WO2005086825A2 - Methods and compositions for treatment of diseases associated with aberrant microsatellite expansion - Google Patents

Methods and compositions for treatment of diseases associated with aberrant microsatellite expansion Download PDF

Info

Publication number
WO2005086825A2
WO2005086825A2 PCT/US2005/007631 US2005007631W WO2005086825A2 WO 2005086825 A2 WO2005086825 A2 WO 2005086825A2 US 2005007631 W US2005007631 W US 2005007631W WO 2005086825 A2 WO2005086825 A2 WO 2005086825A2
Authority
WO
WIPO (PCT)
Prior art keywords
mbnll
mouse
protein
splicing
exon
Prior art date
Application number
PCT/US2005/007631
Other languages
French (fr)
Other versions
WO2005086825A3 (en
Inventor
Maurice S. Swanson
Rahul N. Kanadia
Charles A. Thornton
Original Assignee
University Of Florida
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by University Of Florida filed Critical University Of Florida
Priority to AU2005220900A priority Critical patent/AU2005220900A1/en
Priority to EP05725031A priority patent/EP1734827A4/en
Priority to US10/591,883 priority patent/US7964570B2/en
Publication of WO2005086825A2 publication Critical patent/WO2005086825A2/en
Publication of WO2005086825A3 publication Critical patent/WO2005086825A3/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/1703—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • A61K38/1709—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P21/00—Drugs for disorders of the muscular or neuromuscular system
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/90—Stable introduction of foreign DNA into chromosome
    • C12N15/902—Stable introduction of foreign DNA into chromosome using homologous recombination
    • C12N15/907—Stable introduction of foreign DNA into chromosome using homologous recombination in mammalian cells
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering N.A.
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
    • C12N2750/14143—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector

Definitions

  • DRPLA Dentatorubral pallidoluysian atrophy
  • HD Huntington chorea
  • OPMD Oculopharyngeal muscular dystrophy
  • SBMA Spinobulbar muscular atrophy
  • SCA1 SCA2, SCA3, SCA6, SCA7, SCA17
  • the characterized non- coding region expansion diseases include Fragile XA, Fragile XE, Friedrich's ataxia, Myotonic Dystrophy type 1 (DM1), Myotonic Dystrophy type 2 (DM2), and Spinocerebellar ataxia types 8, 10, and 12 (SCA8, SCA10, SCA12).
  • Huntington's disease-like type 2 is likewise caused by a microsatellite expansion.
  • Microsatellite expansion diseases have been most commonly associated with trinucleotide expansion mutations. In fact, at least 16 of the microsatellite expansion diseases reported to date have been characterized as trinucleotide expansion diseases. More recently, however, microsatellite expansion diseases have also been associated with tetranucleotide and even pentanucleotide expansion mutations. Disease severity and age of onset have both been related to the size of the expansion mutation, eventually leading to muscle weakness and premature cataract formation, and, in severe cases, to hypotonia, muscle heart block, and nervous system dysfunction (Korade-Mirnics, Z, Babitzke, P, Hoffman, E (1998) Nuc. Acids Res. 26(6): 1363-1368).
  • Myotonic dystrophy (dystrophia myotonica, DM) is a multisystemic, dominantly inherited disorder often characterized by myotonia, or, delayed muscle relaxation due to repetitive action potentials in myofibers, and muscle degeneration. Manifestations of DM may also include heart block, ocular cataracts, hypogonadism, and nervous system dysfunction.
  • Myotonic dystrophy type 1 (DM1) is caused by a trinucleotide
  • CCG Dystrophia myotonica-protein kinase
  • DM2 Dystrophia myotonica-protein kinase
  • CCTG tetranucleotide
  • ZNF9 zinc finger protein 9
  • both DM1 and DM2 mutant transcripts accumulate as foci within muscle nuclei (Liquori, et al, 2001).
  • An indication that these transcripts are pathogenic comes from studies on HSA LR mice, which express a large CTG repeat in the 3'-UTR of a human skeletal actin transgene (Mankodi, A, Logigian, E, Callahan, L, McClain, C, White, R, Henderson, D, Krym, M, Thornton, CA ( 2000) Science 289: 1769-1773).
  • HSA LR mice which express a large CTG repeat in the 3'-UTR of a human skeletal actin transgene (Mankodi, A, Logigian, E, Callahan, L, McClain, C, White, R, Henderson, D, Krym, M, Thornton, CA ( 2000) Science 289: 1769-1773).
  • These transgenic mice develop myonuclear RNA foci, myotonia, and degenerative muscle changes
  • the myotonia in HSA LR mice is caused by loss of skeletal muscle chloride (ClC-1) channels due to aberrant pre-mRNA splicing (Mankodi, A, Takahashi, MP, Jiang, H, Beck, CL, Bowers, WJ, Moxley, RT, Cannon, SC, Thornton, CA ( 2002) Mol. Cell 10: 35-44). Similar ClC-1 splicing defects exist in DM1 and DM2. However, the connection between accumulation of mutant DM transcripts in the nucleus and altered splice site selection has not been established (Faustino, NA, Cooper, TA (2003) Genes Dev. 17: 419-437).
  • RNA gain-of-function hypothesis proposes that mutant DM transcripts alter the function and localization of alternative splicing regulators, which are critical for normal RNA processing. Consistent with this proposal, misregulated alternative splicing in DM1 has been demonstrated for six pre-mRNAs: cardiac troponinT (cTNT), insulin receptor (IR), muscle-specific chloride channel (ClC-1), tau, myotubularin-related protein 1 (MTMR1) and fast skeletal troponin T (TNNT3) (Kanadia RN, Johnstone KA, Mankodi A, Lungu C, Thornton CA, Esson D, Timmers AM, Hauswirth WW, Swanson MS (2003), Science 302: 1978-1980).
  • cTNT cardiac troponinT
  • IR insulin receptor
  • ClC-1 muscle-specific chloride channel
  • tau tau
  • MTMR1 myotubularin-related protein 1
  • TNNT3 fast skeletal troponin T
  • CELF proteins have been shown to regulate pre-mRNA alternative splicing and two (CUG-BP1 and ETR-3/CUG-BP2) have been shown to have cytoplasmic RNA-associated functions (Mukhopadhyay D, Houchen CW, Kennedy S, Dieckgraefe BK, Anant S (2003), Mol Cell 11: 113-126).
  • CUG-BP1 regulates alternative splicing of at least three of the pre-mRNAs (cTNT, IR and ClC-1) that are misregulated in DM striated muscle (Charlet-B N, Savkur RS, Singh G, Philips AV, Grice EA, Cooper TA (2002b), Mol Cell 10: 45-53).
  • the splicing patterns observed for all three pre- mRNAs are consistent with increased CUG-BP1 activity and an increase in CUG- BP1 steady-state levels in DM1 striated muscle (Charlet-B N, Savkur RS, Singh G, Philips AV, Grice EA, Cooper TA (2002b), Mol Cell 10: 45-53).
  • cTNT minigenes expressed in DM1 muscle cultures or cTNT and IR pre-mRNAs co-expressed with CUG repeat RNA in normal cells reproduce the aberrant splicing patterns observed for endogenous genes in DM cells (Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737-741; Savkur RS, Philips AV, Cooper TA (2001), Nat Genet 29: 40-47).
  • the CNS symptoms of DM1 may include cognitive impairment, hypersomnolence, heightened sensitivity to anesthetic agents, central hypoventilation, neuroendocrine dysfunction, and effects on personality and behavior [reviewed by Harper (Harper, P.S. (2001), Myotonic dystrophy. Saunders London) and Ashizawa (Ashizawa, T. (1998), Arch. Neurol, 55, 291-293)].
  • Some of these effects such as, mental retardation in individuals with congenital DM1, occur during development (Dyken, P.R., Harper, P.S. (1973), Neurology, 23, 465-473).
  • Other symptoms, such as, hypersomnolence appear during adult life.
  • the mechanism and neuropatho logic correlates for CNS involvement in DM1 are unknown.
  • Microtubule-associated protein tau (MAPT) pre-mRNA is alternatively spliced at exons 2, 3, and 10 (Goedert, M., Spillantini, M.G., Jakes, R., Rutherford, D., and Crowther, R.A. (1989), Neuron, 3, 519-526).
  • Tau transcripts in fetal brain do not include exon 10, whereas -50% of transcripts in adult brain include this exon which encodes an additional microtubule binding domain (Hong, M., Zhukareva, V., Vogelsberg-Ragaglia, V., Wszokek, Z., Reed, L., Miller, B.I., Geschwind, D.H., Bird, T.D., McKeel, D., Goate, A. et al. (1998), Science, 282, 1914-1917).
  • Alternative splicing of exons 2 and 3 also is developmentally regulated (neither exon is included in the fetus, adults mainly include exon 2).
  • RNA-binding proteins that regulate alternative splicing bind to sequence- specific elements in the pre-mRNA to enhance or repress inclusion of alternative exons.
  • Aberrant regulation of alternative splicing can cause the expression of inappropriate splicing patterns leading to human disease (Faustino and Cooper, 2003).
  • Myotonic dystrophy constitutes an example of a disease that alters the function of RNA-binding proteins to cause misregulated alternative splicing.
  • the present disclosure provides methods and compositions for treating diseases associated with aberrant microsatellite expansion employing recombinant adeno-associated virus (rAAV) expressing human muscleblind (MBNL) proteins.
  • rAAV recombinant adeno-associated virus
  • MBNL human muscleblind
  • One embodiment of the invention is directed to a method of treating a disease associated with aberrant microsatellite expansion, comprising administering to a mammal in need thereof, a therapeutically effective amount of recombinant adeno-associated virus (rAAV) containing a transgene that encodes a protein selected from the group consisting of MBNL 1, MBNL2, MBNL3, and combinations thereof.
  • rAAV recombinant adeno-associated virus
  • treating comprises ameliorating or eliminating the symptoms of a neuromuscular or neurological condition caused by the aberrant microsatellite expansion.
  • the neuromuscular condition is myotonic dystrophy.
  • treating comprises reversing the mis-splicing of the Clcnl skeletal muscle chloride channel, reversing the mis- splicing of the Amyloid beta (A4) precursor protein (APP), reversing the mis- splicing of the NMDA receptor NR1 (GRIN1), reversing the mis-splicing of the Microtubule-associated protein tau (MAPT), or reversing the mis-splicing of TNNT2 (cTNT), respectively.
  • A4 precursor protein APP
  • GRIN1 NMDA receptor NR1
  • MTT Microtubule-associated protein tau
  • cTNT TNNT2
  • One embodiment of the invention is directed to a method of treating a disease associated with aberrant microsatellite expansion, comprising administering to a mammal in need thereof, a therapeutically effective amount of recombinant adeno-associated virus (rAAV) containing a transgene that encodes MBNLl.
  • rAAV recombinant adeno-associated virus
  • One embodiment of the invention is directed to a method of treating a disease associated with aberrant microsatellite expansion, comprising administering to a mammal in need thereof, a therapeutically effective amount of recombinant adeno-associated virus (rAAV) containing a transgene that encodes a protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof, wherein the mammal is human.
  • the mammal in need of treatment has RNA inclusions in neuronal cells.
  • One embodiment of the invention is directed to pharmaceutical compositions comprising a recombinant adeno-associated virus (rAAV) containing a transgene that encodes at least one protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof.
  • rAAV recombinant adeno-associated virus
  • the protein is MBNLl.
  • the present disclosure also provides a mouse model for myotonic dystrophy, wherein the mouse has a substantial deletion of a muscleblind exon in its genome.
  • Such an animal model for human disease allows the identification and testing of potential therapeutic and preventive agents.
  • one embodiment of the invention is directed to a mouse model for disease associated with aberrant microsatellite expansion, comprising a mouse having a substantial deletion of MbnlX exon 3 (E3) in the mouse genome, wherein said mouse exhibits symptoms typical of a disease associated with aberrant microsatellite expansion in humans.
  • the invention is directed to a cell isolated from said mouse.
  • the mouse exhibits symptoms such as muscle weakness and ocular cataracts.
  • the invention is directed to a mouse model for disease associated with aberrant microsatellite expansion, comprising a mouse having a substantial deletion of Mbnll exon 3 (E3) in the mouse genome, wherein said mouse exhibits symptoms typical of a disease associated with aberrant microsatellite expansion in humans, wherein the microsatellite repeat expansion disease is caused by a microsatellite expansion in a coding region of DNA.
  • the microsatellite repeat expansion disease is caused by a microsatellite expansion in a non-coding region of DNA.
  • the invention is directed to a mouse model for disease associated with aberrant microsatellite expansion, comprising a mouse having a substantial deletion of Mbnll exon 3 (E3) in the mouse genome, wherein said mouse exhibits symptoms typical of a disease associated with aberrant microsatellite expansion in humans, wherein the mouse exhibits abnormal muscleblind proteins.
  • the mouse may have a loss of functional ClC-1 protein, a loss of functional Amyloid beta (A4) precursor protein, a loss of functional NMDA receptor NR1, a loss of functional Microtubule- associated protein tau, a loss of functional TNNT2 protein, or a loss of functional TNNT3 protein, respectively.
  • One embodiment of the invention is directed to a method of identifying a compound useful in the treatment of disease associated with aberrant microsatellite expansion, comprising administering a test compound to a mouse having a substantial deletion of Mbnll exon 3 (E3) in the mouse genome, wherein said mouse exhibits symptoms typical of a disease associated with aberrant microsatellite expansion in humans, wherein the mouse exhibits abnormal muscleblind proteins, and monitoring said mouse for reduction or inhibition of the symptoms associated with said disease.
  • the mouse may be monitored for effects other than those associated with the disease.
  • the disease is myotonic dystrophy.
  • FIG. 1 A shows targeted disruption of Mbnll.
  • the illustration includes C57BL/6J Mbnll exon organization (open boxes, UTRs black boxes, open reading frame) together with the l29Sl/Svlm] insert (black rectangle), the 129 genomic region with EcoRV ( ⁇ ) ( ⁇ site in C57BL/6] shown by black box with white ⁇ ), Xbal (X), and Bam HI (B) sites, the targeting construct with a thymidine kinase marker (TK), floxed (black triangles, loxP sites), neomycin cassette (stippled box with white N), the 129 region (thick black line) and locations of hybridization probes I and II.
  • TK thymidine kinase marker
  • floxed black triangles, loxP sites
  • neomycin cassette stippled box with white N
  • the 129 region thick black line
  • FIG. IB is a genomic analysis of Mbnll mice with the use of probe 1.
  • the 11-kb EcoRV fragment is derived from C57BL/6; the mutant is 6.5 kb.
  • FIG. IC shows loss of Mbnll ⁇ 3 expression in Mbnll AE3/ ⁇ E3
  • FIG. ID is an immunoblot analysis (total spleen protein) showing absence of Mbnll 41-42kD proteins in Mbnll ⁇ E3/ ⁇ E3 .
  • FIG. 2A shows an electromyograph (EMG) of Mbnll wild-type and mutant knockout vastus muscle.
  • EMG electromyograph
  • FIG. 2B shows ClC-1 splicing in DM mouse models.
  • Functional chloride channels are produced when Clcnl exons 6, 7 and 8 are spliced directly together, whereas isoforms that include cryptic exons 7a or 8a encode truncated nonfunctional proteins.
  • Clcnl exons 7 to 8 are illustrated (open boxes) with the primer positions indicated via horizontal arrows. Inclusion of exons 7a and 8a occurs at low levels in wild-type (FVB wt, Mbnll +/+ ) and Mbnll +/AE3 muscle but at increased levels in Mbnll &E3/AE3 and HSA LR muscle.
  • FIG. 2C and FIG. 2D depict the loss of ClC-1 protein observed in
  • FIG. 2E and FIG. 2F constitute representative images of sections from 11-week-old mice showing equivalent dystrophin (Dys) levels in Mbnll +/+ (E) and Mbnll AE3/ E3 (F) muscle.
  • FIG. 2G and FIG. 2H depict abnormal muscle histology.
  • H&E Hematoxylin and eosin-stained vastus from wild-type (G) and Mbnll AE3/AE3 (H) mice, showing split myofibers (black arrowhead) and centralized myonuclei (white arrowhead). Scale bar, 30 ⁇ m.
  • FIG. 21 to FIG.2L show cataract development.
  • Dilated eyes of 18- week old mice showing a clear wild-type lens (I) but dust-like opacities (white arrowhead) in Mbnll AE3/AE3 mice (K).
  • Center bright spot is the lamp reflection.
  • H&E-stained anterior section (J, L) highlight increased fragmentation (black arrowhead) and opacities (white arrowhead) in Mbnll AE3/ E3 lens (L) compared to wild-type lens (J).
  • FIG. 3 A and 3B constitute representative images of sections from 11- week-old mice showing similar levels of ⁇ -sarcoglycan in (A) wild-type (Mbnll +/+ ) vastus muscle and (B) muscleblind E3 knockout (Mbnll ⁇ E3/ ⁇ E3 ) vastus muscle.
  • FIG. 4A shows adult retention of Tnnt2 exon 5 Mbnll AE3/AE3 heart.
  • RT-PCR products with (+) and without (-) exon 5 are indicated (brackets). Size markers are pBR322 Msp I fragments.
  • FIG. 4B shows Tnnt3 fetal (F) exon inclusion in adult Mbnll AE3/ E3 .
  • the Tnnt3 protein contains variable N-terminal (alternative splicing of exons 4 to 8 and F) and C-terminal regions (exons 16 and 17) (23).
  • RT-PCR 11-week-old mice
  • Tnnt3 exons 2 to 11 left panel
  • F fetal
  • the F exon contains a RyrBI site (arrowhead) resulting in co-migrating smaller fragments in Mbnll AE3/AE3 (right panel).
  • FIG. 4C depicts RT-PCR of Tnnt3 exons 15 to 18 after Mscl digestion.
  • FIG. 4D shows retention of Tnnt3 fetal (F) exon in adult DM1 skeletal muscle (left panel).
  • the right panel shows cDNAs containing the F exon (bracket) cleaved with Bbsl (arrowhead).
  • FIG. 5 A shows reversal of the skeletal muscle major chloride channel
  • (Clcnl) splicing defect following AAV-MBNL1 injection + lanes represent AAV- mycMBNLl injection into the Tibialis anterior (TA) muscles of HSA LR mice, while - lanes represent injection of PBS into the other leg. Boxes indicate Clcnl exons. Shown are the normal (bottom, exons 6, 7, 8 spliced directly together) and aberrant (7a, 8a and intron 6 inclusion) splicing patterns. Mice 190 and 191 are uninjected controls.
  • FIG. 5B shows an electromyogram depicting the results of the myotonia analysis performed.
  • the scale (Y-axis) runs from 0 to 3, with 3 corresponding to severe myotonia. Zero equals no observed myotonic discharges, 1 equals occasional myotonic discharge, 2 equals abundant myotonic discharges and 3 equals myotonic discharge in nearly every insertion.
  • the X-axis shows the mouse number and whether the TA was injected or uninjected with rAAVl Myc-hMBNLl.
  • FIG. 6 shows the results of RT-PCR analysis of exon inclusion.
  • Percent exon inclusion is calculated as ((mRNA+exon)/(mRNA- exon+niRNA+exon)) x 100. Results are derived from at least three independent experiments. Expression of GFP-MBNL1 (-72 kDa), GFP-MBNL2 (-58 kDa), GFP-MBNL3 (-70 kDa) and EGFP (-27 kDa) was detected by Western blot analysis using an anti-GFP monoclonal antibody. All three MBNL proteins promote exon 5 skipping of (A) chicken and (B) human cTNT exon 5 in primary skeletal muscle cultures. (C) All three MBNL proteins promote exon 11 inclusion in a human J_R minigene in HEK293 cells. (D) MBNL proteins have minimal effects on splicing of exon EN in a clathrin light-chain B minigene in primary skeletal muscle cultures.
  • FIG. 7A shows a Western blot confirming depletion of endogenous
  • MBNLl by independent transfection of two different siRNA constructs using the MBNLl monoclonal (mAb) 3A4, which recognizes two MBNLl isoforms generated by alternative splicing (-41 and 42 kDa).
  • GAPDH (-36 kDa) was used as a loading control.
  • FIG. 7B shows the results of immunofiuorescence analysis using mAb 3A4 to confirm depletion of endogenous protein after independent transfection of each MBNLl siRNA construct. Scale bar, 10 ⁇ m.
  • FIG. 7C shows, in bar graph form, the RT-PCR results from at least three transfections.
  • FIG. 8 shows MBNLl binds upstream of exon 5 in human cTNT at a site distinct from the CUG-BPl -binding site.
  • A Binding of recombinant GST- MBNLl to uniformly 32 P-labeled RNA was assayed by UV cross-linking. Scanning mutagenesis was performed by replacing 6 nt blocks with AUAAUA and identified two binding sites 18 and 36 nt upstream of the alternative exon.
  • the MBNL1- binding sites (M) and the CUG-BPl -binding site (C) are located on opposite sides of exon 5. (+) and (-) indicate binding; (•) indicates a putative branch point adenosine.
  • FIG. 9A schematically depicts how the chicken cTNT MSE 1 ⁇ 1 RNA contains an alternative exon flanked by four MSEs.
  • FIG. 9A shows the results of the UV-cross-linking assays, wherein GST-MBNLl bound weakly to MSE1 and strongly to MSE4.
  • FIG. 9B shows UV-cross-linking assay results for competition of
  • FIG. 9C shows the results of the scanning mutagenesis performed, identifying two MBNLl -binding sites within
  • FIG. 9D shows an alignment of the four MBNLl -binding motifs in human and chicken cTNT, which reveals a common motif.
  • FIG. 10A shows, in bar graph form, the results of the over-expression and depletion experiments with respect to the wild-type cTNT minigene, co- transfected with the indicated siRNA constructs, a plasmid expressing a DMPK minigene with 960 CUG repeats (Philips et al 1998) or a GFP-MBNLl expression plasmid in HeLa cells.
  • FIG. 10B shows the results with respect to the mutant cTNT minigene with point mutations that prevent CUG-BPl binding and regulation.
  • FIG. 11A shows, in bar graph form, the results of the over-expression and depletion experiments with respect to the mutant human IR minigene lacking the CUG-BPl -binding site in HEK293 cells.
  • FIG. 1 IB shows the results with respect to the human IR minigene lacking the CUG-BPl -binding site.
  • FIG. 12 shows the results of FISH (left panels) and IF (middle panels) analyses of frozen sections of DM1 brain showing nuclear foci of mutant DMPK mRNA.
  • FISH, IF, and nuclear stain (DAPI, blue) images are merged in panels on the right.
  • FISH without IF
  • Texas Red-labeled CAG repeat probe shows an RNA inclusion in frontal cortical neuron. Autofluorescence from lipofuscin occurs at broad spectrum of wavelengths. It appears in every color channel and as yellow-brown perinuclear material in the merged image.
  • RNA inclusions in cerebral cortex are confined to neurons identified by IF for NeuN (B) or MAP2 (C).
  • RNA foci do not colocalize with PML bodies in cortical neurons. Bar, 5 ⁇ m, applies to all panels.
  • FIG. 13 shows RNA foci in dentate gyrus and subcortical neurons in
  • FISH CAG repeat probe, red
  • IF anti-NeuN antibody, green
  • DAPI nuclear stain
  • FIG. 14 shows foci of mutant RNA in neuronal and muscle nuclei, as visualized by FISH and IF analysis. Processing was carried out on the same slide and imaging under the same exposure settings.
  • FIG. 15 shows the results of FISH and IF analyses of sections of temporal or frontal cortical neurons showing colocalization of mutant DMPK mRNA [(CUG)n] with 20Sa subunit of proteasome (A), MBNL2 (E), and hnRNP F (F).
  • A 20Sa subunit of proteasome
  • E MBNL2
  • F hnRNP F
  • G DM1 cortical neurons
  • H cytoplasm of normal neurons
  • Mutant DMPK mRNA does not colocalize with the PM/ScllOO (nuclear) component of the exosome (B), CUGBP1 (C), or NF90 (D).
  • RAR ⁇ does not colocalize with RNA foci in DM1 cortical neurons (I).
  • the distribution of RAR ⁇ in the DM1 (I) and non-neurologic-disease (J) neuronal nucleus is similar. Bar, 5 ⁇ m, applies to all panels.
  • FIG. 16 shows the results of FISH analysis combined with IF analysis of sections of DM1 temporal or frontal cortex.
  • FISH CAG repeat probe, red, left panels
  • IF middle panels, antibody to indicated protein, green
  • DAPI nuclear stain
  • CUG expansion RNA colocalizes with proteasome 11 S ⁇ subunit (A) and linRNP H (C) but not with double-stranded RNA binding protein ADAR1 (B), hnRNP M (D), or Spl (E). Bar, 5 ⁇ m, applies to all panels.
  • FIG. 17 depicts, in graph form, immunofluorescence (area x intensity) for MBNLl in the nucleus, excluding nucleolus and RNA foci, as determined for 20 neurons in sections of temporal cortex from 3 individuals with DM1 and 3 controls without neurologic disease (C).
  • FIG. 18 shows the regulation of alternative splicing of the NMDA
  • NR1 receptor NBDAR1
  • APP amyloid beta precursor protein
  • MTT microtubule-associated protein tau
  • B provides quantification of RT-PCR splicing assay (triplicates), ex, exon.
  • Human muscleblind genes MBNLl (SEQ ID NO: 1), MBNL2 (SEQ ID NO: 2), and MBNL3 (SEQ ID NO: 3) are homologous to the Drosophila gene muscleblind, which is essential for muscle and eye differentiation.
  • MBNLl the major MBNL gene expressed in human skeletal muscle, encodes multiple protein isoforms, including some that bind to expanded CUG repeats (41 to 42 kD) and others that fail to bind (31 kD isoform), generated by exon 3 skipping.
  • MBNLl was identified in HeLa cells based on its ability to bind double-stranded CUG repeats (Miller JW, Urbinati CR, Teng-Umnuay P, Stenberg MG, Byrne BJ, Thornton CA, Swanson MS (2000), EMBOJ 19: 4439- 4448). All three MBNL gene products colocalize with the expanded repeat RNA foci in vivo (Fardaei M, Rogers MT, Thorpe HM, Larkin K, Hamshere MG, Harper PS, Brook JD (2002), Hum Mol Genet 11: 805-814).
  • Recombinant AAV (rAAV) vectors have been used for expressing gene products in animals, see, for example, U.S. Pat. No. 5,193,941 and WO 94/13788.
  • Other patents and publications describe AAV vectors and uses, the uses generally being related to expression of gene products either in vitro (usually tissue cultures) or in vivo (usually in the lungs or oral mucosa, the normal sites of AAV infection, but expression in other tissues, such as the central nervous system and in cardiac tissue has been observed).
  • AAV vectors have certain advantages over other well-characterized vector systems. First, like adenovirus, AAV infects non-dividing cells. Second, all the AAV viral genes are eliminated in the vector. Since the viral gene expression- induced immune reaction is no longer a concern, AAV vectors are safer than adenovirus vectors. As AAV is an integration virus, integration into the host chromosome will maintain the transgene in the cells. AAV is an extremely stable virus, resistant to many detergents, pH changes and heat (stable at 56 °C for about an hour). AAV can be lyophilized and redissolved without losing significant activity. Finally, AAV causes no known diseases or pathogenic symptoms in humans. Therefore, AAV is a very promising delivery vehicle for gene therapy.
  • T-lymphocytes and B-lymphocytes include: T-lymphocytes and B-lymphocytes, human erythroleukemia cells, different regions of the rat brain, the striatum of the rat brain in a Parkinson's Disease model with the tyrosine hydroxylase gene, heart of the pig and rat with the LacZ gene, the peripheral auditory system of the guinea pig and bronchial epithelia of the rabbit and monkey.
  • the invention provides a vector for effective expression of a protein with MBNLl, MBNL2, or MBNL3 (or combinations thereof) function to treat conditions associated with aberrant microsatellite expansions.
  • the vector of the invention is recombinant adeno-associated virus (rAAV) vectors.
  • the rAAV contains a transgene that expresses an MBNLl, MBNL2, or MBNL3 (or combinations thereof) protein.
  • the invention provides a rAAV containing a transgene that expresses MBNLl (for example, the 41 kD isoform).
  • the rAAV of the invention includes a promoter, which directs the initiation of RNA transcription in the cell of interest.
  • the promoter may be constitutive or regulated. Regulated promoters include inducible promoters and repressible promoters. In an additional embodiment of the invention, the regulation of the promoter is associated with an "operator", to which an inducer or repressor binds.
  • the promoter may be a "ubiquitous" promoter active in essentially all cells of the host organism or may be a promoter with expression more or less specific to the target cells.
  • telomere sequence a promoter sequence functional in the target cell.
  • the rAAV vectors of the invention may feature modified inverted terminal repeats and other sequences, provided that the rAAV vectors can replicate and be packaged with the assistance of helper virus, and establish a nonpathogenic latent infection in target cells.
  • the polynucleotides encoding MBNLl domain sequences and the regulatory elements can have a length of up to about 5,500 bases.
  • susceptible cells are co-transfected with an AAV-derived vector DNA and a suitable AAV-derived helper virus or plasmid harboring the AAV rep gene, AAV cap gene or both and infected by a helper virus, including herpesvirus, adenovirus or a suitable non-AAV helper plasmid using any number of transfection methods, including, inter alia, calcium-phosphate transfection, lipofection or other techniques known to those skilled in the art.
  • the ratio of helper plasmids to the quantity of vector plasmid containing the gene of interest range from 1:1-1:10.
  • the AAV-derived helper virus or helper plasmid may be any virus or plasmid which is capable, on expression of the AAV genes it carries, of providing proteins necessary for the replication and packaging of the rAAV vector in a suitable host cell, for the purpose of producing rAAV vector stock.
  • the target cells of the rAAV vectors of the invention are cells capable of expressing polypeptides with MBNLl activity.
  • the cells are normal cells cultured in vitro.
  • the target cells of the rAAV vectors of the invention are human cells, or cells of other mammals, such as nonhuman primates and mammals of the orders Rodenta (mice, rats, rabbit and hamsters), Carnivora (cats and dogs) and Arteriodactyla (cows, pigs, sheep, goats and horses).
  • the cells are part of a living mammal at the time the rAAV vectors are delivered to the cell.
  • the mammal may be at any stage of development at the time of delivery, e.g, embryonic, fetal, infantile, juvenile or adult. Additionally, the cells may be healthy or diseased.
  • the rAAV vectors of the invention may be administered as viral particles alone, whether as an in vivo direct delivery to the vasculature or as an ex vivo treatment comprising administering the rAAV vector viral particles in vitro to cells from the animal receiving treatment followed by introduction of the transduced cells back into the donor.
  • the rAAV vector virus particles can be used to transduce cells in conjunction with secondary agents known to enhance the efficiency of transduction, see, e.g, WO Ser. No. 95/33824 for a variety of secondary agents.
  • the effective amount of rAAV vectors to be administered will vary from patient to patient.
  • the rAAV construct of the invention expresses human MBNLl (rAAV-MBNLl(rAAV-MBNLl/41)).
  • injection of the rAAV-MBNLl/41 into the tibialis anterior (TA) muscles of a transgenic model for DM that expresses a human skeletal ⁇ -actin transgene carrying 250 CTG repeats results in a functional reversal of a DM-related phenotype, namely, reversal of mis-splicing of the Clcnl skeletal muscle chloride channel, which results in myotonia.
  • the invention is directed to methods for treating or preventing various disorders and conditions associated with aberrant microsatellite expansions in a mammal, said method comprising administering to the mammal a therapeutically effective amount of rAAV containing a transgene that encodes a protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof.
  • the protein is MBNLl.
  • the mammal is a human.
  • the transgene is human.
  • the disease associated with aberrant microsatellite expansion is a neurological or neuromuscular disease.
  • the disease is myotonic dystrophy.
  • the disease is SCA8.
  • the present invention provides methods for treating or preventing a disease or condition related to any physiological process affected by MBNLl, said method comprising administering to the mammal a therapeutically effective amount of rAAV containing a transgene that expresses the MBNLl protein.
  • the invention is directed to methods for treating or preventing various disorders and conditions associated with aberrant microsatellite expansions in a mammal, said method comprising administering to the mammal a therapeutically effective amount of rAAV containing a transgene that encodes a protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof, wherein treating comprises reversing the mis-splicing of the Clcnl skeletal muscle chloride channel.
  • treating comprises reversing the mis-splicing of the Amyloid beta (A4) precursor protein (APP).
  • the mis- splicing may correspond to alternative splicing of exon 7.
  • treating comprises reversing the mis-splicing of the NMDA receptor NR1 (GRLN1).
  • the mis-splicing may correspond to alternative splicing of exon 5.
  • treating comprises reversing the mis- splicing of the Microtubule-associated protein tau (MAPT).
  • the mis-splicing may correspond to alternative splicing of exon 2.
  • treating comprises reversing the mis-splicing of the TNNT2 (cTNT).
  • the mis-splicing may correspond to alternative splicing of exon 5.
  • the invention is directed to methods for treating or preventing various disorders and conditions associated with aberrant microsatellite expansions in a mammal, said method comprising administering to the mammal a therapeutically effective amount of rAAV containing a transgene that encodes a protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof, wherein the mammal has RNA inclusions in neuronal cells.
  • One embodiment of the invention is directed to a pharmaceutical composition
  • a pharmaceutical composition comprising rAAV containing a transgene that encodes at least one protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof.
  • the protein is MBNLl.
  • 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 of the present invention (see, e.g. Remington's Pharmaceutical Sciences, 17.sup.th ed. 1985).
  • Formulations for both ex vivo and in vivo administrations include suspensions in liquid or emulsified liquids.
  • the active ingredient (rAAV vector) is often mixed with excipients that are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients include, for example, water, saline, dextrose, glycerol, ethanol or the like, and combinations thereof.
  • the composition may contain minor amounts of auxiliary substances, such as, wetting or emulsifying agents, pH buffering agents, stabilizing agents or other reagents that enhance the effectiveness of the pharmaceutical composition.
  • Formulations suitable for administration include aqueous and non- aqueous solutions, isotonic sterile solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic, and aqueous and non- aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives.
  • compositions can be administered, for example, orally, nasally, topically, intravenously, intraperitoneally, intravesically or intrathecally.
  • the formulations of compounds can be presented in unit-dose or multi-dose scaled containers, such as ampules and vials. Solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described.
  • the modulators can also be administered as part a of prepared food or drug.
  • the dose administered to a patient in the context of the present invention is often varied to assess the effect of various concentrations of a compound on a transgenic animal.
  • the dose will also be determined by, e.g, the body weight or surface area of the area to be exposed to the compound.
  • the dose equivalent of a modulator is from about 1 ng/kg to 10 mg/kg for a typical subject. Administration can be accomplished via single or divided doses.
  • compositions of the disclosed gene vectors may be administered intravenously, parenterally or intraperitoneally.
  • Solutions of pharmaceutically acceptable salts can be prepared in water suitable mixed with a surfactant, such as hydroxypropylcellulose.
  • Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations will contain a preservative to prevent growth of microorganisms.
  • the pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions.
  • the carrier may be a solvent or dispersion medium containing, for example, water, ethanol, polyol (such as, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils.
  • the proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • microorganisms can be brought about by various antibacterial and antifungal agents, such as, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like.
  • antibacterial and antifungal agents such as, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars or sodium chloride.
  • Solutions of the AAV vector as a free acid (DNA contains acidic phosphate groups) or a pharmacologically acceptable salt can be prepared in water suitably mixed with a surfactant such as hydroxypropylcellulose.
  • a dispersion of AAV particles also can be prepared in glycerol, liquid polyethylene glycols and mixtures thereof and in oils. Under ordinary conditions of storage and use, the preparations contain a preservative to prevent the growth of microorganisms.
  • the sterile aqueous media employed are obtainable by standard techniques well known to those skilled in the art.
  • Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
  • Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above.
  • the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • composition can be formulated in a neutral or salt form.
  • Pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organics acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like.
  • solutions Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective.
  • the formulations are easily administered in a variety of dosage forms such as injectable solutions, drug release capsules and the like.
  • aqueous solutions For parenteral administration in an aqueous solution, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose.
  • aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration.
  • sterile aqueous media that can be employed will be known to those of skill in the art in light of the present disclosure.
  • one dosage could be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion. Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject.
  • preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biologies standards.
  • the pharmaceutical forms suitable for parenteral administration include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases the form must be sterile and must be fluid to the extent that parenteral administration is possible.
  • the formulation must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, liquid polyethylene glycol and the like), suitable mixtures thereof, and vegetable oils.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of a dispersion and by the use of surfactants.
  • the prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal and the like. In many cases it will be preferable to include isotonic agents, for example, sugars or sodium chloride.
  • Prolonged absorption of the injectable compositions can be brought about by use of agents delaying absorption, for example, aluminum monostearate and gelatin.
  • AAV vector in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the sterilized active ingredient into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above.
  • the preferred methods of preparation are vacuum drying and freeze drying which yield a powder of the active ingredient plus any additional desired ingredient from the previously sterile-filtered solution thereof.
  • the rAAV containing a transgene that expresses the MBNLl protein may, for example, be prepared by: culturing a composition comprising cells transiently transfected with an AAV helper plasmid comprising AAV rep and cap nucleic acid sequences encoding AAV rep and cap proteins, an adenoviral helper plasmid comprising essential adenovirus helper genes selected from the group consisting of E1A, E1B, E2A, E4, E4ORF6, E4ORF6/7, VA, and combinations thereof, and an AAV vector comprising first and second AAV ITRs flanking a DNA sequence encoding MBNLl polypeptide, said sequence being operably linked to a promoter DNA sequence, in the absence of adenovirus particles and under conditions suitable for production of recombinant AAV, and purifying rAAV therefrom.
  • the invention is directed to a transgenic animal having a substantial deletion of one or more MBNLl exon(s).
  • the transgenic animals of the invention can be any mammal other than humans.
  • the mammal is a rodent.
  • the rodent is a mouse.
  • An additional embodiment is directed to a cell isolated from the transgenic animal of the invention.
  • the transgenic animal of the invention has a substantial deletion of Mbnll exon 3.
  • Mbnll exon 3 in the transgenic animal of the invention is deleted in its entirety.
  • the transgenic mouse having a substantial deletion of Mbnll exon 3 constitutes an animal model for microsatellite expansion disease in mammals.
  • the mammal is a primate.
  • the primate is a human.
  • the microsatellite expansion disease is caused by a microsatellite expansion in a coding region of DNA.
  • the microsatellite expansion disease is caused by a microsatellite expansion in a non-coding region of DNA.
  • the disease associated with aberrant expansion of microsatellites is myotonic dystrophy. Accordingly, in one embodiment of the invention, the mouse Mbnll gene knockout model exhibits myotonia and ocular cataracts.
  • the invention is directed to a mouse model for disease associated with aberrant microsatellite expansion, comprising a mouse having a substantial deletion of Mbnll exon 3 (E3) in the mouse genome, wherein said mouse exhibits symptoms typical of a disease associated with aberrant microsatellite expansion in humans, wherein said mouse has loss of functional C1C- 1 protein.
  • mouse has loss of functional Amyloid beta (A4) precursor protein.
  • A4 A4 precursor protein.
  • the mouse has loss of functional NMDA receptor NR1.
  • the mouse has loss of functional Microtubule-associated protein tau.
  • the mouse has loss of functional TNNT2 protein.
  • the mouse has loss of functional TNNT3 protein.
  • the transgenic animal of the invention may, for example, be prepared by transfecting a plurality of mouse embryonic stem cells with a nucleic acid comprising an MBNLl gene with a substantial deletion of exon 3, selecting for transgenic embryonic stem cells having incorporated said nucleic acid into their genome, introducing at least one of said transgenic embryonic stem cells into an embryo to produce a chimeric mouse comprising at least one of said transgenic embryonic stem cells, breeding said chimeric mouse with a wild-type mouse to obtain Fl progeny heterozygous for the MBNLl gene with a deletion of exon 3, and breeding a male mouse of said Fl progeny with a female mouse of said Fl progeny to obtain F2 progeny homozygous for MBNLl gene with a deletion of exon 3, wherein the said mouse exhibits a phenotype indicative disease associated with aberrant microsatellite expansion, for example, myotonic dystrophy.
  • Additional embodiments are directed to methods for using the transgenic animals of the invention as animal models to study MBNLl function in vivo, and for evaluating side effects of MBNLl -inhibiting compounds. For example, if a compound known to inhibit MBNLl is administered to an MBNLl knockout mouse, any detected effects of the compound on the mouse can be concluded to be MBNL 1 -independent.
  • the transgenic mammals of the invention can be used as animal models to identify compounds useful in the treatment of diseases associated with aberrant microsatellite expansions (such as, in one embodiment, myotonic dystrophy) and to assess the functional effect of a test compound on cells or animals afflicted with such disease.
  • Such compounds can be any small chemical compound, including polypeptides, polynucleotides, amino acids, nucleotides, carbohydrates, lipids, or any other organic or inorganic molecule.
  • the compounds can be genetically altered versions of the MBNLl gene.
  • assessing the effects of a compound on cells or animals involves providing a combinatorial chemical or peptide library containing a large number of potential therapeutic compounds (potential modulator or binding compounds).
  • potential therapeutic compounds potential modulator or binding compounds.
  • Such "combinatorial chemical libraries” are then screened in one or more assays to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity.
  • the compounds thus identified can serve as conventional "lead compounds" or can themselves be used as potential or actual therapeutics.
  • a combinatorial chemical library is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis, by combining a number of chemical "building blocks” such as reagents. Preparation and screening of combinatorial chemical libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g, U.S. Pat. No. 5,010,175, Furka (1991) Int. J. Pept. Prot. Res, 37:487-493 and Houghton, et al. (1991) Nature, 354:84-88).
  • administering can be achieved by any of the routes normally used for introducing a compound into ultimate contact with the tissue to be treated.
  • the compounds are administered in any suitable manner, optionally with pharmaceutically acceptable carriers. Suitable methods of administering such compounds 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.
  • MBNLl is referred to in the individual descriptions of the embodiments of the invention, MBNL2 and MBNL3 may likewise be contemplated for each embodiment. Definitions
  • a "transgene” refers to genetic material that is introduced, or is capable of being introduced, into cells of a host animal. Typically, once a “transgene” is introduced into the cells of the host animal, it is maintained, either transiently or permanently, by, e.g, insertion into the host genome. In preferred embodiments of the present invention, a transgene is inserted into the host genome by homologous recombination, thereby replacing the endogenous gene with the transgene. Often, a transgene contains a coding sequence, operably linked to a promoter, that encodes a protein, e.g, a marker protein that allows the detection of the transgene in the cell. "Transgenic” refers to any cell or organism that comprises a transgene.
  • a "host" animal or mammal refers to any animal that is used to practice the herein-described methods, i.e. animals into which a transgene is introduced to disrupt an endogenous MBNLl gene.
  • animals include any non-human mammals including, but not limited to, mice, rats, rabbits, and hamsters.
  • Nucleic acid refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form.
  • the term encompasses 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.
  • a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g, degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated.
  • nucleic acid is used interchangeably with gene, cDNA and nucleotide.
  • polypeptide peptide
  • protein protein
  • amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer.
  • amino acid refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids.
  • amino acid sequences one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the substitution of an amino acid with a chemically similar amino acid.
  • Conservative substitution tables providing functionally similar amino acids are well known in the art.
  • conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.
  • a “label” or a “detectable moiety” is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means.
  • useful labels include 32 P, fluorescent dyes, electron-dense reagents, enzymes (e.g, as commonly used in an ELISA), biotin, digoxigenin, or haptens and proteins which can be made detectable, e.g, by incorporating a radiolabel into the peptide or used to detect antibodies specifically reactive with the peptide.
  • recombinant when used with reference, e.g, to a cell, or nucleic acid, protein, or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified.
  • recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all.
  • heterologous when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not found in the same relationship to each other in nature.
  • the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid, e.g, a promoter from one source and a coding region from another source.
  • a heterologous protein indicates that the protein comprises two or more subsequences that are not found in the same relationship to each other in nature (e.g, a fusion protein).
  • a “promoter” is defined as an array of nucleic acid control sequences that direct transcription of a nucleic acid.
  • a promoter includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element.
  • 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.
  • 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 environmental or developmental regulation.
  • operably linked refers to a functional linkage between a nucleic acid expression control sequence (such as a promoter, or array of transcription factor binding sites) and a second nucleic acid sequence, wherein the expression control sequence directs transcription of the nucleic acid corresponding to the second sequence.
  • a nucleic acid expression control sequence such as a promoter, or array of transcription factor binding sites
  • nucleic acids or polypeptide sequences refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., 60% identity, optionally 65%, 70%, 75%, 80%, 85%, 90%, or 95% identity over a specified region), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. Such sequences are then said to be “substantially identical.”
  • immunoassay is an assay that uses an antibody to specifically bind an antigen.
  • the immunoassay is characterized by the use of specific binding properties of a particular antibody to isolate, target, and/or quantify the antigen.
  • the phrase “specifically (or selectively) binds” to an antibody or “specifically (or selectively) immunoreactive with,” when referring to a protein or peptide, refers to a binding reaction that is determinative of the presence of the protein in a heterogeneous population of proteins and other biologies.
  • the specified antibodies bind to a particular protein at least two times the background and do not substantially bind in a significant amount to other proteins present in the sample.
  • Specific binding to an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein
  • polyclonal antibodies raised to an MBNLl polypeptide from specific species such as rat, mouse, or human can be selected to obtain only those polyclonal antibodies that are specifically immunoreactive with the MBNLl protein and not with other proteins, except for polymorphic variants and alleles of the MBNLl protein.
  • transduction refers to the introduction of foreign DNA into cells of an organism (in vivo).
  • transfection refers to the introduction of foreign DNA into cells in culture (in vitro). Genetic modification of eukaryotic cells by introduction of foreign DNA using chemical means. In transient transfection, expression occurs from unintegrated foreign DNA and can be detected for a few days after transfection.
  • titer refers to the number of virus particles produced per ml.
  • the assay system to determine the number of virus particles produced varies considerably depending on the virus in question.
  • High titers are generally essential for successful gene therapy since they allow introduction of the therapeutic gene carried by the virus into the maximum number of cells.
  • treating and “treatment” as used herein include any treatment of a condition or disease in a subject, and include inhibiting the disease or condition, (i.e. arresting its development), relieving the disease or condition (i.e. causing some degree of regression of the condition or delaying progression in the disease), or relieving (to some degree) the conditions caused by the disease (i.e. symptoms of the disease).
  • vehicle refers to a vehicle, usually a biological entity, such as a virus, used for the delivery of genes into an organism. A reagent that facilitates the introduction of foreign genes into cells.
  • packing cells refers to cells that have been transfected with plasmids containing the cap and rep genes from AAV.
  • pharmaceutically acceptable carrier includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like.
  • the use of such media and agents for pharmaceutically-active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.
  • compositions that do not produce an allergic or similar untoward reaction when administered to a human.
  • pharmaceutically-acceptable refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human.
  • aqueous composition that contains a protein as an active ingredient is well understood in the art.
  • injectables either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection can also be prepared.
  • the preparation can also be emulsified.
  • a "substantial" deletion of exon 3 signifies a deletion extensive enough to lend to the phenotype indicative of a disease associated with aberrant microsatellite expansion.
  • mice with a targeted deletion of Mbnll exon 3 (Fig. 1A) were generated.
  • the pMbnll ⁇ E3 " eo targeting plasmid was constructed using pTKflNeo (gift of E. Scott, University of Florida), which contains the Herpes simplex virus - thymidine kinase (HSV-TK) negative selection marker and a loxP-flanked phosphoglycerate kinaseneomycin (PGK-Neo) positive selection cassette.
  • HSV-TK Herpes simplex virus - thymidine kinase
  • PGK-Neo loxP-flanked phosphoglycerate kinaseneomycin
  • a 6 kb Mbnll BamHI fragment was subcloned into pBluescript II KS + (Stratagene, La Jolla, CA), excised with Xhol/Notl, and cloned into the Xhol/Notl sites of pTKflNeo 3' of PGK-Neo.
  • Clones resistant to G418 and FIAU were isolated and screened for homologous recombination by utilizing a forward primer (5'- TGGGATGGAATTGTGGTGTGTTGTTGCTCATG-3') (SEQ ID NO: 4) outside the 5' homologous region and a reverse primer (5'- TCCATTTGTCACGTCCTGCACCGACGC-3') (SEQ ID NO: 5) in PGKNeo.
  • Amplification 25 cycles consisted of 98°C for 20 s followed by 68°C for 4 min.
  • Targeted ES cell clones yielded a 2.9 kb PCR product. This targeting strategy was predicted to approximate the situation in DM by eliminating synthesis of CUG- binding isoforms (Miller, et al, 2000).
  • Genomic DNA analysis of Mbnll mice genomic blot analysis demonstrated successful deletion of Mbnll ⁇ E3 ⁇ E3 mice (Fig. IB). Five ES cell clones (35, 56, 92, 111, 120) that were positive for homologous recombination were confirmed by genomic DNA blot analysis. Based on restriction map analysis of genomic fragments flanking E3, ES genomic DNA digested with EcoRFproduces a 16 kb band when a 300 nt Mbnll BamHI/EcoRV fragment outside the 3' arm of homology is used as a hybridization probe (probe II of Fig. LA).
  • anew EcoRV site (from pBluescript II KS + ) is introduced, generating a novel 6.7 kb EcoRV fragment. All five clones that were positive by PCR were also positive by genomic DNA blot analysis. When the 5' arm of homology (2.5 kb Xbal fragment) was used as probe, two bands at 16 kb (wild type) and 7.5 kb (mutant) were detected. To check for additional insertion events in these five clones, PGK-Neo fragment was used as probe on genomic DNA digested with EcoRV. A single band at 7.5 kb confirmed the absence of any additional insertion events.
  • C57BL/6J blastocysts which were then carried to term by B6D2F1/J recipients.
  • One chimeric male was obtained from each clone.
  • Contribution of CJ.7 (129Sl/SvlmJ) ES cells to the germline was determined by mating the chimeric males with C57BL/6J females. Agouti pups in litters sired by the 1B3 chimeric male indicated germline transmission.
  • GGGTTGAATCTCGTTAGGGACACTGGGTGTCTGTAA-3' (SEQ ID NO: 9)]; [for the wild-type allele (5'-TGGCAGACCCTTTGACACCG-3') (SEQ ID NO: 10)] were used for PCR. Amplification was performed for 30 cycles, each cycle consisting of 96°C for 30 sec, 60°C for 30 sec and 72°C for 2 min. Heterozygotes were then mated to obtain Mbnll AE3/ E3 mice.
  • RT-PCR reverse transcription polymerase chain reaction
  • primers in exons 3 and 6 were used to amplify a cDNA product from either Mbnll +/+ or Mbnll + AES mice that was absent in Mbnll AE3IAE3 mice (Fig. IC).
  • RT-PCR strategy was used with the forward primer positioned in exon 3 (5'-TAGTGTCACACCAATTCGGGACACAAA-3') (SEQ ID NO: 11) and an exon 6 reverse primer (5'-
  • Proteins (30 ⁇ g per lane) were detected following SDS- PAGE and immunoblotting using anti -Mbnll mAb 3A4 (J. W. Miller et al, EMBO J. 19, 4439 (2000), A. Mankodi et al, Ann. Neurol, in press). Total spleen was analyzed (Fig. ID), because this tissue contains relatively high levels of both Mbnlland Cugbpl.
  • Mbnll AE3/AE3 mice monoclonal antibody 3A4 was used, which recognizes Mbnll proteins containing exon 5[MSI].
  • the 41- to 42-kD isoforms in Mbnll + + and Mbnll +/AE3 mice were missing in Mbnll AE3/ E3 (Fig. ID).
  • Previous studies suggested that elevated levels of another RNA-binding protein, CUGBP1, are responsible for DM-associated RNA splicing changes.
  • Mbnll AE3/AE3 mice did not show increased CUGBP1 expression (Fig. ID).
  • Electromyographv electromyography was performed under general anesthesia (intraperitoneal ketamine, 100 mg/kg; xylazine, 10 mg/kg; and acepromazine, 3 mg/kg) using 30 gauge concentric needle electrodes to examine three hindlimb (tibialis anterior, gastrocnemius, vastus), two forelimb (flexor compartment of distal forelimb, triceps), and thoracolumbar paraspinal muscles.
  • First strand cDNA was generated by reverse transcription (RT) using 5 ⁇ g of total RNA and Superscript II RNase H " RT (Invitrogen, Carlsbad, CA) following the manufacturer's protocol. For subsequent PCR reactions, 20% of the RT reaction was used as template. Each PCR reaction was spiked with 10 ⁇ Ci of ( ⁇ i2 P)-dCTP (PerkinElmer Life Sciences, Boston, MA). PCR products were resolved on 5-8% non-denaturing polyacrylamide gels followed by autoradiography using Biomax MS film (Eastman Kodak, Rochester, NY).
  • the forward primer used corresponded to exon 5 (5'GGAATACCTCACACTCAAGGCC-3') (SEQ ID NO: 17) and the reverse primer to exon 8 (5'CACGGAACACAAAGGCACTGAATGT-3') (SEQ ID NO: 18).
  • PCR was performed for 27 cycles each consisting of 45 sec at 95°C, 45 sec at 55°C and 45 sec at 72°C, followed by a final lOmin extension at 72°C.
  • Full- length ClC-1 cDNA clones were generated from muscle RNA by RT-PCR as previously described (A. Mankodi et al, Mol. Cell 10, 35 (2002)).
  • ClC-1, Dys2, and ⁇ -sarcoglycan immunostaining frozen sections of vastus (6 ⁇ m) were immunostained using polyclonal antibodies directed against the C-terminus of ClC-1 (Alpha Diagnostic, San Antonio) or monoclonal antibodies to dystrophin (Dys2) or a-sarcoglycan (NovoCastra, Newcastle upon Tyne) as described in A. Mankodi et al, Mol. Cell 10, 35 (2002).
  • Mbnll AE3/ E3 mice up to 11 weeks of age did not show major degeneration of muscle fibers.
  • Pathological features in Mbnll + &E3/AE3 muscle included an increase in nuclei with an abnormal (central) position and splitting of myofibers (Fig. 2, G and H). Histologic abnormalities were not observed in Mbnll +/+ or Mbnll +/AE3 muscle.
  • mice were sedated using intra-peritoneal injection of 100 mg/kg ketamine (Ketaset, Fort Dodge, IA) and 10 mg/kg xylazine (Xylaject, Phoenix, St Joseph, MO) and anterior chambers and lenses were examined using a slit lamp (Haag Streit, Mason, OH). In vivo images were obtained using a Nikon 990 digital camera attached to the slit-lamp. Immediately after euthanasia, globes were enucleated, fixed in paraformaldehyde and embedded in paraffin blocks before being processed overnight in a Shandon Excelsior tissue processor (Thermo Electron, Waltham, MA).
  • Sections (4 ⁇ m) were cut using an HM-315 microtome (Richard-Allan, Kalamazoo, MI), dried and H&E stained. Sections were photographed using a Canon EOS D60 digital camera attached to an Olympus Vanox microscope.
  • Tnnt2 Abnormal regulation of alternative splicing has been observed in DM1 muscle for cardiac troponin T (TNNT2), insulin receptor (LNSR), and ClC-1. Tnnt2 was analyzed using exon 2 forward (5'GCCGAGGAGGTGGTGGAGGAGTA-3') (SEQ ID NO:
  • Tnnt3 fast skeletal muscle troponin T
  • exon 22 corresponds to exon 11.
  • exon 2 forward (5'- TTCACCATGTCTGACGAGGAAG-3') (SEQ ID NO: 23) and exon 10 reverse (5'CTTCTGGGATCTTAGGAGCAGTG-3') (SEQ ID NO: 24) primers were used.
  • exon 10 reverse 5'CTTCTGGGATCTTAGGAGCAGTG-3' primers were used.
  • 25 PCR cycles were performed each consisting of 45 sec at 95°C, 45 sec at 50°C and 30 sec at 72°C, followed by a final 10-min extension at 72°C.
  • the same amplification protocol was used to amplify the mouse Tnnt3 carboxyl terminal region using an exon 15 forward primer (5 - CCTTGTACCAACTGGAGACTGAC-3') (SEQ ID NO: 25) and an exon 18 reverse primer (5'- TGATGGTCTCTGCTGCAGTG -3') (SEQ ID NO: 26).
  • Partial cDNAs covering the entire Scn4a coding region were generated by PCR using the following primers: set 1 exon 1 (GACCTGGAAGCTGGCAAGAAC) (SEQ ID NO: 27) to exon 6 (TCCCTTCGTCATTGATGTAGGC) (SEQ ID NO: 28); set 2 exon 6 (CCATGAATGACACCAACACCAC) (SEQ ID NO: 29) to exon 12 (CTGAGGGTGACGATGAAGCTG) (SEQ ID NO: 30); set 3 exon 12 (TCTTCACGGGCATCTTCACTG) (SEQ ID NO: 31) to exon 17 (CGCCGCTGTTCAATGTAGATG) (SEQ ID NO: 32); and set 4 exon 16 (TGCCTCTATGTGGACATCTCCC) (SEQ ID NO: 33) to exon 24 (CGACTCTTTCTTGACGTAGGCG) (SEQ ID NO: 34).
  • RT-PCR products from primer sets 1, 2, 3, and 4 was analyzed on 1 % agarose gels before and after restriction digest with Apal, Ncol, BspEl and BsrGl -Hindlll, respectively. Results showed no difference in the length of Scn4a cDNA fragments in Mbnl ⁇ h ' , Mbnl / ⁇ E3 , Mbnil ⁇ E3/ ⁇ E3 or HSA LR mice (data not shown).
  • HSA LR mice were anesthetized using isoflurane, and the left tibialis anterior (TA) muscle was injected with 13.4 ⁇ L PBS containing lxlO 11 rAAVlMyc- hMBNLl, or the right leg was injected with PBS ("uninjected").
  • the mice were anesthetized using 2.5% avertin, and the left and right TAs were collected for total RNA preparation and assayed for recovery of the normal Clcnl pre-mRNA splicing pattern (Fig. 5 A)
  • Reverse transcription was carried out using 5 ⁇ g of total RNA and 300 ng of random hexamers in a final volume of 20 ⁇ l.
  • CACGGAACACAAAGGCACTGAATGT-3' (SEQ ID NO. 41) in exon 8 of Clcnl.
  • the reaction was spiked with 10 ⁇ Ci of dCTP-[oc 32 P]. 27 cycles were carried out at annealing and extension temperatures of 55°C and 72°C, respectively. Thirty percent of the total PCR products were resolved on a 5% acrylamide gel followed by exposure of the gel to an autoradiography film.
  • mice number 188 and 189 were injected on the same day and processed together.
  • Mouse number 190 and 191 were littermates that were neither injected with virus nor with PBS (included as uninjected controls). The results show that the levels of the abnormal splicing products were decreased, while the level of the normal splicing product was increased, following rAAVlMyc-hMBNLl injection.
  • mice were also tested for myotonia by electromyography (EMG).
  • EMG electromyography
  • the Y-axis shows the observed severity of myotonia following insertion of the electrode.
  • the results show that injection of the HSA lR mice with rAAVlMyc-hMBNLl (41 kDa isoform expressed) into the tibialis anterior results in reduced myotonia in as little as four weeks' time.
  • GFP fusion proteins of all three MBNL proteins were transiently expressed with human and chicken cTNT minigenes in primary chicken skeletal muscle cultures.
  • GFP fusions with MBNLl, 2 and 3 were provided by Dr JD Brook (Fardaei M, Rogers MT, Thorpe HM, Larkin K, Hamshere MG, Harper PS, Brook JD (2002), Hum Mol Genet 11: 805-814).
  • the cTNT, IR and clathrin light chain B minigenes were previously described (Kosaki A, Nelson J, Webster NJ (1998), JBiol Chem 273: 10331-10337; Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737- 741 ; Stamm S, Casper D, Hanson V, Helfrnan DM (1999), Brain Res Mol Brain Res 64: 108-118; Ladd AN, Charlet-B N, Cooper TA (2001), Mol Cell Biol 21: 1285- 1296).
  • the MBNL mutant human cTNT minigene was generated by inverse PCR.
  • HEK293 cells were plated at 500 000 cells per well in a six- well plate in DMEM supplemented with 10% ⁇ FBS and Gibco penicillin-streptomycin. At 24 h after plating, the cells were transfected with 1 ⁇ g of minigene and 2 ⁇ g of protein expression plasmid using Fugene ⁇ (Roche, Indianapolis, IN), according to the manufacturer's directions. Protein and RNA were harvested 36-48 h after transfection.
  • Human and chicken cTNT and human IR minigenes were expressed with or without each of the three GFP-MBNL fusion proteins or with GFP alone. Duplicate transfections were used for extraction of RNA and protein. Inclusion of cTNT exon 5 or IR exon 11 was assayed by RT-PCR.
  • RNA isolation and RT-PCR analysis for the cTNT, IR, and clathrin light-chain B minigenes were performed as described previously (Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737-741; Stamm S, Casper D, Hanson V, Helfrnan DM (1999), Brain Res Mol Brain Res 64: 108-118; Savkur RS, Philips AV, Cooper TA (2001), Nat Genet 29: 40-47). [000146] Western blot analysis to investigate alternative splicing related to
  • MBNL cells were harvested in protein loading buffer (62.5 mM Tris-HCl (pH 6.8), 2% SDS, 10% glycerol and 5% 2- ⁇ -mercaptoethanol) and the protein concentration was quantitated with the Non-Interfering Protein Assay (Genotech, St Louis, MO). Total protein lysates from HEK293 (20 ⁇ g) and primary chicken skeletal (30 ⁇ g) cultures were loaded on a 12.5% acrylamide gel and transferred to Immobilon-P membranes (Millipore, Bedford, MA). GFP was detected using JL-8 monoclonal antibody (BD Biosciences, Palo Alto, CA) at a dilution of 1:2000. The secondary antibody was a goat anti-mouse HRP conjugate (Jackson Immunoresearch, West Grove, PA) at a dilution of 1 :5000.
  • HeLa (50 ⁇ g) protein lysates were loaded on a 12.5% acrylamide gel. Blots were probed with the monoclonal 3A4 (16 mg/ml) at a dilution of 1 :500.
  • the secondary antibody was a sheep anti-mouse HRP conjugate (Amersham Biosciences, Piscataway, NJ) at a dilution of 1 :5000.
  • GAPDH in HeLa cells 15 ⁇ g of total protein lysates was run on a 12.5% acrylamide gel, transferred to membranes and detected using the 6G5 monoclonal (Biogenesis, Singer, NH) at a dilution of 1:100 000.
  • the secondary antibody was a goat anti- mouse HRP conjugate (Jackson Immunoresearch, West Grove, PA) at a dilution of 1:5000.
  • GFP-MBNL1, 2 and 3 strongly repressed inclusion of both human and chicken cTNT exon 5 in primary chicken skeletal muscle cultures, while expression of GFP to levels comparable to, or greater than, GFP-MBNL fusion proteins had no effect on splicing ( Figure 6A and 6B).
  • GFP-MBNL1 was found to have a novel MBNLl isoform lacking exons 7, 9 and 10 and containing a frameshift in exon 12.
  • MBNL proteins are directly antagonistic to endogenous CELF activity, which activates cTNT exon inclusion in muscle (Charlet-B N, Logan P, Singh G, Cooper TA (2002a), Mol Cell 9: 649-658).
  • the EN alternative exon in this minigene strongly responds to over-expression of the SR family of proteins and htra2- ⁇ l, but not CELF proteins (Stamm S, Casper D, Hanson V, Helfrnan DM (1999), Brain Res Mol Brain Res 64: 108-118; Singh G, Charlet BN, Han J, Cooper TA (2004), Nucleic Acids Res 32: 1232-1241; data not shown).
  • Over-expression of GFP-MBNL 1, 2 and 3 with the clathrin light-chain minigene had no effect on alternative splicing of exon EN (Figure 6D).
  • MBNL expression also did not affect splicing of an artificial alternative exon flanked by splice sites from human ⁇ -globin intron 1 (data not shown). These results demonstrate that MBNL proteins do not have a general effect on alternative splicing, but, rather regulate specific pre-mRNA targets. In summary, MBNLl, 2 and 3 regulate splicing of cTNT and IR alternative exons.
  • siRNA constructs were designed to target MBNLl, but not MBNL2 and MBNL3. To confirm the specificity of the effects, two siRNA constructs were designed to target different regions of the MBNLl mRNA.
  • SiRNA construct design and transfection two custom siRNA duplexes were designed for RNAi against human MBNLl using the Dharmacon siDESIGN program (www.dharmacon.com (http ://w ww . dharmacon . com/)) and were synthesized by Dharmacon.
  • THH31 mRNA target (AA-N19 format 5' - ⁇ 3') AACAGACAGACUUGAGGUAUG (SEQ ID NO: 35)
  • THH2 mRNA target (AA-N19 format 5' ⁇ 3') AACACGGAAUGUAAAUUUGCA (SEQ ID NO: 36)
  • GFP siRNA duplex (Dharmacon, Lafayette, CO cat. no. D- 001300-01-20).
  • 300 000 HeLa cells were plated in 2 ml of antibiotic-free growth media (DMEM supplemented with 10% FBS) per well in a six-well plate.
  • HeLa cells were chosen because they express MBNLl (Miller JW, Urbinati CR, Teng- Umnuay P, Stenberg MG, Byrne BJ, Thornton CA, Swanson MS (2000), EMBO J 19: 4439-4448) and are amenable to siRNA-mediated depletion (Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001), Nature 411: 494- 498).
  • MBNLl iller JW, Urbinati CR, Teng- Umnuay P, Stenberg MG, Byrne BJ, Thornton CA, Swanson MS (2000), EMBO J 19: 4439-4448
  • siRNA-mediated depletion Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001), Nature 411: 494- 498).
  • the cells were washed once with PBS and incubated with the primary antibody 3A4 (10 mg/ml) ata dilution of 1:1000 in 3% BSA/PBS at room temperature for 1 h. The cells were then washed three times with PBS and incubated with the secondary antibody, Alexa Fluor-labeled goat anti-mouse IgG (2 mg/ml, Molecular Probes, Eugene, OR), at a dilution of 1:100 in 3% BSA/PBS at room temperature for 1 h. The cells were then washed with PBS three times, counterstained with DAPI (Molecular Probes, Eugene, OR) and mounted for visualization by fluorescence microscopy.
  • the primary antibody 3A4 10 mg/ml
  • Alexa Fluor-labeled goat anti-mouse IgG 2 mg/ml, Molecular Probes, Eugene, OR
  • MBNLl depletion and cTNT and IR minigene splicing to determine whether depletion of endogenous MBNLl affected alternative splicing of cTNT, IR and clathrin light chain, the minigenes were transfected with each siRNA construct. Depletion of MBNLl promoted exon inclusion in cTNT, exon skipping in IRand only minimal splicing changes in the clathrin light-chain minigene ( Figure 7C). siRNA-mediated depletion of MBNLl with two independent constructs reproduces the DM splicing patterns for cTNT and IR minigenes. GFP siRNA had no effect on splicing of any of the tested minigenes. MBNLl siRNA had minimal effects on splicing of a rat clathrin light-chain minigene.
  • Example 7 Binding of MBNLl to introns adjacent to the human and chicken cTNT alternative exons
  • UV cross-linking analysis of MBNLl binding to human cTNT to determine whether the splicing effects of MBNLl on pre-mRNA targets were direct or indirect, a UV-cross-linking assay was performed using purified recombinant GST-MBNLl and uniformly labeled in v/tr ⁇ -transcribed segments from the human cTNT gene. Uniformly 32 P-labeled RNAs were transcribed in vitro using [ ⁇ - 32 P]GTP
  • UV-cross-linking assays were performed using radiolabeled transcripts standardized for picomoles of G and U.
  • UV-cross-linking assays included 1 ⁇ g of purified GST-MBNLl in the presence of 1 ⁇ g BSA, 1 ⁇ gtRNA, 0.3 ⁇ g heparin, 0.3 mM magnesium acetate, in 2 mM magnesium acetate, 2 mM ATP, 16 mM HEPES (pH 7.9), 65 mM potassium glutamate, 0.16 mM EDTA, 0.4 mM DTT and 16% glycerol. Bindingwas for 10 min at 30°C.
  • Recombinant GST-MBNLl protein was produced as described (Miller JW, Urbinati CR, Teng-Umnuay P, Stenberg MG, Byrne BJ, Thornton CA, Swanson MS (2000), EMBO J 19: 4439- 4448). Competitions were performed as described previously (Singh G, Charlet BN, Han J, Cooper TA (2004), Nucleic Acids Res 32: 1232-1241). The indicated amounts of non-labeled competitor RNAs were added to the binding reaction 10 min prior to addition of labeled substrate RNA.
  • the human cTNT minigene contains a 732 nucleotide (nt) cTNT genomic fragment that is necessary and sufficient to respond to MBNLl over- expression and depletion ( Figures 6 and 7C).
  • nt nucleotide
  • Figures 6 and 7C To identify MBNLl-binding sites within this cTNT pre-mRNA region, uniformly 32 P-labeled, in vttro-transcribed RNAs covering the entire region were used for UV-cross-linking binding assays.
  • RNAs C, D, E and F the binding of GST-MBNLl on human cTNT was mapped to a 41 nt region within the 3' splice site of exon 5 (compare RNAs C, D, E and F) located between a near-consensus branch point sequence and the 3' cleavage site of the upstream intron.
  • UV cross-linking analysis of MBNLl binding to chicken cTNT UV- cross-linking analysis was performed to identify MBNLl-binding site(s) associated with the chicken cTNT alternative exon 5.
  • the genomic segment of chicken cTNT that responds to MBNL expression contains 99 and 142 nt of upstream and downstream introns flanking the alternative exon, respectively.
  • MSEs muscle-specific splicing enhancers
  • RNAs containing MSEs 1-4 or individual MSEs were transcribed in vitro as uniformly 32 P-labeledRNAs and used for UV cross-linking.
  • GST-MBNLl bound strongly to MSE4 and slightly to MSE1 ( Figure 9A).
  • Figure 9B In competition studies, non-labeled MSE1 RNA poorly competed in the binding of GST-MBNLl to RNA containing MSE 1-4, while MSE4 effectively competed in binding ( Figure 9B), consistent with the UV-cross-linking results.
  • the absence of competition by MSE2 or MSE3 demonstrates the sequence specificity of MBNLl binding ( Figure 9B).
  • scanning mutagenesis was performed.
  • proteins from all three MBNL genes contain two pairs of
  • Miller JW Urbinati CR, Teng-Umnuay P, Stenberg MG, Byrne BJ, Thornton CA, Swanson MS (2000), EMBO J 9: 4439- ⁇ 1448; Fardaei M, Rogers MT, Thorpe HM, Larkin K, Hamshere MG, Harper PS, Brook JD (2002), Hum Mol Genet 11: 805-814; Squillace RM, Chenault DM, Wang EH (2002), Dev Biol 250: 218-230).
  • the Cys3His-type zinc-finger is an evolutionarily conserved motif found in a number of proteins that perform diverse RNA-processing functions, and mutation of this motif results in a loss of RNA binding and disrupts protein function (Bai C, Tolias PP (1996), Mol Cell Biol 16: 6661-6667; Bai C, Tolias PP (1998), Nucleic Acids Res 26: 1597-1604; Lai WS, Carballo E, Strum JR, Kennington EA, Phillips RS, Blackshear PJ (1999), Mol Cell Biol 19: 4311-4323; Stoecklin G, Colombi M, Raineri I, Leuenberger S, Mallaun M, Schmidlin M, Gross B, Lu M, Kitamura T, Moroni C (2002), EMBO J 21: 4709-4718). [000169] MBNLl also binds to specific sequences within single-stranded
  • RNA consistent with the results from other Cys3His zinc-finger proteins (Cheng Y, Kato N, Wang W, Li J, Chen X (2003), Dev Cell 4: 53-66; Michel SL, Guerrerio AL, Berg JM (2003), Biochemistry 42: 4626-4630).
  • the above-delineated results demonstrate that MBNLl binds to cis-elements in chicken cTNT intron 5 required for muscle-specific splicing.
  • Example 8 CELF protein cis-regulatory elements in cTNT and IR and regulation by MBNLl
  • the mutant IR minigenes displayed regulation by MB ⁇ L proteins, which was comparable to the wild-type IR minigenes (compare Figures 11 A and 6C and 1 IB and 7C). These results indicate that regulation of human cT ⁇ T and IR by MB ⁇ L proteins does not require the CUG-BPl -binding site. In other words, the deletion of the human IR CUG-BPl -binding site does not affect regulation by MB ⁇ L1. All three of the MB ⁇ L proteins promoted exon 11 inclusion of the mutant human IR minigene lacking the CUG-BPl -binding site in HEK293 cells (FIG. 11 A). Furthermore, R ⁇ Ai depletion of MB ⁇ L 1 in HeLa cells using the indicated siR ⁇ A constructs promoted exon 11 skipping in the human IR minigene lacking the CUG- BPl-binding site (FIG. 11B).
  • the present results show that the mutated cTNT and IR minigenes are competent to respond to MBNL depletion by RNAi as strongly as the non-mutated minigenes, yet they do not respond to CUG repeat RNA. If expanded CUG repeats affected cTNT and IR splicing simply by sequestering and depleting MBNL, then the co-expression of CUG repeats should have affected splicing of the mutated as well as non-mutated minigenes. It is, thus, indicated that the repeats have a trans-dominant effect on splicing by a mechanism more complex than MBNL depletion alone.
  • Example 9 Fluorescence in situ hybridization (FISH) and i munofluorescence (IF) analysis of DM1 brain
  • FISH Fluorescence in situ hybridization
  • FISH FISH was performed as described (Mankodi, A, Urbinati, CR, Yuan, Q.P, Moxley, R.T, Sansone, V, Krym, M, Henderson, D, Schalling, M, Swanson, M.S, and Thornton, CA. (2001), Hum. Mol. Genet, 10, 2165-2170) with slight modifications. Frozen sections (12 ⁇ m) were fixed in 3% paraformaldehyde PBS for 30 min, permeabilized in 2% acetone PBS (pre-chilled at -20°C) for 5 min, and then prehybridized in 30% formamide and 2 X SSC at room temperature for 10 min.
  • probes were HPLCpurified 2-O-methyl RNA 20-mers (JJDT, Coralville, IA) composed of CAG-, CUG- or GUC- repeats, and labeled with Texas Red at the 5' end. Images were obtained on an Olympus AX70 epifluorescence microscope at 1, 000-fold magnification.
  • RNA foci were processed on the same slide, imaged under the same illumination and exposure settings, and then analyzed using MCED V6.0 software (Imaging Research Inc, St. Catherines, Ontario).
  • FISH Fluorescence in situ hybridization
  • RNA foci ranged in diameter from 0.2 to 2 ⁇ m. Resolution of these small structures required direct fluorescence detection methods. However, the autofluorescent material in brain (lipofuscin) was a complicating factor. The RNA foci were clearly distinguished from lipofuscin when the epifluorescence from three color channels was merged in a single image. As shown in Fig. 12A, the nuclear foci appeared in a single channel determined by the probe label (Texas red).
  • RNA foci were red, sharply demarcated structures in the nucleus. Lipofuscin was yellow-brown perinuclear material with indistinct margins.
  • IF immunofluorescence
  • RNA helicase A C Lee, NJ
  • ADAR1 D. Cho, PA
  • NF90 G. Sen, OH
  • Staufen and NeuN Chemicon, CA
  • proteasome Affiniti, UK
  • Ubiquitin DAKO, DK
  • p80 coilin KL Chan, CA
  • PTB E. Wagner, NC
  • PM-Scl 75 and hn RNP H and F J. Wilusz, NJ and D.
  • MBNLl fluorescence intensity (mean optical density in monochrome mode in arbitrary units) in the region of interest was detennined for 20 cortical neuronal nuclei per subject. Because of the difficulty of estimating background fluorescence from brain sections, the results are not corrected for background. This approach provides a conservative estimate of the fold- reduction for MBNLl in DM1 nucleoplasm.
  • Counts of 100 NeuN-positive cells from temporal and frontal cortex of 4 patients with classical DM1 showed RNA foci in >85% of cortical neurons in each case. More than one focus was visible in -30% of cortical neurons, and occasional neurons had up to 15 small foci.
  • the individual having a small CTG repeat expansion (77 repeats) and mild phenotype (cataracts, mild weakness, and cognitive impairment after age 60 years) had foci in only 39% of NeuN-positive neurons in temporal cortex.
  • RNA foci were also present in the subcortical white matter and corpus callosum in occasional cells expressing 2'3 '-cyclic nucleotide 3'- phosphodiesterase (CNPase), a marker for oligodendrocytes (Fig. 12E). However, these foci were smaller and less intense than those in cortical neurons.
  • CNPase 2'3 '-cyclic nucleotide 3'- phosphodiesterase
  • Fig. 12E a marker for oligodendrocytes
  • RNA inclusions were larger and more intense (3.1 -fold greater, area intensity) in frontal cortical neurons than in skeletal muscle from the same individual (p ⁇ 10- 10 , Fig. 14).
  • mutant RNA was tested for colocalization with proteins that mark different nuclear compartments.
  • These and subsequent experiments localizing protein relative to expanded poly(CUG) RNA were performed on a subset of 4 DM1 and 3 non-disease control samples showing the best preservation of cortical architecture.
  • RNA foci did not colocalize with PML bodies (Fig. 12F).
  • Colocalization of mutant RNA was likewise not found with the nucleolus
  • RNA foci the proteasome and exosome are multisubunit complexes responsible for protein and RNA degradation, respectively.
  • FISH analysis was combined with immunofluorescence using antibodies to components of the proteasome or exosome.
  • Three components of the proteasome (20Sa, 1 lSy and 1 ISa subunits) were recruited to RNA foci in cortical neurons (Fig. 15 A; Fig. 16A). No evidence was found, however, for ubiquitination or sumoylation of the foci (not shown).
  • HuR did not colocalize with RNA foci (representative image for hnRNP M is shown in Fig 16D).
  • hriRNPs H and F colocalized with foci in cortical neurons to a limited extent (Fig. 15F, Fig. 16C), and these results were verified using two different polyclonal antibodies for each protein. The intensity of immunofluorescence for these proteins was greatest at the site of RNA foci; however, there did not appear to be significant depletion of hnRNP H or hnRNP F elsewhere in the neuronal nucleoplasm.
  • MB ⁇ L1, MB ⁇ L2, and MBNL3 showed strong colocalization with RNA foci (not shown).
  • MBNL3 was not examined because its expression in adults is mainly restricted to placenta (Fardaei, M, Rogers, M.T, Thorpe, H.M, Larkin, K. Hamshere, M.G, Harper, P.S, and Brook, J.D. (2002), Hum. Mol.
  • Example 14 DM1 and alternative splicing in the brain
  • NMDA receptor NRl GRINl ex5 AF015730 644-706 ex20 NM_007327 3683-3793 ex21 NM 007327 3794-3910 Alternatively
  • Neurotrophic tyrosine kinase, receptor, type 2 Neurotrophic tyrosine kinase, receptor, type 2
  • the ratio of inclusion versus exclusion isoforms was determined by reverse transcriptasePCR (RT-PCR) using primers flanking the regulated exon.
  • RT-PCR reverse transcriptasePCR
  • An initial screen was performed using total RNA extracted from superior temporal cortex from two controls without neurological disease and four DM1 patients. Among 45 exons screened, 4 appeared to show a change in the ratio of exon inclusion/exclusion splice products in DM1. These differences were then confirmed and quantified in triplicate assays using temporal cortex RNA from 7 patients with DM1 and 5 controls (Fig. 18).
  • DM1 was associated with decreased inclusion of amyloid precursor protein exon 7 (10 ⁇ 1% in DM1, 30 ⁇ 11% in controls, pO.OOl), increased inclusion of NMDA NRl receptor exon 5 (33 ⁇ 11% in DM1, 11 ⁇ 5% in controls, pO.Ol), decreased inclusion of tau exon 2 (5 ⁇ 1% in DM1, 36 ⁇ 10% in controls, p ⁇ 10 "5 ), and decreased inclusion of tau exon 10 (21 ⁇ 1% in DM1, 41 ⁇ 5% in controls, p ⁇ 10 "6 ).
  • MBNL regulates fetal exon skipping in adults.
  • the associated disease constitutes the failure in tissues to splice out specific fetal exons. Without MBNL, the fetal exons are retained. Other exons similarly regulated by MBNL remain to be identified.
  • DM1 is associated with reduced exon 10 inclusion (Fig 18), and
  • FTDP-17 and DM1 are both associated with neurofibrillary tangles and neuronal aggregates of hyperphosphorylated tau (Foster, N.L, Wilhelmsen, K, Sima, A.A, Jones, M.Z, D'Amato, C.J, and Gilman, S. (1997), Ann.Neurol, 41, 706-715; Kiuchi, A, Otsuka, N, Namba,Y, Nakano, I, and Tomonaga, M. (1991), Acta Neuropathol, 82, 1-5; Yoshimura, N, Otake, M, Igarashi, K, Matsunaga, M, Takebe, K, and Kudo, H. (1990), Clin.
  • Neuronal intranuclear inclusions are characteristic of several neurological disorders.
  • the core component of the inclusion is mutant protein or a cleavage product containing the polyglutamine tract (Davies, S.W, Turnaine,k M, Cozens, B.A, DiFiglia, M, Sharp, A.H, Ross, CA, Scherzinger, E, Wanker, E.E, Mangiarini, L, and Bates, G.P. (1997), Cell, 90, 537- 548; DiFiglia, M, Sapp, E, Chase, K.O, Davies, S.W, Bates, G.P, Vonsattel, J.P, and Aronin, N.
  • FMRl mRNA having an expanded CGG repeat leads to formation of nuclear inclusions (Greco, CM, Hagerman, R.J., Tassone, F, Chudley, A.E, Del Bigio, M.R, Jacquemont, S, Leehey, M, and Hagerman, P.J. (2002), Brain, 125, 1760-1771).
  • the above-delineated results indicate that DM1 should be added to the list of disorders characterized by neuronal intranuclear inclusions.
  • RNA inclusions are directly involved in disease pathogenesis, through a mechanism that involves sequestration of muscleblind proteins and mis-regulation of alternative splicing (Kanadia, R.N, Johnstone, K.A., Mankodi, A, Lungu, C, Thornton, CA, Esson, D, Timmers, A,M, Hauswirth, W.W, and Swanson, M.S,. (2003), Science, 302, 1978-1980; Mankodi, A, Logigian, E, Callahan, L, McClain, C, White, R, Henderson, D, Krym, M, and Thornton, CA. (2000), Science, 289, 1769-1773).
  • RNA inclusions The strong expression of expanded poly(CUG) RNA in DM1 neurons, formation of RNA inclusions, redistribution of muscleblind proteins, and altered regulation of alternative splicing shown above indicate that CNS symptoms of DM1 may also be triggered by RNA inclusions.
  • mutant DMPK RNA accumulates to higher levels in cortical neurons (Fig. 14), the cell degeneration is more severe in muscle.
  • the present results also indicate that splicing abnormalities are less frequent and less severe in cerebral cortex than in skeletal muscle (Fig. 18), suggesting that muscleblind proteins are more effectively sequestered in muscle nuclei, or that compensation for muscleblind deficiency is more effective in neurons, perhaps due to expression of additional RNA binding proteins.
  • the exact determinants of cell vulnerability in DM1 are unknown, but the stoichiometry of CUG expansion RNA in relation to muscleblind proteins is likely to play an important role.
  • the mutant DMPK mRNA is widely expressed in cortical and subcortical neurons, the failure to detect DMPK immunologically likely reflects its relatively low concentration in brain homogenates.
  • NMDAR1 NMDA receptor 1
  • NMDARl function is required for nonnal long term potentiation in the hippocampus and learning (Tsien, J.Z, Huerta, P.T. and Tonegawa, S. (1996), Cell, 87, 1327-1338).
  • altered splicing of exon 5 may contribute to the memory impairment observed in DM1 (Rubinsztein, J.S, Rubinsztein, D.C, McKenna, P.J, Goodburn, S, and Holland, A.J. (1997), J. Med. Genet, 34, 229-233).
  • Mus musculus muscleblind-like 1 (Drosophila) (Mbnll), mRNA.
  • Mus musculus muscleblind-like 2 (Mbnl2), transcript variant 2, mRNA.
  • ACCESSION NM_207515 (bases 1 to 4527)
  • Mus musculus muscleblind-like 3 (Drosophila) (Mbnl3), mRNA. ACCESSION NMJ34163 (bases 1 to 1967)
  • SEQ ID NO: 37 Homo sapiens amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease) (APP), transcript variant 1, mRNA.
  • A4 Homo sapiens amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease) (APP), transcript variant 1, mRNA.
  • ACCESSION NM_000484 bases 1 to 3641
  • NMDARl subunit isoform 3b hNMDARl-3b
  • ACCESSION AFO 15730 bases 1 to 3150
  • MTT microtubule-associated protein tau
  • transcript variant 2 mRNA.
  • ACCESSION NM_005910 NM_173727 bases 1 to 2796
  • TNNT2 Homo sapiens troponin T2, cardiac (TNNT2), transcript variant 4, mRNA.
  • ACCESSION NM_001001432 bases 1 to 1114)
  • TNNT3 skeletal, fast

Abstract

The present invention provides methods and compositions for the treatment of diseases associated with aberrant microsatellite expansions. Methods of the present invention comprise use of recombinant adeno-associated virus vectors containing a transgene encoding at least one muscleblind protein. The present invention also provides an animal model for a disease associated with aberrant microsatellite expansion.

Description

METHODS AND COMPOSITIONS FOR TREATMENT OF DISEASES ASSOCIATED WITH ABERRANT MICROSATELLITE EXPANSION
RELATED APPLICATIONS/PATENTS & INCORPORATION BY REFERENCE
[0001] This application claims priority to U.S. Provisional Application Serial
No. 60/551,748, filed on March 10, 2004 as Attorney Docket No. 49163.60677, the contents of which is incorporated herein by reference.
[0002] Each of the applications and patents cited in this text, as well as each document or reference cited in each of the applications and patents (including during the prosecution of each issued patent; "application cited documents"), and each of the PCT and foreign applications or patents corresponding to and/or claiming priority from any of these applications and patents, and each of the documents cited or referenced in each of the application cited documents, are hereby expressly incorporated herein by reference, and may be employed in the practice of the invention. More generally, documents or references are cited in this text, either in a Reference List before the claims, or in the text itself; and, each of these documents or references ("herein cited references"), as well as each document or reference cited in each of the herein cited references (including any manufacturer's specifications, instructions, etc.), is hereby expressly incorporated herein by reference.
STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH
[0003] This work was supported in part by a grant from the National
Institutes of Health (U54-NS48843). The United States Government may have certain rights to the invention.
BACKGROUND OF THE INVENTION
Microsatellite Expansion Diseases
[0004] Aberrant expansion of microsatellites in DNA is associated with a number of neurological and neuromuscular diseases (O'Donnell,WT, Warren, ST (2002), Annu. Rev. Neurosci. 25: 315). These diseases are caused by microsatellite repeat expansions in coding and non-coding regions. The characterized coding region expansion diseases include Dentatorubral pallidoluysian atrophy (DRPLA), Huntington chorea (HD), Oculopharyngeal muscular dystrophy (OPMD), Spinobulbar muscular atrophy (SBMA), and Spinocerebellar ataxia types 1, 2, 3, 6, 1, and 17 (SCA1, SCA2, SCA3, SCA6, SCA7, SCA17). The characterized non- coding region expansion diseases include Fragile XA, Fragile XE, Friedrich's ataxia, Myotonic Dystrophy type 1 (DM1), Myotonic Dystrophy type 2 (DM2), and Spinocerebellar ataxia types 8, 10, and 12 (SCA8, SCA10, SCA12). Huntington's disease-like type 2 (HDL2) is likewise caused by a microsatellite expansion.
[0005] Microsatellite expansion diseases have been most commonly associated with trinucleotide expansion mutations. In fact, at least 16 of the microsatellite expansion diseases reported to date have been characterized as trinucleotide expansion diseases. More recently, however, microsatellite expansion diseases have also been associated with tetranucleotide and even pentanucleotide expansion mutations. Disease severity and age of onset have both been related to the size of the expansion mutation, eventually leading to muscle weakness and premature cataract formation, and, in severe cases, to hypotonia, muscle heart block, and nervous system dysfunction (Korade-Mirnics, Z, Babitzke, P, Hoffman, E (1998) Nuc. Acids Res. 26(6): 1363-1368).
[0006] Myotonic dystrophy (dystrophia myotonica, DM) is a multisystemic, dominantly inherited disorder often characterized by myotonia, or, delayed muscle relaxation due to repetitive action potentials in myofibers, and muscle degeneration. Manifestations of DM may also include heart block, ocular cataracts, hypogonadism, and nervous system dysfunction.
[0007] Myotonic dystrophy type 1 (DM1) is caused by a trinucleotide
(CTG)n expansion (n=50 to >3000) in the 3 '-untranslated region (3'UTR) of the Dystrophia myotonica-protein kinase (DMPK) gene. Myotonic dystrophy type 2 (DM2) is caused by a tetranucleotide (CCTG)n expansion (n=75 to ~11,000) in the first intron of zinc finger protein 9 (ZNF9) gene (Ranum. LPW, Day, JW (2002) Curr. Opin. in Genet, and Dev. 12:266-271). [0008] Although the expansions are located on different chromosomes, there appears to be a common pathogenic mechanism involving the accumulation of transcripts into discrete nuclear RNA foci containing long tracts of CUG or CCUG repeats expressed from the expanded allele (Liquori CL, Ricker K, Moseley ML, Jacobsen JF, Kress W, Naylor SL, Day JW, Ranum LP (2001), Science 293: 864- 867).
[0009] In effect, both DM1 and DM2 mutant transcripts accumulate as foci within muscle nuclei (Liquori, et al, 2001). An indication that these transcripts are pathogenic comes from studies on HSALR mice, which express a large CTG repeat in the 3'-UTR of a human skeletal actin transgene (Mankodi, A, Logigian, E, Callahan, L, McClain, C, White, R, Henderson, D, Krym, M, Thornton, CA ( 2000) Science 289: 1769-1773). These transgenic mice develop myonuclear RNA foci, myotonia, and degenerative muscle changes similar to those seen in human DM. The myotonia in HSALR mice is caused by loss of skeletal muscle chloride (ClC-1) channels due to aberrant pre-mRNA splicing (Mankodi, A, Takahashi, MP, Jiang, H, Beck, CL, Bowers, WJ, Moxley, RT, Cannon, SC, Thornton, CA ( 2002) Mol. Cell 10: 35-44). Similar ClC-1 splicing defects exist in DM1 and DM2. However, the connection between accumulation of mutant DM transcripts in the nucleus and altered splice site selection has not been established (Faustino, NA, Cooper, TA (2003) Genes Dev. 17: 419-437).
[00010] The RNA gain-of-function hypothesis proposes that mutant DM transcripts alter the function and localization of alternative splicing regulators, which are critical for normal RNA processing. Consistent with this proposal, misregulated alternative splicing in DM1 has been demonstrated for six pre-mRNAs: cardiac troponinT (cTNT), insulin receptor (IR), muscle-specific chloride channel (ClC-1), tau, myotubularin-related protein 1 (MTMR1) and fast skeletal troponin T (TNNT3) (Kanadia RN, Johnstone KA, Mankodi A, Lungu C, Thornton CA, Esson D, Timmers AM, Hauswirth WW, Swanson MS (2003), Science 302: 1978-1980).
[00011] In all cases, normal mRNA splice variants are produced, but the normal developmental splicing pattern is disrupted, resulting in expression of fetal protein isoforms that are inappropriate for adult tissues. The insulin resistance and myotonia observed in DM1 correlate with the disruption of splicing of two pre- mRNA targets, IR and ClC-1, respectively (Savkur RS, Philips AV, Cooper TA, Dalton JC, Moseley ML, Ranum LP, Day JW (2004), Am JHum Genet 74: 1309- 1313).
[00012] The mechanism by which expanded repeats alter the regulation of pre-mRNA alternative splicing is unclear. Two families of RNA-binding proteins have been implicated in DM1 pathogenesis: CUG-BP1 and ETR-3-like factors (CELF) and muscleblind-like (MBNL) proteins (Ladd AN, Charlet-B N, Cooper TA (2001), Mol Cell Biol 21: 1285-1296). Six CELF (also called BRUNOL) genes have been identified in humans (Ladd AN, Nguyen NH, Malhotra K, Cooper TA (2004), JBiol Chem 279: 17756-17764). All six CELF proteins have been shown to regulate pre-mRNA alternative splicing and two (CUG-BP1 and ETR-3/CUG-BP2) have been shown to have cytoplasmic RNA-associated functions (Mukhopadhyay D, Houchen CW, Kennedy S, Dieckgraefe BK, Anant S (2003), Mol Cell 11: 113-126).
[00013] A functional link has been established between splicing regulation by
CELF proteins and DM1 pathogenesis. CUG-BP1 regulates alternative splicing of at least three of the pre-mRNAs (cTNT, IR and ClC-1) that are misregulated in DM striated muscle (Charlet-B N, Savkur RS, Singh G, Philips AV, Grice EA, Cooper TA (2002b), Mol Cell 10: 45-53). The splicing patterns observed for all three pre- mRNAs are consistent with increased CUG-BP1 activity and an increase in CUG- BP1 steady-state levels in DM1 striated muscle (Charlet-B N, Savkur RS, Singh G, Philips AV, Grice EA, Cooper TA (2002b), Mol Cell 10: 45-53).
[00014] Furthermore, cTNT minigenes expressed in DM1 muscle cultures or cTNT and IR pre-mRNAs co-expressed with CUG repeat RNA in normal cells reproduce the aberrant splicing patterns observed for endogenous genes in DM cells (Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737-741; Savkur RS, Philips AV, Cooper TA (2001), Nat Genet 29: 40-47). The trarø-dominant effects of endogenous or co-expressed CUG repeat RNA on cTNT and IR splicing regulation require the intronic CUG-BP1 -binding sites, indicating that binding by CUG-BP1 and/or other CELF family members to their cognate intronic regulatory elements is required for induction of aberrant splicing regulation by CUG repeat RNA (Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737-741; Savkur RS, Philips AV, Cooper TA (2001), Nat Genet 29: 40-47).
[00015] The CNS symptoms of DM1 may include cognitive impairment, hypersomnolence, heightened sensitivity to anesthetic agents, central hypoventilation, neuroendocrine dysfunction, and effects on personality and behavior [reviewed by Harper (Harper, P.S. (2001), Myotonic dystrophy. Saunders London) and Ashizawa (Ashizawa, T. (1998), Arch. Neurol, 55, 291-293)]. Some of these effects, such as, mental retardation in individuals with congenital DM1, occur during development (Dyken, P.R., Harper, P.S. (1973), Neurology, 23, 465-473). Other symptoms, such as, hypersomnolence, appear during adult life. The mechanism and neuropatho logic correlates for CNS involvement in DM1 are unknown.
[00016] It is presently unclear whether any steps in the pathogenic sequence of poly (CUG) expression, formation of RNA inclusions, sequestration of RNA binding proteins, and disruption of alternative splicing can take place in the CNS. There is controversy about which cells in the mature brain, if any, express DMPK (Lam, L.T., Pham, Y.C., Nguyen, T.M., and Morris, G.E. (2000), Hum. Mol. Genet, 9, 2167-2173).
[00017] Microtubule-associated protein tau (MAPT) pre-mRNA is alternatively spliced at exons 2, 3, and 10 (Goedert, M., Spillantini, M.G., Jakes, R., Rutherford, D., and Crowther, R.A. (1989), Neuron, 3, 519-526). Tau transcripts in fetal brain do not include exon 10, whereas -50% of transcripts in adult brain include this exon which encodes an additional microtubule binding domain (Hong, M., Zhukareva, V., Vogelsberg-Ragaglia, V., Wszokek, Z., Reed, L., Miller, B.I., Geschwind, D.H., Bird, T.D., McKeel, D., Goate, A. et al. (1998), Science, 282, 1914-1917). Alternative splicing of exons 2 and 3 also is developmentally regulated (neither exon is included in the fetus, adults mainly include exon 2).
[00018] The relative proportion of tau splice products is tightly regulated, as shown by kindreds with frontotemporal dementia and parkinsonism (FTDP-17) due to mutations in MAPT. Silent mutations in MAPT exon 10, or, in the flanking intron, lead to FTDP-17 by disrupting cis elements that regulate splicing of tau pre-mRNA (D'Souza, I., Poorkaj, P., Hong, M., Nochlin, D., LeeN.M., Bird, T.D., and Schellenberg, G.D. (1999), Proc. Natl. Acad. Sci. U.S.A, 96, 5598-5603). Usually these mutations lead to increased inclusion of exon 10 (Lee, V.M., Goedert, M., and Trojanowski, J.Q. (2001), Annu. Rev. Neurosci, 24, 1121-1159). However, some MAPT mutations that segregate with FTDP-17 have the opposite effect of reducing exon 10 inclusion (Stanford, P.M., Shepherd, C.E., Halliday, G.M., Brooks, W.S., Schofield, P.W, Brodaty, H, Martins, R.Ν, Kwok, J.B., and Schofield, P.R. (2003), Brain, 126, 814-826).
[00019] RNA-binding proteins that regulate alternative splicing bind to sequence- specific elements in the pre-mRNA to enhance or repress inclusion of alternative exons. Aberrant regulation of alternative splicing can cause the expression of inappropriate splicing patterns leading to human disease (Faustino and Cooper, 2003). Myotonic dystrophy constitutes an example of a disease that alters the function of RNA-binding proteins to cause misregulated alternative splicing.
BRIEF SUMMARY OF THE INVENTION
[00020] The present disclosure provides methods and compositions for treating diseases associated with aberrant microsatellite expansion employing recombinant adeno-associated virus (rAAV) expressing human muscleblind (MBNL) proteins.
[00021] One embodiment of the invention is directed to a method of treating a disease associated with aberrant microsatellite expansion, comprising administering to a mammal in need thereof, a therapeutically effective amount of recombinant adeno-associated virus (rAAV) containing a transgene that encodes a protein selected from the group consisting of MBNL 1, MBNL2, MBNL3, and combinations thereof. In one embodiment of the invention, treating comprises ameliorating or eliminating the symptoms of a neuromuscular or neurological condition caused by the aberrant microsatellite expansion. In an additional embodiment of the invention, the neuromuscular condition is myotonic dystrophy. [00022] In other embodiments of the invention, treating comprises reversing the mis-splicing of the Clcnl skeletal muscle chloride channel, reversing the mis- splicing of the Amyloid beta (A4) precursor protein (APP), reversing the mis- splicing of the NMDA receptor NR1 (GRIN1), reversing the mis-splicing of the Microtubule-associated protein tau (MAPT), or reversing the mis-splicing of TNNT2 (cTNT), respectively.
[00023] One embodiment of the invention is directed to a method of treating a disease associated with aberrant microsatellite expansion, comprising administering to a mammal in need thereof, a therapeutically effective amount of recombinant adeno-associated virus (rAAV) containing a transgene that encodes MBNLl.
[00024] One embodiment of the invention is directed to a method of treating a disease associated with aberrant microsatellite expansion, comprising administering to a mammal in need thereof, a therapeutically effective amount of recombinant adeno-associated virus (rAAV) containing a transgene that encodes a protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof, wherein the mammal is human. In another embodiment of the invention, the mammal in need of treatment has RNA inclusions in neuronal cells.
[00025] One embodiment of the invention is directed to pharmaceutical compositions comprising a recombinant adeno-associated virus (rAAV) containing a transgene that encodes at least one protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof. In another embodiment of the invention, the protein is MBNLl.
[00026] The present disclosure also provides a mouse model for myotonic dystrophy, wherein the mouse has a substantial deletion of a muscleblind exon in its genome. Such an animal model for human disease allows the identification and testing of potential therapeutic and preventive agents.
[00027] Accordingly, one embodiment of the invention is directed to a mouse model for disease associated with aberrant microsatellite expansion, comprising a mouse having a substantial deletion of MbnlX exon 3 (E3) in the mouse genome, wherein said mouse exhibits symptoms typical of a disease associated with aberrant microsatellite expansion in humans. In another embodiment, the invention is directed to a cell isolated from said mouse. In one embodiment of the invention, the mouse exhibits symptoms such as muscle weakness and ocular cataracts.
[00028] In one embodiment, the invention is directed to a mouse model for disease associated with aberrant microsatellite expansion, comprising a mouse having a substantial deletion of Mbnll exon 3 (E3) in the mouse genome, wherein said mouse exhibits symptoms typical of a disease associated with aberrant microsatellite expansion in humans, wherein the microsatellite repeat expansion disease is caused by a microsatellite expansion in a coding region of DNA. In another embodiment of the invention, the microsatellite repeat expansion disease is caused by a microsatellite expansion in a non-coding region of DNA.
[00029] In one embodiment, the invention is directed to a mouse model for disease associated with aberrant microsatellite expansion, comprising a mouse having a substantial deletion of Mbnll exon 3 (E3) in the mouse genome, wherein said mouse exhibits symptoms typical of a disease associated with aberrant microsatellite expansion in humans, wherein the mouse exhibits abnormal muscleblind proteins. In other embodiments of the invention, the mouse may have a loss of functional ClC-1 protein, a loss of functional Amyloid beta (A4) precursor protein, a loss of functional NMDA receptor NR1, a loss of functional Microtubule- associated protein tau, a loss of functional TNNT2 protein, or a loss of functional TNNT3 protein, respectively.
[00030] One embodiment of the invention is directed to a method of identifying a compound useful in the treatment of disease associated with aberrant microsatellite expansion, comprising administering a test compound to a mouse having a substantial deletion of Mbnll exon 3 (E3) in the mouse genome, wherein said mouse exhibits symptoms typical of a disease associated with aberrant microsatellite expansion in humans, wherein the mouse exhibits abnormal muscleblind proteins, and monitoring said mouse for reduction or inhibition of the symptoms associated with said disease. In an additional embodiment, the mouse may be monitored for effects other than those associated with the disease. In one embodiment of the invention, the disease is myotonic dystrophy. BRIEF DESCRIPTION OF THE FIGURES
[00031] FIG. 1 A shows targeted disruption of Mbnll. The illustration includes C57BL/6J Mbnll exon organization (open boxes, UTRs black boxes, open reading frame) together with the l29Sl/Svlm] insert (black rectangle), the 129 genomic region with EcoRV (Ε) (Ε site in C57BL/6] shown by black box with white Ε), Xbal (X), and Bam HI (B) sites, the targeting construct with a thymidine kinase marker (TK), floxed (black triangles, loxP sites), neomycin cassette (stippled box with white N), the 129 region (thick black line) and locations of hybridization probes I and II.
[00032] FIG. IB is a genomic analysis of Mbnll mice with the use of probe 1.
The 11-kb EcoRV fragment is derived from C57BL/6; the mutant is 6.5 kb.
[00033] FIG. IC shows loss of Mbnll Ε3 expression in MbnllAE3/ΔE3
[00034] FIG. ID is an immunoblot analysis (total spleen protein) showing absence of Mbnll 41-42kD proteins in MbnllΛE3/ΔE3.
[00035] FIG. 2A shows an electromyograph (EMG) of Mbnll wild-type and mutant knockout vastus muscle. The arrow (top panel) indicates normal EMG electrode insertional activity in wild-type muscle, whereas insertion triggers myotonic discharges in Mbnll AE3 E3 muscle (bottom panel).
[00036] FIG. 2B shows ClC-1 splicing in DM mouse models. Functional chloride channels are produced when Clcnl exons 6, 7 and 8 are spliced directly together, whereas isoforms that include cryptic exons 7a or 8a encode truncated nonfunctional proteins. Clcnl exons 7 to 8 are illustrated (open boxes) with the primer positions indicated via horizontal arrows. Inclusion of exons 7a and 8a occurs at low levels in wild-type (FVB wt, Mbnll+/+) and Mbnll+/AE3 muscle but at increased levels in Mbnll &E3/AE3 and HSALR muscle.
[00037] FIG. 2C and FIG. 2D depict the loss of ClC-1 protein observed in
Mbnll AE3/AE3 vastus muscle. Representative images of sections from 11 -week-old mice show reduced ClC-1 immunostaining in Mbnll AE3/AE3 mice (D) relative to wild-type mice (C). Scale bar, 20 μm. [00038] FIG. 2E and FIG. 2F constitute representative images of sections from 11-week-old mice showing equivalent dystrophin (Dys) levels in Mbnll+/+ (E) and Mbnll AE3/ E3 (F) muscle.
[00039] FIG. 2G and FIG. 2H depict abnormal muscle histology.
Hematoxylin and eosin (H&E)-stained vastus from wild-type (G) and Mbnll AE3/AE3 (H) mice, showing split myofibers (black arrowhead) and centralized myonuclei (white arrowhead). Scale bar, 30 μm.
[00040] FIG. 21 to FIG.2L show cataract development. Dilated eyes of 18- week old mice showing a clear wild-type lens (I) but dust-like opacities (white arrowhead) in Mbnll AE3/AE3 mice (K). Center bright spot is the lamp reflection. H&E-stained anterior section (J, L) highlight increased fragmentation (black arrowhead) and opacities (white arrowhead) in Mbnll AE3/ E3 lens (L) compared to wild-type lens (J).
[00041] FIG. 3 A and 3B constitute representative images of sections from 11- week-old mice showing similar levels of α-sarcoglycan in (A) wild-type (Mbnll+/+) vastus muscle and (B) muscleblind E3 knockout (Mbnll ΔE3/ΔE3) vastus muscle.
[00042] FIG. 4A shows adult retention of Tnnt2 exon 5 Mbnll AE3/AE3 heart.
RT-PCR products with (+) and without (-) exon 5 (black box) are indicated (brackets). Size markers are pBR322 Msp I fragments.
[00043] FIG. 4B shows Tnnt3 fetal (F) exon inclusion in adult Mbnll AE3/ E3.
The Tnnt3 protein contains variable N-terminal (alternative splicing of exons 4 to 8 and F) and C-terminal regions (exons 16 and 17) (23). RT-PCR (11-week-old mice) of Tnnt3 exons 2 to 11 (left panel) is shown with alternatively spliced exons 4 to 8 and the fetal (F) exon (black boxes). The F exon contains a RyrBI site (arrowhead) resulting in co-migrating smaller fragments in Mbnll AE3/AE3 (right panel).
[00044] FIG. 4C depicts RT-PCR of Tnnt3 exons 15 to 18 after Mscl digestion.
[00045] FIG. 4D shows retention of Tnnt3 fetal (F) exon in adult DM1 skeletal muscle (left panel). The right panel shows cDNAs containing the F exon (bracket) cleaved with Bbsl (arrowhead). [00046] FIG. 5 A shows reversal of the skeletal muscle major chloride channel
(Clcnl) splicing defect following AAV-MBNL1 injection. + lanes represent AAV- mycMBNLl injection into the Tibialis anterior (TA) muscles of HSALRmice, while - lanes represent injection of PBS into the other leg. Boxes indicate Clcnl exons. Shown are the normal (bottom, exons 6, 7, 8 spliced directly together) and aberrant (7a, 8a and intron 6 inclusion) splicing patterns. Mice 190 and 191 are uninjected controls.
[00047] FIG. 5B shows an electromyogram depicting the results of the myotonia analysis performed. The scale (Y-axis) runs from 0 to 3, with 3 corresponding to severe myotonia. Zero equals no observed myotonic discharges, 1 equals occasional myotonic discharge, 2 equals abundant myotonic discharges and 3 equals myotonic discharge in nearly every insertion. The X-axis shows the mouse number and whether the TA was injected or uninjected with rAAVl Myc-hMBNLl.
[00048] FIG. 6 shows the results of RT-PCR analysis of exon inclusion.
Percent exon inclusion is calculated as ((mRNA+exon)/(mRNA- exon+niRNA+exon)) x 100. Results are derived from at least three independent experiments. Expression of GFP-MBNL1 (-72 kDa), GFP-MBNL2 (-58 kDa), GFP-MBNL3 (-70 kDa) and EGFP (-27 kDa) was detected by Western blot analysis using an anti-GFP monoclonal antibody. All three MBNL proteins promote exon 5 skipping of (A) chicken and (B) human cTNT exon 5 in primary skeletal muscle cultures. (C) All three MBNL proteins promote exon 11 inclusion in a human J_R minigene in HEK293 cells. (D) MBNL proteins have minimal effects on splicing of exon EN in a clathrin light-chain B minigene in primary skeletal muscle cultures.
[00049] FIG. 7A shows a Western blot confirming depletion of endogenous
MBNLl by independent transfection of two different siRNA constructs using the MBNLl monoclonal (mAb) 3A4, which recognizes two MBNLl isoforms generated by alternative splicing (-41 and 42 kDa). GAPDH (-36 kDa) was used as a loading control.
[00050] FIG. 7B shows the results of immunofiuorescence analysis using mAb 3A4 to confirm depletion of endogenous protein after independent transfection of each MBNLl siRNA construct. Scale bar, 10 μm. FIG. 7C shows, in bar graph form, the RT-PCR results from at least three transfections.
[00051] FIG. 8 shows MBNLl binds upstream of exon 5 in human cTNT at a site distinct from the CUG-BPl -binding site. (A) Binding of recombinant GST- MBNLl to uniformly 32P-labeled RNA was assayed by UV cross-linking. Scanning mutagenesis was performed by replacing 6 nt blocks with AUAAUA and identified two binding sites 18 and 36 nt upstream of the alternative exon. The MBNL1- binding sites (M) and the CUG-BPl -binding site (C) are located on opposite sides of exon 5. (+) and (-) indicate binding; (•) indicates a putative branch point adenosine. (B) Four nucleotide substitutions significantly reduce binding of recombinant MBNLl detected by UV cross-linking. Competition of GST-MBNLl binding to 32P-labeled RNA G by the indicated picomoles of non-labeled RNAs G or M shown in A). (C, D) MBNLl -binding site mutations reduce responsiveness to MBNLl, MBNL2 and MBNL3 co-expression but not CUG-BPl in COSM6 cells. Human cTNT minigenes containing the natural sequence (C) or the four nucleotide substitutions (mutation M in A) in the MBNLl -binding site (D) were co-expressed with GFP or the indicated GFP fusion proteins. Exon inclusion was assayed by RT- PCR.
[00052] FIG. 9A schematically depicts how the chicken cTNT MSE 1^1 RNA contains an alternative exon flanked by four MSEs. Below, FIG. 9A shows the results of the UV-cross-linking assays, wherein GST-MBNLl bound weakly to MSE1 and strongly to MSE4.
[00053] FIG. 9B shows UV-cross-linking assay results for competition of
GST-MBNLl binding to labeled chicken cTNT MSE 1-4 RNA by non-labeled MSE RNAs. Picomoles of competitor RNA are indicated. FIG. 9C shows the results of the scanning mutagenesis performed, identifying two MBNLl -binding sites within
MSE4.
[00054] FIG. 9D shows an alignment of the four MBNLl -binding motifs in human and chicken cTNT, which reveals a common motif.
[00055] FIG. 10A shows, in bar graph form, the results of the over-expression and depletion experiments with respect to the wild-type cTNT minigene, co- transfected with the indicated siRNA constructs, a plasmid expressing a DMPK minigene with 960 CUG repeats (Philips et al 1998) or a GFP-MBNLl expression plasmid in HeLa cells. FIG. 10B shows the results with respect to the mutant cTNT minigene with point mutations that prevent CUG-BPl binding and regulation.
[00056] FIG. 11A shows, in bar graph form, the results of the over-expression and depletion experiments with respect to the mutant human IR minigene lacking the CUG-BPl -binding site in HEK293 cells. FIG. 1 IB shows the results with respect to the human IR minigene lacking the CUG-BPl -binding site.
[00057] FIG. 12 shows the results of FISH (left panels) and IF (middle panels) analyses of frozen sections of DM1 brain showing nuclear foci of mutant DMPK mRNA. FISH, IF, and nuclear stain (DAPI, blue) images are merged in panels on the right. In (A), FISH (without IF) using Texas Red-labeled CAG repeat probe shows an RNA inclusion in frontal cortical neuron. Autofluorescence from lipofuscin occurs at broad spectrum of wavelengths. It appears in every color channel and as yellow-brown perinuclear material in the merged image. RNA inclusions in cerebral cortex are confined to neurons identified by IF for NeuN (B) or MAP2 (C). Small foci are present in cerebellar Purkinje cells (D) or oligodendrocytes of the centrum semiovale (E) identified by IF for calbiiidin or CNPase, respectively. (F) RNA foci do not colocalize with PML bodies in cortical neurons. Bar, 5 μm, applies to all panels.
[00058] FIG. 13 shows RNA foci in dentate gyrus and subcortical neurons in
DM1, as visualized by FISH and IF analysis. FISH (CAG repeat probe, red) merged with IF (anti-NeuN antibody, green) and nuclear stain (DAPI, blue). SN, substantia nigra. Bar, 5 μm, applies to all panels.
[00059] FIG. 14 (A) shows foci of mutant RNA in neuronal and muscle nuclei, as visualized by FISH and IF analysis. Processing was carried out on the same slide and imaging under the same exposure settings. (B) depicts, in bar graph form, fluorescence area x intensity of RNA foci in paired samples of frontal cortex and skeletal muscle from the same patient; n=3 patients, 20 nuclei per sample (p<10"10).
[00060] FIG. 15 shows the results of FISH and IF analyses of sections of temporal or frontal cortical neurons showing colocalization of mutant DMPK mRNA [(CUG)n] with 20Sa subunit of proteasome (A), MBNL2 (E), and hnRNP F (F). There is a marked redistribution of MBNLl into RNA foci in DM1 cortical neurons (G), compared to the distribution in the nucleus (excluding nucleolus) and cytoplasm of normal neurons (H). Mutant DMPK mRNA does not colocalize with the PM/ScllOO (nuclear) component of the exosome (B), CUGBP1 (C), or NF90 (D). RARγ does not colocalize with RNA foci in DM1 cortical neurons (I). The distribution of RARγ in the DM1 (I) and non-neurologic-disease (J) neuronal nucleus is similar. Bar, 5 μm, applies to all panels.
[00061] FIG. 16 shows the results of FISH analysis combined with IF analysis of sections of DM1 temporal or frontal cortex. FISH (CAG repeat probe, red, left panels) and IF (middle panels, antibody to indicated protein, green) are merged with nuclear stain (DAPI, blue) in right panels. CUG expansion RNA colocalizes with proteasome 11 Sγ subunit (A) and linRNP H (C) but not with double-stranded RNA binding protein ADAR1 (B), hnRNP M (D), or Spl (E). Bar, 5 μm, applies to all panels.
[00062] FIG. 17 depicts, in graph form, immunofluorescence (area x intensity) for MBNLl in the nucleus, excluding nucleolus and RNA foci, as determined for 20 neurons in sections of temporal cortex from 3 individuals with DM1 and 3 controls without neurologic disease (C).
[00063] FIG. 18 shows the regulation of alternative splicing of the NMDA
NR1 receptor (NMDAR1), amyloid beta precursor protein (APP), and microtubule- associated protein tau (MAPT) in DM1. (A) shows splice products obtained by RT- PCR amplification of RNA isolated from non-disease control (n=5) or DM1 (n=7) temporal cortex. Exon utilization for each splice product is shown in diagram. (B) provides quantification of RT-PCR splicing assay (triplicates), ex, exon.
DETAILED DESCRIPTION OF THE INVENTION
Muscleblind proteins
[00064] Proteins in the muscleblind-like (MBNL) family bind to expanded
CUG repeats in vitro and colocalize with mutant DM and HSALR transcripts in vivo. Human muscleblind genes MBNLl (SEQ ID NO: 1), MBNL2 (SEQ ID NO: 2), and MBNL3 (SEQ ID NO: 3) are homologous to the Drosophila gene muscleblind, which is essential for muscle and eye differentiation. MBNLl, the major MBNL gene expressed in human skeletal muscle, encodes multiple protein isoforms, including some that bind to expanded CUG repeats (41 to 42 kD) and others that fail to bind (31 kD isoform), generated by exon 3 skipping.
[00065] In fact, MBNLl was identified in HeLa cells based on its ability to bind double-stranded CUG repeats (Miller JW, Urbinati CR, Teng-Umnuay P, Stenberg MG, Byrne BJ, Thornton CA, Swanson MS (2000), EMBOJ 19: 4439- 4448). All three MBNL gene products colocalize with the expanded repeat RNA foci in vivo (Fardaei M, Rogers MT, Thorpe HM, Larkin K, Hamshere MG, Harper PS, Brook JD (2002), Hum Mol Genet 11: 805-814). Loss of MBNL function due to sequestration on CUG repeat RNA is proposed to play a role in DM pathogenesis (Miller JW, Urbinati CR, Teng-Umnuay P, Stenberg MG, Byrne B J, Thornton CA, Swanson MS (2000), EMBO J 19: 4439-4448). Thus, while expression of CUG and CCUG expansion RNAs induces MBNL recruitment into nuclear RNA foci, there is no evidence that this relocalization results in muscleblind depletion and functional impairment.
Recombinant adeno-associated vectors
[00066] Recombinant AAV (rAAV) vectors have been used for expressing gene products in animals, see, for example, U.S. Pat. No. 5,193,941 and WO 94/13788. Other patents and publications describe AAV vectors and uses, the uses generally being related to expression of gene products either in vitro (usually tissue cultures) or in vivo (usually in the lungs or oral mucosa, the normal sites of AAV infection, but expression in other tissues, such as the central nervous system and in cardiac tissue has been observed).
[00067] AAV vectors have certain advantages over other well-characterized vector systems. First, like adenovirus, AAV infects non-dividing cells. Second, all the AAV viral genes are eliminated in the vector. Since the viral gene expression- induced immune reaction is no longer a concern, AAV vectors are safer than adenovirus vectors. As AAV is an integration virus, integration into the host chromosome will maintain the transgene in the cells. AAV is an extremely stable virus, resistant to many detergents, pH changes and heat (stable at 56 °C for about an hour). AAV can be lyophilized and redissolved without losing significant activity. Finally, AAV causes no known diseases or pathogenic symptoms in humans. Therefore, AAV is a very promising delivery vehicle for gene therapy.
[00068] Transduction of rAAV vectors harboring the bacterial β-galactosidase gene by single injection into the quadriceps of mice demonstrated that expression was maintained long-term and the expression did not decrease substantially during that time (Xiao et al., J. Virol., 70:8098-8108 (1996)). Other targets successfully transduced with rAAV vectors include: T-lymphocytes and B-lymphocytes, human erythroleukemia cells, different regions of the rat brain, the striatum of the rat brain in a Parkinson's Disease model with the tyrosine hydroxylase gene, heart of the pig and rat with the LacZ gene, the peripheral auditory system of the guinea pig and bronchial epithelia of the rabbit and monkey.
Embodiments of the invention
[00069] In one embodiment, the invention provides a vector for effective expression of a protein with MBNLl, MBNL2, or MBNL3 (or combinations thereof) function to treat conditions associated with aberrant microsatellite expansions. In an additional embodiment, the vector of the invention is recombinant adeno-associated virus (rAAV) vectors. In one embodiment of the invention, the rAAV contains a transgene that expresses an MBNLl, MBNL2, or MBNL3 (or combinations thereof) protein. In an additional embodiment, the invention provides a rAAV containing a transgene that expresses MBNLl (for example, the 41 kD isoform).
[00070] Isolation of the DNA encoding MBNL polypeptides allows one to use methods well-known to the person of ordinary skill in the art to make changes in the codons for specific amino acids such that the codons are "preferred usage" codons for a given species.
[00071] In one embodiment, the rAAV of the invention includes a promoter, which directs the initiation of RNA transcription in the cell of interest. The promoter may be constitutive or regulated. Regulated promoters include inducible promoters and repressible promoters. In an additional embodiment of the invention, the regulation of the promoter is associated with an "operator", to which an inducer or repressor binds. The promoter may be a "ubiquitous" promoter active in essentially all cells of the host organism or may be a promoter with expression more or less specific to the target cells. Known strong promoters that find common use to obtain high levels of recombinant protein expression include the herpes simplex thymidine kinase promoter, SV40 promoter and LTRs such as that obtained from Moloney leukemia retrovirus. For the gene to be expressed, the coding sequence must be operably linked to a promoter sequence functional in the target cell.
[00072] It is not necessary that the AAV-derived sequences correspond exactly with wild-type AAV prototypes. For example, in one embodiment, the rAAV vectors of the invention may feature modified inverted terminal repeats and other sequences, provided that the rAAV vectors can replicate and be packaged with the assistance of helper virus, and establish a nonpathogenic latent infection in target cells. Typically, because of the packaging limitations of AAV, the polynucleotides encoding MBNLl domain sequences and the regulatory elements can have a length of up to about 5,500 bases.
[00073] Numerous applications of the present invention, e.g., making transgenic constructs, involve the cloning, synthesis, maintenance, mutagenesis, and other manipulations of nucleic acid sequences that can be performed using routine techniques in the field of recombinant genetics. Basic texts disclosing the general methods of use in this invention include 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)).
[00074] For propagation of the rAAV vectors in vitro, susceptible cells are co-transfected with an AAV-derived vector DNA and a suitable AAV-derived helper virus or plasmid harboring the AAV rep gene, AAV cap gene or both and infected by a helper virus, including herpesvirus, adenovirus or a suitable non-AAV helper plasmid using any number of transfection methods, including, inter alia, calcium-phosphate transfection, lipofection or other techniques known to those skilled in the art. The ratio of helper plasmids to the quantity of vector plasmid containing the gene of interest range from 1:1-1:10. This procedure produces recombinant AAV vectors; the vector plasmid contains the recombinant AAV genome flanked by the AAV ITRs. The AAV-derived helper virus or helper plasmid may be any virus or plasmid which is capable, on expression of the AAV genes it carries, of providing proteins necessary for the replication and packaging of the rAAV vector in a suitable host cell, for the purpose of producing rAAV vector stock.
[00075] In one embodiment, the target cells of the rAAV vectors of the invention are cells capable of expressing polypeptides with MBNLl activity. In another embodiment of the invention, the cells are normal cells cultured in vitro. In further embodiments, the target cells of the rAAV vectors of the invention are human cells, or cells of other mammals, such as nonhuman primates and mammals of the orders Rodenta (mice, rats, rabbit and hamsters), Carnivora (cats and dogs) and Arteriodactyla (cows, pigs, sheep, goats and horses). In one embodiment of the invention, the cells are part of a living mammal at the time the rAAV vectors are delivered to the cell. The mammal may be at any stage of development at the time of delivery, e.g, embryonic, fetal, infantile, juvenile or adult. Additionally, the cells may be healthy or diseased.
[00076] In one embodiment, the rAAV vectors of the invention may be administered as viral particles alone, whether as an in vivo direct delivery to the vasculature or as an ex vivo treatment comprising administering the rAAV vector viral particles in vitro to cells from the animal receiving treatment followed by introduction of the transduced cells back into the donor. Alternatively, the rAAV vector virus particles can be used to transduce cells in conjunction with secondary agents known to enhance the efficiency of transduction, see, e.g, WO Ser. No. 95/33824 for a variety of secondary agents. The effective amount of rAAV vectors to be administered will vary from patient to patient. Accordingly, effective amounts are best determined by the physician administering the rAAV vectors, and appropriate dosages can be determined readily by one of ordinary skill in the art. [00077] In one embodiment, the rAAV construct of the invention expresses human MBNLl (rAAV-MBNLl(rAAV-MBNLl/41)). In an additional embodiment of the invention, injection of the rAAV-MBNLl/41 into the tibialis anterior (TA) muscles of a transgenic model for DM that expresses a human skeletal α-actin transgene carrying 250 CTG repeats (HSALR -- a mouse model which develops myotonia and muscle degeneration similar to muscle abnormalities seen in DM patients) results in a functional reversal of a DM-related phenotype, namely, reversal of mis-splicing of the Clcnl skeletal muscle chloride channel, which results in myotonia.
[00078] In one embodiment, the invention is directed to methods for treating or preventing various disorders and conditions associated with aberrant microsatellite expansions in a mammal, said method comprising administering to the mammal a therapeutically effective amount of rAAV containing a transgene that encodes a protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof. In a further embodiment of the invention, the protein is MBNLl. In another embodiment of the invention, the mammal is a human. In another embodiment, the transgene is human. In one embodiment of the invention, the disease associated with aberrant microsatellite expansion is a neurological or neuromuscular disease. In an additional embodiment of the invention, the disease is myotonic dystrophy. In yet another embodiment of the invention, the disease is SCA8.
[00079] In additional embodiments, the present invention provides methods for treating or preventing a disease or condition related to any physiological process affected by MBNLl, said method comprising administering to the mammal a therapeutically effective amount of rAAV containing a transgene that expresses the MBNLl protein.
[00080] In one embodiment, the invention is directed to methods for treating or preventing various disorders and conditions associated with aberrant microsatellite expansions in a mammal, said method comprising administering to the mammal a therapeutically effective amount of rAAV containing a transgene that encodes a protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof, wherein treating comprises reversing the mis-splicing of the Clcnl skeletal muscle chloride channel.
[00081] In another embodiment of the invention, treating comprises reversing the mis-splicing of the Amyloid beta (A4) precursor protein (APP). The mis- splicing may correspond to alternative splicing of exon 7. In another embodiment of the invention, treating comprises reversing the mis-splicing of the NMDA receptor NR1 (GRLN1). The mis-splicing may correspond to alternative splicing of exon 5. In yet another embodiment of the invention, treating comprises reversing the mis- splicing of the Microtubule-associated protein tau (MAPT). The mis-splicing may correspond to alternative splicing of exon 2. In yet another embodiment of the invention, treating comprises reversing the mis-splicing of the TNNT2 (cTNT). The mis-splicing may correspond to alternative splicing of exon 5.
[00082] In one embodiment, the invention is directed to methods for treating or preventing various disorders and conditions associated with aberrant microsatellite expansions in a mammal, said method comprising administering to the mammal a therapeutically effective amount of rAAV containing a transgene that encodes a protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof, wherein the mammal has RNA inclusions in neuronal cells.
[00083] One embodiment of the invention is directed to a pharmaceutical composition comprising rAAV containing a transgene that encodes at least one protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof. In one embodiment of the invention, the protein is MBNLl. 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 of the present invention (see, e.g. Remington's Pharmaceutical Sciences, 17.sup.th ed. 1985).
[00084] Formulations for both ex vivo and in vivo administrations include suspensions in liquid or emulsified liquids. The active ingredient (rAAV vector) is often mixed with excipients that are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients include, for example, water, saline, dextrose, glycerol, ethanol or the like, and combinations thereof. In addition, the composition may contain minor amounts of auxiliary substances, such as, wetting or emulsifying agents, pH buffering agents, stabilizing agents or other reagents that enhance the effectiveness of the pharmaceutical composition.
[00085] Formulations suitable for administration include aqueous and non- aqueous solutions, isotonic sterile solutions, which can contain antioxidants, buffers, bacteriostats, and solutes that render the formulation isotonic, and aqueous and non- aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. In the practice of this invention, compositions can be administered, for example, orally, nasally, topically, intravenously, intraperitoneally, intravesically or intrathecally. The formulations of compounds can be presented in unit-dose or multi-dose scaled containers, such as ampules and vials. Solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described. The modulators can also be administered as part a of prepared food or drug.
[00086] The dose administered to a patient, in the context of the present invention is often varied to assess the effect of various concentrations of a compound on a transgenic animal. The dose will also be determined by, e.g, the body weight or surface area of the area to be exposed to the compound. In general, the dose equivalent of a modulator is from about 1 ng/kg to 10 mg/kg for a typical subject. Administration can be accomplished via single or divided doses.
[00087] Pharmaceutical preparations of the disclosed gene vectors may be administered intravenously, parenterally or intraperitoneally. Solutions of pharmaceutically acceptable salts can be prepared in water suitable mixed with a surfactant, such as hydroxypropylcellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations will contain a preservative to prevent growth of microorganisms. [00088] The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier may be a solvent or dispersion medium containing, for example, water, ethanol, polyol (such as, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, such as, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride.
[00089] Solutions of the AAV vector as a free acid (DNA contains acidic phosphate groups) or a pharmacologically acceptable salt can be prepared in water suitably mixed with a surfactant such as hydroxypropylcellulose. A dispersion of AAV particles also can be prepared in glycerol, liquid polyethylene glycols and mixtures thereof and in oils. Under ordinary conditions of storage and use, the preparations contain a preservative to prevent the growth of microorganisms. The sterile aqueous media employed are obtainable by standard techniques well known to those skilled in the art.
[00090] Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin. Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
[00091] The composition can be formulated in a neutral or salt form.
Pharmaceutically-acceptable salts, include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organics acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective. The formulations are easily administered in a variety of dosage forms such as injectable solutions, drug release capsules and the like.
[00092] For parenteral administration in an aqueous solution, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, sterile aqueous media that can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage could be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion. Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject. Moreover, for human administration, preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biologies standards.
[00093] The pharmaceutical forms suitable for parenteral administration include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases the form must be sterile and must be fluid to the extent that parenteral administration is possible. The formulation must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, liquid polyethylene glycol and the like), suitable mixtures thereof, and vegetable oils. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of a dispersion and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal and the like. In many cases it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by use of agents delaying absorption, for example, aluminum monostearate and gelatin.
[00094] Sterile parenteral formulations are prepared by incorporating the
AAV vector in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the sterilized active ingredient into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze drying which yield a powder of the active ingredient plus any additional desired ingredient from the previously sterile-filtered solution thereof.
[00095] The rAAV containing a transgene that expresses the MBNLl protein may, for example, be prepared by: culturing a composition comprising cells transiently transfected with an AAV helper plasmid comprising AAV rep and cap nucleic acid sequences encoding AAV rep and cap proteins, an adenoviral helper plasmid comprising essential adenovirus helper genes selected from the group consisting of E1A, E1B, E2A, E4, E4ORF6, E4ORF6/7, VA, and combinations thereof, and an AAV vector comprising first and second AAV ITRs flanking a DNA sequence encoding MBNLl polypeptide, said sequence being operably linked to a promoter DNA sequence, in the absence of adenovirus particles and under conditions suitable for production of recombinant AAV, and purifying rAAV therefrom.
[00096] In one embodiment, the invention is directed to a transgenic animal having a substantial deletion of one or more MBNLl exon(s). The transgenic animals of the invention can be any mammal other than humans. In one embodiment, the mammal is a rodent. In another embodiment of the invention, the rodent is a mouse. An additional embodiment is directed to a cell isolated from the transgenic animal of the invention.
[00097] In a further embodiment, the transgenic animal of the invention has a substantial deletion of Mbnll exon 3. In one embodiment, Mbnll exon 3 in the transgenic animal of the invention is deleted in its entirety.
[00098] In one embodiment of the invention, the transgenic mouse having a substantial deletion of Mbnll exon 3 constitutes an animal model for microsatellite expansion disease in mammals. In another embodiment of the invention, the mammal is a primate. In yet another embodiment of the invention, the primate is a human.
[00099] In one embodiment of the invention, the microsatellite expansion disease is caused by a microsatellite expansion in a coding region of DNA. In another embodiment of the invention, the microsatellite expansion disease is caused by a microsatellite expansion in a non-coding region of DNA. In one embodiment of the invention, the disease associated with aberrant expansion of microsatellites is myotonic dystrophy. Accordingly, in one embodiment of the invention, the mouse Mbnll gene knockout model exhibits myotonia and ocular cataracts.
[000100] In one embodiment, the invention is directed to a mouse model for disease associated with aberrant microsatellite expansion, comprising a mouse having a substantial deletion of Mbnll exon 3 (E3) in the mouse genome, wherein said mouse exhibits symptoms typical of a disease associated with aberrant microsatellite expansion in humans, wherein said mouse has loss of functional C1C- 1 protein. In another embodiment of the invention, mouse has loss of functional Amyloid beta (A4) precursor protein. In another embodiment of the invention, the mouse has loss of functional NMDA receptor NR1. In yet another embodiment of the invention, the mouse has loss of functional Microtubule-associated protein tau. In another embodiment of the invention, the mouse has loss of functional TNNT2 protein. In another embodiment of the invention, the mouse has loss of functional TNNT3 protein.
[000101] One embodiment is directed to methods for preparing the transgenic animals of the invention. The transgenic animal of the invention may, for example, be prepared by transfecting a plurality of mouse embryonic stem cells with a nucleic acid comprising an MBNLl gene with a substantial deletion of exon 3, selecting for transgenic embryonic stem cells having incorporated said nucleic acid into their genome, introducing at least one of said transgenic embryonic stem cells into an embryo to produce a chimeric mouse comprising at least one of said transgenic embryonic stem cells, breeding said chimeric mouse with a wild-type mouse to obtain Fl progeny heterozygous for the MBNLl gene with a deletion of exon 3, and breeding a male mouse of said Fl progeny with a female mouse of said Fl progeny to obtain F2 progeny homozygous for MBNLl gene with a deletion of exon 3, wherein the said mouse exhibits a phenotype indicative disease associated with aberrant microsatellite expansion, for example, myotonic dystrophy.
[000102] Additional embodiments are directed to methods for using the transgenic animals of the invention as animal models to study MBNLl function in vivo, and for evaluating side effects of MBNLl -inhibiting compounds. For example, if a compound known to inhibit MBNLl is administered to an MBNLl knockout mouse, any detected effects of the compound on the mouse can be concluded to be MBNL 1 -independent.
[000103] In further embodiments, the transgenic mammals of the invention, and cells thereof, can be used as animal models to identify compounds useful in the treatment of diseases associated with aberrant microsatellite expansions (such as, in one embodiment, myotonic dystrophy) and to assess the functional effect of a test compound on cells or animals afflicted with such disease. Such compounds can be any small chemical compound, including polypeptides, polynucleotides, amino acids, nucleotides, carbohydrates, lipids, or any other organic or inorganic molecule. Alternatively, the compounds can be genetically altered versions of the MBNLl gene.
[000104] In one embodiment of the invention, assessing the effects of a compound on cells or animals, e.g, the transgenic animals of the invention having a substantial deletion of MBNLl exon 3, involves providing a combinatorial chemical or peptide library containing a large number of potential therapeutic compounds (potential modulator or binding compounds). Such "combinatorial chemical libraries" are then screened in one or more assays to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as conventional "lead compounds" or can themselves be used as potential or actual therapeutics.
[000105] A combinatorial chemical library is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis, by combining a number of chemical "building blocks" such as reagents. Preparation and screening of combinatorial chemical libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g, U.S. Pat. No. 5,010,175, Furka (1991) Int. J. Pept. Prot. Res, 37:487-493 and Houghton, et al. (1991) Nature, 354:84-88).
[000106] To assess the effect of a compound on an animal, or to treat or prevent a condition associated with aberrant microsatellite expansion, for example, myotonic dystrophy, in an animal, administration of the compound can be achieved by any of the routes normally used for introducing a compound into ultimate contact with the tissue to be treated. The compounds are administered in any suitable manner, optionally with pharmaceutically acceptable carriers. Suitable methods of administering such compounds 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.
[000107] Although MBNLl is referred to in the individual descriptions of the embodiments of the invention, MBNL2 and MBNL3 may likewise be contemplated for each embodiment. Definitions
[000108] A "transgene" refers to genetic material that is introduced, or is capable of being introduced, into cells of a host animal. Typically, once a "transgene" is introduced into the cells of the host animal, it is maintained, either transiently or permanently, by, e.g, insertion into the host genome. In preferred embodiments of the present invention, a transgene is inserted into the host genome by homologous recombination, thereby replacing the endogenous gene with the transgene. Often, a transgene contains a coding sequence, operably linked to a promoter, that encodes a protein, e.g, a marker protein that allows the detection of the transgene in the cell. "Transgenic" refers to any cell or organism that comprises a transgene.
[000109] A "host" animal or mammal refers to any animal that is used to practice the herein-described methods, i.e. animals into which a transgene is introduced to disrupt an endogenous MBNLl gene. For use in the present invention, such animals include any non-human mammals including, but not limited to, mice, rats, rabbits, and hamsters.
[000110] "Nucleic acid" refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. The term encompasses 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. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g, degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. The term nucleic acid is used interchangeably with gene, cDNA and nucleotide.
[000111] The terms "polypeptide," "peptide" and "protein" 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 artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer.
[000112] The term "amino acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.
[000113] A "label" or a "detectable moiety" is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. For example, useful labels include 32 P, fluorescent dyes, electron-dense reagents, enzymes (e.g, as commonly used in an ELISA), biotin, digoxigenin, or haptens and proteins which can be made detectable, e.g, by incorporating a radiolabel into the peptide or used to detect antibodies specifically reactive with the peptide.
[000114] The term "recombinant" when used with reference, e.g, to a cell, or nucleic acid, protein, or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all.
[000115] The term "heterologous" when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid, e.g, a promoter from one source and a coding region from another source. Similarly, a heterologous protein indicates that the protein comprises two or more subsequences that are not found in the same relationship to each other in nature (e.g, a fusion protein).
[000116] A "promoter" is defined as an array of nucleic acid control sequences that direct transcription of a nucleic acid. As used herein, a promoter includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element. 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. 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 environmental or developmental regulation. The term "operably linked" refers to a functional linkage between a nucleic acid expression control sequence (such as a promoter, or array of transcription factor binding sites) and a second nucleic acid sequence, wherein the expression control sequence directs transcription of the nucleic acid corresponding to the second sequence.
[000117] The terms "identical" or percent "identity," in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., 60% identity, optionally 65%, 70%, 75%, 80%, 85%, 90%, or 95% identity over a specified region), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. Such sequences are then said to be "substantially identical."
[000118] The term "immunoassay" is an assay that uses an antibody to specifically bind an antigen. The immunoassay is characterized by the use of specific binding properties of a particular antibody to isolate, target, and/or quantify the antigen. [000119] The phrase "specifically (or selectively) binds" to an antibody or "specifically (or selectively) immunoreactive with," when referring to a protein or peptide, refers to a binding reaction that is determinative of the presence of the protein in a heterogeneous population of proteins and other biologies. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein at least two times the background and do not substantially bind in a significant amount to other proteins present in the sample. Specific binding to an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein For example, polyclonal antibodies raised to an MBNLl polypeptide from specific species such as rat, mouse, or human can be selected to obtain only those polyclonal antibodies that are specifically immunoreactive with the MBNLl protein and not with other proteins, except for polymorphic variants and alleles of the MBNLl protein.
[000120] The term "transduction" refers to the introduction of foreign DNA into cells of an organism (in vivo).
[000121] The term "transfection" refers to the introduction of foreign DNA into cells in culture (in vitro). Genetic modification of eukaryotic cells by introduction of foreign DNA using chemical means. In transient transfection, expression occurs from unintegrated foreign DNA and can be detected for a few days after transfection.
[000122] The term "titer" refers to the number of virus particles produced per ml. The assay system to determine the number of virus particles produced varies considerably depending on the virus in question. High titers are generally essential for successful gene therapy since they allow introduction of the therapeutic gene carried by the virus into the maximum number of cells.
[000123] The terms "treating" and "treatment" as used herein include any treatment of a condition or disease in a subject, and include inhibiting the disease or condition, (i.e. arresting its development), relieving the disease or condition (i.e. causing some degree of regression of the condition or delaying progression in the disease), or relieving (to some degree) the conditions caused by the disease (i.e. symptoms of the disease). [0.00124] The term "vector" refers to a vehicle, usually a biological entity, such as a virus, used for the delivery of genes into an organism. A reagent that facilitates the introduction of foreign genes into cells.
[000125] The phrase "packaging cells" refers to cells that have been transfected with plasmids containing the cap and rep genes from AAV.
[000126] As used herein, "pharmaceutically acceptable carrier" includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutically-active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.
[000127] The phrase "pharmaceutically-acceptable" refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human. The preparation of an aqueous composition that contains a protein as an active ingredient is well understood in the art. Typically, such compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection can also be prepared. The preparation can also be emulsified.
[000128] A "substantial" deletion of exon 3 signifies a deletion extensive enough to lend to the phenotype indicative of a disease associated with aberrant microsatellite expansion.
[000129] Use of the terms "an", "a" and "the" and similar terms used in claiming or describing the invention are intended to be construed as including both the singular and plural, unless clearly otherwise indicated or contraindicated. The terms "including", "having" and "containing" are to be construed as open-ended in the same manner as the terms "comprising" or "comprises" are commonly accepted as including but not limiting to the explicitly set forth subject matter. The term "comprising" and the like are construed to encompass the phrases "consisting of and "consisting essentially of. [000130] The methods and processes described herein may be performed in any suitable order unless otherwise indicated or clearly rendered inoperable by a modification in order.
[000131] Limited and narrow interpretation of descriptive language intended to better illustrate the invention is not to be construed as limiting in any way nor to limit the scope of the invention contemplated by the inventors.
[000132] The invention, now described generally and in some detail, will be understood more readily by reference to the following examples, which are provided by way of reference and are in no manner intended to limit the scope of what the inventors regard as their invention.
EXAMPLES
Example 1. Characterization of MbnIlΔE3 ΛE3 mice.
[000133] Targeted disruption of Mbnll: to test whether or not sequestration of
MBNL proteins contributes to DM pathogenesis, mice with a targeted deletion of Mbnll exon 3 (E3) (Fig. 1A) were generated. The pMbnllΔE3"eo targeting plasmid was constructed using pTKflNeo (gift of E. Scott, University of Florida), which contains the Herpes simplex virus - thymidine kinase (HSV-TK) negative selection marker and a loxP-flanked phosphoglycerate kinaseneomycin (PGK-Neo) positive selection cassette. A 2.5 kb Xbal fragment (5' arm of homology) corresponding to the upstream region bordering Mhnll exon 3, was inserted 5' of PGK-Neo. For the 3' arm of homology, a 6 kb Mbnll BamHI fragment was subcloned into pBluescript II KS+ (Stratagene, La Jolla, CA), excised with Xhol/Notl, and cloned into the Xhol/Notl sites of pTKflNeo 3' of PGK-Neo.
[000134] The pMbnllΔE3"β0 plasmid was linearized with Not/ and electroporated into CJ.7 ES cells (P.J. Swiatek, T. Gridley, Genes & Dev. 7, 2071 (1993)). ES cells were cultured and selected as described in T. Yang et al, Nat. Genet. 19, 25 (1998). Clones resistant to G418 and FIAU were isolated and screened for homologous recombination by utilizing a forward primer (5'- TGGGATGGAATTGTGGTGTGTTGTTGCTCATG-3') (SEQ ID NO: 4) outside the 5' homologous region and a reverse primer (5'- TCCATTTGTCACGTCCTGCACCGACGC-3') (SEQ ID NO: 5) in PGKNeo. Amplification (25 cycles) consisted of 98°C for 20 s followed by 68°C for 4 min. Targeted ES cell clones yielded a 2.9 kb PCR product. This targeting strategy was predicted to approximate the situation in DM by eliminating synthesis of CUG- binding isoforms (Miller, et al, 2000).
[000135] Genomic DNA analysis of Mbnll mice: genomic blot analysis demonstrated successful deletion of Mbnll ΔE3 ΔE3 mice (Fig. IB). Five ES cell clones (35, 56, 92, 111, 120) that were positive for homologous recombination were confirmed by genomic DNA blot analysis. Based on restriction map analysis of genomic fragments flanking E3, ES genomic DNA digested with EcoRFproduces a 16 kb band when a 300 nt Mbnll BamHI/EcoRV fragment outside the 3' arm of homology is used as a hybridization probe (probe II of Fig. LA). In the targeted allele, anew EcoRV site (from pBluescript II KS+) is introduced, generating a novel 6.7 kb EcoRV fragment. All five clones that were positive by PCR were also positive by genomic DNA blot analysis. When the 5' arm of homology (2.5 kb Xbal fragment) was used as probe, two bands at 16 kb (wild type) and 7.5 kb (mutant) were detected. To check for additional insertion events in these five clones, PGK-Neo fragment was used as probe on genomic DNA digested with EcoRV. A single band at 7.5 kb confirmed the absence of any additional insertion events.
[000136] One ΕS clone (ΕS.35) was expanded and transiently transfected with
Crerecombinase to excise PGK-Neo. To detect PGK-Neo loss, forward (5'- CTACGATGGCTGGCTGCAATATGCCTCACTGTAAG-3') (SEQ ID NO: 6) and reverse (5'GGGTTGAATCTCGTTAGGGACACTGGGTGTCTGTAA-3') (SEQ ID NO: 7) primers were used for a PCR screen. PCR was performed for 30 cycles, each cycle consisting of 96°C for 30 see, 60°C for 30 sec and 72°C for 2 min. Clones positive for PGK-Neo deletion yielded a I kb band and cassette excision was confirmed by genomic DNA blot analysis. Utilization of a PCR- generated subfragment of the 5' arm of homology as a hybridization probe yielded EcoR bands at 16 kb and 6.5 kb. The loss of PGK-Neo results in decrease in the size of the mutant allele digested with EcoR from 7.5 to 6.5 kb. The Neo excised allele was designated MbnllΔE3. [000137] Two Mbnll+/ΔE3 ES clones (1B3, 2C1) were transferred to 3.5 dpc
C57BL/6J blastocysts which were then carried to term by B6D2F1/J recipients. One chimeric male was obtained from each clone. Contribution of CJ.7 (129Sl/SvlmJ) ES cells to the germline was determined by mating the chimeric males with C57BL/6J females. Agouti pups in litters sired by the 1B3 chimeric male indicated germline transmission.
[000138] To detect heterozygotes in the Fl population derived from 1 B3, a combination of one forward primer (5'-
CTACGATGGCTGGCTGCAATATGCCTCACTGTAAG-3') (SEQ ID NO: 8) and two reverse primers [for the mutant allele (5'-
GGGTTGAATCTCGTTAGGGACACTGGGTGTCTGTAA-3' (SEQ ID NO: 9)]; [for the wild-type allele (5'-TGGCAGACCCTTTGACACCG-3') (SEQ ID NO: 10)] were used for PCR. Amplification was performed for 30 cycles, each cycle consisting of 96°C for 30 sec, 60°C for 30 sec and 72°C for 2 min. Heterozygotes were then mated to obtain Mbnll AE3/ E3 mice.
[000139] Loss of Mbnll E3 expression in MbnllAE3/ΔE3: loss of E3 expression was confirmed by reverse transcription polymerase chain reaction (RT-PCR); primers in exons 3 and 6 were used to amplify a cDNA product from either Mbnll+/+ or Mbnll+ AES mice that was absent in MbnllAE3IAE3 mice (Fig. IC). To confirm loss of exon 3, an RT-PCR strategy was used with the forward primer positioned in exon 3 (5'-TAGTGTCACACCAATTCGGGACACAAA-3') (SEQ ID NO: 11) and an exon 6 reverse primer (5'-
CCCTTGATGTAATCCATGCAGACAGTGA-3') (SEQ ID NO: 12). Continued transcription of Mbnll mMbnll ΔE3 άE3 fines was examined using exon 10 forward (5*-TGCACGGTGCTACGCCAGCC-3') (SEQ ID NO: 13) and exon 12 reverse (5'- GTGACGACAGCTCTACATCTGGGTAACA-3') (SEQ ID NO: 14) primers, as well as exon 13 forward (5'-CCTGCTGCACACTGTTGCCTACAC-3') (SEQ ID NO: 15) and reverse (5 GTCAGTTCCCTCCCTCACCATGT-3') (SEQ ID NO: 16) primers. For amplification, 27 cycles were performed each consisting of 45 sec at 95°C, 45 sec at 55°C and 45 sec at 72°C, followed by a final 10 min extension at 72°C. As expected, Mbnll expression was not fully eliminated in MbnllAE3AE3 mice; RT-PCR products were apparent with primers in constitutively spliced exons 10 and 12, or within exon 13.
[000140] Immunoblot analysis (total spleen protein): for immunological detection of Mbnll, tissues were placed in homogenization buffer (50 mM Tris-Cl [pH=8.0], 150 mM aCl, 2 mM phenylmethylsulfonyl fluoride, 6 μg/ml aprotinin, 1 μg/ml leupeptin) and disrupted using a Polytron homogenizer and brief sonication (3 X 5 sec using a microtip sonicator). Following addition of IGEPAL CA-630 (Sigma) to 1%, homogenates were incubated on ice for 15 min, centrifuged at 16,000 X g for 10 min. Proteins (30 μg per lane) were detected following SDS- PAGE and immunoblotting using anti -Mbnll mAb 3A4 (J. W. Miller et al, EMBO J. 19, 4439 (2000), A. Mankodi et al, Ann. Neurol, in press). Total spleen was analyzed (Fig. ID), because this tissue contains relatively high levels of both Mbnlland Cugbpl.
[000141] To confirm elimination of the Mbnll 41- to 42-kD proteins in
Mbnll AE3/AE3 mice, monoclonal antibody 3A4 was used, which recognizes Mbnll proteins containing exon 5[MSI]. The 41- to 42-kD isoforms in Mbnll+ + and Mbnll+/AE3 mice were missing in MbnllAE3/ E3 (Fig. ID). Previous studies suggested that elevated levels of another RNA-binding protein, CUGBP1, are responsible for DM-associated RNA splicing changes. However, MbnllAE3/AE3 mice did not show increased CUGBP1 expression (Fig. ID).
Example 2. Myotonia and cataracts
[000142] Electromyographv: electromyography was performed under general anesthesia (intraperitoneal ketamine, 100 mg/kg; xylazine, 10 mg/kg; and acepromazine, 3 mg/kg) using 30 gauge concentric needle electrodes to examine three hindlimb (tibialis anterior, gastrocnemius, vastus), two forelimb (flexor compartment of distal forelimb, triceps), and thoracolumbar paraspinal muscles. At least 10 needle insertions were performed in each muscle and myotonic discharges were graded on a 4 point scale: 0, no myotonia; 1, occasional myotonic discharge in <50% of needle insertions; 2, myotonic discharge with > 50% of insertions; and 3, myotonic discharge with nearly all insertions. The mean score across all MbnllΔE3/AE3 limb muscles was 2.9 in mice age 7 to 11 weeks (n=10). Myotonic discharges were not observed in any muscle in heterozygous Mbnll+/AE3 mice (n=9) or wild-type littermates (n=9).
[000143] Mbnll AB3/AE3 mice display overt myotonia beginning around 6 weeks of age. Delayed muscle relaxation was most noticeable after a period of rest and showed improvement during activity. A similar "warm up" phenomenon is characteristic of myotonia in human DM. Electromyographic recordings confirmed myotonic discharges in all Mbnll E3/ E3 mice tested (n = 10) (Fig. 2A).
[000144] ClC-1 splicing in DM mouse models: because myotonia in DM1 and DM2 muscle is associated with aberrant ClC-1 splicing, RT-PCR assays were used to investigate the effect of loss of Mbnll E3 on ClC-1 (encoded by Clcnl) expression (Fig. 2B). Total cellular RNA was extracted from either quadriceps or heart muscle of Mbnll +/+, Mbnll +/AE3 and Mbnll ΔE3/ΔE3 mice by homogenizing the tissues in TRI-REAGENT (Sigma, St. Louis, MO.) according to manufacturer's protocol. First strand cDNA was generated by reverse transcription (RT) using 5 μg of total RNA and Superscript II RNase H" RT (Invitrogen, Carlsbad, CA) following the manufacturer's protocol. For subsequent PCR reactions, 20% of the RT reaction was used as template. Each PCR reaction was spiked with 10 μCi of (αi2P)-dCTP (PerkinElmer Life Sciences, Boston, MA). PCR products were resolved on 5-8% non-denaturing polyacrylamide gels followed by autoradiography using Biomax MS film (Eastman Kodak, Rochester, NY).
[000145] For ClC-1 mRNA analysis, the forward primer used corresponded to exon 5 (5'GGAATACCTCACACTCAAGGCC-3') (SEQ ID NO: 17) and the reverse primer to exon 8 (5'CACGGAACACAAAGGCACTGAATGT-3') (SEQ ID NO: 18). PCR was performed for 27 cycles each consisting of 45 sec at 95°C, 45 sec at 55°C and 45 sec at 72°C, followed by a final lOmin extension at 72°C. Full- length ClC-1 cDNA clones were generated from muscle RNA by RT-PCR as previously described (A. Mankodi et al, Mol. Cell 10, 35 (2002)). Sequence analysis of 10 clones from Mbnll ΔE3/ΔE3 mice revealed 6 clones with inclusion of exon 7a and 2 clones with retention of intron 2. All splice junctions were normal in 10 clones derived from wild-type littermates. [000146] Remarkably, MbnllAE3/ E3 mice showed abnormal inclusion of Clcnl cryptic exons 7a and 8a in a pattern similar to that seen in HSALR mice. Also, some full-length ClC-1 cDNA clones from Mbnll E3/AE3 mice showed abnormal inclusion of intron 2, as has been observed in DM and HSALR muscle. Notably, these abnormal splice isoforms have premature termination codons and do not encode functional chloride channels. By contrast, splicing of the Scn4a sodium channel, the only other ion channel previously associated with myotonia was normal in MbnllAE3/AE3 muscle. These results suggested that changes in splice site selection result in the loss of functional ClC-1 from myofiber membranes.
[000147] ClC-1, Dys2, and α-sarcoglycan immunostaining: frozen sections of vastus (6 μm) were immunostained using polyclonal antibodies directed against the C-terminus of ClC-1 (Alpha Diagnostic, San Antonio) or monoclonal antibodies to dystrophin (Dys2) or a-sarcoglycan (NovoCastra, Newcastle upon Tyne) as described in A. Mankodi et al, Mol. Cell 10, 35 (2002).
[000148] Immunofluorescence analysis confirmed a major reduction of ClC-1 protein in Mbnll E3 AE3 muscle relative to the muscle of wild-type sibs (Fig. 2, C and D), whereas the membrane-associated proteins dystrophin (Fig. 2, E and F) and α- sarcoglycan (Fig. 3) were unaffected. Because abnormalities of ClC-1 splicing in MbnllAE3/AE3 muscle are more pronounced than in HSALR muscle, and considering that HSALR mice have a >80% reduction of chloride conductance, it is likely that myotonia in Mbnll E3/AE3 mice is due to improper ClC-1 pre-mRNA splicing.
[000149] Analysis of muscle histology: frozen sections (10 μm) of vastus and gastrocnemius muscle were prepared for routine histologic (hematoxylin and eosin, modified Gomori trichrome, periodic acid-Schiff) and histochemical (cytochrome oxidase, acid phosphatase, nicotinamide adenine dinucleotide-tetrazolium reductase, myosin ATPase, succinate dehydrogenase) stains (V. Dubowitz, Muscle Biopsy, A Practical Approach (Bailliere Tindall, London, ed. 2, 1996)).
[000150] Histological analysis of Mbnll AE3/ E3 mice up to 11 weeks of age did not show major degeneration of muscle fibers. Pathological features in Mbnll+ &E3/AE3 muscle included an increase in nuclei with an abnormal (central) position and splitting of myofibers (Fig. 2, G and H). Histologic abnormalities were not observed in Mbnll+/+ or Mbnll+/AE3 muscle.
[000151] Cataract development: besides muscle abnormalities, distinctive ocular cataracts that progress from subcapsular "dust-like" opacities to mature cataracts are a prominent DM-associated feature. Similar cataracts were observed in all MbnllAE3/ E3 eyes examined (n = 24; 3 to 8 months old) but not in wild-type siblings (Fig. 2, 1 to L).
[000152] For ocular lens evaluation, mice were sedated using intra-peritoneal injection of 100 mg/kg ketamine (Ketaset, Fort Dodge, IA) and 10 mg/kg xylazine (Xylaject, Phoenix, St Joseph, MO) and anterior chambers and lenses were examined using a slit lamp (Haag Streit, Mason, OH). In vivo images were obtained using a Nikon 990 digital camera attached to the slit-lamp. Immediately after euthanasia, globes were enucleated, fixed in paraformaldehyde and embedded in paraffin blocks before being processed overnight in a Shandon Excelsior tissue processor (Thermo Electron, Waltham, MA). Sections (4 μm) were cut using an HM-315 microtome (Richard-Allan, Kalamazoo, MI), dried and H&E stained. Sections were photographed using a Canon EOS D60 digital camera attached to an Olympus Vanox microscope.
Example 3. Pre-mRNA splicing
[000153] Abnormal regulation of alternative splicing - Tnnt2: abnormal regulation of alternative splicing has been observed in DM1 muscle for cardiac troponin T (TNNT2), insulin receptor (LNSR), and ClC-1. Tnnt2 was analyzed using exon 2 forward (5'GCCGAGGAGGTGGTGGAGGAGTA-3') (SEQ ID NO:
19) exon 6 reverse (5'GTCTCAGCCTCACCCTCAGGCTCA-3') (SEQ ID NO:
20) and 27 PCR cycles (45 sec at 96°C, 45 sec at 58°C and 45 sec at 72°C, followed by a final 10-min extension at 72°C). Analysis of INSR is uninformative because human patterns of INSR alternative splicing are not conserved in mice. However, Mbnll AE3/ E3 adult heart shows abnormal retention of the Tnnt2 "fetal" exon 5 (Fig. 4 A), as was observed for DM1.
[000154] Abnormal regulation of alternative splicing - Tnnt3: to determine whether alternative splicing of other genes is disrupted in MbnllAE3/ E3, fast skeletal muscle troponin T (Tnnt3) was assessed. For mouse Tnnt3, the forward primer overlaps exons 2 and 3 (5'TCTGACGAGGAAACTGAACAAG-3*) (SEQ ID NO:
21) while the reverse primer (5'TGTCAATGAGGGCTTGGAG-3') (SEQ ID NO:
22) corresponds to exon 11. For human TNNT3, exon 2 forward (5'- TTCACCATGTCTGACGAGGAAG-3') (SEQ ID NO: 23) and exon 10 reverse (5'CTTCTGGGATCTTAGGAGCAGTG-3') (SEQ ID NO: 24) primers were used. For mouse Tnnt3 and human TNNT3, 25 PCR cycles were performed each consisting of 45 sec at 95°C, 45 sec at 50°C and 30 sec at 72°C, followed by a final 10-min extension at 72°C. The same amplification protocol was used to amplify the mouse Tnnt3 carboxyl terminal region using an exon 15 forward primer (5 - CCTTGTACCAACTGGAGACTGAC-3') (SEQ ID NO: 25) and an exon 18 reverse primer (5'- TGATGGTCTCTGCTGCAGTG -3') (SEQ ID NO: 26).
[000155] Primers in Tnnt3 exons 2 and 11 produced a single major RT-PCR product in adult Mbnll+/+ and Mbnll+/AE3 mice that was undetectable in MbnllAE3/AE3 mice (Fig. 4B). Instead, a cluster of larger cDNAs, all containing a "fetal" (F) exon, was prominent. In contrast, mutually exclusive splicing of Tnnt3 exons 16 and 17 was unaffected in MbnllAE3/ E3 mice; this finding shows that altered Mbnll expression has specific effects on splice site selection even within the same pre-mRNA (Fig. 4C). Similar alterations of TNNT3 splicing in adult DM1 muscle (Fig. 4D) were found.
[000156] Abnormal regulation of alternative splicing - Scn4a: missense mutations in the Scn4a muscle-specific sodium channel are also associated with myotonia. The Scn4a pre-mRNA has two rare AT/AC splice sites but is not known to undergo alternative splicing. To screen for abnormalities of Scn4a splicing that might contribute to myotonia, RT-PCR analysis of muscle RNA was carried out. Partial cDNAs covering the entire Scn4a coding region (GenBank accession# AJ278787) were generated by PCR using the following primers: set 1 exon 1 (GACCTGGAAGCTGGCAAGAAC) (SEQ ID NO: 27) to exon 6 (TCCCTTCGTCATTGATGTAGGC) (SEQ ID NO: 28); set 2 exon 6 (CCATGAATGACACCAACACCAC) (SEQ ID NO: 29) to exon 12 (CTGAGGGTGACGATGAAGCTG) (SEQ ID NO: 30); set 3 exon 12 (TCTTCACGGGCATCTTCACTG) (SEQ ID NO: 31) to exon 17 (CGCCGCTGTTCAATGTAGATG) (SEQ ID NO: 32); and set 4 exon 16 (TGCCTCTATGTGGACATCTCCC) (SEQ ID NO: 33) to exon 24 (CGACTCTTTCTTGACGTAGGCG) (SEQ ID NO: 34). RT-PCR products from primer sets 1, 2, 3, and 4 was analyzed on 1 % agarose gels before and after restriction digest with Apal, Ncol, BspEl and BsrGl -Hindlll, respectively. Results showed no difference in the length of Scn4a cDNA fragments in Mbnlϋh ', Mbnl /ΔE3, MbnilΔE3/ΔE3 or HSALR mice (data not shown).
[000157] Loss of specific Mbnll isoforms that associate with expanded (CUG)„ and (CCUG)„RNAs is sufficient to cause myotonia, cataracts, and RNA splicing defects that are similar to those seen in DM. Although muscleblind-like proteins may influence gene expression at multiple levels, these proteins may play a direct role in splice site selection. Recent co-transfection analysis in HEK293 cells using a Tnnt3 mini-gene indicated that the Mbnll 41 kDa protein regulates alternative splice site choice by binding to a discrete RNA element upstream of the fetal (F) exon. Thus, MBNL proteins bind to distinct RNA sequence elements and influence exon use during splicing.
[000158] Young Mbnll E3/AE3 mice do not develop the severe neonatal muscle weakness associated with congenital DM1, and it is not yet known whether cardiac conduction problems develop in this model. Thus, some aspects of the DM phenotype may not result from loss of MBNLl function alone. Additional muscleblind proteins (MBNL2 and MBNL3) are also recruited to nuclear RNA foci. It is contemplated that their sequestration may be required to fully replicate the multisystemic DM phenotype.
Example 4. AAV-MBNL1 injection and Clcnl splicing
[000159] HSALR mice were anesthetized using isoflurane, and the left tibialis anterior (TA) muscle was injected with 13.4 μL PBS containing lxlO11 rAAVlMyc- hMBNLl, or the right leg was injected with PBS ("uninjected"). Four weeks post- injection, the mice were anesthetized using 2.5% avertin, and the left and right TAs were collected for total RNA preparation and assayed for recovery of the normal Clcnl pre-mRNA splicing pattern (Fig. 5 A) [000160] Reverse transcription was carried out using 5 μg of total RNA and 300 ng of random hexamers in a final volume of 20 μl. After, RNase H treatment for 15 minutes at 37°C, 4 μl of cDNA was used for PCR. The final volume of the PCR reaction was 50 μl, which contained 30 pmoles of forward primer (5'- TGAAGGAATACCTCACACTCAAGGCC-3') (SEQ ID NO: 40) in exon 5 of Clcnl and 30 pmoles of reverse primer (5'-
CACGGAACACAAAGGCACTGAATGT-3') (SEQ ID NO. 41) in exon 8 of Clcnl. In addition, the reaction was spiked with 10 μCi of dCTP-[oc32P]. 27 cycles were carried out at annealing and extension temperatures of 55°C and 72°C, respectively. Thirty percent of the total PCR products were resolved on a 5% acrylamide gel followed by exposure of the gel to an autoradiography film.
[000161] Mice number 188 and 189 were injected on the same day and processed together. Mouse number 190 and 191 were littermates that were neither injected with virus nor with PBS (included as uninjected controls). The results show that the levels of the abnormal splicing products were decreased, while the level of the normal splicing product was increased, following rAAVlMyc-hMBNLl injection.
[000162] The mice were also tested for myotonia by electromyography (EMG). Four weeks post-injection, EMG was performed on the injected and uninjected (the latter corresponding, for this example, to those mice not injected with virus, but, rather, with PBS alone) TA of six HSALR mice. The Y-axis shows the observed severity of myotonia following insertion of the electrode. Five out of six mice showed virtual elimination of myotonia in the injected TA muscles (injected with virus), while, in the uninjected TA of the same animal, robust myotonia (grade level=3) was observed. The results show that injection of the HSAlR mice with rAAVlMyc-hMBNLl (41 kDa isoform expressed) into the tibialis anterior results in reduced myotonia in as little as four weeks' time.
Example 5. Effect of MBNL proteins on alternative splicing
[000142] To determine whether MBNL proteins can alter the splicing patterns of pre-mRNAs known to be abnormally regulated in DM1 striated muscle, GFP fusion proteins of all three MBNL proteins were transiently expressed with human and chicken cTNT minigenes in primary chicken skeletal muscle cultures. GFP fusions with MBNLl, 2 and 3 were provided by Dr JD Brook (Fardaei M, Rogers MT, Thorpe HM, Larkin K, Hamshere MG, Harper PS, Brook JD (2002), Hum Mol Genet 11: 805-814). The cTNT, IR and clathrin light chain B minigenes were previously described (Kosaki A, Nelson J, Webster NJ (1998), JBiol Chem 273: 10331-10337; Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737- 741 ; Stamm S, Casper D, Hanson V, Helfrnan DM (1999), Brain Res Mol Brain Res 64: 108-118; Ladd AN, Charlet-B N, Cooper TA (2001), Mol Cell Biol 21: 1285- 1296). The MBNL mutant human cTNT minigene was generated by inverse PCR. [000143] Transient transfection and RT-PCR analysis: HEK293 cells were plated at 500 000 cells per well in a six- well plate in DMEM supplemented with 10%ι FBS and Gibco penicillin-streptomycin. At 24 h after plating, the cells were transfected with 1 μg of minigene and 2 μg of protein expression plasmid using Fugeneό (Roche, Indianapolis, IN), according to the manufacturer's directions. Protein and RNA were harvested 36-48 h after transfection. [000144] Human and chicken cTNT and human IR minigenes were expressed with or without each of the three GFP-MBNL fusion proteins or with GFP alone. Duplicate transfections were used for extraction of RNA and protein. Inclusion of cTNT exon 5 or IR exon 11 was assayed by RT-PCR.
[000145] Chicken primary muscle cultures were prepared, maintained and transfected as previously described, using 0.5 μg minigene reporter and 1 μg expression plasmid (Xu R, Teng J, Cooper TA (1993), Mol Cell Biol 13: 3660- 3674). COSM6 cells were plated at 150 000 cells per well in a six-well plate in DMEM supplemented with 10% FBS, Gibco penicillin-streptomycin and L- glutamine. At 24 h after plating, the cells were transfected with 500 ng of minigene and 1 μg of protein expression plasmid using Fugeneό (Roche, Indianapolis, IN) according to the manufacturer's directions. Protein and RNA were harvested 36-48 h after transfection. RNA isolation and RT-PCR analysis for the cTNT, IR, and clathrin light-chain B minigenes were performed as described previously (Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737-741; Stamm S, Casper D, Hanson V, Helfrnan DM (1999), Brain Res Mol Brain Res 64: 108-118; Savkur RS, Philips AV, Cooper TA (2001), Nat Genet 29: 40-47). [000146] Western blot analysis to investigate alternative splicing related to
MBNL: cells were harvested in protein loading buffer (62.5 mM Tris-HCl (pH 6.8), 2% SDS, 10% glycerol and 5% 2-β-mercaptoethanol) and the protein concentration was quantitated with the Non-Interfering Protein Assay (Genotech, St Louis, MO). Total protein lysates from HEK293 (20 μg) and primary chicken skeletal (30 μg) cultures were loaded on a 12.5% acrylamide gel and transferred to Immobilon-P membranes (Millipore, Bedford, MA). GFP was detected using JL-8 monoclonal antibody (BD Biosciences, Palo Alto, CA) at a dilution of 1:2000. The secondary antibody was a goat anti-mouse HRP conjugate (Jackson Immunoresearch, West Grove, PA) at a dilution of 1 :5000.
[000147] To detect endogenous MBNLl, HeLa (50 μg) protein lysates were loaded on a 12.5% acrylamide gel. Blots were probed with the monoclonal 3A4 (16 mg/ml) at a dilution of 1 :500. The secondary antibody was a sheep anti-mouse HRP conjugate (Amersham Biosciences, Piscataway, NJ) at a dilution of 1 :5000. For GAPDH in HeLa cells, 15 μg of total protein lysates was run on a 12.5% acrylamide gel, transferred to membranes and detected using the 6G5 monoclonal (Biogenesis, Kingston, NH) at a dilution of 1:100 000. The secondary antibody was a goat anti- mouse HRP conjugate (Jackson Immunoresearch, West Grove, PA) at a dilution of 1:5000.
[000148] GFP-MBNL1, 2 and 3 strongly repressed inclusion of both human and chicken cTNT exon 5 in primary chicken skeletal muscle cultures, while expression of GFP to levels comparable to, or greater than, GFP-MBNL fusion proteins had no effect on splicing (Figure 6A and 6B). Of note, GFP-MBNL1 was found to have a novel MBNLl isoform lacking exons 7, 9 and 10 and containing a frameshift in exon 12. In addition, there were no differences in the splicing activity of GFP fusion proteins compared to Xpress epitope-tagged MBNL proteins (data not shown). Therefore, MBNL proteins are directly antagonistic to endogenous CELF activity, which activates cTNT exon inclusion in muscle (Charlet-B N, Logan P, Singh G, Cooper TA (2002a), Mol Cell 9: 649-658).
[000149] Another pre-mRNA target that is misregulated in DM striated muscle is the IR (Savkur RS, Philips AV, Cooper TA (2001), Nat Genet 29: 40-41; Savkur RS, Philips AV, Cooper TA, Dalton JC, Moseley ML, Ranum LP, Day JW (2004), Am JHum Genet 74: 1309-1313). To test whether the MBNL family can also regulate human IR, the three MBNL family members were co-expressed with a human IR minigene. In contrast to the inhibitory effect of MBNL on cTNT splicing, coexpression of MBNL family members with an IR minigene strongly induces exon inclusion, whereas GFP alone had no effect (Figure 6C). [000150] To determine whether the MBNL family has a general effect on alternative splicing, all three MBNL proteins were co-expressed with a clathrin light- chain minigene containing the neuron-specific exon EN. The EN alternative exon in this minigene strongly responds to over-expression of the SR family of proteins and htra2-βl, but not CELF proteins (Stamm S, Casper D, Hanson V, Helfrnan DM (1999), Brain Res Mol Brain Res 64: 108-118; Singh G, Charlet BN, Han J, Cooper TA (2004), Nucleic Acids Res 32: 1232-1241; data not shown). Over-expression of GFP-MBNL 1, 2 and 3 with the clathrin light-chain minigene had no effect on alternative splicing of exon EN (Figure 6D). MBNL expression also did not affect splicing of an artificial alternative exon flanked by splice sites from human β-globin intron 1 (data not shown). These results demonstrate that MBNL proteins do not have a general effect on alternative splicing, but, rather regulate specific pre-mRNA targets. In summary, MBNLl, 2 and 3 regulate splicing of cTNT and IR alternative exons.
Example 6. siRNA-mediated depletion of MBNLl and splicing of cTNT and IR
[000151] To determine whether depletion of endogenous MBNLl protein could also affect the splicing patterns of known DM pre-mRNA targets in human cells, siRNA constructs were designed to target MBNLl, but not MBNL2 and MBNL3. To confirm the specificity of the effects, two siRNA constructs were designed to target different regions of the MBNLl mRNA. [000152] SiRNA construct design and transfection: two custom siRNA duplexes were designed for RNAi against human MBNLl using the Dharmacon siDESIGN program (www.dharmacon.com (http ://w ww . dharmacon . com/)) and were synthesized by Dharmacon. The sequences are as follows: THH31 mRNA target (AA-N19 format 5' -^ 3') AACAGACAGACUUGAGGUAUG (SEQ ID NO: 35), THH2 mRNA target (AA-N19 format 5' ^ 3') AACACGGAAUGUAAAUUUGCA (SEQ ID NO: 36), GFP siRNA duplex (Dharmacon, Lafayette, CO cat. no. D- 001300-01-20). 300 000 HeLa cells were plated in 2 ml of antibiotic-free growth media (DMEM supplemented with 10% FBS) per well in a six-well plate. HeLa cells were chosen because they express MBNLl (Miller JW, Urbinati CR, Teng- Umnuay P, Stenberg MG, Byrne BJ, Thornton CA, Swanson MS (2000), EMBO J 19: 4439-4448) and are amenable to siRNA-mediated depletion (Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001), Nature 411: 494- 498).
[000153] At 12 h after plating, the media was exchanged with 800 μl serum- free media (DMEM) per well. siRNA duplex (2.66 μg) was transfected using Oligofectamine (Invitrogen, Carlsbad, CA). 1 ml of 3 x serum-containing media (DMEM supplemented with 30% FBS) was added after 4 h. After 12 h, the 3 x serum-containing media was replaced with antibiotic-free growth media and the cells were transfected with 1 μg of minigene and 2.66 μg of siRNA duplex using Lipofectamine 2000 (Invitrogen, Carlsbad, CA). The media was exchanged with antibiotic-free growth media 6 h later. RNA and protein were harvested 48 h after transfection of the minigene.
[000154] Independent transient transfection of each siRNA construct resulted in a knockdown of endogenous MBNLl protein to less than 10-20%, based on comparisons to serial dilutions of the untransfected or mock-transfected lysates (Figure 7A; data not shown).
[000155] Immunofluorescence analysis of MBNLl depletion: HeLa cells were grown on coverslips in six-well plates and transfected with 2.66 μg siRNA using Oligofectamine. The coverslips were washed with cold PBS (pH 7.4) and fixed in 4% paraformaldehyde/PBS for 15 min. After three washes with PBS, the cells were dehydrated with 70% ethanol overnight at 4°C. The coverslips were then rehydrated with PBS for 10 min and incubated with 3% BSA/PBS for 15 min at room temperature. The cells were washed once with PBS and incubated with the primary antibody 3A4 (10 mg/ml) ata dilution of 1:1000 in 3% BSA/PBS at room temperature for 1 h. The cells were then washed three times with PBS and incubated with the secondary antibody, Alexa Fluor-labeled goat anti-mouse IgG (2 mg/ml, Molecular Probes, Eugene, OR), at a dilution of 1:100 in 3% BSA/PBS at room temperature for 1 h. The cells were then washed with PBS three times, counterstained with DAPI (Molecular Probes, Eugene, OR) and mounted for visualization by fluorescence microscopy.
[000156] Analysis of MBNL 1 depletion by immunofluorescence demonstrated predominantly nuclear expression that was greatly reduced in the majority of cells by each siRNA construct (Figure 7B). In addition, the siRNA constructs silenced effectively the expression of GFP-MBNL 1, but not GFP-MBNL2, GFP-MBNL3 or GFP from transiently transfected plasmids, and neither MBNLl siRNA affected the levels of endogenous MBNL2 protein (data not shown). These results indicate that the siRNAs preferentially silence MBNLl.
[000157] MBNLl depletion and cTNT and IR minigene splicing: to determine whether depletion of endogenous MBNLl affected alternative splicing of cTNT, IR and clathrin light chain, the minigenes were transfected with each siRNA construct. Depletion of MBNLl promoted exon inclusion in cTNT, exon skipping in IRand only minimal splicing changes in the clathrin light-chain minigene (Figure 7C). siRNA-mediated depletion of MBNLl with two independent constructs reproduces the DM splicing patterns for cTNT and IR minigenes. GFP siRNA had no effect on splicing of any of the tested minigenes. MBNLl siRNA had minimal effects on splicing of a rat clathrin light-chain minigene.
[000158] These splicing effects were not caused by general activation of the mammalian RNAi machinery because siRNA targeting GFP or luciferase and nonspecific pools of siRNA had minimal effects on splicing of the three minigenes (Figure 7C; plus data not shown). Furthermore, the alteration in cTNT splicing caused by MBNLl depletion in HeLa cells can be reversed by expression of GFP- MBNL2 or GFP-MBNL3, but not GFP (data not shown), demonstrating that adding back MBNL isoforms not targeted by MBNLl siRNA rescues the splicing effects of MBNLl deficiency.
[000159] The data indicate that endogenous MBNLl regulates the splicing of human cTNT and IR minigenes. Interestingly, siRNA-mediated depletion of MBNLl reproduces the splicing pattern observed in DM1 for cTNT (exon inclusion) and IR (exon skipping), and is opposite to the pattern observed when MBNLl is over-expressed. The over-expression and depletion data indicate that endogenous MBNLl regulates the alternative splicing of cTNT and IR minigenes, and suggest that MBNLl regulates these pre-mRNAs via specific cw-regulatory elements. The effects of MBNL on the cTNT and IR alternative exons are the opposite of the splicing patterns induced by CELF proteins, implying an antagonistic relationship between these protein families.
Example 7. Binding of MBNLl to introns adjacent to the human and chicken cTNT alternative exons
[000160] UV cross-linking analysis of MBNLl binding to human cTNT: to determine whether the splicing effects of MBNLl on pre-mRNA targets were direct or indirect, a UV-cross-linking assay was performed using purified recombinant GST-MBNLl and uniformly labeled in v/trø-transcribed segments from the human cTNT gene. Uniformly 32P-labeled RNAs were transcribed in vitro using [α-32P]GTP
and [α-32P]UTP (Perkin-Elmer, Wellesley, MA) from PCR products or cloned regions of the human or chicken introns 4 and 5, as represented in Figures 8 and 9. [000161] UV-cross-linking assays were performed using radiolabeled transcripts standardized for picomoles of G and U. UV-cross-linking assays included 1 μg of purified GST-MBNLl in the presence of 1 μg BSA, 1 μgtRNA, 0.3 μg heparin, 0.3 mM magnesium acetate, in 2 mM magnesium acetate, 2 mM ATP, 16 mM HEPES (pH 7.9), 65 mM potassium glutamate, 0.16 mM EDTA, 0.4 mM DTT and 16% glycerol. Bindingwas for 10 min at 30°C. Recombinant GST-MBNLl protein was produced as described (Miller JW, Urbinati CR, Teng-Umnuay P, Stenberg MG, Byrne BJ, Thornton CA, Swanson MS (2000), EMBO J 19: 4439- 4448). Competitions were performed as described previously (Singh G, Charlet BN, Han J, Cooper TA (2004), Nucleic Acids Res 32: 1232-1241). The indicated amounts of non-labeled competitor RNAs were added to the binding reaction 10 min prior to addition of labeled substrate RNA.
[000162] The human cTNT minigene contains a 732 nucleotide (nt) cTNT genomic fragment that is necessary and sufficient to respond to MBNLl over- expression and depletion (Figures 6 and 7C). To identify MBNLl-binding sites within this cTNT pre-mRNA region, uniformly 32P-labeled, in vttro-transcribed RNAs covering the entire region were used for UV-cross-linking binding assays. As shown in Figure 8 A, the binding of GST-MBNLl on human cTNT was mapped to a 41 nt region within the 3' splice site of exon 5 (compare RNAs C, D, E and F) located between a near-consensus branch point sequence and the 3' cleavage site of the upstream intron.
[000163] Scanning mutagenesis identification of binding sites: scanning mutagenesis identified two MBNLl -binding sites located 18 and 36 nt upstream from exon 5 (Figure 8A). The absence of binding to long intronic segments (RNAs F and C) and RNAs containing nucleotide substitutions (RNAs H, J and M; see below) demonstrate binding specificity. This analysis indicates that, for cTNT, the MBNL1- binding site is distinct from the CUG-BPl -binding site, which is located downstream from the alternative exon (Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737-741).
[000164] UV cross-linking analysis of binding of MBNLl with nucleotide substitutions: nucleotide substitutions that disrupt both MBNLl-binding sites were introduced into the human cTNT minigene to test whether MBNLl binding was required to affect responsiveness to MBNLl expression in vivo. As the MBNL- binding site is located within the 3' splice site of intron 4, only four nucleotide substitutions were introduced to reduce the effects of MBNL-binding site mutations on basal splicing efficiency (RNA M, Figure 8A). These substitutions prevented binding of recombinant MBNLl to an RNA that is otherwise identical to RNA G containing the wild-type sequence (Figure 8B). In addition, non-labeled RNA M was much less efficient than RNA G in competing binding of MBNLl to labeled RNA G (Figure 8B).
[000165] When introduced into the human cTNT minigene, the MBNL 1 - binding site mutation significantly reduced (MBNLl and MBNL3) or eliminated (MBNL2) responsiveness to MBNL proteins (Figures 8C and 8D), demonstrating that loss of MBNLl binding in vitro directly correlates with decreased responsiveness to MBNLl in vivo. These results demonstrate that regulation by MBNL protein is mediated via binding the pre-mRNA, and suggest that all three MBNL proteins regulate human cTNT splicing by binding to the same site. In contrast, the MBNLl -binding site mutations had little effect on responsiveness to CUG-BPl (Figures 8C and 8D). GFP alone had minimal effects on splicing. Thus, MBNL proteins regulate splicing by binding to the human cTNT pre-mRNA, and regulation by CUG-BPl does not require the MBNLl -binding site. [000166] UV cross-linking analysis of MBNLl binding to chicken cTNT: UV- cross-linking analysis was performed to identify MBNLl-binding site(s) associated with the chicken cTNT alternative exon 5. The genomic segment of chicken cTNT that responds to MBNL expression contains 99 and 142 nt of upstream and downstream introns flanking the alternative exon, respectively. Within the intronic segments are four muscle-specific splicing enhancers (MSEs, Figure 9A) previously shown to be required for enhanced exon inclusion in embryonic striated muscle (Ryan KJ, Cooper TA (1996), Mol Cell Biol 16: 4014-4023; Cooper TA (1998), Mol Cell Biol 18: 4519^4525) and required for regulation by all the six CELF family members (Ladd AN, Charlet-B N, Cooper TA (2001), Mol Cell Biol 21: 1285-1296; Ladd AN, Nguyen NH, Malhotra K, Cooper TA (2004), JBiol Chem 279: 17756-17764). RNAs containing MSEs 1-4 or individual MSEs were transcribed in vitro as uniformly 32P-labeledRNAs and used for UV cross-linking. GST-MBNLl bound strongly to MSE4 and slightly to MSE1 (Figure 9A). [000167] In competition studies, non-labeled MSE1 RNA poorly competed in the binding of GST-MBNLl to RNA containing MSE 1-4, while MSE4 effectively competed in binding (Figure 9B), consistent with the UV-cross-linking results. The absence of competition by MSE2 or MSE3 demonstrates the sequence specificity of MBNLl binding (Figure 9B). To define the MBNLl-binding site(s) within MSE4, scanning mutagenesis was performed. Two regions required for MBNLl binding were identified at 94 and 120 nt downstream from the exon (Figure 9C). Alignment of the four MBNLl-binding sites in chicken and human cTNT revealed a common motif of YGCU(U/G)Y (Figure 9D). Taken together, these data indicate that MBNLl directly binds to introns adjacent to the human and chicken cTNT alternative exons.
[000168] Of note, proteins from all three MBNL genes contain two pairs of
Cys3His zinc-fmger-related motifs with identical spacing between cysteine and histidine residues in fingers 1 and 3 (CX7CX6CX3H) and fingers 2 and 4 (CX7CX4CX3H) (Miller JW, Urbinati CR, Teng-Umnuay P, Stenberg MG, Byrne BJ, Thornton CA, Swanson MS (2000), EMBO J 9: 4439-^1448; Fardaei M, Rogers MT, Thorpe HM, Larkin K, Hamshere MG, Harper PS, Brook JD (2002), Hum Mol Genet 11: 805-814; Squillace RM, Chenault DM, Wang EH (2002), Dev Biol 250: 218-230). The Cys3His-type zinc-finger is an evolutionarily conserved motif found in a number of proteins that perform diverse RNA-processing functions, and mutation of this motif results in a loss of RNA binding and disrupts protein function (Bai C, Tolias PP (1996), Mol Cell Biol 16: 6661-6667; Bai C, Tolias PP (1998), Nucleic Acids Res 26: 1597-1604; Lai WS, Carballo E, Strum JR, Kennington EA, Phillips RS, Blackshear PJ (1999), Mol Cell Biol 19: 4311-4323; Stoecklin G, Colombi M, Raineri I, Leuenberger S, Mallaun M, Schmidlin M, Gross B, Lu M, Kitamura T, Moroni C (2002), EMBO J 21: 4709-4718). [000169] MBNLl also binds to specific sequences within single-stranded
RNA, consistent with the results from other Cys3His zinc-finger proteins (Cheng Y, Kato N, Wang W, Li J, Chen X (2003), Dev Cell 4: 53-66; Michel SL, Guerrerio AL, Berg JM (2003), Biochemistry 42: 4626-4630). The above-delineated results demonstrate that MBNLl binds to cis-elements in chicken cTNT intron 5 required for muscle-specific splicing.
Example 8. CELF protein cis-regulatory elements in cTNT and IR and regulation by MBNLl
[000170] The CUG-BPl -binding site located downstream from exon 5 in the human cTNT minigene is required for regulation by all six CELF proteins (Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737-741); T Ho, unpublished data), and is distinct from the MBNL-binding site mapped in Figure 8. The results shown previously demonstrate that CUG-BPl regulates minigenes in which MBNLl-binding site mutations have greatly reduced or eliminated MBNL responsiveness (Figure 8D).
[000171] Analysis of the importance of the CUG-BPl binding site to minigene regulation by MBNLl: to determine whether MBNLl can regulate minigenes lacking the CUG-BPl -binding site, GFP-MBNL1 or MBNLl siRNA was cotransfected with a human cTNT minigene containing mutated CUG-BPl -binding sites. Plasmids expressing DMPK exons 11-15 containing 960 interrupted CUG repeats in exon 15 were cloned using techniques as previously described (Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737-741). The over- expression and depletion results demonstrate that cTNT minigenes containing the mutant and wild-type CUG-BPl -binding sites are equally responsive to MBNLl (Figures 10A and 10B). GFP-MBNL2and 3 also showed similar regulation of wild- type and mutant human cTNT minigenes (data not shown). These results indicate that the regulation of human cTNT by MBNLl is independent of CELF regulation. [000172] Similarly, for the IR minigene, regulation by CUG-BPl requires a
CUG-BPl -binding site in a 110 nt region located upstream of IR exon 11 (Savkur RS, Philips AV, Cooper TA (2001), Nat Genet 29: 40^17). A mutant IR minigene lacking the CUG-BPl -binding site was co-expressed with GFP-MBΝL1, 2 and 3 in HEK293 cells (Figure 11 A) or MBΝL1 siRΝA constructs in HeLa cells (Figure 1 IB) to determine whether regulation byMBΝL proteins requires the CUG-BPl - binding site. The mutant IR minigenes displayed regulation by MBΝL proteins, which was comparable to the wild-type IR minigenes (compare Figures 11 A and 6C and 1 IB and 7C). These results indicate that regulation of human cTΝT and IR by MBΝL proteins does not require the CUG-BPl -binding site. In other words, the deletion of the human IR CUG-BPl -binding site does not affect regulation by MBΝL1. All three of the MBΝL proteins promoted exon 11 inclusion of the mutant human IR minigene lacking the CUG-BPl -binding site in HEK293 cells (FIG. 11 A). Furthermore, RΝAi depletion of MBΝL 1 in HeLa cells using the indicated siRΝA constructs promoted exon 11 skipping in the human IR minigene lacking the CUG- BPl-binding site (FIG. 11B).
[000173] Mutant cTΝT and IR minigenes lacking the CUG-BP 1 -binding site respond as strongly as non-mutated minigenes to MBΝL1 depletion by RΝAi (Figures 10B and 11B). However, neither of these minigenes respond to the trans- dominant effects of co-expressed CUG repeat RΝA as do the non-mutated minigenes (Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737-741; Savkur RS, Philips AV, Cooper TA (2001), Nat Genet 29: 40-47; 960CTG, Figure 9). The RΝAi results demonstrate that the mutated cTΝT and IR minigenes are 'competent' to respond to MBΝL1 depletion, and, yet, they do not respond to co- expression of CUG repeat RΝA. Therefore, while it has been demonstrated that MBNL proteins are alternative splicing regulators of cTNT and IR alternative exons, these results indicate that MBNL depletion by CUG repeat RNA is not sufficient to account for the trarø-dominant effect of CUG repeat RNA on splicing. [000174] As shown previously, and in Figure 10B, here, the cTNT and IR minigenes made insensitive to CELF regulation by mutations in the CUG-BP1- binding site no longer respond to expanded CUG repeat RNA, suggesting that the trαrø-dominant effect is mediated at least in part via an intact CUG-BPl -binding site (Figure 10B; Philips AV, Timchenko LT, Cooper TA (1998), Science 280: 737-741; Savkur RS, Philips AV, Cooper TA (2001), Nat Genet 29: 40^17). The present results show that the mutated cTNT and IR minigenes are competent to respond to MBNL depletion by RNAi as strongly as the non-mutated minigenes, yet they do not respond to CUG repeat RNA. If expanded CUG repeats affected cTNT and IR splicing simply by sequestering and depleting MBNL, then the co-expression of CUG repeats should have affected splicing of the mutated as well as non-mutated minigenes. It is, thus, indicated that the repeats have a trans-dominant effect on splicing by a mechanism more complex than MBNL depletion alone.
Example 9. Fluorescence in situ hybridization (FISH) and i munofluorescence (IF) analysis of DM1 brain
[000175] Origin and preparation of tissue samples: to study the expression and distribution of expanded poly(CUG)RNA in relation to putative RNA binding proteins in the brain, autopsy materials were obtained from ten DM1 patients (mean age 56 years, range 44-78 years, 7 men and 3 women) and 13 controls (6 with no neurologic disease, 2 with Alzheimer disease, 4 with Huntington disease, and one with refractory epilepsy). The mean post-mortem interval for DM1 patients was 6 hours (range 2 to 14 hours). At the time of autopsy, coronal sections of brain were prepared and placed on aluminum slabs cooled on dry ice. In addition, selected regions were dissected and flash frozen in liquid nitrogen. All samples were stored at -70°C.
[000176] Nine of the DM1 patients had signs of classical DM1 before age 30 and died of complications related to the disease (respiratory failure in 7, sudden cardiac death in 2). The other DM1 patient had minimal symptoms of DM1 and died at age 78 yrs of unrelated disease. Genetic confirmation was performed as previously described by PCR or Southern blot on DNA isolated from postmortem brain tissue (Thornton, CA, Johnson, K, an Moxley, R.T. (1994), Ann. Neurol, 35, 104-107). Southern blots of cortical DNA samples showed a broad range of expanded alleles ranging in size from 5 to 12 kb (not shown). The individual with the minimal DM phenotype had a CTG repeat expansion length of 77 repeats in DNA isolated from peripheral blood, brain, and other tissues.
[000177] Fluorescence in situ hybridization (FISH) analysis of brain sections:
FISH was performed as described (Mankodi, A, Urbinati, CR, Yuan, Q.P, Moxley, R.T, Sansone, V, Krym, M, Henderson, D, Schalling, M, Swanson, M.S, and Thornton, CA. (2001), Hum. Mol. Genet, 10, 2165-2170) with slight modifications. Frozen sections (12 μm) were fixed in 3% paraformaldehyde PBS for 30 min, permeabilized in 2% acetone PBS (pre-chilled at -20°C) for 5 min, and then prehybridized in 30% formamide and 2 X SSC at room temperature for 10 min. Next, sections were hybridized with probe (1 ng/μl) for 2 h at 37°C in buffer (30% formamide, 2 X SSC, 0.02 % BSA, 66 μg/ml yeast rRNA, 2 mM vanadyl complex) and then washed for 30 min in 30% formamide/2XSSC at 42°C followed by IX SSC for 30 min at room temperature. Probes were HPLCpurified 2-O-methyl RNA 20-mers (JJDT, Coralville, IA) composed of CAG-, CUG- or GUC- repeats, and labeled with Texas Red at the 5' end. Images were obtained on an Olympus AX70 epifluorescence microscope at 1, 000-fold magnification. To compare the relative fluorescence intensities for RNA foci, sections were processed on the same slide, imaged under the same illumination and exposure settings, and then analyzed using MCED V6.0 software (Imaging Research Inc, St. Catherines, Ontario). [000178] Fluorescence in situ hybridization (FISH) of brain sections with CAG repeat probes revealed nuclear RNA foci in every individual with DM1 (n=10, Fig. 12A) but not in controls with (n=7) or without (n=6) neurologic disease. RNA foci were not observed with CUG (sense) or GUC repeat probes. The hybridization of CAG probes to nuclear foci in DM1 did not require denaturation of genomic DNA. These results indicate that CAG repeat probes recognize CUG expansion RNA rather than a cross-reactive RNA or DNA. [000179] Nuclear RNA foci ranged in diameter from 0.2 to 2 μm. Resolution of these small structures required direct fluorescence detection methods. However, the autofluorescent material in brain (lipofuscin) was a complicating factor. The RNA foci were clearly distinguished from lipofuscin when the epifluorescence from three color channels was merged in a single image. As shown in Fig. 12A, the nuclear foci appeared in a single channel determined by the probe label (Texas red). Lipofuscin, which excites and emits at a broad spectrum of wavelengths, generated signal in all channels and appeared as a different color (typically yellow-brown) in the merged image. These observations formed the basis for distinguishing RNA foci in subsequent experiments. RNA foci were red, sharply demarcated structures in the nucleus. Lipofuscin was yellow-brown perinuclear material with indistinct margins. [000180] Immunofluorescence (IF) combined with FISH: to determine which cells express mutant DMPK and form RNA inclusions, different brain regions were surveyed using FISH in combination with antibodies that mark specific cell types. In cerebral cortex, the nuclear foci were distributed throughout all cortical layers and were confined to neurons, as determined by immunofluorescence (IF) for neuronal markers NeuN (Fig. 12B) or MAP2 (Fig. 12C).
Target Antigen Final Dilution Muscleblind mAb (3B10): 1:1500 (MBNLl) pAb (EXP 42): 1:1500 Muscleblind mAb (2D9): 1:10,000 (MBNL2) CUGBP1 mAb (3Bl): 1:500 CELF4 pAb (#440): 1:500 ETR3 pAb (#163): 1:1500 PKR pAb (pT451): 1:500 pAb (M515): 1:500 pAb (D20): 1:500 mAb (B10): 1:500 RNA helicase A pAb 1:500 ADAR1 mAb: 1:500 Target Antigen Final Dilution HRBP pAb (#1683): 1:500 NF90 (DRBP76) pAb (p90 AB4): 1:500 Staufen pAb 1:500 (AB 5819) Proteasome 19S SlOa pAb: 1:500 HS α pAb: 1:1000 HS γ pAb: 1:1000 20S β3 (HC10) mAb: 1:500 20S α pAb: 1:1000 Ubiquitin pAb: 1:1000 p80 coilin pAb: (R288): 1:500 C23 nucleolin mAb: 1:500 PML pAb: 1:500 PTB pAb: 1:500 PM-Scl 75 pAb: 1:500 hnRNP H C-terminal pAb: 1:100 N-terminal pAb: 1:500 hnRNP F pAb: 1:1000 hnRNP H pAb: 1:1000 hnRNP F pAb: 1:1000 hnRNPI/PTB pAb: 1:1000 KSRP pAb: 1:1000 4F4 (hnRNP C) mAb: 1:500 1D8 (hnRNP M) mAb: 1:500 CNPase mAb: 1:1000 MAP2 mAb: 1:500 NeuN mAb: 1:500 Spl (sc-59) pAb: 1:500 RARγ(sc-550) pAb: 1:500 Staufen (AB5819) pAb: 1:500 SUMO-1 mAb
[000181] Following the 1 X SSC post-hybridization wash of the FISH procedure, sections were incubated in primary antibodies (Table 1, above) overnight at 4°C, washed five times with PBS for 2 min, and then incubated in secondary antibody (Alexa 488- labeled goat anti-rabbit polyclonal or Alexa 488-labeled goat anti-mouse polyclonal, Molecular Probes) and 33 nM diamidino-2-phenylindole (DAPI) for 30 min at room temperature. The antibody sources were as follows: CELF4 and ETR3 (T. Cooper, TX), PKR and C23 nucleolin and PML (Biosource Intl, CA), RNA helicase A (C Lee, NJ), ADAR1 (D. Cho, PA), NF90 (G. Sen, OH), Staufen and NeuN (Chemicon, CA), proteasome (Affiniti, UK), Ubiquitin (DAKO, DK), p80 coilin (KL Chan, CA), PTB (E. Wagner, NC), PM-Scl 75 and hn RNP H and F (J. Wilusz, NJ and D. Black, CA), CNPase and MAP2 (Sigma, MO), Spl and RARγ (Santa Cruz Biotechnology, CA), and SUMO-1 (Zymed Laboratories, Inc, CA). Sections were washed five times in PBS prior to mounting. [000182] To estimate relative MBNLl concentration in nucleoplasm in DM1 nuclei vs. controls, sections of temporal cortex were processed on the same slide and imaged under the same exposure settings. Merged images for Texas red (to visualize RNA foci), Alexa 488 (for MBNLl) and DAPI (for nuclear DNA) were obtained. Regions of interest were manually defined as nuclear area excluding nucleolus, RNA foci, and overlapping lipofuscin. MBNLl fluorescence intensity (mean optical density in monochrome mode in arbitrary units) in the region of interest was detennined for 20 cortical neuronal nuclei per subject. Because of the difficulty of estimating background fluorescence from brain sections, the results are not corrected for background. This approach provides a conservative estimate of the fold- reduction for MBNLl in DM1 nucleoplasm.
[000183] Counts of 100 NeuN-positive cells from temporal and frontal cortex of 4 patients with classical DM1 (selected for best relative preservation of cortical architecture) showed RNA foci in >85% of cortical neurons in each case. More than one focus was visible in -30% of cortical neurons, and occasional neurons had up to 15 small foci. In contrast, the individual having a small CTG repeat expansion (77 repeats) and mild phenotype (cataracts, mild weakness, and cognitive impairment after age 60 years) had foci in only 39% of NeuN-positive neurons in temporal cortex.
Example 10. FISH and BF analysis of other neuronal populations in DM1
[000184] RNA foci were widely distributed in other neuronal populations, including the hippocampus (all sectors), dentate gyrus, thalamus, and also the substantia nigra and brain stem tegmentum (each of 4 patients examined) (Fig. 13). The main exception was in cerebellar cortex, where small foci were detected in some Purkinje cells but not in neurons of the molecular or granular cell layers (n=6 patients examined) (Fig. 12D).
[000185] RNA foci were also present in the subcortical white matter and corpus callosum in occasional cells expressing 2'3 '-cyclic nucleotide 3'- phosphodiesterase (CNPase), a marker for oligodendrocytes (Fig. 12E). However, these foci were smaller and less intense than those in cortical neurons. In sections processed on the same slide and imaged under the same exposure settings, quantitation of FISH signals indicated that the amount of CUG expansion RNA in frontal cortical neurons was 2.9-fold greater (area x intensity) than in Purkinje cells (p<10"10) and 18-fold greater than in oligodendrocytes (p<10"10) within the same individual (n=3 patients, 60 nuclei per patient).
Example 11. FISH and IF analysis of neuronal and muscle populations in DM1
[000186] Paired samples of frontal cortex and biceps muscle were available for three patients. When sections of skeletal muscle and cerebral cortex from same patient were processed on the same slide and imaged under the same exposure settings, the RNA inclusions were larger and more intense (3.1 -fold greater, area intensity) in frontal cortical neurons than in skeletal muscle from the same individual (p<10-10, Fig. 14).
Example 12. Localization of mutant RNA
[000187] To determine if mutant RNA resides in a previously identified nuclear domain, mutant RNA was tested for colocalization with proteins that mark different nuclear compartments. These and subsequent experiments localizing protein relative to expanded poly(CUG) RNA were performed on a subset of 4 DM1 and 3 non-disease control samples showing the best preservation of cortical architecture. In contrast to nuclear inclusions of polyglutamine proteins (Skinner, P.J, Koshy, B.T, Cummings. C.J, Klement, LA, Helin, K, Servadio, A, Zoghbi, H.Y., and Orr, H.T. (1997), Nature, 389, 971-974), RNA foci did not colocalize with PML bodies (Fig. 12F). [000188] Colocalization of mutant RNA was likewise not found with the nucleolus
(visualized by DNA staining or antibodies to C23 nucleolin), perinucleolar compartment (antibodies to polypyrimidine tract binding protein), or "speckles" (antibodies to hnRNP C) (data not shown). The possibility of colocalization with Cajal bodies cannot be eliminated, because p80 coilin antibodies did not consistently identify Cajal bodies in cortical neurons stained by the presently described methods.
Example 13. FISH and IF analysis of temporal and frontal cortical neurons
[000189] Recruitment of proteasome and exosome to nuclear RNA foci: the proteasome and exosome are multisubunit complexes responsible for protein and RNA degradation, respectively. To determine if these complexes are recruited to nuclear RNA foci, FISH analysis was combined with immunofluorescence using antibodies to components of the proteasome or exosome. Three components of the proteasome (20Sa, 1 lSy and 1 ISa subunits) were recruited to RNA foci in cortical neurons (Fig. 15 A; Fig. 16A). No evidence was found, however, for ubiquitination or sumoylation of the foci (not shown). In contrast, antibodies to the PM/Scl75 or PM/ScllOO components of the exosome did not colocalize with RNA foci (Fig. 15B). This observation indicates that the proteasome may be recruited by conformational changes in MBNLl, MBNL2, or other poly(CUG) binding proteins. In such a case, loss of muscleblind function in DM1 may result from the combined effects of sequestration and accelerated degradation.
[000190] Monoclonal antibody 3B 1 showed strong expression of CUGBPl in cortical neurons (Fig. 15C). The distribution of this protein in neuronal nucleus and cytoplasm appears similar in DM1 patients and controls, and FISH/IF analysis shows that CUGBPl is not recruited into RNA foci. Polyclonal antibodies to other members of the CUGBPl family, ETR3 and CELF4, also fail to colocalize with foci (not shown). None of six different dsRNA binding proteins in neuronal nuclei (staufen, NF90, ADAR1, PACT, PKR, RNA helicase A) colocalize with RNA foci (representative images for NF90 are shown in Fig. 15D and ADARl in Fig. 16B). [000191] The RNA binding proteins hnRNP Al , hnRNP I, hnRNP M, KSRP and
HuR did not colocalize with RNA foci (representative image for hnRNP M is shown in Fig 16D). In contrast, hriRNPs H and F colocalized with foci in cortical neurons to a limited extent (Fig. 15F, Fig. 16C), and these results were verified using two different polyclonal antibodies for each protein. The intensity of immunofluorescence for these proteins was greatest at the site of RNA foci; however, there did not appear to be significant depletion of hnRNP H or hnRNP F elsewhere in the neuronal nucleoplasm. [000192] The splicing of neuron-specific exon Nl of c-src, which is promoted by hnRNPs H and F (Min, H, Chan, R.C, and Black, D.L. (1995), Genes Dev., 9, 2659-2671; Chou, MN, Rooke, Ν, Turck, CW, and Black, D.L. (1999), Mol. Cell Biol, 19, 69-77) was not reduced in DM1 cerebral cortex. Indeed, inclusion of the Νl exon showed a slight (1.3-fold, p<0.02) increase in DM1 with respect to controls, opposite to the predicted effect of hnRΝP F or H depletion (not shown). This fits with expectations that the number and density of binding sites on a single transcript, hence the capacity for protein sequestration, is much greater for proteins that bind to expanded poly(CUG) than for proteins that bind DMPK mRΝA outside of the repeat tract.
[000193] Mutant DMPK mRΝA is reported to interact with transcription factors retinoic acid receptor gamma (RARγ) and Spl (Ebralidze, A, Wang, Y, Petkova, V, Ebralidse, K., and Junghans, R.P. (2004), Science, 303, 383-387). In cortical neurons, these transcription factors were readily detected by immunofluorescence but they did not colocalize with RΝA foci (Figs. 151 and 16E) and their distribution was similar in DM1 patients and controls (Fig. 151 and 15J).
[000194] Polyclonal antisera recognizing all members of the muscleblind family
(MBΝL1, MBΝL2, and MBNL3) showed strong colocalization with RNA foci (not shown). We used monoclonal antibodies raised against epitopes specific for MBNLl or MBNL2 to determine which muscleblind proteins interact with CUG expansion RNA in neurons. MBNL3 was not examined because its expression in adults is mainly restricted to placenta (Fardaei, M, Rogers, M.T, Thorpe, H.M, Larkin, K. Hamshere, M.G, Harper, P.S, and Brook, J.D. (2002), Hum. Mol. Genet, 11, 805- 814; Kanadia, R.N, Urbinati, CR, Crusselle, V.J, Luo, D, Lee, Y.J., Harrison, J.K, Oh, S.P, and Swanson, M.S. (2003), Gene Expr. Patterns, 3, 459-462). In normal controls, monoclonal antibody 3A4 showed expression of MBNLl in nuclei and cytoplasm of cortical neurons (Fig. 15H). [000195] In DM1, MBNLl was strongly recruited into RNA foci, whereas staining elsewhere in the nucleus was markedly reduced (Fig. 15G). Quantitative analysis was performed on 3 DM1 patients and non-neurologic disease controls having the shortest postmortem intervals and best preservation of cortical architecture (Fig. 17). The mean immunofluorescence intensity for MBNLl in the nucleoplasm (excluding RNA foci and nucleoli) was 2.3-fold lower in DM1 neurons than in non- disease controls (26 ± 9 area x intensity units in DM1 patients vs 61 ± 17 in controls, 20 neuronal nuclei per subject, p<0.00001). Monoclonal antibody 2D9 showed that MBNL2 was also recruited into RNA foci (Fig. 15E). However, immunofluorescence signals in neurons with MoAb 2D9 were lower in relation to background staining in the neuropil, precluding a reliable quantification of its distribution. The finding of depletion of MBNLl in the nucleoplasm of DM1 cells supports a model where CUG expansion RNA accumulates to levels sufficient to sequester and compromise the nuclear functions of MBNLl.
Example 14. DM1 and alternative splicing in the brain
[000196] To determine if DM1 is associated with altered regulation of alternative splicing in brain, 45 exons (in 31 genes) known to undergo alternative splicing in brain (Table 2, below) were examined.
Alternatively
Gene Name Unigene spliced exon Acc. No. Nucleotides
Amyloid beta (A4) APP ex2 NM_000484 205-372 precursor protein ex7 NM_000484 1013-1180 exl5 NM_000484 1181-1237
Actin-related protein ARP3BETA ex2 BC008682.1 134-189 3 -beta
Beta-site APP- BACE2 ex9 NM_012105 1448-1597 cleaving enzyme 2 exlO NM 012105 1598-1766 Alternatively
Gene Name Unigene isμ vvu AV** Ace. No. Nucleotides
Neuronal apoptosis BΓRCI exlO-11 NM_004536 1314-1453 inhibitory protein
Calcium channel, CACNA1A ex38 AF004883 5783-5879 voltage-dependent,
P/Q type, alpha 1A subunit
Calcium/calmodulin CAMK2D alt splice NM_172127 1709-1981 protein kinase II donor in dependent delta ex21(44bp)
Clathrin light chain B CLTB exon cassette NM_007097 641-694
Homo sapiens discs, DLG1 ex8 NM_004087 771-824 large homolog 1
Dopamine receptor DRD2 ex6 NM_000795 889-975 type 2 EPB41L1 ex5 NM_012156 514-618
Erythrocyte membrane protein band 4.1 -like 1 ex21 NM_012156 2356-2439
GABA receptor GABRA4 ex3-8 NM_000809 345-1274 alpha 2
Gephyrin GPHN ex9 NM_020806 742-840 exl2 NM_020806 976-1018
LIM domain binding LDB3 exlO AB 014513 918-1106 3
NMDA receptor NRl GRINl ex5 AF015730 644-706 ex20 NM_007327 3683-3793 ex21 NM 007327 3794-3910 Alternatively
Gene Name Unigene Ace. No. Nucleotides NTRK2 exon cassette AF410901 1878-1926
Neurotrophic tyrosine kinase, receptor, type 2
C-Jun N-terminal JNK2 E6b, E6a NM_002752 666-737 kinase 2
Netrin Gl Ntng2 E5 NM_032536 1115-1138
Neogenin NEO1 ex26 NM_002499 3879-4037
Neurofibromin 1 NF1 ex9a NT010799 108004- 108033
Neuronatin NNAT ex2 NM_005386 200-280
Neurorexin 1 NRXN1 ex3a NM_004801 965-1024 ex4 ex5 ex7a NM_004801 1327-1250 exl2 NM_004801 2540-2566
Neurorexin 2 NRXN2 exl2 NM_015080 2829-2855 ex20 NM_015080 4197-4286
Neurorexin 3 NRXN3 exl2 NM_004796 1621-1647
NUMB NUMB ex8 AF015040 480-512 exl5 AF015040 1367-1510
Presynaptic PICO exlO AB011131 3056-3082 cytomatrix protein
Peanut-like 2 PNUTL2 ex2 NM_004574 189-579
Protein phosphatase PPP2R2B ex6 MN_181674 364-557 2, regulatory subunit B Alternatively sπliced exon
Gene Name Unigene Ace. No. Nucleotides
(PR 52), beta isoform
REST/NRSF/SBR REST ex5 AF228045 410-459
Microtubule- MAPT ex2 NM_005910 370-456 associated protein tau exlO NM_005910 1059-1151
Sarcolemma SLMAP ex4 NM_007159 273-395 associated protein SRC exon cassette NM_005417 additional exon cassette (lδbp or 50bp) v-src sarcoma (Schmidt-Ruppin A- 2) viral oncogene homolog (avian)
Table 2. List of exons screened for abnormal regulation of alternative splicing in DM1 compared to controls without neurologic disease. "Nucleotides" indicates which portion of the specified cDNA (GenBank accession number) was amplified by RT-PCR.
[000197] RT-PCR analysis of alternative splicing: total RNA was isolated from temporal cortex gray matter of 7 DM1 patients and 5 non-neurologic disease controls using TriReagent (Molecular Research Center, Cincinnati). cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen) with a mixture of oligo(dT)12-18 and random hexamer primers. The cDNA was digested with RNase H and then amplified using PCR primers flanking alternatively spliced exons (Table 2).
[000198] PCR products were resolved on agarose gels, stained with
SybrGreenll (Molecular Probes), and analyzed on a fluorimager. An initial screen was performed on a subset of samples (4 DM1 and 2 control). Four exons appeared to show deregulated splicing in DM1. These differences were quantified in a second experiment including the full panel of 7 DM1 and 5 control samples. The fraction of exon inclusion was determined on triplicate reactions using ImageQuant software (Amersham, Piscataway).
[000199] For each exon, the ratio of inclusion versus exclusion isoforms was determined by reverse transcriptasePCR (RT-PCR) using primers flanking the regulated exon. An initial screen was performed using total RNA extracted from superior temporal cortex from two controls without neurological disease and four DM1 patients. Among 45 exons screened, 4 appeared to show a change in the ratio of exon inclusion/exclusion splice products in DM1. These differences were then confirmed and quantified in triplicate assays using temporal cortex RNA from 7 patients with DM1 and 5 controls (Fig. 18). DM1 was associated with decreased inclusion of amyloid precursor protein exon 7 (10 ± 1% in DM1, 30 ± 11% in controls, pO.OOl), increased inclusion of NMDA NRl receptor exon 5 (33 ± 11% in DM1, 11 ± 5% in controls, pO.Ol), decreased inclusion of tau exon 2 (5 ± 1% in DM1, 36 ± 10% in controls, p<10"5), and decreased inclusion of tau exon 10 (21 ± 1% in DM1, 41 ± 5% in controls, p<10"6).
[000200] MBNL regulates fetal exon skipping in adults. The associated disease constitutes the failure in tissues to splice out specific fetal exons. Without MBNL, the fetal exons are retained. Other exons similarly regulated by MBNL remain to be identified.
[000201] Notably, DM1 is associated with reduced exon 10 inclusion (Fig 18), and
FTDP-17 and DM1 are both associated with neurofibrillary tangles and neuronal aggregates of hyperphosphorylated tau (Foster, N.L, Wilhelmsen, K, Sima, A.A, Jones, M.Z, D'Amato, C.J, and Gilman, S. (1997), Ann.Neurol, 41, 706-715; Kiuchi, A, Otsuka, N, Namba,Y, Nakano, I, and Tomonaga, M. (1991), Acta Neuropathol, 82, 1-5; Yoshimura, N, Otake, M, Igarashi, K, Matsunaga, M, Takebe, K, and Kudo, H. (1990), Clin. Neuropathol, 9, 234-239; Vermersch, P, Sergeant, N, Ruchoux, M.M, Hofmann-Radvanyi, H, Wattez, A, Petit, H, Dwailly, P, and Delacourte, A. (1996), Neurology, 47, Ill-Ill.
[000202] Neuronal intranuclear inclusions are characteristic of several neurological disorders. In the polyglutamine disorders, the core component of the inclusion is mutant protein or a cleavage product containing the polyglutamine tract (Davies, S.W, Turnaine,k M, Cozens, B.A, DiFiglia, M, Sharp, A.H, Ross, CA, Scherzinger, E, Wanker, E.E, Mangiarini, L, and Bates, G.P. (1997), Cell, 90, 537- 548; DiFiglia, M, Sapp, E, Chase, K.O, Davies, S.W, Bates, G.P, Vonsattel, J.P, and Aronin, N. (1997), Science, 277, 1990-1993). In Fragile X tremor ataxia syndrome (FXTAS), FMRl mRNA having an expanded CGG repeat leads to formation of nuclear inclusions (Greco, CM, Hagerman, R.J., Tassone, F, Chudley, A.E, Del Bigio, M.R, Jacquemont, S, Leehey, M, and Hagerman, P.J. (2002), Brain, 125, 1760-1771). The above-delineated results indicate that DM1 should be added to the list of disorders characterized by neuronal intranuclear inclusions.
[000203] Furthermore, in DM1 muscle tissue, evidence indicates that RNA inclusions are directly involved in disease pathogenesis, through a mechanism that involves sequestration of muscleblind proteins and mis-regulation of alternative splicing (Kanadia, R.N, Johnstone, K.A., Mankodi, A, Lungu, C, Thornton, CA, Esson, D, Timmers, A,M, Hauswirth, W.W, and Swanson, M.S,. (2003), Science, 302, 1978-1980; Mankodi, A, Logigian, E, Callahan, L, McClain, C, White, R, Henderson, D, Krym, M, and Thornton, CA. (2000), Science, 289, 1769-1773). The strong expression of expanded poly(CUG) RNA in DM1 neurons, formation of RNA inclusions, redistribution of muscleblind proteins, and altered regulation of alternative splicing shown above indicate that CNS symptoms of DM1 may also be triggered by RNA inclusions.
[000204] Despite evidence that mutant DMPK RNA accumulates to higher levels in cortical neurons (Fig. 14), the cell degeneration is more severe in muscle. The present results also indicate that splicing abnormalities are less frequent and less severe in cerebral cortex than in skeletal muscle (Fig. 18), suggesting that muscleblind proteins are more effectively sequestered in muscle nuclei, or that compensation for muscleblind deficiency is more effective in neurons, perhaps due to expression of additional RNA binding proteins. The exact determinants of cell vulnerability in DM1 are unknown, but the stoichiometry of CUG expansion RNA in relation to muscleblind proteins is likely to play an important role. Of note, while the present studies establish that the mutant DMPK mRNA is widely expressed in cortical and subcortical neurons, the failure to detect DMPK immunologically likely reflects its relatively low concentration in brain homogenates.
[000205] The 3-fold increase in the fraction of NMDA receptor 1 (NMDAR1) mRNA that includes exon 5 observed in DM1 brain is of significance, since inclusion of this exon influences the phannacologic behavior, gating, and cellular distribution (somatic rather than somatodendritic expression) of NMDARl (Pal, R, Agbas, A, Bao, X, Hui, D, Leary, C, Hunt, J, Naniwadekar, A, Michaelis, M.L, Kumar, K.N, and Michaelis, E.K. (2003), Brain Res, 994, 1-18).
[000206] NMDARl function is required for nonnal long term potentiation in the hippocampus and learning (Tsien, J.Z, Huerta, P.T. and Tonegawa, S. (1996), Cell, 87, 1327-1338). Thus, altered splicing of exon 5 may contribute to the memory impairment observed in DM1 (Rubinsztein, J.S, Rubinsztein, D.C, McKenna, P.J, Goodburn, S, and Holland, A.J. (1997), J. Med. Genet, 34, 229-233).
[000207] Inclusion of tau exon 2 is reduced in DM1, confirming previous observations (Sergeant, N, Sablonniere, B, Schraen-Maschke, S, Ghestem, A, Maurage, CA, Wattez, A, Vermersch, P, and Delacourte, A. (2001), Hum. Mol. Genet, 10, 2143-2155). These results predict that fetal isoforms of tau (excluding exons 2, 3, and 10) are inappropriately expressed in adult DM1 brain, findings that correlate well with previous studies of tau protein in DM1 brain (Sergeant, N, Sablonniere, B, Schraen-Maschke, S, Ghestem, A, Maurage, CA, Wattez, A, Vermersch, P, and Delacourte, A. (2001), Hum. Mol. Genet., 10, 2143-2155).
[000208] Expression of human fetal tau in transgenic mice leads to formation of neurofibrillary tangles and axonopathy (Ishihara, T, Zhang, B, Higuchi, M, Yoshiyama, Y, Trojanowksi, J.Q., and Lee, V.M. (2001), Am. J. Pathol, 158, 555- 562). It is unclear, however, whether the extent of the tau missplicing in DM1 is sufficient to cause neuronal dysfunction. Together with the above-described finding that DM1 is associated with increased expression of fetal splice isoforms for APP (exon 7 exclusion products), it is indicated that accumulation of mutant DMPK mRNA in the neuronal nucleus compromises a specific developmental program of alternative splicing.
[000209] The methods, techniques and compositions disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been illustrated with several examples and preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the methods and compositions, in the steps or in the sequence of steps and in modifications of the compositions without departing from the concept, spirit and scope of the invention. Accordingly, the exclusive rights sought to be patented are as described in the claims below.
ADDITIONAL SEQUENCES
SEQ ID NO: 1
Mus musculus muscleblind-like 1 (Drosophila) (Mbnll), mRNA.
ACCESSION NM_020007
(bases 1 to 5588)
ORIGIN 1 ggcgacatgc cacagtctct cgccgcagcc cgtcgagtcg gggcgctcgc catgctcccg 61 tgacccggac ccggccagtt ccctttcccg tggcgggcat cccggagtcg cgatcccaca 121 atgccccggg cagtcggggc cccggcgggc agcctgcacg gccacgtgag aggttggtac 181 taagaagtgc ctttcctgac gtctctgctg cttggaaccg cttctagagc agcctctgct 241 tttgccttgc ttgctgccag ctagactgac gacagcacat ccgccctcca cctctagccc 301 agacacccca tttctacttc taatcaggag aaaagctctg agtatctgcc attgccctag 361 gctgctttag tttagaagaa aagtttgctg aaaaagtaag ataccttctg ccaggaaatc 421 aaggaggaaa aaaaaaaatc attttctcga ttttgctcta aactgctgca tctgtctatg 481 ccaaactaat caataccgat tgcaccacca aactccatcg caaatcagct gtgaggagat 541 tccctgtcag acaactttgc tgaaagcagc ttggaaattc ggtgtcaaag ggtctgccac 601 gttttcatgc ttgcattttg ggctccaaat tggcactggg aaggggttac tgagcacacg 661 gctgagtcca ggcctcctct aaacacccat ctacttacag tcctggtatt cctctcaaaa 721 ccaaaacctc tttgaattaa cagtttcatg ctgtgaattt ctagcggagg tctttccctt 781 tatattgaag tcacactttt ccatgtgccg ttaaatcggg gacgggggaa gcagcctttc 841 ggacattttc acagttatct cacactctga gttttatcag ttcctatttt gtttagtttt 901 tgtcttttgt tttggttgct gatttttttt ttctattttt ctttttcttt ttcttttctt 961 tttttctttt tgttttttcc tttttttttt tttggagagg ggttgggttt gttggtttca 1021 ttgaacattt aactacctgt aaaatataaa catggctgtt agtgtcacac caattcggga 1081 cacaaaatgg ctaacactgg aagtatgtag agagtttcaa agggggactt gctcacgacc 1141 agacacggaa tgtaaatttg cacatccttc gaaaagctgc caagttgaaa atggacgagt 1201 aatcgcctgc tttgattcac tgaaaggtcg ttgctccaga gagaactgca aatatcttca 1261 tccaccccca cacttaaaaa cacagttaga gataaatggg cggaataact tgattcagca 1321 gaagaacatg gccatgctgg cccagcaaat gcagttagcc aatgccatga tgcccggtgc 1381 cccgttgcag cccgtgccaa tgttttcagt tgcaccaagc ttagccacca gtgcatcagc 1441 agcctttaac ccttacctgg ggcctgtttc cccaagcctg gttccagcag agatcttgcc 1501 gactgcacca atgttggtca cggggaatcc tggagttcca gtgccagcag ctgccgcagc 1561 tgctgcacag aagttaatgc ggacagacag actggaggtg tgtcgagagt accagcgtgg 1621 caattgcaac agaggagaaa atgactgtcg gtttgctcat cctgctgaca gcacaatgat 168 tgataccaat gacaacacag tcactgtctg catggattac atcaagggga gatgctctcg
174 ggaaaagtgc aaatacttcc atcctcccgc acacctgcaa gccaagatca aggctgccca 180 ataccaggtc aaccaggctg cagcagcaca ggctgcagct actgcagctg ccatgggaat 186 tcctcaagct gtacttcccc cattgccaaa gaggcctgct cttgaaaaaa ccaacggtgc 192 caccgcagtc tttaacactg gtattttcca ataccaacag gctctagcca acatgcagtt 198 acagcagcat acagcatttc tcccaccagg ctcaatattg tgcatgacac ccgctacaag 204 tgttgttccc atggtgcacg gtgctacgcc agccactgtg tccgcagcaa caacatctgc 210 cacaagtgtt cccttcgctg caacagccac agccaaccag atacccataa tatctgccga 216 acatctgact agccacaagt atgttaccca gatgtagagc tgtcgtcaca aaacaatcat 222 acaaagagga aaggacagtg tgcttgatta gagtaaggac gacgtcatta gccatattgt 228 atataccgtc aagcaacaca tacaaaaatc cctcagccac aagacatcca catattgcat 234 gttaaccaga agaaacgaca acatgggaac ctgctgcaca ctgttgccta cacactttgt 240 acattcagtt ggtatttgtg ctgaggtgat attcctatct aaaacaacaa cattgtcttt 246 cttttgtagc acagagttat gcattaaaat atgcatacgt aattagtttc ctatatattc 252 atgccatctt gaaaagacag actatggtgt gaccatgatt ctattatgta ttggtacgtc 258 tgtagaccaa gatataattt tttaaaaata agtttatttc tttcaaggtt tacaagtaac 264 caaggtgcac cttgtattta aaatcgccgt tagagctgag agcgcgcatg cagagtcatt 270 tttgtttgag agtaatattt ttactgtaat agattgtacg acatggtgag ggagggaact 276 gacagatgaa tgtgccaagc aaaaccacaa ctgtgtatat tttaaagcac accatggctt 282 taagtaccat gttgttaagg attctcatga agtgccatag actgtacatc aaattagagt 288 attatttctt cagtgttatt gtttctggag ccacattttg ttgcttattt gctagtacta 294 atcaatcaaa gggcaccatt cttttctttt ttgtttttga aaccaaagct gtctcagaaa 300 tggccaattt aactttacag taacaataga cagcacaaca caaactcaat acagataacc 306 tttcacatac tggagatata tatgatagat atataaaatt attttaatgc attgtagtgt 312 aatatttatg catactctac tatataacat gttattcaaa agggatatgc catttctgag 318 acacaataac aaaaaatgtt tgaggaaatt attttgcttc tatttatagc ctctgtcaaa 324 agtcaaaaga ctataaatgc tttgcagaaa tgggttcacg tttgcttaaa cgcttcatca 330 cagtcacatt caaaatagtg actctaaaca aagagaacag cactgtcatc agatgcatga 336 taaaccaaaa tatgaaaatg ggaaatgttt aattaaccta gtaattgggt gggttaagta 342 catgggtgaa ttttatatgt gattcttttg ttcagattaa ctgcttatag ccttagaaag 348 ccttttaaaa aattttaaaa atagatgtgc attcagtttt taagaatgga ttcatccaaa 354 ggaattcccc ttttttgtgg tttggatgtt gcagctagga aaggctattt ttgctctgtt 360 cagcagttct aaaatcgctg agtaggggcc aggtcactgg cagttctagt gtggaatggg 366 agaagtgaga gttctgttat agaactttcc atacttccaa gtttactgca agtttttatg 372 cttgagagag atgctttcta atataagact gatgtgttga ttttcctgat tgtactgtac 378 atctattaaa gccttagatt attacattac gggttggaac ccataccaat gtaatttcaa 384 tcgtgttaag agagtaatgg tgacttcaca tgttattgta gttagttacg ttatagaata 390 ttacttattt ttcttgttaa aatgtagttt ttcatttcct acatttattg gattttcatt 396 ttctattaac agttgaatac catttcagtt tttagactat tgttttatta gattttacca 402 atgaattttt caaaatacaa aaaaattaaa gtagtttttt cttcataaca tactcagttt 408 taaattacat gtagtgtcat atgaatatcc gtattattgt taactaaatg atttatattt 414 tactgattta atattacagt gtaagaatgt cagtcattgt tcttgtctag ttttcattaa 420 aagaacaaag atcttttata tggatatctt ataaatatat aatcattgct aagtaagaag 426 ttaagttgtt gctatggcaa caatcctggc agacaattga gtaatatttt gatgatttat 432 tttgtttgta attagttatt atgagaagat ctagatccta gatattagaa taaaatttat 438 tttctactgt atccatttca aatgttaaag tattgtttaa tatttttgaa atccctgaat 444 atcaggcctt gttataaata agctgcataa tcaataaata gaacaaggga ctttttgttg 450 ataatccaaa tactcaaagt ttacgtaatg agaattttag cgtgtgtgca aactcttgag 4561 ggttgatgat gctgcaattt agcatgttgg aaagtctaga gagaaggttg actttttgca 4621 cttctgtata tagtcaaaag agagaaacct gtataatagc aagatcttat tttgaataaa 4681 aacgtctata attacaagga gttttgttaa ggctaatgaa atgacagact gagcaaaatt 4741 gcttgcaaaa gtggcacaga gttagcactc catacccttc aaacacgtcg ctttgctttt 4801 tgtggacagc ttgtagtttg ccaggatttt tcagctggaa agatttgcca tccttccaag 4861 atctcatgac tgacaaaact ccattgggcc aaatctgcct gaagatcatt accaaaaaat 4921 agcaggtact tcagccacta agatgaaatc atggatcaga tatcccttac attgttttca 4981 aaactactgc atgtttaaaa cttcaacaaa aagagagaaa gaactatgct aaggacatat 5041 attattcaga tcgatatcta ccaatttcag tggtttaatg ttcacaaaat gaaatcttga 5101 aaataactat tgactttcac aaaattttaa ccataaacag gcaaaccaaa cagcacacct 5161 gtagttgttc tgtgattgtt ttttaattgc tgtagatcat gttctttccg caggtggaaa 5221 aaaaaaaaaa aaaaaaaaaa gaagttcaaa tttcacagtt ttaattttca actcagaagc 5281 aaaagagcaa aatgtgacaa tggccacttg tttaatgact tggttgccca gctgtcactg 5341 cagctggcta ctgatgttgc acttaccagc aacccaccca ccttcatctg ccgaaaggac 5401 agtgagcttg gttttacgat tatgtaatca caacttactt tctgcttgta gtggcttaaa 5461 attatgtatt ttgtctaggg ctgcaatttg ttttatgctt actttattat tactgcagta 5521 gttgactttg ctgtatggaa aaataaagcg aaattgccct aataaaactt ctctttctta 5581 agtaaaaa
SEQ ID NO: 2
Mus musculus muscleblind-like 2 (Mbnl2), transcript variant 2, mRNA. ACCESSION NM_207515 (bases 1 to 4527)
ORIGIN 1 agcagtggta acaacgcaga gtacgggggg tgggaaggaa gggctgcagc tcacagcaac 61 agagtttaga ctgtctttgc ttcatcatct gaaggtaaaa ttttccagcc acggccggcg 121 gctcgcagag tacaataaac agggacggag aactatttgc atggaccccc cttcctcatg 181 atgcggtgga gaagccacgg ccactcggtc ctgccagatg ttcttggggt tactgtacat 241 ggggaagacg agcagagcta aacaagaatt taaagaggac gaaggaagga aagcgccatc 301 ctgctcaaat acaaagatct aagagggttg ttttcccaca tcctccaaag ctgtgagcat 361 tagaactaat attttcccaa agagtgccat cgtattaaag ccactttatt aaggaggggt 421 gtatctgcaa aacagtcaag agactagaac cctgggagcc agagatgaca gtgagcacgc 481 actgcttgtg gctcacagtc ttccagtggg gcctatcgat cggtgactga cttcctgctt 541 gctgacacat tccccctccc cggtttcctg gattggactg cattaaagaa ttcactgctt 601 accttcaaac ttacatgttg gagttttcac ggcggttgtt ttgagatcat tgagactcgg 661 attgatttcg acatttaacc gaaaggaaca gagcccaaag tagttctcat catggccttg 721 aacgttgccc ccgtgagaga cacaaagtgg ctgacgctgg aggtctgcag acagtaccag 781 agaggaacgt gctcacgctc cgacgaagaa tgcaagtttg ctcacccccc caaaagttgc 841 caggttgaaa atggaagagt aattgcctgc tttgattccc tcaagggccg ctgttcaaga 901 gagaactgca aatatcttca tcctccgaca cacttaaaaa cccagctaga gattaatggg 961 aggaacaatt tgatccagca aaaaactgca gcagcgatgc ttgcccagca gatgcaattt 1021 atgtttccag gaacgccgct ccatcctgtg cccacttttc ctgtaggtcc caccataggg 1081 acaaatgcgg ctattagctt tgctccttac ttagcgcctg tcacccctgg agttgggtta 1141 gtcccaacag aggttctacc cactacaccg gtcattgttc ccggaagtcc accggtcact 1201 gtcccgggct caactgcaac tcagaaactt ctcaggactg ataaactgga ggtatgcagg 1261 gagttccagc gaggaaactg tgcccgggga gagacagact gccgctttgc acacccggca 132 gacagcacca tgatcgacac aaacgacaac accgtaaccg tttgtatgga ttacataaag 138 gggcgttgca tgagggagaa atgcaaatat tttcaccctc ctgcacactt gcaggccaaa 144 atcaaagctg cgcagcacca agccaaccag gccgcggtgg ccgcccaggc agccgcggcc 150 gcggccacag tcatggcctt ccctccgggt gctcttcatc ccttaccaaa gagacaagca 156 cttgaaaaaa gcaacggggc cagcacggtc ttcaacccca gcgtcttgca ctaccagcag 162 gctctgacca gtgcgcagct gcagcagcac acggcgttca tccccacagt acccatgatg 168 cacagcgcta cgtccgccac tgtctctgca gcaacaactc ctgcaacaag tgtccccttc 174 gcagcaacag ccacagccaa tcagataatt ctgaaataat caacagaaat ggaatggaat 180 gccaagaatc tgcattgaga ataactaaac attgttactg tacatattac cccgtttcct 186 cctcaataga attgccacaa actgcatgct aaatttagtt cttctggaca gaccacaacc 192 ctaaggctag ttctgctatg tcatatatga gtattaaata tggtatgctt agtatactcc 198 agcctaagat agttaaccac ctgagaccag ctgtgatgtt cgaagacata caggatgagg 204 ttttctttca cagggttctg agcatagttt ctgtcccagg aatattgtct tatctccata 210 actatagctg atgcagaaag tccagacaat atactcattt cgactcagaa tatttcaaat 216 ttagcaataa acagttagct ttagttttaa gtacctattc caagggcagg ttcgattgta 222 actccaatca caaccatttc atttcctgac tggatcgaag ggtatgattc acttcttgag 228 gagacggaca gtcgcagcag agagaagtga agtaaaacat acgcctgcct cgcaggtcta 234 aagtctgagt ggcagctcaa gcacaattgc caggggacac atcagagtgt ggggttcgct 240 ttgccaggag atgccgcact gaatcatggg attctagaat aacattgcat agattgaaaa 246 aaaaaaaaaa actttgcacg gtatgagctt catacccaac ccaacaaagt cttgaaggta 252 ttattttaca agtatatttt taaagttgtt ttataagaga gactttgtag aagtgcctag 258 attttgccag acttcatcca gcttgacaag aatgaaaggc tcatgccaat agtcgaatct 264 aagggattgg tctttcaaac tcgccctccg gttgcctgtt accgaataac tcttctaaac 270 taaaacctag tcaaacaggg aagctgtagg tgaggaggtc tgtataatat tccagtttaa 276 gtacgtctga gtttagtcac tacagatgca aactgtgact ttaatctaaa ttactatgta 282 aacgaaaaaa aaaagtagat agtttcactt tttaaaaact ccattactgt ttttgcattt 288 taagagttgg attaaagggt tgtaagtaac tgcagcatgg aaaaatagtt cttttaattc 294 tttcacctta aagcatattt tatgtctcaa aagtataaaa aactttaata caagtacaca 300 catattatat atacacatac atatatatac tatatatgga tgaaacatat tttaatgttg 306 tttacttttt ttaaatactt ggttgatctt caaggtaata gcgatacaat taaattttgt 312 tcagaaagtt tgttttaaag tttattttaa gcactatcgt accaaatatt tcatatttca 318 cattttatat gttgcacata gcctacacag tacctacata gtttttaaat tattgtttaa 324 gaaatgaaac agctgttata aatggatatt atgtgtaatt gtttaaaaca tccattttct 330 ttgtgaacat tttagtgatt gaagtatttt gacttttgag attgaatgta aaatatttta 336 aattttggta tcatcgcctg ttctgaaaac tagaggcatc caaccatatc attttttttg 342 attgaaaaaa gatctgcatt taattcatgt tggtcaaagt ctaattacta tttatcttac 348 atcatagatc tgataactgt atcgaaaaga gaaatcacat tctgagtgta atcttgcata 354 gtgcttgtgt cgtgtttgtt tttaatttgt ggaaaggtat tgtatctaac ttgtatcacc 360 ttgatagttc tcatctttat gtattattga tatttgtaat ttcctcagct ataacaatgt 366 agttacgcta caacttgcct aaaacactca tacttttttt tttctttact tactcattta 372 aactcattga gaagatagta gactaaaaag gtaaattatg ggaatcactg aaatattttt 378 gtagactaat tgttgtaact gtcctttctt cctttcattt catgattttt attttaaaaa 384 ttattagcac atagctattt tcagcccttt aataactgat catcaaaaca tcacctgtat 390 cccccagcca atatagatga ctgtattttt tactatgata tccattttcc agaattgtga 396 ttataatatg cagagtcaaa tatgccattt acaataagga ggaggccagg caaatgcata 402 gatgtacaaa tatatgtaca acagattttg ctttttattt atttataatg taattttata 408 gaataattct gggatttgag aggatctaaa actatttttc tgtataaata ttatttgcca 414 aaagtttgtt tatattcaga agtctgacta tgatggataa atcttaaatg ctttgtttaa 4201 ttacaaaaac aaaatcacca atatccaaga caggaagatc tcagttcaac agctccggta 4261 gttagggaac taactccact tgcacaggac ttcatttcac tcttggtttt caggctataa 4321 cagcacttca cagaactatt ctttcagcca tacaccactg gtcacatttc tactaaatct 4381 ttctgtaaca cttcttaaag aattccctca ttcgttatct tacagtgtaa acaggactct 4441 aatttgtatc aattatatgt tttggttgta atattcagtt cactcaccca atgtacaacc 4501 aatgaaataa aagaagcatt taaaagg
SEQ ID NO: 3
Mus musculus muscleblind-like 3 (Drosophila) (Mbnl3), mRNA. ACCESSION NMJ34163 (bases 1 to 1967)
ORIGIN 1 ctgaaggatc acgtaactca gaaaatctaa aacacattat gtgtccaaat cagttcttct 61 gagttacgcg gacgcgtggg tttcacgacg caagtgcgtc ctacaggaag aaagtgcccc 121 cagtcggagc gcgagcagga gcgcgacttt ttggcgctct ttgcgagcga gccgcaagga 181 ggcggaagac ggtcccgggc cggggcgcgg gaatcggggc agcgagcgcc gcacggggga 241 gttcctgcgc gtggcgtcct cgcagcgaga cgccgctgga gtcgctcact cggagagatt 301 ccttgaacca tctgcagtca taatattctc tgaagagggt gcacttgatt gccaatttgc 361 tctcagtatg acacctgtca atgtagctct aatccgtgat accaagtggc tgactttaga 421 agtctgtaga gaatttcaga gaggaacttg ctctcgagct gatgcagagt gcaggtttgc 481 ccatccgcca agagtttgcc atgtggaaaa tggccgagtg gtggcctgtt ttgattcact 541 aaagggtcgg tgcactcgtg agaactgcaa gtacctccac cctccaccgc acttaaagtc 601 gcagctagaa gttaatggga gaaacaatct gattcaacag aagactgccg cagccatgtt 661 cgcccagcac atgcaactca tgctgcagaa cgctcagatg tcatctcttg cgtcttttcc 721 tatgaatcca tcacttgcag ctaatcctgc catggctttc aatccttaca tgactcatcc 781 tggcatgggc ctggttcctg ctgagctttt accaaatggt ccggttctga tttctggaaa 841 ccctcctctt gcactgccag gagttcctgg tccaaagcca attcgtacag atagactgga 901 ggtttgccgt gaatttcagc gtggaaattg tacccgtggg gagagcgagt gccgctatgc 961 tcaccctacg gatgtttcca tgattgaagt cactgataat tctgtgacaa tctgcatgga 1021 ttacattaaa ggccgatgct cccgggagaa atgcaagtac tttcatcctc ctccccactt 1081 gcaggccaaa ctcagggcag ctcatcacca gatgaaccat tctgctgcca atgcaatggc 1141 cctgccgcat ggtgcacttc aactgatacc aaagaggtca gcccttgaca aggccaatgg 1201 tgccactcca gtctttaacc ccagtgtttt ccactgccaa caggctctgg ctaacatgca 1261 gattcctcag caggctttta tcccaacagt gcccatgatg cacggtgcta caccttccac 1321 tgtgtctaca gcaacaccac ctgccagcaa cgttccctac gttccaacaa ctacaggcaa 1381 ccagttgaaa tattgagcag cagagttaca gagtatcaga atctctcaac aagaaactcc 1441 gtgtggcctt tctatatgta ttctcgtatg tcttcttgta ccaacacgac aataagcatg 1501 gtgcagtcaa tatactaaag cgcatatacc tgttgacaaa ttcaaatttt aaaaatctgt 1561 ggagatgtta aagcaaatag aaaattaacc agtatgtgtt accttatacg gattcattgt 1621 atatgaatta gcatacaata tacaaccata caggtttgtc atgtatatga attatcagat 1681 ccatattaca tgaattttcc atatgatatg aattaccata ttgaatataa ctgtaaaatg 1741 ttgtgactgc tttccagtaa tggtttataa taaatgaact tccacagtgt actgtaggct 1801 tactgtatac tcttggtgga taaattctgt tttggaagtg ttaccttact gttttgttta 1861 caagatagtc tataggattg atgtagaatg taactgatat ttcccacacc attttcctcc 1921 attggtatat tgtattaaat tgggttctgc ttaaaaaaaa aaaaaaa
SEQ ID NO: 37 Homo sapiens amyloid beta (A4) precursor protein (protease nexin-II, Alzheimer disease) (APP), transcript variant 1, mRNA. ACCESSION NM_000484 (bases 1 to 3641)
ORIGIN 1 gctgactcgc ctggctctga gccccgccgc cgcgctcggg ctccgtcagt ttcctcggca 61 gcggtaggcg agagcacgcg gaggagcgtg cgcgggggcc ccgggagacg gcggcggtgg 121 cggcgcgggc agagcaagga cgcggcggat cccactcgca cagcagcgca ctcggtgccc 181 cgcgcagggt cgcgatgctg cccggtttgg cactgctcct gctggccgcc tggacggctc 241 gggcgctgga ggtacccact gatggtaatg ctggcctgct ggctgaaccc cagattgcca 301 tgttctgtgg cagactgaac atgcacatga atgtccagaa tgggaagtgg gattcagatc 361 catcagggac caaaacctgc attgatacca aggaaggcat cctgcagtat tgccaagaag 421 tctaccctga actgcagatc accaatgtgg tagaagccaa ccaaccagtg accatccaga 481 actggtgcaa gcggggccgc aagcagtgca agacccatcc ccactttgtg attccctacc 541 gctgcttagt tggtgagttt gtaagtgatg cccttctcgt tcctgacaag tgcaaattct 601 tacaccagga gaggatggat gtttgcgaaa ctcatcttca ctggcacacc gtcgccaaag 661 agacatgcag tgagaagagt accaacttgc atgactacgg catgttgctg ccctgcggaa 721 ttgacaagtt ccgaggggta gagtttgtgt gttgcccact ggctgaagaa agtgacaatg 781 tggattctgc tgatgcggag gaggatgact cggatgtctg gtggggcgga gcagacacag 841 actatgcaga tgggagtgaa gacaaagtag tagaagtagc agaggaggaa gaagtggctg 901 aggtggaaga agaagaagcc gatgatgacg aggacgatga ggatggtgat gaggtagagg 961 aagaggctga ggaaccctac gaagaagcca cagagagaac caccagcatt gccaccacca 1021 ccaccaccac cacagagtct gtggaagagg tggttcgaga ggtgtgctct gaacaagccg 1081 agacggggcc gtgccgagca atgatctccc gctggtactt tgatgtgact gaagggaagt 1141 gtgccccatt cttttacggc ggatgtggcg gcaaccggaa caactttgac acagaagagt 1201 actgcatggc cgtgtgtggc agcgccatgt cccaaagttt actcaagact acccaggaac 1261 ctcttgcccg agatcctgtt aaacttccta caacagcagc cagtacccct gatgccgttg 1321 acaagtatct cgagacacct ggggatgaga atgaacatgc ccatttccag aaagccaaag 1381 agaggcttga ggccaagcac cgagagagaa tgtcccaggt catgagagaa tgggaagagg 1441 cagaacgtca agcaaagaac ttgcctaaag ctgataagaa ggcagttatc cagcatttcc 1501 aggagaaagt ggaatctttg gaacaggaag cagccaacga gagacagcag ctggtggaga 1561 cacacatggc cagagtggaa gccatgctca atgaccgccg ccgcctggcc ctggagaact 1621 acatcaccgc tctgcaggct gttcctcctc ggcctcgtca cgtgttcaat atgctaaaga 1681 agtatgtccg cgcagaacag aaggacagac agcacaccct aaagcatttc gagcatgtgc 1741 gcatggtgga tcccaagaaa gccgctcaga tccggtccca ggttatgaca cacctccgtg 1801 tgatttatga gcgcatgaat cagtctctct ccctgctcta caacgtgcct gcagtggccg 1861 aggagattca ggatgaagtt gatgagctgc ttcagaaaga gcaaaactat tcagatgacg 1921 tcttggccaa catgattagt gaaccaagga tcagttacgg aaacgatgct ctcatgccat 1981 ctttgaccga aacgaaaacc accgtggagc tccttcccgt gaatggagag ttcagcctgg 2041 acgatctcca gccgtggcat tcttttgggg ctgactctgt gccagccaac acagaaaacg 2101 aagttgagcc tgttgatgcc cgccctgctg ccgaccgagg actgaccact cgaccaggtt 2161 ctgggttgac aaatatcaag acggaggaga tctctgaagt gaagatggat gcagaattcc 2221 gacatgactc aggatatgaa gttcatcatc aaaaattggt gttctttgca gaagatgtgg 2281 gttcaaacaa aggtgcaatc attggactca tggtgggcgg tgttgtcata gcgacagtga 2341 tcgtcatcac cttggtgatg ctgaagaaga aacagtacac atccattcat catggtgtgg 2401 tggaggttga cgccgctgtc accccagagg agcgccacct gtccaagatg cagcagaacg 2461 gctacgaaaa tccaacctac aagttctttg agcagatgca gaactagacc cccgccacag 2521 cagcctctga agttggacag caaaaccatt gcttcactac ccatcggtgt ccatttatag 2581 aataatgtgg gaagaaacaa acccgtttta tgatttactc attatcgcct tttgacagct 2641 gtgctgtaac acaagtagat gcctgaactt gaattaatcc acacatcagt aatgtattct 2701 atctctcttt acattttggt ctctatacta cattattaat gggttttgtg tactgtaaag 2761 aatttagctg tatcaaacta gtgcatgaat agattctctc ctgattattt atcacatagc 2821 cccttagcca gttgtatatt attcttgtgg tttgtgaccc aattaagtcc tactttacat 2881 atgctttaag aatcgatggg ggatgcttca tgtgaacgtg ggagttcagc tgcttctctt 2941 gcctaagtat tcctttcctg atcactatgc attttaaagt taaacatttt taagtatttc 3001 agatgcttta gagagatttt ttttccatga ctgcatttta ctgtacagat tgctgcttct 3061 gctatatttg tgatatagga attaagagga tacacacgtt tgtttcttcg tgcctgtttt 3121 atgtgcacac attaggcatt gagacttcaa gcttttcttt ttttgtccac gtatctttgg 3181 gtctttgata aagaaaagaa tccctgttca ttgtaagcac ttttacgggg cgggtgggga 3241 ggggtgctct gctggtcttc aattaccaag aattctccaa aacaattttc tgcaggatga 3301 ttgtacagaa tcattgctta tgacatgatc gctttctaca ctgtattaca taaataaatt 3361 aaataaaata accccgggca agacttttct ttgaaggatg actacagaca ttaaataatc 3421 gaagtaattt tgggtgggga gaagaggcag attcaatttt ctttaaccag tctgaagttt 3481 catttatgat acaaaagaag atgaaaatgg aagtggcaat ataaggggat gaggaaggca 3541 tgcctggaca aacccttctt ttaagatgtg tcttcaattt gtataaaatg gtgttttcat 3601 gtaaataaat acattcttgg aggagcaaaa aaaaaaaaaa a
SEQ ID NO: 38
Homo sapiens NMDARl subunit isoform 3b (hNMDARl-3b) mRNA, complete eds. ACCESSION AFO 15730 (bases 1 to 3150)
ORIGIN 1 aagcttatcg atccgtcgac ctcgaggggg ggcccgcgtt cgccgcgcag agccaggccc 61 gccgggcgag cccatgagca ccatgcgcct gctgacgctc gccctgctgt tctcctgctc 121 cgtcgcccgt gccgcgtgcg accccaagat cgtcaacatt ggcgcggtgc tgagcacgcg 181 gaagcacgag cagatgttcc gcgaggccgt gaaccaggcc aacaagcggc acggctcctg 241 gaagattcag ctcaatgcca cctccgtcac gcacaagccc aacgccatcc agatggctct 301 gtcggtgtgc gaggacctca tctccagcca ggtctacgcc atcctagtta gccatccacc 361 tacccccaac gaccacttca ctcccacccc tgtctcctac acagccggct tctaccgcat 421 acccgtgctg gggctgacca cccgcatgtc catctactcg gacaagagca tccacctgag 481 cttcctgcgc accgtgccgc cctactccca ccagtccagc gtgtggtttg agatgatgcg 541 tgtgtacagc tggaaccaca tcatcctgct ggtcagcgac gaccacgagg gccgggccgc 601 tcagaaacgc ctggagacgc tgctggagga gcgtgagtcc aagagtaaaa aaaggaacta 661 tgaaaacctc gaccaactgt cctatgacaa caagcgcgga cccaaggcag agaaggtgct 721 gcagtttgac ccagggacca agaacgtgac ggccctgctg atggaggcga aagagctgga 781 ggcccgggtc atcatccttt ctgccagcga ggacgatgct gccactgtat accgagcagc 841 cgcgatgctg aacatgacgg gctccgggta cgtgtggctg gtcggcgagc gcgagatctc 901 ggggaacgcc ctgcgttacg ccccggacgg catcctcggg ctgcagctca tcaacggcaa 961 gaacgagtcg gcccacatca gcgacgccgt aggcgtggtg gcccaggccg tgcacgagct 1021 cctcgagaag gagaacatca ccgacccgcc gcggggctgc gtgggcaaca ccaacatctg 1081 gaagaccggg ccgctcttca agagagtgct gatgtcttcc aagtatgcgg atggggtgac 1141 tggtcgcgtg gagttcaatg aggatgggga ccggaagttc gccaactaca gcatcatgaa 1201 cctgcagaac cgcaagctgg tgcaagtggg catctacaat ggcacccacg tcatccctaa 126 tgacaggaag atcatctggc caggcggaga gacagagaag cctcgagggt accagatgtc 132 caccagactg aagattgtga cgatccacca ggagcccttc gtgtacgtca agcccacgct 138 gagtgatggg acatgcaagg aggagttcac agtcaacggc gacccagtca agaaggtgat 144 ctgcaccggg cccaacgaca cgtcgccggg cagcccccgc cacacggtgc ctcagtgttg 150 ctacggcttt tgcatcgacc tgctcatcaa gctggcacgg accatgaact tcacctacga 156 ggtgcacctg gtggcagatg gcaagttcgg cacacaggag cgggtgaaca acagcaacaa 162 gaaggagtgg aatgggatga tgggcgagct gctcagcggg caggcagaca tgatcgtggc 168 gccgctaacc ataaacaacg agcgcgcgca gtacatcgag ttttccaagc ccttcaagta 174 ccagggcctg actatgctgg tcaagaagga gattccccgg agcacgctgg actcgttcat 180 gcagccgttc cagagcacac tgtggctgct ggtggggctg tcggtgcacg tggtggccgt 186 gatgctgtac ctgctggacc gcttcagccc cttcggccgg ttcaaggtga acagcgagga 192 ggaggaggag gacgcactga ccctgtcctc ggccatgtgg ttctcctggg gcgtcctgct 198 caactccggc atcggggaag gcgcccccag aagcttctca gcgcgcatcc tgggcatggt 204 gtgggccggc tttgccatga tcatcgtggc ctcctacacc gccaacctgg ccgctttcct 210 ggtgctggac cggccggagg agcgcatcac gggcatcaac gaccctcggc tgaggaaccc 216 ttctgacaag tttatctact ccacggtgaa gcagagctcc gtggatatct acttccggcg 222 ccaggtggag ctgagcacca tgtaccggca tatggagaag cacaactacg agagtgcggc 228 ggaagccatc caggccgtga gagacaacaa gctgcatgcc ttcatctggg actcggcggt 234 gctggagttc gaggcctcgc agaagtgcga cctggtgacg actggagagc tgtttttccg 240 ctcgggcttc ggcataggca tgcgcaaaga cagcccctgg aagcagaacg tctccctgtc 246 catcctcaag tcccacgaga atggcttcat ggaagacctg gacaagacgt gggttcggta 252 tcaggaatgt gactcgcgca gcaacgcccc tgcgaccctt acttttgaga acatggccgg 258 ggtcttcatg ctggtagctg ggggcatcgt ggccgggatc ttcctgattt tcatcgagat 264 tgcctacaag cggcacaagg atgctcgccg gaagcagatg cagctggcct ttgccgccgt 270 taacgtgtgg cggaagaacc tgcagcagta ccatcccact gatatcacgg gcccgctcaa 276 cctctcagat ccctcggtca gcaccgtggt gtgaggcccc cggaggcgcc cacctgccca 282 gttagcccgg ccaaggacac tgatgggtcc tgctgctcgg gaaggcctga gggaagccca 288 cccgccccag agactgccca ccctgggcct cccgtccgtc cgcccgccca ccccgctgcc 294 tggcgccacc ctgctggacc aaggtgcgga ccggagcggc tgaggacggg gcagagctga 300 gtcggctggg cagggcgcag gcgcgtgcac ggcagaggca gggcctgggg tctctgagca 306 gtggggagcg ggggctaact ggcccaggcg gagggccttg gagcagagac ggcagcccca 312 tccttcccgg cagcaccagc gtgagggcca
SEQ ID NO: 39
Homo sapiens microtubule-associated protein tau (MAPT), transcript variant 2, mRNA. ACCESSION NM_005910 NM_173727 (bases 1 to 2796)
ORIGIN 1 cctcccctgg ggaggctcgc gttcccgctg ctcgcgcctg ccgcccgccg gcctcaggaa 61 cgcgccctct cgccgcgcgc gccctcgcag tcaccgccac ccaccagctc cggcaccaac 121 agcagcgccg ctgccaccgc ccaccttctg ccgccgccac cacagccacc ttctcctcct 181 ccgctgtcct ctcccgtcct cgcctctgtc gactatcagg tgaactttga accaggatgg 241 ctgagccccg ccaggagttc gaagtgatgg aagatcacgc tgggacgtac gggttggggg 301 acaggaaaga tcaggggggc tacaccatgc accaagacca agagggtgac acggacgctg 361 gcctgaaaga atctcccctg cagaccccca ctgaggacgg atctgaggaa ccgggctctg 421 aaacctctga tgctaagagc actccaacag cggaagatgt gacagcaccc ttagtggatg 481 agggagctcc cggcaagcag gctgccgcgc agccccacac ggagatccca gaaggaacca 541 cagctgaaga agcaggcatt ggagacaccc ccagcctgga agacgaagct gctggtcacg 601 tgacccaagc tcgcatggtc agtaaaagca aagacgggac tggaagcgat gacaaaaaag 661 ccaagggggc tgatggtaaa acgaagatcg ccacaccgcg gggagcagcc cctccaggcc 721 agaagggcca ggccaacgcc accaggattc cagcaaaaac cccgcccgct ccaaagacac 781 cacccagctc tggtgaacct ccaaaatcag gggatcgcag cggctacagc agccccggct 841 ccccaggcac tcccggcagc cgctcccgca ccccgtccct tccaacccca cccacccggg 901 agcccaagaa ggtggcagtg gtccgtactc cacccaagtc gccgtcttcc gccaagagcc 961 gcctgcagac agcccccgtg cccatgccag acctgaagaa tgtcaagtcc aagatcggct 1021 ccactgagaa cctgaagcac cagccgggag gcgggaaggt gcagataatt aataagaagc 1081 tggatcttag caacgtccag tccaagtgtg gctcaaagga taatatcaaa cacgtcccgg 1141 gaggcggcag tgtgcaaata gtctacaaac cagttgacct gagcaaggtg acctccaagt 1201 gtggctcatt aggcaacatc catcataaac caggaggtgg ccaggtggaa gtaaaatctg 1261 agaagcttga cttcaaggac agagtccagt cgaagattgg gtccctggac aatatcaccc 1321 acgtccctgg cggaggaaat aaaaagattg aaacccacaa gctgaccttc cgcgagaacg 1381 ccaaagccaa gacagaccac ggggcggaga tcgtgtacaa gtcgccagtg gtgtctgggg 1441 acacgtctcc acggcatctc agcaatgtct cctccaccgg cagcatcgac atggtagact 1501 cgccccagct cgccacgcta gctgacgagg tgtctgcctc cctggccaag cagggtttgt 1561 gatcaggccc ctggggcggt caataattgt ggagaggaga gaatgagaga gtgtggaaaa 1621 aaaaagaata atgacccggc ccccgccctc tgcccccagc tgctcctcgc agttcggtta 1681 attggttaat cacttaacct gcttttgtca ctcggctttg gctcgggact tcaaaatcag 1741 tgatgggagt aagagcaaat ttcatctttc caaattgatg ggtgggctag taataaaata 1801 tttaaaaaaa aacattcaaa aacatggcca catccaacat ttcctcaggc aattcctttt 1861 gattcttttt tcttccccct ccatgtagaa gagggagaag gagaggctct gaaagctgct 1921 tctgggggat ttcaagggac tgggggtgcc aaccacctct ggccctgttg tgggggttgt 1981 cacagaggca gtggcagcaa caaaggattt gaaaactttg gtgtgttcgt ggagccacag 2041 gcagacgatg tcaaccttgt gtgagtgtga cgggggttgg ggtggggcgg gaggccacgg 2101 gggaggccga ggcaggggct gggcagaggg gaggaggaag cacaagaagt gggagtggga 2161 gaggaagcca cgtgctggag agtagacatc cccctccttg ccgctgggag agccaaggcc 2221 tatgccacct gcagcgtctg agcggccgcc tgtccttggt ggccgggggt gggggcctgc 2281 tgtgggtcag tgtgccaccc tctgcagggc agcctgtggg agaagggaca gcgggttaaa 2341 aagagaaggc aagcctggca ggagggttgg cacttcgatg atgacctcct tagaaagact 2401 gaccttgatg tcttgagagc gctggcctct tcctccctcc ctgcagggta gggcgcctga 2461 gcctaggcgg ttccctctgc tccacagaaa ccctgtttta ttgagttctg aaggttggaa 2521 ctgctgccat gattttggcc actttgcaga cctgggactt tagggctaac cagttctctt 2581 tgtaaggact tgtgcctctt gggagacgtc cacccgtttc caagcctggg ccactggcat 2641 ctctggagtg tgtgggggtc tgggaggcag gtcccgagcc ccctgtcctt cccacggcca 2701 ctgcagtcac cccgtctgcg ccgctgtgct gttgtctgcc gtgagagccc aatcactgcc 2761 tatacccctc atcacacgtc acaatgtccc gaattc
SEQ ID NO: 54
Homo sapiens troponin T2, cardiac (TNNT2), transcript variant 4, mRNA. ACCESSION NM_001001432 (bases 1 to 1114)
ORIGIN 1 ccccgctgag actgagcaga cgcctccagg atctgtcggc agctgctgtt ctgagggaga 61 gcagagacca tgtctgacat agaagaggtg gtggaagagt acgaggagga ggagcaggaa 121 gagcaggagg aggcagcgga agaggatgct gaagcagagg ctgagaccga ggagaccagg 181 gcagaagaag atgaagaaga agaggaagca aaggaggctg aagatggccc aatggaggag 241 tccaaaccaa agcccaggtc gttcatgccc aacttggtgc ctcccaagat ccccgatgga 301 gagagagtgg actttgatga catccaccgg aagcgcatgg agaaggacct gaatgagttg 361 caggcgctga tcgaggctca ctttgagaac aggaagaaag aggaggagga gctcgtttct 421 ctcaaagaca ggatcgagag acgtcgggca gagcgggccg agcagcagcg catccggaat 481 gagcgggaga aggagcggca gaaccgcctg gctgaagaga gggctcgacg agaggaggag 541 gagaacagga ggaaggctga ggatgaggcc cggaagaaga aggctttgtc caacatgatg 601 cattttgggg gttacatcca gaaggcccag acagagcgga aaagtgggaa gaggcagact 661 gagcgggaaa agaagaagaa gattctggct gagaggagga aggtgctggc cattgaccac 721 ctgaatgaag atcagctgag ggagaaggcc aaggagctgt ggcagagcat ctataacttg 781 gaggcagaga agttcgacct gcaggagaag ttcaagcagc agaaatatga gatcaatgtt 841 ctccgaaaca ggatcaacga taaccagaaa gtctccaaga cccgcgggaa ggctaaagtc 901 accgggcgct ggaaatagag cctggcctcc ttcaccaaag atctgctcct cgctcgcacc 961 tgcctccggc ctgcactccc ccagttcccg ggccctcctg ggcaccccag gcagctcctg 1021 tttggaaatg gggagctggc ctaggtggga gccaccactc ctgcctgccc ccacacccac 1081 tccacaccag taataaaaag ccaccacaca ctga
SEQ ID NO: 55
Homo sapiens troponin T3, skeletal, fast (TNNT3), mRNA.
ACCESSION NM_006757
(bases 1 to 1000)
ORIGIN 1 cccaccttca ccatgtctga cgaggaagtt gaacaggtgg aggagcagta cgaagaagaa 61 gaggaagccc aggaggaaga ggaagttcaa gaagacaccg cagaggagga cgcggaagag 121 gagaaaccga gacccaaact cactgctcct aagatcccag aaggggagaa agtggacttc 181 gatgacatcc agaagaagcg tcagaacaaa gacctaatgg agctccaggc cctcatcgac 241 agccactttg aagcccggaa gaaggaggag gaggagctgg tcgctctcaa agagagaatc 301 gagaagcgcc gtgcagagag agcggagcag cagaggattc gtgcagagaa ggagagggag 361 cgccagaaca gactggcgga ggaaaaggcc agaagggagg aggaggatgc caagaggagg 421 gcagaggacg acctgaagaa gaagaaagcg ctgtcctcca tgggcgccaa ctacagcagc 481 tacctggcca aggctgacca gaagagaggc aagaagcaga cagcccgaga gatgaagaag 541 aagattctgg ctgagagacg caagccgctc aacatcgatc accttggtga agacaaactg 601 agggacaagg ccaaggagct ctgggagacc ctgcaccagc tggagattga caagttcgag 661 tttggggaga agctgaaacg ccagaaatat gacatcacca cgctcaggag ccgcattgac 721 caggcccaga agcacagcaa gaaggctggg accccagcca agggcaaagt cggcgggcgc 781 tggaagtaga gaggccagaa aggccctcga ggcagagacc ctccgccctc ttgcacacca 841 gggccgctcg tgggactcca catcctccag cccccacaat cctgtcaggg gtctccctga 901 cgtcctgggg gtggagaggc catcccgggg cgtcccccgc gtctgtgtcc ttgctgcctt 961 catcccctgg ggcctgtgaa taaagctgca gaaccccctt

Claims

WHAT IS CLAIMED IS:
1. A method of treating a disease associated with aberrant microsatellite expansion, comprising administering to a mammal in need thereof, a therapeutically effective amount of recombinant adeno-associated virus (rAAV) containing a transgene that encodes a protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof.
2. The method of claim 1, wherein treating comprises ameliorating or eliminating the symptoms of a neuromuscular or neurological condition caused by the aberrant microsatellite expansion.
3. The method of claim 2, wherein the neuromuscular condition is myotonic dystrophy.
4. The method of claim 1, wherein treating comprises reversing the mis- splicing of the Clcnl skeletal muscle chloride channel.
5. The method of claim 1, wherein treating comprises reversing the mis- splicing of the Amyloid beta (A4) precursor protein (APP).
6. The method of claim 1, wherein treating comprises reversing the mis- splicing of the NMDA receptor NRl (GRINl).
7. The method of claim 1, wherein treating comprises reversing the mis- splicing of the Microtubule-associated protein tau (MAPT).
8. The method of claim 1, wherein treating comprises reversing the mis- splicing of the TNNT2 (cTNT) protein.
9. The method of claim 1 , wherein the protein is MBNL 1.
10. The method of claim 1, wherein the mammal is human.
11. The method of claim 1, wherein the mammal in need of treatment has RNA inclusions in neuronal cells.
12. A pharmaceutical composition comprising a recombinant adeno-associated virus (rAAV) containing a transgene that encodes at least one protein selected from the group consisting of MBNLl, MBNL2, MBNL3, and combinations thereof.
13. The composition of claim 12, wherein the protein is MBNLl.
14. A mouse model for disease associated with aberrant microsatellite expansion, comprising a mouse having a substantial deletion of Mbnll exon 3 (E3) in the mouse genome, wherein said mouse exhibits symptoms typical of a disease associated with aberrant microsatellite expansion in humans.
15. A cell isolated from the mouse of claim 14.
16. The mouse model of claim 14, wherein the symptoms comprise muscle weakness and ocular cataracts.
17. The mouse model of claim 14, wherein the microsatellite repeat expansion disease is caused by a microsatellite expansion in a coding region of DNA.
18. The mouse model of claim 14, wherein the microsatellite repeat expansion disease is caused by a microsatellite expansion in a non-coding region of DNA.
19. The mouse model of claim 14, wherein said mouse exhibits abnormal muscleblind proteins.
20. The mouse model of claim 14, wherein the disease is myotonic dystrophy.
21. The mouse model of claim 14, wherein said mouse has loss of functional ClC-1 protein.
22. The mouse model of claim 14, wherein said mouse has loss of functional Amyloid beta (A4) precursor protein.
23. The mouse model of claim 14, wherein said mouse has loss of functional NMDA receptor NRl .
24. The mouse model of claim 14, wherein said mouse has loss of functional Microtubule-associated protein tau.
25. The mouse model of claim 14, wherein said mouse has loss of functional TNNT2 protein.
26. The mouse model of claim 14, wherein said mouse has loss of functional TNNT3 protein.
27. A method of identifying a compound useful in the treatment of disease associated with aberrant microsatellite expansion, comprising administering a test compound to the mouse of claim 14 and monitoring said mouse for reduction or inhibition of the symptoms associated with said disease.
28. The method of claim 27, further comprising monitoring said mouse for effects other than those associated with the disease.
29. The method of claim 27, wherein the disease is myotonic dystrophy.
PCT/US2005/007631 2004-03-10 2005-03-10 Methods and compositions for treatment of diseases associated with aberrant microsatellite expansion WO2005086825A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
AU2005220900A AU2005220900A1 (en) 2004-03-10 2005-03-10 Methods and compositions for treatment of diseases associated with aberrant microsatellite expansion
EP05725031A EP1734827A4 (en) 2004-03-10 2005-03-10 Methods and compositions for treatment of diseases associated with aberrant microsatellite expansion
US10/591,883 US7964570B2 (en) 2004-03-10 2005-03-10 Methods and compositions for treatment of myotonia

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US55174804P 2004-03-10 2004-03-10
US60/551,748 2004-03-10

Publications (2)

Publication Number Publication Date
WO2005086825A2 true WO2005086825A2 (en) 2005-09-22
WO2005086825A3 WO2005086825A3 (en) 2006-04-27

Family

ID=34976171

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2005/007631 WO2005086825A2 (en) 2004-03-10 2005-03-10 Methods and compositions for treatment of diseases associated with aberrant microsatellite expansion

Country Status (4)

Country Link
US (1) US7964570B2 (en)
EP (1) EP1734827A4 (en)
AU (1) AU2005220900A1 (en)
WO (1) WO2005086825A2 (en)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2007297535A1 (en) * 2006-09-21 2008-03-27 University Of Florida Research Foundation, Inc. Compositions and methods related to protein displacement therapy for myotonic distrophy
EP4046631A1 (en) * 2021-02-18 2022-08-24 Universitat de València Msi2 as a therapeutic target for the treatment of myotonic dystrophy

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012145597A2 (en) * 2011-04-21 2012-10-26 Nationwide Children's Hospital, Inc. Recombinant virus products and methods for inhibition of expression of myotilin
US10196636B2 (en) 2011-04-21 2019-02-05 Nationwide Children's Hospital, Inc. Recombinant virus products and methods for inhibition of expression of myotilin
CA2752947A1 (en) * 2011-06-30 2012-12-30 Benjamin J. Blencowe Foxp1 splice variants and methods and uses thereof
WO2013138662A1 (en) 2012-03-16 2013-09-19 4S3 Bioscience, Inc. Antisense conjugates for decreasing expression of dmpk
CA2998597A1 (en) * 2015-09-14 2017-03-23 Research Institute At Nationwide Children's Hospital Recombinant virus products and methods for inhibition of expression of myotilin
WO2018175443A1 (en) * 2017-03-20 2018-09-27 University Of Pittsburgh - Of The Commonwealth System Of Higher Education Targeted gene therapies for pain and other neuro-related disorders
WO2021087007A1 (en) * 2019-10-28 2021-05-06 University Of Florida Research Foundation, Incorporated Gene therapy vectors

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See references of EP1734827A4 *

Cited By (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2007297535A1 (en) * 2006-09-21 2008-03-27 University Of Florida Research Foundation, Inc. Compositions and methods related to protein displacement therapy for myotonic distrophy
WO2008036406A3 (en) * 2006-09-21 2009-04-30 Univ Rochester Compositions and methods related to protein displacement therapy for myotonic distrophy
JP2010504098A (en) * 2006-09-21 2010-02-12 ユニバーシティー オブ ロチェスター Compositions and methods for protein replacement therapy for myotonic dystrophy
EP2560001A3 (en) * 2006-09-21 2013-07-17 University of Rochester Compositions and methods related to protein displacement therapy for myotonic distrophy
US9371527B2 (en) 2006-09-21 2016-06-21 University Of Rochester Compositions and methods related to protein displacement therapy for myotonic distrophy
AU2007297535C1 (en) * 2006-09-21 2017-11-23 University Of Florida Research Foundation, Inc. Compositions and methods related to protein displacement therapy for myotonic distrophy
EP4046631A1 (en) * 2021-02-18 2022-08-24 Universitat de València Msi2 as a therapeutic target for the treatment of myotonic dystrophy
WO2022175478A1 (en) * 2021-02-18 2022-08-25 Universitat De València Msi2 as a therapeutic target for the treatment of myotonic dystrophy

Also Published As

Publication number Publication date
AU2005220900A1 (en) 2005-09-22
WO2005086825A3 (en) 2006-04-27
EP1734827A4 (en) 2009-01-28
EP1734827A2 (en) 2006-12-27
US7964570B2 (en) 2011-06-21
US20080213182A1 (en) 2008-09-04

Similar Documents

Publication Publication Date Title
US7964570B2 (en) Methods and compositions for treatment of myotonia
EP2986635B1 (en) Effective delivery of large genes by dual aav vectors
KR102584873B1 (en) Gene editing of deep intronic mutations
US8389487B2 (en) siRNA-mediated gene silencing of synuclein
US20180256752A1 (en) Selective gene therapy expression system
CN106456660B (en) Gene therapy for retinitis pigmentosa
KR20200056428A (en) Variant RNAi
US7604798B2 (en) Methods and compositions for importing nucleic acids into cell nuclei
CA3136004A1 (en) Gene therapies for lysosomal disorders
CN116685329A (en) Nucleic acid constructs and their use for the treatment of spinal muscular atrophy
US20200404890A1 (en) Modeling tdp-43 proteinopathy
US20160256571A1 (en) Invention
JP2023099082A (en) Treatment of myotonic dystrophy
CN114381465B (en) Optimized CYP4V2 gene and application thereof
CN113874512A (en) Compositions and methods for inducing hair cell differentiation
KR20210057720A (en) CLRN1-related hearing loss and/or vision loss treatment method
US20230293727A1 (en) Overexpression of lemd2, lemd3, or chmp7 as a therapeutic modality for tauopathy
Tian et al. Improved gene therapy for MFRP deficiency-mediated retinal degeneration by knocking down endogenous bicistronic Mfrp and Ctrp5 transcript
RU2814137C2 (en) Non-viral dna vectors and options for their use for expression of therapeutic agent based on phenylalanine hydroxylase (pah)
US20230346979A1 (en) Gene therapies for neurodegenerative disorders
WO2024052413A1 (en) Beta-hexosaminidase vectors
CN115484975A (en) Adeno-associated virus compositions for IDS gene transfer and methods of use thereof
Al-Rafiah PLASTIN3 AS A THERAPEUTIC TARGET IN SPINAL MUSCULAR ATROPHY

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BW BY BZ CA CH CN CO CR CU CZ DE DK DM DZ EC EE EG ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NA NI NO NZ OM PG PH PL PT RO RU SC SD SE SG SK SL SM SY TJ TM TN TR TT TZ UA UG US UZ VC VN YU ZA ZM ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): BW GH GM KE LS MW MZ NA SD SL SZ TZ UG ZM ZW AM AZ BY KG KZ MD RU TJ TM AT BE BG CH CY CZ DE DK EE ES FI FR GB GR HU IE IS IT LT LU MC NL PL PT RO SE SI SK TR BF BJ CF CG CI CM GA GN GQ GW ML MR NE SN TD TG

NENP Non-entry into the national phase

Ref country code: DE

WWW Wipo information: withdrawn in national office

Country of ref document: DE

WWE Wipo information: entry into national phase

Ref document number: 2005220900

Country of ref document: AU

WWE Wipo information: entry into national phase

Ref document number: 2005725031

Country of ref document: EP

ENP Entry into the national phase

Ref document number: 2005220900

Country of ref document: AU

Date of ref document: 20050310

Kind code of ref document: A

WWP Wipo information: published in national office

Ref document number: 2005220900

Country of ref document: AU

121 Ep: the epo has been informed by wipo that ep was designated in this application
WWP Wipo information: published in national office

Ref document number: 2005725031

Country of ref document: EP

WWE Wipo information: entry into national phase

Ref document number: 10591883

Country of ref document: US