WO2005118614A1 - Methodes et compositions de traitement de la douleur neuropathique - Google Patents

Methodes et compositions de traitement de la douleur neuropathique Download PDF

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WO2005118614A1
WO2005118614A1 PCT/US2005/012048 US2005012048W WO2005118614A1 WO 2005118614 A1 WO2005118614 A1 WO 2005118614A1 US 2005012048 W US2005012048 W US 2005012048W WO 2005118614 A1 WO2005118614 A1 WO 2005118614A1
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gene
zfp
expression
protein
cells
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PCT/US2005/012048
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John F.M. Forsayeth
Raymond A. Chavez
Trevor Collingwood
Andrew Mcnamara
Yann Jouvenot
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Avigen, Inc.
Sangamo Biosciences, Inc.
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Publication of WO2005118614A1 publication Critical patent/WO2005118614A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4702—Regulators; Modulating activity
    • C07K14/4703—Inhibitors; Suppressors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides

Definitions

  • BACKGROUND Neuropathic pain also referred to as a chronic pain
  • a chronic pain is a complex disorder resulting from injury to the nerve, spinal cord or brain.
  • nerve fibers in subjects with neuropathic pain develop abnormal excitability, particularly hyper- excitability, Zimmerman (2001) Eur J Pharmacol 429(l-3):23-37.
  • Zimmerman 2001
  • Eur J Pharmacol 429(l-3):23-37 Although the American Pain Society estimates that nearly 50 million Americans are totally or partially disabled by pain, there are currently very few effective, well-tolerated treatments available. Wetzel et al. (1997) Ann Pharmacother 31(9):1082-3). Indeed, existing therapeutics cause a range of undesirable side effects primarily due to the difficulty in developing small-molecule drugs capable of specifically targeting the receptor/channel of choice.
  • Transduction of noxious stimuli in nociception is mediated by cellular receptors that typically include non-selective ion channels (e.g., vanilloid receptor, VR1), sodium ion channels (e.g., PN3/NaV ⁇ .g), tyrosine receptor kinases (e.g., Trl A), and GPCRs (e.g., bradykinin receptors).
  • non-selective ion channels e.g., vanilloid receptor, VR1
  • sodium ion channels e.g., PN3/NaV ⁇ .g
  • tyrosine receptor kinases e.g., Trl A
  • GPCRs e.g., bradykinin receptors
  • Navl.8 correlates with inhibition of neuropathic pain in the rat spinal nerve injury model of chronic pain.
  • modulation of genes aberrantly expressed in neuropathic pain has not been previously described.
  • the ability to alter expression of these genes may have utility in treating and/or preventing many forms of pain.
  • ZFPs zinc finger proteins
  • methods utilizing such proteins are provided for use in treating neuropathic pain.
  • ZFPs that bind to a target site in genes that are aberrantly expressed in subjects having neuropathic pain are described, i addition, ZFPs that bind to a target site in genes expressed at normal levels in subjects experiencing neuropathic pain, modulation of whose expression results in decreased pain perception, are also provided.
  • genes that are over-expressed in the dorsal root ganglia (DRG) of pain patients ⁇ e.g., VR1, TRKA and/or Navl.8 can be repressed, while genes that are under- expressed in the same populations can be activated.
  • DDG dorsal root ganglia
  • the ZFPs can be fused to a regulatory domain as part of a fusion protein. By selecting either an activation domain or a repression domain for fusion with the ZFP, one can either activate or repress gene expression. Thus, by appropriate choice of the regulatory domain fused to the ZFP, one can selectively modulate the expression of a target gene and hence various physiological processes correlated with neuropathic pain.
  • a physiological process e.g., pain
  • a plurality of ZFPs (or fusions comprising these ZFPs) is administered. These ZFPs can then bind to different target sites located within a single target gene (e.g., VR1, TRKA, Navl.8, etc.). Alternatively, the ZFPs can bind to target sites in different genes (e.g., two or more of VR1, TRKA, NAV1.8, etc.). Such ZFPs can in some instances have a synergistic effect.
  • the plurality of fusion proteins includes different regulatory domains.
  • compositions containing the nucleic acids and/or ZFPs are also provided.
  • certain compositions include a nucleic acid that encodes one of the ZFPs described herein operably linked to a regulatory sequence, combined with a pharmaceutically acceptable carrier or diluent, wherein the regulatory sequence allows for expression of the nucleic acid in a cell.
  • Protein-based compositions include a ZFP as disclosed herein and a pharmaceutically acceptable carrier or diluent.
  • FIG. 1 is a graph depicting repression of VR1 gene expression in rat cells transfected with a plasmid encoding a fusion of a KOX repression domain and a VR1- targeted ZFP (designated 6332, 6337, 6338).
  • the fusion proteins are designated 6332- KOX, 6337-KOX, and 6338-KOX.
  • NTC refers to a non-transfected control.
  • FIG. 2 is a graph depicting repression of VR1 gene expression in rat cells transfected with a plasmid encoding a fusion of a KOX repression domain and a VR1- targeted ZFP (designated 6144, 6149, 6150).
  • the fusion proteins are designated 6144- KOX, 6149-KOX, and 6150-KOX.
  • eGFP refers to an enhanced Green Fluorescent Protein (GFP) control.
  • FIG. 3 is a graph depicting results of FACS and shows repression of VR1 protein levels in rat cells transfected with a plasmid encoding 6144-KOX, 6149-KOX, 6150- KOX a fusion of a KOX repression domain and a VR1 -targeted ZFP (designated 6144, 6149, 6150).
  • the fusion proteins are designated 6144-KOX, 6149-KOX, 6150-KOX, 6332-KOX, 6337-KOX, and 6338-KOX.
  • “GFP” refers to FACS results obtained with a GFP control.
  • FIG. 4 is a graph depicting repression of TrkA gene expression by in rat cells transfected with a plasmid encoding a fusion of a KOX repression domain and a TrkA- targeted ZFP (designated 6182, 6297) and a plasmid encoding puromycin resistance. Puromycin selection is used to kill untransfected cells. The fusion proteins are designated 6182-KOX and 6297-KOX. "Puromycin cntrl" refers to controls co- transfected with a control plasmid and the plasmid encoding puromycin resistance.
  • FIG. 5 is a graph depicting results of FACS and showing repression ofTrkA protein levels in rat cells co-transfected with a plasmid encoding 6182-KOX or 6297- KOX and a plasmid encoding puromycin resistance.
  • Puromycin cntrl refers to controls co-transfected with a control plasmid and the plasmid encoding puromycin resistance.
  • FIG. 6 is a graph depicting repression of NAV1.8 in human cells transfected with a plasmid encoding a fusion of a KOX repression domain and a NAV1.8-targeted ZFP (designated 6584, 6585, 6586, 6587, 6590, 6591, 6621, and 6622).
  • the fusion proteins are designated 6584-KOX, 6585-KOX, 6586-KOX, 6587-KOX, 6590-KOX, 6591-KOX, 6621 -KOX, and 6622-KOX.
  • eGFP refers to an enhanced Green Fluorescent Protein (GFP) control.
  • EF-la refers to the promoter controlling expression of the fusion protein
  • Kox refers to the presence of a KOX repression domain in the encoded protein
  • the number refers to the particular TrkA-targeted zinc finger binding domain (see Tables 1 and 5 for DNA target sequences and recognition domain amino acid sequences, respectively, for these zinc finger domains).
  • EF-laGFPKox and pBluescript are control plasmids: EF-laGFPKox lacks an engineered zinc finger binding domain; pBluescript is a vector lacking sequences encoding a fusion protein. Bars show the standard error of the mean for duplicate determinations.
  • FIG. 8 is an autoradiographic image of a protein blot in which lysates from cells transfected with plasmids encoding TrkA-targeted ZFP/KOX fusion proteins were analyzed.
  • the top panel shows assays for the presence ofTrkA and TFILB.
  • the lower panel shows assays for the presence of the zinc finger/Kox fusion proteins, using a primary mouse anti-FLAG M2 monoclonal antibody and a donkey anti-mouse IgG- horseradish peroxidase secondary antibody.
  • Abbreviations and protein identifications are the same as in Figure 7.
  • MOLECULAR CLONING A LABORATORY MANUAL, Second edition, Cold Spring Harbor .Laboratory Press, 1989 and Third edition, 2001; Ausubel et al., CURRENT PROTOCOLS LN MOLECULAR BIOLOGY, John Wiley & Sons, New York, 1987 and periodic updates; the series METHODS IN ENZYMOLOGY, Academic Press, San Diego; Wolffe, CHROMATIN STRUCTURE AND FUNCTION, Third edition, Academic Press, San Diego, 1998; METHODS IN ENZYMOLOGY, Vol. 304, "Chromatin" (P .M. Wassarman and A. P.
  • ZFP zinc finger protein
  • a ZFP has least one finger, typically two, three, four, five, six or more fingers. Each finger binds from two to four base pairs of DNA, typically three or four base pairs of DNA.
  • a ZFP binds to a nucleic acid sequence called a target site or target segment. Each finger typically comprises an approximately 30 amino acid, zinc- chelating, DNA-binding subdomain.
  • C 2 H 2 class An exemplary motif characterizing one class of these proteins (C 2 H 2 class) is -Cys-(X)2-4-Cys-(X)12-His-(X)3-5-His (where X is any amino acid) (SEQ LD NO: 1).
  • Additional classes of zinc finger proteins are known and are useful in the practice of the methods, and in the manufacture and use of the compositions disclosed herein (see, e.g., Rhodes et al. (1993) Scientific American 268:56- 65 and US Patent Application Publication No. 2003/0108880).
  • a “target site” is the nucleic acid sequence recognized by a ZFP.
  • a single target site typically has about four to about ten base pairs.
  • a two-fingered ZFP recognizes a four to seven base pair target site
  • a three-fingered ZFP recognizes a six to ten base pair target site
  • a four.finger ZFP recognizes a 12-14 bp target sequence
  • a six-fingered ZFP recognizes an 18-20 bp target sequence, which can comprise two adjacent nine to ten base pair target sites or three adjacent 6-7 bp target sites.
  • a "target subsite” or “subsite” is the portion of a DNA target site that is bound by a single zinc finger, excluding cross-strand interactions. Thus, in the absence of cross- strand interactions, a subsite is generally three nucleotides in length.
  • Kd refers to the dissociation constant for a binding molecule, i.e., the concentration of a compound (e.g., a zinc finger protein) that gives half maximal binding on the of the compound to its target under given conditions (i.e., when (target] «Kd), as measured using a given assay system (see, e.g., U.S. Pat. No. 5,789,538).
  • a compound e.g., a zinc finger protein
  • the assay system used to measure the Kd should be chosen so that it gives the most accurate measure of the actual Kd of the ZFP. Any assay system can be used, as long is it gives an accurate measurement of the actual Kd of the ZFP.
  • the Kd for a ZFP is measured using an electrophoretic mobility shift assay ("EMSA "). Unless an adjustment is made for ZFP purity or activity, the Kd calculations may result in an overestimate of the true Kd of a given ZFP.
  • the Kd of a ZFP used to modulate transcription of a gene is less than about 100 nM, more preferably less than about 75 nM, more preferably less than about 50 nM, most preferably less than about 25 nM.
  • nucleic acids or polypeptides refer to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned for maximum correspondence, as measured using a sequence comparison algorithm such as those described below for example, or by visual inspection.
  • substantially identical in the context of two nucleic acids or polypeptides, refers to two or more sequences or subsequences that have at least 75%, preferably at least 85%, more preferably at least 90%, 95% or higher or any integral value therebetween nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using a sequence comparison algoritlim such as those described below for example, or by visual inspection.
  • the substantial identity exists over a region of the sequences that is at least about 10, preferably about 20, more preferably about 40-60 residues in length or any integral value therebetween, preferably over a longer region than 60-80 residues, more preferably at least about 90-100 residues, and most preferably the sequences are substantially identical over the full length of the sequences being compared, such as the coding region of a nucleotide sequence for example.
  • sequence comparison typically one sequence acts as a reference sequence, to which test sequences are compared.
  • test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated.
  • sequence comparison algorithm calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
  • Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homo logy alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Natl. Acad. Sci.
  • HSPs high scoring sequence pairs
  • T some positive-valued threshold score
  • Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always ⁇ 0).
  • M forward score for a pair of matching residues; always >0
  • N penalty score for mismatching residues; always ⁇ 0.
  • a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
  • sequence similarity the default parameters of the BLAST programs are suitable.
  • the BLASTP program uses as defaults a word length 15 (W) of3, an expectation (E) of 10, and the BLOSUM62 scoring matrix.
  • the TBLATN program (using protein sequence for nucleotide sequence) uses as defaults a word length (W) of 3, an expectation (E) of 10, and a BLOSUM 62 scoring matrix, (see Henikoff& Henikoff, Proc. Natl. Acad. Set USA 89:10915 (1992)).
  • the BLAST algorithm In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5877 (1993)).
  • One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance.
  • P(N) the smallest sum probability
  • a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
  • hybridizes substantially refers to complementary hybridization between a probe nucleic acid and a target nucleic acid and embraces minor mismatches that can be accommodated by reducing the stringency of the hybridization media to achieve the desired detection of the target polynucleotide sequence.
  • hybridizing specifically to refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent conditions when that sequence is present in a complex mixture (e.g., total cellular) DNA or RNA.
  • nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the polypeptide encoded by the second nucleic acid, as described below.
  • Consatively modified variations of a particular polynucleotide sequence refers to those polynucleotides that encode identical or essentially identical amino acid sequences, or where the polynucleotide does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given polypeptide.
  • the codons CGU, CGC, CGA, CGG, AGA, and AGG all encode the amino acid arginine.
  • the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide.
  • Such nucleic acid variations are "silent variations," which are one species of “conservatively modified variations.” Every polynucleotide sequence described herein that encodes a polypeptide also describes every possible silent variation, except where otherwise noted.
  • each codon in a nucleic acid except AUG, which is ordinarily the only codon for methionine
  • each "silent variation" of a nucleic acid that encodes a polypeptide is implicit in each described sequence.
  • a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions.
  • a "conservative substitution,” when describing a protein, refers to a change in the amino acid composition of the protein that does not substantially alter the protein's activity.
  • “conservatively modified variations" of a particular amino acid sequence refers to amino acid substitutions of those amino acids that are not critical for protein activity or substitution of amino acids with other amino acids having similar properties (e.g., acidic, basic, positively or negatively charged, polar or non-polar, etc.) such that the substitutions of even critical amino acids do not substantially alter activity.
  • Conservative substitution tables providing functionally similar amino acids are well known in the art. See, e.g., Creighton (1984) Proteins, W. H. Freeman and Company.
  • a “functional fragment” or “functional equivalent” 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 ore more amino acid or nucleotide substitutions.
  • nucleic acid e.g., coding .function, ability to hybridize to another nucleic acid, binding to a regulatory molecule
  • protein function are well known.
  • DNA-binding function of a polypeptide can be determined, for example, by filter-binding, electrophoretic mobility- shift, or immunoprecipitation assays. 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.
  • nucleic acid “polynucleotide,” and “oligonucleotide” are used interchangeably and refer to a deoxyribonucleotide or ribonucleotide polymer 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.
  • an analogue of a particular nucleotide has the same base-pairing specificity; i.e., an analogue of A will base-pair with T.
  • polynucleotide sequence is the alphabetical representation of a polynucleotide molecule. This alphabetical representation can be input into databases in a computer having a central processing unit and used for bioinformatics applications such as functional genomics and homology searching.
  • the , terms additionally encompass nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides.
  • Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-0-methyl ribonucleotides, and peptide- nucleic acids (PNAs).
  • the nucleotide sequences are displayed herein in the conventional 5 '-3' orientation.
  • 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 HI is generally associated with the linker DNA.
  • 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.
  • 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.
  • 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, hpoprotein, 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.
  • exogenous molecule can be the same type of molecule as an endogenous molecule, e.g., protein or nucleic acid (i.e., an exogenous gene), providing it has a sequence that is different from an endogenous molecule.
  • Methods for the introduction of exogenous molecules into cells 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 "endogenous molecule” is one that is normally present in a particular cell at a particular developmental stage under particular environmental conditions.
  • An “endogenous gene” is a gene that is present in its normal genomic and chromatin context. An endogenous gene can be present, e.g., in a chromosome, an episome, a bacterial genome or a viral genome.
  • the phrase "adjacent to a transcription initiation site” refers to a target site that is within about 50 bases either upstream or downstream of a transcription initiation site.
  • "Upstream" of a transcription initiation site refers to a target site that is more than about 50 bases 5' of the transcription initiation site (i.e., in the non-transcribed region of the gene).
  • Downstream of a transcription initiation site refers to a target site that is more than about 50 bases 3' of the transcription initiation site.
  • a "fusion molecule” is a molecule in which two or more subunit molecules are linked, typically 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 polypeptides (for example, a fusion between a ZFP DNA-binding domain and a transcriptional activation domain) and fusion nucleic acids (for example, a nucleic acid encoding the fusion polypeptide 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.
  • 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 a mRNA.
  • Gene products also include RNAs that 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.
  • Gene activation refers to any process that results in an increase in production of a gene product.
  • a gene product can be either RNA (including, but not limited to, mRNA, rRNA, tRNA, and structural RNA) or protein. Accordingly, gene activation includes those processes that increase transcription of a gene and/or translation of a mRNA.
  • Examples of gene activation processes that increase transcription include, but are not limited to, those that facilitate formation of a transcription initiation complex, those that increase transcription initiation rate, those that increase transcription elongation rate, those that increase processivity of transcription and those that relieve transcriptional repression (by, for example, blocking the binding of a transcriptional repressor). Gene activation can constitute, for example, inhibition of repression as well as stimulation of expression above an existing level. Examples of gene activation processes that increase translation include those that increase translational initiation, those that increase translational elongation and those that increase mRNA stability.
  • gene activation comprises any detectable increase in the production of a gene product, in some instances an increase in production of a gene product by about 2-fold, in other instances from about -2- to about 5-fold or any integer therebetween, in still other instances between about 5- and about 10-fold or any integer therebetween, in yet other instances between about 10- and about 20- fold or any integer therebetween, sometimes between about 20- and about 50-fold or any integer therebetween, in other instances between about 50- and about 100-fold or any integer therebetween, and in yet other instances between 100-fold or more.
  • “Gene repression” and “inhibition of gene expression” refer to any process that results in a decrease in production of a gene product.
  • a gene product can be either RNA (including, but not limited to, mRNA, rRNA, tRNA, and structural RNA) or protein. Accordingly, gene repression includes those processes that decrease transcription of a gene and/or translation of a mRNA. Examples of gene repression processes which decrease transcription include, but are not limited to, those which inhibit formation of a transcription initiation complex, those which decrease transcription initiation rate, those which decrease transcription elongation rate, those which decrease processivity of transcription and those which antagonize transcriptional activation (by, for example, blocking the binding of a transcriptional activator). Gene repression can constitute, for example, prevention of activation as well as inhibition of expression below an existing level.
  • gene repression processes that decrease translation include those that decrease translational initiation, those that decrease translational elongation and those that decrease mRNA stability.
  • Transcriptional repression includes both reversible and i ⁇ eversible inactivation of gene transcription.
  • gene repression comprises any detectable decrease in the production of a gene product, in some instances a decrease in production of a gene product by about 2-fold, in other instances from about 2- to about 5- fold or any integer therebetween, in yet other instances between about 5- and about 10- fold or any integer therebetween, in still other instances between about 10- and about 20- fold or any integer therebetween, sometimes between about 20- and about 50-fold or any integer therebetween, in other instances between about 50- and about 100-fold or any integer therebetween, in still other instances 100-fold or more.
  • modulation refers to a change in the level or magnitude of an activity or process. The change can be either an increase or a decrease.
  • modulation of gene expression includes both gene activation and gene repression. Modulation can be assayed by determining any parameter that is indirectly or directly affected by the expression of the target gene (e.g. VR1, TRKA, Navl.8).
  • Such parameters include, e.g., changes in RNA or protein levels, changes in protein activity, changes in product levels, changes in downstream gene expression, changes in reporter gene transcription, (luciferase, CAT, /3-galactosidase, /3-glucuronidase, green fluorescent protein (see, e.g., Mistili & Spector, Nature Biotechnology 15:961-964 (1997)); changes in signal transduction, phosphorylation and dephosphorylation, receptor-ligand interactions, second messenger concentrations (e.g., cGMP, cAMP, IP3, and Ca 2+ ), cell growth, and vascularization.
  • reporter gene transcription e.g., luciferase, CAT, /3-galactosidase, /3-glucuronidase, green fluorescent protein (see, e.g., Mistili & Spector, Nature Biotechnology 15:961-964 (1997)
  • changes in signal transduction, phosphorylation and dephosphorylation, receptor-ligand interactions
  • Such functional effects can be measured by any means known to those skilled in the art, e.g., measurement of RNA or protein levels, measurement of RNA stability, identification of downstream or reporter gene expression, e.g., via chemiluminescence, fluorescence, colorimetric reactions, antibody binding, inducible markers, ligand binding assays; changes in intracellular second messengers such as caMP and mositol triphosphate (IP3); changes in intracellular calcium levels; cytokine release, and the like.
  • a "regulatory domain” or “functional domain” refers, to a protein or a protein domain that has transcriptional modulation activity when tethered to a DNA binding domain, i.e., a ZFP.
  • a regulatory domain is covalently or non-covalently linked to a ZFP (e.g., to form a fusion molecule) to effect transcription modulation.
  • Regulatory domains can be activation domains or repression domains.
  • Activation domains include, but are not limited to, VP16, VP64 and the p65 subunit of nuclear factor Kappa-B.
  • Repression domains include, but are not limited to, KRAB, KOX, MBD2B and v-ErbA.
  • Additional regulatory domains include, e.g., transcription factors and co- factors (e.g., MAD, ERD, SLD, early growth response factor 1, and nuclear hormone receptors), endonucleases, integrases, recombinases, methyltransferases, histone acetyltransferases, histone deacetylases etc.
  • Activators and repressors include co- activators and co- repressors (see, e.g., Utley et al, Nature 394:498-502 (1998)).
  • a ZFP can act alone, without a regulatory domain, to effect transcription modulation.
  • operably linked or "operatively linked” is used 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.
  • a transcriptional regulatory- sequence such as a promoter
  • An operatively linked transcriptional regulatory sequence is generally joined in cis with a coding sequence, but need not be directly adjacent to it.
  • an enhancer can constitute a transcriptional regulatory sequence that is operatively linked to a coding sequence, even though they are not contiguous.
  • operably linked or "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.
  • the ZFP DNA-binding domain and the transcriptional activation domain (or functional fragment thereof) are in operative linkage if, in the fusion polypeptide, the ZFP DNA-binding domain portion is able to bind its target site and/or its binding site, while the transcriptional activation domain (or functional fragment thereof) is able to activate transcription.
  • the term "recombinant,” when used with reference to a cell, indicates that the cell replicates an exogenous nucleic acid, or expresses a peptide or protein encoded by an exogenous nucleic acid.
  • Recombinant cells can contain genes that are not found within the native (non-recombinant) form of the cell.
  • Recombinant cells can also contain genes found in the native form of the cell wherein the genes are modified and re-introduced into the cell by artificial means.
  • the term also encompasses cells that contain a nucleic acid endogenous to the cell that has been modified without removing the nucleic acid from the cell; such modifications include those obtained by gene replacement, site-specific mutation, and related techniques.
  • a “recombinant expression cassette,” “expression cassette” or “expression construct” is a nucleic acid construct, generated recombinantly or synthetically, that has control elements that are capable of effecting expression of a structural gene that is operatively linked to the control elements in hosts compatible with such sequences.
  • Expression cassettes include at least promoters and optionally, transcription termination signals.
  • the recombinant expression cassette includes at least a nucleic acid to be transcribed (e.g., a nucleic acid encoding a desired polypeptide) and a promoter. Additional factors necessary or helpful in effecting expression can also be used as described herein.
  • an expression cassette can also include nucleotide sequences that encode a signal sequence that directs secretion of an expressed protein from the host cell. Transcription termination signals, enhancers, and other nucleic acid sequences that influence gene expression, can also be included in an expression cassette.
  • a “promoter” is defined as an a ⁇ ay of nucleic acid control sequences that direct transcription.
  • a promoter typically includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of certain RNA polymerase II type promoters, a TATA element, CCAAT box, SP-1 site, etc.
  • a promoter also optionally includes distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription.
  • the promoters often have an element that is responsive to transactivation by a DNA- binding moiety such as a polypeptide, e.g., a nuclear receptor, Gal4, the lac repressor and the like.
  • a “constitutive” promoter is a promoter that is active under most environmental and developmental conditions.
  • An “inducible” promoter is a promoter that is active ' under certain environmental or developmental conditions.
  • a “weak promoter” refers to a promoter having about the same activity as a wild type herpes simplex virus (“HSV”) thymidine kinase (“tk”) promoter or a mutated HSV tk promoter, as described in Eisenberg & McKnight, Mol. Cell. Biol. 5;1940-1947 (1985).
  • an "expression vector” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a host cell, and optionally integration or replication of the expression vector in a host cell.
  • the expression vector can be part of a plasmid, virus, or nucleic acid fragment, of viral or non- viral origin.
  • the expression vector includes an "expression cassette,” which comprises a nucleic acid to be transcribed operably linked to a promoter.
  • expression vector also encompasses naked DNA operably linked to a promoter.
  • host cell is meant a cell that contains an expression vector or nucleic acid, either of which optionally encodes a ZFP or a ZFP fusion protein.
  • the host cell typically supports the replication or expression of the expression vector.
  • Host cells can be prokaryotic cells such as, for example, E. coli, or eukaryotic cells such as yeast, fungal, protozoal, higher plant, insect, or amphibian cells, or mammalian cells such as CHO, HeLa, 293, CDS-I, and the like, e.g., cultured cells (in vitro), explants and primary cultures (in vitro and ex vivo), and cells in vivo.
  • polypeptide As applied to an object, means that the object can be found in nature, as distinct from being artificially produced by humans.
  • polypeptide polypeptide
  • peptide and protein
  • polypeptides are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an analog or mimetic of a co ⁇ esponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers.
  • Polypeptides can be modified, e.g., by the addition of carbohydrate residues to form glycoproteins.
  • polypeptide polypeptide
  • peptide and protein
  • glycoproteins as well as non-glycoproteins.
  • polypeptide sequences are displayed herein in the conventional N-terminal to C-terminal orientation.
  • a "subsequence” or “segment” when used in reference to a nucleic acid or polypeptide refers to a sequence of nucleotides or amino acids that comprise a part of a longer sequence of nucleotides or amino acids (e.g., a polypeptide), respectively.
  • the terms “treating” and “treatment” as used herein refer to reduction in severity and/or frequency of symptoms, elimination of symptoms and/or underlying cause, prevention of the occurrence of symptoms and/or their underlying cause, and improvement or remediation of damage.
  • an “effective” amount (or “therapeutically effective” amount) of a pharmaceutical composition is meant a sufficient, but nontoxic amount of the agent to provide the desired effect.
  • the term refers to an amount sufficient to treat a subject.
  • therapeutic amount refers to an amount sufficient to remedy a disease state or symptoms, by preventing, hindering, retarding or reversing the progression of the disease or any other undesirable symptoms whatsoever.
  • prophylactically effective amount refers to an amount given to a subject that does not yet have the disease, and thus is an amount effective to prevent, hinder or retard the onset of a disease.
  • compositions and methods are provided herein for modulating the expression of target genes that are over- or under-expressed in subjects with neuropathic pain.
  • zinc finger proteins that are capable of modulating expression of one or more target genes involved in nerve excitability are provided, thereby modulating chronic pain.
  • methods for treating neuropathic pain by contacting a cell or population of cells such as in an organism, with one or more zinc finger proteins (ZFPs) that bind to specific sequences in target genes involved in, e.g., nerve excitability and pain.
  • ZFPs zinc finger proteins
  • one ZFP is administered and is able to bind to a target site in a single target gene.
  • Other methods involve administering a plurality of different ZFPs that bind to a multiple target sites within a single target gene or, alternatively, within multiple target genes.
  • ZFPs that are engineered to specifically recognize and bind to particular nucleic acid segments (target sites) in genes involved in neuropathic pain, modulate expression of these genes and thereby treat pain.
  • the ZFPs are linked to regulatory domains to create chimeric transcription factors to activate or repress transcription of one or more genes involved in pain. With such ZFPs, expression of the target gene(s) can be enhanced; with certain other ZFPs, expression can be repressed.
  • the target site can be adjacent to, upstream of, and/or downstream of the transcription start site (defined as nucleotide + 1).
  • one or more ZFPs can be used to modulate expression of one or more target genes.
  • exemplary target genes include the VR1, TrkA and NaV1.8 genes.
  • the Capsaicin and Vanilloid Receptor (VR1) is located exclusively on small nerve fibers of the dorsal root ganglia (DRG). It is activated by noxious heat, lipid, and the low pH that is often associated with tissue damage.
  • TrkA tyrosine Kinase Receptor A
  • TrkA is the receptor for NGF, which is a key regulator of nociceptive thresholds. TrkA expression is restricted to the neuronal subpopulation that is principally concerned with nociception. It functions at primary sensory nerve terminals in the DRG to promote thermal hypersensitivity. TrkA both, facilitates VR1 function, and requires VR1 for its own function.
  • mice deficient in TrkA exhibit impaired nociception.
  • the tetrodotoxin-resistant sodium channel (NaV 1.8, also known as PN3, SNS, and SCNIOa) is restricted to the peripheral small diameter sensory neurons in DRGs and is believed to play a unique role in transmission of nociceptive information to the spinal cord. Its expression is also influenced by NGF and TrkA.
  • NaV 1.8 " mice are apparently normal but show deficits in thermoreception and the development of inflammatory pain, and their behavioral responses to noxious mechanical stimulation appear to be completely abolished.
  • the ZFPs can be used to treat a wide range of neuropathic pain. For example, repression ofVRl, TRKA and/or Navl.8 expression can be achieved using the ZFPs described herein, thereby ameliorating or eliminating neuropathic pain.
  • the ZFPs can be used to repress expression of genes overexpressed in subjects with neuropathic pain, both in vitro and in vivo. Such repression can be utilized, for example, as treatment for chronic pain.
  • Additional genes whose repression results in reduction of chronic pain include, for example, Dynorphin, NT3, and CCK-b.
  • BDNF BDNF
  • NGF GDNF
  • GDNF GDNF
  • Activation and repression of gene expression can be achieved by any method known in the art (e.g., antisense, siR ⁇ A).
  • Prefe ⁇ ed methods for modulation of gene expression involve the use of engineered zinc finger proteins comprising a transcriptional regulatory domain.
  • ZFPs zinc finger proteins
  • the zinc finger proteins (ZFPs) disclosed herein are proteins that can bind to DNA in a sequence-specific manner. As indicated above, these ZFPs can be used to modulate expression of a target gene (e.g., a gene involved in nerve excitability) in vivo or in vitro and by so doing treat chronic pain.
  • a target gene e.g., a gene involved in nerve excitability
  • An exemplary motif characterizing one class of these proteins, the C 2 H 2 class is -Cys-(X) 2-4 -Cys-(X) 12 -His-(X) 3-5 -His (where X is any amino acid) (SEQ. ID. NO:l).
  • the finger domain contains an alpha helix containing the two invariant histidine residues and two invariant cysteine residues in a beta turn coordinated through zinc.
  • the ZFPs provided herein are not limited to this particular class. Additional classes of zinc finger proteins are known and can also be used in the methods and compositions disclosed herein (see, e.g., Rhodes, et al. (1993) Scientific American 268:56-65 and US Patent Application Publication No. 2003/0108880).
  • a single finger domain is about 30 amino acids in length. Zinc finger domains are involved not only in DNA-recognition, but also in RNA binding and in protein-protein binding.
  • the structure suggests that each finger interacts independently with DNA over 3 base-pair intervals, with side-chains at positions -1, 2, 3 and 6 on each recognition helix making contacts with their respective DNA triplet subsites.
  • the amino terminus of Zif268 is situated at the 3' end of the DNA strand with which it makes most contacts.
  • the target strand If the strand with which a zinc finger protein makes most contacts is designated the target strand, some zinc finger proteins bind to a three base triplet in the target strand and a fourth base on the non-target strand.
  • the fourth base is complementary to the base immediately 3' of the three base subsite.
  • the target sites can be located upstream or downstream of the transcriptional start site (defined as nucleotide +1).
  • Target sites can include, for example, 9 nucleotides, 12 nucleotides or 18 nucleotides.
  • the target sites can be located adjacent the transcription initiation site or be located significantly upstream or downstream of the transcription start site.
  • a single target site is recognized by the ZFP(s).
  • - multiple ZFPs can be used, each recognizing different targets in a single gene (e.g., VR1, TRKA or NAV1.8) or in multiple genes.
  • the ZFPs that bind to these target sites typically include at least one zinc finger but can include a plurality of zinc fingers (e.g., 2, 3, 4, 5, 6 or more fingers). Usually, the ZFPs include at least three fingers. Certain of the ZFPs include four or six fingers. The ZFPs that include three fingers typically recognize a target site that includes 9 or 10 nucleotides; four-finger ZFPs recognize a 12-14-nucleotide target site, and ZFPs having six fingers can recognize target sites that include 18 to 21 nucleotides.
  • the ZFPs can also be fusion proteins that include one or more regulatory domains, which domains can be transcriptional activation or repression domains.
  • Exemplary zinc finger proteins that bind to a target site in a VR1, TRK-A or NAV1.8 gene are described in detail in the Examples and Tables 1, 2, 3 and 4.
  • Table 1 shows the nucleotide sequence of the target site for each zinc finger protein and the location of the target site relative to the transcription start site. Negative numbers refer to bp upstream of the transcription start site and positive numbers refer to bp downstream of the transcription start site, where the transcription start site is defined as nucleotide +1. Nucleotides shown in lower case represent nucleotides that are not contacted by a zinc finger. In these cases, the zinc finger protein is designed with a long, non-canonical linker between fingers that bind DNA to either side of the skipped nucleotide.
  • rat VR1 see GenBank accession number NW _047336
  • rat TRK-A GenBank No. NW _047626
  • human TrkA GenBank No. NT_079484
  • humanNAVl.8 GenBan No. NT_022517
  • Table 2 shows the amino acid sequences included in the recognition region of each finger (FI through F6) of the various zinc finger proteins designed to bind to a target sequence in rat VRl.
  • the amino acid sequences shown depict residues -1 through +6, as numbered relative to the first amino acid residue in the alpha-helical portion of the zinc finger. 1 Table 2
  • Table 3 shows the amino acid sequences included in the recognition region of each finger (FI through F6) of the zinc finger proteins designed to bind to a target sequence in rat TRK-A.
  • the amino acid sequences shown depict residues -1 through +6, as numbered relative to the first amino acid residue in the alpha-helical portion of the zinc finger.
  • Table 4 shows the amino acid sequences included in the recognition region of each finger (F 1 through F6) of the various zinc finger proteins designed to bind to a target sequence in human NA VI.8.
  • the amino acid sequences shown depict residues -1 through +6, as numbered relative to the first amino acid residue in the alpha-helical portion of the zinc finger.
  • Table 5 shows the amino acid sequences included in the recognition region of each finger (FI through F6) of the various zinc finger proteins designed to bind to a target sequence in the human TrkA gene.
  • the amino acid sequences shown depict residues -1 through +6, as numbered relative to the first amino acid residue in the alpha-helical portion of the zinc finger.
  • the target sites may be any length, but are preferably 9-10, 12-14, or 18-21 nucleotides in length.
  • one or more ZFPs described herein can be utilized to modulate expression of one or more genes involved in neuropathic pain, and by so doing treat this pain. By judicious selection of various ZFPs and/or combinations thereof, one can tailor targeted gene modulation and, accordingly, tailor treatment for neuropathic pain.
  • Zinc finger proteins are formed from zinc finger components.
  • zinc finger proteins can have one to thirty-seven fingers, commonly having 2, 3, 4, 5 or 6 fingers.
  • a zinc finger protein recognizes and binds to a target site (sometimes refe ⁇ ed to as a target segment) that represents a relatively small subsequence within a target gene.
  • Each component finger of a zinc finger protein can bind to a subsite within the target site.
  • the sub site includes a triplet of three contiguous bases all on the same strand (sometimes refe ⁇ ed to as the target strand).
  • the subsite may or may not also include a fourth base on the opposite strand that is the complement of the base immediately 3' of the three contiguous bases on the target strand.
  • a zinc finger binds to its triplet subsite substantially independently of other fingers in the same zinc finger protein. Accordingly, the binding specificity of zinc finger protein containing multiple fingers is usually approximately the aggregate of the specificities of its component fingers. For example, if a zinc finger protein is formed from first, second and third fingers that individually bind to triplets XXX, YYY, and ZZZ, the binding specificity of the zinc finger protein is 3'XXX YYY ZZZ5*.
  • the relative order of fingers in a zinc finger protein from N-terminal to C- terminal determines the relative order of triplets in the 3' to 5' direction in the target.
  • a zinc finger protein comprises from N-terminal to C-terminal first, second and third fingers that individually bind, respectively, to triplets 5'GAC3', 5'GTA3' and 5'GGC3' then the zinc finger protein binds to the target segment 3'CAGATGCGG5' (SEQ ID NO:2). If the zinc finger protein comprises the fingers in another order, for example, second finger, first finger, third finger, then the zinc finger protein binds to a target segment comprising a different permutation of triplets, in this example, 3 ⁇ TGCAGCGG5' (SEQ ID NO:3). See Berg & Shi, Science 271,1081-1086 (1996).
  • the assessment of binding properties of a zinc finger protein as the aggregate of its component fingers may, in some cases, be influenced by context-dependent interactions of multiple fingers binding in the same protein.
  • Two or more zinc finger proteins can be linked to have a target specificity that is the aggregate of that of the component zinc finger proteins (see e.g., Kim & Pabo, Proc. Natl. Acad. Sci. U.S.A. 95:2812-2817 (1998)).
  • a first zinc finger protein having first, second and third component fingers that respectively bind to XXX, YYY and ZZZ can be linked to a second zinc finger protein having first, second and third component fingers with binding specificities, AAA, BBB and CCC.
  • the binding specificity of the combined first and second proteins is thus
  • 3'XXXYYYZZZ_AAABBBCCC5* where the underline indicates a short intervening region (typically 0-5 bases of any type).
  • the target site can be viewed as comprising two target segments separated by an intervening segment.
  • Linkage can be accomplished using any of the following peptide linkers: T G E K P: (SEQ LD NO:4) (Liu et al., 1997, supra.); (G4S)n (SEQ LD NO:5) (Kim et al., Proc. Natl. Acad. Sci. U.S.A.
  • flexible linkers can be rationally designed using computer programs capable of modeling both DNA-binding sites and the peptides themselves or by phage display methods.
  • noncovalent linkage can be achieved by fusing two zinc finger proteins with domains promoting heterodimer formation of the two zinc finger proteins. For example, one zinc finger protein can be fused with fos and the other with jun (see Barbas et al., WO 95/119431).
  • a typical mammalian diploid genome consists of 3 x 10 9 bp. Assuming that the four nucleotides A, C, G, and T are randomly distributed, a given 9 bp sequence is present approximately 23,000 times. Thus a ZFP recognizing a 9 bp target with absolute specificity would have the potential to bind to about 23,000 sites within the genome. An 18 bp sequence is present about once in a random DNA sequence whose complexity is ten times that of a mammalian genome.
  • a component finger of zinc finger protein typically contains about 30 amino acids and, in one embodiment, has the following motif (N-C):
  • ZFPs The ZFPs provided herein are engineered to recognize a selected target site in a gene involved in neuropathic pain (e.g., VRl, TRKA, or NAV1.8). Non-limiting examples of ZFPs suitable for modulating expression of these and other genes are described herein.
  • the process of designing or selecting a ZFP typically starts with a natural ZFP as a source of framework residues.
  • the process of design or selection serves to define nonconserved positions (i.e., positions -1 to +6) so as to confer a desired binding specificity.
  • One suitable ZFP is the DNA binding domain of the mouse transcription factor Zif268.
  • the DNA binding domain of this protein has the amino acid sequence:
  • YACPVESCDRRFSRSDEL TRHIRIHTGQKP (FI) (SEQ LD NO: 10) FQCRICMRNFSRSDHL TTHIR THTGEKP (F2) (SEQ ID NO: 11) FACDICGRKFARSDERKRHTKIHLRQK (F3) SEQ ID NO: 12) and binds to a target 5' GCG TGG GCG 3' (SEQ ID NO: 13).
  • Another suitable natural zinc finger protein as a source of framework residues is Sp-1.
  • the Sp-1 sequence used for construction of zinc finger proteins co ⁇ esponds to amino acids 531 to 624 in the Sp-1 transcription factor. This sequence is 94 amino acids in length. See, e.g., U.S. Patent Application No.
  • Sp-1 binds to a target site 5'GGG GCG GGG3' (SEQ ID NO: 14).
  • SEQ ID NO: 14 There are a number of substitution rules that assist rational design of some zinc finger proteins.
  • ZFP DNA-binding domains can be designed and/or selected to recognize a particular target site as described in WO 00/42219; WO 00/41566; and U.S. Ser. No. 09/444,241 filed Nov. 19, 1999; Ser. No. 09/535,088 filed Mar. 23, 2000; as well as U.S. Pat. Nos.
  • a target site for a zinc finger DNA-binding domain is identified according to site selection rules disclosed in WO 00/42219.
  • a ZFP is selected as described in WO 02/077227; See also WO 96/06166; Desjarlais & Berg, Proc. Natl. Acad. Sci. USA 90, 2256-2260 (1993); Choo & Klug, Proc. Natl. Acad. Sci.
  • substitution rule is that a G in the middle of a subsite can be recognized by including a histidine residue at position 3 of a zinc finger.
  • a further substitution rule is that asparagine can be incorporated to recognize A in the middle of a triplet, aspartic acid, glutamic acid, serine or threonine can be incorporated to recognize C in the middle of a triplet, and amino acids with small side chains such as alanine can be incorporated to recognize T in the middle of a triplet.
  • a further substitution rule is that the 3' base of a triplet subsite can be recognized by incorporating the following amino acids at position -1 of the recognition helix: arginine to recognize G, glutamine to recognize A, glutamic acid (or aspartic acid) to recognize C, and threonine to recognize T.
  • these substitution rules are useful in designing zinc finger proteins they do not take into account all possible target sites.
  • the assumption underlying the rules namely that a particular amino acid in a zinc finger is responsible for binding to a particular base in a subsite is only approximate. Context-dependent interactions between proximate amino acids in a finger or binding of multiple amino acids to a single base or vice versa can cause variation of the binding specificities predicted by the existing substitution rules.
  • a ZFP DNA-binding domain of predetermined specificity is obtained according to the methods described in WO 02/077227.
  • Any suitable method known in the art can be used to design and construct nucleic acids encoding ZFPs, e.g., phage display, random mutagenesis, combinatorial libraries, computer/rational design, affinity selection, PCR, cloning from cDNA or genomic libraries, synthetic construction and the like, (see, e.g., U.S. Pat. No. 5,786,538; Wu et al., Proc. Natl. Acad. Sci.
  • the binding specificity of a DNA-binding domain is determined by identifying accessible regions in the sequence in question (e.g., in cellular chromatin). Accessible regions can be determined as described in WO 01/83732. See, also, U.S. Patent Application No. 20030021776A1. A DNA-binding domain is then designed and/or selected as described herein to bind to a target site within the accessible region.
  • nucleic acids less than about 100 bases can be custom ordered from any of a variety of commercial sources, such as The Midland Certified Reagent Company (mcrc@oligos.com), The 15 Great American Gene Company (more information may be found on the internet at www.genco.com), ExpressGen Inc. (more information may be found on the internet at www.expressgen.com), Operon Technologies Inc. (Alameda, Calif.).
  • peptides can be custom ordered from any of a variety of sources, such as PeptidoGenic (pkim@ccnet.com), HTI Bio-products, Inc. (more information may be found on the internet at www.htibio.com), BMA Biomedicals Ltd (U.K.), Bio.
  • Oligonucleotides can be chemically synthesized according to the solid phase phosphoramidite triester method first described by Beaucage & Caruthers, Tetrahedron Letts. 22:1859-1862 (1981), using an automated synthesizer, as described in Van Devanter et al, Nucleic Acids Res. 12:6159-6168 (1984). Purification of oligonucleotides is by either denaturing polyacrylamide gel electrophoresis or by reverse phase HPLC.
  • the sequence of the cloned genes and synthetic oligonucleotides can be verified after cloning using, e.g., the chain teraiination method for sequencing double- stranded templates of Wallace et al., Gene 16:21-26 (1981).
  • Two alternative methods are typically used to create the coding sequences required to express newly designed DNA-binding peptides.
  • One protocol is a PCR-based assembly procedure that utilizes six overlapping oligonucleotides.
  • Three oligonucleotides co ⁇ espond to "universal" sequences that encode portions of the DNA- binding domain between the recognition helices. These oligonucleotides typically remain constant for all zinc finger constructs.
  • the other three "specific" oligonucleotides are designed to encode the recognition helices. These oligonucleotides contain substitutions primarily at positions -1, 2, 3 and 6 on the recognition helices making them specific for each of the different DNA-binding domains.
  • the PCR synthesis is carried out in two steps.
  • a double stranded DNA template is created by combining the six oligonucleotides (three universal, three specific) in a four cycle PCR reaction with a low temperature annealing step, thereby annealing the oligonucleotides to form a DNA "scaffold."
  • the gaps in the scaffold are filled in by high-fidelity thermostable polymerase, the combination of Taq and Pfu polymerases also suffices.
  • the zinc finger template is amplified by external primers designed to incorporate restriction sites at either end for cloning into a shuttle vector or directly into an expression vector.
  • An alternative method of cloning the newly designed DNA-binding proteins relies on annealing complementary oligonucleotides encoding the specific regions of the desired ZFP.
  • This particular application requires that the oligonucleotides be phosphorylated prior to the final ligation step. This is usually performed before setting up the annealing reactions.
  • the "universal" oligonucleotides encoding the constant regions of the proteins oligos 1, 2 and 3 of above
  • the "specific" oligonucleotides encoding the finger recognition helices are annealed with their respective complementary oligonucleotides.
  • oligos are designed to fill in the region that was previously filled in by polymerase in the above-mentioned protocol.
  • Oligonucleotides complementary to oligos 1 and 6 are engineered to leave overhanging sequences specific for the restriction sites used in cloning into the vector of choice in the following step.
  • the second assembly protocol differs from the initial protocol in the following aspects: the "scaffold" encoding the newly designed ZFP is composed entirely of synthetic DNA thereby eliminating the polymerase fill-in step, additionally the fragment to be cloned into the vector does not require amplification.
  • the design of leaving sequence- specific overhangs eliminates the need for restriction enzyme digests of the inserting fragment.
  • changes to ZFP recognition helices can be created using conventional site-directed mutagenesis methods. Both assembly methods require that the resulting fragment encoding the newly designed ZFP be ligated into a vector. Ultimately, the ZFP-encoding sequence is cloned into an expression vector.
  • Expression vectors that are commonly utilized include, but are not limited to, a modified pMAL-c2 bacterial expression vector (New England BioLabs, Beverly, Mass.) or a eukaryotic expression vector, pcDNA (Promega, Madison, Wis.). The final constructs are verified by sequence analysis. Any suitable method of protein purification known to those of skill in the art can be used to purify ZFPs (see, Ausubel, supra, Sambrook, supra).
  • any suitable host can be used for expression, e.g., bacterial cells, insect cells, yeast cells, mammalian cells, and the like.
  • Expression of a zinc finger protein fused to a maltose binding protein (MBP-ZFP) in bacterial strain JM109 allows for straightforward purification through an amylose column (New England BioLabs, Beverly, Mass.).
  • High expression levels of the zinc finger chimeric protein can be obtained by induction with IPTG since the MBP-ZFP fusion in the pMal-c2 expression plasmid is under the control of the tac promoter (New England BioLabs, Beverly, Mass.).
  • Bacteria containing the MBP-ZFP fusion plasmids are inoculated into 2xYT medium containing 10 ⁇ M ZnCl , 0.02% glucose, plus 50 ⁇ g/ml ampicillin and shaken at 37°C. At mid-exponential growth IPTG is added to 0.3 mM and the cultures are allowed to shake. After 3 hours the bacteria are harvested by centrifugation, disrupted by sonication or by passage through a pressure cell or through the use of lysozyme, and insoluble material is removed by centrifugation.
  • the MBP-ZFP proteins are captured on an amylose-bound resin, washed extensively with buffer containing 20 mM Tris-HCl (pH 7.5), 200 mM NaCl, 5 mM DTT and 50 . ⁇ M Zn Cl 2 , then eluted with maltose in essentially the same buffer (purification is based on a standard protocol from New England BioLabs). Purified proteins are quantitated and stored for biochemical analysis.
  • the dissociation constant of a purified protein e.g., Kd, is typically characterized via electrophoretic mobility shift assays (EMSA) (Buratowski & Chodosh, in Current Protocols in Molecular Biology pp.
  • ESA electrophoretic mobility shift assays
  • Affinity is measured by titrating purified protein against a fixed amount of labeled double-stranded oligonucleotide target.
  • the target typically comprises the natural binding site sequence flanked by the 3 bp found in the natural sequence and additional, constant flanking sequences.
  • the natural binding site is typically 9 bp for a three-finger protein and 2.times.9 bp +intervening bases for a six finger ZFP.
  • the annealed oligonucleotide targets possess a 1 base 5' overhang that allows for efficient labeling of the target with T4 phage polynucleotide kinase.
  • the target is added at a concentration of 1 nM or lower (the actual concentration is kept at least 10-fold lower than the expected dissociation constant), purified ZFPs are added at various concentrations, and the reaction is allowed to equilibrate for at least 45 min.
  • the reaction mixture also contains 10 mM Tris (pH 7.5), 100 mM KC1, 1 mM MgCl 2 , 0.1 mM Zn Cl 2 , 5 mM DTT, 10% glycerol, 0.02% BSA.
  • the equilibrated reactions are loaded onto a 10% polyacrylamide gel, which has been pre-run for 45 min in Tris/glycine buffer, then bound and unbound labeled target is resolved by electrophoresis at 150V.
  • 10-20% gradient Tris-HCI gels containing a 4% polyacrylamide stacking gel
  • the dried gels are visualized by autoradiography or phosphorimaging and the apparent Kd is determined by calculating the protein concentration that yields half-maximal binding.
  • the assays can also include a determination of the active fraction in the protein preparations. Active fraction is deteraiined by stoichiometric gel shifts in which protein is titrated against a high concentration of target DNA. Titrations are done at 100, 50, and 25% ⁇ of target (usually at micromolar levels).
  • phage display provides a largely empirical means of generating zinc finger proteins with desired target specificity (see e.g., Rebar, U.S. Pat. No. 5,789,538; Choo et al., WO 96/06166; Barbas et al., WO 95/19431 and WO 98/543111; Jamieson et al., supra).
  • the method can be used in conjunction with, or as an alternative to rational design.
  • the method involves the generation of diverse libraries of mutagenized zinc finger proteins, followed by the isolation of proteins with desired DNA-binding properties using affinity selection methods. To use this method, the experimenter typically proceeds as follows.
  • a gene for a zinc finger protein is mutagenized to introduce diversity into regions important for binding specificity and/or affinity. In a typical application, this is accomplished via randomization of a single finger at positions -1, +2, +3, and +6, and sometimes accessory positions such as +1, +5,+8 and +10.
  • the mutagenized gene is cloned into a phage or phagemid vector as a fusion with gene III of a . filamentous phage, which encodes the coat protein p III.
  • the zinc finger gene is inserted between segments of gene III encoding the membrane export signal peptide and the remainder of pill, so that the zinc finger protein is expressed as an amino-terminal fusion with pffl or in the mature, processed protein.
  • the mutagenized zinc finger gene may also be fused to a truncated version of gene ill encoding, minimally, the C-terminal region required for assembly of pill into the phage particle.
  • the resultant vector library is transformed into E. coli and used to produce filamentous phage that express variant zinc finger proteins on their surface as fusions with the coat protein pill. If a phagemid vector is used, then this step requires superinfection with helper phage.
  • the phage library is then incubated with a target DNA site, and affinity selection methods are used to isolate phage that bind target with high affinity from bulk phage.
  • the DNA target is immobilized on a solid support, which is then washed under conditions sufficient to remove all but the tightest binding phage. After washing, any phage remaining on the support are recovered via elution under conditions which disrupt zinc finger— DNA binding. Recovered phage are used to infect fresh E. coli, which is then amplified and used to produce a new batch of phage particles. Selection and amplification are then repeated as many times as is necessary to enrich the phage pool for tight binders such that these may be identified using sequencing and/or screening methods. Although the method is illustrated for pill fusions, analogous principles can be used to screen ZFP variants as pVIII fusions.
  • the sequence bound by a particular zinc finger protein is determined by conducting binding reactions (see, e.g., conditions for determination of Kd, supra) between the protein and a pool of randomized double-stranded oligonucleotide sequences.
  • the binding re d action is analyzed by an electrophoretic mobility shift assay (EMS A), in which protein-DNA complexes undergo retarded migration in a gel and can be separated from unbound nucleic acid.
  • Oligonucleotides that have bound the finger are purified from the gel and amplified, for example, by a polymerase chain reaction.
  • the selection i.e. binding reaction and EMSA analysis
  • Zinc finger proteins are often expressed with an exogenous domain (or functional fragment thereof) as fusion proteins.
  • Common domains for addition to theZFP include, e.g., transcription factor domains (activators, repressors, co-activators, co-repressors), silencers, oncogenes (e.g., myc, jun, fos, myb, max, mad, rel, ets, bcl, myb, mos family members etc.); DNA repair enzymes and their associated factors and modifiers; DNA rea ⁇ angement enzymes and their associated factors and modifiers; chromatin associated proteins and their modifiers (e.g.
  • a prefe ⁇ ed domain for fusing with a ZFP when the ZFP is to be used for repressing expression of a target gene is a KRAB repression domain from the human KOX-1 protein (Thiesen et al., New Biologist 2,363-3 r 4 (1990); Margolin et al., Proc. Natl. Acad. Sci.
  • Prefe ⁇ ed domains for achieving activation include the HSV VP16 activation domain (see, e.g., Hagmann et al., J. Virol. 71, 5952-5962 (1997)) nuclear hormone receptors (see, e.g., Torchia et al., Curr. Opin. Cell. Biol.
  • compositions and methods disclosed herein involve fusions between a DNA-binding domain specifically targeted to one or more regulatory regions of a target gene involved in neuropathic pain and a functional (e.g., repression or activation) domain (or a polynucleotide encoding such a fusion).
  • a functional domain e.g., repression or activation domain
  • the repression or activation domain is brought into proximity with a sequence in the gene that is bound by the DNA-binding domain.
  • the transcriptional regulatory function of the functional domain is then able to act on the selected regulatory sequences.
  • targeted remodeling of chromatin as disclosed in WO 01/83793 can be used to generate one or more sites in cellular chromatin that are accessible to the binding of a DNA binding molecule.
  • Fusion molecules are constructed by methods of cloning and biochemical conjugation that are well known to those of skill in the art. Fusion molecules comprise a DNA-binding domain and a functional domain (e.g., a transcriptional activation or repression domain). Fusion molecules also optionally comprise nuclear localization signals (such as, for example, that from the SV 40 medium T -antigen) and epitope tags (such as, for example, FLAG and hemagglutinin). Fusion proteins (and nucleic acids encoding them) are designed such that the translational reading frame is preserved among the components of the fusion.
  • nuclear localization signals such as, for example, that from the SV 40 medium T -antigen
  • epitope tags such as, for example, FLAG and hemagglutinin
  • Fusions between a polypeptide component of a functional domain (or a functional fragment thereof) on the one hand, and a non-protein DNA-binding domain (e.g., antibiotic, intercalator, minor groove binder, nucleic acid) on the other, are constructed by methods of biochemical conjugation known to those of skill in the art. See, for example, the Pierce Chemical Company (Rockford, IL) Catalogue. Methods and compositions for making fusions between a minor groove binder and a polypeptide have been described. Mapp et al. (2000) Proc. Natl. Acad. Sci. USA 97:3930-3935.
  • the target site bound by the zinc finger protein is present in an accessible region of cellular chromatin.
  • Accessible regions can be determined as i described, for example, in International Publication WO 01/83732. If the target site is not present in an accessible region of cellular chromatin, one or more accessible regions can be generated as described in WO 01/83793.
  • the DNA- binding domain of a fusion molecule is capable of binding to cellular chromatin regardless of whether its target site is in an accessible region or not.
  • such DNA-binding domains are capable of binding to linker DNA and/or nucleosomal DNA. Examples of this type of "pioneer" DNA binding domain are found in certain steroid receptor and in hepatocyte nuclear factor 3 (HNF3). Cordingley et al. (1987) Cell 48:261-270; Pina et al.
  • the fusion molecule is typically formulated with a pharmaceutically acceptable carrier, as is known to those of skill in the art. See, for example, Remington's Pharmaceutical Sciences, 17th ed., 1985; and WO 00/42219.
  • the functional component/domain of a fusion molecule can be selected from any of a variety of different components capable of influencing transcription of a gene once the fusion molecule binds to a target sequence via its DNA binding domain.
  • the functional component can include, but is not limited to, various transcription factor domains, such as activators, repressors, co-activators, co-repressors, and silencers.
  • An exemplary functional domain for fusing with a DNA-binding domain such as, for example, a ZFP, to be used for repressing expression of a gene is a KRAB repression domain from the human KOX-1 protein (see, e.g., Thiesen et al., New Biologist 2,363- 374 (1990); Margolin et al., Proc. Natl. Acad. Sci. USA 91, 4509-4513 (1994); Pengue et al., Nucl. Acids Res.
  • MBD-2B methyl binding domain protein 2B
  • Another useful repression domain is that associated with the v-ErbA protein. See, for example, Damm, et al. (1989) Nature 339:593-597; Evans (1989) Lnt. J. Cancer Suppl. 4:26-28; Pain et al. (1990) New Biol. 2:284-294; Sap et al.
  • Suitable domains for achieving activation include the HSV VP16 activation domain (see, e.g., Hagmann et al., J. Virol. 71, 5952-5962 (1997)) nuclear hormone receptors (see, e.g., Torchia et al., Curr. Opin. Cell. Biol. 10:373-383 (1998)); the p65 subunit of nuclear factor kappa B (Bitko & Barik, J. Virol.
  • VP64 Stevial et al.
  • Additional exemplary activation domains include, but are not limited to, VP16, VP64, p300, CBP, PCAF, SRC1 PvALF, AtHD2A and ERF -2. See, for example, Robyr et al. (2000) Mol. Endocrinol. 14:329-347; CoUingwood et al. (1999) J. Mol.
  • Additional exemplary activation domains include, but are not limited to, OsGAI, HALF-I, CI, API, ARF-5, -6, -7, and -8,
  • Additional exemplary repression domains include, but are not limited to, KRAB
  • Additional exemplary repression domains include, but are not limited to, ROM2 and AtHD2A. See, for example, Chern et al. (1996) Plant Cell 8:305-321; and Wu et al. (2000) Plant J.
  • the nucleic acid encoding the ZFP of choice is typically cloned into intermediate vectors for transformation into prokaryotic or eukaryotic cells for replication and/or expression, e.g., for determination of Kd.
  • Intermediate vectors are typically prokaryote vectors, e.g., plasmids, or shuttle vectors, or insect vectors, for storage or manipulation of the nucleic acid encoding ZFP or production of protein.
  • the nucleic acid encoding a ZFP is also typically cloned into an expression vector, for administration to a plant cell, animal cell, preferably a mammalian cell or a human cell, fungal cell, bacterial cell, or protozoal cell.
  • a ZFP is typically subcloned into an expression vector that contains a promoter to direct transcription.
  • Suitable bacterial and eukaryotic promoters are well known in the art and described, e.g., in Sambrook et al., Molecular Cloning, A Laboratory Manual (2nd ed. 1989); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al., eds., 1994).
  • Bacterial expression systems for expressing the ZFP are available in, e.g., E. coli, Bacillus sp., and Salmonella (Palva et al, Gene 22:229-235 (1983)). Kits for such expression systems are commercially available.
  • Eukaryotic expression systems for mammalian cells, yeast, and insect cells are well known in the art and are also commercially available.
  • the promoter used to direct expression of a ZFP nucleic acid depends on the particular application. For example, a strong constitutive promoter is typically used for expression and purification of ZFP. In contrast, when a ZFP is administered in vivo for gene regulation, either a constitutive or an inducible promoter is used, depending on the particular use of the ZFP.
  • a prefe ⁇ ed promoter for administration of a ZFP can be a weak promoter, such as HSV TK or a promoter having similar activity.
  • the promoter typically can also include elements that are responsive to transactivation, e.g., hypoxia response elements, Gal4 response elements, lac repressor response element, and small molecule control systems such as tet-regulated systems and the RU-486 system (see, e.g., Gossen & Bujard, Proc. Natl. Acad. Sci. USA 89:5547 (1992); Oligino.et al., Gene Ther. 5:491-496 25 (1998); Wang et al., Gene Ther. 4:432-441 (1997); Neering et al., Blood 88:1147-1155 (1996); and Rendahl et al, Nat. Biotechnol. 16:757-761 (1998)).
  • elements that are responsive to transactivation e.g., hypoxia response elements, Gal4 response elements, lac repressor response element, and small molecule control systems such as tet-regulated systems and the RU-486 system
  • small molecule control systems such
  • the expression vector typically contains a transcription unit or expression cassette that contains all the additional elements required for the expression of the nucleic acid in host cells, either prokaryotic or eukaryotic.
  • a typical expression cassette thus contains a promoter operably linked, e.g., to the nucleic acid sequence encoding the ZFP, and signals required, e.g., for efficient polyadenylation of the transcript, transcriptional termination, ribosome binding sites, or translation termination. Additional elements of the cassette may include, e.g., enhancers, and exogenous spliced intronic signals.
  • the particular expression vector used to transport the genetic information into the cell is selected with regard to the intended use of the ZFP.
  • Standard bacterial expression vectors include plasmids such as pBR322 based plasmids, pSKF, pET23D, and commercially available fusion expression systems such as GST and LacZ.
  • a prefe ⁇ ed fusion protein is the maltose binding protein, "MBP.”
  • MBP maltose binding protein
  • Such fusion proteins are used for purification of the ZFP.
  • Epitope tags can also be added to recombinant proteins to provide convenient methods of isolation, for monitoring expression, and for monitoring cellular and subcellular localization, e.g., c-myc or FLAG.
  • Expression vectors containing regulatory elements from eukaryotic viruses are often used in eukaryotic expression vectors, e.g., SV 40 vectors, papilloma virus vectors, and vectors derived from Epstein-Ban virus.
  • eukaryotic vectors include pMSG, pA V009/A+, pMTO10/A+, pMAMneo-5, baculovirus pDSVE, and any other vector allowing expression of proteins under the direction of the SV 40 early promoter, SV40 late promoter, metallothionein promoter, murine mammary tumor virus promoter, Rous sarcoma virus promoter, polyhedrin promoter, or other promoters shown effective for expression in eukaryotic cells.
  • Some expression systems have markers for selection of stably transfected cell lines such as thymidine kinase, hygromycin B phosphotransferase, and dihydrofolate reductase.
  • High yield expression systems are also suitable, such as using a baculovirus vector in insect cells, with a ZFP encoding sequence under the direction of the polyhedrin promoter or other strong baculovirus promoters.
  • the elements that are typically included in expression vectors also include a replicon that functions in E. coli, a gene encoding antibiotic resistance to permit selection of bacteria that harbor recombinant plasmids, and unique restriction sites in nonessential regions of the plasmid to allow insertion of recombinant sequences.
  • Standard transfection methods are used to produce bacterial, mammalian, yeast or insect cell lines that express large quantities of protein, which are then purified using standard techniques (see, e.g., Colley et al., J Biol. Chem. 264: 17619-17622 (1989); Guide to Protein Purification, in. Methods in Enzymology, vol. 182 (Deutscher, ed., . 1990)). Transformation of eukaryotic and prokaryotic cells are performed according to standard techniques (see, e.g., Morrison, J. Bad.
  • Any of the well known procedures for introducing foreign nucleotide sequences into host cells may be used. These include the use of calcium phosphate transfection, polybrene, protoplast fusion, electroporation, liposomes, microinjection, naked DNA, plasmid vectors, viral vectors, both episomal and integrative, and any of the other well known methods for introducing cloned genomic DNA, cDNA, synthetic DNA or other foreign genetic material into a host cell (see, e.g., Sambrook et al., supra).
  • the particular genetic engineering procedure used be capable of successfully introducing at least one gene into the host cell capable of expressing the protein of choice.
  • ASSAYS Once a ZFP has been designed and prepared according to the procedures just set forth, an initial assessment of the activity of the designed ZFP is undertaken. ZFP proteins showing the ability to modulate the expression of a gene of interest can then be further assayed for more specific activities depending upon the particular application for which the ZFPs have been designed. Thus, for example, the ZFPs provided herein can be initially assayed for their ability to modulate expression of genes involved in neuropathic pain. More specific assays of the ability of the ZFP to modulate expression of the target genes involved in neuropathic pain to treat this pain are then typically undertaken.
  • the activity of a particular ZFP can be assessed using a variety of in vitro and in vivo assays, by measuring, e.g., protein or mRNA levels, product levels, enzyme activity, tumor growth; transcriptional activation or repression of a reporter gene; second messenger levels (e.g., cGMP, cAMP, IP3, DAG, Ca2+); cytokine and hormone production levels; and neovascularization, using, e.g., immunoassays (e.g., ELISA and immunohistochemical assays with antibodies), hybridization assays (e.g., RNase protection, Northerns, in situ hybridization, oligonucleotide a ⁇ ay studies), colorimetric assays, amplification assays, enzyme activity assays, tumor growth assays, phenotypic assays, and the like.
  • immunoassays e.g., ELISA and immunohistochemical assays with antibodies
  • hybridization assays
  • ZFPs are typically first tested for activity in vitro using cultured cells, e.g., 293 cells, CHO cells, VERO cells, BHK cells, HeLa cells, COS cells, and the like. Preferably, human cells are used.
  • the ZFP is often first tested using a transient expression system with a reporter gene, and then regulation of the target endogenous gene is tested in cells and in animals, both in vivo and ex vivo.
  • the ZFP can be recombinantly expressed in a cell, recombinantly expressed in cells transplanted into an animal, or recombinantly expressed in a transgenic animal, as well as administered as a protein to an animal or cell using delivery vehicles described below.
  • the cells can be immobilized, be in solution, be injected into an animal, or be naturally occurring in a transgenic or non-transgenic animal. Modulation of gene expression is tested using one of the in vitro or in vivo assays described herein. Samples or assays are treated with a ZFP and compared to untreated control samples, to examine the extent of modulation. As described above, for regulation of endogenous gene expression, the ZFP typically has a Kd of 200 nM or less, more preferably 100 nM or less, more preferably 50 nM, most preferably 25 nM or less. The effects of the ZFPs can be measured by examining any of the parameters described above.
  • Any suitable gene expression, phenotypic, or physiological change can be used to assess the influence of a ZFP.
  • the functional consequences are determined using intact cells or animals, one can also measure a variety of effects such as neurotrophism, transcriptional changes to both known and uncharacterized genetic markers (e.g., Northern blots or oligonucleotide a ⁇ ay studies), changes in cell metabolism such as cell growth or pH changes, and changes in intracellular second messengers such as cAMP or cGMP.
  • Prefe ⁇ ed assays for ZFP regulation of endogenous gene expression can be performed in vitro.
  • ZFP regulation of endogenous gene expression in cultured cells is measured by examining protein production using an ELISA assay.
  • the test sample is compared to control cells treated with a vector lacking ZFP-encoding sequences or a vector encoding an unrelated ZFP that is targeted to another gene.
  • ZFP regulation of endogenous gene expression is determined in vitro by measuring the level of gene mRNA expression (e.g., expression level of VRl, TrKA and/or NaVl .8 gene).
  • the level of gene expression is measured using amplification, e.g., using PCR, LCR, or hybridization assays, e.g., Northern hybridization, dot blotting and RNase protection.
  • RT -PCR techniques i.e., the so-called TaqMan® assays
  • the level of protein or mRNA is detected using directly or indirectly labeled detection agents, e.g., fiuorescently or radioactively labeled nucleic acids, radioactively or enzymatically labeled antibodies, and the like, as described herein.
  • directly or indirectly labeled detection agents e.g., fiuorescently or radioactively labeled nucleic acids, radioactively or enzymatically labeled antibodies, and the like, as described herein.
  • a reporter gene system can be devised using a gene promoter from the selected target gene (e.g., VRl, TRKA, and/or NA V1.8) operably linked to.
  • a reporter gene such as luciferase, green fluorescent protein, CAT, GAPDH, jS-gal, etc.
  • the reporter construct is typically co-transfected into a cultured cell. After treatment with the ZFP of choice, the amount of reporter gene transcription, translation, or activity is measured according to standard techniques known to those of skill in the art.
  • Another example of a prefe ⁇ ed assay format useful for monitoring ZFP regulation of endogenous gene expression is performed in vivo. This assay is particularly useful for examining genes involved in chronic pain. In this assay, the ZFP of choice is administered (e.g., intramuscular or intravenous injection) into an animal exhibiting abe ⁇ ant nerve excitability.
  • nerve function and/or gene expression are compared to control animals that also have abe ⁇ ant nerve excitability but did not receive a ZFP.
  • Nerve excitability that is significantly different as between control and test animals using, e.g., Student's T test) are determined to have been affected by the ZFP.
  • the ZFPs provided herein, and more typically the nucleic acids encoding them, can optionally be formulated with a pharmaceutically acceptable carrier as a pharmaceutical composition.
  • NUCLEIC ACLD BASED COMPOSITIONS Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids encoding the present ZFPs in mammalian cells or target tissues. Such methods can be used to administer nucleic acids encoding ZFPs to cells in vitro. In some instances, the nucleic acids encoding ZFPs are administered for in vivo or ex vivo gene therapy uses.
  • Non- viral vector delivery systems include DNA plasmids, naked nucleic acid, and nucleic acid complexed with a delivery vehicle such as poloxamers or liposomes.
  • Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell.
  • Methods of non- viral delivery of nucleic acids encoding the ZFPs provided herein include lipofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipid:nucleic acid conjugates, naked DNA, artificial virions, and agent- enhanced uptake of DNA.
  • 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. Delivery can be to cells (ex vivo administration) or target tissues (in vivo administration).
  • 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.
  • RNA or DNA viral based systems for the delivery of nucleic acids encoding engineered ZFP 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 can include retroviral, lentivirus, adenoviral, adeno-associated and herpes simplex virus (HSV) vectors for gene transfer.
  • Viral vectors are cu ⁇ ently the most efficient and versatile method of gene transfer in target cells and tissues. 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.
  • Lentiviral vectors are retroviral vector that are able to transduce or infect non-dividing cells and typically produce high viral titers. Selection of a retroviral gene transfer system can therefore depend 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 Immuno deficiency virus (SrV), human immuno deficiency 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.
  • MiLV murine leukemia virus
  • GaLV gibbon ape leukemia virus
  • SrV Simian Immuno deficiency virus
  • HAV human immuno deficiency virus
  • adenoviral based systems are typically 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 levels of expression have been obtained. This vector can be produced in large quantities in a relatively simple system.
  • Adeno-associated virus 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 AA V vectors are described in a number of publications, including U.S. Pat. No.
  • pLASN and MFG-S are examples are retroviral vectors that have been used in clinical trials (Dunbar et al., Blood 85:3048-305 (1995); Kohn et al., Nat. Med. 1: 1 017- 102 (1995); Malech et al, Proc. Natl. Acad. Sci. USA 94:12133-12138 (1997)).
  • PA317/pLASN was the first therapeutic vector used in a gene therapy trial. (Blaese ⁇ ?t al., Science 270:475-480 25 (1995)). Transduction efficiencies of 50% or greater have been observed for MFG-S packaged vectors. (Ellem et al., Immunol Immunother.
  • rAAV Recombinant adeno-associated virus vectors
  • All vectors are derived from a plasmid that retains only the AAV 145 bp inverted terminal repeats flanking the trans gene 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.
  • Ad vectors are predominantly used for colon cancer gene therapy, because they can be produced at high titer and they readily infect a number of different cell types. Most adeno virus vectors are engineered such that a transgene replaces the Ad El a, Elb, and 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 nondividing, differentiated cells such as those found in the liver, kidney and muscle system tissues. Conventional Ad vectors have a large carrying capacity.
  • Ad vector An example of the use of an Ad vector in a clinical trial involved polynucleotide therapy for antitumor 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. 9:71083-1089 (1998); Welsh et al, Hum. Gene Titer. 2:205-18 (1995); Alvarez et al., Hum. Gene Ther. 5:597-613 (1997); Topfet al., Gene Ther.
  • 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 .psi.2 cells or P A317 cells, which package retrovirus.
  • Viral vectors used in gene therapy are usually generated by 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, other viral sequences being replaced by an expression cassette for the protein to be expressed. The missing viral functions are supplied in trans by the packaging cell line.
  • AAV vectors used in gene therapy typically only possess ITR sequences from the AAV genome that are required for packaging and integration into the host genome.
  • Viral DNA is packaged in a cell line that contains a helper plasmid encoding the other AA V 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 AA V vector and expression of AA V 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.
  • an accessory function vector may be used to provide the helper virus functions necessary for AAV production, obviating the need for helper virus infection during AAV production and ensuring that the resulting AAV stock will not be contaminated with helper virus particles (whether active or inactive).
  • Examples of such accessory function vectors are disclosed at U.S. Pat. No. 6.004,797, the disclosure of which is hereby incorporated by reference in its entirety.
  • a viral vector is typically modified to have specificity for a given cell type by expressing a ligand as a fusion protein with a viral coat protein on the viruses outer surface.
  • 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.
  • filamentous phage can be engineered to display antibody fragments (e.g.., FAB or Fv) having specific binding affinity for virtually any chosen cellular receptor.
  • FAB fragment-binding protein
  • Fv antibody fragment-binding protein
  • 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.
  • vectors can be delivered to cells ex vivo, such as cells explanted from an individual patient (e.g., lymphocytes, bone ma ⁇ ow aspirates, tissue biopsy) or universal donor hematopoietic stem cells, followed by reimplantation of the cells into a patient, usually after selection for cells that have incorporated the vector.
  • Ex vivo cell transfection for diagnostics, research, or for gene therapy is well known to those of skill in the art.
  • cells are isolated from the subject organism, transfected with a ZFP nucleic acid (gene or cDNA), and re-infused back into the subject organism (e.g., 30 patient).
  • a ZFP nucleic acid gene or cDNA
  • Various cell types suitable for ex vivo transfection are well known to those of skill in the art (see, e.g., Freshney et al., Culture of Animal Cells, A Manual of Basic Technique (3rd ed. 1994)) and the references cited therein for a discussion of how to isolate and culture cells from patients).
  • stem cells are used in ex vivo procedures for cell transfection and gene therapy.
  • the advantage to using stem cells is that they can be differentiated into other cell types in vitro, or can be introduced into a mammal (such as the donor of the cells) where they will engraft in the bone marrow.
  • Methods for differentiating CD34+cells in vitro into clinically important immune cell types using cytokines such a GM-CSF, LFN- Y and TNF-a are known (see Inaba et al, J Exp. Med. 176:1693-1702 (1992)).
  • cytokines such as GM-CSF, LFN- Y and TNF-a are known (see Inaba et al, J Exp. Med. 176:1693-1702 (1992)).
  • Stem cells are isolated for transduction and differentiation using known methods.
  • stem cells are isolated from bone ma ⁇ ow cells by panning the bone marrow cells with antibodies that bind unwanted cells, such as CD4+ and CQ8+ (T cells), CD45+ (panB cells), GR-1 (granulocytes), and lad (differentiated antigen presenting cells) (see Inaba et al., J. Exp. Med. 176:1693-1702 (1992)).
  • Vectors e.g., retroviruses, adenoviruses, liposomes, etc.
  • therapeutic ZFP nucleic acids can be also administered directly to the organism for transduction of cells in vivo.
  • 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.
  • 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.
  • 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, as described below (see, e.g., Remingtons Pharmaceutical Sciences, 17th ed., 1989). B.
  • PROTEIN COMPOSITIONS An important factor in the administration of polypeptide compounds, such as the present ZFPs, is ensuring that the polypeptide has the ability to traverse the plasma membrane of a cell, or the membrane of an intra-cellular compartment such as the nucleus.
  • Cellular membranes are composed of lipid-protein bilayers that are freely permeable to small, nonionic lipophilic compounds and are inherently impermeable to polar compounds, macromolecules, and therapeutic or diagnostic agents.
  • proteins and other compounds such as liposomes have been described, which have the. ability to translocate polypeptides such as ZFPs across a cell membrane.
  • membrane translocation polypeptides have amphiphilic or hydrophobic amino acid subsequences that have the ability to act as membrane- translocating carriers.
  • homeodomain proteins have the ability to translocate across cell membranes.
  • the shortest internalizable peptide of a homeodomain protein, Antennapedia was found to be the third helix of the protein, from amino acid position 43 to 58 (see, e.g., Prochiantz, Current Opinion in Neurobiology 6:629-634 (1996)).
  • Examples of peptide sequences that can be linked to a ZFP for facilitating uptake ofZFP into cells include, but are not limited to: an 11 amino acid peptide of the tat protein of HI V; a 20 residue peptide sequence which co ⁇ esponds to amino acids 84- 103 of the pl6 protein (see Fahraeus et al., Current Biology 6:84 (1996)); the third helix of the 60- amino acid long homeodomain of Antennapedia (Derossi et al., J. Biol. Chem.
  • Membrane translocation domains can also be selected from libraries of randomized peptide sequences. See, for example, Yeh et al. (2003) Molecular Therapy 7(5):S461, Abstract #1191. Toxin molecules also have the ability to transport polypeptides across cell membranes.
  • such molecules are composed of at least two parts (called “binary toxins”): a translocation or binding domain or polypeptide and a separate toxin domain or polypeptide.
  • the translocation domain or polypeptide binds to a cellular receptor, and then the toxin is transported into the cell.
  • Clostridium perfringens iota, toxin, diphtheria toxin (DT), Pseudomonas exotoxin A (PE), pertussis toxin (PT), Bacillus anthracis toxin, and pertussis adenylate cyclase (CYA) have been used in attempts to deliver peptides to the cell cytosol as internal or amino-te ⁇ ninal fusions (Arora et al., J. Biol. Chem.; 268:3334-3341 (1993); Perelle et al., Infect. Immun., 61 :5147-5156 (1993); Stemnark et al., J.
  • ZFPs can be conveniently fused to or derivatized with such sequences.
  • the translocation sequence is provided as part of a fusion protein.
  • a linker can be used to link the ZFP and the translocation sequence. Any suitable linker can be used, e.g., a peptide linker.
  • the ZFP can also be introduced into an animal cell, preferably a mammalian cell, via a liposomes and liposome derivatives such as immunoliposomes.
  • liposome refers to vesicles comprised of one or more concentrically ordered lipid bilayers, which encapsulate an aqueous phase.
  • the aqueous phase typically contains the compound to be delivered to the cell, i.e., a ZFP.
  • the liposome fuses with the plasma membrane, thereby releasing the drug into the cytosol.
  • the liposome is phagocytosed or taken up by the cell in a transport vesicle. Once in the endosome or phagosome, the liposome either degrades or fuses with the membrane of the transport vesicle and releases its contents.
  • the liposome ultimately becomes permeable and releases the encapsulated compound (in this case, a ZFP) at the target tissue or cell.
  • liposome membranes can be constructed so that they become destabilized when the environment becomes acidic near the liposome membrane (see, e.g., Proc. Natl. Acad. Sci. USA 84:7851 (1987); Biochemistry 28:908 (1989)).
  • liposomes When liposomes are endocytosed by a target cell, for example, they become destabilized and release their contents. This destabilization is termed fusogenesis.
  • Dioleoylphosphatidylethanolamine is the basis of many "fusogenic" systems.
  • Such liposomes typically comprise a ZFP and a lipid component, e.g., a neutral and/or cationic lipid, optionally including a receptor-recognition molecule such as an antibody that binds to a predetermined cell surface receptor or ligand (e.g., an antigen).
  • a lipid component e.g., a neutral and/or cationic lipid, optionally including a receptor-recognition molecule such as an antibody that binds to a predetermined cell surface receptor or ligand (e.g., an antigen).
  • a receptor-recognition molecule such as an antibody that binds to a predetermined cell surface receptor or ligand (e.g., an antigen).
  • Suitable methods include, for example, sonication, extrusion, high pressure/homogenization, microfluidization, detergent dialysis, calcium-induced fusion of small liposome vesicles and ether-fusion methods, all of which are well known in the art.
  • liposomes are targeted using targeting moieties that are specific to a particular cell type, tissue, and the like.
  • targeting moieties e.g., ligands, receptors, and monoclonal antibodies
  • Standard methods for coupling targeting agents to liposomes can be used. These methods generally involve incorporation into liposomes lipid components, e.g., phosphatidylethanolamine, which can be activated for attachment of targeting agents, or derivatized lipophilic compounds, such as lipid derivatized bleomycin.
  • Antibody targeted liposomes can be constructed using, for instance, liposomes that incorporate protein A (see Renneisen et al., J. Biol. Chem., 265:16337-16342 (1990) and Leonetti et al., Proc. Natl. Acad. Sci. USA 87:2448-2451 (1990).
  • the dose administered to a patient should be sufficient to affect a beneficial therapeutic response in the patient over time.
  • the dose will be determined by the efficacy and Kd of the particular ZFP employed, the nuclear volume of the target cell, and the condition of the patient, as well as the body weight or surface area of the patient to be treated.
  • the size of the dose also will be determined by the existence, nature, and extent of any adverse side effects that accompany the administration of a particular compound or vector in a particular patient.
  • the physician evaluates circulating plasma levels of the ZFP or nucleic acid encoding the ZFP, potential ZFP toxicities, progression of the disease, and the production of anti-ZFP antibodies. Administration can be accomplished via single or divided doses.
  • GENERAL ZFPs and the nucleic acids encoding the ZFPs can be administered directly to a subject (e.g., patient) for modulation of gene expression and for therapeutic or prophylactic applications.
  • phrases referring to introducing a ZFP into an animal or patient can mean that a ZFP or ZFP fusion protein is introduced and/or that a nucleic acid encoding a ZFP or ZFP fusion protein is introduced in a form that can be expressed in the animal.
  • the ZFPs and/or nucleic acids can be used in the treatment of chronic pain.
  • Administration of therapeutically effective amounts is by any of the routes normally used for introducing ZFP into ultimate contact with the tissue to be treated.
  • the ZFPs are administered in any suitable manner, preferably with pharmaceutically acceptable carriers (e.g., poloxamer and/or buffer). Suitable methods of administering such modulators 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.
  • 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 are a wide variety of suitable formulations of pharmaceutical compositions (see, e.g., Remington's Pharmaceutical Sciences, 17th ed. 1985)).
  • the ZFPs can be made into aerosol formulations (i.e., they can be "nebulized") to be administered via inhalation. Aerosol formulations can be placed into pressurized acceptable propellants, such as dichlorodifluoromethane, propane, nitrogen, and the like.
  • Formulations suitable for parenteral administration include aqueous and non-aqueous, isotonic sterile injection solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives, hi the practice of the disclosed methods, compositions can be administered, for example, by intravenous infusion, orally, topically, intraperitoneally, intravesically or intrathecally.
  • the formulations of compounds can be presented in unit-dose or multi-dose sealed containers, such as ampules and vials.
  • Injection solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described.
  • compositions provided herein so as to modulate expression of genes involved in neuropathic pain.
  • the compositions can be targeted to specific areas or tissues of a subject.
  • one delivers compositions to specific regions of the body to treat pain.
  • Other treatments in contrast, involve administering the composition in a general manner without seeking to target delivery to specific regions.
  • a number of approaches can be used to localize the delivery of agents to particular regions. Certain of these methods involve delivery to the body lumen or to a tissue (see, e.g., U.S. Pat. Nos.
  • compositions to modulate genes involved in neuropathic pain include systemic administration using intravenous or subcutaneous administration, and tissue engineering (U.S. Pat. No. 5,944,754).
  • Various vectors can be used to deliver polynucleotides to sensory neurons and/or ganglia. See, e.g., Glorioso et al. (2003) Curr. Opin. Mol. Ther. 5(5):483-488. See also Fleming et al.
  • a target site of a nucleic acid within a cell or population of cells is contacted with a ZFP that has binding specificity for that target site.
  • Methods can be performed in vitro with cell cultures or in vivo. Certain methods are performed such that chronic pain is treated by repressing expression of one or more genes involved hyper-excitability (e.g., VRl, TRK-A, and/or NAV1.8).
  • transgenic animals can be generated using standard techniques.
  • gene knockouts e.g., of VRl, TRK-A, and/or NAVl .8 or knockdowns can also be generated.
  • a ZFP as described herein which is targeted to one or more genes involved in neuropathic pain, is administered to any animal in order to create a knockout or knockdown animal. These animals are useful as models for disease and for drug testing.
  • ZFP repressors as described herein make it possible to reduce or eliminate gene (e.g., VRl, TRK-A, and/or NAVl .8) activity in any animal model, for which no feasible ways cu ⁇ ently exist to generate knockouts.
  • gene e.g., VRl, TRK-A, and/or NAVl .8 activity
  • ZFPs as many accepted animal models for studying chronic pain and evaluating candidate drugs are non-mouse models, the ability to create these knockouts/knockdowns in any animal using the ZFPs described herein represents an important advance in the field.
  • animal models for screening can be generated by using ZFPs comprising a transcriptional activation domain to up-regulate expression of, e.g., VRl, TrkAorNaVl.8 genes.
  • ZFPs provided herein and the nucleic acids encoding them such as in the pharmaceutical compositions described herein can be utilized to modulate (e.g., activate or repress) expression of one or more genes involved in nerve excitability, thereby modulating chronic pain. Modulation of nerve excitability can result in the amelioration or elimination of chronic pain. For example, genes overexpressed in chronic pain can be repressed using targeted ZFPs both in cell cultures (i.e., in in vitro applications) and in vivo to decrease nerve hyper-excitability and thereby treat chronic pain.
  • ZFP repressors as described herein do not significantly change the expression levels of any other genes (see, Examples), they are likely to be more specific than antisense methods. Unlike the antisense approach, which needs to target a large number of copies of mRNA, there are a limited number of binding sites in each cell to be targeted by a ZFP, i. e., the chromosomal copies of the target gene(s), therefore, ZFPs can function at a relatively low expression level.
  • certain methods for treating chronic pain involve introducing a ZFP targeted to one or more of VRl, TRK-A, and/orNAVl.8 into an animal.
  • Binding of the ZFP bearing a repression domain to its target site results in decreased nerve excitability and amelioration (or elimination) of neuropathic pain.
  • a repression domain fused to the ZFP represses the expression of the target gene.
  • electrophysiological recordings e.g.. to determine hyper-excitability and/or spontaneous activity
  • compositions provided herein can also be used to activate expression of genes in therapeutic applications.
  • a ZFP engineered to bind a target site in a gene is fused to a transcriptional activation domain.
  • Exemplary genes whose activation can be used to treat neuropathic pain include those encoding brain-derived neurotrophic factor (BDNF), glial-derived neurotrophic factor (GDNF) and nerve growth factor (NGF).
  • BDNF brain-derived neurotrophic factor
  • GDNF glial-derived neurotrophic factor
  • NGF nerve growth factor
  • Rat C6 cells were cultured in DMEM with 10% FBS. Nucleofection was carried out according the manufacture's protocol (Amaxa Biosystems, Cologne, Germany). In brief, 2xl0 6 cells and 2 ⁇ g plasmid DNA were mixed with 100 ⁇ l Nucleofector Solution V. After electroporation with the Nucleofector program U-30, the cells were plated into 6-well plates. Cells were harvested 72 hours post-transfection. Rat ND8/34 cells were cultured in DMEM with 20% FHS. Cells were seeded into 24- well plates at the density of -1.5x 10 5 cells/well 16 to 24 hours prior to transfection.
  • Duplicate transfections were performed for each construct using FuGENE 6 transfection reagents (Roche, Indianapolis, LN). 0.25 ⁇ g of the ZFP-TF expression plasmid or control plasmid and 0.05 ⁇ g of the puromycin resistance plasmid were transfected into each well using 0.75 ⁇ l of Fugene 6 reagent. Transfection reagent-containing media was removed after 8-16 hours and fresh media containing 2 ⁇ g/ml puromycin was added. Cells were harvested 72 hours post-transfection for RNA isolation. Human IMR32 cells were cultured in DMEM with 20% FBS. Cells were seeded into 24- well plates at the density of ⁇ 1.5x 10 5 cells/well 16 to 24 hours prior to transfection.
  • TaqMan was performed in 96-well plate format on ABI 7700 SDS machine (Perkin Elmer, Boston, MA) and analyzed with SDS version 1.6.3 software.
  • RNA samples 25ng were mixed with 0.1 ⁇ M of probe and optimal amount of each primer, 5.5 mM MgCl 2 and 0.3 mM (each) dNTP, 0.625 unit of AmpliTaq Gold DNA Polymerase, 6.25 units of MultiScribe Reverse Transcriptase, and 5 units of RNase Inhibitor in IX TaqMan buffer A from PE.
  • the reverse transcription reactions were performed at 48°C for 30 minutes.
  • PCR amplification reactions were conducted for 40 cycles at 95°C for 15 seconds and at 60°C for 1 minute.
  • the levels of the target gene and 18S mRNA were quantified using standard curves spanning a 125-fold concentration range (relative levels of 0.2 to 25; five-fold dilution series). Each RNA sample was assayed in duplicate Taqman reactions. The ratio of target/18S was used to determine the relative levels of the target RNA in various samples. Sequences and concentrations of primers and probes are provided in Table 1.
  • the reverse transcription step is performed using a poly dT primer instead of the gene specific primer pair.
  • oligo dT (12-18) primer Invitrogen
  • the reverse transcription reaction is performed at 48°C for 60 minutes and then the reverse transcriptase is inactivated at 95°C for 5 minutes.
  • the gene-specific primers are then added to the reaction, and the PCR reaction is performed as described above. Sequences and concentrations of primers and probes are provided in Table 6. Table 6
  • Probe ends are labeled with: 5' --6FAM; and 3'- - BHQ1 ("Black Hole Quencher 1 " ® -Biosearch).
  • the cells were washed three times in a PBS + 1% Tween 20 solution, and resuspended in the secondary antibody solution (goat anti-rabbit IgG-PE, Santa Cruz Biotechnology, sc 3739, diluted at 1/100 in PBS + 1% Tween 20 + 1% powdered milk). The cells were incubated at 4°C for 1 hour. Following this step, the cells were washed three times in a PBS + 1% Tween 20 solution, and resuspended in the tertiary antibody solution (bovine anti-goat IgG-PE, Santa Cruz Biotechnology, sc 3747, diluted at 1/100 in PBS + 1% Tween 20 + 1% powdered milk).
  • the cells were incubated at 4°C for 1 hour. After three washes in a PBS + 1% Tween 20 solution, the cells were resuspended in a PBS solution containing 1% fetal bovine serum. The analysis was performed using a Facscalibur (Becton Dickinson) flow cytometer according to the manufacturer's instructions and the intensity of the phycoerythrin fluorescent labeling in the different samples was measured.
  • Facscalibur Becton Dickinson
  • EXAMPLE 2 REPRESSION OF VRl IN C6 CELLS Fusion proteins comprising 6-fingered zinc finger proteins designed to recognize a target site in rat VRl (rVRl) and a repression domain were designed as described above in and in U.S. Patent No. 6,607,882.
  • the designed ZFPs and the target sites recognized by these ZFPs are shown in Tables 1 and 2. In order to test the ZFPs designed as above and shown in Table 2, the following experiments were conducted.
  • A. GENE EXPRESSION Sequences encoding a fusion protein comprising a rVRl-targeted ZFP (6150, 6332,6337 and 6338) and a repression domain (KOX) were introduced into a pcDNA3.1 plasmid backbone (Invitrogen, Carlsbad, CA) to create rVRl -targeted ZFP expression plasmids.
  • the fusion proteins were designated 6150-KOX, 6332-KOX, 6337-KOX and 6338-KOX.
  • Empty pcDNA3.1 plasmid vectors were also prepared for use as controls.
  • Plasmids vectors including one of 6150-KOX, 6332-KOX, 6337-KOX and 6338- KOX were transfected into cultured Rat C6 cells as described in Example 1. Empty vectors were used as controls. ZFP expression was measured by Taqman assay as described in Example 1. FIGs. 1 and 2 show the results of repression of rat VRl expression using 6332- KOX, 6337-KOX or 6338-KOX. Administration of rVRl -targeted ZFPs significantly repressed rat VRl expression.
  • ZFP repressors expression plasmids were transfected into rat C6 cell cultures using Fugene 6 reagent (Roche, Cat. #1 814 443). To increase the proportion of cells having received the expression plasmid, a puromycin-resistance plasmid was co-transfected with either the ZFP plasmid or the control vector (cells were selected with 2 ⁇ g/ml puromycin for two days to kill untransfected cells).
  • the primary antibody used for detection of rVRl protein is anti-rat VRl (rabbit polyclonal), ABR PA1- 747 (see Immunodetection protocol, Example 1).
  • This experiment revealed that 6144, 6149, 6150, 6332, 6337 and 6338 down-regulate the expression of rVRl at the protein level.
  • FIG. 3. In this analysis, the average fluorescence was determined using the cell population between the fluorescence values of 2 and 100. For each sample, this encompassed >95% of the cells. FIG. 3. Thus, VRl-targeted ZFPs repress expression of rVRl at the nucleotide and protein levels.
  • GENE EXPRESSION Expression plasmids comprising ZFP repressors shown in Table 3 were transfected into ND8/34 cell cultures (mouse neuroblastoma/rat DRG neuron hybrid cell line) using the Fugene 6 reagent. To increase the proportion of cells having received the expression plasmid, a puromycin-resistance plasmid was co-transfected with either the ZFP plasmid or the control vector. Cells were selected with 2 ⁇ g/ml puromycin for two days to kill untransfected cells. As shown FIG. 4, 6182-KOX and 6297-KOX down- regulate the expression of rTrkA at the mRNA level.
  • ZFP repressors expression plasmids were transfected into ND8/34 cell cultures using Fugene 6 reagent. To increase the proportion of cells having received the expression plasmid, a puromycin- resistance plasmid was co-transfected with either the ZFP plasmid or the control vector (cells were selected with 2 ⁇ g/ml puromycin for two days to kill untransfected cells). The primary antibody used in this assay was anti TrkA (rabbit polyclonal), Upstate #06574 (see Immunodetection protocol, Example 1).
  • EXAMPLE 5 REPRESSION OF HUMAN TRKA EXPRESSION Plasmids encoding fusions of various human TrkA-targeted zinc finger proteins (Table 5) with a KOX repression domain were constructed using stajidard molecular biological techniques. See, for example, U.S. Patents 6,453,242 and 6,534,261. Expression of the fusion proteins was controlled by a human EF-l ⁇ promoter, included in the plasmid in operative linkage to sequences encoding the fusion proteins. The EF-la promoter was chosen because it functions effectively in neural cells and cell lines, and its activity can be enhanced by the presence of all-trans-retinoic acid in the cellular culture medium.
  • the chronic myelogenous leukemia cell line K562 was chosen for testing TrkA repression, because they grow well in suspension, express TrkA and can be transfected with high efficiency.
  • Cells were cultured in 6-well dishes to a concentration of 2x10 6 cells per well in the presence of 1 mM all-tr ⁇ s-retinoic acid. Plasmids were introduced into K562 cells by nucleofection (Amaxa, Solution V, Program T -16), and transfection efficiencies of >90% were routinely achieved.
  • TrkA protein levels were analyzed for TrkA protein levels (i.e., at 72 hours after transfection).
  • Cell lysates were prepared in RIPA buffer and passed through a QIAshredder column (Qiagen, Valencia, CA) and analyzed on a NuPAGE 4-12% BisTris (1mm X 10 well) gel (Cat # NP0321BOX, Invitrogen) on the Novex minigel system. The gel was blotted onto 0.2 ⁇ m pore nitrocellulose membrane (Cat # LC2000, Invitrogen) on the Xcell II blot module (Invitrogen).
  • the blot was exposed to rabbit anti-TrkA (1:1, 000 dilution, Upstate Biotechnology, NY) and rabbit anti-TFIIB (1:1,000 dilution, Santa Cruz Biotechnology) overnight at 4°C on a rocking platform, then washed and exposed to horseradish peroxidase-conjugated goat anti-rabbit IgG (1:5,000 dilution, Santa Cruz Biotechnology) at room temperature for 2 hours with agitation. Signal was detected using a SuperSignal WestDura Extended Duration substrate and Chemiluminescence Detection Kit, both obtained from Pierce Chemical Co. (Rockland, IL). The results, shown in Figure 8, indicate that levels of TrkA protein are reduced after transfection of cells with TrkA-targeted ZFP/KOX fusion proteins, confirming the results obtained by analysis of TrkA mRNA.

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Abstract

L'invention concerne des compositions et des méthodes de traitement de la douleur neuropathique. Les compositions de l'invention peuvent contenir des protéines dotées d'un domaine à doigts de zinc fondu sur un domaine régulateur capable soit d'activer soit d'inhiber l'expression d'un gène cible impliqué dans la douleur neuropathique. Dans une variante, les compositions de l'invention peuvent contenir une séquence nucléotidique codant une protéine de l'invention, laquelle séquence peut éventuellement être fournie sous forme de plasmide ou dans un virus ou tout autre vecteur pour pénétrer dans une cellule ou un tissu cible. Par ailleurs, l'invention concerne des méthodes de traitement de la douleur neuropathique qui consistent à traiter un sujet au moyen des compositions de l'invention. Des gènes cibles modèles destinés au traitement de la douleur neuropathique incluent VR1, NaV1.8, et TrkA.
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Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2250184A1 (fr) * 2008-02-08 2010-11-17 Sangamo BioSciences, Inc. Traitement de la douleur chronique par des protéines en doigt de zinc
US9340590B2 (en) 2011-03-16 2016-05-17 Amgen Inc. Potent and selective inhibitors of NaV1.3 and NaV1.7
US9636418B2 (en) 2013-03-12 2017-05-02 Amgen Inc. Potent and selective inhibitors of NAV1.7
EP3354275A1 (fr) * 2009-02-04 2018-08-01 Sangamo Therapeutics, Inc. Procédés et compositions permettant de traiter des neuropathies
US10344060B2 (en) 2013-03-12 2019-07-09 Amgen Inc. Potent and selective inhibitors of Nav1.7
CN111712252A (zh) * 2017-12-13 2020-09-25 纽约州立大学研究基金会 用于治疗疼痛和提高疼痛敏感性的肽和其它药剂

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
DIETZ G.P.H. AND BAHR M.: "Delivery of bioactive molecules into the cell: the Trojan horse approach", MOLECULAR AND CELLULAR NEUROSCIENCE, vol. 27, October 2004 (2004-10-01), pages 85 - 131, XP004599335 *
PARDRIDGE W.M.: "Blood-Brain Barrier Drug Targeting: The Future of Brain Drug Development", MOLECULAR INTERVENTIONS, vol. 3, no. 2, March 2003 (2003-03-01), pages 90 - 105, XP002993086 *
REBAR ET AL: "Induction of angiogenesis in a mouse model using engineered transcription factors", vol. 8, no. 12, December 2002 (2002-12-01), pages 1427 - 1432, XP002993087 *

Cited By (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2250184A1 (fr) * 2008-02-08 2010-11-17 Sangamo BioSciences, Inc. Traitement de la douleur chronique par des protéines en doigt de zinc
EP2250184A4 (fr) * 2008-02-08 2011-05-04 Sangamo Biosciences Inc Traitement de la douleur chronique par des protéines en doigt de zinc
EP3354275A1 (fr) * 2009-02-04 2018-08-01 Sangamo Therapeutics, Inc. Procédés et compositions permettant de traiter des neuropathies
US9340590B2 (en) 2011-03-16 2016-05-17 Amgen Inc. Potent and selective inhibitors of NaV1.3 and NaV1.7
US9796766B2 (en) 2011-03-16 2017-10-24 Amgen Inc. Potent and selective inhibitors of NAV1.3 and NAV1.7
US9636418B2 (en) 2013-03-12 2017-05-02 Amgen Inc. Potent and selective inhibitors of NAV1.7
US10344060B2 (en) 2013-03-12 2019-07-09 Amgen Inc. Potent and selective inhibitors of Nav1.7
CN111712252A (zh) * 2017-12-13 2020-09-25 纽约州立大学研究基金会 用于治疗疼痛和提高疼痛敏感性的肽和其它药剂

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