Patent Application
20220195369
The present disclosure relates to an information processing apparatus, an information processing method, and an information processing program.
JP2009-44974A discloses a method for constructing an estimation model for estimating a quality of cells. In the method, for two or more samples in which cells of the same species are cultured, images are acquired by capturing images of cells of each sample are captured at two or more time points with different culture times, and each acquired image is analyzed, thereby generating numerical data for two or more indicators of morphology of the cells. In the method, actual measurement data of the estimation target is provided for each sample, the generated numerical data is used as an input value, and the provided actual measurement data is used as a teacher value for fuzzy neural network analysis, thereby building an estimation model that indicates a combination of indicators effective for estimation that calculate an output value on the basis of the fuzzy rule.
Perfusion culture is a culture method of cells used in the production of biopharmaceutical drugs using antibodies produced from cells. Perfusion culture is a culture method in which a culture liquid containing cells is continuously filtered and discharged, while a fresh culture medium containing nutritional components is continuously supplied to a culture tank. Perfusion culture is also referred to as continuous culture.
Since the number of process conditions for cell cultures that can be changed in perfusion culture and the set values of each process condition are very large, it is difficult to experiment with all combinations to find the optimum process conditions. Therefore, cell culture is performed under a certain number of different process conditions, and the process conditions with the most desirable experimental results are selected. The selected process condition is optimal among the process conditions within the range of experiments, but more suitable process conditions may exist. In a case where such appropriate process conditions can be derived, it is possible to effectively support perfusion culture.
The technique described in JP2009-44974A estimates the quality of cells from images obtained by capturing cells at two different time points using an estimation model, and does not derive process conditions.
The present disclosure has been made in view of the above-mentioned circumstances, and provides an information processing apparatus, an information processing method, and an information processing program capable of effectively supporting perfusion culture.
The information processing apparatus of the present disclosure comprises: an estimation unit that estimates a quality of an antibody produced from cells and a quality of the cells on the basis of a culture state of the cells, a search unit that searches for the culture state of the cells, which improves the quality of the antibody and the quality of the cells estimated by the estimation unit, and a derivation unit that derives process conditions for cell culture in which a culture state of the cells is the culture state searched by the search unit.
In the information processing apparatus of the present disclosure, the culture state may include the number of the cells, a pH of a culture medium, a concentration of a dissolved gas in the culture medium, and a gas transfer capacity coefficient of the culture medium.
Further, in the information processing apparatus of the present disclosure, the process conditions may include a rotation speed of a stirring device, which is for stirring the culture medium, per unit time and a gas aeration amount of the culture medium per unit volume.
Further, in the information processing apparatus of the present disclosure, the estimation unit may estimate the quality of the antibody and the quality of the cells, on the basis of the culture state of the cells and a trained model which is trained in advance using the culture state, the quality of the antibody, and the quality of the cells.
Further, in the information processing apparatus of the present disclosure, the derivation unit may derive the process conditions, on the basis of the culture state of the cells and a trained model which is trained in advance using the process conditions and the culture state.
Further, in the information processing apparatus of the present disclosure, the search unit may search for the culture state of the cells in accordance with a predetermined search algorithm.
Further, in the information processing apparatus of the present disclosure, the search algorithm may be a genetic algorithm.
Further, the information processing method of the present disclosure executed by a computer, the method comprises: estimating a quality of an antibody produced from cells and a quality of the cells on the basis of a culture state of the cells; searching for the culture state of the cells that improves the estimated quality of the antibody and the estimated quality of the cells; and deriving process conditions for cell culture in which a culture state of the cells is the searched culture state.
In addition, the information processing program of the present disclosure causes a computer to execute processing of: estimating a quality of an antibody produced from cells and a quality of the cells on the basis of a culture state of the cells, searching for the culture state of the cells that improves the estimated quality of the antibody and the estimated quality of the cells; and deriving process conditions for cell culture in which a culture state of the cells is the searched culture state.
According to the present disclosure, it is possible to effectively support perfusion culture.
Examples of embodiments for carrying out the technique of the present disclosure will be hereinafter described in detail with reference to the drawings.
A configuration of a cell culture device 100 according to the present embodiment will be described with reference to
The cells used in expressing the antibody are not particularly limited, and examples thereof include animal cells, plant cells, eukaryotic cells such as yeast, prokaryotic cells such as grass Bacillus, Escherichia coli, and the like. Animal cells such as CHO cells, BHK-21 cells, and SP2/0-Ag14 cells are preferable, and CHO cells are more preferable.
The antibody expressed in animal cells is not particularly limited, and includes, for example, anti-IL-6 receptor antibody, anti-IL-6 antibody, anti-glypican-3 antibody, anti-CD3 antibody, anti-CD20 antibody, anti-GPIIb/IIIa antibody, anti-TNF antibody, anti-CD25 antibody, anti-EGFR antibody, anti-Her2/neu antibody, anti-RSV antibody, anti-CD33 antibody, anti-CD52 antibody, anti-IgE antibody, anti-CD11a antibody, anti-VEGF antibody, anti-VLA4 antibody, and the like. The antibody includes not only monoclonal antibodies derived from animals such as humans, mice, rats, hamsters, rabbits, and monkeys, but also artificially modified antibodies such as chimeric antibodies, humanized antibodies, and bispecific antibodies.
The obtained antibody or fragment thereof can be purified to be uniform. For the separation and purification of the antibody or a fragment thereof, the separation and purification method used in a conventional polypeptide may be used. For example, an antibody can be separated and purified by appropriately selecting and combining a chromatography column such as affinity chromatography, a filter, ultrafiltration, salting out, dialysis, SDS polyacrylamide gel electrophoresis, and isoelectric point electrophoresis. However, the present invention is not limited thereto. The obtained concentration of the antibody can be measured by measurement of the absorbance or by an enzyme-linked immunosorbent assay (ELISA) or the like.
As shown in
The culture container 10 is a container for containing a cell suspension including cells and a culture medium used in expressing an antibody. Inside the culture container 10, a stirring device 11 having a stirring blade is provided. By rotating the stirring blade of the stirring device 11, the culture medium contained together with the cells in the culture container 10 is stirred, and the homogeneity of the culture medium is maintained.
In the cell culture device 10, in order to prevent the concentration of cells in the culture container 10 from becoming excessively high, a cell bleeding treatment is performed, which is for bleeding off a part of the cells in the culture container 10 (for example, about 10%) at an appropriate timing during the culture period. In the cell bleeding treatment, the cells in the culture container 10 are discharged to the outside of the culture container 10 through the flow passage 39.
One end of the flow passage 31 is connected to the bottom of the culture container 10, and the other end is connected to an inlet 20a of the filter unit 20. In the middle of the flow passage 31, a pump P1, which extracts the cell suspension contained in the culture container 10 and sends the cell suspension to the filter unit 20, is provided.
The filter unit 20 comprises a container 21 and a filter membrane 24 that separates the space inside the container 21 into a supply side 22 and a permeation side 23 and performs a membrane separation treatment on the cell suspension extracted from the culture container 10. Further, the filter unit 20 has the inlet 20a through which the cell suspension flows in and an outlet 20b through which the cell suspension flows out on the supply side 22. The cell suspension extracted from the culture container 10 passes through the filter membrane 24 while flowing into the inside of the container 21 from the inlet 20a and flowing out to the outside of the container 21 from the outlet 20b. The filter unit 20 performs the membrane separation treatment by a tangential flow (cross flow) method of sending permeation components to the permeation side 23 while flowing a liquid subjected to the membrane separation treatment along the membrane surface of the filter membrane 24 subjected to the membrane separation treatment (that is, in a direction parallel to the membrane surface). The tangential flow method, which is a method for membrane separation treatment using the filter membrane 24, may be a method of forming a flow in which the cell suspension extracted from the culture container 10 circulates in one direction in parallel along the membrane surface of the filter membrane 24, or may be a method of forming a flow in which the cell suspension extracted from the culture container 10 reciprocates alternately in parallel along the membrane surface of the filter membrane 24. In a case of forming a circulating flow, for example, a KrosFlo perfusion culture flow path device (KML-100, KPS-200, and KPS-600) manufactured by Spectrum Laboratories Corp. can be suitably used. Further, in a case of forming a flow that reciprocates alternately, the ATF system manufactured by REPLIGEN Corp. can be suitably used.
The relatively large-sized components included in the cell suspension do not permeate through the filter membrane 24, flow out to the outside of the container 21 from the outlet 20b, and are returned to the inside of the culture container 10 through the flow passage 32. That is, in the cell suspension extracted from the culture container 10, the components blocked by the filter membrane 24 are returned to the inside of the culture container 10 through the flow passage 32. On the other hand, the relatively small-sized components included in the cell suspension permeate through the filter membrane 24 and are discharged to the outside of the container 21 from a discharge port 20c provided on the permeation side 23. A flow passage 33 provided with a pump P2 is connected to the discharge port 20c of the filter unit 20, and the components discharged to the permeation side 23 are discharged from the discharge port 20c to the outside of the container 21 through the flow passage 33.
In the cell culture device 100 according to the present embodiment, the filter membrane 24 is used for the purpose of separating cells and components unnecessary for cell culture. Examples of components unnecessary for cell culture include cell carcasses, cell crushed products, DNA, HCP, antibodies, waste products, and the like. That is, the filter membrane 24 has a separation performance suitable for blocking the permeation of cells while allowing components unnecessary for cell culture to permeate.
The components unnecessary for cell culture discharged from the culture container 10 as described above are sent to the next process, which is an antibody purification process.
In the contract development of antibody drugs, cells are contracted from customers and antibodies are produced by culturing the contracted cells. In the contract development, as shown in
In the present embodiment, an example of deriving more appropriate process conditions to be used in the next medium-quantity trial production in the above-mentioned small-quantity test will be described.
Next, referring to
The storage unit 43 is realized by a hard disk drive (HDD), a solid state drive (SSD), a flash memory, or the like. A learning program 50 and an information processing program 52 are stored in the storage unit 43 as a storage medium. The CPU 41 reads the learning program 50 from the storage unit 43, expands the program into the memory 42, and executes the expanded learning program 50. Further, the CPU 41 reads the information processing program 52 from the storage unit 43, expands the program into the memory 42, and executes the expanded information processing program 52. Further, the storage unit 43 stores first learning data 54 and second learning data 55. Further, the storage unit 43 stores the first trained model 56 and the second trained model 57.
The measurement unit 48 includes various measurement devices that measure a culture state of cells in the cell culture using the cell culture device 100. Examples of the culture state include: for example, the number of cells contained in the culture container 10 (hereinafter, simply referred to as “number of cells”); a pH of the culture medium; a concentration of the dissolved gas in the culture medium (for example, a concentration of dissolved oxygen); a gas transfer capacity coefficient (for example, oxygen transfer capacity coefficient: kLA) of the culture medium; and the like. The number of cells means a sum of the number of living cells and the number of dead cells.
Referring to
As shown in
Referring to
As shown in
The trained model 56 is a model that is trained in advance using the learning data 54, and the trained model 57 is a model that is trained in advance using the learning data 55. Examples of the trained model 56 and the trained model 57 include a neural network model. The trained model 56 and the trained model 57 are generated by the information processing apparatus 40 in the learning phase to be described later.
Next, referring to
The acquisition unit 60 acquires the learning data 54 and the learning data 55 from the storage unit 43. The learning unit 62 generates the trained model 56 by training the model using the learning data 54 acquired by the acquisition unit 60 as training data. Then, the learning unit 62 stores the generated trained model 56 in the storage unit 43.
As an example, as shown in
Further, the learning unit 62 generates the trained model 57 by training the model using the learning data 55 acquired by the acquisition unit 60 as training data. Then, the learning unit 62 stores the generated trained model 57 in the storage unit 43.
As an example, as shown in
Next, referring to
In step S10 of
Further, as described above, the learning unit 62 generates the trained model 57 by training the model using the learning data 55 acquired in step S10 as the training data. Then, the learning unit 62 stores the generated trained model 57 in the storage unit 43. In a case where step S12 ends, the learning processing ends.
Next, referring to
The acquisition unit 70 acquires the culture state of the cells in the cell culture using the cell culture device 100, which was measured by the measurement unit 48 at the time point at which the cell proliferation period has elapsed. In the present embodiment, the acquisition unit 70 acquires the culture state from each of the plurality of cell culture devices 100 in the small-quantity test.
The estimation unit 72 estimates a quality of the antibody produced from the cells and a quality of the cells, on the basis of the trained model 56 and the culture state acquired by the acquisition unit 70. Specifically, the estimation unit 72 inputs the culture state acquired by the acquisition unit 70 to the trained model 56. As described above, the trained model 56 is a model that is trained using the culture state as an input and the quality of the antibody and the quality of the cells after the elapse of a predetermined period m as the output. Therefore, the output from the trained model 56 is estimated values of the quality of the antibody and the quality of the cells after the predetermined period m has elapsed from the time point at which the acquisition unit 70 acquires the culture state. As described above, the estimation unit 72 estimates the final quality of the antibody and the final quality of the cells from the culture state in each cell culture device 100 in which the small-quantity test is performed (refer to also
As shown in
Specifically, first, the search unit 74 sets the most desirable quality of the antibody and quality of the cells among the quality of the antibody and the quality of the cells estimated by the estimation unit 72 for each cell culture device 100 as evaluation standard in the genetic algorithm. Next, the search unit 74 randomly generates a group of individuals at the initial stage. The individual described herein is a culture state of the cells in cell culture.
Next, the search unit 74 derives an evaluation value of each individual. In the present embodiment, the search unit 74 inputs each individual to the trained model 56, and derives the quality of the antibody and the quality of the cells output from the trained model 56 as evaluation values of each individual.
Next, as shown in
Then, the search unit 74 derives the evaluation value of each individual of the next generation by inputting each individual of the next generation to the trained model 56. The search unit 74 repeats generation of the individual of the next generation as described above until the evaluation value of the individual is greater than a set evaluation standard. Through the above-mentioned processing, the search unit 74 searches for the individual that is greater than the set evaluation standard. The individual thus searched is a culture state of the cells that improves the quality of the antibody and the quality of the cells estimated by the estimation unit 72.
As shown in
The output unit 78 displays the process conditions which are derived by the derivation unit 76 by outputting the process conditions to the display unit 44. On the basis of the output, the process condition display screen shown in
Next, referring to
In step S20 of
In step S22, as described above, the estimation unit 72 estimates the quality of the antibody, which is produced from the cells, and the quality of the cells, on the basis of the trained model 56 and the culture state for each of the culture states acquired in step S20. In step S24, as described above, the search unit 74 searches for the culture state of the cells that improves the quality of the antibody and the quality of the cells estimated in step S22, in accordance with a predetermined search algorithm.
In step S26, as described above, the derivation unit 76 derives the process conditions in which a culture state of the cells is the culture state searched in step S24, on the basis of the trained model 57 and the culture state which is searched in step S24. In step S28, the output unit 78 displays the process conditions which are derived in step S26 by outputting the process conditions to the display unit 44. In a case where the processing of step S28 is completed, the quality estimation processing is completed.
As described above, according to the present embodiment, the process conditions are not derived directly from the quality of the antibody and the quality of the cells, but the process conditions are derived from the quality of the antibody and the quality of the cells through the culture state. As compared with the quality of the antibody and the quality of the cells, and the process conditions, the process conditions and the culture state and the culture state and the quality of the antibody and the quality of the cells are highly related. Therefore, it is possible to derive more appropriate process conditions with high accuracy. As a result, it is possible to effectively support perfusion culture.
In the above-mentioned embodiment, the case where the genetic algorithm is applied as the search algorithm has been described, but the present invention is not limited thereto. For example, as a search algorithm, an algorithm other than a genetic algorithm such as Bayesian optimization may be applied.
Further, in the above-mentioned embodiment, the type of the cells used in learning in the learning phase and the cells used in the operation phase may be different. In such a case, for example, the trained models 56 and 57 are generated from the learning data 54 and 55 for certain cells. In such a case, in the operation phase, relatively small amounts of learning data 54 and 55 are collected for the cells used in the operation phase as compared with the learning phase. Then, the trained models 56 and 57 are subjected to retraining using the small amounts of learning data 54 and 55. Such retraining is also referred to as transfer training. By such retraining, the learning period can be shortened. At the time of the retraining, parameters such as the number of layers and the number of nodes in the interlayers of the trained models 56 and 57 may be changed.
Further, as the hardware structure of the processing unit that executes various processes such as each functional unit of the information processing apparatus 40 in the above-mentioned embodiment, it is possible to use various processors to be described below. As described above, various processors include not only a CPU as a general-purpose processor which functions as various processing units by executing software (programs) but also a programmable logic device (PLD) as a processor capable of changing a circuit configuration after manufacturing a field programmable gate array (FPGA); and a dedicated electrical circuit as a processor, which has a circuit configuration specifically designed to execute specific processing, such as an application specific integrated circuit (ASIC).
One processing unit may be configured as one of the various processors, or may be configured as a combination of two or more of the same or different kinds of processors (for example, a combination of a plurality of FPGAs or a combination of a CPU and an FPGA). Further, the plurality of processing units may be composed of one processor.
As an example of the plurality of processing units composed of one processor, first, as represented by computers such as a client and a server, there is a form in which one processor is composed of a combination of one or more CPUs and software and this processor functions as a plurality of processing units. Second, as represented by a system on chip (SoC), there is a form in which a processor that realizes the functions of the whole system including a plurality of processing units with a single integrated circuit (IC) chip is used. As described above, the various processing units are configured by using one or more of the various processors as a hardware structure.
Furthermore, as the hardware structure of these various processors, more specifically, it is possible to use an electric circuit (circuitry) in which circuit elements such as semiconductor elements are combined.
Further, in the above-mentioned embodiment, the configuration in which the learning program 50 and the information processing program 52 are stored (installed) in the storage unit 43 in advance has been described, but the present invention is not limited thereto. The learning program 50 and the information processing program 52 may be provided in a form in which the programs are stored in a storage medium such as a compact disc read only memory (CD-ROM), a digital versatile disc read only memory (DVD-ROM), and a universal serial bus (USB) memory. Further, the learning program 50 and the information processing program 52 may be downloaded from an external device through a network.
From the above-mentioned description, the technology relating to the following supplementary items can be found.
[Additional Notes]
An information processing apparatus comprising:
a processor; and
a memory that is built into or connected to the processor,
in which the processor is configured to
estimate a quality of an antibody produced from cells and a quality of the cells on the basis of a culture state of the cells,
search for the culture state of the cells that improves the estimated quality of the antibody and the estimated quality of the cells, and
derive process conditions for cell culture in which a culture state of the cells is the searched culture state.
The present disclosure of JP2019-173365 filed on Sep. 24, 2019 is incorporated herein by reference in its entirety. Further, all documents, patent applications, and technical standards described in the present specification are incorporated into the present specification by reference to the same extent as in a case where the individual documents, patent applications, and technical standards were specifically and individually stated to be incorporated by reference.
| Number | Date | Country | Kind |
|---|---|---|---|
| 2019-173365 | Sep 2019 | JP | national |
This application is a continuation application of International Application No. PCT/JP2020/018809 filed May 11, 2020, the disclosure of which is incorporated herein by reference in its entirety. Further, this application claims priority from Japanese Patent Application No. 2019-173365 filed on Sep. 24, 2019, the disclosures of which is incorporated herein by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/JP2020/018809 | May 2020 | US |
| Child | 17690147 | US |
