Patent Application
20210355503
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Sep. 23, 2019, is named NIGH-015/001WO_SL.txt and is 308 kilobytes in size.
The disclosure relates to the fields of human therapeutics, biologic drug products, viral delivery of human DNA sequences and methods of manufacturing same.
There is a long-felt and unmet need for AAV-based delivery vectors and improved methods of manufacturing these AAV-based delivery vectors.
The disclosure provides a method of purifying a recombinant AAV (rAAV) particle from a mammalian host cell culture, comprising the steps of: (a) purifying the plurality of rAAV particles through hydrophobic interaction chromatography (HIC) to produce a HIC eluate comprising the plurality of rAAV particles; (b) purifying the HIC eluate of (a) through cation exchange chromatography (CEX) to produce a CEX eluate comprising a plurality of rAAV particles; (c) isolating a plurality of full rAAV particles from the CEX eluate of (b) by anion exchange (AEX) chromatography to produce a AEX eluate comprising a purified and enriched plurality of full rAAV particles; and (d) diafiltering and concentrating the AEX eluate from (c) into a formulation buffer by tangential flow filtration (TFF) to produce a final composition comprising a purified and enriched plurality of full rAAV particles and the final formulation buffer. In some embodiments, the method further comprises the steps of contacting a plurality of transfected mammalian host cells and a virus release solution under conditions suitable for the release of the plurality of rAAV particles into a harvest media to produce a composition comprising a plurality of rAAV particles, virus release solution and harvest media; and purifying the plurality of rAAV particles from the composition through hydrophobic interaction chromatography (HIC) to produce a HIC eluate comprising the plurality of rAAV particles. In some embodiments, the method further comprises the step of culturing a plurality of mammalian host cells in a harvest media under conditions suitable for the formation of a plurality of rAAV particles, wherein the plurality of mammalian host cells have been transfected with a plasmid vector comprising an exogenous sequence, a helper plasmid vector, and a plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein to produce a plurality of transfected mammalian host cells, prior to the contacting step. In some embodiments, the AAV is an AAV8 or a derivative thereof. In some embodiments, the AAV comprises an AAV8 capsid protein or a derivative thereof.
In some embodiments of the methods of the disclosure, the harvest media comprises one or more of Dulbecco's Modified Eagle's medium (DMEM), stabilized glutamine, stabilized glutamine dipeptide and Benzonase.
In some embodiments of the methods of the disclosure, the harvest media comprises glycine, L-Arginine hydrochloride, L-Cystine dihydrocholoride, L-Glutamine, L-Histidine hydrochloride-H2O, L-Isoleucine, L-Leucine, L-Lysine hydrochloride, L-Methionine, L-Phenylalanine, L-Serine, L-Threonine, L-Tryptophan, L-Tyrosine disodium salt dehydrate, L-Valine, Choline chloride, D-Calcium pantothenate, Folic Acid, Niacinamide, Pyridoxine hydrochloride, Riboflavin, Thiamine hydrochloride, i-Inositol, Calcium Chloride (CaCl2) (anhyd.), Ferric Nitrate (Fe(NO3)3″9H2O), Magnesium Sulfate (MgSO4) (anhyd.), Potassium Chloride (KCl), Sodium Bicarbonate (NaHCO3), Sodium Chloride (NaCl), Sodium Phosphate monobasic (NaH2PO4-H2O), and D-Glucose (Dextrose).
In some embodiments of the methods of the disclosure, the harvest media comprises 4 mM stabilized glutamine or stabilized glutamine dipeptide.
In some embodiments of the methods of the disclosure, the harvest media comprises a serum-free media. In some embodiments of the methods of the disclosure, the harvest media consists of a serum-free media.
In some embodiments of the methods of the disclosure, the harvest media comprises a protein-free media. In some embodiments of the methods of the disclosure, the harvest media consists of a protein-free media.
In some embodiments of the methods of the disclosure, the harvest media comprises a clarified media. In some embodiments of the methods of the disclosure, the harvest media consists of a clarified media.
In some embodiments of the methods of the disclosure, the exogenous sequence comprises: (a) a sequence encoding a rhodopsin kinase promoter; (b) a sequence encoding a retinitis pigmentosa GTPase regulator ORF15 isoform (RPGRORF15); and (c) a sequence encoding a polyadenylation (polyA) signal.
In some embodiments of the methods of the disclosure, the rhodopsin kinase promoter is a GRK1 promoter. In some embodiments, wherein the sequence encoding the GRK1 promoter comprises or consists of:
In some embodiments of the methods of the disclosure, the sequence encoding the RPGRORF15 is a codon optimized human RPGRORF15 sequence. In some embodiments, the sequence encoding RPGRORF15 comprises a nucleotide sequence encoding an amino acid sequence of:
In some embodiments, the sequence encoding RPGRORF15 comprises or consists of a nucleotide sequence of:
In some embodiments of the methods of the disclosure, the sequence encoding the polyA signal comprises a bovine growth hormone (BGH) polyA sequence. In some embodiments, the sequence encoding the BGH polyA signal comprises a nucleotide sequence of:
In some embodiments of the methods of the disclosure, the exogenous sequence comprises a sequence encoding an ATP Binding Cassette, Subfamily Member 4 (ABCA4) protein or a portion thereof. In some embodiments, the exogenous sequence comprises a 5′ sequence encoding an ABCA4 protein or a portion thereof. In some embodiments, the exogenous sequence comprises a 3′ sequence encoding an ABCA4 protein or a portion thereof.
In some embodiments of the methods of the disclosure, the exogenous sequence further comprises a sequence encoding a promoter. In some embodiments, the exogenous sequence further comprises a sequence encoding a rhodopsin kinase (RK) promoter. In some embodiments, the RK promoter is a GRK1 promoter.
In some embodiments of the methods of the disclosure, the sequence encoding the GRK1 promoter comprises or consists of:
In some embodiments of the methods of the disclosure, the exogenous sequence further comprises a sequence encoding a chicken beta-actin (CBA) promoter. In some embodiments, the sequence encoding the CBA promoter comprises or consists of:
In some embodiments of the methods of the disclosure, the sequence encoding the ABCA4 is a human ABCA4 sequence. In some embodiments, the sequence encoding ABCA4 comprises a 5′ nucleotide sequence comprising nucleotides 1-4500 of SEQ ID NO: 2 or SEQ ID NO: 1, or a 3′ truncation variant thereof of either. In some embodiments, the sequence encoding ABCA4 comprises a 5′ nucleotide sequence comprising nucleotides 1-3701 or 1-4326 of SEQ ID NO: 2 or SEQ ID NO: 1. In some embodiments, the sequence encoding ABCA4 comprises a 3′ nucleotide sequence comprising nucleotides 3000-6822 of SEQ ID NO: 2 or SEQ ID NO: 1, or a 5′ truncation variant thereof of either. In some embodiments, the sequence encoding ABCA4 comprises a 3′ nucleotide sequence comprising nucleotides 3154-6822, 3196-6822, 3494-6822, 3603-6822, 3653-6822, 3678-6822, 3702-6822 or 3494-6822 of SEQ ID NO:2 or SEQ ID NO: 1. In some embodiments, the sequence encoding ABCA4 comprises a 5′ nucleotide sequence comprising nucleotides 1-4326 of SEQ ID NO: 2 or SEQ ID NO: 1 and the sequence encoding ABCA4 comprises a 3′ nucleotide sequence comprising nucleotides 3154-6822 of SEQ ID NO: 2 or SEQ ID NO: 1. In some embodiments, the sequence encoding ABCA4 comprises a 5′ nucleotide sequence comprising nucleotides 1-3701 and the sequence encoding ABCA4 comprises a 3′ nucleotide sequence comprising nucleotides 3196-6822 of SEQ ID NO: 2. or SEQ ID NO: 1. In some embodiments, the sequence encoding ABCA4 comprises a 5′ nucleotide sequence comprising nucleotides 1-3701 and the sequence encoding ABCA4 comprises a 3′ nucleotide sequence comprising nucleotides 3494-6822 of SEQ ID NO:2 or SEQ ID NO: 1. In some embodiments, the sequence encoding ABCA4 comprises a 5′ nucleotide sequence comprising nucleotides 1-3701 and the sequence encoding ABCA4 comprises a 3′ nucleotide sequence comprising nucleotides 3603-6822 of SEQ ID NO:2 or SEQ ID NO: 1. In some embodiments, the sequence encoding ABCA4 comprises a 5′ nucleotide sequence comprising nucleotides 1-3701 and the sequence encoding ABCA4 comprises a 3′ nucleotide sequence comprising nucleotides 3653-6822 of SEQ ID NO:2 or SEQ ID NO: 1. In some embodiments, the sequence encoding ABCA4 comprises a 5′ nucleotide sequence comprising nucleotides 1-3701 and the sequence encoding ABCA4 comprises a 3′ nucleotide sequence comprising nucleotides 3678-6822 of SEQ ID NO:2 or SEQ ID NO: 1. In some embodiments, the sequence encoding ABCA4 comprises a 5′ nucleotide sequence comprising nucleotides 1-3701 and the sequence encoding ABCA4 comprises a 3′ nucleotide sequence comprising nucleotides 3702-6822 of SEQ ID NO:2 or SEQ ID NO: 1. In some embodiments, the sequence encoding ABCA4 comprises a 5′ nucleotide sequence comprising nucleotides 1-3701 and the sequence encoding ABCA4 comprises a 3′ nucleotide sequence comprising nucleotides 3494-6822 of SEQ ID NO:2 or SEQ ID NO: 1.
SEQ ID NO: 1 is the human ABCA4 nucleic acid sequence corresponding to NCBI Reference Sequence NM_000350.2. SEQ ID NO: 1 is identical to NCBI Reference Sequence NM_000350.2. The ABCA4 coding sequence spans nucleotides 105 to 6926 of SEQ ID NO: 1.
SEQ ID NO: 2 is identical to SEQ ID NO: 1 with the exception of the following mutations: nucleotide 1640 G>T, nucleotide 5279 G>A, nucleotide 6173 T>C. These mutations do not alter the encoded amino acid sequence, and thus the ABCA4 protein encoded by SEQ ID NO: 2 is identical to the ABCA4 protein encoded by SEQ ID NO: 1.
In some embodiments of the methods of the disclosure, the plasmid vector comprising an exogenous sequence further comprises a sequence encoding a 5′ inverted terminal repeat (ITR) and a sequence encoding a 3′ ITR. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ ITR are derived from a 5′ITR sequence and a 3′ ITR sequence of an AAV of serotype 2 (AAV2). In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ ITR comprise sequences that are identical to a sequence of a 5′ITR and a sequence of a 3′ ITR of an AAV2. In some embodiments, the sequence encoding the 5′ ITR comprises or consists of the nucleotide sequence of:
In some embodiments, the sequence encoding the 3′ ITR comprises or consists of the nucleotide sequence of:
In some embodiments of the compositions of the disclosure, the polynucleotide further comprises a Kozak sequence. In some embodiments, the Kozak sequence comprises or consists of the nucleotide sequence of GGCCACCATG (SEQ ID NO: 73).
In some embodiments of the compositions of the disclosure, the polynucleotide comprises or consists of the sequence of:
In some embodiments of the methods of the disclosure, the plasmid vector comprising an exogenous sequence, the helper plasmid vector or the plasmid vector comprising the sequence encoding a viral Rep protein and a viral Cap protein further comprises a sequence encoding a selection marker.
In some embodiments of the methods of the disclosure, the sequence encoding the viral Rep protein and the sequence encoding the viral Cap protein comprise sequences isolated or derived from AAV serotype 8 (AAV8) viral Rep protein and viral Cap protein sequences.
In some embodiments of the methods of the disclosure, the harvest media comprises DMEM, 4 mM stabilized glutamine or stabilized glutamine dipeptide, and Benzonase.
In some embodiments of the methods of the disclosure, the mammalian host cells have been transfected with a composition comprising one or more of a polymer (e.g. a polyethylenimine (PEI) composition), calcium phosphate, a lipid, a vector capable of traversing a cell membrane (e.g. a liposome, a micelle, a nanoparticle (e.g. carbon, silicon, polymer and gold). In some embodiments, the mammalian host cells have been transfected with a composition comprising polyethylenimine (PEI) (i.e. a PEI composition).
In some embodiments of the methods of the disclosure, the virus release solution comprises a salt and a high pH. In some embodiments, the salt comprises NaCl. In some embodiments, the high pH is a basic pH. In some embodiments, the high pH is greater than 7.0. In some embodiments, high pH comprises a pH greater than or equal to 7.0, 7.1, 7.2, 7.3, 7.4, 7.5, 7.6, 7.7, 7.8, 7.9, 8.0, 8.1, 8.2, 8.3, 8.4, 8.5, 8.6, 8.7, 8.8, 8.9, 9.0, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10.0, 10.1, 10.2, 10.3, 10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11.0, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 12.0, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9, 13.0, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14.0.
In some embodiments of the methods of the disclosure, the conditions suitable for the formation of a plurality of rAAV particles comprise incubating the mammalian host cells at conditions recapitulating in vivo physiology for at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 hours. In some embodiments, conditions recapitulating in vivo physiology include 5% CO2 at a temperature that is minimally human internal body temperature. In some embodiments, conditions suitable for the formation of a plurality of rAAV particles comprises incubating the mammalian host cells at a CO2 level equal to or less than 10% CO2. In some embodiments, human internal body temperature is at least 36° C.
In some embodiments of the methods of the disclosure, the HIC step of (a) further comprises the steps of: (i) generating a HIC chromatogram; and (ii) selecting a fraction on the HIC chromatogram containing rAAV particles to produce the HIC eluate comprising a plurality of rAAV viral particles. In some embodiments, the HIC step further comprises diluting the harvest media into a high salt buffer prior to generating the HIC chromatogram. In some embodiments, the plurality of rAAV particles are eluted using a step gradient. In some embodiments, the step gradient comprises a decrease in salt concentration at each step gradient. In some embodiments of the methods of the disclosure, the CEX step of (b) further comprises the steps of: (i) generating a CEX chromatogram; and (ii) selecting a fraction from the CEX chromatogram containing rAAV particles to produce the CEX eluate comprising a plurality of rAAV viral particles. In some embodiments, the CEX chromatography comprises an SO3− cation exchange matrix. In some embodiments, the CEX chromatography step further comprises adjusting the HIC eluate into a low salt buffer prior to generating the CEX chromatogram. In some embodiments, the adjustment comprises a dilution step. In some embodiments, the adjustment step comprises a TFF step. In some embodiments, the TFF step is performed using a 100 kDa hollow fiber filter (HFF). In some embodiments, the TFF step is performed using at least a 70 kDa HFF. In some embodiments, the TFF step is performed using at least a 50 kDa HFF. In some embodiments, the TFF step is performed using at least a 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 kDa HFF or any number of kDa in between. In some embodiments, the pH of the HIC eluate is adjusted to pH 3.0 to pH 4.0, inclusive of the endpoints. In some embodiments, the pH of the HIC eluate is adjusted to pH 3.5 to pH 3.7, inclusive of the endpoints. In some embodiments, the CEX step further comprises filtering the HIC eluate. In some embodiments, filtering the HIC eluate comprises a 0.8/0.45 μm polyethersulfone (PES) filter. In some embodiments, the plurality of rAAV particles are eluted using a step gradient. In some embodiments, the step gradient comprises a pH gradient, a salt gradient or a combination thereof. In some embodiments, the plurality of rAAV particles are eluted using a linear gradient. In some embodiments, the linear gradient comprises a pH gradient, a salt gradient or a combination thereof. In some embodiments, the CEX step further comprises neutralizing the pH of the CEX eluate. In some embodiments, the pH of the neutralized CEX eluate is pH 9.0.
In some embodiments of the methods of the disclosure, the AEX Chromatography step of (c) further comprises the steps of: (i) generating an AEX chromatogram; and (ii) selecting a fraction from the AEX chromatogram containing full rAAV particles to produce the AEX eluate comprising a purified and enriched plurality of full rAAV particles. In some embodiments, the AEX chromatography comprises an Anion Exchange (QA) matrix. In some embodiments, the AEX chromatography step further comprises diluting the CEX eluate into a low salt buffer prior to generating the AEX chromatogram. In some embodiments, the adjustment comprises a dilution step. In some embodiments, the adjustment step comprises a TFF step. In some embodiments, the adjustment step comprises a first TFF step and a second TFF step. In some embodiments, the TFF step is performed using a 100 kDa hollow fiber filter (HFF). In some embodiments, the diluted CEX eluate is pH 9.0. In some embodiments, the purified and enriched plurality of full rAAV particles are eluted using a linear gradient. In some embodiments, the purified and enriched plurality of full rAAV particles are eluted using a step gradient. In some embodiments, the CEX step further comprises neutralizing the pH of the eluate comprising the purified and enriched plurality of full rAAV particles.
In some embodiments of the methods of the disclosure, the TFF step of (d) is performed using a 100 kDa hollow fiber filter (HFF). In some embodiments, step (f) the method further comprises a second TFF step, and wherein both the first and second TFF steps are performed using a 100 kDa HFF. In some embodiments, the final formulation buffer comprises Tris, MgCl2, and NaCl. In some embodiments, the final formulation buffer comprises 20 mM Tris, 1 mM MgCl2, and 200 mM NaCl at pH 8. In some embodiments, the final formulation buffer further comprises poloxamer 188 at 0.001%.
In some embodiments of the methods of the disclosure, the methods further comprise adding poloxamer 188 to the final composition.
In some embodiments of the methods of the disclosure, the final composition comprising the purified and enriched plurality of full rAAV particles and the final formulation buffer is frozen at −80° C.
The disclosure provides a composition comprising a plurality of rAAV particles produced by a method of the disclosure.
In some embodiments of the compositions of the disclosure, the composition comprises (a) between 0.5×1011 vg/mL and 1×1013 vg/mL, inclusive of the endpoints and (b) less than 50% empty capsids. In some embodiments of the compositions of the disclosure, the composition comprises (a) between 0.5×1011 vg/mL and 1×1013 vg/mL, or between 1×1011 vg/mL and 1×1013 vg/mL, inclusive of the endpoints and (b) less than 30% empty capsids. In some embodiments, the composition comprises (a) between 0.5×1011 vg/mL and 1×1013 vg/mL, or between 1×1011 vg/mL and 1×1013 vg/mL, inclusive of the endpoints and (b) less than 25% empty capsids In some embodiments, the composition comprises (a) between 0.5×1011 vg/mL and 1×1013 vg/mL, or between 1×1011 vg/mL and 1×1013 vg/mL, inclusive of the endpoints and (b) less than 99%, 97%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, 2%, 1%, or any percentage in between of empty capsids. In some embodiments, the composition comprises about 5×1012 vg/mL.
In some embodiments of the compositions of the disclosure, the composition comprises (a) between 0.5×1011 vg/mL and 1×1013 vg/mL, or between 1×1011 vg/mL and 1×1013 vg/mL, inclusive of the endpoints and (b) at least 70% full capsids. In some embodiments, the composition comprises (a) between 0.5×1011 vg/mL and 1×1013 vg/mL, or between 1×1011 vg/mL and 1×1013 vg/mL, inclusive of the endpoints and (b) at least 1%, 2%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99%, 100%, or any percentage in between of full capsids. In some embodiments, the composition comprises 5×1012 vg/mL.
In some embodiments of the compositions of the disclosure, a portion of the plurality of rAAV comprises a functional vector genome, wherein each functional vector genome is capable of expressing an exogenous sequence in a cell following transduction. In some embodiments, the portion of the plurality of rAAV comprising a functional vector genome expresses the exogenous sequence at a 2-fold increase when compared to a level of expression of a corresponding endogenous sequence in a nontransduced cell. In some embodiments, the portion of the plurality of rAAV comprising a functional vector genome expresses the exogenous sequence at a 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13-fold, 14-fold, 15-fold, 16-fold, 17-fold, 18-fold, 19-fold, 20-fold, or any other increment fold increase in between, when compared to a level of expression of a corresponding endogenous sequence in a nontransduced cell.
In some embodiments of the compositions of the disclosure, including those wherein a portion of the plurality of rAAV comprises a functional vector genome, wherein each functional vector genome is capable of expressing an exogenous sequence in a cell following transduction, the exogenous sequence and the corresponding endogenous sequence are not identical. In some embodiments, the exogenous sequence and the corresponding endogenous sequence are not identical, but a protein encoded by the exogenous sequence and a protein encoded by the endogenous sequence are identical. In some embodiments, the exogenous sequence and the corresponding endogenous sequence have at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or any percentage in between of identity. In some embodiments, the exogenous sequence is codon-optimized when compared to the endogenous sequence. In some embodiments, the exogenous sequence and the corresponding endogenous sequence have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or any percentage in between of identity. In some embodiments of the composition of the disclosure, following transduction of a cell with a composition of the disclosure, the exogenous sequence encodes a protein. In some embodiments, the protein encoded by the exogenous sequence has an activity level equal to or greater than an activity level of a protein encoded by a corresponding sequence of a nontransduced cell. In some embodiments, the exogenous sequence and the corresponding endogenous sequence are identical. In some embodiments, the exogenous sequence and the corresponding endogenous sequence are not identical. In some embodiments, the exogenous sequence and the corresponding endogenous sequence have at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or any percentage in between of identity. In some embodiments, following transduction of a cell with a composition of the disclosure, the exogenous sequence encodes a protein.
In some embodiments of the methods of the disclosure, including those wherein the method comprises the step of culturing a plurality of mammalian host cells in a harvest media under conditions suitable for the formation of a plurality of rAAV particles, wherein the plurality of mammalian host cells have been transfected with a plasmid vector comprising an exogenous sequence, a helper plasmid vector, and a plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein to produce a plurality of transfected mammalian host cells, prior to the contacting step, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided at a molar ratio of about 0.5:1:1 to about 10:1:1, about 1:1:1 to about 10:1:1, about 2:1:1 to about 10:1:1, or about 3:1:1 to about 10:1:1, respectively, optionally about 0.5:1:1, about 1:1:1, about 2:1:1, about 3:1:1, about 4:1:1, about 5:1:1, about 6:1:1, about 7:1:1, about 8:1:1, about 9:1:1, or about 10:1:1. In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 1:1:1, respectively. In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 3:1:1, respectively. In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 10:1:1, respectively.
In some embodiments of the methods of the disclosure, including those wherein the method comprises the step of culturing a plurality of mammalian host cells in a harvest media under conditions suitable for the formation of a plurality of rAAV particles, wherein the plurality of mammalian host cells have been transfected with a plasmid vector comprising an exogenous sequence, a helper plasmid vector, and a plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein to produce a plurality of transfected mammalian host cells, prior to the contacting step, the plasmid vector comprising an exogenous sequence (pITR) and the helper plasmid vector (pHELP) is provided in a molar ratio of between 1:1 and 20:19 or between 1:20 and 20:1, or between 1:20 and 1:1 (e.g., any of the ratios shown below in Table A). In some embodiments, the molar ratio of pITR and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein (pREPCAP) is between 1:1 and 20:19, or between 1:20 and 20:1, or between 1:20 and 1:1 (e.g., any of the ratios shown below in Table A). In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 3:1:1, respectively. In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 10:1:1, respectively. In certain embodiments, the transfection is conducted using CaPO4 or PEI. In particular embodiments, the transfection is conducted using PEI at a PEI:DNA ratio (mL:mg) of about 1:1 to about 5:1, respectively, optionally about 2:1 to about 4:1, about 4:1, about 3:1, or about 2:1. In certain embodiments, the transection is conducted using PEI, wherein the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 1:1:1, respectively. In certain embodiments, the transfection is conducted using PEI at a PEI:DNA ratio (mL:mg) of about 0.5:1 to 5:1 or about 1:1 to about 5:1, respectively, optionally about 2:1 to about 4:1, about 4:1, about 3:1, or about 2:1, wherein the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 0.5:1:1 to about 10:1:1, about 1:1:1 to about 10:1:1, about 2:1:1 to about 10:1:1 optionally about 0.5:1:1, about 1:1:1, about 2:1:1, about 3:1:1, about 4:1:1, about 5:1:1, about 6:1:1, about 7:1:1, about 8:1:1, about 9:1:1, or about 10:1:1. In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 1:1:1, respectively. In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 3:1:1, respectively. In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 10:1:1, respectively. In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 2:1:1, about 3:1:1, about 4:1:1, about 5:1:1, about 6:1:1, about 7:1:1, about 8:1:1, or about 9:1:1, respectively.
In some embodiments of the methods of the disclosure, including those wherein the method comprises the step of culturing a plurality of mammalian host cells in a harvest media under conditions suitable for the formation of a plurality of rAAV particles, wherein the plurality of mammalian host cells have been transfected with a plasmid vector comprising an exogenous sequence, a helper plasmid vector, and a plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein to produce a plurality of transfected mammalian host cells, prior to the contacting step, and in which a molar ratio of the plasmid vector to either the helper plasmid vector or the RepCap vector comprises a greater value for the plasmid vector than either the helper plasmid vector or the RepCap vector, the culturing a plurality of mammalian host cells in a harvest media under conditions suitable for the formation of a plurality of rAAV particles comprises a transfection agent. In some embodiments, the transfection agent comprises polyethylenimine. In some embodiments, the transfection agent comprises calcium phosphate (CaPO4).
In certain related embodiments, the disclosure provides a method of producing a recombinant AAV vector, comprising transfecting mammalian host cells with: (i) a plasmid vector comprising an exogenous sequence; (ii) a plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein; and (iii) a helper plasmid vector, wherein the mammalian host cells are contacted with a transfection medium comprising the plasmid vector comprising the exogenous sequence, the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein, and the helper plasmid at a molar ratio of about 0.5:1:1 to about 10:1:1, or about 1:1:1 to about 10:1:1, respectively, optionally about 2:1:1, about 3:1:1, about 4:1:1, about 5:1:1, about 6:1:1, about 7:1:1, about 8:1:1, about 9:1:1, or about 10:1:1. In some embodiments, the transfection medium comprises a transfection agent selected from polyethylenimine (PEI) and CaPO4. In certain embodiments, the transfection agent is PEI, and wherein the tranfection medium comprises PEI and DNA at a ratio of about 5:1 to about 1:1, about 2:1 to about 4:1, about 4:1, about 3:1, about 2:1, or about 1:1.
In particular embodiments of the methods of producing a recombinant AAV vector disclosed herein, the exogenous sequence comprises: (a) a sequence encoding a rhodopsin kinase promoter; (b) a sequence encoding a retinitis pigmentosa GTPase regulator ORF15 isoform (RPGRORF15); and (c) a sequence encoding a polyadenylation (polyA) signal. In some embodiments, the rhodopsin kinase promoter is a GRK1 promoter, e.g., a GRK1 promoter comprising or consisting of:
In some embodiments, the sequence encoding the RPGRORF15 is a codon optimized human RPGRORF15 sequence, including but not limited to any of those disclosed herein.
In particular embodiments of the methods of producing a recombinant AAV vector disclosed herein, the sequence encoding the polyA signal comprises a bovine growth hormone (BGH) polyA sequence, including but not limited to any of those disclosed herein.
In particular embodiments of the methods of producing a recombinant AAV vector disclosed herein, the plasmid vector comprising an exogenous sequence further comprises a sequence encoding a 5′ inverted terminal repeat (ITR) and a sequence encoding a 3′ ITR. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ ITR are derived from a 5′ITR sequence and a 3′ ITR sequence of an AAV of serotype 2 (AAV2). In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ ITR comprise sequences that are identical to a sequence of a 5′ITR and a sequence of a 3′ ITR of an AAV2. In other embodiments, the ITRs comprise one or more modifications as compared to a wild type AAV2, e.g., one or more nucleotide deletions, insertions or substitutions. In certain embodiments, the ITRs are derived from a 3′ AAV2 ITR in forward and reverse orientation with subsequent deletions to produce stabilized ITRs. In certain embodiment, the sequence encoding the 5′ ITR comprises or consists of the nucleotide sequence of:
In certain embodiments, the sequence encoding the 3′ ITR comprises or consists of the nucleotide sequence of:
In particular embodiments of the methods of producing a recombinant AAV vector disclosed herein, the exogenous sequence further comprises a sequence encoding a Kozak sequence. In certain embodiments, the Kozak sequence comprises the nucleotide sequence of GGCCACCATG (SEQ ID NO: 73).
In particular embodiments of the methods of producing a recombinant AAV vector disclosed herein, the exogenous sequence comprises the sequence of:
In particular embodiments of the methods of producing a recombinant AAV vector disclosed herein, the exogenous sequence comprises a sequence encoding an ATP Binding Cassette, Subfamily Member 4 (ABCA4) protein or a portion thereof. In some embodiments, the exogenous sequence comprises a 5′ sequence encoding an ABCA4 protein or a portion thereof. In some embodiments, the exogenous sequence comprises a 3′ sequence encoding an ABCA4 protein or a portion thereof. In some embodiments, the exogenous sequence further comprises a sequence encoding a promoter. In some embodiments, the exogenous sequence comprises a sequence encoding a rhodopsin kinase (RK) promoter. In certain embodiments, the RK promoter is a GRK1 promoter. In some embodiments, the sequence encoding the GRK1 promoter comprises or consists of:
In certain embodiments, the exogenous sequence comprises a sequence encoding a chicken beta-actin (CBA) promoter. In some embodiments, the sequence encoding the CBA promoter comprises or consists of:
In some embodiments, the sequence encoding the ABCA4 is a human ABCA4 sequence or a variant thereof. In certain embodiments, the sequence encoding ABCA4 comprises a 5′ nucleotide sequence comprising nucleotides 1-3701 or 1-4326 of SEQ ID NO: 2 or SEQ ID NO: 1. In certain embodiments, the sequence encoding ABCA4 comprises a 3′ nucleotide sequence comprising nucleotides 3154-6822, 3196-6822, 3494-6822, 3603-6822, 3653-6822, 3678-6822, 3702-6822 or 3494-6822 of SEQ ID NO: 2 or SEQ ID NO: 1. In particular embodiments, the methods disclosed herein are used to produce upstream and/or downstream ABCA4 vectors that may be used according to a dual vector system disclosed herein. In particular embodiments, the ABCA4 vectors include, but are not limited to, those disclosed in or comprising sequences disclosed in any of
In particular embodiments of the methods of producing a recombinant AAV vector disclosed herein, the plasmid vector comprising an exogenous sequence, the helper plasmid vector or the plasmid vector comprising the sequence encoding a viral Rep protein and a viral Cap protein further comprises a sequence encoding a selection marker.
In particular embodiments of the methods of producing a recombinant AAV vector disclosed herein, the sequence encoding the viral Rep protein and the sequence encoding the viral Cap protein comprise sequences isolated or derived from AAV serotype 8 (AAV8) viral Rep protein and viral Cap protein sequences, including variants thereof.
The file of this patent contains at least one drawing/photograph executed in color. Copies of this patent with color drawings(s)/photographs(s) will be provided by the Office upon request and payment of the necessary fee.
Several of the drawings are chromatograms. Generally, the green line indicates fluorescence, the red line indicated absorbance (260 nm), the blue line indicates absorbance (280 nm), and the black line indicates conductibity. Viewed in black and white, the conductivity line typically starts low and increases over time, and the absorbance (260 nm) and absorbance (280 nm) lines largely track each other.
The disclosure provides a method of purifying a recombinant AAV (rAAV) particle from a mammalian host cell culture, comprising the steps of: (a) culturing a plurality of mammalian host cells in a growth media under conditions suitable for the formation of a plurality of rAAV particles, wherein the plurality of mammalian host cells have been transfected with a plasmid vector comprising an exogenous sequence, a helper plasmid vector, and a plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein to produce a plurality of transfected mammalian host cells; (b) contacting the plurality of transfected mammalian host cells and a virus release solution under conditions suitable for the release of rAAV particles into a harvest media to produce a composition comprising a plurality of rAAV particles, virus release solution and harvest media; (c) purifying the plurality of rAAV particles from the composition of (b) through hydrophobic interaction chromatography (HIC) to produce a HIC eluate comprising the plurality of rAAV particles; (d) purifying the plurality of rAAV viral particles from the HIC eluate of (b) through cation exchange chromatography (CEX) to produce a CEX eluate comprising a plurality of rAAV particles; (e) isolating a plurality of full rAAV particles from the CEX eluate of (d) by anion exchange (AEX) chromatography to produce a AEX eluate comprising a purified and enriched plurality of full rAAV particles; and (f) diafiltering and concentrating the AEX eluate of (e) into a final formulation buffer by tangential flow filtration (TFF) to produce a final composition comprising a purified and enriched plurality of full rAAV particles and the final formulation buffer.
The disclosure further related to methods of producing a recombinant AAV (rAAV) particle, comprising the steps of: (a) transfecting a plurality of mammalian host cells with a plasmid vector comprising an exogenous sequence, a helper plasmid vector, and a plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein to produce a plurality of transfected mammalian host cells, wherein the cells are transfected using PEI as a transfection reagent, and wherein the cells are contacted with the PEI and the vectors at specified ratios of the plasmid vectors.
The disclosure provides a composition manufactured using the methods of the disclosure. In some embodiments, the composition comprises (a) between 0.5×1011 vector genomes (vg)/mL and 1×1013 vg/mL of replication-defective and recombinant adeno-associated virus (rAAV), (b) less than 50% empty capsids; and (c) a plurality of functional vg/mL, wherein each of functional vector genomes is capable of expressing an RPGRORF15 sequence in a cell following transduction. In some embodiments, the composition comprises (a) between 0.5×1011 vector genomes (vg)/mL and 1×1013 vg/mL of replication-defective and recombinant adeno-associated virus (rAAV), (b) less than 30% empty capsids; and (c) a plurality of functional vg/mL, wherein each of functional vector genomes is capable of expressing an RPGRORF15 sequence in a cell following transduction. In some embodiments, the composition comprises (a) between 0.5×1011 vector genomes (vg)/mL and 1×1013 vg/mL of replication-defective and recombinant adeno-associated virus (rAAV), (b) less than 99%, 97%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, 2%, 1%, or any percentage in between of empty capsids; and (c) a plurality of functional vg/mL, wherein each of functional vector genomes is capable of expressing an RPGRORF15 sequence in a cell following transduction. In some embodiments, following transduction of a cell with a composition of the disclosure, the RPGRORF15 sequence encodes a RPGRORF15 protein. In some embodiments, the protein encoded by the RPGRORF15 sequence has an activity level equal to or greater than an activity level of an RPGRORF15 encoded by a corresponding sequence of a nontransduced cell. In some embodiments, the exogenous RPGRORF15 sequence and the corresponding endogenous RPGRORF15 sequence are identical. In some embodiments, the exogenous RPGRORF15 sequence and the corresponding endogenous RPGRORF15 sequence are not identical. In some embodiments, the exogenous RPGRORF15 sequence and the corresponding endogenous RPGRORF15 sequence have at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or any percentage in between of identity.
In some embodiments of the compositions of the disclosure, the composition comprises (a) between 0.5×1011 vg/mL and 1×1013 vg/mL, inclusive of the endpoints, (b) at least 70% full capsids and (c) a plurality of functional vg/mL, wherein each of functional vector genomes is capable of expressing an RPGRORF15 sequence in a cell following transduction. In some embodiments, the composition comprises (a) between 0.5×1011 vg/mL and 1×1013 vg/mL, inclusive of the endpoints, (b) at least 1%, 2%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99%, 100%, or any percentage in between of full capsids and (c) a plurality of functional vg/mL, wherein each of functional vector genomes is capable of expressing an RPGRORF15 sequence in a cell following transduction. In some embodiments, the composition comprises 0.5×1011 vg/mL. In some embodiments, the composition comprises 1×1012 vg/mL.
Compositions of the disclosure comprise a therapeutic RPGRORF15 construct suitable for systemic or local administration to a mammal, and preferable, to a human. Exemplary RPGRORF15 constructs of the disclosure comprise a sequence encoding a RPGRORF15 or a portion thereof. Preferably, RPGRORF15 constructs of the disclosure comprise a sequence encoding a human RPGRORF15 or a portion thereof. Exemplary RPGRORF15 constructs of the disclosure may further comprise one or more sequence(s) encoding regulatory elements to enable or to enhance expression of the gene or a portion thereof. Exemplary regulatory elements include, but are not limited to, promoters, introns, enhancer elements, response elements (including post-transcriptional response elements or post-transcriptional regulatory elements), polyadenosine (polyA) sequences, and a gene fragment to facilitate efficient termination of transcription (including a β-globin gene fragment and a rabbit β-globin gene fragment).
In some embodiments of the compositions of the disclosure, the RPGRORF15 construct comprises a human gene or a portion thereof corresponding to a human Retinitis Pigmentosa GTPase Regulator (RPGR) protein or a portion thereof. Human RPGR comprises multiple spliced isoforms. Isoform ORF15 RPGR (RPGRORF15) localizes to the photoreceptors. In some embodiments, the RPGR protein is RPGRORF15. In some embodiments, the RPGRORF15 construct comprises a human gene or a portion thereof comprising a codon-optimized sequence. In some embodiments, the sequence is codon-optimized for expression in mammals. In some embodiments, the sequence is codon-optimized for expression in humans.
In some embodiments of the compositions of the disclosure, the AAV-RPGRORF15 product consists of a purified recombinant serotype 2 (rAAV) encoding the cDNA of RPGRORF15. In some embodiments, each 20 nm AAV virion contains a single stranded DNA insert sequence comprising: an AAV2 5′ inverted terminal repeat (ITR), a 199 bp GRK1 promoter, a 3459 bp human RPGRORF15 cDNA, a 270 bp Bovine growth hormone polyadenylation sequence (BGH-polyA), and an AAV2 3′ ITR, as well a short cloning sequences flanking the elements.
In some embodiments, the RPGRORF15 construct comprises a sequence encoding RPGRORF15 In some embodiments, the sequence encoding the RPGRORF15 is a human RPGRORF15 sequence. In some embodiments, the sequence encoding RPGRORF15 comprises a nucleotide sequence encoding an amino acid sequence that has at least 80% identity, at least 90% identity, at least 95% identity, at least 97% identity, at least 99% identity or is identical to the amino acid sequence of:
In some embodiments, the sequence encoding RPGRORF15 comprises a wild type nucleotide sequence. In some embodiments, the sequence encoding RPGRORF15 comprises a nucleotide sequence that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99% or any percentage in between of identity to the nucleotide sequence of:
In some embodiments, the sequence encoding RPGRORF15 comprises a codon optimized nucleotide sequence. RPGRORF15 contains a highly repetitive purine-rich region at the 3′-end and a splice site immediately upstream, which can create significant challenges in cloning an AAV.RPGR vector. In some embodiments, codon optimization can be used to disable the endogenous splice site and stabilize the purine-rich sequence in the RPGRORF15 transcript without altering the amino acid sequence of the RPGRORF15 protein. In some embodiments, post-translation modifications such as glutamylation of RPGR protein are preserved following codon-optimization. In some embodiments, the RPGRORF15 nucleotide sequence is codon optimized for expression in a mammal. In some embodiments, the RPGRORF15 nucleotide sequence is codon optimized for expression in a human.
In some embodiments, the codon optimized 3459 bp human RPGRORF15 cDNA comprises a nucleotide sequence that has at least 70% identity, at least 75% identity, at least 80% identity, at least 85% identity, at least 90% identity, at least 95% identity, at least 97% identity, at least 99% identity or any percentage in between of identity to the nucleotide sequence of:
In some embodiments, the codon optimized 3459 bp human RPGRORF15 cDNA comprises or consists of the nucleotide sequence of:
In some embodiments of the compositions of the disclosure, the RPGRORF15 construct comprises a promoter. In some embodiments, the promoter comprises a rhodopsin kinase promoter. In some embodiments, the rhodopsin kinase promoter is isolated or derived from the promoter of the G protein-coupled receptor kinase 1 (GRK1) gene. In some embodiments, the promoter is a GRK1 promoter. In some embodiments, the sequence encoding the GRK1 promoter comprises a sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 97% identity or at least 99% identity to:
In some embodiments, the GRK1 promoter comprises or consists of:
In some embodiments of the compositions of the disclosure, the RPGRORF15 construct comprises a polyadenylation signal. In some embodiments, the sequence encoding the polyA signal comprises a polyA signal isolated or derived from a bovine growth hormone (BGH) polyA signal. In some embodiments, the BGH polyA signal comprises a nucleotide sequence that has at least 80% identity, at least 97% identity or 100% identity to the nucleotide sequence of:
In some embodiments, the sequence encoding the BGH polyA comprises or consists of the nucleotide sequence of:
In some embodiments of the compositions of the disclosure, the RPGRORF15 construct further comprises a sequence corresponding to a 5′ inverted terminal repeat (ITR) and a sequence corresponding to a 3′ inverted terminal repeat (ITR). In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR are identical. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR are not identical. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR are isolated or derived from an adeno-associated viral vector of serotype 2 (AAV2) In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR comprise a wild type sequence. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR comprise a truncated wild type AAV2 sequence. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR comprise a variation when compared to a wild type AAV2 sequence. In some embodiments, the variation comprises a substitution, an insertion, a deletion, an inversion, or a transposition. In some embodiments, the variation comprises a truncation or an elongation of a wild type or a variant sequence.
In some embodiments of the compositions of the disclosure, an AAV comprises a sequence corresponding to a 5′ inverted terminal repeat (ITR) and a sequence corresponding to a 3′ inverted terminal repeat (ITR). In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR are identical. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR are not identical. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR are isolated or derived from an adeno-associated viral vector of serotype 2 (AAV2) In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR comprise a wild type sequence. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR comprise a truncated wild type AAV2 sequence. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR comprise a variation when compared to a wild type AAV2 sequence. In some embodiments, the variation comprises a substitution, an insertion, a deletion, an inversion, or a transposition. In some embodiments, the variation comprises a truncation or an elongation of a wild type or a variant sequence.
In some embodiments of the compositions of the disclosure, an AAV comprises a viral sequence essential for formation of a replication-deficient AAV. In some embodiments, the viral sequence is isolated or derived from an AAV of the same serotype as one or both of the sequence encoding the 5′ITR or the sequence encoding the 3′ITR. In some embodiments, the viral sequence, the sequence encoding the 5′ITR or the sequence encoding the 3′ITR are isolated or derived from an AAV2.
In some embodiments of the compositions of the disclosure, an AAV comprises a viral sequence essential for formation of a replication-deficient AAV, a sequence encoding the 5′ITR and a sequence encoding the 3′ITR, but does not comprise any other sequence isolated or derived from an AAV. In some embodiments, the AAV is a recombinant AAV (rAAV), comprising a viral sequence essential for formation of a replication-deficient AAV, a sequence encoding the 5′ITR, a sequence encoding the 3′ITR, and a sequence encoding an RPGRORF15 construct of the disclosure.
In some embodiments, a plasmid DNA used to create the rAAV in a host cell comprises a selection marker. Exemplary selection markers include, but are not limited to, antibiotic resistance genes. Exemplary antibiotic resistance genes include, but are not limited to, ampicillin and kanamycin. Exemplary selection markers include, but are not limited to, drug or small molecule resistance genes. Exemplary selection markers include, but are not limited to, dapD and a repressible operator including but not limited to a lacO/P construct controlling or suppressing dapD expression, wherein plasmid selection is performed by administering or contacting a transformed cell with a plasmid capable of operator repressor titration (ORT). Exemplary selection markers include, but are not limited to, a ccd selection gene. In some embodiments, the ccd selection gene comprises a sequence encoding a ccdA selection gene that rescues a host cell line engineered to express a toxic ccdB gene. Exemplary selection markers include, but are not limited to, sacB, wherein an RNA is administered or contacted to a host cell to suppress expression of the sacB gene in sucrose media. Exemplary selection markers include, but are not limited to, a segregational killing mechanism such as the parAB+ locus composed of Hok (a host killing gene) and Sok (suppression of killing).
The AAV-RPGRORF15 construct product consists of a purified recombinant serotype 2 adeno-associated viral vector (rAAV) encoding the cDNA encoding a therapeutic construct.
In some embodiments, the AAV-RPGRORF15 construct comprises one or more of a sequence encoding a 5′ ITR, a sequence encoding a 3′ ITR and a sequence encoding a capsid protein that is isolated and/or derived from a serotype 8 adeno-associated viral vector (AAV8). In some embodiments, the AAV-RPGRORF15 construct comprises a sequence encoding a 5′ ITR, a sequence encoding a 3′ ITR and a sequence encoding a capsid protein that is isolated and/or derived from a serotype 8 adeno-associated viral vector (AAV8). In some embodiments, the AAV-RPGRORF15 construct comprises a truncated sequence encoding a 5′ ITR and a sequence encoding a 3′ ITR that is isolated and/or derived from a serotype 2 adeno-associated viral vector (AAV2) and a sequence encoding a capsid protein that is isolated and/or derived from a serotype 8 adeno-associated viral vector (AAV8). In some embodiments, the AAV-Construct comprises wild type AAV2 ITRs (a wild type 5′ ITR and a wild type 3′ ITR).
In some embodiments, each 20 nm AAV virion contains a single stranded DNA insert sequence (plus short cloning sites flanking each element) comprising: (a) a 5′ inverted terminal repeat (ITR), (b) a promoter suitable for expression in mammalian cells, (c) a cDNA encoding RPGRORF15, and (d) a 3′ ITR.
In some embodiments, each 20 nm AAV virion contains a single stranded DNA insert sequence (plus short cloning sites flanking each element) comprising: (a) a 5′ inverted terminal repeat (ITR), (b) a promoter suitable for expression in mammalian cells, (c) a cDNA encoding RPGRORF15, (c) a polyadenylation signal, and (d) a bp 3′ ITR.
In some embodiments, each 20 nm AAV virion contains a single stranded DNA insert sequence (plus short cloning sites flanking each element) comprising: (a) a 5′ inverted terminal repeat (ITR), (b) a promoter suitable for expression in mammalian cells, (c) a cDNA encoding RPGRORF15, (d) a post-transcriptional regulatory element (PRE), (e) a polyadenylation sequence (polyA), and (f) a 3′ ITR.
In some embodiments, each 20 nm AAV virion contains a single stranded DNA insert sequence (plus short cloning sites flanking each element) comprising: (a) a 5′ inverted terminal repeat (ITR), (b) a promoter, optionally, a 199 bp GRK1 promoter, (c) a cDNA encoding RPGRORF15, (d) a 270 bp Bovine growth hormone polyadenylation sequence (BGH-polyA), and (e) a 3′ ITR.
In some embodiments, each 20 nm AAV virion contains a single stranded DNA insert sequence (plus short cloning sites flanking each element) comprising: (a) a 5′ inverted terminal repeat (ITR), (b) a promoter, optionally, a 199 bp GRK1 promoter, (c) a cDNA encoding RPGRORF15, (d) a 270 bp Bovine growth hormone polyadenylation sequence (BGH-polyA), and (e) a 3′ ITR.
AAVs or RPGRORF15 constructs of the disclosure may comprise a sequence encoding a promoter capable of expression in a mammalian cell. Preferably, AAVs or RPGRORF15 constructs of the disclosure may comprise a sequence encoding a promoter capable of expression in a human cell. Exemplary promoters of the disclosure include, but are not limited to, constitutively active promoters, cell-type specific promoters, viral promoters, mammalian promoters, and hybrid or recombinant promoters. In some embodiments of the compositions of the disclosure, the therapeutic Construct of an AAV-Construct is under the control of a G protein-coupled receptor kinase 1 (GRK1) promoter.
AAVs or RPGRORF15 constructs of the disclosure may comprise a polyadenosine (polyA) sequence. Exemplary polyA sequences of the disclosure include, but are not limited to, a bovine growth hormone polyadenylation (BGH-polyA) sequence. The BGH-polyA sequence is used to enhance gene expression and has been shown to yield three times higher expression levels than other polyA sequences such as SV40 and human collagen polyA. This increased expression is largely independent of the type of upstream promoter or transgene. Increasing expression levels using a BGH-polyA sequence allows a lower overall dose of AAV or plasmid vector to be injected, which is less likely to generate a host immune response.
In some embodiments of the compositions of the disclosure, the composition comprises a Drug Substance. As used herein, a Drug Substance comprises a rAAV of the disclosure comprising a RPGRORF15 construct of the disclosure.
AAV-ABCA4
The disclosure provides a composition manufactured using the methods of the disclosure. In some embodiments, the composition comprises (a) between 0.5×1011 vector genomes (vg)/mL and 5×1013 vg, or between 0.5×1011 vg/mL and 1×1013 vg/mL, of replication-defective, recombinant adeno-associated virus (rAAV) upstream or downstream vector, respectively, (b) less than 50% empty capsids; and (c) a plurality of functional vg/mL, wherein a pair of upstream and downstream functional vector genomes is capable of expressing an ABCA4 sequence in a cell following transduction. In some embodiments, the composition comprises (a) between 0.5×1011 vector genomes (vg)/mL and 5×1013 vg/mL, or between 0.5×1011 vg/mL and 1×1013 vg/mL, of replication-defective, recombinant adeno-associated virus (rAAV) upstream or downstream vector, respectively, (b) less than 30% empty capsids; and (c) a plurality of functional vg/mL, wherein a pair of upstream and downstream functional vector genomes is capable of expressing an ABCA4 sequence in a cell following transduction. In some embodiments, the composition comprises (a) between 0.5×1011 vector genomes (vg)/mL and 5×1013 vg/mL, or between 0.5×1011 vg/mL and 1×1013 vg/mL, of replication-defective, recombinant adeno-associated virus (rAAV) upstream or downstream vector, respectively, (b) less than 99%, 97%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, 5%, 2%, 1%, or any percentage in between of empty capsids; and (c) a plurality of functional vg/mL, wherein a pair of upstream and downstream functional vector genomes is capable of expressing an ABCA4 sequence in a cell following transduction. In some embodiments, following transduction of a cell with a composition of the disclosure, the ABCA4 sequence encodes an ABCA4 protein. In some embodiments, the protein encoded by the ABCA4 sequence has an activity level equal to or greater than an activity level of an ABCA4 encoded by a corresponding sequence of a nontransduced cell. In some embodiments, the exogenous ABCA4 sequence and the corresponding endogenous ABCA4 sequence are identical. In some embodiments, the exogenous ABCA4 sequence and the corresponding endogenous ABCA4 sequence are not identical. In some embodiments, the exogenous ABCA4 sequence and the corresponding endogenous ABCA4 sequence have at least 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or any percentage in between of identity.
In some embodiments of the compositions of the disclosure, the composition comprises (a) between 0.5×1011 vg/mL and 5×1013 vg/mL, or between 0.5×1011 vg/mL and 1×1013 vg/mL, inclusive of the endpoints, of upstream or downstream vector, respectively (b) at least 70% full capsids and (c) a plurality of functional vg/mL, wherein a pair of upstream and downstream functional vector genomes is capable of expressing an ABCA4 sequence in a cell following transduction. In some embodiments, the composition comprises (a) between 0.5×1011 vg/mL and 5×1013 vg/mL, or between 0.5×1011 vg/mL and 1×1013 vg/mL, inclusive of the endpoints, of upstream or downstream vector, respectively (b) at least 1%, 2%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99%, 100%, or any percentage in between of full capsids and (c) a plurality of functional vg/mL, wherein a pair of upstream and downstream functional vector genomes is capable of expressing an ABCA4 sequence in a cell following transduction.
Compositions of the disclosure comprise a therapeutic ABCA4 construct suitable for systemic or local administration to a mammal, and preferable, to a human. Exemplary ABCA4 constructs of the disclosure comprise a sequence encoding an ABCA4 or a portion thereof. Preferably, ABCA4 constructs of the disclosure comprise a sequence encoding a human ABCA4 or a portion thereof. Exemplary ABCA4 constructs of the disclosure may further comprise one or more sequence(s) encoding regulatory elements to enable or to enhance expression of the gene or a portion thereof. Exemplary regulatory elements include, but are not limited to, promoters, introns, enhancer elements, response elements (including post-transcriptional response elements or post-transcriptional regulatory elements), polyadenosine (polyA) sequences, and a gene fragment to facilitate efficient termination of transcription (including a β-globin gene fragment and a rabbit β-globin gene fragment).
In some embodiments of the compositions of the disclosure, the ABCA4 construct comprises a human gene (or variant thereof) or a portion thereof corresponding to a human ATP-Binding Cassette, Subfamily A, Member 4 (ABCA4) protein or a portion thereof. Human ABCA4 localizes to the photoreceptors. In some embodiments, the ABCA4 construct comprises a human gene or a portion thereof comprising a wild type or codon-optimized sequence. In some embodiments, the sequence is codon-optimized for expression in mammals. In some embodiments, the sequence is codon-optimized for expression in humans. In some embodiments, an upstream ABCA4 construct comprises a 5′ portion of a human ABCA4 gene and a downstream ABCA4 construct comprises a 3′ portion of a human ABCA4 gene. In some embodiments, the 5′ portion of a human ABCA4 gene and the 3′ portion of a human ABCA4 gene each comprise a sequence that “overlaps” with the other, meaning that the overlapping sequence forms a duplex in which the sequence of the overlapping portion of the 5′ portion of a human ABCA4 gene is complementary to the sequence of the overlapping portion of the 3′ portion of a human ABCA4 gene. In some embodiments the sequence of the overlapping portion of the 5′ portion of a human ABCA4 gene comprises or consists of at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500 or any number of nucleotides in between. In some embodiments the sequence of the overlapping portion of the 5′ portion of a human ABCA4 gene comprises or consists of 20 nucleotides. In some embodiments the sequence of the overlapping portion of the 3′ portion of a human ABCA4 gene comprises or consists of at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500 or any number of nucleotides in between. In some embodiments the sequence of the overlapping portion of the 3′ portion of a human ABCA4 gene comprises or consists of 20 nucleotides.
In some embodiments of the compositions of the disclosure, the AAV-ABCA4 product comprises or consists of a purified recombinant serotype 8 (rAAV8) encoding a cDNA of ABCA4. In some embodiments, the AAV-ABCA4 product comprises a purified mutant rAAV8 capsid protein where the mutant rAAV8 comprises a substitution of a Phenylalanine for a Tyrosine at amino acid position 733 (AAV8 Y773F mutant). In some embodiments, an AAV-ABCA4 upstream product comprises or consists of a purified recombinant serotype 8 (rAAV8) encoding a cDNA of a 5′ portion of ABCA4. In some embodiments, an AAV-ABCA4 downstream product comprises or consists of a purified recombinant serotype 8 (rAAV8) encoding a cDNA of a 3′ portion of ABCA4. In some embodiments, the ABCA4 or the portion thereof is a human ABCA4.
In some embodiments of an AAV-ABCA4 product of the disclosure, each 20 nm AAV virion contains a single stranded DNA insert sequence comprising: an AAV2 5′ inverted terminal repeat (ITR), an ABCA4 cDNA and an AAV2 3′ ITR, as well a short cloning sequences flanking the elements.
In some embodiments of an AAV-ABCA4 upstream product of the disclosure, each 20 nm AAV virion contains a single stranded DNA insert sequence comprising: an AAV2 5′ inverted terminal repeat (ITR), a promoter, an ABCA4 cDNA and an AAV2 3′ ITR, as well a short cloning sequences flanking the elements. In some embodiments, the ABCA4 cDNA comprises a sequence encoding a 5′ portion of a human ABCA4 gene. In some embodiments, the promoter comprises a GRK1 promoter. In some embodiments, the promoter comprises a chicken beta-actin (CBA) promoter alone or in combination with one or more of a cytomegalovirus (CMV) enhancer and a rabbit beta-Globin (RBG) splice acceptor site. In some embodiments, the promoter comprises a chicken beta-actin (CBA) promoter, a CMV enhancer and a RBG splice acceptor site, otherwise referred to herein as a “CAG” promoter. In some embodiments, the each 20 nm AAV virion contains a single stranded DNA insert sequence further comprising a sequence encoding an intron and/or a sequence encoding an exon.
In some embodiments of an AAV-ABCA4 downstream product of the disclosure, each 20 nm AAV virion contains a single stranded DNA insert sequence comprising: an AAV2 5′ inverted terminal repeat (ITR), an ABCA4 cDNA and an AAV2 3′ ITR, as well a short cloning sequences flanking the elements. In some embodiments, the ABCA4 cDNA comprises a sequence encoding a 3′ portion of a human ABCA4 gene. In some embodiments, the each 20 nm AAV virion contains a single stranded DNA insert sequence further comprising a sequence encoding a posttranslational regulatory element (PRE). In some embodiments, the each 20 nm AAV virion contains a single stranded DNA insert sequence further comprising a sequence encoding a Woodchuck PRE (WPRE). In some embodiments, the each 20 nm AAV virion contains a single stranded DNA insert sequence further comprising a sequence encoding a polyadenylation signal. In some embodiments, the each 20 nm AAV virion contains a single stranded DNA insert sequence further comprising a sequence encoding a bovine growth hormone (BGH) polyadenylation signal.
In some embodiments, the ABCA4 construct comprises a sequence encoding a human ABCA4 or a portion thereof. In some embodiments, the sequence encoding ABCA4 comprises a nucleotide sequence or a portion thereof encoding an amino acid sequence that has at least 80% identity, at least 90% identity, at least 95% identity, at least 97% identity, at least 99% identity or is identical to the amino acid sequence of:
In some embodiments, the sequence encoding ABCA4 comprises a wild type nucleotide sequence. In some embodiments, the sequence encoding ABCA4 comprises a nucleotide sequence that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99% or any percentage in between of identity to the nucleotide sequence of:
In some embodiments, the sequence encoding ABCA4 comprises a modified nucleotide sequence. In some embodiments, the sequence encoding ABCA4 comprises a nucleotide sequence that has at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 99% or any percentage in between of identity to the nucleotide sequence of:
In some embodiments of the compositions of the disclosure, the ABCA4 construct comprises a promoter. In some embodiments, the promoter comprises a rhodopsin kinase promoter. In some embodiments, the rhodopsin kinase promoter is isolated or derived from the promoter of the G protein-coupled receptor kinase 1 (GRK1) gene. In some embodiments, the promoter is a GRK1 promoter. In some embodiments, the sequence encoding the GRK1 promoter comprises a sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 97% identity or at least 99% identity to:
In some embodiments, the GRK1 promoter comprises or consists of:
In some embodiments of the compositions of the disclosure, the ABCA4 construct comprises a promoter. In some embodiments, the promoter comprises a chicken beta-actin (CBA) promoter. In some embodiments, the sequence encoding the CBA promoter comprises a sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 97% identity or at least 99% identity to:
In some embodiments, the CBA promoter comprises or consists of:
In some embodiments of the compositions of the disclosure, the ABCA4 construct comprises a promoter variant, e.g., a CMV.CBA promoter, a CBA.RBG promoter, or a CBA.InEx promoter.
In some embodiments, the promoter comprises a CMV.CBA promoter variant, e.g., comprising CMV enhancer and a CBA promoter. In some embodiments, the sequence encoding the CMV.CBA promoter comprises a sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 97% identity or at least 99% identity to:
In some embodiments, the promoter comprises a CBA.RBG promoter variant, e.g., comprising a CBA promoter and a RGB intron. In some embodiments, the sequence encoding the CBA.RBG promoter comprises a sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 97% identity or at least 99% identity to:
In some embodiments, the promoter comprises a CBA.InEx promoter variant, e.g., comprising a CBA promoter, an intron, and an exon. In some embodiments, the sequence encoding the CBA.InEx promoter comprises a sequence having at least 80% identity, at least 90% identity, at least 95% identity, at least 97% identity or at least 99% identity to (the intron is italicized):
In some embodiments of the compositions of the disclosure, the ABCA4 construct comprises a polyadenylation signal. In some embodiments, the sequence encoding the polyA signal comprises a polyA signal isolated or derived from a bovine growth hormone (BGH) polyA signal. In some embodiments, the BGH polyA signal comprises a nucleotide sequence that has at least 80% identity, at least 97% identity or 100% identity to the nucleotide sequence of:
In some embodiments, the sequence encoding the BGH polyA comprises or consists of the nucleotide sequence of:
In some embodiments of the compositions of the disclosure, the ABCA4 construct further comprises a sequence corresponding to a 5′ inverted terminal repeat (ITR) and a sequence corresponding to a 3′ inverted terminal repeat (ITR). In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR are identical. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR are not identical. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR are isolated or derived from an adeno-associated viral vector of serotype 2 (AAV2). In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR comprise a wild type sequence. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR comprise a truncated wild type AAV2 sequence. In some embodiments, the sequence encoding the 5′ ITR and the sequence encoding the 3′ITR comprise a variation when compared to a wild type AAV2 sequence. In some embodiments, the variation comprises a substitution, an insertion, a deletion, an inversion, or a transposition. In some embodiments, the variation comprises a truncation or an elongation of a wild type or a variant sequence. In some embodiments, the ITRs are derived from a 3′ AAV2 ITR in forward and reverse orientation with subsequent deletions, to produce stabilized ITRs. In certain embodiments, the 5′ ITR comprises or consists of the following sequence:
In some embodiments, the 3′ ITR comprises or consists of the following sequence:
In some embodiments, the sequence encoding the 5′ ITR comprises the sequence of
In some embodiments, the sequence encoding a 3′ ITR comprises a wild type sequence isolated or derived of an AAV2. In some embodiments, the sequence encoding the 3′ ITR comprises the sequence of
In some embodiments of the compositions of the disclosure, an AAV comprises a viral sequence essential for formation of a replication-deficient AAV. In some embodiments, the viral sequence is isolated or derived from an AAV of the same serotype as one or both of the sequence encoding the 5′ITR or the sequence encoding the 3′ITR. In some embodiments, the viral sequence, the sequence encoding the 5′ITR or the sequence encoding the 3′ITR are isolated or derived from an AAV2.
In some embodiments of the compositions of the disclosure, an AAV comprises a viral sequence essential for formation of a replication-deficient AAV, a sequence encoding the 5′ITR and a sequence encoding the 3′ITR, but does not comprise any other sequence isolated or derived from an AAV. In some embodiments, the AAV is a recombinant AAV (rAAV), comprising a viral sequence essential for formation of a replication-deficient AAV, a sequence encoding the 5′ITR, a sequence encoding the 3′ITR, and a sequence encoding an ABCA4 construct of the disclosure.
In some embodiments, a plasmid DNA used to create the rAAV in a host cell comprises a selection marker. Exemplary selection markers include, but are not limited to, antibiotic resistance genes. Exemplary antibiotic resistance genes include, but are not limited to, ampicillin and kanamycin. Exemplary selection markers include, but are not limited to, drug or small molecule resistance genes. Exemplary selection markers include, but are not limited to, dapD and a repressible operator including but not limited to a lacO/P construct controlling or suppressing dapD expression, wherein plasmid selection is performed by administering or contacting a transformed cell with a plasmid capable of operator repressor titration (ORT). Exemplary selection markers include, but are not limited to, a ccd selection gene. In some embodiments, the ccd selection gene comprises a sequence encoding a ccdA selection gene that rescues a host cell line engineered to express a toxic ccdB gene. Exemplary selection markers include, but are not limited to, sacB, wherein an RNA is administered or contacted to a host cell to suppress expression of the sacB gene in sucrose media. Exemplary selection markers include, but are not limited to, a segregational killing mechanism such as the parAB+ locus composed of Hok (a host killing gene) and Sok (suppression of killing).
AAV-ABCA4 Dual Vector Constructs
AAV is a small virus that presents very low immunogenicity and is not associated with any known human disease. The lack of an associated inflammatory response means that AAV does not cause retinal damage when injected into the eye.
However, the size of the AAV capsid imposes a limit on the amount of DNA that can be packaged within it. The AAV genome is approximately 4.7 kilobases (kb) in size, and it is believed that the corresponding upper size limit for DNA packaging in AAV is approximately 5 kb. The coding sequence of the ABCA4 gene is approximately 6.8 kb in size (with further genetic elements being required for gene expression), making it too large to be incorporated into a standard AAV vector.
“Dual” Vectors
An alternative approach has been to prepare dual vector systems, in which a transgene larger than the approximately 5 kb limit is split approximately in half into two separate vectors of defined sequence: an “upstream” vector containing the 5′ portion of the transgene, and a “downstream” vector containing the 3′ portion of the transgene. Transduction of a target cell by both upstream and downstream vectors allows a full-length transgene to be re-assembled from the two fragments using a variety of intracellular mechanisms. Methods disclosed herein may be used to produce either or both vector of a dual vector system. Compositions disclosed herein may comprise one or both vectors of a dual vector system.
Dual vector systems of the disclosure use an “overlapping” approach. In an overlapping dual vector system, part of the coding sequence at the 3′ end of the upstream coding sequence portion overlaps with a homologous sequence at the 5′ of the downstream coding sequence portion. Upon transduction of a target cell by upstream and downstream vectors, homologous recombination between the upstream and downstream portions of coding sequence allows for the recreation of a full-length transgene, from which a corresponding mRNA can be transcribed and full-length protein expressed.
Without wishing to be bound by any particular theory, a full length transgene (e.g. ABCA4) may be generated from an overlapping dual vector system by second strand synthesis, followed by homologous recombination. Upon transduction of cell by an upstream AAV particle and a downstream particle, a corresponding ssDNA upstream AAV vector and a downstream AAV vector is released into the cell or a nucleus thereof, and a dsDNA comprising the 5′ (upstream) portion of the transgene and the 3′ (downstream) portion of the transgene are generated from each of the ssDNAs by second strand synthesis. The dsDNA then undergoes homologous recombination at the region of overlap between the upstream and downstream portions of coding sequence, which allows for the recreation of a full-length transgene, from which a corresponding mRNA can be transcribed and full-length protein expressed. For example, WO 2014/170480 describes a dual AAV vector system encoding a human ABCA4 protein (the contents of which are incorporated herein in their entirety).
In some embodiments of the compositions and methods of the disclosure, a first AAV vector comprises a 5′ portion of an ABCA4 coding sequence. In some embodiments, a second AAV vector comprises a 3′ portion of an ABCA4 coding sequence. In some embodiments, the 5′ end portion and the 3′ end portion overlap by at least about 20 nucleotides. In some embodiments, the first AAV vector and the second AAV vector each comprise a single stranded DNA (ssDNA). In some embodiments, the first AAV vector comprises a sequence of the ABCA4 coding sequences and/or a sequence complementary to the ABCA4 coding sequence. In some embodiments, the second AAV vector comprises a sequence of the ABCA4 coding sequences and/or a sequence complementary to the ABCA4 coding sequence. In some embodiments, the first AAV vector comprises a sequence of the 5′ ABCA4 coding sequences and a sequence complementary to a portion of the 3′ ABCA4 coding sequence. In some embodiments, the second AAV vector comprises a sequence of the 3′ ABCA4 coding sequence and a sequence complementary to a portion of the 5′ ABCA4 coding sequence. In some embodiments, the first AAV vector and the second AAV vector undergo second strand synthesis to generate a first dsDNA AAV vector and a second dsDNA AAV vector. In some embodiments, the first dsDNA AAV vector and the second dsDNA AAV vector generate a full length ABCA4 transgene through homologous recombination.
Without wishing to be bound by any particular theory, a full length transgene may also be generated from an overlapping dual vector system through single-strand annealing and second strand synthesis. Upon transduction of a cell by an upstream AAV vector and a downstream AAV vector, wherein each of the upstream AAV vector and the downstream AAV vector comprises a ssDNA, and wherein the upstream AAV vector comprises a sequence encoding a 5′ portion of the transgene and the downstream AAV vector comprises a sequence encoding a 3′ portion of the transgene, the complementary upstream and downstream vectors are released into the cell or a nucleus thereof. In some embodiments, the upstream AAV vector comprises a sequence encoding a 5′ portion of the transgene and a sequence complementary to a 3′ portion of the transgene. In some embodiments, the upstream AAV vector comprises a sense sequence encoding a 5′ portion of the transgene and a sequence complementary to a 3′ portion of the transgene. In some embodiments, the upstream AAV vector comprises an antisense sequence encoding a 5′ portion of the transgene and a sequence complementary to a 3′ portion of the transgene. In some embodiments, the downstream AAV vector comprises a sequence encoding a 3′ portion of the transgene and a sequence complementary to a 5′ portion of the transgene. In some embodiments, the downstream AAV vector comprises an antisense sequence encoding a 3′ portion of the transgene and a sequence complementary to a 5′ portion of the transgene. In some embodiments, the downstream AAV vector comprises a sense sequence encoding a 3′ portion of the transgene and a sequence complementary to a 5′ portion of the transgene. In some embodiments, the upstream and downstream vectors hybridize at the region of complementarity (overlap). Following hybridization, a full length transgene is generated by second strand synthesis.
In some embodiments of the compositions and methods of the disclosure, a first AAV vector comprises a 5′ portion of an ABCA4 coding sequence, a second AAV vector comprises a 3′ portion of an ABCA4 coding sequence, and the 5′ portion and the 3′ portion overlap by at least 20 contiguous nucleotides. In some embodiments, the first AAV vector and the second AAV vector each comprise a single stranded DNA (ssDNA). In some embodiments, the first AAV vector comprises a sequence of the ABCA4 coding sequence and the second AAV vector comprises a sequence complementary to the ABCA4 coding sequence. In some embodiments, the second AAV vector comprises a sequence of the ABCA4 coding sequence and the first AAV vector comprises a sequence complementary to the ABCA4 coding sequence. In some embodiments, the first AAV vector and the second AAV vector anneal at a complementary overlapping region to generate a full length dsDNA ABCA4 transgene by subsequent second strand synthesis. In some embodiments, the full length dsDNA ABCA4 transgene is generated in vitro or in vivo (in a cell or in a subject).
The disclosure addresses the above prior art problems by providing adeno-associated viral (AAV) vector systems as described in the claims.
Dual vector approaches increase the capacity of AAV gene therapy, but may also substantially reduce levels of target protein which may be insufficient to achieve a therapeutic effect. In some embodiments of dual vector systems, the efficacy of recombination of dual vectors depends on the length of DNA overlap between the plus and minus strands (sense and antisense strands). The size of the ABCA4 coding sequence allows for the exploration of various lengths of overlap between the plus and minus strands to identify zones for optimal dual vector strategies for the treatment of disorders caused by mutations in large genes. These strategies can lead to production of enough target protein to provide therapeutic effect. In the Stargardt mouse model, therapeutic effect can be readily assessed as the target protein, ABCA4, is required in abundance in the photoreceptor cells of the retina and its absence induces the accumulation of bisretinoid compounds, which in turn leads to an increase in 790 nm autofluorescence. The therapeutic potential of the overlapping dual vector system can be validated in vivo by observing a reduction in this bisretinoid accumulation and subsequent 790 nm autofluorescence levels following treatment.
Advantageously, the AAV vector system of the disclosure provides surprisingly high levels of expression of full-length ABCA4 protein in transduced cells, with limited production of unwanted truncated fragments of ABCA4. With an optimized recombination, the full length ABCA4 protein is expressed in the photoreceptor outer segments in Abca4−/− mice and at levels sufficient to reduce bisretinoid formation and correct the autofluorescent phenotype on retinal imaging. These observations support a dual vector approach for AAV gene therapy to treat Stargardt disease.
In a first aspect, the invention provides an adeno-associated viral (AAV) vector system for expressing a human ABCA4 protein in a target cell, the AAV vector system comprising a first AAV vector comprising a first nucleic acid sequence and a second AAV vector comprising a second nucleic acid sequence; wherein the first nucleic acid sequence comprises a 5′ end portion of an ABCA4 coding sequence (CDS) and the second nucleic acid sequence comprises a 3′ end portion of an ABCA4 CDS, and the 5′ end portion and the 3′ end portion together encompass the entire ABCA4 CDS; wherein the first nucleic acid sequence comprises a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3597 of SEQ ID NO: 1 or SEQ ID NO: 2; wherein the second nucleic acid sequence comprises a sequence of contiguous nucleotides corresponding to nucleotides 3806 to 6926 of SEQ ID NO: 1 or SEQ ID NO:2, wherein the first nucleic acid sequence and the second nucleic acid sequence each comprise a region of sequence overlap with the other; and wherein the region of sequence overlap comprises at least about 20 contiguous nucleotides of a nucleic acid sequence corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2.
The term “AAV vector system” is used to embrace the fact that the first and second AAV vectors are intended to work together in a complementary fashion.
The first and second AAV vectors of the AAV vector system of the invention together encode an entire ABCA4 transgene. Thus, expression of the encoded ABCA4 transgene in a target cell requires transduction of the target cell with both first (upstream) and second (downstream) vectors.
The AAV vectors of the AAV vector system of the invention are typically in the form of AAV particles (also referred to as virions). An AAV particle comprises a protein coat (the capsid) surrounding a core of nucleic acid, which is the AAV genome. The present invention also encompasses nucleic acid sequences encoding AAV vector genomes of the AAV vector system described herein.
SEQ ID NO: 1 is the human ABCA4 nucleic acid sequence corresponding to NCBI Reference Sequence NM_000350.2. SEQ ID NO: 1 is identical to NCBI Reference Sequence NM_000350.2. The ABCA4 coding sequence spans nucleotides 105 to 6926 of SEQ ID NO: 1.
SEQ ID NO: 2 is identical to SEQ ID NO: 1 with the exception of the following mutations: nucleotide 1640 G>T, nucleotide 5279 G>A, nucleotide 6173 T>C. These mutations do not alter the encoded amino acid sequence, and thus the ABCA4 protein encoded by SEQ ID NO: 2 is identical to the ABCA4 protein encoded by SEQ ID NO: 1.
In some embodiment, the first AAV vector comprises a first nucleic acid sequence comprising a 5′ end portion of an ABCA4 CDS. A 5′ end portion of an ABCA4 CDS is a portion of the ABCA4 CDS that includes its 5′ end. Because it is only a portion of a CDS, the 5′ end portion of an ABCA4 CDS is not a full-length (i.e. is not an entire) ABCA4 CDS. Thus, the first nucleic acid sequence (and thus the first AAV vector) does not comprise a full-length ABCA4 CDS.
In some embodiments, the second AAV vector comprises a second nucleic acid sequence comprising a 3′ end portion of an ABCA4 CDS. A 3′ end portion of an ABCA4 CDS is a portion of the ABCA4 CDS that includes its 3′ end. Because it is only a portion of a CDS, the 3′ end portion of an ABCA4 CDS is not a full-length (i.e. is not an entire) ABCA4 CDS. Thus, the second nucleic acid sequence (and thus the second AAV vector) does not comprise a full-length ABCA4 CDS.
The 5′ end portion and 3′ end portion together encompass the entire ABCA4 CDS (with a region of sequence overlap, as discussed below). Thus, a full-length ABCA4 CDS is contained in the AAV vector system of the invention, split across the first and second AAV vectors, and can be reassembled in a target cell following transduction of the target cell with the first and second AAV vectors.
In some embodiments, the first nucleic acid sequence as described above comprises a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3597 of SEQ ID NO: 1. The ABCA4 CDS begins at nucleotide 105 of SEQ ID NO: 1 or SEQ ID NO: 2.
In some embodiments, the second nucleic acid sequence as described above comprises a sequence of contiguous nucleotides corresponding to nucleotides 3806 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2.
In order to encompass the entire ABCA4 CDS, the first and second nucleic acid sequences each further comprise at least a portion of the ABCA4 CDS corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2, such that when the first and second nucleic acid sequences are aligned the entirety of ABCA4 CDS corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2 is encompassed. Thus, when aligned, the first and second nucleic acid sequences together encompass the entire ABCA4 CDS.
Furthermore, the first and second nucleic acid sequences comprise a region of sequence overlap allowing reconstruction of the entire ABCA4 CDS as part of a full-length transgene inside a target cell transduced with the first and second AAV vectors of the invention.
When the first and second nucleic acid sequences are aligned with each other, a region at the 3′ end of the first nucleic acid sequence overlaps with a corresponding region at the 5′ end of the second nucleic acid sequence. Thus, both the first and second nucleic acid sequences comprise a portion of the ABCA4 CDS that forms the region of sequence overlap.
Particularly advantageous results are obtained when the region of overlap between the first and second nucleic acid sequences comprises at least about 20 contiguous nucleotides of the portion of the ABCA4 CDS corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2.
The region of overlap may extend upstream and/or downstream of said 20 contiguous nucleotides. Thus, the region of overlap may be more than 20 nucleotides in length.
The region of overlap may comprise nucleotides upstream of the position corresponding to nucleotide 3598 of SEQ ID NO: 1 or SEQ ID NO: 2. Alternatively, or in addition, the region of overlap may comprise nucleotides downstream of the position corresponding to nucleotide 3805 of SEQ ID NO: 1 or SEQ ID NO: 2.
Alternatively, the region of nucleic acid sequence overlap may be contained within the portion of the ABCA4 CDS corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2.
Thus, in one embodiment, the region of nucleic acid sequence overlap is between 20 and 550 nucleotides in length; preferably between 50 and 250 nucleotides in length; preferably between 175 and 225 nucleotides in length; preferably between 195 and 215 nucleotides in length.
In one embodiment, the region of nucleic acid sequence overlap comprises at least about 50 contiguous nucleotides of a nucleic acid sequence corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2; preferably at least about 75 contiguous nucleotides; preferably at least about 100 contiguous nucleotides; preferably at least about 150 contiguous nucleotides; preferably at least about 200 contiguous nucleotides; preferably all 208 contiguous nucleotides.
In a preferred embodiment, the region of nucleic acid sequence overlap commences at the nucleotide corresponding to nucleotide 3598 of SEQ ID NO: 1 or SEQ ID NO: 2. The term “commences” means that the region of nucleic acid sequence overlap runs in the direction 5′ to 3′ starting from the nucleotide corresponding to nucleotide 3598 of SEQ ID NO: 1 or SEQ ID NO: 2. Thus, in a preferred embodiment, the most 5′ nucleotide of the region of nucleic acid sequence overlap corresponds to nucleotide 3598 of SEQ ID NO: 1 or SEQ ID NO: 2.
In a further preferred embodiment, the region of nucleic acid sequence overlap between the first nucleic acid sequence and the second nucleic acid sequence vector corresponds to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2.
A further advantage of the present invention is that construction of dual AAV vectors comprising a region of nucleic acid sequence overlap as described above can advantageously reduce the level of translation of unwanted truncated ABCA4 peptides.
The problem of translation of truncated ABCA4 peptides may arise in dual AAV vector systems when translation is initiated from mRNA transcripts derived from the downstream vector only. In this regard, AAV ITRs such as the AAV2 5′ ITR may have promoter activity; this together with the presence in a downstream vector of WPRE and bGH poly-adenylation sequences (as discussed below) may lead to the generation of stable mRNA transcripts from unrecombined downstream vectors. The wild-type ABCA4 CDS carries multiple in-frame AUG codons in its downstream portion that cannot be substituted for other codons without altering the amino acid sequence. This creates the possibility of translation occurring from the stable transcripts, leading to the presence of truncated ABCA4 peptides.
In preferred embodiments of the invention wherein the region of nucleic acid sequence overlap commences at the nucleotide corresponding to nucleotide 3598 of SEQ ID NO: 1 or SEQ ID NO: 2, the starting sequence of the overlap zone includes an out-of-frame AUG (start) codon in good context (regarding the potential Kozak consensus sequence) prior to an in-frame AUG codon in weaker context in order to encourage the translational machinery to initiate translation of unrecombined downstream-only transcripts from an out-of-frame site. In particularly preferred embodiments of the invention, there are in total four out-of-frame AUG codons in various contexts prior to the in-frame AUG. All of these will translate to a STOP codon within 10 amino acids, thus preventing the translation of unwanted truncated ABCA4 peptides.
Preferably, the first nucleic acid sequence comprises a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3805 of SEQ ID NO: 1 or SEQ ID NO:2, and the second nucleic acid sequence comprises a sequence of contiguous nucleotides corresponding to nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2, so encompassing the particularly preferred region of nucleic acid sequence overlap as described above.
Thus, in a preferred embodiment, the 5′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2, and the 3′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2.
In a further preferred embodiment, the 5′ end portion of an ABCA4 CDS consists of nucleotides 105 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2, and the 3′ end portion of an ABCA4 CDS consists of nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2.
Thus, in a preferred embodiment, the invention provides an AAV vector system for expressing a human ABCA4 protein in a target cell, the AAV vector system comprising a first AAV vector comprising a first nucleic acid sequence and a second AAV vector comprising a second nucleic acid sequence, wherein the first nucleic acid sequence comprises a 5′ end portion of an ABCA4 coding sequence (CDS) and the second nucleic acid sequence comprises a 3′ end portion of an ABCA4 CDS, and the 5′ end portion and the 3′ end portion together encompass the entire ABCA4 CDS; wherein the 5′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2, and wherein the 3′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2.
In a further preferred embodiment, the disclosure provides an AAV vector system for expressing a human ABCA4 protein in a target cell, the AAV vector system comprising a first AAV vector comprising a first nucleic acid sequence and a second AAV vector comprising a second nucleic acid sequence, wherein the first nucleic acid sequence comprises a 5′ end portion of an ABCA4 coding sequence (CDS) and the second nucleic acid sequence comprises a 3′ end portion of an ABCA4 CDS, and the 5′ end portion and the 3′ end portion together encompass the entire ABCA4 CDS; wherein the 5′ end portion of an ABCA4 CDS consists of nucleotides 105 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2, and wherein the 3′ end portion of an ABCA4 CDS consists of nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2.
In accordance with the term “consists of”, in embodiments wherein the 5′ end portion of an ABCA4 CDS and the 3′ end portion of an ABCA4 CDS consist of specific sequences of contiguous nucleotides as described above, then the first nucleic acid sequence and the second nucleic acid sequence each do not comprise any additional ABCA4 CDS.
Typically, each of the first AAV vector and the second AAV vector comprises 5′ and 3′ Inverted Terminal Repeats (ITRs).
Typically, the AAV genome of a naturally derived serotype, isolate or clade of AAV comprises at least one inverted terminal repeat sequence (ITR). An ITR sequence acts in cis to provide a functional origin of replication and allows for integration and excision of the vector from the genome of a cell. AAV ITRs are believed to aid concatemer formation in the nucleus of an AAV-infected cell, for example following the conversion of single-stranded vector DNA into double-stranded DNA by the action of host cell DNA polymerases. The formation of such episomal concatemers may serve to protect the vector construct during the life of the host cell, thereby allowing for prolonged expression of the transgene in vivo.
Thus, in one embodiment, the ITRs are AAV ITRs (i.e. ITR sequences derived from ITR sequences found in an AAV genome).
The first and second AAV vectors of the AAV vector system of the invention together comprise all of the components necessary for a fully functional ABCA4 transgene to be re-assembled in a target cell following transduction by both vectors. A skilled person will be aware of additional genetic elements commonly used to ensure transgene expression in a viral vector-transduced cell. These may be referred to as expression control sequences. Thus, the AAV vectors of the AAV viral vector system of the invention typically comprise expression control sequences (e.g. comprising a promoter sequence) operably linked to the nucleotide sequences encoding the ABCA4 transgene.
5′ expression control sequences components are suitably located in the first (“upstream”) AAV vector of the viral vector system, while 3′ expression control sequences are suitably located in the second (“downstream”) AAV vector of the viral vector system.
Thus, the first AAV vector typically comprises a promoter operably linked to the 5′ end portion of an ABCA4 CDS. The promoter is required by its nature to be located 5′ to the ABCA4 CDS, hence its location in the first AAV vector.
Any suitable promoter may be used, the selection of which may be readily made by the skilled person. The promoter sequence may be constitutively active (i.e. operational in any host cell background), or alternatively may be active only in a specific host cell environment, thus allowing for targeted expression of the transgene in a particular cell type (e.g. a tissue-specific promoter). The promoter may show inducible expression in response to presence of another factor, for example a factor present in a host cell. In any event, where the vector is administered for therapy, it is preferred that the promoter should be functional in the target cell background.
In some embodiments, it is preferred that the promoter shows retinal-cell specific expression in order to allow for the transgene to only be expressed in retinal cell populations. Thus, expression from the promoter may be retinal-cell specific, for example confined only to cells of the neurosensory retina and retinal pigment epithelium.
An example promoter suitable for use in the present invention is the chicken beta-actin (CBA) promoter, optionally in combination with a cytomegalovirus (CMV) enhancer element. Another example promoter for use in the invention is a hybrid CBA/CAG promoter, for example the promoter used in the rAVE expression cassette (GeneDetect.com). Any of the promoters disclosed herein may be used.
Examples of promoters based on human sequences that would induce retina-specific gene expression include rhodopsin kinase for rods and cones, PR2.1 for cones only, and RPE65 for the retinal pigment epithelium.
The present inventors have found that particularly advantageous levels of gene expression may be achieved using a GRK1 promoter. Thus, in one embodiment, the promoter is a human rhodopsin kinase (GRK1) promoter.
The GRK1 promoter sequence of the invention may be 199 nucleotides in length and comprise nucleotides −112 to +87 of the GRK1 gene. In a preferred embodiment, the promoter comprises the nucleic acid sequence of SEQ ID NO: 5 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4 or 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
The first AAV vector may comprise an untranslated region (UTR) located between the promoter and the upstream ABCA4 nucleic acid sequence (i.e. a 5′ UTR).
Any suitable UTR sequence may be used, the selection of which may be readily made by the skilled person.
The UTR may comprise one or more of the following elements: a Gallus gallus 13 actin (CBA) intron 1 fragment, an Oryctolagus cuniculus 13 globin (RBG) intron 2 fragment, and an Oryctolagus cuniculus (3 globin exon 3 fragment.
The UTR may comprise a Kozak consensus sequence. Any suitable Kozak consensus sequence may be used, the selection of which may be readily made by the skilled person.
In a preferred embodiment, the UTR comprises the nucleic acid sequence specified in SEQ ID NO: 6 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
The UTR of SEQ ID NO: 6 is 186 nucleotides in length and includes a Gallus gallus 13 actin (CBA) intron 1 fragment (with predicted splice donor site), Oryctolagus cuniculus 13 globin (RBG) intron 2 fragment (including predicted branch point and splice acceptor site) and Oryctolagus cuniculus 13 globin exon 3 fragment immediately prior to a Kozak consensus sequence.
The present inventors have surprisingly found that the presence of a UTR as described above, in particular a UTR sequence as specified in SEQ ID NO: 6 or a variant thereof having at least 90% sequence identity, advantageously increases translational yield from the ABCA4 transgene.
The second (“downstream”) AAV vector of the AAV vector system of the invention may comprise a post-transcriptional response element (also known as post-transcriptional regulatory element) or PRE. Any suitable PRE may be used, the selection of which may be readily made by the skilled person. The presence of a suitable PRE may enhance expression of the ABCA4 transgene.
In a preferred embodiment, the PRE is a Woodchuck Hepatitis Virus PRE (WPRE). In a particularly preferred embodiment, the WPRE has a sequence as specified in SEQ ID NO: 7 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
The second AAV vector may comprise a poly-adenylation sequence located 3′ to the downstream ABCA4 nucleic acid sequence. Any suitable poly-adenylation sequence may be used, the selection of which may be readily made by the skilled person.
In a preferred embodiment, the poly-adenylation sequence is a bovine Growth Hormone (bGH) poly-adenylation sequence. In a particularly preferred embodiment, the bGH poly-adenlylation sequence has a sequence as specified in SEQ ID NO: 8 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In a preferred embodiment of the AAV vector system of the invention, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9, and the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10.
In another preferred embodiment of the AAV vector system of the invention, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 3, and the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 4.
The AAV vector system of the invention is suitable for expressing a human ABCA4 protein in a target cell.
Thus, in one aspect, the invention provides a method for expressing a human ABCA4 protein in a target cell, the method comprising the steps of: transducing the target cell with the first AAV vector and the second AAV vector as described above, such that a functional ABCA4 protein is expressed in the target cell.
Expression of human ABCA4 protein requires that the target cell be transduced with both the first AAV vector and the second AAV vector; however, the order is not important. Thus, the target cell may be transduced with the first AAV vector and the second AAV vector in any order (first AAV vector followed by second AAV vector, or second AAV vector followed by first AAV vector) or simultaneously.
Methods for transducing target cells with AAV vectors are known in the art and will be familiar to a skilled person.
The target cell is preferably a cell of the eye, preferably a retinal cell (e.g. a neuronal photoreceptor cell, a rod cell, a cone cell, or a retinal pigment epithelium cell).
The present invention also provides the first AAV vector, as defined above. There is also provided the second AAV vector, as defined above.
In another aspect, the invention provides an AAV vector, comprising a nucleic acid sequence comprising a 5′ end portion of an ABCA4 CDS, wherein the 5′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3805 of SEQ ID NO: 1. Accordingly, this AAV vector does not comprise any additional ABCA4 CDS beyond said sequence of contiguous nucleotides.
The first AAV vector may comprise 5′ and 3′ ITRs, preferably AAV ITRs; a promoter, preferably a GRK1 promoter; and/or a UTR; said elements being as described above in relation to the AAV vector system of the invention.
In one embodiment, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9.
In one embodiment, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In one embodiment, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9 with the proviso that the nucleotide at the position corresponding to nucleotide 1640 of SEQ ID NO: 1 is G, or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In one embodiment, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 3.
In one embodiment, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 3 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In one embodiment, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 3 with the proviso that the nucleotide at the position corresponding to nucleotide 1640 of SEQ ID NO: 1 is G, or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In another aspect, the invention provides an AAV vector, comprising a nucleic acid sequence comprising a 3′ end portion of an ABCA4 CDS, wherein the 3′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2. Accordingly, this AAV vector does not comprise any additional ABCA4 CDS beyond said sequence of contiguous nucleotides.
The second vector may comprise 5′ and 3′ ITRs, preferably AAV ITRs; a PRE, preferably a WPRE; and/or a poly-adenylation sequence, preferably a bGH poly-adenylation sequence; said elements being as described above in relation to the AAV vector system of the invention.
In one embodiment, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10.
In one embodiment, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In one embodiment, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10 with the proviso that the nucleotide at the position corresponding to nucleotide 5279 of SEQ ID NO: 1 is G and the nucleotide at the position corresponding to nucleotide 6173 of SEQ ID NO: 1 is T, or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In one embodiment, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 4.
In one embodiment, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 4 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In one embodiment, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 4 with the proviso that the nucleotide at the position corresponding to nucleotide 5279 of SEQ ID NO: 1 is G and the nucleotide at the position corresponding to nucleotide 6173 of SEQ ID NO: 1 is T, or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
The invention also provides nucleic acids comprising the nucleic acid sequences described above.
The invention also provides an AAV vector genome derivable from an AAV vector as described above.
An example AAV vector system of the invention comprises a first AAV vector and a second AAV vector; wherein the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9; and the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10.
A further example AAV vector system of the invention comprises a first AAV vector and a second AAV vector; wherein the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity; and the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In particular embodiments, the methods and compositions disclosed herein relate to any of the following vectors: CMVCBA.In.GFP.pA vector (SEQ ID NO: 17); CMVCBA.GFP.pA vector (SEQ ID NO: 18); CBA.IntEx.GFP.pA vector (SEQ ID NO: 19); CAG.GFP.pA vector (SEQ ID NO: 20); AAV.5′CMVCBA.In.ABCA4.WPRE.kan vector (SEQ ID NO: 21); AAV.5′CMVCBA.ABCA4.WPRE.kan vector (SEQ ID NO: 22); or AAV.5′CBA.IntEx.ABCA4.WPRE.kan vector (SEQ ID NO: 23).
In particular embodiments, the methods and compositions disclosed herein are directed to any of the following sequences: (i) the ITR to ITR portion of pAAV.RK.5′ABCA4.kan (SEQ ID NO: 26), comprising a sequence encoding a 5′ ITR (SEQ ID NO: 27), a sequence encoding an RK promoter (SEQ ID NO: 28), a sequence encoding a Rabbit Beta-Globin (RBG) Intron/Exon (Int/Ex) (SEQ ID NO: 39), a sequence encoding a 5′ portion of the coding sequence of an ABCA4 gene (SEQ ID NO: 29), and a sequence encoding a 3′ ITR (SEQ ID NO: 30); or (ii) a sequence of the ITR to ITR portion of pAAV.3′ABCA4.WPRE.kan (SEQ ID NO: 30), comprising a sequence encoding a 5′ ITR (SEQ ID NO: 27), a sequence encoding a 3′ portion of the coding sequence of an ABCA4 gene (SEQ ID NO: 31), a sequence encoding WPRE (SEQ ID NO: 32), a sequence encoding bGH polyA and a sequence encoding a 3′ ITR (SEQ ID NO: 33).
The present invention may also be performed where SEQ ID NO: 2 is used as a reference sequence in place of SEQ ID NO: 1.
In this regard, SEQ ID NO: 2 is identical to SEQ ID NO: 1 with the exception of the following mutations: nucleotide 1640 G>T, nucleotide 5279 G>A, nucleotide 6173 T>C. These mutations do not alter the encoded amino acid sequence, and thus the ABCA4 protein encoded by SEQ ID NO: 2 is identical to the ABCA4 protein encoded by SEQ ID NO: 1.
Thus, in alternative embodiments of the invention, references above to SEQ ID NO: 1 may be replaced with references to SEQ ID NO: 2. In addition, any of the constructs disclosed herein may alternatively comprise a different promoter, such as, e.g., a CMV.CBA promoter, a CBA.RBG promoter, or a CBA.InEx promoter. Similarly, any of the constructs may comprises a 5′ ITR comprising or consisting of SEQ ID NO: 6 and/or a 3′ ITR comprising or consisting of SEQ ID NO: 37.
Sequence Correspondence
As used herein, the term “corresponding to” when used with regard to the nucleotides in a given nucleic acid sequence defines nucleotide positions by reference to a particular SEQ ID NO. However, when such references are made, it will be understood that the invention is not to be limited to the exact sequence as set out in the particular SEQ ID NO referred to but includes variant sequences thereof. The nucleotides corresponding to the nucleotide positions in SEQ ID NO: 1 can be readily determined by sequence alignment, such as by using sequence alignment programs, the use of which is well known in the art. In this regard, a skilled person would readily appreciate that the degenerate nature of the genetic code means that variations in a nucleic acid sequence encoding a given polypeptide may be present without changing the amino acid sequence of the encoded polypeptide. Thus, identification of nucleotide locations in other ABCA4 coding sequences is contemplated (i.e. nucleotides at positions which the skilled person would consider correspond to the positions identified in, for example, SEQ ID NO: 1).
By way of example, SEQ ID NO: 2 is identical to SEQ ID NO: 1 with the exception of three specific mutations, as described above (these three mutations do not alter the amino acid sequence of the encoded ABCA4 polypeptide). In this case, a skilled person would therefore consider that a given nucleotide position in SEQ ID NO: 2 corresponded to the equivalent numbered nucleotide position in SEQ ID NO: 1.
Typically, a derivative of an AAV genome will include at least one inverted terminal repeat sequence (ITR), preferably more than one ITR, such as two ITRs or more. One or more of the ITRs may be derived from AAV genomes having different serotypes, or may be a chimeric or mutant ITR. A preferred mutant ITR is one having a deletion of a trs (terminal resolution site). This deletion allows for continued replication of the genome to generate a single-stranded genome which contains both coding and complementary sequences, i.e. a self-complementary AAV genome. This allows for bypass of DNA replication in the target cell, and so enables accelerated transgene expression.
AAV vectors of the disclosure include transcapsidated forms wherein an AAV genome or derivative having an ITR of one serotype is packaged in the capsid of a different serotype. AAV vectors of the invention also include mosaic forms wherein a mixture of unmodified capsid proteins from two or more different serotypes makes up the viral capsid. An AAV vector may also include chemically modified forms bearing ligands adsorbed to the capsid surface. For example, such ligands may include antibodies for targeting a particular cell surface receptor.
Thus, for example, AAV vectors of the invention include those with an AAV2 genome and AAV2 capsid proteins (AAV2/2), those with an AAV2 genome and AAV5 capsid proteins (AAV2/5) and those with an AAV2 genome and AAV8 capsid proteins (AAV2/8).
An AAV vector of the invention may comprise a mutant AAV capsid protein. In one embodiment, an AAV vector of the invention comprises a mutant AAV8 capsid protein. Preferably the mutant AAV8 capsid protein is an AAV8 Y733F capsid protein.
The disclosure provides an adeno-associated viral (AAV) vector system for expressing a human ABCA4 protein in a target cell, the AAV vector system comprising a first AAV vector comprising a first nucleic acid sequence and a second AAV vector comprising a second nucleic acid sequence; wherein the first nucleic acid sequence comprises a 5′ end portion of an ABCA4 coding sequence (CDS) and the second nucleic acid sequence comprises a 3′ end portion of an ABCA4 CDS, and the 5′ end portion and the 3′ end portion together encompass the entire ABCA4 CDS; wherein the first nucleic acid sequence comprises a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3597 of SEQ ID NO: 1 or SEQ ID NO: 2; wherein the second nucleic acid sequence comprises a sequence of contiguous nucleotides corresponding to nucleotides 3806 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2; wherein the first nucleic acid sequence and the second nucleic acid sequence each comprise a region of sequence overlap with the other; and wherein the region of sequence overlap comprises at least about 20 contiguous nucleotides of a nucleic acid sequence corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2.
AAV vectors in general are well known in the art and a skilled person is familiar with general techniques suitable for their preparation from his common general knowledge in the field. The skilled person's knowledge includes techniques suitable for incorporating a nucleic acid sequence of interest into the genome of an AAV vector.
The term “AAV vector system” is used to embrace the fact that the first and second AAV vectors are intended to work together in a complementary fashion.
The first and second AAV vectors of the AAV vector system of the disclosure together encode an entire ABCA4 transgene. Thus, expression of the encoded ABCA4 transgene in a target cell requires transduction of the target cell with both first (upstream) and second (downstream) vectors.
The AAV vectors of the AAV vector system of the disclosure can be in the form of AAV particles (also referred to as virions). An AAV particle comprises a protein coat (the capsid) surrounding a core of nucleic acid, which is the AAV genome. The present disclosure also encompasses nucleic acid sequences encoding AAV vector genomes of the AAV vector system described herein.
SEQ ID NO: 1 is the human ABCA4 nucleic acid sequence corresponding to NCBI Reference Sequence NM_000350.2. SEQ ID NO: 1 is identical to NCBI Reference Sequence NM_000350.2. The ABCA4 coding sequence spans nucleotides 105 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2.
The first AAV vector comprises a first nucleic acid sequence comprising a 5′ end portion of an ABCA4 CDS. A 5′ end portion of an ABCA4 CDS is a portion of the ABCA4 CDS that includes its 5′ end. Because it is only a portion of a CDS, the 5′ end portion of an ABCA4 CDS is not a full-length (i.e. is not an entire) ABCA4 CDS. Thus, the first nucleic acid sequence (and thus the first AAV vector) does not comprise a full-length ABCA4 CDS.
The second AAV vector comprises a second nucleic acid sequence comprising a 3′ end portion of an ABCA4 CDS. A 3′ end portion of an ABCA4 CDS is a portion of the ABCA4 CDS that includes its 3′ end. Because it is only a portion of a CDS, the 3′ end portion of an ABCA4 CDS is not a full-length (i.e. is not an entire) ABCA4 CDS. Thus, the second nucleic acid sequence (and thus the second AAV vector) does not comprise a full-length ABCA4 CDS.
The 5′ end portion and 3′ end portion together encompass the entire ABCA4 CDS (with a region of sequence overlap, as discussed below). Thus, a full-length ABCA4 CDS is contained in the AAV vector system of the disclosure, split across the first and second AAV vectors, and can be reassembled in a target cell following transduction of the target cell with the first and second AAV vectors.
The first nucleic acid sequence as described above comprises a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3597 of SEQ ID NO: 1 or SEQ ID NO: 2. The ABCA4 CDS begins at nucleotide 105 of SEQ ID NO: 1 or SEQ ID NO: 2.
The second nucleic acid sequence as described above comprises a sequence of contiguous nucleotides corresponding to nucleotides 3806 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2.
In order to encompass the entire ABCA4 CDS, the first and second nucleic acid sequences each further comprise at least a portion of the ABCA4 CDS corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2, such that when the first and second nucleic acid sequences are aligned the entirety of ABCA4 CDS corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2 is encompassed. Thus, when aligned, the first and second nucleic acid sequences together encompass the entire ABCA4 CDS.
Furthermore, the first and second nucleic acid sequences comprise a region of sequence overlap allowing reconstruction of the entire ABCA4 CDS as part of a full-length transgene inside a target cell transduced with the first and second AAV vectors of the disclosure.
When the first and second nucleic acid sequences are aligned with each other, a region at the 3′ end of the first nucleic acid sequence overlaps with a corresponding region at the 5′ end of the second nucleic acid sequence. Thus, both the first and second nucleic acid sequences comprise a portion of the ABCA4 CDS that forms the region of sequence overlap.
In some embodiments, the region of overlap between the first and second nucleic acid sequences comprises at least about 20 contiguous nucleotides of the portion of the ABCA4 CDS corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2.
In some embodiments, the region of overlap may extend upstream and/or downstream of said 20 contiguous nucleotides. Thus, the region of overlap may be more than 20 nucleotides in length.
The region of overlap may comprise nucleotides upstream of the position corresponding to nucleotide 3598 of SEQ ID NO: 1 or SEQ ID NO: 2. Alternatively, or in addition, the region of overlap may comprise nucleotides downstream of the position corresponding to nucleotide 3805 of SEQ ID NO: 1 or SEQ ID NO: 2.
Alternatively, the region of nucleic acid sequence overlap may be contained within the portion of the ABCA4 CDS corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2.
Thus, in one embodiment, the region of nucleic acid sequence overlap is between 20 and 550 nucleotides in length; preferably between 50 and 250 nucleotides in length; preferably between 175 and 225 nucleotides in length; preferably between 195 and 215 nucleotides in length.
In one embodiment, the region of nucleic acid sequence overlap comprises at least about 50 contiguous nucleotides of a nucleic acid sequence corresponding to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2; preferably at least about 75 contiguous nucleotides; preferably at least about 100 contiguous nucleotides; preferably at least about 150 contiguous nucleotides; preferably at least about 200 contiguous nucleotides; preferably all 208 contiguous nucleotides.
In certain preferred embodiments, the region of nucleic acid sequence overlap commences at the nucleotide corresponding to nucleotide 3598 of SEQ ID NO: 1 or SEQ ID NO: 2. The term “commences” means that the region of nucleic acid sequence overlap runs in the direction 5′ to 3′ starting from the nucleotide corresponding to nucleotide 3598 of SEQ ID NO: 1 or SEQ ID NO: 2. Thus, in a preferred embodiment, the most 5′ nucleotide of the region of nucleic acid sequence overlap corresponds to nucleotide 3598 of SEQ ID NO: 1 or SEQ ID NO: 2.
In certain preferred embodiments, the region of nucleic acid sequence overlap between the first nucleic acid sequence and the second nucleic acid sequence vector corresponds to nucleotides 3598 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2.
A construction of dual AAV vectors comprising a region of nucleic acid sequence overlap as described above can reduce the level of translation of unwanted truncated ABCA4 peptides.
The problem of translation of truncated ABCA4 peptides may arise in dual AAV vector systems when translation is initiated from mRNA transcripts derived from the downstream vector only. In this regard, AAV ITRs such as the AAV2 5′ ITR may have promoter activity; this together with the presence in a downstream vector of WPRE and bGH poly-adenylation sequences (as discussed below) may lead to the generation of stable mRNA transcripts from unrecombined downstream vectors. The wild-type ABCA4 CDS carries multiple in-frame AUG codons in its downstream portion that cannot be substituted for other codons without altering the amino acid sequence. This creates the possibility of translation occurring from the stable transcripts, leading to the presence of truncated ABCA4 peptides.
In certain preferred embodiments of the disclosure wherein the region of nucleic acid sequence overlap commences at the nucleotide corresponding to nucleotide 3598 of SEQ ID NO: 1, the starting sequence of the overlap zone includes an out-of-frame AUG (start) codon in good context (regarding the potential Kozak consensus sequence) prior to an in-frame AUG codon in weaker context in order to encourage the translational machinery to initiate translation of unrecombined downstream-only transcripts from an out-of-frame site. In certain particularly preferred embodiments of the disclosure, there are in total four out-of-frame AUG codons in various contexts prior to the in-frame AUG. All of these translate to a STOP codon within 10 amino acids, thus preventing the translation of unwanted truncated ABCA4 peptides.
In certain preferred embodiments, the first nucleic acid sequence comprises a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3805 of SEQ ID NO: 1, and the second nucleic acid sequence comprises a sequence of contiguous nucleotides corresponding to nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2, so encompassing the region of nucleic acid sequence overlap as described above.
Thus, in certain preferred embodiments, the 5′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2, and the 3′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2.
In certain preferred embodiments, the 5′ end portion of an ABCA4 CDS consists of nucleotides 105 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2, and the 3′ end portion of an ABCA4 CDS consists of nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2.
Thus, in certain preferred embodiments, the disclosure provides an AAV vector system for expressing a human ABCA4 protein in a target cell, the AAV vector system comprising a first AAV vector comprising a first nucleic acid sequence and a second AAV vector comprising a second nucleic acid sequence, wherein the first nucleic acid sequence comprises a 5′ end portion of an ABCA4 coding sequence (CDS) and the second nucleic acid sequence comprises a 3′ end portion of an ABCA4 CDS, and the 5′ end portion and the 3′ end portion together encompass the entire ABCA4 CDS; wherein the 5′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2, and wherein the 3′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2.
In certain preferred embodiments, the disclosure provides an AAV vector system for expressing a human ABCA4 protein in a target cell, the AAV vector system comprising a first AAV vector comprising a first nucleic acid sequence and a second AAV vector comprising a second nucleic acid sequence, wherein the first nucleic acid sequence comprises a 5′ end portion of an ABCA4 coding sequence (CDS) and the second nucleic acid sequence comprises a 3′ end portion of an ABCA4 CDS, and the 5′ end portion and the 3′ end portion together encompass the entire ABCA4 CDS; wherein the 5′ end portion of an ABCA4 CDS consists of nucleotides 105 to 3805 of SEQ ID NO: 1 or SEQ ID NO: 2, and wherein the 3′ end portion of an ABCA4 CDS consists of nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2.
In accordance with the term “consists of”, in embodiments wherein the 5′ end portion of an ABCA4 CDS and the 3′ end portion of an ABCA4 CDS consist of specific sequences of contiguous nucleotides as described above, then the first nucleic acid sequence and the second nucleic acid sequence each do not comprise any additional ABCA4 CDS.
In certain embodiments, each of the first AAV vector and the second AAV vector comprises 5′ and 3′ Inverted Terminal Repeats (ITRs).
In certain embodiments, the AAV genome of a naturally derived serotype, isolate or clade of AAV comprises at least one inverted terminal repeat sequence (ITR). An ITR sequence acts in cis to provide a functional origin of replication and allows for integration and excision of the vector from the genome of a cell. AAV ITRs are believed to aid concatemer formation in the nucleus of an AAV-infected cell, for example following the conversion of single-stranded vector DNA into double-stranded DNA by the action of host cell DNA polymerases. The formation of such episomal concatemers may serve to protect the vector construct during the life of the host cell, thereby allowing for prolonged expression of the transgene in vivo.
Thus, in some embodiments, the ITRs are AAV ITRs (i.e. ITR sequences derived from ITR sequences found in an AAV genome).
The first and second AAV vectors of the AAV vector system of the disclosure together comprise all of the components necessary for a fully functional ABCA4 transgene to be re-assembled in a target cell following transduction by both vectors. A skilled person is aware of additional genetic elements commonly used to ensure transgene expression in a viral vector-transduced cell. These may be referred to as expression control sequences. Thus, the AAV vectors of the AAV viral vector system of the disclosure may comprise expression control sequences (e.g. comprising a promoter sequence) operably linked to the nucleotide sequences encoding the ABCA4 transgene.
5′ expression control sequences components can be located in the first (“upstream”) AAV vector of the viral vector system, while 3′ expression control sequences can be located in the second (“downstream”) AAV vector of the viral vector system.
Thus, in some embodiments, the first AAV vector may comprise a promoter operably linked to the 5′ end portion of an ABCA4 CDS. The promoter may be required by its nature to be located 5′ to the ABCA4 CDS, hence its location in the first AAV vector.
Any suitable promoter may be used, the selection of which may be readily made by the skilled person. The promoter sequence may be constitutively active (i.e. operational in any host cell background), or alternatively may be active only in a specific host cell environment, thus allowing for targeted expression of the transgene in a particular cell type (e.g. a tissue-specific promoter). The promoter may show inducible expression in response to presence of another factor, for example a factor present in a host cell. In those embodiments where the vector is administered for therapy, the promoter should be functional in the target cell background.
In some embodiments, the promoter shows retinal-cell specific expression in order to allow for the transgene to only be expressed in retinal cell populations. Thus, expression from the promoter may be retinal-cell specific, for example confined only to cells of the neurosensory retina and retinal pigment epithelium.
Elements may be included in both the upstream and downstream vectors of the disclosure to increase expression of ABCA4 protein. For example, the inclusion of an intron in a vector, such as the upstream vector of the disclosure, can increase the expression of an RNA or protein of interest from that vector. An intron is a nucleotide sequence within a gene that is removed by RNA splicing during RNA maturation. Introns can vary in length from tens of base pairs to multiple megabases. However, spliceosomal introns (i.e. introns that are spliced by the eukaryotic spliceosome) may comprise a splice donor (SD) site at the 5′ end of the intron, a branch site in the intron near the 3′ end, and a splice acceptor (SA) site at the 3′ end. These intron elements facilitate proper intron splicing. SD sites may comprise a consensus GU at the 5′ end of the intron and the SA site at the 3′ end of the intron may terminate with “AG.” Upstream of the SA site, introns often contain a region high in pyrimidines, which is between the branch point adenine nucleotide and the SA. Without wishing to be bound by any particular theory, the presence of an intron can affect the rate of RNA transcription, nuclear export or RNA transcript stability. Further, the presence of an intron may also increase the efficiency of mRNA translation, yielding more of a protein of interest (e.g. ABCA4).
In some embodiments of the vectors of the disclosure, the intron, the IntEx or the SA/SD (including a RBD SA/SD) may be one of several elements that function to increase protein expression from the vector. For example, the promoter and, optionally, an enhancer, can affect not just cell or tissue specificity of gene expression, but also the levels of mRNA that are transcribed from the vector. Promoters are regions of DNA that initiate RNA transcription. Depending on the specific sequence elements of the promoter, promoters may vary in strength and tissue specificity. Enhancers are DNA sequences that regulate transcription from promoters by affecting the ability of the promoter to recruit RNA polymerase and initiate transcription. Therefore, the choice of promoter, and optionally, the inclusion of an enhancer and/or the choice of the enhancer itself, in a vector can significantly affect the expression of a gene encoded by the vector. Exemplary promoters, such as the rhodopsin kinase promoter or chicken beta actin promoter, optionally combined with a CMV enhancer, are shown in
Elements in the non-coding sequences of the mRNA transcript itself can also affect protein levels of a sequence encoded in a vector. Without wishing to be limited by any particular theory, sequence elements in the mRNA untranslated regions (UTRs) can effect mRNA stability, which, in turn, affects levels of protein translation. An exemplary sequence element is a Posttranscriptional Regulatory Element (PRE) (e.g. a Woodchuck Hepatitis PRE (WPRE)), which increases mRNA stability. Exemplary promoters, enhancers, PREs, and the arrangement of these elements in vectors of the disclosure, are shown in
In some embodiments of the first AAV vector of the disclosure, the promoter may be operably linked with an intron and an exon sequence. In some embodiments of the first AAV vector of the disclosure, a nucleic acid sequence may comprise the promoter, an intron and an exon sequence. The intron and the exon sequence may be downstream of the promoter sequence. The intron and the exon sequence may be positioned between the promoter sequence and the upstream ABCA4 nucleic acid sequence (US-ABCA4). The presence of an intron and an exon may increase levels of protein expression. In some embodiments, the intron is positioned between the promoter and the exon. In some embodiments, including those embodiments wherein the intron is positioned between the promoter and the exon, the exon is positioned 5′ of the US-ABCA4 sequence. In some embodiments, the promoter comprises a promoter isolated or derived from a vertebrate gene. In some embodiments, the promoter is GRK1 promoter or a chicken beta actin (CBA) promoter. In some embodiments, the promoter is a CMV.CBA promoter, a CBA.RGB promoter, or a CBA.InEx promoter.
The exon may comprise a coding sequence, a non-coding sequence, or a combination of both. In some embodiments, the exon comprises a non-coding sequence. In some embodiments, the exon is isolated or derived from a mammalian gene. In embodiments, the mammal is a rabbit (Oryctolagus cuniculus). In some embodiments, the mammalian gene comprises a rabbit beta globin gene or a portion thereof. In some embodiments, the exon comprises or consists of a nucleic acid sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the nucleic acid sequence of: CTCCTGGGCA ACGTGCTGGT TATTGTGCTG TCTCATCATT TTGGCAAAGA ATT (SEQ ID NO: 14).
In some embodiments, the exon comprises or consists of a nucleic acid sequence having 100% identity to the nucleic acid sequence of:
Introns may comprise a splice donor site, a splice acceptor site or a branch point. Introns may comprise a splice donor site, a splice acceptor site and a branch point. Exemplary splice acceptor sites comprise nucleotides “GT” (“GU” in the pre-mRNA) at the 5′ end of the intron. Exemplary splice acceptor sites comprise an “AG” at the 3′ end of the intron. In some embodiments, the branch point comprises an adenosine (A) between 20 and 40 nucleotides, inclusive of the endpoints, upstream of the 3′ end of the intron. The intron may comprise an artificial or non-naturally occurring sequence. Alternatively, the intron may be isolated or derived from a vertebrate gene. The intron may comprise a sequence encoding a fusion of two sequences, each of which may be isolated or derived from a vertebrate gene. In some embodiments, a vertebrate gene from which the intron nucleic acid sequence or a portion thereof is derived comprises a chicken (Gallus gallus) gene. In some embodiments, the chicken gene comprises a chicken beta actin gene. In some embodiments, a vertebrate gene from which the intron nucleic acid sequence or a portion thereof is derived comprises a rabbit (Oryctolagus cuniculus) gene. In some embodiments, the rabbit gene comprises a rabbit beta globin gene or a portion thereof. In some embodiments, the intron comprises or consists of a nucleic acid sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identity to the nucleic acid sequence of:
In some embodiments, the intron comprises or consists of a nucleic acid sequence having 100% identity to the nucleic acid sequence of:
In some embodiments of the first (or upstream) AAV vector, the promoter comprises a hybrid promoter (a Cytomegalovirus (CMV) enhancer with a chicken beta actin (CBA) promoter). In some embodiments, the CMV enhancer sequence comprises or consists of a nucleic acid sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least any percentage identity in between to the nucleic acid sequence of:
In some embodiments, the sequence encoding the first (or upstream) AAV vector comprises a sequence encoding a CBA promoter (without a CMV enhancer element), a sequence encoding an intron and a sequence encoding an exon. In some embodiments, the CBA promoter sequence comprises or consists of a nucleic acid sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least any percentage identity in between to the nucleic acid sequence of:
In some embodiments, the CBA promoter sequence comprises or consists of a nucleic acid sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least any percentage identity in between to the nucleic acid sequence of:
In some embodiments, the sequence encoding the intron comprises or consists of the nucleic acid sequence of SEQ ID NO: 13. In some embodiments, the sequence encoding the exon comprises or consists of the nucleic acid sequence of SEQ ID NO: 14.
The first AAV vector may comprise an untranslated region (UTR) located between the promoter and the upstream ABCA4 nucleic acid sequence (i.e. a 5′ UTR).
Any suitable UTR sequence may be used, the selection of which may be readily made by the skilled person.
The UTR may comprise or consist of one or more of the following elements: a Gallus β-actin (CBA) intron 1 or a portion thereof, an Oryctolagus cuniculus β-globin (RBG) intron 2 or a portion thereof, and an Oryctolagus cuniculus β-globin exon 3 or a portion thereof.
The UTR may comprise a Kozak consensus sequence. Any suitable Kozak consensus sequence may be used.
In certain preferred embodiments, the UTR comprises the nucleic acid sequence specified in SEQ ID NO: 6, a variant or a portion thereof having at least 90% (e.g. at least 90%, 95%, 96%, 97%, 98%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8% or 99.9%) sequence identity.
The UTR of SEQ ID NO: 6 is 186 nucleotides in length and includes a Gallus β-actin (CBA) intron 1 fragment (with predicted splice donor site), Oryctolagus cuniculus β-globin (RBG) intron 2 fragment (including predicted branch point and splice acceptor site) and Oryctolagus cuniculus β-globin exon 3 fragment immediately prior to a Kozak consensus sequence.
The presence of a UTR as described above, in particular a UTR sequence as specified in SEQ ID NO: 6 or a variant thereof having at least 90% sequence identity, may increase translational yield from the ABCA4 transgene.
The second (“downstream”) AAV vector of the AAV vector system of the disclosure may comprise a post-transcriptional response element (also known as post-transcriptional regulatory element) or PRE. Any suitable PRE may be used, the selection of which may be readily made by the skilled person. In certain embodiments, the presence of a suitable PRE may enhance expression of the ABCA4 transgene.
In certain preferred embodiments, the PRE is a Woodchuck Hepatitis Virus PRE (WPRE). In certain particularly preferred embodiments, the WPRE has a sequence as specified in SEQ ID NO: 7 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
The second AAV vector may comprise a poly-adenylation sequence located 3′ to the downstream ABCA4 nucleic acid sequence. Any suitable poly-adenylation sequence may be used, the selection of which may be readily made by the skilled person.
In certain preferred embodiments, the poly-adenylation sequence is a bovine Growth Hormone (bGH) poly-adenylation sequence. In a particularly preferred embodiment, the bGH poly-adenlylation sequence has a sequence as specified in SEQ ID NO: 8 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity. In certain embodiments, the sequence encoding the polyadenylation sequence comprises or consists of a nucleic acid sequence having at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least any percentage identity in between to the nucleic acid sequence of:
In certain preferred embodiments of the AAV vector system of the disclosure, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9, and the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10.
In certain preferred embodiments of the AAV vector system of the disclosure, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 3, and the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 4.
The AAV vector system of the disclosure may be suitable for expressing a human ABCA4 protein in a target cell.
The disclosure provides a method for expressing a human ABCA4 protein in a target cell, the method comprising the steps of: transducing the target cell with the first AAV vector and the second AAV vector as described above, such that a functional ABCA4 protein is expressed in the target cell.
Expression of human ABCA4 protein requires that the target cell be transduced with both the first AAV vector and the second AAV vector. In certain embodiments, the target cell may be transduced with the first AAV vector and the second AAV vector in any order (first AAV vector followed by second AAV vector, or second AAV vector followed by first AAV vector) or simultaneously.
Methods for transducing target cells with AAV vectors are known in the art and will be familiar to a skilled person.
The target cell is may be a cell of the eye, preferably a retinal cell (e.g. a neuronal photoreceptor cell, a rod cell, a cone cell, or a retinal pigment epithelium cell).
The disclosure also provides the first AAV vector, as defined above. There is also provided the second AAV vector, as defined above.
The disclosure provides an AAV vector, comprising a nucleic acid sequence comprising a 5′ end portion of an ABCA4 CDS, wherein the 5′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 105 to 3805 of SEQ ID NO: 1. In certain embodiments, this AAV vector does not comprise any additional ABCA4 CDS beyond said sequence of contiguous nucleotides.
The first AAV vector may comprise 5′ and 3′ ITRs, preferably AAV ITRs; a promoter, for example a GRK1 promoter; and/or a UTR; said elements being as described above in relation to the AAV vector system of the disclosure. In some embodiments, the promoter is a CMV.CBA promoter, a CBA.RGB promoter, or a CBA.InEx promoter.
In some embodiments, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9.
In some embodiments, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In some embodiments, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9 with the proviso that the nucleotide at the position corresponding to nucleotide 1640 of SEQ ID NO: 1 is G, or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In some embodiments, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 3.
In some embodiments, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 3 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In some embodiments, the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 3 with the proviso that the nucleotide at the position corresponding to nucleotide 1640 of SEQ ID NO: 1 is G, or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
The disclosure provides an AAV vector, comprising a nucleic acid sequence comprising a 3′ end portion of an ABCA4 CDS, wherein the 3′ end portion of an ABCA4 CDS consists of a sequence of contiguous nucleotides corresponding to nucleotides 3598 to 6926 of SEQ ID NO: 1 or SEQ ID NO: 2. In some embodiments, this AAV vector does not comprise any additional ABCA4 CDS beyond said sequence of contiguous nucleotides.
The second vector may comprise 5′ and 3′ ITRs, preferably AAV ITRs; a PRE, preferably a WPRE; and/or a poly-adenylation sequence, preferably a bGH poly-adenylation sequence; said elements being as described above in relation to the AAV vector system of the disclosure.
In some embodiments, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10.
In some embodiments, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In some embodiments, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10 with the proviso that the nucleotide at the position corresponding to nucleotide 5279 of SEQ ID NO: 1 is G and the nucleotide at the position corresponding to nucleotide 6173 of SEQ ID NO: 1 is T, or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In some embodiments, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 4.
In some embodiments, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 4 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In some embodiments, the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 4 with the proviso that the nucleotide at the position corresponding to nucleotide 5279 of SEQ ID NO: 1 is G and the nucleotide at the position corresponding to nucleotide 6173 of SEQ ID NO: 1 is T, or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
The disclosure also provides nucleic acids comprising the nucleic acid sequences described above. The disclosure also provides an AAV vector genome derivable from an AAV vector as described above.
Also provided is a kit comprising the first AAV vector and the second AAV vector as described above. The AAV vectors may be provided in the kits in the form of AAV particles.
Further provided is a kit comprising a nucleic acid comprising the first nucleic acid sequence and a nucleic acid comprising the second nucleic acid sequence, as described above.
The disclosure also provides a pharmaceutical composition comprising the AAV vector system as described above and a pharmaceutically acceptable excipient.
The AAV vector system of the disclosure, the kit of the disclosure, and the pharmaceutical composition of the disclosure, may be used in gene therapy. For example, AAV vector system of the disclosure, the kit of the disclosure, and the pharmaceutical composition of the disclosure, may be used in preventing or treating disease.
In some embodiments, use of the compositions and methods of the disclosure to prevent or treat disease comprises administration of the first AAV vector and second AAV vector to a target cell, to provide expression of ABCA4 protein.
In some embodiments, the disease to be prevented or treated is characterized by degradation of retinal cells. An example of such a disease is Stargardt disease. In some embodiments, the first and second AAV vectors of the disclosure may be administered to an eye of a patient, for example to retinal tissue of the eye, such that functional ABCA4 protein is expressed to compensate for the mutation(s) present in the disease.
The AAV vectors of the disclosure may be formulated as pharmaceutical compositions or medicaments.
An example AAV vector system of the disclosure comprises a first AAV vector and a second AAV vector; wherein the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9; and the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10.
A further exemplary AAV vector system of the disclosure comprises a first AAV vector and a second AAV vector; wherein the first AAV vector comprises the nucleic acid sequence of SEQ ID NO: 9 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity; and the second AAV vector comprises the nucleic acid sequence of SEQ ID NO: 10 or a variant thereof having at least 90% (e.g. at least 90, 95, 96, 97, 98, 99, 99.1, 99.2, 99.3, 99.4, 99.5, 99.6, 99.7, 99.8 or 99.9%) sequence identity.
In some embodiments, the methods and uses of the disclosure may also be performed where SEQ ID NO: 2 is used as a reference sequence in place of SEQ ID NO: 1.
In this regard, SEQ ID NO: 2 is identical to SEQ ID NO: 1 with the exception of the following mutations: nucleotide 1640 G>T, nucleotide 5279 G>A, nucleotide 6173 T>C. These mutations do not alter the encoded amino acid sequence, and thus the ABCA4 protein encoded by SEQ ID NO: 2 is identical to the ABCA4 protein encoded by SEQ ID NO: 1.
Thus, in alternative embodiments of the disclosure, references above to SEQ ID NO: 1 may be replaced with references to SEQ ID NO: 2.
In addition, any of the constructs disclosed herein may alternatively comprise a different promoter, such as, e.g., a CMV.CBA promoter, a CBA.RBG promoter, or a CBA.InEx promoter. Similarly, any of the constructs may comprises a 5′ ITR comprising or consisting of SEQ ID NO: 6 and/or a 3′ ITR comprising or consisting of SEQ ID NO: 37.
Sequence Correspondence
As used herein, the term “corresponding to” when used with regard to the nucleotides in a given nucleic acid sequence defines nucleotide positions by reference to a particular SEQ ID NO. However, when such references are made, it will be understood that the disclosure is not to be limited to the exact sequence as set out in the particular SEQ ID NO referred to but includes variant sequences thereof. The nucleotides corresponding to the nucleotide positions in SEQ ID NO: 1 can be readily determined by sequence alignment, such as by using sequence alignment programs, the use of which is well known in the art. In this regard, a skilled person would readily appreciate that the degenerate nature of the genetic code means that variations in a nucleic acid sequence encoding a given polypeptide may be present without changing the amino acid sequence of the encoded polypeptide. Thus, identification of nucleotide locations in other ABCA4 coding sequences is contemplated (i.e. nucleotides at positions which the skilled person would consider correspond to the positions identified in, for example, SEQ ID NO: 1).
By way of example, SEQ ID NO: 2 is identical to SEQ ID NO: 1 with the exception of three specific mutations, as described above (these three mutations do not alter the amino acid sequence of the encoded ABCA4 polypeptide). In this case, a skilled person would therefore consider that a given nucleotide position in SEQ ID NO: 2 corresponded to the equivalent numbered nucleotide position in SEQ ID NO: 1.
The viral vectors of the disclosure comprise adeno-associated viral (AAV) vectors. An AAV vector of the disclosure may be in the form of a mature AAV particle or virion, i.e. nucleic acid surrounded by an AAV protein capsid.
The AAV vector may comprise an AAV genome or a derivative thereof.
An AAV genome is a polynucleotide sequence, which may, in some embodiments, encode functions for the production of an AAV particle. These functions include, for example, those operating in the replication and packaging cycle of AAV in a host cell, including encapsidation of the AAV genome into an AAV particle. Naturally occurring AAVs are replication-deficient and rely on the provision of helper functions in trans for completion of a replication and packaging cycle. Accordingly, an AAV genome of a vector of the disclosure may be replication-deficient.
The AAV genome may be in single-stranded form, either positive or negative-sense, or alternatively in double-stranded form. In some embodiments, the use of a double-stranded form allows bypass of the DNA replication step in the target cell and so can accelerate transgene expression.
In some embodiments, the AAV genome of a vector of the disclosure may be in single-stranded form.
The AAV genome may be from any naturally derived serotype, isolate or clade of AAV. Thus, the AAV genome may be the full genome of a naturally occurring AAV. As is known to the skilled person, AAVs occurring in nature may be classified according to various biological systems.
AAVs are referred to in terms of their serotype. A serotype corresponds to a variant subspecies of AAV which, owing to its profile of expression of capsid surface antigens, has a distinctive reactivity which can be used to distinguish it from other variant subspecies. A virus having a particular AAV serotype does not efficiently cross-react with neutralizing antibodies specific for any other AAV serotype.
AAV serotypes include AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10 and AAV11, and also recombinant serotypes, such as Rec2 and Rec3, recently identified from primate brain. Any of these AAV serotypes may be used in the disclosure. Thus, in one embodiment of the disclosure, an AAV vector of the disclosure may be derived from an AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, Rec2 or Rec3 AAV.
Reviews of AAV serotypes may be found in Choi et al. (2005) Curr. Gene Ther. 5: 299-310 and Wu et al. (2006) Molecular Therapy 14: 316-27. The sequences of AAV genomes or of elements of AAV genomes including ITR sequences, rep or cap genes may be derived from the following accession numbers for AAV whole genome sequences: Adeno-associated virus 1 NC 002077, AF063497; Adeno-associated virus 2 NC 001401; Adeno-associated virus 3 NC 001729; Adeno-associated virus 3B NC 001863; Adeno-associated virus 4 NC 001829; Adeno-associated virus 5 Y18065, AF085716; Adeno-associated virus 6 NC 001862; Avian AAV ATCC VR-865 AY186198, AY629583, NC 004828; Avian AAV strain DA-1 NC_006263, AY629583; Bovine AAV NC_005889, AY388617.
AAV may also be referred to in terms of clades or clones. This refers, for example, to the phylogenetic relationship of naturally derived AAVs, or to a phylogenetic group of AAVs which can be traced back to a common ancestor, and includes all descendants thereof. Additionally, AAVs may be referred to in terms of a specific isolate, i.e. a genetic isolate of a specific AAV found in nature. The term genetic isolate describes a population of AAVs which has undergone limited genetic mixing with other naturally occurring AAVs, thereby defining a recognizably distinct population at a genetic level.
The skilled person can select an appropriate serotype, clade, clone or isolate of AAV for use in the disclosure on the basis of their common general knowledge. For instance, the AAV5 capsid has been shown to transduce primate cone photoreceptors efficiently as evidenced by the successful correction of an inherited color vision defect (Mancuso et al. (2009) Nature 461: 784-7).
The AAV serotype can determine the tissue specificity of infection (or tropism) of an AAV virus. Accordingly, in some preferred embodiments the AAV serotypes for use in AAVs administered to patients of the disclosure are those which have natural tropism for or a high efficiency of infection of target cells within the eye. In one embodiment, AAV serotypes for use in the disclosure are those which infect cells of the neurosensory retina, retinal pigment epithelium and/or choroid.
In some embodiments, the AAV genome of a naturally derived serotype, isolate or clade of AAV comprises at least one inverted terminal repeat sequence (ITR). An ITR sequence may act in cis to provide a functional origin of replication and allows for integration and excision of the vector from the genome of a cell. The AAV genome may also comprise packaging genes, such as rep and/or cap genes which encode packaging functions for an AAV particle. The rep gene encodes one or more of the proteins Rep78, Rep68, Rep52 and Rep40 or variants thereof. The cap gene encodes one or more capsid proteins such as VP1, VP2 and VP3 or variants thereof. These proteins may make up the capsid of an AAV particle. Capsid variants are discussed below.
In some embodiments, a promoter can be operably linked to each of the packaging genes. Specific examples of such promoters include the p5, p19 and p40 promoters (Laughlin et al. (1979) Proc. Natl. Acad. Sci. USA 76: 5567-5571). For example, the p5 and p19 promoters may be used to express the rep gene, while the p40 promoter may be used to express the cap gene.
In some embodiments, the AAV genome used in a vector of the disclosure may therefore be the full genome of a naturally occurring AAV. For example, a vector comprising a full AAV genome may be used to prepare an AAV vector in vitro. In some embodiments, such a vector may in principle be administered to patients. In some preferred embodiments, the AAV genome will be derivative for the purpose of administration to patients. Such derivatization is known in the art and the disclosure encompasses the use of any known derivative of an AAV genome, and derivatives which could be generated by applying techniques known in the art. Derivatization of the AAV genome and of the AAV capsid are reviewed in Coura and Nardi (2007) Virology Journal 4: 99, and in Choi et al. and Wu et al., referenced above.
Derivatives of an AAV genome include any truncated or modified forms of an AAV genome which allow for expression of a transgene from a vector of the disclosure in vivo. In some embodiments, it is possible to truncate the AAV genome to include minimal viral sequence yet retain the above function. This may contribute to the safety of the AAV genome, by example reducing the risk of recombination of the vector with wild-type virus, and also avoiding triggering a cellular immune response by the presence of viral gene proteins in the target cell.
A derivative of an AAV genome may include at least one inverted terminal repeat sequence (ITR). In some embodiments, a derivative of an AAV genome may include more than one ITR, such as two ITRs or more. One or more of the ITRs may be derived from AAV genomes having different serotypes, or may be a chimeric or mutant ITR. An exemplary mutant ITR is one having a deletion of a trs (terminal resolution site). This deletion allows for continued replication of the genome to generate a single-stranded genome which contains both coding and complementary sequences, i.e. a self-complementary AAV genome. This allows for bypass of DNA replication in the target cell, and so enables accelerated transgene expression.
The inclusion of one or more ITRs may aid concatamer formation of a vector of the disclosure in the nucleus of a host cell, for example following the conversion of single-stranded vector DNA into double-stranded DNA by the action of host cell DNA polymerases. The formation of such episomal concatamers protects the vector construct during the life of the host cell, thereby allowing for prolonged expression of the transgene in vivo.
In some preferred embodiments, ITR elements will be the only sequences retained from the native AAV genome in the derivative. Thus, a derivative may not include the rep and/or cap genes of the native genome and any other sequences of the native genome. This may also reduce the possibility of integration of the vector into the host cell genome. Additionally, reducing the size of the AAV genome allows for increased flexibility in incorporating other sequence elements (such as regulatory elements) within the vector in addition to the transgene.
The following portions may be removed in a derivative of the disclosure: one inverted terminal repeat (ITR) sequence, the replication (rep) and capsid (cap) genes. However, in some embodiments, derivatives may additionally include one or more rep and/or cap genes or other viral sequences of an AAV genome. Naturally occurring AAV integrates with a high frequency at a specific site on human chromosome 19, and shows a negligible frequency of random integration, such that retention of an integrative capacity in the vector may be tolerated in a therapeutic setting.
Where a derivative comprises capsid proteins i.e. VP1, VP2 and/or VP3, the derivative may be a chimeric, shuffled or capsid-modified derivative of one or more naturally occurring AAVs. The disclosure encompasses the provision of capsid protein sequences from different serotypes, clades, clones, or isolates of AAV within the same vector (i.e. a pseudotyped vector).
Chimeric, shuffled or capsid-modified derivatives may be selected to provide one or more functionalities for the viral vector. For example, these derivatives may display increased efficiency of gene delivery, decreased immunogenicity (humoral or cellular), an altered tropism range and/or improved targeting of a particular cell type compared to an AAV vector comprising a naturally occurring AAV genome, such as that of AAV2. Increased efficiency of gene delivery may be effected by improved receptor or co-receptor binding at the cell surface, improved internalization, improved trafficking within the cell and into the nucleus, improved uncoating of the viral particle and improved conversion of a single-stranded genome to double-stranded form. Increased efficiency may also relate to an altered tropism range or targeting of a specific cell population, such that the vector dose is not diluted by administration to tissues where it is not needed.
Chimeric capsid proteins include those generated by recombination between two or more capsid coding sequences of naturally occurring AAV serotypes. This may be performed, for example, by a marker rescue approach in which non-infectious capsid sequences of one serotype are co-transfected with capsid sequences of a different serotype, and directed selection is used to select for capsid sequences having desired properties. The capsid sequences of the different serotypes can be altered by homologous recombination within the cell to produce novel chimeric capsid proteins.
Chimeric capsid proteins of the disclosure also include those generated by engineering of capsid protein sequences to transfer specific capsid protein domains, surface loops or specific amino acid residues between two or more capsid proteins, for example between two or more capsid proteins of different serotypes.
Shuffled or chimeric capsid proteins may also be generated by DNA shuffling or by error-prone PCR. Hybrid AAV capsid genes can be created by randomly fragmenting the sequences of related AAV genes e.g. those encoding capsid proteins of multiple different serotypes and then subsequently reassembling the fragments in a self-priming polymerase reaction, which may also cause crossovers in regions of sequence homology. A library of hybrid AAV genes created in this way by shuffling the capsid genes of several serotypes can be screened to identify viral clones having a desired functionality. Similarly, error prone PCR may be used to randomly mutate AAV capsid genes to create a diverse library of variants which may then be selected for a desired property.
The sequences of the capsid genes may also be genetically modified to introduce specific deletions, substitutions or insertions with respect to the native wild-type sequence. For example, capsid genes may be modified by the insertion of a sequence of an unrelated protein or peptide within an open reading frame of a capsid coding sequence, or at the N- and/or C-terminus of a capsid coding sequence.
The unrelated protein or peptide may be one which acts as a ligand for a particular cell type, thereby conferring improved binding to a target cell or improving the specificity of targeting of the vector to a particular cell population. The unrelated protein may also be one which assists purification of the viral particle as part of the production process, i.e. an epitope or affinity tag. The site of insertion may be selected so as not to interfere with other functions of the viral particle e.g. internalization, trafficking of the viral particle. The skilled person can identify suitable sites for insertion based on their common general knowledge. Particular sites are disclosed in Choi et al., referenced above.
The disclosure additionally encompasses the provision of sequences of an AAV genome in a different order and configuration to that of a native AAV genome. The disclosure also encompasses the replacement of one or more AAV sequences or genes with sequences from another virus or with chimeric genes composed of sequences from more than one virus. Such chimeric genes may be composed of sequences from two or more related viral proteins of different viral species.
AAV vectors of the disclosure include transcapsidated forms wherein an AAV genome or derivative having an ITR of one serotype is packaged in the capsid of a different serotype. AAV vectors of the disclosure also include mosaic forms wherein a mixture of unmodified capsid proteins from two or more different serotypes makes up the viral capsid. An AAV vector may also include chemically modified forms bearing ligands adsorbed to the capsid surface. For example, such ligands may include antibodies for targeting a particular cell surface receptor.
Thus, for example, AAV vectors of the disclosure may include those with an AAV2 genome and AAV2 capsid proteins (AAV2/2), those with an AAV2 genome and AAV5 capsid proteins (AAV2/5) and those with an AAV2 genome and AAV8 capsid proteins (AAV2/8).
An AAV vector of the disclosure may comprise a mutant AAV capsid protein. In one embodiment, an AAV vector of the disclosure comprises a mutant AAV8 capsid protein. In some embodiments, the mutant AAV8 capsid protein is an AAV8 Y733F capsid protein. In some embodiments, the AAV8 Y733F mutant capsid protein comprises an amino acid sequence with at least 95% identity to SEQ ID NO: 12 with a substitution of phenylalanine for tyrosine at position 733 of SEQ ID NO: 12. In some embodiments, the AAV8 Y733F mutant capsid protein comprises an amino acid sequence of SEQ ID NO: 12 with a substitution of phenylalanine for tyrosine at position 733 of SEQ ID NO: 12.
In some embodiments of the compositions of the disclosure, the composition comprises a Drug Product. As used herein, a Drug Product comprises a drug substance, formulated for administration to a subject for the treatment or prevention of a disease or disorder.
The components of an exemplary Drug Product of the disclosure, their functions and specifications are listed in Table 1A.
Compositions of the disclosure may be formulated for systemic or local administration.
Compositions of the disclosure may be formulated as a Suspension for Injection or Infusion.
Compositions of the disclosure may be formulated for injection or infusion by any route, including but not limited to, an intravitreous injection or infusion, a subretinal injection or infusion, or a suprachoroidal injection or infusion.
In some embodiments, compositions of the disclosure may be formulated at a concentration of between 0.5×10{circumflex over ( )}11 DRP/mL and 1.0×10{circumflex over ( )}12 DRP/mL, inclusive of the endpoints. In some embodiments, compositions of the disclosure may be formulated at a concentration of about 0.5×10{circumflex over ( )}11 or 0.5×10{circumflex over ( )}11 DRP/ml. In some embodiments, compositions of the disclosure may be formulated at a concentration of about 0.5×10{circumflex over ( )}11 DRP/mL. In some embodiments, compositions of the disclosure may be formulated at a concentration of about 1×10{circumflex over ( )}12 DRP/mL.
Compositions of the disclosure may be diluted prior to administration using a using a diluent of the disclosure. In some embodiments, the diluent is identical to a formulation buffer used for preparation of the AAV-RPGRORF15 Drug Product. In some embodiments, the diluent is not identical to a formulation buffer used for preparation of the AAV-Construct Drug Product.
Compositions of the disclosure, including the AAV-RPGRORF15 construct Drug Product described in Table 1A, may be formulated as a Suspension for Injection containing between 0.5×10{circumflex over ( )}11 DRP/mL to 1.0×10{circumflex over ( )}13 DRP/mL of AAV particles, inclusive of the endpoints. Compositions of the disclosure, including the AAV-RPGRORF15 construct Drug Product described in Table 1A, may be formulated as a Suspension for Injection containing between 2.5×10{circumflex over ( )}12 DRP/mL to 5×10{circumflex over ( )}12 DRP/mL DRP/mL of AAV particles. In some embodiments, the AAV-RPGRORF15 Drug Product described in Table 1A, may be formulated as a Suspension for Injection containing 0.5×10{circumflex over ( )}11 DRP/mL, 2.5×10{circumflex over ( )}12 DRP/mL, 0.5×10{circumflex over ( )}12 DRP/mL, 5×10{circumflex over ( )}12 DRP/mL or 1.0×10{circumflex over ( )}13 DRP/mL of AAV particles. If required by the protocol, AAV-RPGRORF15 Drug Product may be diluted in the clinic (i.e. by a medical professional) before administration using a diluent of the disclosure. In some embodiments, this diluent is the same formulation buffer used for preparation of the AAV-RPGRORF15 Drug Product.
Compositions of the disclosure may comprise full and empty AAV particles. In some embodiments, a full AAV particle comprises a single stranded DNA encoding an AAV-RPGRORF15 construct of the disclosure. The ordinarily skilled artisan can determine whether an AAV particle is full or empty through, for example, transmission electron microscopy analysis, qPCR or ddPCR. In some embodiments of the composition of the disclosure, the composition comprises at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, 65%, at least 67%, at least 69%, at least 70%, at least 71%, at least 72%, at least 73%, at least 76%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% full AAV particles. In some embodiments, the composition comprises at least 70% full AAV particles.
Compositions of the disclosure may be diluted prior to administration using a using a diluent of the disclosure. In some embodiments, the diluent is identical to a formulation buffer used for preparation of the AAV-RPGRORF15 Drug Product. In some embodiments, the diluent is not identical to a formulation buffer used for preparation of the AAV-RPGRORF15 Drug Product.
Compositions of the disclosure, including the AAV-RPGRORF15 Drug Product described in Table 1A, may be formulated as a Suspension for Injection containing between 0.5×10{circumflex over ( )}11 DRP/mL and 1.0×10{circumflex over ( )}12 DRP/mL, inclusive of the endpoints. In some embodiments, compositions of the disclosure, including the AAV-RPGRORF15 Drug Product described in Table 1A, may be formulated as a Suspension for Injection containing 1.0×10{circumflex over ( )}12 DRP/mL to 5×10{circumflex over ( )}12 DRP/mL, e.g., 2.5×10{circumflex over ( )}12 DRP/mL or 5×10{circumflex over ( )}12 DRP/mL. In some embodiments, compositions of the disclosure, including the AAV-RPGRORF15 Drug Product described in Table 1A, may be formulated as a Suspension for Injection containing 0.5×10{circumflex over ( )}11 DRP/mL, 2.5×10{circumflex over ( )}12 DRP/mL, 5×10{circumflex over ( )}12 DRP/mL or 1.0×10{circumflex over ( )}12 DRP/mL. If required by the protocol, AAV-RPGRORF15 Drug Product may be diluted in the clinic (i.e. by a medical professional) before administration using a diluent of the disclosure. In some embodiments, this diluent is the same formulation buffer used for preparation of the AAV-RPGRORF15 Drug Product.
In some embodiments of the compositions of the disclosure, the composition comprises a Drug Product. As used herein, a Drug Product comprises a drug substance, formulated for administration to a subject for the treatment or prevention of a disease or disorder.
The components of an illustrative Drug Product of the disclosure, their functions and specifications are listed in Table 1B.
Compositions of the disclosure may be formulated for systemic or local administration.
Compositions of the disclosure may be formulated as a Suspension for Injection or Infusion.
Compositions of the disclosure may be formulated for injection or infusion by any route, including but not limited to, an intravitreous injection or infusion, a subretinal injection or infusion, or a suprachoroidal injection or infusion.
Compositions of the disclosure may be formulated at a concentration of between 0.5×10{circumflex over ( )}11 DRP/mL and 1.0×10{circumflex over ( )}12 DRP/mL, inclusive of the endpoints, for an upstream and/or downstream vector, respectively.
Compositions of the disclosure may be diluted prior to administration using a using a diluent of the disclosure. In some embodiments, the diluent is identical to a formulation buffer used for preparation of an AAV-ABCA4 Drug Product. In some embodiments, the diluent is not identical to a formulation buffer used for preparation of the AAV-Construct Drug Product.
Compositions of the disclosure, including an AAV-ABCA4 construct Drug Product described in Table 1B, may be formulated as a Suspension for Injection containing between 0.5×10{circumflex over ( )}11 DRP/mL to 1.0×10{circumflex over ( )}13 DRP/mL of AAV particles, inclusive of the endpoints, for an upstream and/or downstream vector, respectively. If required by the protocol, AAV-ABCA4 Drug Product may be diluted in the clinic (i.e. by a medical professional) before administration using a diluent of the disclosure. In some embodiments, this diluent is the same formulation buffer used for preparation of the AAV-ABCA4 Drug Product.
Compositions of the disclosure may comprise full and empty AAV particles. In some embodiments, a full AAV particle comprises a single stranded DNA encoding an AAV-ABCA4 construct of the disclosure. The ordinarily skilled artisan can determine whether an AAV particle is full or empty through, for example, transmission electron microscopy analysis, qPCR or ddPCR. In some embodiments of the composition of the disclosure, the composition comprises at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, 65%, at least 67%, at least 69%, at least 70%, at least 71%, at least 72%, at least 73%, at least 76%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% full AAV particles. In some embodiments, the composition comprises at least 70% full AAV particles.
Compositions of the disclosure may be diluted prior to administration using a using a diluent of the disclosure. In some embodiments, the diluent is identical to a formulation buffer used for preparation of the AAV-ABCA4 Drug Product. In some embodiments, the diluent is not identical to a formulation buffer used for preparation of the AAV-ABCA4 Drug Product.
Compositions of the disclosure, including the AAV-ABCA4 Drug Product described in Table 1B, may be formulated as a Suspension for Injection containing between 0.5×10{circumflex over ( )}11 DRP/mL and 1.0×10{circumflex over ( )}12 DRP/mL, inclusive of the endpoints, for an upstream and/or downstream vector, respectively. If required by the protocol, AAV-ABCA4 Drug Product may be diluted in the clinic (i.e. by a medical professional) before administration using a diluent of the disclosure. In some embodiments, this diluent is the same formulation buffer used for preparation of the AAV-ABCA4 Drug Product.
Compositions of the disclosure may comprise a Drug Substance. In some embodiments, the Drug Substance comprises or consists of an AAV-RPGRORF15. In some embodiments, the Drug Substance comprises or consists of an AAV-RPGRORF15 and a formulation buffer. In some embodiments, the formulation buffer comprises 20 mM Tris, 1 mM MgCl2, and 200 mM NaCl at pH 8. In some embodiments, the formulation buffer comprises 20 mM Tris, 1 mM MgCl2, and 200 mM NaCl at pH 8 with poloxamer 188 at 0.001%.
Compositions of the disclosure may comprise a Drug Product. In some embodiments, the Drug Product comprises or consists of a Drug Substance and a formulation buffer. In some embodiments, the Drug Product comprises or consists of a Drug Substance diluted in a formulation buffer. In some embodiments, the Drug Product comprises or consists of an AAV8-RPGRORF15 Drug Substance diluted to a final Drug Product AAV-RPGRORF15 vector genome (vg) concentration in a formulation buffer.
Compositions of the disclosure may be formulated to comprise, consist essentially of or consist of an AAV-RPGRORF15 Drug Substance at an optimal concentration for ocular injection or infusion.
Compositions of the disclosure may comprise one or more buffers that increase or enhance the stability of an AAV of the disclosure. In some embodiments, compositions of the disclosure may comprise one or more buffers that ensure or enhance the stability of an AAV of the disclosure. Alternatively, or in addition, compositions of the disclosure may comprise one or more buffers that prevent, decrease, or minimize AAV particle aggregation. In some embodiments, compositions of the disclosure may comprise one or more buffers that prevent, decrease, or minimize AAV particle aggregation.
Compositions of the disclosure may comprise one or more components that induce or maintain a neutral or slightly basic pH. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a neutral or slightly basic pH of between 7 and 9, inclusive of the endpoints. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a pH of about 8. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a pH of between 7.5 and 8.5. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a pH of between 7.7 and 8.3. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a pH of between 7.9 and 8.1. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a pH of 8.
Following contact of a composition of the disclosure and a cell, the AAV-Construct expresses a gene or a portion thereof, resulting in the production of a product encoded by the gene or a portion thereof. In some embodiments, the cell is a target cell. In some embodiments, the target cell is a retinal cell. In some embodiments, the retinal cell is a neuron. In some embodiments, the neuron is a photoreceptor. In some embodiments, the cell is in vivo, in vitro, ex vivo or in situ. In some embodiments, including those wherein the cell is in vivo, the contacting occurs following administration of the composition to a subject. In some embodiments, the AAV-Construct expresses a gene or a portion thereof, results in the production of a product encoded by the gene or a portion thereof at a therapeutically-effective level of expression of the gene product. In some embodiments, the gene product is a protein.
Compositions of the disclosure may be manufactured at a scale of between 1 to 1000 vials per batch, inclusive of the endpoints. In some embodiments of the compositions of the disclosure, a composition, Drug Substance, or Drug Product may be manufactured at a scale of between 50 to 500 vials per batch, inclusive of the endpoints. In some embodiments of the compositions of the disclosure, a composition, Drug Substance, or Drug Product may be manufactured at a scale of between 100 to 250 vials per batch, inclusive of the endpoints.
Exemplary batches of the disclosure may comprise between 0.01 mL and 100 mL, inclusive of the endpoints, of a composition, Drug Substance, or Drug Product of the disclosure.
In some embodiments of the methods of the disclosure for preparation of the Drug Product, a Drug Substance is thawed at +35±2° C., and diluted as required in sterile formulation buffer to the target concentration (e.g., 0.5×10{circumflex over ( )}12 DRP/mL, 5×10{circumflex over ( )}12 DRP/mL or 1.0×10{circumflex over ( )}13 DRP/mL).
In some embodiments of the compositions of the disclosure, the target final DRP titre of the AAV-RPGRORF15 Drug Product is 1×10{circumflex over ( )}13 DRP/mL, the minimum and maximum acceptable titre is 1.0×10{circumflex over ( )}12 DRP/mL and 3.0×10{circumflex over ( )}13 DRP/mL, respectively. In some embodiments of the compositions of the disclosure, the target final DRP titre of the AAV-RPGRORF15 Drug Product is 5×10{circumflex over ( )}12 DRP/mL. In some embodiments, the AAV-RPGRORF15 Drug Product is sterile filtered and filled into 0.5 ml polypropylene tubes or 0.5 mL Crystal Zenith® (cyclic olefin polymer) vials for either administration following up to a 10× dilution or without dilution.
The vials are then frozen and stored at ≤−60° C. For labelling and storage prior to QP release and distribution to site, the Drug Product is transferred to the qualified clinical distributor. The Drug Product is stored at ≤−60° C. in a temperature monitored freezer until QP release and distribution.
AAV-RPGRORF15 Drug Product may be pre-filled into a microdelivery device for subretinal delivery. Microdelivery devices suitable for subretinal delivery may comprise a microneedle and the AAV-RPGRORF15 Drug Product may be further formulated for prefilled, room temperature or pre-filled cold storage in a microdelivery device.
Compositions of the disclosure may be manufactured at a scale of between 1 to 1000 vials per batch, inclusive of the endpoints. In some embodiments of the compositions of the disclosure, a composition, Drug Substance, or Drug Product may be manufactured at a scale of between 50 to 500 vials per batch, inclusive of the endpoints. In some embodiments of the compositions of the disclosure, a composition, Drug Substance, or Drug Product may be manufactured at a scale of between 100 to 250 vials per batch, inclusive of the endpoints.
Exemplary batches of the disclosure may comprise between 0.01 mL and 500 mL, inclusive of the endpoints, of a composition, Drug Substance, or Drug Product of the disclosure.
In some embodiments of the methods of the disclosure for preparation of the Drug Product, a Drug Substance is thawed at +35±2° C., and diluted as required in sterile formulation buffer to the target concentration (e.g., 0.5×10{circumflex over ( )}12 DRP/mL, 5×10{circumflex over ( )}12 DRP/mL or 1.0×10{circumflex over ( )}13 DRP/mL).
In some embodiments of the compositions of the disclosure, the target final DRP titre of the AAV-RPGRORF15 Drug Product is 1×10{circumflex over ( )}13 DRP/mL, the minimum and maximum acceptable titre is 1.0×10{circumflex over ( )}12 DRP/mL and 3.0×10{circumflex over ( )}13 DRP/mL, respectively. In some embodiments of the compositions of the disclosure, the target final DRP titre of the AAV-RPGRORF15 Drug Product is 5×10{circumflex over ( )}12 DRP/mL. In some embodiments, the AAV-RPGRORF15 Drug Product is sterile filtered and filled into 0.5 ml polypropylene tubes or 0.5 mL Crystal Zenith® (cyclic olefin polymer) vials for either administration following up to a 10× dilution or without dilution.
The vials are then frozen and stored at ≤−60° C. For labelling and storage prior to QP release and distribution to site, the Drug Product is transferred to the qualified clinical distributor. The Drug Product is stored at ≤−60° C. in a temperature monitored freezer until QP release and distribution.
AAV-RPGRORF15 Drug Product may be pre-filled into a microdelivery device for suprachoroidal delivery. Microdelivery devices suitable for suprachoroidal delivery may comprise a microcatheter and the AAV-RPGRORF15 Drug Product may be further formulated for prefilled, room temperature or pre-filled cold storage in a microdelivery device.
Compositions of the disclosure may comprise a Drug Substance. In some embodiments, the Drug Substance comprises or consists of an AAV-ABCA4. In some embodiments, the Drug Substance comprises or consists of an AAV-ABCA4 and a formulation buffer. In some embodiments, the formulation buffer comprises 20 mM Tris, 1 mM MgCl2, and 200 mM NaCl at pH 8. In some embodiments, the formulation buffer comprises 20 mM Tris, 1 mM MgCl2, and 200 mM NaCl at pH 8 with poloxamer 188 at 0.001%.
Compositions of the disclosure may comprise a Drug Product. In some embodiments, the Drug Product comprises or consists of a Drug Substance and a formulation buffer. In some embodiments, the Drug Product comprises or consists of a Drug Substance diluted in a formulation buffer. In some embodiments, the Drug Product comprises or consists of an AAV8-ABCA4 Drug Substance diluted to a final Drug Product AAV-ABCA4 vector genome (vg) concentration in a formulation buffer.
Compositions of the disclosure may be formulated to comprise, consist essentially of or consist of an AAV-ABCA4 Drug Substance at an optimal concentration for ocular injection or infusion.
Compositions of the disclosure may comprise one or more buffers that increase or enhance the stability of an AAV of the disclosure. In some embodiments, compositions of the disclosure may comprise one or more buffers that ensure or enhance the stability of an AAV of the disclosure. Alternatively, or in addition, compositions of the disclosure may comprise one or more buffers that prevent, decrease, or minimize AAV particle aggregation. In some embodiments, compositions of the disclosure may comprise one or more buffers that prevent, decrease, or minimize AAV particle aggregation.
Compositions of the disclosure may comprise one or more components that induce or maintain a neutral or slightly basic pH. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a neutral or slightly basic pH of between 7 and 9, inclusive of the endpoints. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a pH of about 8. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a pH of between 7.5 and 8.5. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a pH of between 7.7 and 8.3. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a pH of between 7.9 and 8.1. In some embodiments, compositions of the disclosure comprise one or more components that induce or maintain a pH of 8.
Following contact of a composition of the disclosure and a cell, the AAV-Construct expresses a gene or a portion thereof, resulting in the production of a product encoded by the gene or a portion thereof. In some embodiments, the cell is a target cell. In some embodiments, the target cell is a retinal cell. In some embodiments, the retinal cell is a neuron. In some embodiments, the neuron is a photoreceptor. In some embodiments, the cell is in vivo, in vitro, ex vivo or in situ. In some embodiments, including those wherein the cell is in vivo, the contacting occurs following administration of the composition to a subject. In some embodiments, the AAV-Construct expresses a gene or a portion thereof, results in the production of a product encoded by the gene or a portion thereof at a therapeutically-effective level of expression of the gene product. In some embodiments, the gene product is a protein.
Compositions of the disclosure may be manufactured at a scale of between 1 to 1000 vials per batch, inclusive of the endpoints. In some embodiments of the compositions of the disclosure, a composition, Drug Substance, or Drug Product may be manufactured at a scale of between 50 to 500 vials per batch, inclusive of the endpoints. In some embodiments of the compositions of the disclosure, a composition, Drug Substance, or Drug Product may be manufactured at a scale of between 100 to 250 vials per batch, inclusive of the endpoints.
Exemplary batches of the disclosure may comprise between 0.01 mL and 100 mL, inclusive of the endpoints, of a composition, Drug Substance, or Drug Product of the disclosure.
In some embodiments of the methods of the disclosure for preparation of the Drug Product, a Drug Substance is thawed at +35±2° C., and diluted as required in sterile formulation buffer to the target concentration (e.g., 0.5×10{circumflex over ( )}12 DRP/mL, 5×10{circumflex over ( )}12 DRP/mL or 1.0×10{circumflex over ( )}13 DRP/mL).
In some embodiments of the compositions of the disclosure, the target final DRP titre of the AAV-ABCA4 Drug Product is 1×10{circumflex over ( )}13 DRP/mL, the minimum and maximum acceptable titre is 1.0×10{circumflex over ( )}12 DRP/mL and 3.0×10{circumflex over ( )}13 DRP/mL, respectively. In some embodiments, the AAV-ABCA4 Drug Product is sterile filtered and filled into 0.5 ml polypropylene tubes or 0.5 mL Crystal Zenith® (cyclic olefin polymer) vials for either administration following up to a 10× dilution or without dilution.
The vials are then frozen and stored at ≤−60° C. For labelling and storage prior to QP release and distribution to site, the Drug Product is transferred to the qualified clinical distributor. The Drug Product is stored at ≤−60° C. in a temperature monitored freezer until QP release and distribution.
AAV-ABCA4 Drug Product may be pre-filled into a microdelivery device for subretinal delivery. Microdelivery devices suitable for subretinal delivery may comprise a microneedle and the AAV-ABCA4 Drug Product may be further formulated for prefilled, room temperature or pre-filled cold storage in a microdelivery device.
Compositions of the disclosure may be manufactured at a scale of between 1 to 1000 vials per batch, inclusive of the endpoints. In some embodiments of the compositions of the disclosure, a composition, Drug Substance, or Drug Product may be manufactured at a scale of between 50 to 500 vials per batch, inclusive of the endpoints. In some embodiments of the compositions of the disclosure, a composition, Drug Substance, or Drug Product may be manufactured at a scale of between 100 to 250 vials per batch, inclusive of the endpoints.
Exemplary batches of the disclosure may comprise between 0.01 mL and 500 mL, inclusive of the endpoints, of a composition, Drug Substance, or Drug Product of the disclosure.
In some embodiments of the methods of the disclosure for preparation of the Drug Product, a Drug Substance is thawed at +35±2° C., and diluted as required in sterile formulation buffer to the target concentration (e.g., 0.5×10{circumflex over ( )}12 DRP/mL, 5×10{circumflex over ( )}12 DRP/mL or 1.0×10{circumflex over ( )}13 DRP/mL).
In some embodiments of the compositions of the disclosure, the target final DRP titre of the AAV-ABCA4 Drug Product is 1×10{circumflex over ( )}13 DRP/mL, the minimum and maximum acceptable titre is 1.0×10{circumflex over ( )}12 DRP/mL and 3.0×10{circumflex over ( )}13 DRP/mL, respectively. In some embodiments, the AAV-ABCA4 Drug Product is sterile filtered and filled into 0.5 ml polypropylene tubes or 0.5 mL Crystal Zenith® (cyclic olefin polymer) vials for either administration following up to a 10× dilution or without dilution.
The vials are then frozen and stored at ≤−60° C. For labelling and storage prior to QP release and distribution to site, the Drug Product is transferred to the qualified clinical distributor. The Drug Product is stored at ≤−60° C. in a temperature monitored freezer until QP release and distribution.
AAV-ABCA4 Drug Product may be pre-filled into a microdelivery device for suprachoroidal delivery. Microdelivery devices suitable for suprachoroidal delivery may comprise a microcatheter and the AAV-ABCA4 Drug Product may be further formulated for prefilled, room temperature or pre-filled cold storage in a microdelivery device.
In some embodiments of the compositions of the disclosure, including those wherein the composition comprises a Drug Product and the composition is supplied in a sterile vial, the composition may be stored at below zero (° C.). In some embodiments, the compositions may be thawed and frozen without loss of efficacy of the Drug Product or integrity to the sterile packaging. In some embodiments, the compositions may undergo multiple rounds of thawing and freezing without loss of efficacy of the Drug Product or integrity to the sterile packaging.
In some embodiments of the compositions of the disclosure, including those wherein the composition comprises a Drug Product and the composition is supplied in a sterile vial, the composition may be stored at room temperature.
Starting materials used in the preparation of buffers and media of the disclosure are certified as free from material of animal origin.
Nonlimiting examples of filters used for the filtration of the Drug Substance and Drug Product are Sartopore 0.45 μm and 0.2 μm filters. The filters are non-sterile when purchased and are sterilized in house at the contract manufacturer by autoclaving. In some embodiments, filters are integrity tested by bubble point testing at a threshold pressure (e.g. 3.2 Bars).
All chromatographic materials are released on a Certificate of Analysis prior to use. Columns are purchased prepacked and are sanitized prior to use.
An exemplary passaging protocol comprising 10 passages is shown in
T25 Flask to T175 Flask: Media is discarded and cells washed with pre-warmed PBS. The cells are loosened with TrypLE cell dissociation reagent. The T-flasks or Cell Stacks are incubated 5 to 10 minutes in an incubator set at 37±1° C. and the cells are fully dislodged by gently tapping the vessel. Growth medium is added to inhibit the TrypLE. The volumes of growth medium, PBS and TrypLE used for different supports are presented in Table 6. All cell suspensions are then pooled.
Cell count and cell viability is determined and the cells are seeded, incubated and passaged in accordance with Table 4.
Cell build processes of the disclosure may be scaled up or down according to the number of HYPERstacks to be used. The use of HYPERstacks provides superior scalability and efficiency of cell culture.
Temperatures, durations, spin speed, and volumes below may be adjusted for optimal results depending upon, among other factors, the cell type used. For the exemplary embodiment described below, conditions were optimized for the use of HEK293 Cells. These methods may be optimized for larger scale production.
An exemplary transfection process used in manufacturing AAV constructs of the disclosure comprises or consists of the steps. Plasmid DNA (e.g., a plasmid encoding an AAV Construct comprising an RPGRORF15 or an ABCA4 sequence, a plasmid encoding Ad5 helper functions and a plasmid encoding AAV8 rep and cap genes) and a transfection composition (for example, comprising a polymer or PEI) are diluted separately into transfection solution to produce a DNA transfection composition and a diluted transfection composition, respectively. The diluted transfection composition is added to the DNA transfection composition and incubated at room temperature to produce a Transfectable DNA Composition. The resulting Transfectable DNA Composition is added to the Transfection Medium. Growth Medium is removed from the HYPERstack, and Transfection Medium comprising the Transfectable DNA Composition is added to the empty HYPERstack. The HYPERstack is incubated at 37° C., 5% CO2 for at least 12, 16, 20, 24, 28, 32, 36, 40, 44, or 48 hours.
A summary of an exemplary transfection process used in manufacturing AAV constructs of the disclosure is shown in
The plasmids and the PEI are prepared with Transfection Medium (Table 5).
In certain embodiments, the amount of plasmid DNA is presented in Table 6.
In particular embodiments, the PEIpro® to DNA ratio (mL:mg) is about 0.5:1 to about 5:1, or about 1:1 to about 5:1, respectively, optionally about 2:1 to about 4:1, about 4:1, about 3:1, or about 2:1. In certain embodiments, the transfection is conducted using PEI, wherein the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of 1:1:1, respectively. In certain embodiments, the transfection is conducted using PEI at a PEI:DNA ratio (mL:mg) of about 0.5:1 to 5:1 or about 1:1 to about 5:1, respectively, optionally about 2:1 to about 4:1, about 4:1, about 3:1, or about 2:1, wherein the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 0.5:1:1 to about 10:1:1, about 1:1:1 to about 10:1:1, about 2:1:1 to about 10:1:1 optionally about 0.5:1:1, about 1:1:1, about 2:1:1, about 3:1:1, about 4:1:1, about 5:1:1, about 6:1:1, about 7:1:1, about 8:1:1, about 9:1:1, or about 10:1:1. In certain embodiments, the transfection is conducted using PEI (e.g., PEIpro®) at a PEI:DNA (mL:mg) ratio of about 1:1 to about 5:1, respectively, optionally about 2:1 to about 4:1, about 4:1, about 3:1, or about 2:1, wherein the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of 1:1:1, respectively. In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of 3:1:1, respectively. In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of 10:1:1, respectively. In some embodiments, the plasmid vector comprising an exogenous sequence, the helper plasmid vector, and the plasmid vector comprising a sequence encoding a viral Rep protein and a viral Cap protein are provided in a molar ratio of about 2:1:1, about 3:1:1, about 4:1:1, about 5:1:1, about 6:1:1, about 7:1:1, about 8:1:1, or about 9:1:1, respectively.
Following transfection, Transfection Medium is removed from the HYPERstack, and Harvest Medium is added. Cells are incubated in Harvest Medium at 37° C., 5% CO2 for 72 hours. Virus Release Solution is added to the HYPERstack at a ratio of 1:20 by volume, and cells are incubated at 37° C., 5% CO2 for 18 hours.
Exemplary formulations of the different types of Media and solutions used to culture cells, transfect cells, and release AAV viral particles are disclosed in Table 7.
Following incubation with Virus Release Solution, Harvest Media containing AAV viral particles released from the transfected HEK293 cells is removed from the HYPERstack. In some embodiments, the AAV viral particles are purified from the Harvest Media.
A summary of exemplary down stream processing steps is shown in
Hydrophobic Interaction Chromatography (HIC) captures rAAV viral particles based on the binding of viral capsid proteins to the matrix of the chromatography column through hydrophobic interactions. In some embodiments, a high salt concentration is used to promote clustering of hydrophobic surfaces.
A process summary of an exemplary Hydrophobic Interaction Chromatography (HIC) step of the manufacturing processes of the disclosure is shown in
In some embodiments, the HIC step comprises the steps of: (i) diluting the harvest media comprising a plurality of released rAAV particles; (ii) loading the diluted harvest media on a HIC column; (iii) generating a HIC chromatogram; and (iv) selecting a peak on the HIC chromatogram containing rAAV particles to produce the HIC eluate comprising a plurality of rAAV viral particles. In some embodiments, the chromatography matrix used in the HIC column is a Hydrophobic Interaction (OH) matrix. In some embodiments, the HIC column is an 800 mL monolith. In some embodiments, the harvest media is diluted into a high salt buffer. In some embodiments, a step gradient to elute the rAAV particles. In some embodiments, an isocratic elution to elute the rAAV particles. Illustrative buffer conditions are provided, e.g., in
In some embodiments, the HIC eluate is diluted and filtered prior to additional purification, i.e. prior to Cation Exchange Chromatography (CEX). A suitable filter is chosen to minimize loss of rAAV particles during filtration. In some embodiments, the HIC eluate is filtered using a 0.8/0.45 μM polyethersulfone (PES) filter.
In some embodiments of the methods of the disclosure, Cation Exchange Chromatography (CEX) can be used to further purify the plurality of rAAV particles in the HIC eluate produced by the HIC step. CEX is a type of ion exchange chromatography, which separates molecules based on their net surface charge. In some embodiments, CEX uses a negatively charged ion exchange resin with an affinity for positively charged molecules. When the pH is below the isoelectric point (pI) of the AAV particles, the AAV viral particles have a positive charge and can be purified by CEX.
A process summary of an exemplary Cation Exchange Chromatography (CEX) step of the manufacturing processes of the disclosure is shown in
In some embodiments of the methods of the disclosure, the CEX step comprises the steps of: (i) diluting the HIC eluate comprising a plurality of rAAV viral particles from the HIC step, and optionally, filtering the HIC eluate; (ii) loading the diluted HIC eluate on a CEX column; (iii) generating a CEX chromatogram; and (iv) selecting a fraction from the CEX chromatogram containing rAAV particles to produce the CEX eluate comprising a plurality of rAAV viral particles. In some embodiments, the CEX chromatography comprises an SO3− cation exchange matrix in the chromatography column. In some embodiments, the chromatography column is an 80 mL monolith. In some embodiments, the HIC eluate is diluted into a low salt buffer prior to the CEX step. In some embodiments, the diluted HIC eluate is adjusted to pH 3.0-4.0. In some embodiments, the diluted HIC eluate is adjusted to pH 3.6+/−0.1. In some embodiments, this brings the pH below that of pI of the rAAV viral particles, producing positively charged rAAV viral particles. In some embodiments, a step gradient is used to elute the rAAV particles. In some embodiments, the method further comprises neutralizing the pH of the CEX eluate. Illustrative buffer conditions are provided, e.g., in
In some embodiments of the methods of the disclosure, Anion Exchange Chromatography (AEX) can be used to enrich the plurality of rAAV particles for full rAAV particles. Full rAAV particles are AAV particles comprising a single stranded DNA comprising an AAV-Construct of the disclosure. In some embodiments, the full rAAV particles comprise a sequence encoding a 5′ ITR, a sequence encoding a GRK1 promoter, a sequence encoding RPGRORF15, a sequence encoding a BGH polyA signal and a sequence encoding a 3′ ITR. In some embodiments, the full rAAV particles comprise a sequence encoding a 5′ ITR, a sequence encoding ABCA4 or a portion thereof and a sequence encoding a 3′ ITR.
AEX is a type of ion exchange chromatography which separates molecules based on net surface charge. Full, empty and damaged and/or aggregated AAV viral particles have different isoelectric points (pI). In some embodiments, full and empty particles are separated based on the differing charges of the particles. Full particles are slightly more negatively charged than empty particles due to the present of the DNA genome. In some embodiments, rAAV particles are diluted into solution with a pH that is higher than the pI of the AAV particles. In some embodiments, separation is further enhanced by the removal of MgCl2 from the solutions.
A process summary of an exemplary Anion Exchange Chromatography (AEX) step of the manufacturing processes of the disclosure is shown in
In some embodiments of the methods of the disclosure, the AEX Chromatography step comprises the steps of: (i) diluting the CEX eluate comprising a plurality of rAAV viral particles; (ii) loading the diluted CEX eluate on a AEX column; (iii) generating an AEX chromatogram; and (iv) selecting a fraction from the AEX chromatogram containing full rAAV particles to produce the AEX eluate comprising a purified and enriched plurality of full rAAV particles. In some embodiments, the AEX chromatography comprises an Anion Exchange (QA) matrix in the chromatography column. In some embodiments, the column is an 80 mL macroporous matrix composition. In some embodiments, the CEX eluate is diluted into a low salt buffer prior to the AEX step. In some embodiments, the linear gradient is used to elute the full rAAV particles. In some embodiments, the method further comprises neutralizing the pH of the eluate comprising a purified and enriched plurality of full rAAV particles. Illustrative buffer conditions are provided, e.g., in
In some embodiments of the methods of the disclosure, the AEX eluate comprising a purified and enriched plurality of full rAAV particles is diafiltered and concentrated into a final formulation buffer (FFB) using Tangential Flow Filtration (TFF). Tangential Flow Filtration is a membrane filtration technique which can be classified as a microfiltration or ultrafiltration process, depending on membrane porosity in the specific TFF embodiment. In TFF, the feed stream passes parallel to the membrane face as one portion permeates the membrane, while the retentate is recirculated back to the reservoir. This process achieves volume reduction and additional purification using the principle of Tangential Flow Filtration (TFF).
This process utilizes diafiltration to formulate the AAV product into the desired Final Formulation buffer (20 mM Tris, pH 8, 1 mM MgCl2, 200 mM NaCl, optionally with poloxamer at 0.001%).
Tangential flow filtration of the Elution product is conducted using a hollow fiber filter (HFF) cartridge with a molecular weight cut-off of 100 kDa (Spectrum). The cartridge and the system are equilibrated with Tris 20 mM, MgCl2 1 mM, NaCl 200 mM pH 8 buffer to obtain a pH 8.0±0.2 on the Permeate side.
In some embodiments of the methods of the disclosure, the method comprises a two TFF steps, both the first and second TFFs are performed using a 100 kDa HFF.
The product is concentrated to the minimum volume before the diafiltration in continuous mode against minimum 6 volumes of Formulation Buffer. The retentate is collected. The system is rinsed with Formulation Buffer. This rinse is collected in a different vessel.
If required for longer term storage (>60 days), in some nonlimiting examples of long term storage methods, the product is submicron filtered using a 0.2 μm filter. Once the Drug Substance is completely filtered, the filter is rinsed with the final formulation buffer.
After QC sampling, the purified bulk Drug Substance is stored at <−80° C. Optionally, poloxamer 188 is added to the Drug Substance prior to freezing and storage at <−80° C.
Method of Making a Drug Product from a Drug Substance
Compositions of the disclosure may be supplied as liquids. In some embodiments of the compositions of the disclosure, including those wherein the composition comprises a Drug Product, the Drug Product is supplied in sterile glass vials. In some embodiments, the sterile glass vials are sterile clear glass vials. In some embodiments, the sterile glass vials are capped with stoppers. In some embodiments, the stoppers are plastic. In some embodiments, the sterile glass vials are capped and further enclosed with overseals.
Exemplary Drug Substances are characterized by the tests listed in Table 8.
Analytical Procedures
Physical Titre:
In some embodiments, the genomic titre is determined using qPCR. This method allows quantification of genomic copy number. Samples of the vector stock are diluted in buffer. The samples are DNase treated and the viral capsids lysed with proteinase K to release the genomic DNA. A dilution series is then made. Replicates of each sample are subjected to qPCR using a Taqman based Primer/Probe Set. A standard curve is produced by taking the average for each point in the linear range of the standard plasmid dilution series and plotting the log copy number against the average CT value for each point. In some embodiments, the plasmid DNA used in the standard curve is in the supercoiled conformation and in others it is in the linear conformation. Linearized plasmid can be prepared, for example by digestion with HindIII restriction enzyme, visualized by agarose gel electrophoresis and purified using the QIAquick Gel Extraction Kit (Qiagen) following manufacturer's instructions. Other restriction enzymes that cut within the plasmid used to generate the standard curve may also be appropriate. In some embodiments, the use of supercoiled plasmid as the standard increased the titre of the AAV vector compared to the use of linearized plasmid. The titre of the rAAV vector can be calculated from the standard curve and is expressed as DNase Resistant Particles (DRP)/mL.
In some embodiments, the genomic titre is determined using droplet digital PCR (ddPCR). A samples of AAV or the genomic DNA thereof may be fractionated into a plurality of nanoliter scaled droplets (e.g. 20,000 droplets) comprising an oil/water emulsion. The PCR occurs in each droplet of the plurality. This technique provides the advantage of requiring less sample and smaller volumes of reagents compared with reactions performed without the use of a droplet. Following PCR, each droplet is analyzed or read to determine the fraction of PCR-positive droplets in the original sample. These data are then analyzed using Poisson statistics to determine the target DNA template concentration in the original sample. During droplet generation, template molecules are distributed randomly into droplets. Some droplets contain no template, some contain one template molecule, and others contain more than one. Due to the random nature of the partitioning, the fluorescence data after amplification are well fit by a Poisson distribution. The number of positive droplets corresponds to the concentration of target sequence in the sample. The ddPCR system can accurately analyze samples in which multiple targets are amplified in the same droplet, thereby removing any requirement for one template per droplate at the beginning of a reaction or for one target per droplate following a reaction to quantify the target copies per droplet. ddPCR may use the same PCR reagents as standard PCR.
Infectious Unit (IU) Titre: This assay quantifies the number of infectious particles of AAV. Quantification is performed by infecting RC32 cells (HeLa expressing AAV8 Rep/Cap) with serial dilutions of the vector sample and uniform concentrations of wild type adenovirus to provide helper function. Several days post infection, the cells are lysed diluted to reduce PCR inhibitors and assayed by qPCR in the same manner as described in the physical titre assay above, except that the DNase and Proteinase K digestion is omitted and only the qPCR portion is performed. Individual wells are scored as Positive or Negative for AAV amplification. The scored wells are used to determine the TCID50 in IU/mL using the Karber Method.
Total Particles: The assay uses an ELISA technique (AAV8 Titration ELISA KIT). A monoclonal antibody specific for a conformational epitope on assembled AAV8 capsids is coated onto microtitre strips and is used to capture AAV8 particles from the specimen. Captured AAV particles are detected in two steps. First a biotin-conjugated monoclonal antibody to AAV8 is bound to the immune complex. In the second step streptavidin peroxidase conjugate reacts with the biotin molecules. Addition of substrate solution results in a color reaction which is proportional to the amount of specifically bound viral particles. The absorbance is measured photometrically at 450 nm.
Full:empty Ratio (Transmission Electron Microscopy): The full:empty ratio of AAV2 particles may be determined using negative staining transmission electron microscopy (TEM). Samples are applied to a grid fixed. Samples are visualized using a transmission electron microscope and counts are performed of the full (i.e. containing DNA) and empty AAV2 capsid particles based on their morphology. The ratio of full:empty particles is calculated from the particle counts.
Full:empty Ratio (Analytical Ultracentrifugation): The full:empty ratio of AAV8 particles may be determined using analytical ultracentrifugation (AUC). AUC has an advantage over other methods of being non-destructive, meaning that samples may be recovered following AUC for additional testing. Samples comprising empty and full AAV8 particles are applied to a liquid composition through which the AAV8 move during an ultracentrifugation. A measurement of sedimentation velocity of one or more AAV8 particles provides hydrodynamic information about the size and shape of the AAV particles. A measure of sedimentation equilibrium provides thermodynamic information about the solution molar masses, stoichiometries, association constants, and solution nonideality of the AAV8 particles. Exemplary measurements acquired during AUC are radial concentration distributions, or “scans”. In some embodiments, scans are acquired at intervals ranging from minutes (for velocity sedimentation) to hours (for equilibrium sedimentation). The scans of the methods of the disclosure may contain optical measurements (e.g. light absorbance, interference and/or fluorescence). Ultracentrifugation speeds may range from between 10,000 rotations per minute (rpm) and 75,000 rpm, inclusive of the endpoints. As full AAV8 particles and empty AAV8 particles demonstrate distinct measurements by AUC, the full/empty ratio of a sample may be determined using this method.
Vector Identity (DNA): This assay provides a confirmation of the viral DNA sequence. The assay is performed by digesting the viral capsid and purifying the viral DNA. The DNA is sequenced with a minimum of 2 fold coverage both forward and reverse where possible (some regions, e.g., ITRs are problematic to sequence). The DNA sequencing contig is compared to the expected sequences to confirm identity.
Total Protein: This assay quantifies the total amount of protein present in the test article by using a Micro-BCA kit. In order to eliminate matrix effects of the formulation buffer samples are precipitated with acetone and the precipitated protein re-suspended in an equal volume of water prior to analysis. The protein concentration determination is performed by mixing test article or diluted test article with a Micro-BCA reagent provided in the kit. The same is performed using dilutions of a Bovine Serum Albumin (BSA) Standard. The mixtures are incubated at 60° C. and the absorbance measured at 562 nm. A standard curve is generated from the standard absorbance and the known concentrations using a linear regression fit. The unknown samples are quantified according to the linear regression.
Purity: This assay provides a semi-quantitative determination of AAV purity. Based on the results of the AAV8 capsid particle ELISA, samples are concentrated by SpeedVac and either 4×10{circumflex over ( )}10 or 1×10{circumflex over ( )}11 particles are loaded and the capsid proteins are separated on an SDS-PAGE gel. Densitometry analysis of the SYPRO Orange stained gels allows calculation of the approximate impurity levels relative to the capsid proteins (Vp1, Vp2 and Vp3).
Replication Competent AAV: Test article is used to transduce HEK293 cells in the presence or the absence of wild type adenovirus. Three successive rounds of cell amplification will be conducted and total genomic DNA is extracted at each amplification step.
The rcAAV8 are detected by real-time quantitative PCR. Two sequences are isolated genomic DNA; one specific to the AAV2 Rep gene and one specific to an endogenous gene of the HEK293 cells (human albumin). The relative copy number of the Rep gene per cell is determined. The positive control is the wild type AAV virus serotype 8 tested alone or in the presence of the rAAV vector preparation.
The limit of detection of the assay is challenged for each tested batch. The limit of detection is “X” rcAAV per “Y” genome copies of test sample. If a test sample is negative for Rep sequence, the result for this sample will be reported as: NO REPLICATION, <“X” rcAAV per “Y” genome copies of test sample. If a test sample is positive for Rep sequence, the result for this sample will be reported as: REPLICATION, >“X” rcAAV per “Y” genome copies of test sample.
HEK293 Host Cell Protein: The HEK293 host cell protein (HCP) assay is an immunoenzymetric assay. Samples of purified virus are reacted in microtitre strips coated with an affinity purified capture antibody. A secondary horseradish peroxidase (HRP) conjugated enzyme is reacted simultaneously, resulting in the formation of a sandwich complex of solid phase antibody-HCP-enzyme labelled antibody. The microtitre strips are washed to remove any unbound reactants. The quantity of HEK293 HCPs is detected by the addition of 3,3′,5,5′ tetramethyl benzidine peroxidase, an HRP substrate, to each well. The amount of hydrolyzed substrate is read on a plate reader and is directly proportional to the concentration of HEK293 HCPs present.
Total DNA: Picogreen reagent is an ultra-sensitive fluorescent nucleic acid stain that binds double-stranded DNA and forms a highly luminescent complex (λexcitation=480 nm-λemission=520 nm). This fluorescence emission intensity is proportional to dsDNA quantity in solution. Using a DNA standard curve with known concentrations, DNA content in test samples is obtained by converting measured fluorescence.
HEK293 Host Cell DNA: The original process measured size and quantity of 3 different amplicons whereas the improved process measures total hcDNA including high molecular weight and sheared DNA. The qualification data the improved process demonstrates that the assay is specific and sufficiently sensitive to meet the requirements in assessing hcDNA per dose of <10 ng/dose (WHO Expert Committee on Biological Standardization, 2013).
Residual BSA: Residual BSA is quantified using a commercially available ELISA kit manufactured and marketed by Bethyl. The scientific principle to the ELISA kit is very similar to that specified for the Host Cell Protein ELISA.
Residual Benzonase: This assay uses purified polyclonal antibodies specific to Benzonase endonuclease to detect residual Benzonase in the test sample by sandwich ELISA. Accurate measurement is achieved by comparing the signal of the sample to the Benzonase endonuclease standards assayed at the same time.
Bioburden Assay: This procedure is used to determine quantitatively (if detectable) the amount of bioburden present in a sample. The method used involves membrane filtration of half of the sample onto each of two membranes. The membranes are placed onto separate agar media plates which are incubated in aerobic and anaerobic conditions sequentially at 20-25° C. and 30-35° C. At the conclusion of incubation; aerobe, anaerobe, and fungal counts are expressed as CFU/mL of sample.
Endotoxin Assay: This assay is used to determine if bacterial endotoxins are present in the test article. A quantitative procedure is performed by the kinetic-chromogenic method. Known amounts of endotoxin are tested in parallel with the test article for an accurate determination of the level of bacterial endotoxin. The potential for interference by the test article is examined by spiking the test article plus LAL reagent with specified levels of endotoxin. Following the inhibition/enhancement test, the endotoxin content of the test article is determined.
Quantitative PCR (qPCR): qPCR can be used to confirm HPLC chromatogram results (also referred to as real-time PCR or reverse-transcription PCR, both abbreviated as RT-PCR). qPCR uses polymerase (e.g. a Taq polymerase) in a standard PCR reaction to amplify a target DNA fragment from a complex sample using a pre-validated primer or primer/probe assay. The PCR reaction uses a fluorescent reporter to measure the generation of amplified DNA at every cycle of PCR, thereby providing either an absolute or relative measure of DNA quantity. When the DNA is in the log linear phase of amplification, the amount of fluorescence produced by the PCR increases above the background. The point at which the fluorescence becomes measurable is called the threshold cycle (CT) or crossing point. By comparing the CT of the test sample to a known sample or a standard curve (using a series of dilutions of a known sample), the amount of DNA in the test sample can be determined. In preferred embodiments, the amount of sample/test DNA is compared against an invariant or endogenous gene of the host cell (e.g. a housekeeping gene including but not limited to β-actin).
Droplet Digital PCR (ddPCR): ddPCR can be used to confirm HPLC chromatogram results. ddPCR uses Taq polymerase in a standard PCR reaction to amplify a target DNA fragment from a complex sample using a pre-validated primer or primer/probe assay. The PCR reaction is partitioned into thousands of individual reaction vessels prior to amplification, and the data is acquired at the reaction end point. ddPCR offers direct and independent quantification of DNA without standard curves, and can give a precise and reproducible data. End point measurement enables nucleic acid quantitation independent of reaction efficiency. ddPCR can be used for extremely low target quantitation from variably contaminated samples.
Compositions of the disclosure maintain long term stability when stored at <−60° C. For example, compositions of the disclosure maintain long term stability when stored at temperature between −80° C. and 40° C. (approximately human body temperature), inclusive of the endpoints. For example, compositions of the disclosure maintain long term stability when stored at temperature between −80° C. and 5° C., inclusive of the endpoints. For example, compositions of the disclosure maintain long term stability when stored at −80° C., −20° C. or 5° C. In some embodiments, compositions of the disclosure are formulated as liquids or suspensions, aliquotted into one or more containers (e.g. vials), and stored at <−60° C. In some embodiments, compositions of the disclosure are formulated as liquids or suspensions, aliquotted into one or more containers (e.g. vials), and stored at −80° C., −20° C. or 5° C.
Compositions of the disclosure may be provided in a container with an optimal surface area to volume ratio for maintaining long term stability when stored at <−60° C. Compositions of the disclosure may be provided in a container with an optimal surface area to volume ratio for maintaining long term stability when stored at −80° C., −20° C. or 5° C. In some embodiments, compositions of the disclosure are formulated as liquids or suspensions, aliquotted into one or more containers (e.g. vials), and stored in one or more containers with a surface area to volume ratio as large as possible when all storage requirements are considered.
Compositions of the disclosure maintain long term stability when stored at ambient relative humidity.
Total particle high performance liquid chromatography (HPLC) chromatogram the preferred method for screening purposes as it has a quick turnaround time (<24 hours). This method is the main reporting assay for the recovery determination of experiments. Verification of HPLC results are confirmed with Droplet Digital PCR (ddPCR) measurements.
Following HIC capture, proteinaceous hair-like material was observed in the HIC eluate which led to unsustainable pressure increase during the subsequent chromatography step. A 0.45 μm cellulose acetate (CA) filter was used to retain the fibers but this led to a loss of 50% of the vector. Subsequently, filters were screened for rAAV retention to find a suitable alternative (
Both the gradient elution and the isocratic elution methods were tested for the HIC step (
HIC development confirmed the need for a three step process including an intermediate CEX SO3− polishing step (
A TEM analysis of an exemplary CEX SO3− eluate containing rAAV particles revealed that 27.2% of the particles were full, and 51.1% of the particles were empty or damaged (
Optimal resolution of full and empty peaks depends on pH the concentration of MgCl2. MG2+ has been shown to have preferential interactions with empty AAV particles that aids separation between empty and full particles.
An exemplary HIC chromatogram showing the purification of rAAV particles of the disclosure from Harvest Media is shown in
Estimated process recoveries for the process are shown in
X-linked retinitis pigmentosa (XLRP) is a very severe form of retinitis pigmentosa (RP), resulting in rapid disease progression and severe retinal dysfunction. The worldwide prevalence of XLRP is approximately 1:30,000 to 1:40,000 (Tee et al., 2016). Patients with XLRP typically experience onset of night blindness in the first decade, followed by reduction of visual field and acuity and progressively severe visual impairment. Most patients are legally blind by the end of the fourth decade.
To date, 3 genes have been mapped to XLRP: RP2; RP3, also known as the RP GTPase regulator (RPGR) gene; and OFD1, which has been identified as a rare cause of XLRP (Webb et al., 2012). Approximately 75% of cases of XLRP are due to RPGR variants, and the worldwide prevalence of XLRP due to RPGR variants is approximately 1:40,000 to 1:53,000 (Pelletier et al., 2007; Shu et al., 2008). RPGR is involved in protein distribution in photoreceptors and plays a role in the transport of photo-transduction components and other outer segment proteins across the connecting cilium (Tee et al., 2016). Essential for photoreceptor viability, the RPGR gene product is localised in the outer segment of rod photoreceptors (Ferrari et al., 2011). Loss of RPGR function in the retina causes the progressive loss of rod and cone vision.
Nightstar Therapeutics is developing AAV8-RPGR as a potential gene therapy medicinal product (GTMP) for the treatment of XLRP due to mutations in RPGR. Replacing the deficient RPGR in XLRP patients with new and viable RPGR is expected to slow or stop retinal degeneration and maintain or improve visual function.
This document describes the upstream and primary harvest processes used for the manufacture of AAV8-RPGR product. This document includes all the upstream and primary harvest processing steps.
Manufacturing Process Description and Process Controls
Batch Definition
A batch of product defined as a single production campaign consisting of 20 Corning 36-layer HYPERStack® vessels containing plasmid DNA transfected HEK293 cells that produce the AAV8-RPGR biologic product. The cell culture media is harvested and pooled from the 20 Corning 36-HYPERStack® vessels and followed by a single purification process.
Summary of the Upstream Process
Cells are expanded using Corning flasks and stacks to allow sufficient cell mass to be generated for seeding twenty HYPERStack® units for vector production. Transfection of the cells takes place with a two-production plasmid system using an optimised calcium phosphate co-precipitation method.
After transfection, the medium is changed and Benzonase® endonuclease is added to the media to digest free genomic and plasmid DNA present in the media. To promote vector release into the media, the 36 layer HYPERStack® units are spiked with a HEPES buffered Na2HPO4 solution and incubated prior to harvest. The media from each 36-layer HYPERStack® is harvested aseptically using disposable bioprocess bags and pooled into a single volume (˜82 L).
The pooled media containing the recombinant AAV (rAAV) is then clarified using a capsule 0.65 μm pore pre-filter, followed by a 0.2 μm sterilising grade capsule filter.
Manufacturing Flow Diagram
An overview of the upstream and primary recovery steps of the manufacturing process for AAV8-RPGR is illustrated in
Upstream Manufacturing Process Description
Vial Thaw
A vial from the HEK293 MCB is removed from −150° C. storage and subsequently thawed in a water bath that is set to a temperature of 37±1° C. A visual check is performed to ensure that the cells are thawed. It is anticipated that the WCB will be used for any further production runs.
The thawed cells are added to a T-25 flask that contains 4 mL of growth media (DMEM+10% serum) that has been pre-warmed to 37±1° C. The cells are placed in a humidified CO2 incubator that is set to 37° C. and 5% CO2 and left overnight.
Cell Expansion
Cells are expanded from the initial T-25 flask through to the 36-layer HYPERStack® units through a series of passages. Cells are grown in humidified incubators set at 37° C. and 5% CO2. Cells are passaged when cell confluency reaches 80%, which is typically every three to five days.
The generic passaging protocol consists of the following:
Remove media from the current cell flask/stack.
Transient Transfection, Benzonase® Addition, Media Release and Harvesting
Following 3 days of growth post seeding, the HYPERStack® media is replaced with fresh DMEM media containing serum and chloroquine; this is performed 2-8 hours before transfection. The cells are then transfected with the two production plasmids using an optimized calcium phosphate co-precipitation method.
Sufficient DNA plasmid transfection precipitate is prepared in a biological safety cabinet to transfect 5×36-layer HYPERStacks®. Initially a DNA/calcium mix is prepared containing the vector plasmid, the pDP8.ape helper plasmid and CaCl2). After mixing well, the plasmid/CaCl2) solution is added to an equal volume of 2×HEPES buffered NaHPO4 with concurrent gentle agitation in a disposable process bag to obtain an optimal precipitate. The solution is sat at room temperature for at least 5 minutes and then added to the five 5 HYPERStacks® linked with a manifold. This procedure is repeated four times to complete the transfection of the required 20 HYPERStack® units.
Post transfection, the cells are incubated in an incubator set at 37° C. and 5% CO2. Approximately 22 hours after transfection, the medium is changed using serum-free DMEM. At this time the Benzonase® endonuclease is added to the media, at a concentration of 90 U/mL, to digest free genomic DNA and plasmid DNA present in the media. This step is performed to minimize the amount of residual host cell DNA in the final vector product. The cells are then incubated in an incubator set at 37° C. and 5% CO2 for an additional 69-75 hours. To promote vector release, the 36-layer HYPERStacks® are spiked with a HEPES buffered NaHPO4 solution and incubated for approximately 18 hours in an incubator set at 39° C. and 5% CO2 prior to harvest. The media from each 36-layer HYPERStack® is harvested aseptically using disposable bioprocess bags and pooled into a single volume (˜82 L).
Clarification by Filtration
The pooled media containing the recombinant AAV (rAAV) is then clarified through a capsule pre-filter, followed by a sterilising grade capsule filter. A second back-up pre-filter is installed as part of the filtration set up and is to be used if the inlet pressure reaches 10 psi when the first pre-filter is in use. The pre-filter has a pore size of 0.65 μm and is constructed of, glass fibre. The bioburden reduction filter is a 0.2 μm sterilizing grade filter constructed of polyethersulfone (PES). To achieve maximal recovery, after product filtration, filters are blown down aseptically and chased with buffer.
Preferred Chemicals for Solution Preparation
Compendial or multi-compendial chemicals are to be used wherever possible.
X-linked retinitis pigmentosa (XLRP) is a very severe form of retinitis pigmentosa (RP), resulting in rapid disease progression and severe retinal dysfunction. The worldwide prevalence of XLRP is approximately 1:30,000 to 1:40,000 (Tee et al., 2016). Patients with XLRP typically experience onset of night blindness in the first decade, followed by reduction of visual field and acuity and progressively severe visual impairment. Most patients are legally blind by the end of the fourth decade.
To date, 3 genes have been mapped to XLRP: RP2; RP3, also known as the RP GTPase regulator (RPGR) gene; and OFD1, which has been identified as a rare cause of XLRP (Webb et al., 2012). Approximately 75% of cases of XLRP are due to RPGR variants, and the worldwide prevalence of XLRP due to RPGR variants is approximately 1:40,000 to 1:53,000 (Pelletier et al., 2007; Shu et al., 2008). RPGR is involved in protein distribution in photoreceptors and plays a role in the transport of photo-transduction components and other outer segment proteins across the connecting cilium (Tee et al., 2016). Essential for photoreceptor viability, the RPGR gene product is localised in the outer segment of rod photoreceptors (Ferrari et al., 2011). Loss of RPGR function in the retina causes the progressive loss of rod and cone vision.
Nightstar Therapeutics is developing AAV8-RPGR as a potential gene therapy medicinal product (GTMP) for the treatment of XLRP due to mutations in RPGR. Replacing the deficient RPGR in XLRP patients with new and viable RPGR is expected to slow or stop retinal degeneration and maintain or improve visual function.
This document describes the upstream and primary harvest processes used for the manufacture of AAV8-RPGR product. This document includes all the upstream and primary harvest processing steps.
Manufacturing Process Description and Process Controls
Batch Definition
A batch of product defined as a single production campaign consisting of 20 Corning 36-layer HYPERStack® vessels containing plasmid DNA transfected HEK293 cells that produce the AAV8-RPGR biologic product. The cell culture media is harvested and pooled from the 20 Corning 36-HYPERStack® vessels and followed by a single purification process.
Summary of the Upstream Process
Cells are expanded using Corning flasks and stacks to allow sufficient cell mass to be generated for seeding twenty HYPERStack® units for vector production. Transfection of the cells takes place with a three-production plasmid system using either an optimized calcium phosphate or PEIpro® mediated method.
After transfection, the medium is changed and Benzonase® endonuclease is added to the media to digest free genomic and plasmid DNA present in the media. To promote vector release into the media, the 36-layer HYPERStack® units are spiked with a HEPES buffered Na2HPO4 solution and incubated prior to harvest. The media from each 36-layer HYPERStack® is harvested aseptically using disposable bioprocess bags and pooled into a single volume (˜82 L).
The pooled media containing the recombinant AAV (rAAV) is then clarified using a capsule 0.65 μm pore pre-filter, followed by a 0.2 μm sterilising grade capsule filter.
Manufacturing Flow Diagram
An overview of the upstream and primary recovery steps of the manufacturing process for AAV8-RPGR is illustrated in
Upstream Manufacturing Process Description
Vial Thaw
A vial from the HEK293 MCB is removed from −150° C. storage and subsequently thawed in a water bath that is set to a temperature of 37±1° C. A visual check is performed to ensure that the cells are thawed. It is anticipated that the WCB will be used for any further production runs.
The thawed cells are added to a T-25 flask that contains 4 mL of growth media (DMEM+10% serum) that has been pre-warmed to 37±1° C. The cells are placed in a humidified CO2 incubator that is set to 37° C. and 5% CO2 and left overnight.
Cell Expansion
Cells are expanded from the initial T-25 flask through to the 36-layer HYPERStack® units through a series of passages. Cells are grown in humidified incubators set at 37° C. and 5% CO2. Cells are passaged when cell confluency reaches 80%, which is typically every three to five days.
The generic passaging protocol consists of the following:
Transient Transfection, Benzonase® Addition, Media Release and Harvesting
Following 3 days of growth post seeding, the HYPERStack® media is replaced with fresh DMEM media containing serum and chloroquine (the chloroquine is only required for the calcium phosphate transfection method); this is performed 2-8 hours before transfection. The cells are then transfected with the three production plasmids using either an optimised calcium phosphate or PEIpro® mediated method.
Sufficient DNA plasmid transfection precipitate is prepared in a biological safety cabinet to transfect 5×36-layer HYPERStacks®. The option exists to perform either a calcium phosphate mediated transfection or a transfection that uses PEIpro®. Both methods will be described in this section of the process description. Many of the steps will be common between the two methods, however when there are differences, explicit instructions will be given as to which transfection method is under discussion.
Calcium Phosphate Specific Transfection
Initially a DNA/calcium mix is prepared containing the transgene plasmid, the AV helper plasmid, the capsid plasmid and CaCl2. After mixing well, the plasmid/CaCl2 solution is added to an equal volume of 2×HEPES buffered NaHPO4 with concurrent gentle agitation in a disposable process bag to obtain an optimal precipitate. The solution is sat at room temperature for at least 5 minutes and then added to the five HYPERStacks® linked with a manifold. This procedure is repeated four times to complete the transfection of the 20 HYPERStack® units.
PEIpro® Specific Transfection
The transgene plasmid, the AV helper plasmid and the capsid plasmid DNA are diluted in serum-free media and stirred gently. Diluted PEIpro® is added to the DNA solution; all at once. The resulting solution then needs to be gently agitated and left to equilibrate to room temperature. The PEIpro®/DNA complex solution is then added to the five HYPERStacks® linked with a manifold. This procedure is repeated four times to complete the transfection of the 20 HYPERStack® units.
Post transfection, the cells are incubated in an incubator set at 37° C. and 5% CO2. Approximately 22 hours after transfection, the medium is changed using serum-free DMEM. At this time the Benzonase® endonuclease is added to the media, at a concentration of 90 U/mL, to digest free genomic DNA and plasmid DNA present in the media. This step is performed to minimize the amount of residual host cell DNA in the final vector product. The cells are then incubated in an incubator set at 37° C. and 5% CO2 for an additional 69-75 hours. To promote vector release, the 36-layer HYPERStacks® are spiked with a HEPES buffered NaHPO4 solution and incubated for approximately 18 hours in an incubator set at 39° C. and 5% CO2 prior to harvest. The media from each 36-layer HYPERStack® is harvested aseptically using disposable bioprocess bags and pooled into a single volume (˜82 L).
Clarification by Filtration
The pooled media containing the recombinant AAV (rAAV) is then clarified through a capsule pre-filter, followed by a sterilising grade capsule filter. A second back-up pre-filter is installed as part of the filtration set up and is to be used if the inlet pressure reaches 10 psi when the first pre-filter is in use. The pre-filter has a pore size of 0.65 μm and is constructed of, glass fibre. The bioburden reduction filter is a 0.2 μm sterilizing grade filter constructed of polyethersulfone (PES). To achieve maximal recovery, after product filtration, filters are blown down aseptically and chased with buffer.
Preferred Chemicals for Solution Preparation
Compendial or multi-compendial chemicals are to be used wherever possible.
X-linked retinitis pigmentosa (XLRP) is a very severe form of retinitis pigmentosa (RP), resulting in rapid disease progression and severe retinal dysfunction. The worldwide prevalence of XLRP is approximately 1:30,000 to 1:40,000 (Tee et al., 2016). Patients with XLRP typically experience onset of night blindness in the first decade, followed by reduction of visual field and acuity and progressively severe visual impairment. Most patients are legally blind by the end of the fourth decade.
To date, 3 genes have been mapped to XLRP: RP2; RP3, also known as the RP GTPase regulator (RPGR) gene; and OFD1, which has been identified as a rare cause of XLRP (Webb et al., 2012). Approximately 75% of cases of XLRP are due to RPGR variants, and the worldwide prevalence of XLRP due to RPGR variants is approximately 1:40,000 to 1:53,000 (Pelletier et al., 2007; Shu et al., 2008). RPGR is involved in protein distribution in photoreceptors and plays a role in the transport of photo-transduction components and other outer segment proteins across the connecting cilium (Tee et al., 2016). Essential for photoreceptor viability, the RPGR gene product is localised in the outer segment of rod photoreceptors (Ferrari et al., 2011). Loss of RPGR function in the retina causes the progressive loss of rod and cone vision.
Nightstar Therapeutics is developing AAV8-RPGR as a potential gene therapy medicinal product (GTMP) for the treatment of XLRP due to mutations in RPGR. Replacing the deficient RPGR in XLRP patients with new and viable RPGR is expected to slow or stop retinal degeneration and improve visual function.
This document describes the upstream and primary harvest processes used for the manufacture of AAV8-RPGR product. This document includes all the downstream and primary fill & finish processing steps.
Manufacturing Process Description and Process Controls
Batch Definition
A batch of product defined as a single production campaign consisting of 20 Corning 36-stack HYPERStack® vessels containing plasmid DNA transfected HEK293 cells that produce the AAV8 RPGR biologic product. The cell culture media is harvested and pooled from the 20 Corning 36-HYPERStack® vessels and followed by a single purification process.
Summary of the Downstream Process
After the clarification of the process stream a tangential flow filtration (TFF) step is used to perform a 100 fold volumetric concentration factor of the product followed by diafiltration step into the TMN500T buffer. A 100 kDA modified polyethersulfone (mPES) membrane is employed for this step.
The TFF concentrated media is further purified using a discontinuous iodixanol gradient. This step serves to enrich the preparation for DNA-containing rAAV particles, while removing the bulk of rAAV particles that are devoid of DNA (empty particles) based on the differential buoyant density of these particles. For maximal throughput, the process is completed in two gradient steps.
The iodixanol fraction is further purified on a Sepharose High Performance (SPHP) column which is cation exchange step which captures the positively charged AAV vector whilst other residual impurities and iodixanol are removed from the process stream.
Final vector concentration and diafiltration is achieved using a 100 kDa, TFF mPES membrane. The product is diafiltered into the final formulation buffer (20 mM Tris pH 8.0, 1 mM MgCl2, 200 mM NaCl). Prior to final formulation, in-process samples are analysed for vector recovery using a qPCR method to determine vector titre and yield of DNase Resistant Particles (DRP). This data is used to estimate the final volume required to achieve the final target titre. The excipient poloxamer 188 is added manually to process stream at a final concentration of 0.001% (v/v). After final formulation, the product is terminally sterile filtered through a 0.22 μm filter to yield the Purified Bulk Drug Substance (PBDS). Filling the PBDS completes the process and yields the Final Drug Product (FDP). Release testing takes place on both the PBDS and FDP.
Manufacturing Flow Diagram
An overview of the downstream and fill and finish steps of the manufacturing process for AAV8-RPGR is illustrated in
Downstream Manufacturing Process Description
Large Scale Tangential Flow Filtration
The SSS (salt and surfactant solution) is added to the clarified harvest using 1 part SSS buffer to 9 parts clarified media. The addition of the SSS buffer is performed to maintain the solubility of proteins in the clarified media. A 100 kDA mPES hollow fibre membrane is utilised to perform a 100-fold volumetric concentration of the product. The concentration is followed by four dia-filtrations which buffer exchange the product into TMN500T (20 mM Tris, 1 mM MgCl2, 500 mM NaCl, 0.1% Tween 20). A final concentration takes place after the diafiltration step to reach the target volumetric concentration factor.
Additional Comments—Take care not to allow air into the flow loop during the final concentration step as this can initiate frothing of the product.
Initial Iodixanol Concentration
An initial ultra-centrifugation concentration step is performed to reduce the volume that will be processed in the subsequent iodixanol gradient step. The reduction in volume is necessary as the volumetric throughput of the iodixanol gradient separation is limited.
The product from the preceding TFF step is aliquoted into 32 mL volumes and placed into centrifuge tubes. 1×TMNK buffer can be used to top up the last centrifuge tube in the likely event that it is less than 32 mL. A single layer of 3 mL of 57% iodixanol solution is underlaid into each product containing tubes. The centrifuge tubes are loaded into a centrifuge and spun at 65,000 rpm for 30 minutes utilising a temperature of 4° C. The centrifugation is repeated as necessary to process the entire product stream. The entire 57% iodixanol band is harvested alongside 1 mL of the 57% interface. The harvested product is then diluted in a 1×TMNK buffer.
Additional Comments
Iodixanol Gradient Purification
The centrifuged concentrated media is further purified using a discontinuous iodixanol gradient. This step serves to enrich the preparation for DNA-containing rAAV particles, while removing the bulk of rAAV particles that are devoid of DNA (empty particles) based on the differential buoyant density of these particles in the iodixanol gradient medium following ultracentrifugation. The discontinuous gradient is formed of 25, 40 and 57% iodixanol phases. After centrifugation the DNA enriched vector is harvested from just below the 40/57% interface. The bulk of the empty particles are contained in the 25/40% interface. The harvested pooled vector is diluted in 1×TMNK buffer to prevent aggregation of the AAV vector.
Additional Comments
Cation Exchange Chromatography
The iodixanol harvest fraction is purified over a cation exchange (CEX) chromatography column which serves to remove residual contaminants, including iodixanol.
The iodixanol pool is firstly diluted 7-fold using a dilution buffer (6:1 ratio—dilution buffer to iodixanol pool). This is then followed by a 2-fold dilution using WFI (1:1 ratio—WFI to diluted iodixanol pool). The dilution of the iodixanol pool is necessary to allow the vector to bind to the cation exchange column by reducing the conductivity and lowering the pH of the sample.
The 14-fold, fully diluted, iodixanol pool becomes the load for the cation exchange step which utilises an SP Sepharose™ HP resin. The binding of the vector takes place in a low conductivity and low pH citrate based buffer and the elution is achieved by the use of a high salt buffer. The vector containing elution peak is then diluted with an AMPD buffer (1:9 ratio—AMPD buffer to CEX eluate) before it is stored at 2-8° C. before subsequent processing. An overview of the CEX unit operation is illustrated in
Small Scale Tangential Flow Filtration and Excipient Addition
Final vector formulation is achieved using a 100 kDa, TFF mPES membrane. Prior to final formulation, in-process samples are analysed for vector recovery using a qPCR method to determine vector titre and yield of DNase Resistant Particles (DRP). This data is used to estimate the final volume required to achieve the final target titre. The product is diafiltered into the final formulation buffer (20 mM Tris pH 8.0, 1 mM MgCl2, 200 mM NaCl). The excipient poloxamer 188 is added manually to a final concentration of 0.001% (v/v).
Sterile Filtration and Vialling
After final formulation, the final titre is determined and then the product is terminally sterile filtered through a 0.22 μm filter to yield the Purified Bulk Drug Substance (PBDS). The PBDS is filled into sterile tubes, upon which the product becomes the Final Drug Product (FDP). The FDP is inspected before it is stored at <−60° C.
In-Process Hold Conditions
Preferred Chemicals for Solution Preparation
Compendial or multi-compendial chemicals are to be used wherever possible.
The aim of the project was to develop an industrial chromatographic downstream process (DSP) for rAAV8 RPGR late stage clinical and commercial program. The project included all developed steps—capture, intermediate polishing and separation of empty-full (E/F) AAV8 capsids using Macro-porous OH, SO3 and QA columns, and a tangent flow filtration (TFF) following client's protocol. Development was based on clarified harvest material where calcium phosphate was used as a transfecting agent.
Materials and Methods
Sample
Sample was formulated in clarified DMEM medium. Two different experimental runs were conducted on different dates, Experiment A and Experiment B.
FPLC Systems (Preparative Runs)
HPLC Systems (Analytical Runs)
Monolith Stationary Phases
Analytics runs (3 columns):
Buffers
Buffers were prepared in fresh purified water and filtered through 0.22 μm filters.
Chromotographic Methods
Preparative Runs:
Analytic Runs:
Total Protein Assay
Samples were tested for total protein concentration following two assays. Either BCA Pierce method or Bradford method was used depending on buffer composition. Manufacturer protocol was followed.
Total DNA Assay
For total DNA quantification in samples a Quant-IT™ PicoGreen® assay was used. Manufacturer protocol was followed.
SDS-PAGE
SDS-PAGE was carried out with a Mini-Protean II electrophoresis Cell (Bio-Rad) using 4-20% gradient gels under reducing conditions according to the manufacturer's instructions (Bio-Rad). The gels were run at 200 V for 35 min using a discontinuous Tris-glycine buffering system. Protein bands were visualized by Plus one Silver staining reagent (GE Healthcare). A 10-200 kDa molecular weight standard was used (Fermentas Life Sciences). Each time 20 ul of sample in appropriate dilution, was loaded to the well.
TEM
Samples were prepared for examination with TEM using negative staining method. Thawed samples were mixed gently and applied on freshly glow-discharged copper grids (400 mesh, formvar-carbon coated) for 5 minutes, washed and stained with 1 droplet of 1% (w/v) water solution of uranyl acetate.
The grids were observed with transmission electron microscope Philips CM 100 (FEI, The Netherlands), operating at 80 kV. At least 10 grid squares were examined thoroughly and several micrographs (camera ORIUS SC 200, Gatan, Inc.) were taken to evaluate the ratio between full and empty particles. Micrographs were taken coincidentally at different places on the grid.
ddPCR
Samples (and control) were DNAze treated and diluted in three points in duplicates (6 reactions for each sample). Reaction mix: ddPCR Supermix for Probes (no dUTP). Reaction volume: 20 uL, DNA volume 5 uL, Droplet volume 0.000739. Equipment used: Bio-Rad QX100™ Droplet Digital™ PCR System, Bio-Rad QX200™ AutoDG™ Droplet Digital™ PCR System, Fluidigm Biomark HD. Primers and probes used based on clients recommendation.
Capture Step on Hydrophobic Interaction Chromatography (HIC) Using Macro-Porous OH Columns HPLC Analytical Methods
Preparative Run
Clarified harvest material (8 L divided in 1 L bottles) was thawed overnight at room temperature. Next day it was pooled and diluted 1:1 (8 L harvest+8 L buffer) with dilution buffer using peristaltic pump at speed 400 mL/min. Loading to the column using system pump at 1 CV/min. Tech transfer run was the twenty-fifth (25) run for HIC conditions (HIC-25) for Experiment A.
HPLC Total Analytics
Total particle method was used on HPLC for determination of chromatographic recovery. Fractions were desalted using Amicon Ultra 0.5. Main elution was further diluted 10× prior injection.
Recovery of Preparative Run
Recoveries for capture step HIC-OH comparing to starting clarified harvest material are 102% and 68% for ddPCR and HPLC Total analytics, respectively. The discrepancy between two methods is mainly caused by high salt concentration in sample, moreover the mass balances are not 100% in both cases, so normalization of two would result in more accurate results with average 80-90% recovery of AAV in main fraction.
SDS-PAGE
All fractions were desalted first and then loaded to the gel either neat or diluted under reducing conditions.
Intermediate Polishing on Cation Exchange Chromatography (CEX) Using Macro-Porous SO3 Column
Preparative Run
Entire elution (E1) from HIC-OH was prepared to match binding conditions and loaded to CEX-SO3 column. Tech transfer run was a sixteenth (16) run for CEX conditions (SO3-16) for Experiment A.
Tech transfer run was a seventeenth (17) run for CEX conditions (SO3-17) for Experiment B.
HPLC Total Analytics
Total particle method was used on HPLC for determination of chromatographic recovery. Fractions were 100-fold (E1) or 2.5-fold (other fractions) diluted prior injection.
SDS-PAGE
All fractions were loaded to the gel either neat or diluted under reducing conditions.
Empty and Full AAV Capsids Separation on Anion Exchange Chromatography (AEX) Using Macro-Porous QA Column
Preparative Run
Entire elution (E1) from SO3-16 was diluted to match binding conditions and loaded to AEX-QA column for Experiment A. Tech transfer run was a fourteenth (14) run for AEX conditions (QA-14).
Entire elution (E1) from SO3-17 was diluted to match binding conditions and loaded to AEX-QA column for Experiment B. Tech transfer run was a fifteenth (15) run for AEX conditions (QA-15).
HPLC Empty-Full Analysis
Empty-full method was used on HPLC for determination of chromatographic recovery and purity (ratio of E/F capsids). Fractions were diluted prior injection.
Tangent Flow Filtration
Concentration and buffer exchange was achieved by implementation of TFF on QA-14 E3 sample for Experiment A. End volume of sample was 25 mL (10 mL sample+15 mL system hold-up volume).
Concentration and buffer exchange was achieved by implementation of TFF on QA-15 E3 sample for Experiment B. End volume of sample was 35 mL (10 mL sample+25 mL system hold-up volume).
Recovery of Preparative Run
Recoveries for full capsid enrichment step (empty and full separation) step AEX-QA comparing to starting SO3-16 E1 material are 73% and 67% for ddPCR and HPLC Total analytics, respectively, for Experiment A. The discrepancy between two methods is minor. In case of HPLC analytics, and ddPCR mass balance is not 100%. For HPLC E/F analytics only A260 and A280 areas are accounted since fluorescence gives lower response of full AAV capsid recovery due to DNA (insert) quenching FLD signal. Approximately 60-70% recovery is obtained after TFF, meaning the entire downstream yield is 43% or 73% if comparing QA eluate to clarified harvest material.
Recoveries for full capsid enrichment step (empty and full separation) step AEX-QA comparing to starting SO3-17 E1 material are 62% and 64% for ddPCR and HPLC Total analytics, respectively, for Experiment B. The discrepancy between two methods is minor. In case of HPLC analytics, and ddPCR mass balance is not 100%. For HPLC E/F analytics only A260 and A280 areas are accounted since fluorescence gives lower response of full AAV capsid recovery due to DNA (insert) quenching FLD signal. Approximately 70-80% recovery is obtained after TFF, meaning the entire downstream yield is 55% or 82% if comparing QA eluate to clarified harvest material.
Purity (Ration Between Empty and Full AAV Capsids)
For Experiment A, purity was additionally tested by TEM, for E2 (empty capsids) and E3 (full capsids) however for full capsids a different stage—QA-14 E3 sample after TFF was evaluated. Sample TFF AAV8-RPGR FULLS contained different kind of impurities in contrast to sample QA-14 E2, which contained only small aggregates of damaged particles. Ratio between full and empty/damaged viruses were similar in both samples, 62% in sample TFF AAV8-RPGR FULLS and 65% in sample QA-14 E2. Relatively high percentages represented unclassified particles. Viruses from this group were not electron lucent on the whole surface, but displayed just electron dense spot on the surface. Such viruses could be not completely full, not correctly formed or damaged.
Filamentous impurities were found only in sample after TFF, which was later confirmed that derived from TFF that was not properly sanitized. The large portion of full capsids found in empty peak is explained by fraction collection approach, where E2 fraction is prolonged until absorbance crossing where full particles are already eluting and therefore contaminating the empty fraction E2.
For Experiment B, purity was additionally tested by TEM, for QA-15 E3 (full capsids) and sample after TFF (TT BB RPGR-FULLS). Samples TT BB AAV8-RPGR FULLS and QA-15 E3 contained only small aggregates of damaged particles. In both sample some aggregates included also structures usually called discs and most probably represented proteins. In both samples full particles prevailed, but at the time of grid examination we noticed difference in sample QA-15 E3, between non-diluted and diluted samples. We counted and calculated the particles separately for diluted and non-diluted samples. We propose that only calculations from non-diluted samples are taken into account. Sample TT BB AAV8-RPGR FULLS contained 76% of full particles and sample QA-15 E3 contained 84% of full particles.
SDS-PAGE
All fractions were loaded to the gel either neat or diluted under reducing conditions.
HPLC Analytics—Partial Separation Method
Conclusions
A seamless downstream purification run was performed using clarified harvest as starting material. Capture and concentration of AAV was achieved by HIC-OH step, where proteins were found in flow through and AAV was bound to the column. Protein impurities were removed in either W2 or W3 fractions.
Large portion of protein impurities were still present in main elution fraction (E1) after HIC step. The majority of protein impurities were removed by the intermediate polishing step using CEX-SO3 column, where additional concentration of AAV was achieved by implementation of a 10-fold lower column scale. The percentage of full capsid at this stage was approximately 55% for Experiment A and 34% for Experiment B, so full particle enrichment using AEX-QA was performed.
After separating full capsid from empty capsids a buffer exchange in to formulation buffer was performed using TFF. The entire downstream process yield from clarified harvest to completion of TFF was 43% and 73% from clarified harvest to completion of QA full particle enrichment step for Experiment A. The entire downstream process yield from clarified harvest to completion of TFF was 55% and 82% from clarified harvest to completion of QA full particle enrichment step for Experiment B.
The disclosure provides an industrial chromatographic downstream process (DSP) for Stargardt (ABCA4) late stage clinical and commercial program. The project included all developed steps—capture, intermediate polishing and separation of empty-full (E/F) AAV8 capsids using Macro-porous OH, SO3 and QA columns, and a tangent flow filtration (TFF).
A compatability study was performed for ABACA4 vector wherein a proxy vector was used. The proxy vector has the same capsid (AAV8/Y733F) as the ABCA4 vector. The capsid is the determining factor for the behavior of the vector across the HIC and SO3 steps.
The packaged genome was a construct comprising a Bestrophin-1 gene (which is smaller than the ABCA4 gene and does not require a dual vector, allowing for proof of concept studies on the vector itself). The packaged genome has an effect on the behavior over the QA step. This step employs a linear gradient, therefore it was anticipated that there would be no changes to the operating conditions for the QA step when the ABCA4 transgene is used.
Optimal representation of purity (E/F) ratio is given by FLD and MALS detectors. Enrichment from approximately 55% to 94% of full AAV particles is achieved by the QA step.
The downstream process for the AAV-ABCA4 vector is centred around the use of three monolith chromatography columns of different chemistries, which forms the basis an efficient and robust solution for AAV vector purification. Monoliths are especially suited to the purification of macromolecules, such as viral vectors, due to their large flow channels which allow ligand-target interactions to take place in a diffusion independent manner.
The first unit operation in the purification train is a hydrophobic interaction chromatography (HIC) capture step which is operated in a bind and elute mode. To facilitate binding of the vector to the column it is necessary to increase the concentration of the salting out agent by the dilution of the feed stream with a high molarity stock solution. Product elution is achieved using a step change to a lower molarity salt buffer.
Post the HIC step, the feed stream requires further conditioning to allow the vector to bind the negatively charged strong cation exchange (CEX SO3) column. The conditioning buffer protonates the AAV vector and reduces the counter ion concentration, thereby allowing the vector to bind to the negatively charged ligands. A filtration step is performed after the feed conditioning to remove any particulates and to preserve the effectiveness of the SO3 chromatography column. The SO3 step is also operated in a bind and elute mode with the elution taking place under a step increase in the salt concentration.
The enrichment, for full AAV particles, is achieved by exploiting the minor charge variation that exists between full and empty particles. A linear salt gradient elution utilising a strong anion exchange chromatography (AEX QA) column, allows an adequate resolution between the full and empty species. As with all the other unit operations, a conditioning of the feed is required to allow the vector to bind to the chromatography support.
Final vector concentration and dia-filtration is achieved using a 100 kDa, TFF mPES membrane. The product is diafiltered into the final formulation buffer (20 mM Tris pH 8.0, 1 mM MgCl2, 200 mM NaCl, 0.001% poloxamer 188). Prior to final formulation, in-process samples are analysed for vector recovery using a qPCR method to determine vector titre and yield of DNase Resistant Particles (DRP). This data is used to estimate the final volume required to achieve the final target titre. The excipient poloxamer 188 is added manually to process stream at a final concentration of 0.001% (v/v). After final formulation, the product is terminally sterile filtered through a 0.22 μm filter to yield the Purified Bulk Drug Substance (PBDS). Filling the PBDS completes the process and yields the Final Drug Product (FDP). Release testing takes place on both the PBDS and FDP.
Downstream Manufacturing Process Description
Hydrophobic Interation Chromatography Capture Step
The capture step of the clarified harvest material is performed using a hydrophobic interaction chromatography column. To ensure that the vector binds to the hydrophobic support, an increase in the molarity is required, and is achieved by the addition of a 2.6 M potassium phosphate, 2% sorbitol, pH 7 spike buffer. A 1:1 volumetric addition is performed by adding the dilution buffer to the clarified harvest, whilst the resulting solution is adequately agitated.
An OH monolith column (2 μm pore) is used as the chromatography unit for this unit step. A pulse test is to be performed on the column before use to ensure that the integrity of the column has not been compromised.
After sanitization and equilibration of the column, the product is loaded onto the monolith. Two washes are performed in order of decreasing molarity before product elution is achieved using an isocratic change to a lower molarity salt buffer (0.73 M potassium phosphate, 1% sorbitol, pH 7).
The eluate can be stored at 2-8° C. overnight, prior to forward processing (limit of storage duration to be determined).
Cation Exchange Chromatography
A cation exchange based intermediate polishing chromatography step further reduces process impurities. The eluate from the HIC step needs to be conditioned to allow the vector to bind to the negatively charged ligands. The first part of the conditioning entails lowering the pH of the process stream which is required to be below the iso-electric point (pI), thereby giving the vector an overall positive surface charge. The dilution step also reduces the conductivity of the load, which reduces competitive binding from counter ions in solution. After adjustment of the process stream, a filtration step (0.8/0.45 μm combination filter) is performed to remove any particulates and preserve the effectiveness of the SO3 chromatography column. The neutralisation buffer is added to the added to restore the pH to near physiological levels. The eluate can be stored at 2-8° C. overnight, prior to forward processing (limit of storage duration to be determined).
An SO3 monolith column (2 μm pore) is used as the chromatography unit for this unit step. A pulse test is to be performed on the column before use to ensure that the integrity of the column has not been compromised.
QA Chromatography Step
The enrichment, for full AAV particles, is achieved by exploiting the minor charge variation that exists between full and empty particles. A linear gradient elution utilising an anion exchange chromatography column, allows an adequate resolution between the full and empty species, which permits peak cutting methods to be employed. Due to the minimal charge variation that exists, a step elution would not form the basis of a robust separation operation. A bioprocess system that can accurately and reproducibly form gradients, along with the ability to monitor UV absorbance signals is required to allow elution profile to be effectively formed and monitored. The neutralisation buffer is added to the added to restore the pH to near physiological levels. The eluate can be stored at 2-8° C. overnight, prior to forward processing (limit of storage duration to be determined).
A QA monolith column (2 μm pore) is used as the chromatography unit for this unit step. A pulse test is to be performed on the column before use to ensure that the integrity of the column has not been compromised.
The elution collection criteria has been developed using the A260 and A280 wavelengths. The start of the collection is initiated at the crossing point of the A260 and A280 traces, which corresponds to the E3 fraction. Note: the A260 and A280 wavelengths need to be represented on the same scale for the criteria to be meaningful. The end of the peak collection takes place 3.5 CVs after the start of the collection. A collection criteria that achieves the same goal but uses a different method is acceptable; which will be the case where only one wavelength can be monitored.
Tangential Flow Filtration and Excipient Addition
Final vector formulation is achieved using a 100 kDa, TFF mPES membrane. Prior to final formulation, in-process samples are analysed for vector recovery using a qPCR method to determine vector titre and yield of DNase Resistant Particles (DRP). This data is used to estimate the final volume required to achieve the final target titre. The product is diafiltered into the final formulation buffer (20 mM Tris pH 8.0, 1 mM MgCl2, 200 mM NaCl, 0.001% poloxamer 188).
In-Process Hold Conditions
Proxy Vector
A proxy vector was used for the compatability study. The proxy vector has the same capsid (AAV8/Y773F) as the ABCA4 vector. The capsid is the determining factor for the behavior of the vector across the HIC and SO3 steps. The packaged genome has an effect on the behavior over the QA step. The exemplary packaged genome used was wild type Bestrophin-1 due to its small size, however, this step employs a linear gradient and it is therefore anticipated that there would be no changes to the operating conditions for the QA step when using, for example, an ABCA4 transgene or other transgene of similar size.
Optimization of the HIC Capture Step
Optimization of the chromatography process for the ABCA4 vector has been performed. Changes were made to the wash buffer for the HIC process and the elution buffer for the CEX process.
Optimization of the CEX Step
The CEX step was optimized by the use of a gradient elution run.
The aim of this project was to identify transfection conditions that produce high quality AAV product. HEK293 cells were transfected with various ratios of plasmid DNA, (i.e., a plasmid encoding an AAV Construct comprising an RPGRORF15 sequence (ITR), a plasmid encoding AAV8 rep and cap genes (RepCap), and a pHelper plasmid) using a polyethylenimine (PEI) transfection reagent, PEIpro® (Polyplus Transfection). The plasmid DNA/PEIpro® mixture was added to the cells, which were incubated at 37° C., 5% CO2 for 96 hours before being harvested, and the resulting AAV viral particles were evaluated. Four transfection conditions were evaluated, and the number of vector particles (Capsid ELISA) and the number of particles that contain the genome insert (Genomic titre) were quantified for each condition.
Orthogonal Full to Empty Quantification
It is believed that the full particle analysis in
Effect of Transfection Agent (PEI vs. CaPO4) on AAV Full to Empty Ratios
A PEI vs. CaPO4 comparison transfection study was conducted to determine which reagent resulted in superior product. Material generated from PEI transfection or CaPO4 was used to quantify full to empty vector ratios by HPLC. The material had not been through a process setep that would enrich for full particles. Previous variable conditions were kept constant between the two transfection conditions, including total DNA, PEI/DNA ratio and ratio of transfection plasmids.
The aim of the project was to develop an industrial chromatographic downstream process (DSP) for rAAV/Y733F ABCA4 late stage clinical and commercial program. The project included all developed steps—capture, intermediate polishing and separation of empty-full (E/F) AAV8 capsids using Macro-porous OH, SO3 and QA columns, and buffer exchange achieved by dialysis. Development was based on crude harvest material where PEI was used as a transfecting agent.
Materials and Methods
Sample
Sample was Berzonase™ treated and formulated in DMEM medium. The sample was an ABCA4 proxy vector having the same capsid (AAV8/Y733F) as the ABCA4 vector. The volume shipped was 4 L, the titer was 2.24E+10 vp/mL, and the total vector was 8.96+13 vector genomes (vg).
FPLC Systems (Preparative Runs)
HPLC Systems (Analytical Runs)
Monolith Stationary Phases
Analytics runs (2 columns):
Buffers
Buffers were prepared in fresh purified water and filtered through 0.22 μm filters.
Chromotographic Methods
Preparative Runs:
Analytic Runs:
SDS-PAGE
SDS-PAGE was carried out with a Mini-Protean II electrophoresis Cell (Bio-Rad) using 4-20% gradient gels under reducing conditions according to the manufacturer's instructions (Bio-Rad). The gels were run at 200 V for 35 min using a discontinuous Tris-glycine buffering system. Protein bands were visualized by Plus one Silver staining reagent (GE Healthcare). A 10-200 kDa molecular weight standard was used (PageRuler™ Unstained, thermos Fisher Scientific). Each time 20 ul of sample in appropriate dilution, was loaded to the well.
TEM
Samples were prepared for examination with TEM using negative staining method. Thawed samples were mixed gently and applied on freshly glow-discharged copper grids (400 mesh, formvar-carbon coated) for 5 minutes, washed and stained with 1 droplet of 1% (w/v) water solution of uranyl acetate.
The grids were observed with transmission electron microscope Philips CM 100 (FEI, The Netherlands), operating at 80 kV. At least 10 grid squares were examined thoroughly and several micrographs (camera ORIUS SC 200, Gatan, Inc.) were taken to evaluate the ratio between full and empty particles. Micrographs were taken coincidentally at different places on the grid.
ddPCR
Samples (and control) were DNAze treated and diluted in three points in duplicates (6 reactions for each sample). Reaction mix: ddPCR Supermix for Probes (no dUTP). Reaction volume: 20 uL, DNA volume 5 uL, Droplet volume 0.000739. Equipment used: Bio-Rad QX100™ Droplet Digital™ PCR System, Bio-Rad QX200™ AutoDG™ Droplet Digital™ PCR System, Fluidigm Biomark HD. Primers and probes used were determined based on the target detected.
Results and Discussion
Capture Step on Hydrophobic Interaction Chromatography (HIC) Using Macro-Porous OH Columns HPLC Analytical Methods
Preparative Run
Clarified harvest material (1.2 L divided in two bottles each containing 0.6 L) was thawed at room temperature, pooled and diluted 1:1 (1.2 L harvest+1.2 L buffer) with dilution buffer. Loading to the column using system pump at 5 CV/min. The run was the eighth (8) run for HIC conditions (HIC-8).
HPLC Total Analytics
Total particle method was used on HPLC for determination of chromatographic recovery. Fractions were desalted using Amicon Ultra 0.5. Main elution was further diluted 10× prior injection.
Recovery of Preparative Run
Recoveries for capture step HIC-OH comparing to starting clarified harvest material were 76% and 71% for ddPCR and HPLC Total analytics (MALS), respectively. The discrepancy between other methods in other detectors (A260, A280, FLD) was mainly caused by high salt concentration in sample, moreover the mass balances are not 100% in both cases, so normalization of two (ddPCR and HPLC Total analytics (MALS) would result in more accurate results with average 72%±2% recovery of AAV in main fraction.
Intermediate Polishing on Cation Exchange Chromatography (CEX) Using SO3 Column
Entire elution (E1) from HIC-OH was prepared to match binding conditions and loaded to CEX-SO3 column (SO3-7).
HPLC Total Analysis
Total particle method was used on HPLC for determination of chromatographic recovery. Fraction E1 was 5-fold diluted prior to injection.
SDS-PAGE
All fractions were loaded to the gel either neat or diluted under reducing conditions.
Empty and Full AAV Capsids Separation on Anion Exchange Chromatography (AEX) Using CIM QA Column
Preparative Run
Entire elution (E1) from SO3-7 was diluted to match binding conditions and loaded to AEX-QA column. The run was the third (3) run for AEX conditions (QA-3).
HPLC Total Analytics
Empty-full method was used on HPLC for determination of chromatographic recovery and purity (ratio of E.F capsids). Fractions were diluted prior injection.
Dialysis
Buffer exchange was achieved by implementation of dialysis on QA-3 E3 sample. Details of the dialysis method are provided in
Recovery of Preparative Run
Recoveries for the preparative run are summarized in
Based only on initial volume and end volume and their genomic value a DSP yield of 28% (after dialysis) or 45% (QA main fraction) was obtained, however it must be taken into account that sampling of main fractions after each purification step had a significant impact on overall recovery on smaller scale where end volumes are low. More accurate representation of DSP yield was achieved by accounting for losses after each purification step. By accounting normalized values (
Purity
Purity was additionally tested by TEM, for ratio after SO3 intermediate step, QA-3 E3 (full capsids) and final sample after dialysis (FULL AAV). All grids expressed appropriate quality for observation and all three samples, SO3-7 E1, FULL AAV, and QA-3 E3 were clear, without impurities and without aggregation of particles. Sample SO3-7 E1 contained only 50% of full particles, while the percentage of full particles in other two samples was higher (79% in sample FULL AAV and 88% in sample QA-3 E3;
SDS-PAGE
All fractions were loaded to the gel either neat or diluted under reducing conditions.
HPLC Analysis—Fingerprint Method
A downstream purification run was performed using clarified harvest as a starting material.
Capture and concentration of AAV was achieved by HIC-OH step, where proteins were found in flow through and AAV was bound to the column. Protein impurities were removed in either W2 or W3 fractions. The majority of protein impurities remaining in main elution fraction (E1) after HIC step were removed by the intermediate polishing step using CEX-SO3 column, where additional concentration of AAV was achieved by implementation of an 8-fold lower column scale. The percentage of full capsid at this state was approximately 50-65%, so full particle enrichment using AEX-QA was performed. After separating full capsids from empty capsids, a buffer exchange into formulation buffer was performed using dialysis. The entire downstream process yield from clarified harvest to completion of dialysis was 42% (after chromatography steps—58%) and purity of approximately 90% full AAV capsids was reached. The process was successfully performed at manufacturing scale.
Every document cited herein, including any cross referenced or related patent or application is hereby incorporated herein by reference in its entirety unless expressly excluded or otherwise limited. The citation of any document is not an admission that it is prior art with respect to any invention disclosed or claimed herein or that it alone, or in any combination with any other reference or references, teaches, suggests or discloses any such invention. Further, to the extent that any meaning or definition of a term in this document conflicts with any meaning or definition of the same term in a document incorporated by reference, the meaning or definition assigned to that term in this document shall govern.
While particular embodiments of the disclosure have been illustrated and described, various other changes and modifications can be made without departing from the spirit and scope of the disclosure. The scope of the appended claims includes all such changes and modifications that are within the scope of this disclosure.
This application claims priority to U.S. Provisional Application No. 62/734,505, filed on Sep. 21, 2018; which is incorporated by reference herein in its entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2019/052501 | 9/23/2019 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62734505 | Sep 2018 | US |
