Aav vector compositions and methods for gene transfer to cells, organs and tissues

Abstract

The invention relates to adeno-associated virus (AAV) serotype AAV-Rh74 and related AAV vectors, and AAV-Rh74 and related AAV vector mediated gene transfer methods and uses. In particular, AAV-Rh74 targets polynucleotides to cells, tissues or organs for expression (transcription) of genes encoding therapeutic proteins and peptides, and polynucleotides that function as or are transcribed into inhibitory nucleic acid sequences.

What is claimed: 
     
         1 . A method for delivering or transferring a heterologous polynucleotide sequence into a mammal or a cell of a mammal, comprising administering an adeno-associated virus (AAV) vector, said vector comprising a heterologous polynucleotide sequence, to said mammal or a cell of said mammal, thereby delivering or transferring the heterologous polynucleotide sequence into the mammal or cell of the mammal. 
     
     
         2 . The method of  claim 1 , wherein the heterologous polynucleotide sequence is operably linked to an expression control element conferring transcription of said heterologous polynucleotide sequence. 
     
     
         3 . A method of treating a mammal deficient in protein expression or function, comprising: (a) providing adeno-associated virus (AAV) vector, said vector comprising a heterologous polynucleotide encoding a polypeptide that can correct for the deficient protein expression or function, wherein the heterologous polynucleotide sequence is operably linked to an expression control element conferring transcription of said heterologous polynucleotide sequence; and (b) administering an amount of the AAV vector to the mammal wherein said polypeptide is expressed in the mammal. 
     
     
         4 . The method of  claim 1  or  3 , wherein said adeno-associated virus (AAV) vector comprises an AAV with a VP1 sequence having 90% or more sequence identity to: 
       
         
           
                 
               
                   MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDNGRGLVLP 
                 
                     
                 
                   GYKYLGPFNGLDKGEPVNAADAAALEHDKAYDQQLQAGDNPYLRYNHA 
                 
                     
                 
                   DAEFQERLQEDTSFGGNLGRAVFQAKKRVLEPLGLVESPVKTAPGKKR 
                 
                     
                 
                   PVEPSPQRSPDSSTGIGKKGQQPAKKRLNFGQTGDSESVPDPQPIGEP 
                 
                     
                 
                   PAGPSGLGSGTMAAGGGAPMADNNEGADGVGSSSGNWHCDSTWLGDRV 
                 
                     
                 
                   ITTSTRTWALPTYNNHLYKQISNGTSGGSTNDNTYFGYSTPWGYFDFN 
                 
                     
                 
                   RFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTQNEGTKTIA 
                 
                     
                 
                   NNLTSTIQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLN 
                 
                     
                 
                   NGSQAVGRSSFYCLEYFPSQMLRTGNNFEFSYNFEDVPFHSSYAHSQS 
                 
                     
                 
                   LDRLMNPLIDQYLYYLSRTQSTGGTAGTQQLLFSQAGPNNMSAQAKNW 
                 
                     
                 
                   LPGPCYRQQRVSTTLSQNNNSNFAWTGATKYHLNGRDSLVNPGVAMAT 
                 
                     
                 
                   HKDDEERFFPSSGVLMFGKQGAGKDNVDYSSVMLTSEEEIKTTNPVAT 
                 
                     
                 
                   EQYGVVADNLQQQNAAPIVGAVNSQGALPGMVWQNRDVYLQGPIWAKI 
                 
                     
                 
                   PHTDGNFHPSPLMGGFGLKHPPPQILIKNTPVPADPPTTFNQAKLASF 
                 
                     
                 
                   ITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYYKSTNVDFAVNTE 
                 
                     
                 
                   GTYSEPRPIGTRYLTRNL, 
                 
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
       or 1-50 amino acid substitutions, deletions or additions thererto;
 a VP2 sequence having 90% or more sequence identity to: 
 
       
         
           
                 
               
                   TAPGKKRPVEPSPQRSPDSSTGIGKKGQQPAKKRLNFGQTGDSESVPDP 
                 
                     
                 
                   QPIGEPPAGPSGLGSGTMAAGGGAPMADNNEGADGVGSSSGNWHCDSTW 
                 
                     
                 
                   LGDRVITTSTRTWALPTYNNHLYKQISNGTSGGSTNDNTYFGYSTPWGY 
                 
                     
                 
                   FDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTQNEGTK 
                 
                     
                 
                   TIANNLTSTIQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLT 
                 
                     
                 
                   LNNGSQAVGRSSFYCLEYFPSQMLRTGNNFEFSYNFEDVPFHSSYAHSQ 
                 
                     
                 
                   SLDRLMNPLIDQYLYYLSRTQSTGGTAGTQQLLFSQAGPNNMSAQAKNW 
                 
                     
                 
                   LPGPCYRQQRVSTTLSQNNNSNFAWTGATKYHLNGRDSLVNPGVAMATH 
                 
                     
                 
                   KDDEERFFPSSGVLMFGKQGAGKDNVDYSSVMLTSEEEIKTTNPVATEQ 
                 
                     
                 
                   YGVVADNLQQQNAAPIVGAVNSQGALPGMVWQNRDVYLQGPIWAKIPHT 
                 
                     
                 
                   DGNFHPSPLMGGFGLKHPPPQILIKNTPVPADPPTTFNQAKLASFITQY 
                 
                     
                 
                   STGQVSVEIEWELQKENSKRWNPEIQYTSNYYKSTNVDFAVNTEGTYSE 
                 
                     
                 
                   PRPIGTRYLTRNL, 
                 
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
       or 1-50 amino acid substitutions, deletions or additions thererto; and/or
 a VP3 sequence having 90% or more sequence identity to: 
 
       
         
           
                 
               
                   MAAGGGAPMADNNEGADGVGSSSGNWHCDSTWLGDRVITTSTRTWALP 
                 
                     
                 
                   TYNNHLYKQISNGTSGGSTNDNTYFGYSTPWGYFDFNRFHCHFSPRDW 
                 
                     
                 
                   QRLINNNWGFRPKRLNFKLFNIQVKEVTQNEGTKTIANNLTSTIQVFT 
                 
                     
                 
                   DSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSF 
                 
                     
                 
                   YCLEYFPSQMLRTGNNFEFSYNFEDVPFHSSYAHSQSLDRLMNPLIDQ 
                 
                     
                 
                   YLYYLSRTQSTGGTAGTQQLLFSQAGPNNMSAQAKNWLPGPCYRQQRV 
                 
                     
                 
                   STTLSQNNNSNFAWTGATKYHLNGRDSLVNPGVAMATHKDDEERFFPS 
                 
                     
                 
                   SGVLMFGKQGAGKDNVDYSSVMLTSEEEIKTTNPVATEQYGVVADNLQ 
                 
                     
                 
                   QQNAAPIVGAVNSQGALPGMVWQNRDVYLQGPIWAKIPHTDGNFHPSP 
                 
                     
                 
                   LMGGFGLKHPPPQILIKNTPVPADPPTTFNQAKLASFITQYSTGQVSV 
                 
                     
                 
                   EIEWELQKENSKRWNPEIQYTSNYYKSTNVDFAVNTEGTYSEPRPIGT 
                 
                     
                 
                   RYLTRNL, 
                 
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
       or 1-50 amino acid substitutions, deletions or additions thererto. 
     
     
         5 . The method of  claim 1  or  3 , wherein said adeno-associated virus (AAV) vector comprises an AAV with a VP1, VP2, or VP3 sequence having 95% or more identity to one or more VP1, VP2, or VP3 sequences set forth in  FIG. 3 . 
     
     
         6 . The method of  claim 1  or  3 , wherein said adeno-associated virus (AAV) vector comprises a VP1, VP2, or VP3 sequence having 96% or more identity to one or more VP1, VP2, or VP3 sequences set forth in  FIG. 3 . 
     
     
         7 . The method of  claim 1  or  3 , wherein said adeno-associated virus (AAV) vector comprises a VP1, VP2, or VP3 sequence having 97% or more identity to one or more VP1, VP2, or VP3 sequences set forth in  FIG. 3 . 
     
     
         8 . The method of  claim 1  or  3 , wherein said adeno-associated virus (AAV) vector comprises a VP1, VP2, or VP3 sequence having 98% or more identity to one or more VP1, VP2, or VP3 sequences set forth in  FIG. 3 . 
     
     
         9 . The method of  claim 1  or  3 , wherein said adeno-associated virus (AAV) vector comprises a VP1, VP2, or VP3 sequence having 99% or more identity to one or more VP1, VP2, or VP3 sequences set forth in  FIG. 3 . 
     
     
         10 . The method of  claim 1  or  3 , wherein said adeno-associated virus (AAV) vector comprises a VP1, VP2, or VP3 sequence having 99.5% or more identity to one or more VP1, VP2, or VP3 sequences set forth in  FIG. 3 . 
     
     
         11 . The method of  claim 1  or  3 , wherein said adeno-associated virus (AAV) vector comprises a VP1, VP2, or VP3 sequence of AAV-Rh74 set forth in  FIG. 3 , an AAV vector related to AAV-Rh74 or AAV-Rh74. 
     
     
         12 . The method of  claim 1  or  3 , wherein said heterologous polynucleotide sequence, or said protein, is expressed at levels having a therapeutic effect on the mammal. 
     
     
         13 . The method of  claim 1  or  3 , wherein said adeno-associated virus (AAV) vector has increased tropism for hepatocytes compared to AAV2 or AAV8. 
     
     
         14 . The method of  claim 1  or  3 , wherein said heterologous polynucleotide sequence or said protein is expressed in a cell, tissue or organ of said mammal. 
     
     
         15 . The method of  claim 14 , wherein the cell comprises a secretory cell. 
     
     
         16 . The method of  claim 14 , wherein the cell comprises an endocrine cell. 
     
     
         17 . The method of  claim 14 , wherein the cell comprises hepatocyte, a neural cell, a glial cell, a retinal cell, an epithelial cell, a lung cell or a totipotent, pluripotent or multipotent stem cell. 
     
     
         18 . The method of  claim 14 , wherein the tissue or organ of said mammal comprises liver, brain, central nervous system, spinal cord, eye, retina or lung. 
     
     
         19 . The method of  claim 1  or  3 , wherein the mammal produces an insufficient amount of a protein, or a defective or aberrant protein. 
     
     
         20 . The method of  claim 19 , wherein the protein comprises CFTR (cystic fibrosis transmembrane regulator protein), a blood coagulation (clotting) factor (Factor XIII, Factor IX, Factor X, Factor VIII, Factor VIIa, protein C, etc.) a gain of function blood coagulation factor, an antibody, retinal pigment epithelium-specific 65 kDa protein (RPE65), erythropoietin, LDL receptor, lipoprotein lipase, ornithine transcarbamylase, β-globin, α-globin, spectrin, α-antitrypsin, adenosine deaminase (ADA), a metal transporter (ATP7A or ATP7), sulfamidase, an enzyme involved in lysosomal storage disease (ARSA), hypoxanthine guanine phosphoribosyl transferase, β-25 glucocerebrosidase, sphingomyelinase, lysosomal hexosaminidase, branched-chain keto acid dehydrogenase, a hormone, a growth factor, insulin-like growth factor 1 or 2, platelet derived growth factor, epidermal growth factor, nerve growth factor, neurotrophic factor-3 and -4, brain-derived neurotrophic factor, glial derived growth factor, transforming growth factor α and β, a cytokine, α-interferon, β-interferon, interferon-γ, interleukin-2, interleukin-4, interleukin 12, granulocyte-macrophage colony stimulating factor, lymphotoxin, a suicide gene product, herpes simplex virus thymidine kinase, cytosine deaminase, diphtheria toxin, cytochrome P450, deoxycytidine kinase, tumor necrosis factor, a drug resistance protein, a tumor suppressor protein (e.g., p53, Rb, Wt-1, NF1, Von Hippel-Lindau (VHL), adenomatous polyposis coli (APC)), a peptide with immunomodulatory properties, a tolerogenic or immunogenic peptide or protein Tregitope or hCDR1, insulin, glucokinase, guanylate cyclase 2D (LCA-GUCY2D), Rab escort protein 1 (Choroideremia), LCA 5 (LCA-Lebercilin), ornithine ketoacid aminotransferase (Gyrate Atrophy), Retinoschisin 1 (X-linked Retinoschisis), USH1C (Usher's Syndrome 1C), X-linked retinitis pigmentosa GTPase (XLRP), MERTK (AR forms of RP: retinitis pigmentosa), DFNB1 (Connexin 26 deafness), ACHM 2, 3 and 4 (Achromatopsia), PKD-1 or PKD-2 (Polycystic kidney disease), TPP1, CLN2, a gene product implicated in lysosomal storage diseases (e.g., sulfatases, N-acetylglucosamine-1-phosphate transferase, cathepsin A, GM2-AP, NPC1, VPC2, a sphingolipid activator protein, or one or more zinc finger nucleases for genome editing, or donor sequences used as repair templates for genome editing. 
     
     
         21 . The method of  claim 1  or  3 , wherein the heterologous polynucleotide sequence comprises a gene encoding a polypeptide, peptide or a protein. 
     
     
         22 . The method of  claim 21 , wherein the gene encodes a therapeutic peptide or protein. 
     
     
         23 . The method of  claim 21 , wherein the gene comprises or encodes CFTR (cystic fibrosis transmembrane regulator protein), a blood coagulation (clotting) factor (Factor XIII, Factor IX, Factor X, Factor VII, Factor VIIa, protein C, etc.) a gain of function blood coagulation factor, an antibody, retinal pigment epithelium-specific 65 kDa protein (RPE65), erythropoietin, LDL receptor, lipoprotein lipase, ornithine transcarbamylase, β-globin, α-globin, spectrin, α-antitrypsin, adenosine deaminase (ADA), a metal transporter (ATP7A or ATP7), sulfamidase, an enzyme involved in lysosomal storage disease (ARSA), hypoxanthine guanine phosphoribosyl transferase, β-25 glucocerebrosidase, sphingomyelinase, lysosomal hexosaminidase, branched-chain keto acid dehydrogenase, a hormone, a growth factor, insulin-like growth factor 1 or 2, platelet derived growth factor, epidermal growth factor, nerve growth factor, neurotrophic factor-3 and -4, brain-derived neurotrophic factor, glial derived growth factor, transforming growth factor α and β, a cytokine, α-interferon, β-interferon, interferon-γ, interleukin-2, interleukin-4, interleukin 12, granulocyte-macrophage colony stimulating factor, lymphotoxin, a suicide gene product, herpes simplex virus thymidine kinase, cytosine deaminase, diphtheria toxin, cytochrome P450, deoxycytidine kinase, tumor necrosis factor, a drug resistance protein, a tumor suppressor protein (e.g., p53, Rb, Wt-1, NF1, Von Hippel-Lindau (VHL), adenomatous polyposis coli (APC)), a peptide with immunomodulatory properties, a tolerogenic or immunogenic peptide or protein Tregitope or hCDR1, insulin, glucokinase, guanylate cyclase 2D (LCA-GUCY2D), Rab escort protein 1 (Choroideremia), LCA 5 (LCA-Lebercilin), ornithine ketoacid aminotransferase (Gyrate Atrophy), Retinoschisin 1 (X-linked Retinoschisis), USH1C (Usher's Syndrome 1C), X-linked retinitis pigmentosa GTPase (XLRP), MERTK (AR forms of RP: retinitis pigmentosa), DFNB1 (Connexin 26 deafness), ACHM 2, 3 and 4 (Achromatopsia), PKD-1 or PKD-2 (Polycystic kidney disease), TPP1, CLN2, a gene product implicated in lysosomal storage diseases (e.g., sulfatases, N-acetylglucosamine-1-phosphate transferase, cathepsin A, GM2-AP, NPC1, VPC2, a sphingolipid activator protein or one or more zinc finger nucleases for genome editing, or donor sequences used as repair templates for genome editing. 
     
     
         24 . The method of  claim 1 , wherein the heterologous polynucleotide sequence comprises an inhibitory nucleic acid. 
     
     
         25 . The method of  claim 24 , wherein the inhibitory nucleic acid comprises micro-RNA (miRNA), siRNA, shRNA, trans-splicing RNA, antisense RNA or triplex forming RNA. 
     
     
         26 . The method of  claim 24 , wherein the inhibitory nucleic acid binds to a pathogenic gene, a transcript of a pathogenic gene, or a gene transcript associated with a polynucleotide repeat disease, a huntingtin (HTT) gene, a gene associated with dentatorubropallidolusyan atropy (atrophin 1, ATN1), androgen receptor on the X chromosome in spinobulbar muscular atrophy, human Ataxin-1, -2, -3, and -7, Ca v 2.1 P/Q voltage-dependent calcium channel is encoded by the (CACNA1A), TATA-binding protein, Ataxin 8 opposite strand, also known as ATXN8OS, Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform in spinocerebellar ataxia (type 1, 2, 3, 6, 7, 8, 12 17), FMR1 (fragile X mental retardation 1) in fragile X syndrome, FMR1 (fragile X mental retardation 1) in fragile X-associated tremor/ataxia syndrome, FMR1 (fragile X mental retardation 2) or AF4/FMR2 family member 2 in fragile XE mental retardation; Myotonin-protein kinase (MT-PK) in myotonic dystrophy; Frataxin in Friedreich's ataxia; a mutant of superoxide dismutase 1 (SOD1) gene in amyotrophic lateral sclerosis; a gene involved in pathogenesis of Parkinson's disease and/or Alzheimer's disease; apolipoprotein B (APOB) and proprotein convertase subtilisin/kexin type 9 (PCSK9), hypercoloesterolemia; HIV Tat, human immunodeficiency virus transactivator of transcription gene, in HIV infection; HIV TAR, HIV TAR, human immunodeficiency virus transactivator response element gene, in HIV infection; C—C chemokine receptor (CCR5) in HIV infection; Rous sarcoma virus (RSV) nucleocapsid protein in RSV infection, liver-specific microRNA (miR-122) in hepatitis C virus infection; p53, acute kidney injury or delayed graft function kidney transplant or kidney injury acute renal failure; protein kinase N3 (PKN3) in advance recurrent or metastatic solid malignancies; LMP2, LMP2 also known as proteasome subunit beta-type 9 (PSMB 9), metastatic melanoma; LMP7, also known as proteasome subunit beta-type 8 (PSMB 8), metastatic melanoma; MECL1 also known as proteasome subunit beta-type 10 (PSMB 10), metastatic melanoma; vascular endothelial growth factor (VEGF) in solid tumors; kinesin spindle protein in solid tumors, apoptosis suppressor B-cell CLL/lymphoma (BCL-2) in chronic myeloid leukemia; ribonucleotide reductase M2 (RRM2) in solid tumors; Furin in solid tumors; polo-like kinase 1 (PLK1) in liver tumors, diacylglycerol acyltransferase 1 (DGAT1) in hepatitis C infection, beta-catenin in familial adenomatous polyposis; beta2 adrenergic receptor, glaucoma; RTP801/Redd1 also known as DAN damage-inducible transcript 4 protein, in diabetic macular oedma (DME) or age-related macular degeneration; vascular endothelial growth factor receptor I (VEGFR1) in age-related macular degeneration or choroidal neivascularization, caspase 2 in non-arteritic ischaemic optic neuropathy; Keratin 6A N17K mutant protein in pachyonychia congenital; influenza A virus genome/gene sequences in influenza infection; severe acute respiratory syndrome (SARS) coronavirus genome/gene sequences in SARS infection; respiratory syncytial virus genome/gene sequences in respiratory syncytial virus infection; Ebola filovirus genome/gene sequence in Ebola infection; hepatitis B and C virus genome/gene sequences in hepatitis B and C infection; herpes simplex virus (HSV) genome/gene sequences in HSV infection, coxsackievirus B3 genome/gene sequences in coxsackievirus B3 infection; silencing of a pathogenic allele of a gene (allele-specific silencing) like torsin A (TOR1A) in primary dystonia, pan-class I and HLA-allele specific in transplant; or mutant rhodopsin gene (RHO) in autosomal dominantly inherited retinitis pigmentosa (adRP). 
     
     
         27 . The method of  claim 1  or  3 , wherein the mammal has a lung disease (e.g., cystic fibrosis), a bleeding disorder (e.g., hemophilia A or hemophilia B with or without inhibitors), thalassemia, a blood disorder (e.g., anemia), Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis (ALS), epilepsy, lysosomal storage diseases, a copper or iron accumulation disorders (e.g., Wilson's or Menkes disease) lysosomal acid lipase deficiency, a neurological or neurodegenerative disorder, cancer, type 1 or type 2 diabetes, Gaucher's disease, Hurler's disease, adenosine deaminase deficiency, a metabolic defect (e.g., glycogen storage diseases), a retinal degenerative disease (such as RPE65 deficiency, choroideremia, and other diseases of the eye), a disease of solid organs (e.g., brain, liver, kidney, heart), or an infectious viral (e.g., hepatitis B and C, HIV, etc.), bacterial or fungal disease. 
     
     
         28 . The method of  claim 1  or  3 , wherein the expression control element comprises a constitutive or regulatable control element. 
     
     
         29 . The method of  claim 1  or  3 , wherein the expression control element comprises a tissue-specific expression control element or promoter. 
     
     
         30 . The method of  claim 1  or  3 , wherein the AAV vector is delivered intravenously, intraarterially, intramuscularly, subcutaneously, orally, by intubation, via catheter, dermally, ultra-cranially, via inhalation, intra-cavity, or mucosally. 
     
     
         31 . The method of  claim 1  or  3 , wherein the mammal is human. 
     
     
         32 . The method of  claim 1  or  3 , wherein the mammal is sero-positive for an AAV serotype other than AAV-Rh74. 
     
     
         33 . The method of  claim 1  or  3 , wherein the mammal is sero-positive for an AAV serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10 or AAV11. 
     
     
         34 . The method of  claim 1  or  3 , wherein the mammal is sero-negative for AAV-Rh74. 
     
     
         35 . The method of  claim 1  or  3 , further comprising administering empty capsid AAV. 
     
     
         36 . The method of  claim 1  or  3 , further comprising administering empty capsid AAV-Rh74. 
     
     
         37 . The method of  claim 4 , wherein the VP1, VP2 or VP3 sequence has 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, conservative, non-conservative, or conservative and non-conservative amino acid substitutions. 
     
     
         38 . The method of  claim 1  or  3 , wherein the AAV comprises a pharmaceutical composition. 
     
     
         39 . The method of  claim 38 , wherein the pharmaceutical composition comprises empty capsid AAV. 
     
     
         40 . The method of  claim 38 , wherein the pharmaceutical composition comprises empty capsid AAV-Rh74.