Patent Grant
11434261
The material in the accompanying sequence listing is hereby incorporated by reference into this application. The accompanying sequence listing text file, name HBI1130_3WO_Sequence_Listing.txt was created on Jul. 25, 2017, and is 58 kb. The file can be assessed using Microsoft Word on a computer that uses Windows OS.
The invention relates generally to the design of optimized Zika virus envelope genes and expression thereof and more specifically to Zika virus vaccines.
Zika virus (ZIKV) is a mosquito transmitted flavivirus whose recent spread through the Americas has caused the WHO to declare Zika a public health emergency of international concern (WHO 12 Feb. 2016; PAHO 14 Feb. 2016). Transmitted primarily by Aedes mosquitoes, infection with the positive strand RNA virus can lead to mild, dengue like symptoms: fever and rash sometimes associated with conjunctivitis, arthralgia or myalgia. Originally isolated in 1947 from a rhesus macaque during a yellow fever surveillance study in Uganda, ZIKV had caused sporadic outbreaks of acute, but mild disease in Africa, Asia and the Pacific Islands (Dick et al, 1952). During an intensive ZIKV outbreak in 2007 on Yap Island, 18% had clinical illness while 82% of those infected with ZIKV were asymptomatic (Duffy et al, 2009). ZIKV arrived in the Western hemisphere, Easter Island and Chile in 2014 (Tognarelli et al, 2014), then appeared in Brazil in early 2015 and since has spread to 33 countries and territories in the Caribbean, Central and South America and Mexico (PAHO 2 Apr. 2016). In addition to transmission by mosquitoes, there are reports of ZIKV being sexually transmitted. The first indication that ZIKV may also cause more severe neurological symptoms was the report of a 20-fold increase in the incidence of Guillain-Barré syndrome (GBS) during a 2013/2014 outbreak in French Polynesia (Oehler et al, 2014). A similar increase in GBS has been observed in the Americas coincident with the spread of ZIKV (WHO 2 Apr. 2016). In Bahia, Brazil, 26 of 42 GBS patients had historical symptoms consistent with ZIKV infection (PAHO 14 Feb. 2016; Schuller-Faccini et al, 2015). El Salvador and Colombia have reported a 3-fold increase in the incidence of GBS; 12 of 22 patients had febrile rash 7 to 15 days prior to onset (Schuller-Faccini et al, 2015; WHO 14 Feb. 2016). Honduras, Venezuela and Suriname also have reported an increase in GBS incidence; GBS cases have been reported during the ZIKV outbreak in Puerto Rico, Martinique, Panama, French Guiana, and Haiti (WHO 2 Apr. 2016). During the large and ongoing ZIKV pandemic in Brazil, there has been an increase in reports of infants born with microcephaly; up to 6480 suspected microcephaly cases have been reported in Brazil (PAHO 14 Feb. 2016; WHO 2 Apr. 2016). Given the association of GBS, microcephaly, and other birth defects with ZIKV infection, the development of a safe and effective vaccine for ZIKV is of paramount importance.
There is currently no approved vaccine for ZIKV. Multiple vaccine candidates have been discussed; all are in preclinical development (WHO 2 Apr. 2016). There have been at least 18 active vaccine research efforts identified by the WHO using the gamut of vaccine technologies including inactivated Zika virus, live attenuated viruses, viral vectors expressing ZIKV antigens, DNA vaccines, RNA vaccines, peptide vaccines, VLP vaccines and recombinant protein vaccines. It has been suggested that DNA vaccine candidates being developed by the Vaccine Research Center at NIH and Innovio Pharmaceuticals, Inc. may be able to start Phase 1 clinical testing this year. The target population for a ZIKV vaccine may include women of child bearing age and pregnant women. The risks of any replicating or genetic vaccine vector in this population would be significant. Therefore, a non-replicating, recombinant subunit protein is an attractive approach for a ZIKV vaccine as vaccines based on purified recombinant proteins provide for an improved safety profile. The key to success with the recombinant subunit approach for vaccines is the ability to efficiently produce high quality proteins that result in immune responses equivalent to, or better than, traditional live or inactivated virus approaches.
The choice of a recombinant protein expression system to employ is dependent on the desired application. The system of choice must meet key criteria such as proper folding and processing, consistency, and productivity (cost effectiveness) of the desired protein product (Schmidt, Appl. Microbiol. Biotechnol. (2004) 65:363-372). Insect cell-based expression systems have the potential to meet capacity requirements based on ease of culture, higher tolerance to osmolality and by-product concentrations during large scale culture, and generally higher expression levels (Ikonomou et al., Appl. Microbiol Biotechnol. (2003) 62:1-20). Recently, the use of expression systems based on insect cells has become more common. These systems provide most of the characteristics desired of eukaryotic systems, but have added benefits such as lower cost of goods. Insect cell systems are either based on infection of host cells with insect virus vectors (e.g., baculovirus) or on the generation of stable cell lines by integration of expression plasmids into the genome of the host cells.
The baculovirus expression system (BES) has emerged as the primary insect cell culture system utilized for recombinant protein expression. This system is based on the use of vectors derived from the insect viruses known as baculovirus. These vectors are used to generate recombinant viruses that encode the desired protein product. The recombinant viruses are used to infect host insect cells that then express the desired recombinant proteins. While there are advantages to this system in regards to ease of cloning and “time to product”, there are also several disadvantages. The primary challenge in the use of BES is that it is based on the viral infection of the host cells. This results in cellular lysis and cell death 72-96 hrs post infection (Farrell et al., Biotech. Biogen. (1998) 60:656-663; Deo and Park, Biotechnol. Appl. Biochem. (2006) 43:129-135). As a result, during the late stages of infection the processing machinery of the insect cells is compromised to the extent that the processing of the desired product is also compromised. This limits the time that the cells can produce product and possibly more importantly leads to altered forms of the product being produced. Furthermore, the lysis of cells releases cellular enzymes that can also affect the quality of the desired product.
The use of stably transformed insect cells for the expression of recombinant proteins is an alternative to the use of BES. Expression systems based on stably transformed insect cell lines are non-lytic and provide for steady long term production of secreted products that require proper folding and post translational modifications. The secretion of the product into the culture medium provides a cleaner starting material for the purification process and allows for the final protein product to be purified with basic methods. This leads to products that are of higher quality (Kirkpatrick and Shatzman in Gene Expression Systems: Using Nature for the Art of Expression (1999) pp 289-330).
The Drosophila melanogaster cell expression system (“Drosophila expression system”) is an established heterologous protein expression system based on the use of expression vectors containing Drosophila promoters and Drosophila S2 cells (“S2 cells”) (Schneider, Embryol. Exp. Morph. (1972) 27:353-365). S2 cells are transformed with these vectors in order to establish stable cell lines expressing proteins corresponding to the heterologous sequences introduced into the vector (Johansen, H. et al., Genes Dev. (1989) 3:882-889; Ivey-Hoyle, M., Curr. Opin. Biotechnol. (1991) 2:704-707; Culp, J. S., et al., Biotechnology (NY) (1991) 9:173-177; U.S. Pat. Nos. 5,550,043; 5,681,713; 5,705,359; 6,046,025). This insect cell expression system has been shown to successfully produce a number of proteins from different sources. Examples of proteins that have been successfully expressed in the Drosophila S2 cell system include HIV gp120 (Culp, J. S., et al., Biotechnology (NY) (1991) 9:173-177; Ivey-Hoyle, M., Curr. Opin. Biotechnol. (1991) 2:704-707), human dopamine β-hydrolase (Bin et al., Biochem. J. (1996) 313:57-64), human vascular cell adhesion protein (Bernard et al., Cytotechnol. (1994) 15:139-144). In each of these examples, expression levels were greater than other expression systems that had been previously utilized.
In addition to high levels of expression, the Drosophila expression system has been shown to be able to express heterologous proteins that maintain native-like biological function (Bin et al., Biochem. J. (1996) 313:57-64), (Incardona and Rosenberry, Mol. Biol. Cell. (1996) 7:595-611). More recent examples have shown by means of X-ray crystallography studies that this expression system is capable of producing molecules with native-like structure (Modis et al., Proc. Natl. Acad. Sci. USA (2003) 100:6986-6991), (Modis et al., Nature (2004) 427:313-319), (Xu et al., Acta. Crystallogr. D Biol. Crystallogr (2005) 61:942-950). Two other recent publications have also demonstrated the ability of the Drosophila expression system to produce high quality products. In the first report, Schmetzer et al. (J. Immun. (2005) 174: 942-952) compares baculovirus-expressed EpCAM protein to Drosophila-expressed EpCAM protein for protein folding and native conformation. Specifically, BES-expressed EpCAM and Drosophila-expressed EpCAM were compared to denatured Drosophila-expressed EpCAM. It was determined that the BES-expressed EpCAM was in a partial folded state relative to the non-denatured and denatured Drosophila-expressed EpCAM protein. This indicates that the BES-expressed protein is in an incompletely folded state. The Drosophila-expressed EpCAM protein, on the other hand, adopted a more completely folded state. The authors of this paper considered the Drosophila-expressed protein to be in the “natural” state while the baculovirus-expressed protein was not. In the second report, Gardsvoll et al. (Prot. Exp. Purif. (2004) 34:284-295) demonstrate that the expression of the urokinase-type plasminogen activator receptor (uPAR) in S2 cells results in a more homogeneous product in regards to glycosylation (5 N-linked sites) than uPAR expressed in CHO cells.
The development of a recombinant subunit vaccine for ZIKV requires the selection of appropriate gene sequences from the ZIKV genome that encode proteins that are the target of neutralizing antibodies. Like other members of the flavivirus family, the envelope glycoprotein of ZIKV is the primary target of neutralizing antibodies. In addition to selection of an appropriate ZIKV gene sequence, efforts to optimize the expression of the selected gene sequences are also desirable to enhance the ability to effectively express the selected sequences such that the resultant products are soluble, stable and conformationally relevant.
While there are examples of flavivirus envelope gene sequences being expressed, there are no clear examples of optimizing the expression of these gene sequences as most examples are on the use of naturally occurring sequences of the parent viruses. Various means exist to optimize expression. However, each selected sequence requires several rounds of experimentation to determine which methods or combination of methods will result in the most effective expression in a given expression system while maintaining the appropriate native, or biologically relevant characteristics, which have the immunogenic potential to induce a neutralizing antibody response in the case of the ZIKV envelope gene sequence.
Problems are often encountered with virus envelope sequences that require maintenance of appropriate native or biologically relevant characteristic which can hamper optimal expression. These problems include non-optimal truncations that define the amino-terminus and the carboxy-terminus of the expressed product, poor or ineffective post translation processing, poor matching of the native codon usage with the codon usage of the selected expression system's host cells.
The efficiency of heterologous protein expression in eukaryotic systems is dependent on many factors, such as promoter and associated regulatory elements, transcription initiation sequences, and poly-adenylation signals. As the expression vectors used in a typical system are optimized for the given host cell utilized, the optimization of the gene sequence of interest is often of great importance to ensure optimal express of the desired protein product. This is typically done by adaptation of the codon usage of the gene sequence to the typical codon usage of the host cells. While the gene sequence is altered through codon optimization the amino acid sequence of the encoded protein in not modified through the optimization process (Gustafsson et al, 2004). Basic codon usage optimization involves substituting rare codons in the target gene sequence to ones used more frequently by the host cells. Alternatively, the entire gene sequence can be altered to be in line with the codon usage of the host cells used to express the desired product. With the current efficiency of de novo gene synthesis, the later approach has become the preferred method of codon optimization. As the expression of heterologous proteins is an important part of the biotechnology industry, methods such as codon optimization are often useful in improving expression levels.
Most proteins that are secreted from cells contain an N-terminal signal sequence that directs the protein into the cell's secretion pathway. Optimization of internal secretion signal or signal peptide sequence that interact with the endoplasmic membrane to initiate the secretion process has the potential to increase the efficiency of processing and hence and increase in protein expression. The eukaryotic signal sequence has been divided into three structural regions, basic, hydrophobic, and polar, starting from the N-terminus and proceeding to the C-terminus respectively (von Heijne, 1986 and Bendtsen et al 2004). Over the years numerous secretion signals have been identified and used to direct the secretion of recombinant proteins. Although many different signal sequences have been used and shown to be functional, few studies have been reported that define optimal sequences for a given cell type. The general characteristics and rules related to the three structural regions are well established, as detailed by von Heijne (1986) and by Bendtsen et al (2004), however, little comparative experimental data exist as to what constitutes an optimal secretion signal in a given expression system or a given heterologous protein being expressed. Most published reports deal with the characterization and optimization of gram positive bacterial or yeast secretion signals (Le Loir et al, 2005 and Hofmann and Schultz, 1991). One report that describes the optimization of the IL-2 secretion signal clearly demonstrates the benefits of optimization (Zhang et al, 2005).
Many eukaryotic proteins are modified by N-linked glycosylation (asparagine-linked). The of number sites and the efficiency of glycosylation by the enzyme oligosaccharyltransferase can vary for each protein expressed can vary based on a number of factors. This can influence its expression and function. N-Linked glycosylation usually occurs at the Asn residues in the Asn-X-Ser/Thr motif, where X is any amino acid accept for Pro. However, many Asn-X-Ser/Thr sequences are not glycosylated or are glycosylated inefficiently (Mellquist et al, 1998). Inefficient glycosylation at one or more Asn-X-Ser/Thr sequences in a protein results in the production of heterogeneous glycoprotein products. The work of Mellquist et al has revealed that the amino acid at the Y position (amino acid residue immediately following the Ser or THr residue) is an important determinant of core glycosylation efficiency. This provides an example of a means to optimize the glycosylation efficiency of heterologously expressed proteins.
The methods above describe methods to alter the structural aspects of the gene sequence to enhance the expression level of the desired protein product. Alternatively, modification of internal protein sequences to enhance selected epitopes or to remove selected epitopes can be employed to create a more desired product, as in, a protein product that has an altered immunogenic potential. As an example, epitopes in the dengue E protein that are believed to generate flavivirus cross-reactivity antibody responses were altered to reduce the potential of immune enhancement (Hughes et al, 2012). These included the immunodominant B cell epitope of the fusion peptide and domain III epitopes.
While the structure of flavivirus envelope proteins has been well studied and the structures established by cryo-EM and x-ray crystallography, what constitutes an optimal gene sequence for the expression of heterologous proteins in eukaryotic host cell expression systems is not currently well defined. Current technology and methods provide the potential to assemble gene sequences and make modification to internal sequences and define new end points that can lead to improvements in structure and function. While the potential exists to make such modifications, it is common knowledge that not all attempts to do so result in success. The modifications or attempts to optimize that work with one protein and in a given expression system do not always work on other proteins or in other expression systems. For example, the removal of the first 58 amino acids from the N-terminus of the West Nile envelope protein ectodomain abolishes expression. In another example, the expression of the C-terminal domain (domain III) as of the West Nile or Tick-borne encephalitis envelope protein is easily expressed, however, these subunit proteins are suboptimal in their ability to prime functional immune responses, although it is not obvious why this occurs. Therefore, a systematic evaluation is required to determine the potential of various efforts to modify and optimize a given gene sequence such that high levels of high quality heterologous protein are expressed and that such alterations do not negatively impact the desired functional attributes. In the biotechnology field, the ability to efficiently produce recombinant proteins at a favorable cost of goods is a key to success. In order to achieve this goal for a particular protein, in this case the Zika virus envelope protein using the Drosophila S2 cell expression system, requires further experimentation to define the parameters that result in optimal expression of a high quality protein product.
The combination of multiple optimizations directed at different aspects of a protein's gene sequence and or structure in an appropriate manner such that an additive benefit is achieved can further enhance the utility of the optimized protein product. In the case of flavivirus envelope proteins, several examples exist of expression of various truncated products as soluble recombinant proteins; however, all of these examples relied on sequences derived from native viral sequences or synthetic versions of the native sequence. No significant efforts have been made to optimize expression and secretion other than work to define the carboxy-terminus of the envelope protein that is best suited for expression of a soluble product. There are no examples of combining multiple optimizations to further enhance the expression and secretion of soluble flavivirus envelope proteins. Therefore, the technical problems to be solved are: (1) identification of translational, posttranslational, or structural components of the envelope protein or associated components that when optimized result in improved expression levels and potentially enhance structural quality of the protein such that it is a more potent immunogen; (2) the design of synthetic of component where possible to aid in the optimization; and (3) determining the optimal combination of multiple components such that the combination results in an additive increase in the productivity and quality of protein expression. Further improvements in the expression of the Zika envelope protein could potentially provide for effective immunogens at an improved cost of goods which would bolster the ability to manufacture recombinant proteins suitable for use in vaccines to combat the spread of the Zika virus. The use of such improvements could also be applied to other members of the flavivirus family, including but not limited to West Nile virus, dengue virus, tick-borne encephalitis virus, yellow fever virus, Zika virus and several other viruses which may cause encephalitis, en.wikipedia.org/wiki/Flavivirus-cite_note-ShiP-Y-2 as well as insect-specific flaviviruses (ISFs) such as cell fusing agent virus (CFAV), Palm Creek virus (PCV), and Parramatta River virus (PaRV).
The invention provides optimized expression of a soluble ZIKV envelope recombinant subunit protein that results in high levels of expression of a native-like or biological relevant protein; and is therefore, an effective immunogen for the production of neutralizing antibodies. Specifically, the invention is directed to expression of the optimized ZIKA gene sequences when Drosophila melanogaster S2 cells are used as the host cell.
The optimized ZIKV gene sequence for expression of a soluble and stable envelope protein is composed of a prM-E contiguous sequence that has been codon optimized, that contains an optimized secretion signal for the E protein segment, and that has an optimized C-terminus that enhances expression and stability of the expressed E product. The optimized gene sequence is contained in an expression vector for use in Drosophila S2 cells. The codon optimization of the gene sequence is designed for optimal expression in Drosophila S2 cells. The synthetic optimized secretion signal that is utilized is designed to result in effective post-translation processing at the pM-E junction by host cell signal peptide protease. The newly defined C-terminal end for the envelope protein, Glycine436, provides for interaction between the domain III region and the domain I region that helps to stabilize the expressed and secreted ZIKA envelope protein. The combination of the optimization methods has resulted in a unique gene sequence that provides for the expression of a soluble Zika envelope protein with enhanced stability and at high levels. This improved Zika envelope protein is suitable for use as a vaccine to protect against disease caused by Zika virus infection.
The optimized ZIKV gene sequences of the present invention are capable of high level expression and secretion of the encoded envelope protein into the culture medium of transformed S2 cells. Specifically, the described ZIKV envelope gene sequence has been optimized for 1) codon usage in Drosophila S2 cells, 2) a synthetic, optimized secretion signal sequence and processing site, and 3) a C-terminal truncation point that adds stability to the expressed product.
The invention also provides methods for utilizing the products encoded by the optimized ZIKV gene sequences in vaccine formulations for protecting against disease caused by infection with ZIKV.
One aspect of the present invention is to provide an expression vector that includes a codon optimized DNA sequence encoding a Zika virus pre-membrane and envelope protein. The expression of the DNA sequence results in secretion of a soluble envelope protein in the culture medium.
In one embodiment, the codon optimized DNA sequence includes SEQ ID NO:1.
In another embodiment, the codon optimized DNA sequence is further optimized to enhance secretion of the soluble envelope protein by optimizing the E protein secretion signal sequence. This improved secretion signal codon optimized sequence includes SEQ ID NO:2.
In another embodiment, the codon optimized DNA sequence is further optimized to expression of the soluble envelope protein the carboxy-terminus has been extended to stabilize the expressed envelope protein. This extended codon optimized sequence includes SEQ ID NO:3.
In another embodiment, the codon optimized DNA sequence is further optimized to combine the improved E secretion signal the extended carboxy-terminus to enhance the expression and secretion of the soluble envelope protein. This codon optimized sequence with combined improvements includes SEQ ID NO:4.
In another embodiment, the Drosophila expression vector pHH202 that includes SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4 is used to express and secrete the encoded heterologous ZIKV E protein from cultured insect cells. This expression cassette of the pHH202 vector includes SEQ ID NO:7.
In one embodiment, the expression vectors are used in Drosophila cells.
In another embodiment, the expression vectors are used in Drosophila S2 cells.
In one embodiment, the invention provides a vaccine comprising an effective amount of purified Zika virus envelope protein (E), wherein the protein is secreted into the growth medium when expressed recombinantly in a host cell; and an effective amount of aluminum-based adjuvant, wherein the vaccine induces the production of neutralizing antibodies in human subjects. In one aspect, the E protein is recombinantly produced and expressed in insect host cells. In one aspect, the E protein is recombinantly produced and expressed in Drosophila melanogaster Schneider 2 (S2) host cells. Preferably, the vaccine is in a pharmaceutically acceptable excipient. In one aspect, the E protein is encoded by a nucleic acid sequence beginning at nucleotide 505 of SEQ ID NO:1, SEQ ID NO:2 SEQ ID NO:3, SEQ ID NO:4, or SEQ ID NO: 5 which correlates with amino acid residue 169 of SEQ ID NO:6.
Another aspect of the present invention is to provide a method to elicit an immune response that provides protection against disease caused by Zika virus. The method includes administering to a subject in need thereof a composition that includes a soluble envelope protein expressed and secreted by an expression vector that includes a codon optimized DNA sequence that includes SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4.
In one embodiment, the composition includes an adjuvant to enhance the immune response. The vaccine may further include an effective amount of a saponin adjuvant, for example QS21, an aluminum-based adjuvant (collectively referred to as Alum), for example Alhydrogel®, or a stable oil-in-water emulsion (SE) adjuvant which may include squalene. In embodiments, a TLR-4 agonist is a fully synthetic lipid A (SLA) derivative. In one embodiment, the vaccine includes a mixture of SLA and a saponin-based adjuvant, such as QS21, wherein the mixture is a liposomal formulation with these adjuvant components (SLA-LSQ).
Other aspects and advantages of the invention will be apparent from the following description and the appended claims.
The invention provides an optimized ZIKV gene sequence for expression of a soluble and stable envelope protein that is composed of a prM-E contiguous sequence that has been codon optimized, contains an optimized secretion signal for the E protein segment, and has an optimized C-terminus that enhances expression and stability of the expressed E product. The optimized gene sequence is inserted into a Drosophila S2 cell expression vector which drives the expression of high levels of high quality Zika envelope protein in S2 cells that have been stably transformed with the expression vectors carrying the optimized gene sequence. The use of the optimized gene sequence results in an increase in the productivity and quality of the expressed Zika envelope protein. The enhanced expression of the Zika envelope protein provides for an effective immunogen at an improved cost of goods which can bolster the ability to manufacture recombinant proteins suitable for use in vaccines to combat the spread of the Zika virus.
The term “gene sequence” refers to a sequence of DNA that is transcribed into an RNA molecule that may function directly or be translated into an amino acid chain.
The term “optimized” refers to sequences that were derived from naturally occurring sequences and have been altered to enhance their functions.
The term “codon optimized” refers to a nucleic acid coding region that has been adapted for expression in the cells of a given host by replacing at least one, or more than one, or a significant number, of codons with one or more codons that are more frequently used in the genes of that host.
The term “synthetic” refers to sequences that are not found to occur naturally. More specifically, the synthetic elements described herein are not found in the gene sequences of Zika virus or related flaviviruses.
The term “operably linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner.
“Expression cassette” means the combination of promoter elements with other transcriptional and translational regulatory control elements which are operably linked to a gene sequence to be expressed. A gene sequence can be inserted into the expression cassette for the purpose of expression of said gene sequence. The expression cassette is capable of directing transcription which results in the production of an mRNA for the desired gene product which is then translated to protein by the host cell translational systems. The expression cassette is integral to the expression vector (plasmid). Such an expression vector directs expression of the protein encoded by the gene sequence once introduced into host cells.
The term “transformed” refers to the DNA-mediated transformation of cells. This refers to the introduction of plasmid DNA into insect cells in the process of generating stable cell lines following the integration of the introduced DNA into the genome of the cells. This term is used in place of the term “transfection” which is often used in the same context. The term transformation is used for the introduction of plasmid DNA to cultured cells to distinguish from the introduction of viral DNA into cultured cells which was originally referred to as transfection. As there are no viral DNA sequences in the present invention which are introduced into the host that results in the production of virus-like particles or cell lysis the term transformed is preferred.
“Expression” or “expressed” means the production of proteins using expression vectors and host cells, for instance, Drosophila S2 cells to produce a recombinant protein product that is readily detectable as a cell associated product or as a secreted product in the culture medium.
“Secretion” means secretion of an expressed recombinant protein from cultured host cells into culture medium. The expressed and secreted protein is the result of a given gene sequence being operably linked to an expression cassette such that the sequence codes for the given protein.
The term “product” refers to any recombinant protein, full length or subunit thereof, which is expressed by a host cell into which an expression vector carrying the gene sequence encoding the product has been introduced.
Insect cells are an alternative eukaryotic expression system that provide the ability to express properly folded and post-translationally modified proteins while providing simple and relatively inexpensive growth conditions. The use of stably transformed insect cell expression systems provide benefits over those based on baculovirus infection of the host insect cells. On this basis, S2 cells were selected as the insect host cells of choice. As a result, the efforts to optimize the expression vectors for stably transformed insect cells were based on data derived from the analysis of specific Drosophila genes as well as the complete Drosophila genome.
In a preferred embodiment of the invention, the E protein secretion signal located at the carboxy end of the prM sequence and immediately preceding the E sequence N-terminus, is a synthetic sequence designed to enhance the processing of these sequences. This synthetic secretion sequence has an increase core hydrophobic region and the −2 and −1 amino acid residues have been optimized to increase the recognition of the signal protease cleavage site at the prM-E junction. The amino acid residues at +1 and +4 of the E sequence have also been optimized to aid in the recognition of the signal protease cleavage site. The amino acid sequence of the synthetic secretion signal including the optimized residues in the E sequence are shown in
In a preferred embodiment of the invention, the C-terminus of the E protein has been extended beyond the 80E terminus has been extended to stabilize the soluble envelope protein that is expressed. Specifically, the C-terminus of the soluble E protein has been extended from Gly-404 to Ile-436 as shown in
In a more preferred embodiment of the invention, the combination of the optimized and synthetic elements have been combined into a single gene sequence for the expression of the Zika envelope protein that results in an enhanced efficiency and yield of the product. The product is also enhanced in terms of stability as a soluble product and as an immunogen for use as a vaccine. The prM-E nucleotide sequence containing the assembled optimized Zika virus envelope protein components, codon optimization, synthetic secretion signal, and the E-436 C-terminal extension (OpE-436-CoOp) is presented in SEQ ID NO:4.
Thus, the present invention provides the combination of multiple optimizations directed at different aspects of the Zika virus prM-E gene sequence in such a manner that an additive benefit is achieved and results in high levels of the envelope protein being expressed. The optimized Zika prM-E sequence when used to express the envelope protein in Drosophila S2 cells results in the economic production of large quantities of high quality proteins. The Examples below show that using the individual optimized elements in the Zika gene sequence results in improved or enhanced expression of the envelope protein. The highest levels of envelope protein expression are achieved in the gene sequence in which all of the identified optimized elements are combined.
Although the descriptions presented above and the examples that follow are primarily directed at the use of the optimized expression vectors with Drosophila S2 cells, the vectors and methods can be applied to other insect cell lines that result in stable cell lines following transformation of host cells with plasmid DNA.
The following examples are offered by way of illustration and not by way of limitation.
The following examples describe the development of the optimized ZIKV gene sequences for the expression of the envelope protein in insect cells. The examples demonstrate the ability to effectively express the proteins in Drosophila S2 cells at levels that are commercially suitable for product development.
The examples demonstrate the ability of the individual regulatory elements to enhance the ability to express proteins in S2 cells and the efforts made to determine what changes contributed to the enhanced function of these elements. The results presented below demonstrate that different elements and modifications of these elements can result in high levels of expression or in very little or no detectable expression. Thus, the selection of functional and effective regulatory elements must be determined thorough experimentation. Hence, the invention described herein is unique in that the expression cassette described is mostly synthetic in composition and directs high levels of protein expression.
In an effort to identify optimized gene sequences for driving high levels of high quality ZIKV envelope protein in S2 cells, the wild type prM-E gene sequence was compared to a codon optimized prM-E gene sequence. Both the WT and codon optimized sequences were produced synthetically (DNA2.0, Menlo Park, Calif.). For codon optimization, the standard Drosophila melanogaster codon table was used (Kazusa DNA Research Institute, kazusa.or.ip/codori/). As the objective is to improve the efficiency of expression, which is in part controlled by the translation process, a threshold of 10% usage was used in assigning codons (any codon that is used <10% is excluded). Additionally, based on our analysis of highly expressed proteins in Drosophila, we have added the exclusion of the following codons, CGA for Arg, ATA for He, and GTA for Val. The synthesized gene sequences included appropriate restriction enzyme sites at the ends and a stop codon was included at the end of the envelope protein coding region.
For the expression of the ZIKV envelope protein, the genomic sequence representing the ZIKV pre-membrane protein and carboxy-truncated envelope protein (prM-80E) is used. The sequence utilized for expression is based on the 2013 French Polynesia strain H/PF/2013, (GenBank Accession #KJ776791). The WT 2013 French Polynesia strain H/PF/2013 prM-80E sequence along with translation is provided in
The synthetic DNA fragments were digested with appropriate restriction enzymes and inserted with in the expression cassette (SEQ ID NO:7) of the pHH202 expression vector that has been digested with Nhe I and Xho I. The pHH202 expression cassette contains the following elements: metallothionein promoter, optimized Kozak sequence, influenza HA secretion signal, and the SV40 early 3′UTR. The hygromycin encoding gene is also incorporated into the pHH202 expression plasmid downstream of the expression cassette. The pHH202 expression plasmid is designed to allow directional cloning of the gene of interest into unique Nhe I and Xho I sites. The junctions and full inserts of all constructs were sequenced to verify that the various components that have been introduced are correct and that the proper reading frame has been maintained.
For this work standard methods of culturing and transformation of S2 cells were utilized (Van der Straten, Methods in Mol. and Cell Biol. (1989) 1:1-8; Culp et al., Biotechnology (1991) 9:173-177; Kirkpatrick and Shatzman, In Gene Expression Systems: Using Nature for the Art of Expression, Eds. Fernandez and Hoeffler, Academic Press, (1999) 289-330). Drosophila S2 cells (Schneider, J. Embryol. Exp. Morph. (1972) 27:353-365) obtained from ATCC were utilized. The S2 cells have been adapted to growth in Excell 420 medium (SAFC, St Louis, Mo.) and all procedures and culturing described herein were in Excell 420 medium. Cultures are typically seeded at a density of 1×106 cells/ml and are passed between days 5 and 7. All cultures were incubated at 26° to 27° C. Expression plasmids into which genes of interest were inserted were transformed into S2 cells using the ExpreS2 TR reagent (Expres2ion Bio, Horsholm, Denmark). Following transformation, cells resistant to hygromycin B, 0.3 mg/ml, were selected. Once stable cell lines were selected, they were evaluated for expression of the appropriate products. For the evaluation of expression, 5 ml cultures of selected cell lines were seeded at 2×106 cells/ml and cultured in the presence of 0.2 mM copper sulfate at 26° C. for 7 days. Cultures were evaluated for expression of recombinant proteins in both the cell associated fractions and the culture medium. Proteins were separated by SDS-PAGE and either stained with Coomassie blue or blotted onto nitrocellulose for Western blot analysis. Expression levels ≥1 μg/ml (1 mg/L) are readily detected in S2 cultures by Coomassie staining of SDS-PAGE gels.
Parental S2 cell lines expressing the ZIKFP 80E-WT and ZIKFP-80E-CoOp have been established using standard methods developed at HBI (23). The expression of the ZIKFP-80E products has been identified using the conformationally sensitive monoclonal antibody (mAb) 4G2 that recognizes most flavivirus envelope proteins (24). The expression data for two parental S2 cell lines expressing codon optimized ZIKFP-80E-CoOp is shown in
The use of the codon optimized prM-E gene sequence in transformed S2 resulted in the expression ZIKFP-80E-CoOp at approximately 30 μg/ml. A coomassie stained SDS-PAGE gel is shown in
Another adjuvant which may be utilized in the presently described vaccine formulation is a stable oil based emulsion. In one embodiment the emulsion is a stable oil-in-water emulsion (SE) which may optionally include squalene.
Another adjuvant which may be utilized in the presently described vaccine formulation is a saponin-based adjuvant, such as QS21. QS21 is a purified plant extract that enhances the ability of the immune system to respond to vaccine antigens. It is derived from the Soap bark tree (Quillaja saponaria) and contains water soluble triterpene glucoside compounds, which are members of a family of plant-based compounds called saponins. In one embodiment, a saponin-based adjuvant is combined with SLA forming a liposome formulation. In one embodiment, SLA is combined with QS21 to form a liposome formulation (SLA-LSQ).
The vaccine formulation of the present invention may further include one or more additional pharmaceutically acceptable diluents, carriers, solubilizers, emulsifiers, preservatives and/or adjuvants.
The secretion signal peptide plays an important role in the expression of proteins that are targeted for secretion from the cell. Therefore, the use of optimal sequences that target the desired recombinant protein for secretion into the culture medium during production is important to the efficiency of processing the protein and potentially increasing the yield of the product. The example of secretion signal optimization presented by Zhang et al. (J. Gene Med. (2005) 7:354-365) clearly demonstrates the benefits of secretion signal optimization. However, this specific example applies to plants and it is not clear that the changes to the secretion signal described apply to other eukaryotic cell types. Furthermore, as Zika envelope expression is achieved through the expression of the prM-E polypeptide, the secretion is directed by the integral sequence of the prM protein that serves as a component of the transmembrane anchor for the prM protein. The second membrane spanning sequence of the prM protein also serves as the secretion signal peptide for the E protein. No clear guidance exists on how to best optimize this transmembrane anchor/secretion signal peptide sequence to improve the secretion and yield of the envelope protein. Therefore, a survey of flavivirus prM-E secretion signals was conducted. The putative secretion signals from prM and the E protein N-terminus were analyzed using the SignalP program described by Petersen et al (Nat. Methods, (2011) 8(10): 785-6), which predicts the strength of the secretion signal based on an established algorithm and also predicts the cleavage site of the sequence analyzed.
Surprisingly, as shown in
The Synthetic+ secretion signal is operatively linked to the prM-80E codon optimized Zika sequence (SEQ ID NO:1) to create the combination of codon optimization and secretion signal optimization as detailed in SEQ ID NO:2. SEQ ID NO:2 is then inserted into the expression cassette (SEQ ID NO: 7) of the pHH202 vector. The expressed and secreted E protein is referred to as ZIKFP-Op80E-CoOp.
The C-terminus of the flavivirus E ectodomain is typically defined by the Gly residue in the sequence motif W-X-K/R-X-G. In the case of Zika this is Gly404. While this truncation results in secretion of the ZIKFP-80E product as shown in Example 1, efforts to improve the stability of the expressed E protein, both in terms of expression levels and structural integrity are desirable. An analysis of the Zika virus cyro EM data (Sirohi et al, 2016) suggests that an extension of the E ectodomain from Gly404 to Gly436 may provide a stabilizing effect. The extension of the C-terminus to Gly436 has the potential to provide for interaction between the domain III region and the domain I region and help to stabilize the expressed and secreted ZIKV envelope protein. In the extended E protein, the Phe431 residue has the potential to interact with a hydrophobic pocket in domain I composed of Val12, Val23 and Val24. An extension of the E protein in this manner could lead to enhancement of proper protein folding (native-like structure) and stability.
The codon optimized Zika prM-E sequence that extends the E protein to amino acid residue 436 is referred to as prM-E-436 and is detailed in SEQ ID NO:3. SEQ ID NO:3 is then inserted into the expression cassette (SEQ ID NO: 7) of the pHH202 vector. The expressed and secreted E protein is referred to as ZIKFP-E-436-CoOp.
A fully optimal Zika prM-E sequence that combines the three features, codon optimization, optimized synthetic secretion signal, and the extended E sequence was also generated as detailed in SEQ ID NO:4. SEQ ID NO:4 is then inserted into the expression cassette (SEQ ID NO: 7) of the pHH202 vector. The expressed and secreted E protein is referred to as ZIKFP-OpE-436-CoOp. The expression and secretion of the ZIKFP-80E-WT, ZIKFP-80E-CoOp, and ZIKFP-OpE-436-CoOp from S2 cells was evaluated by SDS-PAGE. A coomassie stained gel is shown in
The immunogenicity of the Drosophila S2 expressed ZIKFP-80E-CoOp subunit protein was evaluated in both inbred and outbred mice with several different adjuvants to assess the immunogenic potential. Mice were immunized intra-muscularly with either two doses or 3 doses of ZIKFP-80E separated by 3 week intervals. Two amounts of ZIKFP-80E-CoOp were evaluated, 5.0 μg and 2.5 μg. The adjuvants tested were Alhydrogel, GPI-0100 and GLA-SE. Mice were bled 2 weeks after the 2 or third dose to prepare serum samples for antibody analysis. The design of the immunogenicity study is presented in Table 1.
Mice were immunized intra-muscularly two or three times at 3 week intervals with the purified subunit protein at a dose of 5.0 μg or 2.5 μg. Five mice were bled two weeks after dose two and 5 mice were bled two weeks after dose three. The sera were then assessed for anti-80E antibody titers by ELISA. The sera were also evaluated for virus neutralizing antibodies using the plaque reduction neutralization test (PRNT).
The ELISA results for the serum collected following two or three doses of ZIKFP-80E-CoOp formulated with multiple adjuvants is presented in
The following references are each relied upon and incorporated herein in their entirety.
CTGCTCGTGAGCGGTGCCCACGCC
AGCCGTTGCGTGGGCGTCAGCAACCGCGATTTCGTG
CTGCTCGTGAGCGGTGCCCACGCC
AGCCGTTGCGTGGGCGTCAGCAACCGCGATTTCGTG
Although the present invention has been described in terms of specific exemplary embodiments and examples, it will be appreciated that the embodiments disclosed herein are for illustrative purposes only and various modifications and alterations might be made by those skilled in the art without departing from the spirit and scope of the invention as set forth in the following claims.
This application is a 35 USC § 371 National Stage application of International Application No. PCT/US2017/044008 filed Jul. 26, 2017, now pending; which claims the benefit under 35 USC § 119(e) to U.S. Application Ser. No. 62/442,346 filed Jan. 4, 2017, U.S. Application Ser. No. 62/410,572 filed Oct. 20, 2016 and U.S. Application Ser. No. 62/367,310 filed Jul. 27, 2016, all now expired. The disclosure of each of the prior applications is considered part of and is incorporated by reference in the disclosure of this application.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2017/044008 | 7/26/2017 | WO |
| Publishing Document | Publishing Date | Country | Kind |
|---|---|---|---|
| WO2018/022790 | 2/1/2018 | WO | A |
| Number | Name | Date | Kind |
|---|---|---|---|
| 6165477 | Ivy et al. | Dec 2000 | A |
| 7838006 | Jirathitikal et al. | Nov 2010 | B2 |
| 9267114 | Yamshchikov | Feb 2016 | B2 |
| 20030175304 | Peters et al. | Sep 2003 | A1 |
| 20090226489 | Jira et al. | Sep 2009 | A1 |
| 20120263754 | Dubensky et al. | Oct 2012 | A1 |
| Number | Date | Country |
|---|---|---|
| 2007202304 | Jun 2007 | AU |
| 105749268 | Jul 2016 | CN |
| 2221368 | Aug 2010 | EP |
| 16162688.2 | Mar 2016 | EP |
| WO 2017109222 | Jun 2017 | WO |
| Entry |
|---|
| Dai et al., Cell Host & Microbe, May 11, 2016, 19:696-704. (Year: 2016). |
| Dai et al., “Structures of the Zika Virus Envelope Protein and its Complex with a Flavivirus Broadly Protective Antibody,” Cell Host & Microbe (2016), 19:696-704, Elsevier Inc. |
| Number | Date | Country | |
|---|---|---|---|
| 20210332084 A1 | Oct 2021 | US |
| Number | Date | Country | |
|---|---|---|---|
| 62442346 | Jan 2017 | US | |
| 62410572 | Oct 2016 | US | |
| 62367310 | Jul 2016 | US |
