WO2009137911A1 - Process, vectors and engineered cell lines for enhanced large-scale transfection - Google Patents

Process, vectors and engineered cell lines for enhanced large-scale transfection Download PDF

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WO2009137911A1
WO2009137911A1 PCT/CA2009/000263 CA2009000263W WO2009137911A1 WO 2009137911 A1 WO2009137911 A1 WO 2009137911A1 CA 2009000263 W CA2009000263 W CA 2009000263W WO 2009137911 A1 WO2009137911 A1 WO 2009137911A1
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gene
interest
cells
ebna1
expression
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PCT/CA2009/000263
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French (fr)
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Yves Durocher
Martin Loignon
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National Research Counsil Of Canada
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Priority to CA2722835A priority Critical patent/CA2722835C/en
Priority to US12/989,898 priority patent/US8637315B2/en
Priority to EP09745326A priority patent/EP2285969B1/en
Priority to DK09745326.0T priority patent/DK2285969T3/en
Publication of WO2009137911A1 publication Critical patent/WO2009137911A1/en
Priority to US14/068,336 priority patent/US9353382B2/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/70—Fusion polypeptide containing domain for protein-protein interaction
    • C07K2319/71—Fusion polypeptide containing domain for protein-protein interaction containing domain for transcriptional activaation, e.g. VP16
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2710/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA dsDNA viruses
    • C12N2710/00011—Details
    • C12N2710/16011—Herpesviridae
    • C12N2710/16211—Lymphocryptovirus, e.g. human herpesvirus 4, Epstein-Barr Virus
    • C12N2710/16222—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2710/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA dsDNA viruses
    • C12N2710/00011—Details
    • C12N2710/16011—Herpesviridae
    • C12N2710/16611—Simplexvirus, e.g. human herpesvirus 1, 2
    • C12N2710/16622—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2800/00—Nucleic acids vectors
    • C12N2800/10—Plasmid DNA
    • C12N2800/108—Plasmid DNA episomal vectors
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2800/00—Nucleic acids vectors
    • C12N2800/40—Systems of functionally co-operating vectors

Definitions

  • the present invention relates to processes vectors and engineered cell lines for large-scale transfection and protein production
  • an expression system for stable expression of a gene of interest comprising one vector having an Epstein-Barr virus nuclear ant ⁇ gen-1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein, a promoter and a polyadenylation signal for the EBNA1 nucleotide sequence an o ⁇ P nucleotide sequence the gene of interest and a promoter and a polyadenylation signal for the gene of interest
  • EBNA1 Epstein-Barr virus nuclear ant ⁇ gen-1
  • a method of stably expressing a gene of interest in mammalian cells comprising transfecting a mammalian cell with a vector having an Epstein-Barr virus nuclear ant ⁇ gen-1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein, a promoter and a polyadenylation signal for the EBNA1 nucleotide sequence, an oriP nucleotide sequence the gene of interest and a promoter and a polyadenylation signal for the gene of interest and replicating the cell to provide mammalian cells that stably express the gene of interest
  • EBNA1 Epstein-Barr virus nuclear ant ⁇ gen-1
  • an expression system for stable expression of a gene of interest comprising a first vector having an Epstein-Barr virus nuclear ant ⁇ gen-1 (EBNA1) nucleotide sequence encoding a truncated EBNA1 protein a promoter and a polyadenyiation signal for the EBNA1 nucleotide sequence and an oriP nucleotide sequence and, a second vector having a gene of interest a promoter and a polyadenylation signal for the gene of interest and an oriP nucleotide sequence
  • EBNA1 Epstein-Barr virus nuclear ant ⁇ gen-1
  • transfecting the cell with the first and second vectors may be accomplished simultaneously, or the cell may be transfected by one of the vectors first to produce a stable clone followed by transfection with the other vector to produce a clone that stably expresses the gene of interest
  • a method of transiently expressing a gene of interest in Chinese Hamster Ovary (CHO) cells comprising transfecting a CHO cell with a first vector having an
  • Epstem-Barr virus nuclear antigen- 1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein, a promoter and a polyadenylation signal for the EBNA1 nucleotide sequence and an oriP nucleotide sequence and a second vector having the gene of interest and a promoter and a polyadenylation signal for the gene of interest, and, replicating the cell to provide CHO cells that transiently express the gene of interest
  • transfecting the CHO cell with the first and second vectors may be accomplished simultaneously or the CHO cell may be transfected by one of the vectors first to produce a clone followed by transfection with the other vector to produce a clone that transiently expresses the gene of interest
  • EBNA1 Epstem-Barr virus nuclear ant ⁇ gen-1
  • a fusion protein comprising a truncated Epstem-Barr virus nuclear antigeni c (EBNAIc) protein and, a herpes simplex virus protein VP16
  • a use of a 40 kDa fully deacetylated poly(ethylen ⁇ m ⁇ ne) as a transfection reagent for improving transfection efficiency in transfection of Chinese Hamster Ovary (CHO) cells
  • a use of co-expression of a fibroblast growth factor (FGF) to increase heterologous gene expression in Chinese Hamster Ovary (CHO) cells FGF
  • Fig 1 depicts schematic diagrams of EBNA1 constructs
  • Fig 2 depicts graphs of SEAP activity in CHO cells co-transfected with pTT vectors encoding various EBNA1 constructs
  • Fig 3A depicts genetic maps of pTT vectors encoding EBNAI c in as under a strong (EFI ⁇ -HTLV, pTT31 ) or a weak (RSV, pTT34) promoter
  • Fig 3B depicts a graph of SEAP activity in CHO cells transfected with pTT vectors encoding EBNAI c in cis under a weak or strong promoter
  • Fig 4A depicts a Western blot of extracts from CHO cells transfected with a linearized pTT-EBNA1c vector containing a blasticidin resistance cassette
  • Fig 4B depicts a Western blot of ahquots of cultures of the CHO cells of Fig 4A at various time intervals without selection pressure
  • Figs 5A-C depict Western blots of codon optimized EBNA1 expression in HEK293 and CHO cells
  • Fig 5D depicts a graph of secreted alkaline phosphatase (SEAP) activity in CHO cells co-expressing VP16-EBNA1 c fusion protein compared to control cells or cells expression an EBNAI c protein
  • Fig 6 depicts graphs of SEAP activity in HEK293 and CHO cells transfected with pTT plasmids using LPEI or LPEI-Max
  • Fig 7 depicts a graph of SEAP activity in transiently transfected CHO-EBNAI c cells illustrating the transactivating activity of oriP
  • Fig 8 depicts a graph of SEAP activity in transfected CHO-EBNAI c cells illustrating the effect of the CMV5 promoter vs the Elongation Factor 1 alpha-HTLV (EFI ⁇ -HTLV) hybrid promoter
  • Fig 9 depicts graphs of SEAP activity illustrating the effect of FGF2 (bFGF) co- expression on transient gene expression in HEK293-EBNA1t and CHO-EBNAIc cells
  • Fig 10 depicts a graph of SEAP expression in CHO-EBNA1 c cells illustrating protein kinase B (AKT) potentiation of valproic acid (VPA) enhancement of transient gene expression
  • AKT protein kinase B
  • VPA valproic acid
  • Fig 11 depicts genetic maps of SEAP-encoding pTT plasmids pTT22 (+or ⁇ P) and pTT30 (-oriP) and graphs of SEAP activity in CHO-EBNAIc cells transfected with linearized pTT22 and pTT30 plasmids illustrating the effect of oriP on linearized vectors in
  • Fig 12 depicts a graph of SEAP activity in CHO-EBNAIc cells after integration of linearized pTT22 (+or ⁇ P) and pTT30 (-oriP) piasmids in their chromosomes
  • Cell culture CHO cells are grown at 37 0 C in FreestyleCHO medium (Invitrogen) supplemented with 8 mM glutamine in Erlenmeyer flasks shaken at 120 rpm in a humidified atmosphere containing 5% CO 2 Cells are routinely maintained between O 1 x10 6 and 3 0x1 O ⁇ cells/ml HEK293-EBNA1 cells (clone 6E) are grown at 37 0 C in F17 medium (Invitrogen) supplemented with 4 mM glutamine and O 1 % pluronic F68 in
  • CHO or HEK293 cells are grown in maintenance medium until they reach a density of 1 5x10 6 to 2 0x10 s cells/ml and then the transfection mixture is added to the cells
  • 1 ⁇ g of plasmid DNA is mixed with 2 ⁇ g of 25 kDa linear polyethylenimine as previously described (Durocher Perret & Kamen 2002)
  • 2 ⁇ g of 25 kDa linear polyethylenimine as previously described (Durocher Perret & Kamen 2002)
  • For every ml of CHO ceils to be transfected 1 ⁇ g of plasmid DNA is mixed with 8 ⁇ g of 25 kDa linear polyethylenimine or with 6 ⁇ g of 40 kDa linear and deacetylated PEI (PEIMAX " " from Polysciences lnc catalog #24765-2)
  • SEAP activity is measured as previously described using the colo ⁇ met ⁇ c substrate paranitrophenyl phosphate (Durocher et al 2000)
  • Mammalian cells transfected with an expression system in which a single vector contains an Epstein-Barr virus nuclear antigen- 1 (EBNA1) nucleotide sequence encoding a truncated EBNA1 protein, an Epstein-Barr Virus (EBV) o ⁇ P nucleotide sequence and a gene of interest unexpectedly provide enhanced stable expression of the gene of interest
  • Truncated EBNA1 proteins include for example, EBNAI c, EBNAIt and EBNAI s These truncated forms are shown in Fig 1 EBNAIt is a 417 ammo acid protein having
  • DNA Linking Region 1 containing Transcriptional Activation Domain (TAD) and DNA Linking Region 2 (LR2) without the GIy-AIa repeats of the 641 amino acid full length protein
  • EBNAIc is a 306 amino acid protein in which LR2 is present but LR1 is absent and EBNAI s is a 337 ammo acid protein in which LR1 is present but LR2 is absent EBNA1 nucleotide sequences encoding EBNAI c are preferred in the vector
  • the amino acid sequences for the full length EBNA1 protein as well as the truncated forms EBNAIt, EBNAIc and EBNAI s are shown in SEQ ID NO 1-4 respectively
  • the corresponding nucleotide sequences of the nucleic acid molecules encoding full length EBNA1 and the truncated forms are shown in SEQ ID NO 5-8, respectively
  • EBV oriP complete nucleotide sequence (pTT3 vector) is shown in SEQ ID NO 9 and a functional EBV o ⁇ P truncated nucleotide sequence (pTT5 vector) is shown in SEQ ID NO 10
  • the o ⁇ P sequence comprises the Family of Repeats (FR) component and the dyad symmetry (DS) component
  • FR Family of Repeats
  • DS dyad symmetry
  • the oriP sequence particularly the FR component contributes to increased expression and stability of expression of the integrated truncated EBNA1 gene
  • the gene of interest may be any gene that encodes a protein product of interest Expression of the gene of interest in the transfected cells permits stable, large-scale production of the protein product for industrial purposes
  • Some particular genes of interest include for example genes that encode monoclonal antibodies erythropoietins interferons vascular endothelial growth factors stem cell growth factors growth hormones insulin-like growth factor binding proteins etc
  • the single vector also preferably comprises a selection gene to permit selection of the transfected cells for the propagation of stable cell lines
  • Any suitable selection gene may be used
  • One example of a class of such genes are genes that confer antibiotic resistance on the cell when the vector is transfected into the cell. Some examples within this class include genes that confer resistance to puromycin, blasticidin, geneticin, zeocin or hygromycin
  • the blasticidin resistance cassette as found in the pYD7 vector is particularly preferred
  • the cell may be permitted to replicate Clones possessing the expression system may be selected on the basis of the selection gene, for example, by treating the cells with an antibiotic and cultu ⁇ ng the cells that survive In this way a cell line stably expressing the gene of interest may be created
  • any or all of the nucleotide sequences and/or genes in the integrated vector may be under the control of a promoter also incorporated in the vector Generally each gene has its own promoter Thus, there is preferably a promoter for the EBNA1 , a promoter for the gene of interest and a promoter for the selection gene Strong or weak promoters may be used Some promoters include, for example the cytomegalovirus (CMV) promoter Elongation Factor 1 alpha-HTLV (EFI ⁇ -HTLV) hybrid promoter, and Rous sarcoma virus (RSV) promoter Also, any or all genes may have a polyadenylation signal Alternatively, two genes, separated by an Internal Ribosome Entry Site (IRES), can be expressed by using only one promoter and one polyadenylation signal
  • CMV cytomegalovirus
  • RSV Rous sarcoma virus
  • any or all genes may have a polyadenylation signal
  • pTT31-SSH is a 8014 bp vector in which the EBNAIc gene is under the control of a strong promoter (EFI ⁇ -HTLV) and the gene of interest (secreted alkaline phosphatase (SEAP) gene) is under the control of a strong promoter (CMV)
  • pTT34-SSH is a 8040 bp vector in which the EBNAIc gene is under the control of a weaker promoter (RSV) and the gene of interest (secreted alkaline phosphatase (SEAP) gene) is under the control of a strong promoter (CMV)
  • Fig 3B depicts a graph of SEAP activity in CHO cells transfected with pTT vectors (oriP-containing vectors) encoding EBNAI c in cis under a weak (RSV) or strong (EFI ⁇ - HTLV) promoter
  • pTT vectors oriP-containing vectors
  • EFI ⁇ - HTLV strong promoter
  • the single vector EBV o ⁇ P-EBNA1 expression system is useful in different types of mammalian cells for example Chinese Hamster Ovary (CHO) cells human embryonic kidney 293 (HEK293) cells Madin-Darby Canine Kidney (MDCK) cells, Vero cells and
  • Mammalian cells transfected with an expression system comprising two separate vectors a first vector containing an Epstein-Barr virus nuclear ant ⁇ gen-1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein and an Epstein-Barr Virus
  • EBNA1 Epstein-Barr virus nuclear ant ⁇ gen-1
  • both vectors contain selection genes. Selection genes are described above For example a stable CHO cell clone expressing EBNAI c driven from an integrated oriP vector containing a blasticidin resistance cassette (pYD7) stably expressed the gene of interest for over 6 months in the absence of selection
  • Stable mammalian cell lines can be produced either by simultaneously transfecting a cell with both vectors and then propagating the cell or by transfecting a cell with one of the vectors (either the EBNA1 -containing or the gene of interest-containing vector) to produce a stable clone and then transfecting a stable clone cell with the other of the vectors to produce a stable clone stably expressing the gene of interest
  • Truncated EBNA1 proteins and corresponding genes as well as the oriP and genes of interest are described above As described previously genes may be under the control of promoters
  • the two vector EBV or ⁇ P-EBNA1 stable expression system is also useful in different types of mammalian cells, for example Chinese Hamster Ovary (CHO) cells human embp/onic kidney 293 (HEK293) cells Madin-Darby Canine Kidney (MDCK) cells and PER C6 "V1 cells especially CHO cells
  • FIGs 1 1 and 12 Chinese Hamster Ovary (CHO) cells stably expressing EBNAI c were produced by transfecting CHO cells with an EBNAIc o ⁇ P- containing plasmid (pYD7 vector) using generally known methods with a linear 25 kDa polyethylenimine (PEI) and stable clones were propagated
  • EBNAIc o ⁇ P- containing plasmid pYD7 vector
  • PEI polyethylenimine
  • clone 3E7 CHO-EBNAIc clone (clone 3E7) so produced was transfected with secreted alkaline phosphatase (SEAP)- encoding and linearized pTT22 (+or ⁇ P) or pTT30 (-o ⁇ P) vectors
  • SEAP secreted alkaline phosphatase
  • the pTT22 and pTT30 vectors both contain a puromycin resistance cassette
  • the pTT22 vector contains o ⁇ P ( ⁇
  • CHO-EBNAI c cells transfected with the pTT22 and pTT30 vectors were transferred in 96-well plates at a density of 100 cells/well Puromycin was added 24 hours post-transfection and selection was maintained for two weeks
  • Chinese Hamster Ovary (CHO) cells transfected with an expression system comprising two separate vectors, a first vector containing an Epstem-Barr virus nuclear ant ⁇ gen-1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein and an Epstem-Barr Virus (EBV) o ⁇ P nucleotide sequence and a second vector comprising a gene of interest and an Epstem-Barr Virus (EBV) oriP nucleotide sequence also unexpectedly provide enhanced transient expression of the gene of interest in the CHO cells
  • EBNA1 Epstem-Barr virus nuclear ant ⁇ gen-1
  • EBV Epstem-Barr Virus
  • CHO cell lines can be produced either by simultaneously transfecting a cell with both vectors and then propagating the cell, or by transfecting a cell with one of the vectors (either the EBNA1 -containing or the gene of interest-containing vector) to produce a clone and then transfecting a clone cell with the other of the vectors to produce a clone transiently expressing the gene of interest
  • Truncated EBNA1 proteins and corresponding genes, as well as the oriP and genes of interest are described above As described previously, genes may be under the control of promoters
  • Fig 2 illustrates transient expression of secreted alkaline phosphatase (SEAP) in CHO cells co-transfected with one vector containing oriP plus the SEAP gene and another vector containing oriP plus truncated EBNA1 constructs (EBNAIt 1 EBNAIc and EBNAI s)
  • CHO cells were co-transfected with 50% of pTT-EBNA1 constructs or 50% salmon testis DNA (stDNA) and (45% pTT-SEAP + 5% pTT-GFP) plasmids SEAP activity was compared to activity in CHO cells transfected with 95% pTT-SEAP + 5% pTT- GFP SEAP activity (OD/min at 410 nm) was measured 5 days post-transfection
  • Fig 2 show an increase in transient SEAP activity of 2-fold or higher in CHO cells co-transfected with o ⁇ P/EBNA1 and o ⁇ P/SEAP plasmids over CHO cells that are not co-transfected with or ⁇ P/EBNA1 plasmids
  • the Transcriptional Activation Domain ' (aa 65-89) in the LR1 domain of EBNA1 is essential for transcriptional activation of integrated oriP vectors
  • Fig 2 surprisingly shows that the truncated Ef NA1 c construct lacking the LR1 domain but containing the LR2 domain is capable of increasing gene expression from non-integrated o ⁇ P plasmids to the same level as EBNAIt (that contains both the LR1 and LR2 domains) or EBNAI s (that contains only the LR1 domain)
  • CHO cells were transfected with a linearized pTT-EBNA1 c vector containing a blasticidin resistance cassette (pYD7 vector) Linearization of the vector was achieved following restriction enzyme digestion using Pvul enzyme Following transfection cells having stably integrated the pYD7 vector were selected by adding blasticidin to the culture medium After a few days of blasticidin selection, blasticidin- resistant cells were seeded in 96-well plates without blasticidin selection Emerging clones were tested for EBNAIc expression An EBNAIc-positive clone 3E7 (Fig 4A) was then selected for further testing A master cell bank (MCB) and Working cell bank (WCB) were made at this point The CHO-EBNAI c (clone 3E7) cells were cultured for over 130 days in the absence of blasticidin selection At various culture time points an aliquot of the cells were taken for EBNAIc expression analysis by Western blot using an ant ⁇ -EBNA1 antibody Fig 4B shows that the clone
  • CHO cells containing integrated EBNA1-express ⁇ ng plasmids were produced by transfecting CHO cells with a pTT-EBNA1 c vector, and the clone propagated (clone 3E7) Resulting CHO-EBNAIc clone was transfected with SEAP-encoding pTT plasmids with complete o ⁇ P (pTT-SMH), with DS-deleted o ⁇ P (pTTi-SMH), with FR- deleted o ⁇ P (pTTj-SMH) or with o ⁇ P-deleted (pTTI-SMH) pTT vectors SEAP activity (OD/min at 410 nm) was measured in the supernatant at 5 days post-transfection Transfections were accomplished using generally known methods with a linear 25 kDa polyethylenimine (PEI)
  • CHO-EBNA1 cells is due to the transactivating activity of the o ⁇ P family of repeats (FR) element, and not to plasmid replication
  • FR o ⁇ P family of repeats
  • DS dyad symmetry
  • Fig 8 compares the effect of the cytomegalovirus (CMV5) promoter and elongation factor 1 alpha-HTLV (EF1 - ⁇ HTLV) promoter on transgene expression in CHO- EBNAIc cells (clone 3E7) CHO-EBNA1 c-3E7 cells were transfected with increasing amount SEAP-encoding oriP-containing (pTT) plasrrids containing either the CMV5 or EF1 -GHTLV promoter to control the SEAP gene (the overall content of DNA was kept constant by compensating with non-codirg StDNA) SEAP activity (OD/min at 410 nm) was measured in the supernatant at day 6 post-transfection
  • the results clearly demonstrate that the CMV5 promoter is at least 5 times more potent than the EF1 - ⁇ HTLV promoter at low plasmid doses (e g 5%) Further CMV5-based plasmid needs 2-4 times less coding plasmid DNA for maximum expression
  • Epstem-Barr virus nuclear ant ⁇ gen-1 (EBNA1 ) nucleotide sequence strongly enhances expression of EBNA1 in mammalian cells especially
  • EBNAIc-CO SEQ ID NO 13 Codon-optimized EBNAIc nucleotide sequence codes for a 308 amino acid protein (SEQ ID NO 1 1 ) Codon-optimized EBNAIs nucleotide sequence (EBNAIs-CO SEQ ID NO 14) codes for a 337 amino acid protein (SEQ ID NO 12)
  • EBNA1 constructs (EBNAIc and EBNAIs) were codon- optim zed (human codon usage - CO) pTT vectors containing EBNAIc EBNAI s or their codon-optimized versions (EBNAIc-CO (SEQ ID NO 13) and EBNAIs-CO (SEQ ID NO 14)) and empty pTT vector (CTRL) were transfected in separate HEK293 cells or CHO cells by generally known methods with a linear 25 kDa polyethylenimine (PEI) Three days post-transfection cells were lyzed and cell extracts analyzed by Western blot using an ant ⁇ -EBNA1 antibody Fig 5A is a Western blot for cell extracts from HEK293 cells and Fig 5B is a Western blot for cell extracts from CHO cells In both cell lines it is evident that codon optimization enhances transient expression of EBNA1 in the cells when compared to the control (CTRL) and the cells
  • HEK293 cells were transfected with increasing amounts (1 25% 5% and 20%) of pTT vectors containing EBNAI c EBNAIc CO EBNAI s or EBNAI s-CO Again it is evident from the Western blots in Fig 5C that codon optimization enhances transient expression of EBNA1 in cells when compared to cells transfected with non- codon-optimized EBNA1
  • CHO cells were co-transfected with pTT-SEAP (50%) plus 5% pTT- GFP vectors (Control) with or without 10% of pTT-EBNA1 c, pTT-EBNAI cCO or pTT- VP16/EBNA1 cCO (EBNAIcCO fused at its N-terminus to VP16 - see below)
  • Non- coding DNA stDNA was used as stuffer DNA to complete the amounts of DNA to 100% SEAP activity measured 5 days later
  • a fusion protein comprising a truncated Epstein-Barr virus nuclear antigeni c (EBNAIc) protein and a herpes simplex virus protein VP16 provides significantly enhanced transactivating activity in mammalian cells, particularly Chinese Hamster Ovary (CHO) cells and human embryonic kidney (HEK) cells
  • a fusion protein is constructed by fusing VP16 to the N-terminus of codon- optimized EBNAIc
  • the VP16 cDNA encoding for the following protein sequence was used APPTDVSLGDELHLDGEDVAMAHADALDDFDLDMLGDGDSPGPGFTPHDSAPY GALDMADFEFEQMFTDALGI DEYGG (SEQ I D NO 15)
  • the VP16 cDNA sequence was cloned in-frame to the 5 region of codon-optimized EBNAIc using generally known methods
  • the VP16-EBNA1 cCO fusion protein in a pTT plasmid (10%) was co-transfected in CHO cells with pTT-SEAP plasmid (50%) and pTT-GFP plasmid (5%) with a linear 40 kDa deacetylated polyethylenimine (see below)
  • the CHO cells were transfected with 10% pTT/VP16-EBNA1 cCO, 50% SEAP, 35% stDNA and 5% GFP Non-coding DNA
  • stDNA was used as stuffer DNA to complete the amounts of DNA to 100%
  • OD/min SEAP activity
  • Fig 5D The results in Fig 5D clearly demonstrate that a VP16-EBNA1 cCO chimera fur t her increases transient gene expression in CHO cells compared to EBNAI c or EBNAIcCO
  • LPEI-MAX fully deacetyiated poly(ethylen ⁇ m ⁇ ne)
  • HEK human embryonic kidney
  • Fig 6 HEK293-EBNA1 t (clone 6E) and CHO-EBNAI c (clone 3E7) cells were used
  • the results in the upper panel show that LPEI-Max is not better than LPEI in HEK293 cells
  • CHO-EBNA1 cells were transfected with pTT- SEAP plasmids using LPEI-MAX at various DNA PEI ratios SEAP activity (OD/min at 410 nm) was measured in the supernatant 6 days post transfection and compared to the best condition found
  • FGF fibroblast growth factor
  • FIG 9 graphs are shown illustrating the effect of FGF2 (bFGF) co- expression on transient gene expression in HEK293-EBNA1t (clone 6E) cells (upper panel) and CHO-EBNAIc (clone 3E7) cells (lower panel)
  • the HEK293-EBNAU and CHO-EBNAI c cells were transfected with 25% pTT-SEAP vector and increasing amounts (0%, 15%, 30% 45%, 60% and 70%) of FGF2-encod ⁇ ng pTT plasmid (the overall content of DNA was kept constant with non-coding StDNA) SEAP activity (OD/min at 410 nm) was measured in the supernatant 7 days post-transfection From the upper panel it is evident that SEAP activity in HEK293-EBNA1t cells is decreased by co-expression of FGF2 From the lower panel it is evident that SEAP activity in CHO-EBNAI c cells is increased by co-expression of FGF2 This clearly demonstrates that the co-
  • FGF2 enhances transgene expression in CHO cells but not in HEK293 cells Increased productivity in CHO cells may be due to a FGF-induced rRNA synthesis PKB Potentiation of VPA
  • PKA protein kinase B
  • VPA valproic acid
  • Valproic acid a histone deacetylase inhibitor enhances transient gene expression in cells
  • VPA also induces apoptosis thereby killing ceils and reducing overall gains in productivity
  • co-expressing PKB also known as AKT
  • a constitutively active PKB mutant potentiates the action of valproic acid in gene expression by inhibiting apoptosis
  • Fig 10 the effect of PKB (AKT) and valproic acid (VPA) on transient gene expression in CHO-EBNAI c (clone 3E7) cells is illustrated
  • the CHO-EBNAI c cells were transfected with a mixture of SEAP-encoding o ⁇ P plasmids (pTT-SEAP) and stuffer DNA or pTT-AKTdd vector (AKTdd is a dominant-positive mutant of AKT)
  • pTT-SEAP SEAP-encoding o ⁇ P plasmids
  • pTT-AKTdd is a dominant-positive mutant of AKT
  • O 25 mM VPA was added 24 hours post-transfection SEAP activity ( ⁇ A410/m ⁇ n) was measured at days 5 to 8 post-transfection
  • Fig 10 clearly demonstrates that valproic acid increases transient gene expression in CHO cells and that transient co-expression of AKTdd greatly potentiates this effect

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Abstract

Processes vectors and engineered cell lines for large-scale transfection and protein production in mammalian cells, especially Chinese Hamster Ovary (CHO) cells are described in which transfection efficiencies are realized through the use of a single vector system, the use of functional oriP sequences in all plasmids, the use of codon- optimized Epstein-Barr virus nuclear antigen-1 (EBNA1 ) constructs the use of a fusion protein between a truncated Epstein-Barr virus nuclear antigenen-1c (EBNA1c) protein and a herpes simplex virus protein VP16, the use of a 40 kDa fully deacetylated poly(ethylenimine) as a transfection reagent, the use of co-expression of a fibroblast growth factor (FGF) and/or the use of protein kinase B to potentiate heterologous gene expression enhancement by valproic acid (VPA).

Description

PROCESS VECTORS AND ENGINEERED CELL LINES FOR ENHANCED LARGE- SCALE TRANSFECTION
Cross-reference to Related Applications
Tnis application claims the benefit of United States Provisional Patent Application USSN 61/071 760 filed May 15, 2008 the entire contents of which is herein incorporated by reference
Field of the Invention
The present invention relates to processes vectors and engineered cell lines for large-scale transfection and protein production
Background of the Invention
Large-scale transfection of Chinese Hamster Ovary (CHO) cells with cost-effective reagents for the production of r-proteins suffers from low efficiency and low productivity In addition, plasmid vectors used in CHO cells are not fully optimized for transient gene expression
There are some very efficient and commercially available cationic lipids formulation that can be used to transfect CHO cells in serum-free medium for example FreestyleMax~y from Invitrogen However, these cationic lipids are very expensive Also, to improve productivity, it is becoming current practice to lower the cultivation temperature following transfection to prolong the production phase and to enhance productivity This temperature shift is not "user friendly" when working at large-scale or when using non- refπgerated culture devices (Wave bioreactors etc) Also, the exact temperature at which the shifts are done may be critical for getting optimal enhancement (e g 29 vs 30 vs 31 vs 32 degrees Celsius)
International patent publication WO 2007/048601 reports an expression system in CHO cells stably expressing EBNA1 for the production of r-proteins However this document specifically admonishes that the cell lines shall not contain a functional copy of the Epstein-Barr virus (EBV) oπP sequence Further the full length EBNA1 structural gene encoding a full length EBNA1 protein is transfected into the cell line and the oriP sequence is never in the same vector as the EBNA1 gene construct
International patent publication WO 2002/090533 describes enhanced production of recombinant proteins by transient tiansfection of suspension-growing mammalian cells However only full length EBNA1 structural genes are used encoding full length EBNA1 proteins and only transient expression of a gene of interest is achieved
International patent publication 2006/096989 describes expression vectors for enhanced transient gene expression and mammalian cells expressing them However only HEK293 cell lines are exemplified and the expression system used does not contain both the EBNA1 gene construct and the oriP sequence in the same vector Further only transient expression of a gene of interest is achieved
There is a need in the art for processes vectors and engineered cell lines for more efficient and productive transfection of cells at a large scale
Summary of the Invention
In accordance with a first aspect of the present invention, there is provided an expression system for stable expression of a gene of interest the expression system comprising one vector having an Epstein-Barr virus nuclear antιgen-1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein, a promoter and a polyadenylation signal for the EBNA1 nucleotide sequence an oπP nucleotide sequence the gene of interest and a promoter and a polyadenylation signal for the gene of interest
In accordance with a second aspect of the present invention, there is provided a method of stably expressing a gene of interest in mammalian cells, the method comprising transfecting a mammalian cell with a vector having an Epstein-Barr virus nuclear antιgen-1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein, a promoter and a polyadenylation signal for the EBNA1 nucleotide sequence, an oriP nucleotide sequence the gene of interest and a promoter and a polyadenylation signal for the gene of interest and replicating the cell to provide mammalian cells that stably express the gene of interest
In accordance with a third aspect of the present invention, there is provided an expression system for stable expression of a gene of interest, the expression system comprising a first vector having an Epstein-Barr virus nuclear antιgen-1 (EBNA1) nucleotide sequence encoding a truncated EBNA1 protein a promoter and a polyadenyiation signal for the EBNA1 nucleotide sequence and an oriP nucleotide sequence and, a second vector having a gene of interest a promoter and a polyadenylation signal for the gene of interest and an oriP nucleotide sequence In accordance with a fourth aspect of the present invention there is provided a method of stably expressing a gene of interest in mammalian cells the method comprising transfecting a mammalian cell with a first vector having an Epstem-Barr virus nuclear antιgen-1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein a promoter and a polyadenylation signal for the EBNA1 nucleotide sequence and an oriP nucleotide sequence and, a second vector having the gene of interest a promoter and a polyadenylation signal for the gene of interest and an oriP nucleotide sequence to provide mammalian cells that stably express the gene of interest
In the fourth aspect, transfecting the cell with the first and second vectors may be accomplished simultaneously, or the cell may be transfected by one of the vectors first to produce a stable clone followed by transfection with the other vector to produce a clone that stably expresses the gene of interest
In accordance with a fifth aspect of the present invention there is provided a method of transiently expressing a gene of interest in Chinese Hamster Ovary (CHO) cells the method comprising transfecting a CHO cell with a first vector having an
Epstem-Barr virus nuclear antigen- 1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein, a promoter and a polyadenylation signal for the EBNA1 nucleotide sequence and an oriP nucleotide sequence and a second vector having the gene of interest and a promoter and a polyadenylation signal for the gene of interest, and, replicating the cell to provide CHO cells that transiently express the gene of interest
In the fifth aspect, transfecting the CHO cell with the first and second vectors may be accomplished simultaneously or the CHO cell may be transfected by one of the vectors first to produce a clone followed by transfection with the other vector to produce a clone that transiently expresses the gene of interest
In accordance with a sixth aspect of the present invention, there is provided a use of a codon-optimized Epstem-Barr virus nuclear antιgen-1 (EBNA1) nucleotide sequence in an expression system for expressing a gene of interest in mammalian cells
In accordance with a seventh aspect of the present invention, there is provided a fusion protein comprising a truncated Epstem-Barr virus nuclear antigeni c (EBNAIc) protein and, a herpes simplex virus protein VP16
In accordance with an eighth aspect of the present invention, there is provided a use of a 40 kDa fully deacetylated poly(ethylenιmιne) as a transfection reagent for improving transfection efficiency in transfection of Chinese Hamster Ovary (CHO) cells In accordance with a ninth aspect of the present invention there is provided a use of co-expression of a fibroblast growth factor (FGF) to increase heterologous gene expression in Chinese Hamster Ovary (CHO) cells
In accordance with a tenth aspect of the present invention there is provided a use of protein kinase B to potentiate valproic acid (VPA) to increase heterologous gene expression in mammalian cells
Further features of the invention will be described or will become apparent in the course of the following detailed description
Brief Description of the Drawings
In order that the invention may be more clearly understood embodiments thereof will now be described in detail by way of example with reference to the accompanying drawings in which
Fig 1 depicts schematic diagrams of EBNA1 constructs
Fig 2 depicts graphs of SEAP activity in CHO cells co-transfected with pTT vectors encoding various EBNA1 constructs
Fig 3A depicts genetic maps of pTT vectors encoding EBNAI c in as under a strong (EFI α-HTLV, pTT31 ) or a weak (RSV, pTT34) promoter
Fig 3B depicts a graph of SEAP activity in CHO cells transfected with pTT vectors encoding EBNAI c in cis under a weak or strong promoter
Fig 4A depicts a Western blot of extracts from CHO cells transfected with a linearized pTT-EBNA1c vector containing a blasticidin resistance cassette
Fig 4B depicts a Western blot of ahquots of cultures of the CHO cells of Fig 4A at various time intervals without selection pressure
Figs 5A-C depict Western blots of codon optimized EBNA1 expression in HEK293 and CHO cells
Fig 5D depicts a graph of secreted alkaline phosphatase (SEAP) activity in CHO cells co-expressing VP16-EBNA1 c fusion protein compared to control cells or cells expression an EBNAI c protein Fig 6 depicts graphs of SEAP activity in HEK293 and CHO cells transfected with pTT plasmids using LPEI or LPEI-Max
Fig 7 depicts a graph of SEAP activity in transiently transfected CHO-EBNAI c cells illustrating the transactivating activity of oriP
Fig 8 depicts a graph of SEAP activity in transfected CHO-EBNAI c cells illustrating the effect of the CMV5 promoter vs the Elongation Factor 1 alpha-HTLV (EFIα-HTLV) hybrid promoter
Fig 9 depicts graphs of SEAP activity illustrating the effect of FGF2 (bFGF) co- expression on transient gene expression in HEK293-EBNA1t and CHO-EBNAIc cells
Fig 10 depicts a graph of SEAP expression in CHO-EBNA1 c cells illustrating protein kinase B (AKT) potentiation of valproic acid (VPA) enhancement of transient gene expression
Fig 11 depicts genetic maps of SEAP-encoding pTT plasmids pTT22 (+orιP) and pTT30 (-oriP) and graphs of SEAP activity in CHO-EBNAIc cells transfected with linearized pTT22 and pTT30 plasmids illustrating the effect of oriP on linearized vectors in
CHO-EBNAIc cells
Fig 12 depicts a graph of SEAP activity in CHO-EBNAIc cells after integration of linearized pTT22 (+orιP) and pTT30 (-oriP) piasmids in their chromosomes
Description of Preferred Embodiments
Materials and Methods
Cell culture CHO cells are grown at 370C in FreestyleCHO medium (Invitrogen) supplemented with 8 mM glutamine in Erlenmeyer flasks shaken at 120 rpm in a humidified atmosphere containing 5% CO2 Cells are routinely maintained between O 1 x106 and 3 0x1 Oδ cells/ml HEK293-EBNA1 cells (clone 6E) are grown at 370C in F17 medium (Invitrogen) supplemented with 4 mM glutamine and O 1 % pluronic F68 in
Erlenmeyer flasks shaken at 120 rpm in a humidified atmosphere containing 5% CO2 Cells are routinely maintained between O 1 x106 and 2 0x10s cells/ml
Cell transfection For transfection CHO or HEK293 cells are grown in maintenance medium until they reach a density of 1 5x106 to 2 0x10s cells/ml and then the transfection mixture is added to the cells For every ml of HEK293 cells to be transfected 1 μg of plasmid DNA is mixed with 2 μg of 25 kDa linear polyethylenimine as previously described (Durocher Perret & Kamen 2002) For every ml of CHO ceils to be transfected 1 μg of plasmid DNA is mixed with 8 μg of 25 kDa linear polyethylenimine or with 6 μg of 40 kDa linear and deacetylated PEI (PEIMAX"" from Polysciences lnc catalog #24765-2)
Secreted alkaline phosphatase activity determination SEAP activity is measured as previously described using the coloπmetπc substrate paranitrophenyl phosphate (Durocher et al 2000)
Single Vector EBV orιP-EBNA 1 Stable Expression System
Mammalian cells transfected with an expression system in which a single vector contains an Epstein-Barr virus nuclear antigen- 1 (EBNA1) nucleotide sequence encoding a truncated EBNA1 protein, an Epstein-Barr Virus (EBV) oπP nucleotide sequence and a gene of interest unexpectedly provide enhanced stable expression of the gene of interest
Truncated EBNA1 proteins include for example, EBNAI c, EBNAIt and EBNAI s These truncated forms are shown in Fig 1 EBNAIt is a 417 ammo acid protein having
DNA Linking Region 1 (LR1 ) containing Transcriptional Activation Domain (TAD) and DNA Linking Region 2 (LR2) without the GIy-AIa repeats of the 641 amino acid full length protein EBNAIc is a 306 amino acid protein in which LR2 is present but LR1 is absent and EBNAI s is a 337 ammo acid protein in which LR1 is present but LR2 is absent EBNA1 nucleotide sequences encoding EBNAI c are preferred in the vector The amino acid sequences for the full length EBNA1 protein as well as the truncated forms EBNAIt, EBNAIc and EBNAI s are shown in SEQ ID NO 1-4 respectively The corresponding nucleotide sequences of the nucleic acid molecules encoding full length EBNA1 and the truncated forms are shown in SEQ ID NO 5-8, respectively
All or any functional part of the complete nucleotide sequence may be used in the vector The EBV oriP complete nucleotide sequence (pTT3 vector) is shown in SEQ ID NO 9 and a functional EBV oπP truncated nucleotide sequence (pTT5 vector) is shown in SEQ ID NO 10 The oπP sequence comprises the Family of Repeats (FR) component and the dyad symmetry (DS) component The oriP sequence particularly the FR component contributes to increased expression and stability of expression of the integrated truncated EBNA1 gene
The gene of interest may be any gene that encodes a protein product of interest Expression of the gene of interest in the transfected cells permits stable, large-scale production of the protein product for industrial purposes Some particular genes of interest include for example genes that encode monoclonal antibodies erythropoietins interferons vascular endothelial growth factors stem cell growth factors growth hormones insulin-like growth factor binding proteins etc
The single vector also preferably comprises a selection gene to permit selection of the transfected cells for the propagation of stable cell lines Any suitable selection gene may be used One example of a class of such genes are genes that confer antibiotic resistance on the cell when the vector is transfected into the cell Some examples within this class include genes that confer resistance to puromycin, blasticidin, geneticin, zeocin or hygromycin The blasticidin resistance cassette as found in the pYD7 vector is particularly preferred After transfection of a cell with the vector, the cell may be permitted to replicate Clones possessing the expression system may be selected on the basis of the selection gene, for example, by treating the cells with an antibiotic and cultuπng the cells that survive In this way a cell line stably expressing the gene of interest may be created
Any or all of the nucleotide sequences and/or genes in the integrated vector may be under the control of a promoter also incorporated in the vector Generally each gene has its own promoter Thus, there is preferably a promoter for the EBNA1 , a promoter for the gene of interest and a promoter for the selection gene Strong or weak promoters may be used Some promoters include, for example the cytomegalovirus (CMV) promoter Elongation Factor 1 alpha-HTLV (EFI α-HTLV) hybrid promoter, and Rous sarcoma virus (RSV) promoter Also, any or all genes may have a polyadenylation signal Alternatively, two genes, separated by an Internal Ribosome Entry Site (IRES), can be expressed by using only one promoter and one polyadenylation signal
Genetic maps of two embodiments (pTT31 -SSH and pTT34-SSH) of the single vector are shown in Fig 3A pTT31-SSH is a 8014 bp vector in which the EBNAIc gene is under the control of a strong promoter (EFI α-HTLV) and the gene of interest (secreted alkaline phosphatase (SEAP) gene) is under the control of a strong promoter (CMV) pTT34-SSH is a 8040 bp vector in which the EBNAIc gene is under the control of a weaker promoter (RSV) and the gene of interest (secreted alkaline phosphatase (SEAP) gene) is under the control of a strong promoter (CMV)
Fig 3B depicts a graph of SEAP activity in CHO cells transfected with pTT vectors (oriP-containing vectors) encoding EBNAI c in cis under a weak (RSV) or strong (EFI α- HTLV) promoter Referring to Fig 3B CHO cells were transfected with increasing amounts of the SEAP gene-containing plasmids pTT-SSH (with oπP but without EBNA1 c) pTT31 -SSH (with oriP and with EBNA1 c under the control of the strong EF1 α- HTLV promoter) and pTT34-SSH (with oriP and with EBNAI c under the control of the weak RSV promoter) Both EBNAIc-containing pTT vectors (pTT31 -SSH and pTT34- SSH) lead to an increase in SEAP activity in CHO cells over the non-EBNA1c-contaιnιng vector (pTT-SSH) Use of a strong promoter to control EBNA1 expression optimizes levels of transactivating activity thereby optimizing expression of the gene of interest
The single vector EBV oπP-EBNA1 expression system is useful in different types of mammalian cells for example Chinese Hamster Ovary (CHO) cells human embryonic kidney 293 (HEK293) cells Madin-Darby Canine Kidney (MDCK) cells, Vero cells and
PER C6"vl cells especially CHO cells
Two Vector EBV ortP-EBNA 1 Stable Expression System
Mammalian cells transfected with an expression system comprising two separate vectors a first vector containing an Epstein-Barr virus nuclear antιgen-1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein and an Epstein-Barr Virus
(EBV) oriP nucleotide sequence and a second vector comprising a gene of interest and an Epstein-Barr Virus (EBV) oriP nucleotide sequence unexpectedly provide enhanced stable expression of the gene of interest The use of oriP in both vectors contributes to stability of expression and increased expression of the gene of interest To facilitate production of stable cell lines that stably express the gene of interest, both vectors contain selection genes Selection genes are described above For example a stable CHO cell clone expressing EBNAI c driven from an integrated oriP vector containing a blasticidin resistance cassette (pYD7) stably expressed the gene of interest for over 6 months in the absence of selection
Stable mammalian cell lines can be produced either by simultaneously transfecting a cell with both vectors and then propagating the cell or by transfecting a cell with one of the vectors (either the EBNA1 -containing or the gene of interest-containing vector) to produce a stable clone and then transfecting a stable clone cell with the other of the vectors to produce a stable clone stably expressing the gene of interest
Truncated EBNA1 proteins and corresponding genes as well as the oriP and genes of interest are described above As described previously genes may be under the control of promoters The two vector EBV orιP-EBNA1 stable expression system is also useful in different types of mammalian cells, for example Chinese Hamster Ovary (CHO) cells human embp/onic kidney 293 (HEK293) cells Madin-Darby Canine Kidney (MDCK) cells and PER C6"V1 cells especially CHO cells
Referring to Figs 1 1 and 12 Chinese Hamster Ovary (CHO) cells stably expressing EBNAI c were produced by transfecting CHO cells with an EBNAIc oπP- containing plasmid (pYD7 vector) using generally known methods with a linear 25 kDa polyethylenimine (PEI) and stable clones were propagated One CHO-EBNAIc clone (clone 3E7) so produced was transfected with secreted alkaline phosphatase (SEAP)- encoding and linearized pTT22 (+orιP) or pTT30 (-oπP) vectors The pTT22 and pTT30 vectors both contain a puromycin resistance cassette The pTT22 vector contains oπP (ι e the DS and FR elements are present) while the pTT30 vector does not contain oπP
(ι e the DS and FR elements are removed) CHO-EBNAI c cells transfected with the pTT22 and pTT30 vectors were transferred in 96-well plates at a density of 100 cells/well Puromycin was added 24 hours post-transfection and selection was maintained for two weeks
Referring to Fig 11 , after selection, SEAP activity (mOD/min at 410 nm) was measured in the supernatant at day 14 post-transfection The results clearly demonstrate the transactivating action of EBNAI c on linearized oπP-beaπng expression plasmids integrated in CHO cells Linearization of the vector abolishes the replication potential of the orιP-EBNA1c system thus eliminating the possibility that the increased SEAP expression is due to plasmid replication The average SEAP activity for the 96 wells are
46 5 and 5 8 mOD/min for oπP-containing and non-oπP-containing SEAP-encoding vectors respectively
Referring to Fig 12, after selection the best positive clones (7 clones for pTT22- oπP vector and 6 clones for pTT30-non-oπP vector) were amplified and maintained in 6- well plates with or without puromycin Twenty days later, clones were seeded in a 6-well plate at 0 25 million cells per ml and SEAP activity (OD/min at 410 nm) was measured 5 days later Also shown in Fig 12 is the SEAP activity found in the non-cloned ("pools" or "bulk") transfected cells maintained in the presence of puromycin for 34 days SEAP activity in the oriP bulk is 10 times higher than in the non-oπP bulk These results clearly demonstrate the transactivating action of EBNAIc on integrated oπP-beaπng expression plasmids in CHO cells For clones 4B10 and 4F4 the increased SEAP activity in the presence of puromycin suggests that these two clones are non-clonal and probably contaminated by a cellular population expressing lower levels of SEAP SEAP activity is expressed as increase in absorbance unit at 410 nm per mm (OD/min) Thus, the presence of oπP in the integrated expression plasmid confers higher expression levels of the gene of interest in EBNA1 -expressing mammalian cells particularly CHO cells vs non-oriP-containing plasmids
Two Vector Transient Expression System in CHO Cells
Chinese Hamster Ovary (CHO) cells transfected with an expression system comprising two separate vectors, a first vector containing an Epstem-Barr virus nuclear antιgen-1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein and an Epstem-Barr Virus (EBV) oπP nucleotide sequence and a second vector comprising a gene of interest and an Epstem-Barr Virus (EBV) oriP nucleotide sequence also unexpectedly provide enhanced transient expression of the gene of interest in the CHO cells
CHO cell lines can be produced either by simultaneously transfecting a cell with both vectors and then propagating the cell, or by transfecting a cell with one of the vectors (either the EBNA1 -containing or the gene of interest-containing vector) to produce a clone and then transfecting a clone cell with the other of the vectors to produce a clone transiently expressing the gene of interest Truncated EBNA1 proteins and corresponding genes, as well as the oriP and genes of interest are described above As described previously, genes may be under the control of promoters
Fig 2 illustrates transient expression of secreted alkaline phosphatase (SEAP) in CHO cells co-transfected with one vector containing oriP plus the SEAP gene and another vector containing oriP plus truncated EBNA1 constructs (EBNAIt1 EBNAIc and EBNAI s) In Fig 2 CHO cells were co-transfected with 50% of pTT-EBNA1 constructs or 50% salmon testis DNA (stDNA) and (45% pTT-SEAP + 5% pTT-GFP) plasmids SEAP activity was compared to activity in CHO cells transfected with 95% pTT-SEAP + 5% pTT- GFP SEAP activity (OD/min at 410 nm) was measured 5 days post-transfection
Transfection was accomplished using generally known methods with a linear 25 kDa polyethylenimine (PEI)
The results in Fig 2 show an increase in transient SEAP activity of 2-fold or higher in CHO cells co-transfected with oπP/EBNA1 and oπP/SEAP plasmids over CHO cells that are not co-transfected with orιP/EBNA1 plasmids Further, while it has been previously shown that the Transcriptional Activation Domain ' (aa 65-89) in the LR1 domain of EBNA1 is essential for transcriptional activation of integrated oriP vectors Fig 2 surprisingly shows that the truncated Ef NA1 c construct lacking the LR1 domain but containing the LR2 domain is capable of increasing gene expression from non-integrated oπP plasmids to the same level as EBNAIt (that contains both the LR1 and LR2 domains) or EBNAI s (that contains only the LR1 domain)
In Fig 4 CHO cells were transfected with a linearized pTT-EBNA1 c vector containing a blasticidin resistance cassette (pYD7 vector) Linearization of the vector was achieved following restriction enzyme digestion using Pvul enzyme Following transfection cells having stably integrated the pYD7 vector were selected by adding blasticidin to the culture medium After a few days of blasticidin selection, blasticidin- resistant cells were seeded in 96-well plates without blasticidin selection Emerging clones were tested for EBNAIc expression An EBNAIc-positive clone 3E7 (Fig 4A) was then selected for further testing A master cell bank (MCB) and Working cell bank (WCB) were made at this point The CHO-EBNAI c (clone 3E7) cells were cultured for over 130 days in the absence of blasticidin selection At various culture time points an aliquot of the cells were taken for EBNAIc expression analysis by Western blot using an antι-EBNA1 antibody Fig 4B shows that the clone 3E7 is very stable over 130 days in culture without blasticidin selection pressure
In Fig 7, CHO cells containing integrated EBNA1-expressιng plasmids were produced by transfecting CHO cells with a pTT-EBNA1 c vector, and the clone propagated (clone 3E7) Resulting CHO-EBNAIc clone was transfected with SEAP-encoding pTT plasmids with complete oπP (pTT-SMH), with DS-deleted oπP (pTTi-SMH), with FR- deleted oπP (pTTj-SMH) or with oπP-deleted (pTTI-SMH) pTT vectors SEAP activity (OD/min at 410 nm) was measured in the supernatant at 5 days post-transfection Transfections were accomplished using generally known methods with a linear 25 kDa polyethylenimine (PEI)
The results in Fig 7 illustrate that increased expression in transiently transfected
CHO-EBNA1 cells is due to the transactivating activity of the oπP family of repeats (FR) element, and not to plasmid replication Removal of the dyad symmetry (DS) element (EBNA1-dependent origin of replication) from the oriP does not inhibit expression while removing the FR element (responsible for EBNA1 -dependent transcriptional activation) strongly reduces expression The results also show that the DS element has a slight inhibitory effect on gene expression
Fig 8 compares the effect of the cytomegalovirus (CMV5) promoter and elongation factor 1 alpha-HTLV (EF1 -αHTLV) promoter on transgene expression in CHO- EBNAIc cells (clone 3E7) CHO-EBNA1 c-3E7 cells were transfected with increasing amount SEAP-encoding oriP-containing (pTT) plasrrids containing either the CMV5 or EF1 -GHTLV promoter to control the SEAP gene (the overall content of DNA was kept constant by compensating with non-codirg StDNA) SEAP activity (OD/min at 410 nm) was measured in the supernatant at day 6 post-transfection The results clearly demonstrate that the CMV5 promoter is at least 5 times more potent than the EF1 -σHTLV promoter at low plasmid doses (e g 5%) Further CMV5-based plasmid needs 2-4 times less coding plasmid DNA for maximum expression
Codon-optimized EBNA 1 Constructs
Codon-optimization of Epstem-Barr virus nuclear antιgen-1 (EBNA1 ) nucleotide sequence strongly enhances expression of EBNA1 in mammalian cells especially
Chinese Hamster Ovary (CHO) and human embryonic kidney (HEK) cells A codon- optimized EBNA1 cDNA instead of non-codon-oDtimized EBNA1 cDNA may be used in any of the aspects of the present invention Full length or truncated EBNA1 cDNA may be codon-optimized Advantageously such codon-optimized EBNA1 nucleotide sequences permit the use of weaker promoters to express EBNA1 thereby reducing the likelihood of promoter competition between two strong promoters in a single expression system Codon-optimized EBNAIc nucleotide sequence (EBNAIc-CO SEQ ID NO 13) codes for a 308 amino acid protein (SEQ ID NO 1 1 ) Codon-optimized EBNAIs nucleotide sequence (EBNAIs-CO SEQ ID NO 14) codes for a 337 amino acid protein (SEQ ID NO 12)
Referring to Fig 5 EBNA1 constructs (EBNAIc and EBNAIs) were codon- optim zed (human codon usage - CO) pTT vectors containing EBNAIc EBNAI s or their codon-optimized versions (EBNAIc-CO (SEQ ID NO 13) and EBNAIs-CO (SEQ ID NO 14)) and empty pTT vector (CTRL) were transfected in separate HEK293 cells or CHO cells by generally known methods with a linear 25 kDa polyethylenimine (PEI) Three days post-transfection cells were lyzed and cell extracts analyzed by Western blot using an antι-EBNA1 antibody Fig 5A is a Western blot for cell extracts from HEK293 cells and Fig 5B is a Western blot for cell extracts from CHO cells In both cell lines it is evident that codon optimization enhances transient expression of EBNA1 in the cells when compared to the control (CTRL) and the cells transfected with non-codon-optimized
EBNA1
For Fig 5C HEK293 cells were transfected with increasing amounts (1 25% 5% and 20%) of pTT vectors containing EBNAI c EBNAIc CO EBNAI s or EBNAI s-CO Again it is evident from the Western blots in Fig 5C that codon optimization enhances transient expression of EBNA1 in cells when compared to cells transfected with non- codon-optimized EBNA1
For Fig 5D CHO cells were co-transfected with pTT-SEAP (50%) plus 5% pTT- GFP vectors (Control) with or without 10% of pTT-EBNA1 c, pTT-EBNAI cCO or pTT- VP16/EBNA1 cCO (EBNAIcCO fused at its N-terminus to VP16 - see below) Non- coding DNA (stDNA) was used as stuffer DNA to complete the amounts of DNA to 100% SEAP activity measured 5 days later This clearly demonstrates that, by improving its expression, codon optimization of EBNAIc provides an increased transactivating activity A VP16-EBNA1cCO chimera also further increases transient gene expression in CHO cells compared to EBNAI c and EBNAIcCO (see below)
EBN A 1 c-VP 16 Fusion Protein
A fusion protein comprising a truncated Epstein-Barr virus nuclear antigeni c (EBNAIc) protein and a herpes simplex virus protein VP16 provides significantly enhanced transactivating activity in mammalian cells, particularly Chinese Hamster Ovary (CHO) cells and human embryonic kidney (HEK) cells
A fusion protein is constructed by fusing VP16 to the N-terminus of codon- optimized EBNAIc The VP16 cDNA encoding for the following protein sequence was used APPTDVSLGDELHLDGEDVAMAHADALDDFDLDMLGDGDSPGPGFTPHDSAPY GALDMADFEFEQMFTDALGI DEYGG (SEQ I D NO 15) The VP16 cDNA sequence was cloned in-frame to the 5 region of codon-optimized EBNAIc using generally known methods
The VP16-EBNA1 cCO fusion protein in a pTT plasmid (10%) was co-transfected in CHO cells with pTT-SEAP plasmid (50%) and pTT-GFP plasmid (5%) with a linear 40 kDa deacetylated polyethylenimine (see below) The CHO cells were transfected with 10% pTT/VP16-EBNA1 cCO, 50% SEAP, 35% stDNA and 5% GFP Non-coding DNA
(stDNA) was used as stuffer DNA to complete the amounts of DNA to 100% Five days post-transfection SEAP activity (OD/min) was measured and compared to activities in cells transfected with stuffer DNA in place of pTT/EBNA1 vectors (CTRL) or a pTT/EBNA1c vector or a pTT/EBNA1cCO vector in place of pTT/VP16-EBNA1c (Fig 5D) The results in Fig 5D clearly demonstrate that a VP16-EBNA1 cCO chimera further increases transient gene expression in CHO cells compared to EBNAI c or EBNAIcCO
Transfection with Fully Deacylated PEI Use of a 40 kDa fully deacetyiated poly(ethylenιmιne) (LPEI-MAX) as a transfection reagent unexpectedly improves transfection efficiency and/or productivity in Chinese Hamster Ovary (CHO) cells in comparison to the use of the usual linear 25 kDa poly(ethylenιmιne) (LPEI) Such an improvement is not realized in human embryonic kidney (HEK) cells
Referring to Fig 6 HEK293-EBNA1 t (clone 6E) and CHO-EBNAI c (clone 3E7) cells were used For the upper panel of Fig 6 HEK293-EBNA1t cells were transfected with pTT-SEAP plasmids using LPEI-MAX at various DNA PEI ratios (R) and polyplexes amounts (%) SEAP activity (OD/min at 410 nm) was measured in the supernatant 6 days post transfection and compared to the best condition found for LPEI (75% polyplexes R=1 2) The results in the upper panel show that LPEI-Max is not better than LPEI in HEK293 cells For the lower panel CHO-EBNA1 cells were transfected with pTT- SEAP plasmids using LPEI-MAX at various DNA PEI ratios SEAP activity (OD/min at 410 nm) was measured in the supernatant 6 days post transfection and compared to the best condition found for LPEI (1 8) The results in the lower panel clearly demonstrate that LPEI-MAX is significantly more potent than LPEI in CHO cells for transient gene expression
Co-expression of FGF
Co-expression of a fibroblast growth factor (FGF) increases heterologous gene expression in Chinese Hamster Ovary (CHO) cells
Referring to Fig 9 graphs are shown illustrating the effect of FGF2 (bFGF) co- expression on transient gene expression in HEK293-EBNA1t (clone 6E) cells (upper panel) and CHO-EBNAIc (clone 3E7) cells (lower panel) The HEK293-EBNAU and CHO-EBNAI c cells were transfected with 25% pTT-SEAP vector and increasing amounts (0%, 15%, 30% 45%, 60% and 70%) of FGF2-encodιng pTT plasmid (the overall content of DNA was kept constant with non-coding StDNA) SEAP activity (OD/min at 410 nm) was measured in the supernatant 7 days post-transfection From the upper panel it is evident that SEAP activity in HEK293-EBNA1t cells is decreased by co-expression of FGF2 From the lower panel it is evident that SEAP activity in CHO-EBNAI c cells is increased by co-expression of FGF2 This clearly demonstrates that the co-expression of
FGF2 enhances transgene expression in CHO cells but not in HEK293 cells Increased productivity in CHO cells may be due to a FGF-induced rRNA synthesis PKB Potentiation of VPA
Use of protein kinase B (PKB) to potentiate valproic acid (VPA) increases heterologous gene expression in mammalian cells especially Chinese Hamster Ovary (CHO) cells
Valproic acid (VPA) a histone deacetylase inhibitor enhances transient gene expression in cells However, VPA also induces apoptosis thereby killing ceils and reducing overall gains in productivity It has now been found that co-expressing PKB (also known as AKT) or a constitutively active PKB mutant in the cells potentiates the action of valproic acid in gene expression by inhibiting apoptosis
Referring to Fig 10 the effect of PKB (AKT) and valproic acid (VPA) on transient gene expression in CHO-EBNAI c (clone 3E7) cells is illustrated The CHO-EBNAI c cells were transfected with a mixture of SEAP-encoding oπP plasmids (pTT-SEAP) and stuffer DNA or pTT-AKTdd vector (AKTdd is a dominant-positive mutant of AKT) In some cases, O 25 mM VPA was added 24 hours post-transfection SEAP activity (ΔA410/mιn) was measured at days 5 to 8 post-transfection Fig 10 clearly demonstrates that valproic acid increases transient gene expression in CHO cells and that transient co-expression of AKTdd greatly potentiates this effect
References The contents of the entirety of each of which are incorporated by this reference
Mizuguchi H, Hosono T, Hayakawa T Long-term replication of Epstein-Barr virus-derived episomal vectors in the rodent cells FEBS Lett 2000 Apr 28,472(2-3) 173-8
Durocher, Y Perret, S, Thibaudeau E, Gaumond MH, Kamen, A Stocco R, Abramovitz, M A reporter gene assay for high-throughput screening of G-protein-coupled receptors stably or transiently expressed in HEK293 EBNA cells grown in suspension culture Analytical Biochemistry 2000 Sep 10 284 (2) 316-26
Boussif O Zanta MA, Behr JP Optimized galenics improve in vitro gene transfer with cationic molecules up to 1000-fold Gene 7Λer 1996 Dec 3(12) 1074-80
Thomas M Lu JJ, Ge Q Zhang C Chen J Klibanov AM Full deacylation of polyethylenimine dramatically boosts its gene delivery efficiency and specificity to mouse lung Proc Natl Acad Sci U S A 2005 Apr 19 102(16) 5679-84 Kang MS Hung SC Kieff E Epstem-Barr virus nuclear antigen 1 activates transcription from episomal but not integrated DNA and does not alter lymphocyte growth Proc Natl Acad Sci U S A 2001 Dec 18 98(26) 15233-8
Sears J Kolman J Wan I GM Aiyar A Metaphase chromosome tethering is necessary for 5 the DNA synthesis and maintenance of oriP plasmids but is insufficient for transcription activation by Epstem-Barr nuclear antigen 1 J Virol 2003 Nov 77(21 ) 1 1767-80
Kennedy G Sugden B EBNA1 a bifunctional transcriptional activator MoI Cell Biol 2003 Oct 23(19) 6901 -8
Phiel CJ, Zhang F, Huang EY, Guenther MG, Lazar MA, Klein PS Histone deacetylase is I O a direct target of valproic acid a potent anticonvulsant mood stabilizer and teratogen J
Biol Chem 2001 Sep 28 276(39) 36734-41
Chen J, Ghazawi FM Bakkar W, Li Q Valproic acid and butyrate induce apoptosis in human cancer cells through inhibition of gene expression of Akt/protein kinase B MoI Cancer 2006,5 71
15 Sheng Z Liang Y, Lm CY, Comai L Chiπco WJ Direct regulation of rRNA transcription by fibroblast growth factor 2 MoI Cell Biol 2005 Nov,25(21 ) 9419-26
Kishida T Asada H Kubo K Sato YT Shιn-Ya M lmanishi J Yoshikawa K Mazda O Pleiotrophic functions of Epstem-Barr virus nuclear antigen- 1 (EBNA1 ) and oπP differentially contribute to the efficacy of transfection/expression of exogenous gene in .0 mammalian cells Journal of Biotechnology 2007
Ettehadieh E, Wong-Madden S Aldrich T, Lane K Morris AE Over-expression of protein kinase Ba enhances recombinant protein expression in transient systems Cytotechnology 2002, 38 1 1 -14
Krysan PJ Calos MP Epstem-Barr virus-based vectors that replicate in rodent cells 15 Gene 1993 137-143
Tomiyasu K Satoh E Oda Y Nishizaki K Kondo M lmanishi J Mazda O Gene transfer in vivo and in vitro wit hEpstein-Barr virus-based episomal vector results in markedly high transient expression in rodent cells Biochem Biophys Res Comm 1998 253 733-738
Goepfert U Kopetzki E Protein expression in rodent cells International Patent 30 Publication WO 2007/048601 published 3 May 2007 Sunstrcm NA Kunaparaju R Rodent expression system utilising polyoma virus and Epstein-Barr virus sequences International Patent Publication WO 2005/024030 published 17 March 2005
Durocher Y Perret S Pham PL St-Laurent G Kamen A Enhanced production of recombinant proteins by transient transfection of suspension-growing mammalian cells International Patent Publication WO 2002/090533 published 14 November 2002
Durocher Y Expression vectors for enhanced transient gene expression and mammalian cells expressing them International Patent Publication WO 2006/096989 published 21 September 2006
Other advantages that are inherent to the structure are obvious to one skilled in the art The embodiments are described herein illustratively and are not meant to limit the scope of the invention as claimed Variations of the foregoing embodiments will be evident to a person of ordinary skill and are intended by the inventor to be encompassed by the following claims

Claims

Claims
1 A fusion protein comprising a truncated Epstein-Barr virus nuclear antigenic (EBNAI c) protein, and a herpes simplex virus protein VP16
2 Use of the fusion protein as defined in claim 1 in an expression system for expressing a gene of interest in mammalian cells
3 Use of a 40 kDa fully deacetylated poly(ethylenιmιne) as a transfection reagent for improving transfection efficiency in transfection of Chinese Hamster Ovary (CHO) cells
4 Use of co-expression of a fibroblast growth factor (FGF) to increase heterologous gene expression in Chinese Hamster Ovary (CHO) cells
5 Use of protein kinase B to potentiate valproic acid (VPA) to increase heterologous gene expression in mammalian cells
6 An expression system for stable expression of a gene of interest, the expression system comprising one vector having an Epstein-Barr virus nuclear antιgen-1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein, a promoter and a polyadenylation signal for the EBNA1 nucleotide sequence, an oπP nucleotide sequence the gene of interest and a promoter and a polyadenylation signal for the gene of interest
7 A method of stably expressing a gene of interest in mammalian cells, the method comprising transfecting a mammalian cell with an expression system as defined in claim 6, and replicating the cell to provide mammalian cells that stably express the gene of interest
8 An expression system for stable expression of a gene of interest, the expression system comprising a first vector having an Epstein-Barr virus nuclear antigen- 1 (EBNA1 ) nucleotide sequence encoding a truncated EBNA1 protein a promoter and a polyadenylation signal for the EBNA1 nucleotide sequence and an oriP nucleotide sequence and a second vector having a gene of interest a promoter and a polyadenylation signal for the gene of interest and an oriP nucleotide sequence
9 A method of stably expressing a gene of interest in mammalian cells the method comprising transfecting a mammalian cell with an expression system as defined in claim 8 and replicating the cell to provide mammalian cells that stably express the gene of interest 10 The method according to claim 9 wherein transfecting the cell with the first and second vectors is accomplished simultaneously or the cell is transfected by one of the vectors first to produce a stable clone followed by transfection with the other vector to produce a clone that stably expresses the gene of interest
11 A method of transiently expressing a gene of interest in Chinese Hamster Ovary
(CHO) cells the method comprising transfecting a CHO cell with a first vector having an Epstein-Barr virus nuclear antigen- 1 (EBNA1) nucleotide sequence encoding a truncated EBNA1 protein a promoter and a polyadenylation signal for the EBNA1 nucleotide sequence and an oriP nucleotide sequence and a second vector having the gene of interest and a promoter and a polyadenylation signal for the gene of interest, and, replicating the cell to provide CHO cells that transiently express the gene of interest
12 The method according to claim 11 wherein transfecting the CHO cell with the first and second vectors is accomplished simultaneously or the CHO cell is transfected by one of the vectors first to produce a clone followed by transfection with the other vector to produce a clone that transiently expresses the gene of interest
13 Use of a codon-optimized Epstein-Barr virus nuclear antιgen-1 (EBNA1) nucleotide sequence in an expression system for expressing a gene of interest in mammalian cells
PCT/CA2009/000263 2007-03-26 2009-03-09 Process, vectors and engineered cell lines for enhanced large-scale transfection WO2009137911A1 (en)

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