ES2357131T3 - PROCEDURES TO PRODUCE PREPARATIONS OF VIRIONS OF AAV RECOMBINANTS SUBSTANTIALLY EXEMPT FROM EMPTY CAPSIDES. - Google Patents

Abstract

A method for purifying AAV vector particles from an AAV preparation comprising AAV vector particles and empty AAV capsids, to provide a product substantially free of empty AAV capsids, said method comprising: a) providing a host cell comprising AAV vector particles; b) lyse said host cell to obtain a crude cell lysate comprising AAV vector particles and empty AAV capsids; c) applying said crude cell lysate to a first cation exchange chromatography column under conditions in which said AAV vector particles and said empty AAV capsids are attached to the column; d) eluting said AAV vector particles and said AAV empty capsids under non-separation conditions to provide an AAV preparation comprising AAV vector particles and empty AAV capsids; e) applying the AAV preparation from (d) to a second column of cation exchange chromatography under conditions under which said AAV vector particles and said empty AAV capsids are attached to the column; f) adding a low salt buffer to the column of (e) under conditions in which the AAV vector particles are eluted and the empty AAV capsids remain attached to the column; and g) collecting the eluted fractions of (f) comprising AAV vector particles to provide an AAV product substantially free of empty AAV capsids.

Description

TECHNICAL FIELD

[0001] The present invention relates to methods for purifying adeno-associated virus (AAV) virions. More particularly, the invention relates to methods for purifying recombinant AAV virions (rAAV) containing packaged genomes from mixtures of AAV virions. which contain packed rAAV virions and empty AAV capsids that lack such genomes.

BACKGROUND OF THE INVENTION

[0002] The developing gene therapy procedures safely and persistently administer therapeutically effective amounts of gene products to patients. Using these procedures, a nucleic acid molecule can be directly introduced into a patient (in vivo gene therapy), or into cells isolated from a patient or donor, which are then subsequently returned to the patient (ex vivo gene therapy). The introduced nucleic acid then directs the patient's own cells or grafted cells to produce the desired therapeutic product. Gene therapy also allows doctors to select specific cellular organs or targets (for example, muscles, blood cells, brain cells, etc.) for therapy.

[0003] Nucleic acids can be introduced into the patient's cells in various ways, including virus-mediated gene administration, administration of pure DNA, and transfection procedures. Virus-mediated gene administration has been used in a majority of gene therapy tests. C. P. Hodgson Biotechnology (1995) 13: 222-225. The most frequently used recombinant viruses are based on retroviruses, adenoviruses, herpes viruses, smallpox viruses, and adeno-associated viruses (AAV).

[0004] Recombinant adeno-associated virus vectors are promising as gene delivery vectors in human gene therapy. However, a significant obstacle to using such vectors as drugs is the development of a truly scalable procedure to produce and purify the vector at commercially viable levels. For a review of the challenges involved in producing a scalable AAV vector for commercial use, see Qu and Wright, Cur. Opin. Drug Disc and Develop. (2000) 3: 750-755. Recently, some column chromatography techniques have been developed to purify rAAV virions. Although these purification procedures based on column chromatography have demonstrated that large-scale rAAV virions can be purified, the preparation of purified virions using column chromatography contains a significant amount of empty AAV capsids. The typical ratio of empty capsids to virions containing a heterologous gene of interest ("AAV vector particles") is approximately 10 or more, that is, 90% of the vectors recovered are empty capsids.

[0005] The presence of a large number of empty capsids may prevent clinical applications, for example by stimulating unwanted immune responses to the capsid protein or by competing for the surface-binding sites of the target cell. Consequently, techniques have been developed to remove empty capsids from the 35 virion preparations of rAAV. These techniques are normally based on ultracentrifugation, for example, gradient centrifugation of cesium chloride or iodixanol. Such centrifugation techniques are extremely laborious, resulting in low yield of the vector, and are not scalable. Kaludov et al., (2002) Hum. Gene Ther. 13: 1235-1243, describe methods of purifying vectors of rAAV-2, rAAV-4 and rAAV-5 using anion exchange columns. However, the experimenters were only able to recover 2%, 0.6% and 6.3%, respectively, as packaged genomes, even after combining the eluates and concentrating the fractions.

[0006] In this way there remains a need for new ways of eliminating or reducing the number of empty capsids of the stock solutions of AAV vector particles in order to improve manufacturing capacity.

SUMMARY OF THE INVENTION

[0007] The present invention is based on the discovery of effective and commercially viable methods of preparing stock solutions of rAAV virions with reduced amounts of empty capsids. The inventors have found herein that empty capsids can be separated from rAAV virions containing genetic material ("AAV vector particles") using column chromatography techniques. This result is surprising since it was previously believed that empty and packaged capsules had identical surface properties. As far as the knowledge of the inventors goes, this is the first demonstration that the charge of the viral particles and / or the charge density are different between the empty particles and the full particles. The techniques described herein provide efficient and scalable procedures for separating empty AAV capsids from AAV vector particles.

[0008] Accordingly, in one embodiment, the invention is directed to a method for purifying AAV vector particles from an AAV preparation comprising AAV vector particles and AAV empty capsids, 55 to provide an AAV product. substantially free of empty AAV capsids. The procedure

understands:

(a) providing a host cell comprising AAV vector particles;

(b) lysing the host cell to obtain a crude cell lysate comprising AAV vector particles and empty AAV capsids;

(c) applying the crude cell lysate to a first cation exchange chromatography column under conditions in which AAV vector particles and AAV capsids are attached to the column;

(d) eluting the AAV vector particles and the empty AAV capsids under non-separation conditions to provide an AAV preparation comprising AAV vector particles and empty AAV capsids;

(e) applying the AAV preparation from (d) to a second column of cation exchange chromatography under conditions where AAV vector particles and empty capsids are attached to the column;

(f) adding a low salt buffer to the column of (e) under conditions where the AAV vector particles elute and the empty AAV capsids remain attached to the column; Y

(g) collecting the eluted fractions of (f) comprising AAV vector particles to provide an AAV product substantially free of empty AAV capsids. fifteen

[0009] In additional embodiments, the above procedure further comprises:

(h) applying the fractions from step (g) to an anion exchange chromatography column under conditions where AAV vector particles and empty AAV capsids, if present, are attached to the column;

(i) adding a low salt buffer to the column of (h) under conditions where the empty AAV capsids are eluted and the AAV vector particles remain attached to the column;

(j) adding a high salt buffer to the column of (i) under conditions in which the AAV vector particles are eluted;

(k) collecting fractions of (i) comprising AAV vector particles to provide an AAV product substantially free of empty AAV capsids. 25

[0010] In a further embodiment, the invention is directed to a method for purifying AAV vector particles from an AAV preparation comprising AAV vector particles and AAV empty capsids, to provide a substantially free AAV product. of empty AAV capsules. The procedure includes:

(a) providing a host cell comprising AAV vector particles; 30

(b) lysing the host cell to obtain a crude cell lysate comprising AAV vector particles and empty AAV capsids;

(c) clarifying the crude cell lysate to provide a clarified cell lysate;

(d) applying the clarified cell lysate to a first cation exchange column comprising a matrix of the functional ligand R-SO3- under conditions where AAV vector particles and AAV empty capsids 35 bind to the column;

(e) eluting AAV vector particles and empty AAV capsids under non-separation conditions to provide an AAV preparation comprising AAV vector particles and empty AAV capsids;

(f) applying the AAV preparation from (e) to a second column of cation exchange chromatography under conditions under which the AAV vector particles and the empty AAV capsids are attached to the column;

(g) adding a low salt buffer to the column of (f) under conditions in which the vector particles elute and the empty AAV capsids remain attached to the column;

(h) collect eluted fractions from (g) comprising AAV vector particles;

(i) applying the fractions of step (h) to an anion exchange chromatography column under conditions under which said AAV vector particles and empty AAV capsids, if present, are attached to the column;

(j) adding a low salt buffer to the column of (i) under conditions where the empty AAV capsids are eluted and the AAV vector particles remain attached to the column;

(k) adding a high salt buffer to the column of (j) under conditions where the AAV vector particles 50 are eluted; Y

(l) collect the eluted fractions of (k) comprising the AAV vector particles to provide an AAV product substantially free of empty AAV capsids.

In another embodiment, the invention is directed to a method for purifying AAV vector particles from an AAV preparation comprising AAV vector particles and empty AAV capsids, to provide an AAV product substantially free of empty capsids of AAV The procedure includes:

(a) providing a host cell comprising AAV vector particles;

(b) lysing the host cell to obtain a crude cell lysate comprising AAV vector particles and empty AAV capsids;

(c) apply the crude cell lysate to a cation exchange chromatography column under conditions in the 60s

that AAV vector particles and AAV empty capsids bind to the column;

(d) eluting the AAV vector particles and the empty AAV capsids under non-separation conditions to provide an AAV preparation comprising AAV vector particles and empty AAV capsids;

(e) applying the AAV preparation from (d) to an anion exchange chromatography column under conditions where AAV vector particles and empty AAV capsids bind to column 5

(f) adding a low salt buffer to the column of (e) under conditions where the empty AAV capsids are eluted and the AAV vector particles remain attached to the column;

(g) adding a high salt buffer to the column of (f) under conditions in which the AAV particles are eluted;

(h) collecting eluted fractions from (g) comprising AAV vector particles to provide an AAV product substantially free of empty AAV capsids. 10

[0011] In additional embodiments, the above procedure further comprises:

(i) applying the AAV preparation of (h) to a second column of anion exchange chromatography and conditions under which AAV vector particles and empty AAV capsids, if present, are attached to the column;

(j) adding a low salt buffer to the column of (i) under conditions where the empty AAV capsids are eluted and the AAV vector particles remain attached to the column;

(k) add a high salt buffer to the column of (j) under conditions in which the AAV vector particles are eluted;

(l) collect the eluted fractions from (k) comprising the AAV vector particles to provide an AAV product substantially free of empty AAV capsids. twenty

[0012] In alternative embodiments, the method further comprises:

(i) applying the AAV preparation from (h) to a second column of cation exchange chromatography under conditions where AAV vector particles and empty AAV capsids are attached to the column;

(j) adding a low salt buffer to the column of (i) under conditions where the AAV vector particles 25 are eluted and the empty AAV capsids remain attached to the column; Y

(k) collecting the eluted fractions of (j) comprising AAV vector particles to provide an AAV product substantially free of empty AAV capsids.

[0013] In some embodiments of all of the above methods, the first cation exchange column and / or the second cation exchange column comprises a carboxymethylated or sulphonated matrix, such as a matrix 30 comprising the functional ligand R-SO3-.

[0014] In further embodiments of all the above procedures, the AAV vector particles are present in the AAV vector in an amount of at least 50%, such as in an amount of at least 75%, for example, in an amount of at least 85%, or at least 90%.

[0015] In other additional embodiments of all the above procedures, the AAV vector particles are derived from AAV-2 or AAV-5.

[0016] Those skilled in the art will readily produce these and other embodiments of the invention subject to the disclosure herein.

BRIEF DESCRIPTION OF THE FIGURES

[0017] Figures 1A and 1B. They show the binding characteristics of a crude lysate containing particles of 40 AAV vectors and empty AAV capsids. In Figure 1A, the resins tested were as follows: Band 1: control; Bands 2 and 3: MACRO PREP Q (strong anion exchanger available from BioRad, Hercules, CA); Bands 4 and 5: UNO-SPHERE Q (strong anion exchanger available from BioRad, Hercules, CA); bands 6 and 7: POROS 50HQ (strong anion exchanger available from Applied Biosystems, Foster City, CA); bands 8 and 9: POROS 50D (weak anion exchanger available from Applied Biosystems, Foster City, CA). In Figure 1B, the resins tested were as follows: Band 1: control; Bands 2 and 3: POROS 50PI (weak anion exchanger available from Applied Biosystems, Foster City, CA); Bands 4 and 5: SOURCE 30Q (strong anion exchanger available from Amersham Biosciences, Piscataway, NJ); Bands 6 and 7: DEAE SEPHAROSE (weak anion exchanger available from Amersham Biosciences, Piscataway, NJ); Bands 8 and 9: Q SEPHAROSE (strong anion exchanger available from Amersham Biosciences, Piscataway, NJ). For Figures 1A and 1B, Bands 2, 4, 6 and 8 used a low salt wash fraction (50 mM NaCl); Bands 3, 5, 7 and 8 used a high salt wash fraction (1M NaCl).

[0018] Figure 2. Shows an analysis of empty AAV capsids and AAV vector particles (Vgs) before and after separation using an anion exchange column as described in the examples.

[0019] Figure 3. It is a silver-stained SDS-PAGE graphic representation of the fractions of an anion exchange column as detailed in the examples. Band 1; AAV vector particles; Bands 2-5; elution fractions of vectors; Band 6: molecular weight patterns of proteins.

[0020] Figure 4. It is a graphic representation of a silver-stained SDS-PAGE gel showing the elution fractions (Bands 12-21) of a cation exchange column as described in the examples.

[0021] Figure 5. It is a graphic representation of a silver-stained SDS-PAGE gel showing the separation of empty AAV particles from AAV vector particles using cation exchange column chromatography. Band 1: starting material; Bands 2-4: three independent samples of vectors eluted from 5 cation exchange columns.

DETAILED DESCRIPTION OF THE INVENTION

[0022] The practice of the present invention will employ, unless otherwise indicated, conventional methods of virology, molecular biology and recombinant DNA techniques that fall within the skill of the person skilled in the art. These techniques are fully explained in the bibliography. See, for example, Sambrook et al. Molecular Cloning: A Laboratory Manual (Current Edition); DNA Cloning: A Practical Approach, Vol. I and II (D. Glover, ed.); Oligonucleotide Synthesis (N. Gait, ed., Current Edition); Nucleic Acid Hybridization (B. Hames & S. Higgins, eds., Current Edition); Transcription and Translation (B. Hames & S. Higgins, eds., Current Edition); CRC Handbook of Parvoviruses, vol. I and II (P. Tijssen, ed.); Fundamental Virology, 2nd Edition, vol. I and II (B.N. Fields and D.M. Knipe, eds.); Freshney Culture of Animal Cells, A Manual of Basic Technique (Wiley-Liss, Third Edition); and Ausubel and 15 col. (1991) Current Protocols in Molecular Biology (Wiley Interscience, NY).

1. DEFINITIONS

[0023] In the description of the present invention, the following terms will be used, and it is desired to define as indicated below.

[0024] It should be noted that, as used herein and in the appended claims, the singular forms "a", "one" and "the" include plural references unless the content clearly dictates otherwise . Thus, for example, the reference to "a packaged capsid" includes a mixture of two or more of said capsids, and the like.

[0025] By "vector" is meant any genetic element, such as a plasmid, phage, transposon, cosmid, chromosome, virus, virion, etc., which is capable of replication when associated with the appropriate control elements and that It can transfer gene sequences between cells. Thus, the term includes cloning and expression vehicles, as well as viral vectors.

[0026] By "AAV vector" is meant a vector derived from an adeno-associated virus serotype, which includes without limitation, AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6 , AAV-7 and AAV-8. AAV vectors may have one or more of the natural AAV genes removed in whole or in part, preferably the rep and / or cap genes, but retain the 30 functional flanking ITR frequencies. Functional ITR sequences are necessary for the rescue, replication and packaging of the AAV virion. Thus, an AAV vector is defined herein to include at least those sequences required for replication and cis packaging (eg, functional ITRs) of the virus. RTIs do not need to be natural nucleotide sequences, and may be altered, for example, by insertion, deletion or replacement of nucleotides, provided the sequences provide functional rescue, replication and packaging.

[0027] "AAV auxiliary functions" refers to AAV-derived coding sequences that can be expressed to provide AAV gene products that, at the same time, function in trans for the replication of productive AAV. Thus, AAV auxiliary functions include the main AAV open reading frames (ORF), rep and chap. Rep expression products have proven to possess many functions, including, among 40 others; recognition, binding and heterosis of the origin of AAV DNA replication; the activity of DNA helicase, and the transcription modulation of AAV promoters (or other heterologists). Cap expression products provide the necessary packaging functions. The auxiliary functions of AAV are used herein to complement the functions of AAV in trans that are disappearing from AAV vectors. Four. Five

[0028] The term "AAV auxiliary construct" refers in general to a nucleic acid molecule that includes nucleotide sequences that provide AAV functions removed from an AAV vector to be used to produce a transduction vector for administration of a nucleotide sequence of interest. Auxiliary AAV constructs are frequently used to provide transient expression of the AAV rep and / or cap genes to complement the disappearance of AAV functions that are necessary for AAV 50 replication; however, auxiliary constructions lack AAV ITRs and cannot replicate or package themselves. The auxiliary AAV constructs may be in the form of a plasmid, phage, transposon, cosmid, virus or virion. Numerous AAV auxiliary constructs have been described, such as the frequently used pAAV / Ad and pIM29 + 45 plasmids encoding Rep and Cap expression products. See, for example, Samulski et al. (1989) J. Virol. 63: 3822-3828; and Mc-Carty et al. (1991) J. Virol. 65: 2936-2945. Numerous 55 different vectors have been described encoding the Rep and / or Cap expression products. See, for example, U.S. Patent Nos. 5,139,941 and 6,376,237.

[0029] The term "accessory functions" refers to viral and / or cellular functions not derived from AAV on which AAV is dependent for replication. Thus, the term includes the proteins and RNAs that are necessary in AAV replication, including those residues involved in the activation of AAV gene transcription, the splicing of the stage-specific AAV mRNA, the replication of the AAV DNA, the synthesis of Cap expression products and the AAV capsid assembly. Accessory virus-based functions can be derived from any of the auxiliary viruses such as adenovirus, herpes virus (other than herpes simplex virus type 1) and vaccinia virus.

[0030] The term "accessory function vector" generally refers to a nucleic acid molecule that includes nucleotide sequences that provide accessory functions. An accessory function vector can be transfected into a suitable host cell, in which the vector is then able to support the production of AAV virions 10 in the host cell. Expressly excluded from the term are infectious viral particles that exist in nature, such as viral particles of adenovirus, herpes virus or vaccinia. In this way, the accessory function vectors can be in the form of a plasmid, phage, transposon or cosmid. In particular, it has been shown that the complete complement of adenovirus genes is not required for accessory auxiliary functions. For example, adenovirus mutants incapable of DNA replication and late gene synthesis 15 have proven to be permissive for AAV replication. Ito et al., (1970) J. Gen. Virol. 9: 243; Ishibashi et al. (1971) Virology 45: 317. Similarly, mutants within regions E2B and E3 have been shown to support AAV replication, indicating that regions E2B and E3 are probably not involved in providing accessory functions. Carter et al. (1983) Virology 126: 505. However, adenoviruses defective in the E1 region, or having the E4 region removed, are unable to support AAV replication. Thus, regions E1A and E4 are probably needed for AAV replication, both directly and indirectly. Laughlin et al., (1982) J. Virol. 41: 868; Janik et al., (1981) Proc. Natl Acad. Sci. USA 78: 1925; Carter et al., (1983) Virology 126: 505. Other characterized Ad mutants include: E1B (Laughlin et al. (1982), above; Janik et al. (1981), above; Ostrove et al., (1980 ) Virology 104: 502); E2A (Handa et al., (1975) J. Gen. Virol. 29: 239; Strauss et al. (1976) J. Virol. 17: 140; Myers et al. (1980) J. Virol. 35: 665; Jay et al. (1981) Proc. Natl. Acad. Sci. USA 78: 2927; Myers et al. (1981) J. Biol. Chem. 256: 25 567); E2B (Carter, Adeno-Associated Virus Helper Functions, in I CRC Handbook of Parvoviruses (P. Tijssen ed., 1990)); E3 (Carter et al. (1983), above); and E4 (Carter et al. (1983), above; Carter (1995)). Although studies of accessory functions provided by adenoviruses that have mutations in the E1B coding region have produced conflicting results, Samulski et al. (1988) J. Virol. 62: 206-210, they recently reported that E1B55k was needed for the production of AAV virions, while E1B19k was not. Additionally, International Publication 30 WO 97/17458 and Matshushita et al. (1998) Gene Therapy 5: 938-945, describes vectors with accessory functions encoding various Ad genes.

[0031] Particularly preferred accessory function vectors comprise an RNA coding region of the adenovirus VA, an ORF6 coding region of the adenovirus E4 a coding region of the adenovirus E2A of 72 kDa, a coding region of the adenovirus E1A and a E1B adenovirus coding region lacking an intact E1B55k coding region. Such vectors are described in International Publication No. WO 01/83797.

[0032] By "recombinant virus" is meant a virus that has been genetically altered, for example, by the addition or insertion of a heterologous nucleic acid construct in the particle.

[0033] By "AAV virion" is meant a complete virus particle such as a natural AAV virus particle 40 (wt) (comprising a single-stranded AAV nucleic acid genome associated with a protein coat of the capsid protein). AAV). In this regard, single-stranded AAV nucleic acid molecules of any complementary sense chain, for example "direct sense" or "opposite direction", may be packaged in any AAV virion and both chains are equally infectious.

[0034] The terms "recombinant AAV virion", "rAAV virion", "AAV vector particle", "full capsids", "full", and "full particles" are defined herein as infectious viruses of defective replication that include the structure of the AAV protein, encapsidating a heterologous nucleotide sequence of interest that is flanked on both sides by the AAV ITRs. A virion of rAAV is produced in a suitable host cell that has had sequences that specify an AAV vector, AAV auxiliary functions and accessory functions introduced therein. In this way, the host cell becomes capable of encoding AAV polypeptides 50 that are needed for the packaging of the AAV vector (which contains a sequence of recombinant nucleotides of interest) in the infectious recombinant virion particles for subsequent gene administration.

[0035] The terms "empty capsid," "empty particle" and "empty" refer to an AAV virion that includes an AAV protein structure but which lacks all or part of the polynucleotide construct comprising the sequence. of heterologous nucleotides of interest flanked on both sides by AAV ITRs. According to this, the empty capsid does not work to transfer the gene of interest in the host cell.

[0036] The term "host cell" denotes, for example, microorganisms, which may be, or have been, used as recipients of an AAV auxiliary construct, an AAV vector plasmid, an accessory function vector, or other DNA. transfer. The term includes the progeny of the original cell that has been transfected. Thus, a host cell as used herein generally refers to a cell that has been

transfected with an exogenous DNA sequence. It is understood that the progeny of an individual parental cell may not necessarily be completely identical in the morphology or in the complement of genomic or total DNA than the original parental due to a natural, accidental, or deliberate mutation.

[0037] The term "transfection" is used to refer to the uptake of foreign DNA by a cell, and a cell has been "transfected" when exogenous DNA has been introduced into the cell membrane. Numerous transfection techniques are generally known in the art. See, for example, Graham et al. (1973) Virology, 52: 456, Sambrook et al. (1989) Molecular Cloning, a laboratory manual, Cold Spring Harbor Laboratories, New York, Davis et al. (1986) Basic Methods in Molecular Biology, Elsevier, and Chu et al. (1981) Gene 13: 197. Such techniques can be used to introduce one or more exogenous DNA residues into suitable host cells.

[0038] As used herein, the term "cell line" refers to a population of cells capable of continuous or prolonged growth and division in vitro. Often, cell lines are clonal populations derived from an individual progenitor cell. It is also known in the art that spontaneous or induced changes in the karyotype can occur during storage or transfer of said clonal populations. Therefore, the cells of the referred cell line may not be precisely identical to the ancestral cells or cultures, and the referred cell line includes such variants. fifteen

[0039] A stock solution or stock preparation of rAAV virions comprising AAV vector particles (packaged genomes) is "substantially free of" empty AAV capsids when at least about 50% -99% or more of the virions present in The stock solution is rAAV virions with packaged genomes (i.e. AAV vector particles). Preferably, the AAV vector particles comprise at least about 75% to 85%, more preferably about 90% of virions present in the stock solution, even more preferably about 95%, or even 99%. or more by weight of the virions present in the stock solution, or any integer between these intervals. Thus, a stock solution is substantially free of empty AAV capsids when between about 40% to about 1% or less, preferably about 25% to about 15% or less, more preferably about 10% or less. , even more preferably about 5% to about 1% or less of the resulting stock solution comprises empty capsids.

[0040] A "nucleic acid" sequence refers to a DNA or RNA sequence. The term comprises sequences that include any of the known base analogs of DNA and RNA such as, but not limited to 4-acetylcytosine, 8-hydroxy-N6-methyladenosine, aziridinylcytosine, pseudoisocytosine, 5- (carboxyhydroxymethyl) uracil, 5- fluorouracil, 5-bromouracil, 5-carboxymethylaminomethyl-2-thiouracil, 5-carboxymethylaminomethyluracil, dihydrouracil, 30 inosine, N6-isopentenyladenine, 1-methyladenine, 1-methylpseudouracil, 1-methylguanine, 1-methylguanine, 1-methylguanine, 1-methylguanine, 1-methylguanine, 1-methylguanine, 1-methylguanine, 1-methylguanine, 1,2 -methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-methyladenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylkeosine, 5 ′ -methoxycarbonylmethyluracyloxyuracyloxyuracyloxyuracyloxyuracil 2-Methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid methyl ester, uracil-5-oxyacetic acid, oxybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil 5-methyluracil, 35 methyl ester of urac acid il-5-oxyacetic, uracil-5-oxyacetic acid, pseudouracil, queosine, 2-thiocytosine, and 2,6-diaminopurine.

[0041] A "coding sequence", or a sequence that "encodes" a selected polypeptide, is a nucleic acid molecule that is transcribed (in the case of DNA) and translated (in the case of mRNA) into a polypeptide in vivo when placed under the control of appropriate regulatory sequences. The limits of the coding sequence 40 are determined by a start codon at the 5 ′ end (amino) and a translation stop codon at the 3 ′ end (carboxy). A transcription termination sequence may be located 3 'with respect to the coding sequence.

[0042] The term "control sequences" of DNA collectively refers to promoter sequences, polyadenylation signals, transcription termination sequences, regulatory domains in the 5 ′ direction, origins of replication, internal ribosome entry sites (" IRES ”), enhancers, and the like, which collectively provide replication, transcription and translation of a coding sequence in a recipient cell. Not all of these control sequences need to be perpetually present as long as the selected coding sequence is capable of replicating, transcribing and translating into an appropriate host cell.

[0043] The term "promoter" is used herein in its ordinary sense to refer to a 50 nucleotide region comprising a DNA regulatory sequence, in which the regulatory sequence is derived from a gene that is capable of binding. to RNA polymerase and to initiate transcription of the coding sequence in address 3 ‟(address 3‟). Transcription promoters may include "inducible promoters" (in which expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.), "repressible promoters" (in the that the expression of an operably linked polynucleotide sequence is repressed by an analyte, cofactor, regulatory protein, etc.), and "constitutive promoters."

[0044] "Operatively linked" refers to an arrangement of elements in which the components thus described are determined in order to carry out their usual function. In this way, the linked control sequences of

operable way to a coding sequence are capable of effecting the expression of the coding sequence. Control sequences do not need to be contiguous with the coding sequence, as long as they function to direct the expression thereof. Thus, for example, the intervention of additionally untranslated transcribed sequences between a promoter sequence and the coding sequence may be present and the promoter sequence can still be considered "operably linked" to the coding sequence. 5

[0045] In order to describe the relative position of the nucleotide sequences in a particular nucleic acid molecule, such as when a particular nucleic acid sequence is described as being located "in the 5‟ direction, "" in the 3 direction ‟”, “3‟ ”, or“ 5 ‟” with respect to another sequence, it should be understood that this is the position of the sequences in the “direct sense” or “coding” chain of a DNA molecule to which He is referring as conventional in the field. 10

[0046] The term "heterologous" as it refers to nucleic acid sequences such as coding sequences and control sequences, denotes sequences that are not normally linked together, and / or that are not associated with a particular cell. Thus, a "heterologous" region of a construct or a nucleic acid vector is a segment of nucleic acid contained or linked to another nucleic acid molecule that is not found in association with the other molecule in nature. For example, a heterologous region of a nucleic acid construct would include a coding sequence flanked by sequences not found in association with the coding sequence in nature. Another example of a heterologous coding sequence is a construct in which the coding sequence is not found in nature (for example, synthetic sequences that have different codons that differ from those of the natural gene). Similarly, a cell transformed with a construct that is not normally present in the cell would be considered heterologous for the purposes of this invention. Allelic variation or episodes of naturally occurring mutations do not provide an increase in heterologous DNA, as used herein.

[0047] By "isolated" when referring to a nucleotide sequence, it is understood that the indicated molecule is present in the substantial absence of other biological macromolecules of the same type. Thus, an "isolated nucleic acid molecule encoding a particular polypeptide" refers to a nucleic acid molecule that is substantially free of other nucleic acid molecules that do not encode the subject polypeptide; however, the molecule may include some additional bases or moieties that do not adversely affect the basic characteristics of the composition.

2. MODES OF CARRYING OUT THE INVENTION

[0048] Before describing the present invention in detail, it should be understood that this invention is not limited to 30 formulations or parameters of particular procedures since said formulations or process parameters may, of course, vary. It should also be understood that the terminology used herein is solely for the purpose of describing specific embodiments of the invention, and is not intended to be limiting.

[0049] Although numerous methods and materials similar or equivalent to those described herein can be used during the practice of the present invention, preferred materials and procedures are described herein.

[0050] The present invention involves reducing the number, or elimination, of the empty AAV capsids contained in the purified stock solutions of AAV virions, with a minimal loss of AAV vector particles contained therein. The methods of the present invention can be used without taking into account the 40 procedures in which rAAV virions are generated.

[0051] There are some methods that are well known in the art to generate rAAV virions: for example, transfection using a vector and AAV helper sequences together with simultaneous infection with one of the AAV helper viruses (eg, adenovirus, virus of herpes, or vaccinia virus) or transfection with a recombinant AAV vector, an AAV auxiliary vector, and an accessory function vector. For detailed descriptions of the 45 procedures for generating rAAV virions see US Pat. Nos. 6,001,650 and 6,004,797.

[0052] Natural AAVs and helper viruses can be used, for example, to provide the replicative functions necessary to produce rAAV virions (see, for example, U.S. Patent No. 5,139,941). Alternatively, a plasmid can be used, which contains auxiliary function genes in combination with infection by one of the auxiliary viruses well known as a source of replicative functions (see, for example, U.S. Patent No. 5,622,856 and U.S. Patent No. 5,139,941). Similarly, a plasmid, which contains genes with accessory function, in combination with a natural AAV infection, can be used to provide the necessary replicative functions. These three approaches, when used in combination with a rAAV vector, are each sufficient to produce rAAV virions. Other approaches, well known in the art by the person skilled in the art, can also be used to produce rAAV virions. 55

[0053] In a preferred embodiment of the present invention, a triple transfection method (described in detail in US Patent No. 6,001,650) is used to produce rAAV virions because this procedure does not require the use of an infectious auxiliary virus, allowing rAAV virions to occur without

No detectable auxiliary virus present. This is accomplished through the use of three vectors for the production of the rAAV virion: an AAV auxiliary function vector, an accessory function vector, and an rAAV expression vector. One skilled in the art will appreciate, however, that nucleic acid sequences encoded by these vectors can be provided in two or more vectors in various combinations.

[0054] As explained herein, the AAV auxiliary function vector encodes the sequences of the "AAV auxiliary function" (ie, rep and cap), which function in trans for replication and producer-producing encapsidation of AAC Preferably, the AAV auxiliary function vector supports efficient production of AAV vector without generating any detectable AAV wt virions (i.e., AAV virions containing functional rep and cap genes) An example of said vector, pHLP19, It is described in US Patent No. 6,001,650. The rep and cap genes of the AAV auxiliary function vector can be derived from any of the known AAV serotypes, as explained above. For example, the AAV auxiliary function vector may have a rep gene derived from AAV-2 and a cap gene derived from AAV-6; one skilled in the art will recognize that other combinations of rep and cap genes are possible, the defining characteristic being the ability to support the production of rAAV virions.

[0055] The accessory function vector encodes nucleotide sequences for viral and / or cellular functions not derived from AAV on which AAV is dependent for replication (ie, "accessory functions"). The 15 accessory functions include those functions required for AAV replication, including, without limitation, the residues involved in the activation of AAV gene transcription, the cutting and splicing of stage-specific AAV mRNA, AAV DNA replication , the synthesis of cap expression products, and the AAV capsid assembly. Accessory virus-based functions can be derived from any of the well-known helper viruses such as adenovirus, herpes virus (other than herpes virus type 1), and vaccinia virus. In a preferred embodiment, the accessory function plasmid pLadeno5 is used (details are described with respect to pLadeno5 in US Patent No. 6,004,797). This plasmid provides a complete set of adenovirus accessory functions for the production of the AAV vector, but lacks the necessary components to form an adenovirus competent for replication.

[0056] Once the stock solutions of AAV virions are produced, numerous procedures, detailed below, can be used to determine infectious titres and to purify the AAV vector particles of the AAV empty capsids.

[0057] In order to deepen the understanding of the invention, a more detailed discussion regarding recombinant AAV expression vectors, AAV auxiliary and accessory functions, compositions comprising AAV virions, as well as of the administration of virions. 30

RECOMBINANT AAV EXPRESSION VECTORS

[0058] Recombinant AAV (rAAV) expression vectors were constructed using known techniques to provide as operably linked components in the direction of transcription, control elements that included a transcription initiation region, the polynucleotide of interest and a region of termination of transcription. The control elements are selected to be functional in the host cell of interest. The resulting construct containing the operably linked components binds (5 'to 3') with the functional AAV ITR sequences.

[0059] The nucleotide sequences of the ITR regions of AAV are known. See, for example, Kotin, R.M. (1994) Human Gene Therapy 5: 793-801; Berns, K.I. "Parvoviridae and their Replication" in Fundamental Virology, 2nd Edition, (B.N. Fields and D.M. Knipe, eds.) For the AAV-2 sequence. The AAV ITRs used in the vectors of the invention do not need to have a terminal nucleotide sequence, and can be altered, for example, by insertion, deletion or replacement of nucleotides. Additionally, an AAV ITR can be derived from any of the various AAV serotypes, including without limitation, AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV-7 and AAV -8, etc. In addition, the 5 ‟and 3 ′ ITRs that flank a selected nucleotide sequence in an AAV expression vector do not necessarily need to be identical or derived from the same AAV serotype or isolate, provided that functions such as 45 are intended, that is, to allow excision and rescue of the sequence of interest of a genome or host cell vector, and to allow the integration of the DNA molecule into the genome of the recipient cell when AAV Rep gene products are present in the cell .

[0060] Polynucleotide molecules suitable for use in AAV vectors will be less than about 5 kilobases (kb) in size. The selected polynucleotide sequence is operably linked to the control elements 50 that direct transcription or expression thereof in the subject in vivo. Said control elements may comprise the control sequences normally associated with the selected gene. Alternatively, heterologous control sequences can be used. Useful heterologous control sequences generally include those derived from sequences encoding mammalian or virus genes. Examples include, but are not limited to, a neuron specific enolase promoter, a GFAP promoter, the SV40 early promoter, the LTR promoter of the mouse mammary tumor virus; the late adenovirus major promoter (AD MLP); a herpes simplex virus (VSH) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter (CMVIE) region, a Rous sarcoma virus (VSR) promoter, the CAG promoter, synthetic promoters , hybrid promoters, and the like. Additionally, sequences derived from non-gene genes will find use herein.

viral, such as the murine metallothionein gene. Such promoter sequences are commercially available from, for example, Stratagene (San Diego, CA).

[0061] The AAV expression vector that houses the bound polynucleotide molecule of interest can be constructed by AAV ITRs by inserting the selected sequence (s) into an AAV genome that has had the frames of AAV Open reading of main AAVs (“ORF”) split from the previous one. Other portions of the AAV genome can also be removed, as long as a sufficient portion of the ITR remains to allow replication and packaging functions. Such constructions can be designed using techniques well known in the art. See, for example, US Patent Nos. 5,173,414 and 5,139,941; International Publications Nos WO 92/01070 (published on January 23, 1992) and WO 93/03769 (published on March 4, 1993); Lebkowski et al. (1988) Molec. Cell Biol. 8: 3988-3996; Vincent et al. (1990) Vaccines 90 (Cold Spring Harbor Laboratory Press); Carter 10 (1992) Current Opinion in Biotechnology 3: 533-539; Muzyczka (1992) Current Topics in Microbiol. and Immunol. 158: 97-129; Kotin (1994) Human Gene Therapy 5: 793-801; Shelling and Smith (1994) Gene Therapy 1: 165-169; and Zhou et al. (1994) J. Exp. Med. 179: 1867-1875.

[0062] Alternatively, the AAV ITRs of the viral genome or of an AAV vector containing the same can be cleaved and fused into 5 ′ and 3 ′ of a selected nucleic acid construct that is present in another vector 15 using techniques of standardized ligation, such as those described in Sambrook et al., above. For example, ligatures can be carried out in 20 mM Tris-Cl pH 7.5, 10 mM MgCl2, 10 mM DTT, 33 µg / ml BSA, 10 mM-50 mM NaCl, and any of 40 µM ATP, 0.01-0.02 units (Weiss) of T4 DNA ligase at 0 ° C (for ligation of the "sticky end") or 1 mM ATP, 0.3-0.6 units (Weiss) of T4 DNA ligase at 14 ° C ( for ligation of the enromado end). Intermolecular ligation of the "sticky end" is usually carried out at concentrations of 30-100 µg / ml of total DNA (total final concentration of 5-100 nm). AAV vectors containing the ITRs have been described in, for example, U.S. Patent No. 5,139,941. In particular, some AAV vectors that are available from the American Type Culture Collection ("ATCC") with Access Numbers 53222, 53223, 53224, 53225 and 53226 are described in the foregoing.

[0063] For the purposes of the invention, host cells suitable for producing rAAV virions of the 25 AAV expression vectors include microorganisms, yeast cells, insect cells, and mammalian cells, which may be, or have been , used as receptors of a heterologous DNA molecule and that are capable of growing in, for example, a suspension culture, a bioreactor, or the like. The term includes the progeny of the original cell that has been transfected. Thus, a "host cell" as used herein generally refers to a cell that has been transfected with an exogenous DNA sequence. Stable human cell line 293 cells (readily available through, for example, from the American Type Culture Collection under Accession Number ATCC CRL1573) are preferred in the practice of the present invention. Specifically, the human cell line 293 is a human embryonic kidney cell line that has been transformed with DNA fragments of adenovirus type 5 (Graham et al. (1977) J. Gen. Virol. 36:59), and which expresses the adenoviral E1a and E1b genes (Aiello et al. (1979) Virology 94: 460). Cell line 293 is easily transfected, and provides a particularly convenient platform in which to produce rAAV virions.

AAV AUXILIARY FUNCTIONS

[0064] Host cells containing the AAV expression vectors described above may become capable of providing auxiliary functions in order to replicate and encapsidate nucleotide sequences flanked by AAV ITRs to produce rAAV virions: The functions AAV auxiliaries are generally AAV-derived coding sequences that can be expressed to provide AAV gene products that, at the same time, function in trans for productive AAV replication. In this document, the AAV auxiliary functions are used to complement the necessary AAV functions that are disappearing from the AAV expression vectors. Thus, AAV auxiliary functions include one, or both of the main AAV ORFs, namely, the rep and cap coding regions, or the functional homologs thereof.

[0065] "AAV rep coding region" means the region recognized by the AAV genome technique that encodes Rep 78, Rep 68, Rep 52 and Rep 40 replication proteins. These Rep expression products have demonstrated possess many functions, including recognition, binding and heterosis of AAV DNA replication origin, helicase DNA activity and transcription modulation of AAV promoters (or 50 other heterologists). Rep expression products are collectively required to replicate the AAV genome. For a description of the AAV rep coding region, see, for example, Muzyczka, N. (1992) Current Topics in Microbiol. and Immunol. 158: 97-129; and Kotin, R.M. (1994) Human Gene Therapy 5: 793-801. Suitable homologs of the AAV rep coding region include the human herpes virus 6 (VHH-6) rep gene that is also known to mediate AAV-2 DNA replication (Thomson et al. (1994) Virology 204: 304-311). 55

[0066] "AAV cap coding region" means the region recognized by the AAV genome technique that encodes the VP1, VP2, and VP3 proteins of the capsid, or functional homologs thereof. These Cap expression products provide the packaging functions that are collectively required to package the viral genome. For a description of the AAV cap coding region, see, for example, Muzyczka, N. and Kotin, R.M. (higher). 60

[0067] AAV auxiliary functions are introduced into the host cell by transfecting the host cell with an AAV auxiliary construct both before and in parallel with the transfection of the AAV expression vector. Auxiliary AAV constructs are used in this way to provide at least transient expression of the AAV rep and / or cap genes to complement the disappearing AAV functions that are necessary for productive AAV infection. AAV auxiliary constructs lack AAV ITRs and cannot replicate or package themselves.

[0068] These constructs may be in the form of a plasmid, phage, transposon, cosmid, virus, or virion. Numerous AAV auxiliary constructs have been described, such as the frequently used pAAV / Ad and pIM29 + 45 plasmids encoding Rep and Cap expression products. See, for example, Samulski et al. (1989) J. Virol. 63: 3822-3828; and McCarty et al. (1991) J. Virol. 65: 2936-2945. Numerous additional vectors have been described which encode the expression products of Rep and / or Cap. See, for example, U.S. Patent 5,139,941.

AAV ACCESSORY FUNCTIONS

[0069] The host cell (or packaging cell) must also become capable of providing functions not derived from AAV, or "accessory functions" in order to produce rAAV virions. Accessory functions are viral and / or cellular functions not derived from AAV on which AAV is dependent for replication. Thus, accessory functions include at least those non-AAV proteins and RNA that are required in AAV replication, including those involved in the activation of AAV gene transcription, the splicing of AAV-specific mRNA from stage, AAV DNA replication, the synthesis of Cap expression products and the AAV capsid assembly. Accessory virus-based functions can be derived from any of the known auxiliary viruses. twenty

[0070] In particular, accessory functions can be introduced into and then expressed in host cells using methods known to those skilled in the art. Normally, accessory functions are provided by infection of the host cells with an unrelated auxiliary virus. Numerous suitable auxiliary viruses are known, including adenovirus; herpes virus such as types 1 and 2 of the herpes simplex virus; and vaccinia virus. Non-viral accessory functions, such as those provided by cellular synchronization using any of the various known agents, will find use herein. See, for example, Buller et al. (1981) J. Virol. 40: 241-247; McPherson et al. (1985) Virology 147: 21 7-222; Schlehofer et al. (1986) Virology 152: 110-117.

[0071] Alternatively, accessory functions may be provided using an accessory function vector as defined above. See, for example, U.S. Patent No. 6,004,797 and International Publication No. WO 01/83797.

[0072] Nucleic acid sequences that provide the accessory functions of natural sources, such as the genome of an adenovirus particle, can be obtained or constructed using recombinant or synthetic methods known in the art. As explained above, it has been shown that the complete complement of adenovirus genes is not required for accessory auxiliary functions. In particular, it has been shown that mutant adenoviruses incapable of DNA replication and late gene synthesis are permissive for AAV replication. Ito et al., (1970) J. Gen. Virol. 9: 243; Ishibashi et al. (1971) Virology 45: 317. Similarly, mutants within regions E2B and E3 have been shown to support AAV replication, indicating that regions E2B and E3 are not likely involved in providing accessory functions. Carter et al. (1983) Virology 126: 505. However, adenoviruses defective in the E1 region, or having an E4 region removed, are unable to support AAV replication. Thus, regions E1A and E4 are probably required for AAV replication, both directly and indirectly. Laughlin et al., (1982) J. Virol. 41: 868; Janik et al., (1981) Proc. Natl Acad. Sci. USA 78: 1925; Carter et al., (1983) Virology 126: 505. Other characterized Ad mutants include: E1B (Laughlin et al. (1982), supra; Janik et al. (1981), above; Ostrove et al., (1980) Virology 104: 502); E2A (Handa et al., (1975) J. Gen. Virol. 29: 239; Strauss et al. (1976) J. Virol. 17: 140; Myers et al., 45 (1980) J. Virol. 35 : 665; Jay et al. (1981) Proc. Natl. Acad. Sci. USA 78: 2927; Myers et al. (1981) J. Biol. Chem. 256: 567); E2B (Carter, Adeno-Associated Virus Helper Functions, in I CRC Handbook of Parvoviruses (P. Tijssen ed., 1990)); E3 (Carter et al. (1983), above); and E4 (Carter et al. (1983), above; Carter (1995)). Although studies of accessory functions provided by adenoviruses that have mutations in the E1B coding region have produced conflicting results, Samulski et al. (1988) J. Virol. 62: 206-210, they recently reported that E1B55k was needed for the production of AAV virions, while E1B19k was not. In addition, International Publication WO 97/17458 and Matshushita et al. (1998) Gene Therapy 5: 938-945, describe vectors with accessory functions encoding several Ad genes. Vectors with particularly preferred accessory functions comprise an adenovirus VA RNA coding region, an E4 adenovirus ORF6 coding region, a 72 kD adenovirus E2A coding region, an adenovirus E1A coding region, and a region 55 Adenovirus E1B lacking an intact E1B55k coding region. Such vectors are described in International Publication No. WO 01/83797.

[0073] As a consequence of the infection of the cell with the auxiliary virus, or the transfection of the host cell with an accessory function vector, the accessory functions that are expressed transactivate the auxiliary construction of AAV to produce Rep and / or Cap protein of AAV. Rep expression products cleave recombinant DNA 60

(including the DNA of interest) of the AAV expression vector. Rep proteins also serve to duplicate the AAV genome. The expressed Cap proteins are assembled into capsids, and the recombinant AAV genome is packaged into the capsids. In this way, AAV replication continues, and the DNA is packaged in rAAV virions.

PURIFICATION OF RAAV 5 VIRIONS

[0074] Following the replication of recombinant AAV, rAAV virions from the host cell can be purified using a variety of conventional purification procedures, such as column chromatography, CsCl gradients, and the like. For example, a plurality can be used. of column purification steps, such as purification in an anion exchange column, an affinity column and / or a cation exchange column. See, for example, International Publication No. WO 02/12455. In addition, if the infection is used to express the accessory functions, the residual auxiliary virus can be inactivated using known procedures. For example, the adenovirus can be inactivated by heating at temperatures of about 60 ° C for, for example, 20 minutes or more. This treatment effectively inactivates only the auxiliary virus because the AAV is extremely heat stable while the auxiliary adenovirus is heat labile.

[0075] Recombinant AAV vectors containing any number of reporter genes can be used to determine infectious titres. For example, alkaline phosphatase, β-galactosidase (LacZ), green fluorescent protein, or luciferase can be used. After harvesting the transfected host cell, a lysate was formed by breaking up the transfected host cells using techniques suitable for large-scale production such as microfluidization. The lysate was then filtered (for example, through a 0.45 µm filter), and purified using column chromatography procedures as described herein. 20 other techniques for determining the infectious titer of any AAV vector have also been reported. See for example, Zhen et al., "An Infectious Titer Assay for Adeno-associated Virus (AAV) Vectors with Sensitivity Sufficient to Detect Single Infectious Events." Hum. Gene Ther. (2004) In Press.

[0076] The purified AAV stock solution was then treated to remove empty capsids using column chromatography techniques. In a particularly preferred method of the invention, 25 rAAV preparations were obtained by lysing transfected cells to obtain a crude cell lysate. The crude cell lysate can then be clarified to remove cell debris by techniques well known in the art, such as filtration, centrifugation, and the like, to return a clarified cell lysate. The crude cell lysate or the clarified cell lysate, containing AAV vector particles and empty AAV capsids, was then applied to a first cation exchange column to further separate the AAV vector particles and the 30 empty AAV capsids. of the cellular part and other components present in the preparation of the cell lysate. The procedures for carrying out the initial purification of the cell lysate are known. A representative procedure is described in U.S. Patent No. 6,593,123.

[0077] Next, the fractions collected from the first cation exchange column were applied to a second ion exchanger, that is, a second cation exchange column and / or an anion exchange column, using different elution conditions separating the AAV empty capsids of AAV vector particles.

[0078] Cation exchangers suitable for the first cation exchange column and the second cation exchange column, if used, include a wide variety of materials known in the art. Particularly preferred are strong cation exchangers capable of binding rAAV virions over a wide pH range. For example, carboxymethylated and sulfonated cation exchange matrices are particularly useful for use herein. Useful matrix materials include, but are not limited to, cellulose matrices, such as microgranular and perlified fibrous matrices; agarose, dextran, polyacrylate, polyvinyl, polystyrene, silica and polyether; and composite materials. Particularly preferred herein are matrices containing the R-SO3-functional ligand, preferably sulfopropyl or sulfoethyl resins. Representative matrices 45 include, but are not limited to POROS HS, POROS SP, POROS S (all strong cation exchangers available from Applied Biosystems, Foster City, CA), POROS CM (weak cation exchangers available from Applied Biosystems, Foster City, CA), TOSOHAAS TOYOPEARL SP550C and MERCK FRACTOGEL EMD SO3-650 (m), as well as SOURCE 15S, SOURCE 30S, SEPHAROSE SP FF, SEPHAROSE SP XL (all available from Amersham Bioscience, Piscataway, NJ). fifty

[0079] For all column chromatography protocols provided below, column can be prepared using standard protocols known in the art with the appropriate buffer solutions. The sample was then loaded. For the first cation exchange column used, the conditions are such that empty capsids and AAV vector particles were attached to the column resin and subsequently eluted together, but separated from other components and cellular debris present. in the cell lysate. For example, empty and filled capsids were eluted using an appropriate ionic strength buffer. Suitable buffers include, for example, 10-50 mM sodium phosphate, preferably 15-40, such as 15 ... 20 ... 25 ... 30 ... 35 ... 40, etc. The mM sodium phosphate contains salt such as NaCl or KCl at a concentration of, for example, 100-700 mM, such as 200-400 mM, for example, 200 ... 300 ... 325 ... 350 .. 370 ... 380 ... 400, etc., or any concentration included in these intervals. The pH of the buffer can be between about 3 and about 9.5, such 60

such as 4-8, for example, pH 4 ... 4.5 ... 5 ... 5.5 ... 6, etc., or any pH within these ranges. The fractions were collected and then advanced in an anion exchange column and / or a second cation exchange column under separation conditions.

[0080] If a second cation exchange column was used at a later stage to separate the empty AAV capsids from the AAV vector particles, two elution buffers, a low salt buffer and a high salt buffer, were used. . In particular, the empty capsids were separated from the AAV vector particles using an appropriate buffer at a pH of between approximately pH 6 to pH 12, preferably pH 7 to pH 10, and even more preferably pH 7.5 to pH 9, 5, such as pH 7.5 ... 8.0, 8.1, 8.2, 8.3, 8.4, 8.5 ... 9.0, 9.1, 9.2, 9 , 3, 9.4, 9.5, or any pH between the defined intervals. Appropriate buffers are well known in the art and include, without limitation, buffers with the following buffer ions: acetic acid; malonic acid; MONTH; phosphate; HEPES, BICINE and the like. To elute the sample, the ionic strength of the starting buffer was increased using a salt, such as NaCl, KCl, ammonium sulfate or any other salt containing sulfate, formate, acetate, citrate, and / or phosphate. In one embodiment of the invention, the column was first treated with a low salt concentration, for example, 10-200 mM of ammonium acetate, such as 20 ... 25 ... 30 ... 35 .. 40 ... 45 ... 50 ... 55 ... 60 ... 65 ... 100 mM, or any concentration within these ranges. This treatment resulted in the elution of AAV vector particles from the resin in the column. Subsequently, the column was treated with a higher concentration of salt in order to elute the empty AAV capsids. An example for use as the second buffer is ammonium acetate with a concentration of 10-800 mM, preferably 500-700 mM, such as 500 ... 550 ... 600 ... 650 ... 700 ... 800 mM, or any concentration within these defined intervals. Using these conditions, AAV vector particles elute initially in the fractions and later in the empty particles. twenty

[0081] As explained above, in an alternative method of the invention, the preparation of the first cation exchange column was applied to an anion exchange column both instead of and additionally in the second cation exchange column. If an anion exchange column is used in addition to the second cation exchange column, it can be used both before and after the second cation exchange column. In addition, a second anion exchange column can be used after the first anion exchange column. Numerous anion exchangers suitable for use with the present invention are known, and include without limitation, MACRO PREP Q (strong anion exchanger available from BioRad, Hercules, CA); UNOSPHERE Q (strong anion exchanger available from BioRad, Hercules, CA); POROS 50HQ (strong anion exchanger available from Applied Biosystems, Foster City, CA); POROS 50D (weak anion exchanger available from Applied Biosystems, Foster City, CA); POROS 50PI (weak anion exchanger 30 available from Applied Biosystems, Foster City, CA); SOURCE 30Q (strong anion exchanger available from Amersham Biosciences, Piscataway, NJ); DEAE SEPHAROSE (weak anion exchanger available from Amersham Biosciences, Piscataway, NJ); Q SEPHAROSE (strong anion exchanger available from Amersham Biosciences, Piscataway, NJ).

[0082] The anion exchange column was first equilibrated using standard buffers and according to the manufacturer's specifications. For example, the column can be equilibrated with, for example, a 5 to 50 mM sodium phosphate buffer, preferably 7-20 mM, such as 10 mM. The sample was then loaded and two elution buffers, a low salt buffer and a high salt buffer were used. The fractions were collected after washing with the low salt and high salt buffers and the protein was detected in the fractions using standard techniques, such as monitoring UV absorption at 260 and 280 nm. Using an anion exchanger, the peaks of the lower salt 40 eluate proteins contain the empty AAV capsids and the higher salt fractions contain the AAV vector particles.

[0083] In particular, in the anion exchange column, the capsids were separated from the AAV vector particles using an appropriate buffer at a pH of between about pH 5 to pH 12, preferably pH 6 to pH 10, and even of more preferably pH7 to pH 9.5, such as pH 7.1, 7.2, 7.3, 7.4 ... 8.0, 8.1, 8.2, 8.3, 8.4 , 8.5 ... 9.0, 9.1, 9.2, 45 9.3, 9.4, 9.5, or any pH between the defined intervals. Buffers suitable for use with anion exchange columns are well known in the art and are generally cationic or hybrid ion in nature. Such buffers include, without limitation, buffers with the following buffer ions: N-methylpiperazine; piperazine; Bis-Tris; Bis-Tris propane; Triethanolamine; Tris; N-methyldiethanolamine; 1-3-diaminopropane; ethanolamine; acetic acid, and the like. To elute the sample, the ionic strength of the starting buffer is increased using a salt, such as NaCl, KCl, sulfate, formate or acetate, at an appropriate pH.

[0084] In one embodiment of the invention, the anion exchange column was first treated with a low salt concentration, for example, 10-100 mM NaCl, such as 10 ... 20 ... 25 .. 30 ... 35 ... 40 ... 45 ... 50 ... 55 ... 60 ... 65 ... 100 n + 4, or any concentration within these intervals After the initial treatment, The column was then treated with a higher concentration of salt in order to elute the empty capsids, such as a higher concentration of NaCl, or with another buffer with a greater ionic strength. An example for use as the second buffer is a sodium acetate buffer or a Tris-based buffer with a concentration of 100-300 mM, preferably 125-200 mM, such as 125 ... 130 ... 140 ... 150 ... 160 ... 170 ... 180 ... 190 ... 200 mM, or any concentration within these defined intervals. After the empty capsids were eluted from the column, AAV vector particles could be recovered using a higher salt concentration. An example for use as the elution buffer is 10 mM Tris buffer containing sodium acetate at a concentration in the range of 100-500 mM, preferably 130-300 mM, such as 100 ... 130 ... 150. .. 200 ... 250 ... 300 ... 350 ... 400 ...

450 ... 500 mM, or any concentration within these defined intervals.

[0085] Using the techniques described above, more than 90% of the empty AAV capsids can be separated from the AAV vector particles. In addition, a high recovery of AAV vector particles was easily achieved, that is, more than 10%, preferably more than 25%, even more preferably more than 50%, such as more than one, can be recovered. 60% AAV vector particles. 5

[0086] Methods for testing empty capsids and AAV vector particles with packaged genomes are known in the art. See, for example, Grimm et al., Gene Therapy (1999) 6: 1322-1330; Sommer et al., Molec. Ther. (2003) 7: 122-128. To test the denatured capsid, the procedures include subjecting the AAV stock solution treated to polyacrylamide gel electrophoresis with SDS, consisting of some gel capable of separating the three capsid proteins, for example, a gel gradient containing Tris-acetate 3-8% in the buffer, 10 then advance the gel until the sample material separates, and transfer the gel into nylon or nitrocellulose membranes, preferably nylon. Antibodies directed against the AAV capsid were then used as the primary antibodies that bind to the proteins of the denatured capsid, preferably a monoclonal antibody directed against the AAV capsid, most preferably the B1 monoclonal antibody directed against AAV-2 ( Wobus et al., J. Virol. (2000) 74: 9281-9293). A secondary antibody was then used, which binds with the primary antibody and contains a means to detect binding with the primary antibody, more preferably, an antibody directed against IgG containing a detection molecule covalently bound to it, most preferably a sheep antibody directed against mouse IgG covalently bound to horseradish peroxidase. A detection procedure was used that semiquantitatively determines the binding between the primary and secondary antibodies, preferably a detection procedure capable of detecting emissions of radioactive isotopes, electromagnetic radiation, or most preferably colorimetric changes, a chemiluminescence detection kit.

[0087] To test the infectious titer, the procedures include planting approximately 100,000 host cells, preferably of human origin, most preferably HeLa cells, in treated tissue culture plates, preferably 24 well treated tissue culture plates, and were incubated for approximately 24 hours after the adenovirus, preferably adenovirus serotype 2, and the treated rAAV 25 stock solution was added to the host cells. The host cells, the adenovirus, and the rAAV stock solution, were allowed to incubate for 24 hours, after which the host cells were fixed, preferably with formaldehyde and glutaraldehyde, and stained with an appropriate agent that will detect the transgene expressed in the rAAV; for example, with rAAV-LacZ, X-gal was contemplated as the staining agent. Other agents of other indicator genes are well known in the art. More general procedures for determining the infectivity titers of 30 vectors containing some transgene are well known in the art. See, for example, Zhen et al., "An Infectious Titer Assay for Adenoassociated Virus (AAV) Vectors with Sensitivity Sufficient to Detect Single Infectious Events." Hum. Gene Ther. (2004) In Press.

3. EXPERIMENTAL PROCEDURE

[0088] Examples of specific embodiments for carrying out the present invention are shown below. The examples are offered for illustrative purposes only, and are not intended in any way to limit the scope of the present invention.

[0089] Efforts have been made to ensure accuracy with respect to the numbers used (eg, quantities, temperature, etc.), but should, of course, be assumed, some error and experimental deviation.

MATERIAL AND PROCEDURES:

RAV 40 PRODUCTION AND PURIFICATION

[0090] Recombinant AAV virions were produced containing the gene encoding human factor IX (rAAV-hFIX) by the triple transfection procedure described in US Patent Nos. 6,001,650 and 6,004,797. The plasmids used were the accessory function plasmid „plade5‟, the AAV auxiliary function plasmid „pHLP19‟, and the recombinant AAV plasmid „phFIX-16‟. Human embryonic kidney (HEK) 293 cells were used as host cells for the production of rAAV virions. Four. Five

[0091] Transfected 293 cells were harvested approximately 72 hours after transfection and disrupted by microfluidization using a Microfluidizer ™ (Microfluidics International Corp., Newton, MA) and the crude lysate was collected and filtered through serial filters. to remove cell debris to create a clarified cell lysate Next, the clarified cell lysate was introduced into a POROS 50HS column to purify AAV vector particles and empty AAV capsids from other cellular components. The 50 AAV vector particles and the empty capsids were eluted from the 50HS POROS column using a buffer containing 20 mM sodium phosphate, 370 mM NaCl, pH 5.5. The AAV preparation containing the AAV vector particles and the empty capsids was diluted 2 times to reduce the salt concentration and was further purified through a Q SEPHAROSE column, the vector particles and the capsules were collected in piston flow AAV vacuums, and buffer concentration and exchange was performed using ultrafiltration and diafiltration techniques. 55

[0092] The final purified product in the POROS 50HS column contained the empty AAV capsids, as well as the AAV vector particles containing recombinant vector genomes. In order to generate samples of

control of each, cesium chloride was added to the purified material of the POROS 50HS column at a density of 1.41 g / ml with mixing, and then subjected to ultracentrifugation at 45.00 rpm using a Ti 70 rotor for 23 hours. Visibly empty bands and those of AAV vector particles were dragged using syringes separately. Empty capsids and purified AAV vector particles were dialyzed separately against a buffer composed of 10 mM sodium phosphate pH 7.4, 140 mM NaCl and 5% sorbital using dialysis cassettes 5 (Pierce) at 4 ° C with Three buffer exchanges.

RESINS AND COLOR CHROMATOGRAPHY:

[0093] Several types of chromatography resins were tested that included anion exchange, cation exchange resins, a chromato-focusing resin and hydrophobic interaction resins (HIC), for their potential to separate empty AAV capsids and AAV vector particles. . A high performance sleeve was used for the resin screening. The resins were packed in a disposable empty column with a bed height of 3 cm (Bio-Rad Laboratories) that were installed in a sleeve. The columns were equilibrated using a buffer containing 10 mM sodium phosphate. The AAV vectors of the clarified HEK293 cell lysate were filtered through a 0.2 µm filter and the empty capsids were then diluted in column equilibration buffer at a 50 mM NaCl (salt) concentration and then They were introduced in the columns. The columns were washed with the equilibrium buffer first and additionally washed with buffer containing 10 mM sodium phosphate and 40 mM NaCl pH 7.4 (low salt wash) to wash the unbound materials. The columns were then treated with elution buffer containing 10 mM sodium phosphate and 1 M NaCl (high salt wash). Materials washed away using the low salt wash were collected as a fraction, and the materials eluted using the high salt wash were collected as a separate fraction. twenty

[0094] After initial screening using disposable columns, larger-scale column chromatography performed on a BIOCAD 700 (Applied Biosystems) column was used to further investigate promising resins and conditions. XK16Glass columns (Amersham Pharmacia) were packaged with different resins using constant flow packing procedures with a linear velocity of 150 cm / hour. Chromatography parameters were programmed using various procedures (see details in each experiment result 25). In general, the programs contain functional blocks of column equilibrium, sample loading, low salt washing, linear or stepwise gradient and a high salt cleaning stage. AAV vector particles and eluted empty capsids in several fractions were monitored and analyzed using the techniques described below.

SDS-PAGE AND WESTERN TRANSFER: 30

[0095] Samples of column fractions were obtained and heated in SDS-PAGE loading buffer containing reducing agent (DTT), and the capsid proteins were resolved in pre-cast gradient polyacrylamide gels (Novex) . Silver staining was performed using SilverXpress (Invitrogen, CA) according to the manufacturer's instructions. Similarly, Western blot analysis was performed after protein transfer resolved by SDS-PAGE on nitrocellulose membranes. A monoclonal antibody (B1, American 35 Research Products, MA) was used as the primary antibody to detect AAV capsid proteins (VP1 VP2 and VP3) by Western blotting. Sheep antibody directed against HRP-conjugated mouse IgG (Promega, WI) was used as the secondary antibody and was detected by the ECL kit (Amersham, United Kingdom).

QUANTITATIVE PCR IN REAL TIME

[0096] The concentration of AAV vector genomes (eg) was measured by quantitative real-time PCR (Q-40 PCR). Samples were diluted and digested with DNase I to remove exogenous DNA. After DNase inactivation, the samples were further diluted and amplified using primers and a TaqManTM fluorogenic probe specific to the DNA sequence between the primers. The number of cycles necessary to achieve a defined level of fluorescence (threshold cycle, Ct) for each sample was measured in an Applied Biosystems Prsim 7700 Sequence Detection System. Plasmid DNA containing sequences identical to the one contained in the AAV vector was used to generate a standard curve in the Q-PCR reaction. The Ct values obtained from the samples were used to determine the genome titer of the vector by normalizing it to the Ct value of the plasmid standard curve.

EXAMPLE 1

UNION PROPERTIES OF EMPTY CAPSIDES AND AAV VECTOR PARTICLES WITH 50 PACKAGED GENOME

[0097] To test whether AAV vector particles were attached to the anion exchange columns, some resins were screened using a high performance sleeve technique. The cell lysate of the 293 cell culture containing AAV vector particles and empty capsids was diluted using 20 mM sodium phosphate buffer to reduce the NaCl concentration to approximately 50 mM and introduced into each column. The columns were then washed and eluted following the procedure described above. The collected samples were subjected to Western Transfer to detect the distribution of AAV particles in the fractions. As shown in Figures 1 and 1B, the AAV capsid protein specific monoclonal antibody detected proteins only

in elution fractions with a high salt concentration (1M NaCl) (Figure 1, Band 3, 5, 7 and 9). These data clearly indicated that AAV vector particles and empty capsids bound to all anion exchange resins (weak and strong exchangers) screened.

EXAMPLE 2

LOAD DIFFERENCES BETWEEN EMPTY CAPSIDES AND AAV VECTOR PARTICLES 5

[0098] Empty capsids and AAV vector particles were separated using CsCl gradient centrifugation. Empty capsids resulted in a visible band at a higher salt density (approximately 1.3 g / cc) and AAV vector particles were distributed as a visible band at a higher salt density (1.38- 1.41 g / cc). Empty capsids and AAV vector particles were prepared as described above and introduced into the columns separately. Three resins, Q 10 SEPHAROSE, POROS 50HQ and UNOSPHERE Q, were used for the column chromatography cycles that were carried out using the same programs to compare elution profiles between empty and full particles. The empty AAV capsids eluted at a lower salt concentration (eluted in the most initial fractions) compared to the AAV vector particles (which eluted in the final fractions); This phenomenon was observed in the three anionic resins tested. In the case of the UNOSPHERE Q resin, the empty capsids were eluted in the 10-15 fraction in a saline gradient of 0 to 500 mM NaCl, while the AAV vector particles were eluted in the 11th fraction; in the case of column Q SEPHAROSE, the empty capsids were eluted in fractions 11, 12 and 13 while AAV vector particles eluted in fractions 13, 14 and 15. The same phenomenon was observed with the POROS column 50HQ when a lower gradient of sodium acetate concentration was used; empty capsids were eluted in fractions 30 to 36, while AAV vector particles were eluted 20 in fractions 36 to 40. These data clearly indicate that there are fundamental load differences between empty AAV capsids and particles of AAV vectors and that the two populations can be separated using these properties by column chromatography techniques. Confirming the separation of empty capsids and AAV vector particles by these resins, the ratio of UV absorption at 260 nm / 280 nm gradually increased in eluted fractions, consistent with differential elution (first eluting place the 25 empty capsids that have a lower 260/280 ratio because they lack DNA).

EXAMPLE 3

EFFECT OF RESINS AND SALTS ON THE EFFECTIVENESS AND RESOLUTION OF THE ELUTION BETWEEN EMPTY CAPSIDES AND AAV VECTOR PARTICLES

[0099] The resins screened in this procedure were all anion exchange resins, but presented 30 differences (charge density, size and composition of the pearl, etc.). The efficiency in binding and separation of empty capsids and AAV vector particles varied from resin to resin. Empty capsids eluted using 110 nM NaCl in column Q SEPHAROSE. In contrast, approximately 65 mM NaCl was sufficient to elute the empty capsids using the UNOSPHERE column, and in the case of the POROS HQ column, 130 mM NaCl was sufficient to elute the empty capsids. 35

[0100] Some different salts were also used in the studies of elution profiles. Sodium chloride, sodium acetate, ammonium acetate and sodium citrate were subjected to comparisons with each other. Using the same program to perform column chromatography cycles, elution of the empty capsids of some fractions was delayed when sodium acetate or ammonium acetate was used compared to sodium chloride, suggesting that different salts have different properties in anionic column chromatography and these properties can be used to enhance resolution in the separation of empty capsids from AAV vector particles.

EXAMPLE 4

DEFINITION OF THE CONDITIONS OF ELUTION OF THE EMPTY CAPSIDES

[0101] Based on the experimental data discussed above, the POROS 50HQ column was used to develop a technique based on column chromatography to separate the empty capsids from the particles of 45 AAV vectors. Empty capsids prepared using CsCl gradient centrifugation as described above were introduced into a column packed with 50HQ POROS resin. In separate cycles, after the initial washing steps with low salt concentrations (50 mM NaCl), the column was washed with either 150 mM sodium acetate, 160 mM sodium acetate or 170 mM sodium acetate. The empty capsids were eluted more effectively when 170 mM NaAc was used. In a separate chromatography cycle using the same salt elution profile, the 50 AAV vector particles remained in the column and then eluted when a linear salt concentration was applied using a higher concentration of sodium chloride.

EXAMPLE 5

SEPARATION OF EMPTY CAPSIDES FROM AAV VECTOR PARTICLES USING ANION EXCHANGE CHROMATOGRAPHY

[0102] To demonstrate that empty capsids and AAV vector particles could be separated using column chromatography techniques, empty capsids and purified AAV particles were mixed together. 3 ml of empty capsids with a concentration of 9E + 13 particles / ml were mixed with 2 ml of filled particles with the concentration of 7E + 12 vector genomes (eg) / ml. The materials were further diluted 3 times using 20 mM sodium phosphate buffer at pH 7.4. 14 ml of this diluted material was introduced into a 50HQ POROS column with a bed volume of 20 ml. The elution profile of the column chromatography described above was used, and the data indicated that the empty capsids were eluted in the saline condition of 10 mM 170 sodium acetate while the AAV vector particles remained in the column and eluted then using a linear gradient of NaCl salt. The UV absorption model (260: 280 nm ratio) of column eluted material during the course of separation was completely consistent with and further demonstrated the effective separation of empty capsids from AAV vector particles. The various eluted fractions of the column were further analyzed using ELISA, Q-PCR, SDS-PAGE and OD analysis of the capsids. All data obtained indicated that the separation of the empty capsids from the AAV vector particles was complete and that the ratio of particles to vector genomes in the fraction of AAV vector particles was 1: 1. In this way, the AAV vector particles were completely separated from the empty capsids, although the starting material (introduced in the column) contained approximately 16 times more empty capsids than vector particles (Figure 2). twenty

EXAMPLE 6

PH EFFECT ON SEPARATION OF EMPTY CAPSIDES OF AAV VECTOR PARTICLES USING ANION EXCHANGE CHROMATOGRAPHY

[0103] To develop a complete column-based purification procedure to remove empty capsids, virions recovered from a cation exchange column (POROS HS) containing 25 empty capsids and AAV vector particles were applied to the POROS 50HQ column. When a similar procedure was used to separate empty capsids and AAV vector particles from samples purified with CsCl, a clear separation was not obtained as observed for prepurified and gradient mixed samples of CsCl, although the two types of particles they remained distinguishable, that is, a partial but incomplete separation of empty capsids and AAV vector particles was observed. Some parameters that can affect the resolution of column chromatography were tested to optimize separation efficiency. Among the parameters tested, it was found that the pH increased the resolution of the separation significantly. Buffers with pH 7.4, pH 8.0, pH 8.5 and pH 9.0 were tested. Empty AAV capsids in the initial column fractions were selectively removed when higher pHs, such as pH 9.0, were used in the procedure, while AAV vector particles eluted at a higher salt concentration in the final fractions. Using pH 9.0, the 35 empty capsids were removed as an individual peak with the UV signature signature model of the highest UV 280 signal and the lowest UV260 signal. In contrast, the second peak contained the AAV vector particles and showed the opposite UV absorption model, dominating UV260 over UV280, as expected for particles filled with AAV vectors containing DNA. The observation was further confirmed by the Q-PCR and SDS-PAGE assays, indicating that the second peak contained the AAV vector particles and the first peak the empty capsids.

EXAMPLE 7

PROCEDURE TO SEPARATE EMPTY AAV CAPSIDES FROM AAV VECTOR PARTICLES USING CHROME IN ANION EXCHANGE COLUMN

[0104] Based on the observation described above, a procedure was designed to separate empty AAV capsids from AAV vector particles using Tris based buffer at pH 8.5 and a 50HQ POROS column resin on a glass column. XK-16 (Amersham Bioscience, Piscataway, NJ). The materials eluted in the initial segments contained the empty capsids and the final segments the AAV vector particles as indicated by the UV absorption models. This was further confirmed by Q-PCR analysis. Vectors eluted at a higher salt concentration in SDS-PAGE were analyzed to determine purity. 50 Vector genomes were determined by Q-PCR and replicated samples were loaded into SDS-PAGE and stained by silver staining. To serve as a control, rAAV virions were purified containing only AAV vector particles using CsCl gradient centrifugation techniques and the same vector genomes were advanced in the SDS-PAGE gels.

[0105] Using these techniques, approximately 60% of the vector was recovered. The recovered vector was essentially free of empty capsids (<10 of the particles were empty capsids) based on the silver staining analysis of the SDS-PAGE (Figure 3). As shown in Figure 3, there was no significant difference in band density (corresponding to total protein) between the control of the empty capsid free vector (lane 1) and

the vector contained in the eluted column fractions (bands 2-5), when all bands were loaded with an equal number of vector genomes.

EXAMPLE 8

SEPARATION OF EMPTY VACUUM PARTICLE CAPSIDES OF AAV USING CHROMATOGRAPHY IN CATIONIC EXCHANGE COLUMN 5

[0106] Cation exchange column chromatography was also investigated for its potential to separate empty capsids from AAV vector particles. The AAV preparation of the first cation exchange column (described in the materials and procedures section) containing the empty capsids and the AAV vector particles was applied to a POROS HS resin. The column was first equilibrated with 20 mM sodium phosphate buffer containing 200 mM NaCl at pH 7.4. The AAV preparation containing AAV 10 vector particles and empty capsids obtained from the first cation exchange column was diluted using 20 mM sodium phosphate, pH 7.4 to reduce the salt concentration to approximately 200 mM NaCl. This material was then introduced in the POROS HS column. A 500 to 700 mM ammonium acetate gradient containing 10 mM Tris at pH 8.5 was then applied to the column. Using this gradient the elution protocol, the AAV particles eluted first, and effectively separated from the empty capsids eluted at a higher concentration of 15 ammonium acetate. This contrast in separation was observed using the anion exchange resin (Example 7 above) in which the empty capsids were eluted at a lower salt concentration with respect to the AAV vector particles.

[0107] Additional information was provided regarding the binding and elution models of empty capsids and AAV vector particles in the cation exchange column by UV absorbance of the column eluate. For example, when the cation exchange column was advanced to pH 8.5, the chromatograph demonstrated a UV absorbance model with absorption at 260 nm (corresponding to AAV vector particles) dominant, in the initial fractions and a absorption at 280 nm (corresponding to empty capsids) dominant in the final elution fractions. As shown in Figure 4, when the same vector genomes were subjected to the silver staining analysis of the SDS-PAGE, the amount of protein increased significantly from the initial fractions to the final fractions, indicating that the initial fractions They contained less empty capsids.

[0108] Based on these observations, separation of empty AAV capsids from AAV vector particles (containing DNA) can be achieved using cation exchange chromatography. Figure 5 shows an SDS-PAGE gel demonstrating separation. Next, a preparation of AAV vectors containing empty capsids and AAV vector particles eluted from a cation exchange column was introduced into the cation exchange column 30. that the conditions required to achieve separation were not used) and was eluted in a step gradient using ammonium acetate. Fractions containing vector genomes were identified using the Q-PCR, and aliquots of these fractions were subjected to the silver staining analysis of the SDS-PAGE. It is clear that the protein signals in the eluted fractions contained less protein signal per 35g input with respect to the material that was introduced in the second column, demonstrating that the empty capsids were removed from the AAV vector particles. The eluted vectors of the three independent experiments are shown in band 2 to 4, indicating the consistency and repeatability of the observations.

[0109] In this manner, the procedures for separating empty capsids from AAV vector particles are described. Although the preferred embodiments of the subject invention have been described in some detail, it is understood that obvious variations can be made without departing from the spirit and scope of the invention as defined by the appended claims.

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Claims (15)

1. A method for purifying AAV vector particles from an AAV preparation comprising AAV vector particles and empty AAV capsids, to provide a product substantially free of empty AAV capsids, said method comprising: a) providing a host cell comprising AAV vector particles; 5 b) lyse said host cell to obtain a crude cell lysate comprising AAV vector particles and empty AAV capsids; c) applying said crude cell lysate to a first cation exchange chromatography column under conditions in which said AAV vector particles and said empty AAV capsids are attached to the column; 10 d) eluting said AAV vector particles and said AAV empty capsids under non-separation conditions to provide an AAV preparation comprising AAV vector particles and empty AAV capsids; e) applying the AAV preparation from (d) to a second column of cation exchange chromatography under conditions under which said AAV vector particles and said empty AAV capsids are attached to the column; f) adding a low salt buffer to the column of (e) under conditions in which the AAV vector particles are eluted and the empty AAV capsids remain attached to the column; Y g) collecting the eluted fractions of (f) comprising AAV vector particles to provide an AAV product substantially free of empty AAV capsids. twenty 2. The method of claim 1, wherein said first cation exchange column comprises a carboxymethylated or sulfonated matrix. 3. The method of claim 2, wherein said matrix comprises the functional ligand R-SO3-. 4. The method of claim 1 wherein said second cation exchange column comprises a carboxymethylated or sulfonated matrix. 25 5. The method of claim 4, wherein said matrix comprises the functional ligand RSO3-. 6. The method of claim 1, further comprising: h) applying the fractions of step (g) to an anion exchange chromatography column under conditions where said AAV vector particles and AAV capsids, if present, are attached to the column; 30 i) adding a low salt buffer to the column of (h) under conditions in which the empty AAV capsids are eluted and the AAV vector particles remain attached to the column; j) adding a high salt buffer to the column of (i) under conditions where the AAV vector particles are eluted; k) collecting the fractions of (j) comprising AAV vector particles to provide a product of AAV substantially free of empty AAV capsids. 7. A method for purifying AAV vector particles from an AAV preparation comprising AAV vector particles and empty AAV capsids, to provide an AAV product substantially free of empty AAV capsids, said process comprising: a) providing a host cell comprising AAV vector particles; 40 b) lyse said host cell to obtain a crude cell lysate comprising AAV vector particles and empty AAV capsids; c) clarifying said crude cell lysate to provide a clarified cell lysate; d) applying said clarified cell lysate to a first cation exchange chromatography column comprising a matrix with the functional ligand R-SO3-, under conditions where said AAV vector particles 45 and said empty capsids are attached to the column ; e) eluting said AAV vector particles and said empty AAV capsids under non-separation conditions to provide an AAV preparation comprising AAV vector particles and empty AAV capsids; f) applying the AAV preparation from (e) to a second column of cation exchange chromatography under conditions under which said AAV vector particles and said empty AAV capsids are attached to the column; 5 g) adding a low salt buffer to the column of (f) under conditions where AAV vector particles elute and empty AAV capsids remain attached to the column; h) collect the eluted fractions of (g) comprising AAV vector particles; i) applying the fractions of step (h) to an anion exchange chromatography column under conditions where said AAV vector particles and empty AAV capsids, if present, are attached to the column; j) adding a low salt buffer to the column of (i) under conditions in which the empty AAV capsids are eluted and the AAV vector particles remain attached to the column; k) adding a high salt buffer to the column of (j) under conditions where the AAV vector particles are eluted; and 15 l) collecting eluted fractions of (k) comprising AAV vector particles to provide an AAV product substantially free of empty AAV capsids. A method for purifying AAV vector particles from an AAV preparation comprising AAV vector particles and empty AAV capsids, to provide an AAV product substantially free of empty AAV capsids, said process comprising: a) providing a host cell comprising AAV vector particles; b) lyse said host cell to obtain a crude cell lysate comprising AAV vector particles and empty AAV capsids; c) applying said crude cell lysate to a cation exchange chromatography column under conditions where said AAV vector particles and said empty AAV capsids are attached to the column; 25 d) eluting said AAV vector particles and said AAV empty capsids under non-separation conditions to provide an AAV preparation comprising AAV vector particles and empty AAV capsids; e) applying the AAV preparation from (d) to an anion exchange chromatography column under conditions where said AAV vector particles and said empty AAV capsids are attached to the column; f) adding a low salt buffer to the column of (e) under conditions in which the empty AAV capsids are eluted and the AAV vector particles remain attached to the column; g) adding a high salt buffer to the column of (f) under conditions where the AAV vector particles are eluted; 35 h) collecting eluted fractions from (g) comprising AAV vector particles to provide an AAV product substantially free of empty AAV capsids. 9. The method of claim 8, further comprising: i) applying the AAV preparation from (h) to a second column of anion exchange chromatography under conditions under which said AAV vector particles and said empty AAV capsids, if present, are attached to the column; j) adding a low salt buffer to the column of (i) under conditions in which the empty AAV capsids are eluted and the AAV vector particles remain attached to the column; k) adding a high salt buffer to the column of (j) under conditions where the AAV vector particles are eluted; Four. Five l) collecting eluted fractions of (k) comprising AAV vector particles to provide an AAV product substantially free of empty AAV capsids. 10. The method of claim 8, further comprising: i) applying the AAV preparation of (h) to a second cation exchange chromatography column under conditions where said AAV vector particles and said empty AAV capsids are attached to the column; j) adding a low salt buffer to the column of (i) under conditions in which the AAV vector particles elute and the empty AAV capsids remain attached to the column; and 5 k) collecting the eluted fractions of (j) comprising AAV vector particles to provide an AAV product substantially free of empty AAV capsids. 11. The method of any of claims 1-10 wherein the AAV vector particles are present in said AAV product in an amount of at least 75%. 12. The method of any of claims 1-10, in which the AAV vector particles are present in said AAV product in an amount of at least 85%. 13. The method of any of claims 1-10, wherein the AAV vector particles are present in said AAV product in an amount of at least 90%. 14. The method of any of claims 1-10, wherein said AAV vector particles are derived from AAV-2. fifteen 15. The method of any of claims 1-10, wherein said AAV vector particles are derived from AAV-5.