Patent Application
20220290259
The Sequence Listing for this application is labeled “Seq-List-replace.txt” which was created on Oct. 8, 2021 and is 3 KB. The entire content of the sequence listing is incorporated herein by reference in its entirety.
The present invention relates to biologic systems and more specifically to the use of genomic and computational analysis for bioproduction of biological molecules. In particular it relates to methods for the identification of specific cell lineage and cell bank characterization, SNPs as well as primers for amplification useful in said methods.
The production of recombinant therapeutic is more and more important to the pharmaceutical industry. Chinese hamster ovary (CHO) cell lines are part of the most used cells for producing recombinant proteins. Other well-known and commonly used cell lines in pharmaceutical industry are for instance NSO or SP2/0. These cells have been repeatedly approved by regulatory agencies. They can be easily cultured in suspension and can produce high titers of human-compatible therapeutic proteins.
Health Authorities, not only before, but also after approval of a drug produced recombinantly via cells in culture require an identity test for the confirmation of the mammalian host cell. Identity tests are needed for instance to show that the cell banks that are used are stable over time and that there are no cross-contaminations. Traditional tests were based on isoenzyme analysis, which can show specie-specific mobility patterns on an electrophoresis gel. These tests are based on the difference in electrophoretic mobility of four different isoenzymes, which allows distinction to be made between human, murine and hamster species. However these enzymatic tests require reagents that may become scarce and are cumbersome to carry out. Other drawbacks include that the sensitivity of these test is not sufficient to comply with the most current acceptable standards.
Therefore, there is a need for alternative and effective methods for the identification of specific cell lineages and cell bank characterization.
In a first aspect the present invention discloses a method for identifying the specific cell lineage of cells in culture comprising the steps of: 1) determining from the nucleic acid molecules isolated from said recombinant cells in culture the presence of polymorphisms or SNPs at at least 5 different positions, more advantageously at at least 10 different positions, even more advantageously at at least 20 different positions, within at least five genes contained in said nucleic acid molecules, 2) obtaining a genetic profile from the determination of step 1), and 3) identifying the cell lineage of said cells in culture from said genetic profile; wherein the at least five genes are: Argonaute RISC catalytic component 1 (Ago1), Cytochrome b (Cytb), Histone deacetylase 1 (Hdac1), Serine/arginine-rich splicing factor 1 (Srsf1) and Topoisomerase II beta (Top2b), and wherein the recombinant cells produce a recombinant protein.
In a second aspect of the invention, herein described is an analytic method comprising the steps of: 1) analyzing the nucleic acid molecules isolated from recombinant cells in culture to determine the presence of polymorphisms or SNPs at at least 5 different positions, more advantageously at at least 10 different positions, even more advantageously at at least 20 different positions, within at least five genes contained in said nucleic acid molecules, 2) obtaining a genetic profile from the analysis of step 1), and 3) determining the species of said recombinant cells in culture from said genetic profile; wherein the at least five genes are: Argonaute RISC catalytic component 1 (Ago1), Cytochrome b (Cytb), Histone deacetylase 1 (Hdac1), Serine/arginine-rich splicing factor 1 (Srsf1) and Topoisomerase II beta (Top2b), and wherein the recombinant cells produce a recombinant protein.
In a third aspect, the present invention relates to a method for cell bank characterization of recombinant cells in culture comprising the steps of: 1) determining, in nucleic acid molecules isolated from said recombinant cells in culture, the presence of polymorphisms or SNPs at at least 5 different positions, more advantageously at at least 10 different positions, even more advantageously at at least 20 different positions, within at least five genes, 2) obtaining a genetic profile from the detection of step 1), and 3) characterizing the origin of the cell bank of the recombinant cells in culture from said genetic profile; wherein the at least five genes are: Argonaute RISC catalytic component 1 (Ago1), Cytochrome b (Cytb), Histone deacetylase 1 (Hdac1), Serine/arginine-rich splicing factor 1 (Srsf1) and Topoisomerase II beta (Top2b), and wherein the recombinant cells produce a recombinant protein.
Described herein is a combination of single species-specific nucleotides (SNPs) allowing identification of the specific cell lineage and cell bank characterization of cells. Thanks to these combinations of SNPs, it is possible to easily differentiate between species (e.g. Mouse, CHO, Human, etc.).
In summary, the method is based on the analysis of differences between animal species (such as mammalian species) in SNPs found in the sequences of 5 highly preserved genes, using PCR (Polymerase Chain Reaction) and sequencing methods. The differences in the SNPs allow the creation of a species-specific pattern that is analyzed by bioinformatics software to confirm the cell line identity and detect any contamination by cell lines of other species. Various advantages of the methods are the following: 1) No reagents for Isoenzyme analysis, 2) Robustness (5, 10, or 20 SNPs only on 5 different genes are needed; “Forensic-like” approach), 3) Sensitivity, 4) Identification of potential contamination and 5) Cost efficient.
Table 1 shows some of the SNPs of each species for the 5 genes tested which can be used according to the present invention. The five genes are Argonaute RISC catalytic component 1 (Ago1), Cytochrome b (Cytb), Histone deacetylase 1 (Hdac1), Serine/arginine-rich splicing factor 1 (Srsf1) and Topoisomerase II beta (Top2b). The identity of the species of origin is given by the presence of at least 5, more advantageously at least 10, even more advantageously at least 20, SNPs in the test sample.
According to the present invention as a whole, the preferred at least 20 SNPs are selected from any combination of the SNP's as described in Table 1. Indeed it was shown by the inventors that using these SNPs allowed for a very accurate identification/characterization of a cell line/cell lineage.
Summary of the method: The method involves culturing the cell line to be analyzed (sample) and preparing cell pellets. The genomic DNA extracted from the sample undergoes 5 different PCR reactions using a pair of primers specific for each of the five genes of interest. These primers amplify the region of the gene in which the SNPs are located. Subsequently, starting from purified PCR products, libraries are prepared for loading on the MiSeq (Illumina) sequencer for sequencing. The data produced are then analyzed using a specific bioinformatics pipeline, which allows the sample cell line of origin to be identified, as well as the presence of cell lines of any other species.
This method can be used to analyze (non-limiting examples):
The cells to be analyzed were isolated from various test cultures and pelleted.
Pellet production from cells in suspension: The cells were resuspended in culture medium and then centrifuged for 10 minutes at 1000 rpm at +4° C. The supernatant was then removed. The resulting pellet can be stored at −80° C. for 5 years maximum from preparation should it be needed.
Pellet production from adherent cells: when the cell monolayer reaches confluence, the culture medium is aspirated from the flask using a sterile pipette. Then the monolayer is washed with PBS. After removal of PBS, trypsin is distribute it evenly over the monolayer by gently moving the flask several times (e.g. 12-15 times). Once the cell monolayer has completely detached, the cells are resuspended in culture medium to block the effect of the trypsin. The cells are then centrifuged for 10 minutes at 1000 rpm at +4° C. The supernatant is then removed, The resulting pellet can be stored at −80° C. for 5 years maximum from preparation should it be needed.
Before proceeding with cell pellet preparation, the following acceptance criterion were checked: cell viability >80%. If cell viability was <80% but between 50% and 79%, cell culturing in flasks was continued until cell viability increases. If cell viability was less than 50%, the cells in culture were discarded.
Genomic DNA was extracted using the Qiagen QiaAmp DNA Blood kit according to the instructions provided in the kit. Once extraction done, DNA was quantified using the NanoDrop method. Two measurements were made for each sample and the final concentration was the mean result. Quantitation on the NanoDrop enabled the degree of purity of each sample to be verified by assessing the 260/280 ratio. To be used in subsequent test phases, the genomic DNA from a sample should respect the following: the 260/280 ratio must be within a 1.7-2.1 range (inclusive). If a sample did not meet the acceptance criterion, it could not be used in subsequent test phases and genomic DNA extraction was repeated only once.
The genomic DNA extracted from samples underwent 5 different PCR reactions using a specific pair of primers for each of the 5 genes (Ago1, Cytb, Hdac1, Srsf1 and Top2b). Standard methods were used for such amplifications. It is noted that if lyophilized, the primers were resuspended in ultrapure water. Each PCR reaction included a negative amplification control consisting of PCR mix with water instead of genomic DNA. In addition, two replicates of the reaction were prepared for each sample.
The reagents in the amplification mix were used at the final concentrations as below:
The amplification reaction was checked by an agarose gel electrophoretic run (prepared according to standard procedures). To go on to the subsequent PCR amplification product purification phase, the following acceptance criteria were checked:
The molecular weight (bp) of the expected band for each gene in each species is shown in the table below:
If the results meet the acceptance criteria, the PCR amplification products can be purified. If the sample PCR reaction acceptance criteria are not met for a certain gene, the PCR reaction is to be repeated for that sample for that gene and the electrophoretic run only once.
After checking the PCR reaction on agarose gel, the remaining volumes of amplification product were purified using the Qiagen MinElute PCR Purification Kit as instructed in the instructions provided with the kit. The PCR purification products were subsequently quantified using the Qubit dsDNA HS Assay Kit.
In order to go on to the subsequent test phases, the following acceptance criterion was checked: the lowest concentration of PCR purification product obtained for each sample must be ≥1 ng/μL. If the minimum sample purification product concentration was not achieved for a certain gene, the PCR reaction for that sample for that gene, the electrophoretic run and purification were repeated.
The sample library was prepared by mixing the PCR purification products of the 5 genes of the sample. Libraries belonging to different samples can be loaded on a single flow cell and analyzed as a single pool for sequencing. The Illumina Experiment Manager (IEM) software installed on the MiSeq system was used to confirm the validity of the choice of the SNPs, i.e. those nucleotide sequences that allowed each sample to be univocally identified. Once the SNPs chosen, the libraries were prepared using the Illumina Nextera XT kit following the instructions provided with the kit. For each sample, the PCR purification product of each of the 5 genes was taken to a concentration of 1 ng/μL based on the quantitation from the Qubit measurement.
Before proceeding with the subsequent phases, the quality of the libraries produced was assessed. This was performed in two steps: analysis on a Qubit fluorometer (to determine the concentration) and capillary electrophoresis analysis on a Bioanalyzer (to determine the concentration and size). In both case standard procedures were used. Subsequently, 1 μl of library was analyzed using the Agilent High Sensitivity DNA Kit as instructed in the kit.
To be used in subsequent test phases, the following acceptance criteria were checked for each sample library:
If the acceptance criteria were met, the flow cell was loaded and run on the MiSeq sequencer. If the library produced for a certain sample did not respect these criteria, library preparation was repeated.
The libraries produced were loaded either on a Nano or on a Micro flow cell. The flow cell was chosen depending on the number of samples to be tested. A Nano flow cell was used for 2 samples, while for a Micro flow cell the number of samples was 10. Libraries were loaded and run as instructed in the MiSeq sequencer.
The MiSeq sequencer run parameters respected the following acceptance criteria:
If any of the parameters were out of these acceptance criteria, he sequencing run was repeated.
The data produced by the MiSeq sequencer run were analyzed using the MAGNETO bioinformatics pipeline.
In the genomic sequences produced by the samples, the bioinformatics pipeline seeks the profile of 22 SNPs distributed over the 5 genes listed in Table 2. At the end of the analysis, the pipeline produced a report containing one or more tables depending on the species-specific profiles identified. This allowed confirmation of the species of origin of the test cell line and assessment of any cross-contamination with cells of other species.
The test was considered valid if the following conditions occurred during the various test phases:
The control validity criteria and sample acceptance criteria of the various phases are specified above.
Result analysis consisted of assessing the species identified by the MAGNETO bioinformatics pipeline. The report produced by the pipeline contained a table for the species identified in the sample as follows:
The report may therefore contain 1, 2 or 3 tables depending on the species identified.
The test result for a certain sample was deemed compliant when:
The report produced by the MAGNETO pipeline on sample analysis should therefore contain only the table for the species of origin of that sample.
During validation, tests were carried out with the aim of checking the ability of the method to identify cell lines of various species. In particular, specificity was proven checking:
In the first test (i.e. ability of the method to confirm the species of origin of a human, murine or hamster cell line), specificity was assessed using the following samples:
Below are the results of the specificity check giving the species identified for each sample.
In the second test (i.e. ability of the method to confirm the species of origin of a cell bank previously tested using the “Isoenzyme analysis in cell lines” method), specificity was assessed using the following samples:
Below are the results of the specificity check giving the species identified for each sample.
All the results obtained in both tests for checking method specificity are valid according to the acceptance criteria (see main methods section), and comply with the acceptance criterion, since the species of origin was confirmed for all the samples tested. Based on these results, it can be stated that the method is specific.
Tests were carried out with the aim of checking the limit of detection, intended as the lowest percentage of contamination among the test species (man, mouse and hamster) that the method is able to identify. To check the limit of detection, cell pellets were prepared mixing different percentages of human (MRC-5), mouse (SP2/0-Ag14) and hamster (CHO-K1) cells lines, as shown below (Table 4).
The samples were prepared, sequenced on a Micro flow cell and analyzed along with samples for checking specificity, as per main methods section. Three repetitions of the test were done using 3 different cell pellets of each mix.
In the mixes containing 5% or more of contaminating species, the contaminating species was identified in 3 repetitions out of 3 of the test (100% success). Based on these results it can therefore be concluded that the method is able to detect cross-contamination among the cell lines of the 3 different test species (man, mouse and hamster) with a 5% minimum limit of contamination detectable (LOD).
Robustness, intended as the ability of the method to remain unchanged in spite of the introduction of deliberate changes in some parameters considered critical, was assessed.
In particular, each experimental phase of the method was subjected to risk analysis in order to identify critical phases for robustness checking.
The experimental phases found to be critical were:
As regards the genomic DNA amplification phase, the PCR (quantity of Taq polymerase enzyme in the reaction) and visualization of bands obtained on agarose gel (different intercalators of DNA in the gel and gel acquisition and analysis using different instruments) conditions were varied.
In the library preparation phase, the quantity of starting DNA was changed, as was the quantity of tagmentation enzyme needed to fragment the DNA.
Finally, as regards the library loading phase and run on the MiSeq sequencer, a check was done on robustness of the method in sequencing samples consisting of recombinant cell banks loaded on a Nano flow cell.
Robustness of this phase was also checked during method validation by assessing the results from samples loaded on two different types of flow cell for sequencing, Nano or Micro. In particular, robustness was proven by checking:
1. Robustness check intended as the ability of the method to confirm the species of origin of a cell line loaded and sequenced on a Nano or on a Micro flow cell. Robustness was assessed on the results from samples prepared and analyzed for the method specificity check (Example 1). The samples used were:
The acceptance criterion for checking robustness was to have confirmation of the species of origin of the samples loaded and sequenced both on the Nano and on the Micro flow cell. Below are the results of samples loaded and sequenced on a Micro flow cell:
Below are the results of samples loaded and sequenced on a Nano flow cell:
2. Robustness check intended as the ability of the method to identify the contaminating species present at the LOD in samples of murine and of hamster origin loaded and sequenced on a Nano or on a Micro flow cell. Robustness was assessed using the following samples:
Robustness of the method in identifying the contaminating species present at the LOD in samples loaded and sequenced on a Micro flow cell was assessed on the results of assay 3 of the test for method limit of detection check (see Example 2). Robustness of the method in identifying the contaminating species present at the LOD in samples loaded and sequenced on a Nano flow cell was assessed using the same samples. In particular, the libraries of samples of the CHO-K1 cell line mixed at the LOD with Sp2-0/Ag14 and of the Sp2-0/Ag14 cell line mixed at the LOD with CHO-K1 of the third repetition of the limit of detection test were loaded and sequenced on a Nano flow cell.
Below are the results from samples loaded and sequenced on the Micro flow cell.
Below are the results from samples loaded and sequenced on the Nano flow cell.
All the results of both method robustness checking tests (point 1 and point 2) are valid according to the acceptance criteria, and comply with these criteria. The method can therefore be considered as being robust with respect to the parameters considered critical for its performance.
The method was classified as a “Limit test for impurities”. The parameters validated were specificity, limit of detection (LOD) and robustness.
critical for its performance.
Consequently, the “Mammalian cell line identity by Next Generation Sequencing” method used to confirm the species of origin of cell lines and to assess any cross-contamination with cells of other species, is to be considered VALIDATED. It can efficiently replace the typical Isoenzyme analysis routinely used for confirm the species of origin of cell lines.
| Number | Date | Country | Kind |
|---|---|---|---|
| 18206755.3 | Nov 2018 | EP | regional |
This application is the U.S. national stage application of International Patent Application No. PCT/EP2019/067091, filed Jun. 26, 2019.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2019/067091 | 6/26/2019 | WO |
