Patent Application
20240044869
The contents of the text file submitted electronically herewith are incorporated herein by reference in their entirety: A computer readable format copy of the Sequence Listing (filename: PRVL_017_01WO_SeqList_ST25.txt, date recorded: Oct. 15, 2021, file size ˜7,474 bytes).
The disclosure relates generally to the field of gene therapy. More specifically, the disclosure provides a cell-based assay for analyzing potency of compositions comprising a recombinant viral vector expressing a transgene.
Recombinant viral vectors encoding glucocerebrosidase (GCase; encoded by the GBA1 gene) are useful for treating disorders such as Parkinson's disease and Gaucher disease. There is a need for an assay to measure relative potency of recombinant viral compositions delivering GCase that are intended to be used for gene therapy.
Provided herein is a method for measuring the relative potency of a test sample comprising a first recombinant virus comprising a transgene encoding glucocerebrosidase (GCase), the method comprising: a) transducing a first plurality of cells with the test sample; b) incubating the transduced first plurality of cells under conditions sufficient to express GCase; c) harvesting a first cell lysate from the transduced first plurality of cells; d) combining the first cell lysate with resorufin-beta-D-glucopyranoside; e) imaging the first cell lysate to obtain a first fluorescence reading; f) transducing a second plurality of cells with a reference standard comprising a second recombinant virus comprising a transgene encoding GCase; g) incubating the transduced second plurality of cells under conditions sufficient to express GCase; h) harvesting a second cell lysate from the transduced second plurality of cells; i) combining the second cell lysate with resorufin-beta-D-glucopyranoside; j) imaging the second cell lysate to obtain a second fluorescence reading; and k) comparing the first fluorescence reading with the second fluorescence reading using parallel line analysis to calculate the relative potency of the test sample.
In some embodiments of the methods disclosed herein, the first recombinant virus and the second recombinant virus comprise identical transgenes encoding GCase.
In some embodiments of the methods disclosed herein, the first recombinant virus and/or the second recombinant virus is a recombinant adeno-associated virus (rAAV). In some embodiments, the rAAV comprises an AAV9 capsid protein. In some embodiments, the rAAV comprises an AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10 or AAV11 capsid protein, or a variant of any of these capsid proteins.
In some embodiments of the methods disclosed herein, the GCase comprises SEQ ID NO:1. In some embodiments, the transgene encoding GCase comprises a codon-optimized nucleotide sequence. In some embodiments, the codon-optimized nucleotide sequence comprises SEQ ID NO: 2.
In some embodiments of the methods disclosed herein, the first plurality of cells and/or the second plurality of cells are HEK-293T or HEK-293 cells.
In some embodiments of the methods disclosed herein, about 1.25 mM resorufin-beta-D-glucopyranoside is combined with the first cell lysate and/or the second cell lysate.
In some embodiments of the methods disclosed herein, the first plurality of cells and the second plurality of cells are seeded in a multi-well plate. In some embodiments, the first plurality of cells and/or the second plurality of cells are seeded at about 20,000 cells per well.
In some embodiments of the methods disclosed herein, the test sample and/or the reference standard are serially diluted before transduction.
In some embodiments of the methods disclosed herein, the first plurality of cells and the second plurality of cells are incubated from about 68 hours to about 81 hours before cell lysate harvesting. In some embodiments, the first plurality of cells and the second plurality of cells are incubated from about 66 hours to about 78 hours after transduction and before cell lysate harvesting.
In some embodiments of the methods disclosed herein, the first plurality of cells is transduced by the test sample at at least two different multiplicities of infection (MOI) of the first recombinant virus. In some embodiments, the second plurality of cells is transduced by the reference standard at at least two different multiplicities of infection (MOI) of the second recombinant virus.
In some embodiments of the methods disclosed herein, the first fluorescence reading and/or the second fluorescence reading reflect a measurement of GCase activity. In some embodiments, the measurement of GCase activity is in relative fluorescence units (RFU)/hour.
In some embodiments of the methods disclosed herein, the comparing step (k) comprises performing a log transformation of the recombinant virus amount and RFU/hour and plotting a standard curve of the log of recombinant virus amount versus the log of RFU/hour for each of the test sample and the reference standard. In some embodiments, the comparing step (k) comprises calculating a linear regression of the log of recombinant virus amount versus the log of RFU/hour for each of the test sample and the reference standard, thereby deriving a test sample slope and a reference standard slope. In some embodiments, the comparing step (k) comprises calculating a linear regression with a common slope using the linear regressions obtained for each of the test sample and the reference standard. In some embodiments, the relative potency is calculated using the formula: Relative potency (%)=10{circumflex over ( )}((b−breference)/A)×100. In some embodiments, the ratio of the slope of the test sample to the common slope is from about 0.60 to about 1.40. In some embodiments, the ratio of the slope of the reference standard to the common slope is from about 0.60 to about 1.40.
In some embodiments, a method disclosed herein further comprises calculating an R2 value for the linear regression of the test sample and the reference standard. In some embodiments, the R2 value for the test sample and the reference standard is greater than or equal to 0.9.
The disclosure relates to cell-based transduction assays to measure relative potency of recombinant viral compositions delivering a transgene encoding glucocerebrosidase (e.g., human glucocerebrosidase). Glucocerebrosidase (also referred to as beta-glucocerebrosidase, lysosomal acid β-glucocerebrosidase, GCase and GBA) is encoded by the GBA1 gene. Subjects with mutations in only one allele of GBA1 are at highly increased risk of Parkinson's disease. Subjects with mutations in both copies of GBA1 suffer from Gaucher disease. Viral compositions delivering a transgene encoding GCase are useful for gene therapy for Parkinson's disease (e.g., Parkinson's disease with a GBA1 mutation) and Gaucher disease.
In some embodiments, a recombinant viral vector encoding GCase is a recombinant adeno-associated virus (rAAV) vector.
The methods disclosed herein utilize the fluorogenic substrate resorufin-β-D-glucopyranoside which, in the presence of GCase, is catalyzed to form the fluorescent product resorufin. Resorufin production is monitored directly as the reaction proceeds to calculate the rate of product formation. In the presence of an excess of resorufin-β-D-glucopyranoside substrate and under the assayed conditions the rate of product formation is linearly proportional to the amount of GCase protein.
The term “recombinant virus” refers to a virus that has been genetically altered, e.g., by the addition or insertion of a heterologous nucleic acid construct into the viral particle.
The term “heterologous” is used herein interchangeably with the term “exogenous”, and refers to a substance coming from some source other than its native source. For example, the term “exogenous protein” or “exogenous gene” refers to a protein or gene from a non-AAV source that has been artificially introduced into an AAV genome or AAV particle.
The term “recombinant adeno-associated virus” or “rAAV” refers to a AAV particle or AAV virion comprising a rAAV vector encapsidated by one or more AAV capsid proteins.
The term “rAAV vector” refers to nucleic acids, either single-stranded or double-stranded, having an AAV 5′ inverted terminal repeat (ITR) sequence and an AAV 3′ ITR flanking a protein-coding sequence operably linked to transcription regulatory elements that are heterologous to the AAV viral genome, for example, one or more promoters and/or enhancers and, optionally, a polyadenylation sequence and/or one or more introns inserted between exons of the protein-coding sequence.
The term “IU” refers to infectious units.
The term “TCID50” refers to the 50% cell culture infectious dose.
The term “USP” refers to the United States Pharmacopeia.
The term “test sample” refers to a sample comprising a rAAV vector comprising a sequence encoding an exogenous protein of interest (e.g., GCase) whose potency is unknown and will be determined using the methods described herein.
The term “reference standard” refers to a composition comprising a rAAV vector encoding an exogenous protein of interest (e.g., GCase) whose potency is known.
In some aspects, provided herein is a method for measuring the relative potency of a test sample comprising a first recombinant virus comprising a transgene encoding glucocerebrosidase (GCase), the method comprising: a) transducing a first plurality of cells with the test sample; b) incubating the transduced first plurality of cells under conditions sufficient to express GCase; c) harvesting a first cell lysate from the transduced first plurality of cells; d) combining the first cell lysate with resorufin-beta-D-glucopyranoside; e) imaging the first cell lysate to obtain a first fluorescence reading; f) transducing a second plurality of cells with a reference standard comprising a second recombinant virus comprising a transgene encoding GCase: g) incubating the transduced second plurality of cells under conditions sufficient to express GCase; h) harvesting a second cell lysate from the transduced second plurality of cells; i) combining the second cell lysate with resorufin-beta-D-glucopyranoside; j) imaging the second cell lysate to obtain a second fluorescence reading; and k) comparing the first fluorescence reading with the second fluorescence reading using parallel line analysis to calculate the relative potency of the test sample.
In some embodiments, the first recombinant virus and the second recombinant virus are identical. In some embodiments, the first recombinant virus and the second recombinant virus are not identical. In some embodiments, the first recombinant virus and the second recombinant virus comprise identical transgenes encoding GCase but are from different manufacturing lots or production lots. In some embodiments, the GCase comprises the amino acid sequence of SEQ ID NO: 1.
In some embodiments, the first plurality of cells and/or the second plurality of cells are HEK-293T or HEK-293 cells.
Methods disclosed herein may be performed in multi-well plates. In some embodiments, a method disclosed herein is performed in a 96-well plate. In some embodiments, the first plurality of cells and the second plurality of cells are seeded in a multi-well plate. In some embodiments, the first plurality of cells and/or the second plurality of cells are seeded at about 20,000 cells per well before transduction with the test sample and the reference standard, respectively. In some embodiments, the cells are allowed to attach overnight at 37° C. and 5% CO2.
In some embodiments, the transduction takes place about 24 hours after cells are seeded.
In some embodiments, the test sample and/or the reference standard are serially diluted before transduction. In some embodiments, the test sample is diluted to 50%, 100%, and 200% of the reference standard. In some embodiments, the serial dilutions produce the following total vector genome (vg) amounts per well: 5.00E+10 vg/well, 3.33E+10 vg/well, 2.22E+10 vg/well, 1.48E+10 vg/well, 9.88E+9 vg/well, and 6.58E+9 vg/well.
In some embodiments, a standard curve of purified recombinant GCase (rGBA, 0 to 333 ng/ml, R&D cat #7410-GHB-020, >95% purity) is run in parallel to the test sample.
In some embodiments, the first plurality of cells is transduced by the test sample at at least two different multiplicities of infection (MOI) of the first recombinant virus. In some embodiments, the second plurality of cells is transduced by the reference standard at at least two different MOIs of the second recombinant virus.
In some embodiments, the first plurality of cells and the second plurality of cells are incubated from about 68 hours to about 81 hours after transduction and before cell lysate harvesting. In some embodiments, the first plurality of cells and the second plurality of cells are incubated from about 2 to about 2.5 hours before a recovery medium (e.g., 10% FBS/DMEM/1 μM Hoechst 33342) is added to the cells. In some embodiments, the first plurality of cells and the second plurality of cells are incubated about 72 hours±6 hours (e.g., from about 66 hours to about 78 hours) after transduction and before cell lysate harvesting. In some embodiments, the incubation takes place at 37° C. and 5% CO2.
In some embodiments, about 1.25 mM resorufin-beta-D-glucopyranoside is combined with the first cell lysate in the combining step (d) and/or the second cell lysate in the combining step (i).
In some embodiments, the imaging step (e) and/or (j) is performed with a plate reader.
In some embodiments, the first fluorescence reading and/or the second fluorescence reading reflect a measurement of GCase activity. In some embodiments, the measurement of GCase activity is in relative fluorescence units (RFU)/hour.
In some embodiments, the comparing step (k) comprises performing a log transformation of the recombinant virus amount and RFU/hour and plotting a standard curve of the log of recombinant virus amount versus the log of RFU/hour for each of the test sample and the reference standard. In some embodiments, the comparing step (k) comprises calculating a linear regression of the log of recombinant virus amount versus the log of RFU/hour for each of the test sample and the reference standard, thereby deriving a test sample slope and a reference standard slope. In some embodiments, the comparing step (k) comprises calculating a linear regression with a common slope using the linear regressions obtained for each of the test sample and the reference standard. In some embodiments, the relative potency of the test sample is calculated using the formula: Relative potency (%)=10{circumflex over ( )}((b−breference)/A)×100. In some embodiments, the ratio of the slope of the test sample to the common slope is from about 0.60 to about 1.40. In some embodiments, the ratio of the slope of the reference standard to the common slope is from about 0.60 to about 1.40.
In some embodiments, the method for measuring the relative potency of a test sample further comprises calculating an R2 value for the linear regression of the test sample and the reference standard. In some embodiments, the R2 value for the test sample and the reference standard is greater than or equal to 0.9. In some embodiments, the R2 value for the test sample and the reference standard is greater than or equal to 0.96.
In some embodiments, the relative potency of the viral vector is at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, 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%, at least 99%, at least 99.5%, at least 99.9%, at least 100%, at least 110%, at least 120%, at least 130% or at least 140% relative to a reference standard. In some embodiments, the relative potency of the viral vector is at least 90% relative to a reference standard.
The infectious titer (also referred to as functional titer) of rAAV vectors is the concentration of viral particles that can infect cells. In some embodiments, cell transduction assays are used for determining infectious titer. In some embodiments, the infectious titer of the viral vector is determined using the method provided in Example 1. In some embodiments, the infectious titer of a composition disclosed herein is from about 8.0E+9 μU/mL to about 1.2E+10 IU/mL. In some embodiments, the infectious titer of a composition disclosed herein is about 8.0E+9 IU/mL, about 8.15E+9 IU/mL, about 8.5E+9 IU/mL, about 9.0E+9 μU/mL, about 9.5E+9 IU/mL, about 9.99E+9 IU/mL, about 1E+10 IU/mL, about 1.12E+10 IU/mL or about 1.2E+10 IU/mL. In some embodiments, the TCID50 of a composition disclosed herein is from about 4,500 vg/IU to about 10,000 vg/IU. In some embodiments, the TCID50 of a composition disclosed herein is about 4,500 vg/IU, about 5,000 vg/IU, about 5,500 vg/IU, about 6,000 vg/IU, about 6,290 vg/IU, about 6,500 vg/IU, about 7,000 vg/IU, about 7,500 vg/IU, about 8,000 vg/IU, about 8,500 vg/IU, about 9,000 vg/IU, about 9,500 vg/IU, about 9,980 vg/IU or about 10,000 vg/IU.
Examples of suitable rAAV vectors that can be used in the methods disclosed herein are disclosed in WO2019/070891, WO2019/070893, WO2019/070894, and WO2019/084068, the disclosure of each of which is incorporated by reference herein in its entirety.
In some embodiments of the methods disclosed herein, a rAAV vector further comprises one or more of the following: a chicken beta actin (CBA) promoter; a cytomegalovirus (CMV) enhancer; a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE); a Bovine Growth Hormone polyA signal tail; an artificial intron; an artificial exon; and one or more of the following transcriptional regulatory activation sites in a promoter region: TATA, RBS, and YY1 (Francois et al., (2005) J. Virol. 79(17):11082-11094). The TATA, RBS and YY1 transcriptional regulatory activation sites may be located at the 5′ end of the promoter region.
In some embodiments of the methods disclosed herein, a rAAV vector comprises a first AAV inverted terminal repeat (ITR) and a second ITR flanking the polynucleotide encoding a gene product of interest and the related regulatory sequences. In some embodiments, each ITR is a wild-type AAV2 ITR (SEQ ID NO: 3). In some embodiments, each ITR is derived from a wild-type AAV2 ITR.
In some embodiments of the methods disclosed herein, a rAAV vector comprises, in sequential order, a first AAV inverted terminal repeat (ITR), a cytomegalovirus (CMV) enhancer, a chicken beta actin (CBA) promoter, the polynucleotide encoding a human GCase protein, a Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE), a Bovine Growth Hormone polyA signal tail and a second AAV ITR. In some embodiments, the polynucleotide encoding a human GCase protein is codon optimized (e.g., codon optimized for expression in human cells). In some embodiments, the polynucleotide encoding a human GCase protein comprises SEQ ID NO: 2. In some embodiments, a rAAV particle comprising a rAAV vector comprising a polynucleotide comprising SEQ ID NO: 2 is referred to as “PR001”.
In some embodiments of the methods disclosed herein, a rAAV vector is a self-complementary recombinant adeno-associated virus (scAAV) vector. scAAV vectors are described in, for example, McCarty et al., Gene Ther. 2001; 8(16):1248-54.
In some embodiments of the methods disclosed herein, the recombinant virus is AAV. In some embodiments of the methods disclosed herein, a rAAV comprises an AAV9 capsid protein. In some embodiments of the methods disclosed herein, a rAAV comprises an AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10 or AAV11 capsid protein, or a variant of any of these capsid proteins.
All publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how the compounds, compositions, articles, devices, and/or methods described and claimed herein are made and evaluated, and are intended to be purely illustrative and are not intended to limit the scope of what the inventors regard as their invention.
The purpose of this assay is to measure in vitro relative potency of an AAV (e.g. AAV9) encapsulated vector encoding glucocerebrosidase (GCase; encoded by the GBA1 gene) using a cell-based assay.
The purpose of this method is to measure a dose response of an AAV encapsulated vector encoding glucocerebrosidase (GCase; encoded by the GBA1 gene) in vitro using a cell-based functional assay. This test method may be used for research purposes, such as comparing the responses of different AAV gene therapy product lots.
Background/Theory of Method: PR001 is an exemplary rAAV expressing GBA1. A transduction assay introduces PR001 to the HEK293T cells and results in GCase enzyme expression. Enzyme activity derived from the transduction was assayed in cell lysate using the fluorogenic substrate 4-methylumbelliferyl-β-D-glucopyranoside, which generates the fluorescent product resorufin by GCase catalysis. Relative potency between two or more rAAVs was calculated from the enzymatic activity resulting from the transduction at different amounts of PR001 using parallel line analysis.
Procedure: HEK293T cells were plated at 20,000 cells/well in a 96-well plate and allowed to attach overnight at 37° C. and 5% C02. Serial dilutions of the AAV were prepared in its excipient as shown in Table 4.
10 μl of AAV dilutions or vehicle were transferred to wells following the plate map in
Cells were incubated for 2 to 2.5 hrs. in a 37° C., 5% CO2 incubator. After incubation, 100 μl of Recovery Medium was added to the cells/transduction medium to the wells for a total volume of 150 μL. Cells were incubated for 72+6 hours at 37° C. and 5% CO2 to allow virally-derived GCase expression.
Cell lysates were harvested. GCase activity was measured by adding 10 μl of 1.25 mM Resorufin-β-D glucopyranoside working solution to black plate with clear flat bottom followed by 40 μL of cell lysate. The plate was immediately read on a Varioskan plate reader at 37° C.
Analysis: A parallel analysis of the data to calculate the relative potency was performed as follows:
Relative potency (%)=10{circumflex over ( )}((b−breference)/A)×100
Obiective: The purpose of this qualification plan is to define the test method to measure relative potency of PR001 in vitro using a cell-based assay. This protocol will demonstrate that the method produces reliable data and is fit for analysis of AAV samples for research and process development purposes (non-GXP).
Qualification plan: The validation will be performed according to the validation of analytical test methods, a procedure described in the International Conference on Harmonization (ICH) Q2 (R), USP<1032> and USP<1033>. Validation testing will consist of testing AAV9-GBA DP at 50%, 100%, and 200% relative potency levels as well as specificity. To evaluate method linearity, accuracy and precision (repeatability and intermediate precision), each level will be tested by two analysts. Relative potency from each assay is independent and regarded as a single assay determination. Each plate will contain one reference standard and up to two test samples. If system suitability fails on a plate, then the plate will be repeated. If system suitability fails for a sample, then only the failed sample will be repeated. All samples should meet the assay acceptance criteria defined in the method and the validation criteria defined in this protocol. Determination of specificity will also be performed using an unrelated AAV product that does not carry GBAL. Detection and quantitation limits have not been included because they are not relevant to a method that reports relative potency as explained in USP<1032>. Table 8 summarizes the validation procedures and the acceptance criteria that will be used to assess the performance of the method.
Linearity: AAV9-GBA test samples will be diluted to 50%, 100%, and 200% of the reference standard, and will be tested in seven assays by two analysts. The mean (measured) relative potency will be plotted versus the expected relative potency and analyzed using linear regression. The resulting linearity equation and coefficient of determination (R2) will be reported. Assay plates that fail system suitability not be used for analysis.
Accuracy: The linearity data will be evaluated to assess accuracy. The mean % recovery will be calculated at each level using the following formula:
The % recovery values at each level will be reported.
Repeatability: The linearity data will be evaluated to assess repeatability. The percent relative standard deviation (% RSD) will be calculated at each level for each assay (i.e. same analyst and same week) and reported.
Intermediate Precision: The linearity data will be evaluated to assess repeatability. The overall % RSD will be calculated at each level and reported.
Range: The lowest and highest potency tested that meet the criteria for linearity, accuracy and precision experiments will be used to determine the method range and will be reported.
Specificity: An alternate molecule (specificity sample) will be tested in one assay by one analyst. The specificity sample will be diluted into the assay as if they were AAV9-GBA test samples. The specificity sample is an alternate molecule (AM): PR006.
Data Handling and Reporting: Raw data will be acquired by the SkanIt RE 5.0 software and parallel line analysis will be performed as indicated in the test method above. This data will be exported into a spreadsheet for calculating additional assay parameters (e.g., accuracy and precision). All resulting data, including details of the experiments such as materials, reagents, equipment used and test conditions, will be recorded and reviewed by a second analyst.
Based on the results from all the valid assay runs and all valid concentrations of the reference standard virus and research virus, the overall average relative potency across all runs from the qualification will be used to establish the nominal RP value for these samples for use in further assay executions.
An example of the potency assay data from several PR001 samples is shown in
Notwithstanding the appended claims, the disclosure sets forth the following numbered embodiments:
This application claims the benefit of U.S. Provisional Patent Application No. 63/092,189, filed on Oct. 15, 2020, the disclosure of which is hereby incorporated by reference in its entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/055200 | 10/15/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63092189 | Oct 2020 | US |
