The present invention relates to polynucleotides for enhancing protein expression and to expression systems comprising the polynucleotides.
High level and stable recombinant protein (r-protein) production in mammalian cells is important for cost-effective biotherapeutic manufacturing. S/MARs (Scaffold/Matrix Attachment Regions) are 70% AT-rich sequences, which are believed to play many important roles in chromatin function. In addition to their structural function, S/MARs play important roles in temporal and spatial organization of gene expression (Alvarez 2000; Liu 1997). The inclusion of an S/MAR sequence in an expression vector can thus help increase the level of expression and prevent silencing of the transgene (Phi-Van 1990; Jenke 2004; Zahn-Zabal 2001; Kim 2004). MAR elements have been shown to work either after integration into the host genome or as part of episomal vectors (Halweg 2005; Girod 2005).
Genomic elements such as UCOE (from Millipore) or MAR (from Selexis) are available and have proven to enhance expression level and stability when provided in cis or in trans in expression vectors used to generate stable cell lines. There are many S/MARs in the human genome that can be incorporated into expression vectors for enhancing productivity and stability of clonal cell lines (Girod 2007). However, not all of these sequences show beneficial effects (Sass 2005) and these sequences are very often very large (1.5 to 4 kb) and as such not practical to incorporate in expression vectors. There is a need to identify S/MAR sequences that are short (<1 kb) while still efficient, but the only way to achieve this is through a trial-and-error approach.
It has now been found that a short human genomic nucleotide sequence from the SAR3 region of the human interferon α2 gene permits enhanced expression stability in the absence of drug selection and permits generation of stable clones or stable pools of cells for producing recombinant proteins. Although stable clones may be generated, the ability to generate stable pools reduces the burden of generating stable clones.
Thus, in one aspect of the present invention there is provided an isolated polynucleotide comprising no more than 755 nucleotides and comprising at least 500 contiguous nucleotides from the nucleotide sequence as set forth in SEQ ID NO: 1.
In another aspect of the present invention there is provided an expression system for producing recombinant protein in a host cell comprising: a gene for encoding a protein of interest; nucleotide sequences for operation of the expression system; and, an expression enhancer incorporated in cis in the expression system for enhancing expression of the gene, the expression enhancer comprising a nucleotide sequence from human interferon alpha2 upstream scaffold associated region 3 (SAR3) comprising no more than 755 nucleotides and comprising at least 500 contiguous nucleotides from the nucleotide sequence as set forth in SEQ ID NO: 1.
In another aspect of the present invention, there is provided a host cell comprising the expression system of the present invention.
In another aspect of the present invention, there is provided a method of producing recombinant protein comprising: transfecting a host cell with an expression system of the present invention; growing the host cells under conditions suitable for expression of the gene to produce the protein of interest; and, recovering the protein of interest.
In another aspect of the present invention, there is provided a use of the polynucleotide of the present invention as an expression enhancer in cis in an expression system for producing recombinant protein.
The isolated polynucleotide comprises no more than 755 nucleotides and comprises at least 500 contiguous nucleotides from the nucleotide sequence as set forth in SEQ ID NO: 1. Preferably, the isolated polynucleotide comprises at least 550, 600, 650, 700 or 750 contiguous nucleotides from the nucleotide sequence as set forth in SEQ ID NO: 1. The isolated polynucleotide may be incorporated in cis in the expression system for enhancing r-protein expression in host cells transfected with the expression system. Advantageously, the expression enhancement is realized even in the absence of drug selection.
The expression system comprises a gene for encoding a protein of interest. Some particular proteins of interest include, for example, monoclonal antibodies (e.g. trastuzumab), erythropoietins, interferons, vascular endothelial growth factors, stem cell growth factors, growth hormones, insulin-like growth factor binding proteins, regulatory proteins (e.g. cumate operator, tetracycline repressor, steroid hormone receptors, transmembrane receptors), etc. The amino acid sequences of proteins of interest and the nucleotide sequences of the genes that encode such proteins are generally known in the art.
The expression system may comprise any suitable vector, for example plasmid vectors, episomal vectors (e.g. oriP/EBV vectors), viral vectors (e.g. Bacman) and cosmid vectors. The type of vector utilized in the expression system will depend on the intended host cell, among other factors, which can be readily determined by one skilled in the art. The vector comprises various nucleotide sequences for operation of the expression system. Such nucleotide sequences include, for example, promoters, origins of replication (e.g. bacterial origin of replication (pMBlori), Epstein-Barr Virus origin of replication (oriP)), leaders (e.g. adenovirus tripartite leader (TPL)), splice donors (SD), introns possibly including other enhancers (e.g. adenovirus major late promoter enhancer (Enh MLP)), splice acceptors (SA), selectable markers (e.g. antibiotic resistance genes), cloning sites (preferably multiple cloning sites) with restriction enzyme consensus sites (preferably multiple restriction enzyme consensus sites, e.g. EcoRV, Cla1, Sfol), and polyadenylation signals (e.g. rabbit beta-globin polyadenylation signal (pA)), among others. The expression system preferably comprises a plasmid vector.
Promoters are useful for controlling expression of various protein-encoding polynucleotides in the expression system. Strong or weak promoters may be used. Some promoters include, for example, cytomegalovirus (CMV) promoters, simian virus 40 promoter (SV40p), Elongation Factor 1 alpha-HTLV (EF1α-HTLV) hybrid promoter and Rous sarcoma virus (RSV) promoter. Selectable markers allow the selection of positively transfected cells. Common selectable markers include, for example, antibiotic resistance genes such as puromycin and hygromycin B for eukaryotic cells, and ampicilin and kanamycin for prokaryotic cells.
The expression system of the present invention may be transfected into a host cell by any suitable method. Such methods are generally known in the art (Kim 2010). The host cell is preferably a eukaryotic cell, more preferably a mammalian cell, for example, a Human Embryonic Kidney 293 (HEK293) cell, a Chinese Hamster Ovary (CHO) cell, a Baby Hamster Kidney (BHK21) cell, a PerC6 cell or a COS7 cell. Human Embryonic Kidney 293 (HEK293) and Chinese Hamster Ovary (CHO) cells are particularly preferred.
Transfected host cells are grown under conditions suitable to permit expression of the polynucleotide for encoding the protein of interest. Such conditions are generally well known for known host cells, for example mammalian cells such as HEK and CHO cells. Growth of cells is typically done in a culture medium and recovering the protein of interest from the cultured cells may also be conveniently done by known methods (Hauser 1997).
Advantageously, the isolated polynucleotide of the present invention can enhance stable expression in host cells when incorporated in cis in an expression system, permits enhanced expression stability in the absence of drug selection, can be combined with an episomal expression system (e.g. an oriP/EBNA1 system) for enhancing expression stability in the absence of drug selection even though pools generated with an episomal expression system (e.g. an oriP/EBNA1 system) are not stable without selection, and permits generation of stable pools for producing r-proteins without the burden of generating stable clones.
Further features of the invention will be described or will become apparent in the course of the following detailed description.
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:
An example of a SAR of the present invention (SAR-BRI) is set forth in SEQ ID NO: 1, which is a 751 nucleotide sequence corresponding to by numbers 1000-1750 of the human interferon α2 upstream scaffold associated region 3 (SAR3) sequence (gi|1791229|gb|U82705.1|HSU82705). SEQ ID NO: 1, which is 73.4% AT-rich (38.9% A, 34.5% T, 12.2% C, 14.4% G), was identified as a potential expression insulator and Geneart was contracted to synthesize it using generally known methods. The sequence possesses two base mutations that were generated to destroy endogeneous EcoRl and EcoRV restriction sites (C1639→G and G1695→T, respectively). The sequence was also flanked by EcoRV and Sfol restriction sites on the 5′ and 3′ ends, respectively, for cloning purposes, as shown in
Previously, a 0.7 kb “strong” SAR element from the SAR3 region of IFN-α2 was identified (Strissel 1998). As shown in
Further, the strength of the SARs disclosed in Strissel 1998 is based on repartion of the DNA fragment between the pellet (nuclei) fraction and the supernatant, as indicated in the Strissel reference:
The SAR-BRI sequence synthesized in Example 1 was inserted in a pTT55-EPO vector (
The pTT55-EPO and pTT54-EPO plasmids were transfected into Chinese Hamster Ovary (CHO) cells and the cells were cultured under puromycin selection to form stable CHO-DG44 EPO pools. To generate the CHO-DG44 pools expressing EPO, cells grown in CHO CD-DG44 medium (Invitrogen) were transfected with PEImax (Polysciences) using 1 μg/ml of supercoiled plasmid DNA at a DNA:PEI ratio of 1:5 (w:w). Puromycin was then added 24 hours post-transfection (hpt) at a concentration of 10 μg/ml. The culture medium was regularly replaced with fresh medium containing puromycin for over 60 days.
After 20 and 60 days post-transfection, EPO expression between pools generated with pTT54-EPO and pTT55-EPO vectors was compared (
It is evident from
Further, an EPO clone (+S/MAR element) maintained for 50 days without selection was compared in parallel to a freshly thawed batch of EPO clone (+S/MAR element) as a control (Ctrl). The western blot (
Furthermore, cells from the pools obtained with pTT54-EPO and pTT55-EPO vectors were plated at low cell density in semi-solid medium (Caron 2009) in the absence of selection. Once the colonies reached 4-10 cells, these were randomly picked and transferred into 96-well plates. After one week in culture, an aliquot of the supernatant from each well was spotted on a nitrocellulose membrane and the presence of EPO detected using an anti-EPO antibody. It is clear from
These results demonstrate that use of a SAR of the present invention permits generation of stable clones for producing r-protein at high levels.
HERCEPTIN is a trade name for the monoclonal antibody trastuzumab. Codon-optimized HERCEPTIN heavy chain cDNA (Geneart) was cloned into pTT54 or pTT55 vectors to yield pTT54-TZMHc plasmid (
To generate stable CMO-DG44 pools expressing HERCEPTIN, cells were transfected as described for EPO in Example 2 except that two vectors were co-transfected at a 1:1 (w:w) ratio (pTT54-TZMHc+pTT52-TZMLc or pTT55-TZMHc+pTT52-TZMLc). Selection was done as for EPO. Expression of HERCEPTIN by the resulting pools was compared 6 days or 25 days post-transfection by western blot under reducing or non-reducing condition using an anti-hFc antibody (
It is evident from
The chimeric heavy chain antibody EG2 (Zhang 2009) was cloned into pTT44 vector to yield pT44-EG2Fc plasmid (
To generate CHO-DG44 clones expressing EG2Fc, cells were transfected as described for EPO in Example 2 except that the plasmid was linearized by digestion with Pvul enzyme. Following transfection, cells were selected in the presence of 10 μglml of puromycin for eight days. Then, puromycin resistant cells were plated at a density of 250 cells/ml in a semi-solid medium without puromycin selection as previously described (Caron 2009). The presence of EG2Fc was monitored by inclusion of fluorescent-labeled anti-IgG antibodies in the semi-solid medium and clones expressing high levels of the cHCAb were identified by fluorescence microscopy and transferred in 96 well-plates using a CELLCELECTOR clone picker (Caron 2009).
As depicted in
EG2Fc titers in Batch 1 and Batch 2 cultures after 4 days and 8 days were compared by SDS-PAGE and Coomassie staining (
It is well known that EBV's episomes are lost at a rate of 1-4% per generation in the absence of selection pressure (Lindner 2007). To enhance retention of EBV episomes, attempts to combine a S/MAR element to an oriP plasmid have hitherto failed (Giannakopoulos 2009).
Pools of HEK293-EBNA1 cells transfected with the oriP-containing pTT22-GFP vector lose GFP expression when selection pressure is removed after 72 days in culture. However, in preliminary unpublished studies, the inclusion of one or two S/MAR sequences from human beta-globin and/or beta-interferon in the pTT22-GFP vector enhances episome stability upon removal of selection pressure as significantly higher percentage of GFP-positive cells can be observed after 125 days (53 days without selection). Likewise, it is expected that the inclusion of SAR-BRI in an episomal vector will also enhance episome stability upon removal of selection pressure.
Free listing of sequences:
References: The contents of the entirety of each of which are incorporated by this reference.
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.
This application is a national stage filing under 35 U.S.C. §371 of International Patent Application PCT/CA2012/000254 filed Mar. 20, 2012, which claims the benefit of U.S. Provisional Application Ser. No. 61/474,879 filed Apr. 13, 2011, the disclosure of each of which is incorporated by reference herein in its entirety.
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/CA2012/000254 | 3/20/2012 | WO | 00 | 10/10/2013 |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2012/139195 | 10/18/2012 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 20050170450 | Durocher | Aug 2005 | A1 |
| 20080070232 | Durocher | Mar 2008 | A1 |
| 20080124760 | Enenkel | May 2008 | A1 |
| Number | Date | Country |
|---|---|---|
| 1524875 | Sep 2004 | CN |
| WO2005040377 | May 2005 | WO |
| WO2005040384 | May 2005 | WO |
| WO2006096989 | Sep 2006 | WO |
| WO2008023247 | Feb 2008 | WO |
| WO2008116931 | Oct 2008 | WO |
| Entry |
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| Number | Date | Country | |
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| 20140038234 A1 | Feb 2014 | US |
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| 61474879 | Apr 2011 | US |