US20160272976A1 - Products and methods for treatment of familial amyotrophic lateral sclerosis - Google Patents

Products and methods for treatment of familial amyotrophic lateral sclerosis Download PDF

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US20160272976A1
US20160272976A1 US14/914,861 US201414914861A US2016272976A1 US 20160272976 A1 US20160272976 A1 US 20160272976A1 US 201414914861 A US201414914861 A US 201414914861A US 2016272976 A1 US2016272976 A1 US 2016272976A1
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sod1
seq
shrna
aav
aav9
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Brian K. Kaspar
Kevin Foust
Don W. Cleveland
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Ludwig Institute for Cancer Research Ltd
Research Institute at Nationwide Childrens Hospital
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Definitions

  • the present invention relates to RNA-based methods for inhibiting the expression of the superoxide dismutase 1 (SOD-1) gene.
  • Recombinant adeno-associated viruses of the invention deliver DNAs encoding RNAs that knock down the expression of SOD-1.
  • the methods have application in the treatment of amyotrophic lateral sclerosis (ALS).
  • ALS amyotrophic lateral sclerosis
  • ALS is an adult-onset, rapidly progressive and fatal neurodegenerative disease, characterized by selective degeneration of both upper and lower motor neurons.
  • ALS is responsible for one in every 2000 deaths, affecting nearly 5 out of 100,000 individuals.
  • ALS occurs when specific nerve cells in the brain and spinal cord that control voluntary movement degenerate.
  • the loss of these motor neurons leads to progressive atrophy of skeletal muscles, which results in loss of muscular function resulting in paralysis, speech deficits, and death due to respiratory failure.
  • SOD1 superoxide dismutase 1
  • mutant SOD1 protein expression within motor neurons themselves contributes to disease onset and early disease progression 6 , as does mutant synthesis in NG2 + cells' that are precursors to oligodendrocytes.
  • mutant SOD1 protein expression in microglia and astrocytes significantly drives rapid disease progression 6,8 , findings which have lead to the conclusion that ALS pathophysiology is non-cell autonomous 3 .
  • astrocytes have been found to be toxic to motor neurons in multiple in vitro models where mutant forms of human SOD1 were overexpressed 9-11 .
  • a recent study derived astrocytes from post-mortem spinal cords of ALS patients with or without SOD1 mutations. In all cases, astrocytes from sporadic ALS patients were as toxic to motor neurons as astrocytes carrying genetic mutations in SOD1 12 . Even more strikingly, reduction of SOD1 in astrocytes derived from both sporadic and familial ALS patients decreased astrocyte-derived toxicity that is selective for motor, but not GABA, neurons.
  • riluzole is the only drug currently approved by the FDA as a therapy for ALS, providing a modest survival benefit 21 .
  • attempts at improving therapy by reducing synthesis of SOD1 have been the focus of multiple therapeutic development approaches.
  • Antisense oligonucleotides and viral delivered RNA interference (RNAi) were tested in rat 22 and mouse models 23-25 that develop fatal paralysis from overexpressing human SOD1 G93A .
  • Antisense oligonucleotides infused at disease onset produced SOD1 reduction and a modest slowing of disease progression 22 .
  • Adeno-associated virus (AAV) vectors have been used in a number of recent clinical trials for treatment of neurological disorders [Kaplitt et al., Lancet 369: 2097-2105 (2007); Marks et al., Lancet Neurol 7: 400-408 (2008); Worgall et al., Hum Gene Ther (2008)].
  • AAV is a replication-deficient parvovirus, the single-stranded DNA genome of which is about 4.7 kb in length including 145 nucleotide inverted terminal repeat (ITRs).
  • ITRs nucleotide inverted terminal repeat
  • AAV2 AAV serotype 2
  • Cis-acting sequences directing viral DNA replication (rep), encapsidation/packaging and host cell chromosome integration are contained within the ITRs.
  • AAV promoters Three AAV promoters (named p5, p19, and p40 for their relative map locations) drive the expression of the two AAV internal open reading frames encoding rep and cap genes.
  • the two rep promoters (p5 and p19), coupled with the differential splicing of the single AAV intron (at nucleotides 2107 and 2227), result in the production of four rep proteins (rep 78, rep 68, rep 52, and rep 40) from the rep gene.
  • Rep proteins possess multiple enzymatic properties that are ultimately responsible for replicating the viral genome.
  • the cap gene is expressed from the p40 promoter and it encodes the three capsid proteins VP1, VP2, and VP3.
  • AAV possesses unique features that make it attractive as a vector for delivering foreign DNA to cells, for example, in gene therapy.
  • AAV infection of cells in culture is noncytopathic, and natural infection of humans and other animals is silent and asymptomatic.
  • AAV infects many mammalian cells allowing the possibility of targeting many different tissues in vivo.
  • AAV transduces slowly dividing and non-dividing cells, and can persist essentially for the lifetime of those cells as a transcriptionally active nuclear episome (extrachromosomal element).
  • the AAV proviral genome is infectious as cloned DNA in plasmids which makes construction of recombinant genomes feasible.
  • the signals directing AAV replication, genome encapsidation and integration are contained within the ITRs of the AAV genome, some or all of the internal approximately 4.3 kb of the genome (encoding replication and structural capsid proteins, rep-cap) may be replaced with foreign DNA such as a gene cassette containing a promoter, a DNA of interest and a polyadenylation signal.
  • the rep and cap proteins may be provided in trans.
  • Another significant feature of AAV is that it is an extremely stable and hearty virus. It easily withstands the conditions used to inactivate adenovirus (56° to 65° C. for several hours), making cold preservation of AAV less critical. AAV may even be lyophilized. Finally, AAV-infected cells are not resistant to superinfection.
  • serotypes of AAV exist and offer varied tissue tropism.
  • Known serotypes include, for example, AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11 and AAVrh74.
  • Advances in the delivery of AAV6 and AAV8 have made possible the transduction by these serotypes of skeletal and cardiac muscle following simple systemic intravenous or intraperitoneal injections. See Pacak et al., Circ. Res., 99(4): 3-9 (1006) and Wang et al., Nature Biotech., 23(3): 321-8 (2005).
  • the use of AAV to target cell types within the central nervous system has involved surgical intraparenchymal injection.
  • the present invention provides products and methods useful for reducing mutant SOD1 protein levels in subjects in need thereof.
  • the invention provides AAV-mediated delivery of RNAs including, but not limited to short hairpin RNAs, to reduce synthesis of ALS-causing human SOD1 mutants in subjects in need thereof.
  • Recombinant AAV (rAAV) contemplated by the invention include, but are not limited to, rAAV9, rAAV2 and rAAVrh74.
  • Delivery routes contemplated by the invention include, but are not limited to, systemic delivery and intrathecal delivery. Use of the methods and products of the invention is indicated, for example, in treating ALS.
  • the invention provides rAAV genomes comprising one or more AAV ITRs flanking a polynucleotide encoding one or more RNAs (including, but not limited to, small hairpin RNAs, antisense RNAs and/or microRNAs) that target mutant SOD1 polynucleotides.
  • RNAs including, but not limited to, small hairpin RNAs, antisense RNAs and/or microRNAs
  • shRNAs small hairpin RNAs
  • the shRNA-encoding polynucleotide is operatively linked to transcriptional control DNA, specifically promoter DNA that is functional in target cells.
  • Commercial providers such as Ambion Inc. (Austin, Tex.), Darmacon Inc.
  • the rAAV genome comprises a DNA encoding a SOD1 shRNA such as:
  • the rAAV genomes of the invention lack AAV rep and cap DNA.
  • AAV DNA in the rAAV genomes may be from any AAV serotype for which a recombinant virus can be derived including, but not limited to, AAV serotypes AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV-7, AAV-8, AAV-9, AAV-10 and AAV-11.
  • the nucleotide sequences of the genomes of the AAV serotypes are known in the art. For example, the complete genome of AAV-1 is provided in GenBank Accession No. NC_002077; the complete genome of AAV-2 is provided in GenBank Accession No.
  • AAV-9 genome is provided in Gao et al., J.
  • the AAVrh74 genome is provided in International Publication No. WO 2013/078316.
  • the invention provides DNA plasmids comprising rAAV genomes of the invention.
  • the DNA plasmids are transferred to cells permissible for infection with a helper virus of AAV (e.g., adenovirus, E1-deleted adenovirus or herpesvirus) for assembly of the rAAV genome into infectious viral particles.
  • helper virus of AAV e.g., adenovirus, E1-deleted adenovirus or herpesvirus
  • rAAV genome a rAAV genome
  • AAV rep and cap genes separate from (i.e., not in) the rAAV genome
  • helper virus functions The AAV rep and cap genes may be from any AAV serotype for which recombinant virus can be derived and may be from a different AAV serotype than the rAAV genome ITRs, including, but not limited to, AAV serotypes AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV-7, AAV-8, AAV-9, AAV-10 and AAV-11.
  • AAV capsid proteins may be modified to enhance delivery of the recombinant vector. Modifications to capsid proteins are generally known in the art. See, for example, US 20050053922 and US 20090202490, the disclosures of which are incorporated by reference herein in their entirety.
  • a method of generating a packaging cell is to create a cell line that stably expresses all the necessary components for AAV particle production.
  • a plasmid (or multiple plasmids) comprising a rAAV genome lacking AAV rep and cap genes, AAV rep and cap genes separate from the rAAV genome, and a selectable marker, such as a neomycin resistance gene, are integrated into the genome of a cell.
  • AAV genomes have been introduced into bacterial plasmids by procedures such as GC tailing (Samulski et al., 1982, Proc. Natl. Acad. S6.
  • the packaging cell line is then infected with a helper virus such as adenovirus.
  • a helper virus such as adenovirus.
  • packaging cells that produce infectious rAAV.
  • packaging cells may be stably transformed cancer cells such as HeLa cells, 293 cells and PerC.6 cells (a cognate 293 line).
  • packaging cells are cells that are not transformed cancer cells such as low passage 293 cells (human fetal kidney cells transformed with E1 of adenovirus), MRC-5 cells (human fetal fibroblasts), WI-38 cells (human fetal fibroblasts), Vero cells (monkey kidney cells) and FRhL-2 cells (rhesus fetal lung cells).
  • the invention provides rAAV (i.e., infectious encapsidated rAAV particles) comprising a rAAV genome of the invention.
  • the rAAV genome is a self-complementary genome.
  • the genomes of the rAAV lack AAV rep and cap DNA, that is, there is no AAV rep or cap DNA between the ITRs of the genomes.
  • Embodiments include, but are not limited to, the exemplary rAAV including a genome encoding the SOD1 shRNA named “AAV-SOD1-shRNA.”
  • a sequence including the AAV-SOD1-shRNA genome is set out below as an inverted sequence from a plasmid used in production.
  • the rAAV of the invention may be purified by methods standard in the art such as by column chromatography or cesium chloride gradients.
  • Methods for purifying rAAV vectors from helper virus are known in the art and include methods disclosed in, for example, Clark et al., Hum. Gene Ther., 10(6): 1031-1039 (1999); Schenpp and Clark, Methods Mol. Med., 69: 427-443 (2002); U.S. Pat. No. 6,566,118 and WO 98/09657.
  • compositions comprising rAAV of the present invention.
  • Compositions of the invention comprise rAAV in a pharmaceutically acceptable carrier.
  • the compositions may also comprise other ingredients such as diluents and adjuvants.
  • Acceptable carriers, diluents and adjuvants are nontoxic to recipients and are preferably inert at the dosages and concentrations employed, and include buffers such as phosphate, citrate, or other organic acids; antioxidants such as ascorbic acid; low molecular weight polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming
  • Titers of rAAV to be administered in methods of the invention will vary depending, for example, on the particular rAAV, the mode of administration, the treatment goal, the individual, and the cell type(s) being targeted, and may be determined by methods standard in the art. Titers of rAAV may range from about about 1 ⁇ 10 2 , about 1 ⁇ 10 3 , about 1 ⁇ 10 4 , about 1 ⁇ 10 5 , about 1 ⁇ 10 6 , about 1 ⁇ 10 7 , about 1 ⁇ 10 8 , about 1 ⁇ 10 9 , about 1 ⁇ 10 10 , about 1 ⁇ 10 11 , about 1 ⁇ 10 12 , about 1 ⁇ 10 13 to about 1 ⁇ 10 14 or more DNase resistant particles (DRP) per ml.
  • DNase resistant particles DNase resistant particles
  • Dosages may also be expressed in units of viral genomes (vg). Dosages may also vary based on the timing of the administration to a human. These dosages of rAAV may range from about 1 ⁇ 10 4 , about 1 ⁇ 10 5 , about 1 ⁇ 10 6 , about 1 ⁇ 10 7 , about 1 ⁇ 10 8 , about 1 ⁇ 10 9 , about 1 ⁇ 10 10 , about 1 ⁇ 10 11 , about 1 ⁇ 10 12 , about 1 ⁇ 10 13 , about 1 ⁇ 10 14 , about 1 ⁇ 10 15 , about 1 ⁇ 10 16 or more viral genomes per kilogram body weight in an adult.
  • vg viral genomes
  • the dosages of rAAV may range from about about 1 ⁇ 10 4 , about 3 ⁇ 10 4 , about 1 ⁇ 10 5 , about 3 ⁇ 10 5 , about 1 ⁇ 10 6 , about 3 ⁇ 10 6 , about 1 ⁇ 10 7 , about 3 ⁇ 10, about 1 ⁇ 10 8 , about 3 ⁇ 10 8 , about 1 ⁇ 10 9 , about 3 ⁇ 10 9 , about 1 ⁇ 10 10 , about 3 ⁇ 10 10 , about 1 ⁇ 10 11 , about 3 ⁇ 10 11 , about 1 ⁇ 10 12 , about 3 ⁇ 10 12 , about 1 ⁇ 10 13 , about 3 ⁇ 10 13 , about 1 ⁇ 10 14 , about 3 ⁇ 10 14 , about 1 ⁇ 10 15 , about 3 ⁇ 10 15 , about 1 ⁇ 10 16 , about 3 ⁇ 10 16 or more viral genomes per kilogram body weight.
  • compositions comprising rAAV of the present invention.
  • Compositions of the invention comprise rAAV in a pharmaceutically acceptable carrier.
  • the compositions may also comprise other ingredients such as diluents and adjuvants.
  • Acceptable carriers, diluents and adjuvants are nontoxic to recipients and are preferably inert at the dosages and concentrations employed, and include buffers such as phosphate, citrate, or other organic acids; antioxidants such as ascorbic acid; low molecular weight polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming
  • the invention provides methods of transducing a target cell with a rAAV of the invention, in vivo or in vitro.
  • the in vivo methods comprise the step of administering an effective dose, or effective multiple doses, of a composition comprising a rAAV of the invention to a subject, a subject (including a human being), in need thereof. If the dose is administered prior to onset/development of a disorder/disease, the administration is prophylactic. If the dose is administered after the onset/development of a disorder/disease, the administration is therapeutic.
  • an effective dose is a dose that alleviates (eliminates or reduces) at least one symptom associated with the disorder/disease state being treated, that slows or prevents progression to a disorder/disease state, that slows or prevents progression of a disorder/disease state, that diminishes the extent of disease, that results in remission (partial or total) of disease, and/or that prolongs survival.
  • a disease contemplated for treatment with methods of the invention is ALS.
  • “Treatment” thus alleviates (eliminates or reduces) at least one symptom associated with the disorder/disease state being treated (for example, weight loss is eliminated or reduced by at least 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100% or greater), that slows or prevents progression to (onset/development) of a disorder/disease state, that slows or prevents progression of a disorder/disease state, that diminishes the extent of disease, that results in remission (partial or total) of disease, and/or that prolongs survival.
  • a symptom associated with the disorder/disease state being treated for example, weight loss is eliminated or reduced by at least 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%
  • survival is prolonged by at least 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100% or greater.
  • Combination therapies are also contemplated by the invention.
  • Combination as used herein includes both simultaneous treatment or sequential treatments.
  • Combinations of methods of the invention with standard medical treatments e.g., riluzole are specifically contemplated, as are combinations with novel therapies.
  • Administration of an effective dose of the compositions may be by routes standard in the art including, but not limited to, systemic intramuscular, parenteral, intravenous, oral, buccal, nasal, pulmonary, intracranial, intrathecal, intraosseous, intraocular, rectal, or vaginal.
  • Route(s) of administration and serotype(s) of AAV components of the rAAV (in particular, the AAV ITRs and capsid protein) of the invention may be chosen and/or matched by those skilled in the art taking into account the infection and/or disease state being treated and the target cells/tissue(s) that are to express the SOD1 shRNAs.
  • the route of administration is systemic.
  • the route of administration is intrathecal.
  • the route of administration is introcerebroventricular.
  • the route of administration is cisterna magna.
  • the route of administration is by lumbar puncture.
  • Transduction of cells with rAAV of the invention results in sustained expression of SOD1 shRNAs.
  • the present invention thus provides methods of administering/delivering rAAV which express SOD1 shRNA to a subject, preferably a human being.
  • the term “transduction” is used to refer to the administration/delivery of SOD1 shRNAs to a recipient cell either in vivo or in vitro, via a replication-deficient rAAV of the invention resulting in expression of a SOD1 shRNA by the recipient cell.
  • the invention provides methods of administering an effective dose (or doses, administered essentially simultaneously or doses given at intervals) of rAAV that encode SOD1 shRNAs to a subject in need thereof.
  • the invention provides methods of delivering a polynucleotide encoding an shRNA of the invention across the BBB comprising systemically administering a rAAV with a genome including the polynucleotide to a subject.
  • the rAAV genome is a self complementary genome.
  • the rAAV genome is a single-stranded genome.
  • the rAAV is a rAAV9.
  • the rAAV is a rAAV2.
  • the rAAV is a rAAVrh74.
  • the methods systemically deliver polynucleotides across the BBB to the central and/or peripheral nervous system. Accordingly, a method is provided of delivering a polynucleotide to the central nervous system comprising systemically administering a rAAV with a self-complementary genome including the genome to a subject. In some embodiments, the polynucleotide is delivered to brain. In some embodiments, the polynucleotide is delivered to the spinal cord. Also provided is a method of delivering a polynucleotide to the peripheral nervous system comprising systemically administering a rAAV with a self-complementary genome including the polynucleotide to a subject is provided.
  • the polynucleotide is delivered to a lower motor neuron.
  • the rAAV genome is a self complementary genome.
  • the rAAV genome is a single-stranded genome.
  • the rAAV is a rAAV9.
  • the rAAV is a rAAV2.
  • the rAAV is a rAAVrh74.
  • the invention provides methods of delivering a polynucleotide to the central nervous system of a subject in need thereof comprising intrathecal delivery of rAAV with a genome including the polynucleotide.
  • the rAAV genome is a self complementary genome.
  • the rAAV genome is a single-stranded genome.
  • the rAAV is a rAAV9.
  • the rAAV is a rAAV2.
  • the rAAV is a rAAVrh74.
  • a non-ionic, low-osmolar contrast agent is also delivered to the subject, for example, iobitridol, iohexol, iomeprol, iopamidol, iopentol, iopromide, ioversol or ioxilan.
  • Embodiments of the invention employ rAAV to deliver polynucleotides to nerve, glial cells and endothelial cells.
  • the nerve cell is a lower motor neuron and/or an upper motor neuron.
  • the glial cell is a microglial cell, an oligodendrocyte and/or an astrocyte.
  • the rAAV is used to deliver a polynucleotide to a Schwann cell.
  • FIG. 1 AAV9 transduction pattern and persistence in SOD1 G93A mice.
  • Spinal cords were examined for GFP, ChAT (motor neuron marker) and GFAP (astrocyte marker) expression.
  • Temporal vein injection of AAV9-CB-GFP at P1 resulted in efficient transduction of motor neurons and glia in SOD1 G93A mice (a,f,k,p).
  • Tail vein injection at P21 (b,g,l,q) predominantly targeted astrocytes with few GFP positive motor neurons.
  • AAV9-CB-GFP was intravenously injected at P1 and P21 in SOD1 G93A animals that were sacrificed at end stage ( ⁇ P130).
  • Immunofluorescence analysis of lumbar ventral horn (c,d,h,i,m,n,r,s) demonstrated that GFP expression was maintained in astrocytes throughout the disease course.
  • SOD1 mediated inflammation and damage would affect AAV9 transduction, we intravenously injected SOD1 G93A mice at P85 and harvested their spinal cords at endstage. There was no difference observed in the transduction pattern of SOD1 G93A mice treated at P21 or P85.
  • Insets in (r-t) show co-localization between GFP and GFAP signal.
  • AAV adeno-associated virus; P1, postnatal day 1; P21, postnatal day 21; P85, postnatal day 85; GFP, green fluorescent protein; ChAT, choline acetyltransferase; GFAP, glial fibrillary acidic protein.
  • FIG. 2 shRNA constructs show efficient reduction of human SOD1 protein in vitro and in vivo.
  • shRNA 130 was packaged into AAV9 and injected into SOD1 G93A mice at either P1 or P21.
  • FIG. 3 Intravenous delivery of AAV9-SOD1-shRNA improves survival and motor performance in SOD1 G93A mice.
  • FIG. 4 Intravenous injection of AAV9-SOD1-shRNA reduces mutant protein in spinal cords of SOD1 G93A mice.
  • (a-d) Images of lumbar spinal cord sections from uninjected (a), P1 injected (b), P21 injected (c) and P85 injected (d) mice were captured with identical microscope settings to qualitatively show SOD1 levels at end stage. SOD1 levels inversely correlate with survival.
  • FIG. 5 AAV9-SOD1-shRNA improves survival and motor performance in SOD1 G37R mice treated after disease onset.
  • FIG. 6 Intravenous injection of AAV9 in adult SOD1 G37R mice targets astrocytes and motor neurons within the spinal cord.
  • a-h Immunofluorescence analysis revealed neuronal as well as glial transduction in both AAV9-CB-GFP (a-d) and AAV9-SOD1-shRNA treated (e-h) mice.
  • GFP green fluorescent protein
  • ChAT choline acetyltransferase
  • GFAP glial fibrillary acidic protein
  • SOD1 superoxide dismutase 1.
  • FIG. 7 Intrathecal infusion of AAV9-SOD1-shRNA in non-human primates leads to efficient reduction in SOD1 levels.
  • a myelogram shortly after intrathecal infusion of AAV9-SOD1-shRNA mixed with contrast shows proper delivery into the subarachnoid space of a cynomolgus macaque . Arrows show diffusion of the contrast agent along the entire spinal cord.
  • SOD1 Superoxide dismutase 1.
  • FIG. 8 Lumbar intrathecal infusion of AAV9-SOD1-shRNA leads to efficient transduction of motor neurons and non-neuronal cells in the cervical, thoracic and lumbar cord resulting in reduction of SOD1.
  • GFP+/Chat+ cell counts show a caudal to rostral gradient of motor neuron transduction ranging from 85% of transduced cells in the lumbar region to more than 50% in the cervical region.
  • SOD1 mRNA levels in cervical, thoracic and lumbar cord section homogenates analyzed by qRT-PCR show significant reduction in SOD1 transcript, consistently with motor neuron transduction.
  • SOD1 levels were normalized to ⁇ -actin and AAV9-SOD1-shRNA injected animals were compared to an AAV9-CB-GFP injected control.
  • FIG. 9 Design of a clinical SOD1 shRNA construct.
  • Original AAV SOD1 shRNA construct contains shRNA sequence against human SOD1 under H1 promoter followed by the expression cassette for GFP which includes CMV enhancer, CBA promoter, modified SV40 intron, and GFP transgene sequence followed by bGH PolyA terminator.
  • SOD1 shRNA expression cassette and GFP expression cassette are flanked by AAV2 ITRs which ensures the packaging of the complete flanked sequence in AAV9 capsid.
  • the GFP expression cassette is replaced by a stuffer element that contains tandem, noncoding sequences from FDA approved DNA vaccines.
  • ITR inverted terminal repeats
  • shRNA small hairpin RNA
  • SOD1 superoxide dismutase 1
  • CMV cytomegalo virus enhancer
  • CBA Chicken ⁇ -actin promoter
  • GFP green fluorescent protein
  • bGH pA bovine growth hormone poly A terminator.
  • FIG. 10 Schematic of clinical SOD1 shRNA construct. Different restriction sites are placed in the clinical SOD1 shRNA construct that allow the cloning of multiple shRNA expression cassettes while maintaining the total distance between the two ITRs.
  • FIG. 11 In vitro transfection of clinical SOD1 shRNA construct efficiently reduces human SOD1 protein in HEK293 cells. Representative microscopic fields showing bright-field images of non-transfected control (a), AAV SOD1 shRNA transfected (b) and shuttle vector pJet SOD1 shRNA transfected (c,d) HEK 293 cells, 72 hrs post transfection. Corresponding fluorescence images reveal the lack of GFP fluorescence from pJet SOD1 shRNA transfected HEK 293 cells (g,h) as compared to AAV SOD1 shRNA transfected cells (f).
  • FIG. 12 Schematic of cloning strategy for clinical AAV SOD1 shRNA vector.
  • Clinical SOD1 shRNA construct was cloned into AAV CB MCS vector using Kpn1/SPh1 sites.
  • Kpn1/SPh1 double digest of AAV CB MCS plasmid results in the release of the complete transgene expression cassette from this vector which is further replaced with clinical SOD1 shRNA construct carrying SOD1 shRNA expression cassette and stuffer sequence.
  • FIG. 13 Clinical AAV SOD1 shRNA efficiently reduces human SOD1 levels in vitro.
  • HEK293 cells were transfected with clinical AAV SOD1 shRNA plasmid by Calcium phosphate method. Representative microscopic fields showing brightfield images of non-transfected control, AAV SOD1 shRNA and Clinical AAV SOD1 shRNA transfected cells respectively, 72 hrs post-transfection (a-c). Successful removal of GFP from clinical AAV SOD1 shRNA was confirmed by lack of GFP expression in Clinical AAV SOD1 shRNA transfected cells (f,g).
  • FIGS 1 AAV9-shRNA-SOD1 administration is well tolerated in WT mice.
  • Female and male WT animals were injected with AAV9-SOD1-shRNA at P1 or P21 and monitored up to 6 months of age.
  • (a,b) Both male and female treated mice showed steady increase in body mass as compared to control animals.
  • (c,d) Rotarod performance and (e,f) hind limb grip strength were not affected by P1 or P21 treatment in both groups as compared to respective controls.
  • n 5 per group.
  • WT wild type; P1, postnatal day 1; P21, postnatal day 21.
  • FIGS 2 Hematology and Serum Chemistry of AAV9-SOD1-shRNA treated WT animals.
  • a-m Blood was collected from P1 (green) or P21 (red) treated and control (gray) WT animals at 150 days of age for hematology studies. No significant differences were observed between treated and control animals.
  • FIG. 1 u a diagram illustrating the percent astrocyte transduction achieved in these mice.
  • FIG. 4 Intravenous injection of AAV9-SOD1-shRNA efficiently reduces levels of mutant SOD1 protein in spinal cords of SOD1 G37R mice.
  • AAV9-CB-GFP or AAV9-SOD1-shRNA was injected in SOD1 G37R mice and spinal cords were harvested at end stage and analyzed by western blot for human SOD1 protein levels.
  • FIG. 5 shRNA 130 efficiently reduces the levels of monkey SOD1 in vitro.
  • Transduction efficiency was high in SOD1 G93A astrocytes with GFP expressed in 34 ⁇ 2% and 54 ⁇ 3%, respectively, of P1 and P21 injected spinal grey matter astrocytes (defined by immunoreactivity for GFAP). This efficiency was similar to our previous report of 64 ⁇ 1% in P21 injected wild type animals 18 . Motor neurons were a prominent cell type transduced at all levels of the spinal cords of P1 injected SOD1 G93A animals (62 ⁇ 1%), compared with significantly lower targeting to motor neurons in P21 injected animals (8 ⁇ 1%).
  • SOD1 mutant mediated damage including astrocytic and microglial activation and early changes in the blood brain barrier develop during disease in mice in SOD1 mutant mice 20
  • this damage affected AAV9 transduction.
  • Analysis of the spinal cords revealed that the transduction pattern seen in P85 animals was similar to P21 treated animals with astrocytes as the predominant cell type transduced at all levels (51 ⁇ 6% GFP+/GFAP+ cells in lumbar grey matter).
  • shRNA constructs targeting human SOD1 were generated and obtained from the Life Technologies design tool.
  • the constructs that had a minimum of four base mismatches compared to the mouse mRNA sequence correspond to record number CCDS33536.1 in the NCBI CCDS database.
  • These constructs were cloned in pSilencer 3.1 (Genscript) under the human H1 promoter and tested in vitro.
  • shRNA 130 along with H1 promoter was further cloned into an AAV vector along with a reporter GFP under Chicken Beta-Actin promoter to identify the transduced cells. Human 293 cells were transfected with each cassette.
  • the HEK-293 cells were maintained in IMDM medium containing 10% FBS, 1% L-glutamine and 1% penicillin/streptomycin. Upon reaching ⁇ 60% confluence, cells were transfected with pSilencer 3.1 containing the shRNAs being tested. Protein lysates were prepared 72 hours post transfection and analyzed for SOD1 levels by western blot. All four sequences reduced SOD1 protein levels by >50% ( FIGS. 2 b,c ).
  • shRNA130 was selected for further experiments because it produced the most consistent knockdown across three separate transfection experiments. It was cloned into a self-complementary AAV9 vector that also contained a GFP gene whose expression would identify transduced cells (referred to as AAV9-SOD1-shRNA). Self-complementary AAV9-SOD1-shRNA was produced by transient transfection procedures using a double-stranded AAV2-ITR-based CB-GFP vector, with a plasmid encoding Rep2Cap9 sequence as previously described along with an adenoviral helper plasmid pHelper (Stratagene, Santa Clara, Calif.) in 293 cells 18 .
  • AAV9-SOD1-shRNA self-complementary AAV9 vector that also contained a GFP gene whose expression would identify transduced cells
  • AAV9-SOD1-shRNA For neonatal mouse injections, postnatal day 1-2 SOD1 G93A pups were utilized. Total volume of 50 ⁇ l containing 5 ⁇ 10 11 DNAse resistant viral particles of AAV9-SOD1-shRNA (Virapur LLC, San Diego, Calif.) was injected via temporal vein as previously described 18 . A correct injection was verified by noting blanching of the vein. After the injection, pups were returned to their cage.
  • AAV9-SOD1-shRNA is Safe and Well Tolerated in Wild Type Mice
  • animals were placed in a restraint that positioned the mouse tail in a lighted, heated groove. The tail was swabbed with alcohol then injected intravenously with AAV9-SOD1-shRNA.
  • loxSOD1 G37R ALS mice carrying a human mutant SOD1 G37R transgene flanked by lox p sites under its endogenous promoter, were maintained in as previously described 37 .
  • FIG. 6 Histological examination of end-stage SOD1 G37R treated animals revealed similar levels of intraspinal cell transduction in animals treated with AAV9-SOD1-shRNA or AAV9-GFP ( FIG. 6 ). GFP expression was predominantly observed within motor neurons and astrocytes of both groups, and SOD1 expression was detectably decreased only in animals that received AAV9-SOD1-shRNA ( FIGS. 6 k,o ). Immunoblotting of whole spinal cord extracts from end stage SOD1 G37R mice revealed an 80% reduction in hSOD1 protein levels in AAV9-SOD1-shRNA treated animals compared to controls ( Figure S4 ).
  • AAV9 was injected intrathecally via lumbar puncture. This method was chosen over systemic delivery to decrease the amount of virus required and to minimize any effects from reduction of SOD1 in peripheral tissues.
  • One year old cynomolgus macaques ( Macaca fascicularis ) with average body weight of 2 kg were used for this study at the Mannheimer Foundation. Regular monitoring of overall health and body weight was performed prior and after the injections to assess the welfare of the animals.
  • cDNA was prepared using RT 2 First strand synthesis kit (SABiosciences). SOD1 transcript levels were analyzed by qRT-PCR which revealed that the monkey SOD1 mRNA was reduced by ⁇ 75% in 130 shRNA transduced cells compared to mock transduced control cells ( Figure S 5 ).
  • the AAV9-SOD1-shRNA virus (1 ⁇ 10 13 vg/kg) was infused along with contrast agent via lumbar puncture into the subarachnoid space of three male cynomolgus macaques and one control subject was injected with AAV9-CB-GFP (1 ⁇ 10 13 vg/kg) ( FIG. 7 a ).
  • Each intrathecal injection was performed by lumbar puncture into the subarachnoid space of the lumbar thecal sac.
  • AAV9 was resuspended with omnipaque (iohexol), an iodinated compound routinely used in the clinical setting.
  • Iohexol is used to validate successful subarachnoid space cannulation and was administered at a dose of 100 mg/Kg.
  • the subject was placed in the lateral decubitus position and the posterior midline injection site at ⁇ L4/5 level identified (below the conus of the spinal cord). Under sterile conditions, a spinal needle with stylet was inserted and subarachnoid cannulation was confirmed with the flow of clear CSF from the needle.
  • 0.8 ml of CSF was drained, immediately followed by injection with a mixture containing 0.7 mL iohexol (300 mg/ml formulation) mixed with 2.1 mL of virus (2.8 ml total).
  • FIGS. 8 a - c Motor neuron counts revealed a caudal to rostral gradient in cell transduction, with the cervical region showing more than 50% of GFP/Chat+ motor neurons, increasing to 65% in the thoracic region and reaching a remarkable 80% in the lumbar region ( FIG. 8 d ).
  • qRT-PCR for SOD1 was performed on whole section homogenates from cervical, thoracic and lumbar cord segments.
  • mice Control and treated SOD1 G93A mice were sacrificed at either 21 days post injection or at endstage for immunohistochemical analysis. Animals were anesthetized with xylazene/ketamine cocktail, transcardially perfused with 0.9% saline, followed by 4% paraformaldehyde. Spinal cords were harvested, cut into blocks of tissue 5-6 mm in length, and then cut into 40 ⁇ m thick transverse sections on a vibratome (Leica, Bannockburn, Ill.). Serial sections were kept in a 96-well plate that contained 4% paraformaldehyde and were stored at 4° C.
  • End stage loxSOD1 G37R mice were anesthetized using isoflurane and perfused with 4% paraformaldehyde.
  • Spinal cord segments including cervical, thoracic and lumbar segments were dissected.
  • spinal cords were frozen in isopentane at ⁇ 65° C., and serial 30 ⁇ m coronal sections were collected free floating using sliding microtome.
  • mice were sacrificed at 180 days of age. Animals were anesthetized using xylazene/ketamine cocktail and perfused with 0.9% saline. Different tissues were removed and stored in 10% buffered formalin. These tissues were further processed, blocked and mounted for hematoxilin & eosin staining by the Nationalwide Children's Hospital Morphology Core.
  • Cynomolgus monkeys injected with virus were euthanized 2 weeks post injection. Animals were anesthetized with sodium pentobarbital at the dose of 80-100 mg/kg intravenously and perfused with saline solution. Brain and spinal cord dissection were performed immediately and tissues were processed either for nucleic acid isolation (snap frozen) or post-fixed in 4% paraformaldehyde and subsequently cryoprotected with 30% sucrose and frozen in isopentane at ⁇ 65° C. 12 ⁇ m coronal sections were collected from lumbar cord using a cryostat for free floating immunostaining.
  • Primary antibodies used were as follows: rabbit anti-GFP (1:400, Invitrogen, Carlsbad, Calif.), rabbit anti-SOD1 (1:200, Cell signaling, Danvers, Mass.), goat anti-ChAT (1:50 Millipore, Billerica, Mass.), mouse anti-GFAP (1:200, Millipore, Billerica, Mass.), chicken anti GFAP (1:400, Abcam, Cambridge, Mass.), and rabbit anti-Ibal (1:400, Wako, Richmond Va.). Tissues were incubated in primary antibody at 4° C. for 48-72 hours then washed three times with TBS.
  • tissue were incubated for 2 hours at room temperature in the appropriate FITC-, Cy3-, or Cy5-conjugated secondary antibodies (1:200 Jackson Immunoresearch, Westgrove, Pa.) and DAPI (1:1000, Invitrogen, Carlsbad, Calif.). Tissues were then washed three times with TBS, mounted onto slides then coverslipped with PVA-DABCO. All images were captured on a Zeiss-laser-scanning confocal microscope.
  • monkey spinal cord sections were washed three times in TBS, blocked for 2 h at RT in 10% donkey serum and 1% Triton X-100. Sections were then incubated overnight at 4° C. with rabbit anti-GFP primary antibody (1:1000 Invitrogen, Carlsbad, Calif.) diluted in blocking buffer. The following day, tissues were washed with TBS 3 times, incubated with biotinylated secondary antibody anti-rabbit (1:200 Jackson Immunoresearch, Westgrove, Pa.) in blocking buffer for 30 min at RT, washed 3 times in TBS and incubated for 30 min at RT with ABC (Vector, Burlingame, Calif.).
  • Sections were then washed for 3 times in TBS and incubated for 2 min with DAB solution at RT and washed with distilled water. These were then mounted onto slides and covered with coverslips in mounting medium. All images were captured with the Zeiss Axioscope.
  • Spinal cords were harvested from P1, P21 injected and control SOD1 G93A mice 21 days post injection and from treated and control monkeys 2 weeks post injection of AAV9-SOD1-shRNA.
  • Spinal cords were homogenized and protein lysates were prepared using T-Per (Pierce) with protease inhibitor cocktail. Samples were resolved on SDS-PAGE according to manufacturer's instructions.
  • RNA from laser captured cells or whole spinal cord sections from the cervical, thoracic and lumbar segments was isolated using the RNaqueous Micro Kit (Ambion, Grand Island, N.Y.) according to manufacturer's instructions. RNA was then reverse-transcribed into cDNA using the RT 2 HT First Strand Kit (SABiosciences, Valencia, Calif.). 12.5 ng RNA were used in each Q-PCR reaction using SyBR Green (Invitrogen, Carlsbad, Calif.) to establish the relative quantity of endogenous monkey SOD1 transcript in animals who had received the AAV9-SOD1-shRNA compared to animals who had received only AAV9-GFP. Each sample was run in triplicate and relative concentration calculated using the ddCt values normalized to endogenous actin transcript.
  • SOD1 G93A mice were monitored for changes in body mass twice a week.
  • loxSOD1 G37R mice were weighed on a weekly basis. Motor coordination was recorded using a rotarod instrument (Columbus Instruments, Columbus, Ohio). Each weekly session consisted of three trials on the accelerating rotarod beginning at 5 rpm/min. The time each mouse remained on the rod was registered.
  • Both SOD1 G93A and loxSOD1 G37R mice were subjected to weekly assessment of hindlimb grip strength using a grip strength meter (Columbus Instruments, Columbus, Ohio). Each weekly session consisted of 3 (SOD1 G93A mice) or 5 (loxSOD1 G37R mice) tests per animal.
  • End stage was defined as an artificial death point when animals could no longer “right” themselves within 30 sec after being placed on its back.
  • Onset and disease progression were determined from retrospective analysis of the data.
  • Disease onset is defined as the age at which the animal reached its peak weight.
  • Disease duration is defined as the time period between disease onset and end stage.
  • Early disease duration is the period between peak weight and loss of 10% of body weight while late disease duration is defined as the period between 10% loss of body weight until disease end stage. Due to shorter life span of SOD1 G93A animals, we did not assess the distinction between the early and late progression.
  • mice For toxicity analysis following injection at P1 or P21, treated and control WT mice were subjected to behavioral analysis starting at ⁇ 30 days of age and monitored up to 6 months. Body mass was recorded weekly while rotarod performance and hindlimb grip strength were recorded biweekly.
  • Blood samples were collected in (K2) EDTA microtainer tubes (BD) from treated and control WT mice at 150 days of age by mandibular vein puncture. The same animals were bled at 180 days of age and blood was collected in serum separator microtainer tubes. The blood was allowed to clot for an hour and was then centrifuged at 10,000 rpm for 5 minutes. The clear upper phase (serum) was collected and frozen at ⁇ 80° C. Hematological and serum analysis were conducted by Ani Lytics Inc, Gaithersburg, Md.
  • the AAV SOD1 shRNA vector described in Example 2 carries shRNA against human SOD1 sequence under the H1 promoter ( FIG. 9 a ).
  • the same vector also contains a GFP expression cassette which expresses GFP under a CBA promoter.
  • the other regulatory elements present in this cassette include CMV enhancer, SV40 intron and bGH PolyA terminator sequence.
  • the SOD1 shRNA construct of Example 2 was modified by replacing the GFP expression cassette with a non-coding stuffer sequence while maintaining the size of the total DNA construct flanked by the ITRs ( FIG. 9 b ). This is important as the distance between the two ITR sequences greatly affects the packaging capacity of the flanked construct into AAV9 capsids[321-324].
  • Clinical SOD1 shRNA construct has shRNA against human SOD1 under H1 promoter which is followed by the non-coding stuffer sequence.
  • This construct is designed in such a way that multiple shRNA expression cassettes can be added to the final vector by simultaneous removal of the stuffer sequence. Restriction endonuclease sites have been added to the stuffer sequence so that a part of the stuffer can be removed when another shRNA expression cassette is added ( FIG. 10 ). This simultaneous removal and addition of DNA sequences would help maintaining the optimal size of the whole construct between the ITRs ( ⁇ 2.0 kb) to achieve efficient packaging.
  • HEK293 cells were transfected with pJet SOD1 shRNA plasmid using Calcium Phosphate method.
  • AAV SOD1 shRNA plasmid was used as a positive control.
  • Immunofluorescence analysis of HEK293 cells, 72 hrs post transfection revealed the lack of native GFP fluorescence from pJet SOD1 shRNA transfected cells as compared to AAV9 SOD1 shRNA transfected cells. Immunoblot analysis of cell lysates from these cells further confirmed the successful replacement of GFP from pJet SOD1 shRNA plasmid.
  • pJet SOD1 shRNA resulted in efficient downregulation of SOD1 protein levels (>50%), similar to AAV SOD1 shRNA plasmid. See FIG. 11 .
  • Clinical SOD1 shRNA construct was further cloned into an AAV.CB.MCS vector using Kpn1/Sph1 sites to generate clinical AAV SOD1 shRNA plasmid ( FIG. 12 ).
  • AAV.CB.MCS was generated from AAV.CB.GFP plasmid obtained from merion Scientific by replacing GFP with a multiple cloning site (MCS).
  • Cloning of clinical SOD1 shRNA construct at Kpn1/Sph1 sites puts it between the two AAV2 ITRs which facilitates the packaging of the construct in AAV9 viral capsids. See FIG. 12 .
  • Clinical AAV SOD1 shRNA plasmid was screened with restriction endonucleases to confirm the presence of SOD1 shRNA expression cassette (Xba1 digest), stuffer sequence (EcoRV/Pme1 double digest) and also intact ITR sequences (Sma1 digest).
  • Clinical AAV SOD1 shRNA plasmid was transfected in HEK293 cells to determine its knockdown efficiency. Similar to the pJet SOD1 shRNA plasmid, clinical AAV SOD1 shRNA transfected cells were devoid of any GFP expression as evident by immunofluorescence ( FIG. 13 a - f ) and immunoblot assay ( FIG. 13 g ). More importantly, clinical AAV SOD1 shRNA efficiently reduced human SOD1 protein levels in HEK293 cells by more than 50% ( FIG. 13 g,h ). Altogether, these results confirmed the successful generation of clinical AAV SOD1 shRNA vector with functional SOD1 shRNA expression cassette and complete removal of the transgene expression cassette.

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