# Patent

## Title
Composition and methods for highly efficient gene transfer using AAV capsid variants

## Abstract

Compositions and methods for AAV mediated gene therapy are disclosed. AAV vectors comprise protein capsid variants comprising therapeutically beneficial transgenes. AAV variants are provided which exhibit increased transduction efficiency when compared to AAV serotypes (e.g., AAV1, AAV2, AAV8, AAV-rh74), which lack the modifications disclosed herein. Such improved vectors are useful for transduction of a variety of tissues.

## Background
RELATED APPLICATIONS
This application is the National Phase of International Application No. PCT/US2013/037170, filed Apr. 18, 2013, which designated the U.S. and that International Application was published under PCT Article 21(2) in English, which claims priority to U.S. Provisional Application No. 61/635,273, filed Apr. 18, 2012 and U.S. Provisional Application No. 61/794,995, filed Mar. 15, 2013, all of which applications are expressly incorporated herein by reference in their entirety.


SEQUENCE LISTING
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Oct. 14, 2014, is named CHOP_0434479_SEQLIST.txt and is 34,266 bytes in size.
FIELD OF THE INVENTION
This application relates to the fields of gene therapy and molecular biology. More specifically, this invention provides adeno-associated viral vectors comprising protein capsid variants which improve the transduction efficiency of AAV vectors comprising therapeutically beneficial transgenes.
BACKGROUND OF THE INVENTION
Several publications and patent documents are cited throughout the specification in order to describe the state of the art to which this invention pertains. Each of these citations is incorporated herein by reference as though set forth in full.
Adeno-associated virus (AAV) is a small (20 nm), replication-defective, non-enveloped virus. Many distinct AAV serotypes have been characterized in human and nonhuman primates. The AAV genome is comprised of single-stranded DNA with 145 bp inverted terminal repeats (ITRs) at both ends. There are two open reading frames (ORFs), rep and cap. While the rep products are essential for AAV replication, 3 capsid proteins (VP1, VP2, and VP3) are expressed from the cap gene. VP1, VP2 and VP3 come together at 1:1:10 ratio to form an icosahedral capsid (Xie Q et al, 2002). During recombinant AAV (rAAV) vector production, an expression cassette flanked by ITRs is packaged into AAV capsid. The genes required for replication of AAV are not included in the cassette. Recombinant AAV is considered the safest and one of the most widely used viral vectors for in vivo gene transfer. The vectors can infect cells from multiple tissue types providing strong and persistent transgene expression. They are also non-pathogenic and have a low immunogenicity profile (High K A, 2011).
One of the immediate goals for gene therapy trials is optimizing vectors to maximize tissue transduction while minimizing the vector dose. Upon entry into the cell, AAV capsid proteins are subject to proteasome mediated degradation. Phosphorylation of surface-exposed tyrosine residues of AAV capsid represents one of the first steps that leads to degradation of the virus via the ubiquitin-proteasome pathway (Zhong L et al, 2007). Most of the regulated proteolysis in the cell occurs through this pathway. Ubiquitin is a small protein ( ̃8.5 kDa) that can be found in all eukaryotic cells. Ubiquitin is attached to the side-chain of amino-acids of a substrate protein. After additional ubiquitin proteins are attached to the substrate via the initially attached ubiquitin, a polyubiquitin chain is formed and the substrate is marked for degradation (Thrower J S et al 2000, Peng J et al 2003, Bedford L et al 2011). It has been shown that mutation of surface-exposed tyrosine residues leads to an increase in transduction efficiency of AAV2 vectors (Zhong L et al, 2008). More recently, several groups have shown that the strategy is effective also with other AAV serotypes in several tissues, including AAV serotype 6 and 8.
Clearly, a need exists in the art for compositions and methods which improve the transduction of AAV carrying clinically important transgenes in patients in need thereof.
SUMMARY OF THE INVENTION
In accordance with the present invention, novel AAV variants are provided which exhibit increased transduction efficiency when compared to AAV serotypes (e.g., AAV1, AAV2, AAV8, AAV-rh74), which lack the modifications disclosed herein. Such improved vectors are useful for transduction of a variety of tissues, including liver, muscle, brain, and retina.
In one embodiment, an adeno-associated virus (AAV) vector comprising an altered VP1 capsid protein is provided, the altered capsid protein comprising lysine residue substitutions, thereby reducing ubiquination of the capsid and increasing the transduction efficiency of variant AAV into target tissues and cells. In one embodiment, the vector further comprises a heterologous nucleic acid, (e.g., a minigene comprising AAV inverted terminal repeats and a heterologous nucleic acid sequence) operably linked to regulatory sequences which direct expression of a product from the heterologous nucleic acid sequence in a host cell. In a preferred embodiment, the AAV vector comprises one or more lysine substitutions in VP1 as provided in the tables set forth herein. In another embodiment, the AAV vector is of the AAV8 serotype and contains an alteration provided in Table 3.
In a preferred embodiment, the AAV vectors of the invention comprising the variant capsid proteins are useful for expression of therapeutic peptides or therapeutic nucleic acids. Such peptides include, without limitation, an anti-viral RNAi molecule, Factor VIII, Factor IX or a functional fragment thereof. Additional expression products include for example, IgG, IgM, IgA, IgD, IgE, chimeric immunoglobulins, humanized antibodies, or single chain antibodies. In one aspect the expression product is an RNAi that is useful for inhibiting HCV infection and replication. In another embodiment, the expression product is an antisense nucleic acid useful for down modulating a target cell of interest.
In another embodiment of the invention, a pharmaceutical composition comprising the variant AAV vectors of the invention in a biologically compatible carrier is provided. Also encompassed by the present invention are cell cultures comprising the vectors disclosed herein.
The invention also encompasses a method of delivering a transgene to a cell in a subject, said method comprising the step of contacting the cell with an AAV vector as disclosed herein, wherein said AAV vector comprises the transgene, wherein the presence of lysine substitution in the VP1 capsid sequence in said vector is associated with reduced ubiquitination and increased transduction efficiency.
In a final aspect, the invention provides decoy viral variants that are inefficient at infecting cells but are effective to block antibody neutralization of viral variants carrying beneficial transgenes due to the structural similarities of the two viral variants. Exemplary capsid variants for this purpose include for example, K38R, K143R, KS10R and K709R.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1: Lysines on the surface of AAV1, AAV2 and AAV8: PDB numbers of AAV serotypes used here are as follows: AAV1: 3NG9, AAV2: 1LP3, and AAV8: 2QA0. The arrows represent the respective Lysine residues. (A) There are 11 Lysines on the surface of AAV1 VP3. Residue colors are as follows: K258 red, K459 blue, K491 yellow, K493 magenta, K508 cyan, K528 dark salmon, K533 light green, K545 light blue (slate), K567 dark salmon, K666 light cyan, K707 gray. (B) There are 10 Lysines on the surface of AAV2 VP3. Residue colors are as follows: K258 red, K490 yellow, K507 cyan, K527 dark salmon, K532 light green, K544 light blue (slate), K549 light yellow, K556 light magenta, K665 light cyan, K706 gray (C) There are 8 Lysines on the surface of AAV8 VP3. Residue colors are as follows: K259 red, K333 green, K510 cyan, K530 dark salmon, K547 light blue (slate), K569 dark salmon, K668 light cyan, K709 gray. Note that K528 and K567 of AAV1 and K530 and K569 of AAV8 are side by side in the structure and showed with the same color.
FIG. 2: Several Lysine residues of AAV8 capsid were mutated to Arginine. Blood from the animals was collected 8 weeks after virus injection via tail vein. hF.IX levels are detected by ELISA (A) The residues that are predicted to be ubiqutinated by the software with high and medium confidence levels were mutated to arginine. 2.5×1010 virus particles per mouse were injected via tail vein (B,C) The residues that are predicted with low confidence to be ubiqutinated by the software were mutated to arginine. 2.5×109 virus particles per mouse were injected via tail vein. (B) K569R and K668R capsid mutations (C) Affect of K38R, K143R, K259R, K510R, K547R capsid mutations are compared to affect of K530R mutation.
FIG. 3: Combination of the K to R capsid mutations (A) Combination of K137R, K33R and K530R mutations are still higher than the wild type but not statistically different from the K530R. (B) K709R mutation negatively affects the AAV8 transduction, Addition of K709R mutation to K(137/333/530)R mutant also decreases the transduction of the virus. C) Combination of multiple Lysine to arginine mutations does not increase the transduction rate. (D) Combination of three lysine to arginine residues with four or six tyrosine to phenylalanine residues decreases the transduction rate.
FIG. 4: AAV1 transduction (A) CTL killing of HHL5-B7 hepatocytes transduced with AAV-1 lysine mutants at three different MOIs 5K, 50K and 500K. Peptide (IPQYGYLTL (SEQ ID NO:61) for AAV1; VPQYGYLTL (SEQ ID NO:62) for AAV2) was used as a positive control. LDH release correlates with the cell killing. (B) Total number of GFP positive cells and GFP expression was compared among different constructs at 50K and 500K MOIs.
FIG. 5: AAV2 transduction: A) AAV2 K137R, K527R or K532R mutants were compared to WT AAV2 in terms of HHL5 cell line transduction rate. The cells were transfected at 10K, 50K, 100K and 500K MOIs and checked 24 hours later for GFP expression. B) A graph showing cytotoxicity as measured by LDL release of variants tested.
FIG. 6: CTL assay in which target hepatocyte cells were transduced with AAV-2 vector at increasing concentrations and then incubated with HLA-matched effector cells. AAV vectors encoded wild-type AAV-2 capsid or single lysine mutations as indicated. Effectors were derived from PBMC expanded in vitro against AAV-2 MHC Class I epitope VPQYGYLTL (SEQ ID NO:62) and effector-to-target ratio was 10:1. Results are expressed as percentage of CTL activity (% cytotoxicity compared to cells treated with 10% SDS as a maximum cytotoxicity control after background subtraction) with respect to the wild type vector.
FIG. 7: RH74 data: Human F.IX transgene expression levels in plasma measured by an ELISA specific for human F.IX.A) Definition of TMR=K(137/333/530)R, Definition of HMF=Y(253/275/447/703/707/733)F. B) Definition of HMR: K(137/259/333/530/552/569)R, Definition of 195/202: G195A+L199V+S201P+G202N. While HMR+195/202, HMR+195/202+K(38)R, HMR+195/202+K(51)R, HMR+195/202+K(61)R, and HMR+195/202+K(77)R produced higher hFIX production upon injection to mice, HMR+195/202+K(122/123)R or HMR+195/202+K(142/413)R injection did not produce any detectable hFIX at all. C): RHM13_1 mutant produced similar hFIX levels compared to Rh74 WT whereas hFIX levels derived from RHM17_1-treated mice were barely above background levels. D) RHM14_2 mutant produced similar hFIX levels compared to Rh74 WT; RHM15_1 performance was in-between that of AAV8 and AAVrh74 WT.



DETAILED DESCRIPTION OF THE INVENTION
In accordance with the present invention, we have found that mutating the lysine residues on AAV capsids to arginine residues increases AAV transduction efficiency. Our initial experiments showed that a single substitution of a lysine residue predicted to be a target for ubiquitination resulted in higher levels of expression of the human factor IX (FIX) transgene in mice compared to animals receiving unmodified AAV vectors. The AAV lysine mutants described herein could be used to advantage to generate vectors that target the liver, CNS, muscle, and other organs with higher efficiency compared to the wild type AAV capsids. Thus, this discovery can be used to develop therapeutics to treat hemophilia A, B, Huntington's disease, and virtually any other disease that requires increased transduction levels of desirable transgenes into a target tissue of interest.
The following definitions are provided to facilitate an understanding of the present invention.
I. Definitions
“Gene therapy” is the insertion of genes into an individual's cells and/or tissues to treat a disease, commonly hereditary diseases wherein a defective mutant allele is replaced or supplemented with a functional one.
“Adeno-associated viruses”, from the parvovirus family, are small viruses with a genome of single stranded DNA. These viruses can insert genetic material at a specific site on chromosome 19 and are preferred because they are not associated with pathogenic disease in humans.
A “therapeutic” peptide or protein is a peptide or protein that may alleviate or reduce symptoms that result from an absence or defect in a protein in a cell or subject. Alternatively, a “therapeutic” peptide or protein is one that otherwise confers a benefit to a subject, e.g., anti-cancer effects. Therapeutic peptides and proteins include, but are not limited to, CFTR (cystic fibrosis transmembrane regulator protein), dystrophin (including the protein product of dystrophin mini-genes, see, e.g, Vincent et al., (1993) Nature Genetics 5:130), utrophin (Tinsley et al., (1996) Nature 384:349), clotting factors (Factor XIII, Factor IX, Factor X, etc.), monoclonal antibodies (Lewis et al., 2002), erythropoietin, the LDL receptor, lipoprotein lipase, ornithine transcarbamylase, β-globin, α-globin, spectrin, α-antitrypsin, adenosine deaminase, hypoxanthine guanine phosphoribosyl transferase, β-glucocerebrosidase, sphingomyelinase, lysosomal hexosaminidase, branched-chain keto acid dehydrogenase, hormones, growth factors (e.g., insulin-like growth factors 1 and 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, and the like), cytokines (e.g., α-interferon, β-interferon, interferon-γ, interleukin-2, interleukin-4, interleukin 12, granulocyte-macrophage colony stimulating factor, lymphotoxin), suicide gene products (e.g., herpes simplex virus thymidine kinase, cytosine deaminase, diphtheria toxin, cytochrome P450, deoxycytidine kinase, and tumor necrosis factor), proteins conferring resistance to a drug used in cancer therapy, tumor suppressor gene products (e.g., p53, Rb, Wt-1, NF1, VHL, APC, and the like), and any other peptide or protein that has a therapeutic effect in a subject in need thereof.
Further exemplary therapeutic peptides or proteins include those that may be used in the treatment of a disease condition including, but not limited to, cystic fibrosis (and other diseases of the lung), hemophilia A, hemophilia B, thalassemia, anemia and other blood disorders, AIDS, Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, epilepsy, and other neurological disorders, cancer, diabetes mellitus, muscular dystrophies (e.g., Duchenne, Becker), Gaucher's disease, Hurler's disease, adenosine deaminase deficiency, glycogen storage diseases and other metabolic defects, retinal degenerative diseases (and other diseases of the eye), and diseases of solid organs (e.g., brain, liver, kidney, heart).
The term “promoters” or “promoter” as used herein can refer to a DNA sequence that is located adjacent to a DNA sequence that encodes a recombinant product. A promoter is preferably linked operatively to an adjacent DNA sequence. A promoter typically increases an amount of recombinant product expressed from a DNA sequence as compared to an amount of the expressed recombinant product when no promoter exists. A promoter from one organism can be utilized to enhance recombinant product expression from a DNA sequence that originates from another organism. For example, a vertebrate promoter may be used for the expression of jellyfish GFP in vertebrates. In addition, one promoter element can increase an amount of recombinant products expressed for multiple DNA sequences attached in tandem. Hence, one promoter element can enhance the expression of one or more recombinant products. Multiple promoter elements are well-known to persons of ordinary skill in the art.
In one embodiment, high-level constitutive expression will be desired. Examples of such promoters include, without limitation, the retroviral Rous sarcoma virus (RSV) LTR promoter/enhancer, the cytomegalovirus (CMV) immediate early promoter/enhancer (see, e.g., Boshart et al, Cell, 41:521-530 (1985)), the SV40 promoter, the dihydrofolate reductase promoter, the cytoplasmic β-actin promoter and the phosphoglycerol kinase (PGK) promoter.
In another embodiment, inducible promoters may be desired. Inducible promoters are those which are regulated by exogenously supplied compounds, either in cis or in trans, including without limitation, the zinc-inducible sheep metallothionine (MT) promoter; the dexamethasone (Dex)-inducible mouse mammary tumor virus (MMTV) promoter; the T7 polymerase promoter system (WO 98/10088); the tetracycline-repressible system (Gossen et al, Proc. Natl. Acad. Sci. USA, 89:5547-5551 (1992)); the tetracycline-inducible system (Gossen et al., Science, 268:1766-1769 (1995); see also Harvey et al., Curr. Opin. Chem. Biol., 2:512-518 (1998)); the RU486-inducible system (Wang et al., Nat. Biotech., 15:239-243 (1997) and Wang et al., Gene Ther., 4:432-441 (1997)]; and the rapamycin-inducible system (Magari et al., J. Clin. Invest., 100:2865-2872 (1997); Rivera et al., Nat. Medicine. 2:1028-1032 (1996)). Other types of inducible promoters which may be useful in this context are those which are regulated by a specific physiological state, e.g., temperature, acute phase, or in replicating cells only.
In another embodiment, the native promoter for the transgene or nucleic acid sequence of interest will be used. The native promoter may be preferred when it is desired that expression of the transgene or the nucleic acid sequence should mimic the native expression. The native promoter may be used when expression of the transgene or other nucleic acid sequence must be regulated temporally or developmentally, or in a tissue-specific manner, or in response to specific transcriptional stimuli. In a further embodiment, other native expression control elements, such as enhancer elements, polyadenylation sites or Kozak consensus sequences may also be used to mimic the native expression.
In one embodiment, the recombinant viral genome comprises a transgene operably linked to a tissue-specific promoter. For instance, if expression in skeletal muscle is desired, a promoter active in muscle may be used. These include the promoters from genes encoding skeletal α-actin, myosin light chain 2A, dystrophin, muscle creatine kinase, as well as synthetic muscle promoters with activities higher than naturally-occurring promoters. See Li et al., Nat. Biotech., 17:241-245 (1999). Examples of promoters that are tissue-specific are known for liver albumin, Miyatake et al. J. Virol., 71:5124-32 (1997); hepatitis B virus core promoter, Sandig et al., Gene Ther. 3:1002-9 (1996); alpha-fetoprotein (AFP), Arbuthnot et al., Hum. Gene Ther., 7:1503-14 (1996)], bone (osteocalcin, Stein et al., Mol. Biol. Rep., 24:185-96 (1997); bone sialoprotein, Chen et al., J. Bone Miner. Res. 11:654-64 (1996)), lymphocytes (CD2, Hansal et al., J. Immunol., 161:1063-8 (1998); immunoglobulin heavy chain; T cell receptor a chain), neuronal (neuron-specific enolase (NSE) promoter, Andersen et al. Cell. Mol. Neurobiol., 13:503-15 (1993); neurofilament light-chain gene, Piccioli et al., Proc. Natl. Acad. Sci. USA, 88:5611-5 (1991); the neuron-specific vgf gene, Piccioli et al., Neuron, 15:373-84 (1995)]; among others.
The term “enhancers” or “enhancer” as used herein can refer to a DNA sequence that is located adjacent to the DNA sequence that encodes a recombinant product. Enhancer elements are typically located upstream of a promoter element or can be located downstream of or within a DNA coding sequence (e.g., a DNA sequence transcribed or translated into a recombinant product or products). Hence, an enhancer element can be located 100 base pairs, 200 base pairs, or 300 or more base pairs upstream or downstream of a DNA sequence that encodes recombinant product Enhancer elements can increase an amount of recombinant product expressed from a DNA sequence above increased expression afforded by a promoter element. Multiple enhancer elements are readily available to persons of ordinary skill in the art.
“Nucleic acid” or a “nucleic acid molecule” as used herein refers to any DNA or RNA molecule, either single or double stranded and, if single stranded, the molecule of its complementary sequence in either linear or circular form. In discussing nucleic acid molecules, a sequence or structure of a particular nucleic acid molecule may be described herein according to the normal convention of providing the sequence in the 5′ to 3′ direction. With reference to nucleic acids of the invention, the term “isolated nucleic acid” is sometimes used. This term, when applied to DNA, refers to a DNA molecule that is separated from sequences with which it is immediately contiguous in the naturally occurring genome of the organism in which it originated. For example, an “isolated nucleic acid” may comprise a DNA molecule inserted into a vector, such as a plasmid or virus vector, or integrated into the genomic DNA of a prokaryotic or eukaryotic cell or host organism.
A “vector” is a replicon, such as a plasmid, cosmid, bacmid, phage or virus, to which another genetic sequence or element (either DNA or RNA) may be attached so as to bring about the replication of the attached sequence or element.
An “expression operon” refers to a nucleic acid segment that may possess transcriptional and translational control sequences, such as promoters, enhancers, translational start signals (e.g., ATG or AUG codons), polyadenylation signals, terminators, and the like, and which facilitate the expression of a polypeptide coding sequence in a host cell or organism.
The terms “transform”, “transfect”, “transduce”, shall refer to any method or means by which a nucleic acid is introduced into a cell or host organism and may be used interchangeably to convey the same meaning. Such methods include, but are not limited to, transfection, electroporation, microinjection, infection, PEG-fusion and the like.
The introduced nucleic acid may or may not be integrated (covalently linked) into nucleic acid of the recipient cell or organism. In bacterial, yeast, plant and mammalian cells, for example, the introduced nucleic acid may be maintained as an episomal element or independent replicon such as a plasmid. Alternatively, the introduced nucleic acid may become integrated into the nucleic acid of the recipient cell or organism and be stably maintained in that cell or organism and further passed on to or inherited by progeny cells or organisms of the recipient cell or organism. Finally, the introduced nucleic acid may exist in the recipient cell or host organism only transiently.
The term “selectable marker gene” refers to a gene that when expressed confers a selectable phenotype, such as antibiotic resistance, on a transformed cell or plant.
The term “operably linked” means that the regulatory sequences necessary for expression of the coding sequence are placed in the DNA molecule in the appropriate positions relative to the coding sequence so as to effect expression of the coding sequence. This same definition is sometimes applied to the arrangement of transcription units and other transcription control elements (e g enhancers) in an expression vector.
The term “oligonucleotide” as used herein refers to sequences, primers and probes of the present invention, and is defined as a nucleic acid molecule comprised of two or more ribo- or deoxyribonucleotides, preferably more than three. The exact size of the oligonucleotide will depend on various factors and on the particular application and use of the oligonucleotide.
The phrase “specifically hybridize” refers to the association between two single-stranded nucleic acid molecules of sufficiently complementary sequence to permit such hybridization under pre-determined conditions generally used in the art (sometimes termed “substantially complementary”). In particular, the term refers to hybridization of an oligonucleotide with a substantially complementary sequence contained within a single-stranded DNA or RNA molecule of the invention, to the substantial exclusion of hybridization of the oligonucleotide with single-stranded nucleic acids of non-complementary sequence.
The term “primer” as used herein refers to a DNA oligonucleotide, either single-stranded or double-stranded, either derived from a biological system, generated by restriction enzyme digestion, or produced synthetically which, when placed in the proper environment, is able to functionally act as an initiator of template-dependent nucleic acid synthesis. When presented with an appropriate nucleic acid template, suitable nucleoside triphosphate precursors of nucleic acids, a polymerase enzyme, suitable cofactors and conditions such as a suitable temperature and pH, the primer may be extended at its 3′ terminus by the addition of nucleotides by the action of a polymerase or similar activity to yield a primer extension product. The primer may vary in length depending on the particular conditions and requirement of the application. For example, in diagnostic applications, the oligonucleotide primer is typically 15-25 or more nucleotides in length. The primer must be of sufficient complementarity to the desired template to prime the synthesis of the desired extension product, that is, to be able to anneal with the desired template strand in a manner sufficient to provide the 3′ hydroxyl moiety of the primer in appropriate juxtaposition for use in the initiation of synthesis by a polymerase or similar enzyme. It is not required that the primer sequence represent an exact complement of the desired template. For example, a non-complementary nucleotide sequence may be attached to the 5′ end of an otherwise complementary primer. Alternatively, non-complementary bases may be interspersed within the oligonucleotide primer sequence, provided that the primer sequence has sufficient complementarity with the sequence of the desired template strand to functionally provide a template-primer complex for the synthesis of the extension product.
Polymerase chain reaction (PCR) has been described in U.S. Pat. Nos. 4,683,195, 4,800,195, and 4,965,188, the entire disclosures of which are incorporated by reference herein.
The term “isolated” may refer to a compound or complex that has been sufficiently separated from other compounds with which it would naturally be associated. “Isolated” is not meant to exclude artificial or synthetic mixtures with other compounds or materials, or the presence of impurities that do not interfere with fundamental activity or ensuing assays, and that may be present, for example, due to incomplete purification, or the addition of stabilizers.
The term “immune response” is meant to refer to any response to an antigen or antigenic determinant by the immune system of a vertebrate subject. Exemplary immune responses include humoral immune responses (e.g. production of antigen-specific antibodies) and cell-mediated immune responses (e.g. lymphocyte proliferation), as defined herein below.
II. Methods of Using and Methods of Administration of the Variant Adenoassociated Viral Vectors of the Invention
The methods of the present invention provide a means for delivering heterologous nucleic acid sequences into a broad range of host cells, including both dividing and non-dividing cells. The vectors and other reagents, methods and pharmaceutical formulations of the present invention are additionally useful in a method of administering a protein or peptide to a subject in need thereof, as a method of treatment or otherwise. In this manner, the protein or peptide may thus be produced in vivo in the subject. The subject may be in need of the protein or peptide because the subject has a deficiency of the protein or peptide, or because the production of the protein or peptide in the subject may impart some therapeutic effect, as a method of treatment or otherwise, and as explained further below.
In general, the present invention may be employed to deliver any foreign nucleic acid with a biological effect to treat or ameliorate the symptoms associated with any disorder related to gene expression. Illustrative disease states include, but are not limited to: cystic fibrosis (and other diseases of the lung), hemophilia A, hemophilia B, thalassemia, anemia and other blood coagulation disorders, AIDs, Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, epilepsy, and other neurological disorders, cancer, diabetes mellitus, muscular dystrophies (e.g., Duchenne, Becker), Gaucher's disease, Hurler's disease, adenosine deaminase deficiency, glycogen storage diseases and other metabolic defects, retinal degenerative diseases (and other diseases of the eye), diseases of solid organs (e.g., brain, liver, kidney, heart), and the like.
In addition, the present invention may be employed to deliver nucleic acids encoding monoclonal antibodies or fragments thereof that are known to provide beneficial biological effects to treat or ameliorate the symptoms associated with cancers, infectious diseases, and autoimmune diseases such as rheumatoid arthritis. Other sequences may encode for example cytokines such as interferon-alpha that may modulate the course of a disease.
Gene transfer has substantial potential use in understanding and providing therapy for disease states. There are a number of inherited diseases in which defective genes are known and have been cloned. In some cases, the function of these cloned genes is known. In general, the above disease states fall into two classes: deficiency states, usually of enzymes, which are generally inherited in a recessive manner, and unbalanced states, at least sometimes involving regulatory or structural proteins, which are inherited in a dominant manner. For deficiency state diseases, gene transfer could be used to bring a normal gene into affected tissues for replacement therapy, as well as to create animal models for the disease using antisense mutations. For unbalanced disease states, gene transfer could be used to create a disease state in a model system, which could then be used in efforts to counteract the disease state. Thus the methods of the present invention permit the treatment of genetic diseases. As used herein, a disease state is treated by partially or wholly remedying the deficiency or imbalance that causes the disease or makes it more severe. The use of site-specific integration of nucleic sequences to cause mutations or to correct defects is also possible.
Finally, the instant invention finds further use in diagnostic and screening methods, whereby a gene of interest is transiently or stably expressed in a cell culture system, or alternatively, a transgenic animal model.
III. Subjects, Pharmaceutical Formulations, Vaccines, and Modes of Administration
The present invention finds use in both veterinary and medical applications. Suitable subjects include both avians and mammals, with mammals being preferred. The term “avian” as used herein includes, but is not limited to, chickens, ducks, geese, quail, turkeys and pheasants. The term “mammal” as used herein includes, but is not limited to, humans, bovines, ovines, caprines, equines, felines, canines, lagomorphs, etc. Human subjects are the most preferred. Human subjects include fetal, neonatal, infant, juvenile and adult subjects.
In particular embodiments, the present invention provides a pharmaceutical composition comprising a virus particle of the invention in a pharmaceutically-acceptable carrier or other medicinal agents, pharmaceutical agents, carriers, adjuvants, diluents, etc. For injection, the carrier will typically be a liquid. For other methods of administration, the carrier may be either solid or liquid, such as sterile, pyrogen-free water or sterile pyrogen-free phosphate-buffered saline solution. For inhalation administration, the carrier will be respirable, and will preferably be in solid or liquid particulate form. As an injection medium, it is preferred to use water that contains the additives usual for injection solutions, such as stabilizing agents, salts or saline, and/or buffers.
In other embodiments, the present invention provides a pharmaceutical composition comprising a cell in which an AAV provirus is integrated into the genome in a pharmaceutically-acceptable carrier or other medicinal agents, pharmaceutical agents, carriers, adjuvants, diluents, etc.
By “pharmaceutically acceptable” it is meant a material that is not biologically or otherwise undesirable, e.g., the material may be administered to a subject without causing any undesirable biological effects. Thus, such a pharmaceutical composition may be used, for example, in transfection of a cell ex vivo or in administering a viral particle or cell directly to a subject.
The present invention further provides a method of delivering a nucleic acid to a cell. For in vitro methods, the virus -may be administered to the cell by standard viral transduction methods, as are known in the art. Preferably, the virus particles are added to the cells at the appropriate multiplicity of infection according to standard transduction methods appropriate for the particular target cells. Titers of virus to administer can vary, depending upon the target cell type and the particular virus vector, and may be determined by those of skill in the art without undue experimentation. Alternatively, administration of a parvovirus vector of the present invention can be accomplished by any other means known in the art.
Recombinant virus vectors are preferably administered to the cell in a biologically-effective amount. A “biologically-effective” amount of the virus vector is an amount that is sufficient to result in infection (or transduction) and expression of the heterologous nucleic acid sequence in the cell. If the virus is administered to a cell in vivo (e.g., the virus is administered to a subject as described below), a “biologically-effective” amount of the virus vector is an amount that is sufficient to result in transduction and expression of the heterologous nucleic acid sequence in a target cell.
The cell to be administered the inventive virus vector may be of any type, including but not limited to neural cells (including cells of the peripheral and central nervous systems, in particular, brain cells), lung cells, retinal cells, epithelial cells (e.g., gut and respiratory epithelial cells), muscle cells, pancreatic cells (including islet cells), hepatic cells, myocardial cells, bone cells (e.g., bone marrow stem cells), hematopoietic stem cells, spleen cells, keratinocytes, fibroblasts, endothelial cells, prostate cells, germ cells, and the like. Alternatively, the cell may be any progenitor cell. As a further alternative, the cell can be a stem cell (e.g., neural stem cell, liver stem cell). Moreover, the cells can be from any species of origin, as indicated above.
In particular embodiments of the invention, cells are removed from a subject, the parvovirus vector is introduced therein, and the cells are then replaced back into the subject. Methods of removing cells from subject for treatment ex vivo, followed by introduction back into the subject are known in the art. Alternatively, the rAAV vector is introduced into cells from another subject, into cultured cells, or into cells from any other suitable source, and the cells are administered to a subject in need thereof.
Suitable cells for ex vivo gene therapy include, but are not limited to, liver cells, neural cells (including cells of the central and peripheral nervous systems, in particular, brain cells), pancreas cells, spleen cells, fibroblasts (e.g., skin fibroblasts), keratinocytes, endothelial cells, epithelial cells, myoblasts, hematopoietic cells, bone marrow stromal cells, progenitor cells, and stem cells.
Dosages of the cells to administer to a subject will vary upon the age, condition and species of the subject, the type of cell, the nucleic acid being expressed by the cell, the mode of administration, and the like. Typically, at least about 102 to about 108, preferably about 102 to about 106 cells, will be administered per dose. Preferably, the cells will be administered in a “therapeutically-effective amount”.
A “therapeutically-effective” amount as used herein is an amount that is sufficient to alleviate (e.g., mitigate, decrease, reduce) at least one of the symptoms associated with a disease state. Alternatively stated, a “therapeutically-effective” amount is an amount that is sufficient to provide some improvement in the condition of the subject.
A further aspect of the invention is a method of treating subjects in vivo with the inventive virus particles. Administration of the parvovirus particles of the present invention to a human subject or an animal in need thereof can be by any means known in the art for administering virus vectors.
Exemplary modes of administration include oral, rectal, transmucosal, topical, transdermal, inhalation, parenteral (e.g., intravenous, subcutaneous, intradermal, intramuscular, and intraarticular) administration, and the like, as well as direct tissue or organ injection, alternatively, intrathecal, direct intramuscular, intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspenions in liquid prior to injection, or as emulsions. Alternatively, one may administer the virus in a local rather than systemic manner, for example in a depot or sustained-release formulation.
In particularly preformed embodiments of the invention, the nucleotide sequence of interest is delivered to the liver of the subject. Administration to the liver may be achieved by any method known in art, including, but not limited to intravenous administration, intraportal administration, intrabilary administration, intra-arterial administration, and direct injection into the liver parenchyma.
Preferably, the cells (e.g., liver cells) are infected by a recombinant parvovirus vector encoding a peptide or protein, the cells express the encoded peptide or protein and secrete it into the circulatory system in a therapeutically-effective amount (as defined above). Alternatively, the vector is delivered to and expressed by another cell or tissue, including but not limited to, brain, pancreas, spleen or muscle.
In other preferred embodiments, the inventive parovirus particles are administered intramuscularly, more preferably by intramuscular injection or by local administration (as defined above). In other preferred embodiments, the parovirus particles of the present invention are administered to the lungs.
The parovirus vector disclosed herein may be administered to the lungs of a subject by any suitable means, but are preferably administered by administering an aerosol suspension of respirable particles comprised of the inventive parvovirus vectors, which the subject inhales. The respirable particles may be liquid or solid. Aerosols of liquid particles comprising the inventive parvovirus vectors may be produced by any suitable means, such as with a pressure-driven aerosol nebulizer or an ultrasonic nebulizer, as is known to those of skill in art. See, e.g. U.S. Pat. No. 4,501,729. Aerosols of solid particles comprising the inventive virus vectors may likewise be produced with any solid particulate medicament aerosol generator, by techniques known in the pharmaceutical art.
Dosages of the inventive parvovirus particles will depend upon the mode of administration, the disease or condition to be treated, the individual subject's condition, the particular virus vector, and the gene to be delivered and can be determined in a routine manner. Exemplary doses for achieving therapeutic effects are virus titers of at least about 105, 106, 107, 108, 109, 1010, 1011, 1012, 1013, 1014, 1015, 1016 transducting units or more, preferably about 108 to 1013 transducting units, yet more preferably 1012 transducing units.
In summary, the parvovirus vectors, reagents, and methods of the present invention can be used to direct a nucleic acid to either dividing or non-dividing cells, and to stably express the heterologous nucleic acid therein. Using this vector system, it is now possible to introduce into cells, in vitro or in vivo, genes that encode proteins that affect cell physiology. The vectors of the present invention can thus be useful in gene therapy for disease states or for experimental modification of cell physiology.
The following example is provided to illustrate certain embodiments of the invention. It is not intended to limit the invention in anyway.
Example I
Lysine to Arginine Mutations Affect AAV Transduction Rate and MHC Delivery
Identification of Lysine Residues to be Targeted in AAV1 and AAV8 Vectors
We used the UbPred software to predict the possible ubiquitination sites on AAV1, AAV2, AAV8 and Rh74 capsid proteins (Radivojac P et al, 2010). UbPred software is available online at www-ubpred-org-index-html. The output of the analysis is the prediction of the lysine residues important for ubiquitination within the indicated AAV serotype capsid sequence. See FIG. 1 and Table 1. These are the following:












AAV1 Capsid Protein VP1 Sequence:


(SEQ ID NO: 1)


MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDDGRGLVLPGYKYLGPFNGL


 


DKGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHADAEFQERLQEDTSFGGNLGRAVF


 


QAKKRVLEPLGLVEEGAKTAPGKKRPVEQSPQEPDSSSGIGKTGQQPAKKRLNFGQTGDSES


 


VPDPQPLGEPPATPAAVGPTTMASGGGAPMADNNEGADGVGNASGNWHCDSTWLGDRVIT


 


TSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINN


 


NWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQGCLPP


 


FPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEEVPFHSSYAHS


 


QSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRV


 


SKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDEDKFFPMSGVMIFGKESAGAS


 


NTALDNVMITDEEEIKATNPVATERFGTVAVNFQSSSTDPATGDVHAMGALPGMVWQDRD


 


VYLQGPIWAKIPHTDGHFHPSPLMGGFGLKNPPPQILIKNTPVPANPPAEFSATKFASFITQYST


 


GQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYLTRP













Lysine





position
Score
Ubiquitinated





26
0.59
No



 


31
0.55
No



 


33
0.47
No



 


38
0.61
No



 


51
0.54
No



 


61
0.72
Yes
Medium confidence


 


77
0.63
Yes
Low confidence


 


84
0.72
Yes
Medium confidence


 


122
0.17
No



 


123
0.26
No



 


137
0.90
Yes
High confidence


 


142
0.62
Yes
Low confidence


 


143
0.81
Yes
Medium confidence


 


161
0.70
Yes
Medium confidence


 


168
0.25
No



 


169
0.26
No



 


258
0.49
No



 


310
0.14
No



 


315
0.15
No



 


322
0.48
No



 


459
0.81
Yes
Medium confidence


 


476
0.43
No



 


491
0.20
No



 


493
0.28
No



 


508
0.62
Yes
Low confidence


 


528
0.67
Yes
Low confidence


 


533
0.70
Yes
Medium confidence


 


545
0.65
Yes
Low confidence


 


567
0.66
Yes
Low confidence


 


621
0.50
No



 


641
0.50
No



 


650
0.45
No



 


666
0.58
No



 


689
0.65
Yes
Low confidence


 


693
0.65
Yes
Low confidence


 


707
0.78
Yes
Medium confidence










Legend










Label
Score range
Sensitivity
Specificity





Low confidence
0.62 < s < 0.69
0.464
0.903


 


Medium confidence 
0.69 < s < 0.84
0.346
0.950


 


High confidence
0.84 < s < 1.00
0.197
0.989



















Desirable mutants in AAV-1










ID
AAV-1 mutant







MUT1-1
K61R



MUT1-2
K84R



MUT1-3
K137R



MUT1-4
K143R



MUT1-5
K161R



MUT1-6
K459R



MUT1-7
K528R



MUT1-8
K533R



MUT1-9
K707R






















AAV8 capsid protein VP1 sequence:


(SEQ ID NO: 2)


MAADGYLPDWLEDNLSEGIREWWALKPGAPKPKANQQKQDDGRGLVLPGYKYLGPFNGL


 


DKGEPVNAADAAALEHDKAYDQQLQAGDNPYLRYNHADAEFQERLQEDTSFGGNLGRAVF


 


QAKKRVLEPLGLVEEGAKTAPGKKRPVEPSPQRSPDSSTGIGKKGQQPARKRLNFGQTGDSE


 


SVPDPQPLGEPPAAPSGVGPNTMAAGGGAPMADNNEGADGVGSSSGNWHCDSTWLGDRVI


 


TTSTRTWALPTYNNHLYKQISNGTSGGATNDNTYFGYSTPWGYFDFNRFHCHFSPRDWQRLI


 


NNNWGFRPKRLSFKLFNIQVKEVTQNEGTKTIANNLTSTIQVFTDSEYQLPYVLGSAHQGCLP


 


PFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFQFTYTFEDVPFHSSYAH


 


SQSLDRLMNPLIDQYLYYLSRTQTTGGTANTQTLGFSQGGPNTMANQAKNWLPGPCYRQQR


 


VSTTTGQNNNSNFAWTAGTKYHLNGRNSLANPGIAMATHKDDEERFFPSNGILIFGKQNAAR


 


DNADYSDVMLTSEEEIKTTNPVATEEYGIVADNLQQQNTAPQIGTVNSQGALPGMVWQNRD


 


VYLQGPIWAKIPHTDGNFHPSPLMGGFGLKHPPPQILIKNTPVPADPPTTFNQSKLNSFITQYST


 


GQVSVEIEWELQKENSKRWNPEIQYTSNYYKSTSVDFAVNTEGVYSEPRPIGTRYLTRNL













Lysine





position
Score
Ubiquitinated





26
0.52
No



 


31
0.51
No



 


33
0.16
No



 


38
0.62
Yes
Low confidence


 


51
0.56
No



 


61
0.68
Yes
Low confidence


 


77
0.65
Yes
Low confidence


 


122
0.17
No



 


123
0.32
No



 


137
0.92
Yes
High confidence


 


142
0.53
No



 


143
0.65
Yes
Low confidence


 


162
0.28
No



 


163
0.29
No



 


170
0.24
No



 


259
0.49
No



 


312
0.09
No



 


317
0.12
No



 


324
0.43
No



 


333
0.75
Yes
Medium confidence


 


478
0.59
No



 


510
0.50
No



 


530
0.71
Yes
Medium confidence


 


547
0.40
No



 


569
0.66
Yes
Low confidence


 


623
0.47
No



 


643
0.44
No



 


652
0.51
No



 


668
0.64
Yes
Low confidence


 


691
0.66
Yes
Low confidence


 


695
0.67
Yes
Low confidence


 


709
0.68
Yes
Low confidence










Legend










Label
Score range
Sensitivity
Specificity





Low confidence
0.62 < s < 0.69
0.464
0.903


 


Medium confidence
0.69 < s < 0.84
0.346
0.950


 


High confidence
0.84 < s < 1.00
0.197
0.989









Table 3 appended hereto provides the yield of vector obtained using the different capsid mutants, including AAV8 of the invention. The table also indicates whether the mutation resulted in increased, decreased or comparable transduction efficiencies when compared to wild type vectors of the same serotype.












AAV2 capsid protein VP1 sequence:


(SEQ ID NO: 3)


MAADGYLPDWLEDTLSEGIRQWWKLKPGPPPPKPAERHKDDSRGLVLPGYKYLGPFNGLDK


 


GEPVNEADAAALEHDKAYDRQLDSGDNPYLKYNHADAEFQERLKEDTSFGGNLGRAVFQA


 


KKRVLEPLGLVEEPVKTAPGKKRPVEHSPVEPDSSSGTGKAGQQPARKRLNFGQTGDADSVP


 


DPQPLGQPPAAPSGLGTNTMATGSGAPMADNNEGADGVGNSSGNVVHCDSTWMGDRVITTS


 


TRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNW


 


GFRPKRLNFKLFNIQVKEVTQNDGTTTIANNLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPA


 


DVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNETFSYTFEDVPFHSSYAHSQS


 


LDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPGPCYRQQRVSKT


 


SADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVLIFGKQGSEKTNV


 


DIEKVMITDEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGVLPGMVWQDRDVYL


 


QGPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPSTTFSAAKFASFITQYSTGQ


 


VSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVYSEPRPIGTRYLTRNL













Lysine





position
Score
Ubiquitinated





24
0.20
No



 


26
0.49
No



 


33
0.38
No



 


39
0.89
Yes 
High confidence


 


51
0.53
No



 


61
0.67
Yes 
Low confidence


 


77
0.68
Yes 
Low confidence


 


92
0.56
No



 


105
0.58
No



 


122
0.14
No



 


123
0.18
No



 


137
0.87
Yes
High confidence


 


142
0.58
No



 


143
0.77
Yes
Medium confidence


 


161
0.70
Yes
Medium confidence


 


169
0.31
No



 


258
0.51
No



 


309
0.14
No



 


314
0.17
No



 


321
0.46
No



 


490
0.73
Yes
Medium confidence


 


507
0.61
No



 


527
0.78
Yes
Medium confidence


 


532
0.75
Yes
Medium confidence


 


544
0.61
No



 


549
0.68
Yes
Low confidence


 


556
0.62
Yes
Low confidence


 


620
0.47
No



 


640
0.45
No



 


649
0.42
No



 


665
0.54
No



 


688
0.68
Yes
Low confidence


 


692
0.68
Yes
Low confidence


 


706
0.66
Yes
Low confidence










Legend











Score
Sensi-
Specif-


Label
range
tivity
icity





Low confidence
0.62 ≦ s ≦ 0.69 
0.464
0.903


 


Medium confidence
0.69 ≦ s ≦ 0.84 
0.346
0.950


 


High confidence
0.84 ≦ s ≦ 1.00 
0.197
0.989





















AAV-Rh74 capsid protein VP1 sequence


(SEQ ID NO: 4)


MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDNGRGLVLPGYKYLGPFNGL


 


DKGEPVNAADAAALEHDKAYDQQLQAGDNPYLRYNHADAEFQERLQEDTSEGGNLGRAVF


 


QAKKRVLEMMAESPVKTAPGKKRPVEPSPQRSPDSSTGIGKKGQQPAKKRLNFGQTGDSES


 


VPDPQPIGEPPAGPSGLGSGTMAAGGGAPMADNNEGADGVGSSSGNWHCDSTWLGDRVITT


 


STRTWALPTYNNHLYKQISNGTSGGSTNDNTYFGYSTPWGYEDENRETICHESPRDWQRLINN


 


NWGFRPKRLNFKLFNIQVKEVTQNEGTKTIANNLTSTIQVFTDSEYQLPYVLGSAHQGCLPPF


 


PADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFEFSYNFEDVPFHSSYAHS


 


QSLDRLMNPLIDQYLYYLSRTQSTGGTAGTQQLLFSQAGPNNMSAWAKNWLPGPCYRQQRV


 


STTLSQNNNSNFAWTGATKYHLNGRDSLVNPGVAMATHKDDEERFFPSSGVLMFGKQGAG


 


KDNVDYSSVMLTSEEEIKTTNPVATEQYGVVADNLQQQNAAPIVGAVNSQGALPGMVWQN


 


RDVYLQGPIWAKIPHTDGNFHPSPLMGGFGLKHPPPQILIKNTPVPADPPTTFNQAKLASFITQ


 


YSTGQVSVEIEWELQKENSKRWNPEIQYTSNYYKSTNVDFAVNTEGTYSEPRPIGTRYLTRNL













Lysine





position
Score
Ubiquitinated





26
0.60
No



 


31
0.53
No



 


33
0.27
No



 


38
0.23
No



 


51
0.38
No



 


61
0.68
Yes
Low confidence


 


77
0.65
Yes
Low confidence


 


122
0.17
No



 


123
0.30
No



 


137
0.90
Yes
High confidence


 


142
0.35
No



 


143
0.35
No



 


162
0.36
No



 


163
0.33
No



 


169
0.27
No



 


170
0.25
No



 


259
0.46
No



 


312
0.13
No



 


317
0.16
No



 


324
0.46
No



 


333
0.77
Yes
Medium confidence


 


478
0.51
No



 


510
0.49
No



 


530
0.67
Yes
Low confidence


 


547
0.52
No



 


552
0.69
Yes
Medium confidence


 


569
0.67
Yes
Low confidence


 


623
0.49
No



 


643
0.44
No



 


652
0.54
No



 


668
0.56
No



 


691
0.68
Yes
Low confidence


 


695
0.67
Yes
Low confidence


 


709
0.69
Yes
Medium confidence










Legend










Label
Score range
Sensitivity
Specificity





Low confidence
0.62 < s < 0.69
0.464
0.903


 


Medium confidence
0.69 < s < 0.84
0.346
0.950


 


High confidence
0.84 < s < 1.00
0.197
0.989



















Desirable mutants in AAV-rh74 (also see Table 3)










ID
AAV-rh74 mutant







Mut74-1
K26R



Mut74-2
K31R



Mut74-3
K33R



Mut74-4
K38R



Mut74-5
K51R



Mut74-6
K77R



Mut74-7
K137R



Mut74-8
K163R



Mut74-9
K169R



Mut74-10
K259R



Mut74-11
K333R



Mut74-12
K530R



Mut74-13
K547R



Mut74-14
K552R



Mut74-15
K569R



Mut74-16
K668R



Mut74-17
K691R



Mut74-18
K695R



Mut74-19
K709R










The following primer sets were utilized to create the lysine containing capsid variants of the invention:










Primers used for mutagenesis:







AAV1 primers:


AAV1 K61R


Sense: 5′-CTT CAA CGG ACT CGA CAG GGG GGA GCC-3′


(SEQ ID NO: 5)


Antisense: 5′-GGC TCC CCC CTG TCG AGT CCG TTG AAG-3′


(SEQ ID NO: 6)


 


AAV1 K84R


Sense: 5′-GCC TAC GAC CAG CAG CTC AGA GCG GGT GAC-3′


(SEQ ID NO: 7)


Antisense: 5′-GTC ACC CGC TCT GAG CTG CTG GTC GTA GGC-3′


(SEQ ID NO: 8)


 


AAV1 K137R


Sense: 5′-TGG TTG AGG AAG GCG CTA GGA CGG CTC CT-3′


(SEQ ID NO: 9)


Antisense: 5′-AGG AGC CGT CCT AGC GCC TTC CTC AAC CA-3′


(SEQ ID NO: 10)


 


AAV1 K143R


Sense: 5′-CTA AGA CGG CTC CTG GAA AGA GAC GTC CGG TAG-3′


(SEQ ID NO: 11)


Antisense: 5′-CTA CCG GAC GTC TCT TTC CAG GAG CCG TCT TAG-3′


(SEQ ID NO: 12)


 


AAV1 K161R


Sense: 5′-CGG GCA TCG GCA GGA CAG GCC AGC A-3′


(SEQ ID NO: 13)


Antisense: 5′-TGC TGG CCT GTC CTG CCG ATG CCC G-3′


(SEQ ID NO: 14)


 


AAV1 K459R


Sense: 5′-AGT CCG GAA GTG CCC AAA ACA GGG ACT TGC TGT-3′


(SEQ ID NO: 15)


Antisense: 5′-ACA GCA AGT CCC TGT TTT GGG CAC TTC CGG ACT-3′


(SEQ ID NO: 16)


 


AAV1 K528R


Sense: 5′-GCA CTG CTA TGG CCT CAC ACA GAG ACG ACG AAG-3′


(SEQ ID NO: 17)


Antisense: 5′-CTT CGT CGT CTC TGT GTG AGG CCA TAG CAG TGC-3′


(SEQ ID NO: 18)


 


AAV1 K533R


Sense: 5′-CAA AGA CGA CGA AGA CAG GTT CTT TCC CAT GAG CG-3′


(SEQ ID NO: 19)


Antisense: 5′-CGC TCA TGG GAA AGA ACC TGT CTT CGT CGT CTT TG-3′


(SEQ ID NO: 20)


 


AAV1 K707R


Sense: 5′-TGCAGTACACATCCAATTATGCAAGATCTGCCAACG TTG-3′


(SEQ ID NO: 21)


Antisense: 5′-CAACGTTGGCAGATCTTGCATAATTGGATGTGTACTGCA-3′


(SEQ ID NO: 22)


 


AAV8 Primers


AAV8 K137R


Sense: 5′-GGT TGA GGA AGG CGC TAG GAC GGC TCC TGG-3′


(SEQ ID NO: 23)


Antisense: 5′-CCA GGA GCC GTC CTA GCG CCT TCC TCA ACC-3′


(SEQ ID NO: 24)


 


AAV8 K333R


Sense: 5′-GCA GAA TGA AGG CAC CAG GAC CAT CGC CAA TAA CC-3′


(SEQ ID NO: 25)


Antisense: 5′-GGT TAT TGG CGA TGG TCC TGG TGC CTT CAT TCT GC-3′


(SEQ ID NO: 26)


 


AAV8 K530R


Sense: 5′-GCA TCG CTA TGG CAA CAC ACA GAG ACG ACG AGG-3′


(SEQ ID NO: 27)


Antisense: 5′-CCT CGT CGT CTC TGT GTG TTG CCA TAG CGA TGC-3′


(SEQ ID NO: 28)


 


AAV8 K709R


Sense: 5′-GTACACCTCCAACTACTACAGATCTACAAGTGTGGACTTTG-3′


(SEQ ID NO: 29)


Antisense: 5′-CAAAGTCCACACTTGTAGATCTGTAGTAGTTGGAGGTGTAC-3′


(SEQ ID NO: 30)


 


AAV2 Primers


AAV2 K39R


Sense: 5′-GCCCGCAGAGCGGCATAGGGACGACAG-3′


(SEQ ID NO: 31)


Antisense: 5′ -CTGTCGTCCCTATGCCGCTCTGCGGGC-3′


(SEQ ID NO: 32)


 


AAV2 K137R


Sense: 5′-CCTGGTTGAGGAACCTGTTAGGACGGCTCCGG-3′


(SEQ ID NO: 33)


Antisense: 5′-CCGGAGCCGTCCTAACAGGTTCCTCAACCAGG-3′


(SEQ ID NO: 34)


 


AAV2 K143R


Sense: 5′-AGACGGCTCCGGGAAAAAGGAGGCCGGTA-3′


(SEQ ID NO: 35)


Antisense: 5′-TACCGGCCTCCTTTTTCCCGGAGCCGTCT-3′


(SEQ ID NO: 36)


 


AAV2 K161R


Sense: 5′-CCTCGGGAACCGGAAGGGCGGGCC-3′


(SEQ ID NO: 37)


Antisense: 5′-GGCCCGCCCTTCCGGTTCCCGAGG-3′


(SEQ ID NO: 38)


 


AAV2 K490R


Sense: 5′-CCGCCAGCAGCGAGTATCAAGGACATCTGCGG-3′


(SEQ ID NO: 39)


Antisense: 5′-CCGCAGATGTCCTTGATACTCGCTGCTGGCGG-3′


(SEQ ID NO: 40)


 


AAV2 K527R


Sense: 5′-CGGCCATGGCAAGCCACAGGGACGATGAA-3′


(SEQ ID NO: 41)


Antisense: 5′-TTCATCGTCCCTGTGGCTTGCCATGGCCG-3′


(SEQ ID NO: 42)


 


AAV2 K532R


Sense: 5′-ACAAGGACGATGAAGAAAGGTTTTTTCCTCAGAGCGG-3′


(SEQ ID NO: 43)


Antisense: 5′-CCGCTCTGAGGAAAAAACCTTTCTTCATCGTCCTTGT-3′


(SEQ ID NO: 44)


 


AAV-rh74 Primers


AAV-rh74 K137R


Sense: 5′-CTGGTTGAATCGCCGGTTAGGACGGCTCCTG-3′


(SEQ ID NO: 45)


Antisense: 5′-GACCAACTTAGCGGCCAATCCTGCCGAGGAC-3′


(SEQ ID NO: 46)


 


AAV-rh74 K333R


Sense: 5′-GCAGAATGAAGGCACCAGGACCATCGCCAATAACC-3′


(SEQ ID NO: 47)


Antisense: 5′-GGTTATTGGCGATGGTCCTGGTGCCTTCATTCTGC-3′


(SEQ ID NO: 48)


 


AAV-rh74 K530R


Sense: 5′-GTTGCCATGGCTACCCACAGGGACGACGAA-3′


(SEQ ID NO: 49)


Antisense: 5′-TTCGTCGTCCCTGTGGGTAGCCATGGCAAC-3′


(SEQ ID NO: 50)


 


AAV-rh74 K552R


Sense: 5′-GGAAACAGGGAGCTGGAAGAGACAACGTGGACTAT-3′


(SEQ ID NO: 51)


Antisense: 5′-ATAGTCCACGTTGTCTCTTCCAGCTCCCTGTTTCC-3′


(SEQ ID NO: 52)


 


AAV-rh74 K569R


Sense: 5′-CTAACCAGCGAGGAAGAAATAAGGACCACCAACCC-3′


(SEQ ID NO: 53)


Antisense: 5′-GGGTTGGTGGTCCTTATTTCTTCCTCGCTGGTTAG-3′


(SEQ ID NO: 54)


 


AAV-rh74 K691R


Sense: 5′-CGAGTGGGAGCTGCAGAGGGAGAACAGCAA-3′


(SEQ ID NO: 55)


Antisense: 5′-TTGCTGTTCTCCCTCTGCAGCTCCCACTCG-3′


(SEQ ID NO: 56)


 


AAV-rh74 K695R


Sense: 5′-GCTGCAGAAGGAGAACAGCAGACGCTGGAACC-3′


(SEQ ID NO: 57)


Antisense: 5′-GGTTCCAGCGTCTGCTGTTCTCCTTCTGCAGC-3′


(SEQ ID NO: 58)


 


AAV-rh74 K709R


Sense: 5′-AGTACACTTCCAACTACTACAGATCTACAAATGTGGACTTTGC-3′


(SEQ ID NO: 59)


Antisense: 5′-GCAAAGTCCACATTTGTAGATCTGTAGTAGTTGGAAGTGTACT-3′


(SEQ ID NO: 60)









Table 5 provides a series of AAV vectors derived from mutagenesis that were used to package liver-specific AAV transgene expression cassettes for FIX. Packaging efficiency was indistinguishable from that observed with wild type, unmodified AAV8 vectors.















Preparation size
Yield per roller bottle


Lot number
Lysine mutant
(Roller Bottles)
(vector genomes)







KA712
AAV8 K137R
10
1.53E13


KA713
AAV8 K333R
10
9.46E12


KA714
AAV8 K530R
10
1.61E13


KA535
AAV8 (wild
10
6.63E12



type)









Capsid mutants which contain 2, 3, 4, 5, 6, 7 or more altered lysine residues in any of the capsid proteins described herein to further increase transduction efficiency are also within the scope of the invention. The data also reveals that certain mutations result in variants which exhibited significantly reduced transduction efficiency. Such variants could be used in combination with variants which exhibit increased transduction efficiencies, to act as decoys to neutralize or saturate an antibody directed immune response to the incoming vectors, thereby enabling vectors carrying desirable transgenes to more efficiently enter cells.
FIG. 1 shows schematic diagrams of the capsid surface. The data presented in FIGS. 2A, 2B and 2C demonstrate that altering lysine residues in the VP1 capsid on AAV8 alters the level of transgene produced due to altered transduction levels. FIGS. 3A, 3B and 3C show the effects of single and multiple mutations on HF.IX production in transduced cells. FIG. 3D demonstrates that a combination mutations, e.g., three lysine to arginine residues with four or six tyrosine to phenylalanine residues decreases transduction rates.
CTL Killing of HHL5-B7 Hepatocytes Using AAV Lysine Mutants
We assessed CTL killing of hepatocytes transduced with certain of the AAV lysine mutants disclosed here. The following materials and methods were employed to assess CTL killing of transduced hepatocytes.
Vector Generation
AAV vectors were produced in HEK-293 cells using a triple transfection approach as previously described (Matsushita, 1998) and purified with cesium chloride gradient centrifugation methods (Ayuso, 2010). AAV epitope peptides were synthesized by Genemed Synthesis and resuspended at a concentration of 5 mg/ml in 100% DMSO.
In Vitro Expansion of T Cells
Human PBMCs (Cellular Technology LTD) were thawed, washed, counted, and resuspended at a concentration of 2×106 cells/ml in AIM-V lymphocyte media (Gibco) containing 3% human serum (Bioreclamation), 1% L-glutamine (Gibco), and 1% penicillin/streptomycin (Gibco). For each expansion condition, 1×106 (500 μl) cells were added per well in a 24 well plate (BD Falcon) in a volume of 500 μl. An additional 1×106 (500 μl) of autologous irradiated splenocytes (3000 rad) were also added to each well as feeder cells, along with 2.5 μg/ml of human β-2-microglobulin (Lee Biosolutions), and 10 ng/ml of human recombinant IL-7 (R&D Systems). Cells were expanded in the presence of AAV peptide at a final concentration of 10 μg/ml at 37° C. in 5% CO2. Human IL-2 (Roche) at a concentration of 10 ng/ml was added to the cell culture after the first 24 hours and replenished every 48 hours thereafter. Cells were divided into new wells as necessary and antigenic stimulation (antigen and feeder cells) was repeated every 7-10 days for up to 3 rounds of restimulation.
CTL Assay
CTL assay was performed as previously described (Pien, 2009). Briefly, lactate dehydrogenase (LDH) release following CTL-mediated target lysis was measured with the CytoTox 96 Non Radioactive Cytotoxicity Assay (Promega). Four thousand HHL5 hepatocyte target cells were plated in each well of a Microtest Primaria flat-bottom 96-well plate (BD Falcon) in DMEM containing no serum. Target cells were transduced at an MOI of 5000, 50,000, and 500,000 of AAV capsid and incubated for 18 hours at 37° C. 5% CO2. Following treatment and incubation, plated target cells were washed once with media prior to the addition of epitope-specific cytotoxic T lymphocytes, expanded as described above. CTLs were added at an effector-target cell ratio of 10:1 for 4 hours at 37° C., 5% CO2 and LDH was measured after a 30 minute incubation at room temperature with enzymatic substrate read at 490 nm using a spectrophotometer (Spectramax).
Flow Cytometry
GFP expression following AAV transduction was measured by flow cytometry. Human hepatocytes from cell lines HHL5 or Huh7 were plated in DMEM containing 10% fetal bovine serum, 1% L-glutamine (Gibco), and 1% penicillin/streptomycin (Gibco) at a density of 250,000 cells/well in a Primaria Multiwell 24-well plate (BD Falcon). Cells were transduced with 5000, 50000, or 5000000 MOI of AAV vector and incubated for 18 hours at 37° C. 5% CO2. Following incubation, cells were trypsinized, washed twice with PBS 2% FBS, and fixed with 2% paraformaldehyde. Samples were acquired on a FACS Canto II flow cytometer using the FACSDiva® (BD Biosciences) and further analysis was performed using Flowjo® software (Treestar).
CTL Assay Results
In order to further test effect of the lysine mutations on viral transduction, we utilized an in vitro CTL-mediated cytotoxicity assay previously developed by our lab to test the functionality of AAV vectors (Pien et al.). AAV1 and AAV2 transduction results are shown in FIGS. 4 and 5 and 6. In FIG. 4, all lysine mutations in the AAV-1 capsid resulted in a decrease in CTL-mediated killing of target cells, suggesting that the lysine mutations led to less efficient processing and presentation of surface antigen upon transduction. Furthermore, the effect of lysine mutations appears to be additive, with the triple and quadruple lysine mutants showing the greatest decrease of CTL-mediated killing (FIG. 4A, B). Mutations to the AAV-2 capsid showed a similar effect. See FIGS. 5 and 6. FIG. 7 shows the transduction results obtained when Rh74 variants were tested.
In summary, we have found that mutating the lysine residues on AAV capsids to arginine residues increases AAV transduction efficiency. Our experiments identified several variants that upon transduction, resulted in higher levels of expression of the human factor IX (FIX) transgene in mice compared to animals receiving unmodified AAV vectors.
REFERENCES


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While certain of the preferred embodiments of the present invention have been described and specifically exemplified above, it is not intended that the invention be limited to such embodiments. Various modifications may be made thereto without departing from the scope and spirit of the present invention, as set forth in the following claims.

## Claims

1. An adeno-associated virus (AAV) vector comprising a VP1 capsid protein comprising one or more lysine substitutions at position 61, K61R, at position 84, K84R, at position 137, K137R, at position 143, K143R, at position 161, K161R, at position 459, K459R, at position 533, K533R, or at position 707, K707R of AAV1 VP1 capsid protein, said vector further comprising a minigene comprising AAV inverted terminal repeats and a heterologous nucleic acid sequence operably linked to regulatory sequences which direct expression of a product from the heterologous nucleic acid sequence in a host cell, said lysine substitution being effective to inhibit ubiquitination of said capsid protein, thereby increasing transduction of said AAV vector into a target cell, compared to an AAV vector comprising the AAV1 VP1 capsid protein without the one or more lysine substitutions.

2. An adeno-associated virus (AAV) vector comprising a VP1 capsid protein comprising one or more lysine substitutions at position 39, K39R, at position 137, K137R, at position 143, K143R, at position 161, K161R, at position 490, K490R, at position 527, K527R, or at position 532, K532R of AAV2 VP1 capsid protein, said vector further comprising a minigene comprising AAV inverted terminal repeats and a heterologous nucleic acid sequence operably linked to regulatory sequences which direct expression of a product from the heterologous nucleic acid sequence in a host cell, said lysine substitution being effective to inhibit ubiquitination of said capsid protein, thereby increasing transduction of said AAV vector into a target cell, compared to an AAV vector comprising the AAV2 VP1 capsid protein without the one or more lysine substitutions.

3. An adeno-associated virus (AAV) vector comprising a VP1 capsid protein comprising one or more lysine substitutions at position 137, K137R, at position 259, K259R, at position 333, K333R, at position 530, K530R, at position 569, K569R, or at position 668, K668R, of AAV8 VP1 capsid protein, said vector further comprising a minigene comprising AAV inverted terminal repeats and a heterologous nucleic acid sequence operably linked to regulatory sequences which direct expression of a product from the heterologous nucleic acid sequence in a host cell, said lysine substitution being effective to inhibit ubiquitination of said capsid protein, thereby increasing transduction of said AAV vector into a target cell, compared to an AAV vector comprising the AAV8 VP1 capsid protein without the one or more lysine substitutions.

4. An adeno-associated virus (AAV) vector comprising a VP1 capsid protein comprising one or more lysine substitutions at position 26, K26R, at position 38, K38R, at position 51, K51R, at position 61, K61R, at position 77, K77R, at position 137, K137R, at position 169, K169R, at position 259, K259R, at position 333, K333R, at position 530, K530R, at position 547, K547R, at position 552, K552R, at position 569, K569R or at position 709, K709R of AAV-rh74 VP1 capsid protein, said vector further comprising a minigene comprising AAV inverted terminal repeats and a heterologous nucleic acid sequence operably linked to regulatory sequences which direct expression of a product from the heterologous nucleic acid sequence in a host cell, said lysine substitution being effective to inhibit ubiquitination of said capsid protein, thereby increasing transduction of said AAV vector into a target cell, compared to an AAV vector comprising the AAV-rh74 VP1 capsid protein without the one or more lysine substitutions.

5. The AAV vector according to any one of claims 1-4, wherein the expression product of the heterologous nucleic acid sequence is a therapeutic peptide or nucleic acid.

6. The AAV vector according to claim 5, wherein the therapeutic peptide is a coagulation factor selected from the group consisting of Factor VIII, Factor IX or a functional fragment thereof.

7. The AAV vector according to any one of claims 1-4, wherein the expression product of the heterologous nucleic acid sequence is an IgG, IgM, IgA, IgD, IgE, chimeric immunoglobulin, humanized antibody, or a single chain antibody.

8. The AAV vector according to claim 7, wherein the expression product of the heterologous nucleic acid sequence is a chimeric immunoglobulin.

9. The AAV vector according to any one of claims 1-4, wherein the expression product of the heterologous nucleic acid sequence is a single chain antibody.

10. The AAV vector according to any one of claims 1-4, wherein the expression product is an antiviral RNAi.

11. The AAV vector of claim 10, wherein said inhibitory RNA is effective to inhibit HCV infection and replication.

12. The AAV vector of claim 10, wherein said inhibitory RNA is effective to inhibit expression of a eukaryotic target gene.

13. The AAV vector according to any one of claims 1-4, wherein the expression product of the heterologous nucleic acid sequence is a disease-modifying cytokine.

14. The AAV vector according to any one of claims 1-4, wherein the expression product of the heterologous nucleic acid sequence is a pair of zinc finger nucleases.

15. The AAV vector according to any one of claims 1-4 comprising 2, 3, or 4 lysine substitutions.

16. The AAV vector according to any one of claims 1-4, wherein the expression product is Factor VIII.

17. The AAV vector according to any one of claims 1-4, wherein the expression product is Factor IX.

18. A pharmaceutical composition comprising the AAV vector according to any one of claims 1-4, and a physiological compatible carrier therefor.

19. A cell culture comprising the AAV vector according to any one of claims 1-4.