US20170368198A1 - Optimized mini-dystrophin genes and expression cassettes and their use - Google Patents

Optimized mini-dystrophin genes and expression cassettes and their use Download PDF

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US20170368198A1
US20170368198A1 US15/628,268 US201715628268A US2017368198A1 US 20170368198 A1 US20170368198 A1 US 20170368198A1 US 201715628268 A US201715628268 A US 201715628268A US 2017368198 A1 US2017368198 A1 US 2017368198A1
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vector
dystrophin
mini
dmd
human
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Xiao Xiao
Juan Li
Chunping Qiao
Scott W.J. McPhee
Richard J. Samulski
Maritza Mclntyre
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University of North Carolina at Chapel Hill
Bamboo Therapeutics Inc
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Bamboo Therapeutics Inc
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Definitions

  • This invention relates to polynucleotides encoding mini-dystrophin proteins, viral vectors comprising the same, and methods of using the same for delivery of mini-dystrophin to a cell or a subject.
  • Duchenne muscular dystrophy is a severe, x-linked, progressive neuromuscular disease affecting approximately one in 3,600 to 9200 live male births.
  • the disorder is caused by frame shift mutations on the dystrophin gene abolishing the expression of the dystrophin protein.
  • Progressive weakness and muscle atrophy begins in childhood, starting in the lower legs and pelvis before spreading into the upper arms.
  • Other symptoms include loss of certain reflexes, waddling gait, frequent falls, difficulty rising from a sitting or lying position, difficulty climbing stairs, changes to overall posture, impaired breathing, and cadiomyopathy.
  • Becker muscular dystrophy has less severe symptoms than DMD, but still leads to premature death. Compared to DMD, BMD is characterized by later-onset skeletal muscle weakness. Whereas DMD patients are wheelchair dependent before age 13 , those with BMD lose ambulation and require a wheelchair after age 16 . BMD patients also exhibit preservation of neck flexor muscle strength, unlike their counterparts with DMD. Despite milder skeletal muscle involvement, heart failure from DMD-associated dilated cardiomyopathy (DCM) is a common cause of morbidity and the most common cause of death in BMD, which occurs on average in the mid-40s.
  • DCM DMD-associated dilated cardiomyopathy
  • Dystrophin is a cytoplasmic protein encoded by the dmd gene, and functions to link cytoskeletal actin filaments to membrane proteins. Normally, the dystrophin protein, located primarily in skeletal and cardiac muscles, with smaller amounts expressed in the brain, acts as a shock absorber during muscle fiber contraction by linking the actin of the contractile apparatus to the layer of connective tissue that surrounds each muscle fiber. In muscle, dystrophin is localized at the cytoplasmic face of the sarcolemma membrane.
  • the dmd gene is the largest known human gene at approximately 2.5 Mb.
  • the gene is located on the X chromosome at position Xp21 and contains 79 exons.
  • the most common mutations that cause DMD or BMD are large deletion mutations of one or more exons (60-70%), but duplication mutations (5-10%), and single nucleotide variants, (including small deletions or insertions, single-base changes, and splice site changes accounting for approximately 25%-35% of pathogenic variants in males with DMD and about 10%-20% of males with BMD) can also cause pathogenic dystrophin variants.
  • Full-length dystrophin is a large (427 kDa) protein comprising a number of subdomains that contribute to its function. These subdomains include, in order from the amino-terminus toward the carboxy-terminus, the N-terminal actin-binding domain, a central so-called “rod” domain, a cysteine-rich domain and lastly a carboxy-terminal domain or region.
  • the rod domain is comprised of 4 proline-rich hinge domains (abbreviated H), and 24 spectrin-like repeats (abbreviated R) in the following order: a first hinge domain (H1), 3 spectrin-like repeats (R1, R2, R3), a second hinge domain (H2), 16 more spectrin-like repeats (R4, R5, R6, R7, R8, R9, R10, R11, R12, R13, R14, R15, R16, R17, R18, R19), a third hinge domain (H3), 5 more spectrin-like repeats (R20, R21, R22, R23, R24), and finally a fourth hinge domain (H4).
  • Subdomains toward the carboxy-terminus of the protein are involved in connecting to the dystrophin-associated glycoprotein complex (DGC), a large protein complex that forms a critical link between the cytoskeleton and the extra-cellular matrix.
  • DGC dystrophin-associated glycoprotein complex
  • AAV adeno-associated virus
  • AAV-mediated mini-dystrophin gene therapy has shown promise in mdx mice, an animal model for DMD, with widespread expression in muscle and evidence of improved muscle function (See, e.g., Wang et al., J. Orthop. Res. 27:421 (2009)).
  • mdx mice an animal model for DMD
  • a micro-dystrophin vector were attempted in the GRMD DMD dog model, however, powerful immunosuppressant drugs were required to achieve significant transduction of muscle cells (Yuasa et al., Gene Ther. 14:1249 (2007)).
  • AAV vectors encoding mini-dystrophins that can be expressed at high levels in transduced cells of subjects with DMD while minimizing immune responses to the mini-dystrophin protein.
  • mini-dystrophin proteins Disclosed and exemplified hereto are mini-dystrophin proteins, codon-optimized genes for expressing such mini-dystrophin proteins, AAV vectors for transducing cells with such genes, and methods of prevention and treatment using such AAV vectors, in particular for preventing and treating dystrophinopathies in subjects in need thereof.
  • AAV vectors of the disclosure are capable of guiding production of significant levels of mini-dystrophin in transduced cells while causing no or only muted immune response against the mini-dystrophin protein.
  • FIG. 1 shows construction of highly truncated mini-dystrophin genes.
  • Wild-type muscle dystrophin has four major domains: the N-terminal domain (N); the central rod domain, which contains 24 rod repeats (R) and four hinges (H); a cysteine-rich (CR) domain, and the carboxy-terminal (CT) domain.
  • the mini-dystrophin genes were constructed by deleting a large portion of the central rods and hinges and most of the CT domain.
  • the mini-dystrophin genes were codon-optimized, fully synthesized and subsequently cloned between a CMV promoter or a muscle-specific synthetic hybrid promoter at the 5′ end of the gene, and a small poly(A) sequence at the 3′ end of the gene.
  • This gene segment containing promoter, codon-optimized mini-dystrophin gene, and polyA signal, was then cloned into a plasmid containing left and right AAV inverted terminal repeats (ITRs) so that the gene segment was flanked by the ITRs.
  • FIG. 2 shows codon-optimization effectively enhances mini-dystrophin gene expression.
  • the top panels show immunofluorescence (IF) staining of mini-dystrophin protein in (A) untransfected 293 cells or after transfection of original un-optimized (B), or optimized (C) mini-dystrophin Dys3978 vector plasmids.
  • the bottom panels show Western blots of the mini-dystrophin in the transfected 293 cells. Blot on the left used an equal amount of cell lysates and shows overwhelming expression by the optimized cDNA.
  • Blot on the right used a 100 ⁇ dilution of the cell lysate from 293 cells transfected with optimized mini-dystrophin cDNA, while the non-optimized sample was not diluted. Note that the signal of the optimized one is still stronger after 100 ⁇ dilution.
  • FIG. 3 shows IF staining of human mini-dystrophin expression in dystrophin/utrophin double knockout (dKO) mice treated with AAV9 vector.
  • Muscle and heart samples from wild-type control mice C57BL/10 (C57), untreated dKO mice, and AAV9-CMV-Hopti-Dys3978 treated dKO mice (T-dKO) were thin-sectioned and stained with an antibody that also recognizes both the mouse wild-type dystrophin and human mini-dystrophin protein. Highly efficient expression was achieved in all samples examined.
  • FIG. 4 shows normalization of body weight of dKO mice as a result of AAV9-CMV-Hopti-Dys3978 treatment. Data were obtained at 4 months of age from wild-type control B10 mice (C57BL/10), untreated mdx mice, untreated dKO mice, and vector-treated dKO mice.
  • FIG. 5 shows improvement of grip force and treadmill running of dKO mice as a result of AAV9-CMV-Hopti-Dys3978 treatment. Data were obtained at 3 months of age from wild-type control B10 mice (C57BL/10), untreated mdx mice, untreated dKO mice, and vector-treated dKO mice (T-dKO).
  • FIGS. 6A-6B show amelioration of dystrophic pathology of dKO mice as a result of AAV9-CMV-Hopti-Dys3978 treatment.
  • FIG. 6A Cryosections (8 ⁇ m) of tibialis anterior muscles from wild-type control C57BK/10 mice, untreated dKO mice, and vector-treated dKO (T-dKO) mice were subjected to hematoxylin and eosin (H&E) staining for histopatology (10 ⁇ magnification).
  • FIG. 6B Quantitative analyses of muscle mass, heart mass, percentage of centrally localized nuclei and serum creatine kinase activities.
  • FIG. 7 shows survival curves of dKO mice treated with human codon-optimized mini-dystrophin Dys3978 vector (AAV9-CMV-Hopti-Dys3978) compared to untreated dKO mice and wildtype mice. Greater than 50% of the treated dKO mice survived longer than 80 weeks (duration of the experiment).
  • FIG. 8 shows improvement in cardiac functions of dKO mice is a result of AAV9-CMV-Hopti-Dys3978 treatment. Hemodynamic analysis was performed on wild-type control C57BL/10 mice, untreated mdx mice, and AAV9 vector-treated dKO mice. The untreated dKO mice were too sick to sustain the procedure. Data were collected from the three groups of mice without or with dobutamine challenge.
  • FIGS. 9A-9B show improvement in electrocardiography (ECG) of dKO mice as a result of AAV9-CMV-Hopti-Dys3978 treatment.
  • FIG. 9A The PR interval of the ECG was improved in vector-treated dKO mice.
  • FIG. 9B Quantitative data of the analysis. The experiment was done to carefully monitor the heart rate of the three groups so that the ECG was not affected by the variation in heart rate. *p ⁇ 0.05.
  • FIG. 10 shows a comparison of the non-tissue specific CMV promoter and the muscle-specific hCK promoter in driving human codon-optimized mini-dystrophin Dys3978 in mdx mice after tail vein injection of AAV9-Hopti-Dys3978 vectors containing CMV or hCK promoter.
  • the human mini-dystrophin Dys3978 showed robust expression in limb muscle and heart muscle as well. It appeared that the hCK promoter was more effective over the CMV promoter.
  • FIG. 11 shows magnetic resonance imaging (MRI) images of the hind limb of GRMD dog “Jelly” after isolated limb vein perfusion of the AAV9-CMV-Hopti-Dys3978 vector.
  • the vector was infused with pressure in the right hind leg which had a tight tourniquet placed at the groin area.
  • the whitish signals indicated vector solution retention in the perfused limb.
  • FIG. 12 shows IF staining of human mini-dystrophin Dys3978 expression at 2 months post vector injection in GRMD dog “Jelly.” Biopsy samples of 5 different muscle groups in both right and left hind legs were examined. The non-injected left leg also had detectable dys3978, suggesting that the AAV9 vector had traveled from the site of injection to the contralateral leg.
  • FIG. 13 shows IF staining of human mini-dystrophin Dys3978 expression at 7 months post vector injection in GRMD dog “Jelly.” Biopsy samples of 4 different muscle groups in both right and left hind legs were examined. The non-injected left leg also had detectable Dys3978, suggesting that the AAV9 vector had traveled from the site of injection to the contralateral leg. Western blot analysis of Dys3978 was done on the same samples.
  • FIG. 14 shows IF staining of human mini-dystrophin Dys3978 expression at 12 months post vector injection in GRMD dog “Jelly.” Biopsy samples of 4 different muscle groups in both right and left hind legs and 1 sample in the forelimb were examined. The non-injected left leg also had detectable Dys3978, suggesting that the AAV9 vector had traveled from the site of injection to the contralateral leg.
  • FIG. 15 shows IF staining of human mini-dystrophin Dys3978 expression at 2 years post vector injection in GRMD dog “Jelly.” Biopsy samples of 2 different muscles groups in both right and left hind legs were examined. Note the non-injected left leg appeared to have more detectable Dys3978 than the injected leg.
  • FIG. 16 shows IF staining of human mini-dystrophin Dys3978. Biopsy samples of two additional (compared with FIG. 15 ) muscle groups in both right and left hind legs and one sample in the forelimb were examined from GRMD dog “Jelly.” Samples were also collected at 2 years post vector injection.
  • FIG. 17 shows IF staining of human mini-dystrophin Dys3978 at 4 years post vector injection in the non-injected left hind leg from GRMD dog “Jelly.”
  • FIG. 18 shows IF staining of human mini-dystrophin Dys3978 at greater than 8 years post vector injection in GRMD dog “Jelly.” Necropsy muscle samples of 5 different muscle groups and heart were examined.
  • FIG. 19 shows IF staining of human mini-dystrophin Dys3978 and endogenous revertant dystrophin at greater than 8 years post vector injection in GRMD dog “Jelly.”
  • Necropsy muscle samples of three different muscle groups were stained with an antibody that recognized both human and dog dystrophin (upper panel) or an antibody that only recognized dog revertant dystrophin (lower panel).
  • the revertant dystrophin positive myofibers were highlighted by arrows.
  • Revertant fibers are rare muscle fibers that stain positively for dystrophin protein that occur in human DMD patients, as well as the mdx mouse and GRMD dogs.
  • FIG. 20 shows Western blot analyses of human mini-dystrophin Dys3978 present in muscle samples of GRMD dog “Jelly” at necropsy more than 8 years after AAV9 vector injection.
  • Western blot showed human mini-dystrophin Dys3978 was present in all skeletal muscles examined. Muscle from an age and sex matched normal dog named “Molly” was used as a positive control with serial 2-fold dilutions to indicate the quantitation of dystrophin protein.
  • the molecular weight of wildtype full length dystrophin is about 400 kDa white the mini-dystrophin Dys3978 protein is about 150 kDa.
  • FIG. 21 shows muscle contractile force improvement in GRMD dog “Jelly” after injection of the AAV9-CMV-Hopti-Dys3978 vector and body wide gene expression.
  • the top curve represents the muscle force of a normal dog, while the bottom curve represents the muscle force of the untreated GRMD dog.
  • the two curves extended into more time points represents the muscle force of dog “Jelly.”
  • Two more GRMD dogs treated with AAV9-CMV-canine-mini-dystrophin Dys3849 vector (Wang, et al., PNAS 97(25):13714-9 (2000)) were also examined for muscle force, and showed improvement (“Jasper” and “Peridot”).
  • FIG. 22 shows muscle biopsy IF staining of human mini-dystrophin expression at 4 months post AAV9-hCK-Copti-Dys3978 vector injection in GRMD dog “Dunkin.”
  • the vector was delivered by intravenous injection to achieve body wide gene expression. Biopsy samples of 4 different muscle groups in the hind limbs were examined. Note nearly uniform mini-dystrophin Dys3978 detected in all muscle groups.
  • FIG. 23 shows IF staining of human mini-dystrophin expression at 14 months post AAV9-hCK-Copti-Dys3978 vector injection in GRMD dog “Dunkin.” Necropsy samples were taken and examined. Note widespread and robust levels of mini-dystrophin Dys3978 detected in heart and all muscle groups. Magnification 4 ⁇ .
  • FIG. 24 shows IF staining of diaphragm muscle with robust levels of human mini-dystrophin detected at 14 months post AAV9-hCK-Copti-Dys3978 vector injection in GRMD dog “Dunkin.”
  • FIG. 25 shows IF staining of peroneus longus muscle with robust levels of human mini-dystrophin detected at 14 months post AAV9-hCK-Copti-Dys3978 vector injection in GRMD dog “Dunkin.”
  • FIG. 26 shows IF staining of semi-membranosus muscle with robust levels of human mini-dystrophin detected at 14 months post AAV9-hCK-Copti-Dys3978 vector injection in GRMD dog “Dunkin.”
  • FIG. 27 shows IF staining of heart left ventricle (LV) muscle with robust levels of human mini-dystrophin detected at 14 months post AAV9-hCK-Copti-Dys3978 vector injection in GRMD dog “Dunkin.”
  • FIG. 28 shows detection by Western blot of human mini-dystrophin Dys3978 in muscle samples of GRMD dog “Dunkin” at 4 months and 14 months post vector injection. Muscle from an age matched normal dog was used as a positive control with serial 2-fold dilutions to indicate the quantitation of dystrophin protein. The molecular weight of wildtype full length dystrophin is about 400 kDa while the mini-dystrophin Dys3978 is about 150 kDa. Note that no mini-dystrophin Dys3978 was detected in the liver.
  • FIG. 29 shows detection by Western blot of human mini-dystrophin Dys3978 expression in heart (LV) sample of GRMD dog “Dunkin” at 14 months post vector injection.
  • Heart sample from an age-matched normal dog was used as a positive control with serial 2-fold dilutions to indicate the quantitation of dystrophin protein.
  • FIG. 30 shows restoration of dystrophin associated protein complex as shown by IF staining of human mini-dystrophin Dys 3978 as well as gamma-sarcoglycan (r-SG) of various muscle groups.
  • FIG. 31 shows analysis of AAV9-CMV-Copti-Dys3978 vector DNA copy in various muscle and tissues. Quantitative PCR (qPCR) was performed to determine the AAV vector DNA genome copy numbers, which were normalized on a per diploid cell basis.
  • qPCR Quantitative PCR
  • FIG. 32 shows improvement of dystrophic histopathology in the heart of AAV9-CMV-Copti-Dys3978 vector GRMD dog “Dunkin” compared to age-matched normal and untreated GRMD dog. HE staining.
  • FIG. 33 shows improvement of dystrophic histopathology in the diaphragm muscle of AAV9-CMV-Copti-Dys3978 vector GRMD dog “Dunkin.” Compared to age-matched normal and untreated GRMD dog. HE staining.
  • FIG. 34 shows improvement of dystrophic histopathology in the limb muscles of AAV9-CMV-Copti-Dys3978 vector GRMD dog “Dunkin” compared to age-matched untreated GRMD dog. HE staining.
  • FIG. 35 shows inhibition of fibrosis in limb muscle and diaphragm of GRMD dog “Dunkin” compared to age-matched untreated GRMD dog. Mason Trichrome blue staining.
  • FIG. 36A provides photomicrographs showing immunolabeling with anti-dystrophin DYSB antibody of biceps femoris muscle obtained from a WT rat mock treated with PBS (left panel), a mock treated DMD rat (central panel), and a Dmd dmx rat treated with AAV9.hGK.Hopti-Dys3978.spA vector (right panel).
  • the dark outline around the fibers shows the subsarcolemmal localization of the dystrophin in WT rat and mini-dystrophin in vector treated Dmd mdx rat.
  • FIG. 36B provides photomicrographs showing haematoxylin and eosin (HES) stained biceps femoris muscle obtained from a mock treated WT rat (left panel), a mock treated Dmd mdx rat (central panel) and a DMD rat treated with AAV9.hGK.Hopti-Dys3978.spA vector (right panel). Cluster of necrotic fibers (*) and endomysial mild fibrosis (black arrowhead) are shown.
  • HES haematoxylin and eosin
  • FIG 36C provides photomicrographs showing immunolabeling with anti-dystrophin DYSB antibody of cardiac muscle obtained from a mock treated WT rat (left panel), a mock treated Dmd mdx rat (central panel) and a Dmd mdx rat treated with AAV9.hCK.Hopti-Dys3978.spA vector (right panel).
  • the dark outline around the fibers shows the subsarcolemmal localization of the dystrophin in WT rat and mini-dystrophin in vector treated Dmd mdx rat.
  • FIG. 36D provides photomicrographs showing HES stained cardiac muscle obtained from a mock treated WT rat (left panel), a mock treated Dmd mdx rat (central panel) and a Dmd mdx rat treated with AAV9.hCK.Hopti-Dys3978spA vector (right panel).
  • a focus of fibrosis is shown in the center panel, and a focus of mononuclear cell infiltration is illustrated in the right panel.
  • FIG. 37 shows average body weight in grams of WT rats treated with vehicle (buffer) and Dmd mdx rats treated with vehicle and increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector over time to 25 weeks after dosing.
  • WT refers to wild type rats
  • DMD refers to Dmd mdx rats
  • n refers to sample size
  • D refers to number days since dosing
  • W refers to number of weeks since dosing
  • E is notation for the specified coefficient times ten raised to the power of the specified exponent (thus, “1E13” stands for 1 ⁇ 10 13 , “3E13”stands for 3 ⁇ 10 13 , “1E14” stands for 1 ⁇ 10 14 , and “3E14” stands for 3 ⁇ 10 14 );
  • vg/kg stands for vector genomes per kilogram body weight; and “w/o HAS” refers to a treatment arm where the vector was administered in PBS without human serum albumin.
  • FIG. 38A provides exemplary photomicrographs of skeletal muscle from Dmd mdx rats stained for histological examination illustrating a semi-quantitative scoring scheme used to estimate the degree of severity of muscle lesions caused by the absence of dystrophin.
  • a score of 0 corresponded to the absence of lesions
  • 1 corresponded to the presence of some regenerative activity as evidenced by centronucleated fibers and small foci of regeneration
  • 2 corresponded to the presence of degenerated fibers; isolated or in small clusters
  • 3 corresponded to tissue remodeling and fiber replacement by fibrotic or adipose tissue. Scoring for heart used different criteria as explained in the text.
  • FIG. 38B shows total DMD lesion scores for rats (that is, average of lesion subscores for biceps femoris, pectoralis, diaphragm and cardiac muscles) at 3 months post-injection are shown, individually as well as the mean among all rats in each treatment arm, and compared to show a vector dose-responsive reduction in lesion score.
  • WT mock refers to WT rats treated with vehicle
  • KO mock refers to Dmd mdx rats treated with vehicle
  • “KO 1E13”, “3E13”, and “1E14” refer to Dmd mdx rats treated with the indicated doses of AAV9.hGK.Hopti-Dys3978.spA vector in vg/kg. Letters above bars indicate that the underlying data is not statistically different from other bars over which the same letters appear. Conversely, bars over which different letters appear are statistically different from each other. Statistics were calculated using the Kruskal-Wallis and Dunn's tests.
  • FIG. 39A provides representative sections from biceps femoris muscle samples from Dmd mdx rats treated with increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector, and negative controls. Samples were dual labeled with an antibody that specifically binds to full length rat dystrophin and human mini-dystrophin, and wheat germ agglutinin conjugate which stains connective tissue. Top panel are micrographs from animals sacrificed at 3 months post-injection. Bottom panel are micrographs from animals sacrificed at 6 months post-injection.
  • FIG. 39B provides percent fibers in random sections from biceps femoris muscle samples from Dmd dmx rats treated with increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector, and negative controls, that stained positive for presence of dystrophin protein. Data for 3 and 6 months post-injection are included. Letters above bars indicate that the underlying data is not statistically different from other bars over which the same letters appear. Conversely, bars over which different letters appear are statistically different from each other. Statistics were calculated using ANOVA analysis and Fisher's post-hoc bilateral test.
  • FIG. 39C provides percent area in random sections of biceps femoris muscle samples from Dmd mdx rats treated with increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector, and negative controls, that stained positive for presence of connective tissue. Data for 3 and 6 months post-injection are included. Letters above bars indicate that the underlying data is not statistically different from other bars over which the same letters appear. Conversely, bars over which different letters appear are statistically different from each other. Statistics were calculated using ANOVA analysis and Fisher's post-hoc bilateral test.
  • FIG. 40A provides representative sections from diaphragm muscle samples from Dmd mdx rats treated with increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector, and negative controls, sacrificed at 3 months post-injection. Samples were dual labeled with an antibody that specifically binds to full length rat dystrophin and human mini-dystrophin, and wheat germ agglutinin conjugate which stains connective tissue.
  • FIG. 40B provides percent fibers in random sections from diaphragm muscle samples from Dmd mdx rats treated with increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector, and negative controls, that stained positive for presence of dystrophin. Data for 3 and 6 months post-injection are included. Letters above bars indicate that the underlying data is not statistically different from other bars over which the same letters appear. Conversely, bars over which different letters appear are statistically different from each other. Statistics were calculated using ANOVA analysis and Fisher's post-hoc bilateral test.
  • FIG. 40C provides percent fibers in random sections from diaphragm muscle samples from Dmd mdx rats treated with increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector, and negative controls, that stained positive for presence of connective tissue. Data for 3 and 6 months post-injection are included. Letters above bars indicate that the underlying data is not statistically different from other bars over which the same letters appear. Conversely, bars over which different letters appear are statistically different from each other. Statistics were calculated using ANOVA analysis and Fisher's post-hoc bilateral test.
  • FIG. 41A shows representative transverse sections of heart at one-third from the apex taken from Dmd mdx rats treated with increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector (top panel), and negative controls (bottom panel), sacrificed at 3 months and 6 months post-injection. Histology sections were stained with picrosirius red to permit visualization of connective tissue.
  • the middle panel contains representative sections of heart muscle taken from vector and vehicle treated Dmd mdx rats dual labeled with an antibody that specifically binds to full length rat dystrophin and human mini-dystrophin, and wheat germ agglutinin conjugate which stains connective tissue.
  • FIG. 41B provides percent fibers in random sections from heart muscle samples from Dmd mdx rats treated with increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector, and negative controls, stained for presence of dystrophin protein. Data for 3 and 6 months post-injection are included. Letters above bars indicate that the underlying data is not statistically different from other bars over which the same letters appear. Conversely, bars over which different letters appear are statistically different from each other. Statistics were calculated using ANOVA analysis and Fisher's post-hoc bilateral test.
  • FIG. 41C provides percent fibers in random sections of heart muscle samples from Dmd mdx rats treated with increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector, and negative controls, stained for presence of connective tissue. Data for 3 and 6 months post-injection are included. Letters above bars indicate that the underlying data is not statistically different from other bars over which the same letters appear. Conversely, bars over which different letters appear are statistically different from each other. Statistics were calculated using ANOVA analysis and Fisher's post-hoc bilateral test.
  • FIG. 42A provides data regarding muscle fatigue in Dmd mdx rats treated with increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector compared to Dmd mdx and WT rats treated with vehicle measured by repeating five closely spaced grip strength tests. Tests were conducted 3 months post-injection in rats injected at 7-9 weeks of age, or when the rats were approximately 4.5 months old. Graph shows the decrease in forelimb grip force measured between trials 1 and 5 (expressed as percentage of trial 1 force). Results are represented as mean ⁇ SEM. Statistics compare Dmd mdx rats treated with vector against WT rats receiving vehicle (*p ⁇ 0.05; ***p ⁇ 0.001), and Dmd mdx rats receiving vehicle ( p ⁇ 0.01; p ⁇ 0.001), both as negative controls.
  • FIG. 42B provides data regarding muscle fatigue in Dmd mdx treated with increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector compared to Dmd mdx and WT rats treated with vehicle measured by repeating five closely spaced grip strength tests. Tests were conducted 6 months post-injection in rats injected at 7-9 weeks of age, or when the rats were approximately 7.5 months old. Graph shows the decrease in forelimb grip force measured between trials 1 and 5 (expressed as percentage of trial 1 force). Results are represented as mean ⁇ SEM.
  • FIG. 43 provides left ventricular (LV) end-diastolic diameter measured during diastole from long-axis images obtained by M-mode echocardiography 6 months post-injection in WT and Dmd mdx rats administered vehicle or AAV9.hCK.Hopti-Dys3978.spA vector. Descriptive statistics shown are mean ⁇ SEM.
  • FIG. 44 provides ejection fractions measured during diastole from long-axis images obtained by M-mode echocardiography 6 months post-injection in WT and Dmd mdx rats administered vehicle or AAV9.hCK.Hopti-Dys3978.spA vector. Descriptive statistics shown are mean ⁇ SEM, and the “$” symbol indicates a statistically significant difference between the data over which it is placed and the data for Dmd mdx rats treated with vehicle (buffer) (p ⁇ 0.05).
  • FIG. 45A provides E/A ratios measured using pulsed Doppler with an apical four-chamber orientation 3 months post-injection in WT and Dmd mdx rats administered vehicle or AAV9.hCK.Hopti-Dys3978.spA vector. Descriptive statistics shown are mean ⁇ SEM, and the “*” symbol indicates a statistically significant difference between the data over which it is placed and the data for WT rats treated with vehicle (buffer) (p ⁇ 0.05).
  • FIG. 45B provides E/A ratios measured using pulsed Doppler with an apical four-chamber orientation 6 months post-injection in WT and Dmd mdx rats administered vehicle or AAV9.hCK.Hopti-Dys3978.spA vector. Descriptive statistics shown are mean ⁇ SEM, and the “**” symbol indicates a statistically significant difference between the data over which it is placed and the data for WT rats treated with vehicle (buffer) (p ⁇ 0.01).
  • FIG. 46A provides isovolumetric relaxation time measured using pulsed Doppler with an apical four-chamber orientation 3 months post-injection in WT and Dmd mdx rats administered vehicle or AAV9.hCK.Hopti-Dys3978.spA vector. Descriptive statistics shown are mean ⁇ SEM.
  • FIG. 46B provides isovolumetric relaxation time measured using pulsed Doppler with an apical four-chamber orientation 6 months post-injection in WT and Dmd mdx rats administered vehicle or AAV9.hCK.Hopti-Dys3978.spA vector. Descriptive statistics shown are mean ⁇ SEM, and the “$” symbol indicates a statistically significant difference between the data over which it is placed and the data for Dmd mdx rats treated with vehicle (buffer) (p ⁇ 0.05).
  • FIG. 47 provides deceleration time measured using pulsed Doppler with an apical four-chamber orientation 6 months post-injection in WT and Dmd mdx rats administered vehicle or AAV9.hCK.Hopti-Dys3978.spA vector. Descriptive statistics shown are mean ⁇ SEM, and the “*” symbol indicates a statistically significant difference between the data over which it is placed and the data for WT rats treated with vehicle (buffer) (p ⁇ 0.05).
  • FIG. 48A shows effect in Dmd mdx rats of increasing doses of AAV9.hCK.Hopti-Dys3978.spA vector on blood AST levels 3 months post-injection. Results are represented as mean ⁇ SEM. Statistical analyses were performed using the non-parametric Kruskal Wallis test and a post-hoc Dunn's multiple comparison test. Statistics compare Dmd mdx rats treated with vector against WT rats that received buffer (vehicle) as a negative control (**p ⁇ 0.1, *p ⁇ 0.05).
  • FIG. 48B shows effect in Dmd mdx rats of different doses of AAV9.hCK.Hopti-Dys3978.spA vector on blood AST levels 6 months post-injection. Results are represented as mean ⁇ SEM. Statistical analyses were performed using the non-parametric Kruskal Wallis test and a post-hoc Dunn's multiple comparison test. Statistics compare Dmd mdx rats treated with vector against WT rats that received buffer (vehicle) as a negative control (***p ⁇ 0.001, **p ⁇ 0.01).
  • FIG. 49A shows effect in Dmd mdx rats of different doses of AAV9.hCK.Hopti-Dys3978.spA vector on blood AST levels 3 months post-injection. Results are represented as mean ⁇ SEM. Statistical analyses were performed using the non-parametric Kruskal Wallis test and a post-hoc Dunn's multiple comparison test. Statistics compare Dmd mdx rats treated with vector against WT rats that received buffer (vehicle) (***p ⁇ 0.001, *p ⁇ 0.05), or against Dmd mdx rats that received buffer (##p ⁇ 0.01, #p ⁇ 0.05), as negative controls.
  • FIG. 49B shows effect in Dmd mdx rats of different doses of AAV9.hCK.Hopti-Dys3978.spA vector on blood AST levels 6 months post-injection. Results are represented as mean ⁇ SEM. Statistical analyses were performed using the non-parametric Kruskal Wallis test and a post-hoc Dunn's multiple comparison test. Statistics compare Dmd mdx rats treated with vector against WT rats that received buffer (vehicle) as a negative control (**p ⁇ 0.01).
  • FIG. 50A shows effect in Dmd mdx rats of different doses of AAV9.hCK.Hopti-Dys3978.spA vector on blood LDH levels 3 months post-injection. Results are represented as mean ⁇ SEM. Statistical analyses were performed using the non-parametric Kruskal Wallis test and a post-hoc Dunn's multiple comparison test. Statistics compare Dmd mdx rats treated with vector against WT rats that received buffer (vehicle) (***p ⁇ 0.001, **p ⁇ 0.01), or against Dmd mdx rats that received buffer (#p ⁇ 0.05), as negative controls.
  • FIG. 50B shows effect in Dmd mdx rats of different doses of AAV9.hCK.Hopti-Dys3978.spA vector on blood LDH levels 6 months post-injection. Results are represented as mean ⁇ SEM. Statistical analyses were performed using the non-parametric Kruskal Wallis test and a post-hoc Dunn's multiple comparison test. Statistics compare Dmd mdx rats treated with vector against WT rats that received buffer (vehicle) as a negative control (**p ⁇ 0.01).
  • FIG. 51A shows effect in Dmd mdx rats of different doses of AAV9.hCK.Hopti-Dys3978.spA vector on blood total creatine kinase (CK) levels 3 months post-injection. Results are represented as mean ⁇ SEM. Statistical analyses were performed using the non-parametric Kruskal Wallis test and a post-hoc Dunn's multiple comparison test. Statistics compare Dmd mdx rats treated with vector against WT rats that received buffer (vehicle) (**p ⁇ 0.01), or compare Dmd mdx rats dosed with 3 ⁇ 10 14 vg/kg vector against Dmd mdx rats that received buffer or 1 ⁇ 10 13 vg/kg vector (##p ⁇ 0.01).
  • FIG. 51B shows effect in Dmd mdx rats of different doses of AAV9.hCK.Hopti-Dys3978.spA vector on blood total creatine kinase (CK) levels 6 months post-injection. Results are represented as mean ⁇ SEM. Statistical analyses were performed using the non-parametric Kruskal Wallis test and a post-hoc Dunn's multiple comparison test.
  • FIG. 52A provides total creatine-kinase (CK) evolution between day of injection (D0) of vehicle of vector and sacrifice 3 months post-injection. Solid bars indicate data from D0, whereas hatched bars indicate data at 3 months. Results are represented as mean ⁇ SEM.
  • FIG. 52B provides total creatine-kinase (CK) evolution between day of injection (D0) of vehicle of vector and sacrifice 6 months post-injection. Solid bars indicate data from D0, whereas hatched bars indicate data at 3 months. Results are represented as mean ⁇ SEM.
  • FIG. 53A provides average absolute maximum forelimb grip strength of older Dmd mdx rats treated with 1 ⁇ 10 14 vg/kg AAV9.hCK.Hopti-Dys3978.spA vector compared to Dmd mdx and WT rats treated with vehicle. Tests were conducted 3 months post-injection in rats injected at 4 months of age, or when the rats were approximately 7 months old. Results are represented as mean ⁇ SEM. Statistics compare Dmd mdx rats treated with vector against Dmd mdx rats treated with vehicle (*p ⁇ 0.01).
  • FIG. 53B provides average maximum forelimb grip strength relative to body weight of older Dmd mdx rats treated with 1 ⁇ 10 14 vg/kg AAV9.hCK.Hopti-Dys3978.spA vector compared to Dmd mdx and WT rats treated with vehicle. Tests were conducted 3 months post-injection in rats injected at 4 months of age, or when the rats were approximately 7 months old. Results are represented as mean ⁇ SEM. Statistics compare Dmd mdx rats treated with vector against Dmd mdx rats treated with vehicle (*p ⁇ 0.01).
  • FIG. 53C shows evolution of forelimb grip force as a measure of muscle fatigue in older Dmd mdx rats treated with 1 ⁇ 10 14 vg/kg AAV9.hCK.Hopti-Dys3978.spA vector compared to Dmd mdx and WT rats treated with vehicle. Test was conducted by measuring average maximum grip force 5 times with short intervals between each trial. Tests were conducted 3 months post-injection in rats injected at 4 months of age, or when the rats were approximately 7 months old. Results are provided relative to body weight and as the mean ⁇ SEM.
  • FIG. 54A provides average absolute maximum forelimb grip strength of older Dmd mdx rats treated with 1 ⁇ 10 14 vg/kg AAV9.hCK.Hopti-Dys3978.spA vector compared to Dmd mdx and WT rats treated with vehicle. Tests were conducted 3 months post-injection in rats injected at 6 months of age, or when the rats were approximately 9 months old. Results are represented as mean ⁇ SEM. Statistics compare Dmd mdx rats treated with vector against WT rats treated with vehicle (**p ⁇ 0.01).
  • FIG. 54B provides average maximum forelimb grip strength relative to body weight of older Dmd mdx rats treated with 1 ⁇ 10 14 vg/kg AAV9.hCK.Hopti-Dys3978.spA vector compared to Dmd mdx and WT rats treated with vehicle. Tests were conducted 3 months post-injection in rats injected at 4 months of age, or when the rats were approximately 9 months old. Results are represented as mean ⁇ SEM. Statistics compare Dmd mdx rats treated with vehicle against WT rats treated with vehicle (*p ⁇ 0.05) or Dmd mdx rats treated with vector against Dmd mdx rats treated with vehicle ( p ⁇ 0.05).
  • FIG. 54C shows evolution of forelimb grip force as a measure of muscle fatigue in older Dmd mdx rats treated with 1 ⁇ 10 14 vg/kg AAV9.hCK.Hopti-Dys3978.spA vector compared to Dmd mdx and WT rats treated with vehicle. Test was conducted by measuring average maximum grip force 5 times with short intervals between each trial. Tests were conducted 3 months post-injection in rats injected at 6 months of age, or when the rats were approximately 9 months old. Results are provided relative to body weight and as the mean ⁇ SEM.
  • FIGS. 55A-55C provide an alignment between the amino acid sequences of the mini-dystrophin protein ⁇ 3990 (SEQ ID NO:27) and the mini-dystrophin protein Dys3978 (SEQ ID NO:7).
  • FIGS. 56A-56I provide an alignment between the nucleic acid sequence encoding mini-dystrophin protein ⁇ 3990 (SEQ ID NO:28), which is derived from the wildtype nucleic acid sequence encoding human dystrophin protein, and the human codon-optimized nucleic acid sequence encoding mini-dystrophin Dys3978 (called Hopti-Dys3978; SEQ ID NO:1).
  • Nucleotide sequences are presented herein by single strand only, in the 5′ to 3′ direction, from left to right, unless specifically indicated otherwise. Nucleotides and amino acids are represented herein in the manner recommended by the IUPAC-IUB Biochemical Nomenclature Commission, or (for amino acids) by either the one-letter code, or the three letter code, both in accordance with, 37 CFR ⁇ 1.822 and established usage. See, e.g., Patent In User Manual , 99-102 (November 1990) (U.S. Patent and Trademark Office).
  • rAAV parvovirus and AAV
  • packaging vectors expressing the parvovirus Rep and/or Cap sequences transiently and stably transacted packaging cells.
  • Such techniques are known to those skilled in the art. See, e.g., S AMBROOK et al., M OLECULAR C LONING : A L ABORATORY M ANUAL 2nd Ed. (Cold Spring Harbor, N.Y., 1989); A USUBEL el al., C URRENT P ROTOCOLS IN M OLECULAR B IOLOGY (Green Publishing Associates, Inc. and John Wiley Sons, Inc., New York).
  • amino acid can be selected from any subset of these amino acid(s) for example A, G, I or L; A, G, I or V; A or G; only L; etc. as if each such subcombination is expressly set forth herein.
  • amino acid can be disclaimed.
  • the amino acid is not A, G or I; is not A; is not G or V; etc. as if each such possible disclaimer is expressly set forth herein.
  • the term “about,” as used herein when referring to a measurable value such as an amount of the length of a polynucleotide or polypeptide sequence, dose, time, temperature, and the like, is meant to encompass variations of 20%, 10%, 5%, 1%, 0.5%, or even 0.1% of the specified amount.
  • AAV adeno-associated virus
  • AAV includes but is not limited to, AAV type 1 (AAV1), AAV type 2 (AAV2), AAV type 3 (AAV3, including types 3A and 3B), AAV type 4 (AAV4), AAV type 5 (AAV5), AAV type 6 (AAV6), AAV type 7 (AAV7), AAV type 8 (AAV8), AAV type 9 (AAV9), AAV type 10 (AAV10), AAV type 11 (AAV11), AAV type 12 (AAV12), AAV type 13 (AAV13), Avian AAV ATCC VR-865, Avian AAV strain DA-1, Bb1, Bb2, Ch5, Cy2, Cy3, Cy4, Cy5, Cy6, Hu1, Hu10, Hu11, Hu13, Hu15, Hu16, Hu17, Hu18, Hu19, Hu2, Hu20, Hu21, Hu22, Hu23, Hu24, Hu25, Hu26, Hu27, Hu28, Hu29, Hu3, Hu31, Hu32, Hu34
  • Capsids may be derived from a number of AAV serotypes disclosed in U.S. Pat. No. 7,906,111; Gao et al., 2004, J. Virol.
  • AAV-TT true type AAV (AAV-TT) variants disclosed in WO 2015/121501, and RHM-4-1, RHM15-1 through RHM15-6, and variants thereof, disclosed in WO 2015/013313, and one skilled in the art would know there are likely other variants not yet identified that perform the same or similar function, or may include components from two or more AAV capsids.
  • a full complement of AAV cap proteins includes VP1, VP2, and VP3.
  • the open reading frame comprising nucleotide sequences encoding AAV capsid proteins may comprise less than a full complement AAV cap proteins or the full complement of AAV cap proteins may be provided.
  • AAV is a small non-enveloped virus with an icosahedral capsid about 20-30 nm in diameter.
  • AAV are not able to replicate without the contribution of so-called helper proteins from other viruses (e.g., adenovirus, herpes simplex virus, Vaccinia virus and human papillomavirus), and so were placed into a special genus, called Dependovirus (because they depend on other viruses for replication) within the family of parvoviridae.
  • helper proteins e.g., adenovirus, herpes simplex virus, Vaccinia virus and human papillomavirus
  • Dependovirus because they depend on other viruses for replication
  • AAV2 AAV2
  • AAV2 AAV2
  • AAV2 or any other AAV serotype infect and replicate inside cells are provided merely to aid in the understanding of the inventions disclosed herein, and are not intended to limit their scope in any way. Even if some of this information is later found to be incorrect or incomplete, it should not be construed as detracting from the utility or enablement of the inventions disclosed and claimed herein. Further information about AAV lifecycle can be found in M.
  • the wild type genome of AAV2 is linear DNA approximately 4.7 kilobases in length. Although mostly single-stranded, the 5′ and 3′ ends of the genome consist of so-called inverted terminal repeats (ITR), each 145 basepairs long and containing palindromic sequences that self-anneal through classic Watson-Crick base-pairing to form T-shaped hairpin structures.
  • ITR inverted terminal repeats
  • One of these structures contains a free 3′ hydroxyl group that, relying on cellular DNA polymerases, permits initiation of viral DNA replication through a self-priming strand-displacement mechanism. See, for example, M. Goncalves, Adeno-associated virus: from defective virus to effective vector, Virology J 2:43 (2005).
  • the wild type AAV2 genome contains two genes, rep and cap, that code respectively for four replication proteins (Rep 78, Rep 68, Rep 52, and Rep 40) and three capsid proteins (VP1, VP2, and VP3) through efficient use of alternative promoters and splicing.
  • the large replication proteins, Rep 78 and 68 are multifunctional and play a role in AAV transcription, viral DNA replication, and site-specific integration of the viral genome into human chromosome 19.
  • the smaller Rep proteins have been implicated in packing the viral genome into the viral capsids in infected cell nuclei.
  • capsid proteins are produced through a combination of alternative splicing and use of alternative translational start sites, so that all three proteins share sequence towards their carboxy-termini, but VP2 includes additional amino-terminal sequence absent from VP3, and VP1 includes additional amino-terminal sequence absent from both VP2 and VP3. It is estimated that capsids contain a total of 60 capsid proteins in an approximate VP1:VP2:VP3 stoichiometry of 1:1:10, although these ratios can apparently vary.
  • AAV has been identified as a leading viral vector for gene therapy.
  • Advantages of using AAV compared to other viruses that have been proposed as gene therapy vectors include the ability of AAV to support long term gene expression in transduced cells, to transduce both dividing and nondividing cells, to transduce a wide variety of different types of cells depending on serotype, the inability to replicate without a helper virus, and an apparent lack of pathogenicity associated with wild type infections.
  • AAV capsids can physically accommodate a single stranded DNA genome that is at most about 4.7-5.0 kilobases in length. Without modifying the genome, there would not be enough room to include a heterolous gene, such as coding sequence for a therapeutic protein, and gene regulatory elements, such as a promoter and optionally an enhancer. To create more room, the rep and cap genes can be removed and replaced with desired heterologous sequences, as long as the flanking ITRs are retained. The functions of the rep and cap genes can be provided in trans on a different piece of DNA. By contrast, the ITRs are the only AAV viral elements that must remain in cis with the heterologous sequence.
  • ITRs with a heterologous gene and removing the rep and cap genes to a different plasmid lacking ITRs also prevents production of infectious wild type AAV at the same time that AAV vector for gene therapy is being produced. Removing rep and cap also means that AAV vectors for gene therapy cannot replicate in the cells they transduce.
  • the genome of AAV vectors is linear single-stranded DNA flanked by AAV ITRs.
  • the single stranded DNA genome must be converted to double-stranded form by cellular DNA polymerases that utilize the free 3′-OH of one of the self-priming ITRs to initiate second-strand synthesis.
  • full length-single stranded genomes of opposite polarity can anneal to generate a full length double-stranded genome, and can result when a plurality of AAV vectors carrying genomes of opposite polarity simultaneously transduce the same cell. After double-stranded vector genomes form, by whatever mechanism, the cellular gene transcription machinery can act on the double-stranded DNA to express the heterologous gene.
  • the vector genome can be designed to be self-complementary (scAAV), having a wild type ITR at each end and a mutated ITR in the middle.
  • scAAV self-complementary
  • scAAV self-complementary
  • a wild type ITR at each end
  • a mutated ITR in the middle.
  • TR Adeno-associated virus terminal repeat
  • AAV vectors for gene therapy have been developed, but one of the most common is the triple transfection technique, in which three different plasmids are transfected into producer cells. See, for example, N. Clement and J. Grieger, Mol Ther Methods Clin Dev, 3:16002 (2016), Grieger, J C, et al., Mol Ther 24 (2):287-97 (2016), and the references cited therein.
  • a plasmid is created that includes the sequence of the vector genome including, for example a heterologous promoter and optionally an enhancer, and a heterologous gene to express a desired RNA or protein, flanked by the left and right ITRs.
  • the vector plasmid would be co-transfected into producer cells, such as HEK293 cells, with a second plasmid containing the rep and cap genes, and a third plasmid containing adenovirus (or other virus) helper genes required to replicate and package the vector genome into AAV capsids.
  • rep, cap and adenovirus helper genes all reside on the same plasmid, and two plasmids are co-transfected into producer cells.
  • adenovirus helper genes include E1a, E1b, E2a, E4orf6, and VA RNA genes.
  • an AAV gene therapy vector could use an AAV9 capsid and a vector genome containing AAV2 ITRs flanking a heterologous gene (which can be designated “AAV2/9”), such as a mini-dystrophin.
  • AAV2/9 a heterologous gene
  • the parvovirus particles and genomes of the present invention can be from, but are not limited to AAV.
  • the genomic sequences of various serotypes of AAV and the autonomous parvoviruses, as well as the sequences of the native ITRs, Rep proteins, and capsid subunits are known in the art. Such sequences may be found in the literature or in public databases such as GenBank.
  • ITR sequences from AAV1, AAV2 and AAV3 are provided by Xiao, X., (1996), “Characterization of Adeno-associated virus (AAV) DNA replication and integration,” Ph.D. Dissertation, University of Pittsburgh, Pittsburgh, Pa. (incorporated herein in its entirety).
  • transduction of a cell by AAV refers to AAV-mediated transfer of genetic material into the cell. See, e.g., FIELDS et al., VIROLOGY, volume 2, chapter 69 (3d ed., Lippincott-Raven Publishers).
  • a “3′ portion” of a polynucleotide indicates a segment of the polynucleotide that is downstream of another segment.
  • the term “3′ portion” is not intended to indicate that the segment is necessarily at the 3′ end of the polynucleotide, or even that it is necessarily in the 3′ half of the polynucleotide, although it may be.
  • a “5′ portion” of a polynucleotide indicates a segment of the polynucleotide that is upstream of another segment.
  • the term “5′ portion” is not intended to indicate that the segment is necessarily at the 5′ end of the polynucleotide, or even that it is necessarily in the 5′ of the polynucleotide, although it may be.
  • polypeptide encompasses both peptides and proteins, unless indicated otherwise.
  • a “polynucleotide” is a linear sequence of nucleotides in which the 3′-position of each monomeric unit is linked to the 5′-position of the neighboring monomeric unit via a phosphate group.
  • Polynucleotides may be RNA (containing RNA nucleotides only), DNA (containing DNA nucleotides only), RNA and DNA hybrids (containing RNA and DNA nucleotides), as well as other hybrids containing naturally occurring and/or non-naturally occurring nucleotides.
  • the linear order of bases of the nucleotides in a polynucleotide is called the “nucleotide sequence,” “nucleic acid sequence,” “nucleobase sequence,” or sometimes, just “sequence” of the polynucleotide.
  • the order of bases is provided starting from the 5′ end of the polynucleotide and ending at the 3′ end of the polynucleotide.
  • polynucleotides can adopt secondary structures, such as regions of self-complementarity. Polynucleotides can also hybridize with fully or partially complementary polynucleotides through classic Watson-Crick base pairing, or other mechanisms familiar to those of ordinary skill.
  • a “gene” is a section of a polynucleotide, typically but not necessarily of DNA, that encodes a polypeptide or protein.
  • genes can be interrupted by introns.
  • polynucleotide can encode more than one polypeptide or protein due to mechanisms such as alternative splicing, use of alternate start codons, or other biological mechanisms familiar to those of ordinary skill in the art.
  • codon-optimized refers to a gene coding sequence that has been optimized to increase expression by substituting one or more codons normally present in a coding sequence (for example, in a wildtype sequence, including, e.g., a coding sequence for dystrophin or a mini-dystrophin) with a codon for the same (synonymous) amino acid.
  • a coding sequence for example, in a wildtype sequence, including, e.g., a coding sequence for dystrophin or a mini-dystrophin
  • the optimization substitutes one or more rare codons (that is, codons for tRNA that occur relatively infrequently in cells from a particular species) with synonymous codons that occur more frequently to improve the efficiency of translation.
  • one or more codons in a coding sequence are replaced by codons that occur more frequently in human cells for the same amino acid. Codon optimization can also increase gene expression through other mechanisms that can improve efficiency of transcription and/or translation.
  • a codon-optimized gene exhibits improved protein expression, for example, the protein encoded thereby is expressed at a detectably greater level in a cell compared with the level of expression of the protein provided by the wildtype gene in an otherwise similar cell.
  • sequence identity has the standard meaning in the art. As is known in the art, a number of different programs can be used to identify whether a polynucleotide or polypeptide has sequence identity or similarity to a known sequence. Sequence identity or similarity may be determined using standard techniques known in the art, including, but not limited to, the local sequence identity algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the sequence identity alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Natl. Acad. Sci.
  • PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments. It can also plot a tree showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng & Doolittle, J. Mol. Evol. 35:351 (1987); the method is similar to that described by Higgins & Sharp, CABIOS 5:151 (1989).
  • BLAST BLAST algorithm
  • WU-BLAST-2 WU-BLAST-2 uses several search parameters, which are preferably set to the default values. The parameters are dynamic values and are established by the program itself depending upon the composition of the particular sequence and composition of the particular database against which the sequence of interest is being searched; however, the values may be adjusted to increase sensitivity.
  • a percentage amino acid sequence identity value is determined by the number of matching identical residues divided by the total number of residues of the “longer” sequence in the aligned region.
  • the “longer” sequence is the one having the most actual residues in the aligned region (gaps introduced by WU-Blast-2 to maximize the alignment score are ignored).
  • percent nucleic acid sequence identity is defined as the percentage of nucleotide residues in the candidate sequence that are identical with the nucleotides in the polynucleotide specifically disclosed herein.
  • the alignment may include the introduction of gaps in the sequences to be aligned.
  • the percentage of sequence identity will be determined based on the number of identical nucleotides in relation to the total number of nucleotides.
  • sequence identity of sequences shorter than a sequence specifically disclosed herein will be determined using the number of nucleotides in the shorter sequence, in one embodiment.
  • percent identity calculations relative weight is not assigned to various manifestations of sequence variation, such as insertions, deletions, substitutions, etc.
  • identities are scored positively (+1) and all forms of sequence variation including gaps are assigned a value of “0,” which obviates the need for a weighted scale or parameters as described below for sequence similarity calculations.
  • Percent sequence identity can be calculated, for example, by dividing the number of matching identical residues by the total number of residues of the “shorter” sequence in the aligned region and multiplying by 100. The “longer” sequence is the one having the most actual residues in the aligned region.
  • “Substantial homology” or “substantial similarity,” means, when referring to a nucleic acid or fragment thereof, indicates that, when optimally aligned with appropriate nucleotide insertions or deletions with another nucleic acid (or its complementary strand), there is nucleotide sequence identity in at least about 95 to 99% of the sequence.
  • an “isolated” polynucleotide e.g., an “isolated DNA” or an “isolated RNA” means a polynucleotide separated or substantially free from at least some of the other components of the naturally occurring organism or virus, for example, the cell or viral structural components or other polypeptides or nucleic acids commonly found associated with the polynucleotide.
  • an “isolated” polypeptide means a polypeptide that is separated or substantially free from at least some of the other components of the naturally occurring organism or virus, for example, the cell or viral structural components or other polypeptides or nucleic acids commonly found associated with the polypeptide.
  • a “therapeutic polypeptide” is a polypeptide that may alleviate or reduce symptoms that result from an absence or defect in a protein in a cell or subject.
  • a “therapeutic polypeptide” is one that otherwise confers a benefit to a subject, e.g., anti-cancer effects or improvement in transplant survivability.
  • modified refers to a sequence that differs from a wild-type sequence due to one or more deletions, additions, substitutions, or any combination thereof.
  • virus vector As used herein, by “isolate” or “purify” (or grammatical equivalents) a virus vector, it is meant that the virus vector is at least partially separated from at least some of the other components in the starting material.
  • treat By the terms “treat,” “treating,” or “treatment of” (and grammatical variations thereof) it is meant that the severity of the subject's condition is reduced, at least partially improved or stabilized and/or that some alleviation, mitigation, decrease, or stabilization in at least one clinical symptom is achieved and/or there is a delay in the progression of the disease or disorder.
  • prevent refers to prevention and/or delay of the onset of a disease, disorder and/or a clinical symptom(s) in a subject and/or a reduction in the severity of the onset of the disease, disorder and/or clinical symptom(s) relative to what would occur in the absence of the methods of the invention.
  • the prevention can be complete, e.g., the total absence of the disease, disorder and/or clinical symptom(s).
  • the prevention can also be partial, such that the occurrence of the disease, disorder and/or clinical symptom(s) in the subject and/or the severity of onset is less than what would occur in the absence of the present invention.
  • a “treatment effective” amount as used herein is an amount that is sufficient to provide some improvement or benefit to the subject.
  • a “treatment effective” amount is an amount that will provide some alleviation, mitigation, decrease or stabilization in at least one symptom in the subject.
  • the therapeutic effects need not be complete or curative, as long as some benefit is provided to the subject.
  • a “prevention effective”, amount as used herein is an amount that is sufficient to prevent and/or delay the onset of a disease, disorder and/or clinical symptoms, in a subject and/or to reduce and/or delay the severity of the onset of a disease, disorder and/or clinical symptoms in a subject relative to what would occur in the absence of the methods of the invention.
  • the level of prevention need not be complete, as long as some benefit is provided to the subject.
  • heterologous or “exogenous” nucleotide or nucleic acid sequence are used interchangeably herein and refer to a nucleic acid sequence that is not naturally occurring in the virus or a cell.
  • the heterologous nucleic acid comprises an open reading frame that encodes a polypeptide or nontranslated RNA of interesting (e.g., for delivery to a cell or subject).
  • virus vector refers to a virion or virus particle that functions as a nucleic acid delivery vehicle and which comprises a vector genome packaged within the virion or virus particle.
  • Vectors can be infectious or non-infectious. Non-infectious vectors cannot replicate themselves without exogenously added factors.
  • Vectors may be AAV particles or virions comprising an AAV capsid within which is packaged an AAV vector genome. These vectors may also be referred to herein as “recombinant AAV” (abbreviated “rAAV”) vectors, particles or virions.
  • rAAV recombinant AAV
  • a vector genome is a polynucleotide for packaging within a vector particle or virion for delivery into a cell (which cell may be referred to as a “target cell”).
  • a vector genome is engineered to contain a heterologous nucleic acid sequence, such as a gene, for delivery into the target cell.
  • a vector genome may also contain one or more nucleic acid sequences that function as regulatory elements to control expression of the heterologous gene in the target cell.
  • a vector genome may also contain wildtype or modified viral nucleic acid sequencer(s) required for the production and/or function of the vector, such as, without limitation, replication of the vector genome in a host and packaging into vector particles.
  • the vector genome is an “AAV vector genome,” which is capable of being packaged into an AAV capsid.
  • an AAV vector genome includes one or two inverted terminal repeats (ITRs) in cis with the heterologous gene to support replication and packaging. All other structural and non-structural protein coding sequences required for AAV vector production may be provided in trans (e.g., from a plasmid, or by stably integrating the sequences into a host cell).
  • an AAV vector genome comprises at least one ITR (e.g., an AAV ITR), optionally two ITRs (e.g., two AAV ITRs), which typically will be at the 5′ and 3′ ends of the vector genome and flank the heterologous nucleic acid sequence, but need not be contiguous thereto.
  • the ITRs can be the same or different from each other, and from the same or different AAV serotypes.
  • host cell refers to cells into which exogenous nucleic acid has been introduced, including the progeny of such cell.
  • Host cells include “transformants,” “transformed cells,” and “transduced cells,” which include the primary transformed cell and progeny derived therefrom without regard to the number of passages.
  • certain host cells may be used as “producer” or “packaging” cells that contain all the genes required to assemble functional virus particles including a capsid and vector genome.
  • different host cells can usefully serve as producer cells, such as HEK293 cells, or the Pro10 cell line, but others are possible.
  • the required genes for viron assembly include the vector genome as described elsewhere herein, AAV rep and cap genes, and certain helper genes from other viruses, including without limitation adenovirus.
  • AAV rep and cap genes include the vector genome as described elsewhere herein, AAV rep and cap genes, and certain helper genes from other viruses, including without limitation adenovirus.
  • the requisite genes for AAV production can be introduced into producer cells in various ways, including without limitation transfection of one or more plasmids, however, certain of the genes can already be present in the producer cells, either integrated into the genome or carried on an episome.
  • inverted terminal repeat includes any palindromic viral terminal repeat, or synthetic sequence that forms a hairpin structure and functions as an inverted terminal repeat (i.e., mediates certain viral functions such as replication, virus packaging, integration and/or provirus rescue, and the like).
  • the ITR can be an AAV ITR or a non-AAV ITR.
  • a non-AAV ITR sequence such as those of other parvoviruses (e.g., canine parvovirus, bovine parvovirus, mouse parvovirus, porcine parvovirus, human parvovirus B-19) or the SV40 hairpin that serves as the origin of SV40 replication can be used as an ITR, which can further be modified by truncation, substitution, deletion, insertion and/or addition.
  • the ITR can be partially or completely synthetic, such as the “double-D sequence” as described in U.S. Pat. No. 5,478,745 to Samulski et al. See also FIELDS et al., VIROLOGY, volume 2, chapters 69 & 70 (4th ed., Lippincott-Raven Publishers).
  • An “AAV inverted terminal repeat” or “AAV ITR” may be from any AAV, including but not limited to serotypes 1, 2, 3a, 3b, 4, 5, 6, 7, 8, 9, 10, 11, or 13, snake AAV, avian AAV, bovine AAV, canine AAV, equine AAV, ovine AAV, goat AAV, shrimp AAV, or any other AAV now known or later discovered.
  • An AAV ITR need not have the native terminal repeat sequence (e.g., a native AAV ITR sequence may be altered by insertion, deletion, truncation and/or missense mutations), as long as the terminal repeat mediates the desired functions, e.g., replication, virus packaging, persistence, and/or provirus rescue, and the like.
  • the sequence of the AAV2 ITRs are 145 base pairs long, and are provided herein as SEQ ID NO:14 and SEQ ID NO:15.
  • Cross-motifs includes conserved sequences such as found at or close to the termini of the genomic sequence and recognized for initiation of replication; cryptic promoters or sequences at internal positions likely used for transcription initiation, splicing or termination.
  • flanking indicates the presence of one or more the flanking elements upstream and/or downstream, i.e., 5′ and/or 3′, relative to the sequence.
  • the term “flanked” is not intended to indicate that the sequences are necessarily contiguous. For example, there may be intervening sequences between the nucleic acid encoding the transgene and a flanking element.
  • a sequence e.g., a transgene
  • TRs two other elements
  • Transection of a cell means that genetic material is introduced into a cell for the purpose of genetically modifying the cell. Transection can be accomplished by a variety of means known in the art, such as calcium phosphate, polyethyleneimine, electroporation, and the like.
  • Gene transfer or “gene delivery” refers to methods or systems for reliably inserting foreign DNA into host cells. Such methods can result in transient expression of non-integrated transferred DNA, extrachromosomal replication and expression of transferred replicons (e.g. episomes), or integration of transferred genetic material into the genomic DNA of host cells.
  • transferred replicons e.g. episomes
  • Transgene is used to mean any heterologous nucleotide sequence incorporated in a vector, including a viral vector, for delivery to and including expression in a target cell (also referred to herein as a “host cell”), and associated expression control sequences, such as promoters. It is appreciated by those of skill in the art that expression control sequences will be selected based on ability to promote expression of the transgene in the target cell.
  • a transgene is a nucleic acid encoding a therapeutic polypeptide.
  • the virus vectors of the invention can further be “targeted” virus vectors (e.g., having a directed tropism) and/or a “hybrid” parvovirus (i.e., in which the viral ITRs and viral capsid are from different parvoviruses) as described in international patent publication WO 00/28004 and Chao et al., (2000) Mol. Therapy 2:619.
  • targeted virus vectors e.g., having a directed tropism
  • a “hybrid” parvovirus i.e., in which the viral ITRs and viral capsid are from different parvoviruses
  • viral capsid or genomic elements can contain other modifications, including insertions, deletions and/or substitutions.
  • parvovirus or AAV “Rep coding sequences” indicate the nucleic acid sequences that encode the parvoviral or AAV non-structural proteins that mediate viral replication and the production of new virus particles.
  • the parvovirus and AAV replication genes and proteins have been described in, e.g., F IELDS et al., V IROLOGY , volume 2, chapters 69 & 70 (4th ed., Lippincott-Raven Publishers).
  • the “Rep coding sequences” need not encode all of the parvoviral or AAV Rep proteins.
  • the Rep coding sequences do not need to encode all four AAV Rep proteins (Rep78, Rep 68, Rep52 and Rep40), in fact, it is believed that AAV5 only expresses the spliced Rep68 and Rep40 proteins.
  • the Rep coding sequences encode at least those replication proteins that are necessary for viral or vector genome replication and packaging into new virions.
  • the Rep coding sequences will generally encode at least one large Rep protein (i.e., Rep78/68) and one small Rep protein (i.e., Rep52/40).
  • the Rep coding sequences encode the AAV Rep78 protein and the AAV Rep52 and/or Rep40 proteins. In other embodiments, the Rep coding sequences encode the Rep68 and the Rep52 and/or Rep40 proteins. In a still further embodiment, the Rep coding sequences encode the Rep68 and Rep52 proteins, Rep68 and Rep40 proteins, Rep78 and Rep52 proteins, or Rep78 and Rep40 proteins.
  • large Rep protein refers to Rep68 and/or Rep78.
  • Large Rep proteins of the claimed invention may be either wild-type or synthetic.
  • a wild-type large Rep protein may be from any parvovirus or AAV, including but not limited to serotypes 1, 2, 3a, 3b, 4, 5, 6, 7, 8, 9, 10, 11, or 13, or any other AAV now known or later discovered.
  • a synthetic large Rep protein may be altered by insertion, deletion, truncation and/or missense mutations.
  • Rep proteins are encoded by a single gene through use of two different promoters and alternative splicing.
  • Rep proteins can be expressed in producer cells from a single gene, or from distinct polynucleotides, one sequence for each Rep protein to be expressed.
  • a Rep encoding gene can be engineered to inactivate the p5 or p19 promoter so that only small or only large Rep proteins are expressed the respective modified genes.
  • Expression of the large and small Rep proteins from different genes can be advantageous when one of the viral promoters is inactive in a host cell, in which case a constitutively active promoter can be used instead, or where it is desired to express the Rep proteins at different levels under the control of separate transcriptional and/or translational control elements.
  • the parvovirus of AAV “cap boding sequences” encode the structural proteins that form a functional parvovirus or AAV capsid (i.e., can package DNA and infect target cells).
  • the cap coding sequences will encode all of the parvovirus for AAV capsid subunits, but less than all of the capsid subunits may be encoded as long as a functional capsid is produced.
  • the cap coding sequences will be present on a single nucleic acid molecule.
  • a “micro-dystrophin” or a “mini-dystrophin” is an engineered protein comprising certain subdomains or portions of subdomains present in full length muscle dystrophin or isoforms thereof that possess at least some of the functionality of dystrophin when expressed in a muscle cell. Micro-dystrophins and mini-dystrophins are smaller than full length muscle dystrophin (Dp427m). Relative to full length muscle dystrophin, micro-dystrophins and mini-dystrophins may contain deletions at the N-terminus, the C-terminus, internally, or any combination thereof.
  • a “dystrophinopathy” is a muscle disease caused by pathogenic variants in DMD, the gene encoding the protein dystrophin.
  • Dystrophinopathies manifest as a spectrum of phenotypes depending on the nature of the underlying genetic lesion. The mild end of the spectrum includes without limitation the phenotypes of asymptomatic increase in serum concentration of creatine phosphokinase (CK) and muscle cramps with myoglobinuria.
  • CK creatine phosphokinase
  • the severe end of the spectrum includes without limitation the progressive muscle diseases Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD), in which skeletal muscle is primarily affected and heart to a lesser degree, and DMD-associated dilated cardiomyopathy (DCM), in which the heart is primarily affected.
  • DMD Duchenne muscular dystrophy
  • BMD Becker muscular dystrophy
  • DCM DMD-associated dilated cardiomyopathy
  • the present disclosure provides codon-optimized mini-dystrophin gene sequences and expression cassettes containing the same. Such genes and expression cassettes are useful for, among other applications, gene therapy to prevent or treat dystrophinopathies, such as DMD, in subjects in need thereof. Expression of mini-dystrophin proteins in transduced muscle cells is able to replicate and replace at least some of the function normally attributable to full-length dystrophin, such as supporting a mechanically strong link between the extra-cellular matrix and the cytoskeleton.
  • the codon-optimized sequences are designed to fit within the size limitations of parvovirus vectors, e.g., AAV vectors, as well as provide enhanced expression of mini-dystrophin compared to non-optimized sequences.
  • the optimized mini-dystrophin sequences provide increased expression of mini-dystrophin protein in muscle cells, or in muscle in animals that is at least about 5% greater than the expression of non-codon-optimized dystrophin sequences, e.g., at least about 5, 10, 20, 30, 40, 50, 75, 100, 200, 300, 400, or 500% or more, where the non-codon-optimized sequence is based on the mRNA encoding wildtype human full-length muscle dystrophin, as exemplified by NCBI Reference Sequence NM_004006.2, which is incorporated by reference.
  • one aspect of the invention relates to a polynucleotide encoding a mini-dystrophin protein, the polynucleotide comprising, consisting essentially of, or consisting of: (a) the nucleotide sequence of SEQ ID NO:1 or a sequence at least about 90% identical thereto; (b) the nucleotide sequence of SEQ ID NO:2 or a sequence at least about 90% identical thereto; or (c) the nucleotide sequence of SEQ ID NO:3 or a sequence at least about 90% identical thereto.
  • the polynucleotide is at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the nucleotide sequence of one of SEQ ID NOS: 1-3.
  • the polynucleotide has a length that is within the capacity of a viral vector, e.g., a parvovirus vector, e.g., an AAV vector.
  • the polynucleotide is about 5000, 4900, 4800, 4700, 4600, 4500, 4400, 4300, 4200, 4100, or about 4000 nucleotides, or fewer.
  • the mini-dystrophin protein encoded by the polynucleotide comprises, consists essentially of, or consists of the N-terminus, hinge H1, rods R1 and R2, hinge H3, rods R22, R23, and R24, hinge H4, the cysteine-rich domain (CR domain), and in some embodiments, all or a portion of the carboxy-terminal domain (CT domain) of wild-type dystrophin protein.
  • the mini-dystrophin protein encoded by the polynucleotide comprises, consists essentially of, or consists of the N-terminus, Actin-Binding Domain (ABD), hinge H1, rods R1 and R2, rods R22, R23, and R24, hinge H4, the CR domain, and in some embodiments, all or a portion of the CT domain of wild-type dystrophin protein.
  • the mini-dystrophin protein does not comprise the last three amino acids at the C-terminus of the wild-type dystrophin protein (SEQ ID NO:25).
  • the polynucleotide encodes a mini-dystrophin protein comprising, consisting essentially of, or consisting of the amino acid sequence of SEQ ID NO:7 or SEQ ID NO:8 or a sequence at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the nucleotide sequence of SEQ ID NO:7 or SEQ ID NO:8.
  • dystrophin The nucleotide sequence of dystrophin is well known in the art and may be found in sequence databases such as GenBank.
  • human dystrophin mRNA sequence may be found at GenBank Accession No. M18533 or NCBI Reference Sequence NM_004006.2, which are incorporated by reference herein in their entirety.
  • the polynucleotide is part of an expression cassette for production of dystrophin protein.
  • the expression cassette may further comprise expression elements useful for increasing expression of dystrophin.
  • the polynucleotide of the invention is operably linked to a promoter.
  • the promoter may be a constitutive promoter or a tissue-specific or tissue-preferred promoter such as a muscle-specific or muscle-preferred promoter.
  • the promoter is a creatinine kinase promoter, e.g., a promoter comprising, consisting essentially of, or consisting of the nucleotide sequence of SEQ ID NO: 4 or SEQ ID NO: 5.
  • the polynucleotide of the invention is operably linked to a polyadenylation element.
  • the polyadenylation element comprises the nucleotide sequence of SEQ ID NO: 6.
  • the polynucleotide is part of an expression cassette comprising, consisting essentially of, or consisting or the polynucleotide operably linked to a promoter and a polyadenylation element.
  • the gene expression cassette comprises, consists essentially or, or consists of the nucleotide sequence of any one of SEQ ID NOS: 9-12 or a sequence at least about 90% identical thereto, e.g., at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical.
  • Suitable vectors include, but are not limited to, a plasmid, phage, phagemid, viral vector (e.g., AAV vector, an adenovirus vector, a herpesvirus vector, an alphavirus, or a baculovirus vector), bacterial artificial chromosome (BAC), or yeast artificial chromosome (YAC).
  • viral vector e.g., AAV vector, an adenovirus vector, a herpesvirus vector, an alphavirus, or a baculovirus vector
  • BAC bacterial artificial chromosome
  • YAC yeast artificial chromosome
  • the nucleic acid can comprise, consist of, or consist essentially of an AAV vector comprising a 5′ and/or 3′ terminal repeat (e.g., 5′ and/or 3′ AAV terminal repeat).
  • the vector is a viral vector, e.g., a parvovirus vector, e.g., an AAV vector, e.g., an AAV9 vector.
  • the viral vector may further comprise a nucleic acid comprising a recombinant viral template, wherein the nucleic acid is encapsidated by the parvovirus capsid.
  • the invention further provides a recombinant parvovirus particle (e.g., a recombinant AAV particle) comprising the polynucleotides of the invention. Viral vectors and viral particles are discussed further below.
  • the viral vector exhibits modified tissue tropism compared to vectors from which the modified vector is derived.
  • the parvovirus vector exhibits systemic tropism for skeletal, cardiac, and/or diaphragm muscle.
  • the parvovirus vector has reduced tropism for liver compared to a virus vector comprising a wild-type capsid protein.
  • Tissue tropism can be modified by altering certain viral capsid amino acids, for example, those present in AAV capsid VP1, VP2, and/or VP3 proteins, according to the knowledge of those ordinarily skilled in the art.
  • the vector genome is self-complementary or duplexed, and AAV virions containing such vector genomes are known as scAAV vectors.
  • scAAV vectors are described in international patent publication WO 01/92551 (the disclosure of which is incorporated herein by reference in its entirety).
  • Use of scAAV to express a mini-dystrophin may provide an increase in the number of cells transduced, the copy number per transduced cell, or both.
  • An additional aspect of the invention relates to a transformed cell comprising the polynucleotide and/or vector of the invention.
  • the cell may be an in vitro, ex vivo, or in vivo cell.
  • a further aspect of the invention relates to a non-human transgenic animal comprising the polynucleotide and/or vector and/or transformed cell of the invention.
  • the transgenic animal is a laboratory animal, e.g., an animal model of a disease, e.g., an animal model of muscular dystrophy.
  • Another aspect of the invention relates to a mini-dystrophin protein encoded by the polynucleotides of the invention.
  • the mini-dystrophin protein contains all of the sequences necessary for a functional dystrophin protein.
  • the domains of dystrophin are well known in the art and sequences may be found in sequence databases such as GenBank.
  • GenBank For example, the human dystrophin amino acid sequence may be found at NCBI Reference Sequence: NP_03997.1 and GenBank Accession No: AAA53189, which are incorporated by reference herein in their entirety.
  • the mini-dystrophin protein comprises, consists essentially of, or consists of the N-terminus, hinge H1, rods R1 and R2, hinge H3, rods R22, R23, and R24, hinge H4, the CR domain, and in some embodiments, all or a portion of the CT domain, wherein the mini-dystrophin protein does not comprise the last three amino acids at the C-terminus of wild-type dystrophin protein (SEQ ID NO:25).
  • the N-terminal actin binding domain comprises, consists essentially of, or consists of amino acid numbers 1-240 from SEQ ID NO:25, the amino acid sequence of full length human dystrophin protein; H1 comprises, consists essentially of, or consists of amino acid numbers 253-327 from SEQ ID NO:25; R1 comprises, consists essentially of, or consists of amino acid numbers 337-447 from SEQ ID NO:25; R2 comprises, consists essentially of, or consists of amino acid numbers 448-556 from SEQ ID NO:25; H3 comprises, consists essentially of, or consists of amino acid numbers 2424-2470, from SEQ ID NO:25; R22 comprises, consists essentially of, or consists of amino acid numbers 2687-2802 from SEQ ID NO:25; R23 comprises, consists essentially of, or consists of amino acid numbers 2803-2931 from SEQ ID NO:25; R24 comprises, consists essentially of, or consists of amino acid numbers 2932-3040 from S
  • the mini-dystrophin protein comprises, consists essentially of, or consists of the N-terminus, hinge H1, rods R1 and R2 rods R22, R23, and R24, hinge H4, the CR domain, and in some embodiments, all or a portion of the CT domain. In certain embodiments, the mini-dystrophin protein does not comprise the last three amino acids at the C-terminus of wild-type dystrophin protein.
  • the N-terminal actin binding domain comprises, consists essentially of, or consists of amino acid numbers 1-240 from SEQ ID NO:25, the amino acid sequence of full length human dystrophin protein; H1 comprises, consists essentially of, or consists of amino acid numbers 253-327 from SEQ ID NO:25; R1 comprises, consists essentially of, or consists of amino acid numbers 337-447 from SEQ ID NO:25; R2 comprises, consists essentially of, or consists of amino acid numbers 448-556 from SEQ ID NO:25; R22 comprises, consists essentially of, or consists of amino acid numbers 2687-2802 from SEQ ID NO:25; R23 comprises, consists essentially of, or consists of amino acid numbers 2803-2931 from SEQ ID NO:25; R24 comprises, consists essentially of, or consists of amino acid numbers 2932-3040 from SEQ ID NO:25; H4 comprises, consists essentially of, or consists of amino acid numbers 3041-3112 from S
  • a further aspect of the invention relates to a method of producing mini-dystrophin protein in a cell, comprising contacting the cell with the polynucleotide or vector of the invention, thereby producing the mini-dystrophin in the cell.
  • the cell may be an in vitro, ex vivo, or in vivo cell, e.g., a cell line or a primary cell. Methods of producing a protein in a cell by introduction of a polynucleotide encoding the protein are well known in the art.
  • Another aspect of the invention relates to a method of producing a mini-dystrophin protein in a subject, comprising delivering to the subject the polynucleotide, vector and/or transformed cell of the invention, thereby producing the mini-dystrophin protein in the subject.
  • An additional aspect of the invention relates to a method of treating muscular dystrophy in a subject in need thereof, comprising delivering to the subject a therapeutically effective amount of the polynucleotide, vector, and/or transformed cell of the invention, thereby treating muscular dystrophy in the subject.
  • the muscular dystrophy may be any form of muscular dystrophy, e.g., Duchenne muscular dystrophy or Becker muscular dystrophy.
  • the virus vectors of the present invention are useful for the delivery of polynucleotides encoding mini-dystrophin to cells in vitro, ex vivo, and in vivo.
  • the virus vectors can be advantageously employed to deliver or transfer polynucleotides encoding mini-dystrophin to animal, including mammalian, cells.
  • the virus vector may also comprise a heterologous nucleic acid that shares homology with and recombines with a locus on a host chromosome. This approach can be utilized, for example, to correct a genetic defect in the host cell.
  • the polynucleotides encoding mini-dystrophin can be used to produce mini-dystrophin protein in a cell in vitro, ex vivo, or in vivo.
  • the virus vectors may be introduced into cultured cells and the expressed mini-dystrophin protein isolated therefrom.
  • the polynucleotide encoding mini-dystrophin can be operably associated with appropriate control sequences.
  • the polynucleotide can be operably associated with expression control elements, such as transcription/translation control signals, origins of replication, polyadenylation signals, internal ribosome entry sites (IRES), promoters, and/or enhancers, and the like.
  • expression control elements such as transcription/translation control signals, origins of replication, polyadenylation signals, internal ribosome entry sites (IRES), promoters, and/or enhancers, and the like.
  • promoter and optionally enhancer elements can be used depending on the level and tissue-specific expression desired.
  • the promoter/enhancer can be constitutive of inducible, depending on the pattern of expression desired.
  • the promoter/enhancer can be native or foreign and can be a natural or a synthetic sequence. By foreign, it is intended that the transcriptional initiation region is not found in the wild-type host into which the transcriptional initiation region is introduced.
  • An enhancer if employed, can be chosen from the same gene and species as the promoter, from the orthologous gene in a different species as the promoter, from a different gene in the same species as the promoter, or from a different gene in a different species as the promoter.
  • the promoter/enhancer elements can be native to the target cell or subject to be treated.
  • the promoters/enhancer element can be native to the heterologous nucleic acid sequence.
  • the promoter/enhancer element is generally chosen so that it functions in the target cell(s) of interest. Further, in particular embodiments the promoter/enhancer element is a mammalian promoter/enhancer element.
  • the promoter/enhancer element may be constitutive or inducible.
  • Inducible expression control elements are typically advantageous in those applications in which it is desirable to provide regulation over expression of the heterologous nucleic acid sequence(s).
  • Inducible promoters/enhancer elements for gene delivery can be tissue-specific or—preferred promotor/enhancer elements, and include muscle specific or preferred (including cardiac, skeletal and/or smooth muscle specific or preferred) promoter/enhancer elements.
  • Other inducible promoter/enhancer elements include hormone-inducible and metal-inducible elements.
  • Exemplary inducible promoters/enhancer elements include, but are not limited to, a Tet on/off element, a RU486-inducible promoter, an ecdysone-inducible promoter, a rapamycin-inducible promoter, and a metallothionein promoter.
  • polynucleotide encoding mini-dystrophin is transcribed and then translated in the target cells
  • specific initiation signals are generally included for efficient translation of inserted protein coding sequences.
  • exogenous translational control sequences which may include the ATG initiation codon and adjacent sequences, can be of a variety of origins, both natural and synthetic.
  • the virus vectors according to the present invention provide a means for delivering polynucleotide encoding mini-dystrophin into a broad range of cells, including dividing and non-dividing cells.
  • the virus vectors can be employed to deliver the polynucleotide to a cell in vitro, e.g., to produce mini-dystrophin in vitro or for ex vivo gene therapy.
  • the virus vectors are additionally useful in a method of delivering the polynucleotide to a subject in need thereof e.g., to express mini-dystrophin. In this manner, the protein can be produced in vivo in the subject.
  • the subject can be in need of mini-dystrophin because the subject has a deficiency of functional dystrophin. Further, the method can be practiced because the production of mini-dystrophin in the subject may impart some beneficial effect.
  • the virus vectors can also be used to produce mini-dystrophin in cultured cells or in a subject (e.g., using the subject as a bioreactor to produce the protein or to observe the effects of the protein on the subject, for example, in connection with screening methods).
  • virus vectors of the present invention can be employed to deliver the polynucleotide encoding mini-dystrophin to treat and/or prevent any disease state for which it is beneficial to deliver mini-dystrophin.
  • disease states include, but are not limited to muscular dystrophies including Duchenne and Becker.
  • Virus vectors according to the instant invention find use in diagnostic and screening methods, whereby a polynucleotide encoding mini-dystrophin is transiently or stably expressed in a cell culture system, or alternatively, a transgenic animal model.
  • the virus vectors of the present invention can also be used for various non-therapeutic purposes, including but not limited to use in protocols to assess gene targeting, clearance, transcription, translation, etc., as would be apparent to one skilled in the art.
  • the virus vectors can also be used for the purpose of evaluating safety (spread, toxicity, immunogenicity, etc.). Such data, for example, are considered by the United States Food and Drug Administration as part of the regulatory approval process prior to evaluation of clinical efficacy.
  • the disclosure provides AAV vectors or particles including AAV capsids from an AAV serotype that has tropism for striated muscle including without limitation, skeletal muscle, including the diaphragm, and cardiac muscle.
  • AAV capsids having tropism for striated muscle are AAV1, AAV6, AAV7, AAV8, and AAV9.
  • other embodiments include AAV capsids that are not known to occur naturally, but rather have been engineered for the express purpose of creating novel AAV capsids that preferentially transduce striated muscle compared to other tissues.
  • Such engineered capsids are known in the art, but the disclosure encompasses new muscle-specific AAV capsids yet to be developed.
  • Non-limiting examples of muscle-specific engineered AAV capsids were reported in Yu, C Y, et al., Gene Ther 16(8):953-62 (2009), Asokan, A, et al., Nat Biotech 28(1):79-82 (2010 (describing AAV2i8), Bowles, D E, et al., Mol Therapy 20(2):443-455 (2012) (describing AAV 2.5), and Asokan, A, et al., Mol Ther 20(4):699-708 (2012).
  • amino acid sequences of the capsid proteins including VP1, VP2, and VP3 proteins, for many naturally and non-naturally occurring AAV serotypes are known in the art.
  • amino acid sequence for the AAV9 serotype is provided as the amino acid sequence of SEQ ID NO:13.
  • the AAV particles of the disclosure for treating dystrophinopathy include a vector genome for expressing a mini-dystrophin protein with dystrophin subdomains selected to at least partially restore in transduced muscle cells the function supplied by the missing full length dystrophin protein.
  • the mini-dystrophin protein is constructed from subdomains from the full length wild type human dystrophin protein.
  • the mini-dystrophin protein includes the following subdomains from the human dystrophin protein in the following order from N-terminus to C-terminus: N-terminal actin binding domain (ABD); H1 hinge domain; R1 and R2 spectrin-like repeat domains; H3 hinge domain; R22, R23 and R24 spectrin-like repeat domains; H4 hinge domain; cysteine rich (CR) domain; and carboxy-terminal (CT) domain.
  • N-terminal actin binding domain (ABD)
  • H1 hinge domain R1 and R2 spectrin-like repeat domains
  • H3 hinge domain R22, R23 and R24 spectrin-like repeat domains
  • H4 hinge domain cysteine rich (CR) domain
  • CT carboxy-terminal
  • the N-terminal actin binding domain comprises, consists essentially of, or consists of amino acid numbers 1-240 from SEQ ID NO:25, the amino acid sequence of full length human dystrophin, protein; H1 comprises, consists essentially of, or consists of amino acid numbers 253-327 from SEQ ID NO:25; R1 comprises, consists essentially of, or consists of amino acid numbers 337-447 from SEQ ID NO:25; R2 comprises, consists essentially of, or consists of amino acid numbers 448-556 from SEQ ID NO:25; H3 comprises, consists essentially of, or consists of amino acid numbers 2424-2470 from SEQ ID NO:25; R22 comprises, consists essentially of, or consists of amino acid numbers 2687-2802 from SEQ ID NO:25; R23 comprises, consists essentially of, or consists of amino acid numbers 2803-2931 from SEQ ID NO:25; R24 comprises, consists essentially of, or consists of amino acid numbers 2932-3040 from SEQ ID NO:25; R
  • the vector genome of the AAV particles of the disclosure for treating dystrophinopathy includes a gene for expressing a mini-dystrophin.
  • the vector genome will lack the rep and cap genes normally present in wild type AAV to provide room for the gene expressing the mini-dystrophin.
  • the gene encodes a mini-dystrophin protein with the following subdomains from full length human dystrophin protein: ABD-H1-R1-R2-H3-R22-R23-R24-H4-CRD-CTD.
  • the CTD is only a portion of the CTD found in wildtype muscle dystrophin, and in some embodiments does not include the last three amino acids present in wildtype muscle dystrophin (SEQ ED NO:25).
  • the gene encodes for a human mini-dystrophin protein having the amino acid sequence of SEQ ID NO:7.
  • the gene encoding the human mini-dystrophin protein is codon-optimized with respect to the species of the subject to which the AAV particles of the disclosure will be administered to effect gene therapy. Without wishing to be bound by theory, it is believed that codon-optimization improves the efficiency with which transduced cells are able to transcribe the gene into mRNA and/or translate the mRNA into protein, thereby increasing the amount of mini-dystrophin protein produced compared to expression of a mini-dystrophin encoding gene that is non-codon-optimized.
  • the codon-optimization is human codon-optimization, but codon-optimization can be performed with respect to other species, including canine.
  • codon-optimization substitutes one or more codons that pair with relatively rare tRNAs present in a species, such as human, with synonymous codons that pair with more prevalent tRNAs for the same amino acid. This approach can increase the efficiency of translation.
  • codon-optimization eliminates certain cis-acting motifs that can influence the efficiency of transcription or translation. Non-limiting examples of codon-optimization include adding a strong Kozak sequence at the intended start of the coding sequence, or eliminating internal ribosome entry sites downstream of the intended start codon.
  • codon-optimization increases the GC content (that is, the number of G and C nucleobases present in a nucleic acid sequence, usually expressed as a percentage) relative to the wildtype sequence from which the mini-dystrophin gene was assembled.
  • the GC contends at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, or greater than the GC content of the corresponding wildtype gene.
  • the GC content of a codon-optimized gene is about or at least 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, or greater.
  • codon-optimization increases the codon adaptation index (CAI) of the gene encoding the mini-dystrophin protein.
  • CAI codon adaptation index
  • the CAI is a measure of synonymous codon usage bias in a particular species.
  • the CAI value (which ranges from 0 to 1) in a particular species is positively correlated with gene expression levels. See, for example, Sharp, P M and W-H Lie, Nuc Acids Res 15(3): 1281-95 (1987).
  • codon-optimization increases the CAI of the mini-dystrophin gene in reference to highly expressed human genes to a value that is at least 0.70, 0.71, 0.72, 0.73, 0.74, 0.75, 0.76, 0.77, 0.78, 0.79, 0.80, 0.81, 0.82, 0.83, 0.84, 0.85, 0.86, 0.87, 0.88, 0.89, 0.90, 0.91, 0.92, 0.93, 0.94, 0.95, 0.96, 0.97, 0.98, or 0.99.
  • codon-optimization reduces the number of CpG dinucleotides in the coding sequence of a mini-dystrophin. Without wishing to be bound by any particular theory of operation, it is believed that methylation at CpG dinucleotides can silence gene transcription, such that reducing the number of CpG dinucleotides in a gene sequence can reduce the level of methylation, thereby resulting in enhanced transcription efficiency.
  • the number of CpG dinucleotides is reduced by about or at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55% 60%, or more compared to the wildtype sequence from which the mini-dystrophin gene was assembled.
  • a non-limiting example of a human codon-optimized human mini-dystrophin gene is provided by the DNA sequence of SEQ ID NO:1.
  • This DNA sequence which is 3978 nucleobases long (including a stop codon) is referred to herein as Hopti-Dys3978, although the particular terminology is merely used for convenience and is not intended to be limiting.
  • the mini-dystrophin protein sequence encoded by SEQ ID NO:1, which is called Dys3978 is provided by SEQ ID NO:7.
  • An example of a canine codon-optimized human mini-dystrophin gene is provided by SEQ ID NO:3, which also encodes Dys3978.
  • the coding sequence for the mini-dystrophin of SEQ ID NO:7 was assembled from subsequences of the wildtype full-length human muscle dystrophin gene (as exemplified by NCBI Reference Sequence NM_004006.2, which is incorporated by reference) corresponding to certain subdomains present in the dystrophin protein (SEQ ID NO:25).
  • the resulting gene sequence is provided herein as SEQ ID NO:26, which was then human codon-optimized, resulting in the DNA sequence of SEQ ID NO:1.
  • codon-optimization increased the GC content, decreased the use of infrequent codons (that is, increased the codon-adaptation index (CAI)), and included a strong translation initiation site (Kozak consensus sequence or similar), compared to the gene sequence before codon-optimization.
  • CAI codon-adaptation index
  • the vector genome of the AAV particles of the disclosure for treating dystrophinopathy, such as DMD further include AAV inverted terminal repeats (ITR) flanking the codon-optimized gene encoding mini-dystrophin protein.
  • ITRs are from the same AAV serotype as the capsid (for example, without limitation AAV9 ITRs used with AAV9 capsid), but in other embodiments, AAV ITRs from a different serotype may be used.
  • ITRs from the AAV2 serotype may be used in a vector genome in combination with an AAV capsid from a different, non-AAV2 serotype.
  • Non-limiting examples include use of AAV2 ITRs with a capsid from the AAV1, AAV6, AAV7, AAV8, or AAV9 serotypes, or a different naturally or non-naturally occurring AAV serotype.
  • AAV2 ITRs may be used in combination with the capsid from the AAV9 serotype. From the perspective of the plus or sense DNA strand of the vector genome, the sequence of the left, 5′, or upstream AAV2 ITR is provided as the DNA sequence of SEQ ID NO:14, and the sequence of the right, 3′, or downstream AAV2 ITR is provided as the DNA sequence of SEQ ID NO:15.
  • the vector genome of the AAV vectors of the disclosure for treating dystrophinopathy further includes a transcriptional regulatory element operably linked with the gene encoding the mini-dystrophin protein so that the vector genome, once converted into its double stranded form can express the mini-dystrophin gene in transduced cells.
  • Transcriptional regulatory elements typically include a promoter, but optionally one or more enhancer elements that can act to augment the rate of transcription initiation from the promoter.
  • Operable linkage of a transcriptional regulatory element with respect to the mini-dystrophin coding sequence means that the transcriptional regulatory element can function to control transcription and expression of the gene, but does not necessarily require any particular structural or spatial relationship. Because vector genomes of the disclosure are typically packaged into AAV capsids as single-stranded DNA molecules, it should be understood that the operable linkage may not be functional until the vector genome is converted into double-stranded form. Usually, a promoter will be positioned 5′ or upstream of a gene sequence encoding the mini-dystrophin protein, but other transcriptional regulatory elements, such as enhancers, may be positioned 5′ or elsewhere, such as 3′, of the gene.
  • the transcriptional regulatory element can be a strong constitutively active promoter, such those found in certain viruses that infect eukaryotic cells.
  • a well-known example from the art include the promoter from the cytomegalovirus (CMV), but others are known as well such at the promoter from the Rous sarcoma virus (RSV).
  • Strong viral promoters, such as CMV or RSV are typically not tissue specific, so that if used the mini-dystrophin protein would be expressed not only in muscle cells, but any other cell type, such as liver, transduced by the AAV particles of the disclosure.
  • a muscle-specific transcriptional regulatory element can be used to reduce the amount of mini-dystrophin protein expressed in non-muscle cells, such as liver cells, that may also be transduced by the AAV particles of the disclosure.
  • Muscle-specific transcriptional regulatory elements can be derived from Muscle-specific genes from any species, including mammalian species, such as without limitation, human or mouse muscle genes. Muscle-specific transcriptional regulatory elements will typically include at minimum a promoter from a muscle-specific gene as well as one of more enhancers from the same or a different muscle specific gene. Such enhancers can originate from many parts of the native gene, such as enhancers positioned 5′ or 3′ of the gene, or even reside in introns. Muscle-specific transcriptional regulatory elements can be removed en bloc from a muscle-specific gene and inserted into a plasmid for producing the AAV vector genomes of the disclosure, or can be engineered to tailor their activity and reduce their size as much as possible.
  • Non-limiting examples of muscle-specific genes from which muscle-specific transcriptional regulatory elements can be derived include the muscle creatine kinase gene, myosin heavy chain gene, or myosin light chain gene, or the alpha 1 actin gene from skeletal muscle, though others are possible as well. These genes can be from human, mouse, or other species.
  • Muscle-specific transcriptional regulatory elements that have been created for use in gene therapy applications are described in the art, and may be used in the AAV vectors of the disclosure for treating muscular dystrophy.
  • Hauser described muscle-specific transcriptional regulatory elements known as CK4, CK5, and CK6 derived from the mouse creatine kinase (MCK) gene (Hauser, M A, et al., Mol Therapy 2(1):16-25 (2000)), Salva described muscle-specific transcriptional regulatory elements known as CK1 and CK7, derived from the MCK gene, and MHCK1 and MHCK7, which additionally include enhancers from the mouse ⁇ -MHC gene (Salva, M Z, et al., Mol Therapy 15(2):320-9 (2007)), and Wang described muscle-specific transcriptional regulatory elements known as enh358MCK, dMCK and tMCK (Wang, B, et al., Gene Therapy 15:1489-9 (2008)).
  • Non-limiting examples of muscle-specific transcriptional regulatory elements that may be used in the AAV vectors of the disclosure for treating muscular dystrophy include CK4, CK5, CK6, CK1, CK7, MHCK1, MHCK7, enh358MCK, dMCK and tMCK, each as described in the art, or those disclosed herein as having the DNA sequences of SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:16.
  • Other muscle-specific transcriptional regulatory elements may be used as well.
  • the vector genome of the AAV vectors of the disclosure for treating dystrophinopathy further includes a transcription termination sequence positioned 3′ of the coding sequence for the mini-dystrophin gene.
  • transcription termination sequence ensures that the mRNA transcript encoding the mini-dystrophin protein will be appropriately polyadenylated by the transduced cell thereby ensuring efficient translation of the message into protein.
  • mammalian transcription termination sequences identified a consensus sequence in the 3′ UTR of genes that serves to terminate transcription and signal polyadenylation of the growing transcript. Specifically, these sequences typically include the motif AATAAA, followed by 15-30 nucleotides, and then CA. See, for example, N.
  • transcription termination sequences are known in the art and can be used in the AAV vectors of the disclosure. Non-limiting examples include the polyadenylation signal from the SV40 virus early or late genes (SV40 early or late polyA) or the polyadenylation signal from the bovine growth hormone gene (bGH poly A). Transcription termination sequences from other genes of any species may be used in the AAV vectors of the disclosure. Alternatively, synthetic transcription termination sequences may be designed and used to signal transcription termination and polyadenylation. Additional non-limiting examples of transcription termination sequences that may be used in the AAV vectors of the disclosure include those disclosed herein as having the DNA sequences of SEQ ID NO:6 and SEQ ID NO:17.
  • the disclosure provides an AAV viral particle or vector for treating dystrophinopathy, such as DMD, comprising an AAV capsid and a vector genome encoding a mini-dystrophin-protein.
  • the mini-dystrophin protein includes the following subdomains from full length human dystrophin protein: ABD-H1-R1-R2-H3-R22-R23-R24-H4-CRD-CTD.
  • the CTD is only a portion of the CTD found in wildtype muscle dystrophin, and in some embodiments does not include the last three amino acids present in wildtype muscle dystrophin (SEQ ID NO:25).
  • the gene encoding the mini-dystrophin protein of SEQ ID NO:7 is human codon-optimized and has the DNA sequence of SEQ ID NO:1.
  • the AAV capsid is from the AAV9 serotype.
  • single-stranded AAV vector genomes are packaged into capsids as the plus strand or minus strand in about equal proportions. Consequently, embodiments of the vector or particle include AAV particles in which the vector genome is in the plus strand polarity (that is, has the nucleobase sequence of the sense or coding DNA strand), as well as AAV particles in which the vector genome is in the minus strand polarity (that is, has the nucleobase sequence of the antisense or template DNA strand).
  • nucleobase sequence of the plus strand in its regular 5′ to 3′ order the nucleobase sequence of the minus strand in its 5′ to 3′ order can be determined as the reverse-complement of the nucleobase sequence of the plus strand.
  • the vector genome when in plus polarity, comprises a muscle-specific transcriptional regulatory element derived from the creatine kinase gene having the DNA sequence of SEQ ID NO:16 positioned 5′ of and operably linked with SEQ ID NO:1, the DNA sequence of the human codon-optimized gene encoding mini-dystrophin protein.
  • Particles comprising the corresponding minus strand are also possible, where the sequence of nucleobases from its 5′ end would be the reverse complement of the sequence of the aforementioned plus strand.
  • the vector genome when in plus polarity comprises a first AAV2 ITR followed by the DNA sequence of SEQ ED NO:16 positioned 5′ of and operably linked with the DNA sequence of SEQ ID NO:1, and a transcription termination sequence comprising the DNA sequence of SEQ ID NO:17 positioned 3′ of the mini-dystrophin gene, followed by a second AAV2 ITR.
  • Particles comprising the corresponding minus strand are also possible, where the sequence of nucleobases from its 5′ end would be the reverse complement of the sequence of the aforementioned plus strand.
  • the vector genome when in plus polarity, comprises in 5′ to 3′ order a first AAV2 ITR, a transcriptional regulatory element sequence defined by the DNA sequence of SEQ ID NO:16, a human codon optimized gene sequence for expressing a mini-dystrophin, the gene sequence defined by the DNA sequence of SEQ ID NO:1 in operable linkage with the transcriptional regulatory element, a transcription termination sequence defined by the DNA sequence of SEQ ID NO:17, and a second AAV2 ITR.
  • Particles comprising the corresponding minus strand are also possible, where the sequence of nucleobases from its 5′ end would be the reverse complement of the sequence of the aforementioned plus strand.
  • an AAV vector for treating dystrophinopathy such as DMD, which may be referred to herein as AAV9.hCK.Hopti-Dys3978.spA, comprises a capsid from the AAV9 serotype and a vector genome, which vector genome may be referred to herein as hCK.Hopti-Dys3978.spA, comprising, consisting essentially of, or consisting of, when the genome is in plus polarity, the DNA sequence of SEQ ID NO:18 or, when the genome is in the minus polarity, the reverse-complement of the DNA sequence of SEQ ID NO: 18 (that is, when the vector genome sequence is read 5′ to 3′).
  • the present disclosure further provides methods of producing AAV vectors.
  • the present disclosure provides a method of producing a recombinant parvovirus particle, comprising providing to a cell permissive for AAV replication and packaging a recombinant AAV vector genome, comprising a mini-dystrophin gene, associated genetic control elements and flanking AAV ITRs, and AAV replication and packaging functions, such as those provided by the AAV rep and cap genes, under conditions sufficient for the replication and packaging of the recombinant AAV particles, whereby rAAV particles are produced by the cell.
  • Conditions sufficient for the replication and packaging of the rAAV particles include without limitation helper functions, such as those from adenovirus and/or herpesvirus.
  • the rAAV particle vector genome, replication and packaging functions and, where required, helper functions can be provided via viral or non-viral vectors, such as plasmids, and can exist within the packaging cells stably or transiently, either integrated into the cell's genome or in an episome.
  • Recombinant AAV vectors of the disclosure can be made by several methods known to skilled artisans (see, e.g., WO 2013/063379).
  • An exemplary method is described in Grieger, et al. 2015, Molecular Therapy 24(2):287-297, the contents of which are incorporated by reference. Briefly, efficient transfection of HEK293 cells is used as a starting point, wherein an adherent HEK293 cell line from a qualified clinical master cell bank is used to grow in animal component-free suspension conditions in shaker flasks and WAVE bioreactors that allow for rapid and scalable rAAV particle production.
  • the suspension HEK293 cell line is capable of generating, in some embodiments, greater than 1 ⁇ 10 5 vector genome (vg) containing particles per cell, or greater than 1 ⁇ 10 14 vg/L of cell culture when harvested 48 hours post-transfection.
  • Triple transfection refers to the fact that the packaging cell is transfected with three plasmids: one plasmid encodes the AAV rep and cap genes, another plasmid encodes various helper functions (e.g., adenovirus or HSV proteins such as E1a, E1b, E2a, E4, and VA RNA, and another plasmid encodes the vector genome, i.e., the mini-dystrophin gene and its various control elements flanked by AAV ITRs.
  • helper functions e.g., adenovirus or HSV proteins such as E1a, E1b, E2a, E4, and VA RNA
  • another plasmid encodes the vector genome, i.e., the mini-dystrophin gene and its various control elements flanked by AAV ITRs.
  • a number of variables can be optimized such as selection of a compatible serum-free suspension media that supports both growth and transection, selection of a transfection reagent, transfection
  • the packaging functions include genes for viral vector replication and packaging.
  • the packaging functions may include, as needed, functions necessary for viral gene expression, viral vector replication, rescue of the viral vector from the integrated state, viral gene expression, and packaging of the viral vector into a viral particle.
  • the packaging functions may be supplied together or separately to the packaging cell using a genetic construct such as a plasmid or an amplicon, a Baculovirus, or HSV helper construct.
  • the packaging functions may exist extrachromosomally within the packaging cell, but may also be integrated into the cell's chromosomal DNA. Examples include genes encoding AAV Rep and Cap proteins. Rep and cap genes can be provided to packaging cell together as part of the same viral or non-viral vector.
  • the rep and cap sequences may be provided by a hybrid adenovirus vector (e.g., inserted into the E1a or E3 regions of a deleted adenovirus vector) or herpesvirus vector, such as an EBV vector.
  • AAV rep and cap genes can be provided separately. Rep and cap genes can also be stably integrated into the genome of a packaging cell, or exist on an episome. Typically, rep and cap genes will not be flanked by ITRs to avoid packaging of these sequences into rAAV vector particles.
  • the helper functions include helper virus elements needed for establishing active infection of the packaging cell which is required to initiate packaging of the viral vector. Examples include functions derived from adenovirus, baculovirus and/or herpes virus sufficient to result in packaging of the viral vector.
  • adenovirus helper functions will typically include adenovirus components E1a, E1b, E2a, E4, and VA RNA.
  • the packaging functions may be supplied by infection of the packaging cell with the required virus. Alternatively, use of infectious virus can be avoided, whereby the packaging functions may be supplied together or separately to the packaging cell using a non-viral vector such as a plasmid of an amplicon.
  • the packaging functions may exist extrachromosomally within the packaging cell, but may also be integrated into the cell's chromosomal DNA (e.g., E1 or E3 in HEK 293 cells).
  • any method of introducing the nucleotide sequence carrying the helper functions into a cellular host for replication and packaging may be employed, including but not limited to electroporation, calcium phosphate precipitation, microinjection, cationic or anionic liposomes, and liposomes in combination with a nuclear localization signal.
  • the helper functions are provided by transfection using a virus vector or infection using a helper virus; standard methods for producing viral infection may be used.
  • any suitable permissive or packaging cell known in the art may be employed in the production of the packaged viral vector.
  • Mammalian cells or insect cells are preferred.
  • Examples of cells useful for the production of packaging cells in the practice pf the invention include, for example, human cell lines, such as VERO, WI38, MRC5, A549, HEK 293 cells (which express functional adenoviral E1 under the control of a constitutive promoter), B-50 or any other HeLa cells, HepG2, Saos-2, HuH7, and HT1080 cell lines.
  • the packaging cell is capable of growing in suspension culture, especially in serum-free growth media.
  • the packaging cell is a HEK293 that grows in suspension in serum free medium.
  • the packaging cell is the HEK293 cell described in U.S. Pat. No. 9,441,206 and deposited as ATCC No. PTA 13274.
  • Numerous rAAV particle packaging cell lines are known in the art, including, but not limited to, those disclosed in WO 2002/46359.
  • Cell lines for use as packaging cells include insect cell lines, particularly when baculoviral vectors are used to introduce the genes required for rAAV particle production as described herein. Any insect cell that allows for replication of AAV and that can be maintained in culture can be used in accordance with the present disclosure. Examples include Spodoptera frugiperda , such as the Sf9 or Sf21 cell lines, Drosophila spp. cell lines, or mosquito cell lines, e.g., Aedes albopictus -derived cell lines.
  • AAV vector particles of the disclosure After AAV vector particles of the disclosure have been produced and purified, they can be titered to prepare compositions for administration to subjects, such as human subjects with muscular dystrophy. AAV vector titering can be accomplished using methods known in the art. In certain embodiments, AAV vector particles can be titered using quantitative PCR (qPCR) using primers against sequences in the vector genome. for example, AAV2 ITR sequences if present, or other sequences in the vector genome.
  • qPCR quantitative PCR
  • a standard curve can be generated permitting the concentration of the AAV vector to be calculated as the number of vector genomes (vg) per unit volume, such as microliters or milliliters.
  • the number of AAV vector particles containing genome scan be determined using dot blot using a suitable probe for the vector genome.
  • the disclosure provides methods for treating a dystrophinopathy by administering to a subject in need of treatment for dystrophinopathy a therapeutically effective dose or amount of an AAV vector of the disclosure, such as, without limitation, the vector known as AAV9.hCK.Hopti-Dys3978.spA.
  • the dystrophinopathy is a muscular dystrophy, including without limitation Duchenne muscular dystrophy (DMD), Becker muscular dystrophy (BMD), DMD-associated dilated cardiomyopathy (DCM), and symptomatic carrier states in females.
  • the disclosure provides methods for treating muscular dystrophy by administering to a subject in need of treatment for muscular dystrophy a therapeutically effective dose or amount of an AAV vector of the disclosure, such as, without limitation, the vector known as AAV9.hCK.Hopti-Dys3978.spA.
  • the disclosure provides methods for treating Duchenne muscular dystrophy (DMD), Becker muscular dystrophy (BMD), DMD-associated dilated cardiomyopathy (DCM), and symptomatic carrier states in females, in subjects in need of treatment therefore.
  • DMD Duchenne muscular dystrophy
  • BMD Becker muscular dystrophy
  • DCM DMD-associated dilated cardiomyopathy
  • symptomatic carrier states in females, in subjects in need of treatment therefore.
  • an AAV vector or pharmaceutical composition of the disclosure in the manufacture of a medicament for use in the methods of treatment disclosed herein.
  • an AAV vector or pharmaceutical composition of the disclosure for use in a method of treatment disclosed herein is also provided.
  • Treatment of subjects with a dystrophinopathy need not result in a cure to be considered effective, where cure is defined as either halting disease progression, or partially or completely restoring the subject's muscle function. Rather a therapeutically effective dose or amount of an AAV vector of the disclosure is one that serves to reduce or ameliorate the symptoms of, slow the progression of, or improve the quality of life of a subject with the dystrophinopathy, such as DMD.
  • a therapeutically effective dose or amount of an AAV vector of the disclosure is one that serves to reduce or ameliorate the symptoms of, slow the progression of, or improve the quality of life of a subject with the dystrophinopathy, such as DMD.
  • treatment of subjects with a dystrophinopathy can improve their mobility, delay the time to their loss of ambulation or other mobility, and in the bases of severe dystrophinopathy, such as DMD, extend the life of subjects with the disorder.
  • the methods of treatment of the disclosure can be used to treat male or female subjects with a dystrophinopathy, such as DMD.
  • a dystrophinopathy such as DMD.
  • treatment can be provided to symptomatic carriers, or to the rare female subject with full blown disease.
  • the methods of the disclosure can also be used to treat subjects of any age with a dystrophinopathy, including subjects less than 1 year old, or about or at least 1 year old, or about or at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 years old or older.
  • Subjects, when treated, may be ambulatory, or non-ambulatory.
  • the methods of treatment of the disclosure can be used to treat subjects with a dystrophinopathy regardless of the underlying genetic lesion (for example, deletions, duplications, splice site variants, or nonsense mutations in the dystrophin gene), so long as the lesion results in a reduction or loss in the function of the native human dystrophin gene.
  • a dystrophinopathy regardless of the underlying genetic lesion (for example, deletions, duplications, splice site variants, or nonsense mutations in the dystrophin gene), so long as the lesion results in a reduction or loss in the function of the native human dystrophin gene.
  • treating a subject with a therapeutically effective dose or amount of an AAV mini-dystrophin vector will reduce tissue concentrations of one or more biomarkers that are associated with the existence or progression of muscular dystrophy.
  • the biomarkers are certain enzymes released from damaged skeletal muscle or cardiac muscle cells into the blood (including serum or plasma).
  • Non-limiting examples include creatinine kinase (CK), the transaminases alanine aminotransferase (ALT) and aspartate aminotransferase (AST), and lactic acid dehydrogenase (LDH), the average levels of which are all known to be elevated in subjects with DMD.
  • a therapeutically effective dose or amount of an AAV mini-dystrophin vector of the disclosure is effective to reduce elevated ALT levels in blood of DMD patients to within about 7-, 6-, 5-, 4-, 3-, or 2-fold greater than that typically found in healthy subjects of similar age and sex. In other embodiments, a therapeutically effective dose or amount of an AAV mini-dystrophin vector of the disclosure is effective to reduce elevated AST levels in blood of DMD patients to within about 7-, 6-, 5-, 4-, 3-, or 2-fold greater than that typically found in healthy subjects of similar age and sex.
  • a therapeutically effective dose or amount of an AAV mini-dystrophin vector of the disclosure is effective to reduce elevated LDH levels in blood of DMD patients to within about 7-, 6-, 5-, 4-, 3-, or 2-fold greater than that typically found in healthy subjects of similar age and sex.
  • a therapeutically effective dose or amount of an AAV mini-dystrophin vector of the disclosure is effective to reduce elevated total CK levels in blood of DMD patients to within about 50-, 48-, 46-, 44-, 42-, 40-, 38-, 36-, 34-, 32, 30-, 28-, 26-, 24-, 22-, 20-, 18-, 16-, 14-, 12-, 10-, 9, 8-, 7-, 6, 5-, 4-, 3-, or 2-fold greater than that typically found in healthy subjects of similar age and sex. It has also been found that matrix metalloproteinase-9 (MMP-9), an enzyme associated with degradation or remodeling of the extracellular matrix, is elevated in the blood of DMD patients.
  • MMP-9 matrix metalloproteinase-9
  • a therapeutically effective dose or amount of an AAV mini-dystrophin vector of the disclosure is effective to reduce elevated MMP-9 levels in blood of DMD patients to within about 15-, 14-, 13-, 12-, 11-, 10-, 9-, 8-, 7-, 6-, 5-, 4-, 3-, or 2-fold greater than that typically found in healthy subjects of similar age and sex.
  • a therapeutically effective dose or amount of an AAV mini-dystrophin vector of the disclosure is effective to alter the levels of ALT, AST, LDH, CK and MMP-9 as indicated above alone or in combination with one or more of these same or other biomarkers.
  • a therapeutically effective dose or amount of an AAV mini-dystrophin vector of the disclosure is effective to reduce ALT and AST, ALT and LDH, AST and CK, or AST and MMP-9, etc.
  • an effective dose or amount of an AAV vector is one that improves average subject performance in the 6 minute walk-test (6MWT).
  • the 6MWT has been established as a reproducible and valid measure of muscle function and mobility of human subjects with muscular dystrophy, in particular, DMD. See, for example, McDonald, C M, et al., Muscle Nerve 41(4):500-1 (2010); Henricson, E, et al., PLOS Currents Musc Dys, 8 Jul. 2013; McDonald, C M, et al., Muscle Nerve 48:343-56 (2013).
  • the distance in meters that a subject can, starting from rest, walk continually and unaided during a 6 minute period is recorded.
  • This distance is also known as the 6 minute walk distance (6MWD).
  • 6MWD 6 minute walk distance
  • an individual subject may be tested more than once over a period of days, and the results averaged. Due to its advantages, the 6MWT has been adopted as a primary clinical endpoint in drug trials involving ambulatory DMD patients. See, for example, Bushby, K, et al., Muscle Nerve 50:477-87 (2014); Mendell, J R, et al., Ann Neurol 79:257-71 (2016); Campbell, C, et al., Muscle Nerve 55(4):458-64 (2017). Usually, in these trials, each subject in the treatment group has his ambulation tested using the 6MWT over a period of months or years to determine if a treatment effect exists.
  • therapeutic efficacy is determined statistically by comparing the treatment effect of AAV vectors of the disclosures on the average 6MWT performance of treated subjects, such as those with DMD, in comparison with the average 6MWT performance of untreated control subjects with the same type of dystrophinopathy, such as DMD.
  • Such controls can have been included in the same studies used to evaluate the therapeutic efficacy of AAV vectors of the disclosure, or can be similar subjects drawn from natural history studies of the progression of DMD or other dystrophinopathies.
  • Controls can be age matched (or stratified, for example and without limitation, into those subjects younger than or older than some threshold age, such as 6, 7, 8, 9, or 10 years), matched for status of prior corticosteroid treatment (that is, yes or no, or length of time of previous treatment), matched for baseline performance in the 6MWT before any treatment (except perhaps with corticosteroids) (or stratified, for example and without limitation, into those subjects whose baseline performance is below and above some threshold, such as 200 m, 250 m, 300 m, 350 m, 400 m, 450 m, or 500 m), or some other attribute determined to be clinically relevant.
  • some threshold age such as 6, 7, 8, 9, or 10 years
  • matched for status of prior corticosteroid treatment that is, yes or no, or length of time of previous treatment
  • baseline performance in the 6MWT before any treatment except perhaps with corticosteroids
  • stratified, for example and without limitation, into those subjects whose baseline performance is below and above some threshold such as 200 m, 250 m
  • a therapeutically effective dose or amount of an AAV vector of the disclosure is effective to increase the average 6MWD of subjects with dystrophinopathy, such as DMD, by about or at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 meters or more compared to similar matched or stratified controls 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, or 36 months after administration of the vector.
  • dystrophinopathy such as DMD
  • the AAV vector comprises the AAV9 capsid and a genome including a human codon-optimized gene encoding a mini-dystrophin protein, such as, without limitation, the vector designated as AAV9.hCK.Hopti-Dys3978.spA.
  • a therapeutically effective dose of amount of an AAV vector of the disclosure is effective to increase the average 6MWD of subjects with dystrophinopathy, such as DMD, by about or at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 meters or more compared to similar matched or stratified controls 30, 60, 90, 120, 150, 180, 210, 240, 270, 300, 330, 360, 390, 420, 450, 480, 510, 540, 570, 600, 630, 660, 690 or 720 days after administration of the vector.
  • dystrophinopathy such as DMD
  • the AAV vector comprises the AAV9 capsid and a genome including a human codon-optimized gene encoding a mini-dystrophin protein such as, without limitation, the vector designated as AAV9.hCK.Hopti-Dys3978.spA.
  • therapeutic efficacy can be expressed as reduction in the time it takes a subject to ascend 4 standardized stairs, a test known as the 4 stair climb test. This test has been used to assess the effectiveness of corticosteroid treatment in DMD patients. Griggs, R C, et al., Arch Neurol 48(4):383-8 (1991).
  • a therapeutically effective dose or amount of an AAV vector of the disclosure is effective to reduce the average time it takes for subjects with dystrophinopathy, such as DMD, to perform the 4 stair climb test by about or at least 0.2, 0.4, 0.6, 0.8, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0, 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, 3.6, 3.8, or 4.0 seconds or more compared to similar matched or stratified controls 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, or 36 months after administration of the vector.
  • dystrophinopathy such as DMD
  • the AAV vector comprises the AAV9 capsid and a genome including a human codon-optimized gene encoding a mini-dystrophin protein, such as, without limitation, the vector designated as AAV9.hCK.Hopti-Dys3978.spA.
  • a therapeutically effective dose or amount of an AAV vector of the disclosure is effective to reduce the average time it takes for subjects with dystrophinopathy, such as DMD, to perform the 4 stair climb test by about or at least 0.2, 0.4, 0.6, 0.8, 1.0, 1.2, 1.4, 1.6, 1.8, 2.0, 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, 3.6, 3.8, or 4.0 seconds or more compared to similar matched or stratified controls 30, 60, 90, 120, 150, 180, 210, 240, 270, 300, 330, 360, 390, 420, 450, 480, 510, 540, 570, 600, 630, 660, 690 or 720 days after administration of the vector.
  • dystrophinopathy such as DMD
  • the AAV vector comprises the AAV9 capsid and a genome including a human codon-optimized gene encoding a mini-dystrophin protein, such as, without limitation, the vector designated as AAV9.hCK.Hopti-Dys3978.spA.
  • Therapeutic efficacy can also be expressed as a reduction over time in the percentage of subjects that experience loss of ambulation a specified time after treatment compared to controls. Loss of ambulation is defined as start of continuous reliance on wheelchair use.
  • a therapeutically effective dose or amount of an AAV vector of the disclosure reduces, 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, or 36 months after administration to subjects with dystrophinopathy, such as DMD, the average number of subjects that have lost ambulation by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65% or more compared to similar matched or stratified controls.
  • the AAV vector comprises the AAV9 capsid and a genome including a human codon-optimized gene encoding a mini-dystrophin protein, such as, without limitation, the vector designated as AAV9.hCK.Hopti-Dys3978.spA.
  • a therapeutically effective dose or amount of an AAV vector of the disclosure is effective to delay the onset of one of more symptoms in a subject having a dystrophinopathy, such as DMD.
  • Diagnosis before onset of symptoms can be accomplished through prenatal, perinatal or postnatal genetic testing for mutations in the DMD gene.
  • treatment with an AAV vector of the disclosure is effective to delay onset of one or more symptoms of DMD by at least or about 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 20, 22, 24, 25, 26, 28, 30, 32, 34, 35, 36, 38, 40, 42, 44, 45, 46, 48, 50, 52, 54, 55, 56, 28, 60, 62, 64, 65, 66, 68, 70, 72, 74, 75, 76, 78, or 80 months, or more compared to similar matched or stratified controls.
  • early symptoms of DMD include without limitation delay in walking ability (to an average age of about 18 months, compared to an average of 12-15 months in babies without DMD); difficulty jumping, running or climbing stairs; proneness to falling; proximal muscle weakness, evidenced, for example, by exhibiting the Gowers' maneuver when rising from the floor; enlarged calves, due to pseudohypertrophy; waddling gait due to subjects' walking on toes and/or balls of feet; tendency to maintain balance by sticking out bellies and pulling back shoulders; and cognitive impairments, such as diminished receptive language, expressive language, visuospatial ability, fine motor skills, attention, and memory skills.
  • the AAV vector comprises the AAV9 capsid and a genome including a human codon-optimized gene encoding a mini-dystrophin protein, such as, without limitation, the vector designated as AAV9.hCK.Hopti-Dys3978.spA.
  • Therapeutic efficacy can also be expressed as a reduction over time in the percentage of vector treated subjects that experience an increase in the amount of adipose tissue that replaces lean muscle tissue compared to untreated controls.
  • this progression toward increased adiposity can be determined using MRI analysis of the leg muscles of DMD patients and expressed as the fat fraction (FF), as explained further in Willcocks, R J, et al., Multicenter prospective longitudinal study of magnetic resonance biomarkers in a large Duchenne muscular dystrophy cohort, Ann Neurol. 79:535-47 (2016).
  • FF fat fraction
  • treatment of DMD subjects with an AAV vector of the disclosure is effective to reduce the average FF in their lower extremities as determined by MRI by about or at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, or more 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, or 36 months after treatment compared to matched controls.
  • the AAV vector comprises the AAV9 capsid and a genome including a human codon-optimized gene encoding a mini-dystrophin protein, such as, without limitation, the vector designated as AAV9.hCK.Hopti-Dys3978.spA.
  • a therapeutically effective dose or amount of an AAV vector of the disclosure is one that results in at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or more of skeletal muscle fibers expressing the mini-dystrophin protein 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, or 36 months after treatment.
  • the percentage of muscle fibers that are positive for mini-dystrophin protein expression may be determined by immunolabeling sections of biopsied muscle from treated subjects with an anti-dystrophin antibody capable of specifically binding the mini-dystrophin protein.
  • the AAV vector comprises the AAV9 capsid and a genome including a human codon-optimized gene encodings mini-dystrophin protein, such as, without limitation, the vector designated as AAV9.hCK.Hopti-Dys3978.spA.
  • a dose or amount of an AAV vector of the disclosure for treating dystrophinopathy is determined to be therapeutically effective and at the same time causes either no cellular (T cell) immune response specific for the mini-dystrophin protein in treated subjects, or in only a low percentage of such subjects.
  • T cell no cellular immune response specific for the mini-dystrophin protein in treated subjects, or in only a low percentage of such subjects.
  • Existence or extent of a T cell response against the mini-dystrophin protein can be determined using the ELISPOT assay to detect peripheral blood mononuclear cells (PBMCs) isolated from subject blood that produce gamma interferon (IFN ⁇ ) in response to exposure to an overlapping peptide library covering the mini-dystrophin protein amino acid sequence.
  • PBMCs peripheral blood mononuclear cells isolated from subject blood that produce gamma interferon (IFN ⁇ ) in response to exposure to an overlapping peptide library covering the mini-dystrophin protein amino acid sequence.
  • the threshold for a positive IFN ⁇ response can be set as greater than 50 spot-forming cells per million PBMCs tested.
  • Use of other assays to detect a T cell response against the mini-dystrophin protein are also possible including without limitation detection of T cell infiltrates in biopsies of muscle or other tissues expressing mini-dystrophin protein obtained from vector treated subjects.
  • Subjects can be human subjects or animal subjects, such as animal models of DMD, such as the mdx mouse, mdx rat, or GRMD dog models.
  • a dose or amount of an AAV vector of the disclosure for treating dystrophinopathy is determined to be therapeutically effective and at the same time causes either no inflammatory response against the capsid, vector genome (or any component thereof), or mini-dystrophin protein expressed by transduced cells, or in only a low percentage of such subjects.
  • dystrophinopathy such as muscular dystrophy, such as DMD
  • inflammation in response to an AAV vector may be caused by an innate immune response. Inflammation, if any exists, in the muscles of vector treated subjects can be detected using magnetic resonance imaging.
  • Subjects can be human subjects or animal subjects, such as animal models of DMD, such, as the mdx mouse, mdx rat, or GRMD dog models.
  • existence or absence of cellular immune response of inflammation is determined 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36 months after treatment, or some other time after treatment.
  • a low percentage of subjects exhibiting a cellular immune response to the mini-dystrophin protein would be less than or equal to about 0%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19% or 20% of subjects administered vector.
  • the AAV vector comprises the AAV9 capsid and a genome including a human codon-optimized gene encoding a mini dystrophin protein, such as, without limitation, the vector designated as AAV9.hCK.Hopti-Dys3978. spA.
  • a dose or amount of an AAV vector of the disclosure for treating dystrophinopathy is therapeutically effective without need for concomitant immune suppression in treated subjects.
  • treatment of a subject with dystrophinopathy, such as DMD is effective without need to administer to the subject before, during or after treatment with AAV vector one or more immune-suppressing drugs (apart from steroid treatment, which is the current standard of care).
  • immune-suppressing drugs include but are not limited to calcineurin inhibitors, such as tacrolimus and cyclosporin, antiproliferative agents, such as mycophenolate, leflunomide, and azathioprine, or mTOR inhibitors, such as sirolimus and everolimus.
  • calcineurin inhibitors such as tacrolimus and cyclosporin
  • antiproliferative agents such as mycophenolate, leflunomide, and azathioprine
  • mTOR inhibitors such as sirolimus and everolimus.
  • efficacy of the AAV vectors of the disclosure can be tested in animal models of Duchenne muscular dystrophy, and results used to predict efficacious doses of such vectors in human DMD patients.
  • Various animal models are known in the art, including the mdx mouse model, the Golden Retriever muscular dystrophy model, and more recently, the Dmd mdx rat model, which is described in greater detail in the Examples.
  • AAV vectors of the disclosure including the vector designated as AAV9.hCK.Hopti-Dys3978.spA, can be established with respect to various biological parameters and aspects of the disease course in the rats.
  • treatment of Dmd mdx rats with a dose of AAV9.hCK.Hopti-Dys3978.spA of at least 1 ⁇ 10 14 vg/kg or 3 ⁇ 10 14 vg/kg is effective to reduce serum AST, ALT, LDH, or total creatine kinase levels at 3 months or 6 months post-injection compared to controls.
  • treatment of Dmd mdx rats with a dose of AAV9.hCK.Hopti-Dys3978.spA of at least 1 ⁇ 10 14 vg/kg or 3 ⁇ 10 14 vg/kg is effective to reduce fibrosis in biceps femoris, diaphragm, or heart muscle at 3 months or 6 months post-injection compared to controls.
  • treatment of Dmd mdx rats with a dose of AAV9.hCK.Hopti-Dys3978.spA of at least 1 ⁇ 10 14 vg/kg or 3 ⁇ 10 14 vg/kg is effective to increase forelimb grip force at 3 months or 6 months post-injection compared to controls.
  • treatment of Dmd mdx rats with a dose of AAV9.hCK.Hopti-Dys3978.spA of at least 1 ⁇ 10 14 vg/kg or 3 ⁇ 10 14 vg/kg is effective to reduce muscle fatigue as measured over 5 closely spaced trials testing forelimb grip force at 3 months or 6 months post-injection compared to controls.
  • treatment of Dmd mdx rats with a dose of AAV9.hCK.Hopti-Dys3978.spA of at least 1 ⁇ 10 14 vg/kg or 3 ⁇ 10 14 vg/kg is effective to increase the left ventricular ejection fraction as measured using echocardiography at 6 months post-injection compared to controls.
  • treatment of Dmd mdx rats with a dose of AAV9.hCK.Hopti-Dys3978.spA of at least 1 ⁇ 10 14 vg/kg or 3 ⁇ 10 14 vg/kg is effective to increase the ratio of the velocity of early to late left ventricular filling (i.e., E/A ratio) as measured using echocardiography at 3 months or 6 months post-injection compared to controls.
  • treatment of Dmd mdx rats with a dose of AAV9.hCK.Hopti-Dys3978.spA of at least 1 ⁇ 10 14 vg/kg or 3 ⁇ 10 14 vg/kg is effective to decrease the isovolumetric relaxation time (IVRT) or the time in milliseconds between peak E velocity and its return to baseline (i.e., the E wave deceleration time (DT)) as measured using echocardiography at 3 months or 6 months post-injection compared to controls.
  • IVRT isovolumetric relaxation time
  • DT E wave deceleration time
  • the increase or decrease of the physiologic measurement in vector-treated animals compared to control animals can, in some embodiments, be tested for statistical significance.
  • the choice of which statistical test to apply is within the knowledge of those ordinarily skilled in the art.
  • a p-value is adopted as the way in which to assess statistical significance, such p-values, once calculated, can be compared to a predefined significance level, and if the p-value is smaller than the significance level, the treatment effect can be determined to be statistically significant.
  • the significance level can be predefined as 0.25, 0.20, 0.15, 0.10, 0.05, 0.04, 0.03, 0.02, 0.01, 0.005, or some other significance level.
  • the significance level is predefined as 0.05
  • calculation of a p-value ⁇ 0.05 would be interpreted to represent a statistically significant difference between vector-treated and control groups.
  • the controls can be age matched animals of the same sex and genetic background that are untreated, or treated only with vehicle and not vector. Other controls are also possible however.
  • treatment of Dmd mdx rats with a dose of AAV9.hCK.Hopti-Dys3978.spA of at least 3 ⁇ 10 14 vg/kg is effective to transduce biceps femoris, diaphragm, heart muscle, or other striated muscles, and express the mini-dystrophin protein encoded by the opti-Dys3978 gene without inducing a cellular immune response against the mini-dystrophin protein by 3 months or 6 months post-injection.
  • Cellular immune response against the mini-dystrophin protein can be assessed by isolating splenocytes, or blood lymphocytes, such as peripheral blood mononuclear cells (PBMCs), from test animals, incubating the cells with peptides from an overlapping peptide library covering the mini-dystrophin protein amino acid sequence (for example, peptides 15 amino acids long overlapping by 10 amino acids each) in pools (for example, 5 pools), and determining whether the cells produce gamma interferon (IFN ⁇ ) in response to being exposed to the peptides. Production of IFN ⁇ can be determined using the ELISPOT assay according to the knowledge of those ordinarily skilled in the art.
  • PBMCs peripheral blood mononuclear cells
  • the threshold for a positive IFN ⁇ response can be set as greater than 50 spot-forming cells per million cells tested, or in other embodiments, as at least 3-times the number of spot-forming cells detected using a negative control (for example, medium only without added peptides), so that a negative response would be considered below these thresholds.
  • an AAV vector for treating dystrophinopathy is administered to a subject in need of treatment for dystrophinopathy, such as DMD, jointly with at least a second agent established or believed to be effective for treating dystrophinopathy, such as DMD.
  • Joint administration of the AAV vector means treating a subject before, contemporaneously with, or after treatment of the second agent.
  • the AAV vector is jointly administered with an antisense oligonucleotide that causes exon skipping of the DMD gene, for example of exon 51 of the dystrophin gene, or some other exon of the dystrophin gene.
  • the AAV vector is jointly administered with an agent that inhibits myostatin function in the subject, such as an anti-myostatin antibody, examples of which are provided in U.S. Pat. Nos. 7,888,486, 8,992,913, and 8,415,459.
  • the AAV vector is jointly administered with an agent that promote ribosomal read-through of nonsense mutations, such as ataluren, or with an agent that suppresses premature stop codons, such as an aminoglycoside, such as gentamicin.
  • the AAV vector is jointly administered with an anabolic steroid, such as oxandrolone.
  • the AAV vector is jointly administered with a corticosteroid, such as without limitation prednisone, deflazacort, or prednisolone.
  • the AAV vector is an AAV9 vector comprising a genome including a human codon-optimized gene encoding a mini-dystrophin protein, such as, without limitation, the vector designated as AAV9.hCK.Hopti-Dys3978.spA.
  • Virus vectors and capsids find use in both veterinary and human medical applications. Suitable subjects include both avians and mammals.
  • avian as used herein includes, but is not limited to, chickens, ducks, geese, quail, turkeys, pheasant, parrots, parakeets, and the like.
  • mammal as used herein includes, but is not limited to, humans, non-human primates, bovines, ovines, caprines, equines, felines, canines, lagomorphs, etc. Human subjects include neonates, infants, juveniles and adults.
  • the subject is “in need of” the methods of the present invention, e.g., because the subject has or is believed at risk for a disorder including those described herein or that would benefit from the delivery of a polynucleotide including those described herein.
  • the subject can be a laboratory animal and/or an animal model of disease.
  • the present invention provides a pharmaceutical composition
  • a pharmaceutical composition comprising a virus vector (such as an rAAV particle) and/or capsid of the invention in a pharmaceutically acceptable carrier and, optionally, other medicinal agents, pharmaceutical agents, stabilizing agent, buffers, carriers, adjuvants, diluents, etc.
  • the carrier will typically be a liquid.
  • the carrier may be either solid or liquid.
  • the carrier will be respirable, and optionally can be in solid or liquid particulate form.
  • pharmaceutically acceptable it is meant a material that is not toxic or otherwise undesirable, i.e., the material may be administered to a subject without causing any undesirable biological effects.
  • the virus vector may be introduced into the cells at the appropriate multiplicity of infection according to standard transduction methods suitable for the particular target cells. Titers of virus vector to administer can vary, depending upon the target cell type, and number, and the particular virus vector, and can be determined by those of skill in the art without undue experimentation. In representative embodiments, at least about 10 3 infectious units, more preferably at least about 10 5 infectious units are introduced to the cell.
  • the cell(s) into which the virus vector is introduced can be of any type, including but not limited to muscle cells (e.g., skeletal muscle cells, cardiac muscle cells, smooth muscle cells and/or diaphragm muscle cells), stem cells, germ cells, and the like.
  • the cell can be any progenitor cell.
  • the cell can be a stem cell (e.g., muscle stem cell).
  • the cell can be from any species of origin, as indicated above.
  • the virus vector can be introduced into cells in vitro for the purpose of administering the modified cell to a subject.
  • the cells have been removed from a subject, the virus vector is introduced therein, and the cells are then administered back into the subject.
  • Methods of removing cells from subject for manipulation ex vivo, followed by introduction back into the subject are known in the art (see, e.g., U.S. Pat. No. 5,399,346).
  • the recombinant virus vector can be introduced into cells from a donor subject, into cultured cells, or into cells from any other suitable source, and the cells are administered to a subject in need thereof (i.e., a “recipient” subject).
  • Suitable cells for ex vivo gene delivery are as described above. Dosages of the cells to administer to a subject will vary upon the age, condition and species of the subject, the type of cell, the nucleic acid being expressed by the cell, the mode of administration, and the like. Typically, at least about 10 2 to about 10 8 cells or at least about 10 3 to about 10 6 cells will be administered per dose in a pharmaceutically acceptable carrier. In particular embodiments, the cells transduced with the virus vector are administered to the subject in a treatment effective or prevention effective amount in combination with a pharmaceutical carrier.
  • a further aspect of the invention is a method of administering the virus vector to subjects.
  • Administration of the virus vectors and/or capsids according to the present invention to a human subject or an animal in need thereof can be by any means known in the art.
  • the virus vector and/or capsid is delivered in a treatment effective or prevention effective dose in a pharmaceutically acceptable carrier.
  • Dosages of the virus vector and/or capsid to be administered to a subject depend upon the mode of administration, the disease or condition to be treated and/or prevented, the individual subject's condition, the particular virus vector or capsid, and the nucleic acid to be delivered, and the like, and can be determined in a routine manner.
  • Exemplary doses for achieving therapeutic effects are titers of at least about 10 5 , 10 6 , 10 7 , 10 8 , 10 9 , 10 10 , 10 11 , 10 12 , 10 13 , 10 14 , 10 15 transducing units, optionally about 10 8 -10 13 transducing units.
  • more than one administration may be employed to achieve the desired level of gene expression over a period of various intervals, e.g., daily, weekly, monthly, yearly, etc.
  • an AAV vector or particle of the disclosure can be administered to a subject in compositions comprising empty AAV capsids of the same or a different serotype.
  • Empty capsids are AAV capsids comprising the typical arrangement and ratios of VP1, VP2 and VP3 capsid proteins, but do not contain a vector genome. Without wishing to be bound by any particular theory of operation, is hypothesized that the presence of empty capsids can reduce the immune response against the capsid of the AAV vector, and thereby increase transduction efficiency.
  • Empty capsids can occur naturally in a preparation of AAV vector, or be added in known quantities to achieve known ratios of empty capsids to AAV vector (that is, capsids containing vector genomes). Preparation, purification and quantitation of empty capsids is within the knowledge of those ordinarily skilled in the art.
  • Compositions comprising AAV vectors of the disclosure and empty capsids can be formulated with an excess of empty capsids relative to AAV vectors, or an excess of genome containing AAV vectors relative to empty capsids.
  • compositions of the disclosure comprise AAV vectors of the disclosure and empty capsids of the same or a different serotype, wherein the ratio of empty capsids to AAV vectors is about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2, 3.3, 3.4, 3.5, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4.0, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, 5.0, 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.8, 5.9, 6.0, 6.1, 6.2, 6.3, 6.4, 6.5, 6.6,
  • the disclosure provides exemplary efficacious doses of AAV vector particles for treating dystrophinopathy, such as muscular dystrophy, such as DMD, quantified as vector genomes (vg) per kilogram of subject body weight (kg), abbreviated vg/kg.
  • dystrophinopathy such as muscular dystrophy, such as DMD
  • vg vector genomes per kilogram of subject body weight
  • an efficacious dose of an AAV vector of the disclosure is about 1 ⁇ 10 12 vg/kg, 2 ⁇ 10 12 vg/kg, 3 ⁇ 10 12 vg/kg, 4 ⁇ 10 12 vg/kg, 5 ⁇ 10 12 vg/kg, 6 ⁇ 10 12 vg/kg, 7 ⁇ 10 12 vg/kg, 8 ⁇ 10 12 vg/kg, 9 ⁇ 10 12 vg/kg, 1 ⁇ 10 13 vg/kg, 2 ⁇ 10 13 vg/kg, 3 ⁇ 10 13 vg/kg, 4 ⁇ 10 13 vg/kg, 5 ⁇ 10 13 vg/kg, 6 ⁇ 10 13 vg/kg, 7 ⁇ 10 13 vg/kg, 8 ⁇ 10
  • the AAV vector may be administered to a subject in a pharmaceutically acceptable composition alone, or with empty capsids of the same, capsid serotype at an empty capsid to vector ratio of about 0.5:1, 1:1, 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, 8:1, 9:1, 10:1, or some other ratio.
  • Exemplary modes of administration include oral, rectal, transmucosal, intranasal, inhalation (e.g., via an aerosol), buccal (e.g., sublingual), vaginal, intrathecal, intraocular, transdermal, intraendothelial, in utero (or in ovo), parenteral, (e.g., intravenous, subcutaneous, intradermal, intracranial, intramuscular (including administration to skeletal, diaphragm and/or cardiac muscle), intrapleural, intracerebral, and intra-articular), topical (e.g., to both skin and mucosal surfaces; including airway surfaces, and transdermal administration), intra-lymphatic, and the like, as well as direct tissue or organ injection (e.g., to skeletal muscle, cardiac muscle, or diaphragm muscle).
  • parenteral e.g., intravenous, subcutaneous, intradermal, intracranial, intramuscular (including administration to skeletal, diaphrag
  • Administration can be to any site in a subject, including, without limitation, a site selected from the group consisting of a skeletal muscle, a smooth muscle, the heart, and the diaphragm.
  • Administration to skeletal muscle according to the present invention includes but is not limited to administration to skeletal muscle in the limbs (e.g., upper arm, lower arm, upper leg, and/or lower leg), back, neck, head (e.g., tongue), thorax, abdomen, pelvis/perineum, and/or digits.
  • limbs e.g., upper arm, lower arm, upper leg, and/or lower leg
  • head e.g., tongue
  • thorax e.g., abdomen, pelvis/perineum, and/or digits.
  • Suitable skeletal muscles include but are not limited to abductor digiti minimi (in the hand), abductor digiti minimi (in the foot), abductor hallucis, abductor ossis metatarsi quinti, abductor pollicis brevis, abductor pollicis longus, adductor brevis, adductor hallucis, adductor longus, adductor magnus, adductor pollicis, anconeus, anterior scalene, articularis genus, biceps brachii, biceps femoris, brachialis, brachioradialis, buccinator, coracobrachialis, corrugator supercilii, deltoid, depressor anguli oris, depressor labii inferioris, digastric, dorsal interossei (in the hand), dorsal interossei (in the foot), extensor carpi radialis brevis, exten
  • the virus vector can be delivered to skeletal muscle by intravenous administration, intra-arterial administration, intraperitoneal administration, limb perfusion, (optionally, isolated limb perfusion of a leg and/or arm; see, e.g. Arruda et al., (2005) Blood 105: 3458-3464), and/or direct intramuscular injection.
  • the virus vector and/or capsid is administered to a limb (arm and/or leg) of a subject (e.g., a subject with muscular dystrophy such as DMD) by limb perfusion, optionally isolated limb perfusion (e.g., by intravenous or intra-articular administration.
  • the virus vectors and/or capsids of the invention can advantageously be administered without employing “hydrodynamic” techniques.
  • Tissue delivery (e.g., to muscle) of prior art vectors is often enhanced by hydrodynamic techniques, (e.g., intravenous/intravenous administration in a large volume), which increase pressure in the vasculature and facilitate the ability of the vector to cross the endothelial cell barrier.
  • the viral vectors and/or capsids of the invention can be administered in the absence of hydrodynamic techniques such as high volume infusions and/or elevated intravascular pressure (e.g., greater than normal systolic pressure, for example, less than or equal to a 5%, 10%, 15%, 20%, 25% increase in intravascular pressure over normal systolic pressure).
  • hydrodynamic techniques such as high volume infusions and/or elevated intravascular pressure (e.g., greater than normal systolic pressure, for example, less than or equal to a 5%, 10%, 15%, 20%, 25% increase in intravascular pressure over normal systolic pressure).
  • Administration to cardiac muscle includes administration to the left atrium, right atrium, left ventricle, right ventricle and/or septum.
  • the virus vector and/or capsid can be delivered to cardiac muscle by intravenous administration, intra-arterial administration such as intra-aortic administration, direct cardiac injection (e.g., into left atrium, right atrium, left ventricle, right ventricle), and/o. coronary artery perfusion.
  • Administration to diaphragm muscle can be by any suitable method including intravenous administration, intra-arterial administration, and/or intra-peritoneal administration.
  • Administration to smooth muscle can be by any suitable method including intravenous administration, intra-arterial administration, and/or intra-peritoneal administration.
  • administration can be to endothelial cells present in, near, and/or on smooth muscle.
  • Delivery to a target tissue can also be achieved by delivering a depot comprising the virus vector and/or capsid.
  • a depot comprising the virus vector and/or capsid is implanted into skeletal, smooth, cardiac and/or diaphragm muscle tissue or the tissue can be contacted with a film or other matrix comprising the virus vector and/or capsid.
  • implantable matrices or substrates are described in U.S. Pat. No. 7,201,898.
  • a virus vector according to the present invention is administered to skeletal muscle, diaphragm muscle and/or cardiac muscle (e.g., to treat and/or prevent muscular dystrophy).
  • the invention is used to treat and/or prevent disorders of skeletal, cardiac and/or diaphragm muscle.
  • the invention provides a method of treating and/or preventing muscular dystrophy in a subject in need thereof, the method comprising: administering a treatment or prevention effective amount of a virus vector of the invention to a mammalian subject, wherein the virus vector comprises a heterologous nucleic acid encoding dystrophin, a mini-dystrophin, or a micro-dystrophin.
  • the virus vector can be administered to skeletal, diaphragm and/or cardiac muscled described elsewhere herein.
  • Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions.
  • one may administer the virus vector and/or virus capsids of the invention in a local rather than systemic manner, for example, in a depot or sustained-release formulation.
  • the virus vector and/or virus capsid can be delivered adhered to a surgically implantable matrix (e.g., as described in U.S. Patent Publication No. 2004-0013645).
  • ⁇ 3990 One of these mini-dystrophin proteins, named ⁇ 3990, was described in U.S. Pat. No. 7,510,867 under SEQ ID NO:6.
  • the protein sequence of ⁇ 3990 and the DNA encoding it are provided herein by SEQ ID NO:27 and SEQ ID NO:28, respectively.
  • Dys3978 is 1325 amino acids in length, and includes the following portions or subdomains from wildtype full-length human muscle dystrophin (SEQ ID NO:25): the N-terminus and actin-binding domain (ABD), hinge H1, rods R1 and R2, hinge H3, rods R22, R23 and R24, hinge H4, the cysteine-rich domain (CR-domain) and part of the carboxy-terminal domain (CT domain).
  • SEQ ID NO:25 wildtype full-length human muscle dystrophin
  • the gene encoding Dys3978 was constructed by combining subsequences from the wildtype dystrophin coding sequence corresponding to the protein subdomains described above. The resulting gene is provided by SEQ ID NO:26. To increase the expression of Dys3978, the gene sequence was codon-optimized using human codon algorithms. The resulting human codon-optimized gene, called Hopti-Dys3978, is provided as SEQ ID NO:1. A canine codon-optimized gene encoding Dys3978, called Copti-Dys3978, was also generated, the sequence of which is provided as SEQ ID NO:3. An alignment comparing the DNA sequences of Hopti-Dys3978 and the non-codon-optimized gene encoding ⁇ 3990 is provided in FIGS. 56A-56I .
  • codon-optimization of the gene encoding Dys3978 increased total GC content from about 46% in the non-codon-optimized gene to about 61% in the human codon-optimized gene (i.e., Hopti-Dys3978).
  • Increasing GC content can result in increased mRNA levels in mammalian cells. See, for example, Grzegorz, K, et al., PLoS Biol, 4(6):e180 (2006); and Newman, Z R, et al., PNAS, E1362-71 (2016).
  • Codon-optimization also increased the codon adaptation index (CAI) and included addition of a Kozak consensus transcription initiation recognition site at the beginning of the coding sequence.
  • CAI codon adaptation index
  • the Hopti-Dys3978 gene was cloned into an AAV vector expression cassette containing the constitutively active CMV promoter and a small synthetic polyadenylation (polyA) signal sequence (SEQ ID NO: 6). After transfection into human HEK 293 cells, the vector plasmid containing the Hopti-Dys3978 gene showed surprisingly greater protein expression than the non-optimized gene encoding Dysp3978, as determined qualitatively using immunofluorescent staining and Western blot against dystrophin protein ( FIG. 2 ).
  • Hopti-Dys3837 (SEQ ID NO: 2 ) encodes a human mini-dystrophin protein, of 1278 amino acids called Dys3837 (SEQ ID NO: 8), which is also illustrated schematically in FIG. 1 .
  • the human and canine codon-optimized Dys3978 genes were placed under the control of one of two different synthetic muscle-specific promoter and enhancer combinations derived from the muscle creatine kinase gene identified below:
  • the following vectors were constructed using standard molecular cloning techniques.
  • the gene expression cassettes of the specified promoter, mini-dystrophin gene and polyA sequence were cloned into an AAV vector plasmid backbone containing AAV2 inverted terminal repeats (ITRs) flanking the expression cassette.
  • ITRs inverted terminal repeats
  • AAV-CMV-Hopti-Dys3978 2) (SEQ ID NO: 9) AAV-hCK-Hopti-Dys3978 3) (SEQ ID NO: 10) AAV-hCK-Hopti-Dys3837 4) (SEQ ID NO: 11) AAV-hCKplus-Hopti-Dys3837 5) (SEQ ID NO: 12) AAV-hCK-Copti-Dys3978
  • the treated dKO mice also showed amelioration of dystrophic pathology ( FIGS. 6A-6B ) and great improvement of overall health.
  • the dKO mice treated with Hopti-Dys3978 gene showed a much prolonged life-span (50% survival rate: 22 weeks vs. more than 80 weeks) ( FIG. 7 ).
  • the fertility of both male and female dKO mice were restored (Table 1 ), suggesting overall function improvement and possibly improvement in smooth muscle function as well.
  • the untreated dKO mice are completely infertile. However fertility was restored by AAV-CMV-Hopti-Dys3978 in both males and females of treated dKO (T-dKO) mice.
  • mice While measurement by echocardiography showed mdx mice had no apparent cardiac deficit under baseline condition when compared with G57/B10 wildtype mice, they did show apparent deficits as measured by hemodynamics at baseline ( FIG. 8 , open bars).
  • the results herein show that the AAV9-treated dKO mice displayed similar baseline cardiac hemodynamics to that of the mdx mice, including end-systolic pressure; end-diastolic volume, maximal rate of isovolumic contraction (dp/dt max ) and maximal rate of isovolumic relaxation (dp/dt min ).
  • treated dKO mice displayed similar baseline cardiac hemodynamics to that of the mdx mice, including end-systolic pressure, end-diastolic volume, maximal rate of isovolumic contraction (dp/dt max and dp/dt min ), whereas the AAV9-treated dKO mice performed significantly better than mdx mice in every parameter examined ( FIG. 8 , filled bars). Furthermore, greater than 50% of the mdx mice died within the 30-min dobutamine challenge window, consistent with our previous report (Wu et al., Proc. Natl. Acad. Sci. USA 105:14814 (2008)).
  • the same vector, AAV9-CMV-Hopti-Dys3978 was tested in the golden retriever muscular dystrophy (GRMD) dog, a large animal DMD model. Specifically, the vector was administered to a 2.5-month-old GRMD dog, “Jelly,” and then followed for more than 8 years post injection.
  • GRMD golden retriever muscular dystrophy
  • GRMD dog “Jelly” 2.5 months old female; 6.3 kg; serum CK: 20262 units/L before treatment
  • AAV9-CMV-Hopti-Dys3978 vector at a dose of 1 ⁇ 10 13 vg/kg via the right hind limb.
  • a rubber tourniquet was positioned at the proximal pelvic extremity (the groin area) to cover a majority of muscles in the right hind limb.
  • the AAV9 vector was injected via the great saphenous vein using a Harvard pump set at injection speed 1 ml/sec.
  • the vector volume was 20 ml/kg body weight (130 ml total).
  • the tourniquet was released after 10 minutes accounting from the start of injection.
  • mini-dystrophin-positive myofibers varied among different muscles, certain muscles had greater than 90% of myofibers positive upon necropsy ( FIG. 18 ).
  • Co-staining of mini-dystrophin and revertant myofibers (anti-C-terminus antibody) showed co-existence of both ( FIG. 19 ).
  • Mini-dystrophin was also observed in approximately 20% of the cardiomyocytes ( FIG. 18 ).
  • Overall gene expression was largely stable. For example, positive myofibers in the cranial sartorius muscle remained comparable throughout the 6 time points, from 2 and 7 months to 1, 4 and 8 years (compare FIGS. 12, 13, 14, 17 and 18 ).
  • Western blot confirmed the IF staining results ( FIG. 20 ).
  • AAV9-hCK-Copti-Dys3978 vector (a modified creatine kinase promoter driving a canine codon-optimized human mini-dystrophin 3978) was used in a GRMD dog named “Dunkin”.
  • the gene encodes the same human mini-dystrophin Dys3978 protein used in other studies, but was canine codon-optimized.
  • the DNA sequence is 94% identical to the human codon-optimized gene.
  • Transfection experiments in human HEK 293 cells comparing CK-Copti-Dys3978 (canine codon-optimized) and CK-Hopti-Dys3978 (human codon-optimized) revealed essentially the same level of expression. Multiple experiments comparing both constructs in mdx mice also showed essentially the same expression levels.
  • GRMD dog “Dunkin” female, 2.5 m old, 6.5 kg was intravenously injected with AAV9-hCK-Copti-Dys3978 vector at the dose of 4 ⁇ 10 13 vg/kg via the great saphenous vein. The dog was not sedated during injection. There was no noticeable adverse reaction or behavior change. A muscle biopsy was done 4 months post vector injection and necropsy was done at 14 months post-injection.
  • Dys3978 from the canine codon-optimized gene Copti-Dys3978 effectively restored dystrophin associated protein complex including gamma-sarcoglycan ( FIG. 30 ).
  • Quantitative PCR of vector DNA copy numbers showed a consistent trend to the mini-dystrophin protein expression levels ( FIG. 31 ).
  • Dystrophic pathology was largely ameliorated as shown by H&E staining for histology of the heart ( FIG. 32 ), diaphragm ( FIG. 33 ) and limb muscles ( FIG. 34 ). Trichrome Mason blue staining also showed significant reduction of fibrosis in limb muscle and diaphragm ( FIG. 35 ).
  • the AAV9.hCK.Hopti-Dys3978.spA vector used in Dmd mdx rat studies describe further in Examples 7, 8 and 9 includes an AAV9 capsid and an expression cassette designed to express a miniaturized version of human dystrophin protein including the N-terminus region, hinge 1 (H1), rod 1 (R1), rod 2 (R2), hinge 3 (H3), rod 22 (R22), rod 23 (R23), rod 24 (R24), hinge 4 (H4), cysteine-rich (CR) domain, and portion of the carboxy-terminal (CT) domain from full length human Dp427m dystrophin protein (SEQ ID NO:25), which are domains minimally required for function.
  • the protein sequence of the mini-dystrophin protein is provided as the amino acid sequence of SEQ ID NO:7, which is encoded by the human codon-optimized DNA sequence provided as the nucleic acid sequence of SEQ ID NO:1.
  • the vector genome of the AAV9.hGK.Hopti-Dys3978.spA vector is provided as the nucleic acid sequence of SEQ ID NO:18, or its reverse complement when the single-stranded genome is packaged in its minus polarity.
  • the vector genome comprises 5′ and 3′ flanking AAV2 inverted terminal repeats (ITRs) (having the DNA sequence of SEQ ID NO:14 or SEQ ID NO:15, respectively), a synthetic hybrid enhancer and promoter derived from the creatine kinase (CK) gene to serve as a muscle specific transcription regulatory element (hCK; having the DNA sequence of SEQ ID NO:16), a 3978 base pair long human codon-optimized gene encoding the human mini-dystrophin protein described above (i.e., the Hopti-Dys3978 gene), and a small synthetic transcription termination sequence including a polyadenylation (polyA) signal (spA; having the DNA sequence of SEQ ID NO:17).
  • ITRs inverted terminal repeats
  • Vector was manufactured using the triple transaction technique and a serum free non-adherent cell line derived from HEK 293 cells.
  • the plasmids used included a helper plasmid to express adenovirus helper protein required for efficient replication and packaging of the vector, a packaging plasmid expressing AAV2 rep gene and the AAV9 capsid proteins, and a third plasmid containing the sequence of the expression cassette described above.
  • Cells were grown and expanded from a working cell bank sample, and once sufficient volume and cell density had been reached, the cells were transfected using a transaction reagent. After incubation to permit vector production from the transfected cells, the cells were lysed to release vector, the lysate clarified, and vector purified using a nuclease treatment step to remove contaminating nucleic acids, followed by iodixanol step gradient centrifugation, anion exchange chromatography, dialysis against the formulation buffer, sterile filtration, and then storage at 2-8° C.
  • This example describes testing AAV9.hCK.Hopti-Dys3978.spA in a recently developed Dmd mdx rat models which has certain advantages compared to the classic mdx mouse and GRMD dog models.
  • the skeletal and cardiac disease are both present at an early stage and develop in a sequential manner similar to the disease progression seen in humans.
  • tissue samples were fixed in 10% neutral buffered formalin, embedded in paraffin wax, and 5- ⁇ m-thick sectioned before staining with hematoxylin eosin saffron (HES).
  • HES hematoxylin eosin saffron
  • additional samples liver, heart, biceps, femoris, pectoralis and diaphragm muscles
  • WT rats displayed subsarcolemmal dystrophin detected in skeletal, diaphragm and cardiac muscle fibers, and localization of dystrophin detected did not differ between rats treated with vector compared to only PBS.
  • mini-dystrophin detection in the vector treated WT rats could not be confirmed using this assay because the anti-dystrophin antibody used could not distinguish between wild type dystrophin and the mini-dystrophin protein.
  • one of the Dmd mdx rats displayed rare skeletal muscle fibers (from about 5% to 10%) with subsarcolemmal dystrophin detectable, which is in accordance with the previous description of the presence of scattered revertant fibers in this model with a frequency of about 5% (Larcher et al., PlosOne, 2014). However no dystrophin was detected in diaphragm or cardiac muscle fibers from this rat.
  • mini-dystrophin protein was well tolerated in healthy animals.
  • vector treatment of the Dmd mdx rats resulted in a significant and generalized detection of mini-dystrophin in fibers of all muscles studied (biceps femoris, pectoralis, diaphragm and heart) with a pattern of subsarcolemmal localization similar to that in WT rat muscles.
  • the expression of mini-dystrophin Dys3978 from the vector was associated with reduction in fibrosis and necrosis ( FIGS. 36A-36D ).
  • This example describes the results of treating Dmd mdx rats, an animal model for Duchenne muscular dystrophy, with increasing doses of AAV9.hCK.Hopti-Dys3978.spA, and measuring the effects at 3 months and 6 months after administration.
  • Rats were dosed at 7-8 weeks of age by IV injection into the dorsal penile vein, which resulted in systemic administration of the test articles.
  • Four different vector doses were tested in 10-12 Dmd mdx rats: 1 ⁇ 10 13 vg/kg (5 rats at the 3 month time point and 6 rats at the 6 month time point), 3 ⁇ 10 13 vg/kg ( 6 rats at the 3 month time point and 5 rats at the 6 month time point), and 1 ⁇ 10 14 vg/kg (7 rats at the 3 month time point and 6 rats at the 6 month time point), and 3 ⁇ 10 14 vg/kg (5 rats at the 3 month time point and 5 rats at the 6 month time point).
  • Dmd mdx rats and WT rats each received vehicle only (1 ⁇ PBS, 215 mM NaCl, 1.25% human serum albumin, 5% (w/v) sorbitol) as a negative control (6 Dmd mdx rats at the 3 month time point, 4 Dmd mdx rats at the 6 month time point, 5 WT rats at the 3 month time point, and 7 WT rats at the 6 month time point).
  • Five untreated (that is, no vector and no vehicle either) Dmd mdx rats were also included as further negative controls.
  • rats from each test arm were euthanized and necropsied to take tissue samples for further analysis. Prior to sacrifice, cardiac function and grip strength tests were carried out in the test animals to assess the effect of vector treatment on DMD disease progression.
  • vector doses may be represented in two different numerically equivalent ways in the text and figures.
  • “1 ⁇ 10 13 ” is equivalent to “1E13
  • “”3 ⁇ 10 13 ” is equivalent to “3E13
  • “”1 ⁇ 10 14 ” is equivalent to “1E14”
  • “3 ⁇ 10 14 ” is equivalent to “3E14.”
  • rats in each treatment arm were weighted daily for the first week, and weekly thereafter until sacrifice.
  • the average weight of all rats in each treatment arm is listed in Table 2 (pre-injection until 9 weeks post-injection) and Table 3 (weeks 10-25 post-injection) and are graphed against time in FIG. 37 .
  • error bars represent the standard error of the mean (SEM), which are also reported in the table.
  • SEM standard error of the mean
  • Standard molecular biology techniques were used to quantitate the transgene copy number by quantitative PCR (qPCR), relative expression levels of the mini-dystrophin mRNA transcripts by reverse transcriptase qPCR (RT-qPCR), and the amount of mini-dystrophin protein expression qualitatively by Western blot analysis.
  • genomic DNA was purified from tissues using the Gentra Puregene kit from Qiagen. Samples were then analyzed using a StepOne PlusTM Real Time PGR System (Applied Biosystems®, Thermo Fisher Scientific) using 50 ng gDNA in duplicate. All reactions were performed in duplex in a final volume of 20 ⁇ L containing template DNA, Premix Ex taq (Ozyme), 0.3 ⁇ L of ROX reference Dye (Ozyme), 0.2 ⁇ mol/L of each primer and 0.1 ⁇ mol/L of Taqman® probe.
  • Vector copy numbers were determined using primers and probe designed to amplify a region of the mini-dystrophin transgene:
  • Endogenous gDNA copy numbers were determined using primers and probe designed to amplify the rat HPRT1 gene:
  • threshold cycle (Ct) values were compared with those obtained with different dilutions of linearized standard plasmids (containing either the mini-dystrophin expression cassette or the rat HPRT1 gene).
  • the absence of qPCR inhibition in the presence of gDNA was checked by analyzing 50 ng of gDNA extracted from tissues samples from a control animal, spiked with different dilutions of standard plasmid.
  • Duplex qPCR (amplification of the 2 sequences in the same reaction) was used and results were expressed in vector genome per diploid genome (vg/dg). The sensitivity of the test was 0.003 vg/dg.
  • Duplex qPCR analysis was then performed 1/15-diluted cDNA using the same mini-dystrophin and rat HPRT1 specific primers and probes as for the quantification of transgene copy numbers by qPCR.
  • RNA sample For each RNA sample, the absence of DNA contamination was also confirmed by analysis of “cDNA-like samples” obtained without addition of reverse transcriptase the reaction mix.
  • Membranes were then blocked in 5% skim milk, 1% NP40 (Sigma-Aldrich) in TBST (tris-buffered saline, 0.1% Tween 20) and hybridized with an anti-dystrophin antibody-specific for exons 10 and 11 of the dystrophin protein (1:100, MANEX 1011C monoclonal antibody) and with a secondary anti-mouse IgG HRP-conjugated antibody (1:2000, Dako).
  • the same membrane was also hybridized with an anti-rat alpha-tubulin antibody (1:10000, Sigma) and with a secondary anti-mouse IgG HRP-conjugated antibody (1:2000, Dako). Immunoblots were visualized by ECL Chemiluminescent analysis system (Thermo Fisher Scientific).
  • results of testing for transgene copy numbers (as vector genomes per diploid genome (vg/dg)) in whole blood, spleen, heart, biceps femoris, pectoralis, diaphragm, and liver in Dmd mdx rats treated with vector and vehicle, and in WT rats administered vehicle only are described in the tables below. Data at 3 months post-injection is provided in Table 4, and at 6 months post-injection is provided in Table 5. Data are the mean of results from individual test animals.
  • Mini-dystrophin DNA was detected in Dmd mdx rats that had been injected with vector at both 3 and 6 months post-injection.
  • Transgene copy numbers in the tissues under study followed a pattern of prevalence of liver>heart>biceps femoris ⁇ diaphragm ⁇ pectoralis>spleen.
  • liver was by far the most efficiently transduced, with vector copy numbers reaching up to an average of 80-110 vg/dg in rats administered with 3 ⁇ 10 14 vg/kg vector.
  • Vector copy numbers in liver were 7-45 fold higher than in heart and 40-300 fold higher than in biceps femoris, diaphragm, or pectoralis muscles.
  • vector copy numbers averaged about 1.0 vg/dg in rats dosed with 1 ⁇ 10 14 vg/kg vector and about 5.0 vg/dg in rats dosed with 3 ⁇ 10 14 vg/kg vector.
  • transgene copy numbers in biceps femoris and pectoralis were similar and never exceeded about 0.5 vg/dg.
  • the average transgene copy number increased to about 1.2 vg/dg.
  • the data was particularly variable for diaphragm due to certain unusually high results among 4 animals that had received the two highest dose levels of vector, in which the transgene copy numbers ranged from about 9-15 vg/dg. If these outlying data points are excluded, then the transduction efficiency of diaphragm is relatively low at both the 3 and 6 month time points, with transgene copy numbers averaging about 0.2-0.4 vg/dg at the 1 ⁇ 10 14 vg/kg dose and about 1.05-1.3 vg/dg at the 3 ⁇ 10 14 vg/kg dose.
  • transcripts were detected in any tissue from animals in the negative control arms (WT rats and Dmd mdx rats treated with vehicle), or in spleen of animals treated with vector, regardless of dose. In all other tissues examined, vector-derived transcripts were detected, the levels of which tended to increase in a dose-responsive manner, although with some variability in the data. Transcript levels in the tissues followed the pattern biceps femoris>heart ⁇ diaphragm>liver. As discussed above, liver was the most transduced tissue among those sampled, with vector copy numbers varying about 60-130 fold higher than in biceps femoris muscle. Despite this, the level of mini-dystrophin mRNA in liver was about 5-15 fold lower than in biceps femoris, evidence of the highly muscle-specific activity of the promoter used in the vectors.
  • mini-dystrophin protein levels were also analyzed to determine mini-dystrophin protein levels using Western blot. No mini-dystrophin protein was detected in any tissue from animals in the negative control arms (WT rats and Dmd mdx rats treated with vehicle). At both the 3 and 6 month time points, mini-dystrophin protein was detected in biceps femoris, heart and diaphragm of Dmd mdx rats dosed with vector. At the lowest dose tested (1 ⁇ 10 13 vg/kg), mini-dystrophin protein was detected less frequently in the tissue samples compared to rats dosed with vector at higher levels. These results are summarized qualitatively in Table 8.
  • mini-dystrophin mRNA RQ of approximately 1.5 was required to permit detection of the protein. Consistent with the low levels of mini-dystrophin transcript measured in liver, no mini-dystrophin protein was detected in this tissue, even at the highest vector dose used.
  • tissue samples were obtained for histopathological and immunocytochemical analysis.
  • Tissue samples vehicle treated WT rats, vehicle and vector treated Dmd mdx rats were obtained during whole necropsy evaluation at 3 and 6 months post-injection. Samples were also obtained from untreated Dmd mdx rats sacrificed at 7-9 weeks of age to serve as a baseline comparison. Tissues were immediately fixed in formalin for histopathology or snap frozen for immunohistochemistry (immunolabeling) and stored until processing. For histopathology, tissue samples were fixed in 10% neutral buffered formalin, embedded in paraffin wax, and sectioned (5 ⁇ m) before staining with hematoxylin eosin saffron (HES) stain.
  • HES hematoxylin eosin saffron
  • Quantification of the picrosirius positive areas in heart sections was performed using Nikon Imaging Software (Nikon, Champigny sur Marne, France). Quantification of DYSB positive fibers and WGA positive areas was performed using ImageJ open source image processing software (v 2.0.0-rc-49/1.51a).
  • Tissue samples stained for histology were examined microscopically and lesions related to the DMD phenotype systematically recorded. Lesions in skeletal and cardiac muscle were scored semi-quantitatively as illustrated in FIG. 38A .
  • skeletal muscle biceps femoris, pectoralis and diaphragm
  • a score of 0 corresponded to absence of significant lesion
  • a score of 1 corresponded to the presence of some regeneration activity as evidenced by centro-nucleated fibers and regeneration foci
  • a score of 2 corresponded to degenerative fibers, isolated or in small clusters
  • a score of 3 corresponded to tissue remodeling and fiber replacement by fibrotic or adipose tissue.
  • scoring was based on the intensity of fibrosis (score of 1 for lower, and score of 2 for higher) and the presence of degenerative fibers (score of 3).
  • a total lesion score for each rat was calculated as the mean of the animal's scores for biceps femoris, pectoralis, diaphragm and cardiac muscles. Lesion scores for individual rats within each treatment arm were also averaged.
  • FIG. 38B Total lesion scores of individual rats and averages grouped by treatment arm at 3 months post-injection are shown in FIG. 38B , in which WT mock refers to WT rats treated With vehicle, for which lesion scores were 0.
  • KO mock refers to Dmd mdx rats treated with vehicle
  • KO 1E13, 3E13, and 1E14 refer to Dmd mdx rats treated with the indicated doses (i.e., 1 ⁇ 10 13 , 3 ⁇ 10 13 , and 1 ⁇ 10 14 , respectively) of vector in vg/kg.
  • the prevalence of muscular lesions associated with the dystrophic phenotype in Dmd mdx rats was reduced by vector treatment in a dose-responsive manner.
  • the percentage of positively stained muscle fibers in three randomly selected microscopic fields from each rat was calculated for biceps femoris, diaphragm, and cardiac muscles.
  • the area in three randomly selected microscopic fields staining positively with WGA conjugate was calculated to determine the extent of connective tissue fibrosis in frozen tissue samples from biceps femoris and diaphragm.
  • the amount of connective tissue (collagen) in transverse sections of heart was determined by quantifying the area staining positive with picrosirius red in histological preparations. Results from these studies are provided in FIGS. 39A-39C , FIGS. 40A-40C , and FIGS. 41A-41C .
  • FIG. 39A shows representative photomicrographs of stained tissue sections from biceps femoris muscle samples from WT rats treated with vehicle (WT+buffer), Dmd mdx rats treated with vehicle (DMD+buffer), and Dmd mdx rats treated with vector at increasing doses of 1 ⁇ 10 13 , 3 ⁇ 10 13 , 1 ⁇ 10 14 and 3 ⁇ 10 14 vg/kg (DMD+1E13, 3E13, 1E14, and 3E14, respectively).
  • the top panel of photos are from samples taken at 3 months post-injection and the bottom panel are from samples taken at 6 months post-injection.
  • FIG. 39A shows representative photomicrographs of stained tissue sections from biceps femoris muscle samples from WT rats treated with vehicle (WT+buffer), Dmd mdx rats treated with vehicle (DMD+buffer), and Dmd mdx rats treated with vector at increasing doses of 1 ⁇ 10 13 , 3 ⁇ 10 13 , 1 ⁇ 10 14 and 3
  • FIG. 39B is a graph showing the percentage of dystrophin positive fibers in biceps femoris muscle samples from WT rats and Dmd mdx rats, each treated with vehicle, and Dmd mdx rats treated with increasing doses of vector, at 3 and 6 month time points. Also included are results from untreated Dmd mdx rats 7-9 weeks of age (“DMD pathol status”).
  • FIG. 39C is a graph showing the percentage area occupied by connective tissue (as a measure of fibrosis) in biceps femoris muscle samples from similarly treated WT and Dmd mdx rats at 3 and 6 month time points, and untreated Dmd mdx rats 7-9 weeks of age.
  • the same letter over error bars indicates no statistically significant difference between the data, whereas no common letter indicates there is a significant difference (for example, two bars both having an “a” above them would not be significantly different from each other).
  • FIG. 40A shows representative photomicrographs of stained tissue sections from diaphragm samples from WT rats treated with vehicle (WT+buffer), Dmd mdx rats treated with vehicle (DMD+buffer), and Dmd mdx rats treated with vector at increasing doses of 1 ⁇ 10 13 , 3 ⁇ 10 13 , 1 ⁇ 10 14 and 3 ⁇ 10 14 vg/kg (DMD+1E13, 3E13, 1E14, and 3E14, respectively), all taken at 3 months post-injection.
  • WT+buffer Dmd mdx rats treated with vehicle
  • DMD+buffer Dmd mdx rats treated with vector at increasing doses of 1 ⁇ 10 13 , 3 ⁇ 10 13 , 1 ⁇ 10 14 and 3 ⁇ 10 14 vg/kg
  • FIG. 40B is a graph showing the percentage of dystrophin positive fibers in diaphragm samples from WT rats and Dmd mdx rats, each treated with vehicle, and Dmd mdx rats treated with increasing doses of vector, at 3 and 6 month time points. Also included are results from untreated Dmd mdx rats 7-9 weeks of age (“DMD pathol status”).
  • FIG. 40C is a graph showing the percentage area occupied by connective tissue (as a measure of fibrosis) in diaphragm samples from similarly treated WT and Dmd mdx rats at 3 and 6 month time points, and untreated Dmd mdx rats 7-9 weeks of age.
  • the same letter over error bars indicates no statistically significant difference between the data, whereas no common letter indicates there is a significant difference (for example, two bars both having an “a” above them would not be significantly different from each other).
  • FIG. 41A shows representative photomicrographs of stained tissue sections from heart muscle samples from WT rats treated with vehicle (WT+buffer), Dmd mdx rats treated with vehicle (DMD+buffer), and Dmd mdx rats treated with vector at increasing doses of 1 ⁇ 10 13 , 3 ⁇ 10 13 , 1 ⁇ 10 14 and 3 ⁇ 10 14 vg/kg (DMD+1E13, 3E13, 1E14, and 3E14, respectively).
  • the top and bottom panels show transverse sections of hearts from the third of the apex prepared histologically and stained with picrosirius red taken from test animals sacrificed at 3 and 6 months post-injection, respectively.
  • the black bars indicate length of 2 mm.
  • FIG. 41B is a graph showing the percentage of dystrophin positive fibers in heart muscle samples from WT rats and Dmd mdx rats, each treated with vehicle, and Dmd mdx rats treated with increasing doses of vector, at 3 and 6 month time points. Also included are results from untreated Dmd mdx rats 7-9 weeks of age (“DMD pathol status”).
  • DMD pathol status results from untreated Dmd mdx rats 7-9 weeks of age
  • 41C is a graph showing the percentage area occupied by connective tissue (as a measure of fibrosis) in heart muscle samples from similarly treated WT and Dmd mdx rats at 3 and 6 month time points, and untreated Dmd mdx rats 7-9 weeks of age.
  • connective tissue as a measure of fibrosis
  • Dmd mdx rats Treatment with vector induced mini-dystrophin expression in all muscles analyzed (biceps femoris, diaphragm, and heart), and the percentage of fibers expressing mini-dystrophin was positively correlated with vector dose (p ⁇ 0.001 by linear regression).
  • the number of mini-dystrophin-positive fibers in vector treated Dmd mdx rats was higher in biceps femoris and heart than in diaphragm, suggesting some heterogeneity in biodistribution or expression efficacy.
  • Mini-dystrophin expression was similar in terms of its subsarcolemmal localization, regardless dose, and no abnormal localization was detected eyen at the highest dose analyzed, 3 ⁇ 10 14 vg/kg. In some fibers, discontinuous dystrophin staining was detected along the sarcolemma, although the frequency of this observation decreased with increasing vector dose.
  • Forelimb grip force of Dmd mdx rats injected with vehicle or increasing doses of vector were tested 3 and 6 months post-injection.
  • WT rats injected with vehicle were included as negative controls. Rats were injected when they were 7-9 weeks old so that grip force testing was conducted when they were about 4.5 and 7.5 months old. Maximum grip force and grip force after repeated trials as an indication of fatigue were both measured.
  • a grip meter (Bio-GT3, BIOSEB, France) attached to a force transducer was used to measure the peak force generated when rats were placed with their forepaws on the T-bar and gently pulled backward until they released their grip.
  • Five tests were performed in sequence with a short latency (20-40 seconds) between each test, and the reduction in strength between the first and the last determination taken as an index of fatigue. Results are expressed in grams (g) and are normalized to the body weight (g/g BW). Grip test measurements were performed by an experimenter blind to genotype and treatment arm. Data are presented as the mean ⁇ SEM, and evaluated statistically using the non-parametric Kruskal-Wallis test to analyze differences between groups.
  • Forelimb grip force was also measured during five closely spaced repeated trials to determine the extent to which vector treatment might affect the muscle fatigue known to occur in the Dmd mdx rat model.
  • vehicle treated Dmd mdx rats exhibited a marked decrease of forelimb strength between the first and fifth trials (reduction of 63 ⁇ 5%), whereas WT rats treated with vehicle were just as strong after the fifth trial as after the first, an effect seen before in this model (Larcher, et al., 2014).
  • the Dmd mdx rats showed no statistically significant difference in the extent of fatigue compared to WT rats treated with vehicle. In other words, after five trials, these vector treated Dmd mdx rats were indistinguishable from wild type. In fact, in all trials, the mean grip force of Dmd mdx rats treated with the highest vector dose was higher than that of WT controls, although the difference was not statistically significant.
  • Cardiac function of Dmd mdx rats and WT controls were tested 3 and 6 months post-injection (about 5 and 8 months of age, respectively) to determine if vector treatment could improve the structural or functional effects on heart of the muscular dystrophy disease process in the rat DMD model.
  • Using two-dimensional echocardiography, free wall diastolic thickness, LV end-diastolic diameter, LV ejection fraction, and E/A ratio were measured 3 and 6 months post-injection.
  • Echocardiographic measurements were conducted by an experimenter blind as to genotype and treatment arm. Two-dimensional (2D) echocardiography was performed on test animals using a Vivid 7 Dimension ultrasound (GE Healthcare) with a 14-MHz transducer. To observe possible structural remodeling, left ventricular end-diastolic diameter and free wall end-diastolic thickness were measured during diastole from long and short-axis images obtained with M-mode echocardiography.
  • Systolic function was assessed by the ejection fraction, and diastolic function was determinedly by taking trans-mitral flow measurements of ventricular filling velocity using pulsed Doppler in an apical four-chamber orientation to determine the E/A ratio, isovolumetric relaxation time, and the E wave deceleration time, indicators of diastolic dysfunction explained further below.
  • the E/A ratio is the ratio of the peak velocity of blood movement from the left atrium to the left ventricle during two stages of atrial emptying and ventricular filling.
  • Blood is transferred from the left atrium to the left ventricle in two steps. In the first, the blood in the left atrium moves passively into the ventricle below when the mitral valve opens due to negative pressure created by the relaxing ventricle. The speed at which the blood moves during this initial action is called the “E,” for early, ventricular filling velocity. Later in time, the left atrium contracts to eject any remaining blood in the atrium, and the speed at which the blood moves at this stage is called the “A,” for atrium, ventricular filling velocity.
  • the E/A ratio is the ratio of the early (E) to late (A) ventricular filling velocities. In healthy heart, the E/A ratio is greater than 1. In Duchenne myopathy, however, the left ventricular wall becomes stiff, reducing ventricular relaxation and pull on atrial blood, thereby slowing the early (E) filling velocity and lowering the E/A ratio.
  • the isovolumetric relaxation time (IVRT) is the interval between the closure of the aortic valve to onset of ventricular filling by opening of the mitral valve, or the time until ventricular filling starts after relaxation begins.
  • LV left ventricular
  • DT could only be measured in older rats due to technical difficulties with an anesthesia protocol.
  • DT was significantly elevated in Dmd mdx rats treated with vehicle compared to WT controls, and there was a strong trend toward restoration to normal values after vector treatment at all doses tested ( FIG. 47 ).
  • ALT, AST, CK, and LDH are all enzymes released into the blood from damaged muscle cells, and are known to be elevated in human DMD patients.
  • AST levels were elevated in Dmd mdx rats treated with vehicle compared to WT rats, although due to variability in the data, significance existed only at the 6 month time point.
  • Dmd mdx rats were treated with vector, a trend towards lower AST levels (albeit with wide inter-individual viability) was observed in the 1 ⁇ 10 14 and 3 ⁇ 10 14 vg/kg dose groups at 3 months post-injection and in the 3 ⁇ 10 14 vg/kg dose group at 6 months post-injection. Again, due to variability in the data, these differences did not reach statistical significance.
  • FIG. 48A and FIG. 48B which reports data for the 3 month and 6 month post-injection time points, respectively.
  • ALT, LDH, and total CK levels all responded to age and vector treatment in similar ways.
  • ALT, LDH and total CK levels were all significantly elevated in Dmd mdx rats treated with vehicle compared to WT rats.
  • Treating the Dmd mdx rats with the mini-dystrophin vector resulted in a trend suggesting a dose responsive reduction in ALT, LDH and total CK levels relative to vehicle treated Dmd mdx rats, which in some cases achieved statistical significance.
  • Total CK levels within treatment arms were also compared on the day of injection and 3 and 6 months after. As shown in FIG. 52A and FIG. 52B , blood total CK levels were consistently low in WT rats administered vehicle, while CK levels declined in all Dmd mdx rats, including those treated only with vehicle and the lowest vector dose. In contrast, the reduction of CK levels after 3 and 6 months was much greater for Dmd mdx rats treated with the three highest doses of vector.
  • the humoral and cellular immune response in Dmd mdx rats treated with AAV9.hCK.Hopti-Dys3978.spA vector were measured before treatment and at 3 and 6 months post-injection and compared to negative and positive controls. Serum samples were obtained before injection of vehicle or vector, and at euthanasia 3 months post-injection. Splenocytes for analysis of T cell response were harvested at euthanasia at 3 and 6 months post-injection.
  • Humoral response to expression of the mini-dystrophin protein was assessed qualitatively by Western blot analysis of sera obtained from the test animals and diluted 1:500. Sera from all rats, whether WT or Dmd mdx , were negative for antibodies against mini-dystrophin protein when administered vehicle, or prior to receiving vector. By contrast most Dmd mdx rats treated with vector, even at the lowest dose of 1 ⁇ 10 13 vg/kg, produced IgG antibodies that bound mini-dystrophin in Western blots.
  • Presence of antibodies to the AAV9 vector capsid was tested by ELISA. Serum from WT and Dmd mdx rats treated with vehicle had no detectable IgG that reacted with AAV9. By contrast, all rats treated with vector, regardless of dose or whether sacrificed 3 or 6 months post-injection, produced anti-AAV9 IgG with a titer higher than 1:10240, the highest dilution tested. Neutralizing antibodies against AAV9 were also tested with a cell transduction inhibition assay using a recombinant AAV9 vector that expresses LacZ reporter gene detected using a luminometer. The titer was defined as the lowest dilution that inhibited transduction>50%.
  • Neutralizing antibodies against AAV9 were detected in the serum from all Dmd mdx rats that had received vector, regardless of dose or whether sacrificed 3 or 6 months post-injection, but not in the same animals prior to injection or WT and Dmd mdx rats that had received vehicle only. Titers ranged from 1:5000 to ⁇ 1:500000 with no clear dose effect.
  • Presence of a cellular immune response to vector was evaluated using an IFN ⁇ ELISpot assay on splenocytes isolated from vehicle treated WT and Dmd mdx rats, and Dmd mdx rats that had received vector.
  • T cell-response to the human mini-dystrophin protein expressed by the vector genome was tested using an overlapping peptide bank covering the whole sequence of opti-dys3978 protein (length of 15 amino acids, overlap of 10 amino acids, total of 263 peptides) and a rat specific IFN ⁇ -ELISpot BASIC kit (Mabtech).
  • Negative control consisted of unstimulated splenocytes and positive control consisted of cells stimulated with the mitogen concanavalin A.
  • IFN ⁇ secretion was quantified as the number of spot-forming cells (SFC) per 10 6 cells, and a positive response was defined as >50 SFC/10 6 cells or at least 3-fold the value obtained for the negative control.
  • SFC spot-forming cells
  • No specific T cell response against any peptide sequences derived from the mini-dystrophin protein was found in splenocytes obtained from any of the test animals, at either 3 months or 6 months post-injection, including from Dmd mdx rats treated at the highest vector dose of 3 ⁇ 10 14 vg/kg.
  • T cell response against the AAV9 capsid was also tested using the IFN ⁇ ELISpot assay screened against peptide sequences derived from AAV9 (15-mers overlapping by 10 amino acids divided into 3 pools). There was a positive IFN ⁇ response in between 16%-60% of vector treated Dmd mdx rats sacrificed at 3 months post-injection, and between 16%-66% of vector treated Dmd mdx rats sacrificed at 6 months post-injection, that was positively correlated with vector dose. By contrast, all WT and Dmd mdx rats treated with vehicle were negative for T cell response against AAV9 capsid.
  • Example 8 The studies described in Example 8, above, were initiated in young rats 7-9 weeks of age.
  • This example describes muscle function analysis of older Dmd mdx rats first treated with the AAV9.hCK.Hopti-Dys3978.spA vector when they were 4 months of age and 6 months of age, respectively.
  • the average life span of Sprague Dawley rats is 24-3 months.
  • the goal of these experiments was to determine if treatment with vector later in a Dmd mdx rat's life might be effective. Positive results would suggest that treating older human DMD patients, such as older children, adolescents, or even young adults, with vector might also improve their muscle function.
  • Dmd mdx rats at 4 and 6 months of age were separately treated with 1 ⁇ 10 14 vg/kg of AAV9.hCK.Hopti-Dys3978.spA vector.
  • rats were tested for grip strength as described previously. As with the younger rats, maximum forelimb grip strength and grip strength over multiple repeated trials with short latency periods between each trial were tested. The latter test was intended to measure muscle fatigue.
  • the symbol “*” indicates a statistically significant difference between vector treated Dmd mdx rats and WT rats treated with vehicle (p ⁇ 0.05); “ ” indicates a statistically significant difference between vector versus vehicle treated Dmd mdx rats (p ⁇ 0.01); and “ ⁇ ” and “ ⁇ ” indicate a statistically significant difference between vehicle treated Dmd mdx rats at the 4th and 5th grip tests, respectively, compared to the 1st grip test (at p ⁇ 0.01 and p ⁇ 0.001, respectively).
  • the symbols “*” and “**” indicate a statistically significant difference between vehicle treated Dmd mdx and WT rats (at p ⁇ 0.05 and p ⁇ 0.01, respectively); and “ ” indicates a statistically significant difference between vector versus vehicle treated Dmd mdx rats (p ⁇ 0.05).
  • the symbols “**” and “***” indicate a statistically significant difference between vector treated Dmd mdx rats and WT rats treated with vehicle (at p ⁇ 0.01 and p ⁇ 0.001, respectively); “ ” indicates a statistically significant difference between vector versus vehicle treated Dmd mdx rats (p ⁇ 0.05); and “ ⁇ ” indicates a statistically significant difference between vehicle treated Dmd mdx rats at the 5th grip test compared to the 1st grip test (p ⁇ 0.01).

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CN108660159A (zh) * 2018-04-12 2018-10-16 四川大学 重组蝙蝠腺相关病毒载体及其用途
WO2019204303A3 (en) * 2018-04-16 2019-11-28 The Trustees Of The University Of Pennsylvania Compositions and methods for treating duchenne muscular dystrophy
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