WO2015196179A1 - Methods of packaging multiple adeno-associated virus vectors - Google Patents

Abstract

Provided herein are methods related to co-packaging of multiple rAAV particles, e.g., by introducing multiple nucleic acid vectors encoding proteins or polypeptides or RNAs of interest into a single cell preparation.

Description

METHODS OF PACKAGING MULTIPLE ADENO-ASSOCIATED VIRUS VECTORS

CROSS-REFERENCED TO RELATED APPLICATIONS This application claims the benefit under 35 U.S.C. § 119(e) of U.S. provisional application number 62/015,031, filed June 20, 2014, which is incorporated by reference herein in its entirety.

FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under P01 HL059412 awarded by the National Institutes of Health National Heart, Lung, and Blood Institute and the National Institutes of Health. The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Recombinant adeno-associated virus (rAAV) particles are a promising method for therapeutic gene delivery to treat a multitude of diseases. In some cases, use of multiple rAAV particles, as a mixed population, is desirable. For example, it may be that the transgene is too large to be effectively packaged into a single rAAV particle, such that two rAAV particles must be used to package the entire transgene. Alternatively, multiple transgenes may be required for effective treatment, for instance if multiple proteins are involved in disease progression. Further, it may be desirable to use multiple promoters to target different tissues. For these reasons, mixed populations of rAAV particles may be appropriate for certain types of gene therapy. Unfortunately, hurdles still exist for rapidly and cost-effectively producing mixed populations of rAAV particles.

SUMMARY OF THE INVENTION

Aspects of the disclosure are based, in part, on the development of an efficient and inexpensive method of co-packaging of multiple plasmids containing different expression cassettes using a single transfection step to produce preparations of recombinant adeno- associated virus (rAAV) particles containing a desired ratio of the different expression cassette plasmids. It was found that two plasmids, either encoding different transgenes or encoding the same transgenes but under the control of different promoters, could be transfected simultaneously into cells at several ratios. It was surprisingly found that the transduced cells produced a mixed population of rAAV particles having a ratio that was approximately the same as the input ratio of the two plasmids at the transfection step. This study showed that mixed rAAV particle preparations containing rAAV particles

encapsidating different nucleic acid molecules could be prepared using a single step for introducing the plasmids into producer cells.

Accordingly, aspects of the disclosure relate to methods of co-packaging rAAV particles.

Some aspects of the disclosure relate to methods of producing a recombinant adeno- associated virus rAAV particle preparation having a target ratio of at least a first rAAV particle to a second rAAV particle (e.g., a target ratio of a first rAAV particle to a second rAAV particle, or a target ratio of a first rAAV particle to a second rAAV particle to a third rAAV particle, or a target ratio of a first rAAV particle to a second rAAV particle to a third rAAV particle to a fourth rAAV particle, etc.), the method comprising

(a) contacting a cell preparation with

(i) at least two (e.g., two, three, four, five, or more) nucleic acid vectors described herein (e.g., each containing a construct comprising a heterologous nucleic acid region encoding a protein or polypeptide or an RNA and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region);

wherein the cell preparation is contacted under conditions sufficient for producing at least two (e.g., two, three, four, five, or more) rAAV particles comprising the constructs of the at least two (e.g., two, three, four, five, or more) nucleic acid vectors; and

(b) isolating the at least two (e.g., two, three, four, five, or more) rAAV particles from the cell preparation, thereby producing a rAAV preparation having a target ratio of the at least two (e.g., two, three, four, five, or more) rAAV particles. In some embodiments, a method of producing a recombinant adeno-associated virus (rAAV) particle preparation having a target ratio of a first rAAV particle to a second rAAV particle is provided, the method comprising:

(a) contacting a cell preparation with:

(i) a first nucleic acid vector containing a first construct comprising a heterologous nucleic acid region encoding a first protein or polypeptide and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region;

(ii) a second nucleic acid vector containing a second construct comprising a heterologous nucleic acid region encoding a second protein or polypeptide and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region,

wherein the cell preparation is contacted under conditions sufficient for producing a first rAAV particle comprising the first construct and a second rAAV particle comprising the second construct; and

(b) isolating the first rAAV particle and the second rAAV particle from the cell preparation, thereby producing a rAAV preparation having a target ratio of the first rAAV particle to the second rAAV particle.

In some embodiments, the cell preparation is contacted simultaneously with the first nucleic acid vector and the second nucleic acid vector. In some embodiments, the first nucleic acid vector and the second nucleic acid vector are present in an initial ratio of the first nucleic acid vector to the second nucleic acid vector when contacted with the cell

preparation. In some embodiments, the target ratio of the first rAAV particle and the second rAAV particle is compared to the initial ratio of the first nucleic acid vector to the second nucleic acid vector. In some embodiments, the target ratio of the first rAAV particle to the second rAAV particle is within 10% of the initial ratio of the first nucleic acid vector to the second nucleic acid vector. In some embodiments, the initial ratio is 1: 1, 1:9 or 9: 1 of the first nucleic acid vector to the second nucleic acid vector. In some embodiments, the target ratio of the first rAAV particle to the second rAAV particle is measured after isolating the first rAAV particle and the second rAAV particle from the cell preparation. In some embodiments, the target ratio of the first rAAV particle to the second rAAV particle is measured by measuring a level of DNA from the first rAAV particle and a level of DNA from the second rAAV particle. In some embodiments, the level of DNA is measured using PCR, sequencing or flow cytometry. In some embodiments, the level of DNA is measured using PCR and the PCR is quantitative PCR.

In some embodiments of any one of the methods described herein, step (a) comprises transfecting the cell preparation with the first nucleic acid vector and the second nucleic acid vector. In some embodiments, the first nucleic acid vector and the second nucleic acid vector are a first plasmid and a second plasmid. In some embodiments, the method further comprises contacting the cell preparation with at least one helper plasmid. In some embodiments, the at least one helper plasmid is a first helper plasmid comprising a rep gene and a cap gene and a second helper plasmid comprising a Ela gene, a Elb gene, a E4 gene, a E2a gene, and a VA gene.

In some embodiments of any one of the methods described herein, step (a) comprises infecting the cell preparation with the first nucleic acid vector and the second nucleic acid vector. In some embodiments, the first nucleic acid vector is contained within a first herpes simplex virus type 1 (HSV) particle and the second nucleic acid vector is contained within a second HSV particle. In some embodiments, the first nucleic acid vector is contained within a first baculovirus particle and the second nucleic acid vector is contained within a second baculovirus particle.

In some embodiments of any one of the methods described herein, step (a) comprises incubating the cell preparation for at least 60 hours after contacting the cell preparation with the first nucleic acid vector and the second nucleic acid vector.

In some embodiments of any one of the methods described herein, step (b) comprises lysing the cell preparation and extracting the first rAAV particle and the second rAAV particle. In some embodiments, the first rAAV particle and the second rAAV particle are extracted simultaneously. In some embodiments, two or more vectors are provided in a ratio of interest (e.g., a specified ratio or range of ratios) to produce different rAAVs in the cell preparation, and a preparation of the different rAAV particles is prepared from the cell preparation. In some embodiments, the different rAAV particles are isolated together (e.g., using an isolation procedure that isolates a mixture of the different rAAV particles).

In some embodiments, a preparation of two rAAV particles described herein can be used to deliver different genes, different gene fragments (e.g., different regions of the same gene or different genes), with or without promoters, and/or with or without other regulatory nucleic acid sequences to a cell (e.g., in vitro or in a subject). In some embodiments, the genes or gene fragments are human genes. In some embodiments, a protein or polypeptide encoded by a nucleic acid described herein is a full length protein or polypeptide. In some embodiments, a protein or polypeptide encoded by a nucleic acid described herein is a fragment of a full length protein or polypeptide (e.g., a functional fragment). In some embodiments, the nucleic acids (e.g., genes or gene fragments) are recombinant nucleic acids (e.g., recombinant genes). In some embodiments, the genes or gene fragments are used for gene rescue. In some embodiments, the genes or gene fragments are used to provide one or more RNAs or proteins to a cell or a subject. In some embodiments, the one or more RNAs or proteins are therapeutic RNAs or proteins (e.g., they encode a naturally occurring or recombinant enzyme, cytokine, receptor, kinase, regulatory protein, ligand, antibody, or other RNA or protein that is useful to assist in the treatment of a disease or condition). In some embodiments, a preparation of rAAV particles are delivered to a subject (e.g., a human subject) for example via injection or other delivery route. In some embodiments, the subject is a subject having a disease or condition that can be treated with the one or more nucleic acids that are delivered using the rAAV particles. In some embodiments, a preparation of rAAV particles are contacted to a preparation of cells in vitro. In some embodiments, the cells are cells from a subject (e.g., isolated from a human subject) and the cells are administered (e.g., re-administered to the human subject) after being modified by the nucleic acids in the rAAV particles (e.g., after genome editing or after receiving one or more constructs that express an RNA or protein of interest such as a therapeutic RNA or protein). In some embodiments of any one of the methods described herein, the first rAAV particle and the second rAAV particle are each rAAV 2/9 pseudotyped particles. In some embodiments of any one of the methods described herein, more than two rAAV particles are each rAAV 2/9 pseudotyped particles.

The details of one or more embodiments of the disclosure are set forth in the description below. Other features or advantages of the present disclosure will be apparent from the following drawings and detailed description of several embodiments, and also from the appending claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present disclosure, which can be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

FIG. 1 is a photograph of a DNA gel showing differential packaging of expression cassettes combined prior to transfection. The vectors contained different transgenes which were used for delineation. DNA was amplified from each preparation and ran on 2% agarose gel. GFP band is 171 bp and mCherry is 191 bp. Lanes 1-3 contain DNA amplified from vectors in crude lysate (post-benzonase treatment); lanes 4-6 contain DNA amplified from vectors purified via iodixanol gradient originating from the crude lysates in lanes 1-3. Vector constructs were co-packaged in AAV9 at ratios of GFP to mCherry 1:9, 1: 1 and 9: 1, respectively. Gel is one representative image of three separate co-packaging experiments.

FIG. 2 is a graph showing total vector genomes resulting from co-packaging. DNA was extracted from post-benzonase treated crude lysates (Crude) or after iodixanol purification (Purified) of GFP and mCherry vectors co-packaged at 1:9, 1: 1 or 9: 1 ratios, respectively. Total vector genome titer was determined either directly, using a common CMV enhancer (Single Primer Set), or from the summation of each vector titer using transgene specific primers (Double Primer Set). Data represent the average total titer from crude (final volume of 3 mL) or purified samples (final volume of 0.2 mL) at each ratio assayed in triplicate.

FIG. 3 is a graph showing that two expression cassettes can be packaged at predicted ratios combined prior to transfection. Quantitative PCR using transgene specific primers on iodixanol purified GFP or mCherry vectors was performed to determine the respective contribution of each individual vector in the total preparation when co-packaged at 1:9, 1: 1 and 9: 1 ratios, respectively. Each vector yield is expressed as a percentage of total vector genome, with 100% obtained from the summation of the titers determined using transgene specific primers for either GFP or mCherry. Data represent the average of three separate experiments for each ratio.

FIG. 4 is a graph showing in vitro characterization of co-packaged reporter vectors. The percent contribution of either AAV9-GFP or AAV9-mCherry to the total infectious titer (GFP + mCherry) was determined via single cell fluorescence assay in C12 cells. Data represent the average of two separate experiments for each ratio.

FIGs. 5A and B are a photograph and a graph showing co-packaging of therapeutic constructs. FIG. 5A) AAV9-LSP-coGAA and AAV9-DES-coGAA were co-packaged and purified at 1:9 (lanes 1, 4 and 7), 1: 1 (lanes 2, 5 and 8) and 9: 1 ratios (lanes 3, 6 and 9), respectively. AAV9-LSP-coGAA band is 288 bp and AAV9-DES-coGAA is 453 bp. DNA was amplified from each preparation and ran on 1.5% agarose gel. FIG. 5B) DNA extracted from co-packaged AAV9-LSP-coGAA and AAV9-DES-coGAA was subjected to quantitative PCR to determine the respective contribution of each individual vector in the total preparation when co-packaged at 1:9, 1: 1 and 9: 1 ratios, respectively. Each vector yield is expressed as a percentage of total vector genome, with 100% obtained from the summation of the titers determined using promoter specific primers for either LSP or DES. Data represent the average of three separate experiments for each ratio. LSP, liver specific promoter; DES, desmin promoter; coGAA, human codon-optimized acid a-glucosidase.

FIG. 6 is a photograph of a DNA gel showing vectors co-packaged at ratios 1:9 GFP to mCherry, 1: 1, and 9: 1. Top: Standard of 10¹⁰ to 10⁵ total copies of the combined constructs. GFP band is 171 bp and mCherry is 191 bp. Bottom: Lanes 1-3 contain DNA amplified from vectors in crude lysate (post-benzonase treatment); lanes 4-6 contain DNA amplified from vectors purified via iodixanol gradient.

DETAILED DESCRIPTION OF THE INVENTION

Limiting factors in large pre-clinical and clinical studies utilizing adeno-associated virus (AAV) particles for gene therapy are focused on the restrictive packaging capacity, the overall yields and the versatility of the production methods for single AAV vector production. Furthermore, applications where multiple vectors are needed to provide long expression cassettes, whether due to long cDNA sequences or the need of different regulatory elements, require that each vector be packaged and characterized separately, directly affecting labor and cost associated with such manufacturing strategies.

As described herein, a rapid and inexpensive method was devised for co-packaging multiple expression constructs encoding different proteins or encoded the same proteins with different promoters into multiple recombinant adeno-associated virus (rAAV) particles, to produce a mixed population of rAAV particles. It was surprisingly found that the input ratio of two plasmids containing two different expression constructs correlated well with the output ratio of rAAV particles containing the two different expression constructs, demonstrating that the method could be used to reliably predict output ratios of rAAV particles based on the initial ratio of plasmids. This study showed feasibility and

reproducibility of a method that allows for two constructs, differing in either transgene or control elements, to be efficiently co-packaged and characterized simultaneously, reducing time and cost of manufacturing and release testing.

Accordingly, aspects of the disclosure relate to methods of producing a recombinant adeno-associated virus rAAV particle preparation having a target ratio of at least a first rAAV particle to a second rAAV particle (e.g., a target ratio of a first rAAV particle to a second rAAV particle, or a target ratio of a first rAAV particle to a second rAAV particle to a third rAAV particle, or a target ratio of a first rAAV particle to a second rAAV particle to a third rAAV particle to a fourth rAAV particle, etc.), the method comprising

(a) contacting a cell preparation with (i) at least two (e.g., two, three, four, five, or more) nucleic acid vectors described herein (e.g., each containing a construct comprising a heterologous nucleic acid region encoding a protein or polypeptide or an RNA and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region);

wherein the cell preparation is contacted under conditions sufficient for producing at least two (e.g., two, three, four, five, or more) rAAV particles comprising the constructs of the at least two (e.g., two, three, four, five, or more) nucleic acid vectors; and

(b) isolating the at least two (e.g., two, three, four, five, or more) rAAV particles from the cell preparation, thereby producing a rAAV preparation having a target ratio of the at least two (e.g., two, three, four, five, or more) rAAV particles.

In some embodiments, the method comprises:

(a) contacting a cell preparation with

(i) a first nucleic acid vector described herein (e.g., containing a first construct comprising a heterologous nucleic acid region encoding a first protein or polypeptide and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region);

(ii) a second nucleic acid vector described herein (e.g., containing a second construct comprising a heterologous nucleic acid region encoding a second protein or polypeptide and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region),

wherein the cell preparation is contacted under conditions sufficient for producing a first rAAV particle comprising the first construct and a second rAAV particle comprising the second construct; and

(b) isolating the first rAAV particle and the second rAAV particle from the cell preparation, thereby producing a rAAV preparation having a target ratio of the first rAAV particle to the second rAAV particle.

In some embodiments, the method comprises:

(a) contacting a cell preparation with (i) a first nucleic acid vector described herein (e.g., containing a first construct comprising a heterologous nucleic acid region encoding a first protein or polypeptide or RNA and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region);

(ii) a second nucleic acid vector described herein (e.g., containing a second construct comprising a heterologous nucleic acid region encoding a second protein or polypeptide or RNA and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region),

(iii) a third nucleic acid vector described herein (e.g., containing a third construct comprising a heterologous nucleic acid region encoding a third protein or polypeptide or RNA and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region),

wherein the cell preparation is contacted under conditions sufficient for producing a first rAAV particle comprising the first construct, a second rAAV particle comprising the second construct, and a third rAAV particle comprising the third construct; and

(b) isolating the first rAAV particle, the second rAAV particle, and the third rAAV particle from the cell preparation, thereby producing a rAAV preparation having a target ratio of the first rAAV particle to the second rAAV particle to the third rAAV particle.

In some embodiments, the method comprises:

(a) contacting a cell preparation with

(i) a first nucleic acid vector described herein (e.g., containing a first construct comprising a heterologous nucleic acid region encoding a first protein or polypeptide or RNA and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region);

(ii) a second nucleic acid vector described herein (e.g., containing a second construct comprising a heterologous nucleic acid region encoding a second protein or polypeptide or RNA and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region), (iii) a third nucleic acid vector described herein (e.g., containing a third construct comprising a heterologous nucleic acid region encoding a third protein or polypeptide or RNA and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region),

(iv) a fourth nucleic acid vector described herein (e.g., containing a fourth construct comprising a heterologous nucleic acid region encoding a fourth protein or polypeptide or RNA and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region),

wherein the cell preparation is contacted under conditions sufficient for producing a first rAAV particle comprising the first construct, a second rAAV particle comprising the second construct, a third rAAV particle comprising the third construct, and a fourth rAAV particle comprising the fourth construct; and

(b) isolating the first rAAV particle, the second rAAV particle, the third rAAV particle, and the fourth rAAV particle from the cell preparation, thereby producing a rAAV preparation having a target ratio of the first rAAV particle to the second rAAV particle to the third rAAV particle to the fourth rAAV particle.

Ratios

In some embodiments, the first nucleic acid vector and the second nucleic acid vector are present in an initial ratio of the first nucleic acid vector to the second nucleic acid vector when contacted with the cell preparation. In some embodiments, the initial ratio is determined by adding a known concentration of the first nucleic acid vector and a known concentration of the second nucleic acid vector to a composition and contacting the composition with the cell preparation. In some embodiments, the initial ratio is determined by measuring the concentration of the first nucleic acid vector and the second nucleic acid vector, e.g., when present together in a composition. The measuring may be done using any method known in the art, e.g., by PCR.

The initial ratio of the first nucleic acid vector to the second nucleic acid vector (and optionally third nucleic acid vector, fourth nucleic acid vector, etc.) may be any ratio that is suitable for obtaining a desired target ratio. The target ratio will depend upon the disease to be treated, the proteins or polypeptides to be delivered, the tissue(s) to be targeted, the promoter to be used, the size of nucleic acid vectors and other such considerations within the knowledge of the person skilled in the art. In some embodiments, if the sizes of the nucleic acid vectors are not approximately equal, the ratios may be adjusted to compensate for differences in packaging efficiency. For example, the molar ratios of the nucleic acid vectors may be adjusted to produce equimolar input ratios that result in appropriate ratios of output rAAV particles, as smaller vectors, e.g., of about 4.2-4.7 kb in size, are generally packaged more abundantly. In some embodiments, for instance, if one nucleic acid vector (e.g., pTR-X plasmid) is ¾ the size of the other nucleic acid vector (e.g., pTR-Y plasmid), then the amount of pTR-Y may be increased to compensate for the size difference between the two vectors. An exemplary calculation for determining molar ratio is shown below:

Calculating and producing equimolar ratios of nucleic acid vectors, e.g., upon transfection, can be done using routine techniques. In some embodiments, the initial ratio

(e.g., initial molar ratio) is 1: 1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1: 10, 1:20, 1:30, 1:40,

1:50, 1:60, 1:70, 1:80, 1:90 or 1: 100 (or any ratio in between 1: 1 and 1: 100) of the first nucleic acid vector to the second nucleic acid vector. In some embodiments, if more than two nucleic acid vectors (e.g., three or four nucleic acid vectors) are utilized, then the initial ratio is, for example, 1: 1: 1, 1: 1: 1: 1, 1:2:2, 1:2:2: 1, 1:2:2:2, 1:2:3, 1:2:3:4, 1:2: 1, 1:2: 1:2, 1:2: 1: 1 (or any ratio between 1: 1: 1 and 1: 100: 100 or between 1: 1: 1: 1 and 1: 100: 100: 100) of the more than two nucleic acid vectors. It should be appreciated the ratio of any two particular nucleic acid vectors can be different (e.g., 1:2 or 1:2:3 or 1:2: 1:2). In some embodiments, the target ratio is 1: 1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, 1: 10, 1:20, 1:30, 1:40, 1:50, 1:60, 1:70, 1:80, 1:90 or 1: 100 (or any ratio in between 1: 1 and 1: 100) of the first rAAV particle to the second rAAV particle. In some embodiments, if more than two nucleic acid vectors (e.g., three or four nucleic acid vectors) are utilized, then the target ratio is, for example, 1 : 1: 1, 1: 1: 1: 1, 1:2:2, 1:2:2: 1, 1:2:2:2, 1:2:3, 1:2:3:4, 1:2: 1, 1:2: 1:2, 1:2: 1: 1 (or any ratio between 1: 1: 1 and 1: 100: 100 or between 1: 1: 1: 1 and 1: 100: 100: 100) of the more than two rAAV particles (e.g., three or four rAAV particles). However, it should be appreciated that any initial ratio of interest between two or more vectors or constructs can be used.

In some embodiments, the target ratio is compared to the initial ratio. In some embodiments, the target ratio of the first rAAV particle to the second rAAV particle is compared to the initial ratio of the first nucleic acid vector to the second nucleic acid vector. The comparison may be done, e.g., with the assistance of software on a computer. In some embodiments, the target ratio is within a certain percentage of the initial ratio. In some embodiments, the target ratio is within 20%, 15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% of the initial ratio. In some embodiments, the target ratio of the first rAAV particle to the second rAAV particle is within a certain percentage of the initial ratio of the first nucleic acid vector to the second nucleic acid vector. In some embodiments, the target ratio of the first rAAV particle to the second rAAV particle is within 20%, 15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% of the initial ratio of the first nucleic acid vector to the second nucleic acid vector. The percentage may be determined, e.g., by comparing the amount of the first rAAV particle and the second rAAV particle in the rAAV preparation. In some embodiments, the target ratio is within 0-20%, 0-15%, 0-10%, 0-9%, 0-8%, 0-7%, 0-6%, 0- 5%, 1-10%, 1-9%, 1-8%, 1-7%, 1-6%, 1-5%, 2-10%, 2-9%, 2-8%, 2-7%, 2-6%, 2-5%, 3- 10%, 3-9%, 3-8%, 3-7%, 3-6%, or 3-5% of the initial ratio. In some embodiments, the target ratio of the first rAAV particle to the second rAAV particle is within 0-20%, 0-15%, 0-10%, 0-9%, 0-8%, 0-7%, 0-6%, 0-5%, 1-10%, 1-9%, 1-8%, 1-7%, 1-6%, 1-5%, 2-10%, 2-9%, 2- 8%, 2-7%, 2-6%, 2-5%, 3-10%, 3-9%, 3-8%, 3-7%, 3-6%, or 3-5% of the initial ratio of the first nucleic acid vector to the second nucleic acid vector.

In some embodiments, the initial ratio and/or the target ratio are measured. The initial and/or target ratio may be measured using any method known in the art or described herein (see, e.g., Current Protocols in Molecular Biology, Wiley Intersciences), e.g., using a DNA- detection assay (e.g., PCR, sequencing, or probes), a protein detection assay (e.g., Western blot, silver stain, coomassie stain, immunohistochemistry, flow cytometry or

immunofluorescence), or a virus infectivity assay (e.g., a green cell assay). A PCR assay may be any type of PCR known in the art including, but not limited to quantitative PCR. A sequencing assay may be any type of sequencing known in the art including, Sanger sequencing or massive parallel sequencing (e.g., Ion Torrent, pyrosequencing, sequencing by synthesis, and sequencing by ligation). In some embodiments, the target ratio of the first rAAV particle to the second rAAV particle is measured after isolating the first rAAV particle and the second rAAV particle from the cell preparation. In some embodiments, the target ratio of the first rAAV particle to the second rAAV particle is measured by measuring a level of DNA from the first rAAV particle and a level of DNA from the second rAAV particle. Nucleic acid vectors and rAAV particles

Aspects of the disclosure relate to nucleic acid vectors for co-packaging into rAAV (recombinant adeno-associated virus) particles. The produced rAAV particles have many uses, e.g., in methods and pharmaceutical compositions for treating a disease in a subject in need thereof (e.g., a subject having a disease involving reduced protein expression that may be treated with gene therapy), for infecting cells to screen rAAV particles for a desired phenotype (e.g., upregulation of a protein or polypeptide of interest in the cell), or for infecting animals to screen for pharmacokinetics and/or therapeutic efficacy of an rAAV.

In some embodiments, a first nucleic acid vector and a second nucleic acid vector are contemplated for use in a method described herein. In some embodiments, further nucleic acid vectors are contemplated for use in a method described herein (a first, second, third, fourth, and/or fifth nucleic acid vector, etc.). The terms "first", "second", "third", etc., are not meant to imply a specific order or importance unless explicitly indicated otherwise.

In some embodiments, each nucleic acid vector comprises a construct (e.g., an expression construct) comprising (a) one or more heterologous nucleic acid regions comprising a sequence encoding a protein or polypeptide of interest or encoding an RNA of interest (e.g., a microRNA or a small hairpin RNA (shRNA)) and (b) one or more regions comprising inverted terminal repeat (ITR) sequences (e.g., wild-type ITR sequences or engineered ITR sequences) flanking the one or more heterologous nucleic acid regions. In some embodiments, each nucleic acid vector is circular. In some embodiments, each nucleic acid vector is a plasmid (e.g., comprising an origin of replication (such as an E. coli ORI) and optionally a selectable marker (such as an Ampicillin or Kanamycin selectable marker)). In some embodiments, each nucleic acid vector is single- stranded. In some embodiments, each nucleic acid vector is double-stranded. In some embodiments, a double- stranded nucleic acid vector may be, for example, a self-complimentary vector that contains a region of the nucleic acid vector that is complementary to another region of the nucleic acid vector, initiating the formation of the double-strandedness of the nucleic acid vector. In some embodiments, the nucleic acid vector comprises a baculovirus or a HSV genomic sequence. In some embodiments the genomic sequence is modified to remove genes for replication of a baculovirus or HSV. Baculovirus and HSV nucleic acid vectors and genomic sequences are known in the art (see, e.g., Clement et al. Large-Scale Adeno-Associated Viral Vector Production Using a Herpesvirus-Based System Enables Manufacturing for Clinical Studies. Human Gene Therapy. 20:796-806; and Kotin. Large-scale recombinant adeno-associated virus production. Human Molecular Genetics, 2011, Vol. 20, Review Issue 1, R2-R6).

In some embodiments, as part of a method described herein, each construct contained within each nucleic acid vector is packaged within a viral capsid to produce one or more rAAV particles (e.g., a first rAAV particle comprising a first construct and a second rAAV particle comprising a second construct). Accordingly, in some embodiments, each rAAV particle comprises a viral capsid and a construct as described herein, which is encapsidated by the viral capsid.

In some embodiments, each construct comprises (1) one or more heterologous nucleic acid regions comprising a sequence encoding a protein or polypeptide of interest, (2) one or more nucleic acid regions comprising a sequence that facilitates expression of the

heterologous nucleic acid region (e.g., a promoter and/or enhancer), and (3) one or more nucleic acid regions comprising a sequence that facilitates integration of the heterologous nucleic acid region (optionally with the one or more nucleic acid regions comprising a sequence that facilitates expression) into the genome of the subject. In some embodiments, viral sequences that facilitate integration comprise Inverted Terminal Repeat (ITR) sequences. In some embodiments, each construct comprises one or more heterologous nucleic acid regions comprising a sequence encoding a protein or polypeptide of interest or an RNA of interest operably linked to a promoter, wherein the one or more heterologous nucleic acid regions are flanked on each side (e.g., flanked on each the 5' and 3' side of the one or more heterologous nucleic acid regions) with a nucleic acid region comprising an ITR sequence. The ITR sequences can be derived from any AAV serotype (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) or can be derived from more than one serotype. In some embodiments, the ITR sequences are derived from AAV2. ITR sequences and plasmids containing ITR sequences are known in the art and commercially available (see, e.g., products and services available from Vector Biolabs, Philadelphia, PA; Cellbiolabs, San Diego, CA; Agilent Technologies, Santa Clara, Ca; and Addgene, Cambridge, MA; and Gene delivery to skeletal muscle results in sustained expression and systemic delivery of a therapeutic protein. Kessler PD,

Podsakoff GM, Chen X, McQuiston SA, Colosi PC, Matelis LA, Kurtzman GJ, Byrne BJ. Proc Natl Acad Sci U S A. 1996 Nov 26;93(24): 14082-7; and Curtis A. Machida. Methods in Molecular Medicine™. Viral Vectors for Gene TherapyMethods and Protocols.

10.1385/1-59259-304-6:201 © Humana Press Inc. 2003. Chapter 10. Targeted Integration by Adeno-Associated Virus. Matthew D. Weitzman, Samuel M. YoungJr., Toni Cathomen and Richard Jude Samulski; U.S. Pat. Nos. 5,139,941 and 5,962,313, all of which are incorporated herein by reference).

In some embodiments, each nucleic acid vector comprises a pTR-UF-11 plasmid backbone, which is a plasmid that contains AAV2 ITRs. This plasmid is commercially available from the American Type Culture Collection (ATCC MBA-331).

In some embodiments, the construct comprises one or more regions comprising a sequence that facilitates expression of the heterologous nucleic acid, e.g., expression control sequences operatively linked to the heterologous nucleic acid. Numerous such sequences are known in the art. Non-limiting examples of expression control sequences include promoters, insulators, silencers, response elements, introns, enhancers, initiation sites, termination signals, and poly(A) tails. Any combination of such control sequences is completed herein (e.g., a promoter and an enhancer). To achieve appropriate expression levels of the protein or polypeptide of interest, any of a number of promoters suitable for use in the selected host cell may be employed. The promoter may be, for example, a constitutive promoter, tissue-specific promoter, inducible promoter, or a synthetic promoter. For example, constitutive promoters of different strengths can be used. A construct described herein may include one or more constitutive promoters, such as viral promoters or promoters from mammalian genes that are generally active in promoting transcription. Non-limiting examples of constitutive viral promoters include the Herpes Simplex virus (HSV), thymidine kinase (TK), Rous Sarcoma Virus (RSV), Simian Virus 40 (SV40), Mouse Mammary Tumor Virus (MMTV), Ad E1A and cytomegalovirus (CMV) promoters. Non-limiting examples of constitutive mammalian promoters include various housekeeping gene promoters, as exemplified by the β-actin promoter.

Inducible promoters and/or regulatory elements may also be contemplated for achieving appropriate expression levels of the protein or polypeptide of interest. Non- limiting examples of suitable inducible promoters include those from genes such as cytochrome P450 genes, heat shock protein genes, metallothionein genes, and hormone- inducible genes, such as the estrogen gene promoter. Another example of an inducible promoter is the tetVP16 promoter that is responsive to tetracycline.

Tissue-specific promoters and/or regulatory elements are also contemplated herein. Non-limiting examples of such promoters that may be used include (1) desmin (DES), creatine kinase, myogenin, alpha myosin heavy chain, human brain and natriuretic peptide, specific for muscle cells, and (2) liver specific promoter [LSP, (GeneArt®, Life

Technologies)], albumin, alpha- 1 -antitrypsin, hepatitis B virus core protein promoters, specific for liver cells.

Synthetic promoters are also contemplated herein. A synthetic promoter may comprise, for example, regions of known promoters, regulatory elements, transcription factor binding sites, enhancer elements, repressor elements, and the like.

In some embodiments, a first construct described herein comprises a first promoter and a second construct described herein comprises a second promoter. In some

embodiments, the first promoter and the second promoter are different (e.g., the first promoter is DES and the second promoter is LSP). In some embodiments, the first and second promoters are selected from DES, LSP, parathyroid hormone receptor; kidney- specific promoter (PI), Synapsin, minimal human glucose-6-phosphatase promoter, MTM1, CMV and chicken beta-actin. Exemplary first and second promoter pairs include (a) DES and LSP, (b) LSP and PI, (c) Synapsin and DES, (d) LSP and minimal human glucose-6- phosphatase promoter, and (e) MTM1 and LSP. Such promoters are known in the art and described herein (see, e.g., Synapsin (neuronal specific; commercially available at Addgene. ID#22907);P1 [parathyroid hormone receptor; kidney- specific promoter (McCuaig KA, Lee HS, Clarke JC, Assar H, Horsford J, White JH. Parathyroid hormone/parathyroid hormone related peptide receptor gene transcripts are expressed from tissue-specific and ubiquitous promoters. Nucleic Acids Res 1995; 23: 1948-1955)]; minimal human glucose-6- phosphatase promoter (Lin B, Morris DW, Chou JY. The role of HNFlalpha, HNF3gamma, and cyclic AMP in glucose-6-phosphatase gene activation. Biochemistry 1997; 36: 14096- 14106; Schmoll D, Wasner C, Hinds CJ, Allan BB, Walther R, Burchell A. Identification of a cAMP response element within the glucose- 6-phosphatase hydrolytic subunit gene promoter which is involved in the transcriptional regulation by cAMP and glucocorticoids in H4IIE hepatoma cells. Biochem J 1999; 338: 457-463; Vander Kooi BT, Streeper RS, Svitek CA, Oeser JK, Powell DR, O'Brien RM. The three insulin response sequences in the glucose- 6-phosphatase catalytic subunit gene promoter are functionally distinct. J Biol Chem 2003; 278: 11782-11793); and Endogenous MTM1 promoter (commercially available at

GeneCopoeia; Accession # NM_000252; Product ID: HPRM15185)). In some embodiments, the first promoter and the second promoter are the same (e.g., the first promoter is DES and the second promoter is DES). In some embodiments, the first and second promoter are both CMV promoters, both chicken beta-actin promoters, both LSPs, both PI promoters, both Synapsin promoters, both minimal human glucose-6-phosphatase promoters, or both MTM1 promoters.

In some embodiments, each construct comprises one or more heterologous nucleic acid regions comprising a sequence encoding a protein or polypeptide of interest. In some embodiments, the first construct and the second construct (and optionally third, fourth, fifth constructs, etc.) each comprise a sequence encoding the same protein or polypeptide of interest (e.g., both the first and second constructs encode GAA). In some embodiments, the first construct and the second construct (and optionally third, fourth, fifth constructs, etc.) each comprise a sequence encoding different proteins or polypeptides of interest (e.g., the first construct encodes a first protein or polypeptide of interest and second construct encodes a second protein or polypeptide of interest, etc.). In some embodiments, the constructs each encode a fragment of dystrophin, e.g., three fragments within three constructs (see, e.g., Lostal et al., Full-Length Dystrophin Reconstitution with Adeno-Associated Viral Vectors. Hum. Gene Ther., 2014. PMID: 24580018). In some embodiments, the first construct encodes beta-hexosaminidase alpha and the second construct encodes beta-hexosaminidase- beta (see, e.g., Cachon-Gonzalez et al., Gene transfer corrects acute GM2 gangliosidosis— potential therapeutic contribution of perivascular enzyme flow. Mol. Ther., 2012. PMID: 22453766). In some embodiments, the constructs each encode a fragment of myosin 7A, e.g., two fragments within two constructs (see, e.g., Dyka et al., Dual AAV Vectors Result in Efficient In Vitro and In Vivo expression of an Oversized Gene, MY07A. Hum Gene Ther., 2014. PMID: 24568220). In some embodiments, the first construct encodes Vascular endothelial growth factor-A (VEGF-A, VEGF) and the second construct encodes fibroblast growth factor 4 (FGF4) (see, e.g., Jazwa et al., Arteriogenic therapy based on simultaneous delivery of VEGF-A and FGF4 genes improves the recovery from acute limb ischemia. Vase. Cell. 2013. PMID: 23816205). In some embodiments, the first construct encodes Vascular endothelial growth factor-A (VEGF-A, VEGF) and the second construct encodes

Angiopoietin- 1 (see, e.g., Arsic et al., Induction of functional neovascularization by combined VEGF and Angiopoietin- 1 gene transfer using AAV vectors. Mol. Ther., 2003. PMID: 12727107). In some embodiments, the first construct encodes the heavy chain of factor VIII and the second construct encodes the light chain of factor VII (see, e.g., Mah et al., Dual vectors expressing murine factor VIII result in sustained correction of hemophilia A mice. Hum. Gene Ther., 2003. PMID: 12614565). In some embodiments of any of the constructs above, the promoter for each construct is a tissue-specific or a constitutive promoter. In some embodiments of any of the constructs above, the promoter for each construct is CMV or chicken beta-actin.

In some embodiments, each construct comprises one or more heterologous nucleic acid regions comprising a sequence encoding a protein or polypeptide of interest and a promoter. In some embodiments, the first construct and the construct each encode the same protein or polypeptide of interest but comprise different promoter regions (e.g., the first construct comprises GAA operably linked to a DES promoter and the second construct comprises GAA operably linked to a LSP). In some embodiments, the first construct and the second construct encode the different proteins or polypeptides of interest and comprise different promoter regions (e.g., the first construct comprises hexosaminidase A operably linked to a DES promoter and the second construct comprises hexosaminidase B operably linked to a CMV promoter).

In some embodiments, the first and second constructs do not include a promoter region. In some embodiments, the first and second constructs include different regions of a nucleic acid encoding a protein or polypeptide of interest (e.g., different regions each encoding only a portion of a protein or polypeptide of interest). In some embodiments, the different regions are overlapping regions of the same gene. In some embodiments, the different regions are non- overlapping regions of the same gene. In some embodiments, more than two different constructs (e.g., 3, 4, 5, 6, 7, 8, 9, 10 or more) are packaged together. In some embodiments, the more than two different constructs include more than two different (e.g., overlapping or non- overlapping) regions of a gene of interest. In some embodiments, a resulting AAV preparation can be used to deliver two or more regions of a gene to a cell, for example, to be used as templates for altering (e.g., for correcting one or more mutations associated with a disease or condition) a genomic sequence in the cell (e.g., as a form of gene therapy). In some embodiments, these two or more regions can act as rescue sequences in a procedure that also involves delivering one or more genome editing nucleases to the cell.

The protein or polypeptide of interest may be, e.g., a polypeptide or protein of interest provided in Table 1. The sequences of the polypeptide or protein of interest may be obtained, e.g., using the non-limiting National Center for Biotechnology Information (NCBI) Protein IDs or SEQ ID NOs from patent applications provided in Table 1.

Table 1. Non-limiting examples of proteins or polypeptides of interest and associated diseases, disorders, or phenotypes

The polypeptides and proteins provided in Table 1 are known in the art for use in rAAV particles (see, e.g., Adeno-Associated Virus Vectors in Clinical Trials. Barrie J. Carter. Human Gene Therapy. May 2005, 16(5): 541-550. doi: 10.1089/hum.2005.16.541. Published in Volume: 16 Issue 5: May 25, 2005; Neuropharmacology. 2013 Jun;69:82-8. doi:

10.1016/j.neuropharm.2012.03.004. Epub 2012 Mar 17.; Adeno-associated virus (AAV) gene therapy for neurological disease. Weinberg MSI, Samulski RJ, McCown TJ.Gene therapy for lysosomal storage disorders. Yew NS, Cheng SH. Pediatr Endocrinol Rev. 2013 Nov; 11 Suppl 1:99-109; Directed evolution of novel adeno-associated viruses for therapeutic gene delivery. Bartel MA, Weinstein JR, Schaffer DV.Gene Ther. 2012 Jun;19(6):694-700. doi: 10.1038/gt.2012.20. Epub 2012 Mar 8; Therapeutic in vivo gene transfer for genetic disease using AAV: progress and challenges. Mingozzi F, High KA. Nat Rev Genet. 2011

May;12(5):341-55. doi: 10.1038/nrg2988). In some embodiments, the polypeptide or protein of interest is a human protein or polypeptide.

In some embodiments, each construct comprises one or more heterologous nucleic acid regions comprising a sequence encoding a RNA of interest (e.g., an shRNA or microRNA) and a promoter. Exemplary RNAs of interest and AAV vectors comprising such RNAs include, e.g., AAVsh2.4, AAVsh8.2, AAVsh30.1, AAV-shHD2, siRNAs Targeting TGFpi, TGFPR2, and CTGF, scAAV2-IREl alpha, XBPl and ATF6. Such RNAs are known in the art (see, e.g., McBride et al., Artificial miRNAs mitigate shRNA-mediated toxicity in the brain: Implications for the therapeutic development of RNAi. PNAS, 2008. doi:

10.1073/pnas.0801775105; Franich et al., AAV Vector-mediated RNAi of Mutant

Huntingtin Expression Is Neuroprotective in a Novel Genetic Rat Model of Huntington's Disease. Mol. Ther., 2008. doi: 10.1038/mt.2008.50; Sriram et al., Triple Combination of siRNAs Targeting TGFpi, TGFPR2, and CTGF Enhances Reduction of Collagen I and Smooth Muscle Actin in Corneal Fibroblasts. IOVS., 2013. doi: 10.1167/iovs.l3-12758; and Ruan et al., Development of an anti- angiogenic therapeutic model combining scAAV2- delivered siRNAs and noninvasive photoacoustic imaging of tumor vasculature development. Cancer Letters, 2013. DOI: 10.1016/j.canlet.2012.11.016). Other exemplary RNAs of interest include RNAs (e.g., microRNAs or shRNAs) that target Huntingtin (HTT, see, e.g., NM_002111.7), Ataxin-1 (ATXN1, see, e.g., NM_000332.3 or NM_001128164.1), TGFpi (TGFB1, see, e.g., NM_000660.5), TGFPR2 (TGFBR2, see, e.g., NM_001024847.2 or NM_003242.5), connective tissue growth factor (CTGF, see, e.g., NM_001901.2), IRElalpha (IRE la, see, e.g., NM_001433.3), X-box binding protein 1 (XBP1, see, e.g.,

NM_001079539.1 or NM_005080.3) and activating transcription factor 6 (ATF6, see, e.g., NM_007348.3). Such RNAs of interest may be used to treat, e.g., Huntington's disease, cancer, hypervascularization, and spinocerebellar ataxia type 1.

In some embodiments, a nucleic acid vector or construct described herein may also contain marker or reporter genes, e.g., LacZ or a fl orescent protein.

In some embodiments, a nucleic acid vector or construct described herein can be used to deliver a genome editing nuclease to a cell (for example by delivering a nucleic acid encoding a genome editing nuclease), for example an engineered nuclease that can be useful to target genomic nucleic acid for cleavage (e.g., to create a double-stranded break at a known target position in the genome of a cell that receives the genome editing nuclease). In some embodiments, a genome editing nuclease is a zinc finger nuclease (ZFN), a

transcription activator-like effector nuclease (TALEN), a meganuclease, an RNA-guided DNA endonuclease (e.g., a CRISPR Cas9 related nuclease), or a combination thereof. In some embodiments, a Cas9 related nuclease is a naturally occurring endonuclease. In some embodiments, a Cas9 related nuclease is a sequence variant or a fragment of a naturally occurring Cas9 endonuclease and/or a chimeric nuclease including a naturally occurring or variant Cas9 endonuclease (or a fragment of one or more thereof). In some embodiments, a nucleic acid encoding a Cas9 related nuclease is delivered along with a nucleic acid encoding a guide RNA. In some embodiments, a guide RNA is a synthetic RNA that includes a targeting segment that is complementary to a strand of a target region (e.g., a genomic target region of interest), and a nuclease interacting segment that interacts with (e.g., binds or guides) an RNA-guided nuclease. In some embodiments, a guide RNA includes a sequence that targets a gene to be edited to restore its function (e.g., for therapeutic purposes). In some embodiments, a guide RNA targets a dystrophin gene (e.g., a region of a dystrophin gene that contains a mutation associated with DMD).

In some embodiments, a genome editing nuclease (e.g., a Cas9 related nuclease and a guide RNA) are delivered along with a rescue nucleic acid (e.g., a rescue DNA or RNA molecule) that can be used as a template for genomic repair after cleavage by the genome editing nuclease. In some embodiments, the rescue nucleic acid has a sequence of a target nucleic acid that does not include a mutation associated with a disease. For example, in some embodiments, a rescue nucleic acid includes a portion of a DMD-associated nucleic acid (e.g., a region of a dystrophin gene) that does not contain a mutation associated with DMD (e.g., a wild- type DMD genomic sequence).

In some embodiments, two or more different rAAV particles are used to deliver a rescue nucleic acid and a nucleic acid encoding a genome editing nuclease. In some embodiments, two or more different rAAV particles are used to deliver a Cas9 related nuclease (e.g., a nucleic acid encoding a Cas9 related nuclease) and a guide RNA (e.g., a nucleic acid encoding a guide RNA). In some embodiments, the rescue nucleic acid provides a region of a DMD associated gene that does not contain a mutation associated with DMD, and the guide RNA includes a targeting portion that targets a Cas9 related nuclease to cleave genomic DNA in or near the region of the DMD associated gene corresponding to the rescue nucleic acid. In some embodiments, the different AAV vectors are delivered together (e.g., simultaneously) to a cell (for example a cell from a subject, e.g., a human subject) that is being targeted for genomic editing.

Accordingly, in some embodiments methods and compositions described herein can be used to package two or more different nucleic acid vectors (e.g., including a rescue nucleic acid, and/or a nucleic acid encoding a genomic editing nuclease, and/or a nucleic acid encoding a guide RNA) simultaneously into a rAAV in order to produce an rAAV

preparation including different rAAV particles each containing one of the nucleic acid vectors. For example, methods and compositions described herein can be used to prepare and deliver combinations of these different vectors in different ratios of interest.

Nucleic acid vectors containing constructs (e.g., expression constructs) and methods of producing such nucleic acid vectors are also known in the art and commercially available (see, e.g., Zolotukhin et al. Production and purification of serotype 1, 2, and 5 recombinant adeno-associated viral vectors. Methods 28 (2002) 158-167; and U.S. Patent Publication Numbers US20070015238 and US20120322861, which are incorporated herein by reference; and plasmids and kits available from ATCC and Cell Biolabs, Inc.).

Producing rAAV particle preparations

Other aspects of the disclosure relate to producing rAAV particle preparations, e.g., by contacting a cell preparation with a first nucleic acid vector comprising a first construct as described herein and a second nucleic acid vector comprising a second construct as described herein, permitting the cell preparation to produce a first rAAV particle comprising the first construct and a second rAAV particle comprising the second construct, and isolating the first rAAV particle and the second rAAV particle from the cell preparation. In some

embodiments, further nucleic acid vectors (e.g., third, fourth, fifth, etc.) and further rAAV particles(third, fourth, fifth, etc.) are also contemplated herein.

In some embodiments, the cell preparation is a mammalian cell preparation or an insect cell preparation. In some embodiments, the mammalian cell preparation comprises 293 cells or baby hamster kidney cells (BHK) (available, e.g., from ATCC® CRL-1573™ for 293 cells and ATCC ® CCL-10™ BHK cells). In some embodiments, the insect cell preparation comprises Sf9 cells (available, e.g., from ATCC® CRL-1711™).

In some embodiments, the cell preparation, after contact with the first and second nucleic acid vector (and optionally third, fourth, fifth, etc. nucleic acid vectors), is maintained under conditions sufficient for producing a first rAAV particle comprising the first construct and a second rAAV particle comprising the second construct (and optionally third, fourth, fifth, etc. rAAV particles comprising third, fourth, fifth, etc. constructs). In some

embodiments, the conditions sufficient for producing comprise incubating the cell preparation for an appropriate length of time, in an appropriate medium, and at an appropriate temperature. In some embodiments, the length of time is 12 to 72 hours, 24 to 72 hours, or 48 to 72 hours. In some embodiments, the length of time is at least 24 hours, at least 48 hours, at least 60 hours or at least 72 hours. In some embodiments, the temperature is 37 degrees Celsius. In some embodiments, the medium comprises nutrients for maintaining cell health and/or growth. In some embodiments, the medium comprises Dulbecco's modified Eagle's medium, 293 SFM II , Gibco® FreeStyle™ 293 Expression Medium, CD 293 Medium, Expi293™ Expression Medium, Sf-900™ III SFM, Express Five® SFM, or Sf- 900™ II SFM (available from Life Technologies™).

In some embodiments, the cell preparation is contacted simultaneously with the first nucleic acid vector and the second nucleic acid vector (and optionally third, fourth, fifth, etc. nucleic acid vectors). In some embodiments, the cell preparation is contacted with a composition comprising the first nucleic acid vector and the second nucleic acid vector (and optionally third, fourth, fifth, etc. nucleic acid vectors). In some embodiments, the composition comprises calcium chloride and/or hank's balanced saline solution. In some embodiments, the composition further comprises one or more helper plasmids as described herein.

In some embodiments, contacting a cell preparation with a first and second nucleic acid vector (and optionally third, fourth, fifth, etc. nucleic acid vectors) comprises transfecting the cell preparation with the first nucleic acid vector and the second nucleic acid vector (and optionally third, fourth, fifth, etc. nucleic acid vectors). In some embodiments, the transfection is calcium phosphate transfection. In some embodiments, the method further comprises contacting the cell preparation with at least one helper plasmid described herein. In some embodiments, the cell preparation is transfected simultaneously with the first nucleic acid vector and the second nucleic acid vector (e.g., as plasmids) and the at least one helper plasmid (e.g., one, two, or three helper plasmids). In some embodiments, the first nucleic acid vector and the second nucleic acid vector (e.g., as plasmids) and the at least one helper plasmid are comprised within a composition before contacting with the cell preparation. In some embodiments, the composition comprises calcium chloride and/or hank's balanced saline solution.

In some embodiments, the at least one helper plasmid is a first helper plasmid comprising a rep gene and a cap gene and a second helper plasmid comprising a El a gene, a Elb gene, a E4 gene, a E2a gene, and a VA gene. In some embodiments, the rep gene is a rep gene derived from AAV2 and the cap gene is derived from AAV9. Helper plasmids, and methods of making such plasmids, are described herein and also known in the art and commercially available (see, e.g., pDM, pDG, pDPlrs, pDP2rs, pDP3rs, pDP4rs, pDP5rs, pDP6rs, pDG(R484E/Pv585E), and pDP8.ape plasmids from PlasmidFactory, Bielefeld, Germany; other products and services available from Vector Biolabs, Philadelphia, PA; Cellbiolabs, San Diego, CA; Agilent Technologies, Santa Clara, Ca; and Addgene,

Cambridge, MA; Grimm et al. (1998), Novel Tools for Production and Purification of Recombinant Adenoassociated Virus Vectors, Human Gene Therapy, Vol. 9, 2745-2760;

Kern, A. et al. (2003), Identification of a Heparin-Binding Motif on Adeno-Associated Virus Type 2 Capsids, Journal of Virology, Vol. 77, 11072-11081.; Grimm et al. (2003), Helper Virus-Free, Optically Controllable, and Two-Plasmid-Based Production of Adeno-associated Virus Vectors of Serotypes 1 to 6, Molecular Therapy, Vol. 7, 839-850; Kronenberg et al. (2005), A Conformational Change in the Adeno-Associated Virus Type 2 Capsid Leads to the Exposure of Hidden VPl N Termini , Journal of Virology, Vol. 79, 5296-5303; and MouUier, P. and Snyder, R.O. (2008), International efforts for recombinant adenoassociated viral vector reference standards, Molecular Therapy, Vol. 16, 1185-1188). An exemplary, non-limiting transfection method is described in Example 1. Another exemplary, non-limiting, transfection method is described next. One or more helper plasmids are produced or obtained, which comprise rep and cap genes for the desired AAV serotype or pseudotype (e.g., rep2/cap9) and the adenoviral VA, E2A (DBP), and E4 genes under the transcriptional control of their native promoters. 293 cells are transfected via CaP0₄- mediated transfection with the helper plasmids and a first and second nucleic acid vector described herein (e.g., as plasmids).

In some embodiments, contacting a cell preparation with a first and second nucleic acid vector (and optionally third, fourth, fifth, etc. nucleic acid vectors) comprises infecting the cell preparation with the first nucleic acid vector and the second nucleic acid vector (and optionally third, fourth, fifth, etc. nucleic acid vectors). The cell preparation may be infected using any method known in the art, e.g., herpes simplex virus type 1 (HSV) infection or baculovirus infection (see, e.g., Clement et al. Large-Scale Adeno-Associated Viral Vector Production Using a Herpesvirus-Based System Enables Manufacturing for Clinical Studies. Human Gene Therapy. 20:796-806; and Kotin. Large-scale recombinant adeno-associated virus production. Human Molecular Genetics, 2011, Vol. 20, Review Issue 1, R2-R6).

In some embodiments, the first nucleic acid vector is contained within a first herpes simplex virus type 1 (HSV) particle and the second nucleic acid vector is contained within a second HSV particle (and optionally third, fourth, fifth, etc. nucleic acid vectors are contained within a third, fourth, fifth, etc. HSV particle). In some embodiments, the first

HSV particle and the second HSV particle are contacted with the cell preparation (e.g., comprising 293 cells or BHK cells). In some embodiments, further HSV particles comprising one or more helper nucleic acids (e.g., comprising rep genes, cap genes, a Ela gene, a Elb gene, a E4 gene, a E2a gene, and/or a VA gene) are contacted with the cell preparation. In some embodiments, the one or more helper nucleic acids are stably integrated into the cell preparation such that the further HSV particles are optional.

In some embodiments, the first nucleic acid vector is contained within a first baculovirus particle and the second nucleic acid vector is contained within a second baculovirus particle (and optionally third, fourth, fifth, etc. nucleic acid vectors are contained within a third, fourth, fifth, etc. baculovirus particle). In some embodiments, the first baculovirus particle and the second baculovirus particle are contacted with the cell preparation (e.g., comprising Sf9 cells). In some embodiments, further baculovirus particles comprising one or more helper nucleic acids (e.g., comprising rep genes, cap genes, a Ela gene, a Elb gene, a E4 gene, a E2a gene, and/or a VA gene) are contacted with the cell preparation. In some embodiments, the one or more helper nucleic acids are stably integrated into the cell preparation such that the further baculovirus particles are optional.

An exemplary, non-limiting, infection method is described next. Sf9-based producer stable cell lines are infected with a first recombinant baculovirus comprising the first nucleic acid vector and the second recombinant baculovirus comprising the second nucleic acid vector.

In some embodiments, when the cell preparation is contacted with the first and second nucleic acid vector via infection, the initial ratio of the first nucleic acid vector to the second nucleic acid vector is the ratio of the multiplicity of infection of the first nucleic acid vector to the multiplicity of infection of the second nucleic acid vector. Multiplicity of infection or MOI is a term known in the art and refers to the ratio of infectious agents (e.g., HSV or baculovirus) to infection targets (e.g., cells).

The first and second rAAV particle, once produced by the cell preparation using any method described herein, may be isolated using any method known in the art or described herein. In some embodiments, isolation comprises lysing the cell preparation and extracting the first rAAV particle and the second rAAV particle. The first rAAV particle and the second rAAV particle may be extracted from the cell preparation simultaneously (e.g., a population of rAAV particles that comprises both the first rAAV particle and the second rAAV particle is extracted from the cell preparation such as using a purification method described herein) or separately. In some embodiments, extraction comprises purification, e.g., by iodixanol step gradient, CsCl gradient, chromatography, or polyethylene glycol (PEG) precipitation.

The first and second rAAV particle (and optionally third, fourth, fifth, etc. rAAV particles) produced by a method described herein may be of any AAV serotype, including any derivative or pseudotype (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, or pseudotypes/derivatives thereof). In some embodiments, the first and second rAAV particle (and optionally third, fourth, fifth, etc. rAAV particles) are of the same serotype. In some embodiments, the first and second rAAV particle (and optionally third, fourth, fifth, etc. rAAV particles) are of the different serotypes. Non-limiting examples of derivatives and pseudotypes include rAAV2/l, rAAV2/5, rAAV2/8, rAAV2/9, AAV2-AAV3 hybrid, AAVrh. l0,AAVhu. l4, AAV3a/3b, AAVrh32.33, AAV-HSC15, AAV-HSC17, AAVhu.37, AAVrh.8, CHt-P6, AAV2.5, AAV6.2, AAV2i8, AAV-HSC15/17, AAVM41, AAV9.45, AAV6(Y445F/Y731F),

AAV2.5T, AAV-HAE1/2, AAV clone 32/83, AAVShHIO, AAV2 (Y->F), AAV8 (Y733F), AAV2.15, AAV2.4, AAVM41, and AAVr3.45. Such AAV serotypes and

derivatives/pseudotypes, and methods of producing such derivatives/pseudotypes are known in the art (see, e.g., Mol Ther. 2012 Apr;20(4):699-708. doi: 10.1038/mt.2011.287. Epub 2012 Jan 24. The AAV vector toolkit: poised at the clinical crossroads. Asokan Al, Schaffer DV, Samulski RJ.). In some embodiments, the first and second rAAV particle (and optionally third, fourth, fifth, etc. rAAV particles) are pseudotyped rAAV particles. In some embodiments, the pseudotyped rAAV particle comprises (a) a nucleic acid vector comprising AAV2 ITRs and (b) a capsid comprised of capsid proteins derived from AAVx (e.g., AAV1, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, or AAV10). Exemplary rAAV pseudotyped particles include, but are not limited to rAAV2/l, rAAV2/5, rAAV2/8, and rAAV2/9 particles. Methods for producing and using pseudotyped rAAV particles are known in the art (see, e.g., Duan et al., J. Virol., 75:7662-7671, 2001; Halbert et al., J. Virol., 74: 1524-1532, 2000; Zolotukhin et al., Methods, 28: 158-167, 2002; and Auricchio et al., Hum. Molec. Genet., 10:3075-3081, 2001). Without further elaboration, it is believed that one skilled in the art can, based on the above description, utilize the present disclosure to its fullest extent. The following specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever. All publications cited herein are incorporated by reference for the purposes or subject matter referenced herein. EXAMPLES

Example 1. Exemplary rAAV co-production protocol

Introduction

To date adeno-associated virus (AAV) has been used in over 100 gene therapy clinical trials. The widespread tropism, sustained gene expression and excellent safety data that exist for AAV are only a few of the reasons it has reached such popularity. As a nonpathogenic shuttle for therapeutic genes capable of delivering its payload to many cell types, the basic biological processes governing the behavior of the many AAV serotypes has been an extensive area of research for many years (Zincarelli et al., 2008; Asokan et al., 2012; Gurda et al., 2012; Aschauer et al., 2013; Asokan and Samulski 2013; Rayaprolu et al., 2013). With its success in correcting the pathology associated with diseases such as seen in the multitude of metabolic myopathies and hematological disorders, AAV is quickly becoming the gene therapy vector of choice for initiating large animal studies and clinical trials (Markusic and Herzog 2012; Mah et al., 2013).

However, among its drawbacks are host immune responses against the capsid and/or transgene (Boutin et al., 2010; Rogers et al., 2011; Faust et al., 2013; Mingozzi and High 2013), appropriate transduction of the target tissue (Zincarelli et al., 2008; Pulicherla et al., 2011; Aschauer et al., 2013), size limitation, with an optimal packaging size of ~4.7kb (Dong et al., 1996), and the challenges to produce high titer vectors in a cost and time effective manner (Clement et al., 2009; Doria et al., 2013). Implementation towards large-scale manufacturing of AAV using infection-based systems (herpes simplex virus type 1 and baculovirus systems) rather than transfection will certainly become useful to address the large quantities of virus needed for FDA required extensive pre-clinical studies, as well as clinical studies. Yet transfection remains the current standard of vector production in most laboratories and manufacturing cores. Furthermore, some indications may require the use of two or more vector constructs. To palliate the inability of AAV genomes to carry long therapeutic cDNA, the packaging capacity may be expanded by splitting the genome and rely on what has been referred to as the fragment AAV reassembly model (Rabinowitz et al., 2002; Hirsch et al., 2013). Gene expression using fragmented vectors relies on the host recombination machinery to splice together one expression cassette containing a splice donor site to another encoding a compatible splice acceptor region (Ghosh et al., 2011).

Encouraging results using this strategy have been reported for Duchenne's muscular dystrophy (Lai et al., 2005; Zhang and Duan 2012; Zhang et al., 2013; Koo et al., 2014) and Usher 1 (Lopes et al., 2013; Dyka et al., 2014).

However there are many other instances where the simultaneous delivery of more than one AAV vector may be required. Such as for indications where two or more subunits are needed (e.g., hexosaminidase A and B for Tay-Sachs disease) or indications where the expression of the therapeutic gene needs to be elevated in specific tissues; which could be mediated by the use of different promoters upstream of the same therapeutic transgene (Pacak et al., 2009; Palfi et al., 2012; Fagoe et al., 2013). For instance, targeting gene expression to the liver for the purposes of immune tolerance induction while providing an additional vector to correct systemic pathology would allow for the simultaneous treatment of many congenital metabolic myopathies wherein immune responses have proven deleterious to the efficacy of gene therapy.

Clinical applications using two or more AAV constructs would be time and cost prohibitive if each construct was produced separately. To facilitate the use and production of multiple vectors, a novel production method was investigated that exploited the

stoichiometric properties of AAV in that only one expression plasmid is packaged per encapsidated virus. A method was developed that allowed for the production of multiple vectors in a single transfection step. Combining reporter expression cassettes to be packaged at a known input ratio, it was shown through quantitative PCR (qPCR) and in vitro infectivity assays that the output vector preparation closely recapitulated the input ratios. Additionally, it was shown that therapeutic constructs containing unique promoter elements could be co- packaged and were able to be differentially titrated. These results indicate that, at minimum, two vectors containing either separate transgenes or regulatory elements can be co-packaged and subsequently characterized independently. Methods

Construction of r AAV vector plasmids

Recombinant vectors containing GFP (pTRUFl l) and mCherry (pTRUFl l-mCherry) were assembled using the pTR-UF backbone previously described (Zolotukhin et al., 1996). The sequences of PTR-UF and PTR-UF 11 are provided below.

The red fluorescent protein mCherry was cloned in lieu of GFP in the pTRUFl 1 construct using standard techniques. mCherry was amplified from pRSETB-mCherry (obtained from Dr. R. Tsien, University of California, San Diego) using primers mcherryNotl-F 3 ' AT A AG A ATGCGGCCGCC ACC ATGGTG AG (SEQ ID NO: 3) and mcherryNotl-R 3' ATAAGAATGCGGCCGCCCACGATGGTGTAGTCC (SEQ ID NO: 4) to introduce two Not I sites flanking the amplicon. The amplicon was digested with Notl and ligated into pTRUFl 1 Notl. A human codon- optimized acid a-glucosidase cDNA (coGAA) (GeneArt®, Life Technologies) was cloned into a desmin promoter construct (pTR-DES) previously described (Pacak et al., 2009; Falk et al., 2013). The liver- specific promoter (LSP) (GeneArt®, Life Technologies) contains the apolipoprotein E - hepatocyte control region (Miao et al., 2000; Manno et al., 2006; Cao et al., 2007), the human a 1 -antitrypsin promoter (Cresawn et al., 2005) and 5' UTR and was sub-cloned into pTR-DES-coGAA in lieu of the DES promoter (Bglll and Sail). The sequences of the DES promoter and the LSP are provided below.

ApoE-HCR-hAAT-5 ' UTR [Liver Specific Promoter (LSP)] Sequence:

5'-

AAV9 production

Recombinant adeno-associated viral (AAV) vectors were produced and purified as previously described (Zolotukhin et al., 2002). HEK293 cells were cultured in 5% FBS and antibiotic supplemented Dulbecco's modified Eagle's medium. Plasmid DNA was propagated in SURE2 cells (Agilent Technologies, Inc., Santa Clara, CA) and isolated using Qiagen plasmid purification reagents or obtained from Aldevron (Fargo, ND). Cells were seeded in 150 mm dishes at 5.0xl0⁶ cells 24 hours prior to transfection. The calcium phosphate precipitate was formed by combining the total amount of expression plasmids, with the equivalent concentration of the capsid plasmid rep2/cap9 and twice the concentration of the Ad helper plasmid pXX6-80 in 2.5M CaCl₂ followed by the addition of 2X HBS, pH 7.05. Sequences of these plasmids are below.

For co-packaging experiments, ratios of the two expression constructs were varied between 1:9, 1: 1 and 9: 1 ratios and determined off of the total amount of expression plasmid DNA necessary and the total base pair size of the individual constructs to retain equimolar ratio with the helpers; at the surface area of 148 cm , the final amounts of plasmids were 16 μg of expression plasmids, 16 μg of rep2/cap9, and 38 μg of pXX6-80. Cells were incubated at 37°C at 5% C02 for 60 hours, washed in PBS, harvested in PBS-5 mM EDTA and centrifuged at lOOOg for 10 minutes at 4 °C. Cells were resuspended in lysis buffer (150 mM NaCl, 50 mM Tris, pH 8.4) and subjected to three freeze/thaw cycles between a -80 °C freezer and 37 °C water bath. Benzonase (50 U/mL) and MgCl₂ were added to the cell lysate and incubated for 30 minutes at 37 °C. The crude lysate was clarified by centrifugation at 3400g for 20 minutes at 4 °C. The vector-containing supernatant was used for quantitative PCR (qPCR) or further purified by iodixanol step gradients (Zolotukhin et al., 2002). Final formulations of iodixanol purified vectors were concentrated in PBS (Apollo® Concentrators, Orbital Biosciences, Topsfield, MA). Each ratio of co-packaged vectors was performed independently in triplicate.

Titration of AAV vectors

DNA from all AAV vectors, both from crude lysate or iodixanol purified

preparations, was extracted using Qiagen reagents. 100 μl of vector from clarified lysate or 10 μl of iodixanol purified vector were treated with proteinase K (Qiagen; 0.2 mg/ml, 55°C, 30 min) followed by DNA extraction following manufacturer's instructions.

For AAV9-GFP and AAV9-mCherry, primers designed for the cytomegalovirus enhancer were used to determine total titer (primer set 1; see Table 2 for primer sequences). Additional forward and reverse primers designed uniquely to the GFP and mCherry transgenes (primer sets 2 and 3, respectively) were also used to determine the individual contribution of each construct to the total vector preparation. Endpoint PCR was optimized by amplifying 0.5 ng of extracted DNA on a 3 -step cycling protocol across a temperature gradient (30 cycles: 94 °C for 15 sec, 46-50 °C for 15 sec, 72 °C for 30 sec) preceded by a 2 minute 94 °C incubation and followed by a 1 minute 72 °C elongation. QPCR titration was optimized by amplifying 1 ng of extracted DNA on a 2-step cycling protocol across a temperature gradient (50 cycles: 95 °C for 10 sec, 57-63 °C for 1 min) preceded by a 10 min 95 °C incubation and followed with a melt curve protocol (95 °C for 1 min, 63 °C for 1 min, 65-95 °C for 5 sec in 0.5 °C increments). An annealing temperature of 50 °C was used for all primer sets and combinations for endpoint PCR experiments. For qPCR, CMV targeted primers were annealed at 63 °C, GFP and mCherry primers were annealed at 50 °C. The primers below are SEQ ID NOs: 9-17 from top to bottom. Table 2. Primer Sequences for PCR

CB, CMV enhancer/chicken β-actin promoter

DES, desmin promoter,

LSP, liver specific promoter

coGAA, human codon optimized acid alpha-glucosidase

To titrate co-packaged AAV9-LSP-coGAA and AAV9-DES-coGAA, forward primers unique to the promoter sequences were used in conjunction with a reverse primer anchored within the transgene shared by both constructs (primer set 4). Endpoint and qPCR performed on co-packaged AAV9-LSP-coGAA and AAV9-DES-coGAA was optimized and performed identically as with co-packaged AAV9-GFP and AAV9-mCherry. For qPCR, LSP, DES and coGAA primers were annealed at 60 °C.

Standard curves were generated by using 109-105 total copies, as well as the inclusion of a non-template control, of the relevant expression plasmids either singly or in combination with the additional co-packaged construct. For each endpoint or qPCR reaction of single or combined expression plasmids, the corresponding primers were also used individually or in combination. For example, 4 standard curves of pTRUFl 1 were amplified individually with primers targeting the CMV enhancer (primer set 1), GFP (primer set 2), mCherry (primer set 3), or a combination of GFP and mCherry (primer sets 2 and 3). Likewise, 4 standard curves of combined pTRUFl 1 and pTRUFl 1 -mCherry were amplified individually with primers targeting the CMV enhancer (primer set 1), GFP (primer set 2), mCherry (primer set 3), or a combination of GFP and mCherry (primer sets 2 and 3). Each combination of primer sets and plasmids was investigated to ensure the specificity of amplification.

Endpoint PCR was conducted using Illustra™ PuReTaq™ Ready-To-Go™ PCR beads (GE Healthcare, Buckinghamshire, UK). 0.5 ng of DNA was amplified from each preparation and ran on a 2% agarose gel at 100 V for 90 minutes for GFP and mCherry vectors or on a 1.5% agarose gel at 110 V for 50 minutes for LSP and DES vectors. QPCR was performed with iTaq™ Universal SYBR® Green Supermix using 1 ng of DNA on a Bio- Rad CFX96 Real-Time PCR Detection System and analyzed using Bio-Rad CFX Manager v. 3.1 software (Bio-Rad Laboratories, Inc., Hercules, CA). A multiplication factor of two was included when determining vector genomes per milliliter (vg/mL) to account for the packaging of positive- and negative- sense viral genomes.

Single cell fluorescence assay

The infectious titer of AAV9-GFP and AAV9-mCherry was determined essentially as described previously (Zolotukhin et al., 2002). C12 cells were seeded at 2xl0⁴ cells in a 96- well plate and infected 18 hours later with the co-packaged vectors in a serial 10-fold dilution series. Due to the low in vitro transduction efficiency of AAV9, co-infection with Ad5 (MOI of 20) was implemented. 40 hours later, red and green cells were counted using a fluorescent microscope and the infectious titer was calculated based on dilution. Each ratio, packaged in triplicate, was assayed in duplicate. The particle-to-infectivity ratio was then determined by the qPCR titer divided by the infectious titer.

Statistical analysis

Figures and statistical analysis was performed using GraphPad Prism v. 5.0

(GraphPad Software, La Jolla, CA). Results

AAV packages expression plasmids in a defined stoichiometry

To facilitate the use and production of multiple vectors, a novel co-packaging method was investigated that would allow for the generation of a heterogeneous population of AAV vectors in a single manufacturing step. It was hypothesized that combining plasmids to be packaged at a known input ratio would result in an output vector preparation containing the equivalent ratio. To demonstrate this hypothesis, two vectors that only differed by the reporter gene, GFP or mCherry, were co-packaged into AAV serotype 9 (AAV9). The vectors were co-packaged at 1:9, 1: 1 and 9: 1 molar ratios, respectively. Vector DNA extracted either from crude lysates or from purified vectors were first analyzed by endpoint PCR (FIG. 1). Semi-quantitative end-point PCR revealed that each vector preparation differentially packaged each transgene, recapitulating the ratios that were transfected into the cells.

Each dual vector preparation was then subject to quantitative PCR (qPCR) analysis for a more robust quantification assessment. To determine the overall vector titer primers targeted towards the CMV enhancer region of the shared promoter to both AAV9-GFP and AAV9-mCherry were used (see "Methods - Titration of AAV Vectors"). At a scale of production using 150 mm tissue culture dishes, it was determined that an overall titer ranging from ~1 xlO⁹ to 5xl0⁹ vg/mL in the crude lysate (volume 3mL) and after iodixanol purification (volume 0.2 mL) (FIG. 2). The use of a single primer set or a combination of transgene specific primers simultaneously did not significantly affect the titration outcome (FIG. 2). In addition it was verified that the results obtained from purified vector preparations confirmed those obtained from crude lysates, which excluded potential risks of plasmid carry over or contamination from the transfection precipitate in benzonase-digested crude lysates. Titers determined from the transgene specific primers revealed that the predicted ratios of 1:9, 1: 1 and 9: 1 AAV9-GFP to AAV9-mCherry were recapitulated (FIG. 3). Corroborating what was observed using endpoint PCR, at the 1:9, 1: 1 and 9: 1 GFP to mCherry ratios, the mean percentage of their respective contribution to the total titer was: 11.03% to 88.97%, 64.12% to 35.88%, and 94.19% to 5.81% over the three independent packaging experiments. These data strongly support the hypothesis that AAV can package more than one expression plasmid combined at a predetermined ratio in a reproducible and predictable manner. Ratios of co-packaged vectors are maintained in in vitro cell transduction

An established method of vector quality control is the infectivity or transduction assay. For marker gene carrying vectors, the assay is based on single cell fluorescence (Zolotukhin et al., 2002). To determine the infectious titer, C12 cells were transduced in the presence of Ad5 (MOI of 20), with purified AAV9-GFP and AAV9-mCherry co-packaged at the above ratios. Two days post- infection, green and red cells were visually counted independently. The infectious titer ranged from 8.5xl0³ to 1.25xl0⁴ IU/mL closely mirroring the vector genome titers. Furthermore the average particle-to-infectivity ratios ranged from 2.1xl0⁵ to 4.9xl0⁵, which were consistent with ratios observed for AAV9 preparations, and more importantly, the particle-to-infectivity ratios were not significantly different between the two marker constructs or at the different packaging ratios (data not shown). The mean respective contribution of green and red cells to the total infectious titer was: 10.85% to 89.15%, 59.34% to 40.66%, and 91.22% to 8.78% (FIG. 4). These results indicate that co- packaged vectors also display transduction profiles in the ratios at which they were co- packaged.

Therapeutic constructs can be differentially packaged

It may prove efficacious in some instances to use multiple vectors that target transgene expression to specific tissues. Therefore this method was applied to the production of therapeutically relevant constructs differing in transcription elements. Vectors containing human codon- optimized acid a-glucosidase (coGAA) with different promoter elements that target expression to the liver [ApoE-HCR-hAAT promoter (LSP)] or cardiac, skeletal, and neuronal tissue [desmin promoter (DES)] were co-packaged and purified at the above ratios in AAV9 in 150 mm tissue culture dishes. Dual vector preparations were analyzed in a similar manner as the marker containing vectors. Titers were assessed using forward primers within the individual promoters (LSP or DES) and a shared, reverse primer anchored in the transgene (GAA; Table 2). Endpoint PCR confirmed the differential contribution of the two constructs to the total vector production (FIG. 5A). Resulting overall titers ranged from lxlO⁹ to 3xl0⁹ vg/mL. Similarly, qPCR revealed the output ratio recapitulated the predicted ratios as was observed when AAV9-GFP and AAV9-mCherry were co-packaged (FIG. 5B). The mean percentage of the total titer consisting of AAV9-LSP-coGAA or AAV9-DES- coGAA was: 9.09% to 90.91%, 57.10% to 42.90%, and 93.83% to 6.17%. The data presented support the hypothesis that packaging pre-determined ratios of input plasmid containing different transcriptional elements results in a heterogeneous population containing multiple vectors with the potential of expressing in discrete tissues. These results also indicate that production of multiple vectors in a single transfection step can produce dual, or potentially more, vectors at a predetermined ratio reproducibly and at the proportion of the investigator's choice. Discussion

The widespread use of AAV for gene therapy applications emphasizes its utility and diverse capabilities but the limitations of manufacturing and packaging size have dampened the rapid successes observed in preclinical models to translation in the clinic. Many groups have investigated manners in which greater quantities of vector can be made quickly and efficiently with varying degrees of success. The most standard protocol to produce recombinant AAV, both at research and clinical grade, is a transfection method using two or sometimes three plasmids to provide all the cis and trans functions necessary to package AAV (Zolotukhin et al., 2002). However, transfection-based methods are inherently difficult to adapt to large scale platforms and methods using baculovirus (Kotin 2011; Mietzsch et al., 2014) or herpes simplex virus 1 (HSV) systems (Clement et al., 2009), together with producer cells grown in suspension, are rapidly improving and paving the way to future manufacturing campaigns. Despite these quick and impressive advancements toward infection-based methods, transfection remains the most versatile and cost effective method at small and medium scale preparations enabling researchers to develop proof-of-principle concepts.

Current methods of AAV production are directed towards the manufacturing of a single vector at a purity and titer conducive for preclinical studies or early phase clinical trials. In some instances, the use of more than one AAV may be beneficial or even required as a therapeutic approach. For some diseases, the production of multiple vectors containing fragmented genomes is required when the constructs exceed the carrying capacity of the vector. Duchenne's muscular dystrophy, hemophilia A, Tay-Sachs disease and Usher 1 are only a few of the diseases that would rely on multiple gene products or trans- splicing vectors to provide for therapeutic benefit (Mah et al., 2003; Cachon-Gonzalez et al., 2012; Lopes et al., 2013; Koo et al., 2014; Lostal et al., 2014; Dyka et al., 2014). Similarly, it may prove necessary to coordinate and differentially control transgene expression to different target regions with tissue restricted promoters, such as the central nervous system, eye or systemically, while avoiding expression in antigen presenting cells and provoking a deleterious immune response (Zhang et al., 2012; Palfi et al., 2012; Fagoe et al., 2013). The benefit of altering the construct and not the capsid lies in that the coordination of expression may be contingent upon the tropism of a particular serotype and it has already been shown that much of the population is already seropositive for many of the serotypes in clinical trial (Boutin et al., 2010). It would behoove an investigator then to ensure that all cell and tissue types are transduced at a minimal degree of exposure of the animal or individual to multiple serotypes. This immunization against the various serotypes would preclude any subsequent attempts using different capsid variants without substantial immunomodulation as well as potentially prime innate and adaptive responses against viral components; all of which have been shown to be detrimental to long-term efficacy (Cresawn et al., 2005; Jayandharan et al., 2011; Wang et al., 2011; Sudres et al., 2012; Mingozzi and High 2013). Based on these considerations, the method described herein is being used to develop a single gene therapy product that will allow for the simultaneous induction of immune tolerance and physiologic correction of Pompe disease that may prove beneficial for other metabolic myopathies characterized by systemic pathology and are prone to immune responses to the therapeutic protein.

When more than one vector is necessary to the therapeutic approach, investigators have the sole choice of producing and testing each vector preparation independently, followed by co-administration of the two vectors at time of dosing. As an obvious consequence, processing times are often increased and cost doubled; aspects all the more relevant for clinical manufacturing. Clinical manufacturing and release testing of AAV in compliance with FDA-regulated Good-Manufacturing Practices (GMP) is extremely costly and time consuming, a non-trivial aspect of designing an AAV gene therapy trial.

Furthermore, pre-clinical toxicology studies would need to integrate additional animals and controls to evaluate safety of each single vector separately, as well as in combination, and again, resulting in dramatic increases in cost and time toward protocol validation.

The necessity of novel production methods to provide for multiple constructs in an efficient and reliable manner currently stands as an unmet need in the field. This study focused on the development of such a method. Here it was revealed that vectors containing either different transgenes or transcriptional elements could be combined in predetermined ratios and produce an output of vector that recapitulated that prediction. Although a method for developing mosaic capsids by co-transfection has been previously attempted (Gigout et al., 2005), this study is the first instance of constructing a heterogeneous population of vectors containing different payloads in a single manufacturing step.

Here it was demonstrated that disparate ratios (1:9 or 9: 1) provided for the greatest reliability in titration and infectivity, at least in vitro. In all cases the favored construct was the smaller of the two, emphasizing the care with which the plasmids should be combined when packaging taking into account the total size of the plasmid and maintaining precise molar ratios. Co-packaging may therefore provide as an alternative method of vector production where more than one gene product is necessary, and providing as a novel platform for treating diverse congenital disorders for which AAV mediated gene therapy is applicable. Moreover, this technique could theoretically expand to infection-based systems as the expression cassettes to be packaged could be provided at varying multiplicities of infection to produce a heterogeneous population of vectors similar to results here using transfection. With respect to regulatory aspects of AAV clinical manufacturing, the main advantage of this strategy is related to being extremely cost and time effective, as developed earlier. The dual vector preparation should be considered as one single new investigational drug (IND) for each given ratio. This advantage may also be a challenge, as precise methods to characterize each vector contribution must be developed and well controlled, and reproducibility of the production method established. To facilitate FDA review and approval, the chosen dual vector at the therapeutic ratio, similar to a single AAV drug, will undergo extensive toxicology and dose assessment studies. The ratio must remain unchanged throughout the protocol validation, at least within the margin of errors of the methods used to produce and characterize the vector preparation. Identity testing, including whole genome sequencing, will be a challenge. However new next generation sequencers allow for Massive Parallel Sequencing (MSP) to provide full sequencing of multiple species in one given sample, which would also confirm the ratio of each vector construct. From this study, and for the constructs tested here, it is believed that with appropriate characterization tools, both vectors can be accurately titrated and that predicted ratios are consistent across several production attempts.

Example 2. Exemplary rAAV co-production protocol

To date adeno-associated virus (AAV) has been used in 109 gene therapy clinical trials. The widespread tropism, sustained gene expression and excellent safety data that exist for AAV are only a few of the reasons it has reached such popularity. Among its drawbacks though are size limitation, with an optimal packaging size of ~4.7kb, and the challenges to produce high titer vectors in a cost and time effective manner. Furthermore, some indications may require the use of two or more vector constructs. For instance, different promoters may be used to support specific tissue targeting. For long cDNA, the packaging capacity may be expanded by splitting the cDNA and using cis- or trans-splicing elements. Clinical applications using two or more AAV constructs would be time and cost prohibitive if each construct was produced separately. To facilitate the use and production of multiple vectors, a novel production method was explored that exploited the stoichiometric properties of the virus in that only one expression plasmid is packaged per encapsidated virus. The tested hypothesis was that combining plasmids prior to packaging at a known input ratio would result in an output vector preparation containing the equivalent ratio.

Methods

AAV9 Vector Production and Purification

AAV vectors were produced in 150mm tissue culture dishes via CaP04 transfection GFP + mCherry and LSP + DES vectors were co-packaged at 1:9, 1: 1, and 9: 1 ratios The amount of expression plasmid for co-packaging was determined by the total amount of

DNA necessary and the total base pair size of the individual constructs to retain equimolar ratios. Post-benzonase treated, vector-containing supernatant was used for quantitative PCR (qPCR) or further purified using discontinuous iodixanol step gradients for qPCR and infectivity assays.

Titration of Vectors

Primers were designed for the shared CMV enhancer of the GFP and mCherry vectors as well as unique fragments within the transgenes. The LSP and DES vectors were titrated using unique forward primers within the promoter and a shared reverse primer anchored within the transgene. Standard curves were generated by using 10¹⁰-10⁵ total copies of the relevant expression plasmids either singly or in combination with a non-template control. QPCR was performed with iTaq™ Universal SYBR® Green Supermix on a Bio-Rad CFX96 Real-Time PCR Detection System and analyzed using Bio-Rad CFX Manager v. 3.1. Single Cell Fluorescence Assay

C12 cells were seeded at 2xl0⁴ cells in a 96- well plate and infected 18 hours later with the co-packaged vectors in a 10-fold dilution series in the presence of Ad5 (MOI 20). 40 hours later, red and green cells were counted using a fluorescent microscope and the infectious titer was calculated based on dilution. Results

As shown in Fig. 6, vectors were co-packaged at ratios 1:9 GFP to mCherry, 1: 1, and 9: 1. The differential packaging of the vectors was evident. The use of multiple primer sets and different sources of vector DNA had no effect on PCR efficiency.

As shown in Fig. 2 and Fig. 3, the titer of co-packaged GFP and mCherry (RFP) vectors using a single primer set targeting a shared CMV enhancer compared to the sum of titers determined from transgene specific primers used simultaneously showed no significant difference. Additionally, titers determined from crude lysate or iodixanol purified vector did not impact total quantification. QPCR titration determined from the transgene specific primers revealed that the respective contribution of each vector to the total titer corroborated the predicted ratios of GFP to mCherry prior to transfection.

As shown in Fig. 4, as a measure of infectivity, a single cell fluorescence assay was performed on C12 cells. The individual contribution of each vector to the total infectious titer also repeated the predicted ratios.

As shown in Fig. 5, therapeutic constructs differing in promoter elements (liver specific promoter - LSP; desmin promoter - DES) driving human codon-optimized acid a- glucosidase were co-packaged at 1:9, 1: 1, and 9: 1 ratios. The observed percent contribution of each vector to the total titer validated the predicted ratios.

Conclusion

During transfection, AAV will co-package reporter constructs combined at a predetermined ratio predictably and reproducibly to generate a heterogeneous population of vectors. Co-packaged vectors transduce C12 cells in the predicted ratios. Therapeutic constructs differing in promoter elements were also co-packaged in a reliable method. At least two constructs, differing in either transgene or transcription elements, can be efficiently co-packaged and return vector in equivalent ratios. References

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OTHER EMBODIMENTS

All of the features disclosed in this specification may be combined in any

combination. Each feature disclosed in this specification may be replaced by an alternative feature serving the same, equivalent, or similar purpose. Thus, unless expressly stated otherwise, each feature disclosed is only an example of a generic series of equivalent or similar features.

From the above description, one skilled in the art can easily ascertain the essential characteristics of the present disclosure, and without departing from the spirit and scope thereof, can make various changes and modifications of the disclosure to adapt it to various usages and conditions. Thus, other embodiments are also within the claims.

EQUIVALENTS

While several inventive embodiments have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and/or structures for performing the function and/or obtaining the results and/or one or more of the advantages described herein, and each of such variations and/or modifications is deemed to be within the scope of the inventive embodiments described herein. More generally, those skilled in the art will readily appreciate that all parameters, dimensions, materials, and configurations described herein are meant to be exemplary and that the actual parameters, dimensions, materials, and/or configurations will depend upon the specific application or applications for which the inventive teachings is/are used. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific inventive embodiments described herein. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, inventive embodiments may be practiced otherwise than as specifically described and claimed. Inventive embodiments of the present disclosure are directed to each individual feature, system, article, material, kit, and/or method described herein. In addition, any combination of two or more such features, systems, articles, materials, kits, and/or methods, if such features, systems, articles, materials, kits, and/or methods are not mutually inconsistent, is included within the inventive scope of the present disclosure.

All definitions, as defined and used herein, should be understood to control over dictionary definitions, definitions in documents incorporated by reference, and/or ordinary meanings of the defined terms.

All references, patents and patent applications disclosed herein are incorporated by reference with respect to the subject matter for which each is cited, which in some cases may encompass the entirety of the document.

The indefinite articles "a" and "an," as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean "at least one."

The phrase "and/or," as used herein in the specification and in the claims, should be understood to mean "either or both" of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Multiple elements listed with "and/or" should be construed in the same fashion, i.e., "one or more" of the elements so conjoined. Other elements may optionally be present other than the elements specifically identified by the "and/or" clause, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, a reference to "A and/or B", when used in conjunction with open-ended language such as "comprising" can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.

As used herein in the specification and in the claims, "or" should be understood to have the same meaning as "and/or" as defined above. For example, when separating items in a list, "or" or "and/or" shall be interpreted as being inclusive, i.e., the inclusion of at least one, but also including more than one, of a number or list of elements, and, optionally, additional unlisted items. Only terms clearly indicated to the contrary, such as "only one of or "exactly one of," or, when used in the claims, "consisting of," will refer to the inclusion of exactly one element of a number or list of elements. In general, the term "or" as used herein shall only be interpreted as indicating exclusive alternatives (i.e. "one or the other but not both") when preceded by terms of exclusivity, such as "either," "one of," "only one of," or "exactly one of." "Consisting essentially of," when used in the claims, shall have its ordinary meaning as used in the field of patent law.

As used herein in the specification and in the claims, the phrase "at least one," in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase "at least one" refers, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, "at least one of A and B" (or, equivalently, "at least one of A or B," or, equivalently "at least one of A and/or B") can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another

embodiment, to at least one, optionally including more than one, B, with no A present (and optionally including elements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one, B (and optionally including other elements); etc.

It should also be understood that, unless clearly indicated to the contrary, in any methods claimed herein that include more than one step or act, the order of the steps or acts of the method is not necessarily limited to the order in which the steps or acts of the method are recited. In the claims, as well as in the specification above, all transitional phrases such as "comprising," "including," "carrying," "having," "containing," "involving," "holding," "composed of," and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases "consisting of and "consisting essentially of shall be closed or semi-closed transitional phrases, respectively, as set forth in the United States Patent Office Manual of Patent Examining Procedures, Section 2111.03.

Claims

Claims What is claimed is:

1. A method of producing a recombinant adeno-associated virus (rAAV) particle preparation having a target ratio of a first rAAV particle to a second rAAV particle, the method comprising:

(a) contacting a cell preparation with:

(i) a first nucleic acid vector containing a first construct comprising a heterologous nucleic acid region encoding a first protein or polypeptide and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region;

(ii) a second nucleic acid vector containing a second construct comprising a heterologous nucleic acid region encoding a second protein or polypeptide and nucleic acid regions comprising an inverted terminal repeat (ITR) flanking each side of the heterologous nucleic acid region,

wherein the cell preparation is contacted under conditions sufficient for producing a first rAAV particle comprising the first construct and a second rAAV particle comprising the second construct; and

(b) isolating the first rAAV particle and the second rAAV particle from the cell preparation, thereby producing a rAAV preparation having a target ratio of the first rAAV particle to the second rAAV particle.

2. The method of claim 1, wherein the cell preparation is contacted simultaneously with the first nucleic acid vector and the second nucleic acid vector.

3. The method of claim 1 or 2, wherein the first nucleic acid vector and the second nucleic acid vector are present in an initial ratio of the first nucleic acid vector to the second nucleic acid vector when contacted with the cell preparation.

4. The method of claim 3, wherein the target ratio of the first rAAV particle and the second rAAV particle is compared to the initial ratio of the first nucleic acid vector to the second nucleic acid vector.

5. The method of claim 3 or 4, wherein the target ratio of the first rAAV particle to the second rAAV particle is within 10% of the initial ratio of the first nucleic acid vector to the second nucleic acid vector.

6. The method of any one of claims 3 to 5, wherein the initial ratio is 1: 1, 1:9 or 9: 1 of the first nucleic acid vector to the second nucleic acid vector.

7. The method of any one of claims 1 to 6, wherein the target ratio of the first rAAV particle to the second rAAV particle is measured after isolating the first rAAV particle and the second rAAV particle from the cell preparation.

8. The method of claim 7, wherein the target ratio of the first rAAV particle to the second rAAV particle is measured by measuring a level of DNA from the first rAAV particle and a level of DNA from the second rAAV particle.

9. The method of claim 8, wherein the level of DNA is measured using PCR, sequencing or flow cytometry.

10. The method of claim 9, wherein the level of DNA is measured using PCR and the PCR is quantitative PCR.

11. The method of any one of claims 1 to 10, wherein step (a) comprises transfecting the cell preparation with the first nucleic acid vector and the second nucleic acid vector.

12. The method of any one of claims 1 to 11, wherein the first nucleic acid vector and the second nucleic acid vector are a first plasmid and a second plasmid.

13. The method of claim 12, wherein the method further comprises contacting the cell preparation with at least one helper plasmid.

14. The method of claim 13, wherein the at least one helper plasmid is a first helper plasmid comprising a rep gene and a cap gene and a second helper plasmid comprising a Ela gene, a Elb gene, a E4 gene, a E2a gene, and a VA gene.

15. The method of any one of claims 1 to 10, wherein step (a) comprises infecting the cell preparation with the first nucleic acid vector and the second nucleic acid vector.

16. The method of claim 15, wherein the first nucleic acid vector is contained within a first herpes simplex virus type 1 (HS V) particle and the second nucleic acid vector is contained within a second HSV particle.

17. The method of claim 15, wherein the first nucleic acid vector is contained within a first baculovirus particle and the second nucleic acid vector is contained within a second baculovirus particle.

18. The method of any one of the preceding claims, wherein step (a) comprises incubating the cell preparation for at least 60 hours after contacting the cell preparation with the first nucleic acid vector and the second nucleic acid vector.

19. The method of any one of the preceding claims, wherein step (b) comprises lysing the cell preparation and extracting the first rAAV particle and the second rAAV particle.

20. The method of claim 19, wherein the first rAAV particle and the second rAAV particle are extracted simultaneously.

21. The method of any one of the preceding claims, wherein the first rAAV particle and the second rAAV particle are each rAAV 2/9 pseudotyped particles.