Patent Application
20250188427
The application contains a Sequence Listing which has been submitted electronically in XML format and is hereby incorporated by reference in its entirety. Said .XML copy, created on Jul. 24, 2023, is named “G.xml” and is 55,186 bytes in size. The sequence listing contained in this .XML file is part of the specification and is hereby incorporated by reference herein in its entirety.
The present invention relates to a method of producing a target virus, the method including culturing an animal cell in a predetermined state. The present invention further relates to a culture composition containing an animal cell, a virus, and a culture medium.
The adeno-associated virus (AAV) is a linear single-stranded DNA virus belonging to Parvoviridae. The wild-type AAV genome contains a replication regulatory gene (Rep gene) and a capsid structural gene (Cap gene), and inverted terminal repeat sequences (ITR) are adjacent to these genes for viral replication and packaging. The AAV vector can introduce a gene to proliferating and non-proliferating cells, and can be expressed for a long term particularly in non-dividing cells. In addition, AAV is considered to be non-pathogenic and has low immunogenicity. From the above, the AAV vector has been clinically applied as a vector for gene therapy.
On the other hand, as a method of improving the production amount of the recombinant protein, WO2017/192691A describes that the production amount (titer) of an antibody is improved by treating Chinese hamster ovary cells (CHO cells) into which an antibody gene has been introduced with a bromodomain and extraterminal motif (BET) inhibitor. CN106551939A describes that the production of a virus of HSV infected in a human is improved by a bromodomain inhibitor. US2015/0133434A and US2018/0002699A describe a therapeutic method of reactivating latent HIV in cells to remove infected cells, and describe the use of an inhibitor of a bromodomain protein PCAF or JQ1.
Currently, a gene therapy agent using AAV vectors have been put on the market, and there is a demand for the development of a production method that improves the production amount of viruses such as AAV vectors. An object to be achieved of the present invention is to provide a method of producing a target virus, which is capable of improving the production amount of the virus. Another object to be achieved of the present invention is to provide a culture composition containing an animal cell, a virus, and a culture medium, in which the production amount of the virus is improved.
As a result of intensive studies to achieve the above object, the present inventors have found that the production amount of a target virus can be improved by culturing animal cells into which an exogenous recombinant nucleic acid encoding the target virus has been introduced, in a culture medium in a state in which the function of BET is suppressed. The present invention has been completed based on the above findings.
According to the present invention, the following inventions are provided.
According to the present invention, it is possible to improve the production amount of the target virus.
Hereinafter, an example of the embodiment of the present disclosure will be described. However, the present disclosure is not limited to the following embodiments, and can be implemented with appropriate changes within the scope of the object of the present disclosure. In the present specification, a numerical range indicated using “to” means a range including numerical values described before and after “to” as a minimum value and a maximum value, respectively.
A promoter means a DNA regulatory region/sequence to which an RNA polymerase can be bound and which is involved in the initiation of transcription of a downstream coding sequence or a downstream non-coding sequence.
The vector is a DNA or RNA molecule that is used to artificially transport an exogenous gene to another cell. A vector for expressing a gene is referred to as an expression vector. In a case where a vector containing an exogenous gene to be introduced is introduced into a cell, the exogenous gene is replicated and/or expressed in the cell. Examples of the vector include an episomal (for example, plasmid) vector and a non-episomal vector. The vector can be introduced into a host cell by methods such as transfection, transduction, cell fusion, and lipofection.
In the present specification, a gene means a nucleic acid molecule encoding a polypeptide or RNA, and examples thereof include a nucleic acid molecule such as cDNA or genomic DNA.
The method for producing a target virus according to the embodiment of the present invention includes a virus production step of culturing an animal cell into which an exogenous recombinant nucleic acid encoding a target virus has been introduced, in a culture medium in a state in which a function of BET is suppressed.
Examples of the method of suppressing the function of BET include (1) suppression of the function of BET by a treatment with a BET inhibitor (preferably a bromodomain inhibitor), (2) inhibition of expression of BET by siRNA or gene editing (addition of a mutation to a BET-related gene or change in an expression level), and (3) competitive inhibition by overexpression of a peptide or a protein. In addition, examples thereof include a method of suppressing the function of BET by controlling a protein (for example, acetylated histone or P-TEFb) upstream or downstream of the molecular signal by BET using the same method as described above. Among the above, suppression of the function of BET by treatment with a BET inhibitor (preferably a bromodomain inhibitor) is preferable.
The bromodomain is a protein domain that has a function known to recognize acetylated lysine of histone and to control a chromatin structure and gene expression by collecting control proteins. In humans, about 50 types of bromodomain-containing proteins exist. Examples of the protein containing a bromodomain include a bromodomain and extra-terminal family protein (BET) having a bromodomain repeat sequence and a specific terminal sequence. As the BET, bromodomain-containing protein 2 (BRD2), BRD3, BRD4, and BRDT are known. These proteins each have a bromodomain 1 (BD1) and a bromodomain 2 (BD2), which are N-terminal bromodomains.
Preferably, the function of BET can be suppressed by containing a BET inhibitor (preferably, a bromodomain inhibitor) in the culture medium. The BET inhibitor (preferably a bromodomain inhibitor) is a substance that binds to a bromodomain of a protein and inhibits the function of the bromodomain. BRD2, BRD3, and BRD4 have a bromodomain, and the function of BRD2, BRD3, and/or BRD4 is inhibited by a BET inhibitor (preferably a bromodomain inhibitor).
For the BET inhibitor (preferably a bromodomain inhibitor), the equilibrium dissociation constant: Kd value with respect to any one of BRD2, BRD3, or BRD4 is preferably 150 nmol/L or less, more preferably 100 nmol/L or less, and still more preferably 50 nmol/L or less.
Preferably, the Kd value with respect to the bromodomain 1 within BRD4 is 100 nmol/L or less, and the Kd value with respect to the bromodomain 2 is 250 nmol/L or less. More preferably, the Kd value with respect to the bromodomain 1 is 70 nmol/L or less, and the Kd value with respect to the bromodomain 2 is 200 nmol/L or less.
In a determination device of surface plasmon resonance (SPR), in a case where polarized light is irradiated to a surface of a metal thin film of a sensor chip such that total reflection occurs, an SPR signal in which the intensity of reflected light decreases is observed in a part of the reflected light. Since the angle at which the SPR signal occurs changes depending on the mass on the sensor chip, the angle at which the SPR signal occurs changes as the ligand immobilized on the sensor chip and the added analyte are bound or dissociated. The measurement result can be acquired as a sensor gram showing a change in angle of the SPR signal or a response unit (RU) converted from the change in angle over time. By fitting the acquired sensor grams of binding and dissociation to the theoretical curve, the binding rate constant (ka) and the dissociation rate constant (kd) between the ligand and the analyte can be determined, and further, the equilibrium dissociation constant (Kd=kd/ka) can be determined.
For the BET inhibitor (preferably a bromodomain inhibitor), the IC50 with respect to any one of BRD2, BRD3, or BRD4 is preferably 1 μmol/L or less, more preferably 500 nmol/L or less, still more preferably 200 nmol/L or less, even still more preferably 100 nmol/L or less, and particularly preferably 50 nmol/L or less.
The IC50 with respect to any of BRD2, BRD3, or BRD4 can be determined by plotting the binding inhibition value between the acetylated histone and the bromodomain against the concentration of the inhibitor and calculating the concentration corresponding to an inhibition rate of 50%.
Examples of the BET inhibitor (preferably, a bromodomain inhibitor) include (+)-JQ1 (also known as(S)-(+)-tert-butyl 2-(4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)acetate [Cas #: 1268524-70-4]), PFI-1 (also known as 2-methoxy-N-(3-methyl-2-oxo-1,2,3,4-tetrahydro-quinazolin-6-yl)-benzenesulfonamide [Cas #: 1403764-72-6]), Bromosporine (also known as N-[6-(3-methanesulfonamido-4-methylphenyl)-3-methyl-[1,2,4]triazolo [4,3-b]pyridazin-8-yl]carbamate [Cas #: 1619994-69-2]), I-BET762 (also known as (4S)-6-(4-chlorophenyl)-N-ethyl-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4-acetamide [Cas #: 1260907-17-2]), I-BET151 (also known as 7,3,5-dimethyl-4-isoxazolyl-1,3-dihydro-8-methoxy-1-[1R-1-(2-pyridinyl) ethyl]-2H-imidazo[4,5-c]quinolin-2-one [Cas #: 1300031-49-5]), and OTX015 (also known as 6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepine-6-acetamide [Cas #: 202590-98-5]). Examples of the other compounds include CPI-203 [Cas #: 1446144-04-2], RVX-208 [Cas #: 1044870-39-4], BI-2536 [Cas #: 755038-02-9], and AZD5153 [Cas #: 1869912-39-9].
Among the above, (+)-JQ1, PFI-1, Bromosporine, I-BET762, I-BET151, and OTX015 are preferable, (+)-JQ1, PFI-1, Bromosporine, and I-BET762 are more preferable, and (+)-JQ1 and PFI-1 are still more preferable.
The concentration of the BET inhibitor (preferably, bromodomain inhibitor) in the culture medium is preferably 0.01 μmol/L to 100 μmol/L, more preferably 0.05 μmol/L to 100 μmol/L, still more preferably 0.1 μmol/L to 50 μmol/L, and particularly preferably 1 μmol/L to 10 μmol/L.
The treatment period with the BET inhibitor (preferably, the bromodomain inhibitor), that is, the period in which the BET inhibitor (preferably, the bromodomain inhibitor) is contained in the culture medium is preferably 1 hour or more and 240 hours or less, more preferably 6 hours or more and 240 hours or less, still more preferably 12 hours or more and 240 hours or less, even still more preferably 24 hours or more and 120 hours or less, and particularly preferably 48 hours or more and 96 hours or less. The upper limit of the period in which a BET inhibitor (preferably a bromodomain inhibitor) is contained in the culture medium is not particularly limited, but is generally 240 hours or less, preferably 120 hours or less, and particularly preferably 96 hours or less.
In a case where a doxycycline-inducing promoter is used for expressing the exogenous recombinant nucleic acid, the culture medium may contain doxycycline. The concentration of doxycycline is preferably 5 μg/mL or less, more preferably 1 μg/mL or less, still more preferably 700 ng/ml or less, and particularly preferably 500 ng/ml or less.
The addition time of doxycycline is preferably 1 hour or more, more preferably 6 hours or more, still more preferably 12 hours or more, even still more preferably 24 hours or more, and yet even still more preferably 48 hours or more.
In the present invention, the culture medium is preferably supplied during the culturing, and the supplied culture medium may contain doxycycline and a BET inhibitor (preferably a bromodomain inhibitor).
The supplied culture medium is a culture medium to be added during cell culturing. The culture method using the supplied culture medium is not particularly limited, but perfusion culture is desirable.
The period for which doxycycline and the BET inhibitor (preferably, the bromodomain inhibitor) are allowed to act is preferably 1 hour or more, more preferably 6 hours or more, still more preferably 12 hours or more, even still more preferably 24 hours or more, and yet even still more preferably 48 hours or more.
The method according to the embodiment of the present invention may include stopping the suppression of the function of BET before the produced virus is recovered. The fact that the suppression of the function of BET is stopped means the removal of a factor that inhibits the expression of BET or the removal of an inhibitor from the culture medium. The method of the removal is not particularly limited, but it is preferable to completely or partially replace the culture medium in which the cells are being cultured. Preferably, the function of BET can be stopped by performing culturing in a culture medium in which the BET inhibitor (preferably, a bromodomain inhibitor) is reduced or removed. In this manner, it is possible to avoid the mixing of the BET inhibitor (preferably, a bromodomain inhibitor) in the virus composition to be used as a gene therapy agent.
The period in which the suppression of the function of BET is stopped is preferably 24 to 72 hours.
The period of performing culturing in the culture medium in which the BET inhibitor (preferably, a bromodomain inhibitor) is reduced or removed by completely or partially replacing the culture medium in which the cells are being cultured is preferably 1 hour or more, more preferably 1 to 240 hours, still more preferably 12 to 120 hours, and particularly preferably 24 to 72 hours.
In addition, in a case where a stimulus that induces expression in a condition-specific manner as described later is applied while the function of BET is stopped, it is preferable that the stimulus that induces expression in a condition-specific manner is continued even after the suppression of the function of BET is stopped.
On the contrary, the stimulus that induces the expression in a condition-specific manner may be stopped with the stop of the function of the BET. In a case where the stimulus that induces the expression in a condition-specific manner is the addition of a tetracycline-based drug, the stimulus that induces the expression in a condition-specific manner can be stopped by replacing with a culture medium that does not contain the tetracycline-based drug to reduce the tetracycline-based drug from the culture medium. In addition, in a case where the tetracycline-based drug is doxycycline, the culture medium can be similarly replaced with a culture medium that does not contain doxycycline.
Preferably, the culturing is performed in a culture medium containing a BET inhibitor (preferably, a bromodomain inhibitor) and a tetracycline-based drug for 12 to 48 hours, then the culture medium is replaced with a culture medium not containing a BET inhibitor (preferably, a bromodomain inhibitor), and then the culturing is performed for 24 to 72 hours.
In the present invention, the transcription by an RNA polymerase III is preferably promoted by suppressing the function of BET. The RNA polymerase III is an RNA transcription factor present in eukaryotic cells. Examples of the promoter that promotes transcription by the RNA polymerase III include an H1 promoter and a U6 promoter. The promotion is preferably an increase in the RNA level by 2 times or more.
It is known that the VA-RNA described later is induced to be expressed by the RNA polymerase III.
In the present invention, an animal cell into which an exogenous recombinant nucleic acid encoding a target virus has been introduced is used.
The target virus means a virus that is produced by introducing an exogenous nucleic acid into a cell. Examples of the target virus include an adeno-associated virus, a lentivirus, a baculovirus, and a retrovirus, and among these, an adeno-associated virus is preferable.
Adeno-associated virus (AAV) refers to a small, incompletely replicative, non-enveloped virus containing single-stranded DNA having about 4,700 bases, from the family of Parvoviridae and Dependoparvovirus. It is known that there are more than 100 serum types in AAV, and that the host range and the characteristics of the virus differ depending on the difference in the serum types. Serum type 2 (AAV2) is one of the serum types that have been widely studied for a long time, and it is known that the host range is very wide. The serum type 1 (AAV1), the serum type 5 (AAV5), and the serum type 6 (AAV6) are serum types having higher tissue directivity. It is said that AAV1 has high gene introduction efficiency into muscle, liver, airway, central nervous system, and the like, AAV5 has high gene introduction efficiency into central nervous system, liver, retina, and the like, and AAV6 has high gene introduction efficiency into heart, muscle, liver, and the like. In the present invention, the serum type 2 or the serum type 5 is preferably used. The serum type 5 is particularly preferable.
The adeno-associated virus gene refers to a gene composed of one or a plurality of nucleic acid sequences derived from the serum types of one or a plurality of adeno-associated viruses. The adeno-associated virus gene is preferably a gene involved in replication and packaging of AAV and a gene encoding an AAV constituent protein.
AAV is a non-enveloped virus that proliferates in the presence of helper viruses such as adenovirus and herpesvirus. In the preparation of AAV to be used for gene therapy or nucleic acid introduction, classically, AAV replication has been performed by co-infecting host cells with an adenovirus. In addition, a gene responsible for the helper action of adenovirus has been clarified, and a plasmid incorporating this gene has also been used. For example, a plasmid containing a Rep gene and a Cap gene, an adenovirus helper plasmid, and a plasmid containing a gene for treatment or prevention are simultaneously transfected into cells, and can thus be packaged as recombinant AAV (rAAV).
The Rep gene and the Cap gene encode proteins involved in the replication and packaging of the virion. In the wild type, the Rep gene is expressed from the P5 promoter and the p19 promoter. The Cap region expresses VP1, VP2, and VP3. Examples of the promoter that is naturally carried by the Cap gene can include a p40 promoter.
The adeno-associated virus gene (such as a Rep gene and a Cap gene) may be a wild-type gene, but a gene in which modifications such as substitution, deletion, insertion, or addition of a base have been made to the wild-type gene may be used as long as it exhibits an inherent function.
In a case where modifications such as substitution, deletion, insertion, or addition of a base are made to the wild-type adeno-associated virus gene (such as a Rep gene and a Cap gene), the number of the modified bases is preferably 1 to 20, more preferably 1 to 10, and still more preferably 1 to 3. The modified base sequence of the adeno-associated virus gene exhibits preferably 85% or more sequence identity, more preferably 90% or more sequence identity, still more preferably 95% or more sequence identity, and even still more preferably 98% or more sequence identity with the base sequence of the wild-type adeno-associated virus gene.
In a case where the Rep gene and the Cap gene are introduced into a cell, a vector containing the Rep gene and the Cap gene can be introduced into the cell. The arrangement of the Rep gene and the Cap gene in a vector is not particularly limited, the Rep gene may be located upstream of the Cap gene or downstream of the Cap gene, and the Rep gene is located preferably upstream of the Cap gene.
The Rep gene means a region of the AAV genome encoding a virus replication protein that is known to those skilled in the art and that is collectively required for replication of a virus genome, or its functional homolog, for example, a human herpesvirus 6 (HHV-6) Rep gene (mediating AAV-2 DNA replication is known). Accordingly, the coding region of the Rep gene includes at least a gene encoding REP78 and REP68 (long form of REP protein) and REP52 and REP40 (short form of REP protein) of AAV, or a functional homologue thereof. The coding region of the Rep gene used in the present invention may be derived from any AAV serum type, but is preferably derived from AAV2. Examples of those derived from AAV2 include REP78 and REP68, and REP52 and REP40, and ITR.
The Cap gene means a region in the AAV genome encoding a capsid protein of a virus known to those skilled in the art. Examples of these capsid proteins are AAV capsid proteins VP1, VP2 and VP3. The Cap gene used in the present invention may be derived from any AAV serum type, but is preferably derived from AAV2 or AAV5. AAV5 is particularly preferable.
As the vector containing the Rep gene and the Cap gene, for example, a plasmid, a nucleic acid sequence derived from a virus, or an artificially designed nucleic acid can be used, and a plasmid is preferable.
In the present invention, a gene for treatment or prevention may be introduced into cells. It is preferable that the gene for treatment or prevention is introduced in a state of being sandwiched between ITRs.
As the gene for treatment or prevention, a gene that is incomplete or lost in the genome of the target cell, a gene encoding non-natural protein having a desired biological or therapeutic effect (for example, antiviral function), or the like can be used, but the gene is not particularly limited. Specific examples of the gene for treatment or prevention include a gene used for treatment or prevention of inflammatory diseases, autoimmunity, chronic and infectious diseases (including disorders such as AIDS, cancer, nervous system diseases, cardiovascular diseases, and hypercholesterolemia), various blood diseases such as anemia and hemophilia, or gene deficiency (for example, cystic fibrosis, Gaucher's disease, adenosine deaminase (ADA) deficiency, emphysema, and the like).
The gene for treatment or prevention may be several antisense oligonucleotides (for example, a short-chain oligonucleotide complementary to a sequence around a translation initiation site (AUG codon) of mRNA) that are useful in antisense therapy against cancer and viral disease.
The gene for therapy or prophylaxis may be linked to a promoter for expressing the gene for therapy or prophylaxis. The promoter for expressing a gene for treatment or prevention is not particularly limited, but examples thereof can include a cytomegalovirus-derived promoter (including an enhancer as desired), an SV40 early promoter, a human elongation factor-1α (EF-1α) promoter, a human ubiquitin C promoter, a retrovirus Rous sarcoma virus LTR promoter, a dihydrofolate reductase promoter, a β-actin promoter, and a phosphoglycerate kinase (PGK) promoter. The gene for treatment or prevention and the promoter for expressing the gene are preferably flanked by the ITR sequences.
In the present invention, it is preferable that a virus helper gene derived from an adenovirus is introduced into cells. The virus helper gene is a non-adeno-associated virus gene for enabling replication and packaging of an adeno-associated virus. As the virus helper gene, a gene derived from a virus of another species other than the adeno-associated virus is used. Specific examples of the virus helper gene include a virus helper gene derived from an adenovirus or a herpesvirus, and the virus helper gene is preferably derived from an adenovirus.
Examples of the virus helper gene derived from adenovirus can include E1A, E1B, E2A, E4, and VA-RNA. In the host cell having all or a part of the E1 region, the region of the adenovirus genome required for replicating the AAV genome and packaging of the AAV genome into the capsid to form a virus virion is the E2A region, the E4 region, and the VA-RNA region. For the function by the E4 region, the 34 kDa E4 protein encoded by the open reading frame 6 (E4ORF6) of the E4 region is required for replicating the AAV. Preferably, the virus helper gene is an E2 gene, an E4 gene, or a VA-RNA gene. The VA-RNA gene is preferably a VA-RNAI gene.
The adenovirus-derived virus helper gene (such as an E1A, an E1B, an E2A, an E4, and a VA-RNA) may be a wild-type gene, but a gene in which modifications such as substitution, deletion, insertion, or addition of a base have been made to the wild-type gene may be used as long as it exhibits an inherent function.
In a case where modifications such as substitution, deletion, insertion, or addition of a base is made to the wild-type virus helper gene, the number of the modified bases is preferably 1 to 20, more preferably 1 to 10, and still more preferably 1 to 3. The modified base sequence of the virus helper gene exhibits preferably 85% or more sequence identity, more preferably 90% or more sequence identity, still more preferably 95% or more sequence identity, and even still more preferably 98% or more sequence identity with the base sequence of the wild-type virus helper gene.
In a case of introducing a virus helper gene into a cell, a vector containing the virus helper gene can be introduced into the cell.
As the vector containing a virus helper gene, for example, a plasmid, a virus-derived sequence, an artificially designed nucleic acid, or the like can be used, and a plasmid is preferable.
The virus helper gene is preferably under the control of a promoter and may be under the control of a promoter capable of regulating expression.
As the promoter capable of regulating expression, a promoter capable of regulating expression on and off by the presence or absence of a stimulus that induces expression in a condition-specific manner can be used. Examples of the stimulus that induces expression in a condition-specific manner include a chemical stimulus and a physical stimulus, but the present invention is not particularly limited thereto. Examples of the chemical stimulus include endogenous hormones, stress responses, lactose, tetracycline or a derivative thereof (for example, doxycycline), cumic acid, rapamycin, FKCsA, abscisic acid (ABA), tamoxifen/Cre-loxP (system in which a Cre promoter modified to be able to induce activation by tamoxifen is used), a riboswitch, and the like. Examples of the physical stimulus include blue light, heat, and the like.
Among the above, the promoter capable of regulating expression is preferably a promoter capable of regulating expression by a drug. The drug is preferably a tetracycline-based drug and more preferably doxycycline. That is, the stimulus that induces the expression in a condition-specific manner may be that the culture medium contains doxycycline.
Specifically, examples of the promoter capable of regulating expression include a tetracycline-responsive promoter, a RU486-inductive promoter, an ecdysone-inductive promoter, a rapamycin-inductive promoter, and a metallothionein promoter. Specific examples of the tetracycline-responsive promoter include a Tet-on/off system (manufactured by TET systems GmbH & Co. KG).
The promoter capable of regulating expression may be a Tet-on/off system which is a promoter capable of regulating expression by tetracycline, or a Tet-on system.
In the Tet-on system, the promoter additionally contains at least one Tet operon. By using a Tet operon (tetracycline-controlled transcriptional activation), transcription can be reversibly switched on or off in the presence of one of the tetracycline which is an antibiotic, or a derivative thereof (for example, doxycycline). The Tet repressor protein present in the cell blocks expression by binding to a Tet operator sequence introduced into a promoter. Therefore, no gene expression is observed in a case where the Tet repressor binds to the Tet operator sequence. By adding tetracycline or doxycycline, the Tet repressor is sequestered to allow promoter activity and turn on gene expression. The Tet operon system is widely available, such as the Tet operon used in the pcDNA (trademark) 4/TO mammalian expression vector available from Invitrogen.
In the Tet-on system, the Tet operator sequence may be located upstream or downstream of the promoter for which expression is desired to be regulated. The Tet operator sequence is preferably located downstream of a promoter capable of regulating expression in view of reducing expression leakage in a case where expression is turned off.
The specific examples of the promoter are not particularly limited, but can include a cytomegalovirus-derived promoter (CMV promoter) (including an enhancer as desired), an SV40 early promoter, a human elongation factor-1α (EF-1α) promoter, a human ubiquitin C promoter, a retrovirus Rous sarcoma virus (RSV) LTR promoter, a dihydrofolate reductase promoter, a β-actin promoter, and a phosphoglycerate kinase (PGK) promoter.
The exogenous recombinant nucleic acid means a recombinant nucleic acid introduced from the outside of a cell into the inside of the cell. The exogenous recombinant nucleic acid can be introduced into cells by methods such as transfection, transduction, and lipofection in a form of a vector containing the exogenous recombinant nucleic acid.
Transfection refers to a process of allowing a nucleic acid to cross a membrane of a eukaryotic cell and to be introduced into a cell by a chemical means (for example, using a reagent such as calcium phosphate or polyethyleneimine), a mechanical means (for example, electroporation), or a physical means (for example, delivery by bioballistic).
Transduction refers to introduce of a nucleic acid into a cell across a membrane of a eukaryotic cell via a virus-derived vector.
Lipofection refers to introduce of a nucleic acid into a cell by the formation of a complex between a vector and a positively charged lipid or the like by electrical interaction, and endocytosis or membrane fusion.
Preferably, in the animal cell, the exogenous recombinant nucleic acid is expressed in a constitutive expression system. The constitutive expression system is a method of expressing for 1 month or more. It is possible to maintain the expression of the target gene for a long period of time by inserting a plasmid into a chromosome, introducing an episomal vector, or introducing an exogenous nucleic acid using an artificial chromosome. In this case, in a case where the drug resistance gene is introduced into the plasmid, selection with a drug can be performed.
The recombinant nucleic acid is not particularly limited as long as it is a sequence capable of expressing a virus. Preferably, the recombinant nucleic acid is a sequence that expresses an adeno-associated virus. As described above, a sequence derived from a helper virus and a sequence derived from an adeno-associated virus is known as the sequence that expresses the adeno-associated virus, but the sequence is not limited to these as long as the adeno-associated virus can be expressed. The components derived from the helper virus include E1A, E1B, E2A, E4, and/or VA-RNA, but are not limited thereto. As the sequence derived from the adeno-associated virus, Rep and Cap are known, but the present invention is not limited thereto.
In the present invention, it is preferable that at least one of the exogenous recombinant nucleic acids contain a promoter controlled by an RNA polymerase III.
In the present invention, the exogenous recombinant nucleic acid is preferably a nucleic acid encoding E2A, E4, VA-RNA, Rep, and Cap.
In the present invention, the gene that is transcribed from a promoter controlled by the RNA polymerase III is more preferably VA-RNAi.
In the present invention, the expression of at least one RNA which is a gene transcriptional product of the exogenous recombinant nucleic acid is preferably 10 times or more, more preferably 10 times or more and 100 times or less, and still more preferably 20 times or more and 50 times or less, as compared with a case of culturing in a state in which the function of BET is not suppressed. Preferably, the expression of the VA-RNAI is 20 times or more. The state in which the function of BET is not suppressed is a state in which a BET inhibitor (preferably a bromodomain inhibitor) is not added, or a state in which an endogenous BET gene is not mutated or suppressed in expression, or a full length or a part of an exogenous wild-type or mutant BET gene is not introduced.
In the present invention, the exogenous recombinant nucleic acid preferably includes a nucleic acid encoding at least E2A and VA-RNAI, and the RNA expression ratio between the E2A and the VA-RNAI gene is preferably E2A:VA-RNAI=1:1 to 1:20, more preferably E2A:VA-RNAI=1:1 to 1:15, and still more preferably E2A:VA-RNAI=1:1 to 1:10.
It is preferable that at least one of the exogenous recombinant nucleic acids contains a nucleic acid sequence that induces expression in a condition-specific manner. The promoter induced by a nucleic acid sequence that induces expression in a condition-specific manner is not particularly limited, but is preferably a doxycycline-inducible TET promoter.
As a manufacturing method of the adeno-associated virus, any of a triple transfection (TT) method, a packaging cell method, or a producer cell method may be used. From the viewpoint of the effects of the present invention, the packaging cell method or the Producer cell method is preferable, and the Producer cell method is most preferable.
The TT method is a method in which a plasmid containing a Rep gene and a Cap gene, an adenovirus helper plasmid, and a plasmid containing a transgene (for example, a gene for desired therapy or prophylaxis) are simultaneously transfected into cells, and can thus be packaged as recombinant AAV (rAAV).
The packaging cell method is a method of producing AAV by introducing, to the cell in which a part of the gene in the TT method is incorporated into a chromosome in advance, the remaining genes into a cell by transfection.
The Producer cell method is a method of producing AAV using cells that produce AAV without additional gene introduction. Preferably, the method is a method of producing AAV without a transfection operation using cells in which a gene (containing at least Rep and Cap genes) in the TT method is incorporated into a chromosome. More preferably, the Producer cell method is a method of producing AAV without a transfection operation using cells in which all genes in the TT method are incorporated into a chromosome.
The animal cell is not particularly limited, but is preferably a mammalian cell or an insect cell, and more preferably a mammalian cell. Examples of the mammalian cell include a human cell, a mouse cell, a rat cell, a monkey cell, and a hamster cell, but the cells are not particularly limited. The human cell can be preferably used. Examples of the cell include mouse myeloma (NSO) cell lines, Chinese hamster ovary (CHO) cell lines, HT1080, H9, HepG2, MCF7, MDBK Jurkat, NIH3T3, PC12, a baby hamster kidney (BHK) cell, VERO, SP2/0, YB2/0, Y0, C127, an L cell, COS (for example, COS1 and COS7), QC1-3, a human embryo-derived kidney (HEK293) cell, VERO, PER. C6, HeLa, EB1, EB2, EB3, and oncolytic or hybridoma cell lines. The cell is preferably a HEK293 cell or a CHO cell, and more preferably a HEK293 cell.
The method according to the embodiment of the present invention includes a virus production step of culturing animal cells in a culture medium.
The culturing the cells in the present invention can be performed under normal conditions for culturing the cells.
The cell density at the time of seeding the cells in the virus production step is preferably 1×104 cells/mL or more, more preferably 1×105 cells/mL or more, still more preferably 1×106 cells/mL or more, even still more preferably 1×107 cells/mL or more, and particularly preferably 1×108 cells/mL or more. The upper limit of the cell density at the time of seeding the cells is not particularly limited, but is generally 1×109 cells/mL or less.
In the present invention, a proliferation step of proliferating cells can be performed before the virus production step. The form of the culturing in the proliferation step is not particularly limited, but is preferably perfusion culture.
For example, a proliferation step of culturing cells in a culture medium that does not contain doxycycline and a BET inhibitor (preferably a bromodomain inhibitor) until the cell density reaches 1×104 cells/mL or more (more preferably 1×105 cells/mL or more, still more preferably 1×106 cells/mL or more, even still more preferably 1×107 cells/mL or more, and particularly preferably 1×108 cells/mL or more) is performed before the virus production step, and then the virus production step can be performed using a culture medium containing doxycycline and a BET inhibitor (preferably a bromodomain inhibitor).
The culture temperature of the cells is not particularly limited, and the culture of the cells are performed at a temperature at which the cells can survive. The culture temperature is generally 25° C. to 45° C., preferably 30° C. to 42° C., more preferably 35° C. to 40° C., and 37° C. as an example.
The CO2 concentration is generally 3 to 10% CO2, preferably 5 to 10% CO2, and 8% CO2 as an example.
The period of the virus production step is preferably 24 hours or more and 30 days or less, more preferably 24 hours or more and 20 days or less, still more preferably 24 hours or more and 10 days or less, even still more preferably 24 hours or more and 7 days or less, and particularly preferably 24 hours or more and 72 hours or less.
As the culture, batch culture, fed-batch culture, perfusion culture, or shaking culture can be performed. It is preferable that at least a part of the virus production step is perfusion culture.
As the culture container, a flask or a bioreactor can be used, but it is not particularly limited.
The culture scale is not particularly limited, and the cells can be cultured in a culture medium of any volume, for example, the cells can be cultured in a culture medium of 1 mL to 2,000 L, preferably 1 L to 2,500 L, more preferably 50 L to 2,300 L, and particularly preferably 400 L to 2,200 L.
The culture may be carried out while stirring by shaking. The stirring speed in the case of stirring by shaking is generally 50 rpm to 200 rpm, and preferably 80 to 150 rpm. The stirring culture may be rotary stirring culture using a propeller or the like in a reactor. The stirring speed in the case of stirring by rotating is generally 50 rpm to 200 rpm, and preferably 80 to 150 rpm. In addition, stirring may be performed by wave-type shaking stirring or vertical movement of the stirring blade, but the stirring is not particularly limited.
Examples of the culture medium include, but are not limited to, Expi293 Expression Medium (Thermo Fisher Scientific, Inc., A1435101), a Dalbecco's modified Eagle's medium (DMEM) containing 10% (vol/vol) fetal bovine serum (FBS), a serum-free UltraCULTURE (trademark) culture medium (Lonza), a STEMPRO (trademark)-34 SFM culture medium, a human endothelial-SFM, a GIBCO (registered trademark) FREESTYLE (trademark) 293 expression medium, a CD CHO AGT culture medium, a CHO-S-SFM culture medium, a GIBCO (registered trademark) FREESTYLE (trademark) CHO expression medium, a CD OPTICHO (trademark) culture medium, a CD CHO culture medium, a CD DG44 culture medium, a SF-900 (trademark) culture medium, an Expi293 (trademark) expression medium, a 293 SFM culture medium, a BALANCD (registered trademark) HEK293 culture medium, and any derivates or modifications thereof. In a certain specific non-limiting embodiment, the high-density culture medium may be a CD FORTICHO (trademark) culture medium, a CD CHO AGT culture medium, a CHO-S-SFM culture medium, a GIBCO (registered trademark) FREESTYLE (trademark) CHO expression medium, a CD OPTICHO (trademark) culture medium, a CD CHO culture medium, a CD DG44 culture medium, a GIBCO (registered trademark) FREESTYLE (trademark) 293 expression medium, an Expi293 (trademark) expression medium, an LV-MAX (trademark) production culture medium, a FREESTYLE (trademark) F17 expression medium, a DYNAMIS (trademark) culture medium, a BALANCD (registered trademark) HEK293 culture medium, a similar culture medium, or a modified form thereof.
The culture medium is preferably Expi293 Expression Medium (Thermo Fisher Scientific, A1435101), or a Dulbecco's Modified Eagle's Medium (DMEM) containing 10% (vol/vol) fetal bovine serum (FBS).
The method for producing a target virus according to the embodiment of the present invention may include recovering the virus. The target virus produced in the cell that produces a virus remains in the cell or is released into the culture supernatant.
In a case of recovering a target virus from cells, for example, a specimen containing the target virus can be prepared by subjecting the cells to ultrasonic lysis, freezing and thawing the cells to lyse the cells, or bringing the cells into contact with an acidic solution. The specimen prepared in this way may be used as it is, or may be purified as desired.
In a case of recovering the target virus from the culture supernatant, the culture supernatant may be used as it is as a specimen containing the target virus, or may be purified as desired.
The purification method in a case of purifying the target virus is not particularly limited, and examples thereof include a CsCl gradient ultracentrifugation method, a chromatography method, and an ultrafiltration method. By the above-described purification method, the target virus can be purified from a specimen containing the target virus. Furthermore, the genome DNA (gDNA) or the residual plasmid may be digested by adding MgCl2 and Benzonase to the specimen purified as described above to perform a reaction.
The titer of the target virus produced by the method according to the embodiment of the present invention can be measured by a normal method known to those skilled in the art. For example, the cell culture solution after the culture is collected, the cells are disrupted by freeze-thaw, and then the supernatant is collected by centrifugation. The gDNA (genomic DNA) and the residual plasmid can be digested by adding MgCl2 and Benzonase to the collected supernatant to react. It is possible to measure the titer of a target virus by performing droplet digital PCR (ddPCR) using the sample containing the target virus obtained above as a ddPCR sample.
In an example of the present invention, by suppressing the function of BET, the production amount of a target virus such as AAV can be improved by 2 times or more as compared with the production method in the related art.
According to the present invention, there is provided a culture composition containing an animal cell into which an exogenous recombinant nucleic acid encoding a target virus has been introduced and in which a function of BET is suppressed, a virus, and culture medium.
Specific examples and preferred aspects of the “animal cell in which an exogenous recombinant nucleic acid encoding a target virus has been introduced and a function of BET is suppressed”, “virus”, and “culture medium” are as described in the present specification.
In the culture composition according to the embodiment of the present invention, the virus is preferably an adeno-associated virus.
In the culture composition according to the embodiment of the present invention, the culture medium preferably contains a BET inhibitor (preferably a bromodomain inhibitor).
The present invention will be more specifically described using the following examples; however, it is not limited by the examples.
Floating HEK293 cells (Thermo Fisher Scientific, R79007) were suspended in 12 mL of Expi293 Expression Medium (Thermo Fisher Scientific, A1435101) in a 1×107 cells/mL, and cultured in 125 mL shaking flask for 24 hours. The culture solution was incubated under the conditions of 37° C. and 8% CO2 while being constantly stirred at 120 rpm.
HEK293 cells were seeded in a 24-well plate at a density of 0.75×105 cells/well in a DMEM medium containing 10% FBS (clontech, 631101) (FUJIFILM Wako Pure Chemical Corporation, 041-29775), and then subjected to adhesion culture for 24 hours. The plasmids (seq1 and seq2) were co-introduced into HEK293 cells using TransIT-293 (Takara Bio, MIR2704) reagent. After 0.5 months, the cells were each seeded in a 96-well plate, and after further expansion culture for 1 month, an AAV producer cell strain in which the plasmid was incorporated into the chromosome was produced.
Seq1: all-in-one plasmid (integrated plasmid into which a gene required for AAV production is incorporated). The Rep gene and the Cap gene are controlled by a p5 promoter contained in the wild-type AAV. The E2 gene is controlled by a promoter contained in a wild-type adenovirus. The seq1 is designed as E4ORF6 is under the CMV promoter, and VA-RNA is under the H1 promoter, and the TET operator sequence is incorporated into the promoter to be capable of being controlled by expression by doxycycline.
Seq2: a plasmid (GENEWIZ) obtained by synthesizing the piggyBac transposase gene sequence and inserting the gene sequence into the EcoRV site of the pUC57 vector.
The base sequence of the seq1 is set forth in SEQ ID NO: 1 in the sequence list, and the base sequence of seq2 is set forth in SEQ ID NO: 2 in the sequence list.
The produced AAV producer cell was seeded in a 24-well plate at 5×105 cells/mL, incubated for 6 hours (the number of cells was 5×105 cells/mL or more), and then doxycycline (final concentration of 0.5 μg/mL) and Epigenetics Screening Library (CAYMAN, 11076) (final concentration of 4 μmol/L) were added. After the treatment for 72 hours, the cells were recovered, and the evaluation of the Real-time PCR and the AAV titer measurement were performed.
The HEK cells cultured 72 hours after the gene introduction under the conditions of 37° C. and 8% CO2 were collected by centrifugation at 300×g. mRNA was purified using RNeasy Plus Mini Kit (Qiagen), and cDNA was prepared by reverse transcription using High Capacity RNA to cDNA Kit. The produced cDNA was quantitatively evaluated by detection with primers and probes for various genes (E2: seq3, 4, 5, VA-RNA: seq6, 7, 8, E4ORF6: seq9, 10, 11, Rep: seq12, 13, 14, and Cap: seq15, 16, 17) using TaqMan Gene Expression Master Mix (Applied Biosystems), and by standardization for GAPDH (Thermo Fisher Scientific, Hs02786624_g1) using TaqMan Gene Expression Assay. The base sequences of the seqs. 3 to 17 are each shown in SEQ ID NOs: 3 to 17 in the sequence list.
The HEK cell culture solution, which had been cultured for 72 hours after the gene introduction under the conditions of 37° C. and 8% CO2, was collected, and the cells were disrupted by freezing and thawing at −80° C. Then, the supernatant was collected by centrifugation at 13,800×g, 2 mmol/L (final concentration) MgCl2, and 25 U/mL Benzonase was added thereto, and a reaction was carried out at 37° C. for 2 hours to digest gDNA (genomic DNA) and residual plasmid. The sample after the reaction was incubated at 95° C. for 15 minutes, 70° C. for 3 minutes, 40° C. for 3 minutes, and 20° C. for 3 minutes in this order, to inactivate Benzonase, and the reactant was used as a ddPCR (Droplet Digital PCR) sample. The ddPCR sample was diluted 50-fold with a solution in which 0.05% Pluronic F-68 and 10 μg/mL bovine thymus DNA was mixed to a TE buffer (pH 8.0). 10 μL of ddPCRtm Supermix for Probes (no dUTP) (Bio-Rad Laboratories, Inc.), 2 μL of diluted ddPCR sample, primers (seq18, seq19, final concentration of 900 nmol/L) and probe (seq20, final concentration of 250 nmol/L), nuclease free water (Thermo Fisher Scientific, 10977015) was mixed in a tube on ice, the total liquid volume was adjusted to 22 μL, and ddPCR was performed. The sequences of the seq18, seq19, and seq20 are set forth in SEQ ID NOs: 18 to 20 in the sequence list.
In ddPCR, droplets were formed from the prepared solution using a droplet forming apparatus, and subsequently incubated at 95° C. for 10 minutes, 94° C. for 30 seconds, and 55° C. in this order for 40 cycles, and then incubated at 98° C. for 10 minutes. Measurement was performed using a droplet reader, and the AAV genomic titer (vg/mL) was calculated.
The produced AAV producer cell was seeded in a 96-well plate at 5×105 cells/mL, incubated for 6 hours (the number of cells was 5×105 cells/mL or more), and then doxycycline (final concentration of 0.5 μg/mL) and Epigenetics Screening Library (CAYMAN, 11076) (final concentrations of 0.15, 0.45, and 1.35 μmol/L) were added. After the treatment for 72 hours, the cells were recovered, and the AAV titer was evaluated.
The change in the AAV production amount at the time of each bromodomain inhibitor addition was evaluated. Table 1 and
From the results of
As the Kd value of the bromodomain inhibitor used, the nominal numerical value published by the reagent manufacturer is shown in Table 3.
As the IC50 value of the bromodomain inhibitor used, the nominal numerical value published by the reagent manufacturer is shown in Table 4.
Furthermore, the produced AAV producer cell was seeded at 5×105 cells/mL and incubated for 6 hours, and then doxycycline (final concentration: 0.5 μg/mL) and JQ1 (final concentration: 4 μmol/L) were added.
After the JQ1 treatment, the AAV titer per cell was further improved by removing JQ1 from the culture medium.
[Sequence list] International application 22F00823W1JP23030630 4.xml based on International Patent Cooperation Treaty
| Number | Date | Country | Kind |
|---|---|---|---|
| 2022-134297 | Aug 2022 | JP | national |
This application is a Continuation of PCT International Application No. PCT/JP2023/030630 filed on Aug. 25, 2023, which claims priority under 35 U.S.C § 119(a) to Japanese Patent Application No. 2022-134297 filed on Aug. 25, 2022. Each of the above application(s) is hereby expressly incorporated by reference, in its entirety, into the present application.
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/JP2023/030630 | Aug 2023 | WO |
| Child | 19060910 | US |
