WO2020176732A1 - TREATMENT OF PULMONARY FIBROSIS WITH SERCA2a GENE THERAPY - Google Patents

TREATMENT OF PULMONARY FIBROSIS WITH SERCA2a GENE THERAPY Download PDF

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WO2020176732A1
WO2020176732A1 PCT/US2020/020103 US2020020103W WO2020176732A1 WO 2020176732 A1 WO2020176732 A1 WO 2020176732A1 US 2020020103 W US2020020103 W US 2020020103W WO 2020176732 A1 WO2020176732 A1 WO 2020176732A1
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serca2a
aav
vector
expression
cells
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PCT/US2020/020103
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French (fr)
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Lahouaria HADRI
Malik BISSERIER
Yassine Sassi
Roger Hajjar
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Icahn School Of Medicine At Mount Sinai
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y306/00—Hydrolases acting on acid anhydrides (3.6)
    • C12Y306/03—Hydrolases acting on acid anhydrides (3.6) acting on acid anhydrides; catalysing transmembrane movement of substances (3.6.3)
    • C12Y306/03008—Ca2+-transporting ATPase (3.6.3.8)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/43—Enzymes; Proenzymes; Derivatives thereof
    • A61K38/46—Hydrolases (3)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/0075—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the delivery route, e.g. oral, subcutaneous
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2207/00—Modified animals
    • A01K2207/20—Animals treated with compounds which are neither proteins nor nucleic acids
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2227/00—Animals characterised by species
    • A01K2227/10—Mammal
    • A01K2227/105—Murine
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2267/00—Animals characterised by purpose
    • A01K2267/03—Animal model, e.g. for test or diseases
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
    • C12N2750/14143—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector

Definitions

  • the present disclosure relates generally to treating pulmonary disease, and more specifically, to a method for treating Idiopathic pulmonary fibrosis in a subject by delivering a polynucleotide encoding sarcoplasmic reticulum Ca++ ATPase (SERCA2a) protein in a viral expression vector.
  • SERCA2a sarcoplasmic reticulum Ca++ ATPase
  • Idiopathic pulmonary fibrosis is a devastating rare disease that is refractory to treatment, primarily affecting middle-aged and older adults. It represents a heterogeneous group of lung disorders dealing with a progressive accumulation of scar tissue and a fibro-proliferative process, leading to respiratory failure. To date, despite extensive research efforts in experimental and clinical studies, IPF remains an increasing cause of morbidity and mortality with an average survival of fewer than three years from diagnosis. Therefore, there is a compelling need to develop more effective and reliable therapeutic modalities for the treatment of IPF.
  • SR sarcoplasmic reticulum
  • SERCA calcium ++ ATPase
  • methods of preventing or ameliorating idiopathic pulmonary fibrosis in a subject at risk of developing idiopathic pulmonary fibrosis comprising administering to the subject a vector comprising a nucleic acid that encodes for SERCA.
  • the administering is via intratracheal instillation, bronchial instillation, inhalation; a nasal spray, or an aerosol.
  • the administering is via intratracheal.
  • the vector is an adeno-associated viral (AAV) vector.
  • AAV vector is any one of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, or AAV9.
  • the AAV vector is AAV1.
  • the vector is a recombinant adeno-associated virus (rAAV).
  • the vector comprises a nucleic acid that encodes for any one of SEQ ID NOs: 1-20.
  • the vector comprises a nucleic acid that encodes for any one of SEQ ID NOs: 1-4.
  • the subject is a mammal.
  • the mammal is a human.
  • SERCA SERCA is SERCA isoform 2 (SERCAZa).
  • methods of preventing or ameliorating idiopathic pulmonary fibrosis in a subject at risk of developing idiopathic pulmonary fibrosis comprising administering to a subject a pharmaceutical composition comprising an effective amount of a vector comprising a nucleic acid that encodes for SERCA, and a pharmaceutically acceptable excipient.
  • methods of producing a vector described herein include (a) culturing a host cell so that the vector is expressed; and (b) isolating the vector from the host cell.
  • each when used in reference to a collection of items, is intended to identify an individual item in the collection but does not necessarily refer to every item in the collection, unless expressly stated otherwise, or unless the context of the usage clearly indicates otherwise.
  • FIG. 1C shows representative images of double immunofluorescence staining for SERCA2a (top left), alpha smooth muscle actin (aSMA; top right) was detected by
  • FIG. ID shows SERCA2a mRNA expression level analyzed by quantitative polymerase chain reaction (qPCR) in sham control mice and BLM-challenged mice (n ⁇ 3-6 per group).
  • FIG. IE shows SERCA2a protein expression level analyzed by immunoblotting in sham control mice and BLM-challenged mice (n ⁇ 3-6 per group).
  • FIG. IF shows representative images of double immunofluorescence staining for SERCA2a (top left), alpha smooth muscle actin (aSMA; top right) was detected by
  • FIG. 2A shows SERCA2a mRNA levels in bleomycin-treated mice.
  • FIG. 2B shows IL-6 mRNA levels in bleomycin-treated mice.
  • FIG. 2C shows SERCA2a mRNA levels in bleomycin-treated mice relative to mRNA expression at day 1.
  • FIG. 3A shows immunofluorescence images of GFP (top images), DAPI (bottom left image) and merged image in lung tissue.
  • FIG. 3B shows mRNA expression detecting viral copies of SERCA2a AAV 1 in lung and right ventricle (RV) in sham control, AAV1.LUC- and AAVl.SERCA2a-treated mice.
  • FIG. 3C shows SERCA2a mRNA expression in the cohorts of the therapeutic protocol of
  • FIG. 4A is a diagrammatic representation of FIG. 4A.
  • FIG. 3D shows SERCA2a mRNA expression in the cohorts of the prevention protocol of
  • FIG. 6A is a diagrammatic representation of FIG. 6A.
  • FIG. 4A shows a schematic of the experimental design to assess the therapeutic efficacy of AAVl.SERCA2a gene therapy in the BLM-induced IPF model.
  • Mice received a single intratracheal (IT) aerosolization of BLM (4U/kg) and 2 weeks later were randomly assigned to receive either the vehicle, AAV1-LUC encoding for luciferase as an AAV1 control or AAV1- SERCA2a for 4 weeks.
  • FIG. 4B shows Kaplan-Meier survival curves of mice IT aerosolized either with the vehicle (Control), AAV1.LUC as control (AAV1.LUC) or AAVl .
  • SERC A2a shows Kaplan-Meier survival curves of mice IT aerosolized either with the vehicle (Control), AAV1.LUC as control (AAV1.LUC) or AAVl .
  • FIG. 4C shows viral genome copies were assessed in the mice lungs and the RV to determine the efficiency and specificity of the IT delivery of AAVl. SERC A2a gene transfer.
  • FIG. 4D shows endogenous SERCA2a mRNA level assessed in lung tissues by RT- qPCR.
  • FIG. 4E shows SERCA2a protein expression assessed by immunoblotting in the sham control group, AAVl. LUC and AAVl. SERC A2a-treated BLM groups.
  • FIG. 4F shows arterial blood-gas analysis for the sham control group (Control) and the BLM-challenged mice treated with AAVl.
  • SERC A2a groups 4 weeks after AAV1 delivery in BLM-treated animals.
  • the parameters include pH, Sa02, Pa02, PaC02, base excess in the extracellular fluid compartment (BEECF).
  • FIG. 4G shows representative Masson’s trichrome and hematoxylin and eosin stained lung sections of indicated mice (Left). The graphs represent the quantification of fibrosis (Top) and medial thickness (Bottom).
  • FIG. 41 shows right ventricular systolic pressure (RVSP; Left panel) and Fulton index (Right panel).
  • RVSP right ventricular systolic pressure
  • Fulton index Right panel
  • FIG. 4J shows RV sections stained with fluorescence-tagged wheat germ agglutinin to examine RV cardiomyocyte cross-sectional area.
  • FIG. 4K shows cardiac hypertrophy-related transcripts expression levels (ANP, BNP, b-
  • FIG. 4L shows representative Masson’ s trichrome stained heart sections (top) and quantified fibrosis in the sham control group, AAV 1 LUC and AAV1. SERC A2a-treated BLM groups.
  • FIG. 4M shows fibrosis markers COL1A1, COL3A1 and TGFP mRNA level in the sham control group, AAV 1 LUC and AAVl.SERCA2a-treated BLM groups.
  • FIGs. 5A-5B show mRNA expression of heparan Sulfate 6-O-Sulfotransferase 1 (HS6ST1), versican (VC AN), fibromodulin (FMOD), hyaluronan synthase 2 (HAS2), and syndican 4 (SDC4) in the therapeutic experiment (FIG. 5A) and the prevention experiment (FIG. 5B).
  • HS6ST1 heparan Sulfate 6-O-Sulfotransferase 1
  • VC AN versican
  • FMOD fibromodulin
  • HAS2 hyaluronan synthase 2
  • SDC4 syndican 4
  • FIG. 6A shows a schematic of the experimental design of the prevention protocol. Mice received a single intratracheal aerosolization of either the vehicle, AAV 1.LUC or
  • mice were administered with either bleomycin (4U/kg) or vehicle by IT delivery and hemodynamic studies were performed at week 5 post AAV 1 delivery.
  • FIG. 6B shows viral genome copies assessed in the mice lungs and RV to determine the efficiency and specificity of the IT delivery of AAV 1.
  • FIG. 6C shows endogenous SERCA2a mRNA level assessed in lung tissues by qPCR using specific primers.
  • FIG. 6D shows SERCA2a protein expression was assessed in lung tissues by
  • FIG. 6E shows representative Masson’s trichrome and hematoxylin and eosin stained lung sections of indicated mice (Top).
  • the bar graphs represent the quantification of fibrosis and medial thickness (Bottom).
  • FIG. 6G shows right ventricular systolic pressure (RVSP; Left) and Fulton index (RV weight/LV+ Septum weight; Right).
  • FIG. 6H shows RV cardiomyocyte cross-sectional area stained with fluorescence-tagged wheat germ agglutinin to examine the RV hypertrophy.
  • FIG. 61 shows RV cardiac hypertrophy-related transcripts expression level assessed by qPCR.
  • FIG. 6J shows representative Masson’s trichrome stained heart sections.
  • FIG. 6K Fibrosis markers mRNA level of COL1A1, COL3A1, CTGF and TGFp.
  • FIG. 7B shows a representative blot of SERCA2a, Cyclin D1 and GAPDH in NHLF overexpressing SERCA2a or Ad.CT.
  • FIG. 7D shows representative images of immuno staining showing SERCAZa (red) and aSMA (Red) and nucleus (D API-blue) in Ad.SERCA2a or Ad.CT-transduced NHLF cells. (GFP in green indicates infected cells).
  • FIGs. 7F show IL-6 mRNA expression levels. NHLF were infected with either
  • Ad.SERCA2a or Ad.CT were treated with TGF-b (5 ng/ml) for 48 hrs.
  • FIG. 7G shows IL-6 mRNA expression levels in NHLFs depleted SERCA2a using sh.S2a (sh.S2a) or a non-specific shRNA (sh.CT) for 72 hrs and treated with T ⁇ Rb (5 ng/ml; 48 hrs).
  • FIGs. 7H-7I show NFKB luciferase activity in SERCA2a overexpressing or SERCA2a depleted NHLF with or without TGF-b treatment, respectively.
  • FIGs. 7J-7K show OTUB1 mRNA expression was assessed by RT-qPCR in NHLF infected with Ad.S2a, sh.CT or sh.S2a.
  • L-M NHLF were infected either with Ad.S2a, sh.S2a or controls and treated with T ⁇ Rb for 48 hrs alone.
  • FIGs. 7L-7M show OTUB1 mRNA expression was assessed by RT-qPCR in NHLF infected with Ad.S2a, sh.CT or sh.S2a.
  • L-M NHLF were infected either with Ad.S2a, sh.S2a or controls and treated with THRb for 48 hrs alone or in combination with STAT3 inhibitor (STAT3i), and OTUB1 mRNA level was assessed by RT-qPCR in the indicated conditions.
  • FIG. 7N shows representative immunoblot for the indicated proteins in NHLF overexpressing SERCA2a stimulated with TORb in the absence or presence of STAT3L
  • FIGs. 70-7P show relative cell proliferation using BrdU labeling in the specified conditions of NHLF expressing the specified constructs or either a negative control siRNA or siRNA OTUB1 (siOTUBl) and the cells were treated with medium supplemented with 5% FBS alone or in combination with THRb.
  • FIG. 8A shows SERCA2a mRNA and protein levels in NHLF cells infected with SERCA2a adenovirus.
  • FIG. 8B shows SERCA2a mRNA and protein levels in NHLF cells infected with a specific shRNA against SERCA2a.
  • FIG. 8C shows HS6ST1 and VCAN mRNA levels in NHLF cells transfected with SERCA2a adenovirus and/or TGF-b.
  • FIG. 9A shows COL1 A1 mRNA levels in human pulmonary alveolar epithelial cells infected with SERCA2a adenovirus and treated with and without TGF-b.
  • FIG. 9B shows COLO A1 mRNA levels in human pulmonary alveolar epithelial cells infected with SERCA2a adenovirus and treated with and without TGF-b.
  • FIG. 9C shows CTGF mRNA levels in human pulmonary alveolar epithelial cells infected with SERCA2a adenovirus and treated with and without TGF-b.
  • FIG. 10A shows OTLIBl mRNA and protein levels in fibroblasts transfected with a siRNA against OTLIB 1.
  • FIG. 10B shows COL1 A1 mRNA levels in fibroblasts transfected with a siRNA against OTLIBl alone or in combination with a specific shRNA against SERCA2a with and without TGF-b.
  • FIG. IOC shows COL3 A1 mRNA levels in fibroblasts transfected with a siRNA against OTUB1 alone or in combination with a specific shRNA against SERCA2a with and without TGF-b.
  • FIG. 10D shows CTGF mRNA levels in fibroblasts transfected with a siRNA against OTUB1 alone or in combination with a specific shRNA against SERCA2a with and without TGF-b.
  • FIG. 10E shows FOXM1 mRNA and protein levels in fibroblasts infected with
  • SERCA2a adenovirus SERCA2a adenovirus.
  • FIG. 10F shows FOXM1 mRNA and protein levels in fibroblasts infected with a specific shRNA against SERCA2a.
  • FIGs. 11A-11C show NHLFs were infected either with Ad.S2a, sh.S2a or si.OTUBl and treated with TORb for 48 hrs. FOXMl expression level was assessed in indicated conditions.
  • FIGs. 11D-11E show SnoN (Left) and SKI (Right) mRNA expression levels were assessed by RTqPCR in S2a overexpressing cells or sh.S2a depleted cells, respectively,
  • FIGs. 11F-11G show representative immunoblots of indicated proteins in NHLF overexpressing S2a or a specific non-silencing or sh.SERCA2a and treated with TORb for 48 hrs.
  • FIG. 11H shows SnoN mRNA expression level in NIHLF cells depleted of SERCA2a and FOXMl using a specific sh.RNA and OTUB1 using siRNA.
  • FIG. Ill shows SERCA2a overexpression prevented the interaction between endogenous FOXMl/OTUBl and FOXMl/pSMAD3.
  • Immunoprecipitation (IP) of FOXMl followed by Immunoblotting (IB) of FOXM1, OTUB1, phospho- and total SMAD3 was performed in NHLF cells after infection with Ad.S2a or sh.S2a or controls in the absence or presence of TGF-b.
  • FIG. 11J shows SERCA2a enhanced FOXM1 and SMAD2/3 ubiquitination.
  • Direct IB of NHLF lysates was used to analyze protein levels of OTUB1.
  • FIGs. 11K-11M show OTUB1, FOXM1, SNON, and SKI mRNA and protein expression levels in lung tissue from control non-IPF and IPF patients.
  • FIG. 11N shows double immunostaining of OTUB1 (top panel; top left image in each cohort)/SMA (top panel; second image from left image in top row in each cohort), and FOXM1 (bottom panel; top left image in each cohort)/SMA (bottom panel; second image from left image in top row in each cohort) in control non-IPF and IPF patients.
  • FIGs. 110-1 IP show OTUB1, FOXM1, SNON, and SKI expression assessed by immunoblotting in control untreated and BLM-induced PF in mice. Densitometric quantitation is shown of OTUB1, SNON, and SKI protein expression normalized to GAPDH.
  • FIG. 12A shows OTUB1 mRNA levels in mice treated with bleomycin.
  • FIG. 12B shows FOXM1 mRNA levels in mice treated with bleomycin.
  • FIG. 12C shows SnoN mRNA levels in mice treated with bleomycin.
  • FIG. 12D shows SKI mRNA levels in mice treated with bleomycin.
  • FIG. 13B shows OTUB1 (Top) and FOXM1 (Bottom) mRNA levels were assessed by RT-qPCR in the lungs in the indicated groups in the therapeutic and preventative protocols
  • FIG. 13C shows SnoN (Top) and SKI (Bottom) mRNA levels were assessed by RT- qPCR in the lungs in the indicated groups in the therapeutic and preventative protocols.
  • FIG. 13D shows lung homogenates lysates after immunoblotting analysis for the indicated proteins after the treatment protocol. Representative blots and respective densitometry quantitation for p-NF-kB p65, p-STAT3, OTUB1, FOXM1, p-SMAD2-3, SNON, aSMA and Cyclin D1 are presented. Protein expression was normalized to total NFKB, total-STAT3, total- SMAD2-3 and GAPDH.
  • FIG. 13E shows lung homogenates lysates after immunoblotting analysis for the indicated proteins in the prevention protocol.
  • FIG. 13F shows a schematic representation of the molecular mechanisms by which SERCA2a inhibits lung fibrosis.
  • SERCA2a inhibits STAT3 activation and therefore decreases OTUB1 and FOXM1 expression.
  • Downregulation of OTUB1 expression results in inhibition of the SMAD signaling and the upregulation of the anti-fibrosis SnoN and SKI proteins.
  • FIG. 14A shows a schematic of the experimental design of the treatment protocol.
  • FIG. 14B shows a schematic of the experimental design of the prevention protocol.
  • the present disclosure provides methods for treating idiopathic pulmonary fibrosis (IPF) in a subject by delivering a therapeutic adeno-associated virus (AAV)-SERCA (e.g., SERCAZa) composition to the subject in need thereof.
  • AAV adeno-associated virus
  • SERCAZa SERCAZa
  • references to“the method” includes one or more methods, and/or steps of the type described herein which will become apparent to those persons skilled in the art upon reading this disclosure and so forth.
  • all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs.
  • Idiopathic pulmonary fibrosis is a chronic and fatal lung disease of unknown cause characterized by progressive fibroblast proliferation and differentiation to myofibroblast, destruction of the alveolar architecture and a relentless decline in pulmonary function, leading to respiratory failure and ultimately to death within 3-5 years after the diagnosis.
  • the present disclosure provides a therapeutic strategy to prevent and inhibit lung fibrosis based on the AAVl.SERCA2a target gene therapy.
  • SERCA2a expression was significantly decreased in lung tissue from patients with IPF and in bleomycin-challenged mice.
  • SERCA2a overexpression significantly decreased the proliferation, migration and human lung fibroblast transition to myofibroblast.
  • SERCA2a decreased lung fibrosis and prevented the expression of several fibrosis markers, and lung vascular remodeling.
  • the methods provided herein utilize a viral vector to deliver the SERCAZa gene or its isoforms directly to the lungs and/or to muscle cells associated with lung function.
  • a viral vector to deliver the SERCAZa gene or its isoforms directly to the lungs and/or to muscle cells associated with lung function.
  • One aspect of the present disclosure contemplates transfer of a therapeutic polynucleotide into a cell. Such transfer may employ viral or non-viral methods of gene transfer.
  • the viral vector is an adeno-associated virus (AAV) vector or a human parvovirus.
  • AAV adeno-associated virus
  • the therapeutically significant polynucleotides are incorporated into a viral vector to mediate transfer to a cell.
  • Additional expression constructs encoding other therapeutic agents as described herein may also be transferred via viral transduction using infectious viral particles, for example, by transformation with an adeno-associated virus (AAV) of the present disclosure.
  • AAV adeno-associated virus
  • a retrovirus, bovine papilloma virus, an adenovirus vector, a lentiviral vector, a vaccinia virus, a polyoma virus, or an infective virus may be used.
  • nonviral methods which include, but are not limited to, direct delivery of DNA such as by perfusion, naked DNA transfection, liposome mediated transfection, encapsulation, and receptor-mediated endocytosis may be employed.
  • a viral vector is used for the transduction of pulmonary cells to deliver a therapeutically significant polynucleotide to a cell.
  • the virus may gain access to the interior of the cell by a specific means such as receptor-mediated endocytosis, or by non-specific means such as pinocytosis.
  • ATPase Sarcoplasmic/Endoplasmic Reticulum Ca2+ Transporting 2 (ATP2A2; also known as DD; DAR; ATP2B; or SERCA2a) is a gene that encodes one of the SERCA Ca(2+)- ATPases (i.e., SERCA2a), which are intracellular pumps located in the sarcoplasmic or endoplasmic reticula of the skeletal muscle. SERCA2a catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol into the sarcoplasmic reticulum lumen, and is involved in regulation of the contraction/relaxation cycle.
  • SERCA2a catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol into the sarcoplasmic reticulum lumen, and is involved in regulation of the contraction/relaxation cycle.
  • Polynucleotides e.g., viral vectors described herein encode for a“polypeptide”, for example, SERCA2a or isomers thereof.“Polypeptide” is used in its conventional meaning, i.e., as a sequence of amino acids.
  • the polypeptides are not limited to a specific length of the product; thus, peptides, oligopeptides, and proteins are included within the definition of polypeptide, and such terms may be used interchangeably herein unless specifically indicated otherwise.
  • This term also does not refer to or exclude post-expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like, as well as other modifications known in the art, both naturally occurring and non- naturally occurring.
  • a polypeptide may be an entire protein, or a subsequence thereof.
  • Particular polypeptides of interest in the context of this disclosure are amino acid subsequences comprising epitopes, i.e., antigenic determinants substantially responsible for the immunogenic properties of a polypeptide and being capable of evoking an immune response.
  • SERCA2a polypeptides include but are not limited to, human GenBank sequences such as AAB29701 (Wuytack et al., J Biol Chem (1994) 269(2): 1410- 1416); NP_733765 (Lytton and MacLennan, J Biol Chem (1988) 263(29): 15023-15031);
  • NP_001672 (Otsu et al, Genomics (1993) 17(2):507-509); AAH35588 (Strausberg et al, Proc Natl Acad Sci USA (2002) 99(26): 16899-16903); and mouse GenBank sequences including AAD01889 (Ver Heyen et al, Mamm Genome (2000) 11(2): 159-163); NP_033852 (Hsu et al., Biochem Biophys Res Comm (1993) 197(3): 1483-1491); CAB41018 (Ver Heyen et al., Mamm Genome (2000) 11(2): 159-163); CAB41017 (Id.); CAB72436 (Id.); CAA11450 (Id.);
  • AAH54531 (Strasberg et al, Proc Natl Acad Sci USA (2002) 99(26): 16899-16903); AAH54748 (Id.); and other species including NP_957259 (Ebert et al, Proc Natl Acad Sci USA (2005) 102(49): 17705-17710); ABG90496 (Wu et al, Silurus lanzhouensis SERCA2a, direct submission (23-JUN-2006), Department of Applied Chemistry, College of Science, China Agricultural University, No.
  • NP_001025448 (Sehra H., Danio rerio SERCA2a, direct submission (7-AUG-2005), Welcome Trust Sanger Institute, Hixton, Cambridgeshire, CB 10 ISA, UK);
  • NP 001009216 (Gambel et al, Biochem Biophys Acta (1992) 1131(2):203-206);
  • NP 999030 (Eggermont et al, Biochem J (1989) 260(3):757-761);
  • NP 058986 (Gunteski-Hamblin et al, J Biol Chem (1988)
  • SERCA2a having the sequences recited as SEQ ID NO: 1-20.
  • the polypeptide for SERCA2a has the sequence recited as SEQ ID NO: 1-4.
  • the present disclosure provides variants of the polypeptide compositions described herein.
  • polypeptide variants that exhibit at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or greater sequence identity, along its length, to any one of the polypeptide sequences set forth as SEQ ID NOs: 1-20.
  • a SERCA2a polypeptide is a fusion polypeptide that includes any one of SERCA2a polypeptides set forth as SEQ ID NOs: 1-20 as described herein, or that includes at least one SERCA2a polypeptide as described herein and an unrelated sequence, such as a known viral protein.
  • a fusion partner may, for example, assist in providing epitopes (an immunological fusion partner) recognized by humans, or may assist in expressing the protein (an expression enhancer) at higher yields than the native recombinant protein. Certain fusion partners enhance formation of multimers.
  • polypeptides are defined by structural domains.
  • the signaling domain which is associated with transduction upon receptor binding and is found in the cytoplasmic compartment of cells, is defined as a region of a protein molecule delimited on the basis of function and is related to a receptor's cytoplasmic substrate.
  • Fusion polypeptides may generally be prepared using standard techniques, including chemical conjugation.
  • a fusion SERCA2a polypeptide is expressed as a recombinant polypeptide, allowing the production of increased SERCA2a levels, relative to a non-fused polypeptide, in an expression system.
  • DNA sequences encoding the polypeptide components may be assembled separately, and ligated into an appropriate expression vector. The 3 ' end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5' end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion polypeptide that retains the biological activity of both component polypeptides.
  • the present disclosure also encompasses“peptide” or“peptide portion” or“fragment” or “peptide fragment” and equivalents thereof, which is used broadly herein to mean two or more amino acids linked by a peptide bond.
  • proteolytic fragment also is used herein to refer to a product that can be produced by a proteolytic reaction on a polypeptide, i.e., a peptide produced upon cleavage of a peptide bond in the polypeptide.
  • proteolytic fragment is used generally herein to refer to a peptide that can be produced by a proteolytic reaction, it should be recognized that the fragment need not necessarily be produced by a proteolytic reaction, but also can be produced using methods of chemical synthesis or methods of recombinant DNA technology, as discussed in greater detail below, to produce a synthetic peptide that is equivalent to a proteolytic fragment.
  • functional fragment or “functional portion” or equivalents thereof means that the SERCA2a fragment or peptide has functional SERCA2a activity, for example, a functional fragment or functional proteolytic fragment of SERCA2a or SERCA2a has functional SERCA2a or SERCA2a activity.
  • a peptide of the disclosure contains at least about six amino acids, usually contains about ten amino acids, and can contain fifteen or more amino acids, particularly twenty or more amino acids. It should be recognized that the term“peptide” is not used herein to suggest a particular size or number of amino acids comprising the molecule, and that a peptide of the disclosure can contain up to several amino acid residues or more.
  • the“translation product” or“polypeptide” refers to peptides, polypeptides, oligopeptides and proteins or protein fragments which have a desired biological effect in vivo or in vitro.
  • the term“fragment” refers to a molecule or any peptide subset of the molecule; whereas a“variant” of such molecule refers to a naturally occurring molecule (e.g., isoform such as SERCA2a) substantially similar to either the entire molecule, or a fragment thereof.
  • an“analog” of a molecule refers to a non-natural molecule substantially similar to either the entire molecule or a fragment thereof.
  • a peptide linker sequence may be employed to separate the first and second polypeptide components by a distance sufficient to ensure that each polypeptide folds into its secondary and tertiary structures. Such a peptide linker sequence is incorporated into the fusion polypeptide using standard techniques well known in the art.
  • Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes.
  • the peptide linker sequences contain Gly, Asn, and Ser residues. Other near neutral amino acids, such as Thr and Ala may also be used in the linker sequence.
  • Amino acid sequences which may be usefully employed as linkers are generally known in the art.
  • the linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.
  • SERCAZa polypeptides are highly conserved, hence the skilled artisan can perform an optimal alignment of polypeptide or nucleic acid sequences for comparison using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters.
  • This program embodies several alignment schemes described in the following references: Dayhoff, M. O. (1978) A model of evolutionary change in proteins— Matrices for detecting distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogenes pp.
  • Taxonomy the Principles and Practice of Numerical Taxonomy, Freeman Press, San Francisco, Calif.; Wilbur, W. J. and Lipman, D. J. (1983) Proc. Natl. Acad., Sci. USA 80:726-730, each of which is incorporated herein by reference.
  • optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman (1981) Add. APL. Math 2:482, by the identity alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity methods of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85: 2444, by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.
  • BLAST and BLAST 2.0 are described in Altschul et al. (1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively.
  • BLAST and BLAST 2.0 can be used, for example with the parameters described herein, to determine percent sequence identity for the polynucleotides and polypeptides of the disclosure.
  • Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. For amino acid sequences, a scoring matrix can be used to calculate the cumulative score.
  • Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
  • SERCA sarcoplasmic Reticulum Ca2+-ATPase
  • SERCA resides in the sarcoplasmic reticulum (SR) within muscle cells.
  • Vasoconstriction e.g., vascular smooth muscle cells or VSMC
  • SERCA is a Ca2+ ATPase which transfers Ca2+ from the cytosol of the cell to the lumen of the sarcoplasmic reticulum (SR) at the expense of ATP hydrolysis.
  • SERCA proteins are encoded by three genes (SERCA1,
  • SERCA transcripts are expressed and alternatively spliced in a tissue dependent manner. The resulting mRNA species encode different SERCA protein isoforms and differ in 3 '-untranslated regions (UM). SERCA protein isoforms differ in their Ca2+ affinity, resistance to oxidative stress and modulation by sarcolipin, phospholamban (PLB/PLN), and Ca2+/calmodulin kinase II.
  • nucleic acids that encode for any one of SEQ ID NOs: 1-20.
  • the present disclosure provides variants of nucleotides that encode for any one of SEQ ID NOs: 1-20.
  • nucleotide variants that exhibit at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%,
  • any one of the nucleotides described herein can be included as part of a vector that produces a SERCA2a polypeptide.
  • any one of the nucleotides described herein e.g., any nucleotide encoding for any one of SEQ ID NOs: 1-20 or a variant thereof
  • any one of the nucleotides described herein can be included as part of an adeno-associated viral vector serotype 1.
  • nucleic acid sequences are embodied in the present disclosure.
  • nucleic acid sequence or equivalents thereof refer to a DNA or RNA sequence.
  • the term captures sequences that include any of the known base analogues of DNA and RNA such as, but not limited to 4-acetylcytosine, 8-hydroxy-N-6-methyladenosine, aziridinylcytosine,
  • pseudoisocytosine 5-(carboxyhydroxylmethyl) uracil, 5-fluorouracil, 5-bromouracil, 5- carboxymethylaminomethyl-2-thiouracil, 5-carboxymethyl-aminomethyluracil, dihydrouracil, inosine, N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil, 1-methylguanine, 1- methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5- methylcytosine, N6-methyladenine, 7-methylguanine, 5-methylaminomethyluracil, 5- methoxyamino-methyl-2-thiouracil, beta-D-mannosylqueosine, 5 '-methoxycarbonylmethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid methylester
  • control sequences refer collectively to promoter sequences, polyadenylation signals, transcription termination sequences, upstream regulatory domains, origins of replication, internal ribosome entry sites (“IRES”), enhancers, and the like, which collectively provide for the replication, transcription and translation of a coding sequence in a recipient cell. Not all of these control sequences need always be present so long as the selected coding sequence is capable of being replicated, transcribed and translated in an appropriate host cell.
  • nucleic acids that include one or more “promoter” sequences, which are used herein in its ordinary sense to refer to a nucleotide region comprising a DNA regulatory sequence, wherein the regulatory sequence is derived from a gene which is capable of binding RNA polymerase and initiating transcription of a downstream (3 - direction) coding sequence.
  • Transcription promoters can include“inducible promoters” (where expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.),“repressible promoters” (where expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.), and“constitutive promoters.”
  • nucleic acids embodied in the present disclosure are“operably linked” to each other or linked to a protein or peptide.
  • “operatively linked” refers to an arrangement of elements wherein the components so described are configured so as to perform their usual function.
  • control sequences operably linked to a coding sequence are capable of effecting the expression of the coding sequence.
  • the control sequences need not be contiguous with the coding sequence, so long as they function to direct the expression thereof.
  • intervening untranslated yet transcribed sequences can be present between a promoter sequence and the coding sequence and the promoter sequence can still be considered“operably linked” to the coding sequence.
  • the ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements.
  • the regulatory elements responsible for expression of DNA are located only 5' to the DNA sequence encoding the first polypeptides.
  • stop codons required to end translation and transcription termination signals are only present 3 ' to the DNA sequence encoding the secondary, tertiary, or quaternary, etc., polypeptide (i.e., a stop codon will be present on the ultimate polypeptide depending on the number of distinct polypeptides making up a chimeric protein molecule).
  • SERCA2a polypeptides the present disclosure provides SERCA2a and SERCA2a containing polynucleotide compositions.
  • DNA and“polynucleotide” are used interchangeably herein to refer to a DNA molecule that has been isolated free of total genomic DNA of a particular species.“Isolated,” as used herein, means that a polynucleotide is substantially away from other coding sequences, and that the DNA molecule does not contain large portions of unrelated coding DNA, such as large chromosomal fragments or other functional genes or polypeptide coding regions. Of course, this refers to the DNA molecule as originally isolated, and does not exclude genes or coding regions later added to the segment by the hand of man.
  • SERCA2a gene or“SERCA2a transgene” or other SERCA isomers thereof, refers to DNA or RNA and can include sense and antisense strands as appropriate to the goals of the therapy practiced according to the disclosure.
  • polynucleotide refers to a polymer of deoxyribonucleotides or ribonucleotides, in the form of a separate fragment or as a component of a larger construct.
  • Polynucleotides of the disclosure include functional derivatives of known polynucleotides which operatively encode for SERCAZa protein.
  • polynucleotide sequence can be deduced from the genetic code, however, the degeneracy of the code must be taken into account.
  • Polynucleotides of the disclosure include sequences which are degenerate as a result of the genetic code, which sequences may be readily determined by those of ordinary skill in the art.
  • a“heterologous” region of a nucleic acid construct or a vector is a segment of nucleic acid within or attached to another nucleic acid molecule that is not found in association with the other molecule in nature.
  • a heterologous region of a nucleic acid construct could include a coding sequence flanked by sequences not found in association with the coding sequence in nature.
  • heterologous coding sequence is a construct where the coding sequence itself is not found in nature (e.g., synthetic sequences having codons different from the native gene).
  • a cell transformed with a construct which is not normally present in the cell would be considered heterologous for purposes of this disclosure.
  • Allelic variation or naturally occurring mutational events do not give rise to heterologous DNA, as used herein.
  • a“coding sequence” or a sequence which“encodes” a particular protein is a nucleic acid sequence which is transcribed (in the case of DNA) and translated (in the case of mRNA) into a polypeptide in vitro or in vivo when placed under the control of appropriate regulatory sequences.
  • a coding sequence can include, but is not limited to, cDNA from prokaryotic or eukaryotic mRNA, genomic DNA sequences from prokaryotic or eukaryotic DNA, and even synthetic DNA sequences.
  • a transcription termination sequence will usually be located 3' to the coding sequence.
  • SERCA2a The nucleotide sequence of the SERCA2a and its isoforms is about 90%+ conserved among mammalian species.
  • SERCA2a has been identified and sequenced from various mammalian species, including human GenBank sequences NM 170665 (Lytton and MacLennan, J Biol Chem (1998) 263(29):15024-15031); NM_001681 (Id.); NM_006241 (Park et al, J Biol Chem (1994) 269(2):944-954); NM_001003214 (Autry and Jones, J Biol Chem (1997)
  • human SERCA2a polynucleotide includes use human therapies, e.g., human gene therapies, rat SERCA2a polynucleotide can also be used for purposes of the disclosure described herein.
  • polynucleotides which are structurally or functionally similar, e.g. highly homologous to human SERCA2a are encompassed within the disclosure.
  • DNA and RNA may also be synthesized using automated nucleic acid synthesis by any method known now known or later discovered (e.g., PCR, cDNA synthesis (see, for example, Sambrook et al, Molecular Cloning: A
  • polynucleotide compositions of this disclosure can include genomic sequences, extra-genomic and plasmid-encoded sequences and smaller engineered gene segments that express, or may be adapted to express, proteins, polypeptides, peptides and the like. Such segments may be naturally isolated, or modified synthetically by the hand of man.
  • polynucleotides of the disclosure may be single-stranded or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules.
  • RNA molecules may include HnRNA molecules, which contain introns and correspond to a DNA molecule in a one-to-one manner, and mRNA molecules, which do not contain introns. Additional coding or noncoding sequences may, but need not, be present within a polynucleotide of the present disclosure, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.
  • Polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a polypeptide/protein of the disclosure or a portion thereof) or may comprise a sequence that encodes a variant or derivative, including an immunogenic variant or derivative, of such a sequence. Further, polynucleotides can encode a combination of different sequences, e.g., a transgene, a viral polynucleotide, a nucleic acid encoding a selectable marker and the like.
  • the polynucleotide or nucleic acid can be either a DNA or RNA.
  • the sequences in question can be of natural or artificial origin, and in particular genomic DNA, cDNA, mRNA, tRNA, rRNA, hybrid sequences or synthetic or semi synthetic sequences.
  • the nucleic acid can be very variable in size, ranging from oligonucleotide to chromosome.
  • These nucleic acids may be of human, animal, vegetable, bacterial, viral, and the like, origin. They may be obtained by any technique known to a person skilled in the art, and in particular by the screening of libraries, by chemical synthesis or alternatively by mixed methods including the chemical or enzymatic modification of sequences obtained by the screening of libraries. They can, moreover, be incorporated into vectors, such as plasmid vectors.
  • RNA In vitro transcribed messenger RNA (mRNA) has many advantages as a vehicle for gene delivery. Transfection of mRNA is very efficient and rapid expression of the encoded protein can be achieved. Unlike viral vectors or plasmid DNA, cell-delivered mRNA does not introduce the risk of insertional mutagenesis. Previous studies have shown that RNA can activate a number of innate immune receptors, including Toll-like receptor (TLR)3, TLR7, TLR8 and retinoic acid- inducible gene I (RIG-I). However, activation of these receptors can be avoided by incorporating modified nucleosides, e.g. pseudouridine (Y) or 2-thiouridine (s2U), into the RNA for example.
  • TLR Toll-like receptor
  • TLR8 TLR7, TLR8 and retinoic acid- inducible gene I
  • RIG-I retinoic acid- inducible gene I
  • Y pseudouridine
  • s2U 2-thiouridine
  • RNA-dependent protein kinase is a ubiquitous mammalian enzyme with a variety of cellular functions, including regulation of translation during conditions of cell stress.
  • PKR binds viral double- stranded (ds)RNA, autophosphorylates and subsequently phosphorylates the alpha subunit of translation initiation factor 2 (eIF-2a), thus repressing translation.
  • ds viral double- stranded
  • eIF-2a alpha subunit of translation initiation factor 2
  • PKR can be activated by a variety of RNA structures that include single-stranded (ss)RNA forming hairpins imperfect dsRNA containing mismatches, short dsRNA with ss tails, stem-loop structures with 5 '-triphosphates, and unique elements present in interferon gamma (IFN-g) and tumor necrosis factor-alpha mRNAs and cellular RNAs.
  • IFN-g interferon gamma
  • Y-modified mRNAs are attractive vectors for gene delivery or replacement, vaccine antigen delivery or other RNA-based therapeutic applications.
  • the nucleic acids of the present disclosure have undergone a chemical or biological modification to render them more stable.
  • exemplary modifications to a nucleic acid include the depletion of a base (e.g., by deletion or by the substitution of one nucleotide for another) or modification of a base, for example, the chemical modification of a base.
  • the phrase“chemical modifications” as used herein, includes modifications which introduce chemistries which differ from those seen in naturally occurring nucleic acids, for example, covalent modifications such as the introduction of modified nucleotides, (e.g., nucleotide analogs, or the inclusion of pendant groups which are not naturally found in such nucleic acid molecules).
  • suitable modifications include alterations in one or more nucleotides of a codon such that the codon encodes the same amino acid but is more stable than the codon found in the wild-type version of the nucleic acid.
  • C's cytidines
  • U's uridines
  • RNA devoid of C and U residues have been found to be stable to most RNases (Heidenreich, et al. J Biol Chem 269, 2131-8 (1994)).
  • the number of C and/or U residues in an mRNA sequence is reduced.
  • the number of C and/or U residues is reduced by substitution of one codon encoding a particular amino acid for another codon encoding the same or a related amino acid.
  • Contemplated modifications to the mRNA nucleic acids of the present disclosure also include the incorporation of pseudouridines.
  • the incorporation of pseudouridines into the mRNA nucleic acids of the present disclosure may enhance stability and translational capacity, as well as diminishing immunogenicity in vivo.
  • the constraints on reducing the number of C and U residues in a sequence will likely be greater within the coding region of an mRNA, compared to an untranslated region, (i.e., it will likely not be possible to eliminate all of the C and U residues present in the message while still retaining the ability of the message to encode the desired amino acid sequence).
  • the degeneracy of the genetic code presents an opportunity to allow the number of C and/or U residues that are present in the sequence to be reduced, while maintaining the same coding capacity (i.e., depending on which amino acid is encoded by a codon, several different possibilities for modification of RNA sequences may be possible).
  • the codons for Gly can be altered to GGA or GGG instead of GGU or GGC.
  • modification also includes, for example, the incorporation of non-nucleotide linkages or modified nucleotides into the nucleic acid sequences of the present disclosure (e.g., modifications to one or both the 3' and 5' ends of an mRNA molecule encoding a functional protein or enzyme).
  • modifications include the addition of bases to a nucleic acid sequence (e.g., the inclusion of a poly A tail or a longer poly A tail), the alteration of the 3' UTR, or the 5' UTR, complexing the nucleic acid with an agent (e.g., a protein or a complementary nucleic acid molecule), and inclusion of elements which change the structure of a nucleic acid molecule (e.g., which form secondary structures).
  • the poly A tail is thought to stabilize natural messengers and synthetic sense RNA. Therefore, in one embodiment a long poly A tail can be added to an mRNA molecule thus rendering the RNA more stable.
  • Poly A tails can be added using a variety of art-recognized techniques. For example, long poly A tails can be added to synthetic or in vitro transcribed RNA using poly A polymerase (Yokoe, et al. Nature Biotechnology. 1996; 14: 1252-1256). A transcription vector can also encode long poly A tails. In addition, poly A tails can be added by transcription directly from PCR products.
  • Poly A may also be ligated to the 3' end of a sense RNA with RNA ligase (see, e.g., Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1991 edition)).
  • the length of the poly A tail is at least about 90, 200, 300, 400 at least 500 nucleotides.
  • the length of the poly A tail is adjusted to control the stability of a modified sense mRNA molecule of the disclosure and, thus, the transcription of protein.
  • the length of the poly A tail can influence the half-life of a sense mRNA molecule
  • the length of the poly A tail can be adjusted to modify the level of resistance of the mRNA to nucleases and thereby control the time course of protein expression in a cell.
  • the stabilized nucleic acid molecules are sufficiently resistant to in vivo
  • nucleases degradation (e.g., by nucleases), such that they may be delivered to the target cell without a transfer vehicle.
  • the nucleotide sequences encoding the polypeptide may be inserted into appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence.
  • appropriate expression vector i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence.
  • operatively encoding refers to a polynucleotide which has been modified to include promoter and other sequences necessary for expression and, where desired, secretion of the desired translation product; e.g., a peptide or protein. All the embodiments of the disclosure can be practiced using known recombinant expression vectors including bacterial and viral. In some embodiments, these vectors will include cDNA('s) which encode for the desired translation product. Therefore, unless context otherwise requires, it will be assumed that“polynucleotide” refers to operatively encoding sequences contained in a suitable recombinant expression vector, examples of which are provided herein.
  • control elements or“regulatory sequences” present in an expression vector are those non-translated regions of the vector (e.g., enhancers, promoters, 5' and 3' untranslated regions and the like), which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used.
  • inducible promoters such as the hybrid lacZ promoter of the pBLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or pSPORTl plasmid (Gibco BRL, Gaithersburg, Md.) and the like may be used.
  • promoters include those from CMV, beta-actin, EF2alpha, RSV LTR, HIW LTR, HTLV-1 LTR, and composite promoters (D. H.
  • the promoter is a CMV promoter or a promoter comprising portions of the chicken beta-actin promoter (H. Niwa et al, Efficient selection for high-expression transfectants with a novel eukaryotic vector, Gene 108: 193-199, 1991).
  • the promoter is a CMV promoter, Sm22 promoter, or Tie2 promoter. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding a polypeptide, vectors based on SV40 or EBV may be advantageously used with an appropriate selectable marker.
  • Specific initiation signals may also be used to achieve more efficient translation of sequences encoding a polypeptide of interest. Such signals include the ATG initiation codon and adjacent sequences. In cases where sequences encoding the polypeptide, its initiation codon, and upstream sequences are inserted into the appropriate expression vector, no additional
  • transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a portion thereof, is inserted, exogenous translational control signals including the ATG initiation codon should be provided. Furthermore, the initiation codon should be in the correct reading frame to ensure translation of the entire insert. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers which are appropriate for the particular cell system which is used, such as those described in the literature (Scharf, D. et al. (1994) Results Probl. Cell Differ. 20: 125-162, incorporated herein by reference).
  • a host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion.
  • modifications of the polypeptide include, but are not limited to, acetylation, carboxyl ation, glycosylation, phosphorylation, lipidation, and acylation.
  • Post-translational processing which cleaves a“prepro” form of the protein may also be used to facilitate correct insertion, folding and/or function.
  • Different host cells such as CHO, COS, HeLa, MDCK, HEK293, and WI38, which have specific cellular machinery and characteristic mechanisms for such post-translational activities, may be chosen to ensure the correct modification and processing of the foreign protein.
  • gene delivery involves polymers which form complexes, nanoparticles (defined as less than 1 micron in diameter), or even microparticles (defined as 1 micron in diameter or greater) with DNA plasmids and other nucleic acids.
  • polymers which form complexes, nanoparticles (defined as less than 1 micron in diameter), or even microparticles (defined as 1 micron in diameter or greater) with DNA plasmids and other nucleic acids.
  • Many kinds of polymers have been described that enhance the expression of genes encoded by nucleic acids in cells.
  • cationic polymers such as poly-L-lysine, poly-L-glutamate, or block co polymers may also be delivery agents for nucleic acids.
  • PAG A poly[alpha-(4- aminobutyl)-l -glycolic acid]
  • PAG A poly[alpha-(4- aminobutyl)-l -glycolic acid]
  • PAG A water-soluble lipopolymer
  • WSLP water-soluble lipopolymer
  • Polyethylenimine-based vesicle-polymer hybrid gene delivery as another way to deliver plasmid DNA expression vectors, including the use of poly(propylenimine) dendrimers as delivery agents
  • polyethylene glycol (PEG) copolymers were found to improve plasmid DNA delivery, including various kinds of polymers that can be used for the controlled release of plasmid DNA and other nucleic acids.
  • Such molecules include poly(lactic acid) and its derivatives, PEGylated poly(lactic acid), poly(lactic- co-glycolic acid) and its derivatives, poly(ortho esters) and their derivatives, PEGylated poly(ortho esters), poly(caprolactone) and its derivatives, PEGylated poly(caprolactone), polylysine and its derivatives, PEGylated polylysine, poly(ethylene imine) and its derivatives, PEGylated poly(ethylene imine), poly( acrylic acid) and its derivatives, PEGylated poly( acrylic acid), poly(urethane) and its derivatives, PEGylated poly(urethane), and combinations of all of these.
  • One object of the present disclosure is the use of polymeric lipid-protein-sugar microparticles for the delivery of nucleic acids. These and other polymers are well known in the art.
  • nucleic acid compositions of the present disclosure are delivered by electroporation.
  • Electroporation uses electrical pulses to introduce proteins, nucleic acids, lipids, carbohydrates, or mixtures thereof into the host to produce an effect.
  • a typical use of electroporation is to introduce a nucleic acid into the host so that the protein encoded by the nucleic acid is efficiently produced.
  • nucleic acid compositions of the present disclosure are delivered by particle bombardment.
  • Powderject Novartis Pharmaceutical Corporation
  • AAV Adeno- Associated Virus
  • Adeno-associated virus has shown promise for delivering genes for gene therapy in clinical trials in humans.
  • AAV Adeno-associated virus
  • the AAV genome is a linear, single- stranded DNA molecule containing about 4681 nucleotides.
  • the AAV genome generally comprises an internal nonrepeating genome flanked on each end by inverted terminal repeats (ITRs).
  • ITRs are approximately 145 base pairs (bp) in length.
  • the ITRs have multiple functions, including as origins of DNA replication, and as packaging signals for the viral genome.
  • the internal nonrepeated portion of the genome includes two large open reading frames, known as the AAV replication (rep) and capsid (cap) genes.
  • the rep and cap genes code for viral proteins that allow the virus to replicate and package into a virion.
  • a family of at least four viral proteins is expressed from the AAV rep region, Rep 78, Rep 68, Rep 52, and Rep 40, named according to their apparent molecular weight.
  • the AAV cap region encodes at least three proteins, VP1, VP2, and VP3.
  • the term“vector” means any genetic element, such as a plasmid, phage, transposon, cosmid, chromosome, virus, virion, etc., which is capable of replication when associated with the proper control elements and which can transfer gene sequences between cells.
  • the term includes cloning and expression vehicles, as well as viral vectors previously discussed.
  • “recombinant expression vector” refers to systems of polynucleotide(s) which operatively encode polypeptides expressible in eukaryotes or prokaryotes. Methods of expressing DNA sequences having eukaryotic or viral sequences in prokaryotes are well known in the art. Biologically functional viral and plasmid DNA vectors capable of expression and replication in a host are also well known in the art. Hosts can include microbial, yeast, insect and mammalian organisms.
  • the vectors or recombinant expression vectors provided herein are easily manufactured, and combine the advantages of adenovirus (high titer, high infectivity, large capacity, lack of association with human malignancy) but with the integration capability of AAV, making them particularly suitable for stable gene transfer which is useful in, for example, gene therapy approaches such as that described herein.
  • a further advantage of the described AAV vectors is that, by virtue of containing AAV TR or ITR and D sequences that flank the gene of interest, it is expected that they integrate into cellular chromosomal DNA. Integration is important for stable gene transfer into cells.
  • Another advantage of the AAV vectors provided herein is that they are packaged efficiently into stable virus particles whether small or large polynucleotides are used. Still, another advantage of the AAV vectors provided herein is that they are less cytotoxic than first generation adenovirus vectors since no adenovirus genes are expressed within transduced cells.
  • the AAV-vector and/or AAV-SERCA2a containing virions described herein are “transfected”, which refers to the uptake of foreign DNA by a cell. That is, a cell“transfected” with exogenous DNA and the DNA is introduced inside the cell membrane.
  • transfection techniques are generally known in the art. See, e.g., Graham et al. (1973) Virology, 52:456, Sambrook et al. (1989) Molecular Cloning, a laboratory manual, Cold Spring Harbor Laboratories, New York, Davis et al. (1986) Basic Methods in Molecular Biology, Elsevier, and Chu et al. (1981) Gene 13: 197, incorporated herein by reference.
  • Such techniques can be used to introduce one or more exogenous DNA moieties, such as a nucleotide integration vector and other nucleic acid molecules, into suitable host cells.
  • the term“host cell” or“host” denotes, for example, mammalian cells, that can be, or have been, used as recipients of an AAV helper construct, an AAV vector plasmid, an accessory function vector, or other transfer DNA.
  • the terms“subject”,“individual” or“patient” are used interchangeably herein and refer to a vertebrate, and in some embodiments, a mammal. Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals and pets.
  • the term includes the progeny of the original cell which has been transfected.
  • a “host cell” or“host” as used herein generally refers to a cell which has been transfected with an exogenous DNA sequence. It is understood that the progeny of a single parental cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation.
  • cell line refers to a population of cells capable of continuous or prolonged growth and division in vitro. Often, cell lines are clonal populations derived from a single progenitor cell. It is further known in the art that spontaneous or induced changes can occur in karyotype during storage or transfer of such clonal populations. Therefore, cells derived from the cell line referred to may not be precisely identical to the ancestral cells or cultures, and the cell line referred to includes such variants.
  • Additional viral vectors useful for delivering the polynucleotides encoding polypeptides of the present disclosure by gene transfer include those derived from the pox family of viruses, such as vaccinia virus and avian poxvirus.
  • vaccinia virus recombinants expressing the novel molecules can be constructed as follows. The DNA encoding a polypeptide is first inserted into an appropriate vector so that it is adjacent to a vaccinia promoter and flanking vaccinia DNA sequences, such as the sequence encoding thymidine kinase (TK). This vector is then used to transfect cells which are simultaneously infected with vaccinia.
  • TK thymidine kinase
  • Homologous recombination serves to insert the vaccinia promoter plus the gene encoding the polypeptide of interest into the viral genome.
  • the resulting TK(-) recombinant can be selected by culturing the cells in the presence of 5-bromodeoxyuridine and picking viral plaques resistant thereto.
  • a vaccinia-based infection/transfection system can be conveniently used to provide for inducible, transient expression or coexpression of one or more polypeptides described herein in host cells of an organism.
  • cells are first infected in vitro with a vaccinia virus recombinant that encodes the bacteriophage T7 RNA polymerase.
  • This polymerase displays extraordinar specificity in that it only transcribes templates bearing T7 promoters.
  • RNA RNA
  • the method provides for high level, transient, cytoplasmic production of large quantities of RNA and its translation products. See, e.g., Elroy-Stein and Moss, Proc. Natl. Acad. Sci. USA (1990) 87:6743-6747; Fuerst et al. Proc. Natl. Acad. Sci. USA (1986) 83:8122-8126, incorporated herein by reference.
  • avipoxviruses such as the fowlpox and canarypox viruses
  • canarypox viruses can also be used to deliver the coding sequences of interest.
  • Recombinant avipox viruses expressing immunogens from mammalian pathogens, are known to confer protective immunity when administered to non-avian species.
  • the use of an Avipox vector is particularly desirable in human and other mammalian species since members of the Avipox genus can only productively replicate in susceptible avian species and therefore are not infective in mammalian cells.
  • alphavirus vectors can also be used for delivery of polynucleotide compositions of the present disclosure, such as those vectors described in U.S. Pat. Nos.
  • VEE Venezuelan Equine Encephalitis
  • molecular conjugate vectors such as the adenovirus chimeric vectors described in Michael et al. J. Biol. Chem. (1993) 268:6866-6869 and Wagner et al. Proc. Natl. Acad. Sci. USA (1992) 89:6099-6103, incorporated herein by reference, can also be used for gene delivery under the disclosure.
  • AAV has been engineered to deliver genes of interest by deleting the internal
  • nonrepeating portion of the AAV genome i.e., the rep and cap genes
  • heterologous gene between the ITRs.
  • the heterologous gene is typically functionally or operatively linked to a heterologous promoter (constitutive, cell-specific, or inducible) capable of driving gene expression in the patient's target cells under appropriate conditions.
  • Termination signals such as polyadenylation sites, can also be included.
  • the term“AAV vector” means a vector derived from an adeno-associated virus serotype, including without limitation, AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, and mutated forms thereof.
  • AAV vectors can have one or more of the AAV wild-type genes deleted in whole or part, the rep and/or cap genes, but retain functional flanking ITR sequences.
  • the AAV vector is derived from an adeno- associated virus serotype AAV1. Despite the high degree of homology, the different serotypes have tropisms for different tissues.
  • AAV 1 The receptor for AAV 1 is unknown; however, AAV 1 is known to transduce skeletal and smooth muscle more efficiently than AAV2.
  • AAV 1 is known to transduce skeletal and smooth muscle more efficiently than AAV2.
  • an AAV vector is defined herein to include at least those sequences required in cis for replication and packaging (e.g., functional ITRs) of the virus.
  • the ITRs need not be the wild-type nucleotide sequences, and may be altered, for example, by the insertion, deletion or substitution of nucleotides, as long as the sequences provide for functional rescue, replication and packaging.
  • AAV vectors must have one copy of the AAV inverted terminal repeat sequences (ITRs) at each end of the genome in order to be replicated, packaged into AAV particles and integrated efficiently into cell chromosomes.
  • ITRs AAV inverted terminal repeat sequences
  • the nucleic acid promoted by ITR can be any desired sequence.
  • the nucleic acid encodes a SERCA2a polypeptide or its isoform (e.g., SERCA2a), which has a desired function in the cell in which the vector is expressed.
  • SERCA2a polypeptide increases the control of Ca++ storage and regulation in the cell, thereby lowering blood pressure in the arteries of the lungs.
  • the ITR consists of nucleotides 1 to 145 at the left end of the AAV DNA genome and the corresponding nucleotides 4681 to 4536 (i.e., the same sequence) at the right hand end of the AAV DNA genome.
  • AAV vectors must have a total of at least 300 nucleotides of the terminal sequence. So, for packaging large coding regions into AAV vector particles, it is important to develop the smallest possible regulatory sequences, such as transcription promoters and polyA addition signal.
  • the adeno-associated viral vector comprising the inverted terminal repeat (ITR) sequences of adeno-associated virus and a nucleic acid encoding SERCA (e.g., SERCA2a), its isoforms, fragments and/or variants, wherein the inverted terminal repeat sequences promote expression of the nucleic acid in the absence of another promoter.
  • ITR inverted terminal repeat
  • SERCA e.g., SERCA2a
  • AAV refers to all serotypes of AAV (i.e., 1-9) and mutated forms thereof.
  • ITR sequences from other serotypes of AAV since the ITRs of all AAV serotypes are expected to have similar structures and functions with regard to replication, integration, excision and transcriptional mechanisms.
  • AAV is also a helper-dependent virus. That is, it requires coinfection with a helper virus (e.g., adenovirus, herpesvirus or vaccinia), in order to form AAV virions.
  • a helper virus e.g., adenovirus, herpesvirus or vaccinia
  • AAV establishes a latent state in which the viral genome inserts into a host cell chromosome, but infectious virions are not produced.
  • the helper virus While AAV can infect cells from different species, the helper virus must be of the same species as the host cell. Thus, for example, human AAV will replicate in canine cells coinfected with a canine adenovirus.
  • AAV helper functions refer to AAV-derived coding sequences which can be expressed to provide AAV gene products that, in turn, function in trans for productive AAV replication.
  • AAV helper functions include both of the major AAV open reading frames (ORFs), rep and cap.
  • ORFs major AAV open reading frames
  • Rep expression products have been shown to possess many functions, including, among others: recognition, binding and nicking of the AAV origin of DNA
  • AAV helper functions are used herein to complement AAV functions in trans that are missing from AAV vectors.
  • AAV helper construct refers generally to a nucleic acid molecule that includes nucleotide sequences providing AAV functions deleted from an AAV vector which is to be used to produce a transducing vector for delivery of a nucleotide sequence of interest.
  • AAV helper constructs are commonly used to provide transient expression of AAV rep and/or cap genes to complement missing AAV functions that are necessary for lytic AAV replication; however, helper constructs lack AAV ITRs and can neither replicate nor package themselves.
  • AAV helper constructs can be in the form of a plasmid, phage, transposon, cosmid, virus, or virion. A number of AAV helper constructs and vectors that encode Rep and/or Cap expression products have been described.
  • recombinant AAV (rAAV) virus is made by cotransfecting a plasmid containing the gene of interest flanked by the two AAV terminal repeats and/or an expression plasmid containing the wild-type AAV coding sequences without the terminal repeats, for example pIM45.
  • the cells are also infected and/or transfected with adenovirus and/or plasmids carrying the adenovirus genes required for AAV helper function.
  • rAAV virus stocks made in such fashion are contaminated with adenovirus which must be physically separated from the rAAV particles (for example, by cesium chloride density centrifugation or column
  • adenovirus vectors containing the AAV coding regions and/or cell lines containing the AAV coding regions and/or some or all of the adenovirus helper genes could be used.
  • Cell lines carrying the rAAV DNA as an integrated provirus can also be used.
  • recombinant AAVs rAAVs
  • Methods for obtaining recombinant AAVs having a desired capsid protein are well known in the art. (See, for example, US 2003/0138772), the contents of which are incorporated herein by reference in their entirety).
  • the methods involve culturing a host cell which contains a nucleic acid sequence encoding an AAV capsid protein or fragment thereof; a functional rep gene; a recombinant AAV vector composed of, AAV inverted terminal repeats (ITRs) and a transgene; and sufficient helper functions to permit packaging of the recombinant AAV vector into the AAV capsid proteins.
  • ITRs AAV inverted terminal repeats
  • the recombinant AAV vector, rep sequences, cap sequences, and helper functions required for producing the rAAV of the disclosure may be delivered to the packaging host cell using any appropriate genetic element (vector).
  • the selected genetic element may be delivered by any suitable method, including those described herein.
  • the methods used to construct any embodiment of this disclosure are known to those with skill in nucleic acid manipulation and include genetic engineering, recombinant engineering, and synthetic techniques. See, e.g., Sambrook et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N. Y. Similarly, methods of generating rAAV virions are well known and the selection of a suitable method is not a limitation on the present disclosure. See, e.g., K. Fisher et al, J. Virol., 70:520-532 (1993) and U.S. Pat. No. 5,478,745.
  • recombinant AAVs may be produced using the triple transfection method (described in detail in U.S. Pat. No. 6,001,650).
  • the recombinant AAVs are produced by transfecting a host cell with an recombinant AAV vector (comprising a transgene) to be packaged into AAV particles, an AAV helper function vector, and an accessory function vector.
  • An AAV helper function vector encodes the“AAV helper function” sequences (i.e., rep and cap), which function in trans for productive AAV replication and encapsidation.
  • the AAV helper function vector supports efficient AAV vector production without generating any detectable wild-type AAV virions (i.e., AAV virions containing functional rep and cap genes).
  • vectors suitable for use with the present disclosure include pHLP19, described in U.S. Pat. No. 6,001,650 and pRep6cap6 vector, described in U.S. Pat. No. 6,156,303, the entirety of both incorporated by reference herein.
  • the accessory function vector encodes nucleotide sequences for non-AAV derived viral and/or cellular functions upon which AAV is dependent for replication (i.e.,“accessory functions”).
  • the accessory functions include those functions required for AAV replication, including, without limitation, those moieties involved in activation of AAV gene transcription, stage specific AAV mRNA splicing, AAV DNA replication, synthesis of cap expression products, and AAV capsid assembly.
  • Viral- based accessory functions can be derived from any of the known helper viruses such as adenovirus, herpesvirus (other than herpes simplex virus type-1), and vaccinia virus.
  • the term“accessory functions” refers to non-AAV derived viral and/or cellular functions upon which AAV is dependent for its replication.
  • the term captures proteins and RNAs that are required in AAV replication, including those moieties involved in activation of AAV gene transcription, stage specific AAV mRNA splicing, AAV DNA replication, synthesis of Cap expression products and AAV capsid assembly.
  • Viral-based accessory functions can be derived from any of the known helper viruses such as adenovirus, herpesvirus (other than herpes simplex virus type-1) and vaccinia virus.
  • “accessory function vector” refers generally to a nucleic acid molecule that includes nucleotide sequences providing accessory functions.
  • An accessory function vector can be transfected into a suitable host cell, wherein the vector is then capable of supporting AAV virion production in the host cell.
  • infectious viral particles as they exist in nature, such as adenovirus, herpesvirus or vaccinia virus particles.
  • accessory function vectors can be in the form of a plasmid, phage, transposon or cosmid.
  • adenovirus mutants incapable of DNA replication and late gene synthesis have been shown to be permissive for AAV replication.
  • mutants within the E2B and E3 regions have been shown to support AAV replication, indicating that the E2B and E3 regions are probably not involved in providing accessory functions.
  • adenoviruses defective in the El region, or having a deleted E4 region are unable to support AAV replication.
  • El A and E4 regions are likely required for AAV replication, either directly or indirectly.
  • Other characterized Ad mutants include: E1B; E2A;
  • Exemplary accessory function vectors include an adenovirus VA RNA coding region, an adenovirus E4 ORF6 coding region, an adenovirus E2A 72 kD coding region, an adenovirus El A coding region, and an adenovirus E1B region lacking an intact ElB55k coding region.
  • “capable of supporting efficient rAAV virion production” is meant the ability of an accessory function vector or system to provide accessory functions that are sufficient to complement rAAV virion production in a particular host cell at a level substantially equivalent to or greater than that which could be obtained upon infection of the host cell with an adenovirus helper virus.
  • the ability of an accessory function vector or system to support efficient rAAV virion production can be determined by comparing rAAV virion titers obtained using the accessory vector or system with titers obtained using infection with an infectious adenovirus.
  • an accessory function vector or system supports efficient rAAV virion production substantially equivalent to, or greater than, that obtained using an infectious adenovirus when the amount of virions obtained from an equivalent number of host cells is not more than about 200 fold less than the amount obtained using adenovirus infection; in some embodiments, not more than about 100 fold less; and in some embodiments, equal to, or greater than, the amount obtained using adenovirus infection.
  • AAV virion is meant a complete virus particle, such as a wild-type (wt)
  • AAV virus particle comprising a linear, single-stranded AAV nucleic acid genome associated with an AAV capsid protein coat.
  • single-stranded AAV nucleic acid molecules of either complementary sense, e.g.,“sense” or“antisense” strands can be packaged into any one AAV virion and both strands are equally infectious.
  • a“recombinant AAV virion,” or“rAAV virion” is defined herein as an infectious, replication-defective virus including an AAV protein shell, encapsidating a heterologous nucleotide sequence of interest which is flanked on both sides by AAV ITRs.
  • a rAAV virion is produced in a suitable host cell which has had an AAV vector, AAV helper functions and accessory functions introduced therein. In this manner, the host cell is rendered capable of encoding AAV polypeptides that are required for packaging the AAV vector
  • the AAV system of the disclosure may also include a sequence encoding a selectable marker.
  • selectable marker or“selectable gene product” as used herein, refers to the use of a gene which may include but is not limited to: bacterial aminoglycoside 3'
  • phosphotransferase gene also referred to as the neo gene
  • bacterial hygromycin G phosphotransferase (hyg) gene which confers resistance to the antibiotic hygromycin
  • bacterial xanthine-guanine phosphoribosyl transferase gene also referred to as the gpt gene
  • the AAV system of the disclosure may also include sequences encoding a visual detectable marker, e.g., green fluorescent protein (GFP) or any other detectable marker standard in the art and can be identified and utilized by one skilled in the art without undue experimentation.
  • GFP green fluorescent protein
  • adenovirus“hybrid” viruses which incorporate desirable features from adenovirus as well as from other types of viruses as a means of generating unique vectors with highly specialized properties.
  • viral vector chimeras were generated between adenovirus and adeno-associated virus (AAV).
  • adenovirus expression vector is meant to include those constructs containing adenovirus sequences sufficient (a) to support packaging of the construct and/or (b) to ultimately express a tissue and/or cell-specific construct that has been cloned therein.
  • the expression vector comprises a genetically engineered form of adenovirus.
  • retrovirus the adenoviral infection of host cells does not result in chromosomal integration because adenoviral DNA can replicate in an episomal manner without potential genotoxicity.
  • adenoviruses are structurally stable, and no genome rearrangement has been detected after extensive amplification.
  • Adenovirus growth and manipulation is known to those of skill in the art, and exhibits broad host range in vitro and in vivo. This group of viruses can be obtained in high titers, e.g.,
  • adenovirus 109 to 1011 plaque-forming units per mL, and they are highly infective.
  • the life cycle of adenovirus does not require integration into the host cell genome.
  • the foreign genes delivered by adenovirus vectors are episomal and, therefore, have low genotoxicity to host cells. No side effects have been reported in studies of vaccination with wild-type adenovirus, demonstrating their safety and/or therapeutic potential as in vivo gene transfer vectors.
  • Adenovirus vectors have been used in eukaryotic gene expression and vaccine
  • recombinant adenovirus could be used for gene therapy (see, e.g., Stratford-Perricaudet et al, Hum. Gene. Ther., 1991; 1 :242-256; Rich et al, 1993).
  • Studies in administering recombinant adenovirus to different tissues include muscle injection, peripheral intravenous injections and stereotactic inoculation into the brain.
  • Recombinant adenovirus and adeno-associated virus can both infect and transduce non-dividing human primary cells.
  • adenovirus vectors While the use of adenovirus vectors is contemplated, such use in gene therapy trials is currently limited by short-lived transgene expression. (Vassalli G, et al, Int. J. Cardiol., 2003; 90(2-3) :229-38). This is due to cellular immunity against adenoviral antigens. Improved “gutless” adenoviral vectors have reduced immunogenicity, yet still are ineffective if maximal expression of the transgene for more than six months is needed or desired for therapeutic effect (Gilbert R, et al, Hum. Mol. Genet., 2003; 12(11): 1287-99). AAV vectors have demonstrated long term expression (>1 year) (Daly T M, et al, Gene Then, 2001; 8(17): 1291-8).
  • a polynucleotide may be integrated into the genome of a target cell. This integration may be in the specific location and orientation via homologous
  • the polynucleotide may be stably maintained in the cell as a separate, episomal segment ofDNA.
  • Such polynucleotide segments or “episomes” encode sequences sufficient to permit maintenance and replication independent of or in synchronization with the host cell cycle. The manner in which the expression construct is delivered to a cell and where in the cell the polynucleotide remains is dependent on the type of expression construct employed.
  • a polynucleotide as disclosed herein is included in a retroviral vector.
  • Retroviruses may be chosen as gene delivery vectors due to their ability to integrate their genes into the host genome, transferring a large amount of foreign genetic material, infecting a broad spectrum of species and cell types and for being packaged in special cell-lines.
  • the retroviral genome contains three genes, gag, pol, and env that code for capsid proteins, polymerase enzyme, and envelope components, respectively.
  • a sequence found upstream from the gag gene contains a signal for packaging of the genome into virions.
  • Two long terminal repeat (LTR) sequences are present at the 5' and 3' ends of the viral genome. These contain strong promoter and enhancer sequences and are also required for integration in the host cell genome.
  • LTR long terminal repeat
  • a nucleic acid encoding a gene of interest is inserted into the viral genome in the place of certain viral sequences to produce a virus that is replication-defective.
  • a packaging cell line is constructed containing the gag, pol, and/or env genes but without the LTR and/or packaging components.
  • a recombinant plasmid containing a cDNA, together with the retroviral LTR and packaging sequences is introduced into this cell line (by calcium phosphate precipitation for example), the packaging sequence allows the RNA transcript of the recombinant plasmid to be packaged into viral particles, which are then secreted into the culture media.
  • the media containing the recombinant retroviruses is then collected, optionally concentrated, and used for gene transfer.
  • Retroviral vectors are able to infect a broad variety of cell types. However, integration and stable expression require the division of host cells.
  • herpes simplex virus is neurotropic, it has generated considerable interest in treating certain disorders. Moreover, the ability of HSV to establish latent infections in non dividing cells without integrating into the host cell chromosome or otherwise altering the host cell's metabolism, along with the existence of a promoter that is active during latency makes HSV an attractive vector. And though much attention has focused on the neurotropic applications of HSV, this vector also can be exploited for other tissues given its wide host range.
  • HSV Another factor that makes HSV an attractive vector is the size and organization of the genome. Because HSV is large, incorporation of multiple genes or expression cassettes is less problematic than in other smaller viral systems. In addition, the availability of different viral control sequences with varying performance (temporal, strength, etc.) makes it possible to control expression to a greater extent than in other systems. It also is an advantage that the virus has relatively few spliced messages, further easing genetic manipulations.
  • HSV also is relatively easy to manipulate and can be grown to high titers. Thus, delivery is less of a problem, both in terms of volumes needed to attain sufficient multiplicity of infection (MOI) and in a lessened need for repeat dosing.
  • MOI multiplicity of infection
  • Lentiviral Vectors are complex retroviruses, which, in addition to the common retroviral genes gag, pol, and env, contain other genes with regulatory or structural function. The higher complexity enables the virus to modulate its life cycle, as in the course of latent infection.
  • Some examples of lentivirus include the Human Immunodeficiency Viruses (HTV 1, REV 2) and the Simian Immunodeficiency Virus (SIV).
  • Lentiviral vectors have been generated by multiply attenuating the HIV virulence genes, for example, the genes env, vif, vpr, vpu and nef are deleted making the vector biologically safe.
  • Lentiviral vectors are known in the art, see, e.g., U.S. Pat. Nos. 6,013,516 and 5,994,136, both of which are incorporated herein by reference.
  • the vectors are plasmid-based or virus-based, and are configured to carry the essential sequences for incorporating foreign nucleic acid, for selection and for transfer of the nucleic acid into a host cell.
  • the gag, pol and env genes of the vectors of interest also are known in the art. Thus, the relevant genes are cloned into the selected vector and then used to transform the target cell of interest.
  • Recombinant lentivirus capable of infecting a non-dividing cell wherein a suitable host cell is transfected with two or more vectors carrying the packaging functions, namely gag, pol and env, as well as rev and tat is described in U.S. Pat. No. 5,994,136, incorporated herein by reference.
  • This describes a first vector that can provide a nucleic acid encoding a viral gag and a pol gene and another vector that can provide a nucleic acid encoding a viral env to produce a packaging cell.
  • Introducing a vector providing a heterologous gene into that packaging cell yields a producer cell which releases infectious viral particles carrying the foreign gene of interest.
  • the env is an amphotropic envelope protein which allows transduction of cells of human and other species.
  • Vaccinia virus vectors have been used extensively because of the ease of their construction, relatively high levels of expression obtained, wide host range and large capacity for carrying DNA.
  • Vaccinia contains a linear, double- stranded DNA genome of about 186 kb that exhibits a marked“A-T” preference. Inverted terminal repeats of about 10.5 kb flank the genome. The majority of essential genes appear to map within the central region, which is most highly conserved among poxviruses.
  • Estimated open reading frames in vaccinia virus number from 150 to 200. Although both strands are coding, extensive overlap of reading frames is not common. At least 25 kb can be inserted into the vaccinia virus genome.
  • Prototypical vaccinia vectors contain transgenes inserted into the viral thymidine kinase gene via homologous recombination. Vectors are selected on the basis of a tk-phenotype. Inclusion of the untranslated leader sequence of encephalomyocarditis virus results in a level of expression that is higher than that of conventional vectors, with the transgenes accumulating at 10% or more of the infected cell's protein in 24 h.
  • the empty capsids of papovaviruses have received attention as possible vectors for gene transfer.
  • the use of empty polyoma was first described when polyoma DNA and purified empty capsids were incubated in a cell-free system. The DNA of the new particle was protected from the action of pancreatic DNase. The reconstituted particles were used for transferring a transforming polyoma DNA fragment to rat Fill cells.
  • the empty capsids and reconstituted particles consist of all three of the polyoma capsid antigens ⁇ P1, VP2 and VP3.
  • U.S. Pat. No. 6,046,173, incorporated herein by reference discloses the use of a pseudocapsid formed from papovavirus major capsid antigen and excluding minor capsid antigens, which incorporates exogenous material for gene transfer.
  • viral vectors may be employed as expression constructs in the present disclosure, such as vectors derived from viruses such as Sindbis virus or cytomegalovirus. They offer several attractive features for various mammalian cells (see, e.g., Friedmann, Science, 1989; 244: 1275- 1281; Horwich et al, J. Virol., 1990; 64:642-650).
  • the nucleic acids to be delivered are housed within an infective virus that has been engineered to express a specific binding ligand.
  • the virus particle will thus bind specifically to the cognate receptors of the target cell and deliver the contents to the cell.
  • a novel approach designed to allow specific targeting of retrovirus vectors was developed based on the chemical modification of a retrovirus by the chemical addition of lactose residues to the viral envelope. This modification can permit the specific infection of hepatocytes via sialogly coprotein receptors.
  • DNA constructs of the present disclosure are generally delivered to a cell.
  • the nucleic acid to be transferred is non-infectious, and can be transferred using non-viral methods.
  • Suitable methods for nucleic acid delivery for use with the current disclosure include methods as described herein or as would be known to one of ordinary skill in the art. Such methods include, but are not limited to, direct delivery of“naked” DNA plasmid via the vasculature (U.S. Pat. No.
  • the nucleic acid encoding the therapeutic gene may be positioned and expressed at different sites.
  • the nucleic acid encoding the therapeutic gene may be stably integrated into the genome of the cell. This integration may be in the cognate location and orientation via homologous recombination (gene replacement) or it may be integrated in a random, non-specific location (gene
  • the nucleic acid may be stably maintained in the cell as a separate, episomal segment of DNA.
  • Such nucleic acid segments or“episomes” encode sequences sufficient to permit maintenance and replication independent of or in synchronization with the host cell cycle. How the expression construct is delivered to a cell and where in the cell the nucleic acid remains is dependent on the type of expression construct employed.
  • the expression construct may be entrapped in a liposome.
  • Liposomes are vesicular structures characterized by a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers.
  • the addition of DNA to cationic liposomes causes a topological transition from liposomes to optically birefringent liquid-crystalline condensed globules. These DNA-lipid complexes are potential non- viral vectors for use in gene therapy.
  • Liposome-mediated nucleic acid delivery and expression of foreign DNA in vitro has been very successful.
  • investigators demonstrated the feasibility of liposome-mediated delivery and expression of foreign DNA in cultured chick embryo, HeLa, and hepatoma cells.
  • Successful liposome-mediated gene transfer in rats after intravenous injection has also been accomplished.
  • various commercial approaches involving “lipofection” technology are also included.
  • the liposome may be complexed with a hemagglutinating virus (HVJ). This has been shown to facilitate fusion with the cell membrane and promote cell entry of liposome-encapsulated DNA.
  • HVJ hemagglutinating virus
  • the liposome may be complexed or employed in conjunction with nuclear non-histone chromosomal proteins (HMG-1).
  • HMG-I nuclear non-histone chromosomal proteins
  • receptor-mediated delivery vehicles which can be employed to deliver a nucleic acid encoding a therapeutic gene into cells. These take advantage of the selective uptake of macromolecules by receptor-mediated endocytosis in almost all eukaryotic cells. Because of the cell type-specific distribution of various receptors, the delivery can be highly specific (Wu and Wu, 1993). Where liposomes are employed, other proteins which bind to a cell surface membrane protein associated with endocytosis may be used for targeting and/or to facilitate uptake, e.g., capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, and proteins that target intracellular localization and enhance intracellular half-life.
  • Receptor- mediated gene targeting vehicles generally consist of two components: a cell receptor-specific ligand and a DNA-binding agent.
  • ligands have been used for receptor- mediated gene transfer. The most extensively characterized ligands are asialoorosomucoid (ASOR) and transferring (Wagner et al, Proc. Natl. Acad. Sci. 87(9):3410-14 (1990), incorporated herein by reference).
  • ASOR asialoorosomucoid
  • a synthetic neoglycoprotein which recognizes the same receptor as ASOR, has been used as a gene delivery vehicle.
  • Epidermal growth factor (EGF) has also been used to deliver genes to squamous carcinoma cells.
  • the delivery vehicle may comprise a ligand and a liposome.
  • a ligand for example, investigators have employed lactosyl-ceramide, a galactose-terminal asialganglioside, incorporated into liposomes and observed an increase in the uptake of the insulin gene by hepatocytes.
  • a nucleic acid encoding a therapeutic gene also may be specifically delivered into a cell type such as cardiac cells, by any number of receptor-ligand systems with or without liposomes.
  • the expression construct may simply consist of naked recombinant DNA or plasmids. Transfer of the construct may be performed by any of the methods mentioned above which physically or chemically permeabilize the cell membrane. This is applicable particularly for transfer in vitro, however, it may be applied for in vivo use as well. It is envisioned that therapeutic DNA may also be transferred in a similar manner in vivo.
  • Wolff et al. U.S. Pat. No. 6,867,196, incorporated herein by reference
  • the disclosure provides a method of treating or providing treatment for a subject suffering from idiopathic pulmonary fibrosis.
  • “treating” or“treatment” of the subject is an approach for obtaining beneficial or desired clinical results. Desired clinical results include, but are not limited to, prevention of remodeling of smooth muscle cells on pulmonary arteries, restored lung function, and/or reduction of severity of or inhibition of symptoms associated with idiopathic pulmonary fibrosis.
  • Desired clinical results include, but are not limited to, prevention of remodeling of smooth muscle cells on pulmonary arteries, restored lung function, and/or reduction of severity of or inhibition of symptoms associated with idiopathic pulmonary fibrosis.
  • the desired benefits or clinical results are independent of the mechanism, although the mechanism of activity is encompassed within the result.
  • the particular symptoms which yield to treatment in accordance with the disclosure will depend on severity of the idiopathic pulmonary fibrosis being treated.
  • the therapeutic composition to treat idiopathic pulmonary fibrosis includes a vector that includes a gene encoding SERCA2a or its isoforms.
  • SERCA2a gene or transgene of the disclosure when contained in a therapeutic composition, are typically operatively linked to various regulatory elements which has been modified to include promoter and other sequences necessary for expression and, where desired, secretion of the desired translation product (e.g., a peptide or protein).
  • the desired translation product e.g., a peptide or protein
  • SERCA2a polynucleotides may be conjugated to or used in association with other
  • polynucleotides which operatively code for regulatory proteins that control the expression of these polypeptides or may contain recognition, promoter and secretion sequences.
  • regulatory polynucleotides and incorporate them into SERCA2a polynucleotides of the disclosure without undue experimentation.
  • the therapeutic composition to treat or reduce symptoms associated with idiopathic pulmonary fibrosis includes a polynucleotide encoding a protein capable of indirectly modulating smooth muscle Ca2+ and contractility.
  • the cardiac protein phospholamban is inhibitory to the activity of SERCA2a.
  • the present methods include methods to decrease the level or activity of phospholamban in a pulmonary smooth muscle cell.
  • expression of a pseudophosphorylated mutant of phospholamban is increased.
  • a mutant has replacement of the serine 16 phosphorylation site with the basic amino acid glutamine, thereby introducing a negative charge at position 16 (S16E phospholamban mutant).
  • This pseudophosphorylated form of phospholamban competes with natural phospholamban for binding to SERCA, thereby decreasing the opportunity for the natural protein to negatively affect SERCA activity. See, e.g., WO 2000/025804, incorporated herein by reference.
  • compositions of the present disclosure are
  • “ameliorative,” means to improve or relieve a subject of symptoms associated with a disorder, and includes curing such a disorder.
  • nucleic acids and proteins of SERCA, phospholamban, inhibitor-1 of the type 1 phosphatase, S100A1, and sarcolipin, as well as related nucleic acids and proteins which play a role in Ca2+, are targets for polynucleotides of the present disclosure.
  • a viral vector and transgene is AAV2/l/SERCA2a, which is comprised of an AAV serotype 1 viral capsid enclosing a single-stranded 4486 nucleotide DNA containing the human SERCA2a expression cassette flanked by ITRs derived from AAV serotype 2.
  • the icosahedral capsid consists of three related AAV serotype 1 capsid proteins,
  • the AAV2/l/SERCA2a DNA contains the following components: AAV serotype2 based FIR at the 3' and 5' ends, flanking the CMV-hSERCA2a-polyA expression cassette.
  • the expression cassette contains the cytomegalovirus immediate early
  • CMVie enhancer/promoter driving transcription of sequences including a hybrid intron from the commercial plasmid pCI (Promega— GenBank U47119), the hSERCA2a cDNA (coding sequence identical to GenBank NM-001681), and a bovine growth hormone polyadenylation signal (BGHpA, (GenBank M57764)).
  • the hybrid intron was designed using the 5 '-donor site from the first intron of the human b-globin and 3 '-acceptor site from the intron located between the leader and body of an immunoglobulin gene heavy chain variable region.
  • the therapeutic agents including polynucleotides, polynucleotides in combination with a vector, both viral and non-viral, as discussed above can be used in the preparation of a medicament for the treatment of pulmonary disease (e.g., idiopathic pulmonary fibrosis), where the medicament is administered by direct infusion into the circulatory system or by intra-tracheal or inhalation administration.
  • pulmonary disease e.g., idiopathic pulmonary fibrosis
  • Methods for delivery via inhalation are discussed in, e.g., Moss, et al. Human Gene Therapy, 18:726-732 (August 2007), which is incorporated herein by reference.
  • compositions of the present disclosure are delivered to a“target cell” or “host cell” or“target tissue” and equivalents thereof, which refers to the cell, tissue of the host in which expression of the operatively encoding polynucleotide is sought.
  • a“target cell” or “host cell” or“target tissue” and equivalents thereof which refers to the cell, tissue of the host in which expression of the operatively encoding polynucleotide is sought.
  • adeno- associated viral-SERCA2a compositions delivered in a lung cell or to lung tissue.
  • administering a vector that includes SERCA increases levels of SERCA2a mRNA in one or more lung cells. In some aspects, administering a vector that includes SERCA (e.g., SERCA2a) increases levels of SERCA2a protein in one or more lung cells. In some embodiments, administering a vector that includes SERCA2 decreases IL-6 mRNA in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases IL-6 protein in one or more lung cells.
  • administering a vector that includes SERCA2a decreases the amount of detectable fibrosis in a lung sample.
  • detection of fibrosis can be identified using Hematoxylin & Eosin and/or Masson’s trichrome staining.
  • administering a vector that includes SERCA2a decreases
  • administering a vector that includes SERCA2a decreases COL1A1 protein in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases COL3A1 mRNA in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases COL3 Al protein in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases CTGF mRNA in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases CTGF protein in one or more lung cells.
  • administering a vector that includes SERCA2a decreases TGF- beta mRNA in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases TGF-beta protein in one or more lung cells.
  • administering a vector that includes SERCA2a decreases the mRNA of one or more of heparan Sulfate 6-O-Sulfotransferase 1 (HS6ST1) and Versican (VCAN), hyaluronan synthase 2, fibromodulin, and syndican 4 in one or more lung cells.
  • administering a vector that includes SERCA2a decreases the protein level of one or more of heparan Sulfate 6-O-Sulfotransferase 1 (HS6ST1) and Versican (VC AN), hyaluronan synthase 2, fibromodulin, and syndican 4 in one or more lung cells.
  • An aspect of the present disclosure is packaging of the AAV-SERCA2a virions.
  • Growth and propagation of the virions will require a“defmed-medium conditions”, which refer to environments for culturing cells where the concentration of components therein required for optimal growth are detailed.
  • a“defmed-medium conditions” refer to environments for culturing cells where the concentration of components therein required for optimal growth are detailed.
  • the culture conditions are typically animal-free conditions or free of non-human animal proteins.
  • vectors useful in the present disclosure have varying transduction efficiencies.
  • the viral or non-viral vector transduces more than, equal to, or at least about 10%, 20%, 30%, 40%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, 100% of the cells of the targeted vascular territory.
  • more than one vector can be used simultaneously, or in sequence. This can be used to transfer more than one polynucleotide, and/or target more than one type of cell. Where multiple vectors or multiple agents are used, more than one transduction/transfection efficiency can result.
  • inventions of the present disclosure can be“synergistic” or have“synergy”, which refers to an activity of administering combinations of proteins, lipids, nucleic acids,
  • carbohydrates or chemical compounds that is greater than the additive activity of the proteins, lipids, nucleic acids, carbohydrates, or chemical compounds, if administered individually.
  • the embodiments of the present disclosure can be“co-administered”, which refers to two or more proteins, lipids, nucleic acids, carbohydrates, or chemical compounds of a combination that are administered so that the therapeutic or prophylactic effects of the combination is greater than the therapeutic effect of either proteins, lipids, nucleic acids, carbohydrates, or chemical compounds administered alone.
  • the two or more proteins, lipids, nucleic acids, carbohydrates, or chemical compounds can be administered simultaneously or sequentially. Simultaneously co administered proteins, lipids, nucleic acids, carbohydrates, or chemical compounds may be provided in one or more pharmaceutically acceptable compositions.
  • Sequential co-administration includes, but is not limited to, instances in which the proteins, lipids, nucleic acids, carbohydrates, or chemical compounds are administered so that each protein, lipid, nucleic acid, carbohydrate, or chemical compound can be present at the treatment site at the same time.
  • kits for producing a vector comprising expressing the vector from a host cell.
  • a vector e.g., an AAV vector
  • the methods of producing a vector include culturing a host cell containing the vector.
  • the host cell includes a hybrid vector comprising: (i) adenovirus sequences comprising the adenovirus 5' and 3' cis-elements necessary for replication and virion encapsidation; and (ii) adeno-associated virus (AAV) sequences comprising the 5' and 3' inverted terminal repeat (ITRs) of an AAV, said AAV sequences flanked by the adenovirus sequences of (ii); and (iii) a selected transgene (e.g., any one of SEQ ID NOs:l-20) or a variant thereof) operatively linked to sequences which regulate its expression in a target cell, said gene and regulatory sequences flanked by the AAV sequences of (ii).
  • a hybrid vector comprising: (i) adenovirus sequences comprising the adenovirus 5' and 3' cis-elements necessary for
  • the host further includes an optional helper adenovirus, wherein the host cell and/or the helper virus provide the adenovirus sequences necessary to package the hybrid vector and generate a recombinant hybrid adenovirus.
  • the methods of producing a vector include the step of isolating from said culture the recombinant hybrid adenovirus.
  • cells e.g., host cells
  • the vectors include polynucleotides encoding an AAV vector in host cells.
  • the host cell is a mammalian cell.
  • the host cell is selected from the group consisting of E. coli, Pseudomonas, Bacillus, Streptomyces, yeast, CHO, YB/20, NSO, PER-C6, HEK-293T, NIH- 3T3, HeLa, BHK, Hep G2, SP2/0, R1 .1, B-W, L-M, COS 1, COS 7, BSC1, BSC40, BMT10 cell, plant cell, insect cell, and human cell in tissue culture.
  • disclosed is an isolated AAV vector that includes any one of SEQ ID NO: 1-20, or a variant thereof.
  • the present disclosure also embodies administering“pharmaceutically acceptable” molecular entities and compositions that are physiologically tolerable and do not typically produce an allergic or similar untoward reaction, such as gastric upset, dizziness and the like, when administered to a human.
  • pharmaceutically acceptable means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.
  • carrier refers to a diluent, adjuvant, excipient, or vehicle with which the compound is administered.
  • Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like.
  • water or aqueous solution saline solutions and aqueous dextrose and glycerol solutions are employed as carriers, particularly for injectable solutions.
  • Suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin.
  • the term“therapeutic composition” is defined as one comprising at least a gene encoding SERCA2 or its isoforms (e.g., SERCA2a).
  • the therapeutic composition may also contain other nucleic acid molecules (e.g., a viral vector) and
  • pharmaceutically acceptable entities and substances such as water, minerals, carriers such as proteins, and other excipients known to one skilled in the art.
  • compositions as disclosed herein may be administered in combination with other agents as well, such as, e.g., other proteins or
  • compositions may thus be delivered along with various other agents as required in the particular instance.
  • compositions may be purified from host cells or other biological sources, or alternatively may be chemically synthesized as described herein. Likewise, such compositions may further comprise substituted or derivatized RNA or DNA compositions.
  • any of the pharmaceutical compositions described herein can contain pharmaceutically acceptable salts of the polynucleotides and polypeptides of the disclosure.
  • Such salts can be prepared, for example, from pharmaceutically acceptable non-toxic bases, including organic bases (e.g., salts of primary, secondary and tertiary amines and basic amino acids) and inorganic bases (e.g., sodium, potassium, lithium, ammonium, calcium and magnesium salts).
  • an“adjuvant” or equivalents thereof refers to a compound or mixture that enhances the immune response to an antigen.
  • An adjuvant can serve as a tissue depot that slowly releases the antigen and also as a lymphoid system activator that non-specifically enhances the immune response. Often, a primary challenge with an antigen alone, in the absence of an adjuvant, will fail to elicit a humoral or cellular immune response.
  • Adjuvants include, but are not limited to, complete Freund's adjuvant, incomplete Freund's adjuvant, saponin, mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil or hydrocarbon emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum.
  • the adjuvant is pharmaceutically acceptable.
  • the term“molecular adjuvant” is defined as a protein, lipid, nucleic acid, carbohydrate, or chemical compound for which dendritic cells (DCs), macrophages, B cells, T cells, and/or NK cells have a known receptor whose occupancy leads to a defined sequence of intracellular signal transduction and a change in the phenotype resulting in an improvement in the quantity or quality of the ensuing immune response.
  • DCs dendritic cells
  • macrophages B cells, T cells, and/or NK cells
  • the cells as described above are collectively referred to as“immune cells.”
  • compositions of the present disclosure include those provided by Bioject, Inc. (Portland, Oreg.), some examples of which are described in U.S. Pat. Nos. 4,790,824;
  • compositions of the present disclosure may alternatively be incorporated with one or more excipients in the form of a mouthwash, dentifrice, buccal tablet, oral spray, or sublingual orally- administered formulation.
  • the active ingredient may be incorporated into an oral solution such as one containing sodium borate, glycerin and potassium bicarbonate, or dispersed in a dentifrice, or added in a therapeutically-effective amount to a composition that may include water, binders, abrasives, flavoring agents, foaming agents, and humectants.
  • the compositions may be fashioned into a tablet or solution form that may be placed under the tongue or otherwise dissolved in the mouth.
  • Vaccine formulations can also be delivered to the nasal mucosa, aerosolized for inhalational delivery, or delivered to the mucosal surfaces of the female and male genital track or the rectum. Vaccine formations may also be formulated for transdermal delivery.
  • compositions disclosed herein parenterally, intravenously, intramuscularly, intratracheally, or even
  • compositions of the disclosure may be delivered via inhalation, intravenous injection, intracardiac injection, intratracheally. In another embodiment, the compositions of the disclosure are administered via mechanical ventilation.
  • solutions of the active compounds as free base or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose.
  • Dispersions may also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations generally will contain a preservative to prevent the growth of microorganisms.
  • Illustrative pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions (for example, see U.S. Pat. No. 5,466,468, incorporated herein by reference).
  • the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils.
  • polyol e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like
  • suitable mixtures thereof e.g., vegetable oils
  • vegetable oils e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like
  • Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and/or by the use of surfactants.
  • the prevention of the action of microorganisms can be facilitated by various antibacterial and antifungal agents, for example, parabens,
  • chlorobutanol phenol, sorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars or sodium chloride, will be included.
  • Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
  • the solution for parenteral administration in an aqueous solution, should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose.
  • aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration.
  • a sterile aqueous medium that can be employed will be known to those of skill in the art in light of the present disclosure.
  • one dosage may be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example,“Remington's Pharmaceutical Sciences” 15th Edition, pages 1035- 1038 and 1570-1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. Moreover, for human administration, in some
  • preparations meets sterility, pyrogenicity, and the general safety and purity standards as required by FDA Office of Biologies standards.
  • compositions disclosed herein may be formulated in a neutral or salt form.
  • Illustrative pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective.
  • the carriers can further comprise any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like.
  • solvents dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like.
  • the use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the
  • compositions are pharmaceutically-acceptable.
  • pharmaceutically-acceptable refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human.
  • the pharmaceutical compositions may be delivered by intranasal sprays, inhalation, and/or other aerosol delivery vehicles.
  • Methods for delivering genes, nucleic acids, and peptide compositions directly to the lungs via nasal aerosol sprays has been described, e.g., in U.S. Pat. No. 5,756,353 and U.S. Pat. No. 5,804,212, each of which is incorporated herein by reference.
  • polynucleotides e.g., viral vectors
  • intranasal microparticle resins Takenaga et al, J Controlled Release (1998) 52(l-2):81-7; and Moss, et al.
  • liposomes, nanocapsules, microparticles, lipid particles, vesicles, and the like are used for the introduction of the compositions of the present disclosure into suitable host cells/organisms.
  • the compositions of the present disclosure may be formulated for delivery either encapsulated in a lipid particle, a liposome, a vesicle, a
  • compositions of the present disclosure can be bound, either covalently or non-covalently, to the surface of such carrier vehicles.
  • liposome and liposome-like preparations as potential drug carriers is generally known to those of skill in the art (see for example, Lasic, Trends Biotechnol (1998) 16(7):307-21; Takakura, Nippon Rinsho (1998) 56(3):691-5; Chandran et al, Indian J Exp Biol (1997) 35(8):801-9; Margalit, Crit. Rev Ther Drug Carrier Syst (1995) 12(2-3):233-61; U.S. Pat. No. 5,567,434; U.S. Pat. No. 5,552,157; U.S. Pat. No. 5,565,213; U.S. Pat. No.
  • the disclosure provides for pharmaceutically- acceptable nanocapsule formulations of the compositions of the present disclosure.
  • Nanocapsules can generally entrap compounds in a stable and reproducible way (see, for example, Quintanar- Guerrero et al, Drug Dev India Pharm (1998) 24(12): 1113-28).
  • ultrafme particles sized around 0.1 pm
  • Such particles can be made as described, for example, by Couvreur et al, Crit. Rev Ther Drug Carrier Syst.
  • continuous dosing schedules include daily continuous administration where SERCA2a is administered each day, and continuous bolus administration schedules, where SERCA2a is administered at least once per day by intravenous or subcutaneous injections.
  • Exemplary continuous administration schedules include, but are not limited to, at least 2, 3, 4, 5, 6, or 7 days, at least 1, 2, 3, 4, 5, or 6 weeks or more, or any combination thereof.
  • discontinuous dosing schedules The exact parameters of discontinuous administration schedules will vary according the formulation, method of delivery and the clinical needs of the subject. For example, if the SERCA2a formulation is administered by inhalation, administration schedules comprising a first period of administration followed by a second period in which SERCA2a is not administered which is greater than, equal to, or less than the period where SERCA2a is administered.
  • discontinuous administration schedules for inhalation administration include, but are not limited to, schedules comprising periods selected from 1, 2, 3, 4, 5, 6, or 7 days, 1, 2, 3, 4, 5, 6, or more weeks, or any combination thereof, and off periods selected from 1, 2, 3, 4, 5, 6, or 7 days, 1, 2, 3, 4, 5, 6 or more weeks.
  • Continuous and discontinuous administration schedules by any method also include dosing schedules in which the dose is modulated throughout the effective period, such that, for example, at the beginning of the SERCA2a administration period; the dose is low and increased until the end of the SERCA2a administration period; the dose is initially high and decreased during the SERCA2a administration period; the dose is initially low, increased to a peak level, then reduced towards the end of the SERCA2a administration period; and any combination thereof.
  • the dosing schedules may be performed using any method of standard in the art, such as a catheter system.
  • compositions will comprise sufficient genetic material to produce a therapeutically effective amount of the SERCA2a or portions or fragments or functional fragments of interest, i.e., an amount sufficient to reduce or ameliorate symptoms of the disease state in question or an amount sufficient to confer the desired benefit.
  • the compositions may also contain a
  • compositions include any pharmaceutical agent that does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity.
  • pharmaceutically acceptable excipients include, but are not limited to, sorbitol, any of the various TWEEN compounds, and liquids such as water, saline, glycerol and ethanol.
  • Pharmaceutically acceptable salts can be included therein, for example, mineral acid salts such as hydrochlorides,
  • auxiliary substances such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles.
  • One particularly useful formulation includes recombinant AAV virions in combination with one or more dihydric or polyhydric alcohols, and, optionally, a detergent, such as a sorbitan ester. See, for example, International Publication No. WO 00/32233, incorporated herein by reference.
  • an effective amount of viral vector which must be added can be empirically determined.
  • Administration can be effected in one dose, continuously or intermittently throughout the course of treatment. Methods of determining the most effective means and dosages of administration are well known to those of skill in the art and will vary with the viral vector, the composition of the therapy, the target cells, and the subject being treated. Single and multiple administrations can be carried out with the dose level and pattern being selected by the treating physician.
  • transgene can be expressed by the delivered recombinant virion.
  • separate vectors each expressing one or more different transgenes, can also be delivered as described herein.
  • viral vectors delivered by the methods of the present disclosure be combined with other suitable compositions and therapies.
  • certain systemically delivered compounds such as muristerone, ponasteron, tetracyline or aufin may be administered in order to regulate expression of the transgene.
  • compositions of the present disclosure contain SERCA2a or SERC2a or portions, or functional fragments thereof operatively linked to various regulatory elements in an AAV vector, substantially similar to that previously described above including any excipients or carriers or agents necessary to effectuate efficient, but non-toxic delivery of the therapeutic compositions will be produced. Also control AAV compositions will be produced, e.g. AAV-GFP constructs.
  • an AAV vector can be constructed which encodes a recombinant fusion SERCA2a operatively linked to green fluorescent protein (GFP) tag (AAV-SERCA2a-GFP), for recognition.
  • GFP green fluorescent protein
  • the host cell (or packaging cell) must also be rendered capable of providing nonAAV- derived functions, or“accessory functions”, in order to produce rAAV virions.
  • Accessory functions are nonAAV-derived viral and/or cellular functions upon which AAV is dependent for its replication, including at least those nonAAV proteins and RNAs that are required in AAV replication, including those involved in activation of AAV gene transcription, stage specific AAV mRNA splicing, AAV DNA replication, synthesis of Cap expression products and AAV capsid assembly.
  • Viral-based accessory functions can be derived from any of the known helper viruses.
  • accessory functions can be introduced into and then expressed in host cells using methods known to those of skill in the art.
  • accessory functions are provided by infection of the host cells with an unrelated helper virus.
  • helper viruses include adenoviruses; herpesviruses, e.g., herpes simplex virus types 1 and 2; and vaccinia viruses.
  • Nonviral accessory functions will also find use herein, such as those provided by cell synchronization using any of various known agents. See, e.g., Buller et al. (1981) J. Virol. 40:241 247; McPherson et al. (1985) Virology 147:217 222; Schlehofer et al. (1986) Virology 152: 110 117.
  • accessory functions can be provided using an accessory function vector as defined above. See, e.g., U.S. Pat. No. 6,004,797 and International Publication No. WO
  • Nucleic acid sequences providing the accessory functions can be obtained from natural sources, such as from the genome of an adenovirus particle, or constructed using recombinant or synthetic methods known in the art. Also, the full-complement of adenovirus genes is not required for accessory helper functions. In fact, adenovirus mutants incapable of DNA replication and late gene synthesis have been shown to be permissive for AAV replication. Ito et al, (1970) J. Gen. Virol. 9:243; Ishibashi et al, (1971) Virology 45:317; and Carter et al, (1983) Virology 126:505. For example, reports show that El A and E4 regions are likely required for AAV replication, either directly or indirectly. Laughlin et al, (1982) J. Virol 41:868; Janik et al, (1981) Proc. Natl.
  • Infection of the host cell with a helper virus, or transfection of the host cell with an accessory function vector, allows expression of the accessory functions which transactivate the AAV helper construct to produce AAV Rep and/or Cap proteins.
  • the Rep expression products in turn excise the recombinant DNA (including the DNA of interest, e.g., SERCA2a) from the AAV expression vector.
  • the Rep proteins also serve to duplicate the AAV genome.
  • the expressed Cap proteins assemble into capsids, and the recombinant AAV genome is packaged into the capsids, AAV replication proceeds, and the DNA is packaged into rAAV virions.
  • rAAV virions can be purified from the host cell using a variety of conventional purification methods, such as column chromatography, CsCl gradients, and the like. For example, a plurality of column purification steps can be used, such as purification over an anion exchange column, an affinity column and/or a cation exchange column. See, for example, International Publication No. WO 02/12455.
  • adenovirus can be inactivated by heating to temperatures of approximately 60° C. for, e.g., 20 minutes or more. This treatment effectively inactivates only the helper virus since AAV is extremely heat stable while the helper adenovirus is heat labile.
  • the resulting rAAV virions containing the SERCA2a nucleotide sequence of interest, or fragment, or functional fragment, or portion thereof can then be used for gene delivery using the techniques described below.
  • Recombinant AAV virions may be introduced into smooth muscle cells using either in vivo or in vitro (also termed ex vivo) transduction techniques. If transduced in vitro, the desired recipient cell (e.g., a lung cell) will be removed from the subject, transduced with rAAV virions and reintroduced into the subject. Alternatively, syngeneic or xenogeneic cells can be used where those cells will not generate an inappropriate immune response in the subject.
  • transduced cells can be transduced in vitro by combining recombinant AAV virions (rAAV) with cells to be transduced in appropriate media, and those cells harboring the DNA of interest can be screened using conventional techniques such as Southern blots and/or PCR, or by using selectable markers. Transduced cells can then be formulated into rAAV virions (rAAV) with cells to be transduced in appropriate media, and those cells harboring the DNA of interest can be screened using conventional techniques such as Southern blots and/or PCR, or by using selectable markers. Transduced cells can then be formulated into rAAV virions
  • compositions as described above, and the composition introduced into the subject by various techniques as described below, in one or more doses.
  • Recombinant AAV (rAAV) virions or cells transduced in vitro may be delivered directly to muscle by injection with a needle, catheter or related device, using techniques known in the art.
  • the rAAV virions will be formulated into pharmaceutical compositions and one or more dosages may be administered directly in the indicated manner.
  • a therapeutically effective dose will include on the order of from about 10 8 /kg to about 10 16 /kg of the rAAV virions; or from about 10 10 /kg to about 10 14 /kg; or from about 10 u /kg to about 10 13 /kg of the rAAV virions (or viral genomes, also termed“vg” or“v.g.”), or any value within these ranges.
  • CED convection-enhanced delivery
  • recombinant virions can be delivered to many cells over large areas of muscle.
  • the delivered vectors efficiently express transgenes in muscle cells.
  • Any convection-enhanced delivery device may be appropriate for delivery of viral vectors.
  • the device is an osmotic pump or an infusion pump. Both osmotic and infusion pumps are commercially available from a variety of suppliers, for example Alzet Corporation, Hamilton Corporation, Alza, Inc., Palo Alto, Calif.).
  • a viral vector is delivered via CED devices as follows.
  • a catheter, cannula or other injection device is inserted into appropriate muscle tissue in the chosen subject, such as skeletal muscle.
  • appropriate muscle tissue such as skeletal muscle.
  • the present disclosure describes a perfusion method
  • various perfusion methods are available and standard in the art, and without being held to any one method, any perfusion method which gives the desired result is anticipated, such as a methods utilizing a catheter.
  • the objective of the perfusion methods is to increase the time of contact between the vector (e.g., adenovirus, AAV, lentivirus vectors) and the target cells (e.g., smooth muscle cells).
  • the disclosure encompasses perfusion methods such as closed-circuit perfusion methods carried out at body temperature, and under defined conditions at, for example, 37° C., for about 2, 5, 10, 12, 15, 30, 60 or more minutes, or in larger animals or humans for about 2, 4, 6, 8, 10, 12 or more hours, allowing viral entry into the target cells and to create optimal conditions for gene expression and protein synthesis.
  • perfusion methods such as closed-circuit perfusion methods carried out at body temperature, and under defined conditions at, for example, 37° C., for about 2, 5, 10, 12, 15, 30, 60 or more minutes, or in larger animals or humans for about 2, 4, 6, 8, 10, 12 or more hours, allowing viral entry into the target cells and to create optimal conditions for gene expression and protein synthesis.
  • various excipients e.g., natural and un-natural amino acids, growth factors and the like may be added to provide enough material for protein synthesis.
  • the effect on pulmonary artery pressure and cardiac function may be determined using a pressure-volume measurement system post-injection e.g., one week or one month post-injection. Repeated measurements may be continued in order to monitor the short term and long-terms effects and efficacy of the therapy. For example, if after one week the results are considered not significant, then new trials using higher (or lower) dosages, or multiple dosages may be performed.
  • Studies may be performed to determine gene expression including removal of pulmonary tissues receiving the perfusion as well as surrounding and/or control tissues.
  • the tissues may be histologically processed by methods standard in the art, e.g., fixation methods, vibratome or cutting methods, and the like.
  • fixation methods e.g., fixation methods, vibratome or cutting methods, and the like.
  • immunohisto chemistry using a SERCA2 or SERCA2a
  • polynucleotides or antibodies which are immunogenic against SERCA2 or SERCA2 are polynucleotides or antibodies which are immunogenic against SERCA2 or SERCA2
  • polypeptides may be performed. Further, for those animals receiving the AAV-GFP
  • compositions, expression of GFP in the tissues may be measured using fluorescent microscopy or any other method standard in the art which can measure and detect fluorescence.
  • the methods of the disclosure include administering to a subject in need thereof a therapeutically effective amount of an siRNA in a viral vector, where the RNAi decreases expression and/or activity of phospholamban (PLB), in an amount effective to transduce pulmonary smooth muscle cells of the subject, thereby resulting in expression of the RNAi and treating idiopathic pulmonary fibrosis in the subject.
  • PLB phospholamban
  • PLB nucleic acids include but are not limited to, GenBank Accession Nos. NM 02667 (Simmerman et al, J Biol Chem (1986) 261(28): 13333-13341); NM_023129 (Ganim et al, Cir Res (1992) 71(5): 1021-1030); NM_022707 (Wang and Nadal-Ginard, Adv Exp Med Biol (1991) 304:387-395); BC134584 (Moore et al, direct submission (17 Mar.
  • RNA interference refers generally to a process in which a double-stranded RNA molecule changes the expression of a nucleic acid sequence with which the double- stranded or short hairpin RNA molecule shares substantial or total homology. While not being bound by theory, the mechanism of action may include, but is not limited to, direct or indirect down regulation of the expression of the PLB gene, decrease in PLB mRNA, and/or a decrease in PLB activity.
  • RNAi including“short inhibitory RNA (siRNA),” refer to RNA sequences that elicit RNA interference, and which is transcribed from a vector.
  • RNA short hairpin RNA
  • shRNA RNA structure having a duplex region and a loop region. This term should also be understood to specifically include RNA molecules with stem-loop or panhandle secondary structures. In some embodiments of the present disclosure, RNAis are expressed initially as shRNAs.
  • RNAi is generally optimized by identical sequences between the target and the RNAi.
  • the homology between the RNAi and PLB is at least 70% nucleotide sequence identity, and may be at least 75% nucleotide sequence identity.
  • Homology includes, but is not limited to, at least 80% nucleotide sequence identity, and is at least 85% or even 90% nucleotide sequence identity.
  • sequence homology between the target sequence and the sense strand of the RNAi is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% nucleotide sequence identity.
  • RNAi efficacy it is more important that the antisense strand be homologous to the target sequence. In some circumstances, it is known that 17 out of 21 nucleotides is sufficient to initiate RNAi, but in other circumstances, identity of 19 or 20 nucleotides out of 21 is required. While not being bound by theory, at a general level, greater homology is required in the central part of a double stranded region than at its ends.
  • Some predetermined degree of lack of perfect homology may be designed into a particular construct so as to reduce its RNAi activity which would result in a partial silencing or repression of the target gene's product, in circumstances in which only a degree of silencing was sought. In such a case, only one or two bases of the antisense sequence may be changed.
  • the sense strand is more tolerant of mutations. While not being bound by theory, this may be due to the antisense strand being the one that is catalytically active. Thus, less identity between the sense strand and the transcript of a region of a target gene will not necessarily reduce RNAi activity, particularly where the antisense strand perfectly hybridizes with that transcript.
  • Mutations in the sense strand may be useful to assist sequencing of hairpin constructs and potentially for other purposes, such as modulating dicer processing of a hairpin transcript or other aspects of the RNAi pathway.
  • hybridizing and“annealing” including grammatical equivalents thereof, are used interchangeably in this specification with respect to nucleotide sequences and refer to nucleotide sequences that are capable of forming Watson-Crick base pairs due to their complementarity.
  • non-Watson-Crick base pairing is also possible, especially in the context of RNA sequences. For example a so-called “wobble pair” can form between guanosine and uracil residues in RNA.
  • dsRNA double-stranded RNA
  • dsRNA double-stranded RNA
  • the dsRNA complex comprises a first nucleotide sequence that hybridizes under stringent conditions, including a wash step of 0.2xSSC at 65° C., to a nucleotide sequence of at least one mammalian gene and a second nucleotide sequence which is complementary to the first nucleotide sequence.
  • the first nucleotide sequence might be linked to the second nucleotide sequence by a third nucleotide sequence (e.g., an RNA loop) so that the first nucleotide sequence and the second nucleotide sequence are part of the same RNA molecule; alternatively, the first nucleotide sequence might be part of one RNA molecule and the second nucleotide sequence might be part of another RNA molecule.
  • a dsRNA complex may be formed by intramolecular hybridization or annealing or the ds RNA complex is formed by intermolecular hybridization or annealing.
  • RNA, protein samples and formalin-fixed paraffin -embedded sections of human IPF and healthy control donors, non-IPF were used in the present study.
  • the samples were anonymous and archived specimens.
  • the protocol was approved by the local research and independent ethics committee of the University General Consortium Hospital of Valencia (CEIC/2013). Informed written consent was obtained from each participant.
  • NHLF Normal human lung fibroblast
  • FGM-2 medium supplemented with 5% fetal bovine serum (FBS) in 5% C02 at 37°C and passaged at the confluence.
  • FBS fetal bovine serum
  • shRNA and lentivirus production The SERCA2a shRNA (TRCN0000038529) and FOXM1 shRNA (TRCN0000015543) cloned in the pLKO.l lentiviral expression vector was obtained from Dharmacon.
  • the constructs and viral packaging plasmids pSPAX2 and pMD2.G were co-transfected into 293T cells using Lipofectamine 2000 (Invitrogen Life Technologies) per the manufacturer’s recommendations.
  • the virus was concentrated by incubation with the Lenti-X Concentrator (Clontech) as recommended by the supplier.
  • the concentrated virus particles were used to infect NHLF cells for 72 hrs. siRNA experiments
  • OTUB1 siRNA AM16708
  • A4611 negative control siRNAs
  • 30 nM/well of each siRNA was mixed with Lipofectamine RNAiMax according to the manufacturer’s instructions. Protein and RNA expression was measured by immunoblotting and RT-qPCR after 72 hrs to validate OTUB1 knockdown.
  • NHLFs The proliferation of NHLFs was measured by 5-bromo-2’-deoxyuridine (BrdU) incorporation for 48h using the Cell Proliferation ELISA, BrdU (colorimetric) assay (Roche, Indianapolis, IN), according to the manufacturer’s instructions.
  • cDNA synthesis kit (Applied Biosystems, Foster City, CA) was used to generate cDNA according to the
  • Frozen lung sections (8 pm) were incubated in cold acetone for 20 min. Sections were then blocked with 10% normal goat serum for 1 hr at room temperature and incubated overnight at 4°C with a specific antibody against SERCA2a (1 : 100), OTUB1 (1 : 100), FOXM1 (1 : 100) and alpha-SMA (1 :250). Sections were washed three times with PBS and incubated with a secondary antibody coupled to Alexa Fluor®633 or Alexa Fluor®488 (1 :200, Molecular probes) for lh. Coverslides were mounted with vectashield mounting medium (Vector Laboratories).
  • SERC A2a vector used in this study contains an AAV1 viral capsid and a single- stranded ⁇ 4.5-kb DNA containing the human SERCA2a cDNA driven by a cytomegalovirus immediate-early promoter/enhancer, a hybrid intron, and a bovine growth hormone polyadenylation signal, all flanked by 145-nucleotide AAV2 inverted terminal repeat sequences necessary for replication and packaging of the vector DNA in the capsid.
  • mice were randomly assigned to receive intratracheally aerosolized with either the vehicle, AAV1.LUC encoding for luciferase as an AAV1 control or AAVl-SERCA2a (50 pL; 3.5el 1 vg/mL) using a single-dose IT delivery by using an IA-1C Microsprayer (PennCentury, Wyndmoor, PA).
  • AAV1.LUC encoding for luciferase as an AAV1 control or AAVl-SERCA2a (50 pL; 3.5el 1 vg/mL) using a single-dose IT delivery by using an IA-1C Microsprayer (PennCentury, Wyndmoor, PA).
  • mice were first randomly assigned into three treatment groups: vehicle, AAV1.LUC or AAVl.SERCA2a delivered as previously described and injected with BLM or vehicle control injections 14 days later. Hemodynamic studies were performed 5 weeks after the administration of AAV1.LUC or AAVl.SERCA2a and then mice were sacrificed for lung and RV tissue harvest.
  • mice were anesthetized with (2-4%) isoflurane, intubated via tracheotomy, and mechanically ventilated with 1-2% isoflurane and oxygen (tidal volume, 6 mL/kg; respiratory rate, 100 breaths per minute).
  • the thoracic cavity was opened and the organs were accessed through a sternotomy.
  • an ultrasonic flow probe flow probe 2.5S176; Transonic Systems Inc., Ithaca, NY
  • RVSP right ventricular systolic pressure
  • the heart was removed from the chest and rinsed with PBS to remove blood and any clots. Both atria and connecting vessels are dissected out.
  • the RV was separated from the heart and weighed. The Fulton Index was calculated by the weight ratio of the RV weight to the LV plus septum weight to specifically illustrate the RV hypertrophy.
  • NHLFs were lysed using a buffer containing 20 mmol/L Tris, pH 7.5, 150 mmol/L NaCl, 20 mmol/L MgC12, 0.5% NP40, 0.5 mmol/L EDTA, protease, and phosphatase cocktail inhibitors (Roche).
  • FOXM1 was immunoprecipitated using a specific antibody against FOXM1 (Supplemental Table 3, 1 :50) overnight at 4°C with gentle shaking. Purification steps were performed with protein A/G agarose according to the manufacturer's instructions (Santa Cruz).
  • Ubiquitynation assay was performed in NHLFs cells by transfecting HA-ubiquitin (2pg) in cells overexpressing either Ad.SERCA2a, shRNA against SERCA2a, siRNA OTUB1 alone or in combination with shRNA SERCA2a. 24 hrs after the transfection, the cells were treated with TGFP alone (5nM, 48 hrs) alone or in combination with MG132 (IOmM, 6 hrs). Cells were lysed using a buffer containing 25 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% NP-40, 1 mM EDTA, 5% glycerol and protease, and phosphatase cocktail inhibitors (Roche).
  • Protein lysates (lmg) were incubated with the appropriate IgG control antibody (e.g., 0.25 pg/ml), and suspended with protein A/G agarose beads at 4 °C for 1 h. Samples were centrifuged at 1,000 x g for 1 min at 4°C and supernatants transferred into a clean microcentrifuge tube. Samples were then incubated with a primary antibody HA-Tag (Cell signaling, 1 :50) overnight at 4°C with rotation.
  • IgG control antibody e.g. 0.25 pg/ml
  • agarose beads were then added and incubated at 4°C with rotation for 2 h. Samples were then centrifuged at 1,000 x g for 1 min at 4 °C and supernatant was discarded. Beads were washed with ice-cold RIPA buffer (or PBS) 3 times 15 min with constant rotation at 4°C.
  • NHLF cells were seeded into 24-well plates and transfected using Lipofectamine 2000 with NFK-B luciferase reporter vector (Addgene) for 48 hrs (Invitrogen) according to the manufacturer's instructions. TGFp (5 ng/ml) was then added and the cells were incubated for 48 hrs. NFK-B activity was measured using a luciferase assay kit (Promega). Hematoxylin & Eosin and Masson’s trichrome staining
  • Lung tissue was harvested, inflated with PBS/OCT (50:50), and fixed (frozen) in OCT. Sections were cut to 8 mih and adhered to color frost glass slides (ThermoFisher). Lung tissue sections were stained with hematoxylin and eosin and Masson’s trichrome (Sigma- Aldrich) and visualized using light microscopy. The medial thickness and collagen deposition were then quantified using ImageJ software.
  • RV sections were fixed in 1% paraformaldehyde and stained using fluorescence-tagged wheat germ agglutinin (WGA) (Invitrogen) overnight at 4°C and imaged with on Zeiss Observer Z. l microscope (Carl Zeiss) at x l60 magnification. The outlines of cardiac myocytes were traced and the cardiomyocyte area was calculated using ImageJ software.
  • WGA fluorescence-tagged wheat germ agglutinin
  • Example 2 Decreased expression of SERCA2a in human IPF and in a mouse model of BLM- induced lung fibrosis.
  • SERCA2a mRNA and protein expression levels were measured in lung biopsies of patients diagnosed with IPF and non-IPF lungs (healthy control donors; Tables 2 and 3).
  • SERCA2a expression was significantly decreased at the level of a mRNA and protein in IPF lung tissue specimens compared to control non-IPF lung samples (FIGs. 1 A-B).
  • mice were randomly allocated to a sham control-treated group that received IT saline injections and a PF group that received a single IT aerosolization of BLM (4U/kg). After two weeks, the BLM-challenged group was randomly assigned to receive intratracheally-aerosolized AAV1 encoding human SERCA2a ( AAV1. SERC A2a) or AAVl encoding human luciferase (AAV1.LUC) as a control (FIG. 4 A).
  • Pulmonary hemodynamics, morphometric measurements, as well as fibrosis and pulmonary vascular remodeling were measured 4 weeks post-AAV injection (FIG. 4A).
  • AAVl SERC A2a treatment resulted in significant improvement in the median survival of mice in the BLM-induced PF model compared with A AVI.
  • LUC -treated mice (FIG. 4B).
  • the survival rate was 60% with AAVl- SERC A2a and 15% with the control AAVl.
  • LUC which represents a 45% reduction in mortality (FIG. 4B).
  • SERC A2a on- and off-target of SERCA2a gene transduction was assessed by analyzing the viral genome copies and CMV SERC A2a mRNA levels in the lung and RV of AAVl.SERCA2a and AAV1.LUC- treated BLM challenged mice. The results showed that the number of exogenous SERCA2a genome copies in the lung tissue samples were significantly higher in the AAVl . SERCA2a- treated group in comparison with the AAV l -LUC group. There was no viral genome copy detected in the RV of the AAVl . SERC A2a-treated group, demonstrating the specificity of the local IT aerosol delivery method toward the mice lungs (FIG. 4C).
  • Example 4 1 1 Vl.SERCA2a effectively reverses pulmonary interstitial fibrosis and vascular remodeling.
  • AAVl.SERCA2a gene transfer markedly diminished pulmonary vascular remodeling in comparison with the AAV1.LUC- treated BLM mice group (FIG.4G).
  • the expression of several markers of fibrosis in the lung and bronchoalveolar lavage (BAL) fluid samples was measured by RT-qPCR.
  • PG proteoglycans
  • HS6ST1 heparan Sulfate 6-0- Sulfotransferase 1
  • VC AN Versican
  • hyaluronan synthase 2 fibromodulin
  • syndican 4 which are major components of the ECM implicated in lung tissue remodeling in PF38
  • SERCA2a overexpression decreased CTGF and TGFp transcript levels in BAL fluid (FIG. 4H, lower panel).
  • RVESP right ventricular systolic pressure
  • AAVl -SERC A2a AAVl -SERC A2a
  • AAVl. SERC A2a treatment reduced RV collagen deposition, visualized by Masson’s trichrome staining in comparison with AAVl. LUC-treated mice (FIG. 4L).
  • the expression of fibrosis markers was assessed by RT-qPCR in the RV samples, and the results showed decreased expression of type 1 and III and TGF-bI in AAVl -SERC A2a-treated animals, which is also consistent with the earlier results (FIG. 4M).
  • Example 5 Prevention of bleomycin-induced Lung Fibrosis by intratracheal delivery of 1 1 Vl.SERCA2a in a mouse model
  • mice were randomly assigned to three treatment groups: sham, AAV 1. SERC A2a, and AAV1.LUC (FIG. 6A). Then, two weeks later, the mice were
  • FIG. 6A AAV1 encoding human SERCAZa was only expressed in the lungs of the AAVl.SERCA2a treated group (FIG. 6B, FIG. 3D). Similarly, AAV 1. SERC A2a restored endogenous SERC Za mRNA (FIG. 6C) and protein expression levels in the prevention protocol (FIG. 6D).
  • Example 6 SERCA2a inhibits the proliferation, migration and differentiation of fibroblasts to myofibroblasts in vitro.
  • NHLFs cells were infected for 48 hours with a control adenovirus encoding b-galactosidase (Ad.CT) or an adenovirus encoding human SERCA2a (Ad.S2a) and stimulated either with 0.1% or 5% FBS for 48 hrs in the presence or absence of TGF-bI.
  • Ad.CT control adenovirus encoding b-galactosidase
  • Ad.S2a adenovirus encoding human SERCA2a
  • FIG. 7A After confirming the increased expression of SERCA2a in NHLF transduced by Ad.2a (FIG. 7B, FIG. 8 A), the protein level of Cyclin Dl, a cell cycle marker, was evaluated; and there were decreased protein levels of Cyclin Dl in SERCA2a overexpressing NHLFs cells compared to Ad.CT (FIG. 7B).
  • SERCA2a overexpression inhibits fibroblast to myofibroblast transition as assessed by immunostaining for a-smooth muscle actin (aSMA-a strong marker of myofibroblast differentiation) (FIG. 7D). It was next determined whether SERCA2a regulates the expression of several TGF-bI -regulated pro-fibrosis genes. Thus, SERCA2a was overexpressed in NHLFs cells and treated them with TGF-bI for 48 hrs. Then the mRNA expression of Collagen 1AI (COL1A1), COL3A1 and CTGF was analyzed. Remarkably, SERCA2a overexpression impaired the induction of pro- fibrotic fibrosis markers induced by TGF-b treatment (FIG. 7E), and PG markers such as HS6ST1 and VCAN (FIG. 8C).
  • SERCA2a silencing potentiates the expression of the fibrosis markers induced by TGFP in hAEpiC (FIGs. 9A-9C).
  • Example 7 SERCA2a overexpression blocks NFKB-mediated IL-6 expression in fibroblasts.
  • IL-6 may be an important cytokine that can promote fibrosis.
  • IL-6 produced by various cell types, is a pleiotropic cytokine and functions as a pro-inflammatory factor as well as a profibrotic factor in BLM- induced lung fibrosis.
  • SERCA2a the molecular mechanism underlying the role of SERCA2a in PF was examined. To this end, we determined whether SERCA2a inhibits TGFP-induced fibrosis gene expression via the suppression of IL-6.
  • Treatment of NHLF cells with TGF-bI drastically increased the expression of IL-6, thus, IL-6 expression may depend on TGF ⁇ -mediated signaling (FIG. 7F).
  • SERCA2a overexpression markedly reversed this effect (FIG. 7F), while SERCA2a silencing (sh.S2a) (FIG. 2B) increased IL-6 transcript (FIG. 7G).
  • the promoter region of the IL-6 gene has a putative Nuclear Factor kappa B (NF-KB)-binding site43. Since NF-KB activity can be modulated by increased intracellular Ca2+ levels44 44, it was tested whether SERCA2a affects NF-KB activity. Remarkably, the results show that SERCA2a decreases TGFb-induced NFKB luciferase activity compared to Ad.CT (FIG. 7H) and to
  • Example 8 SERCA2a as a negative regulator of SMAD2/3 complex activity via inhibition of pSTAT3/OTUBl in fibroblast in vitro.
  • OTUB1 is a direct target of SERCA2a.
  • the promoter analysis of OTUB1 revealed the existence of the STAT3 transcription factor binding sites. Therefore, it was tested whether STAT3 inhibition affects OTUB1 expression.
  • STAT3i STAT3 inhibitor
  • the induction of OTUB1 by the TGF-b treatment is reversed by SERCA2a overexpression in a STAT3 -dependent manner (FIGs. 7L-7N).
  • Example 9 SERCA2a inhibition of OTUB1 and FOXM1 mediates SnoN/SKI expression in human lung fibroblasts
  • the TGF-b signaling is regulated by various stimulatory and inhibitory mediators. Since FOXM1 sustained the activation of SMAD3 in cancer, the role of SERCA2a on FOXM1 expression and protein stability in NHLF cells was next assessed. Interestingly, SERCA2a repressed FOXMl expression at both mRNA and protein levels in the absence (FIG. 10E) or presence of TGF-b treatment (FIG. 11 A and 1 IF). However, SERCA2a depletion in NHLFs reversed this effect by increasing FOXM1 expression (FIGs. 10F, 1 IB, and 11G). Interestingly, OTUB1 silencing did not affect FOXM1 mRNA expression but increased FOXM1 protein expression (FIG. 11C). These results suggest that SERCAZa may regulate the FOXM1 expression level directly and also protein stability through the inhibition of OTUB1 expression (FIG. 1 IF).
  • Example 10 SERCA2a overexpression atenuates TGF-b signaling by promoting the ubiquitination and the degradation of FOXM1 and active SMAD 2/3 via the repression of OTUB1
  • Cells were treated with THRb and the proteasome inhibitor MG132 to induce phosphorylation of the SMAD2/3 complex and to inhibit proteasomal degradation, respectively.
  • MG132 and TGF-b treatment decrease polyubiquitylated FOXM1 and p-SMAD2/3 proteins, which decrease their proteasome-mediated degradation (FIG. 11J).
  • Example 11 Expression of OTUB1 is correlated with FOXM1 in human IPF
  • OTUB1, FOXMl, SnoN and SKI expression was examined by assessing their mRNA and protein levels in healthy non-IPF patients and lung human biopsies from IPF patients, as well as in the BLM-challenged mice model of PF.
  • the levels of OTUB1 and FOXMl mRNA and protein expression levels were inversely correlated with SKI and SnoN expression in human lung tissue from IPF patients (FIGs. 1 IK and 11L, respectively).
  • OTUB1 and FOXMl were significantly higher in IPF patients compared to control non-IPF (FIG. 11M). Similar to what has been observed in human lung samples, high OTUB1 and FOXMl mRNA expression levels were correlated with the severity of lung fibrosis disease in a time-dependent manner in the BLM- induced PF mouse model (FIGs. 12A and 12D), while SnoN and SKI expression levels were reduced (FIGs. 12C and 12D). Likewise, OTUB1 and FOXMl protein expression were increased while SnoN and SKI protein expression levels were further decreased (FIG. 1 IN).
  • Example 12 AAVl.SERCA2a gene transfer attenuates lung inflammation, pulmonary fibrosis and remodeling by inhibiting the OTUB1/FOXM1/SMAD2/3 signaling and promoting

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Abstract

The present disclosure provides methods for treating idiopathic pulmonary fibrosis (IPF) in a subject by delivering a therapeutic adeno-associated virus (AAV)-SERCA2 composition to the subject in need thereof.

Description

TREATMENT OF PULMONARY FIBROSIS WITH SERCA2a GENE THERAPY
CROSS REFERENCE TO RELATED APPLICATION
This application claims the benefit of priority under 35 U.S.C. § 119(e) of U.S. Ser. Nos. 62/811,384, filed February 27, 2019, and 62/815,220, filed March 7, 2019. The entire contents of each priority document are herein incorporated by reference.
FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with government support under HL133554; HL117505,
HL119046, HL129814, HL128072, HL131404, and HL135093, a P50 HL112324, each awarded by National Institutes of Health. The government has certain rights in the invention.
FIELD OF THE DISCLOSURE
The present disclosure relates generally to treating pulmonary disease, and more specifically, to a method for treating Idiopathic pulmonary fibrosis in a subject by delivering a polynucleotide encoding sarcoplasmic reticulum Ca++ ATPase (SERCA2a) protein in a viral expression vector.
BACKGROUND
Idiopathic pulmonary fibrosis (IPF) is a devastating rare disease that is refractory to treatment, primarily affecting middle-aged and older adults. It represents a heterogeneous group of lung disorders dealing with a progressive accumulation of scar tissue and a fibro-proliferative process, leading to respiratory failure. To date, despite extensive research efforts in experimental and clinical studies, IPF remains an increasing cause of morbidity and mortality with an average survival of fewer than three years from diagnosis. Therefore, there is a compelling need to develop more effective and reliable therapeutic modalities for the treatment of IPF.
SUMMARY
Disclosed herein are methods of treating idiopathic pulmonary fibrosis in a subject in need thereof, comprising administering to a subject a vector comprising a nucleic acid that encodes for sarcoplasmic reticulum (SR) calcium ++ ATPase (SERCA). Also disclosed herein are methods of preventing or ameliorating idiopathic pulmonary fibrosis in a subject at risk of developing idiopathic pulmonary fibrosis, comprising administering to the subject a vector comprising a nucleic acid that encodes for SERCA. In some embodiments, the administering is via intratracheal instillation, bronchial instillation, inhalation; a nasal spray, or an aerosol. In some embodiments, the administering is via intratracheal. In some embodiments, the vector is an adeno-associated viral (AAV) vector. In some embodiments, the AAV vector is any one of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, or AAV9. In some embodiments, the AAV vector is AAV1. In some embodiments, the vector is a recombinant adeno-associated virus (rAAV). In some embodiments, the vector comprises a nucleic acid that encodes for any one of SEQ ID NOs: 1-20. In some embodiments, the vector comprises a nucleic acid that encodes for any one of SEQ ID NOs: 1-4. In some embodiments, the subject is a mammal. In some embodiments, the mammal is a human. In some embodiments, the SERCA is SERCA isoform 2 (SERCAZa).
Also disclosed herein are methods of treating idiopathic pulmonary fibrosis in a subject in need thereof, comprising administering to a subject a pharmaceutical composition comprising an effective amount of a vector comprising a nucleic acid that encodes for SERCA, and a pharmaceutically acceptable excipient. Finally, also disclosed herein are methods of preventing or ameliorating idiopathic pulmonary fibrosis in a subject at risk of developing idiopathic pulmonary fibrosis, comprising administering to a subject a pharmaceutical composition comprising an effective amount of a vector comprising a nucleic acid that encodes for SERCA, and a pharmaceutically acceptable excipient.
In some embodiments, disclosed herein are methods of producing a vector described herein. In some embodiments, the methods include (a) culturing a host cell so that the vector is expressed; and (b) isolating the vector from the host cell.
All publications, patents, patent applications, and information available on the internet and mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, patent application, or item of information was specifically and individually indicated to be incorporated by reference. To the extent publications, patents, patent applications, and items of information incorporated by reference contradict the disclosure contained in the specification, the specification is intended to supersede and/or take precedence over any such contradictory material. Where values are described in terms of ranges, it should be understood that the description includes the disclosure of all possible sub-ranges within such ranges, as well as specific numerical values that fall within such ranges irrespective of whether a specific numerical value or specific sub-range is expressly stated.
The term“each,” when used in reference to a collection of items, is intended to identify an individual item in the collection but does not necessarily refer to every item in the collection, unless expressly stated otherwise, or unless the context of the usage clearly indicates otherwise.
Various embodiments of the features of this disclosure are described herein. However, it should be understood that such embodiments are provided merely by way of example, and numerous variations, changes, and substitutions can occur to those skilled in the art without departing from the scope of this disclosure. It should also be understood that various alternatives to the specific embodiments described herein are also within the scope of this disclosure.
BRIEF DESCRIPTION OF THE DRAWINGS
The following drawings illustrate certain embodiments of the features and advantages of this disclosure. These embodiments are not intended to limit the scope of the appended claims in any manner. Like reference symbols in the drawings indicate like elements.
FIG. 1A shows SERCA2a mRNA expression level analyzed by quantitative polymerase chain reaction (qPCR) in lung tissues from patients with sporadic IPF (n=8) and human donor lungs (controls, n= 8). All data in figures are presented as mean ±SEM; ns=not significant, * = p<0.05, ** = p O.Ol, *** P < 0.001.
FIG. IB shows SERCA2a protein expression level analyzed by immunoblotting in lung tissues from patients with sporadic IPF (n=8) and human donor lungs (controls, n= 8).
FIG. 1C shows representative images of double immunofluorescence staining for SERCA2a (top left), alpha smooth muscle actin (aSMA; top right) was detected by
immunofluorescence in lungs from control non-IPF and IPF patients. Nuclei were stained with DAPI (bottom left).
FIG. ID shows SERCA2a mRNA expression level analyzed by quantitative polymerase chain reaction (qPCR) in sham control mice and BLM-challenged mice (n~3-6 per group).
FIG. IE shows SERCA2a protein expression level analyzed by immunoblotting in sham control mice and BLM-challenged mice (n~3-6 per group). FIG. IF shows representative images of double immunofluorescence staining for SERCA2a (top left), alpha smooth muscle actin (aSMA; top right) was detected by
immunofluorescence in lungs from sham control mice and BLM-challenged mice. Nuclei were stained with DAPI (bottom left).
FIG. 2A shows SERCA2a mRNA levels in bleomycin-treated mice.
FIG. 2B shows IL-6 mRNA levels in bleomycin-treated mice.
FIG. 2C shows SERCA2a mRNA levels in bleomycin-treated mice relative to mRNA expression at day 1.
FIG. 3A shows immunofluorescence images of GFP (top images), DAPI (bottom left image) and merged image in lung tissue.
FIG. 3B shows mRNA expression detecting viral copies of SERCA2a AAV 1 in lung and right ventricle (RV) in sham control, AAV1.LUC- and AAVl.SERCA2a-treated mice.
FIG. 3C shows SERCA2a mRNA expression in the cohorts of the therapeutic protocol of
FIG. 4A.
FIG. 3D shows SERCA2a mRNA expression in the cohorts of the prevention protocol of
FIG. 6A.
FIG. 4A shows a schematic of the experimental design to assess the therapeutic efficacy of AAVl.SERCA2a gene therapy in the BLM-induced IPF model. Mice received a single intratracheal (IT) aerosolization of BLM (4U/kg) and 2 weeks later were randomly assigned to receive either the vehicle, AAV1-LUC encoding for luciferase as an AAV1 control or AAV1- SERCA2a for 4 weeks.
FIG. 4B shows Kaplan-Meier survival curves of mice IT aerosolized either with the vehicle (Control), AAV1.LUC as control (AAV1.LUC) or AAVl . SERC A2a.
FIG. 4C shows viral genome copies were assessed in the mice lungs and the RV to determine the efficiency and specificity of the IT delivery of AAVl. SERC A2a gene transfer.
FIG. 4D shows endogenous SERCA2a mRNA level assessed in lung tissues by RT- qPCR.
FIG. 4E shows SERCA2a protein expression assessed by immunoblotting in the sham control group, AAVl. LUC and AAVl. SERC A2a-treated BLM groups.
FIG. 4F shows arterial blood-gas analysis for the sham control group (Control) and the BLM-challenged mice treated with AAVl. LUC or AAVl. SERC A2a groups 4 weeks after AAV1 delivery in BLM-treated animals. The parameters include pH, Sa02, Pa02, PaC02, base excess in the extracellular fluid compartment (BEECF).
FIG. 4G shows representative Masson’s trichrome and hematoxylin and eosin stained lung sections of indicated mice (Left). The graphs represent the quantification of fibrosis (Top) and medial thickness (Bottom).
FIG. 4H shows levels of fibrosis markers (COL1, COL3, CTGF, TGFP) were quantified by qPCR in lung tissues (Top) and bronchoalveolar lavage fluid samples (BALF, Bottom) (n=6- 8 per group).
FIG. 41 shows right ventricular systolic pressure (RVSP; Left panel) and Fulton index (Right panel).
FIG. 4J shows RV sections stained with fluorescence-tagged wheat germ agglutinin to examine RV cardiomyocyte cross-sectional area.
FIG. 4K shows cardiac hypertrophy-related transcripts expression levels (ANP, BNP, b-
MHC).
FIG. 4L shows representative Masson’ s trichrome stained heart sections (top) and quantified fibrosis in the sham control group, AAV 1 LUC and AAV1. SERC A2a-treated BLM groups.
FIG. 4M shows fibrosis markers COL1A1, COL3A1 and TGFP mRNA level in the sham control group, AAV 1 LUC and AAVl.SERCA2a-treated BLM groups.
FIGs. 5A-5B show mRNA expression of heparan Sulfate 6-O-Sulfotransferase 1 (HS6ST1), versican (VC AN), fibromodulin (FMOD), hyaluronan synthase 2 (HAS2), and syndican 4 (SDC4) in the therapeutic experiment (FIG. 5A) and the prevention experiment (FIG. 5B).
FIG. 6A shows a schematic of the experimental design of the prevention protocol. Mice received a single intratracheal aerosolization of either the vehicle, AAV 1.LUC or
AAV 1. SERC A2a. After two weeks, the mice were administered with either bleomycin (4U/kg) or vehicle by IT delivery and hemodynamic studies were performed at week 5 post AAV 1 delivery.
FIG. 6B shows viral genome copies assessed in the mice lungs and RV to determine the efficiency and specificity of the IT delivery of AAV 1. SERCA2a gene transfer. FIG. 6C shows endogenous SERCA2a mRNA level assessed in lung tissues by qPCR using specific primers.
FIG. 6D shows SERCA2a protein expression was assessed in lung tissues by
immunoblotting (n=3-5 per group).
FIG. 6E shows representative Masson’s trichrome and hematoxylin and eosin stained lung sections of indicated mice (Top). The bar graphs represent the quantification of fibrosis and medial thickness (Bottom).
FIG. 6F shows fibrosis markers mRNA levels were quantified by qPCR in lung tissues (Top) and BALF (Bottom) (n=6-8 per group).
FIG. 6G shows right ventricular systolic pressure (RVSP; Left) and Fulton index (RV weight/LV+ Septum weight; Right).
FIG. 6H shows RV cardiomyocyte cross-sectional area stained with fluorescence-tagged wheat germ agglutinin to examine the RV hypertrophy.
FIG. 61 shows RV cardiac hypertrophy-related transcripts expression level assessed by qPCR.
FIG. 6J shows representative Masson’s trichrome stained heart sections.
FIG. 6K Fibrosis markers mRNA level of COL1A1, COL3A1, CTGF and TGFp.
FIG. 7A shows normal human pulmonary fibroblasts (NHLFs) were infected for 48 hours either with a control adenovirus encoding b-Galactosidase (Ad.CT) or an adenovirus encoding human SERCA2a (Ad.SERCA2a) and cultured in either 0.1% or 5% FBS in the absence or the presence of 5 ng/ml of TGF-bI for 48 hrs. Proliferation was determined by labeling cells with BrdU (n=3).
FIG. 7B shows a representative blot of SERCA2a, Cyclin D1 and GAPDH in NHLF overexpressing SERCA2a or Ad.CT.
FIG. 7C shows NHLF were infected for 48 h with Ad.SERCA2a (Ad.S2a) or Ad.CT and the migration were assessed using Boyden chamber-based cell migration assay (n=3).
FIG. 7D shows representative images of immuno staining showing SERCAZa (red) and aSMA (Red) and nucleus (D API-blue) in Ad.SERCA2a or Ad.CT-transduced NHLF cells. (GFP in green indicates infected cells). FIG. 7E shows fibrosis markers (COL1A1, COL3A1 and CTGF) mRNA levels were assessed by RT-qPCR (n=3) in NHLF overexpressing Ad.SERCA2a or Ad.CT and treated with TGF-b for 48 hrs.
FIGs. 7F show IL-6 mRNA expression levels. NHLF were infected with either
Ad.SERCA2a or Ad.CT and treated with TGF-b (5 ng/ml) for 48 hrs.
FIG. 7G shows IL-6 mRNA expression levels in NHLFs depleted SERCA2a using sh.S2a (sh.S2a) or a non-specific shRNA (sh.CT) for 72 hrs and treated with TϋRb (5 ng/ml; 48 hrs).
FIGs. 7H-7I show NFKB luciferase activity in SERCA2a overexpressing or SERCA2a depleted NHLF with or without TGF-b treatment, respectively.
FIGs. 7J-7K show OTUB1 mRNA expression was assessed by RT-qPCR in NHLF infected with Ad.S2a, sh.CT or sh.S2a. L-M) NHLF were infected either with Ad.S2a, sh.S2a or controls and treated with TϋRb for 48 hrs alone.
FIGs. 7L-7M show OTUB1 mRNA expression was assessed by RT-qPCR in NHLF infected with Ad.S2a, sh.CT or sh.S2a. L-M) NHLF were infected either with Ad.S2a, sh.S2a or controls and treated with THRb for 48 hrs alone or in combination with STAT3 inhibitor (STAT3i), and OTUB1 mRNA level was assessed by RT-qPCR in the indicated conditions.
FIG. 7N shows representative immunoblot for the indicated proteins in NHLF overexpressing SERCA2a stimulated with TORb in the absence or presence of STAT3L
FIGs. 70-7P show relative cell proliferation using BrdU labeling in the specified conditions of NHLF expressing the specified constructs or either a negative control siRNA or siRNA OTUB1 (siOTUBl) and the cells were treated with medium supplemented with 5% FBS alone or in combination with THRb.
FIG. 8A shows SERCA2a mRNA and protein levels in NHLF cells infected with SERCA2a adenovirus.
FIG. 8B shows SERCA2a mRNA and protein levels in NHLF cells infected with a specific shRNA against SERCA2a.
FIG. 8C shows HS6ST1 and VCAN mRNA levels in NHLF cells transfected with SERCA2a adenovirus and/or TGF-b.
FIG. 9A shows COL1 A1 mRNA levels in human pulmonary alveolar epithelial cells infected with SERCA2a adenovirus and treated with and without TGF-b. FIG. 9B shows COLO A1 mRNA levels in human pulmonary alveolar epithelial cells infected with SERCA2a adenovirus and treated with and without TGF-b.
FIG. 9C shows CTGF mRNA levels in human pulmonary alveolar epithelial cells infected with SERCA2a adenovirus and treated with and without TGF-b.
FIG. 10A shows OTLIBl mRNA and protein levels in fibroblasts transfected with a siRNA against OTLIB 1.
FIG. 10B shows COL1 A1 mRNA levels in fibroblasts transfected with a siRNA against OTLIBl alone or in combination with a specific shRNA against SERCA2a with and without TGF-b.
FIG. IOC shows COL3 A1 mRNA levels in fibroblasts transfected with a siRNA against OTUB1 alone or in combination with a specific shRNA against SERCA2a with and without TGF-b.
FIG. 10D shows CTGF mRNA levels in fibroblasts transfected with a siRNA against OTUB1 alone or in combination with a specific shRNA against SERCA2a with and without TGF-b.
FIG. 10E shows FOXM1 mRNA and protein levels in fibroblasts infected with
SERCA2a adenovirus.
FIG. 10F shows FOXM1 mRNA and protein levels in fibroblasts infected with a specific shRNA against SERCA2a.
FIGs. 11A-11C show NHLFs were infected either with Ad.S2a, sh.S2a or si.OTUBl and treated with TORb for 48 hrs. FOXMl expression level was assessed in indicated conditions.
FIGs. 11D-11E show SnoN (Left) and SKI (Right) mRNA expression levels were assessed by RTqPCR in S2a overexpressing cells or sh.S2a depleted cells, respectively,
SERCA2a with and without TGF-b.
FIGs. 11F-11G show representative immunoblots of indicated proteins in NHLF overexpressing S2a or a specific non-silencing or sh.SERCA2a and treated with TORb for 48 hrs.
FIG. 11H shows SnoN mRNA expression level in NIHLF cells depleted of SERCA2a and FOXMl using a specific sh.RNA and OTUB1 using siRNA.
FIG. Ill shows SERCA2a overexpression prevented the interaction between endogenous FOXMl/OTUBl and FOXMl/pSMAD3. Immunoprecipitation (IP) of FOXMl followed by Immunoblotting (IB) of FOXM1, OTUB1, phospho- and total SMAD3 was performed in NHLF cells after infection with Ad.S2a or sh.S2a or controls in the absence or presence of TGF-b.
FIG. 11J shows SERCA2a enhanced FOXM1 and SMAD2/3 ubiquitination. IP of HA- tag followed by IB of FOXM1 and phospho-SMAD3 in NHLF overexpressing SERCAZa (Ad.S2a) or a specific non-silencing or sh.SERCA2a (sh.S2a), siRNA OTUB1 and transfected with Flag-HA ubiquitin, and treated with TGFP or proteasome inhibitor MG132 for 6 hrs. Direct IB of NHLF lysates was used to analyze protein levels of OTUB1.
FIGs. 11K-11M show OTUB1, FOXM1, SNON, and SKI mRNA and protein expression levels in lung tissue from control non-IPF and IPF patients.
FIG. 11N shows double immunostaining of OTUB1 (top panel; top left image in each cohort)/SMA (top panel; second image from left image in top row in each cohort), and FOXM1 (bottom panel; top left image in each cohort)/SMA (bottom panel; second image from left image in top row in each cohort) in control non-IPF and IPF patients.
FIGs. 110-1 IP show OTUB1, FOXM1, SNON, and SKI expression assessed by immunoblotting in control untreated and BLM-induced PF in mice. Densitometric quantitation is shown of OTUB1, SNON, and SKI protein expression normalized to GAPDH.
FIG. 12A shows OTUB1 mRNA levels in mice treated with bleomycin.
FIG. 12B shows FOXM1 mRNA levels in mice treated with bleomycin.
FIG. 12C shows SnoN mRNA levels in mice treated with bleomycin.
FIG. 12D shows SKI mRNA levels in mice treated with bleomycin.
FIG. 13A shows IL-6 mRNA level was quantified by qPCR in lung tissues (Top) and BAL Fluid (Bottom) in the therapeutic and preventive protocols (n=6-8 per group).
FIG. 13B shows OTUB1 (Top) and FOXM1 (Bottom) mRNA levels were assessed by RT-qPCR in the lungs in the indicated groups in the therapeutic and preventative protocols
FIG. 13C shows SnoN (Top) and SKI (Bottom) mRNA levels were assessed by RT- qPCR in the lungs in the indicated groups in the therapeutic and preventative protocols.
FIG. 13D shows lung homogenates lysates after immunoblotting analysis for the indicated proteins after the treatment protocol. Representative blots and respective densitometry quantitation for p-NF-kB p65, p-STAT3, OTUB1, FOXM1, p-SMAD2-3, SNON, aSMA and Cyclin D1 are presented. Protein expression was normalized to total NFKB, total-STAT3, total- SMAD2-3 and GAPDH. FIG. 13E shows lung homogenates lysates after immunoblotting analysis for the indicated proteins in the prevention protocol. Representative western blots and respective the densitometric quantitation for p-NF-kB p65, p-STAT3, p-SMAD2-3, OTUB1, FOXM1, SNON, SKI, Cyclin D1 and aSMA are presented. Protein expression was normalized to total-STAT3, Total- SMAD2-3 and GAPDH.
FIG. 13F shows a schematic representation of the molecular mechanisms by which SERCA2a inhibits lung fibrosis. SERCA2a inhibits STAT3 activation and therefore decreases OTUB1 and FOXM1 expression. Downregulation of OTUB1 expression results in inhibition of the SMAD signaling and the upregulation of the anti-fibrosis SnoN and SKI proteins. Altogether, our results showed that SERCA2a inhibits pulmonary fibrosis and secondary PH by
downregulating the pro-fibrosis OTUB1 protein and downregulating the anti-fibrosis SnoN/SKI proteins.
FIG. 14A shows a schematic of the experimental design of the treatment protocol.
FIG. 14B shows a schematic of the experimental design of the prevention protocol.
DETAILED DESCRIPTION
I. Introduction
The present disclosure provides methods for treating idiopathic pulmonary fibrosis (IPF) in a subject by delivering a therapeutic adeno-associated virus (AAV)-SERCA (e.g., SERCAZa) composition to the subject in need thereof.
Before the present composition, methods, and treatment methodology are described, it is to be understood that this disclosure is not limited to particular compositions, methods, and experimental conditions described, as such compositions, methods, and conditions may vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting, since the scope of the present disclosure will be limited only in the appended claims.
As used in this specification and the appended claims, the singular forms“a”,“an”, and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, references to“the method” includes one or more methods, and/or steps of the type described herein which will become apparent to those persons skilled in the art upon reading this disclosure and so forth. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the disclosure, the methods and materials are now described.
The practice of the present disclosure will employ, unless indicated specifically to the contrary, conventional methods of virology, immunology, microbiology, molecular biology and recombinant DNA techniques within the skill of the art, many of which are described below for the purpose of illustration. Such techniques are explained fully in the literature. See, e.g., Sambrook, et al. Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Maniatis et al. Molecular Cloning: A Laboratory Manual (1982); DNA Cloning: A Practical Approach, vol. I & II (D. Glover, ed.); Oligonucleotide Synthesis (N. Gait, ed., 1984); Nucleic Acid Hybridization (B. Hames & S. Higgins, eds., 1985); Transcription and Translation (B. Hames & S. Higgins, eds., 1984); Animal Cell Culture (R. Freshney, ed., 1986); Perbal, A Practical Guide to
Molecular Cloning (1984).
Idiopathic pulmonary fibrosis (IPF) is a chronic and fatal lung disease of unknown cause characterized by progressive fibroblast proliferation and differentiation to myofibroblast, destruction of the alveolar architecture and a relentless decline in pulmonary function, leading to respiratory failure and ultimately to death within 3-5 years after the diagnosis. The present disclosure provides a therapeutic strategy to prevent and inhibit lung fibrosis based on the AAVl.SERCA2a target gene therapy. As disclosed herein, SERCA2a expression was significantly decreased in lung tissue from patients with IPF and in bleomycin-challenged mice. In vitro, SERCA2a overexpression significantly decreased the proliferation, migration and human lung fibroblast transition to myofibroblast. In vivo, AAV 1. SERCA2a decreased lung fibrosis and prevented the expression of several fibrosis markers, and lung vascular remodeling.
Thus, the methods provided herein, utilize a viral vector to deliver the SERCAZa gene or its isoforms directly to the lungs and/or to muscle cells associated with lung function. One aspect of the present disclosure contemplates transfer of a therapeutic polynucleotide into a cell. Such transfer may employ viral or non-viral methods of gene transfer. In one embodiment, the viral vector is an adeno-associated virus (AAV) vector or a human parvovirus.
In one embodiment, the therapeutically significant polynucleotides are incorporated into a viral vector to mediate transfer to a cell. Additional expression constructs encoding other therapeutic agents as described herein may also be transferred via viral transduction using infectious viral particles, for example, by transformation with an adeno-associated virus (AAV) of the present disclosure. Alternatively, a retrovirus, bovine papilloma virus, an adenovirus vector, a lentiviral vector, a vaccinia virus, a polyoma virus, or an infective virus may be used. Similarly, nonviral methods which include, but are not limited to, direct delivery of DNA such as by perfusion, naked DNA transfection, liposome mediated transfection, encapsulation, and receptor-mediated endocytosis may be employed. These techniques are well known to those of skill in the art, and the particulars thereof do not lie at the crux of the present disclosure and thus need not be exhaustively detailed herein. For example, a viral vector is used for the transduction of pulmonary cells to deliver a therapeutically significant polynucleotide to a cell. The virus may gain access to the interior of the cell by a specific means such as receptor-mediated endocytosis, or by non-specific means such as pinocytosis.
II. SERCA2a Peptides and Nucleic Acids
1. SERCA2a Peptides
ATPase Sarcoplasmic/Endoplasmic Reticulum Ca2+ Transporting 2 (ATP2A2; also known as DD; DAR; ATP2B; or SERCA2a) is a gene that encodes one of the SERCA Ca(2+)- ATPases (i.e., SERCA2a), which are intracellular pumps located in the sarcoplasmic or endoplasmic reticula of the skeletal muscle. SERCA2a catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol into the sarcoplasmic reticulum lumen, and is involved in regulation of the contraction/relaxation cycle.
Polynucleotides (e.g., viral vectors) described herein encode for a“polypeptide”, for example, SERCA2a or isomers thereof.“Polypeptide” is used in its conventional meaning, i.e., as a sequence of amino acids. The polypeptides are not limited to a specific length of the product; thus, peptides, oligopeptides, and proteins are included within the definition of polypeptide, and such terms may be used interchangeably herein unless specifically indicated otherwise. This term also does not refer to or exclude post-expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like, as well as other modifications known in the art, both naturally occurring and non- naturally occurring. A polypeptide may be an entire protein, or a subsequence thereof. Particular polypeptides of interest in the context of this disclosure are amino acid subsequences comprising epitopes, i.e., antigenic determinants substantially responsible for the immunogenic properties of a polypeptide and being capable of evoking an immune response.
As disclosed herein, SERCA2a polypeptides, include but are not limited to, human GenBank sequences such as AAB29701 (Wuytack et al., J Biol Chem (1994) 269(2): 1410- 1416); NP_733765 (Lytton and MacLennan, J Biol Chem (1988) 263(29): 15023-15031);
NP_001672 (Otsu et al, Genomics (1993) 17(2):507-509); AAH35588 (Strausberg et al, Proc Natl Acad Sci USA (2002) 99(26): 16899-16903); and mouse GenBank sequences including AAD01889 (Ver Heyen et al, Mamm Genome (2000) 11(2): 159-163); NP_033852 (Hsu et al., Biochem Biophys Res Comm (1993) 197(3): 1483-1491); CAB41018 (Ver Heyen et al., Mamm Genome (2000) 11(2): 159-163); CAB41017 (Id.); CAB72436 (Id.); CAA11450 (Id.);
AAH54531 (Strasberg et al, Proc Natl Acad Sci USA (2002) 99(26): 16899-16903); AAH54748 (Id.); and other species including NP_957259 (Ebert et al, Proc Natl Acad Sci USA (2005) 102(49): 17705-17710); ABG90496 (Wu et al, Silurus lanzhouensis SERCA2a, direct submission (23-JUN-2006), Department of Applied Chemistry, College of Science, China Agricultural University, No. 2, Yuanmigyuan West Road, Haidian, Beijing, 100094, China); NP_001025448 (Sehra H., Danio rerio SERCA2a, direct submission (7-AUG-2005), Welcome Trust Sanger Institute, Hixton, Cambridgeshire, CB 10 ISA, UK); NP 001009216 (Gambel et al, Biochem Biophys Acta (1992) 1131(2):203-206); NP 999030 (Eggermont et al, Biochem J (1989) 260(3):757-761); NP 058986 (Gunteski-Hamblin et al, J Biol Chem (1988)
263(29): 15032-15040); CAA37784 (Eggermont et al, Biochem J (1989) 260(3):757-761); and CAA37783 (Id.). All of the above sequences are publicly available and incorporated herein by reference.
Table 1. SERCA2a Polypeptides
Figure imgf000014_0001
Figure imgf000015_0001
Figure imgf000016_0001
Figure imgf000017_0001
Figure imgf000018_0001
Figure imgf000019_0001
Figure imgf000020_0001
Figure imgf000021_0001
Figure imgf000022_0001
Figure imgf000023_0001
Disclosed herein are SERCA2a having the sequences recited as SEQ ID NO: 1-20. In some embodiments, the polypeptide for SERCA2a has the sequence recited as SEQ ID NO: 1-4. In some embodiments, the present disclosure provides variants of the polypeptide compositions described herein. In some embodiments, disclosed herein are polypeptide variants that exhibit at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or greater sequence identity, along its length, to any one of the polypeptide sequences set forth as SEQ ID NOs: 1-20.
In some embodiments, a SERCA2a polypeptide is a fusion polypeptide that includes any one of SERCA2a polypeptides set forth as SEQ ID NOs: 1-20 as described herein, or that includes at least one SERCA2a polypeptide as described herein and an unrelated sequence, such as a known viral protein. A fusion partner may, for example, assist in providing epitopes (an immunological fusion partner) recognized by humans, or may assist in expressing the protein (an expression enhancer) at higher yields than the native recombinant protein. Certain fusion partners enhance formation of multimers.
In one embodiment, polypeptides are defined by structural domains. For example, the signaling domain, which is associated with transduction upon receptor binding and is found in the cytoplasmic compartment of cells, is defined as a region of a protein molecule delimited on the basis of function and is related to a receptor's cytoplasmic substrate.
Fusion polypeptides may generally be prepared using standard techniques, including chemical conjugation. In some embodiments, a fusion SERCA2a polypeptide is expressed as a recombinant polypeptide, allowing the production of increased SERCA2a levels, relative to a non-fused polypeptide, in an expression system. Briefly, DNA sequences encoding the polypeptide components may be assembled separately, and ligated into an appropriate expression vector. The 3 ' end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5' end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion polypeptide that retains the biological activity of both component polypeptides.
The present disclosure also encompasses“peptide” or“peptide portion” or“fragment” or “peptide fragment” and equivalents thereof, which is used broadly herein to mean two or more amino acids linked by a peptide bond. The term“proteolytic fragment” also is used herein to refer to a product that can be produced by a proteolytic reaction on a polypeptide, i.e., a peptide produced upon cleavage of a peptide bond in the polypeptide. Although the term“proteolytic fragment” is used generally herein to refer to a peptide that can be produced by a proteolytic reaction, it should be recognized that the fragment need not necessarily be produced by a proteolytic reaction, but also can be produced using methods of chemical synthesis or methods of recombinant DNA technology, as discussed in greater detail below, to produce a synthetic peptide that is equivalent to a proteolytic fragment. Further, the term“functional fragment” or “functional portion” or equivalents thereof means that the SERCA2a fragment or peptide has functional SERCA2a activity, for example, a functional fragment or functional proteolytic fragment of SERCA2a or SERCA2a has functional SERCA2a or SERCA2a activity.
Generally, a peptide of the disclosure contains at least about six amino acids, usually contains about ten amino acids, and can contain fifteen or more amino acids, particularly twenty or more amino acids. It should be recognized that the term“peptide” is not used herein to suggest a particular size or number of amino acids comprising the molecule, and that a peptide of the disclosure can contain up to several amino acid residues or more.
Also, as used herein, the“translation product” or“polypeptide” refers to peptides, polypeptides, oligopeptides and proteins or protein fragments which have a desired biological effect in vivo or in vitro. As used herein, the term“fragment” refers to a molecule or any peptide subset of the molecule; whereas a“variant” of such molecule refers to a naturally occurring molecule (e.g., isoform such as SERCA2a) substantially similar to either the entire molecule, or a fragment thereof. In contrast, an“analog” of a molecule refers to a non-natural molecule substantially similar to either the entire molecule or a fragment thereof. All these are embodied in the disclosure so long as in vivo delivery of the therapeutic composition containing SERCA2a polypeptide, fragment, or variant to a subject suffering from idiopathic pulmonary fibrosis ameliorates or effectively treats the subject in need thereof. A peptide linker sequence may be employed to separate the first and second polypeptide components by a distance sufficient to ensure that each polypeptide folds into its secondary and tertiary structures. Such a peptide linker sequence is incorporated into the fusion polypeptide using standard techniques well known in the art. Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes. In some embodiments, the peptide linker sequences contain Gly, Asn, and Ser residues. Other near neutral amino acids, such as Thr and Ala may also be used in the linker sequence. Amino acid sequences which may be usefully employed as linkers are generally known in the art. The linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.
As discussed previously, SERCAZa polypeptides are highly conserved, hence the skilled artisan can perform an optimal alignment of polypeptide or nucleic acid sequences for comparison using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters. This program embodies several alignment schemes described in the following references: Dayhoff, M. O. (1978) A model of evolutionary change in proteins— Matrices for detecting distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, Calif.; Higgins, D. G. and Sharp, P. M. (1989) CABIOS 5: 151-153; Myers, E. W. and Muller W. (1988) CABIOS 4: 11-17; Robinson, E. D. (1971) Comb. Theor 11 : 105; Saitou, N. Nei, M.
(1987) Mol. Biol. Evol. 4:406-425; Sneath, P. H. A. and Sokal, R. R. (1973) Numerical
Taxonomy— the Principles and Practice of Numerical Taxonomy, Freeman Press, San Francisco, Calif.; Wilbur, W. J. and Lipman, D. J. (1983) Proc. Natl. Acad., Sci. USA 80:726-730, each of which is incorporated herein by reference.
Alternatively, optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman (1981) Add. APL. Math 2:482, by the identity alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity methods of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85: 2444, by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.
One example of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively. BLAST and BLAST 2.0 can be used, for example with the parameters described herein, to determine percent sequence identity for the polynucleotides and polypeptides of the disclosure. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. For amino acid sequences, a scoring matrix can be used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
2. SERCA2a Nucleic Acids
Also disclosed herein are nucleic acids that encode for SERCA2a. Accordingly, the present disclosure provides polynucleotides encoding a polypeptide called Sarco/Endoplasmic Reticulum Ca2+-ATPase (SERCA). SERCA resides in the sarcoplasmic reticulum (SR) within muscle cells. Vasoconstriction (e.g., vascular smooth muscle cells or VSMC) is reported to be dependent on mobilization Ca2+ from intracellular stores or the SR. SERCA is a Ca2+ ATPase which transfers Ca2+ from the cytosol of the cell to the lumen of the sarcoplasmic reticulum (SR) at the expense of ATP hydrolysis. SERCA proteins are encoded by three genes (SERCA1,
2 and 3) located on separate chromosomes. SERCA transcripts are expressed and alternatively spliced in a tissue dependent manner. The resulting mRNA species encode different SERCA protein isoforms and differ in 3 '-untranslated regions (UM). SERCA protein isoforms differ in their Ca2+ affinity, resistance to oxidative stress and modulation by sarcolipin, phospholamban (PLB/PLN), and Ca2+/calmodulin kinase II. In some embodiments, disclosed herein are nucleic acids that encode for any one of SEQ ID NOs: 1-20. In some embodiments, the present disclosure provides variants of nucleotides that encode for any one of SEQ ID NOs: 1-20. In some embodiments, disclosed herein are nucleotide variants that exhibit at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%,
96%, 97%, 98%, or 99% or greater sequence identity, along its length, to a nucleotide sequence that encodes for any one of SEQ ID NOs: 1-20.
In some embodiments, any one of the nucleotides described herein (e.g., any nucleotide encoding for any one of SEQ ID NOs: 1-20 or a variant thereof) can be included as part of a vector that produces a SERCA2a polypeptide. In some embodiments, any one of the nucleotides described herein (e.g., any nucleotide encoding for any one of SEQ ID NOs: 1-20 or a variant thereof) can be included as part of an adeno-associated viral vector. In some embodiments, any one of the nucleotides described herein (e.g., any nucleotide encoding for any one of SEQ ID NOs: 1-20 or a variant thereof) can be included as part of an adeno-associated viral vector serotype 1.
Various nucleic acid sequences are embodied in the present disclosure. As used herein, “nucleic acid” sequence or equivalents thereof refer to a DNA or RNA sequence. The term captures sequences that include any of the known base analogues of DNA and RNA such as, but not limited to 4-acetylcytosine, 8-hydroxy-N-6-methyladenosine, aziridinylcytosine,
pseudoisocytosine, 5-(carboxyhydroxylmethyl) uracil, 5-fluorouracil, 5-bromouracil, 5- carboxymethylaminomethyl-2-thiouracil, 5-carboxymethyl-aminomethyluracil, dihydrouracil, inosine, N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil, 1-methylguanine, 1- methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5- methylcytosine, N6-methyladenine, 7-methylguanine, 5-methylaminomethyluracil, 5- methoxyamino-methyl-2-thiouracil, beta-D-mannosylqueosine, 5 '-methoxycarbonylmethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2- thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, -uracil-5-oxyacetic acid methylester, uracil- 5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and 2,6-diaminopurine.
In some embodments, the nucleic acids disclosed herein include other nucleic acid sequences, including but not limited to“control sequences.” Control sequences refer collectively to promoter sequences, polyadenylation signals, transcription termination sequences, upstream regulatory domains, origins of replication, internal ribosome entry sites (“IRES”), enhancers, and the like, which collectively provide for the replication, transcription and translation of a coding sequence in a recipient cell. Not all of these control sequences need always be present so long as the selected coding sequence is capable of being replicated, transcribed and translated in an appropriate host cell.
In some embodiments, disclosed herein are nucleic acids that include one or more “promoter” sequences, which are used herein in its ordinary sense to refer to a nucleotide region comprising a DNA regulatory sequence, wherein the regulatory sequence is derived from a gene which is capable of binding RNA polymerase and initiating transcription of a downstream (3 - direction) coding sequence. Transcription promoters can include“inducible promoters” (where expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.),“repressible promoters” (where expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.), and“constitutive promoters.”
The nucleic acids embodied in the present disclosure are“operably linked” to each other or linked to a protein or peptide. As used herein,“operatively linked” refers to an arrangement of elements wherein the components so described are configured so as to perform their usual function. Thus, control sequences operably linked to a coding sequence are capable of effecting the expression of the coding sequence. The control sequences need not be contiguous with the coding sequence, so long as they function to direct the expression thereof. Thus, for example, intervening untranslated yet transcribed sequences can be present between a promoter sequence and the coding sequence and the promoter sequence can still be considered“operably linked” to the coding sequence.
The ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements. The regulatory elements responsible for expression of DNA are located only 5' to the DNA sequence encoding the first polypeptides. Similarly, stop codons required to end translation and transcription termination signals are only present 3 ' to the DNA sequence encoding the secondary, tertiary, or quaternary, etc., polypeptide (i.e., a stop codon will be present on the ultimate polypeptide depending on the number of distinct polypeptides making up a chimeric protein molecule). In addition to SERCA2a polypeptides, the present disclosure provides SERCA2a and SERCA2a containing polynucleotide compositions. The terms“DNA” and“polynucleotide” are used interchangeably herein to refer to a DNA molecule that has been isolated free of total genomic DNA of a particular species.“Isolated,” as used herein, means that a polynucleotide is substantially away from other coding sequences, and that the DNA molecule does not contain large portions of unrelated coding DNA, such as large chromosomal fragments or other functional genes or polypeptide coding regions. Of course, this refers to the DNA molecule as originally isolated, and does not exclude genes or coding regions later added to the segment by the hand of man.
The phrase“SERCA2a gene” or“SERCA2a transgene” or other SERCA isomers thereof, refers to DNA or RNA and can include sense and antisense strands as appropriate to the goals of the therapy practiced according to the disclosure. Also, as used herein,“polynucleotide” refers to a polymer of deoxyribonucleotides or ribonucleotides, in the form of a separate fragment or as a component of a larger construct. Polynucleotides of the disclosure include functional derivatives of known polynucleotides which operatively encode for SERCAZa protein.
The polynucleotide sequence can be deduced from the genetic code, however, the degeneracy of the code must be taken into account. Polynucleotides of the disclosure include sequences which are degenerate as a result of the genetic code, which sequences may be readily determined by those of ordinary skill in the art.
Further, the term“heterologous” as it relates to nucleic acid sequences such as coding sequences and control sequences, denotes sequences that are not normally joined together, and/or are not normally associated with a particular cell. Thus, a“heterologous” region of a nucleic acid construct or a vector is a segment of nucleic acid within or attached to another nucleic acid molecule that is not found in association with the other molecule in nature. For example, a heterologous region of a nucleic acid construct could include a coding sequence flanked by sequences not found in association with the coding sequence in nature. Another example of a heterologous coding sequence is a construct where the coding sequence itself is not found in nature (e.g., synthetic sequences having codons different from the native gene). Similarly, a cell transformed with a construct which is not normally present in the cell would be considered heterologous for purposes of this disclosure. Allelic variation or naturally occurring mutational events do not give rise to heterologous DNA, as used herein. Accordingly, a“coding sequence” or a sequence which“encodes” a particular protein, is a nucleic acid sequence which is transcribed (in the case of DNA) and translated (in the case of mRNA) into a polypeptide in vitro or in vivo when placed under the control of appropriate regulatory sequences. The boundaries of the coding sequence are determined by a start codon at the 5' (amino) terminus and a translation stop codon at the 3' (carboxy) terminus. A coding sequence can include, but is not limited to, cDNA from prokaryotic or eukaryotic mRNA, genomic DNA sequences from prokaryotic or eukaryotic DNA, and even synthetic DNA sequences. A transcription termination sequence will usually be located 3' to the coding sequence.
The nucleotide sequence of the SERCA2a and its isoforms is about 90%+ conserved among mammalian species. Hence, SERCA2a has been identified and sequenced from various mammalian species, including human GenBank sequences NM 170665 (Lytton and MacLennan, J Biol Chem (1998) 263(29):15024-15031); NM_001681 (Id.); NM_006241 (Park et al, J Biol Chem (1994) 269(2):944-954); NM_001003214 (Autry and Jones, J Biol Chem (1997)
272(25): 15872-15880); BC035588 (Strausberg et al, Proc Natl Acad Sci USA (2002)
99(26): 16899-16903); AY186578 (Gelebart et al, Biochem Biophys Res Comm (2003)
303(2):676-684); and mouse GenBank sequences NM_026482 (Du et al, Arch Biochem
Biophys (1995) 316(l):302-310); NM 213616 (Hunter et al, Genomics (1993) 18(3):510-519); NM_009722 (Hsu et al, Biochem Biophys Res Comm (1993) 197(3): 1483-1491); AH31870 (Ver Heyen et al, Mamm Genome (2000) 11(2): 159-163); BC054531 (Strausberg et al, Proc Natl Acad Sci USA (2002) 99(26): 16899-16903); BC054748 (Id.); AJ131821 (Ver Heyen et al, Mamm Genome (2000) 11(2): 159-163); AJ223584 (Id.); AF029982 (Id.); and AF039893 (Schoenfeld and Lowe, direct submission (18 Dec. 1997), Cardiovascular Research, Genentech,
1 DNA Way, South San Francisco, Calif. 94080, USA). All of the above sequences are publicly available.
Although those of ordinary skill in the art will recognize that use of the human SERCA2a polynucleotide includes use human therapies, e.g., human gene therapies, rat SERCA2a polynucleotide can also be used for purposes of the disclosure described herein. Hence, polynucleotides which are structurally or functionally similar, e.g. highly homologous to human SERCA2a are encompassed within the disclosure. It will be obvious to one skilled in the art, that to obtain and use SERCA2a sequences included in this disclosure and those known in the art, DNA and RNA may also be synthesized using automated nucleic acid synthesis by any method known now known or later discovered (e.g., PCR, cDNA synthesis (see, for example, Sambrook et al, Molecular Cloning: A
Laboratory Manual, 3rd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 2001, and Current Protocols in Molecular Biology, M. Ausubel et al., eds., (Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., most recent Supplement)).
As will be understood by those skilled in the art, the polynucleotide compositions of this disclosure can include genomic sequences, extra-genomic and plasmid-encoded sequences and smaller engineered gene segments that express, or may be adapted to express, proteins, polypeptides, peptides and the like. Such segments may be naturally isolated, or modified synthetically by the hand of man.
As will be also recognized by the skilled artisan, polynucleotides of the disclosure may be single-stranded or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules. RNA molecules may include HnRNA molecules, which contain introns and correspond to a DNA molecule in a one-to-one manner, and mRNA molecules, which do not contain introns. Additional coding or noncoding sequences may, but need not, be present within a polynucleotide of the present disclosure, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.
Polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a polypeptide/protein of the disclosure or a portion thereof) or may comprise a sequence that encodes a variant or derivative, including an immunogenic variant or derivative, of such a sequence. Further, polynucleotides can encode a combination of different sequences, e.g., a transgene, a viral polynucleotide, a nucleic acid encoding a selectable marker and the like.
In the compositions of the present disclosure, the polynucleotide or nucleic acid can be either a DNA or RNA. The sequences in question can be of natural or artificial origin, and in particular genomic DNA, cDNA, mRNA, tRNA, rRNA, hybrid sequences or synthetic or semi synthetic sequences. In addition, the nucleic acid can be very variable in size, ranging from oligonucleotide to chromosome. These nucleic acids may be of human, animal, vegetable, bacterial, viral, and the like, origin. They may be obtained by any technique known to a person skilled in the art, and in particular by the screening of libraries, by chemical synthesis or alternatively by mixed methods including the chemical or enzymatic modification of sequences obtained by the screening of libraries. They can, moreover, be incorporated into vectors, such as plasmid vectors.
In vitro transcribed messenger RNA (mRNA) has many advantages as a vehicle for gene delivery. Transfection of mRNA is very efficient and rapid expression of the encoded protein can be achieved. Unlike viral vectors or plasmid DNA, cell-delivered mRNA does not introduce the risk of insertional mutagenesis. Previous studies have shown that RNA can activate a number of innate immune receptors, including Toll-like receptor (TLR)3, TLR7, TLR8 and retinoic acid- inducible gene I (RIG-I). However, activation of these receptors can be avoided by incorporating modified nucleosides, e.g. pseudouridine (Y) or 2-thiouridine (s2U), into the RNA for example. RNA-dependent protein kinase (PKR) is a ubiquitous mammalian enzyme with a variety of cellular functions, including regulation of translation during conditions of cell stress. During viral infection, PKR binds viral double- stranded (ds)RNA, autophosphorylates and subsequently phosphorylates the alpha subunit of translation initiation factor 2 (eIF-2a), thus repressing translation. Originally, potent activation of PKR was thought to require >30-bp-long dsRNA. It has subsequently been shown that PKR can be activated by a variety of RNA structures that include single-stranded (ss)RNA forming hairpins imperfect dsRNA containing mismatches, short dsRNA with ss tails, stem-loop structures with 5 '-triphosphates, and unique elements present in interferon gamma (IFN-g) and tumor necrosis factor-alpha mRNAs and cellular RNAs. Since replacing uridines with pseudouridines also abrogates innate immune activation by RNA, Y-modified mRNAs are attractive vectors for gene delivery or replacement, vaccine antigen delivery or other RNA-based therapeutic applications.
In some embodiments, the nucleic acids of the present disclosure have undergone a chemical or biological modification to render them more stable. Exemplary modifications to a nucleic acid include the depletion of a base (e.g., by deletion or by the substitution of one nucleotide for another) or modification of a base, for example, the chemical modification of a base. The phrase“chemical modifications” as used herein, includes modifications which introduce chemistries which differ from those seen in naturally occurring nucleic acids, for example, covalent modifications such as the introduction of modified nucleotides, (e.g., nucleotide analogs, or the inclusion of pendant groups which are not naturally found in such nucleic acid molecules).
In addition, suitable modifications include alterations in one or more nucleotides of a codon such that the codon encodes the same amino acid but is more stable than the codon found in the wild-type version of the nucleic acid. For example, an inverse relationship between the stability of RNA and a higher number of cytidines (C's) and/or uridines (U's) residues has been demonstrated, and RNA devoid of C and U residues have been found to be stable to most RNases (Heidenreich, et al. J Biol Chem 269, 2131-8 (1994)). In some embodiments, the number of C and/or U residues in an mRNA sequence is reduced. In another embodiment, the number of C and/or U residues is reduced by substitution of one codon encoding a particular amino acid for another codon encoding the same or a related amino acid. Contemplated modifications to the mRNA nucleic acids of the present disclosure also include the incorporation of pseudouridines. The incorporation of pseudouridines into the mRNA nucleic acids of the present disclosure may enhance stability and translational capacity, as well as diminishing immunogenicity in vivo.
(See, e.g., Kariko, K., et al, Molecular Therapy 16 (11): 1833-1840 (2008)). Substitutions and modifications to the nucleic acids of the present disclosure may be performed by methods readily known to one or ordinary skill in the art.
The constraints on reducing the number of C and U residues in a sequence will likely be greater within the coding region of an mRNA, compared to an untranslated region, (i.e., it will likely not be possible to eliminate all of the C and U residues present in the message while still retaining the ability of the message to encode the desired amino acid sequence). The degeneracy of the genetic code, however presents an opportunity to allow the number of C and/or U residues that are present in the sequence to be reduced, while maintaining the same coding capacity (i.e., depending on which amino acid is encoded by a codon, several different possibilities for modification of RNA sequences may be possible). For example, the codons for Gly can be altered to GGA or GGG instead of GGU or GGC.
The term modification also includes, for example, the incorporation of non-nucleotide linkages or modified nucleotides into the nucleic acid sequences of the present disclosure (e.g., modifications to one or both the 3' and 5' ends of an mRNA molecule encoding a functional protein or enzyme). Such modifications include the addition of bases to a nucleic acid sequence (e.g., the inclusion of a poly A tail or a longer poly A tail), the alteration of the 3' UTR, or the 5' UTR, complexing the nucleic acid with an agent (e.g., a protein or a complementary nucleic acid molecule), and inclusion of elements which change the structure of a nucleic acid molecule (e.g., which form secondary structures).
The poly A tail is thought to stabilize natural messengers and synthetic sense RNA. Therefore, in one embodiment a long poly A tail can be added to an mRNA molecule thus rendering the RNA more stable. Poly A tails can be added using a variety of art-recognized techniques. For example, long poly A tails can be added to synthetic or in vitro transcribed RNA using poly A polymerase (Yokoe, et al. Nature Biotechnology. 1996; 14: 1252-1256). A transcription vector can also encode long poly A tails. In addition, poly A tails can be added by transcription directly from PCR products. Poly A may also be ligated to the 3' end of a sense RNA with RNA ligase (see, e.g., Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1991 edition)). In one embodiment, the length of the poly A tail is at least about 90, 200, 300, 400 at least 500 nucleotides. In one embodiment, the length of the poly A tail is adjusted to control the stability of a modified sense mRNA molecule of the disclosure and, thus, the transcription of protein. For example, since the length of the poly A tail can influence the half-life of a sense mRNA molecule, the length of the poly A tail can be adjusted to modify the level of resistance of the mRNA to nucleases and thereby control the time course of protein expression in a cell. In one embodiment, the stabilized nucleic acid molecules are sufficiently resistant to in vivo
degradation (e.g., by nucleases), such that they may be delivered to the target cell without a transfer vehicle.
Accordingly, in order to express a desired polypeptide, the nucleotide sequences encoding the polypeptide, e.g., SERCA2a, or functional equivalents, may be inserted into appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence. Methods that are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding a polypeptide of interest and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described, for example, in Sambrook, J. et al. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Plainview, N.Y., and Ausubel, F. M. et al. (1989) Current Protocols in Molecular Biology, John Wiley & Sons, New York. N. Y, incorporated herein by reference.
The term“operatively encoding” refers to a polynucleotide which has been modified to include promoter and other sequences necessary for expression and, where desired, secretion of the desired translation product; e.g., a peptide or protein. All the embodiments of the disclosure can be practiced using known recombinant expression vectors including bacterial and viral. In some embodiments, these vectors will include cDNA('s) which encode for the desired translation product. Therefore, unless context otherwise requires, it will be assumed that“polynucleotide” refers to operatively encoding sequences contained in a suitable recombinant expression vector, examples of which are provided herein.
The“control elements” or“regulatory sequences” present in an expression vector are those non-translated regions of the vector (e.g., enhancers, promoters, 5' and 3' untranslated regions and the like), which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the pBLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or pSPORTl plasmid (Gibco BRL, Gaithersburg, Md.) and the like may be used. By way of non-limiting examples, promoters include those from CMV, beta-actin, EF2alpha, RSV LTR, HIW LTR, HTLV-1 LTR, and composite promoters (D. H. Barouch et al, A human T-cell leukemia virus type 1 regulatory element enhances the immunogenicity of human immunodeficiency virus type 1 DNA vaccines in mice and nonhuman primates, J. Virol. 79: 8828-8834, 2005, incorporated herein by reference). In one aspect, the promoter is a CMV promoter or a promoter comprising portions of the chicken beta-actin promoter (H. Niwa et al, Efficient selection for high-expression transfectants with a novel eukaryotic vector, Gene 108: 193-199, 1991). In another aspect, the promoter is a CMV promoter, Sm22 promoter, or Tie2 promoter. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding a polypeptide, vectors based on SV40 or EBV may be advantageously used with an appropriate selectable marker.
Specific initiation signals may also be used to achieve more efficient translation of sequences encoding a polypeptide of interest. Such signals include the ATG initiation codon and adjacent sequences. In cases where sequences encoding the polypeptide, its initiation codon, and upstream sequences are inserted into the appropriate expression vector, no additional
transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a portion thereof, is inserted, exogenous translational control signals including the ATG initiation codon should be provided. Furthermore, the initiation codon should be in the correct reading frame to ensure translation of the entire insert. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers which are appropriate for the particular cell system which is used, such as those described in the literature (Scharf, D. et al. (1994) Results Probl. Cell Differ. 20: 125-162, incorporated herein by reference).
In addition, a host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion. Such
modifications of the polypeptide include, but are not limited to, acetylation, carboxyl ation, glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing which cleaves a“prepro” form of the protein may also be used to facilitate correct insertion, folding and/or function. Different host cells such as CHO, COS, HeLa, MDCK, HEK293, and WI38, which have specific cellular machinery and characteristic mechanisms for such post-translational activities, may be chosen to ensure the correct modification and processing of the foreign protein.
Moreover, gene delivery involves polymers which form complexes, nanoparticles (defined as less than 1 micron in diameter), or even microparticles (defined as 1 micron in diameter or greater) with DNA plasmids and other nucleic acids. Many kinds of polymers have been described that enhance the expression of genes encoded by nucleic acids in cells.
For example, cationic polymers such as poly-L-lysine, poly-L-glutamate, or block co polymers may also be delivery agents for nucleic acids. Further, the use of poly[alpha-(4- aminobutyl)-l -glycolic acid] (PAG A) has been used to deliver plasmid DNAs to tumor-bearing mice. Still, the use of water-soluble lipopolymer (WSLP), using branched polyethylenimine and cholesteryl chloroformate has also been described. Polyethylenimine-based vesicle-polymer hybrid gene delivery as another way to deliver plasmid DNA expression vectors, including the use of poly(propylenimine) dendrimers as delivery agents Also, polyethylene glycol (PEG) copolymers were found to improve plasmid DNA delivery, including various kinds of polymers that can be used for the controlled release of plasmid DNA and other nucleic acids. Such molecules include poly(lactic acid) and its derivatives, PEGylated poly(lactic acid), poly(lactic- co-glycolic acid) and its derivatives, poly(ortho esters) and their derivatives, PEGylated poly(ortho esters), poly(caprolactone) and its derivatives, PEGylated poly(caprolactone), polylysine and its derivatives, PEGylated polylysine, poly(ethylene imine) and its derivatives, PEGylated poly(ethylene imine), poly( acrylic acid) and its derivatives, PEGylated poly( acrylic acid), poly(urethane) and its derivatives, PEGylated poly(urethane), and combinations of all of these. One object of the present disclosure is the use of polymeric lipid-protein-sugar microparticles for the delivery of nucleic acids. These and other polymers are well known in the art.
Still in another aspect, nucleic acid compositions of the present disclosure are delivered by electroporation. Electroporation uses electrical pulses to introduce proteins, nucleic acids, lipids, carbohydrates, or mixtures thereof into the host to produce an effect. A typical use of electroporation is to introduce a nucleic acid into the host so that the protein encoded by the nucleic acid is efficiently produced.
In another aspect, nucleic acid compositions of the present disclosure are delivered by particle bombardment. Powderject (Novartis Pharmaceutical Corporation) has developed methods to coat gold particles with nucleic acids and other substances and then forcibly introduce them into the host by particle bombardment. For nucleic acids encoding antigens, this results in an improved immune response to the antigens.
III. Adeno- Associated Virus (AAV)
Adeno-associated virus (AAV) has shown promise for delivering genes for gene therapy in clinical trials in humans. As the only viral vector system based on a nonpathogenic and replication-defective virus, recombinant AAV virions have been successfully used to establish efficient and sustained gene transfer of both proliferating and terminally differentiated cells in a variety of tissues.
The AAV genome is a linear, single- stranded DNA molecule containing about 4681 nucleotides. The AAV genome generally comprises an internal nonrepeating genome flanked on each end by inverted terminal repeats (ITRs). The ITRs are approximately 145 base pairs (bp) in length. The ITRs have multiple functions, including as origins of DNA replication, and as packaging signals for the viral genome. The internal nonrepeated portion of the genome includes two large open reading frames, known as the AAV replication (rep) and capsid (cap) genes. The rep and cap genes code for viral proteins that allow the virus to replicate and package into a virion. In particular, a family of at least four viral proteins is expressed from the AAV rep region, Rep 78, Rep 68, Rep 52, and Rep 40, named according to their apparent molecular weight. The AAV cap region encodes at least three proteins, VP1, VP2, and VP3.
As used herein, the term“vector” means any genetic element, such as a plasmid, phage, transposon, cosmid, chromosome, virus, virion, etc., which is capable of replication when associated with the proper control elements and which can transfer gene sequences between cells. Thus, the term includes cloning and expression vehicles, as well as viral vectors previously discussed. Similarly,“recombinant expression vector” refers to systems of polynucleotide(s) which operatively encode polypeptides expressible in eukaryotes or prokaryotes. Methods of expressing DNA sequences having eukaryotic or viral sequences in prokaryotes are well known in the art. Biologically functional viral and plasmid DNA vectors capable of expression and replication in a host are also well known in the art. Hosts can include microbial, yeast, insect and mammalian organisms.
The vectors or recombinant expression vectors provided herein are easily manufactured, and combine the advantages of adenovirus (high titer, high infectivity, large capacity, lack of association with human malignancy) but with the integration capability of AAV, making them particularly suitable for stable gene transfer which is useful in, for example, gene therapy approaches such as that described herein. A further advantage of the described AAV vectors is that, by virtue of containing AAV TR or ITR and D sequences that flank the gene of interest, it is expected that they integrate into cellular chromosomal DNA. Integration is important for stable gene transfer into cells. Another advantage of the AAV vectors provided herein is that they are packaged efficiently into stable virus particles whether small or large polynucleotides are used. Still, another advantage of the AAV vectors provided herein is that they are less cytotoxic than first generation adenovirus vectors since no adenovirus genes are expressed within transduced cells.
The AAV-vector and/or AAV-SERCA2a containing virions described herein are “transfected”, which refers to the uptake of foreign DNA by a cell. That is, a cell“transfected” with exogenous DNA and the DNA is introduced inside the cell membrane. A number of transfection techniques are generally known in the art. See, e.g., Graham et al. (1973) Virology, 52:456, Sambrook et al. (1989) Molecular Cloning, a laboratory manual, Cold Spring Harbor Laboratories, New York, Davis et al. (1986) Basic Methods in Molecular Biology, Elsevier, and Chu et al. (1981) Gene 13: 197, incorporated herein by reference. Such techniques can be used to introduce one or more exogenous DNA moieties, such as a nucleotide integration vector and other nucleic acid molecules, into suitable host cells.
The term“host cell” or“host” denotes, for example, mammalian cells, that can be, or have been, used as recipients of an AAV helper construct, an AAV vector plasmid, an accessory function vector, or other transfer DNA. Similarly, the terms“subject”,“individual” or“patient” are used interchangeably herein and refer to a vertebrate, and in some embodiments, a mammal. Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals and pets. The term includes the progeny of the original cell which has been transfected. Thus, a “host cell” or“host” as used herein generally refers to a cell which has been transfected with an exogenous DNA sequence. It is understood that the progeny of a single parental cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation.
As used herein, the term“cell line” refers to a population of cells capable of continuous or prolonged growth and division in vitro. Often, cell lines are clonal populations derived from a single progenitor cell. It is further known in the art that spontaneous or induced changes can occur in karyotype during storage or transfer of such clonal populations. Therefore, cells derived from the cell line referred to may not be precisely identical to the ancestral cells or cultures, and the cell line referred to includes such variants.
Additional viral vectors useful for delivering the polynucleotides encoding polypeptides of the present disclosure by gene transfer include those derived from the pox family of viruses, such as vaccinia virus and avian poxvirus. By way of example, vaccinia virus recombinants expressing the novel molecules can be constructed as follows. The DNA encoding a polypeptide is first inserted into an appropriate vector so that it is adjacent to a vaccinia promoter and flanking vaccinia DNA sequences, such as the sequence encoding thymidine kinase (TK). This vector is then used to transfect cells which are simultaneously infected with vaccinia.
Homologous recombination serves to insert the vaccinia promoter plus the gene encoding the polypeptide of interest into the viral genome. The resulting TK(-) recombinant can be selected by culturing the cells in the presence of 5-bromodeoxyuridine and picking viral plaques resistant thereto.
A vaccinia-based infection/transfection system can be conveniently used to provide for inducible, transient expression or coexpression of one or more polypeptides described herein in host cells of an organism. In this particular system, cells are first infected in vitro with a vaccinia virus recombinant that encodes the bacteriophage T7 RNA polymerase. This polymerase displays exquisite specificity in that it only transcribes templates bearing T7 promoters.
Following infection, cells are transfected with the polynucleotide or polynucleotides of interest, driven by a T7 promoter. The polymerase expressed in the cytoplasm from the vaccinia virus recombinant transcribes the transfected DNA into RNA which is then translated into polypeptide by the host translational machinery. The method provides for high level, transient, cytoplasmic production of large quantities of RNA and its translation products. See, e.g., Elroy-Stein and Moss, Proc. Natl. Acad. Sci. USA (1990) 87:6743-6747; Fuerst et al. Proc. Natl. Acad. Sci. USA (1986) 83:8122-8126, incorporated herein by reference.
Alternatively, avipoxviruses, such as the fowlpox and canarypox viruses, can also be used to deliver the coding sequences of interest. Recombinant avipox viruses, expressing immunogens from mammalian pathogens, are known to confer protective immunity when administered to non-avian species. The use of an Avipox vector is particularly desirable in human and other mammalian species since members of the Avipox genus can only productively replicate in susceptible avian species and therefore are not infective in mammalian cells.
Methods for producing recombinant Avipoxviruses are known in the art and employ genetic recombination, as described above with respect to the production of vaccinia viruses. See, e.g., WO 91/12882; WO 89/03429; and WO 92/03545, incorporated herein by reference.
Any of a number of alphavirus vectors can also be used for delivery of polynucleotide compositions of the present disclosure, such as those vectors described in U.S. Pat. Nos.
5,843,723; 6,015,686; 6,008,035 and 6,015,694, incorporated herein by reference. Certain vectors based on Venezuelan Equine Encephalitis (VEE) can also be used, illustrative examples of which can be found in U.S. Pat. Nos. 5,505,947 and 5,643,576, both of which are incorporated herein by reference.
Moreover, molecular conjugate vectors, such as the adenovirus chimeric vectors described in Michael et al. J. Biol. Chem. (1993) 268:6866-6869 and Wagner et al. Proc. Natl. Acad. Sci. USA (1992) 89:6099-6103, incorporated herein by reference, can also be used for gene delivery under the disclosure.
AAV has been engineered to deliver genes of interest by deleting the internal
nonrepeating portion of the AAV genome (i.e., the rep and cap genes) and inserting a
heterologous gene between the ITRs. The heterologous gene is typically functionally or operatively linked to a heterologous promoter (constitutive, cell-specific, or inducible) capable of driving gene expression in the patient's target cells under appropriate conditions. Termination signals, such as polyadenylation sites, can also be included.
As used herein, the term“AAV vector” means a vector derived from an adeno-associated virus serotype, including without limitation, AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, and mutated forms thereof. AAV vectors can have one or more of the AAV wild-type genes deleted in whole or part, the rep and/or cap genes, but retain functional flanking ITR sequences. In some embodiments, the AAV vector is derived from an adeno- associated virus serotype AAV1. Despite the high degree of homology, the different serotypes have tropisms for different tissues. The receptor for AAV 1 is unknown; however, AAV 1 is known to transduce skeletal and smooth muscle more efficiently than AAV2. Without being bound by theory, since most of the studies have been done with pseudotyped vectors in which the vector DNA flanked with AAV2 ITR is packaged into capsids of alternate serotypes, it is clear that the biological differences are related to the capsid rather than to the genomes. Recent evidence indicates that DNA expression cassettes packaged in AAV1 capsids are at least 1 loglO more efficient at transducing cardiomyocytes than those packaged in AAV2 capsids.
Functional ITR sequences are necessary for the rescue, replication and packaging of the AAV virion. Thus, an AAV vector is defined herein to include at least those sequences required in cis for replication and packaging (e.g., functional ITRs) of the virus. The ITRs need not be the wild-type nucleotide sequences, and may be altered, for example, by the insertion, deletion or substitution of nucleotides, as long as the sequences provide for functional rescue, replication and packaging.
AAV vectors must have one copy of the AAV inverted terminal repeat sequences (ITRs) at each end of the genome in order to be replicated, packaged into AAV particles and integrated efficiently into cell chromosomes. However, the nucleic acid promoted by ITR can be any desired sequence. In one embodiment, the nucleic acid encodes a SERCA2a polypeptide or its isoform (e.g., SERCA2a), which has a desired function in the cell in which the vector is expressed. For example, the SERCA2a polypeptide increases the control of Ca++ storage and regulation in the cell, thereby lowering blood pressure in the arteries of the lungs.
The ITR consists of nucleotides 1 to 145 at the left end of the AAV DNA genome and the corresponding nucleotides 4681 to 4536 (i.e., the same sequence) at the right hand end of the AAV DNA genome. Thus, AAV vectors must have a total of at least 300 nucleotides of the terminal sequence. So, for packaging large coding regions into AAV vector particles, it is important to develop the smallest possible regulatory sequences, such as transcription promoters and polyA addition signal. In this system, the adeno-associated viral vector comprising the inverted terminal repeat (ITR) sequences of adeno-associated virus and a nucleic acid encoding SERCA (e.g., SERCA2a), its isoforms, fragments and/or variants, wherein the inverted terminal repeat sequences promote expression of the nucleic acid in the absence of another promoter.
Accordingly, as used herein, AAV refers to all serotypes of AAV (i.e., 1-9) and mutated forms thereof. Thus, it is routine in the art to use the ITR sequences from other serotypes of AAV since the ITRs of all AAV serotypes are expected to have similar structures and functions with regard to replication, integration, excision and transcriptional mechanisms.
AAV is also a helper-dependent virus. That is, it requires coinfection with a helper virus (e.g., adenovirus, herpesvirus or vaccinia), in order to form AAV virions. In the absence of coinfection with a helper virus, AAV establishes a latent state in which the viral genome inserts into a host cell chromosome, but infectious virions are not produced. Subsequent infection by a helper virus“rescues” the integrated genome, allowing it to replicate and package its genome into an infectious AAV virion. While AAV can infect cells from different species, the helper virus must be of the same species as the host cell. Thus, for example, human AAV will replicate in canine cells coinfected with a canine adenovirus.
The term“AAV helper functions” refer to AAV-derived coding sequences which can be expressed to provide AAV gene products that, in turn, function in trans for productive AAV replication. Thus, AAV helper functions include both of the major AAV open reading frames (ORFs), rep and cap. The Rep expression products have been shown to possess many functions, including, among others: recognition, binding and nicking of the AAV origin of DNA
replication; DNA helicase activity; and modulation of transcription from AAV (or other heterologous) promoters. The Cap expression products supply necessary packaging functions. AAV helper functions are used herein to complement AAV functions in trans that are missing from AAV vectors.
Accordingly, the term“AAV helper construct” refers generally to a nucleic acid molecule that includes nucleotide sequences providing AAV functions deleted from an AAV vector which is to be used to produce a transducing vector for delivery of a nucleotide sequence of interest. AAV helper constructs are commonly used to provide transient expression of AAV rep and/or cap genes to complement missing AAV functions that are necessary for lytic AAV replication; however, helper constructs lack AAV ITRs and can neither replicate nor package themselves. AAV helper constructs can be in the form of a plasmid, phage, transposon, cosmid, virus, or virion. A number of AAV helper constructs and vectors that encode Rep and/or Cap expression products have been described.
Typically, recombinant AAV (rAAV) virus is made by cotransfecting a plasmid containing the gene of interest flanked by the two AAV terminal repeats and/or an expression plasmid containing the wild-type AAV coding sequences without the terminal repeats, for example pIM45. The cells are also infected and/or transfected with adenovirus and/or plasmids carrying the adenovirus genes required for AAV helper function. rAAV virus stocks made in such fashion are contaminated with adenovirus which must be physically separated from the rAAV particles (for example, by cesium chloride density centrifugation or column
chromatography). Alternatively, adenovirus vectors containing the AAV coding regions and/or cell lines containing the AAV coding regions and/or some or all of the adenovirus helper genes could be used. Cell lines carrying the rAAV DNA as an integrated provirus can also be used. In some embodiments, recombinant AAVs (rAAVs) have tissue-specific targeting capabilities, such that a transgene of the rAAV will be delivered specifically to one or more predetermined tissue(s).
Methods for obtaining recombinant AAVs having a desired capsid protein are well known in the art. (See, for example, US 2003/0138772), the contents of which are incorporated herein by reference in their entirety). Typically the methods involve culturing a host cell which contains a nucleic acid sequence encoding an AAV capsid protein or fragment thereof; a functional rep gene; a recombinant AAV vector composed of, AAV inverted terminal repeats (ITRs) and a transgene; and sufficient helper functions to permit packaging of the recombinant AAV vector into the AAV capsid proteins. The recombinant AAV vector, rep sequences, cap sequences, and helper functions required for producing the rAAV of the disclosure may be delivered to the packaging host cell using any appropriate genetic element (vector). The selected genetic element may be delivered by any suitable method, including those described herein. The methods used to construct any embodiment of this disclosure are known to those with skill in nucleic acid manipulation and include genetic engineering, recombinant engineering, and synthetic techniques. See, e.g., Sambrook et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N. Y. Similarly, methods of generating rAAV virions are well known and the selection of a suitable method is not a limitation on the present disclosure. See, e.g., K. Fisher et al, J. Virol., 70:520-532 (1993) and U.S. Pat. No. 5,478,745.
In some embodiments, recombinant AAVs may be produced using the triple transfection method (described in detail in U.S. Pat. No. 6,001,650). Typically, the recombinant AAVs are produced by transfecting a host cell with an recombinant AAV vector (comprising a transgene) to be packaged into AAV particles, an AAV helper function vector, and an accessory function vector. An AAV helper function vector encodes the“AAV helper function” sequences (i.e., rep and cap), which function in trans for productive AAV replication and encapsidation. In some embodiments, the AAV helper function vector supports efficient AAV vector production without generating any detectable wild-type AAV virions (i.e., AAV virions containing functional rep and cap genes). Non-limiting examples of vectors suitable for use with the present disclosure include pHLP19, described in U.S. Pat. No. 6,001,650 and pRep6cap6 vector, described in U.S. Pat. No. 6,156,303, the entirety of both incorporated by reference herein. The accessory function vector encodes nucleotide sequences for non-AAV derived viral and/or cellular functions upon which AAV is dependent for replication (i.e.,“accessory functions”). The accessory functions include those functions required for AAV replication, including, without limitation, those moieties involved in activation of AAV gene transcription, stage specific AAV mRNA splicing, AAV DNA replication, synthesis of cap expression products, and AAV capsid assembly. Viral- based accessory functions can be derived from any of the known helper viruses such as adenovirus, herpesvirus (other than herpes simplex virus type-1), and vaccinia virus.
As used herein, the term“accessory functions” refers to non-AAV derived viral and/or cellular functions upon which AAV is dependent for its replication. Thus, the term captures proteins and RNAs that are required in AAV replication, including those moieties involved in activation of AAV gene transcription, stage specific AAV mRNA splicing, AAV DNA replication, synthesis of Cap expression products and AAV capsid assembly. Viral-based accessory functions can be derived from any of the known helper viruses such as adenovirus, herpesvirus (other than herpes simplex virus type-1) and vaccinia virus.
Accordingly,“accessory function vector” refers generally to a nucleic acid molecule that includes nucleotide sequences providing accessory functions. An accessory function vector can be transfected into a suitable host cell, wherein the vector is then capable of supporting AAV virion production in the host cell. Expressly excluded from the term are infectious viral particles as they exist in nature, such as adenovirus, herpesvirus or vaccinia virus particles. Thus, accessory function vectors can be in the form of a plasmid, phage, transposon or cosmid.
In particular, it has been demonstrated that the full-complement of adenovirus genes is not required for accessory helper functions. In particular, adenovirus mutants incapable of DNA replication and late gene synthesis have been shown to be permissive for AAV replication. Similarly, mutants within the E2B and E3 regions have been shown to support AAV replication, indicating that the E2B and E3 regions are probably not involved in providing accessory functions. However, adenoviruses defective in the El region, or having a deleted E4 region, are unable to support AAV replication. Thus, El A and E4 regions are likely required for AAV replication, either directly or indirectly. Other characterized Ad mutants include: E1B; E2A;
E2B; E3; and E4. Although studies of the accessory functions provided by adenoviruses having mutations in the E1B coding region have produced conflicting results, recently it has been reported that E1B55% is required for AAV virion production, while ElB19k is not.
Exemplary accessory function vectors include an adenovirus VA RNA coding region, an adenovirus E4 ORF6 coding region, an adenovirus E2A 72 kD coding region, an adenovirus El A coding region, and an adenovirus E1B region lacking an intact ElB55k coding region.
By“capable of supporting efficient rAAV virion production” is meant the ability of an accessory function vector or system to provide accessory functions that are sufficient to complement rAAV virion production in a particular host cell at a level substantially equivalent to or greater than that which could be obtained upon infection of the host cell with an adenovirus helper virus. Thus, the ability of an accessory function vector or system to support efficient rAAV virion production can be determined by comparing rAAV virion titers obtained using the accessory vector or system with titers obtained using infection with an infectious adenovirus. In some embodiments, an accessory function vector or system supports efficient rAAV virion production substantially equivalent to, or greater than, that obtained using an infectious adenovirus when the amount of virions obtained from an equivalent number of host cells is not more than about 200 fold less than the amount obtained using adenovirus infection; in some embodiments, not more than about 100 fold less; and in some embodiments, equal to, or greater than, the amount obtained using adenovirus infection.
Hence, by“AAV virion” is meant a complete virus particle, such as a wild-type (wt)
AAV virus particle (comprising a linear, single-stranded AAV nucleic acid genome associated with an AAV capsid protein coat). In this regard, single-stranded AAV nucleic acid molecules of either complementary sense, e.g.,“sense” or“antisense” strands, can be packaged into any one AAV virion and both strands are equally infectious.
Similarly, a“recombinant AAV virion,” or“rAAV virion” is defined herein as an infectious, replication-defective virus including an AAV protein shell, encapsidating a heterologous nucleotide sequence of interest which is flanked on both sides by AAV ITRs. A rAAV virion is produced in a suitable host cell which has had an AAV vector, AAV helper functions and accessory functions introduced therein. In this manner, the host cell is rendered capable of encoding AAV polypeptides that are required for packaging the AAV vector
(containing a recombinant nucleotide sequence of interest) into infectious recombinant virion particles for subsequent gene delivery.
The AAV system of the disclosure, may also include a sequence encoding a selectable marker. The phrase,“selectable marker” or“selectable gene product” as used herein, refers to the use of a gene which may include but is not limited to: bacterial aminoglycoside 3'
phosphotransferase gene (also referred to as the neo gene) which confers resistance to the drug G418 in mammalian cells; bacterial hygromycin G phosphotransferase (hyg) gene which confers resistance to the antibiotic hygromycin; and the bacterial xanthine-guanine phosphoribosyl transferase gene (also referred to as the gpt gene) which confers the ability to grow in the presence of mycophenolic acid. In addition, the AAV system of the disclosure may also include sequences encoding a visual detectable marker, e.g., green fluorescent protein (GFP) or any other detectable marker standard in the art and can be identified and utilized by one skilled in the art without undue experimentation. Those of skill in the art have circumvented some of the limitations of adenovirus-based vectors by using adenovirus“hybrid” viruses, which incorporate desirable features from adenovirus as well as from other types of viruses as a means of generating unique vectors with highly specialized properties. For example, viral vector chimeras were generated between adenovirus and adeno-associated virus (AAV). These aspects of the disclosure do not deviate from the scope of the disclosure described herein.
Another method for delivery of the polynucleotide for gene therapy involves the use of an adenovirus expression vector. As used herein, the term“adenovirus expression vector” is meant to include those constructs containing adenovirus sequences sufficient (a) to support packaging of the construct and/or (b) to ultimately express a tissue and/or cell-specific construct that has been cloned therein.
In one embodiment, the expression vector comprises a genetically engineered form of adenovirus. Knowledge of the genetic organization of adenovirus, a 36 kb, linear, double- stranded DNA virus, allows substitution of large pieces of adenoviral DNA with foreign sequences up to 7 kb (Grunhaus and Horwitz, Seminar in Virology, 1992; 3:237-252). In contrast to retrovirus, the adenoviral infection of host cells does not result in chromosomal integration because adenoviral DNA can replicate in an episomal manner without potential genotoxicity. Also, adenoviruses are structurally stable, and no genome rearrangement has been detected after extensive amplification.
Adenovirus growth and manipulation is known to those of skill in the art, and exhibits broad host range in vitro and in vivo. This group of viruses can be obtained in high titers, e.g.,
109 to 1011 plaque-forming units per mL, and they are highly infective. The life cycle of adenovirus does not require integration into the host cell genome. The foreign genes delivered by adenovirus vectors are episomal and, therefore, have low genotoxicity to host cells. No side effects have been reported in studies of vaccination with wild-type adenovirus, demonstrating their safety and/or therapeutic potential as in vivo gene transfer vectors.
Adenovirus vectors have been used in eukaryotic gene expression and vaccine
development. Recently, animal studies suggested that recombinant adenovirus could be used for gene therapy (see, e.g., Stratford-Perricaudet et al, Hum. Gene. Ther., 1991; 1 :242-256; Rich et al, 1993). Studies in administering recombinant adenovirus to different tissues include muscle injection, peripheral intravenous injections and stereotactic inoculation into the brain. Recombinant adenovirus and adeno-associated virus can both infect and transduce non-dividing human primary cells.
While the use of adenovirus vectors is contemplated, such use in gene therapy trials is currently limited by short-lived transgene expression. (Vassalli G, et al, Int. J. Cardiol., 2003; 90(2-3) :229-38). This is due to cellular immunity against adenoviral antigens. Improved “gutless” adenoviral vectors have reduced immunogenicity, yet still are ineffective if maximal expression of the transgene for more than six months is needed or desired for therapeutic effect (Gilbert R, et al, Hum. Mol. Genet., 2003; 12(11): 1287-99). AAV vectors have demonstrated long term expression (>1 year) (Daly T M, et al, Gene Then, 2001; 8(17): 1291-8).
IV Other Delivery Systems
1. Retroviral Vectors
In certain embodiments, a polynucleotide may be integrated into the genome of a target cell. This integration may be in the specific location and orientation via homologous
recombination (gene replacement) or it may be integrated in a random, non-specific location (gene augmentation). In yet further embodiments, the polynucleotide may be stably maintained in the cell as a separate, episomal segment ofDNA. Such polynucleotide segments or “episomes” encode sequences sufficient to permit maintenance and replication independent of or in synchronization with the host cell cycle. The manner in which the expression construct is delivered to a cell and where in the cell the polynucleotide remains is dependent on the type of expression construct employed.
In some embodiments, a polynucleotide as disclosed herein is included in a retroviral vector. Retroviruses may be chosen as gene delivery vectors due to their ability to integrate their genes into the host genome, transferring a large amount of foreign genetic material, infecting a broad spectrum of species and cell types and for being packaged in special cell-lines.
The retroviral genome contains three genes, gag, pol, and env that code for capsid proteins, polymerase enzyme, and envelope components, respectively. A sequence found upstream from the gag gene contains a signal for packaging of the genome into virions. Two long terminal repeat (LTR) sequences are present at the 5' and 3' ends of the viral genome. These contain strong promoter and enhancer sequences and are also required for integration in the host cell genome. In order to construct a retroviral vector, a nucleic acid encoding a gene of interest is inserted into the viral genome in the place of certain viral sequences to produce a virus that is replication-defective. In order to produce virions, a packaging cell line is constructed containing the gag, pol, and/or env genes but without the LTR and/or packaging components. When a recombinant plasmid containing a cDNA, together with the retroviral LTR and packaging sequences is introduced into this cell line (by calcium phosphate precipitation for example), the packaging sequence allows the RNA transcript of the recombinant plasmid to be packaged into viral particles, which are then secreted into the culture media. The media containing the recombinant retroviruses is then collected, optionally concentrated, and used for gene transfer. Retroviral vectors are able to infect a broad variety of cell types. However, integration and stable expression require the division of host cells.
2. Herpes Virus
Because herpes simplex virus (HSV) is neurotropic, it has generated considerable interest in treating certain disorders. Moreover, the ability of HSV to establish latent infections in non dividing cells without integrating into the host cell chromosome or otherwise altering the host cell's metabolism, along with the existence of a promoter that is active during latency makes HSV an attractive vector. And though much attention has focused on the neurotropic applications of HSV, this vector also can be exploited for other tissues given its wide host range.
Another factor that makes HSV an attractive vector is the size and organization of the genome. Because HSV is large, incorporation of multiple genes or expression cassettes is less problematic than in other smaller viral systems. In addition, the availability of different viral control sequences with varying performance (temporal, strength, etc.) makes it possible to control expression to a greater extent than in other systems. It also is an advantage that the virus has relatively few spliced messages, further easing genetic manipulations.
HSV also is relatively easy to manipulate and can be grown to high titers. Thus, delivery is less of a problem, both in terms of volumes needed to attain sufficient multiplicity of infection (MOI) and in a lessened need for repeat dosing. For a review of HSV as a gene therapy vector, see Glorioso et al, Annu. Rev. Microbiol., 1995; 49:675-710. Avirulent variants of HSV have been developed and are readily available for use in gene therapy contexts (U.S. Pat. No.
5,672,344, incorporated herein by reference).
3. Lentiviral Vectors Lentiviruses are complex retroviruses, which, in addition to the common retroviral genes gag, pol, and env, contain other genes with regulatory or structural function. The higher complexity enables the virus to modulate its life cycle, as in the course of latent infection. Some examples of lentivirus include the Human Immunodeficiency Viruses (HTV 1, REV 2) and the Simian Immunodeficiency Virus (SIV). Lentiviral vectors have been generated by multiply attenuating the HIV virulence genes, for example, the genes env, vif, vpr, vpu and nef are deleted making the vector biologically safe.
Lentiviral vectors are known in the art, see, e.g., U.S. Pat. Nos. 6,013,516 and 5,994,136, both of which are incorporated herein by reference. In general, the vectors are plasmid-based or virus-based, and are configured to carry the essential sequences for incorporating foreign nucleic acid, for selection and for transfer of the nucleic acid into a host cell. The gag, pol and env genes of the vectors of interest also are known in the art. Thus, the relevant genes are cloned into the selected vector and then used to transform the target cell of interest.
Recombinant lentivirus capable of infecting a non-dividing cell wherein a suitable host cell is transfected with two or more vectors carrying the packaging functions, namely gag, pol and env, as well as rev and tat is described in U.S. Pat. No. 5,994,136, incorporated herein by reference. This describes a first vector that can provide a nucleic acid encoding a viral gag and a pol gene and another vector that can provide a nucleic acid encoding a viral env to produce a packaging cell. Introducing a vector providing a heterologous gene into that packaging cell yields a producer cell which releases infectious viral particles carrying the foreign gene of interest. In some embodiments, the env is an amphotropic envelope protein which allows transduction of cells of human and other species.
4. Vaccinia Virus Vectors
Vaccinia virus vectors have been used extensively because of the ease of their construction, relatively high levels of expression obtained, wide host range and large capacity for carrying DNA. Vaccinia contains a linear, double- stranded DNA genome of about 186 kb that exhibits a marked“A-T” preference. Inverted terminal repeats of about 10.5 kb flank the genome. The majority of essential genes appear to map within the central region, which is most highly conserved among poxviruses. Estimated open reading frames in vaccinia virus number from 150 to 200. Although both strands are coding, extensive overlap of reading frames is not common. At least 25 kb can be inserted into the vaccinia virus genome. Prototypical vaccinia vectors contain transgenes inserted into the viral thymidine kinase gene via homologous recombination. Vectors are selected on the basis of a tk-phenotype. Inclusion of the untranslated leader sequence of encephalomyocarditis virus results in a level of expression that is higher than that of conventional vectors, with the transgenes accumulating at 10% or more of the infected cell's protein in 24 h.
5. Polyoma Viruses Vectors
The empty capsids of papovaviruses, such as the mouse polyoma virus, have received attention as possible vectors for gene transfer. The use of empty polyoma was first described when polyoma DNA and purified empty capsids were incubated in a cell-free system. The DNA of the new particle was protected from the action of pancreatic DNase. The reconstituted particles were used for transferring a transforming polyoma DNA fragment to rat Fill cells. The empty capsids and reconstituted particles consist of all three of the polyoma capsid antigens \P1, VP2 and VP3. U.S. Pat. No. 6,046,173, incorporated herein by reference, discloses the use of a pseudocapsid formed from papovavirus major capsid antigen and excluding minor capsid antigens, which incorporates exogenous material for gene transfer.
6. Other Viral Vectors
Other viral vectors may be employed as expression constructs in the present disclosure, such as vectors derived from viruses such as sindbis virus or cytomegalovirus. They offer several attractive features for various mammalian cells (see, e.g., Friedmann, Science, 1989; 244: 1275- 1281; Horwich et al, J. Virol., 1990; 64:642-650).
With the recognition of defective hepatitis B viruses, new insight was gained into the structure-function relationship of different viral sequences. In vitro studies showed that the virus could retain the ability for helper-dependent packaging and reverse transcription despite the deletion of up to 80% of its genome (Horwich et al., J. Virol. 64:642-650 (1990)). This suggested that large portions of the genome could be replaced with foreign genetic material. Chang et al. introduced the chloramphenicol acetyltransferase (CAT) gene into duck hepatitis R virus genome in the place of the polymerase, surface, and/or pre-surface coding sequences. It was cotransfected with wild-type virus into an avian hepatoma cell line. Culture media containing high titers of the recombinant virus were used to infect primary duckling hepatocytes. Stable CAT gene expression was detected for at least 24 days after transfection (Chang et al, Hepatology 14: 134 A (1991)).
7. Modified Viruses
In still further embodiments of the present disclosure, the nucleic acids to be delivered are housed within an infective virus that has been engineered to express a specific binding ligand. The virus particle will thus bind specifically to the cognate receptors of the target cell and deliver the contents to the cell. A novel approach designed to allow specific targeting of retrovirus vectors was developed based on the chemical modification of a retrovirus by the chemical addition of lactose residues to the viral envelope. This modification can permit the specific infection of hepatocytes via sialogly coprotein receptors.
Another approach to targeting of recombinant retroviruses was designed in which biotinylated antibodies against a retroviral envelope protein or against a specific cell receptor were used. The antibodies were coupled via the biotin components by using streptavidin. Using antibodies against major histocompatibility complex class I and/or class II antigens, they demonstrated the infection of a variety of human cells that bore those surface antigens with an ecotropic virus in vitro.
8. Non- Viral Transfer
DNA constructs of the present disclosure are generally delivered to a cell. In certain embodiments, however, the nucleic acid to be transferred is non-infectious, and can be transferred using non-viral methods.
Several non-viral methods for the transfer of expression constructs into cultured mammalian cells are contemplated by the present disclosure. Suitable methods for nucleic acid delivery for use with the current disclosure include methods as described herein or as would be known to one of ordinary skill in the art. Such methods include, but are not limited to, direct delivery of“naked” DNA plasmid via the vasculature (U.S. Pat. No. 6,867,196, incorporated herein by reference); by liposome mediated transfection (Nicolau and Sene, 1982; Fraley et al, 1979; Nicolau et al, 1987; Wong et al, 1980; Kaneda et al, 1989; Kato et al, 1991) and receptor-mediated transfection (Wu and Wu, 1987; Wu and Wu, 1988); by agitation with silicon carbide fibers (Kaeppler et al, 1990; U.S. Pat. Nos. 5,302,523 and 5,464,765, each incorporated herein by reference); use of cationic lipids; naked DNA; or by microencapsulated DNA (U.S. Pat. Appl. No. 2005/0037085 incorporated herein by reference). Though the application of techniques such as these, target cells or tissue can be stably or transiently transformed.
Once the construct has been delivered into the cell, the nucleic acid encoding the therapeutic gene may be positioned and expressed at different sites. In certain embodiments, the nucleic acid encoding the therapeutic gene may be stably integrated into the genome of the cell. This integration may be in the cognate location and orientation via homologous recombination (gene replacement) or it may be integrated in a random, non-specific location (gene
augmentation). In yet further embodiments, the nucleic acid may be stably maintained in the cell as a separate, episomal segment of DNA. Such nucleic acid segments or“episomes” encode sequences sufficient to permit maintenance and replication independent of or in synchronization with the host cell cycle. How the expression construct is delivered to a cell and where in the cell the nucleic acid remains is dependent on the type of expression construct employed.
In a particular embodiment of the disclosure, the expression construct may be entrapped in a liposome. Liposomes are vesicular structures characterized by a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers. The addition of DNA to cationic liposomes causes a topological transition from liposomes to optically birefringent liquid-crystalline condensed globules. These DNA-lipid complexes are potential non- viral vectors for use in gene therapy.
Liposome-mediated nucleic acid delivery and expression of foreign DNA in vitro has been very successful. Using the b-lactamase gene, investigators demonstrated the feasibility of liposome-mediated delivery and expression of foreign DNA in cultured chick embryo, HeLa, and hepatoma cells. Successful liposome-mediated gene transfer in rats after intravenous injection has also been accomplished. Also included are various commercial approaches involving “lipofection” technology.
In certain embodiments of the disclosure, the liposome may be complexed with a hemagglutinating virus (HVJ). This has been shown to facilitate fusion with the cell membrane and promote cell entry of liposome-encapsulated DNA. In other embodiments, the liposome may be complexed or employed in conjunction with nuclear non-histone chromosomal proteins (HMG-1). In yet further embodiments, the liposome may be complexed or employed in conjunction with both HVJ and HMG-I. In that such expression constructs have been
successfully employed in transfer and expression of nucleic acid in vitro and in vivo, then they are applicable for the present disclosure.
Other vector delivery systems which can be employed to deliver a nucleic acid encoding a therapeutic gene into cells are receptor-mediated delivery vehicles. These take advantage of the selective uptake of macromolecules by receptor-mediated endocytosis in almost all eukaryotic cells. Because of the cell type-specific distribution of various receptors, the delivery can be highly specific (Wu and Wu, 1993). Where liposomes are employed, other proteins which bind to a cell surface membrane protein associated with endocytosis may be used for targeting and/or to facilitate uptake, e.g., capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, and proteins that target intracellular localization and enhance intracellular half-life.
Receptor- mediated gene targeting vehicles generally consist of two components: a cell receptor-specific ligand and a DNA-binding agent. Several ligands have been used for receptor- mediated gene transfer. The most extensively characterized ligands are asialoorosomucoid (ASOR) and transferring (Wagner et al, Proc. Natl. Acad. Sci. 87(9):3410-14 (1990), incorporated herein by reference). A synthetic neoglycoprotein, which recognizes the same receptor as ASOR, has been used as a gene delivery vehicle. Epidermal growth factor (EGF) has also been used to deliver genes to squamous carcinoma cells.
In other embodiments, the delivery vehicle may comprise a ligand and a liposome. For example, investigators have employed lactosyl-ceramide, a galactose-terminal asialganglioside, incorporated into liposomes and observed an increase in the uptake of the insulin gene by hepatocytes. Thus, it is feasible that a nucleic acid encoding a therapeutic gene also may be specifically delivered into a cell type such as cardiac cells, by any number of receptor-ligand systems with or without liposomes.
In another embodiment of the disclosure, the expression construct may simply consist of naked recombinant DNA or plasmids. Transfer of the construct may be performed by any of the methods mentioned above which physically or chemically permeabilize the cell membrane. This is applicable particularly for transfer in vitro, however, it may be applied for in vivo use as well. It is envisioned that therapeutic DNA may also be transferred in a similar manner in vivo. Wolff et al. (U.S. Pat. No. 6,867,196, incorporated herein by reference) teach that efficient gene transfer into heart tissue can be obtained by injection of plasmid DNA solutions in a vein or artery of the heart. Wolff also teaches the administration of RNA, non-plasmid DNA, and viral vectors.
V. Methods. Uses and Other Compositions
1. Methods of Treatment
In one aspect, the disclosure provides a method of treating or providing treatment for a subject suffering from idiopathic pulmonary fibrosis. As used herein,“treating” or“treatment” of the subject is an approach for obtaining beneficial or desired clinical results. Desired clinical results include, but are not limited to, prevention of remodeling of smooth muscle cells on pulmonary arteries, restored lung function, and/or reduction of severity of or inhibition of symptoms associated with idiopathic pulmonary fibrosis. The desired benefits or clinical results are independent of the mechanism, although the mechanism of activity is encompassed within the result. As will be understood by one of skill in the art, the particular symptoms which yield to treatment in accordance with the disclosure will depend on severity of the idiopathic pulmonary fibrosis being treated.
In one aspect of the disclosure, the therapeutic composition to treat idiopathic pulmonary fibrosis includes a vector that includes a gene encoding SERCA2a or its isoforms. As previously discussed, the SERCA2a gene or transgene of the disclosure, when contained in a therapeutic composition, are typically operatively linked to various regulatory elements which has been modified to include promoter and other sequences necessary for expression and, where desired, secretion of the desired translation product (e.g., a peptide or protein). For example, the
SERCA2a polynucleotides may be conjugated to or used in association with other
polynucleotides which operatively code for regulatory proteins that control the expression of these polypeptides or may contain recognition, promoter and secretion sequences. Those of ordinary skill in the art will be able to select regulatory polynucleotides and incorporate them into SERCA2a polynucleotides of the disclosure without undue experimentation.
In another aspect of the disclosure, the therapeutic composition to treat or reduce symptoms associated with idiopathic pulmonary fibrosis includes a polynucleotide encoding a protein capable of indirectly modulating smooth muscle Ca2+ and contractility. As is known in the art, the cardiac protein phospholamban is inhibitory to the activity of SERCA2a. Accordingly, the present methods include methods to decrease the level or activity of phospholamban in a pulmonary smooth muscle cell. In one embodiment, expression of a pseudophosphorylated mutant of phospholamban is increased. In another embodiment, a mutant has replacement of the serine 16 phosphorylation site with the basic amino acid glutamine, thereby introducing a negative charge at position 16 (S16E phospholamban mutant). This pseudophosphorylated form of phospholamban competes with natural phospholamban for binding to SERCA, thereby decreasing the opportunity for the natural protein to negatively affect SERCA activity. See, e.g., WO 2000/025804, incorporated herein by reference.
In a related aspect, the therapeutic compositions of the present disclosure are
administered to a subject as a prophylactic or ameliorative modality. As used herein,
“ameliorative,” means to improve or relieve a subject of symptoms associated with a disorder, and includes curing such a disorder.
Still other nucleic acids (transgenes) and proteins of SERCA, phospholamban, inhibitor-1 of the type 1 phosphatase, S100A1, and sarcolipin, as well as related nucleic acids and proteins which play a role in Ca2+, are targets for polynucleotides of the present disclosure.
For example, in one aspect, a viral vector and transgene is AAV2/l/SERCA2a, which is comprised of an AAV serotype 1 viral capsid enclosing a single-stranded 4486 nucleotide DNA containing the human SERCA2a expression cassette flanked by ITRs derived from AAV serotype 2. The icosahedral capsid consists of three related AAV serotype 1 capsid proteins,
VP1, VP2, and VP3. The AAV2/l/SERCA2a DNA contains the following components: AAV serotype2 based FIR at the 3' and 5' ends, flanking the CMV-hSERCA2a-polyA expression cassette. The expression cassette contains the cytomegalovirus immediate early
enhancer/promoter (CMVie) driving transcription of sequences including a hybrid intron from the commercial plasmid pCI (Promega— GenBank U47119), the hSERCA2a cDNA (coding sequence identical to GenBank NM-001681), and a bovine growth hormone polyadenylation signal (BGHpA, (GenBank M57764)). The hybrid intron was designed using the 5 '-donor site from the first intron of the human b-globin and 3 '-acceptor site from the intron located between the leader and body of an immunoglobulin gene heavy chain variable region.
The therapeutic agents, including polynucleotides, polynucleotides in combination with a vector, both viral and non-viral, as discussed above can be used in the preparation of a medicament for the treatment of pulmonary disease (e.g., idiopathic pulmonary fibrosis), where the medicament is administered by direct infusion into the circulatory system or by intra-tracheal or inhalation administration. Methods for delivery via inhalation are discussed in, e.g., Moss, et al. Human Gene Therapy, 18:726-732 (August 2007), which is incorporated herein by reference.
The therapeutic compositions of the present disclosure are delivered to a“target cell” or “host cell” or“target tissue” and equivalents thereof, which refers to the cell, tissue of the host in which expression of the operatively encoding polynucleotide is sought. For example, adeno- associated viral-SERCA2a compositions delivered in a lung cell or to lung tissue.
In some aspects, administering a vector that includes SERCA (e.g., SERCA2a) increases levels of SERCA2a mRNA in one or more lung cells. In some aspects, administering a vector that includes SERCA (e.g., SERCA2a) increases levels of SERCA2a protein in one or more lung cells. In some embodiments, administering a vector that includes SERCA2 decreases IL-6 mRNA in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases IL-6 protein in one or more lung cells.
In some embodiments, administering a vector that includes SERCA2a decreases the amount of detectable fibrosis in a lung sample. For example, detection of fibrosis can be identified using Hematoxylin & Eosin and/or Masson’s trichrome staining.
In some embodiments, administering a vector that includes SERCA2a decreases
COL1 Al mRNA in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases COL1A1 protein in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases COL3A1 mRNA in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases COL3 Al protein in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases CTGF mRNA in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases CTGF protein in one or more lung cells.
In some embodiments, administering a vector that includes SERCA2a decreases TGF- beta mRNA in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases TGF-beta protein in one or more lung cells.
In some embodiments, administering a vector that includes SERCA2a decreases the mRNA of one or more of heparan Sulfate 6-O-Sulfotransferase 1 (HS6ST1) and Versican (VCAN), hyaluronan synthase 2, fibromodulin, and syndican 4 in one or more lung cells. In some embodiments, administering a vector that includes SERCA2a decreases the protein level of one or more of heparan Sulfate 6-O-Sulfotransferase 1 (HS6ST1) and Versican (VC AN), hyaluronan synthase 2, fibromodulin, and syndican 4 in one or more lung cells.
An aspect of the present disclosure is packaging of the AAV-SERCA2a virions. Growth and propagation of the virions will require a“defmed-medium conditions”, which refer to environments for culturing cells where the concentration of components therein required for optimal growth are detailed. For example, depending on the use of the cells (e.g., therapeutic applications), removing cells from conditions that contain xenogenic proteins are important; i.e., the culture conditions are typically animal-free conditions or free of non-human animal proteins.
As disclosed herein, vectors useful in the present disclosure have varying transduction efficiencies. As a result, the viral or non-viral vector transduces more than, equal to, or at least about 10%, 20%, 30%, 40%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, 100% of the cells of the targeted vascular territory. In some embodiments, more than one vector (viral or non-viral, or combination thereof) can be used simultaneously, or in sequence. This can be used to transfer more than one polynucleotide, and/or target more than one type of cell. Where multiple vectors or multiple agents are used, more than one transduction/transfection efficiency can result.
The embodiments of the present disclosure can be“synergistic” or have“synergy”, which refers to an activity of administering combinations of proteins, lipids, nucleic acids,
carbohydrates, or chemical compounds that is greater than the additive activity of the proteins, lipids, nucleic acids, carbohydrates, or chemical compounds, if administered individually.
The embodiments of the present disclosure can be“co-administered”, which refers to two or more proteins, lipids, nucleic acids, carbohydrates, or chemical compounds of a combination that are administered so that the therapeutic or prophylactic effects of the combination is greater than the therapeutic effect of either proteins, lipids, nucleic acids, carbohydrates, or chemical compounds administered alone. The two or more proteins, lipids, nucleic acids, carbohydrates, or chemical compounds can be administered simultaneously or sequentially. Simultaneously co administered proteins, lipids, nucleic acids, carbohydrates, or chemical compounds may be provided in one or more pharmaceutically acceptable compositions. Sequential co-administration includes, but is not limited to, instances in which the proteins, lipids, nucleic acids, carbohydrates, or chemical compounds are administered so that each protein, lipid, nucleic acid, carbohydrate, or chemical compound can be present at the treatment site at the same time.
2. Methods of Production
In some embodiments, provided herein are methods of producing a vector (e.g., an AAV vector) described herein, comprising expressing the vector from a host cell. In some
embodiments, the methods of producing a vector (e.g., an AAV vector) described herein include culturing a host cell containing the vector. In some embodiments, the host cell includes a hybrid vector comprising: (i) adenovirus sequences comprising the adenovirus 5' and 3' cis-elements necessary for replication and virion encapsidation; and (ii) adeno-associated virus (AAV) sequences comprising the 5' and 3' inverted terminal repeat (ITRs) of an AAV, said AAV sequences flanked by the adenovirus sequences of (ii); and (iii) a selected transgene (e.g., any one of SEQ ID NOs:l-20) or a variant thereof) operatively linked to sequences which regulate its expression in a target cell, said gene and regulatory sequences flanked by the AAV sequences of (ii). In some embodiments, the host further includes an optional helper adenovirus, wherein the host cell and/or the helper virus provide the adenovirus sequences necessary to package the hybrid vector and generate a recombinant hybrid adenovirus. In some embodiments, the methods of producing a vector (e.g., an AAV vector) described herein include the step of isolating from said culture the recombinant hybrid adenovirus.
In certain aspects, provided herein are cells (e.g., host cells) expressing vectors as described herein. In some embodiments, the vectors include polynucleotides encoding an AAV vector in host cells. In some embodiments, the host cell is a mammalian cell. In some
embodiments, the host cell is selected from the group consisting of E. coli, Pseudomonas, Bacillus, Streptomyces, yeast, CHO, YB/20, NSO, PER-C6, HEK-293T, NIH- 3T3, HeLa, BHK, Hep G2, SP2/0, R1 .1, B-W, L-M, COS 1, COS 7, BSC1, BSC40, BMT10 cell, plant cell, insect cell, and human cell in tissue culture. In some embodiments, disclosed is an isolated AAV vector that includes any one of SEQ ID NO: 1-20, or a variant thereof.
3. Pharmaceutical Compositions and Uses Thereof
The present disclosure also embodies administering“pharmaceutically acceptable” molecular entities and compositions that are physiologically tolerable and do not typically produce an allergic or similar untoward reaction, such as gastric upset, dizziness and the like, when administered to a human. Thus, as used herein, the term“pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans. The term“carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the compound is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. In some embodiments, water or aqueous solution saline solutions and aqueous dextrose and glycerol solutions are employed as carriers, particularly for injectable solutions. Suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin.
Accordingly, as used herein, the term“therapeutic composition” is defined as one comprising at least a gene encoding SERCA2 or its isoforms (e.g., SERCA2a). The therapeutic composition may also contain other nucleic acid molecules (e.g., a viral vector) and
pharmaceutically acceptable entities, and substances such as water, minerals, carriers such as proteins, and other excipients known to one skilled in the art.
It will be understood that, if desired, a composition as disclosed herein may be administered in combination with other agents as well, such as, e.g., other proteins or
polypeptides or various pharmaceutically-active agents. In fact, there is virtually no limit to other components that may also be included, given that the additional agents do not cause a significant adverse effect upon contact with the target cells or host tissues. The compositions may thus be delivered along with various other agents as required in the particular instance. Such
compositions may be purified from host cells or other biological sources, or alternatively may be chemically synthesized as described herein. Likewise, such compositions may further comprise substituted or derivatized RNA or DNA compositions.
It will be apparent that any of the pharmaceutical compositions described herein can contain pharmaceutically acceptable salts of the polynucleotides and polypeptides of the disclosure. Such salts can be prepared, for example, from pharmaceutically acceptable non-toxic bases, including organic bases (e.g., salts of primary, secondary and tertiary amines and basic amino acids) and inorganic bases (e.g., sodium, potassium, lithium, ammonium, calcium and magnesium salts).
Another aspect of the present disclosure administers an“adjuvant” or equivalents thereof, which refers to a compound or mixture that enhances the immune response to an antigen. An adjuvant can serve as a tissue depot that slowly releases the antigen and also as a lymphoid system activator that non-specifically enhances the immune response. Often, a primary challenge with an antigen alone, in the absence of an adjuvant, will fail to elicit a humoral or cellular immune response. Adjuvants include, but are not limited to, complete Freund's adjuvant, incomplete Freund's adjuvant, saponin, mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil or hydrocarbon emulsions, keyhole limpet hemocyanins, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum. In some embodiments, the adjuvant is pharmaceutically acceptable.
In a related aspect, the term“molecular adjuvant” is defined as a protein, lipid, nucleic acid, carbohydrate, or chemical compound for which dendritic cells (DCs), macrophages, B cells, T cells, and/or NK cells have a known receptor whose occupancy leads to a defined sequence of intracellular signal transduction and a change in the phenotype resulting in an improvement in the quantity or quality of the ensuing immune response. Ina related aspect, the cells as described above are collectively referred to as“immune cells.”
In a related embodiment, other devices and methods that may be useful for gas-driven needle-less injection of compositions of the present disclosure include those provided by Bioject, Inc. (Portland, Oreg.), some examples of which are described in U.S. Pat. Nos. 4,790,824;
5,064,413; 5,312,335; 5,383,851; 5,399,163; 5,520,639 and 5,993,412, each of which is incorporated herein by reference.
The present disclosure may be delivered by various modes. For oral administration the compositions of the present disclosure may alternatively be incorporated with one or more excipients in the form of a mouthwash, dentifrice, buccal tablet, oral spray, or sublingual orally- administered formulation. Alternatively, the active ingredient may be incorporated into an oral solution such as one containing sodium borate, glycerin and potassium bicarbonate, or dispersed in a dentifrice, or added in a therapeutically-effective amount to a composition that may include water, binders, abrasives, flavoring agents, foaming agents, and humectants. Alternatively the compositions may be fashioned into a tablet or solution form that may be placed under the tongue or otherwise dissolved in the mouth. Vaccine formulations can also be delivered to the nasal mucosa, aerosolized for inhalational delivery, or delivered to the mucosal surfaces of the female and male genital track or the rectum. Vaccine formations may also be formulated for transdermal delivery.
In certain circumstances it will be desirable to deliver the pharmaceutical compositions disclosed herein parenterally, intravenously, intramuscularly, intratracheally, or even
intrap eritoneally. In some embodiments, delivery is via intratracheal instillation, bronchial instillation, inhalation; a nasal spray, or an aerosol. In some embodiments, delivery is intratracheally. Such approaches are well known to the skilled artisan, some of which are further described, for example, in U.S. Pat. No. 5,543,158; U.S. Pat. No. 5,641,515 and U.S. Pat. No. 5,399,363, each of which is incorporated herein by reference. As such, in one embodiment, the compositions of the disclosure may be delivered via inhalation, intravenous injection, intracardiac injection, intratracheally. In another embodiment, the compositions of the disclosure are administered via mechanical ventilation. In certain embodiments, solutions of the active compounds as free base or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions may also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations generally will contain a preservative to prevent the growth of microorganisms.
Illustrative pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions (for example, see U.S. Pat. No. 5,466,468, incorporated herein by reference). In all cases the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils. Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and/or by the use of surfactants. The prevention of the action of microorganisms can be facilitated by various antibacterial and antifungal agents, for example, parabens,
chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In some embodiments, isotonic agents, for example, sugars or sodium chloride, will be included. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
In one embodiment, for parenteral administration in an aqueous solution, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, a sterile aqueous medium that can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage may be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example,“Remington's Pharmaceutical Sciences” 15th Edition, pages 1035- 1038 and 1570-1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. Moreover, for human administration, in some
embodiments, preparations meets sterility, pyrogenicity, and the general safety and purity standards as required by FDA Office of Biologies standards.
In another embodiment of the disclosure, the compositions disclosed herein may be formulated in a neutral or salt form. Illustrative pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective.
The carriers can further comprise any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the
compositions. The phrase“pharmaceutically-acceptable” refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human.
In certain embodiments, the pharmaceutical compositions may be delivered by intranasal sprays, inhalation, and/or other aerosol delivery vehicles. Methods for delivering genes, nucleic acids, and peptide compositions directly to the lungs via nasal aerosol sprays has been described, e.g., in U.S. Pat. No. 5,756,353 and U.S. Pat. No. 5,804,212, each of which is incorporated herein by reference. Likewise, the delivery of polynucleotides (e.g., viral vectors) using intranasal microparticle resins (Takenaga et al, J Controlled Release (1998) 52(l-2):81-7; and Moss, et al. Human Gene Therapy, 18:726-732 (August 2007), each of which is incorporated herein by reference) and lysophosphatidyl-glycerol compounds (U.S. Pat. No. 5,725,871, incorporated herein by reference) are also well-known in the pharmaceutical arts. Likewise, illustrative transmucosal drug delivery in the form of a polytetrafluoroetheylene support matrix is described in U.S. Pat. No. 5,780,045, incorporated herein by reference.
In certain embodiments, liposomes, nanocapsules, microparticles, lipid particles, vesicles, and the like, are used for the introduction of the compositions of the present disclosure into suitable host cells/organisms. In particular, the compositions of the present disclosure may be formulated for delivery either encapsulated in a lipid particle, a liposome, a vesicle, a
nanosphere, or a nanoparticle or the like. Alternatively, compositions of the present disclosure can be bound, either covalently or non-covalently, to the surface of such carrier vehicles.
The formation and use of liposome and liposome-like preparations as potential drug carriers is generally known to those of skill in the art (see for example, Lasic, Trends Biotechnol (1998) 16(7):307-21; Takakura, Nippon Rinsho (1998) 56(3):691-5; Chandran et al, Indian J Exp Biol (1997) 35(8):801-9; Margalit, Crit. Rev Ther Drug Carrier Syst (1995) 12(2-3):233-61; U.S. Pat. No. 5,567,434; U.S. Pat. No. 5,552,157; U.S. Pat. No. 5,565,213; U.S. Pat. No.
5,738,868 and U.S. Pat. No. 5,795,587.
Alternatively, in other embodiments, the disclosure provides for pharmaceutically- acceptable nanocapsule formulations of the compositions of the present disclosure. Nanocapsules can generally entrap compounds in a stable and reproducible way (see, for example, Quintanar- Guerrero et al, Drug Dev India Pharm (1998) 24(12): 1113-28). To avoid side effects due to intracellular polymeric overloading, such ultrafme particles (sized around 0.1 pm) may be designed using polymers able to be degraded in vivo. Such particles can be made as described, for example, by Couvreur et al, Crit. Rev Ther Drug Carrier Syst. 1988; 5(1): 1-20; zur Muhlen et al, Eur J Pharm Biopharm (1998) 45(2): 149-55; Zambaux et al, J Controlled Release (1998) 50(l-3):31-40; and U.S. Pat. No. 5,145,684.
The present disclosure contemplates a variety of dosing schedules described herein as well as others not described herein but would otherwise be known to one skilled in the art. The disclosure encompasses continuous dosing schedules, in which SERCA2a is administered on a regular (daily, weekly, or monthly, depending on the dose and dosage form) basis without substantial breaks. In some embodiments, continuous dosing schedules include daily continuous administration where SERCA2a is administered each day, and continuous bolus administration schedules, where SERCA2a is administered at least once per day by intravenous or subcutaneous injections. Exemplary continuous administration schedules include, but are not limited to, at least 2, 3, 4, 5, 6, or 7 days, at least 1, 2, 3, 4, 5, or 6 weeks or more, or any combination thereof.
The disclosure also encompasses discontinuous dosing schedules. The exact parameters of discontinuous administration schedules will vary according the formulation, method of delivery and the clinical needs of the subject. For example, if the SERCA2a formulation is administered by inhalation, administration schedules comprising a first period of administration followed by a second period in which SERCA2a is not administered which is greater than, equal to, or less than the period where SERCA2a is administered. Examples of discontinuous administration schedules for inhalation administration include, but are not limited to, schedules comprising periods selected from 1, 2, 3, 4, 5, 6, or 7 days, 1, 2, 3, 4, 5, 6, or more weeks, or any combination thereof, and off periods selected from 1, 2, 3, 4, 5, 6, or 7 days, 1, 2, 3, 4, 5, 6 or more weeks.
Continuous and discontinuous administration schedules by any method also include dosing schedules in which the dose is modulated throughout the effective period, such that, for example, at the beginning of the SERCA2a administration period; the dose is low and increased until the end of the SERCA2a administration period; the dose is initially high and decreased during the SERCA2a administration period; the dose is initially low, increased to a peak level, then reduced towards the end of the SERCA2a administration period; and any combination thereof. Also, the dosing schedules may be performed using any method of standard in the art, such as a catheter system. Compositions will comprise sufficient genetic material to produce a therapeutically effective amount of the SERCA2a or portions or fragments or functional fragments of interest, i.e., an amount sufficient to reduce or ameliorate symptoms of the disease state in question or an amount sufficient to confer the desired benefit. The compositions may also contain a
pharmaceutically acceptable excipient. Such excipients include any pharmaceutical agent that does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity. Pharmaceutically acceptable excipients include, but are not limited to, sorbitol, any of the various TWEEN compounds, and liquids such as water, saline, glycerol and ethanol. Pharmaceutically acceptable salts can be included therein, for example, mineral acid salts such as hydrochlorides,
hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such vehicles. A thorough discussion of pharmaceutically acceptable excipients is available in REMINGTON'S PHARMACEUTICAL SCIENCES (Mack Pub. Co., N.J. 1991).
One particularly useful formulation includes recombinant AAV virions in combination with one or more dihydric or polyhydric alcohols, and, optionally, a detergent, such as a sorbitan ester. See, for example, International Publication No. WO 00/32233, incorporated herein by reference.
As is apparent to those skilled in the art in view of the teachings of this specification, an effective amount of viral vector which must be added can be empirically determined.
Administration can be effected in one dose, continuously or intermittently throughout the course of treatment. Methods of determining the most effective means and dosages of administration are well known to those of skill in the art and will vary with the viral vector, the composition of the therapy, the target cells, and the subject being treated. Single and multiple administrations can be carried out with the dose level and pattern being selected by the treating physician.
It should be understood that more than one transgene can be expressed by the delivered recombinant virion. Alternatively, separate vectors, each expressing one or more different transgenes, can also be delivered as described herein. Furthermore, it is also intended that the viral vectors delivered by the methods of the present disclosure be combined with other suitable compositions and therapies. Where the transgene is under the control of an inducible promoter, certain systemically delivered compounds such as muristerone, ponasteron, tetracyline or aufin may be administered in order to regulate expression of the transgene.
Accordingly, therapeutic compositions of the present disclosure contain SERCA2a or SERC2a or portions, or functional fragments thereof operatively linked to various regulatory elements in an AAV vector, substantially similar to that previously described above including any excipients or carriers or agents necessary to effectuate efficient, but non-toxic delivery of the therapeutic compositions will be produced. Also control AAV compositions will be produced, e.g. AAV-GFP constructs.
Also, in order to distinguish AAV-delivered SERCA2a from its endogenous counterpart, an AAV vector can be constructed which encodes a recombinant fusion SERCA2a operatively linked to green fluorescent protein (GFP) tag (AAV-SERCA2a-GFP), for recognition.
The host cell (or packaging cell) must also be rendered capable of providing nonAAV- derived functions, or“accessory functions”, in order to produce rAAV virions. Accessory functions are nonAAV-derived viral and/or cellular functions upon which AAV is dependent for its replication, including at least those nonAAV proteins and RNAs that are required in AAV replication, including those involved in activation of AAV gene transcription, stage specific AAV mRNA splicing, AAV DNA replication, synthesis of Cap expression products and AAV capsid assembly. Viral-based accessory functions can be derived from any of the known helper viruses.
In particular, accessory functions can be introduced into and then expressed in host cells using methods known to those of skill in the art. Typically, accessory functions are provided by infection of the host cells with an unrelated helper virus. A number of suitable helper viruses are known, including adenoviruses; herpesviruses, e.g., herpes simplex virus types 1 and 2; and vaccinia viruses. Nonviral accessory functions will also find use herein, such as those provided by cell synchronization using any of various known agents. See, e.g., Buller et al. (1981) J. Virol. 40:241 247; McPherson et al. (1985) Virology 147:217 222; Schlehofer et al. (1986) Virology 152: 110 117.
Alternatively, accessory functions can be provided using an accessory function vector as defined above. See, e.g., U.S. Pat. No. 6,004,797 and International Publication No. WO
01/83797, each of which is incorporated herein by reference in its entirety. Nucleic acid sequences providing the accessory functions can be obtained from natural sources, such as from the genome of an adenovirus particle, or constructed using recombinant or synthetic methods known in the art. Also, the full-complement of adenovirus genes is not required for accessory helper functions. In fact, adenovirus mutants incapable of DNA replication and late gene synthesis have been shown to be permissive for AAV replication. Ito et al, (1970) J. Gen. Virol. 9:243; Ishibashi et al, (1971) Virology 45:317; and Carter et al, (1983) Virology 126:505. For example, reports show that El A and E4 regions are likely required for AAV replication, either directly or indirectly. Laughlin et al, (1982) J. Virol 41:868; Janik et al, (1981) Proc. Natl.
Acad. Sci. USA 78: 1925; Carter et al, (1983) Virology 126:505. In addition, International Publication WO 97/17458 and Matshushita et al, (1998) Gene Therapy 5:938 945, describe accessory function vectors encoding various adenoviral genes.
Infection of the host cell with a helper virus, or transfection of the host cell with an accessory function vector, allows expression of the accessory functions which transactivate the AAV helper construct to produce AAV Rep and/or Cap proteins. The Rep expression products in turn excise the recombinant DNA (including the DNA of interest, e.g., SERCA2a) from the AAV expression vector. The Rep proteins also serve to duplicate the AAV genome. The expressed Cap proteins assemble into capsids, and the recombinant AAV genome is packaged into the capsids, AAV replication proceeds, and the DNA is packaged into rAAV virions.
Following recombinant AAV replication, rAAV virions can be purified from the host cell using a variety of conventional purification methods, such as column chromatography, CsCl gradients, and the like. For example, a plurality of column purification steps can be used, such as purification over an anion exchange column, an affinity column and/or a cation exchange column. See, for example, International Publication No. WO 02/12455. Further, if infection is employed to express the accessory functions, residual helper virus can be inactivated, using known methods. For example, adenovirus can be inactivated by heating to temperatures of approximately 60° C. for, e.g., 20 minutes or more. This treatment effectively inactivates only the helper virus since AAV is extremely heat stable while the helper adenovirus is heat labile.
The resulting rAAV virions containing the SERCA2a nucleotide sequence of interest, or fragment, or functional fragment, or portion thereof can then be used for gene delivery using the techniques described below.
Recombinant AAV virions may be introduced into smooth muscle cells using either in vivo or in vitro (also termed ex vivo) transduction techniques. If transduced in vitro, the desired recipient cell (e.g., a lung cell) will be removed from the subject, transduced with rAAV virions and reintroduced into the subject. Alternatively, syngeneic or xenogeneic cells can be used where those cells will not generate an inappropriate immune response in the subject.
Suitable methods for the delivery and introduction of transduced cells into a subject have been described. For example, cells can be transduced in vitro by combining recombinant AAV virions (rAAV) with cells to be transduced in appropriate media, and those cells harboring the DNA of interest can be screened using conventional techniques such as Southern blots and/or PCR, or by using selectable markers. Transduced cells can then be formulated into
pharmaceutical compositions, as described above, and the composition introduced into the subject by various techniques as described below, in one or more doses.
Recombinant AAV (rAAV) virions or cells transduced in vitro may be delivered directly to muscle by injection with a needle, catheter or related device, using techniques known in the art. For in vivo delivery, the rAAV virions will be formulated into pharmaceutical compositions and one or more dosages may be administered directly in the indicated manner. A therapeutically effective dose will include on the order of from about 108/kg to about 1016/kg of the rAAV virions; or from about 1010/kg to about 1014/kg; or from about 10u/kg to about 1013/kg of the rAAV virions (or viral genomes, also termed“vg” or“v.g.”), or any value within these ranges.
One mode of administration of recombinant AAV virions uses a convection-enhanced delivery (CED) system. In this way, recombinant virions can be delivered to many cells over large areas of muscle. Moreover, the delivered vectors efficiently express transgenes in muscle cells. Any convection-enhanced delivery device may be appropriate for delivery of viral vectors. In some embodiments, the device is an osmotic pump or an infusion pump. Both osmotic and infusion pumps are commercially available from a variety of suppliers, for example Alzet Corporation, Hamilton Corporation, Alza, Inc., Palo Alto, Calif.). Typically, a viral vector is delivered via CED devices as follows. A catheter, cannula or other injection device is inserted into appropriate muscle tissue in the chosen subject, such as skeletal muscle. For a detailed description regarding CED delivery, see U.S. Pat. No. 6,309,634, incorporated herein by reference in its entirety.
Although, the present disclosure describes a perfusion method, various perfusion methods are available and standard in the art, and without being held to any one method, any perfusion method which gives the desired result is anticipated, such as a methods utilizing a catheter. The objective of the perfusion methods is to increase the time of contact between the vector (e.g., adenovirus, AAV, lentivirus vectors) and the target cells (e.g., smooth muscle cells). Hence, the disclosure encompasses perfusion methods such as closed-circuit perfusion methods carried out at body temperature, and under defined conditions at, for example, 37° C., for about 2, 5, 10, 12, 15, 30, 60 or more minutes, or in larger animals or humans for about 2, 4, 6, 8, 10, 12 or more hours, allowing viral entry into the target cells and to create optimal conditions for gene expression and protein synthesis. For this reason, various excipients, e.g., natural and un-natural amino acids, growth factors and the like may be added to provide enough material for protein synthesis.
To determine efficacy in animal models which received the AAV-SERCA2a or AAV- SERCA2a compositions, the effect on pulmonary artery pressure and cardiac function may be determined using a pressure-volume measurement system post-injection e.g., one week or one month post-injection. Repeated measurements may be continued in order to monitor the short term and long-terms effects and efficacy of the therapy. For example, if after one week the results are considered not significant, then new trials using higher (or lower) dosages, or multiple dosages may be performed.
Studies may be performed to determine gene expression including removal of pulmonary tissues receiving the perfusion as well as surrounding and/or control tissues. The tissues may be histologically processed by methods standard in the art, e.g., fixation methods, vibratome or cutting methods, and the like. For example, to study gene expression of SERCA2 or SERCA2a or other SERCA2 isoforms, immunohisto chemistry using a SERCA2 or SERCA2a
polynucleotides or antibodies which are immunogenic against SERCA2 or SERCA2
polypeptides may be performed. Further, for those animals receiving the AAV-GFP
compositions, expression of GFP in the tissues may be measured using fluorescent microscopy or any other method standard in the art which can measure and detect fluorescence.
4. RNAi
Thus, in one embodiment, the methods of the disclosure include administering to a subject in need thereof a therapeutically effective amount of an siRNA in a viral vector, where the RNAi decreases expression and/or activity of phospholamban (PLB), in an amount effective to transduce pulmonary smooth muscle cells of the subject, thereby resulting in expression of the RNAi and treating idiopathic pulmonary fibrosis in the subject. Unphosphorylated PLB keeps the Ca2+ affinity of SERCA2a low, resulting in decreased SR Ca2+ uptake, slowed relaxation and decreased SR Ca2+ load.
PLB nucleic acids, include but are not limited to, GenBank Accession Nos. NM 02667 (Simmerman et al, J Biol Chem (1986) 261(28): 13333-13341); NM_023129 (Ganim et al, Cir Res (1992) 71(5): 1021-1030); NM_022707 (Wang and Nadal-Ginard, Adv Exp Med Biol (1991) 304:387-395); BC134584 (Moore et al, direct submission (17 Mar. 2007), BC Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Suite 100, 570 West 7th Avenue, Vancouver, British Columbia V5Z 4S6, Canada); and NM 214213 (Verboomen et al., Biochem J (1989) 262(l):353-356). All of the above sequences are publicly available and incorporated herein by reference.
The term“RNA interference” refers generally to a process in which a double-stranded RNA molecule changes the expression of a nucleic acid sequence with which the double- stranded or short hairpin RNA molecule shares substantial or total homology. While not being bound by theory, the mechanism of action may include, but is not limited to, direct or indirect down regulation of the expression of the PLB gene, decrease in PLB mRNA, and/or a decrease in PLB activity. The term“RNAi,” including“short inhibitory RNA (siRNA),” refer to RNA sequences that elicit RNA interference, and which is transcribed from a vector. The terms“short hairpin RNA” or“shRNA” refer to an RNA structure having a duplex region and a loop region. This term should also be understood to specifically include RNA molecules with stem-loop or panhandle secondary structures. In some embodiments of the present disclosure, RNAis are expressed initially as shRNAs.
RNAi is generally optimized by identical sequences between the target and the RNAi.
The RNA interference phenomenon can be observed with less than 100% homology, but the complementary regions must be sufficiently homologous to each other to form the specific double stranded regions. The precise structural rules to achieve a double-stranded region effective to result in RNA interference have not been fully identified, but approximately 70% identity is generally sufficient. Accordingly, in some embodiments of the disclosure, the homology between the RNAi and PLB is at least 70% nucleotide sequence identity, and may be at least 75% nucleotide sequence identity. Homology includes, but is not limited to, at least 80% nucleotide sequence identity, and is at least 85% or even 90% nucleotide sequence identity. In one embodiment, sequence homology between the target sequence and the sense strand of the RNAi is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% nucleotide sequence identity.
Another consideration is that base-pairing in RNA is subtly different from DNA in that G will pair with U, although not as strongly as it does with C, in RNA duplexes. Moreover, for RNAi efficacy, it is more important that the antisense strand be homologous to the target sequence. In some circumstances, it is known that 17 out of 21 nucleotides is sufficient to initiate RNAi, but in other circumstances, identity of 19 or 20 nucleotides out of 21 is required. While not being bound by theory, at a general level, greater homology is required in the central part of a double stranded region than at its ends. Some predetermined degree of lack of perfect homology may be designed into a particular construct so as to reduce its RNAi activity which would result in a partial silencing or repression of the target gene's product, in circumstances in which only a degree of silencing was sought. In such a case, only one or two bases of the antisense sequence may be changed. On the other hand, the sense strand is more tolerant of mutations. While not being bound by theory, this may be due to the antisense strand being the one that is catalytically active. Thus, less identity between the sense strand and the transcript of a region of a target gene will not necessarily reduce RNAi activity, particularly where the antisense strand perfectly hybridizes with that transcript. Mutations in the sense strand (such that it is not identical to the transcript of the region of the target gene) may be useful to assist sequencing of hairpin constructs and potentially for other purposes, such as modulating dicer processing of a hairpin transcript or other aspects of the RNAi pathway.
The terms“hybridizing” and“annealing” including grammatical equivalents thereof, are used interchangeably in this specification with respect to nucleotide sequences and refer to nucleotide sequences that are capable of forming Watson-Crick base pairs due to their complementarity. The person skilled in the art would understand that non-Watson-Crick base pairing is also possible, especially in the context of RNA sequences. For example a so-called “wobble pair” can form between guanosine and uracil residues in RNA.
The RNA expression products of the RNAi expression cassette lead to the generation of a double-stranded RNA (dsRNA) complex for inducing RNA interference and thus down regulating or decreasing expression of a mammalian gene.“dsRNA” refers to a ribonucleic acid complex comprising two Watson-Crick base-paired complementary RNA strands. The dsRNA complex comprises a first nucleotide sequence that hybridizes under stringent conditions, including a wash step of 0.2xSSC at 65° C., to a nucleotide sequence of at least one mammalian gene and a second nucleotide sequence which is complementary to the first nucleotide sequence. The first nucleotide sequence might be linked to the second nucleotide sequence by a third nucleotide sequence (e.g., an RNA loop) so that the first nucleotide sequence and the second nucleotide sequence are part of the same RNA molecule; alternatively, the first nucleotide sequence might be part of one RNA molecule and the second nucleotide sequence might be part of another RNA molecule. Thus, a dsRNA complex may be formed by intramolecular hybridization or annealing or the ds RNA complex is formed by intermolecular hybridization or annealing.
The present disclosure is more particularly described in the following examples which are intended as illustrative only since numerous modifications and variations therein will be apparent to those skilled in the art. The following examples are intended to illustrate but not limit the disclosure.
EXAMPLES
Example 1: Materials and Methods
Online Methods
Patients. RNA, protein samples and formalin-fixed paraffin -embedded sections of human IPF and healthy control donors, non-IPF were used in the present study. Human lung tissues were obtained from patients with IPF (n=8) who underwent surgery for organ transplantation program, and lung explant healthy control samples were obtained from organ transplant program from the University General Consortium Hospital of Valencia (n=8). The samples were anonymous and archived specimens. The protocol was approved by the local research and independent ethics committee of the University General Consortium Hospital of Valencia (CEIC/2013). Informed written consent was obtained from each participant.
Cell Culture
Normal human lung fibroblast (NHLF) was purchased from Lonza, Inc. (Allendale, NJ) and cultured as recommended in FGM-2 medium supplemented with 5% fetal bovine serum (FBS) in 5% C02 at 37°C and passaged at the confluence. shRNA and lentivirus production. The SERCA2a shRNA (TRCN0000038529) and FOXM1 shRNA (TRCN0000015543) cloned in the pLKO.l lentiviral expression vector was obtained from Dharmacon. For lentivirus production, the constructs and viral packaging plasmids pSPAX2 and pMD2.G were co-transfected into 293T cells using Lipofectamine 2000 (Invitrogen Life Technologies) per the manufacturer’s recommendations. The virus was concentrated by incubation with the Lenti-X Concentrator (Clontech) as recommended by the supplier. The concentrated virus particles were used to infect NHLF cells for 72 hrs. siRNA experiments
Cells were seeded at 250 000 cells/well in 6-well plates and maintained in a 37°C incubator with 5% C02 for 24 hrs before transfection. For siRNA knock-down experiments, human OTUB1 siRNA (AM16708) and negative control siRNAs (AM4611) were purchased from Invitrogen. 30 nM/well of each siRNA was mixed with Lipofectamine RNAiMax according to the manufacturer’s instructions. Protein and RNA expression was measured by immunoblotting and RT-qPCR after 72 hrs to validate OTUB1 knockdown.
Cell proliferation
The proliferation of NHLFs was measured by 5-bromo-2’-deoxyuridine (BrdU) incorporation for 48h using the Cell Proliferation ELISA, BrdU (colorimetric) assay (Roche, Indianapolis, IN), according to the manufacturer’s instructions.
Total RNA isolation, cDNA preparation, and quantitative RT-PCR analysis
The whole left lobe of each lung was used for total RNA isolation using TRIzol™
(Invitrogen) and purified using RNeasy mini columns (Qiagen). The cDNA synthesis kit (Applied Biosystems, Foster City, CA) was used to generate cDNA according to the
manufacturer’s instructions. Quantitative RT-PCR was performed using the PerfeCTa SYBRTM Green FastMix kit (Quantabio) according to the manufacturer’s instructions. Fold changes in gene expression were determined using the relative comparison method with normalization to GAPDH as an internal control. The primer sequences are provided in with the following primers: Supplemental Table 3.
SDS-PAGE and Immunoblot analysis. Cell lysates were prepared using RIP A lysis buffer (Invitrogen) containing a Protease Inhibitor Cocktail (Roche) and a Phosphatase Inhibitor Cocktail (Sigma- Aldrich). After centrifugation for 20 min at 15000 x g, the protein
concentrations were determined using a bicinchoninic acid (BCA) assay (Sigma- Aldrich). The proteins were then separated by SDS-polyacrylamide gel electrophoresis (PAGE) and transferred to polyvinylidene difluoride membranes. The membranes were blocked with 5% Skim milk and hybridized overnight at 4°C with the primary antibodies listed in Supplemental Table 3. The membranes were then incubated with the appropriate secondary HRP-conjugated antibody (Cell signaling) and the blots were developed using the ECL System (Thermo Scientific).
Immunofluorescence
Frozen lung sections (8 pm) were incubated in cold acetone for 20 min. Sections were then blocked with 10% normal goat serum for 1 hr at room temperature and incubated overnight at 4°C with a specific antibody against SERCA2a (1 : 100), OTUB1 (1 : 100), FOXM1 (1 : 100) and alpha-SMA (1 :250). Sections were washed three times with PBS and incubated with a secondary antibody coupled to Alexa Fluor®633 or Alexa Fluor®488 (1 :200, Molecular probes) for lh. Coverslides were mounted with vectashield mounting medium (Vector Laboratories).
Intratracheal bleomycin animal model
All of the animal experiments and handling were performed in accordance with NIH Guide for the Care and Use of Laboratory Animals, and approved by the Icahn School of Medicine at Mount Sinai Institutional Animal Care and Use Committee. Animals were anesthetized by IP injection of xylazine/ketamine and were secured to a tray in the supine position. Using a 20 G angiocath, animals were then intubated. The board was tilted at 45 degrees and the IA-1C Microsprayer tip (PennCentury, Wyndmoor, PA) was inserted through the lumen of the angiocath. BLM was administered via IT delivery (50pL; 4U/Kg) and the tip was removed. The animals were then extubated and returned to their cages.
AA VI vectors delivery
Human AAVl.SERCA2a and AAV1.LUC was produced as previously described (8).
The rAAVl . SERC A2a vector used in this study, contains an AAV1 viral capsid and a single- stranded ~4.5-kb DNA containing the human SERCA2a cDNA driven by a cytomegalovirus immediate-early promoter/enhancer, a hybrid intron, and a bovine growth hormone polyadenylation signal, all flanked by 145-nucleotide AAV2 inverted terminal repeat sequences necessary for replication and packaging of the vector DNA in the capsid. For the treatment protocol, 14 days after aerosolized delivery of BLM (4U/kg), mice were randomly assigned to receive intratracheally aerosolized with either the vehicle, AAV1.LUC encoding for luciferase as an AAV1 control or AAVl-SERCA2a (50 pL; 3.5el 1 vg/mL) using a single-dose IT delivery by using an IA-1C Microsprayer (PennCentury, Wyndmoor, PA). Four weeks after treatment, the mice were for assessed for hemodynamic analysis and then sacrificed and the heart and lungs were collected. In the prevention protocol, mice were first randomly assigned into three treatment groups: vehicle, AAV1.LUC or AAVl.SERCA2a delivered as previously described and injected with BLM or vehicle control injections 14 days later. Hemodynamic studies were performed 5 weeks after the administration of AAV1.LUC or AAVl.SERCA2a and then mice were sacrificed for lung and RV tissue harvest.
Heart Hemodynamic Studies
The mice were anesthetized with (2-4%) isoflurane, intubated via tracheotomy, and mechanically ventilated with 1-2% isoflurane and oxygen (tidal volume, 6 mL/kg; respiratory rate, 100 breaths per minute). The thoracic cavity was opened and the organs were accessed through a sternotomy. Once the pericardium was opened and the heart was fully accessible, an ultrasonic flow probe (flow probe 2.5S176; Transonic Systems Inc., Ithaca, NY) was inserted into the RV to collect the right ventricular systolic pressure (RVSP). Hemodynamic data were recorded using a Scisense PV Control Unit (Scisense, Ontario, Canada).
Right Ventricular Weight Measurement
The heart was removed from the chest and rinsed with PBS to remove blood and any clots. Both atria and connecting vessels are dissected out. The RV was separated from the heart and weighed. The Fulton Index was calculated by the weight ratio of the RV weight to the LV plus septum weight to specifically illustrate the RV hypertrophy.
Immunoprecipitation After the indicated treatments, NHLFs were lysed using a buffer containing 20 mmol/L Tris, pH 7.5, 150 mmol/L NaCl, 20 mmol/L MgC12, 0.5% NP40, 0.5 mmol/L EDTA, protease, and phosphatase cocktail inhibitors (Roche). FOXM1 was immunoprecipitated using a specific antibody against FOXM1 (Supplemental Table 3, 1 :50) overnight at 4°C with gentle shaking. Purification steps were performed with protein A/G agarose according to the manufacturer's instructions (Santa Cruz). Samples were subjected to immunoblotting using a primary antibody against OTUB1, phospho-SMAD2-3, Tot-SMAD2-3 (Cell Signaling). Proteins were then visualized using the appropriate secondary horseradish peroxidase-conjugated goat anti-mouse or anti-rabbit antibody and an enhanced chemiluminescence detection kit (Thermo Scientific).
Ubiquitynation assay
Ubiquitynation assay was performed in NHLFs cells by transfecting HA-ubiquitin (2pg) in cells overexpressing either Ad.SERCA2a, shRNA against SERCA2a, siRNA OTUB1 alone or in combination with shRNA SERCA2a. 24 hrs after the transfection, the cells were treated with TGFP alone (5nM, 48 hrs) alone or in combination with MG132 (IOmM, 6 hrs). Cells were lysed using a buffer containing 25 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% NP-40, 1 mM EDTA, 5% glycerol and protease, and phosphatase cocktail inhibitors (Roche). Protein lysates (lmg) were incubated with the appropriate IgG control antibody (e.g., 0.25 pg/ml), and suspended with protein A/G agarose beads at 4 °C for 1 h. Samples were centrifuged at 1,000 x g for 1 min at 4°C and supernatants transferred into a clean microcentrifuge tube. Samples were then incubated with a primary antibody HA-Tag (Cell signaling, 1 :50) overnight at 4°C with rotation.
Appropriate agarose beads were then added and incubated at 4°C with rotation for 2 h. Samples were then centrifuged at 1,000 x g for 1 min at 4 °C and supernatant was discarded. Beads were washed with ice-cold RIPA buffer (or PBS) 3 times 15 min with constant rotation at 4°C.
Samples were subjected to immunoblotting as previously described.
Lucif erase reporter gene assays
NHLF cells were seeded into 24-well plates and transfected using Lipofectamine 2000 with NFK-B luciferase reporter vector (Addgene) for 48 hrs (Invitrogen) according to the manufacturer's instructions. TGFp (5 ng/ml) was then added and the cells were incubated for 48 hrs. NFK-B activity was measured using a luciferase assay kit (Promega). Hematoxylin & Eosin and Masson’s trichrome staining
Lung tissue was harvested, inflated with PBS/OCT (50:50), and fixed (frozen) in OCT. Sections were cut to 8 mih and adhered to color frost glass slides (ThermoFisher). Lung tissue sections were stained with hematoxylin and eosin and Masson’s trichrome (Sigma- Aldrich) and visualized using light microscopy. The medial thickness and collagen deposition were then quantified using ImageJ software.
Wheat Germ Agglutinin ( WGA ) Immunostaining
RV sections were fixed in 1% paraformaldehyde and stained using fluorescence-tagged wheat germ agglutinin (WGA) (Invitrogen) overnight at 4°C and imaged with on Zeiss Observer Z. l microscope (Carl Zeiss) at x l60 magnification. The outlines of cardiac myocytes were traced and the cardiomyocyte area was calculated using ImageJ software.
Statistical analysis
All the experiments were conducted at least in triplicate. Results are presented as mean±standard error of the mean. Data were analyzed with the use of an unpaired t test for comparisons between 2 conditions or 1-way analysis of variance with the Tukey correction for comparisons between >2 conditions. Statistical analysis was performed using GraphPad Prism software (GraphPad Software, Inc., La Jolla, CA).
Example 2: Decreased expression of SERCA2a in human IPF and in a mouse model of BLM- induced lung fibrosis.
To determine if SERCA2a expression is modulated in the fibrotic lungs of patients with IPF, SERCA2a mRNA and protein expression levels were measured in lung biopsies of patients diagnosed with IPF and non-IPF lungs (healthy control donors; Tables 2 and 3).
Table 2. IPF Patient Clinical Data
Figure imgf000079_0001
Table 3. Control Healthy Non-IPF Subjects
Figure imgf000079_0002
SERCA2a expression was significantly decreased at the level of a mRNA and protein in IPF lung tissue specimens compared to control non-IPF lung samples (FIGs. 1 A-B).
Concomitantly, a significant decrease of SERCA2a protein by immunostaining in human IPF lungs versus control non-IPF was observed (FIG. 1C). In accordance with these findings, SERCA2a expression, at the levels of both mRNA and protein, was markedly diminished in the lung from the in vivo experimental mouse model of PF induced by an IT delivery of bleomycin (BFM) (FIGs. ID- IF).
Interestingly, there were decreased SERCA2a mRNA expression levels that correlated to disease severity in a time-dependent manner (FIG. 2A). Conversely, IF-6 mRNA level was increased (FIG. 2B). Finally, gene expression patterns in lungs from BFM-challenged mice at day 1, 3 and 14 were analyzed; similarly, the decrease of SERCA2a mRNA expression was confirmed at 14 days post-BFM delivery (FIG. 2C). Example 3: Therapeutic intratracheal delivery of AAVl.SERCA2a inhibits lung fibrosis and lung dysfunction in the BLM-induced IPF model
To assess the effects of SERCA2a gene therapy, the gene transfer efficiency of AAV1- mediated gene transfer was first assessed by performing GFP staining to corroborate transduction in lung tissue harvested 30 days after the IT delivery of AAV1 encoding human GFP (FIG. 3 A). The results show that GFP was expressed abundantly throughout the intima and media of small pulmonary arteries, in bronchial epithelial and smooth muscle cells, and pneumocytes, indicating successful AAV1 aerosolized IT delivery gene transfer to the lungs (FIG. 3 A).
To further confirm the implication of SERCA2a downregulation in lung fibrosis, we next evaluated the potential therapeutic effect of targeted gene transfer of SERC A2a using AAV 1 serotype in a mouse model of BLM-induced PF. The BLM murine model induced pulmonary fibrosis and is the most commonly-used animal model in rodents to study interstitial lung disease. BLM aerosolization leads to lung injury with a subsequent fibroproliferative response in mice by inducing an increase in production of reactive oxygen species, thereby causing cellular damage to endothelial cells and other cell types, leading to the production of cytokines and pro- fibrotic mediators such as TGF-b and IL-6. Using a therapeutic strategy, mice were randomly allocated to a sham control-treated group that received IT saline injections and a PF group that received a single IT aerosolization of BLM (4U/kg). After two weeks, the BLM-challenged group was randomly assigned to receive intratracheally-aerosolized AAV1 encoding human SERCA2a ( AAV1. SERC A2a) or AAVl encoding human luciferase (AAV1.LUC) as a control (FIG. 4 A).
Pulmonary hemodynamics, morphometric measurements, as well as fibrosis and pulmonary vascular remodeling were measured 4 weeks post-AAV injection (FIG. 4A). We first noticed that AAVl . SERC A2a treatment resulted in significant improvement in the median survival of mice in the BLM-induced PF model compared with A AVI. LUC -treated mice (FIG. 4B). At 40 days, the survival rate was 60% with AAVl- SERC A2a and 15% with the control AAVl. LUC, which represents a 45% reduction in mortality (FIG. 4B). Altogether, these pre- clinical data elicited that gene transfer of SERCA2a significantly improves survival in a mouse model of lung fibrosis.
Next, the targeting efficiency distribution of aerosolized delivery of AAVl. SERC A2a on- and off-target of SERCA2a gene transduction was assessed by analyzing the viral genome copies and CMV SERC A2a mRNA levels in the lung and RV of AAVl.SERCA2a and AAV1.LUC- treated BLM challenged mice. The results showed that the number of exogenous SERCA2a genome copies in the lung tissue samples were significantly higher in the AAVl . SERCA2a- treated group in comparison with the AAV l -LUC group. There was no viral genome copy detected in the RV of the AAVl . SERC A2a-treated group, demonstrating the specificity of the local IT aerosol delivery method toward the mice lungs (FIG. 4C). Similarly, real-time analysis using specific primers for the synthetic CMV promoter revealed efficient transduction of the lung compared to RV tissues (FIG. 3B). To further demonstrate the efficacy of gene transfer, the expression of SERCA2a in the lungs was measured by real-time qPCR using specific primers designed for mouse and human SERCA2a isoform, and by western blotting using a specific antibody that recognized both the exogenous human and endogenous mouse SERCA2a isoform. The results show an increase in human SERCA2a mRNA levels in the lung samples of
AAV 1. SERC A2a-treated animals compared to controls (FIG. 2D). Surprisingly, specific local instillation of exogenous AAV 1 human SERCA2a in the mouse lungs restored the endogenous mouse SERCA2a transcript in the BLM-PF mice model treated with AAVl human SERCA2a compared to AAVl. LUC-treated mice (FIG. 2C). The protein level of SERCA2a in the lungs of BLM-challenged mice was restored in the AAVl . SERC A2a-treated group compared to controls (FIG. 4E). This confirms the on-target specificity of the AAVl. SERC A2a after in vivo gene IT delivery in the BLM mouse model of PF. In clinical settings, evidence of abnormal gas exchange, as defined by low partial pressure of arterial oxygen (P02)/percentage of inspired oxygen ratio or a decrease in P02, is used as one of the diagnostic criteria for interstitial lung fibrosis 37. The present results demonstrated a significant deterioration of gas exchange in the BLM + AAVl. LUC treated group, and that AAVl . SERC A2a improved blood gas exchange with increased P02 in BLM-challenged mice (FIG. 4F).
Example 4: 1 1 Vl.SERCA2a effectively reverses pulmonary interstitial fibrosis and vascular remodeling.
BLM instillation resulted in substantial histological tissue damage in the AAVl. LUC- treated group compared to the SERCA2a-treated group. To further investigate the potential therapeutic effect of SERCA2a gene transfer in PF, next the interstitial fibrosis level and the vascular remodeling were evaluated by histological analysis. Interestingly, the results demonstrated that both interstitial and perivascular fibrosis was increased in the AAV1.LUC group and significantly decreased in the AAV1. SERC A2a-treated BLM group (FIG. 4G). In addition, morphometric analysis of distal pulmonary arteries demonstrated a significant increase in the medial thickness in BLM-treated mice. Similarly, AAVl.SERCA2a gene transfer markedly diminished pulmonary vascular remodeling in comparison with the AAV1.LUC- treated BLM mice group (FIG.4G). The expression of several markers of fibrosis in the lung and bronchoalveolar lavage (BAL) fluid samples was measured by RT-qPCR. SERCA2a
overexpression was markedly reduced the expression of several fibrosis markers as collagen type I and III, CTGF and TGFp mRNA levels (FIG. 4H, upper panel). There was also a
downregulation of major proteoglycans (PG) markers such as heparan Sulfate 6-0- Sulfotransferase 1 (HS6ST1) and Versican (VC AN), hyaluronan synthase 2, fibromodulin, and syndican 4, which are major components of the ECM implicated in lung tissue remodeling in PF38 (FIG. 5 A). Moreover, SERCA2a overexpression decreased CTGF and TGFp transcript levels in BAL fluid (FIG. 4H, lower panel). Collectively, the results demonstrated that AAVl gene transfer of SERCA2a in BLM-challenged mice decreased pro-fibrotic responses and the vascular remodeling in the BLM-challenged mice model of PF. Interestingly, the reversal of pulmonary vascular thickening was accompanied by a reduction in right ventricular systolic pressure (RVESP) (FIG. 41, left panel). Heart rate was not affected in either sham group or mice challenged with BLM and treated with AAV. SERC A2a or AAVl. LUC (Data not shown). In addition, the treatment of BLM-challenged mice with AAVl.SERCA2a reversed RV
hypertrophy, as was revealed by a decreased Fulton Index (RV/LV + septum weight) compared to the AAVl. LUC group (FIG. 41, right panel). Remarkably, restoration of SERCA2a expression significantly inhibited RV hypertrophy induced by BLM. Histological analysis showed a reduction in cardiomyocyte size in the BLM group treated with AAVl -SERC A2a compared with A AVI. LUC -treated mice (FIG. 4J). In addition, the upregulation of the hypertrophic gene markers, atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), beta-myosin heavy chain (b-MHC), was compromised in AAVl -SERC A2a (FIG. 4K).
In addition, AAVl. SERC A2a treatment reduced RV collagen deposition, visualized by Masson’s trichrome staining in comparison with AAVl. LUC-treated mice (FIG. 4L). The expression of fibrosis markers was assessed by RT-qPCR in the RV samples, and the results showed decreased expression of type 1 and III and TGF-bI in AAVl -SERC A2a-treated animals, which is also consistent with the earlier results (FIG. 4M). Altogether, the results further confirmed the hypothesis that SERCAZa downregulation is critical in the pathogenesis of PF and that AAVl.SERCA2a gene transfer represents a promising therapeutic target.
Example 5: Prevention of bleomycin-induced Lung Fibrosis by intratracheal delivery of 1 1 Vl.SERCA2a in a mouse model
In the prevention protocol, mice were randomly assigned to three treatment groups: sham, AAV 1. SERC A2a, and AAV1.LUC (FIG. 6A). Then, two weeks later, the mice were
administered with an IT instillation of BLM or vehicle as control, and hemodynamic studies were performed five weeks post-AAVl delivery (FIG. 6A). Consistent with the previous results, AAV1 encoding human SERCAZa was only expressed in the lungs of the AAVl.SERCA2a treated group (FIG. 6B, FIG. 3D). Similarly, AAV 1. SERC A2a restored endogenous SERC Za mRNA (FIG. 6C) and protein expression levels in the prevention protocol (FIG. 6D).
Preventive administration of AAVl.SERCA2a significantly decreased interstitial and perivascular fibrosis as well as the medial thickness in the BLM-induced PF (FIG. 6E). The results simultaneously confirmed that SERCA2a gene therapy prevents the expression of pro- fibrosis and PG markers in the lung and B AL fluid samples (FIG. 6F, FIG. 5B). Additionally, SERCA2 decreased RVSP and RV hypertrophy, as illustrated by the lower Fulton index in the BLM-treated mice (FIG. 6G). The quantification of the RV cardiomyocyte size revealed that the overexpression of SERCA2a significantly prevented BLM-induced cardiac myocyte hypertrophy (FIG. 6H). In agreement with these results, the data showed that AAVl.SERCA2a gene therapy impaired the upregulation of the hypertrophic markers ANP, BNP and b-MHC induced in the BLM-challenged mice (FIG. 61). In addition, as expected, SERCA2a-treated BLM-challenged mice displayed reduced RV interstitial fibrosis and the expression of the fibrosis markers compared to the AAV1. LUC-treated group (FIGs. 6J and 6K, respectively). These findings support the hypothesis that IT delivery of aerosolized AAVl.SERCA2a represses lung fibrosis.
Example 6: SERCA2a inhibits the proliferation, migration and differentiation of fibroblasts to myofibroblasts in vitro.
To further investigate the role of SERCA2a in the initiation and progression of pulmonary fibrosis, the effect of SERCA2a overexpression in vitro on the proliferation and migration of normal human pulmonary fibroblasts (NHLFs) was examined using a Bromodeoxyuridine (BrdU) and a Transwell migration assay, respectively. The pro-fibrotic agent TGF-bI is an important mediator of fibrosis and is thought to contribute to the
pathogenesis of lung fibrosisl 1. NHLFs cells were infected for 48 hours with a control adenovirus encoding b-galactosidase (Ad.CT) or an adenovirus encoding human SERCA2a (Ad.S2a) and stimulated either with 0.1% or 5% FBS for 48 hrs in the presence or absence of TGF-bI. The results show that serum stimulation (FBS) and TORb increased NHLFs
proliferation, whereas SERCA2a overexpression significantly decreased their proliferative effects (FIG. 7A). After confirming the increased expression of SERCA2a in NHLF transduced by Ad.2a (FIG. 7B, FIG. 8 A), the protein level of Cyclin Dl, a cell cycle marker, was evaluated; and there were decreased protein levels of Cyclin Dl in SERCA2a overexpressing NHLFs cells compared to Ad.CT (FIG. 7B). Collectively, the results demonstrated that SERCA2a inhibits NHLFs proliferation. Migration of fibroblasts toward the fibrotic lesions plays an important role in PF, thus the role of SERCA2a on NHLFs migration was investigated; it was demonstrated that SERCA2a was capable of inhibiting TGF^-induced NHLFs cells migration in vitro as well (FIG. 7C). Myofibroblasts have long been identified as the chief culprit in fibrosis development and are responsible for the deposition and maintenance of the fibrotic ECM in all organs, which ultimately leads to deleterious tissue architectural changes and organ failure39-41. Therefore, the role of SERCA2a overexpression on fibroblast to myofibroblast differentiation and pro-fibrosis genes in vitro in NHLF treated with TGF-bI for 48 hrs was assessed. Interestingly, SERCA2a overexpression inhibits fibroblast to myofibroblast transition as assessed by immunostaining for a-smooth muscle actin (aSMA-a strong marker of myofibroblast differentiation) (FIG. 7D). It was next determined whether SERCA2a regulates the expression of several TGF-bI -regulated pro-fibrosis genes. Thus, SERCA2a was overexpressed in NHLFs cells and treated them with TGF-bI for 48 hrs. Then the mRNA expression of Collagen 1AI (COL1A1), COL3A1 and CTGF was analyzed. Remarkably, SERCA2a overexpression impaired the induction of pro- fibrotic fibrosis markers induced by TGF-b treatment (FIG. 7E), and PG markers such as HS6ST1 and VCAN (FIG. 8C).
Given epithelial cells constitute the primary source of pro-fibrotic mediators and play a critical role in fibroblast proliferation, migration and ECM accumulation, the role of SERCA2a in human pulmonary alveolar epithelial cells in-vitro (hAEpiC) was evaluated. Similarly, SERCA2a overexpression blocked the differentiation of the hAEpiC toward a fibroblastic-like phenotype by reducing the expression of several fibrosis markers such as COL1 A1 (FIG. 9A), COL3 A1 (FIG. 9B), and CTGF (FIG. 9C). Concomitantly, the expression of SERCA2a expression was knocked down using a specific shRNA (sh.S2a) (FIG. 8B). The results showed that SERCA2a silencing potentiates the expression of the fibrosis markers induced by TGFP in hAEpiC (FIGs. 9A-9C).
Example 7: SERCA2a overexpression blocks NFKB-mediated IL-6 expression in fibroblasts.
In addition to TGF-b, there is substantial evidence that IL-6 may be an important cytokine that can promote fibrosis. Indeed, IL-6, produced by various cell types, is a pleiotropic cytokine and functions as a pro-inflammatory factor as well as a profibrotic factor in BLM- induced lung fibrosis. Then, the molecular mechanism underlying the role of SERCA2a in PF was examined. To this end, we determined whether SERCA2a inhibits TGFP-induced fibrosis gene expression via the suppression of IL-6. Treatment of NHLF cells with TGF-bI drastically increased the expression of IL-6, thus, IL-6 expression may depend on TGF^-mediated signaling (FIG. 7F). Remarkably, SERCA2a overexpression markedly reversed this effect (FIG. 7F), while SERCA2a silencing (sh.S2a) (FIG. 2B) increased IL-6 transcript (FIG. 7G). The promoter region of the IL-6 gene has a putative Nuclear Factor kappa B (NF-KB)-binding site43. Since NF-KB activity can be modulated by increased intracellular Ca2+ levels44 44, it was tested whether SERCA2a affects NF-KB activity. Remarkably, the results show that SERCA2a decreases TGFb-induced NFKB luciferase activity compared to Ad.CT (FIG. 7H) and to
SERCA2a-depleted cells (FIG. 71). Therefore, the data suggest a positive feedback loop between IL-6 and TGF-b that is repressed by SERCA2a through the repression of NF-KB activity.
Example 8: SERCA2a as a negative regulator of SMAD2/3 complex activity via inhibition of pSTAT3/OTUBl in fibroblast in vitro.
Herein, it was questioned whether SERCA2a via STAT3 regulates SMAD2/3 protein activity and stability. Subsequently, since OTUB1 stabilizes and inhibits the ubiquitination of p- SMAD2/318; it was further investigated whether SERCA2a regulates OTUB1 via STAT3. To this end, NHLFs cells were infected with either Ad.S2a or Ad.CT and treated with TGF-b for 48 hrs. SERCA2a significantly diminished OTUB1 mRNA expression induced by TGF-b treatment (FIG. 7J). On the contrary, the silencing of SERCA2a expression potentiates OTUB1 expression upon TGF-b treatment (FIG. 7K). Hence, these results suggested that OTUB1 is a direct target of SERCA2a. Interestingly, the promoter analysis of OTUB1 revealed the existence of the STAT3 transcription factor binding sites. Therefore, it was tested whether STAT3 inhibition affects OTUB1 expression. To test this possibility, we treated NHLFs overexpressing SERCA2a or Ad.CT with TGFP alone or in combination with the STAT3 inhibitor HJC0152 (STAT3i) for 48 hrs, and measured the expression of OTUB1 by RT-qPCR and immunoblotting. Remarkably, the induction of OTUB1 by the TGF-b treatment is reversed by SERCA2a overexpression in a STAT3 -dependent manner (FIGs. 7L-7N). Concurrently, it was successfully demonstrated that the STAT3i repressed OTUB1 mRNA expression induced by the loss of SERCA2a and TGF-b treatment (FIG. 7N). SimilarSERCA2a, STAT3i decreased a-SMA and Cyclin D1 protein expression levels (FIG. 7N). To gain further support of the notion that SERCAZa regulates OTUB1 via STAT3 inhibition, the OTUB1 expression was knocked down using siRNA OTUB1 (si.OTUBl).
Silencing OTUB1 decreased OTUB1 mRNA and protein expression levels (FIG. 10A), while decreasing NHLFs proliferation and strengthening the beneficial effect of SERCA2a overexpression (FIG. 70). Likewise, the data demonstrated that the loss of SERCA2a potentiated the NHLFs proliferation in an OTUB1 -dependent manner (FIG. 7P). The expression of several fibrosis markers in NHLFs cells after the SERCA2a knockdown alone or in combination with si.OTUBl was analyzed. Markedly, OTUB1 inhibition repressed the expression of the fibrosis markers induced by the loss of SERCA2a and TGF-b treatment (FIGs. 10B-10D). Collectively, the results demonstrated that restoration of SERCA2a expression inhibited OTUB1 expression in a ST AT3 -dependent mechanism, and subsequently, the decrease of the expression of TORb- dependent pro-fibrotic genes.
Example 9: SERCA2a inhibition of OTUB1 and FOXM1 mediates SnoN/SKI expression in human lung fibroblasts
Like many other biological mechanisms, the TGF-b signaling is regulated by various stimulatory and inhibitory mediators. Since FOXM1 sustained the activation of SMAD3 in cancer, the role of SERCA2a on FOXM1 expression and protein stability in NHLF cells was next assessed. Interestingly, SERCA2a repressed FOXMl expression at both mRNA and protein levels in the absence (FIG. 10E) or presence of TGF-b treatment (FIG. 11 A and 1 IF). However, SERCA2a depletion in NHLFs reversed this effect by increasing FOXM1 expression (FIGs. 10F, 1 IB, and 11G). Interestingly, OTUB1 silencing did not affect FOXM1 mRNA expression but increased FOXM1 protein expression (FIG. 11C). These results suggest that SERCAZa may regulate the FOXM1 expression level directly and also protein stability through the inhibition of OTUB1 expression (FIG. 1 IF).
Given the critical role of SnoN and SKI in the regulation of SMAD and TGF-b signaling, it was sought to determine whether SERCA2a regulates SnoN and SKI expression. To this end, SnoN and SKI expression levels were analyzed in overexpressing or depleted SERCA2a cells and treated with TGF-bI. The results indicated that SERCA2a overexpression repressed the effects oίTϋRb and restored SnoN and SKI mRNA and protein expression (FIGs. 1 ID and 1 IF), while SERCA2a depletion has opposite effects (FIGs. 5D and 5G). Moreover, SERCA2a overexpression decreased SMAD2/3 phosphorylation (FIGs. 1 IF) compared to control cells, while SERCA2a depletion potentiates SMAD2/3 phosphorylation (FIGs. 11G). These results raise the possibility that SERCA2a may regulate SnoN/SKI expression through the repression of OTUB1 and/or FOXM1. Effectively, silencing FOXM1 and OTUB1 restored SnoN mRNA expression (FIGs. 11H).
Example 10: SERCA2a overexpression atenuates TGF-b signaling by promoting the ubiquitination and the degradation of FOXM1 and active SMAD 2/3 via the repression of OTUB1
In addition to the above results, it was also confirmed the direct interaction of
endogenous FOXM1 with OTUB1 and with SMAD2/3 in NHLF cells using an
immunoprecipitation assay using an anti-FOXMl antibody. As shown in FIG. 6H, endogenous FOXM1 interacts with OTUB1 and FOXMl/pSMAD3 interaction is potentiated in response to TGF-b. However, the interaction between endogenous FOXMl/OTUBl and between
FOXM1/SMAD3 was decreased after SERCA2a overexpression but enhanced after SERCA2a knockdown (FIG. 1 II). Next, it was determined that the effects of SERCA2a on the
ubiquitination of FOXM1 and active SMAD2/3 in SERCA2a overexpressing or SERCAZZa- depleted NHLF cells and transfected together with tagged-HA ubiquitin. Cells were treated with THRb and the proteasome inhibitor MG132 to induce phosphorylation of the SMAD2/3 complex and to inhibit proteasomal degradation, respectively. MG132 and TGF-b treatment decrease polyubiquitylated FOXM1 and p-SMAD2/3 proteins, which decrease their proteasome-mediated degradation (FIG. 11J). However, SERCA2a overexpression and depletion of OTUB1 resulted in enhanced FOXM1 and active SMAD2/3 polyubiquitylation by inhibiting OTUB1, while the cells depleted of SERCA2a expression exhibited lower levels of ubiquitination, suggesting that SERCA2a is necessary and sufficient for the regulation of SMAD/TGFP signaling (FIG. 11 J).
Example 11: Expression of OTUB1 is correlated with FOXM1 in human IPF
Next, the correlation between OTUB1, FOXMl, SnoN and SKI expression was examined by assessing their mRNA and protein levels in healthy non-IPF patients and lung human biopsies from IPF patients, as well as in the BLM-challenged mice model of PF. Remarkably, the levels of OTUB1 and FOXMl mRNA and protein expression levels were inversely correlated with SKI and SnoN expression in human lung tissue from IPF patients (FIGs. 1 IK and 11L, respectively).
Likewise, the immunostaining intensity of OTUB1 (red) and FOXMl (red) was significantly higher in IPF patients compared to control non-IPF (FIG. 11M). Similar to what has been observed in human lung samples, high OTUB1 and FOXMl mRNA expression levels were correlated with the severity of lung fibrosis disease in a time-dependent manner in the BLM- induced PF mouse model (FIGs. 12A and 12D), while SnoN and SKI expression levels were reduced (FIGs. 12C and 12D). Likewise, OTUB1 and FOXMl protein expression were increased while SnoN and SKI protein expression levels were further decreased (FIG. 1 IN).
Example 12: AAVl.SERCA2a gene transfer attenuates lung inflammation, pulmonary fibrosis and remodeling by inhibiting the OTUB1/FOXM1/SMAD2/3 signaling and promoting
SKI/SNON expression in vivo
A single IT instillation of BLM induces acute lung inflammation leading to fibrosis46. In this study, whether the potential anti-fibrotic effect of SERCA2a is mediated through an anti inflammatory mechanism by suppressing IL-6 expression in vivo was explored. The level of IL-6 mRNA was significantly increased in the lungs of AAV1. LUC-treated animals versus the sham non-BLM treated group (Control). Compared with the AAV1. LUC-treated BLM group, AAVl SERCA2a gene transfer significantly reduced IL-6 mRNA levels in the lungs and BLF after the therapeutic or prevention protocols (FIG. 13 A). Given that it was previously demonstrated that, in vitro, SERCA2a silencing potentiated the NHLF proliferation and the expression of several fibrosis markers in an OTUB1 -dependent manner and decreased the expression of the negative regulators of fibrosis SNON and SKI. OTUB1, SnoN and SKI mRNA expression in vivo in the lung tissues from the three groups of animals were analyzed. Similarly, OTUB1 and FOXM1 mRNA levels were markedly increased in AAV1. LUC-treated BLM animals (FIG. 13B) with decreased SnoN and SKI mRNA expression levels (FIG. 13C). Consistently, long-term IT instillation of AAVl.SERCA2a significantly decreased the mRNA expression levels of OTUB1 and FOXM1 and restored SnoN and SKI expression in both prevention and treatment experiments in the same order of magnitude, validating in vitro experiments (FIGs. 13B and 13C).
Moreover, the findings were validated by showing that NFicB-p65 and STAT3 phosphorylation was increased in AAV1. LUC-treated BLM-challenged mice compared to the sham non-treated group in both protocols (FIGs. 13D and 13E). Similarly, OTUB1 and FOXM1 protein expression were highly increased in BLM-induced PF whereas SnoN and SKI were significantly down-regulated (FIGs. 13D and 13E). Subsequently, SERCA2a overexpression reversed the effect of BLM and significantly decreased NFKB-p65 and STAT3 phosphorylation, OTUB1 and FOXM1 protein expression, and consequently, the phosphorylation of SMAD2/3 (FIGs. 13D and 13E). Consistent with the mRNA data, SnoN and SKI were also restored in AAV1. SERC A2a-treated animals compared to AAV1. LUC-treated BLM group (FIGs. 13D and 13E). Consequently, aSMA and Cyclin D1 protein expression were markedly reduced in AAV 1. SERC A2a-treated animals (FIGs. 13D and 13E) Collectively, the data suggest that IT delivery of AAVl.SERCA2a is a safe, efficient and feasible approach to inhibit PF by decreasing myofibroblast differentiation, fibroblast proliferation, migration, and invasion through a transcriptional regulation of STAT3, OTUBl/FOXMl and SnoN/SKI pathway, and therefore, Smad2/3 activity (FIG. 13F).

Claims

WHAT IS CLAIMED IS:
1. A method of treating idiopathic pulmonary fibrosis in a subject in need thereof, comprising administering to a subject a vector comprising a nucleic acid that encodes for sarcoplasmic reticulum (SR) calcium ++ ATPase (SERCA).
2. A method of preventing or ameliorating idiopathic pulmonary fibrosis in a subject at risk of developing idiopathic pulmonary fibrosis, comprising administering to the subject a vector comprising a nucleic acid that encodes for SERCA.
3. The method of claim 1 or 2, wherein the administering is via intratracheal instillation, bronchial instillation, inhalation; a nasal spray, or an aerosol.
4. The method of any one of claims 1-3, wherein the administering is via intratracheal.
5. The method of any one of claims 1-4, wherein the vector is an adeno-associated viral
(AAV) vector.
6. The method of claim 5, wherein the AAV vector is any one of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, or AAV9.
7. The method of claim 5 or 6, wherein the AAV vector is AAV1.
8. The method of any one of claims 1-7, wherein the vector is a recombinant adeno- associated virus (rAAV).
9. The method of any one of claims 1-8, wherein the vector comprises a nucleic acid that encodes for any one of SEQ ID NOs: 1-20.
10. The method of any one of claims 1-9, wherein the vector comprises a nucleic acid that encodes for any one of SEQ ID NOs: 1-4.
11. The method of any one of claims 1-10, wherein the subject is a mammal.
12. The method of claim 11, wherein the mammal is a human.
13. The method of any one of claims 1-12, wherein the SERCA is SERCA isoform 2 (SERCA2).
14. A method of treating idiopathic pulmonary fibrosis in a subject in need thereof, comprising administering to a subject a pharmaceutical composition comprising an effective amount of a vector comprising a nucleic acid that encodes for SERCA, and a pharmaceutically acceptable excipient.
15. A method of preventing or ameliorating idiopathic pulmonary fibrosis in a subject at risk of developing idiopathic pulmonary fibrosis, comprising administering to a subject a pharmaceutical composition comprising an effective amount of a vector comprising a nucleic acid that encodes for SERCA, and a pharmaceutically acceptable excipient.
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