expression of α-synuclein, we differentiated the parental and targeted hESC lines into neurons in order to induce expression of α-synuclein. Mutation analysis RT-PCR confirmed that the levels and ratio of expression of the wild-type and the A53T-mutated transcript in the targeted cell line were similar to those observed in neurons derived from A53T-patient-specific hiPSCs (WIBR-iPS-SNCAA53T(1lox)).
In order to increase the targeting efficiency by reducing non-targeted integrations of the donor vector, as well as integration of donor vector sequences that are outside of the homology arms at the site of ZFN cleavage, we employed a positive-negative selection strategy by incorporating the herpes simplex virus thymidine kinase (HSV-TK) and diphteria toxin A-chain (DT-A) into the vector backbone (FIG. 5).
Using this strategy, 9 out of 41 puromycin- and ganciclovir-resistant colonies resulted in a correctly targeted allele. Four out of these clones had no disruption of the second, wild-type allele and 1 out of the 41 clones resulted in correct targeting and insertion of the A53T (G209A) mutation into both alleles (WIBR3-SNCAA53T/A53T). The targeted clones initially identified by Southern blot analysis were confirmed by sequencing of the genomic locus. None of the clones integrated the transiently transfected ZFNs.
Thus, this single step biallelic modification of a disease-relevant locus, only possible as a result of the significantly increased targeting efficiency due to the positive-negative selection strategy, represents a unique tool to study the role of mutant α-synuclein in the absence of the wild-type protein. Individuals homozygous for this mutation have not been described and the study of a homozygous mutant cell may provide new insights into the pathogenesis of PD.
Example 6
Introduction of the A53T (G209) Point Mutation into the α-Synuclein Gene without a Selection Marker
Genetically-pristine hESCs that contain no exogenous sequences other than the edited base for introducing the disease-causing point mutation were also generated. Given the high gene editing activity of the ZFNs, we constructed a donor vector lacking a selection cassette, including only of  ̃1 kb homology flanking the ZFN cleavage site and including the A53T (G209A) point mutation in order to insert the mutation in the endogenous wild type α-synuclein locus in hESCs (FIG. 6). The hESC line BGO1 was electroporated with the donor construct together with ZFNs and an eGFP expressing plasmid, which allows transfected cells to be enriched by fluorescence-activated cell sorting (FACS).
Colonies derived from single eGFP expressing cells were screened by Southern blot analysis using an A53T (G209A) allele specific Tsp45I restriction digest. Three out of 240 BGO1 clones showed the A53T (G209A) allele specific restriction pattern, indicative of an accurate genetic alteration event resulting in a A53T (G209A) mutation at the endogenous genomic locus. Further analysis by PCR genotyping and sequencing of the genomic locus confirmed one correctly targeted clone with the expected single base pair change of nucleotide 209 on one allele and an unaffected second allele, resulting in a A53T mutated cell line on a genetic BGO1 background (BGO1-SNCAA53T/WT).
The targeted cell line maintained a pluripotent state as shown by the uniform expression of the pluripotency markers OCT4, NANOG, SOX2, Tra-1-60, Tra-1-81 and SSEA4, the ability to form teratomas comprised of cell types originating from all three developmental germ layers and differentiation into dopaminergic neurons in vitro. The stable integration of the ZFNs and GFP expression plasmids was excluded by Southern blot analysis.
These results demonstrate that selection-free, ZFN-driven generation of point mutations was readily achieved in hESCs.
Example 7
Genetic Repair of the A53T (G209) α-Synuclein Mutation in PD Patient-Derived hiPSCs
Fibroblasts, obtained from a patient carrying the A53T (G209A) α-synuclein mutation were reprogrammed using previously described doxycycline-inducible and Cre-recombinase excisable lentiviral vectors (see, e.g., Hockemeyer et al. (2008) Cell Stem Cell. 3(3):346-53; Soldner et al. (2009) Cell 136(5):964-77.
The resulting hiPSCs before (WIBR-iPS-SNCAA53T(2lox) and after Cre-mediated excision of the reprogramming factors (WIBR-iPS-SNCAA53T(11ox)) displayed all basic properties of pluripotent cells as indicated by the uniform expression of the pluripotency marker proteins OCT4, NANOG, SOX2, Tra-1-60, Tra-1-81 and SSEA4, the ability to form teratomas comprised of cell types originating from all three developmental germ layers and a normal karyotype. Sequencing of the genomic α-synuclein locus confirmed the A53T (G209A) mutation in the patient derived hiPSCs. Furthermore, the cells were shown to differentiate into thyrosine-hydroxylase expressing dopaminergic neurons, the cell type primarily affected in PD.
In order to genetically repair the A53T (G209) mutation in the PD patient-derived hiPSCs, we employed a similar selection-free targeting strategy as described above for hESCs with the only difference of using a wild-type sequence containing donor vector.
Six out of 240 WIBR-iPS-SNCAA53T clones demonstrated the loss of the A53T specific Tsp45I restriction site by Southern blot screening, which is either the result of a ZFN-induced DSB followed by non-homologous error-prone end joining or HDR based correction of the allele. Further analysis by PCR genotyping and sequencing of the genomic locus confirmed one correctly repaired patient-derived hiPSC lines with the expected single base pair change of nucleotide 209 of α-synuclein.
Finally, to prevent uncontrollable effects from residual expression of the reprogramming transgenes (see, e.g., Soldner, supra), we excised the reprogramming vectors from the corrected patient derived hiPCs (WIBR-iPS-SNCAA53T-Corr), which subsequently displayed a normal karyotype, maintained a pluripotent state as indicated by the uniform expression of the pluripotency markers OCT4, NANOG, SOX2, Tra-1-60, Tra-1-81 and SSEA4 and the ability to form teratomas comprised of cell types originating from all three developmental germ layers. Stable integration of ZFNs, Cre recombinase and GFP expression plasmids was excluded by Southern blot analysis. The genetic repair of the A53T mutation in the patient-derived hiPSCs did not compromise the ability to differentiate into TH expressing dopaminergic neurons.
To further validate accurate editing of the α-synuclein locus in the repaired patient-derived hiPSC line (WIBR-iPS-SNCAA53T-Corr), we performed mutation analysis RT-PCR of α-synuclein after neuronal differentiation which confirmed the loss of expression of the mutated A53T(G209A) transcript.
Example 8
Additional Genetic Alterations in Engineered ESCs and iPSCs
A potential limitation of ZFN mediated genome editing is the induction of off-target DNA strand breaks at related sequences other than the intended target site. To examine off-target modifications in the targeted cell lines we initially determined the DNA binding specificity for each ZFN employed in this study by SELEX analysis as described previously, for example in Hockemeyer et al. (2009), supra; Perez et al. (2008), supra). This allows for the identification of the most probable off-target cleavage sites genome-wide. A Surveyor endonuclease (Cel-1) assay was subsequently performed to reveal any potential nonhomologous end joining (NHEJ)-mediated indels for the top 12 putative off-target sites in the WIBR3-SNCAA53T/WT-2, WIBR3-SNCAA53T/WT-3 and WLBR3-SNCA-A53T/A53T lines and the top 38 putative off-target sites (representing candidate off target sites for the L1/R1 ZFN heterodimerization, as well as L1 and R1 homodimerization sites) for WIBR3-iPS-SNCAA53T/corr, BGO1-SNCAA53T/WT and WIBR3-SNCAA53T/WT-1. No evidence of off-target cleavage at any of the examined loci was found.
It is well established that prolonged culture of hESCs can lead to adaption such as increased growth rate, reduced apoptosis and the acquisition of chromosomal abnormalities such as copy number variations (CNVs). See, e.g., Narva et al. (2010) Nat Biotechnol. 28(4):371-7). More recently, it has been proposed that the reprogramming process itself compromises the genomic integrity and leads to the accumulating of CNVs and somatic mutations. See, e.g. Gore et al. (2011) Nature 471(7336):63-67; Hussein et al. (2011) Nature 471(7336):58-62. Although all our tested cell lines showed a normal karyotype after genome editing as determined by conventional karyotyping, the low resolution of this technology excludes the detection of smaller CNVs, which are considered a major source for human genome variability and particularly important in the context of genome editing. Such genetic changes involve the induction of DNA double strand breaks and clonal events, which are thought to increase the chance for additional genomic alterations. We therefore performed high-resolution genome wide CNV analysis using an Affymetrix SNP 6.0 array as described previously in Hussein et al., supra and Narva et al., supra on 3 pairs of isogenic parental and genetically modified cell lines.
We identified on average 77 CNVs with an average size of 158 kb per cell line. For human ES cell lines this is slightly higher as described previously and may be due technical variability such as low sample or the higher passage numbers (between Passage P25 and P60 for hESCs and P22 and P40 for hiPSCs) of the cell lines used in this study. 63% of the identified CNVs (number and total genomic area) overlapped between isogenic pairs using pairwise comparison before and after ZFN mediated genome modification. In contrast, we observed only 35% overlap of CNVs between genetically unrelated samples. This degree of overlap is comparable to previously published hESC data comparing identical cell lines at different passage numbers. See, e.g., Narva et al., supra. Furthermore, comparing average number and total genome area of CNVs before and after ZFN mediated gene targeting did not reveal any additional increase other than that observed during regular hESCs in culture.
Thus, our analysis confirms that hESCs and hiPSCs contain a higher number of CNVs than the normal human genome, probably acquired during the reprogramming process and prolonged cell culture. We conclude that the Cre-recombinase mediated excision of the reprogramming factors and ZFN mediated genome editing did not substantially increase the level of genomic alterations.
To further validate that the genome editing approach did not induce major genetic or epigenetic alterations, which would result in aberrant gene expression profiles, we performed whole genome expression analysis of undifferentiated pairs of parental and genetically modified cell lines. Despite very similar gene expression of all pluripotent cell lines hierarchical cluster analysis suggests that the influence of genetic background on gene expression is more significant than the genome editing, since gene expression patterns of pairs of parental and genome edited cell lines are more closely correlated than to genetically independent cell lines (see Soldner et al. (2011) Cell 146(2): 318-331).
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Although disclosure has been provided in some detail by way of illustration and example for the purposes of clarity of understanding, it will be apparent to those skilled in the art that various changes and modifications can be practiced without departing from the spirit or scope of the disclosure. Accordingly, the foregoing descriptions and examples should not be construed as limiting.

## Claims

1. A zinc finger nuclease (ZFN) fusion protein comprising a cleavage domain and a zinc-finger protein (ZFP) that binds to a target site in a leucine rich repeat kinase 2 (LRRK2) or α-synuclein (SCNA) gene in a genome, wherein the ZFP comprises 5 or 6 engineered zinc-finger binding domains, each zinc finger domain comprising a recognition helix region designated F1 to F5 or F1 to F6, wherein the zinc finger protein comprises the recognition helix regions as shown in a single row of Table 2 or Table 4 and further wherein the target site is selected from the group consisting of SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:46, SEQ ID NO:36 and SEQ ID NO:37.

2. A kit comprising a ZFN according to claim 1 and instructions for cleaving a LRRK2 or a SCNA gene.