US20050049219A1

US20050049219A1 - Methods of treatment with mini-dystrophin nucleic acid sequences

Info

Publication number: US20050049219A1
Application number: US10/964,536
Authority: US
Inventors: Jeffrey Chamberlain; Scott Harper
Original assignee: Individual
Current assignee: Individual
Priority date: 2000-10-06
Filing date: 2004-10-13
Publication date: 2005-03-03
Also published as: US8501920B2; AU2001296600A1; ATE400656T1; EP1366160B1; US20030216332A1; WO2002029056A3; EP1366160A2; US20080167260A1; DE60134786D1; WO2002029056A2; US6869777B2

Abstract

The present invention relates to compositions and methods for expressing mini-dystrophin peptides. In particular, the present invention provides compositions comprising nucleic acid sequences that are shorter than wild-type dystrophin cDNA and that express mini-dystrophin peptides that function in a similar manner as wild-type dystrophin proteins. The present invention also provides compositions comprising mini-dystrophin peptides, and methods for expressing mini-dystrophin peptides in target cells.

Description

The present Application claims priority to U.S. Provisional Application Ser. No. 60/238,848, filed Oct. 6, 2000, hereby incorporated by reference.
This invention was made with Government support under contract NIH R01AR40864-10. The government has certain rights in this invention.

FIELD OF THE INVENTION

BACKGROUND OF THE INVENTION

Muscular dystrophy is a group of inherited disorders characterized by progressive muscle weakness and loss of muscle tissue. Muscular dystrophies includes many inherited disorders, including Becker's muscular dystrophy and Duchenne's muscular dystrophy, which are both caused by mutations in the dystrophin gene. Both of the disorders have similar symptoms, although Becker's muscular dystrophy is a slower progressing form of the disease. Duchenne's muscular dystrophy is a rapidly progressive form of muscular dystrophy.
Both disorders are characterized by progressive muscle weakness of the legs and pelvis which is associated with a loss of muscle mass (wasting). Muscle weakness also occurs in the arms, neck, and other areas, but not as severely as in the lower half of the body. Calf muscles initially enlarge (an attempt by the body to compensate for loss of muscle strength), the enlarged muscle tissue is eventually replaced by fat and connective tissue (pseudohypertrophy). Muscle contractions occur in the legs and heels, causing inability to use the muscles because of shortening of muscle fibers and fibrosis of connective tissue. Bones develop abnormally, causing skeletal deformities of the chest and other areas. Cardiomyopathy occurs in almost all cases. Mental retardation may accompany the disorder but it is not inevitable and does not worsen as the disorder progresses. The cause of this impairment is unknown. Becker's muscular dystrophy occurs in approximately 3 out of 100,000 people. Symptoms usually appear in men between the ages of 7 and 26. Women rarely develop symptoms. There is no known cure for Becker's muscular dystrophy. Treatment is aimed at control of symptoms to maximize the quality of life. Activity is encouraged. Inactivity (such as bed rest) can worsen the muscle disease. Physical therapy may be helpful to maintain muscle strength. Orthopedic appliances such as braces and wheelchairs may improve mobility and self-care. Becker's muscular dystrophy results in slowly progressive disability. A normal life span is possible; however, death usually occurs after age 40.
Duchenne's muscular dystrophy occurs in approximately 2 out of 10,000 people. Symptoms usually appear in males 1 to 6 years old. Females are carriers of the gene for this disorder but rarely develop symptoms. There is no known cure for Duchenne's muscular dystrophy. Treatment is aimed at control of symptoms to maximize the quality of life. Activity is encouraged. Inactivity (such as bed rest) can worsen the muscle disease. Physical therapy may be helpful to maintain muscle strength and function. Orthopedic appliances such as braces and wheelchairs may improve mobility and the ability for self-care. Duchenne's muscular dystrophy results in rapidly progressive disability. By age 10, braces may be required for walking, and by age 12, most patients are confined to a wheelchair. Bones develop abnormally, causing skeletal deformities of the chest and other areas. Muscular weakness and skeletal deformities contribute to frequent breathing disorders. Cardiomyopathy occurs in almost all cases. Intellectual impairment is common but is not inevitable and does not worsen as the disorder progresses. Death usually occurs by age 15, typically from respiratory (lung) disorders.
Although there are no available treatments for muscular dystrophy, the usefulness of gene replacement as therapy for the disease has been established in transgenic mouse models. Unfortunately, progress toward therapy for human patients has been limited by lack of a suitable technique for delivery of such vectors to large masses of muscle cells. What is needed in the art is a vector that can carry most of the dystrophin coding sequence, that can be cheaply produced in large quantities, that can be delivered to a large mass of muscle cells, and that provides stable expression of dystrophin after delivery.

SUMMARY OF THE INVENTION

The present invention provides compositions and methods for expressing mini-dystrophin peptides. In particular, the present invention provides compositions comprising nucleic acid sequences that are shorter than wild-type dystrophin cDNA and that express mini-dystrophin peptides that function in a similar manner as wild-type dystrophin proteins. The present invention also provides compositions comprising mini-dystrophin peptides, and methods for expressing mini-dystrophin peptides in target cells.
The present invention provides such shortened nucleic acid sequences in a variety of ways. For example, the present invention provides nucleic acids encoding only 4, 8, 10, 12, 14, 16, 18, 20 and 22 spectrin-like repeat encoding sequences (i.e. nucleic acids encoding an exact number of spectrin-like repeats). As wild-type dystrophin has 24 spectrin-like repeat encoding sequences, providing nucleic acids encoding fewer numbers of repeats reduces the size of the dystrophin gene (e.g. allowing the nucleic acid sequence to fit into vectors with limited cloning capacity). Another example of such shortened nucleic acid sequences are those that lack at least a portion of the carboxy-terminal domain of wild-type dystrophin nucleic acid. A further example of such shortened nucleic acid sequences are those that lack at least a portion of the 3′ untranslated region, or 5′ untranslated region, or both. In certain embodiments, the present invention provides compositions comprising the peptides expressed by the nucleic acid sequences of the present invention.
In certain embodiments, the present invention provides compositions comprising nucleic acid encoding a mini-dystrophin peptide, wherein the mini-dystrophin peptide comprises a spectrin-like repeat domain, and wherein the spectrin-like repeat domain consists of n spectrin-like repeats, wherein n is an even number less than 24. In particular embodiments, the present invention provides nucleic acid encoding a mini-dystrophin peptide, wherein the mini-dystrophin peptide comprises a spectrin-like repeat domain comprising n spectrin-like repeats, wherein the mini-dystrophin peptide contains no more than n spectrin-like repeats, and wherein n is an even number that is less than 24 and at least 4. In some embodiments, the present invention provides nucleic acid encoding a mini-dystrophin peptide, wherein the mini-dystrophin peptide comprises n spectrin-like repeats, wherein the mini-dystrophin peptide contains no more than n spectrin-like repeats, and wherein n is an even number that is less than 24 and at least 4.
In some embodiments, n is 20 or less. In other embodiments, n is 16 or less. In particular embodiments, n is 12 or less. In additional embodiments, n is 8 or less. In preferred embodiments, n is 4. In certain embodiments, n is selected from 4, 8, 10, 12, 14, 16, 18, 20 and 22. In some embodiments, the present invention provides compositions comprising nucleic acid encoding a mini-dystrophin peptide, wherein the mini-dystrophin peptide comprises a spectrin-like repeat domain, and wherein the spectrin-like repeat domain consists of n spectrin-like repeats, wherein n is 4, 8, 12, 16, or 20. In certain embodiments, the present invention provides the peptides encoded by the nucleic acid sequences encoding the mini-dystrophin peptides.
In certain embodiments, the present invention provides compositions comprising nucleic acid encoding a mini-dystrophin peptide, wherein the mini-dystrophin peptide comprises i) a spectrin-like repeat domain comprising 4 dystrophin spectrin-like repeats, ii) an actin-binding domain, and iii) a β-dystroglycan binding domain; and wherein the mini-dystrophin peptide contains no more than 4 dystrophin spectrin-like repeats.
In some embodiments, the present invention provides compositions comprising a mini-dystrophin peptide, wherein the mini-dystrophin peptide comprises a spectrin-like repeat domain comprising n spectrin-like repeats, wherein the mini-dystrophin peptide contains no more than n spectrin-like repeats, and wherein n is an even number that is less than 24 and at least 4. In particular embodiments, the present invention provides a cell (or cell line) containing the nucleic acid and peptide sequences of the present invention.
In certain embodiments, the mini-dystrophin peptide is capable of altering a measurable muscle value in a DMD animal model by at least approximately 10% of the wild type value. In other embodiments, the mini-dystrophin peptide is capable of altering a measurable muscle value in a DMD animal model by at least approximately 20% of the wild type value. In particular embodiments, the mini-dystrophin peptide is capable of altering a measurable muscle value in a DMD animal model by at least approximately 30% of the wild type value. In preferred embodiments, the mini-dystrophin peptide is capable of altering a measurable muscle value in a DMD animal model to a level similar to the wild-type value (e.g. ±4%). In certain embodiments, the nucleic acid comprises at least 2, or at least 4, spectrin-like repeat encoding sequences. In some embodiments, the spectrin-like repeat encoding sequences are precise spectrin-like repeat encoding sequences. In certain embodiments, the nucleic acid is less than 5 kilo-bases in length. In other embodiments, the nucleic acid is less than 6 kilo-bases in length. In particular embodiments, the nucleic acid comprises viral DNA (e.g. adenovirus DNA). In preferred embodiments, the viral DNA comprises adeno-associated viral DNA.
In certain embodiments, the present invention provides compositions comprising nucleic acid encoding a mini-dystrophin peptide, wherein the mini-dystrophin peptide comprises a spectrin-like repeat domain, and wherein the spectrin-like repeat domain consists of n spectrin-like repeats, wherein n is an even number less than 24; and wherein the nucleic acid comprises an actin-binding domain encoding sequence, a β-dystroglycan-binding domain encoding sequence, and at least 2, or at least 4, spectrin-like repeat encoding sequences. In some embodiments, the nucleic acid comprises at least 4 spectrin-like repeat encoding sequences.
In certain embodiments, the present invention provides compositions comprising nucleic acid, wherein the nucleic acid comprises at least 2 spectrin-like repeat encoding sequences, and wherein the nucleic acid encodes a mini-dystrophin peptide comprising a spectrin-like repeat domain, wherein the spectrin-like repeat domain consists of n spectrin-like repeats, and wherein n is an even number less than 24. In some embodiments, the nucleic acid comprises at least 4 spectrin-like repeat encoding sequences.
In some embodiments, the nucleic acid comprises SEQ ID NO:39 (i.e. ΔR4-R23). In other embodiments, the nucleic acid comprises SEQ ID NO:40 (i.e. ΔR2-R21). In certain embodiments, the nucleic acid comprises SEQ ID NO:41 (i.e. ΔR2-R21+H3). In still other embodiments, the nucleic acid comprises SEQ ID NO:42 (i.e. ΔH2-R19).
In certain embodiments, the nucleic acid comprises an expression vector (e.g. plasmid, virus, etc). In some embodiments, the expression vector comprises viral DNA. In certain embodiments, the viral DNA comprises adeno-viral DNA. In some embodiments, the viral DNA comprises lentiviral DNA. In other embodiments, the viral DNA comprises helper-dependent adeno-viral DNA. In preferred embodiments, the viral DNA comprises adeno-associated viral DNA. In some embodiments, the nucleic acid is inserted in a virus (e.g. adeno-associated virus, adenovirus, helper-dependent adeno-associated virus, lentivirus).
In certain embodiments, the nucleic acid comprises an actin-binding domain encoding sequence. In particular embodiments, the actin binding domain comprises at least a portion of SEQ ID NO:6 (e.g. 5%, 10%, 20%, 40%, 50%, or 75% of SEQ ID NO:6). In other embodiments, the actin binding domain comprises at least a portion of a homolog or mutated version of SEQ ID NO:6 (e.g. 5%, 10%, 20%, 40%, 50%, or 75% of a SEQ ID NO:6 homolog or mutated version of SEQ ID NO:6). In certain embodiments, the nucleic acid comprises a β-dystroglycan binding domain. In certain embodiments, the β-dystroglycan binding domain comprises at least a portion of a dystrophin hinge 4 encoding sequence (e.g. the 3′ 50% of SEQ ID NO:34), and at least a portion of dystrophin cysteine-rich domain encoding sequence (e.g. the 5′ 75% of SEQ ID NO:35). In particular embodiments, at least a portion of hinge 4 is the WW domain (SEQ ID NO:45), or a homolog or mutation thereof.
In particular embodiments, the spectrin-like repeat encoding sequences are selected from the group consisting of SEQ ID NOS:8-10, 12-27, and 29-33. In some embodiments, the spectrin-like repeat encoding sequences are selected from the group consisting of SEQ ID NOS:8-10, 12-27, and 29-33, and homologs or mutations of SEQ ID NOS:8-10, 12-27, and 29-33. In preferred embodiments, the spectrin-like repeat encoding sequences are selected from the group consisting of SEQ ID NOS:8-10 and 29-33. In some embodiments, the spectrin-like repeat encoding sequences are identical (e.g. all the sequences are SEQ ID NO:8). In preferred embodiments, the spectrin-like repeat encoding sequences are all different (e.g. the nucleic acid sequence has only 4 spectrin-like repeat encoding sequences, and these 4 are: SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10, and SEQ ID NO:33). In certain embodiments, nucleic acid sequence comprises at least one spectrin-like repeat encoding sequence selected from the group consisting of SEQ ID NOS:8-10, and at least one spectrin-like repeat encoding sequence selected from the group consisting of SEQ ID NOS:29-33.
In certain embodiments, the nucleic acid (or the resulting peptide) comprises at least one dystrophin hinge region. In some embodiments, the nucleic acid comprises at least one dystrophin hinge region selected from hinge region 1, hinge region 2, hinge region 3 and hinge region 4. In some embodiments, the nucleic acid comprises at least one dystrophin hinge region selected from hinge region 1, hinge region 2, and hinge region 3. In particular embodiments, dystrophin hinge region 1 is SEQ ID NO:7, or a homolog (See, e.g. FIG. 11), or a mutant version thereof. In particular embodiments, dystrophin hinge region 2 is SEQ ID NO:11, or a homolog (See, e.g. FIG. 11), or a mutant version thereof. In certain embodiments, dystrophin hinge region 3 is SEQ ID NO:28, or a homolog (See, e.g. FIG. 11), or a mutant version thereof. In other embodiments, dystrophin hinge region 4 is SEQ ID NO:34, or a homolog (See, e.g. FIG. 11), or a mutant version thereof.
In some embodiments, the nucleic acid comprises a sequence encoding at least a portion of wild-type dystrophin C-terminal protein. In other embodiments, the nucleic acid comprises at least a portion of the 5′ untranslated region. In particular embodiments, the nucleic acid comprises at least a portion of the 3′ untranslated region. In different embodiments, the nucleic acid sequence comprises regulatory sequences (e.g. MCK enhancer and promoter elements). In particular embodiments, the nucleic acid sequence is operably linked to regulatory sequences (e.g. MCK enhancer and promoter elements). In certain embodiments, the nucleic acid sequence comprises a mutant muscle-specific enhancer region.
In particular embodiments, the nucleic acid has less than 75% of a wild type dystrophin 5′ untranslated region. In other embodiments, the nucleic acid has less than 50% or 20% or 1% (e.g. 0, 1, 2 nucleotides from a wild type dystrophin 5′ untranslated region). In particularly preferred embodiments, the nucleic acid sequence does not contain any of the wild-type dystrophin 5′ untranslated region. In certain embodiments, the nucleic acid has less than 75% of a wild type dystrophin 3′ untranslated region. In other embodiments, the nucleic acid has less than 50%, preferably less than 40%, more preferably less than 35% of a wild type dystrophin 3′ untranslated region. In certain embodiments, the nucleic acid does not contain a wild-type dystrophin 3′ untranslated region (or, in some embodiments, any type of 3′ untranslated region).
In particular embodiments, the mini-dystrophin peptide (e.g. encoded by the nucleic acid of the present invention) comprises a substantially deleted dystrophin C-terminal domain. In some embodiments, the mini-dystrophin peptide comprises less than 40% of wild type dystrophin C-terminal domain, preferably less than 30%, more preferably less than 20%, even more preferably less than 1%, and most preferably approximately 0% (e.g. 0, 1, 2, 3 or 4 amino acids from the wild type dystrophin C-terminal domain). In some embodiments, the nucleic acid sequence comprises at least one intron sequence.
In some embodiments, the present invention provides methods for expressing a mini-dystrophin peptide in a target cell, comprising; a) providing; i) a vector comprising nucleic acid encoding a mini-dystrophin peptide, wherein the mini-dystrophin peptide comprises a spectrin-like repeat domain, and wherein the spectrin-like repeat domain consists of n spectrin-like repeats, wherein n is an even number less than 24, and ii) a target cell, and b) contacting the vector with the target cell under conditions such that the mini-dystrophin peptide is expressed in the target cells. In certain embodiments, the contacting comprises transfecting. In some embodiments, the contacting is performed in-vitro. In particular embodiments, the contacting is done in-vivo. In other embodiments, the target cell is a muscle cell. In particular embodiments, the target cell further comprises a subject (e.g. with Duchenne muscular dystrophy (DMD) or Becker muscular dystrophy (BMD)). In preferred embodiment, the mini-dystrophin peptide is expressed in the cells of a subject (e.g. such that symptoms of DMD or BMD are reduced or eliminated).
In certain embodiments, the present invention provides methods comprising; a) providing; i) a vector comprising nucleic acid encoding a mini-dystrophin peptide, wherein the mini-dystrophin peptide comprises a spectrin-like repeat domain comprising n spectrin-like repeats, wherein the mini-dystrophin peptide contains no more than n spectrin-like repeats, and wherein n is an even number that is less than 24 and at least 4, and ii) a subject comprising a target cells (e.g. a subject with symptoms of a muscle disease, such as Muscular Dystrophy); and b) contacting the vector with the subject under conditions such that the mini-dystrophin peptide is expressed in the target cell (e.g. such that the symptoms are reduced or eliminated). In preferred embodiments, the nucleic acid encoding the mini-dystrophin peptide is contained within an viral vector (e.g. adeno-associated viral vector), and the contacting is done by means of injecting the viral vector into the subject.
In particular embodiments, the present invention provides compositions comprising nucleic acid, wherein the nucleic acid encodes a mini-dystrophin peptide, and wherein the mini-dystrophin peptide comprises a substantially deleted dystrophin C-terminal domain. In some embodiments, the present invention provides the peptides encoded by the nucleic acid of the present invention. In certain embodiments, the substantially deleted dystrophin C-terminal domain is less than 40% of a wild type dystrophin C-terminal domain. In other embodiments, the substantially deleted dystrophin C-terminal domain is less than 30%, 20%, or 1% of a wild type dystrophin C-terminal domain. In preferred embodiments, the substantially deleted dystrophin C-terminal domain is approximately 0% of a wild type dystrophin C-terminal domain. In certain embodiments, the mini-dystrophin peptide does not contain any portion of the wild type dystrophin C-terminal domain (i.e. it is completely deleted).
In certain embodiments, the mini-dystrophin peptide is capable of altering a measurable muscle value in a DMD animal model by at least 10% of the wild type value. In other embodiments, the mini-dystrophin peptide is capable of altering a measurable muscle value in a DMD animal model by at least 20% of the wild type value. In particular embodiments, the mini-dystrophin-peptide is capable of altering a measurable muscle value in a DMD animal model by at least 30% of the wild type value. In preferred embodiments, the mini-dystrophin peptide is capable of altering a measurable muscle value in a DMD animal model to a level similar to the wild-type value (e.g. ±4%).
In certain embodiments, the nucleic acid comprises an expression vector (e.g. plasmid, virus, etc). In some embodiments, the expression vector comprises viral DNA. In certain embodiments, the viral DNA comprises adeno-viral DNA. In some embodiments, the viral DNA comprises lentiviral DNA. In other embodiments, the viral DNA comprises helper-dependent adeno-viral DNA. In preferred embodiments, the viral DNA comprises adeno-associated viral DNA. In some embodiments, the nucleic acid is inserted in a virus (e.g. adeno-associated virus, adenovirus, helper-dependent adeno-associated virus, lentivirus).
In certain embodiments, the nucleic acid comprises an actin-binding domain encoding sequence. In particular embodiments, the actin binding domain comprises at least a portion of SEQ ID NO:6 (e.g. 5%, 10%, 20%, 40%, 50%, or 75% of SEQ ID NO:6). In other embodiments, the actin binding domain comprises at least a portion of a homolog or mutated version of SEQ ID NO:6 (e.g. 5%, 10%, 20%, 40%, 50%, or 75% of a SEQ ID NO:6 homolog or mutated version of SEQ ID NO:6). In certain embodiments, the nucleic acid comprises a β-dystroglycan binding domain. In certain embodiments, the β-dystroglycan binding domain comprises at least a portion of a dystrophin hinge 4 encoding sequence (e.g. the 3′ 50% of SEQ ID NO:34), and at least a portion of dystrophin cysteine-rich domain encoding sequence (e.g. the 5′ 75% of SEQ ID NO:35). In particular embodiments, at least a portion of hinge 4 is the WW domain (SEQ ID NO:45), or a homolog or mutation thereof.
In certain embodiments, the nucleic acid comprises at least one dystrophin hinge region. In some embodiments, the nucleic acid comprises at least one dystrophin hinge region selected from hinge region 1, hinge region 2, hinge region 3 and hinge region 4. In some embodiments, the nucleic acid comprises at least one dystrophin hinge region selected from hinge region 1, hinge region 2, and hinge region 3. In particular embodiments, dystrophin hinge region 1 is SEQ ID NO:7, or a homolog (See, e.g. FIG. 11), or a mutant version thereof. In particular embodiments, dystrophin hinge region 2 is SEQ ID NO:11, or a homolog (See, e.g. FIG. 11), or a mutant version thereof. In certain embodiments, dystrophin hinge region 3 is SEQ ID NO:28, or a homolog (See, e.g. FIG. 11), or a mutant version thereof. In other embodiments, dystrophin hinge region 4 is SEQ ID NO:34, or a homolog (See, e.g. FIG. 11), or a mutant version thereof.
In other embodiments, the nucleic acid comprises at least a portion of the 5′ untranslated region. In particular embodiments, the nucleic acid comprises at least a portion of the 3′ untranslated region. In different embodiment, the nucleic acid sequence comprises regulatory sequences (e.g. MCK enhancer and promoter elements). In particular embodiments, the nucleic acid sequence is operably linked to regulatory sequences (e.g. MCK enhancer and promoter elements). In certain embodiments, the nucleic acid sequence comprises a mutant muscle-specific enhancer region.
In particular embodiments, the nucleic acid contains less that 75% of a wild type dystrophin 5′ untranslated region. In other embodiments, the nucleic acid contains less than 50% or 20% or 1% (e.g. 0, 1, 2 nucleotides from a wild type dystrophin 5′ untranslated region). In particularly preferred embodiments, the nucleic acid sequence does not contain any of the wild-type dystropllin 5′ untranslated region. In certain embodiments, the nucleic acid has less than 75% of a wild type dystrophin 3′ untranslated region. In other embodiments, the nucleic acid has less than 50%, preferably less than 40%, more preferably less than 35% of a wild type dystrophin 3′ untranslated region. In certain embodiments, the nucleic acid does not contain a wild-type dystrophin 3′ untranslated region (or, in some embodiments, any type of 3′ untranslated region).
In some embodiments, the present invention provides methods for expressing a mini-dystrophin peptide in a target cell, comprising; a) providing; i) a vector comprising nucleic acid, wherein the nucleic acid encodes a mini-dystrophin peptide comprising a substantially deleted dystrophin C-terminal domain, and ii) a target cell, and b) contacting the vector with the target cell under conditions such that the mini-dystrophin peptide is expressed in the target cells. In certain embodiments, the contacting comprises transfecting. In other embodiments, the target cell is a muscle cell.
In certain embodiments, the present invention provides systems and kits with the mini-dystrophin nucleic acid and/or peptide sequences described herein. In certain embodiments, the systems and kits of the present invention comprise a nucleic acid sequence encoding a mini-dystrophin peptide (and/or the mini-dystrophin peptide) and one other component (e.g. an insert component with written instructions for using the mini-dystrophin nucleic acid, or a nucleic acid encoding a vector, or a component for delivering the nucleic acid to a subject, cells for expressing the mini-dystrophin peptide, a buffer, etc.). In certain embodiments, the present invention provides a computer readable medium (e.g. CD, hard drive, floppy disk, magnetic tape, etc.) that contains the nucleic acid or amino acid sequences of the present invention (e.g. a computer readable representation of the nucleotide bases used to make a mini-dystrophin nucleic acid sequence).
In some embodiments, the present invention provides mini-dystrophin nucleic acid sequences for use as a medicament. In other embodiments, the present invention provides mini-dystrophin peptides for use as a medicament. In particular embodiments, the present invention provides the use of mini-dystrophin nucleic acid sequences for preparing a drug for a therapeutic application. In additional embodiments, the present invention provides the use of mini-dystrophin peptides for preparing a drug for a therapeutic application. In some embodiments, the present invention provides mini-dystrophin nucleic acid sequences for the preparation of a composition for the treatment of a muscle disease (e.g. DMD). In other embodiments, the present invention provides mini-dystrophin peptides for the preparation of a composition for the treatment of a muscle disease (e.g. DMD).

DESCRIPTION OF THE FIGURES

FIG. 1 shows the nucleic acid sequence for wild-type human dystrophin cDNA.
FIG. 2 shows the nucleic acid sequence for wild-type mouse dystrophin cDNA.
FIG. 3 shows the nucleic acid sequence for wild-type human utrophin cDNA.
FIG. 4 shows the nucleic acid sequence for wild-type mouse utrophin cDNA FIG. 5 shows various domains of the nucleic acid sequence for wild-type human dystrophin cDNA.
FIG. 6 shows various domains of the nucleic acid sequence for wild-type human dystrophin cDNA.
FIG. 7 shows various domains of the nucleic acid sequence for wild-type human dystrophin cDNA.
FIG. 8 shows various domains of the nucleic acid sequence for wild-type human dystrophin cDNA.
FIG. 9 shows various domains of the nucleic acid sequence for wild-type human dystrophin cDNA.
FIG. 10 shows the 3′ UTR domain nucleic acid sequence for wild-type human dystrophin cDNA.
FIG. 11 shows a sequence alignment between wild-type human dystrophin cDNA and wild-type mouse dystrophin cDNA. The various domains in the human dystrophin sequence have spaces between them with the ends highlighted in bold. In this regard, homologous sequences for various domains in the mouse cDNA sequence are seen.
FIG. 12 shows the nucleic acid sequence for ΔR4-R23, a nucleic acid sequence encoding a mini-dystrophin peptide.
FIG. 13 shows the nucleic acid sequence for ΔR2-R21, a nucleic acid sequence encoding a mini-dystrophin peptide.
FIG. 14 shows the nucleic acid sequence for ΔR2-R21+H3, a nucleic acid sequence encoding a mini-dystrophin peptide.
FIG. 15 shows the nucleic acid sequence for ΔH2-R19, a nucleic acid sequence encoding a mini-dystrophin peptide.
FIG. 16 shows the complete cDNA sequence for human skeletal muscle alpha actinin.
FIG. 17 shows the nucleic acid sequence for ΔR9-R16, a nucleic acid sequence encoding a mini-dystrophin peptide.
FIG. 18 shows the nucleic acid sequence for the WW domain.
FIG. 19 shows various transgenic expression constructs tested in Example 1.
FIG. 20 shows the contractile properties of EDL, soleus, and diaphragm muscles in wild-type, mdx, and dystrophin Δ71-78 mice.
FIG. 21 show the nucleic acid sequence for pBSX.
FIG. 22 shows a restriction map for pBSX.
FIG. 23 shows the ‘full-length’ HDMD sequence.
FIG. 24 shows the cloning procedure for ΔR4-R23.
FIG. 25 shows the cloning procedure for ΔR2-R21+H3.
FIG. 26 shows the cloning procedure for ΔR2-R21.
FIG. 27 shows a schematic illustration of the domains encoded by the truncated and full-length dystrophin sequences tested in Example 5.
FIG. 28 is a graph showing the percentage of myofibers in quadricep muscles of 3 month old mice that display centrally-located nuclei in the indicated strains of transgenic mice.
FIG. 29 shows graphs depicting the force generating capacity in diaphragm (A) or EDL (B) muscles of the indicated strains of dystrophin transgenic mdx mice and control mice.
FIG. 30 shows a graph depicting the force generating capacity in EDL (A) or diaphragm (B) muscles of the indicated strains of dystrophin transgenic mdx mice and control mice.
FIG. 31 is a graph showing the percentage of force generating capacity lost after 1 or 2 lengthening contractions of the tibialis anterior muscle of the indicated strains of dystrophin transgenic mdx mice and control mice.
FIG. 32 is a graph showing the total distance run on a treadmill by animals from the indicated strains of dystrophin transgenic mdx mice and control mice.
FIG. 33 shows a graph depicting the total body mass (A) and mass of the tibialis anterior muscle (B) of the indicated strains of dystrophin transgenic mdx mice and control mice.
FIG. 34 is a schematic illustration of the structure of a mini-dystrophin expression cassette inserted into an adeno-associated viral vector.
FIG. 35 is a schematic illustration of the structure of plasmid pTZ19R (top) and the sequence of the multiple cloning site in the vector (bottom).
FIG. 36 shows the nucleic acid sequence of various MCK enhancer regions (wild-type and mutant).
FIG. 37 shows the nucleic acid sequence of various MCK promoter regions.
FIG. 38 shows a comparison between domains in dystrophin and utrophin.

DEFINITIONS

To facilitate an understanding of the present invention, a number of terms and phrases are defined below:
As used herein, the term “measurable muscle values” refers to measurements of dystrophic symptoms (e.g. fibrosis, an increased proportion of centrally located nuclei, reduced force generation by skeletal muscle, etc.) in an animal. These measurements may be taken, for example, to determine the wild-type value (i.e. the value in a control animal), to determine the value in a DMD (Duchenne muscular dystrophy) animal model (e.g. in an mdx mouse model), and to determine the value in a DMD animal model expressing the mini-dystrophin peptides of the present invention. Various assays may be employed to determine measurable muscle values in an animal including, but not limited to, assays measuring fibrosis, phagocytic infiltration of muscle tissue, variation in myofiber size, an increased proportion of myofibers with centrally located nuclei, elevated serum levels of muscle pyruvate kinase, contractile properties assays, DAP (dystrophin associated protein) assays, susceptibility to contraction induced injuries and measured force assays (See Examples 1 and 4).
As used herein, the term “mini-dystrophin peptide” refers to a peptide that is smaller in size than the full-length wild-type dystrophin peptide, and that is capable of altering (increasing or decreasing) a measurable muscle value in a DMD animal model by at least approximately 10% such that the value is closer to the wild-type value (e.g. a mdx mouse has a measurable muscle value that is 50% of the wild-type value, and this value is increased to at least 60% of the wild-type value; or a mdx mouse has a measurable muscle value that is 150% of the wild-type value, and this value is decreased to at most 140% of the wild-type value). In some embodiments, the mini-dystrophin-peptide is capable of altering a measurable muscle value in a DMD animal model by at least approximately 20% of the wild type value. In certain embodiments, the mini-dystrophin-peptide is capable of altering a measurable muscle value in a DMD animal model by at least approximately 30% of the wild type value. In preferred embodiments, the mini-dystrophin peptide is capable of altering a measurable muscle value in a DMD animal model to a level similar to the wild-type value (e.g. ±4%).
As used herein, the term “wild-type dystrophin cysteine-rich domain” refers to a peptide encoded by the nucleic acid sequences in SEQ ID NO:35 (e.g. in human), as well as wild type peptide homologs encoded by nucleic acid homologs of SEQ ID NO:35 (See, FIG. 11).
As used herein, the term “wild type dystrophin C-terminal domain” refers to a peptide encoded by the nucleic acid sequences in SEQ ID NO:36 (e.g. in human), as well as wild type peptide homologs encoded by nucleic acid homologs of SEQ ID NO:36 (See, FIG. 11).
As used herein, the term “mini-dystrophin peptide comprising a substantially deleted dystrophin C-terminal domain” refers to a mini-dystrophin peptide that has less than 45% of a wild type dystrophin C-terminal domain. In some embodiments, the mini-dystrophin peptide comprises less than 40% of wild type dystrophin C-terminal domain, preferably less than 30%, more preferably less than 20%, even more preferably less than 1%, and most preferably approximately 0% (e.g. 0, 1, 2, 3 or 4 amino acids from the wild type dystrophin C-terminal domain). The construction of mini-dystrophin peptides with a substantially deleted dystrophin C-terminal domain may be accomplished, for example, by deleting all or a portion of SEQ ID NO:36 from human dystrophin SEQ ID NO:1 (See, e.g. Example 3C).
As used herein, the term “wild type dystrophin 5′ untranslated region” refers to the nucleic acid sequence at the very 5′ end of a wild type dystrophin nucleic acid sequence (e.g. SEQ ID NOS:1 and 2) that immediately precedes the amino acid coding regions. For example, for human dystrophin, SEQ ID NO:5 (the first 208 bases) is the 5′ untranslated region (a homolog in mouse may be seen in FIG. 11).
As used herein, the term “wild type dystrophin 3′ untranslated region” refers to the nucleic acid sequence at the very 3′ end of a wild type dystrophin nucleic acid sequence (e.g. SEQ ID NOS:1 and 2) that immediately proceeds the amino acid coding regions. For example, for human dystrophin, SEQ ID NO:38 (the last 2690 bases of the human dystrophin gene) is the 3′ untranslated region (a homolog in mouse may be seen in FIG. 11).
As used herein, the term “actin-binding domain encoding sequence” refers to the portion of a dystrophin nucleic sequence that encodes a peptide-domain capable of binding actin in vitro (e.g. SEQ ID NO:6), as well as homologs (See, FIG. 11), conservative mutations, and truncations of such sequences that encode peptide-domains that are capable of binding actin in vivo. Determining whether a particular nucleic acid sequence encodes a peptide-domain (e.g. homolog, mutation, or truncation of SEQ ID NO:6) that will bind actin in vitro may be performed, for example, by screening the ability of the peptide-domain to bind actin in vitro in a simple actin binding assay (See, Corrado et al., FEBS Letters, 344:255-260 [1994], describing the expression of candidate dystrophin peptides as fusion proteins, absorbing F-actin on to microtiter plates, incubating the candidate peptides in the F-actin coated microtiter plates, washing the plates, adding anti-fusion protein rabbit antibody, and adding an anti-rabbit antibody conjugated to a detectable marker).
As used herein, the term “β-dystroglycan-binding domain encoding sequence” refers to the portion of a dystrophin nucleic sequence that encodes a peptide-domain capable of binding β-dystroglycan in vivo (e.g. SEQ ID NOs:34 and 35), as well as homologs (See, FIG. 11), conservative mutations, and truncations of such sequences that encode peptide-domains that are capable of binding β-dystroglycan in vivo. In preferred embodiments, the β-dystroglycan-binding domain encoding sequence includes at least a portion of a hinge 4 encoding region (e.g. SEQ ID NO:45, the WW domain) and at least a portion of a wild-type dystrophin cysteine-rich domain (e.g. at least a portion of SEQ ID NO:35) (See, e.g Jung et al., JBC, 270 (45):27305 [1995]). Determining whether a particular nucleic acid sequence encodes a peptide-domain (e.g. homolog, mutation, or truncation) that will bind β-dystroglycan in vivo may be performed, for example, by first screening the ability of the peptide-domain to bind β-dystroglycan in vitro in a simple β-dystroglycan binding assay (See, Jung et al., pg 27306—constructing peptide-domain dystrophin-GST fusion peptides and radioactively labelled β-dystroglycan, immobilizing the fusion proteins on glutathione-agarose beads, incubating the beads with the radioactively labelled β-dystroglycan, pelleting the beads, washing the beads, and resolving the sample on an SDS-polyacrylamide gel, staining with Coomasie blue, exposing to film, and quantifying the amount of radioactivity present). Nucleic acid sequences found to express peptides capable of binding β-dystroglycan in such assays may then, for example, be tested in vivo by transfecting a cell line (e.g., COS cells) with two expression vectors, one expressing the dystroglycan peptide and the other expressing the candidate peptide domain (as a fusion protein). After culturing the cells, the protein is then extracted and a co-immunoprecipitation is performed for one of the proteins, followed by a Western blot for the other.
As used herein, the term “spectrin-like repeats” refers to peptides composed of approximately 100 amino acids that are responsible for the rod-like shape of many structural proteins including, but not limited to, dystrophin, utrophin, fodrin, alpha-actin, and spectrin, when the spectrin-like repeats are present in multiple copies (e.g. dystrophin-24, utrophin-22, alpha-actin-4, spectrin-16, etc). Spectrin-like repeats also refers to mutations of these natural peptides, such as conservative changes in amino acid sequence, as well as the addition or deletion of up to 5 amino acids to/from the end of a spectrin-like repeat. Spectrin-like repeats includes ‘precise spectrin-like repeats’ (see below). Examples of spectrin-like repeats include, but are not limited to, peptides encoded by nucleic acid sequences found in wild-type human dystrophin (e.g. SEQ ID NOS:8-10, 12-27, and 29-33).
As used herein, the term “spectrin-like repeat encoding sequences” refers to nucleic acid sequences encoding spectrin-like repeat peptides. This term includes natural and synthetic nucleic acid sequences encoding the spectrin-like repeats (e.g. both the naturally occurring and mutated spectrin-like repeat peptides). Examples of spectrin-like repeat encoding sequences include, but are not limited to, SEQ ID NOS:8-10, 12-27, and 29-33.
As used herein, the term “precise spectrin-like repeat encoding sequences” refers to nucleic acid sequences encoding spectrin-like repeat peptides with up to 1 additional amino acid added to, or deleted from, the spectrin-like repeat. As used herein, the term “spectrin-like repeat domain” refers to the region in a mini-dystrophin peptide that contains the spectrin-like repeats of the mini-dystrophin peptide.
The term “gene” refers to a DNA sequence that comprises control and coding sequences necessary for the production of a polypeptide or precursor thereof. The polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired enzymatic activity is retained. The term “gene” encompasses both cDNA and genomic forms of a given gene.
The tern “wild-type” refers to a gene, gene product, or other sequence that has the characteristics of that gene or gene product when isolated from a naturally occurring source. A wild-type gene is that which is most frequently observed in a population and is thus arbitrarily designated the “normal” or “wild-type” form of the gene. In contrast, the term “modified” or “mutant” refers to a gene, gene product, or other sequence that displays modifications in sequence and or functional properties (e.g. altered characteristics) when compared to the wild-type gene or gene product. It is noted that naturally-occurring mutants can be isolated; these are identified by the fact that they have altered characteristics when compared to the wild-type gene or gene product.
The term “oligonucleotide” as used herein is defined as a molecule comprised of two or more deoxyribonucleotides or ribonucleotide, usually more than three (3), and typically more than ten (10) and up to one hundred (100) or more (although preferably between twenty and thirty). The exact size will depend on many factors, which in turn depends on the ultimate function or use of the oligonucleotide. The oligonucleotide may be generated in any manner, including chemical synthesis, DNA replication, reverse transcription, or a combination thereof.
As used herein, the term “regulatory sequence” refers to a genetic sequence or element that controls some aspect of the expression of nucleic acid sequences. For example, a promoter is a regulatory element that facilitates the initiation of transcription of an operably linked coding region. Other regulatory elements are enhancers, splicing signals, polyadenylation signals, termination signals, etc. Examples include, but are not limited to, the 5′ UTR of the dystrophin gene (SEQ ID NO:5), MCK promoters and enhancers (both wild type and mutant, See U.S. provisional app. Ser. No. 60/218,436, filed Jul. 14, 2000, and International Application PCT/US01/22092, filed Jul. 13, 2001, both of which are hereby incorporated by reference).
Transcriptional control signals in eucaryotes comprise “promoter” and “enhancer” elements. Promoters and enhancers consist of short arrays of DNA sequences that interact specifically with cellular proteins involved in transcription. The present invention contemplates modified enhancer regions.
The term “recombinant DNA vector” as used herein refers to DNA sequences containing a desired coding sequence and appropriate DNA sequences necessary for the expression of the operably linked coding sequence in a particular host organism (e.g., mammal). DNA sequences necessary for expression in procaryotes include a promoter, optionally an operator sequence, a ribosome binding site and possibly other sequences. Eukaryotic cells are known to utilize promoters, polyadenlyation signals and enhancers.
The terms “in operable combination”, “in operable order” and “operably linked” as used herein refer to the linkage of nucleic acid sequences in such a manner that a nucleic acid molecule capable of directing the transcription of a given gene and/or the synthesis of a desired protein molecule is produced. The term also refers to the linkage of amino acid sequences in such a manner so that a functional protein is produced.
“Hybridization” methods involve the annealing of a complementary sequence to the target nucleic acid (the sequence to be detected). The ability of two polymers of nucleic acid containing complementary sequences to find each other and anneal through base pairing interaction is a well-recognized phenomenon.
The “complement” of a nucleic acid sequence as used herein refers to an oligonucleotide which, when aligned with the nucleic acid sequence such that the 5′ end of one sequence is paired with the 3′ end of the other, is in “antiparallel association.” Complementarity need not be perfect; stable duplexes may contain mismatched base pairs or unmatched bases. Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length of the oligonucleotide, base composition and sequence of the oligonucleotide, ionic strength and incidence of mismatched base pairs.
The term “homology” refers to a degree of complementarity. There may be partial homology or complete homology (i.e., identity). A partially complementary sequence is one that at least partially inhibits a completely complementary sequence from hybridizing to a target nucleic acid is referred to using the functional term “substantially homologous.” The inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or Northern blot, solution hybridization and the like) under conditions of low stringency. A substantially homologous sequence or probe will compete for and inhibit the binding (i.e., the hybridization) of a completely homologous to a target under conditions of low stringency. This is not to say that conditions of low stringency are such that non-specific binding is permitted; low stringency conditions require that the binding of two sequences to one another be a specific (i.e., selective) interaction. The absence of non-specific binding may be tested by the use of a second target that lacks even a partial degree of complementarity (e.g., less than about 30% identity); in the absence of non-specific binding the probe will not hybridize to the second non-complementary target.
As used herein the term “stringency” is used in reference to the conditions of temperature, ionic strength, and the presence of other compounds such as organic solvents, under which nucleic acid hybridizations are conducted. Those skilled in the art will recognize that “stringency” conditions may be altered by varying the parameters just described either individually or in concert. With “high stringency” conditions, nucleic acid base pairing will occur only between nucleic acid fragments that have a high frequency of complementary base sequences (e.g., hybridization under “high stringency” conditions may occur between homologs with about 85-100% identity, preferably about 70-100% identity). With medium stringency conditions, nucleic acid base pairing will occur between nucleic acids with an intermediate frequency of complementary base sequences (e.g., hybridization under “medium stringency” conditions may occur between homologs with about 50-70% identity). Thus, conditions of “weak” or “low” stringency are often required with nucleic acids that are derived from organisms that are genetically diverse, as the frequency of complementary sequences is usually less.
Low stringency conditions when used in reference to nucleic acid hybridization comprise conditions equivalent to binding or hybridization at 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCL, 6.9 g/l NaH₂PO₄-H₂O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.1% SDA, 5× Denhardt's reagent [50× Denhardt's contains per 500 ml: 5 g Ficoll (Type 400, Pharmacia), 5 g BSA (Fraction V, Sigma)] and 100 μg/ml denatured salmon sperm DNA followed by washing in solution comprising 5×SSPE, 0.1% SDS at 42° C. when a probe of about 500 nucleotides in length is employed.
High stringency conditions when used in reference to nucleic acid hybridization comprises conditions equivalent to binding or hybridizing at 42° C. in a solution consisting of 5×SSPE (43.8 g/l NaCL, 6.9 g/l NaH₂PO₄-H₂O and 1.85 g/l EDTA, pH adjusted to 7.4 with NaOH), 0.5% SDS, 5× Denhardt's reagent and 100 μg/ml denatured salmon sperm DNA, followed by washing in a solution comprising 0.1×SSPE, 1.0% SDS at 42° C. when a probe of about 500 nucleotides is employed.
The art knows well that numerous equivalent conditions may be employed to comprise low stringency conditions; factors such as the length and nature (DNA, RNA, base composition) of the probe and nature of the target (DNA, RNA, base composition, present in solution or immobilized, etc.) and the concentration of the salts and other components (e.g., the presence or absence of formamide, dextran sulfate, polyethylene glycol) are considered and the hybridization solution may be varied to generate conditions of low stringency hybridization different from, but equivalent to, the above listed conditions. In addition, the art knows conditions that promote hybridization under conditions of high stringency (e.g., increasing the temperature of the hybridization and/or wash steps, the use of formamide in the hybridization solution, etc.).
The term “transfection” as used herein refers to the introduction of foreign DNA into eukaryotic cells. Transfection may be accomplished by a variety of means known to the art including calcium phosphate-DNA co-precipitation, DEAE-dextran-mediated transfection, polybrene-mediated transfection, electroporation, microinjection, liposome fusion, lipofection, protoplast fusion, retroviral infection, and biolistics.
The term “stable transfection” or “stably transfected” refers to the introduction and integration of foreign DNA into the genoine of the transfected cell. The term “stable transfectant” refers to a cell which has stably integrated foreign DNA into the genomic DNA.
As used herein, the terms “nucleic acid molecule encoding,” “DNA sequence encoding,” and “DNA encoding” refer to the order or sequence of deoxyribonucleotides along a strand of deoxyribonucleic acid. The order of these deoxyribonucleotides determines the order of amino acids along the polypeptide (protein) chain. The DNA sequence thus codes for the amino acid sequence.
As used herein, the terms “muscle cell” refers to a cell derived from muscle tissue, including, but not limited to, cells derived from skeletal muscle, smooth muscle (e.g. from the digestive tract, urinary bladder, and blood vessels), and cardiac muscle. The term includes muscle cells in vitro, ex vivo, and in vivo. Thus, for example, an isolated cardiomyocyte would constitute a muscle cell, as would a cell as it exists in muscle tissue present in a subject in vivo. This term also encompasses both terminally differentiated and nondifferentiated muscle cells, such as myocytes, myotubes, myoblasts, cardiomyocytes, and cardiomyoblasts.
As used herein, the term “muscle-specific” in reference to an regulatory element (e.g. enhancer region, promoter region) means that the transcriptional activity driven by these regions is mostly in muscle cells or tissue (e.g. 20:1) compared to the activity conferred by the regulatory sequences in other tissues. An assay to determine the muscle-specificity of a regulatory region is provided in Example 5 below (measuring beta-galactoside in muscle cells and liver cells from a mouse transfected with an expression vector).
As used herein, the term “mutant muscle-specific enhancer region” refers to a wild-type muscle-specific enhancer region that has been modified (e.g. deletion, insertion, addition, substitution), and in particular, has been modified to contain an additional MCK-R control element (See U.S. Prov. App. Ser. No. 60/218,436, hereby incorporated by reference, and section IV below).

DESCRIPTION OF THE INVENTION

The present invention provides compositions and methods for expressing mini-dystrophin peptides. In particular, the present invention provides compositions comprising nucleic acid sequences that are shorter than wild-type dystrophin cDNA and that express mini-dystrophin peptides that function in a similar manner as wild-type dystrophin proteins. The present invention also provides compositions comprising mini-dystrophin peptides, and methods for expressing mini-dystrophin peptides in target cells.
The present invention provides such shortened nucleic acid sequences (and resulting peptides) in a variety of ways. For example, the present invention provides nucleic acid encoding only 4, 8, 12, 16, and 20 spectrin-like repeat encoding sequences (i.e. nucleic acid encoding an exact number of spectrin-like repeats that are multiples of 4). As wild-type dystrophin has 24 spectrin-like repeat encoding sequences, providing nucleic acid encoding fewer numbers of repeats reduces the size of the dystrophin gene (e.g. allowing the nucleic acid sequence to fit into vectors with limited cloning capacity). Another example of such shortened nucleic acid sequences are those that lack at least a portion of the carboxy-terminal domain of wild-type dystrophin nucleic acid. A further example of such shortened nucleic acid sequences are those that lack at least a portion of the 3′ untranslated region, or 5′ untranslated region, or both.
I. Dystrophin
A. Dystrophin Structure
In some embodiments, the present invention provides gene constructs comprising spectrin-like repeats from human dystrophin. Dystrophin is a 427 kDa cytoskeletal protein and is a member of the spectrin/αactinin superfamily (See e.g., Blake et al., Brain Pathology, 6:37 [1996]; Winder, J. Muscle Res. Cell. Motil., 18:617 [1997]; and Tinsley et al., PNAS, 91:8307 [1994]). The N-terminus of dystrophin binds to actin, having a higher affinity for non-muscle actin than for sarcomeric actin. Dystrophin is involved in the submembraneous network of non-muscle actin underlying the plasma membrane. Dystrophin is associated with an oligomeric, membrane spanning complex of proteins and glycoproteins, the dystrophin-associated protein complex (DPC). The N-terminus of dystrophin has been shown in vitro to contain a functional actin-binding domain. The C-terminus of dystrophin binds to the cytoplasmic tail of β-dystroglycan, and in concert with actin, anchors dystrophin to the sarcolemma. Also bound to the C-terminus of dystrophin are the cytoplasmic members of the DPC. Dystrophin thereby provides a link between the actin-based cytoskeleton of the muscle fiber and the extracellular matrix. It is this link that is disrupted in muscular dystrophy.

The central rod domain of dystrophin is composed of a series of 24 weakly repeating units of approximately 110 amino acids, similar to those found in spectrin (i.e., spectrin-like repeats). This domain constitutes the majority of dystrophin and gives dystrophin a flexible rod-like structure. The rod-domain is interrupted by four hinge regions that are rich in proline. It is contemplated that the rod-domain provides a structural link between member of the DPC. Table 1 shows an overview of the structural and functional domains of human dystrophin.

TABLE 1


Full Length Human Dystrophin cDNA

Nucleotides	Feature	SEQ ID NO:

1-208	5′ untranslated region	SEQ ID NO: 5
209-211	Start codon (ATG)	—
209-964	N terminus	SEQ ID NO: 6
965-1219	Hinge 1	SEQ ID NO: 7
1220-1546	Spectrin-like repeat No. 1	SEQ ID NO: 8
1547-1879	Spectrin-like repeat No. 2	SEQ ID NO: 9
1880-2212	Spectrin-like repeat No. 3	SEQ ID NO: 10
2213-2359	Hinge 2	SEQ ID NO: 11
2360-2692	Spectrin-like repeat No. 4	SEQ ID NO: 12
2693-3019	Spectrin-like repeat No. 5	SEQ ID NO: 13
3020-3346	Spectrin-like repeat No. 6	SEQ ID NO: 14
3347-3673	Spectrin-like repeat No. 7	SEQ ID NO: 15
3674-4000	Spectrin-like repeat No. 8	SEQ ID NO: 16
4001-4312	Spectrin-like repeat No. 9	SEQ ID NO: 17
4313-4588	Spectrin-like repeat No. 10	SEQ ID NO: 18
4589-4915	Spectrin-like repeat No. 11	SEQ ID NO: 19
4916-5239	Spectrin-like repeat No. 12	SEQ ID NO: 20
5340-5551	Spectrin-like repeat No. 13	SEQ ID NO: 21
5552-5833	Spectrin-like repeat No. 14	SEQ ID NO: 22
5834-6127	Spectrin-like repeat No. 15	SEQ ID NO: 23
6128-6187	20 amino acid insert (not hinge)	—
6188-6514	Spectrin-like repeat No. 16	SEQ ID NO: 24
6515-6835	Spectrin-like repeat No. 17	SEQ ID NO: 25
6836-7186	Spectrin-like repeat No. 18	SEQ ID NO: 26
7187-7489	Spectrin-like repeat No. 19	SEQ ID NO: 27
7490-7612	Hinge 3	SEQ ID NO: 28
7613-7942	Spectrin-like repeat No. 20	SEQ ID NO: 29
7943-8269	Spectrin-like repeat No. 21	SEQ ID NO: 30
8270-8617	Spectrin-like repeat No. 22	SEQ ID NO: 31
8618-9004	Spectrin-like repeat No. 23	SEQ ID NO: 32
9005-9328	Spectrin-like repeat No. 24	SEQ ID NO: 33
9329-9544	Hinge 4	SEQ ID NO: 34
9545-10431	Start of C terminus	SEQ ID NO: 35
10432-11254	Alternatively spliced exons 71-78	SEQ ID NO: 36
11255-11266	End of Coding Region	SEQ ID NO: 37
11267-13957	3′ untranslated region	SEQ ID NO: 38

*Domain structure based on Winder et al., Febs Letters, 369: 27-33 (1995)

B. Spectrin-Like Repeats
Spectrin-like repeats are about 100 amino acids long and are found in a number of proteins, including the actin binding proteins spectrin, fodrin, a-actinin, and dystrophin, but their function remains unclear (Dhermy, 1991. Biol. Cell, 71:249-254). These domains may be involved in connecting functional domains and/or mediate protein-protein interactions. The many tandem, spectrin-like motifs that comprise most of the mass of the proteins in this superfamily are responsible for their similar flexible, rod-like molecular shapes. Although these homologous motifs are frequently called repeats or repetitive segments, adjacent segments in each protein are only distantly related evolutionarily.
Spectrin is a cytoskeletal protein of red blood cells that is associated with the cytoplasmic side of the lipid bilayer (See e.g., Speicher and Ursitti, Current Biology, 4:154 [1994]). Spectrin is a long-thin flexible rod-shaped protein that constitutes about 25% of the membrane-associated protein mass. Spectrin is composed of two large polypeptide chains, α-spectrin (˜240 kDa) and β-spectrin (˜220 kDa) and serves to cross-link short actin oligomers to form a dynamic two-dimensional submembrane latticework. Spectrin isoforms have been found in numerous cell types and have been implicated in a variety of functions.
The recent determination of the crystal structure of a single domain of spectrin provides insight into the structure function of an entire class of large actin cross-linking proteins (Yan et al., Science, 262:2027 [1993]). The domain is an example of a spectrin-like repeat. Early analysis of spectrin-like repeats by partial peptide sequence analysis demonstrated that most of the antiparallel spectrin heterodimer is made up of homologous 106 residue motifs. Subsequent sequence analyses of cDNAs confirmed that this small motif is the major building block for all spectrin isoforms, as well as for the related actinins and dystrophins (Matsudaira, Trends Biochem Sci, 16:87 [1991]).
Given their similar sequences, all spectrin motifs are expected to have related, but not identical, three-dimensional structures. The structure of a single Drosophila spectrin motif, 14, which has now been determined (Yan et al., Science, 262:2027 [1993]), should therefore provide insight into the overall conformation of spectrins in particular and, to a more limited extent, the other members of the spectrin superfamily. The structure shows that the spectrin motif forms a three-helix bundle, similar to the earliest conformational prediction based on the analysis of multiple homologous motifs (Speicher and Marchesi, Nature, 311:177 [1984]).
II. Variants and Homologs of Dystrophin
The present invention is not limited to the spectrin-like repeat encoding sequences SEQ ID NOS:8-10, 12-27, and 29-33, but specifically includes nucleic acid sequences capable of hybridizing to the spectrin-like repeat encoding sequences SEQ ID NOS:8-10, 12-27, and 29-33, (e.g. capable of hybridizing under high stringent conditions). Those skilled in the art know that different hybridization stringencies may be desirable. For example, whereas higher stringencies may be preferred to reduce or eliminate non-specific binding between the spectrin-like repeat encoding sequences SEQ ID NOS:8-10, 12-27, and 29-33, and other nucleic acid sequences, lower stringencies may be preferred to detect a larger number of nucleic acid sequences having different homologies to the nucleotide sequence of SEQ ID NOS:8-10, 12-27, and 29-33.
Accordingly, in some embodiments, the dystrophin spectrin-like repeats of the compositions of the present invention (e.g., SEQ ID NOs:8-10, 12-27, and 29-33) are replaced with different spectrin-like repeats, including, but not limited to, variants, homologs, truncations, and additions of dystrophin spectrin-like repeats. Candidate spectrin-like repeats are screened for activity using any suitable assay, including, but not limited to, those described below and in illustrative Examples 1 and 5.
A. Homologs
1. Dystrophin From Other Species
In some embodiments, the spectrin-like repeats of the gene constructs of the present invention are replaced with spectrin-like repeats of dystrophin from other species (e.g., homologs of dystrophin), including, but not limited to, those described herein. Homologs of dystrophin have been identified in a variety of organisms, including mouse (Genbank accession number M68859); dog (Genbank accession number AF070485); and chicken (Genbank accession number X13369). The spectrin-like repeats of the mouse dystrophin gene were compared to the human gene (See FIG. 11) and were shown to have significant homology. Similar comparisons can be generated with homologs from other species, including but not limited to, those described above, by using a variety of available computer programs (e.g., BLAST, from NCBI). Candidate homologs can be screened for biological activity using any suitable assay, including, but not limited to, those described herein.
2. Utrophin
In some embodiments, the spectrin-like repeats of the gene constructs of the present invention are replaced with spectrin-like repeats from another peptide (e.g., homologs of dystrophin). For example, in some embodiments, spectrin-like repeats from the utrophin protein (See e.g., Genbank accession number X69086; SEQ ID NO:3; FIG. 3) are utilized. Utrophin is an autosomally-encoded homolog of dystrophin and has been postulated that the proteins play a similar physiological role (For a recent review, See e.g., Blake et al., Brain Pathology, 6:37 [1996]). Human utrophin shows substantial homology to dystrophin, with the major difference occurring in the rod domain, where utrophin lacks repeats 15 and 19 and two hinge regions (See e.g., Love et al., Nature 339:55 [1989]; Winder et al., FEBS Lett., 369:27 [1995]). Utrophin thus contains 22 spectrin-like repeats and two hinge regions. A comparison of the rod domain of Utrophin and Dystrophin is shown in FIG. 38.
In addition, in some embodiments, spectrin-like repeats from a homolog of utrophin are utilized. Homologs of utrophin have been identified in a variety of organisms, including mouse (Genbank accession number Y12229; SEQ ID NO:4; FIG. 4) and rat (Genbank accession number AJ002967). The nucleic acid sequence of these or additional homologs can be compared to the nucleic acid sequence of human utrophin using any suitable methods, including, but not limited to, those described above. Candidate spectrin-like repeats from human utrophin or utrophin homologs can be screened for biological activity using any suitable assay, including, but not limited to, those described herein.
3. Alpha-actinin
In some embodiments, spectrin-like repeats from Dystrophin are replaced with spectrin-like repeats from alpha-actinin. The microfilament protein alpha-actinin exists as a dimer. The N-terminal regions of both polypeptides, arranged in antiparallel orientation, comprise the actin-binding regions, while the C-terminal, larger parts consist of four spectrin-like repeats that interact to form a rod-like structure (See e.g., Winkler et al., Eur. J. Biochem., 248:193 [1997]). In some embodiments, human alpha-actinin spectrin-like repeats are utilized (Genbank accession number M86406; SEQ ID NO:87; FIG. 16). In other embodiments, alpha-actinin homologs from other organisms are utilized (e.g., mouse (Genbank accession number AJ289242); Xenopus (Genbank accession number BE576799), and rat (Genbank accession number AFI90909).
B. Variants
Still other embodiments of the present invention provide mutant or variant forms of spectrin-like repeats (i.e., muteins). It is possible to modify the structure of a peptide having an activity of spectrin-like repeats for such purposes as enhancing therapeutic or prophylactic efficacy, or stability (e.g., ex vivo shelf life, and/or resistance to proteolytic degradation in vivo). Such modified peptides provide additional peptides having a desired activity of the subject spectrin-like repeats as defined herein. A modified peptide can be produced in which the amino acid sequence has been altered, such as by amino acid substitution, deletion, or addition.
Moreover, as described above, variant forms (e.g., mutants) of the subject spectrin-like repeats are also contemplated as finding use in the present invention. For example, it is contemplated that an isolated replacement of a leucine with an isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, or a similar replacement of an amino acid with a structurally related amino acid (i.e., conservative mutations) will not have a major effect on the biological activity of the resulting molecule. Accordingly, some embodiments of the present invention provide variants of spectrin-like repeats containing conservative replacements. Conservative replacements are those that take place within a family of amino acids that are related in their side chains. Genetically encoded amino acids can be divided into four families: (1) acidic (aspartate, glutamate); (2) basic (lysine, arginine, histidine); (3) nonpolar (alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan); and (4) uncharged polar (glycine, asparagine, glutamine, cysteine, serine, threonine, tyrosine). Phenylalanine, tryptophan, and tyrosine are sometimes classified jointly as aromatic amino acids. In similar fashion, the amino acid repertoire can be grouped as (1) acidic (aspartate, glutamate); (2) basic (lysine, arginine histidine), (3) aliphatic (glycine, alanine, valine, leucine, isoleucine, serine, threonine), with serine and threonine optionally be grouped separately as aliphatic-hydroxyl; (4) aromatic (phenylalanine, tyrosine, tryptophan); (5) amide (asparagine, glutamine); and (6) sulfur-containing (cysteine and methionine) (See e.g., Stryer (ed.), Biochemistry, 2nd ed, WH Freeman and Co. [1981]). Whether a change in the amino acid sequence of a peptide results in a functional homolog can be readily determined by assessing the ability of the variant peptide to function in a fashion similar to the wild-type protein. Peptides in which more than one replacement has taken place can readily be tested in the same manner.
The present invention further contemplates a method of generating sets of combinatorial mutants of the present spectrin-like repeats, as well as truncation mutants, and is especially useful for identifying potential variant sequences (i.e., homologs) that possess the biological activity of spectrin-like repeats (e.g., a decrease in muscle necrosis). In addition, screening such combinatorial libraries is used to generate, for example, novel spectrin-like repeat homologs that possess novel biological activities all together.
Therefore, in some embodiments of the present invention, spectrin-like repeat homologs are engineered by the present method to produce homologs with enhanced biological activity. In other embodiments of the present invention, combinatorially-derived homologs are generated which provide spectrin-like repeats that are easier to express and transfer to host cells. Such spectrin-like repeats, when expressed from recombinant DNA constructs, can be used in therapeutic embodiments of the invention described below.
Still other embodiments of the present invention provide spectrin-like repeat homologs which have intracellular half-lives dramatically different than the corresponding wild-type protein. For example, the altered proteins comprising the spectrin-like repeat homologs are rendered either more stable or less stable to proteolytic degradation or other cellular process that result in destruction of, or otherwise inactivate spectrin-like repeats. Such homologs, and the genes that encode them, can be utilized to alter the pharmaceutical activity of constructs expressing spectrin-like repeats by modulating the half-life of the protein. For instance, a short half-life can give rise to more transient biological effects. As above, such proteins find use in pharmaceutical applications of the present invention.
In some embodiments of the combinatorial mutagenesis approach of the present invention, the amino acid sequences for a population of spectrin-like repeat homologs are aligned, preferably to promote the highest homology possible. Such a population of variants can include, for example, spectrin-like repeat homologs from one or more species, or spectrin-like repeat homologs from different proteins of the same species (e.g., including, but not limited to, those described above). Amino acids that appear at each position of the aligned sequences are selected to create a degenerate set of combinatorial sequences.
In a preferred embodiment of the present invention, the combinatorial spectrin-like repeat library is produced by way of a degenerate library of genes encoding a library of polypeptides that each include at least a portion of candidate spectrin-like repeat sequences. For example, a mixture of synthetic oligonucleotides is enzymatically ligated into gene sequences such that the degenerate set of candidate spectrin-like repeat sequences are expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of spectrin-like repeat sequences therein.
There are many ways by which the library of potential spectrin-like repeat homologs can be generated from a degenerate oligonucleotide sequence. In some embodiments, chemical synthesis of a degenerate gene sequence is carried out in an automatic DNA synthesizer, and the synthetic genes are ligated into an appropriate gene for expression. The purpose of a degenerate set of genes is to provide, in one mixture, all of the sequences encoding the desired set of potential spectrin-like repeat sequences. The synthesis of degenerate oligonucleotides is well known in the art (See e.g., Narang, Tetrahedron Lett., 39:3 9 [1983]; Itakura et al., Recombinant DNA, in Walton (ed.), Proceedings of the 3rd Cleveland Symposium on Macromolecules, Elsevier, Amsterdam, pp 273-289 [1981]; Itakura et al., Annu. Rev. Biochem., 53:323 [1984]; Itakura et al., Science 198:1056 [1984]; Ike et al., Nucl. Acid Res., 11:477 [1983]). Such techniques have been employed in the directed evolution of other proteins (See e.g., Scott et al., Science, 249:386-390 [1980]; Roberts et al., Proc. Natl. Acad. Sci. USA, 89:2429-2433 [1992]; Devlin et al., Science, 249: 404-406 [1990]; Cwirla et al., Proc. Natl. Acad. Sci. USA, 87: 6378-6382 [1990]; as well as U.S. Pat. Nos. 5,223,409, 5,198,346, and 5,096,815, each of which is incorporated herein by reference).
A wide range of techniques are known in the art for screening gene products of combinatorial libraries made by point mutations, and for screening cDNA libraries for gene products having a certain property. Such techniques are generally adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of spectrin-like repeat homologs. The most widely used techniques for screening large gene libraries typically comprise cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates relatively easy isolation of the vector encoding the gene whose product was detected. Each of the illustrative assays described below are amenable to high through-put analysis as necessary to screen large numbers of degenerate sequences created by combinatorial mutagenesis techniques.
Accordingly, in one embodiment of the present invention, the candidate genes comprising altered spectrin-like repeats are displayed on the surface of a cell or viral particle, and the ability of particular cells or viral particles to bind to a another member of the DPC complex (e.g., actin) is assayed. In other embodiments of the present invention, the gene library is cloned into the gene for a surface membrane protein of a bacterial cell, and the resulting fusion protein detected by panning (WO 88/06630; Fuchs et al., BioTechnol., 9:1370 [1991]; and Goward et al, TIBS 18:136 [1992]). In other embodiments of the present invention, fluorescently labeled molecules that bind proteins comprising spectrin like repeats (e.g., actin), can be used to score for potentially functional spectrin-like repeat homologs. Cells are visually inspected and separated under a fluorescence microscope, or, where the morphology of the cell permits, separated by a fluorescence-activated cell sorter.
In an alternate embodiment of the present invention, the gene library is expressed as a fusion protein on the surface of a viral particle. For example, foreign peptide sequences are expressed on the surface of infectious phage in the filarnentous phage system, thereby conferring two significant benefits. First, since these phage can be applied to affinity matrices at very high concentrations, a large number of phage can be screened at one time. Second, since each infectious phage displays the combinatorial gene product on its surface, if a particular phage is recovered from an affinity matrix in low yield, the phage can be amplified by another round of infection. The group of almost identical E. coli filamentous phages M13, fd, and fl are most often used in phage display libraries, as either of the phage gIII or gVIII coat proteins can be used to generate fusion proteins without disrupting the ultimate packaging of the viral particle (See e.g., WO 90/02909; WO 92/09690; Marks et al., J. Biol. Chem., 267:16007 [1992]; Griffths et al., EMBO J., 12:725 [1993]; Clackson et al., Nature, 352:624 [1991]; and Barbas et al., Proc. Natl. Acad. Sci., 89:4457 [1992]).
In another embodiment of the present invention, the recombinant phage antibody system (e.g., RPAS, Pharmacia Catalog number 27-9400-01) is modified for use in expressing and screening of spectrin-like repeat combinatorial libraries. The pCANTAB 5 phagemid of the RPAS kit contains the gene that encodes the phage gIII coat protein. In some embodiments of the present invention, the spectrin-like repeat combinatorial gene library is cloned into the phagemid adjacent to the gIII signal sequence such that it is expressed as a gIII fusion protein. In other embodiments of the present invention, the phagemid is used to transform competent E. coli TG1 cells after ligation. In still other embodiments of the present invention, transformed cells are subsequently infected with M13KO7 helper phage to rescue the phagemid and its candidate spectrin-like repeat gene insert. The resulting recombinant phage contain phagemid DNA encoding a specific candidate spectrin-like repeat and display one or more copies of the corresponding fusion coat protein. In some embodiments of the present invention, the phage-displayed candidate proteins that are capable of, for example, binding to actin, are selected or enriched by panning. The bound phage is then isolated, and if the recombinant phage express at least one copy of the wild type gIII coat protein, they will retain their ability to infect E. coli. Thus, successive rounds of reinfection of E. coli and panning will greatly enrich for spectrin-like repeat homologs, which can then be screened for further biological activities.
In light of the present disclosure, other forms of mutagenesis generally applicable will be apparent to those skilled in the art in addition to the aforementioned rational mutagenesis based on conserved versus non-conserved residues. For example, spectrin-like repeat homologs can be generated and screened using, for example, alanine scanning mutagenesis and the like (Ruf et al., Biochem., 33:1565 [1994]; Wang et al., J. Biol. Chem., 269:3095 [1994]; Balint et al. Gene 137:109 [1993]; Grodberg et al., Eur. J. Biochem., 218:597 [1993]; Nagashima et al., J. Biol. Chem., 268:2888 [1993]; Lowman et al., Biochem., 30:10832 [1991]; and Cunningham et al., Science, 244:1081 [1989]), by linker scanning mutagenesis (Gustin el al., Virol., 193:653 [1993); Brown et al., Mol. Cell. Biol., 12:2644 [1992]; McKnight el al., Science, 232:316); or by saturation mutagenesis (Meyers el al., Science, 232:613 [1986]).
C. Truncations and Additions
In yet other embodiments of the present invention, the spectrin-like repeats of human dystrophin are replaced by truncation or additions of spectrin-like repeats from dystrophin or another protein, including, but not limited to, those described above. Accordingly, in some embodiments, amino acids are truncated from either end of one or more of the spectrin-like repeats in a given construct. The activity of truncation mutants is determined using any suitable assay, including, but not limited to, those disclosed herein.
In some embodiments, additional amino acids are added to either or both ends of the spectrin-like repeats in a given construct. In some embodiments, single amino acids are added and the activity of the construct is determined. Amino acids may be added to one or more of the spectrin-like repeats in a given construct. The activity of spectrin-like repeats comprising additional amino acids is determined using any suitable assay, including, but not limited to, those disclosed herein.
III. Carboxy-Terminal Domain Truncated Dystrophin Genes
In some embodiments, the present invention provides compositions comprising nucleic acid, wherein the nucleic acid encodes a mini-dystrophin peptide, and wherein the mini-dystrophin peptide comprises a substantially deleted dystrophin C-terminal domain (e.g., 55% of the dystrophin C-terminal domain is missing). In some embodiments, this type of truncation prevents the mini-dystrophin peptide from binding both syntrophin and dystrobrevin.
The dystrophin COOH-terminal domain is located adjacent to the cysteine-rich domain, and contains an alternatively spliced region and two coiled-coil motifs (Blake et al., Trends Biochem. Sci., 20:133, 1995). The alternatively spliced region binds three isoforms of syntrophin in muscle, while the coiled-coil motifs bind numerous members of the dystrobrevin family (Sadoulet-Puccio et al., PNAS, 94:12413, 1997). The dystrobrevins display significant homology with the COOH-terminal region of dystrophin, and the larger dystrobrevin isoforms also bind to the syntrophins. The importance and functional significance of syntrophin and dystrobrevin remains largely unknown, although they may be involved in cell signaling pathways (Grady et al., Nat. Cell. Biol, 1:215, 1999).
Researchers have previously generated transgenic mdx mouse strains expressing dystrophins deleted for either the syntrophin or the dystrobrevin binding domain (Rafael et al., Hum. Mol. Genet., 3:1725, 1994; and Rafael et al., J. Cell Biol., 134:93 1996). These mice displayed normal muscle function and essentially normal localization of syntrophin, dystrobrevin, and nNOS. Thus, while dystrobrevin appears to protect muscle from damage (Grady et al., Nat. Cell. Biol, 1:215, 1999), removal of the dystrobrevin binding site from dystrophin does not result in a dystrophy. Subsequent studies revealed that syntrophin and dystrobrevin bind each other in addition to dystrophin, so that removal of only one of the two binding sites on dystrophin might not sever the link between dystrophin, syntrophin and dystrobrevin. Surprisingly, the transgenic mice according to the present invention (See Example 1) displayed normal muscle function even though they lacked both the syntrophin and dystrobrevin binding sites.
IV. MCK Regulatory Regions
In certain embodiments, nucleic acid encoding mini-dystrophin peptides of the present invention are operably linked to muscle creatine kinase gene (MCK) regulatory regions and control elements, as well as mutated from of these regions and elements (see See U.S. Provisional App. Ser. No. 60/218,436, filed Jul. 14, 2000, and International Application PCT/US01/22092, filed Jul. 13, 2001, both of which are hereby incorporated by reference). In some embodiments, the nucleic acid encoding mini-dystrophin peptides is operably linked to these sequences to provide muscle specificity and reduced size such that the resulting construct is able to fit into, for example, a viral vector (e.g. adeno-associated virus). MCK gene regulatory regions (e.g. promoters and enhancers) display striated muscle-specific activity and have been characterized in vitro and in vivo. The major known regulatory regions in the mouse MCK gene include a 206 base pair muscle-specific enhancer located approximately 1.1 kb 5′ of the transcription start site in mouse (i.e. SEQ ID NO:87) and a 358 base pair proximal promoter (i.e. SEQ ID NO:93) [Shield, et al, Mol. Cell. Biol., 16:5058 (1996)]. A larger MCK promoter region may also be employed (e.g. SEQ ID NO:92), as well as smaller MCK promoter regions (e.g. SEQ ID NO:94).
The 206 base pair MCK enhancer (SEQ ID NO:87) contains a number of sequence motifs, including two classes of E-boxes (MCK-L and MCK-R), CarG, and AT-rich sites. Similar E-box sequences are found in the enhancers of the human, rat, and rabbit MCK genes [See, Trask, et al., Nucleic Acids Res., 20:2313 (1 992)]. Mutation may be made to this sequence by, for example, inserting an additional MCK-R control element into a wild-type enhancer sequence naturally containing one MCK-R control element (such that the resulting sequence has at least two MCK-R control elements). For example, the inserted MCK-R control element replaces the endogenous MCK-L control element. The 206 base pair mouse enhancer (SEQ ID NO:2) may be modified by replacing the left E-box (MCK-L) with a right E-Box (MCK-R) to generate a mutant muscle-specific enhancer region (e.g. to generate SEQ ID NO:88). A similar approximately 200 base pair wild type enhancer region in human may be modified by replacing the left E-box with a MCK-R to generate a mutant muscle-specific enhancer region (e.g. 2R human enhancer regions).
Another modification that may be made to generate mutant muscle-specific enhancer regions by inserting the S5 sequence GAGCGGTTA (SEQ ID NO:95) into wild type mouse, human, and rat enhancer sequence. Making such a modification to the mouse enhancer SEQ ID NO:87, for example, generates S5 mutant muscle-specific enhancer regions (e.g. SEQ ID NO:89). Another modification that may be made, for example, to the wild type mouse enhancer is replacing the left E-box (MCK-L) with a right E-Box (MCK-R), and also inserting the 5S sequence, to generate 2R5S type sequences (e.g. in mouse, SEQ ID NO:90). These mutant muscle-specific enhancer regions may have additional sequences added to them or sequences that are taken away. For example, the mutant muscle-specific enhancer regions may have a portion of the sequence removed (e.g. the 3′ 41 base pairs). Examples of such mutant truncation 2RS5 sequences in mouse is SEQ ID NO:91 with the 3′ 41 base pairs removed, generating mutant truncated 2RS5 muscle-specific enhancer regions.
Any of these wild-type or mutant muscle-specific enhancer regions described above may be further modified to produce additional mutants. These additional mutants include, but are not limited to, muscle-specific enhancer regions having deletions, insertions or substitutions of different riucleotides or nucleotide analogs so long as the transcriptional activity of the enhancer region is maintained. Guidance in determining which and how many nucleotide bases may be substituted, inserted or deleted without abolishing the transcriptional activity may be found using computer programs well known in the art, for example, DNAStar software or GCG (Univ. of Wisconsin) or may be determined empirically using assays provided by the present invention.
V. Expression Vectors
The present invention contemplates the use of expression vectors with the compositions and methods of the present invention (e.g. with the nucleic acid constructs encoding the mini-dystrophin peptides). Vectors suitable for use with the methods and compositions of the present invention, for example, should be able to adequately package and carry the compositions and cassettes described herein. A number of suitable vectors are known in the art including, but are not limited to, the following: 1) Adenoviral Vectors; 2) Second Generation Adenoviral Vectors; 3) Gutted Adenoviral Vectors; 4) Adeno-Associated Virus Vectors; and 5) Lentiviral Vectors.
Those skilled in the art will recognize and appreciate that other vectors are suitable for use with methods and compositions of the present invention. Indeed, the present invention is not intended to be limited to the use of the recited vectors, as such, alternative means for delivering the compositions of the present invention are contemplated. For example, in various embodiments, the compositions of the present invention are associated with retrovirus vectors and herpes virus vectors, plasmids, cosmids, artificial yeast chromosomes, mechanical, electrical, and chemical transfection methods, and the like. Exemplary delivery approaches are discussed below.
1. Adenoviral Vectors
Self-propagating adenovirus (Ad) vectors have been extensively utilized to deliver foreign genes to a great variety of cell types in vitro and in vivo. “Self-propagating viruses” are those which can be produced by transfection of a single piece of DNA (the recombinant viral genome) into a single packaging cell line to produce infectious virus; self-propagating viruses do not require the use of helper virus for propagation. As with many vectors, adenoviral vectors have limitations on the amount of heterologous nucleic acid they are capable of delivering to cells. For example, the capacity of adenovirus is approximately 8-10 kb, the capacity of adeno-associated virus is approximately 4.8 kb, and the capacity of lentivirus is approximately 8.9 kb. Thus, the mutants of the present invention that provide shorter nucleic acid sequences encoding the mini-dystrophin peptides (compared to full length wild-type dystrophin (14 kb)), improve the carrying capacity of such vectors.
2. Second Generation Adenoviral Vectors
In an effort to address the viral replication problems associated with first generation Ad vectors, so called “second generation” Ad vectors have been developed. Second generation Ad vectors delete the early regions of the Ad genome (E2A, E2B, and E4). Highly modified second generation Ad vectors are less likely to generate replication-competent virus during large-scale vector preparation, and complete inhabitation of Ad genome replication should abolish late gene replication. Host immune response against late viral proteins is thus reduced [See Amalfitano ei al., “Production and Characterization of Improved Adenovirus Vectors With the E1, E2b, and E3 Genes Deleted,” J. Virol. 72:926-933 (1998)]. The elimination of E2A, E2B, and E4 genes from the Ad genome also provide increased cloning capacity. The deletion of two or more of these genes from the Ad genome allows for example, the delivery of full length or cDNA dystrophin genes via Ad vectors [Kumar-Singh et al, Hum. Mol. Genet., 5:913 (1996)].
3. Gutted Adenoviral Vectors
“Gutted,” or helper dependent, Ad vectors contain cis-acting DNA sequences that direct adenoviral replication and packaging but do not contain viral coding sequences [See Fisher et al. “Recombinant Adenovirus Deleted of All Viral Genes for Gene Therapy of Cystic Fibrosis,” Virology 217:11-22 (1996) and Kochanek et al. “A New Adenoviral Vector: Replacement of All Viral Coding Sequences With 28 kb of DNA Independently Expressing Both Full-length Dystrophin and Beta-galactosidase” Proc. Nal. Acad. Sci. USA 93:5731-5736 (1996)]. Gutted vectors are defective viruses produced by replication in the presence of a helper virus, which provides all of the necessary viral proteins in trans. Since gutted vectors do not contain any viral genes, expression of viral proteins is not possible.
Recent developments have advanced the field of gutted vector production [See Hardy et al., “Construction of Adenovirus Vectors Through Cre-lox Recombination,” J. Virol. 71:1842-1849 (1997) and Hartigan-O'Conner et al., “Improved Production of Gutted Adenovirus in Cells Expressing Adenovirus Preterminal Protein and DNA Polymerase,” J. Virol. 73:7835-7841 (1999)]. Gutted Ad vectors are able to maximally accommodate up to about 37 kb of exogenous DNA, however, 28-30 kb is more typical. For example, a gutted Ad vector can accommodate the full length dystrophin or cDNA, but also expression cassettes or modulator proteins.
4. Adeno-Associated Virus Vectors
In preferred embodiments, the nucleic acid encoding the mini-dystrophin peptides of the present invention are inserted in adeno-associated vectors (AAV vectors). AAV vectors evade a host's immune response and achieve persistent gene expression through avoidance of the antigenic presentation by the host's professional APCs such as dendritic cells. Most AAV genomes in muscle tissue are present in the form of large circular multimers. AAV's are only able to carry about 5 kb of exogenous DNA. As such, the nucleic acid of the present invention encoding the mini-dystrophin peptides is well suited, in some embodiments, for insertion into these vectors due the reduced size of the nucleic acid sequences.
The dystrophin expression cassettes of the present invention (containing nucleic acid encoding mini-dystrophin peptides) may be cloned into any of a variety of cis-acting plasmid vectors that contain the adeno-associated virus inverted terminal repeats (ITRs) to allow production of infectious virus. For example, one such plasmid is the cis-acting plasmid (pCisAV) (Yan et al., PNAS, 97:6716-6721, 2000). This plasmid contains the AAV-ITRs separated by a NotI cloning site. The ITR elements were derived from pSub201, a recombinant plasmid from which an infectious adeno-associated virus genome can be excised in vitro and used to study viral replication. After ligation of the dystrophin expression cassette (isolated as a NotI fragment from pCK6DysR4-23-71-78An) into NotI-digested pCisAV, rAAV stocks are generated by cotransfection of pCisAV. CK6DysR4-23-71-78An and pRep/Cap (Fisher, et al., J. Virol. 70:520-532, 1996) together with coinfection of the recombinant adenovirus Ad.CMVlacZ into 293 cells. Recombinant AAV vector, for example, may then be purified on CsCl gradients as described (Duan, et al., Virus Res. 48:41-56, 1997).
5. Lentiviral Vectors
Vectors based on human or feline lentiviruses have emerged as another vector useful for gene therapy applications. Lentivirus-based vectors infect nondividing cells as part of their normal life cycles, and are produced by expression of a package-able vector construct in a cell line that expresses viral proteins. The small size of lentiviral particles constrains the amount of exogenous DNA they are able to carry to about 10 kb. However, once again, the small size nucleic acid encoding the mini-dystrophin peptides of the present invention allow such vectors to be employed.
6. Retroviruses
Vectors based on Moloney murine leukemia viruses (MMLV) and other retroviruses have emerged as useful for gene therapy applications. These vectors stably transduce actively dividing cells as part of their normal life cycles, and integrate into host cell chromosomes. Retroviruses may be employed with the compositions of the present invention (e.g. gene therapy), for example, in the context of infection and transduction of muscle precursor cells such as myoblasts, satellite cells, or other muscle stem cells.
Experimental
The following examples are provided in order to demonstrate and further illustrate certain preferred embodiments and aspects of the present invention and are not to be construed as limiting the scope thereof.
In the experimental disclosure which follows, the following abbreviations apply: N (normal); M (molar); mM (millimolar); μM (micromolar); mol (moles); mmol (millimoles); μmol (micromoles); nmol (nanomoles); pmol (picomoles); g (grams); mg (milligrams); μg (micrograms); ng (nanograms); l or L (liters); ml (milliliters); μl (microliters); cm (centimeters); mm (millimeters); μm (micrometers); nm (nanometers); ° C. (degrees Centigrade); and Sigma (Sigma Chemical Co., St. Louis, Mo.).

EXAMPLE 1

Carboxy-Terminal Domain Truncated Dystrophin Genes

This example describes the generation of carboxy-terminal truncated dystrophin nucleic acid sequences. In particular, this examples describes the construction of dystrophin nucleic acid sequence with the entire carboxy-terminal domain deleted, and testing of this sequence in a mouse model for DMD.
A. Methods
The bases encoding amino acids 3402-3675 (corresponding to exons 71-78) were deleted from the full length murine dystrophin cDNA (SEQ ID NO:2, accession No. M68859) by recombinant PCR, leaving the last three amino acids (exon 79) of the dystrophin protein unaltered. This dystrophin Δ71-78 cDNA was cloned into an expression vector containing bases −2139 to +239 of the human -skeletal actin (HSA) promoter (Brennan, el al., J. Biol. Chem. 268:719, 1993). A splice acceptor from the SV40 VP1 intron (isolated as a 400 bp HindIII/XbaI fragment from pSVL; Amersham Pharmacia Biotech) was inserted immediately 3′ of the HSA fragment, and the SV40 polyadenylation signal (isolated as a BamHI fragment from pCMVβ; MacGregor and Caskey, Nuc. Acid. Res., 17:2365, 1989) was inserted 3′ of the dystrophin cDNA. The excised dystrophin Δ71-78 expression cassette was injected into wild-type C57B1/10×SJL/J F2 hybrid embryos, and F_omice were screened by PCR. Five positive F_o's were backcrossed onto the C57B1/10mdx background, and the line with the most uniform expression levels was selected for analysis. Also employed were previously described transgenic mdx mice that express dystrophin constructs deleted approximately for exons 71-74 (Δ71-74) or exons 75-78 (Δ75-78), which remove amino acids 3402-3511 and 3528-3675, respectively, See Rafael et al., J. Cell Biol., 134:93-102, 1996). Transgenic mdx line Dp71 expresses the Dp71 isoform of dystrophin in striated muscle (Cox et al., Nat. Genet., 8:333-339, 1994).
i. Morphology Methods
Quadriceps, soleus, extensor digitorum longus (EDL), tibialis anterior, and diaphragm muscles were removed from the mice, frozen in liquid nitrogen cooled O.C.T. embedding medium (Tissue-Tek), and cut into 7-μm sections. After fixing in 3.7% formaldehyde, sections were stained in hematoxylin and eosin-phloxine. Stained sections were imaged with a Nikon E1000 microscope connected to a Spot-2 CCD camera. To determine the percentage of fibers containing central nuclei, the number of muscle fibers with centrally-located nuclei was divided by the total number of muscle fibers.
ii. Evans Blue Assays
4 month old control mice and Δ71-78 mice were analyzed after injection with Evans blue, as described previously (Straub et al., J. Cell. Biol., 139:375-385, 1997). In brief, mice were tail vein-injected with 150 μl of a solution containing 10 mg/ml Evans blue dye in PBS (150 mM NaCl, 50 mM Tris, pH 7.4). After 3 hours, the animals were euthanized and mouse tissues were either fixed in 3.7% formaldehyde/0.5% glutaraldehyde to observe gross dye uptake, or frozen unfixed in O.C.T. embedding medium. To examine Evans blue uptake by individual fibers, 7-μm-thick frozen sections were fixed in cold acetone and analyzed by fluorescence microscopy.
iii. Immunofluorescence Assays
Quadriceps and diaphragm muscles from C57B1/10, mdx, and Δ71-78 mice were removed, frozen in O.C.T. embedding medium, and cut into 7-μm sections. Immunofluorescence was performed with previously described antibodies against dystrophin (NH₂terminus), α1-syntrophin (SYN17), β1-syntrophin, α-dystrobrevin-1 (DB670), α-dystrobrevin-2 (DB2), and utrophin. After incubation with primary antibodies, cryosections were incubated with an FITC-conjugated goat anti-rabbit secondary antibody and fluorescent images were viewed on a Nikon E1000 microscope. Antibodies to α-sarcoglycan (Rabbit 98), β-sarcoglycan (Goat 26), γ-sarcoglycan (Rabbit 245), δ-sarcoglycan (Rabbit 215), sarcospan (Rabbit 235), α-dystroglycan (Goat 20), β-dystroglycan (AP 83), or nNOS (Rabbit 200) have been described previously (Duclos el al., J. Cell. Biol., 142:1461, 1998). Cy3-conjugated secondary antibodies were used and images were viewed on a Bio-Rad MRC-600 laser scanning confocal microscope. All digitized images were captured under the same conditions.
iv. Measurements of Contractile Properties Methods
Contractile properties of muscles from 6-month-old Δ71-78 transgenic mice were compared with those of C57B1/10 wild-type and mdx mice using methods described previously (Lynch et al., Am. J. Physiol., 272:C2063, 1997). The samples included eight muscles each from the EDL, soleus, and diaphragm. Mice were deeply anesthetized with avertin and each muscle was isolated and dissected free from the mouse. After removal of the limb muscles, the mice were euthanized with the removal of the diaphragm muscle. The muscles were immersed in a bath filled with oxygenated buffered mammalian Ringer's solution (137 mM NaCl, 24 mM NaHCO₃, 11 mM glucose, 5 mM KCl, 2 mM CaCl₂, 1 mM MgSO₄, 1 mM NaH₂PO₄, and 0.025 mM tubocurarine chloride, pH 7.4). For each muscle, one tendon was tied to a servomotor and the other tendon to a force transducer. Muscles were stretched from slack length to the optimal length for force development and then stimulated at a frequency that produced absolute isometric tetanic force (mN). After the measurements of the contractile properties, the muscles were removed from the bath, blotted and weighed to determine muscle mass. Specific force (kN/m²) was calculated by dividing absolute force by total fiber cross sectional area.
v. Muscle Membrane Isolation Methods
Muscle microsomes from 12-14 month-old C57B1/10, mdx, Δ71-78, Δ71-74, Δ75-78, and Dp71 mice were prepared as described previously (Ohlendieck et al., J. Cell. Biol., 112:135, 1991). In brief, skeletal muscle was homogenized in 7.5-vol homogenization buffer plus protease inhibitor Complete (Boehringer). The homogenate was centrifuged at 14,000 g for 15 min to remove cellular debris. The supernatant was filtered through cheesecloth and spun at 142,000 g for 37 minutes to collect microsomes. The microsome pellet was resuspended in KCl wash buffer (0.6 M KCl, 0.3 M sucrose, 50 mM Tris-HCl, pH 7.4) plus protease inhibitors and recentrifuged at 142,000 g for 37 minutes to obtain KCl-washed microsomes. The final pellet was resuspended in 0.3 M sucrose and 20 mM Tris-maleate, pH 7.0. Samples were quantified by the Coomassie Plus Protein Assay Reagent (Pierce Chemical Co.) and equivalent protein loading was verified by SDS-PAGE. KCl-washed microsomes were analyzed by Western blot using antibodies against β2-syntrophin, pan syntrophin, nNOS (Transduction Laboratories), β-dystroglycan, α-sarcoglycan (Novocastra Laboratories), and other proteins described above.
B. Results
i. Generation of Dystrophin Δ71-78 Transgenic Mice
To test the function of a dystrophin protein lacking both the syntrophin and dystrobrevin binding sites, we prepared a cDNA expression vector deleted for the COOH-terminal domain (corresponding to exons 71-78; See FIG. 19) as described above. The structure of several dystrophin transgenic constructs previously tested are also shown for comparison. Mice expressing the dystrophin Δ71-78 transgene were crossed onto the mdx background and dystrophin levels were analyzed by Western blotting. The expression of the dystrophin Δ71-78 transgene in skeletal muscle was determined to be 10-fold higher than endogenous dystrophin. Immunofluorescent staining of quadriceps muscle using an antibody against the NH₂-terminus of dystrophin revealed that the Δ71-78 protein was localized to the sarcolemma, similar to wild-type dystrophin. Dystrophin Δ71-78 expression was also found to be uniform in the diaphragm, EDL, and soleus muscles, but the tibialis anterior muscle displayed a mosaic expression pattern. The human skeletal muscle -actin promoter used in this study was not expressed in either smooth or cardiac muscle.
ii. Morphology of Dystrophin Δ71-78 Mice Appears Normal
We initially analyzed transgenic mdx mouse muscle tissues for morphological signs of dystrophy. Hematoxylin and eosin-stained limb and diaphragm skeletal muscle sections of dystrophin Δ71-78 mice revealed none of the signs of fibrosis, necrotic fibers, or mononuclear cell infiltration that were apparent in age-matched mdx controls. NMJs (neuromuscular junctions) of transgenic mice stained with rhodamine-labeled-bungarotoxin consistently appeared normal in contrast to the varying degrees of postsynaptic folding observed in mdx NMJs. Mdx muscle fibers have previously been shown to be highly permeable to the vital dye Evans blue in vivo, reflecting damage to the dystrophic fiber sarcolemma (Matsuda et al, J. Biochem. (Tokyo), 118:959, 1995). Skeletal muscle fibers from dystrophin Δ71-78 mice, like wild-type animals, were found not to be permeable to Evans blue dye.
iii. Analysis of Centrally Nucleated Muscle Fibers

Another hallmark of dystrophy in mdx mice is the presence of large numbers of centrally-nucleated muscle fibers, reflecting cycles of fiber degeneration and regeneration (Torres and Duchen, Brain, 110:269, 1987). To estimate the degree of myofiber regeneration occurring in Δ71-78 transgenic mice, centrally nucleated fibers were counted from a variety of muscle groups in age-matched wild-type, mdx, and Δ71-78 mice (See, Table 2). By 4 months of age, 71% of muscle fibers in mdx quadriceps muscles contained central nuclei, whereas wild-type muscles had <1%. Interestingly, 4 month old dystrophin Δ71-78 quadriceps muscles displayed 1% central nuclei, indicating that very little, if any, regeneration was occurring. When 1-year-old mice were compared, a modest increase in centrally nucleated fibers became apparent. Quadriceps muscles from Δ71-78 mice contained 10% centrally nucleated fibers, although diaphragm muscles still displayed <1%. EDL and soleus muscles displayed 5 and 8% centrally nucleated fibers, respectively. For comparison, 1-year-old wild-type mice had <1% centrally nucleated fibers in both limb and diaphragm muscles. Furthermore, 1-year-old mdx limb muscles had 60% centrally nucleated fibers, whereas the diaphragm had 35%.

TABLE 2


Percentage of Centrally Nucleated Fibers in Mouse Skeletal Muscles

Line	Age	Quad	Dia	TA	EDL	Soleus

C57/B110	4	<1	<1	ND	ND	ND
mdx	4	71	58	ND	ND	ND
Δ71-78	4	1	<1	ND	ND	ND
C57/B110	12	<1	<1	<1	<1	<1
mdx	12	65	35	58	50	61
Δ71-78	12	10	<1	ND	5	8
Δ71-74	15	5	<1	<1	<1	ND
Δ75-78	15	8	<1	4	2	7

Quad = quadriceps;
Dia = diaphragm;
TA = tibialis anterior;
Age is in months

Previous studies of transgenic mice expressing dystrophins deleted for exons Δ71-74 (Δ71-74) or exons Δ75-78 (Δ75-78) revealed no increase in the numbers of centrally nucleated fibers by 4 months of age (Rafael et al. 1996, see above). To contrast these mice with the 71-78 transgenics, central nuclei counts were performed on 15-month-old Δ71-74 and 75-78 mice. It was determined that these animals had central nuclei counts in between those of wild-type and Δ71-78 mice. The Δ71-74 and Δ75-78 mice had 5 and 8% centrally nucleated fibers in quadriceps, respectively (Table 2).
iv. Contractile Properties
Compared with muscles of wild-type mice, those from mdx mice displayed a significant amount of necrosis, fibrosis, and infiltrating mononuclear cells. mdx skeletal muscles also displayed a loss of specific force-generating capacities when muscles were stimulated to contract in vitro, providing an extremely sensitive and quantitative measurement of the dystrophic process (FIG. 20A). In contrast, dystrophin Δ71-78 mice had no major abnormalities when subjected to the same analysis (FIG. 20 B). Muscle mass for both EDL and diaphragm were not significantly different between dystrophin Δ71-78 and wild-type mice, whereas dystrophin Δ71-78 soleus muscles were slightly hypertrophied. When stimulated to contract, all three muscle groups displayed specific forces not significantly different from wild-type (P<0.05). These results demonstrate that the dystrophin Δ71-78 protein has essentially the same functional capacity as the full-length protein.
v. Localization of the DAP Complex in Δ71-78 Mice
Immunofluorescent analysis of the peripheral DAP complex revealed α1-syntrophin, β1-syntrophin, α-dystrobrevin-1, and α-dystrobrevin-2 to be localized at the sarcolemma with dystrophin, despite the lack of syntrophin and dystrobrevin binding sites in the transgene-encoded dystrophin. α1-syntrophin levels were similar between wild-type and Δ71-78 mice. However, the levels of β1-syntrophin were elevated at the membrane in Δ71-78 mice, particularly in those fibers that normally express significant levels of this isoform. α-dystrobrevin-1 was primarily located at the NMJ in wild-type mice, and was exclusively located at the NMJs in mdx mice. Surprisingly, in dystrophin Δ71-78 mice, higher levels of α-dystrobrevin-1 were observed at the sarcolemma than in wild-type mice. The Δ71-78 mice also displayed a slight increase in utrophin localization along the sarcolemma, but this increase was less than the increase in mdx fibers. Immunofluorescent localization of the sarcoglycans, α- and β-dystroglycan, sarcospan, and nNOS in Δ71-78 mice revealed no differences in the expression of these proteins when compared with wild-type mice. The proper localization of these proteins to the sarcolemma indicated that membrane targeting of the DAP complex components can proceed in the absence of the COOH-terminal domain of dystrophin.
vi. DAP Complex Protein Levels
To examine the levels of the DAP complex members that associate with dystrophin, muscle microsomes were prepared from wild-type and dystrophin Δ71-78 mice and analyzed by Western blotting. This approach provides information on the relative abundance of individual DAP complex members in muscles of separate lines of mice. Slightly elevated levels of β-dystroglycan were detected in dystrophin Δ71-78 mice, which we have previously observed whenever dystrophin is overexpressed. Isoforms of syntrophin and dystrobrevin were present at slightly different levels when the dystrophin Δ71-78 membranes were compared with those from wild-type mice. α1-syntrophin and β2-syntrophin levels were lower than in wild-type mice, whereas the level of β1-syntrophin was elevated. Although there was approximately the same amount of α-dystrobrevin-2, there were elevated levels of α-dystrobrevin-1 in Δ71-78 microsomes. A reduction in nNOS was observed in dystrophin Δ71-78 muscle, indicating that nNOS binds weakly to the DAP complex in Δ71-78 mice. Levels of a-sarcoglycan were similar in all lines tested, and provided an internal control for protein loading.
Since some DAP complex members exhibited isoform changes in Δ71-78 mice, we examined purified microsomes from dystrophin Δ71-74 and Δ75-78 mice. Transgenic mdx mice that express the dystrophin isoform Dp71 in muscle were also included in this study since these dystrophic mice have the DAP complex present at the sarcolemma. α1-syntrophin levels were lower in all four transgenic lines compared with wild-type mice. Surprisingly, β1-syntrophin was absent in Δ71-74 microsomes but was highly overexpressed in Δ75-78 and Dp71 microsomes. The Δ71-74 microsomes had equivalent β2-syntrophin levels when compared with wild-type microsomes, but this isoform of syntrophin was reduced in both Δ75-78 and Dp71 microsomes. A pan syntrophin antibody, which detects all three isoforms of syntrophin, confirmed the upregulation of syntrophin in Δ75-78 and Dp71 microsomes. Similar to Δ71-78, α-dystrobrevin-1 was elevated in all dystrophin transgenic microsome preparations. However, in comparison with wild-type, α-dystrobrevin-2 was higher in Δ71-74 and Δ75-78, but equal in Dp71 microsomes. Contrary to the Δ71-78 mice, deleting either exons 71-74 or 75-78 restored nNOS to wild-type levels. However, Dp71 mice, which lack the NH₂-terminal and rod domains of dystrophin, did not retain nNOS in the microsome fractions. Previous studies have also shown that utrophin is upregulated in mdx and Dp71 mice (Ohlendieck et al., Neuron, 7:499-508, 1991). Therefore, utrophin levels were compared in all transgenic lines and we found that Δ71-78, Δ71-74, and Δ75-78 mice do not have the elevated levels seen in mdx and Dp71 mice.

EXAMPLE 2

Construction of ΔR4-R23, ΔR2-R21+H3, and ΔR2-R1

This example describes the construction of R4-R23 (micro-dys1), ΔR2-R21+H3 (micro-dys3), and ΔR2-R1 (micro-dys2), three sequences with 4 spectrin-like repeat encoding sequences. The ‘full-length’ human dystrophin cDNA that was started with was actually a sequence slightly smaller than the true full-length human dystrophin cDNA. In particular, the starting sequence, called full-length HDMD (SEQ ID NO:47, see FIG. 23) is the same as the wild-type human dystrophin in SEQ ID NO:1, except the 3′ 1861 base pairs are deleted (at an XbaI site), and the 39 base pair alternatively spliced exon 71 (bases 10432-10470) are deleted. This sequence (SEQ ID NO:47) is originally in pBSX (SEQ ID NO:46, See FIGS. 21 and 22).
A. Cloning ΔR4-R23
The procedure used for cloning ΔR4-R23 is outlined in FIG. 24. Initially, three PCR reactions were performed (employing Pfu polymerase) to create the deletion shown in FIG. 24. The primers employed in the first reaction were 5′ GAA CAA GAT TCA CAC AAC TGG C 3′ (SEQ ID NO:48), which anneals to 1954-1975 of the HDMD clone, and 5′ GTT CCT GGA GTC TTT CAA GAT CCA CAG TAA TCT GCC TC 3′ (SEQ ID NO:49), which is a reversed, tailed primer (the bold sequence anneals to 2359-2341 of the HDMD clone, and the underlined sequence anneals to 9023-9005 the HDMD clone. PCR was conducted employing these primers, and a 425 bp PCR product was produced. The first primer employed in the second reaction was 5′ GAG GCA GAT TAC TGT GGA TCT TGA AAG ACT CCA GGA AC 3′ (SEQ ID NO:50), which is the reverse complement primer of SEQ ID NO:49 (the bold-faced sequence of SEQ ID NO:50) anneals to 234!-2359 of the HDMD clone in the forward direction. The underlined sequence anneals to 9005-9023 of the HDMD clone in the forward direction. The other primer employed for the second reaction was 5′ TGT TTG GCG AGA TGG CTC 3′ (SEQ ID NO:51) which anneals to 9413-9396 of HDMD in the reverse direction. PCR was conducted employing these primers, and a 427 bp PCR product was produced. The third reaction employed the products from steps 1 and 2 and the outside primers SEQ ID NO:48 and SEQ ID NO:51, producing a 814 bp fragment by PCR. This fragment was then digested with NcoI and HindIII to produce a 581 bp DNA fragment.
This 581 bp fragment was then cloned into a 5016 bp NcoI+Hind III fragment from the HDMD clone. The 581 bp fragment contained part of repeat 3, all of Hinge 2, and part of repeat 24. The NcoI site used in the HDMD clone was located at 2055 bp. The Hind III site was located at 9281 bp. The 5016 fragment contained the pBSX cloning vector sequence, and the entire 5′ UTR, the entire N terminus, Hinge 1, Repeats 1, 2, and part of repeat 3 up to the Ncol site of human dstrophin. Ligation of the 5016 bp fragment and 581 bp fragment (step 2) was then performed to created a 5597 bp sequence.
Step 3 was then performed to clone a 2.9 kb HindIII fragment containing part of repeat 24, the C terminus, and the 3′ UTR (See FIG. 24). The 5′ HindIII site is located at 9281 bp of the HDMD clone. The 3′ HindIII site of this fragment is derived from pBSX polylinker. This 2.9 kb fragment was cloned into the HindIII site of the product of Step 2 to yield an 8.5 kb plasmid, composed of the ΔR4-R23 cDNA plus pBSX. The entire ΔR4-R23 cDNA was excised from pBSX with NotI and cloned into the NotI site of the HSA expression vector (HSA promoter-VP1 intron-NotI site-tandem SV40 poly adenylation site).
B. Cloning ΔR2-R21+H3
The procedure used for cloning ΔR2-R21+H3 is outlined in FIG. 25. Initially, four PCR reactions were performed (employing Pfu polymerase) to create the deletion shown in FIG. 25. The primers employed in the first reaction were 5′ GAT GTG GAA GTG GTG AAA GAC 3 (SEQ ID NO:52), which anneals to 1319-1330 of the HDMD clone, and 5′ CCA ATA GTO GTC AGT CCA GGA GCA TGT AAA TTG CTT TG 3′ (SEQ ID NO:53), which is a reverse, tailed primer (the bold-faced sequence anneals to 1546-1532 of the HDMD clone and the underlined sequence anneals to 7512-7490 of the HDMD clone. PCR was conducted with these primers and a 228 bp PCR product was produced. The first primer employed in the second reaction was 5′ CAA AGC AAT TTA CAT GCT CCT GGA CTG ACC ACT ATT GG 3′ (SEQ ID NO:54), which is the reverse complement of SEQ ID NO:53 (the bold-faced sequence of SEQ ID NO:54 anneals to 1532-1546 of the HDMD clone in the forward direction, and the underlined sequence anneals to 7512-7490 of the HDMD clone in the forward direction. The other primer employed in the second reaction was 5′ CTG TTG CAG TAA TCT ATG CTC CAA CAT CAA GGA AGA TG 3′ (SEQ ID NO:55), and the bold-faced sequence anneals to 8287-8270 of the HDMD clone, and the underlined sequence anneals to 7612-7593 of the HDMD clone as a reverse primer. PCR was performed with these primers, and a 123 bp PCR product was produced. The first primer employed in the third reaction was 5′ CAT CTT CCT TGA TGT TGG AGC ATA GAT TAC TGC AAC AG 3′ (SEQ ID NO:56), the underlined sequence anneals to 7593-7612 of the HDMD clone in the forward direction, and the bold-faced sequence anneals to 8270-8287. The second primer employed in the third reaction was SEQ ID NO:51 (see above), which anneals to 9413-9396 in the reverse direction. PCR was performed with these primers, and a 1143 bp fragment was produced. The fourth reaction employed the products from reactions 1, 2, and 3 as template, and the outside primers (SEQ ID NO:52 and SEQ ID NO:51), and a 1494 bp fragment was produced using Pfu polymerase.
This 1494 bp fragment was then digested with Munl and HindIII to produce a 1270 bp band and cloned into a 4320 bp MunI+HindIII fragment from the HDMD clone. The 1270 bp fragment contained the part of repeat 1, all of hinge 3, repeat 22, repeat 23, and part of repeat 24. The 4320 bp fragment contained the 5′ UTR of HDMD, the N terminus, Hinge 1, and part of repeat 1 and pBSX. The MunI site in HDMD is located at base 1409. The HindIII site is at 9281 bp. Ligation of the 4320 bp fragment and the 1270 bp fragment was then performed (See FIG. 25) and a 4490 bp fragment was produced. Step 3 was performed as describe above for ΔR4-R23 to generate ΔR2-R21 +H3.
C. Cloning ΔR2-R21
The cloning of ΔR2-R21 was performed essentially the same way as for ΔR2-R21+H3, with the exception of the recombinant PCR reaction to assemble the rod domain deletion (See, FIG. 26). All other steps are the same. Three PCR reactions were performed (using Pfu polymerase) to create the deletion. The primers employed in the first reaction were SEQ ID NO:52 (see above), and 5′ CTG TTG CAG TAA TCT ATG ATG TAA ATT GCT TTG 3′ (SEQ ID NO:57), the underlined sequence anneals to 8287-8270 of the HDMD clone in the reverse direction, and the bold-faced sequence anneals to 1546-1532 of the HDMD clone in the reverse direction. PCR was performed with these primers, and a 250 bp product was obtained. The first primer employed in the second reaction was 5′ CAA AGC AAT TTA CAT CAT AGA TTA CTG CAA CAG 3′ (SEQ ID NO:58), which is is the reverse complement of SEQ ID NO:57 (the bold-faced sequence of SEQ ID NO:58 anneals to 1532-1546 of the HDMD clone in the forward direction, and the underlined sequence anneals to 8270-8287 of the HDMD clone in the forward direction. The other primer employed in the second reaction was SEQ ID NO:51, which anneals to 9413-9396 in the reverse direction. PCR was performed with these primers and a 1143 bp product was obtained. The third reaction employed the products from reactions 1 and 2 (as template) and the outside primers (SEQ ID NO:52 and SEQ ID NO:51), and a 1383 bp fragment was produced. This fragment was then digested with Munl and HindIII to produce an 1147 bp fragment containing part of repeat 1, repeat 22, repeat 23, and part of repeat 24. This was then cloned into the same MunI+HindIII HDMD fragment described for the ΔR2-R21+H3 clone and all other steps thereafter were the same.

EXAMPLE 3

ΔR4-R23 Deletions

This example describes the construction of 5′ UTR, 3′ UTR, and C-terminal deletions of ΔR4-R23 (making it even smaller), as well as the addition of polyadenylation and promoter sequences. This example also describes the alteration of the Kozak sequence (to become more like that of consensus).
A. Deletion of the 3′ UTR
In order to delete the 3′ UTR, the following two primers were employed 5′ TCT CTC CAA GAT CAC CTC G 3′ (SEQ ID NO:64), which anneals to 9117-9134 of the HDMD full length clone, and 5′ ATG AAG CTT GCG GCC GCA TGC GGG AAT CAG GAG TTG 3′ (SEQ ID NO:65) (the underlined site is a HindIII site that was included in this primer and the bold-faced type is a NotI site). SEQ ID NO:65 is a reverse primer that anneals to 11340-11322 of HDMD in the 3′ UTR. These primers cause the deletion of 707 bp of the 3′ UTR from the XbaI cloning site located at 12057 to the end of this primer (SEQ ID NO:65), leaving 113 bp of native 3′ UTR, and introducing NotI and HindIII cloning sites. The PCR product obtained using the primers corresponding to SEQ ID NOS:64 and 65 on the pΔR4-R23 clone was named HdysΔ3′UTR and was saved for use as a template to generate a further deletion of exons 71-78 (see part C below).
B. Deletion of 5′ UTR and Alteration of Kozak Sequence
A portion of the 5′ UTR was deleted (and the Kozak sequence was altered in the same step). The ‘step 2’ clone from cloning of ΔR4-R23 was utilized (this was the the product of ligating the step 1 PCR product into the 5016 bp NcoI and HindIII fragment from the HDMD full-length clone, and this clone contained pBSX backbone plus the 5′ UTR, N terminus, Hinge 1, Repeats 1, 2, 3, Hinge 2, and part of repeat 24. There is an MunI site located in the first repeat at nucleotide 1409 of the HDMD cDNA. In addition, there is a NotI site that is polylinker derived at the 5′ end of the clone. These two sites were employed, MunI+NotI, to clone a new fragment containing a truncated 5′ UTR and an altered Kozak sequence as follows. PCR was performed, using Pfu polymerase using the following primers. The first primer was 5′ TAG CGG CCG CGG TTT TTT TTA TCG CTG CCT TGA TAT ACA CTT TCC ACC ATG CTT TGG TGG GAA GAA GTA G 3′ (SEQ ID NO:59). We created a Notl site (underlined) in this. primer so the product could be cloned back into the NotI site from the polylinker. The sequence immediately 3′ to this NotI site corresponds to the dystrophin 5′ UTR sequence (the original Kozak sequence was changed with this primer, from TCAAAATGC, changed to CCACCATGC. The second primer was 5′ TTT TCC TGT TCC AAT CAG C 3′ (SEQ ID NO:60) which anneals to sequence 1441-1423 of HDMD full length clone. The final product of this reaction was 1270 bp and was digested with NotI+MunI to produce a 1233 bp fragment that was then cloned into the NotI (polylinker)+MunI site in Repeat 1 of the “Step 2” clones (described above for ΔR4-23). This new clone was named pHDMD5′ Kozak.
C. Deletion of Exons 71-78 (C-Terminal)
Using three PCR reactions, a 71-78 deletion was created. We used the HindIII fragment containing the 3′UTR that was generated by digestion of the HDMD full-length dystrophin cDNA with HindIII as the vector to clone the 71-78 fragment into the HindIII site. The primer employed for the first reaction were 5′ GGC TTC CTA CAT TGT GTC AGT TTC CAT GTT GTC CCC 3′ (SEQ ID NO:66), and 5′ TCT CTC CAA GAT CAC CTC 3′ (SEQ ID NO:67) anneals to 9117-9134 of HDMD. PCR was performed employing these primers and a 1334 bp product was produced. The primers for the second reaction were SEQ ID NO:65, and 5′ GGG GAC AAC ATG GAA ACT GAC ACA ATG TAG GAA GCC 3′ (SEQ ID NO:68), where the bold-face sequence anneals to exon 70 at 10415-10431 in the forward direction, and the underlined sequence anneals to 11216-11233 in the forward direction. PCR was performed and a 150 bp fragment was generated. The product of reactions 1 and 2 were used as template and the outside primers SEQ ID NO:65 and SEQ ID NO:67 were used to prime the reaction which generated the complete 71-78 C terminus (1484 bp). This product was digested with HindIII to produce a 1319 bp fragment and was cloned into the HindIII site of pTZ19R (See FIG. 35). This new clone was named pTZ-HDMD-H3Δ71-78Δ3.
D. Cloning of the SV40 pA Sequence into the Not I site
The next step was the cloning of the SV 40 pA sequence: 5′GATCCAGACATGATAAGATACATTGATGAGTTTGGACAAACCACAACTAGA ATGCAGTGAAAAAAATGCTTTATTTGTGAAATTTGTGATGCTATTGCTTTATT TGTAACCATTATAAGCTGCAATAAACAAGTTAACAACAACAATTGCATTCAT TTTATGTTTCAGGTTCAGGGGGAGGTGTGGGAGGTTTTTTCGGATC3′ (SEQ ID NO:71) into the NotI site of the 3′ HindIII fragment that now contains the 3′ UTR and 71-78. A PCR reaction was performed on the template pHSA with a reverse primer 5′ AGC GGC CGC AAA AAA CCT CCC ACA CCT CC 3′ (SEQ ID NO:69, containing a regenerating NotI site—underlined) and 5′ TAC GGC CGA TCC AGA CAT GAT AAG ATA C 3′ (SEQ ID NO:70, containing a destroying EagI site, in bold). All other sequence (besides the NotI and EagI sites) is SV40 pA. This PCR reaction generated a 195 bp product+cloning sites=209 bp. We then cloned this fragment into the NotI site of pTZ-HDMD-H3Δ71-78Δ3 generated by PCR in the 3′ UTR clone. The upstream (5′—most) NotI site in this clone was destroyed by EagI ligation. This new clone was named pTZ-HDMD-H33′A.
E. Cloning of CK6 Promoter into NotI Site
The CK6 promoter—5′ GGT-ACTACGGGTCTAGGCTGCCCATGTAAGGAGGCAAGGCCTGGGGACACCCGAG ATGCCTGGTTATAATTAACCCCAACACCTGCTGCCCCCCCCCCCCCAACACCT GCTGCCTGAGCCTGAGCGGTTACCCCACCCCGGTGCCTGGGTCTTAGGCTCTG TACACCATGGAGGAGAAGCTCGCTCTAAAAATAACCCTGTCCCTGGTGGGCC CAATCAAGGCTGTGGGGGACTGAGGGCAGGCTGTAACAGGCTTGGGGGCCA GGGCTTATACGTGCCTGGGACTCCCAAAGTATTACTGTTCCATGTTCCCGGCG AAGGGCCAGCTGTCCCCCGCCAGCTAGACTCAGCACTTAGTTTAGGAACCAG TGAGCAAGTCAGCCCTTGGGGCAGCCCATACAAGGCCATGGGGCTGGGCAAG CTGCACGCCTGGGTCCGGGGTGGGCACGGTGCCCGGGCAACGAGCTGAAAGC TCATCTGCTCTCAGGGCCCCTCCCTGGGGACAGCCCCTCCTGGCTAGTCACAC CCTGTAGGCTCCTCTATATAACCCAGGGGCACAGGGGCTGCCCCCGGGTCAC GGGGATCCTCTAGACC-3′ (SEQ ID NO:61) was amplified using two tailed primers: 5′ AGC GGC CGC GGT ACT ACG GGT CTA GG 3′ Forward (SEQ ID NO:62), and 5′ ATC GGC CGT CTA GAG GAT CCC CGT GAC C 3′ Reverse (SEQ ID NO:63). The underlined sequence is a NotI site added to the end of this primer. The remaining sequence is CK6 sequence. The bold-faced type is an EagI site added to the end of this primer. The remaining sequence is from CK6. The CK6 promoter was amplified this way so we could add the NotI and EagI sites (so the entire cassette could be excised when put back together with NotI). This PCR product was therefore digested with NotI and EagI and ligated into the Noti site of pHDMD5′Kozak. This new clone was named pCK6HDMD5′Kozak. NotI and EagI produce compatible cohesive sites, but when EagI ligates to NotI, it destroys the site. So we placed the EagI site at the 3′ end, so that when the final construct was cut with NotI, the entire expression cassette could be excised intact. The same strategy was employed at the 3′ end when placing the SV40 poly A sequence into the 3′ Not I site.
F. Re-Ligating the 5′ and 3′ Ends.
This step was performed as described above in the micro-dystrophin transgene constructs. We reconstituted the same cloning sites but with modifications in the fragments, so the modified 3′ end, isolated as a HindIII fragment from clone pTZ-HDMD-H33′A (example 3 part D), was able to be cloned into the HindIII site of pCK6HDMD5′Kozak (example 3, part E). This final clone, named pCK6R4-R23KozakΔ3′, contains a truncated dystrophin expression cassette that can be excised in its entirety by digestion with NotI. This excised expression cassette can then be used for a variety of purposes. One such purpose is to clone the cassette into a plasmid containing the inverted terminal repeats from adeno-associated virus. By cloning the dystrophin expression cassette HDMD-H33′A into a cloning site between the two ITRs of AAV, a recombinant AAV vector could be produced.

EXAMPLE 4

Construction of Reduced Repeat Dystrophin Constructs

This example describes the construction of ΔH2-R19 (an 8 spectrih-like-repeat sequence), pΔR9RI6 (a 16 spectrin-like-repeat sequence), pΔR1R24 (a zero spectrin-like-repeat sequence), pΔH2-H3 (an 8 spectrin-like repeat sequence), and ΔH2-R19,R20 (a 7 spectrin-like repeat sequence). One starting plasmid was pHBMD, a human dystrophin cDNA (full-length HDMD, SEQ ID NO:47) with a further deletion of the sequences encoded by exons 17-48. The cDNA was cloned into the commercially available plasmid vector pTZ19r (MBI Fermentas; Genbank accession number Y14835, See FIG. 35), into which an EcoRI-SalI adapter (prepared by self-annealing of the oligonucleotide 5′-AATTCGTCGACG-3′, SEQ ID NO:83) had been ligated into the the EcoRI site. Base number 1 of the cDNA is immediately 3′ of the adapter sequence, and the cDNA ends at the XbaI site at base 12,100 of SEQ ID NO:1. This XbaI site had been ligated into the XbaI site of the plasmid ptZ19r. Another starting plasmid is pBSX (SEQ ID NO:46), a modified version of pBluescript KSII+ (Stratagene) which is used to make pBSXA (pBSX into which the SV40 polyadenylation signal (pA) was added). This pA sequence was excised as a 206 bp fragment from pCMVβ (Clonetech), blunt-ended with DNA polymerase I, and ligated into the blunt-ended KpnI site of pBSX.
Another starting plasmid is pCK3, which is pBSX with the 3.3 kb mouse muscle creatine kinase enhancer plus promoter attached to the minx intron (See, Hauser et al., Mol Ther., 2:16-25, 2000). Another staring plasmid is pHDSK, which is pHBMD digested with KpnI, to remove the dystrophin sequences 3′ of the internal KpnI site (base 7,616 of the human dystrophin cDNA sequence, SEQ ID NO:1). A further starting vector is p44.1, which is pBluescript KS− (Stratagene) carrying a human dystrophin cDNA fragment spanning the EcoRI site at base 7,002 to the EcoRI site at base 7,875 of the full-length human dystrophin cDNA sequence, cloned into the EcoRI site of the vector. Another plasmid employed was p30-2, pBluescribe (Stratagene) containing a fragment from the full-length human dystrophin cDNA spanning bases 1,455 to the EcoRI site at base 2,647, cloned into the EcoRI site of the vector. An additional vector employed was p30-1, pBluescribe (Stratagene) containing an EcoRI fragment from the full-length human dystrophin cDNA spanning bases 2,647 to 4,558, cloned into the EcoRI site of the vector. An further plasmid employed is p47-4, pBluescript KS− (Stratagene) carrying the human dystrophin cDNA EcoR1 fragment spanning bases 4,452 to 7,002 of the full-length cDNA sequence, cloned into the EcoRI site of the vector. Another plasmid is p9-7, pBluescribe (Stratagene) containing bases 1-1,538 of the full-length human dystrophin cDNA. Base 1 is attached to a linker of the sequence 5′ GAATTC-3′ and cloned into the EcoRI site of the vector. Base 1,538 is blunt-end cloned into the PstI site of the vector, which had been destroyed by fill-in with T4 DNA polymerase. Another vector employed is p63-1, pBluescript KS− (Stratagene) carrying the human dystrophin cDNA EcoRI fragment spanning bases 7,875 to the 3′ end of the full-length cDNA, cloned into the EcoRI site of the vector (the 3′ end of the cDNA is ligated to a linker of the sequence 5′-GAATTC-3′).
Initially, the MCK promoter plus enhancer and the minx intron were excised from pCK3 by digestion with EagI, yielding a 3.5 kb fragment that was ligated into EagI-digested pBSXA to make pBSXACK3. Truncated dystrophin cDNAs, derived from pHBMD, containing various deletions of dystrophin domains were prepared as described below. The cDNA inserts were excised from the plasmid backbone with SalI, and ligated into pBSXACK3 at the SalI site, which is located between the minx intron and the pA sequence, such that the 3′ end of the cDNA was adjacent to the pA sequence. The isolation of the truncated cDNAs is described below. pBSXACK3-truncated dystrophin plasmids were digested with BssHII to release the expression vectors, which were gel purified and used to generate transgenic mice.
Isolation of ΔH2R19
A PCR product was generated by amplification of plasmid p30-2 with primers 5′-TGTGCTGCAAGGCGATTAAGTTGG-3′ (SEQ ID NO:72) and 5′-GAGCTAGGTCAGGCTGCTGTGAAATCTGTGC-3′ (SEQ ID NO:75). Primer SEQ ID NO:75 overlaps the end of repeat 3 and the beginning of hinge 3. Primer SEQ ID NO:72 corresponds to a sequence in the plasmid vector adjacent to the cloning site. A second PCR product was generated by amplification of plasmid p44-1 using primers 5′-CCAGGCTTTACACTTTATGCTTCC-3′ (SEQ ID NO:73) and 5′-GCACAGATTTCACAGCAGCCTGACCTAGCTC-3′ (SEQ ID NO:74). Primer SEQ ID NO:74 is the reverse complement of primer SEQ ID NO:75. Primer SEQ ID NO:73 corresponds to a sequence in the plasmid vector adjacent to the cloning site. The PCR products were then purified by agarose gel electorphoreses, and quantified. A recombinant PCR product was then prepared by mixing together 10 ng of each of the first two PCR products, then re-PCR amplifying using only primers SEQ ID NO:72 and SEQ ID NO:73. This recombinant PCR product was then digested with NheI and KpnI, and ligated into NheI and KpnI digested pHΔSK to generate plasmid pHBMDΔH2 (NheI-cuts at cDNA base 1,519, and KpnI cuts at base 7,616 of the full-length human dystrophin cDNA sequence). pHBMDΔH2 was then digested with KpnI and XbaI, and ligated to the KpnI-XbaI fragment from pHBMD (this latter fragment contains the full-length human dystrophin cDNA bases 7,616 to 12,100) to obtain plasmid pΔH2R19.
Isolation of pΔR9R16
Plasmid p44-1 was digested with EcoRI and Asp718 to excise a 610 bp cDNA insert, that was ligated into pBSX digested with EcoRI and Asp718, yielding pBSX44AE. pBSX44AE was digested with EcoRI and Xbal, and ligated to the NheI-EcoRI cDNA-containing fragment from p30-2, yielding pBSX44AE/30-2NE. Plasmid pBSX44AE/30-2NE was linearized by digestion with EcoRI, into which was ligated the EcoRI-digested recombinant PCR product ΔR9-R16. This latter recombinant PCR product was generated as follows. Plasmid p30-1 was amplified with primers SEQ ID NO:72 and 5′-CCATTTCTCAACAGATCTTCCAAAGTCTTG-3′ (SEQ ID NO:77), and plasmid p47-4 was amplified by PCR with primers SEQ ID NO:73 and 5′-CAAGACTTTGGAAGATCTGTTGAGAAATGG-3 (SEQ ID NO:76). A recombinant PCR product (ΔR9-R16) was then prepared by mixing together 10 ng of each of the first two PCR products, then re-PCR amplifying using only primers SEQ ID NO:72 and SEQ ID NO:73. This recombinant PCR product was then digested with EcoRI, and ligated into EcoRI digested pBSX44AE/30-2NE to generate plasmid pR9R16int. Plasmid pR9R16int was digested with NcoI and Asp718, and the 3 kb cDNA fragment was isolated and ligated into NcoI and Asp718 digested pHASK to generate pΔR9R16.
Isolation of pΔR1R24
Plasmid p9-7 was PCR amplified with PCR primers 5′-AGTGTGGTTTGCCAGCAGTC (SEQ ID NO:80) and 5′-CAAAGTCCCTGTGGGCGTCTTCAGGAGCTTCC-3′ (SEQ ID NO:79). Plasmid p63-1 was PCR amplified with primers 5′ GGAAGCTCCTGAAGACGCCCACAGGGACTTTG-3′ (SEQ ID NO:78) and 5′-TGGTTGATATAGTAGGGCAC-3′ (SEQ ID NO:81). A recombinant PCR product (ΔR1-R24) was then prepared by mixing together 10 ng of each of the first two PCR products, then re-PCR amplifying using only primers SEQ ID NO:80 and SEQ ID NO:81. This recombinant PCR product was then digested with SexAI and PpuMI, and ligated into SexAI and PpuMI digested pHBMD to generate plasmid pΔR1R24.
Isolation of pΔH2-H3
This clone was prepared exactly as pΔH2-R19, except that primer 5′-CAGATTTCACAGGCTGCTCTGGCAGATTTC-3′ (SEQ ID NO:82) was used in place of primer SEQ ID NO:74, and primer 5′-GAAATCTGCCAGAGCAGCCTGTGAAATCTG-3′ (SEQ ID NO:84) was used in place of primer SEQ ID NO:75.
Isolation of ΔH2-R19,R20
This clone was generated from clone pΔH2R19 as follows. Plasmid p44-1 was amplified with primers SEQ ID NO:72 and 5′-TGAATCCTTTAACATAGGTACCTCCAACAT-3′ (SEQ ID NO:85). Plasmid 63-1 was amplified with primers 5′-ATGTTGGAGGTACCTATGTTAAAGGATTCA-3′ (SEQ ID NO:86) and SEQ ID NO:81. The PCR products were then purified by agarose gel electorphoreses, and quantified. A recombinant PCR product was then prepared by mixing together 10 ng of each of the first two PCR products, then re-PCR amplifying using only primers SEQ ID NO:72 and SEQ ID NO:81. This product was digested with Asp718 and BstXI, and ligated into Asp718 and BstXI digested pHBMD generating clone pBMDΔR20. The Asp718-XbaI cDNA-containing fragment from pBMDΔR20 was isolated and ligated into Asp718 and XbaI digested pΔH2R19 to generate pΔH2-R19,R20.

EXAMPLE 5

Testing Truncated Dystrophin in mdx Mice

This example describes the generation of transgenic mdx mice expressing truncated dystrophin cDNA (see above), and testing these mice in various ways to determine various measurable muscle values. A variety of dystrophin expression cassettes (FIG. 27) were used to generate transgenic mice to test their functional capacity in alleviating muscular dystrophy on the dystrophin null mdx background. FIG. 27 depicts the truncated dystrophin cDNA sequences tested, all of which were linked to an regulatory regions, a minx intron, and the SV40 polyadenylation sequence (the 4-repeat constructs employed the HSA actin promoter, See Crawford et al., J. Cell. Biol., 150:1399, 2000; and the remaining sequences employed an MCK enhancer and promoter, see Niwa et al., Genes Dev. 4:1552, 1990). Each of these constructs was released by digestion from plasmid hosts, were gel purified, and used to generate transgenic mice.
Excised expression cassettes injected into wild type C57B1/10×SJL/J F2 hybrid embryos, and F⁰mice were screened by PCR analysis of DNA isolated from tail snips. Positive F⁰mice were backcrossed onto the C57B1/10mdx background, and individual mouse lines were tested for dystrophin expression by immunofluorescent analysis with dystrophin antibodies for of expression in skeletal muscle fibers. Lines that displayed uniform expression of dystrophin in muscle fibers were selected for further analysis. These lines were further backcrossed onto the mdx mouse background before analysis of dystrophin expression, muscle function and morphology.
A. Truncated Dystrophin cDNAs are Expressed at Various Levels in Muscles of Transgenic mdx Mice.
Muscle extracts were analyzed by western (immuno) blot analysis to determine the amount of dystrophin made in different muscles of the transgenic mdx mice. For these studies, total protein was extracted from the quadriceps and diaphragm muscles of control and transgenic mice, and protein concentrations were determined using the Coomassie Plus Protein Assay Reagent (Pierce). One hundred micrograms of each sample was electrophoresed on a 6% polyacrylamide/SDS gel (29.7:0.3/acryl:bis), transferred for 2 hours at 75 volts onto Biotrace Nitrocellulose (Gelman Science) in 1×Tris-Glycine, 20% methanol, 0.05% SDS, using a wet-transfer apparatus (Hoefer). Membranes were blocked in 10% non-fat dry milk, 1% normal goat serum, and 0.1% Tween-20, and hybridized with DYS1 (Novacastra) at a 1/1000 dilution for 2 hours at room temperature, washed, and then probed with horse radish peroxidase conjugated anti-mouse antibodies at a 1/2,000 dilution (Cappel). Blots were developed using the ECL chemiluminescence system (Amersham). All incubations contained 1% normal goat serum and 0.1% Tween-20. The results of the western blot indicated that R9-R16 was poorly expressed in this line of mice, especially in the diaphragm, and that H2-H3 was very poorly expressed in the diaphragm.
B. Truncated Dystrophin cDNAs Confer Various Degrees of Protection on Muscles of Transgenic mdx Mice.
Various muscle groups from the different lines of transgenic mice expressing truncated dystrophins were examined for morphological abnormalities, and for expression of dystrophin by indirect immunofluorescence (IF) in individual fibers. IF analysis was performed as follows. Skeletal muscle was removed from control and transgenic animals, cut into strips, embedded in Tissue-tek OCT mounting media (Miles, Inc.), and frozen quickly in liquid nitrogen-cooled isopentane. Seven micrometer sections were blocked with 1% gelatin in KPBS for 15 minutes, washed in KPBS+0.2% gelatin (KPBSG), and incubated for 2 hours in KPBSG+1% normal goat serum with affinity-purified dystrophin antibody 18-4 (Cox el al., Nature, 364:725-729, 1993) at a dilution of 1/1000. After washing, the slides were incubated for 1 hour with either biotin-labeled goat anti-rabbit polyclonal antibodies (Pierce), washed again, and incubated with FITC (fluorescein isothiocynate)-conjugated streptavidin. After a final wash, Vectashield (Vector Laboratories, Inc.) with DAPI was applied and sections were photographed through a dual bandpass filter under 40× magnification using a Nikon E1000 microscope.
Morphological analysis of the muscles was performed as follows. Muscle groups from among the following types were chosen for analysis: Quadriceps (Quad), soleus, extensor digitorum longus (EDL), tibialis anterior (TA), and diaphragm muscles. Selected muscles were removed from mice, frozen in liquid nitrogen cooled O.C.T. embedding medium (Tissue-Tek), and cut into 7 μm sections. After fixing in 3.7% formaldehyde, sections were stained in hematoxylin and eosin-phloxine. Stained sections were imaged with a Nikon E1000 microscope and photographed.
The results of this analysis show that micro-dystrophin expression (ΔR4R23 transgene) in the diaphragm prevents the onset of muscular dystrophy in mdx mice. In particular, micro-dystrophin transgenic and wild-type C57B/10 diaphragm sections stained with hematoxylin and eosin (H&E) show morphologically healthy muscle without areas of fibrosis, necrosis, mononuclear cell infiltration, or centrally located nuclei. Conversely, the mdx diaphragm displays a high level of dystrophic morphology by H&E. Also, immuno-fluorescence, using anti-dystrophin polyclonal primary antisera, demonstrates that micro-dystrophin transgenes are expressed at the sarcolemmal membrane in a similar fashion to that of wild-type dystrophin, while mdx mice do not express dystrophin.
H & E staining also shows that truncated dystrophins with 8 or 16 spectrin-like repeats have varying abilities to prevent dystrophy in the diaphragm of transgenic mdx mice. The H2R19 maintains normal muscle morphology that is not different from wild-type C57B1/10 muscle. The ΔH2R19 muscle displays a very low percentage of centrally nucleated fibers, while the ΔH2-R19,R20 and ΔR9-16 constructs display percentages intermediate between ΔH2-R19 and mdx (see FIG. 28). The mdx diaphragm had a large number of centrally nucleated fibers, many necrotic fibers, and large areas of mono-nuclear cell infiltration and fibrosis.
The results also show that quadriceps muscle fibers expressing micro-dystrophin transgene (ΔR4R23 transgene) display normal morphology and exclude Evans Blue Dye. Micro-dystrophin transgenic mdx or C57B1/10 quadriceps sections stained with hematoxylin and eosin (H&E) display morphologically healthy muscle without areas of necrosis, fibrosis, mononuclear cell infiltration, or centrally-located nuclei, as opposed to sections of mdx muscle. The high abundance of central nuclei and mononuclear immune cell infiltration are evidence of muscle cell necrosis. Immunofluorescence results indicate that micro-dystrophins display a subsarcolemmal expression pattern like that of wild-type dystrophin, while mdx mice do not express dystrophin. Evans Blue Dye (EBD) uptake is an indication of a damaged myofiber. For analysis of EBD uptake, mice were tail vein injected with 150 μl of a solution containing 10 mg/ml Evans blue dye in PBS (150 mM NaCl, 50 mM Tris pH 7.4). After three hours, the animals were euthanized and mouse tissues were either fixed in 3.7% formaldehyde/0.5% glutaraldehyde to observe gross dye uptake, or frozen unfixed in O.C.T. embedding medium. To examine Evans blue uptake by individual fibers, 7 μm thick frozen sections were fixed in cold acetone and analyzed by fluorescence microscopy. The results of this testing indicate that fibers expressing micro-dystrophin or wild-type dystrophin exclude EBD, and that damaged mdx muscle cell membranes are permeable to Evans Blue dye.
A hallmark of dystrophy in mdx mice is the presence of large numbers of centrally-nucleated muscle fibers, reflecting cycles of fiber degeneration and regeneration. To estimate the degree of myofiber regeneration occurring in the transgenic mice, centrally-nucleated fibers were counted from quadriceps muscles in age-matched wild-type, mdx, and transgenic mdx mice (FIG. 28). To determine the percentage of fibers containing central nuclei, the number of muscle fibers with centrally-located nuclei was divided by the total number of muscle fibers.
Expression of 8 or 4 repeat micro-dystrophin transgenes on the mdx background significantly reduces the percentage of fibers with centrally-located nuclei to wild-type or near wild-type levels (FIG. 28). Dystrophin molecules with zero repeats are unable to correct the mdx phenotype by this assay. The best constructs were observed to be the 8 repeat H2-R19 and the 4 repeat R2-R23 constructs. Greater percentages of centrally nucleated fibers were observed in mice expression the exon 17-48 deletion, the 4 repeat R2R21 construct, the 7 repeat H2R19,R20 construct, the 16 repeat R9R16 construct, and the zero repeat R1R24 construct (FIG. 28). The results from the R9R16 construct likely do not reflect the full functional capacity of the 16 repeat dystrophin since this line of mice expressed very low levels of the truncated dystrophin protein. All other muscles expressed levels of dystrophin that have been shown to be capable of preventing dystrophy if the expressed protein is functional (Phelps et al., Hum Mol Genet; 4:1251-1258, 1995).
The functional capacity of the truncated dystrophins was also assessed by measuring muscle contractile properties in the transgenic mdx mice. Contractile properties of muscles from transgenic mice were compared with those of C57B1/10 wild type and mdx mice. The samples included 4-8 muscles each from the tibialis anterior (TA), extensor digitorum longus (EDL) or diaphragm. Mice were deeply anesthetized with avertin and each muscle was isolated and dissected free from the mouse. After removal of the limb muscles, the mice were euthanized with the removal of the diaphragm muscle. The muscles were immersed in a bath filled with oxygenated buffered mammalian Ringer's solution (137 mM NaCl, 24 mM NaHCO₃, 11 mM glucose, 5 mM KCl, 2 mM CaCl₂ _{, 1}mM MgSO₄, 1 mM NaH₂PO₄, and 0.025 mM tubocurarine chloride, pH 7.4). For each muscle, one tendon was tied to a servomotor and the other tendon to a force transducer. Muscles were stretched from slack length to the optimal length for force development and then stimulated at a frequency that produced absolute isometric tetanic force (mN). Following the measurements of the contractile properties, the muscles were removed from the bath, blotted and weighed to determine muscle mass. Specific force (kN/m2) was calculated by dividing absolute force by total fiber cross sectional area.
FIG. 29 shows that the 8 repeat dystrophin encoded by H2-R19 supports normal force development in both the diaphragm (FIG. 29 a) and EDL muscle (FIG. 29 b). In contrast, previous studies showed that the exon 17-48 construct, which encodes a dystrophin with 8.25 spectrin-like repeats, supports only 90-95% of normal force development in the diaphragm (Phelps et al., Hum Mol Genet, 4:1251-1258, 1995). The 8 repeat dystrophin lacking a central hinge (H2-H3), and the 7 repeat dystrophin (H2-R19,R20) both fail to support significant force generation compared with dystrophic mdx muscles. The results from the R9-R16 construct likely do not reflect the full functional capacity of the 16 repeat dystrophin, since this line of mice expressed very low levels of the truncated dystrophin.
FIG. 30 shows that the micro-dystrophin transgenic mdr mice develop less specific force than do C57B1/10 mice in the TA, but near wild-type levels in the diaphragm. Micro-dys 1 and −2 refer to transgenes ΔR4-R23, and ΔR2-R21, respectively. FIG. 30A shows that C57B1/10 mice display significantly higher specific force than both transgenic lines and mdx mice in the tibialis anterior (TA) muscle. Data are presented as mean±standard error of the means (s.e.m.) with each bar representing 6 to 8 TA muscles. ANOVA statistical testing was performed. (* indicates significance from C57B1/10, p<0.01; s indicates significance from C57B1/10, p<0.05). FIG. 30B shows that mice expressing Micro-dys I develop wild type levels of specific force in the diaphragm, while mice expressing Micro-dys 2 develop ˜22% less specific force by the same assay when compared with C57B1/10. Both lines of mice develop more specific force than mdx mice in the diaphragm. Data are presented as the percentage of wild type.
Dystrophic mice are susceptible to contraction-induced injury (Petrof, ei al., Proc. Nail. Acad Sci. USA. 90:3710-3714, 1993). In this part of the example tested whether the 4 repeat dystrophin clones would protect muscles of transgenic mdr mice from contraction induced injuries. To test contraction-induced injury, an experimental protocol consisting of two muscle stretches was performed in live, anesthetized animals. The distal tendon of the TA was cut and secured to the lever arm of a servomotor that monitors position and force produced by the muscle. Stimulation voltage and optimal muscle length (L₀) for force production were determined. The muscle was maximally stimulated and then stretched 40% greater than L₀(LC1) for 300 milliseconds. A second lengthening contraction was performed 10 seconds later (LC2). The maximum force that the muscle was able to produce after each stretch was measured and expressed as a percentage of the force produced before stretch. Mdr mice expressing micro-dystrophins were significantly protected from the dramatic force deficit produced after a lengthening contraction compared with mdx mice (FIG. 31). Micro-dys 1 and −2 refer to transgenes ΔR4-R23, and ΔR2-R21, respectively. Furthermore, there was no significant difference between either micro-dystrophin construct studied in this assay and C57B1/10 mice following the second, most damaging lengthening contraction. Data are presented as means±s.e.m. with each bar representing between 6 and 8 TA muscles from 9-11 week old mice.
C. Truncated 4 Repeat Dystrophin cDNAs Restore the Ability to Run Long Distances to mdx Mice.
We have observed that mdx mice are not able to run for long distances on a treadmill, as compared to wild-type mice (see below). Therefore, mice expressing four repeat dystrophins were compared with wild-type and mdx mice for ability to run for extended times on a treadmill. The exercising protocol utilized a six lane, enclosed treadmill with a shock grid to allow forced running at a controlled rate. C57B1/10, C57B1/6×SJL F1, mdx or transgenic mdx mice were run at a 15 degree downward angle to induce damaging eccentric muscle contractions. Mice were given a 15 minute acclimation period prior to exercise, and then ran at 10 meters/minute with a subsequent 5 m/min increase in rate every 10 minutes until exhaustion. Exhaustion was determined to be the time at which a mouse spent more than 5 seconds sitting on the shock grid without attempting a re-entry to the treadmill. As shown in FIG. 32, both lines of four repeat transgenic mice ran significantly farther than mdx mice. Micro-dys 1 and −2 refer to transgenes ΔR4-R23, and ΔR2-R21, respectively. Micro-dystrophin transgenic mice are a genetic mixture of C57B1/6×SJL, and C57BV10 strains, and ran an intermediate distance between the two wild-type lines. Data are presented as means±s.e.m. ANOVA statistical analyses were performed. (* indicates values significantly different from mdx line, p<0.01; s indicates values significantly different from mdx line, p<0.05).
D. Micro-Dystrophin Transgenic mdr Mice do not Display Hypertrophy
As a way to measure the functional capacity of the four-repeat dystrophins, we weighed both whole mice and dissected tibialis anterior muscles from age matched transgenic and control mice. The results shown in FIG. 33 show that the micro-dystrophin transgenic mdx mice do not display the muscle hypertrophy normally observed in mdx mice. FIG. 33A shows that three month old micro-dystrophin transgenic mdr mice weighed significantly less than age-matched mdx control mice. FIG. 11B shows that tibialis anterior (TA) muscle masses in mdx mice were significantly higher than control muscle masses in C57B1/10 and in both lines of mdx mice expressing different micro-dystrophin transgenes. Data are presented as means±s.e.m. with each bar representing between 3 and 4 mice. ANOVA statistical analyses were performed (* indicates difference from mdx line, p<0.01; Y indicates difference from C57B1/10 line, p<0.01; s indicates difference from C57B1/10 line, p<0.05). Micro-dys 1 and −2 refer to transgenes ΔR4-R23, and ΔR2-R21, respectively.

EXAMPLE 6

Mini-Dystrophin-Containing Adeno-Associated Viral Vectors
This example describes a construct that could be made in order to allow adeno-associated virus to express a mini-dystrophin peptide in a target muscle cells. FIG. 34 shows a schematic illustration of a plasmid vector containing the adeno-associated virus inverted terminal repeats (AAV-ITRs), the muscle promoter plus enhancer fragment known as CK6 (SEQ ID NO:61, the ΔR2-R21 four repeat dystrophin cDNA (SEQ ID NO:40) with a further deletion of sequences encoded on exons 71-78, plus a 195 base pair SV40 polyadenylation signal that would have a total insert size of approximately 4.7 kb. The cloning capacity of adeno-associated viral vectors is approximately 4.9 kb. As such, the construct could be efficiently packaged into AAV viral particles (e.g. this plasmid construct could be used to transfect cells such that AAV expressing mini-dystrophin peptide is expressed). These AAV then, for example, may be administered to a subject with DMD or BMD (i.e. gene therapy to correct a muscle deficiency in a subject).
All publications and patents mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in material science, chemistry, and molecular biology or related fields are intended to be within the scope of the following claims.

Claims

1-34. (cancelled).

35. A method comprising;

a) providing;

i) a vector comprising nucleic acid which is less than 5.0 kb in length and which encodes a mini-dystrophin peptide, wherein said mini-dystrophin peptide comprises a spectrin-like repeat domain comprising 4 dystrophin spectrin-like repeats, and wherein said mini-dystrophin peptide is capable of increasing a diaphragm specific force value in a DMD animal model by at least 20% of the wild type value; and

ii) a subject comprising target cells; and

b) contacting said vector with said subject under conditions such that said mini-dystrophin peptide is expressed in said target cells.

36. The method of claim 35, wherein said vector comprises an adeno-associated vector.

37. The method of claim 35, wherein said contacting is done by means of injecting said vector into said subject.

38. The method of claim 35, wherein said mini-dystrophin peptide is capable of increasing a diaphragm specific force value in a DMD animal model by at least 30% of the wild type value.

39. The method of claim 35, wherein said dystrophin spectrin-like repeats are human dystrophin spectrin-like repeats.

40. The method of claim 35, wherein said nucleic acid comprises an actin-binding domain encoding sequence.

41. The method of claim 40, wherein said actin binding domain comprises at least a portion of SEQ ID NO:6.

42. The method of claim 35, wherein said nucleic acid comprises a β-dystroglycan binding domain.

43. The method of claim 42, wherein said β-dystroglycan binding domain comprises at least a portion of a dystrophin hinge 4 encoding sequence, and at least a portion of a dystrophin cysteine-rich domain encoding sequence.

44. The method of claim 35, wherein said spectrin-like repeat encoding sequences are selected from the group consisting of SEQ ID NOS:8-10, 12-27, and 29-33.

45. The method of claim 35, wherein said nucleic acid contains less than 75% of a wild type dystrophin 5′ untranslated region.

46. The method of claim 35, wherein said mini-dystrophin peptide further comprises a substantially deleted dystrophin C-terminal domain.

47. The method of claim 35, wherein said nucleic acid contains less than 50% of a dystrophin 3′ untranslated region.

48. The method of claim 35, wherein said mini-dystrophin peptide further comprises dystrophin hinge region 1 and dystrophin hinge region 4.

49. The method of claim 35, wherein said mini-dystrophin peptide further comprises dystrophin hinge region 2 or dystrophin hinge region 3.

50. The method of claim 35, wherein said nucleic acid comprises a promoter.

51. The method of claim 50, wherein said promoter is an MCK promoter.

52. The method of claim 35, wherein said 4 dystrophin spectrin-like repeats are selected from the group consisting of: dystrophin spectrin-like repeat number 1, dystrophin spectrin-like repeat number 2, dystrophin spectrin-like repeat number 3, dystrophin spectrin-like repeat number 22, dystrophin spectrin-like repeat number 23, and dystrophin spectrin like repeat number 24.