Patent Application
20200148725
The present invention relates to norovirus fusion proteins, VLPs comprising norovirus fusion proteins, and methods of producing the same.
The global disease burden attributed to norovirus infection is high, being associated with an estimated 20% of all worldwide diarrheal cases and causing over 200,000 deaths annually. Noroviruses are the primary cause of foodborne disease outbreaks in North America and are the causative agent for the majority of healthcare-associated outbreaks amongst the elderly. Norovirus strains are also recognized as being the leading cause of pediatric gastrointestinal illness worldwide.
Noroviruses comprise one of a number of genera of the family Caliciviridae. The human norovirus genome is a single-stranded, positive-sense RNA molecule encoding three open reading frames (ORFs) and capped on its 5′ end by a VPg protein. ORF1 encodes six non-structural viral proteins, including VPg, an RNA-dependent RNA polymerase, and a viral protease. ORF2 encodes the major structural capsid protein (VP1). ORF3 encodes a minor capsid protein (VP2).
VP1 is comprised of 2 domains: a shell (S) domain, and a protruding (P) domain. The P domain is further comprised of a P1 sub-domain and a P2 sub-domain. The P2 sub-domain is referred to as the hypervariable domain and is thought to play an important role in receptor binding and immune reactivity.
VP1 proteins form dimers via P domain-mediated protein interactions. Dimerization increases the stability of the virion capsid and results in formation of the protrusions extending from the base core of the norovirus particle formed by S domains. When expressed, norovirus VP1 proteins can automatically assemble to form 2 virion structures: a 180-mer capsid structure with T=3 icosahedral symmetry having a 38-40 nm diameter; and a 60-mer capsid structure with T=1 icosahedral symmetry having a 23 nm diameter.
VP2, the minor structural protein, has a molecular weight (MW) of approximately 21-24 kDa. Studies suggest that VP2 is highly basic and located inside the capsid. The function of VP2 has not yet been fully understood but it is generally believed to play a role in capsid stability by protecting the virions from disassembly and degradation (Bertolotti-Ciarlet A., Crawford S. E., Hutson A. M., Estes M. K. 2003, J. Virol. 77:11603-11615). VP2 may also have a function during RNA genome packaging. The amount of VP2 minor structural protein in virions is relatively low with 1.5 to 8 copies incorporated into the mature virion. Bertolotti-Ciarlet et. al. (2003) report that in insect and mammalian cells, VLPs composed of VP1/VP2 are more resistant to protease cleavage than those with only VP1, and that expression of VP2 in cis, results in an increase in VP1 protein production. In addition, the presence of the 3′UTR downstream of the ORF2 gene increases the steady-state levels of NV ORF2 mRNA. The greatest increase in VP1 expression was observed when ORF2+ORF3+3′UTR, residing on the same construct and under regulation of one promoter, was expressed. Expression of VP2 in trans did not result in any increase in VP1 expression, indicating that the subgenomic organization of ORF2-ORF2-3′UTR was required for the observed increase in VP1 production.
Noroviruses are classified according to their phylogenetic clustering of the VP1 amino acid sequence. Seven genogroups have been classified to date (GI through GVII) with only genogroups GI, GII, and GIV known to infect humans. Of the 32 specific genotypes currently associated with human infections, GII.4 noroviruses have been responsible for the majority of recent norovirus outbreaks. New strains of GII.4 emerge every two to three years, evolving by a process driven by mutations in epitope determining regions of the hypervariable P2 domain of VP1. This process allows the norovirus to escape humoral immune responses acquired by previous exposure to earlier strains.
While faced with the difficulty of rapidly evolving and genetically diverse norovirus strains, the development of effective norovirus vaccines has been exacerbated by additional challenges. For instance, until recently, human norovirus could not be grown in cell culture and even now, robust cell culture systems for both VLPs and live attenuated noroviruses are lacking.
An additional challenge in vaccine development is that immunity to norovirus infection is strain and genotype specific with minimal cross-immunity conferred against other genogroups. Furthermore, immunity to a norovirus strain is not life-long and is estimated to persist from anywhere between six months and nine years.
Various approaches have been undertaken to develop a suitable vaccine against norovirus infection including the production of recombinant norovirus proteins in plants and recombinant generation of fusion/chimeric VP1 proteins.
Mason et al. (Proc Natl Acad Sci U.S.A., 1996, 93(11):5335-40) teach the use of genetically engineered tobacco plants and potato tubers to express GI.1 norovirus VLPs from native VP1 protein. The plant produced norovirus VLPs are morphologically and physically similar to the 38 nm Norwalk VLPs produced in insect cells. Oral administration of purified tobacco-produced Norwalk VLPs from native capsid protein, or potato tubers expressing GI.1 capsid protein induced a humoral immune response in mice and humans (Tacket et al., J. Infect. Dis., 2000, 182(1):302-5).
Huang et al. (Biotechnol. Bioeng., 2009, 103(4):706-14) describe a geminivirus-derived DNA replicon vector for production of GI.1 norovirus VLP in plants. Co-delivery of bean yellow dwarf virus-derived vector and Rep/RepA-supplying vector in Nicotiana benthamiana resulted in rapid and robust protein production.
Coit et al. (WO 2007/081447; U.S. Pat. Nos. 7,527,801; 8,119,145; 8,124,104; 8,142,793; 9,428,739) teach polynucleotides encoding capsid proteins and other immunogenic proteins from norovirus. The production of norovirus-derived multiple epitope fusion antigens comprising a norovirus NTPase-polymerase fusion protein is also described. The fusion protein may comprise a linker sequence. Methods to produce norovirus fusion proteins comprising VP1 are also disclosed.
Steadman et al. (U.S. Pat. No. 8,980,275) describe a chimeric protein comprising a Calicivirus capsid protein and at least one heterologous antigen, and the formation of VLPs when the chimeric protein is expressed in a host cell. A chimeric protein comprising a heterologous antigen, or fragment thereof, inserted into a P2 domain of the Calicivirus protein is also disclosed.
Lin et al. (WO 2016/019890) teach a fusion protein in which an antigen is fused, with or without a linker sequence, on both its N-terminal and C-terminal ends, to viral structural proteins, or fragments thereof, and wherein fusion improves the folding and antigenicity of the antigen. The viral structural protein may be any protein that contributes to the structure of the capsid or protein core of the virus, and the norovirus S domain or P domain are mentioned as examples.
Settembre et al. (U.S. Ser. No. 14/946,324) disclose immunogenic compositions comprising chimeric norovirus VP1 proteins capable of forming VLPs produced in insect cells, mammalian cells, avian cells, bacterial cells, yeast cells, or Tetrahymena cells. The chimeric VP1 proteins have all, or a portion, of a VP1 P domain from one strain of norovirus replaced with all, or a portion, of a P domain from a non-homologous norovirus strain.
Noroviruses are known to bind specific histo-blood group antigens (HBGA). Huo et al. (Virus Res., 2016, 224:1-5) teach the production of chimeric VP1 capsid proteins where the P2 domain of a GII.4 Sydney 2012-like variant norovirus is exchanged for the P2 domain of a GII.3 strain norovirus. Results from in vitro HBGA-binding blockade assays indicate that although GII.3 norovirus VLPs do not bind to any synthetic or salivary HBGAs tested, the chimeric VLPs are capable of binding synthetic blood type A (trimer) and Le(x) HBGAs and blood type A, B and O salivary HBGAs. Furthermore, Huo et al. demonstrate that this binding can be competitively inhibited by anti-GII.3 serum but not anti-GI.2 or anti GII.4 serum.
The present invention relates to norovirus fusion proteins, virus like particles (VLPs) comprising norovirus fusion proteins, and methods of producing the same.
It is an object of the invention to produce norovirus fusion proteins, VLPs comprising norovirus fusion proteins, and to producing VLPs comprising norovirus fusion proteins in plants.
As described herein there is provided a nucleic acid encoding a norovirus VP1 fusion protein comprising, a first sequence encoding an S domain derived from a first norovirus strain, and a second sequence encoding a P domain derived from a second norovirus strain, the first and second sequence are selected from norovirus genogroups GI, GII, and GIV.
Also provided is the nucleic acid encoding the norovirus VP1 fusion protein as described above, wherein the first and second norovirus strains are independently selected from norovirus genotypes GI.1, GI.2, GI.3, GI.4, GI.5, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.12, GII.13, GII.14, GII.17 and GII.21 is also provided. For example, which is not to be considered limiting, the first norovirus strain and the second norovirus strain may be independently selected from norovirus subtypes:
GI.1/US/1968,
GI.2/Leuven/2003/Bel,
GI.3/S29/2008/Lilla Edet/Sweden,
GI.5/AlbertaEI390/2013/CA,
GII.1/Ascension208/2010/USA,
GII.12/HS206/2010/USA,
GII.13/VA173/2010/USA,
GII.14/8610/Saga/2008/JPN,
GII.17/Kawazaki/2014/A0A077KVU6, and
GII.21/Salisbury150/2011/USA.
The nucleic acid as described above may also comprise a fifth sequence encoding a CPMV enhancer, the CPMV enhancer operatively linked with the first, second, third, and fourth sequences. The nucleic acid as described above may also be optimized for human codon usage, increased GC content, or a combination thereof.
A norovirus VP1 fusion protein encoded by the nucleic acid as described above is also described herein. Furthermore, a virus like particle (VLP) comprising the norovirus VP1 fusion protein encoded by the nucleic acid is also disclosed.
Methods to produce an antibody or antibody fragment using the norovirus fusion VP1 fusion protein or the VLP encoded by the nucleic acid, or the VLP comprising the norovirus VP1 fusion protein and norovirus VP2 protein encoded by the nucleic acid complex, are described herein. An antibody, an antibody fragment, or a combination thereof, produced using these methods is also provided.
The present disclosure also describes a method of producing a norovirus VP1 fusion protein in a plant host cell, for example the plant, the portion of a plant, or the plant cell. The method comprises introducing the nucleic acid, or nucleic acid complex, as described above into the plant host cell, and incubating the plant host cell under conditions that permit expression of the norovirus VP1 fusion protein. The method may further comprises a step of harvesting the plant host cell, for example the plant, the portion of a plant, or the plant cell, and purifying the norovirus VP1 fusion protein.
As described herein, there is a method of producing a VLP comprising a norovirus VP1 fusion protein in a plant, portion of the plant, or a plant cell. The method comprises introducing the nucleic acid as described herein into the plant, portion of the plant, or the plant cell, and incubating the plant, portion of the plant, or the plant cell under conditions that permit expression of the nucleic acid and the formation of the VLP. The method of producing the VLP may further comprise a step of harvesting the plant, portion of the plant, or the plant cell, producing a plant extract, and purifying the VLP, wherein the VLP has a diameter of about 15 nm to 50 nm, for example, about 23 nm (for T=1 icosahedral symmetry) or about 38 to about 40 nm (for T=3 icosahedral symmetry). Furthermore, in the step of introducing, a second nucleic acid sequence encoding a norovirus VP2 protein may be introduced in the plant, portion of the plant, or the plant cell, and in the step of incubating, the conditions permit co-expression and co-production, of both the VP1 fusion protein and the VP2 protein in the plant, the portion of a plant, or the plant cell
A plant, portion of a plant, or a plant cell comprising the VLP produced by the method described above is also provided herein. A plant extract comprising the VLP produced by this method is also described.
Also provided is a composition for inducing an immune response. The composition comprises, an effective dose of the norovirus VP1 fusion protein encoded by the nucleic acid as described herein; and a pharmaceutically acceptable carrier, adjuvant, vehicle or excipient. Alternatively, the composition may comprise, an effective dose of the VLP produced by the method described herein, and a pharmaceutically acceptable carrier, adjuvant, vehicle or excipient.
A method of producing an antibody or an antibody fragment is also described. The method comprises, administering the norovirus fusion VP1 fusion protein as described above to a subject in need thereof, or a host animal, thereby producing the antibody or the antibody fragment.
Additionally there is provided a vaccine for inducing an immune response in a subject in need thereof, the vaccine comprising an effective dose of the norovirus VP1 fusion protein encoded by the nucleic acid described herein. Alternatively, the vaccine may comprise an effective dose of VLP produced by the method described herein.
The present disclosure also provides a method of inducing immunity to a norovirus infection in a subject comprising administering the norovirus VP1 fusion protein encoded by the nucleic acid described herein. The norovirus VP1 fusion protein may be administered orally, intranasally, intramuscularly, intraperitoneally, intravenously, or subcutaneously. Also provided is a method of inducing immunity to a norovirus infection in a subject comprising of administering the VLP produced by the method described herein. The VLP may be administered orally, intranasally, intramuscularly, intraperitoneally, intravenously, or subcutaneously.
Also described herein is a nucleic acid complex comprising, a VP1 sequence encoding a norovirus VP1 fusion protein, and a VP2 sequence encoding a norovirus VP2 protein, the VP1 sequence comprising a first and a second nucleic acid sequence, the first nucleic acid sequence encoding an S domain derived from a first norovirus strain, the second nucleic acid sequence encoding a P domain derived from a second norovirus strain, the VP2 sequence comprising a third nucleic acid sequence derived from the first norovirus strain and encoding the norovirus VP2 protein, wherein the VP1 sequence is operatively linked to a first regulatory region, and the VP2 sequence is operatively linked to a second regulatory region, and the VP1 sequence and the VP2 sequence are located on one nucleic acid segment, or the VP1 sequence and the VP2 sequence are located on separate nucleic acid segments. The first regulatory region, the second regulatory region, or the first and second regulatory region of the nucleic acid complex may comprise a CPMV enhancer element that is operatively linked with a promoter active in the plant. For example, the first and the second regulatory region may comprise the CPMV enhancer element, and the first and the second regulatory region may comprise the same promoter. Furthermore, the first and the second regulatory region may comprise a CPMV enhancer element, and the CPMV enhancer sequence of the first and the second regulatory region may be the same CPMV enhancer sequence. The first, the second, the third nucleic acid sequence, or all of the first, second and third nucleic acid sequence, may be optimized for human codon usage, increased GC content, or a combination thereof.
Also provided herein is a VLP comprising the norovirus VP1 fusion protein and the norovirus VP2 protein encoded by the nucleic acid complex as defined above. The VLP may have a diameter of about 15 nm to 50 nm, for example, from about 23 nm or about 38 nm.
A method of producing a virus like particle (VLP) in a plant, portion of a plant, or a plant cell is also described. The method comprises introducing the nucleic acid complex as defined above into the plant, the portion of a plant, or the plant cell, and incubating the plant, the portion of a plant, or the plant cell under conditions that permit the production of the VLP comprising the norovirus VP1 fusion protein and the norovirus VP2 protein. The method may further comprises a step of harvesting the plant, the portion of a plant, or the plant cell. Furthermore, the method may comprises a step of extracting, purifying, or both extracting and purifying, the VLP comprising the norovirus VP1 fusion protein and the norovirus VP2 protein, from the plant, the portion of a plant, or the plant cell.
Also included herein is a plant, portion of the plant, or the plant cell comprising the nucleic acid complex as described above. Furthermore, a plant extract comprising the VLP comprising the norovirus VP1 fusion protein and the norovirus VP2 protein, produced by the method described above is provided
Also described herein is the VLP comprising the norovirus VP1 fusion protein and the norovirus VP2 protein produced by the method described above. The VLP may have a diameter of about 15 nm to 50 nm, for example about 23 nm or about 38 nm. Furthermore, a plant, portion of the plant, or the plant cell comprising the VLP comprising the VP1 fusion protein and the norovirus VP2 protein as described above is also provided.
A composition for inducing an immune response comprising, an effective dose of the VLP comprising the norovirus VP1 fusion protein and the norovirus VP2 protein described above, and a pharmaceutically acceptable carrier, adjuvant, vehicle or excipient is also presented herein. Also provided, is a method for inducing immunity to a norovirus infection in a subject, comprising, administering the composition as just described to the subject. Furthermore, the composition may be administered to the subject orally, intranasally, intramuscularly, intraperitoneally, intravenously, or subcutaneously.
Also described is a method for inducing immunity to a norovirus infection in a subject, the method comprising administering the VLP comprising, an effective dose of the VLP comprising the norovirus VP1 fusion protein and the norovirus VP2 protein as described above, to the subject. The VLP may be administered to the subject orally, intranasally, intramuscularly, intraperitoneally, intravenously, or subcutaneously.
A vaccine is also described herein. The vaccine comprising an effective dose of the VLP of claim 66 for inducing an immune response. Also presented is a method for inducing immunity to a norovirus infection in a subject, comprising administering the vaccine as just described to the subject. The vaccine may be administered to the subject orally, intranasally, intramuscularly, intraperitoneally, intravenously, or subcutaneously.
The present disclosure also describes a method of producing an antibody or an antibody fragment comprising, administering the VLP comprising the norovirus VP1 fusion protein and the norovirus VP2 protein, described above, to a subject in need thereof, or a host animal, thereby producing the antibody or the antibody fragment, is also provided. For example, the antibody or antibody fragment may recognizes an epitope of the P domain.
This summary of the invention does not necessarily describe all features of the invention.
These and other features of the invention will become more apparent from the following description in which reference is made to the appended drawings wherein:
The following description is of a preferred embodiment.
As used herein, the terms “comprising,” “having,” “including” and “containing,” and grammatical variations thereof, are inclusive or open-ended and do not exclude additional, un-recited elements and/or method steps. The term “consisting essentially of” when used herein in connection with a use or method, denotes that additional elements and/or method steps may be present, but that these additions do not materially affect the manner in which the recited method or use functions. The term “consisting of” when used herein in connection with a use or method, excludes the presence of additional elements and/or method steps. A use or method described herein as comprising certain elements and/or steps may also, in certain embodiments, consist essentially of those elements and/or steps, and in other embodiments consist of those elements and/or steps, whether or not these embodiments are specifically referred to. In addition, the use of the singular includes the plural, and “or” means “and/or” unless otherwise stated. The term “plurality” as used herein means more than one, for example, two or more, three or more, four or more, and the like. Unless otherwise defined herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. As used herein, the term “about” refers to an approximately +/−10% variation from a given value. It is to be understood that such a variation is always included in any given value provided herein, whether or not it is specifically referred to. The use of the word “a” or “an” when used herein in conjunction with the term “comprising” may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one” and “one or more than one.”
The term “plant”, “portion of a plant”, “plant portion’, “plant matter”, “plant biomass”, “plant material”, plant extract”, or “plant leaves”, as used herein, may comprise an entire plant, tissue, cells, or any fraction thereof, intracellular plant components, extracellular plant components, liquid or solid extracts of plants, or a combination thereof, that are capable of providing the transcriptional, translational, and post-translational machinery for expression of one or more than one nucleic acids described herein, and/or from which an expressed protein or VLP may be extracted and purified. Plants may include, but are not limited to, agricultural crops including for example canola, Brassica spp., maize, Nicotiana spp., (tobacco) for example, Nicotiana benthamiana, Nicotiana rustica, Nicotiana, tabacum, Nicotiana alata, Arabidopsis thaliana, alfalfa, potato, sweet potato (Ipomoea batatus), ginseng, pea, oat, rice, soybean, wheat, barley, sunflower, cotton, corn, rye (Secale cereale), sorghum (Sorghum bicolor, Sorghum vulgare), safflower (Carthamus tinctorius).
The term “plant portion”, as used herein, refers to any part of the plant including but not limited to leaves, stem, root, flowers, fruits, a plant cell obtained from leaves, stem, root, flowers, fruits, a plant extract obtained from leaves, stem, root, flowers, fruits, or a combination thereof. The term “plant extract”, as used herein, refers to a plant-derived product that is obtained following treating a plant, a portion of a plant, a plant cell, or a combination thereof, physically (for example by freezing followed by extraction in a suitable buffer), mechanically (for example by grinding or homogenizing the plant or portion of the plant followed by extraction in a suitable buffer), enzymatically (for example using cell wall degrading enzymes), chemically (for example using one or more chelators or buffers), or a combination thereof. A plant extract may be further processed to remove undesired plant components for example cell wall debris. A plant extract may be obtained to assist in the recovery of one or more components from the plant, portion of the plant or plant cell, for example a protein (including protein complexes, protein surprastructures and/or VLPs), a nucleic acid, a lipid, a carbohydrate, or a combination thereof from the plant, portion of the plant, or plant cell. If the plant extract comprises proteins, then it may be referred to as a protein extract. A protein extract may be a crude plant extract, a partially purified plant or protein extract, or a purified product, that comprises one or more proteins, protein complexes, protein suprastructures, and/or VLPs, from the plant tissue. If desired a protein extract, or a plant extract, may be partially purified using techniques known to one of skill in the art, for example, the extract may be subjected to salt or pH precipitation, centrifugation, gradient density centrifugation, filtration, chromatography, for example, size exclusion chromatography, ion exchange chromatography, affinity chromatography, or a combination thereof. A protein extract may also be purified, using techniques that are known to one of skill in the art.
The term nucleic acid segment as used herein refers to a sequence of nucleic acids that encodes a protein of interest. In addition to the sequence of nucleic acids, the nucleic acid segment comprise a regulatory region and a terminator that are operatively linked to the sequence of nucleic acids. The regulatory region may for example comprise a promoter, and optionally, an enhancer element operatively linked to the promoter.
The term “nucleic acid complex” as used herein refers to a combination of two or more than two nucleic acid segments. The two or more than two nucleic acid segments may be present in a single nucleic acid, so that the nucleic acid complex comprises two, or more than two nucleic acid segments, with each nucleic acid segment under the control of a regulatory region and a terminator. Alternatively, the nucleic acid complex may comprise two or more separate nucleic acids, each of the nucleic acids comprising one or more than one nucleic acid segment, where each nucleic acid segment is under the control of a regulatory region and a terminator. For example a nucleic acid complex may comprise one nucleic acid that comprises two nucleic acid segments, a nucleic acid complex may comprise two nucleic acids, each nucleic acid comprising one nucleic acid segment, or a nucleic acid complex may comprise two or more than two nucleic acids, with each nucleic acid comprising one or more than one nucleic acid segment.
The term “vector” or “expression vector”, as used herein, refers to a recombinant nucleic acid for transferring exogenous nucleic acid sequences into host cells (e.g. plant cells) and directing expression of the exogenous nucleic acid sequences in the host cells. “Expression cassette” refers to a nucleotide sequence comprising a nucleic acid of interest under the control of, and operably (or operatively) linked to, an appropriate promoter or other regulatory elements for transcription of the nucleic acid of interest in a host cell. As one of skill in the art would appreciate, the expression cassette may comprise a termination (terminator) sequence that is any sequence that is active the plant host. For example the termination sequence may be derived from the RNA-2 genome segment of a bipartite RNA virus, e.g. a comovirus, the termination sequence may be a NOS terminator, or terminator sequence may be obtained from the 3′UTR of the alfalfa plastocyanin gene.
The constructs of the present disclosure may further comprise a 3′ untranslated region (UTR). A 3′ untranslated region contains a polyadenylation signal and any other regulatory signals capable of effecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by effecting the addition of polyadenylic acid tracks to the 3′ end of the mRNA precursor. Polyadenylation signals are commonly recognized by the presence of homology to the canonical form 5′ AATAAA-3′ although variations are not uncommon. Non-limiting examples of suitable 3′ regions are the 3′ transcribed non-translated regions containing a polyadenylation signal of Agrobacterium tumor inducing (Ti) plasmid genes, such as the nopaline synthase (Nos gene) and plant genes such as the soybean storage protein genes, the small subunit of the ribulose-1, 5-bisphosphate carboxylase gene (ssRUBISCO; U.S. Pat. No. 4,962,028; which is incorporated herein by reference), the promoter used in regulating plastocyanin expression.
By “regulatory region” “regulatory element” or “promoter” it is meant a portion of nucleic acid typically, but not always, upstream of the protein coding region of a gene, which may be comprised of either DNA or RNA, or both DNA and RNA. When a regulatory region is active, and in operative association, or operatively linked, with a nucleotide sequence of interest, this may result in expression of the nucleotide sequence of interest. A regulatory element may be capable of mediating organ specificity, or controlling developmental or temporal gene activation. A “regulatory region” includes promoter elements, core promoter elements exhibiting a basal promoter activity, elements that are inducible in response to an external stimulus, elements that mediate promoter activity such as negative regulatory elements or transcriptional enhancers. “Regulatory region”, as used herein, also includes elements that are active following transcription, for example, regulatory elements that modulate gene expression such as translational and transcriptional enhancers, translational and transcriptional repressors, upstream activating sequences, and mRNA instability determinants. Several of these latter elements may be located proximal to the coding region.
In the context of this disclosure, the term “regulatory element” or “regulatory region” typically refers to a sequence of DNA, usually, but not always, upstream (5′) to the coding sequence of a structural gene, which controls the expression of the coding region by providing the recognition for RNA polymerase and/or other factors required for transcription to start at a particular site. However, it is to be understood that other nucleotide sequences, located within introns, or 3′ of the sequence may also contribute to the regulation of expression of a coding region of interest. An example of a regulatory element that provides for the recognition for RNA polymerase or other transcriptional factors to ensure initiation at a particular site is a promoter element. Most, but not all, eukaryotic promoter elements contain a TATA box, a conserved nucleic acid sequence comprised of adenosine and thymidine nucleotide base pairs usually situated approximately 25 base pairs upstream of a transcriptional start site. A promoter element may comprise a basal promoter element, responsible for the initiation of transcription, as well as other regulatory elements that modify gene expression.
There are several types of regulatory regions, including those that are developmentally regulated, inducible or constitutive. A regulatory region that is developmentally regulated, or controls the differential expression of a gene under its control, is activated within certain organs or tissues of an organ at specific times during the development of that organ or tissue. However, some regulatory regions that are developmentally regulated may preferentially be active within certain organs or tissues at specific developmental stages, they may also be active in a developmentally regulated manner, or at a basal level in other organs or tissues within the plant as well. Examples of tissue-specific regulatory regions, for example see-specific a regulatory region, include the napin promoter, and the cruciferin promoter (Rask et al., 1998, J. Plant Physiol. 152: 595-599; Bilodeau et al., 1994, Plant Cell 14: 125-130). An example of a leaf-specific promoter includes the plastocyanin promoter (see U.S. Pat. No. 7,125,978, which is incorporated herein by reference).
An inducible regulatory region is one that is capable of directly or indirectly activating transcription of one or more DNA sequences or genes in response to an inducer. In the absence of an inducer the DNA sequences or genes will not be transcribed. Typically the protein factor that binds specifically to an inducible regulatory region to activate transcription may be present in an inactive form, which is then directly or indirectly converted to the active form by the inducer. However, the protein factor may also be absent. The inducer can be a chemical agent such as a protein, metabolite, growth regulator, herbicide or phenolic compound or a physiological stress imposed directly by heat, cold, salt, or toxic elements or indirectly through the action of a pathogen or disease agent such as a virus. A plant cell containing an inducible regulatory region may be exposed to an inducer by externally applying the inducer to the cell or plant such as by spraying, watering, heating or similar methods. Inducible regulatory elements may be derived from either plant or non-plant genes (e.g. Gatz, C. and Lenk, I. R. P., 1998, Trends Plant Sci. 3, 352-358). Examples, of potential inducible promoters include, but not limited to, tetracycline-inducible promoter (Gatz, C., 1997, Ann. Rev. Plant Physiol. Plant Mol. Biol. 48, 89-108), steroid inducible promoter (Aoyama, T. and Chua, N. H., 1997, Plant J. 2, 397-404) and ethanol-inducible promoter (Salter, M. G., et al, 1998, Plant Journal 16, 127-132; Caddick, M. X., et al, 1998, Nature Biotech. 16, 177-180) cytokinin inducible IB6 and CKI1 genes (Brandstatter, I. and Kieber, J. J., 1998, Plant Cell 10, 1009-1019; Kakimoto, T., 1996, Science 274, 982-985) and the auxin inducible element, DR5 (Ulmasov, T., et al., 1997, Plant Cell 9, 1963-1971).
A constitutive regulatory region directs the expression of a gene throughout the various parts of a plant and continuously throughout plant development. Examples of known constitutive regulatory elements include promoters associated with the CaMV 35S transcript. (p35S; Odell et al., 1985, Nature, 313: 810-812; which is incorporated herein by reference), the rice actin 1 (Zhang et al, 1991, Plant Cell, 3: 1155-1165), actin 2 (An et al., 1996, Plant J., 10: 107-121), or tms 2 (U.S. Pat. No. 5,428,147), and triosephosphate isomerase 1 (Xu et. al., 1994, Plant Physiol. 106: 459-467) genes, the maize ubiquitin 1 gene (Cornejo et al, 1993, Plant Mol. Biol. 29: 637-646), the Arabidopsis ubiquitin 1 and 6 genes (Holtorf et al, 1995, Plant Mol. Biol. 29: 637-646), the tobacco translational initiation factor 4A gene (Mandel et al, 1995 Plant Mol. Biol. 29: 995-1004). the Cassava Vein Mosaic Virus promoter, pCAS, (Verdaguer et al., 1996); the promoter of the small subunit of ribulose biphosphate carboxylase, pRbcS: (Outchkourov et al., 2003), the pUbi (for monocots and dicots).
The term “constitutive” as used herein does not necessarily indicate that a nucleotide sequence under control of the constitutive regulatory region is expressed at the same level in all cell types, but that the sequence is expressed in a wide range of cell types even though variation in abundance is often observed.
The expression constructs as described above may be present in a vector. The vector may comprise border sequences which permit the transfer and integration of the expression cassette into the genome of the organism or host. The construct may be a plant binary vector, for example a binary transformation vector based on pPZP (Hajdukiewicz, et al. 1994). Other example constructs include pBin19 (see Frisch, D. A., L. W. Harris-Hailler, et al. 1995, Plant Molecular Biology 27: 405-409).
The term “native”, “native protein” or “native domain”, as used herein, refers to a protein or domain having a primary amino acid sequence identical to wildtype. Native proteins or domains may be encoded by nucleotide sequences having 100% sequence similarity to the wildtype sequence. A native amino acid sequence may also be encoded by a human codon (hCod) optimized nucleotide sequence or a nucleotide sequence comprising an increased GC content when compared to the wild type nucleotide sequence provided that the amino acid sequence encoded by the hCod-nucleotide sequence exhibits 100% sequence identity with the native amino acid sequence.
By a nucleotide sequence that is “human codon optimized” or a “hCod” nucleotide sequence, it is meant the selection of appropriate DNA nucleotides for the synthesis of an oligonucleotide sequence or fragment thereof that approaches the codon usage generally found within an oligonucleotide sequence of a human nucleotide sequence. By “increased GC content” it is meant the selection of appropriate DNA nucleotides for the synthesis of an oligonucleotide sequence or fragment thereof in order to approach codon usage that, when compared to the corresponding native oligonucleotide sequence, comprises an increase of GC content, for example, from about 1 to about 30%, or any amount therebetween, over the length of the coding portion of the oligonucleotide sequence. For example, from about 1, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30%, or any amount therebetween, over the length of the coding portion of the oligonucleotide sequence. As described below, a human codon optimized nucleotide sequence, or a nucleotide sequence comprising an increased GC contact (when compared to the wild type nucleotide sequence) exhibits increased expression within a plant, portion of a plant, or a plant cell, when compared to expression of the non-human optimized (or lower GC content) nucleotide sequence.
Norovirus VP1 fusion proteins and methods of producing norovirus VP1 fusion proteins in plants are described herein. The norovirus VP1 fusion protein, comprises an S domain derived from a first norovirus strain fused to a P domain, or a portion of the P domain, derived from a second norovirus strain. It has been observed that expression of the VP1 fusion protein increases the yield of the P domain, or a portion of the P domain, derived from the second norovirus strain in plants, when compared to the yield of the P domain, or a portion of the P domain, of the second norovirus strain, when expressed in the same plant and under the same conditions, as a native VP1 protein comprising both an S domain and the P domain (or comprising the P domain that comprises a portion of the P domain), from the same second norovirus strain.
For example, the norovirus VP1 fusion protein, and methods of producing the norovirus VP1 fusion protein, may include a VP1 fusion protein comprising an S domain derived from a first norovirus strain fused to the P1 and P2 subdomains derived from a second norovirus strain:
S1st strain-P1a2nd strain-P22nd strain-P1b2nd strain.
also referred to as: “S1-P1a2-P22-P1b2”, or “S1-P2”.
The VP1 fusion protein, S1-P2, was observed to maintain or increase the yield of the P1 and P2 subdomains (P domain) derived from the second norovirus strain, as compared to the yield of the P subdomain of the second strain, when expressed in the same plant and under the same conditions as a native VP1 protein comprising both an S domain and the P domain, that comprises the P1 and P2 subdomains, from the same second norovirus strain. The sequence encoding the VP1 fusion protein may be optimized for human codon usage, for having an increased GC content, or a combination thereof.
Also provided herein are methods of increasing production of VLPs comprising norovirus VP1 fusion proteins in plants, wherein a nucleic acid encoding a norovirus VP1 fusion protein as described herein, for example S1st strain-P1a2nd strain-P22nd strain-P1b2nd strain (S1-P1a2-P22-P1b2; S1-P2) is introduced into the plant or a portion of the plant. One or more than one type of norovirus fusion protein may be expressed in a plant or portion of the plant in order to produce a VLP comprising one or more than one type of norovirus fusion protein.
The methods of producing a VLP comprising a VP1 fusion protein may also comprise a step of co-expressing a nucleic acid sequence encoding a VP2 protein in the plant or portion of the plant.
The term “single construct” or “single constructs”, as used herein, refers to nucleic acid vectors comprising a single nucleic acid sequence. The term “dual construct” or “dual constructs”, as used herein, refers to a nucleic acid vector comprising two nucleic acid sequences.
By co-expression it is meant the introduction and expression of two or more nucleotide sequences, each of the two or more nucleotide sequences encoding a protein of interest, or a fragment of a protein of interest within a plant, portion of a plant or a plant cell. The two or more nucleotide sequences may be introduced into the plant, portion of the plant or the plant cell within one vector, so that each of the two or more nucleotide sequences is under the control of a separate regulatory region (e.g. comprising a dual construct). Alternatively, the two or more nucleotide sequences may be introduced into the plant, portion of the plant or the plant cell within separate vectors (e.g. comprising single constructs), and each vector comprising appropriate regulatory regions for the expression of the corresponding nucleic acid. For example, two nucleotide sequences, each on a separate vector and introduced into separate A. tumefaciens hosts, may be co-expressed by mixing suspensions of each A. tumefaciens host in a desired volume (for example, an equal volume, or the ratios of each A. tumefaciens host may be altered) before vacuum infiltration. In this manner, co-infiltration of multiple Agrobacterium suspensions permits co-expression of multiple transgenes.
The nucleic acid comprising encoding a norovirus VP1 fusion protein as described herein, for example, S1-P2 may further comprise sequences that enhance expression of the norovirus VP1 fusion protein in the plant, or in a portion of the plant. Sequences that enhance expression may include, a CPMV enhancer element in operative association with the nucleic acid encoding the norovirus VP1 fusion protein. The sequence encoding the VP1 fusion protein may also be optimized for human codon usage, for having an increased GC content, or a combination thereof. Furthermore, a nucleic acid encoding VP2 may be co-expressed along with the sequence encoding the VP1 fusion protein. The co-expression of a nucleic acid encoding VP2 may lead to increased stability, an increased yield, or both an increase in stability and yield, of VLPs that comprise the one or more than one type of VP1 fusion protein.
The term “CPMV enhancer element”, as used herein, refers to a nucleotide sequence encoding the 5′UTR regulating the Cowpea Mosaic Virus (CPMV) RNA2 polypeptide or a modified CPMV sequence as is known in the art. For example, a CPMV enhancer element or a CPMV expression enhancer, includes a nucleotide sequence as described in WO2015/14367; WO2015/103704; WO2007/135480; WO2009/087391; Sainsbury F., and Lomonossoff G. P., (2008, Plant Physiol. 148: pp. 1212-1218), each of which is incorporated herein by reference. A CPMV enhancer sequence can enhance expression of a downstream heterologous open reading frame (ORF) to which they are attached. The CPMV expression enhancer may include CPMV HT, CPMVX, CPMVX+, CPMV-HT+, CPMV HT+[WT115], or CPMV HT+ [511] (WO2015/14367; WO2015/103704 which are incorporated herein by reference). The CPMV expression enhancer may be used within a plant expression system comprising a regulatory region that is operatively linked with the CPMV expression enhancer sequence and a nucleotide sequence of interest. The term “5′UTR” or “5′ untranslated region” or “5′ leader sequence” refers to regions of an mRNA that are not translated. The 5′UTR typically begins at the transcription start site and ends just before the translation initiation site or start codon of the coding region. The 5″ UTR may modulate the stability and/or translation of an mRNA transcript.
By “operatively linked” it is meant that the particular sequences interact either directly or indirectly to carry out an intended function, such as mediation or modulation of expression of a nucleic acid sequence. The interaction of operatively linked sequences may, for example, be mediated by proteins that interact with the operatively linked sequences.
When one or more than one type of the norovirus VP1 fusion protein is expressed in the plant, portion of the plant or the plant cell, the one or more than one type of VP1 fusion proteins auto-assemble into VLPs. The plant or portion of the plant may be harvested under suitable extraction and purification conditions to maintain the integrity of the VLP, and the VLP comprising the one or more than one type of VP1 fusion protein may be purified. The one or more than one VP1 fusion protein may also be co-expressed with nucleotide sequence encoding VP2, so that the VLP may comprise both VP1 fusion protein and VP2 protein. The present disclosure also provides for the production of one or more than one type of VP1 fusion protein as described herein within a plant, portion of a plant, or plant cell, and the extraction and purification of the one or more than one type of VP1 fusion protein from the plant, the portion of the plant, or the plant cell to produce plant matter, a plant extract, or a protein extract, comprising the VP1 fusion protein.
Plant matter, a plant extract, or a protein extract comprising the norovirus VP1 fusion protein, for example S1-P2, or VLPs comprising the norovirus a VP1 fusion protein as described herein, for example S1-P2 is also provided. The plant matter, plant extract, or protein extract may be used to induce immunity to norovirus infection in a subject. Alternatively, the VP1 fusion protein, or the VLP comprising the VP1 fusion protein (and optionally VP2), may be purified or partially purified, and the purified or partially purified preparation may be used in inducing immunity to norovirus infection in a subject.
The present disclosure also provides a composition comprising an effective dose of one or more than one type of norovirus VP1 fusion protein, for example, S1-P2, a combination thereof, or VLPs comprising one or more than one type of norovirus VP1 fusion protein, and optionally VP2, for example S1-P2, for inducing an immune response, and a pharmaceutically acceptable carrier, adjuvant, vehicle, or excipient.
Also provided herein are methods of inducing immunity to a norovirus infection in a subject comprising of administering one or more than one type of norovirus VP1 fusion protein or VLPs comprising one or more than one types of norovirus VP1 fusion proteins to a subject orally, intranasally, intramuscularly, intraperitoneally, intravenously, or subcutaneously.
The term “norovirus”, as used herein, refers to a non-enveloped viral strain of the genus Norovirus of the family Caliciviridae that is characterized as having a single-stranded, positive-sense RNA. The norovirus genome is 7,654 nucleotides in length. The ORF1 encodes a nonstructural polyprotein that is cleaved by viral 3C-like protease into 6 proteins, including an RNA-dependent RNA polymerase. ORF2 and ORF3 encode a major (VP1) and a minor (VP2) capsid proteins, respectively (see
Norovirus strains as disclosed herein include, any known norovirus strain, but also modifications to known norovirus strains that are known to develop on a regular basis over time (See for example Parra G. I. et. al. PLoS Pathog 13(1): e1006136. doi:10.1371/journal. ppat.1006136). For example norovirus strains may include, but are not limited to GI.1/Norwalk/1968/US (GI.1; SEQ ID NO:1;
The terms “percent similarity”, “sequence similarity”, “percent identity”, or “sequence identity”, when referring to a particular sequence, are used for example as set forth in the University of Wisconsin GCG software program, or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology, Ausubel et al., eds. 1995 supplement). Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, using for example the algorithm of Smith & Waterman, (1981, Adv. Appl. Math. 2:482), by the alignment algorithm of Needleman & Wunsch, (1970, J. Mol. Biol. 48:443), by the search for similarity method of Pearson & Lipman, (1988, Proc. Natl. Acad. Sci. USA 85:2444), by computerized implementations of these algorithms (for example: GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.).
An example of an algorithm suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., (1977, Nuc. Acids Res. 25:3389-3402) and Altschul et al., (1990, J. Mol. Biol. 215:403-410), respectively. BLAST and BLAST 2.0 are used, with the parameters described herein, to determine percent sequence identity for the nucleic acids and proteins of the invention. For example the BLASTN program (for nucleotide sequences) may use as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=−4 and a comparison of both strands. For amino acid sequences, the BLASTP program may use as defaults a word length of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, 1989, Proc. Natl. Acad. Sci. USA 89:10915) alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparison of both strands. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (see URL: ncbi.nlm.nih.gov/).
The term “VP1”, as used herein, refers to the norovirus major capsid protein or polypeptide comprising an amino acid sequence similar to the protein or polypeptide encoded by ORF2 of one or more strains of norovirus as described herein. The major capsid protein folds into two principal domains, a shell (S) domain and a protruding (P) domain, which contains two subdomains, P1 and P2 (see
As shown in
The VP1 protein as disclosed herein includes any VP1 protein comprising an amino acid sequence having from about 40 to about 100%, from about 50 to about 100%, from about 60 to about 100%, from about 70 to about 100%, from about 80 to about 100%, from about 85 to about 100% from about 90 to about 100%, or from about 95 to about 100% or any amount therebetween, sequence identity (which may be also termed sequence similarity) with a VP1 amino acid sequenced from a norovirus GI.1 (SEQ ID NO:1;
It is well known in the art that the sequence of the P domain of the norovirus VP1 protein is hypervariable and readily mutates. For example as shown in
The present disclosure therefore includes nucleic acid sequences that exhibit from about 60% to about 100%, or any amount therebetween, sequence identity with any of the nucleic acid sequences encoding VP1, including the S, P or both the S and P domains, between the strains identified above, and as listed in
Similarly, the present invention includes amino acid sequences that exhibit from about 40% to about 100% or any amount therebetween, sequence similarity with any of the VP1 sequences, including the S, P or both the S and P domains, from GI.1 (SEQ ID NO:1), GI.2 (SEQ ID NO:2), GI.3 (SEQ ID NO:3), GII.4 (SEQ ID NO:4), GII.6 (SEQ ID NO:5), GII.13 (SEQ ID NO:6), GII.17 (SEQ ID NO:7). For example, from about 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100% or any amount therebetween, sequence similarity with any of the VP1 amino acid sequences, including the S domain, the P domain, or both the S and P domains. For example, as shown in
By “VP1 fusion protein” or “chimeric VP1 protein” it is meant, a protein comprising an S domain derived from a first norovirus strain fused to the P1 and P2 subdomains derived from a second norovirus strain:
S1st strain-P1a2nd strain-P22nd strain-P1b2nd strain (S1-P1a2-P22-P1b2; S1-P2).
The boundary between the S domain and the P domain of the norovirus VP1 amino acid sequence is well conserved (see
Examples of VP1 fusion protein of the form: S1-P1a2-P22-P1b2 include, but are not limited to:
The VP1 fusion protein is heterologous (or chimeric) in that the fusion protein comprises an S domain from a first VP1 protein and a P domain from a second VP1 protein. The heterologous VP1 fusion protein may comprise an amino acid sequence that falls within, or the amino acid sequence is found within (or maps against) the consensus sequence of the VP1 sequence shown in
Additional non-limiting examples of VP1 fusion proteins include those that comprise an S domain from: GI.1, for example but not limited to, the VP1 fusion shown in
VP1 fusion proteins may also comprise a P domain obtained from GI.1/Norwalk/1968/US (SEQ ID NO:1); GI.5 Siklos/Hun5407/2013/HUN (SEQ ID NO:44); GII.1 Ascension 208/2010/USA (SEQ ID NO:45); GII.2 CGMH47/2011/TW (SEQ ID NO:66); GII.3 Jingzhou/2013402/CHN (SEQ ID NO:67); GII.4/Dresden174/1997/DE(variant:US1995/96); GII.4/FarmingtonHills/2002/US (SEQ ID NO:9); GII.4/Hunter-NSW504D/2004/AU (SEQ ID NO:10); GII.4/Shellharbour-NSW696T/2006/AU (11); GII.4/Orange-NSW001P/2008/AU (variant New Orleans 2009) (SEQ ID NO:12); GII.5 AlbertaEI390/2013/CA (SEQ ID NO:68); GII.7 Musashimurayama/2010/JP (SEQ ID NO:69; GII.14 8610/Saga/2008/JPN (SEQ ID NO:46); GII.21 Salisbury150/2011/USA (SEQ ID NO:47), or a sequence that exhibits from about 40-100% or any amount therebetween, sequence similarity with the amino acid sequence of the P domain from any one of GI.1/Norwalk/1968/US; GI.5 Siklos/Hun5407/2013/HUN; GII.1 Ascension 208/2010/USA; GII.2 CGMH47/2011/TW; GII.3 Jingzhou/2013402/CHN; GII.4/Dresden174/1997/DE(variant:US1995/96); GII.4/FarmingtonHills/2002/US; GII.4/Hunter-NSW504D/2004/AU; GII.4/Shellharbour-NSW696T/2006/AU (11); GII.4/Orange-NSW001P/2008/AU (variant New Orleans 2009); GII.5 AlbertaEI390/2013/CA; GII.7 Musashimurayama/2010/JP; GII.14 8610/Saga/2008/JPN; GII.21 Salisbury150/2011/USA, for example from about 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100% or any amount therebetween sequence similarity with the amino acid sequence of the P or the P2 domain from any one of GI.1/Norwalk/1968/US; GI.5 Siklos/Hun5407/2013/HUN; GII.1 Ascension 208/2010/USA; GII.2 CGMH47/2011/TW; GII.3 Jingzhou/2013402/CHN; GII.4/Dresden174/1997/DE(variant:US1995/96); GII.4/FarmingtonHills/2002/US; GII.4/Hunter-NSW504D/2004/AU; GII.4/Shellharbour-NSW696T/2006/AU (11); GII.4/Orange-NSW001P/2008/AU (variant New Orleans 2009); GII.5 AlbertaEI390/2013/CA; GII.7 Musashimurayama/2010/JP; GII.14 8610/Saga/2008/JPN; GII.21 Salisbury150/2011/USA, provided that the VP1 protein induces immunity to norovirus in a subject, when the VP1 protein is administered to the subject. Furthermore, the VP1 fusion protein may comprise a P domain that comprises an amino acid sequence that falls within (i.e. the amino acid sequence maps against, or is found within) the consensus sequence of the P domain as shown in
In the VP1 fusion protein examples provided above, the S domain may comprise an amino acid sequence that exhibits from about 80-100%, or any amount therebetween, sequence similarity with the amino acid sequence of the S domain from any norovirus, for example but not limited to, the S domain from GI.1 Nor/68 (SEQ ID NO:1; see
As shown in
Expression of native GII.6/Ohio/490/12 VP1 protein has proven to be challenging (e.g.
The term “virus-like particle”, VLP, “virus-like particles”, or “VLPs”, as used herein, refers to a norovirus virus like particles that comprise one or more than one type of norovirus VP1 protein, one or more than one type of VP1 fusion protein, or a combination thereof, and that self-assemble into non-replicating, non-enveloped, non-infectious viral capsid structures lacking all parts of the norovirus genome. For example, the VLP may comprise one type of VP1 fusion protein, or the VLP may comprise two or more different VP1 fusion proteins. Furthermore the VLP may comprise a VP2 protein. VLPs comprising VP1 protein, VP1+VP2 protein, VP1 fusion protein, or VP1 fusion protein+VP2 protein are of the size from about 15 nm to 50 nm or any amount therebetween, for example 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 nm, or any amount therebetween. For example, for T=1 icosahedral symmetry, VLPs may about 23 nm, or for T=3 icosahedral symmetry, VLPs may be from about 38 to about 40 nm.
As shown in
An aspect of the present disclosure provides for the production of norovirus VP1 protein in plants. As shown in
Furthermore, as seen in lanes 7-10 and 15-18 of
This observation is in contrast to that observed in insect and mammalian cells (Bertolotti-Ciarlet A., Crawford S. E., Hutson A. M., Estes M. K. 2003, J. Virol. 77:11603-11615), who reported that an increase in VP1 expression was only observed when VP1 and VP2 (or VP1+VP2+3′UTR) resided in cis, and were co-expressed using the same organization as that found in the viral genome, under the control of one promoter and terminator. No increase in VP1 expression was observed by Bertolotti-Ciarlet (2003) in insect or mammalian cells, when VP1 and VP2 were co-expressed in trans.
As described in more detail below (see “Norovirus VP1 Fusion Proteins”; reference to
The data presented in
Assembly of Plant-Produced Norovirus VP1 into VLPs
Differential Expression of Norovirus VP1 in Plants
The expression levels of norovirus VP1 protein derived from six norovirus strains having the highest occurrence of outbreaks between Sep. 1, 2013 and Aug. 31, 2015 (as reported by the Centers for Disease Control and Prevention, see URL: www.cdc.gov/norovirus/reporting/calicinet/data.html) were compared in N. benthamiana.
VP1 protein production was determined using Coomassie-stained SDS-PAGE analysis (approx. 55-60 kDa band) of extracts obtained from plant leaves vacuum infiltrated with expression vectors comprising human codon optimized sequences of VP1 derived from GI.1/Norwalk/1968/US (SEQ ID NO:18), GI.2/Leuven/2003/Bel (SEQ ID NO:54), GI.3/S29/2008/Lilla Edet/Sweden (SEQ ID NO:55), GII.4/Sydney/NSW0514/2012/AU (SEQ ID NO:56), GII.6/Ohio/490/12 (SEQ ID NO:60), GII.13/VA173/2010/USA (SEQ ID NO:61), GII.17/Kawasaki323/2014/JP (SEQ ID NO:62), strains. As shown in
VP1 protein expression was also observed when GI.3 (/S29/2008/Lilla Edet/Sweden; SEQ ID NO:3,
As shown in the electron micrographs of
Even though expression levels of VP1 protein in leaves infiltrated with vectors expressing GII.4/Sydney/NSW0514/2012/AU (SEQ ID NO:4), GII.6/Ohio/490/12 (SEQ ID NO:5), GII.17/Kawasaki323/2014/JP (SEQ ID NO:7), was either low or undetectable using Coomassie-stained SDS-PAGE analysis (see
Norovirus VP1 Fusion Proteins
Expression vectors were constructed which encoded norovirus VP1 fusion proteins wherein the S domain of GI.1 was fused to the following P domains:
GI.2 (S(GI.1)+P(GI.2); S(GI.1 Nor/68)+P (GI.2/Leuven/03); SEQ ID NO's:22(aa), 57(na),
GI.3 (S(GI.1)+P(GI.3); GI.3 S(GI.1 Nor/68)+P (GI.3/S29/08/Lilla Edet) SEQ ID NO:23(aa), 58(na),
GII.4 (S(GI.1)+P(GII.4); S(GI.1 Nor/68)+P (GII.4/Sydney/NSW0514/12) SEQ ID NO:24(aa), 59na),
GII.6 (S(GI.1)+P(GII.6); S(GI.1 Nor/68)+P(GII.6/Ohio/490/12) SEQ ID NO:25(aa), 63(na),
GII.13 (S(GI.1)+P(GII.13); S(GI.1 Nor/68)+P (GII.13/VA173/10) SEQ ID NO:26(aa); 64(na),
GII.17 (S(GI.1)+P(GII.17); S(GI.1 Nor/68)+P (GII.17/Kawasaki323/14) SEQ ID NO:27(aa), 65(na),
VP1 fusion protein production was determined using Coomassie-stained SDS-PAGE analysis (approx. 55-60 kDa band) of extracts obtained from plant leaves vacuum infiltrated with expression vectors comprising the above nucleotide sequences encoding the various VP1 fusion proteins, and VP2. As shown in
Even though protein product was not observed using SDS-PAGE analysis for the VP1 fusion S(GI.1)+P(GII.4) (S(GI.1 Nor/68)+P (GII.4/Sydney/NSW0514/12; SEQ ID NO:59,
The fusion of the GI.1 Norwalk S domain to the P domains of low-expressing GII.6 (GI.1S-GII.6P) did not result in enhanced expression of norovirus VP1 fusion protein as compared to their native non-fusion counterparts. Without wishing to be bound by theory, these results suggest that the S domain may not be responsible for the low-level of expression in plants for these particular norovirus strains.
When VP1 fusion proteins are expressed in plants, it is preferred that the ORF3 sequence encoding VP2 is obtained from the same norovirus strain as used to obtain the S domain of fusion VP1 sequence. Support for this observation may be found with reference to Panels B and C of
It is also of interest to note that the VLP yield obtained from co-expressing a VP1 fusion along with a VP2, where the S domain and the VP2 area obtained from the same genotype and strain (Panel B;
As shown in the electron micrographs of
However, no VLPs were obtained from plant extracts expressing the VP1 fusion protein GI.1+GII.6/Ohio/490/12 (also see Example 5), consistent with the low or undetectable expression levels of this VP1 fusion protein as shown in
Additional human codon optimized VP1 fusion proteins were prepared and co-expressed with VP2 in N. benthamiana leaves, as described in Example 5 below. The VP1 fusion proteins included:
S(GI.1)+P(X), where X=GI.2, GI.3, GII.4, GII.6, GII.12, GII.13, GII.17;
S(GI.5)+P(Y), where Y=GII.4;
S(GII.1)+P(Z), where Z=GI.3, GII.4, GII.17;
S(GII.12)+P(W), where W=GI.1, GI.2, GI.3, GI.5, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.13, GII.14, GII.17, GII.21;
S(GII.14)+P(T), where T=GII.4;
S(GII.21)+P(Q), where Q=GII.4
Expression of VP1 fusion proteins in a plant, a portion of a plant or a plant cell was observed (see Example 5) with the following VP1 fusion constructs:
S(GI.1)+P(GI.,2), S(GI.1)+P(GI.3), S(GI.1)+P(GII.4), S(GI.1)+P(GII.6), S(GI.1)+P(GII.12), S(GI.1)+P(GII.13), S(GI.1)+P(GII.17),
S(GI.5)+P(GII.4),
S(GII.1)+P(GI.3), S(GII.1)+P(GII.4),
S(GII.12)+P(GI.1), S(GII.12)+P(GI.2), S(GII.12)+P(GI.3), S(GII.12)+P(GI.5), S(GII.12)+P(GII.1), S(GII.12)+P(GII.2), S(GII.12)+P(GII.4), S(GII.12)+P(GII.7), S(GII.12)+P(GII.13), S(GII.12)+P(GII.14), S(GII.12)+P(GII.17), S(GII.12)+P(GII.21).
Enhanced Stability of VLPs Comprising Norovirus VP1 Fusion Proteins
As shown in
However, VLPs comprising S(GI.1 Nor68)+P(GI.2 Leu03) norovirus VP1 fusion proteins (encoded by construct 3360;
A similar shift in density was also observed in VLPs comprising of S(GI.1)+P(GI.3P) norovirus VP1 fusion proteins (
Additionally, as shown with reference to
Induction of Immunity Against Norovirus Infection
An “immune response” generally refers to a response of the adaptive immune system of a subject. The adaptive immune system generally comprises a humoral response, and a cell-mediated response. The humoral response is the aspect of immunity that is mediated by secreted antibodies, produced in the cells of the B lymphocyte lineage (B cell). Secreted antibodies bind to antigens on the surfaces of invading microbes (such as viruses or bacteria), which flags them for destruction. Humoral immunity is used generally to refer to antibody production and the processes that accompany it, as well as the effector functions of antibodies, including Th2 cell activation and cytokine production, memory cell generation, opsonin promotion of phagocytosis, pathogen elimination and the like. The terms “modulate” or “modulation” or the like refer to an increase or decrease in a particular response or parameter, as determined by any of several assays generally known or used, some of which are exemplified herein.
A cell-mediated response is an immune response that does not involve antibodies but rather involves the activation of macrophages, natural killer cells (NK), antigen-specific cytotoxic T-lymphocytes, and the release of various cytokines in response to an antigen. Cell-mediated immunity is used generally to refer to some Th cell activation, Tc cell activation and T-cell mediated responses. Cell mediated immunity may be of particular importance in responding to viral infections.
For example, the induction of antigen specific CD8 positive T lymphocytes may be measured using an ELISPOT assay; stimulation of CD4 positive T-lymphocytes may be measured using a proliferation assay. Anti-norovirus antibody titres may be quantified using an ELISA assay; isotypes of antigen-specific or cross reactive antibodies may also be measured using anti-isotype antibodies (e.g. anti-IgG, IgA, IgE or IgM). Methods and techniques for performing such assays are well-known in the art.
Cytokine presence or levels may also be quantified. For example a T-helper cell response (Th1/Th2) will be characterized by the measurement of IFN-γ and IL-4 secreting cells using by ELISA (e.g. BD Biosciences OptEIA kits). Peripheral blood mononuclear cells (PBMC) or splenocytes obtained from a subject may be cultured, and the supernatant analyzed. T lymphocytes may also be quantified by fluorescence-activated cell sorting (FACS), using marker specific fluorescent labels and methods as are known in the art.
A microneutralization assay may also be conducted to characterize an immune response in a subject, see for example the methods of Rowe et al., 1973. Virus neutralization titers may be quantified in a number of ways, including: enumeration of lysis plaques (plaque assay) following crystal violent fixation/coloration of cells; microscopic observation of cell lysis in in vitro culture; and 2) ELISA and spectrophotometric detection of norovirus.
The term “epitope” or “epitopes”, as used herein, refers to a structural part of an antigen to which an antibody specifically binds.
With reference to
Plant Expression
The constructs of the present invention can be introduced into plant cells using Ti plasmids, Ri plasmids, plant virus vectors, direct DNA transformation, micro-injection, electroporation, etc. For reviews of such techniques see for example Weissbach and Weissbach, Methods for Plant Molecular Biology, Academy Press, New York VIII, pp. 421-463 (1988); Geierson and Corey, Plant Molecular Biology, 2d Ed. (1988); and Miki and Iyer, Fundamentals of Gene Transfer in Plants. In Plant Metabolism, 2d Ed. D T. Dennis, D H Turpin, D D Lefebrvre, D B Layzell (eds), Addison Wesly, Langmans Ltd. London, pp. 561-579 (1997). Other methods include direct DNA uptake, the use of liposomes, electroporation, for example using protoplasts, micro-injection, microprojectiles or whiskers, and vacuum infiltration. See, for example, Bilang, et al. (1991, Gene 100: 247-250), Scheid et al. (1991, Mol. Gen. Genet. 228: 104-112), Guerche et al. (1987, Plant Science 52: 111-116), Neuhause et al. (1987, Theor. Appl Genet. 75: 30-36), Klein et al. (2987, Nature 327: 70-73); Freeman et al. (1984, Plant Cell Physiol. 29: 1353), Howell et al. (1980, Science 208: 1265), Horsch et al. (1985, Science 227: 1229-1231), DeBlock et al. (1989, Plant Physiology 91: 694-701), Methods for Plant Molecular Biology (Weissbach and Weissbach, eds., Academic Press Inc., 1988), Methods in Plant Molecular Biology (Schuler and Zielinski, eds., Academic Press Inc., 1989), WO 92/09696, WO 94/00583, EP 331083, EP 175966, Liu and Lomonossoff (2002, J Virol Meth, 105:343-348), EP 290395; WO 8706614; U.S. Pat. Nos. 4,945,050; 5,036,006; and 5,100,792, U.S. patent application Ser. No. 08/438,666, filed May 10, 1995, and Ser. No. 07/951,715, filed Sep. 25, 1992, (all of which are hereby incorporated by reference).
Transient expression methods may be used to express the constructs of the present invention (see D'Aoust et al., 2009, Methods in molecular biology, Vol 483, pages41-50; Liu and Lomonossoff, 2002, Journal of Virological Methods, 105:343-348; which is incorporated herein by reference). Alternatively, a vacuum-based transient expression method, as described by Kapila et al. (1997, Plant Sci. 122, 101-108; which is incorporated herein by reference), or WO 00/063400, WO 00/037663 (which are incorporated herein by reference) may be used. These methods may include, for example, but are not limited to, a method of Agro-inoculation or Agro-infiltration, syringe infiltration, however, other transient methods may also be used as noted above. With Agro-inoculation, Agro-infiltration, or syringe infiltration, a mixture of Agrobacteria comprising the desired nucleic acid enter the intercellular spaces of a tissue, for example the leaves, aerial portion of the plant (including stem, leaves and flower), other portion of the plant (stem, root, flower), or the whole plant. After crossing the epidermis the Agrobacteria infect and transfer t-DNA copies into the cells. The t-DNA is episomally transcribed and the mRNA translated, leading to the production of the protein of interest in infected cells, however, the passage of t-DNA inside the nucleus is transient.
Also considered part of this invention are transgenic plants, plant cells or seeds containing the gene construct of the present invention that may be used as a platform plant suitable for transient protein expression described herein. Methods of regenerating whole plants from plant cells are also known in the art (for example see Guerineau and Mullineaux (1993, Plant transformation and expression vectors. In: Plant Molecular Biology Labfax (Croy R R D ed) Oxford, BIOS Scientific Publishers, pp 121-148). In general, transformed plant cells are cultured in an appropriate medium, which may contain selective agents such as antibiotics, where selectable markers are used to facilitate identification of transformed plant cells. Once callus forms, shoot formation can be encouraged by employing the appropriate plant hormones in accordance with known methods and the shoots transferred to rooting medium for regeneration of plants. The plants may then be used to establish repetitive generations, either from seeds or using vegetative propagation techniques. Transgenic plants can also be generated without using tissue culture. Methods for stable transformation, and regeneration of these organisms are established in the art and known to one of skill in the art. Available techniques are reviewed in Vasil et al. (Cell Culture and Somatic Cell Genetics of Plants, Vol I, II and III, Laboratory Procedures and Their Applications, Academic Press, 1984), and Weissbach and Weissbach (Methods for Plant Molecular Biology, Academic Press, 1989). The method of obtaining transformed and regenerated plants is not critical to the present invention.
If plants, plant portions or plant cells are to be transformed or co-transformed by two or more nucleic acid constructs, the nucleic acid construct may be introduced into the Agrobacterium in a single transfection event so that the nucleic acids are pooled, and the bacterial cells transfected. Alternatively, the constructs may be introduced serially. In this case, a first construct is introduced into the Agrobacterium as described, the cells are grown under selective conditions (e.g. in the presence of an antibiotic) where only the singly transformed bacteria can grow. Following this first selection step, a second nucleic acid construct is introduced into the Agrobacterium as described, and the cells are grown under doubly-selective conditions, where only the doubly-transformed bacteria can grow. The doubly-transformed bacteria may then be used to transform a plant, plant portion or plant cell as described herein, or may be subjected to a further transformation step to accommodate a third nucleic acid construct.
Alternatively, if plants, plant portions, or plant cells are to be transformed or co-transformed by two or more nucleic acid constructs, the nucleic acid construct may be introduced into the plant by co-infiltrating a mixture of Agrobacterium cells with the plant, plant portion, or plant cell, each Agrobacterium cell may comprise one or more constructs to be introduced within the plant. In order to vary the relative expression levels within the plant, plant portion or plant cell, of a nucleotide sequence of interest within a construct, during the step of infiltration, the concentration of the various Agrobacteria populations comprising the desired constructs may be varied.
The present invention will be further illustrated in the following examples.
The candidate sequences for VP1 and VP2 are available in Genbank (see
GI.1/Norwalk/1968/US (GI.1) NCBI M87661 (SEQ ID NO:1); VP1
GI.2/Leuven/2003/Bel (GI.2) NCBI FJ515294 (SEQ ID NO:2)
GI.3/S29/2008/Lilla Edet/Sweden NCBI JN603244 (SEQ ID NO:3)
GI.5/Siklos/Hun5407/2013/HUN (SEQ ID NO:44)
GII.1/Ascension208/2010/USA (SEQ ID NO:45)
GII.2/CGMH47/2011/TW (SEQ ID NO:66)
GII.3/Jingzhou/2013402/CHN (SEQ ID NO:67)
GII.4/Sydney/NSW0514/2012/AU NCBI JX459908 (SEQ ID NO:4)
GII.5/AlbertaEI390/2013/CA (SEQ ID NO:68)
GII.6/Ohio/490/2012/USA NCBI KC464321 (SEQ ID NO:5; VP1), NCBI J407072 (VP2)
GII.7/Musahimurayama/2010/JP (SEQ ID NO:69)
GII.12/HS206/2010/USA (SEQ ID NO:28)
GII.13/VA173/2010/USA NCBI JN899242 (SEQ ID NO:6)
GII.14/8610/Saga/2008/JP (SEQ ID NO:46)
GII.17/Kawasaki323/2014/JP NCBI AB983218 (SEQ ID NO:7)
GII.21/Salisbury150/2011/USA NCBI XX (SEQ ID NO:47)
A wild-type sequence encoding VP1 from Norovirus strain GI.1/Norwalk/1968/US was cloned into 2X35S/CPMV 160/NOS expression system using the following PCR-based method. A fragment containing the GI.1 VP1 coding sequence was amplified using primers IF-NoV(US68)VP1(ORF2).c (SEQ ID NO: 72) and IF-NoV(US68)VP1(ORF2).r (SEQ ID NO: 73), using native GI.1 VP1 gene sequence (SEQ ID NO: 13;
2X35S/CPMV 160/VP1 GI.1 (hCod)/NOS (Construct number 2724)
A human codon-optimized sequence encoding VP1 from Norovirus strain GI.1/Norwalk/1968/US was cloned into 2X35S/CPMV 160/NOS expression system using the following PCR-based method. A fragment containing the GI.1 VP1 coding sequence was amplified using primers IF-NoV(US68)VP1(ORF2)(hCod).c (SEQ ID NO: 76) and IF-NoV(US68)VP1(ORF2)(hCod).r (SEQ ID NO: 77), using human codon-optimized GI.1 VP1 gene sequence (SEQ ID NO: 18;
2X35S/CPMV 160/VP2 GI.1 (hCod)/NOS (Construct Number 2725)
A human codon-optimized sequence encoding VP2 from Norovirus strain GI.1/Norwalk/1968/US was cloned into 2X35S/CPMV 160/NOS expression system using the following PCR-based method. A fragment containing the GI.1 VP2 coding sequence was amplified using primers IF-NoV(US68)VP2(ORF3)(hCod).c (SEQ ID NO: 79) and IF-NoV(US68)VP2(ORF3)(hCod).r (SEQ ID NO: 80), using human codon-optimized GI.1 VP2 gene sequence (SEQ ID NO: 19;
2X35S/CPMV 160/VP1 GI.2 (hCod)/NOS (Construct Number 3300)
A human codon-optimized sequence encoding VP1 from Norovirus strain GI.2/Leuven/2003/Bel was cloned into 2X35S/CPMV 160/NOS expression system using the following PCR-based method. A fragment containing the GI.2 VP1 coding sequence was amplified using primers IF-GI2Leu03VP1.c (SEQ ID NO: 82) and IF-GI2Leu03VP1.r (SEQ ID NO: 83), using human codon-optimized GI.2 VP1 gene sequence (SEQ ID NO: 54;
A summary of the primers and templates used to preparer the above VP1 and VP2 constructs described above is provided in Table 2 below.
Norovirus VP1 Fusion Constructs
2X35S/CPMV 160/Fusion VP1 S(GI.1)+P(GI.2) (hCod)/NOS (Construct Number 3360)
A human codon-optimized sequence encoding fusion VP1 comprising of S domain from Norovirus strain GI.1/Norwalk/1968/US fused to P domain from Norovirus strain GI.2/Leuven/2003/Bel (VP1 S(GI.1)+P(GI.2)) was cloned into 2X35S/CPMV 160/NOS expression system using the following PCR-based method. In a first round of PCR, a fragment containing S domain from Norovirus strain GI.1/Norwalk/1968/US was amplified using primers IF-NoV(US68)VP1(ORF2).c (SEQ ID NO: 72) and GI2Leu+GI1VP1.r (SEQ ID NO: 85), using human codon-optimized GI.1 VP1 gene sequence (SEQ ID NO: 18;
A summary of the VP1 fusion proteins, primers, templates and products is provided in Table 2 below. The VP1 fusion proteins were constructed using the same methods as described above, with reference to construct #3360.
∧For In-fusion cloning; SEQ ID NO:
∧∧Complete VP1, S domain or P domain; SEQ ID NO:)
Agrobacterium tumefaciens Transfection
Agrobacterium tumefaciens strain AGL1 was transfected by electroporation with the native norovirus VP1, native norovirus VP2, or norovirus VP1 fusion protein expression vectors using the methods described by D'Aoust et al., 2008 (Plant Biotech. J. 6:930-40). Transfected Agrobacterium were grown in YEB medium supplemented with 10 mM 2-(N-morpholino)ethanesulfonic acid (MES), 20 μM acetosyringone, 50 μg/ml kanamycin and 25 μg/ml of carbenicillin pH5.6 to an OD600 between 0.6 and 1.6. Agrobacterium suspensions were centrifuged before use and resuspended in infiltration medium (10 mM MgCl2 and 10 mM MES pH 5.6).
Preparation of Plant Biomass, Inoculum and Agroinfiltration
N. benthamiana plants were grown from seeds in flats filled with a commercial peat moss substrate. The plants were allowed to grow in the greenhouse under a 16/8 photoperiod and a temperature regime of 25° C. day/20° C. night. Three weeks after seeding, individual plantlets were picked out, transplanted in pots and left to grow in the greenhouse for three additional weeks under the same environmental conditions
Agrobacteria transfected with each native norovirus VP1, native norovirus VP2, or norovirus VP1 fusion expression vector were grown in a YEB medium supplemented with 10 mM 2-(N-morpholino)ethanesulfonic acid (MES), 20 μM acetosyringone, 50 μg/ml kanamycin and 25 μg/ml of carbenicillin pH5.6 until they reached an OD600 between 0.6 and 1.6. Agrobacterium suspensions were centrifuged before use and resuspended in infiltration medium (10 mM MgCl2 and 10 mM MES pH 5.6) and stored overnight at 4° C. On the day of infiltration, culture batches were diluted in 2.5 culture volumes and allowed to warm before use. Whole plants of N. benthamiana were placed upside down in the bacterial suspension in an air-tight stainless steel tank under a vacuum of 20-40 Torr for 2-min. Plants were returned to the greenhouse for a 6 or 9 day incubation period until harvest.
Leaf Harvest and Total Protein Extraction
Following incubation, the aerial part of plants was harvested, frozen at −80° C. and crushed into pieces. Total soluble proteins were extracted by homogenizing (Polytron) each sample of frozen-crushed plant material in 3 volumes of cold 100 mM NaOAc pH 5.2+150 mM NaCl, 0.4 μg/ml Metabisulfite and 1 mM phenylmethanesulfonyl fluoride. After homogenization, the slurries were centrifuged at 10,000 g for 10 min at 4° C. and these clarified crude extracts (supernatant) kept for analyses.
The total protein content of clarified crude extracts was determined by the Bradford assay (Bio-Rad, Hercules, Calif.) using bovine serum albumin as the reference standard. Proteins were separated by SDS-PAGE under reducing conditions using Criterion™ TGX Stain-Free™ precast gels (Bio-Rad Laboratories, Hercules, Calif.) and proteins were visualized with Gel Doc™ EZ imaging system (Bio-Rad Laboratories, Hercules, Calif.) and electrotransferred onto polyvinylene difluoride (PVDF) membranes (Roche Diagnostics Corporation, Indianapolis, Ind.) for immunodetection. Prior to immunoblotting, the membranes were blocked with 5% skim milk and 0.1% Tween-20 in Tris-buffered saline (TBS-T) for 16-18 h at 4° C.
Protein Analysis and Immunoblotting
Immunoblotting was performed with a first incubation with a primary mAb 242P antibody specific to VP1 from GI and GII genotypes, diluted 1/500 in 2% skim milk in TBS-Tween 20 0.1%. Peroxydase-conjugated goat anti-mouse (Jackson Immunoresearch, cat #115-035-146) diluted 1/10000 was used as secondary antibody for chemiluminescence detection were as indicated in Table 4, diluted as indicated in 2% skim milk in TBS-Tween 20 0.1% Immunoreactive complexes were detected by chemiluminescence using luminol as the substrate (Roche Diagnostics Corporation). Horseradish peroxidase-enzyme conjugation of human IgG antibody was carried out by using the EZ-Link Plus® Activated Peroxidase conjugation kit (Pierce, Rockford, Ill.).
Analysis of VLP Formation/Iodixanol Gradients
Proteins were extracted from frozen biomass by mechanical extraction in a blender with 2 volumes of extraction buffer (100 mM NaOAc pH 5.2+150 mM NaCl). The slurry was filtered through a large pore nylon filter to remove large debris and centrifuged 5000 g for 5 min at 4° C. The supernatant was collected and centrifuged again at 5000 g for 30 min (4° C.) to remove additional debris. The supernatant is then loaded on a discontinuous iodixanol density gradient. Analytical density gradient centrifugation was performed as follows: 38 ml tubes containing discontinuous iodixanol density gradient in acetate buffer (1 ml at 45%, 2 ml at 35%, 2 ml at 33%, 2 ml at 31%, 2 ml at 29% and 5 ml at 25% of iodixanol) were prepared and overlaid with 25 ml of the extracts containing the rotavirus-like particles. The gradients were centrifuged at 175 000 g for 4 hours (4° C.). After centrifugation, 1 ml fractions were collected from the bottom to the top and fractions were analyzed by SDS-PAGE combined with protein staining or Western blot.
Electron Microscopy
Following centrifugation of partially clarified plant extracts on discontinuous iodixanol density gradients, as described above, fractions (1 ml/fraction) containing the samples were pooled, mixed with 100 mM PBS pH 7.2+150 mM NaCl buffer to completely fill the tube and centrifuged 120 minutes at 100000 g. The pellets were re-suspended in 300-1000 μl of buffer depending of the VP1 quantity.
Carbon-coated copper grids with a 200 nm mesh size were made hydrophilic by placing the carbon side face up on a Whatman paper in a petri dish and incubating overnight at 4 deg C. Pooled fractions (20 μl) from density gradient centrifugation to be observed by transmission electron microscopy (TEM) were deposited on a Parafilm and grids were floated with the carbon side facing down and incubated at room temperature for 5 minutes. Grids were washed 4 times on 20 μl water droplet and the excess water from the last wash drained by touching a Whatman paper with the side of the grid. Grids were incubated 1 minute on a 20 μl droplet of 2% uranyl acetate in water. Grids were allowed to dry 5 minutes on a Whatman paper. Observation was performed under transmission electron microscopy at magnifications ranging from 10,000× to 150,000×.
N. benthamiana leaves were, vacuum infiltrated, as described in Example 2, with Agrobacterium tumifaciens comprising expression vectors encoding wildtype GI.1 VP1 as a single nucleic acid construct, GI.1 VP2 (GI.1/Norwalk/1968/US; SEQ ID NO:15,
Leaves infiltrated with expression vectors comprising nucleotide sequences that correspond to wildtype GI.1 VP1 (GI.1/Norwalk/1968/US; SEQ ID NO:13;
Leaves infiltrated with expression vectors comprising GI.1 VP1 nucleotide sequences that were codon optimized for human expression (hCod GI.1/Norwalk/1968/US; SEQ ID NO:18;
Leaves infiltrated with vectors comprising either wildtype GI.1 VP1 (GI.1/Norwalk/1968/US; SEQ ID NO:13;
Co-expression of human codon optimized GI.1 VP1 (GI.1/Norwalk/1968/US; SEQ ID NO:13;
Components of crude plant extracts prepared from N. benthamiana leaves expressing GI.1 VP1 (single nucleic acid human codon optimized constructs; hCod GI.1/Norwalk/1968/US; SEQ ID NO:18;
The protein components from the high density iodixanol gradient fractions were analyzed by scanning electron microscopy
The expression levels of norovirus human codon optimized sequences encoding VP1 protein from norovirus strains, GI.1/Norwalk/1968/US (SEQ ID NO:18;
Strong, or high, VP1 protein production was observed when human codon optimized GI.1/Norwalk/1968/US (SEQ ID NO:18), GI.3/S29/2008/Lilla Edet/Sweden (SEQ ID NO:55), GII.13/VA173/2010/USA (SEQ ID NO:61), and good, or medium, expression of VP1 was observed when GI.2/Leuven/2003/Bel (SEQ ID NO:54), were expressed in plant leaves (
Strong, or high expression of GI.5/Siklos/HUN5407/2013/HUN; GII.1/Ascension208/2010/USA; GII.12/HS206/2010/USA; GII.12/HS206/2010/USA; and GII.21/Salisbury150/2011/USA, and good or medium expression of GII.2/CGMH47/2011/TW; GII.5/AlbertaE1390/2013/CA; GII.7/Musashimurayama/2010/JP, was also observed in plants.
Electron micrographs (prepared as described in Example 2), of high density iodixanol gradient fractions of several human codon optimized VP1 preparations were observed following expression of the following norovirus strains in plants (see
VP1 proteins derived from the above strains were observed to self-assembled into VLPs having a structural conformation and diameter of about 15 nm to 50 nm (for example, of either about 23 nm, for T=1 icosahedral symmetry; or about 38 to 40 nm, for T=3 icosahedral symmetry), similar to that of wildtype norovirus.
N. benthamiana leaves were, vacuum infiltrated, as described in Example 2, with Argrobacterium tumifaciens comprising expression vectors encoding VP1 fusion proteins described below were co-expressed with VP2 (GI.1/Norwalk/1968/US; SEQ ID NO:15,
Leaves were infiltrated with expression vectors (nucleic acid complex) comprising human codon optimized nucleotide sequences encoding VP1 fusion of the GI.1 Norwalk S domain (GI.1/Norwalk/1968/US (SEQ ID NO:18;
In this example, VP1 and VP2 nucleic acid segments, with each nucleic acid segment comprising a regulatory region and a terminator, were introduced into the plants as a nucleic acid complex. As described below, with reference to
Expression of VP1 fusion proteins comprising S(GI.1)+P(GI.,2), S(GI.1)+P(GI.3), S(GI.1)+P(GII.4), S(GI.1)+P(GII.13), S(GI.1)+P(GII.17), when co-expressed with VP2, resulted in similar or greater levels of expression of norovirus VP1 fusion proteins as compared to their native non-fusion counterparts (see Example 3;
Electron micrographs (prepared as described in Example 2), of high density iodixanol gradient fractions of several human codon optimized VP1 fusion preparations were prepared as shown in
Even though protein product was below detectable levels using SDS-PAGE analysis for the VP1 fusion S(GI.1)+P(GII.4) (S(GI.1 Nor/68)+P (GII.4/Sydney/NSW0514/12; SEQ ID NO:59,
Additional nucleic acid segments encoding human codon optimized VP1 fusion proteins were prepared and co-expressed with nucleic acid segments encoding VP2, in N. benthamiana leaves, as described above. These VP1 fusion proteins included:
S(GI.1)+P(X), where X=GI.2, GI.3, GII.4, GII.6, GII.12, GII.13, GII.17;
S(GI.5)+P(Y), where Y=GII.4;
S(GII.1)+P(Z), where Z=GI.3, GII.4, GII.17;
S(GII.12)+P(W), where W=GI.1, GI.2, GI.3, GI.5, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.13, GII.14, GII.17, GII.21;
S(GII.14)+P(T), where T=GII.4;
S(GII.21)+P(Q), where Q=GII.4
After 6 or 9 days post infiltration (6 DPI and 9 DPI, respectively) with the nucleic acid complex, total crude protein extracts were prepared from leaf homogenates, separated by SDS-PAGE, and stained with Coomassie Brilliant Blue dye to determine VP1 fusion protein production. Expression levels of the various VP1 fusion proteins was determined from the Coomassie stained gels. Additionally electron micrographs of high density iodixanol gradient fractions of several VP1 fusion products were also prepared.
Expression of various a nucleic acid segments encoding VP1 fusion proteins, comprising an S domain fused with heterologous P domain, with both domains obtained from VP1 proteins from a range of norovirus strains was observed, including, an S domain from GI.1, GI.5, GII.1, GII.12, GII.14 and GII.21, and a P domain obtained from GI.1, GI.2, GI.3, GI.5, GII.1, GII.2, GII.4, GII.6, GII.7, GII.12, GII.13, GII.14, GII.17 and GII.21. For example S(GI.1)+P(GI.2), S(GI.1)+P(GI.3), S(GI.1)+P(GII.4), S(GI.1)+P(GII.6), S(GI.1)+P(GII.12), S(GI.1)+P(GII.13), S(GI.1)+P(GII.17); S(GI.5)+P(GII.4); S(GII.1)+P(GI.3), S(GII.1)+P(GII.4), S(GII.12)+P(GI.1), S(GII.12)+P(GI.2), S(GII.12)+P(GI.3), S(GII.12)+P(GI.5), S(GII.12)+P(GII.1), S(GII.12)+P(GII.2), S(GII.12)+P(GII.4), S(GII.12)+P(GII.7), S(GII.12)+P(GII.13), S(GII.12)+P(GII.14), S(GII.12)+P(GII.17), S(GII.12)+P(GII.21), when co-expressed with a nucleic acid segment encoding VP2.
For example, strong, or high levels of expression of VP1 fusion protein in plants was observed using nucleic acid segments encoding: S(GI.1/US/68)+P(X); or S(GI.5/Siklos/HUN5407/2013/HUN)+P(Y), or S(GII.1/Ascension208/2010/USA)+P(Z); S(GII.12/HS206/2010/USA)+P(W); where:
X=P(GI.2/Leuven/2003/BEL); P(GII.4/Sydney/NSW0514/2012/AU); P(GII.12/HS206/2010/USA); P(GII.13/VA173/2010/USA);
Y=P(GII.4/Sydney/NSW0514/2012/AU);
Z=P(GI.3/S29/2008/Lilla Edet/Sweeden); or
W=P(GI.1/US/68): P(GI.3/S29/2008/Lilla Edet/Sweeden); P(GI.5/Siklos/HUN5407/2013/HUN); P(GII.1/Ascension208/2010/USA); P(GII.13/VA173/2010/USA); P(GII.14/8610/Saga/2008/JPN); P(GII.21/Salisbury150/2011/USA).
Good, or medium levels of expression levels in plants were observed using nucleic acid segments encoding VP1 fusion proteins comprising: S(GI.1/US/68)+P(X); S(GII.12/HS206/2010/USA)+P(W); or S(GII.14/8610/Saga/2008/JPN)+P(T), where:
X=P(GI.3/S29/2008/Lilla Edet/Sweeden); P(GII.6/Ohio/490/2012/USA); P(GII.17/Kawasaki323/2014/JP);
W=P(GI.2/Leuven/2003/BEL); P(GII.2/CGMH47/2011/TW); P(GII.7/Musashimurayama/2010/JP); P(GII.17/Kawasaki323/2014/JP); or
T=P(GII.4/Sydney/NSW0514/2012/AU).
Expression that was below detectable levels was observed with nucleic acid segments encoding VP1 fusion proteins comprising: S(GII.12/HS206/2010/USA)+P(GII.4/Sydney/NSW0514/2012/AU); S(GII.1/Ascension208/2010/USA+P(GII.4/Sydney/NSW0514/2012/AU); or S(GII.21/Salisbury150/2011/USA)+P(GII.4/Sydney/NSW0514/2012/AU).
These results demonstrate that VP1 fusion proteins comprising various combinations of S domains and P domains may be produced when expressed in plants.
Increased Expression of VLPs Comprising Norovirus VP1 Fusion Proteins and VP2 Native Proteins from the S Domain Genotype
The expression of a nucleic acid complex comprising norovirus nucleic acid segments encoding VP1 protein or VP1 fusion proteins co-expressed with a nucleic acid segment encoding VP2, were compared in N. benthamiana as described in Example 2. VP1 or VP1 fusion protein production was determined using Coomassie-stained SDS-PAGE analysis of extracts obtained from plant leaves vacuum infiltrated with expression vectors were loaded onto discontinuous iodixanol density gradients. Fractions collected from the bottom to the top and fractions were analyzed by SDS-PAGE. The following constructs were expressed and analyzed:
VP1 GII.4: human codon optimized native VP1 GII.4/Sydney/NSW0514/2012/AU (construct #3304; SEQ ID NO:56;
VP1 GII.4 and VP2 GII.4: human codon optimized native VP1 co-expressed with human codon optimized native VP2 GII.4/Sydney/NSW0514/2012/AU (construct #3305; SEQ ID NO:120;
VP1 fusion S(GI.1)+P(GII.4): human codon optimized VP1 S(GI.1)+P(GII.4) fusion protein (construct 3362; SEQ ID NO:59;
VP1 fusion S(GI.1)+P(GII.4) and VP2 GI.1: human codon optimized native VP1 S(GI.1)+P(GII.4) fusion protein (construct 3362; SEQ ID NO:59;
VP1 fusion S(GI.1)+P(GII.4) and VP2 GII.4: human codon optimized VP1 S(GI.1)+P(GII.4) fusion protein (construct 3362; SEQ ID NO:59;
The results are presented in
The level of expression of the human codon-optimized GII.4/Sydney native VP1 protein (construct #3304) is low when the GII.4 VP1 construct is expressed alone (
The level of expression of the VP1 fusion, human codon optimized VP1 S (GI.1)+P (GII.4; construct #3362), is greatly increased when compared to the native VP1 of the GII.4 genotype (Panel B,
This production of VLPs when co-expressing a VP1 fusion having an S domain and VP2 from same genotype and strain is to be contrast with the co-expression of a VP1 fusion, human codon optimized VP1 S (GI.1)+P (GII.4; construct #3362) with human codon-optimized VP2 from GII.4/Sydney (construct #3305), where the S domain of the VP1 fusion and the VP2 protein are obtained from different genotypes and strains. Co-expression of VP1 fusion comprising an S domain with a VP2 obtained from a different genotype and strain resulted in a dramatic decrease in VLP production (Panel C;
Without wishing to be bound by theory, these results are consistent with the proposal that VP2 is located on the inside of the viral particle and that VP2 may play a role in particle stability. When VP1 fusion proteins are expressed in plants, it is preferred that the ORF3 sequence encoding VP2 is obtained from the same norovirus strain as used to obtain the S domain of fusion VP1 sequence.
Levels of VLPs comprising of high-expressing native VP1 GI.1/Norwalk/1968/US (encoded by construct 2724; SEQ ID NO:78;
In contrast, increased stability of VP1 fusion protein was observed with VLPs comprising S(GI.1 Nor68)+P(GI.2 Leu03) norovirus VP1 fusion proteins (encoded by construct 3360; SEQ ID NO:87;
A similar shift in density was also observed in VLPs comprising S(GI.1)+P(GI.3) norovirus VP1 fusion proteins GI.1 Nor68+GI.3 Lil08 (see
Studies on the immune response to Norovirus native GI.1 (SEQ ID NO:1) VLP administration were performed with 6-8 week old female BALB/c mice (Charles River Laboratories). Thirty seven mice were randomly divided into four groups of eight animals for Norovirus VLP vaccine and a group of five animals for placebo. All groups were injected using intramuscular immunization. All groups were immunized in a two-dose regimen, the boost immunization being administered 3 weeks following the first immunization.
For intramuscular administration in hind legs, two groups (eight animals) of unanaesthetized mice were immunized with the plant-made VLP native VP1 from Norovirus GI.1 genotype vaccine (1 or 10 μg). Placebo group (five animals) was immunized using the same route and regimen as the candidate vaccine using vaccine buffer (PBS at pH 6.0). In a similar manner plant-produced VP1 fusion proteins as described herein, for example VP1 fusion proteins produced using construct #3360, 3361, 3361, 3363, 3364, 3365, or SEQ ID NO's: 22 to 27, 29 to 43, 49 to 53, and 71, may also also administered to mice following the same protocol as described in this example.
To measure the potential benefit of adjuvant, two groups of animals (8 animals) were immunized by intramuscular administration in hind legs on unanaesthetized mice with 1 or 10 μg plant-made VLP Norovirus vaccine plus one volume Alhydrogel 2% (alum, Cedarlane Laboratories Ltd., Burlington, Ontario, Canada). All groups were immunized according to a prime-boost regimen with the boost immunization performed 3 weeks following the first immunization.
Mice were evaluated through clinical observations during the in-life period as followed: daily monitoring for mortality and clinical signs, weekly detailed examinations, injection site observations and body weight measurements. All animals were under observation and sacrificed on Day 42 for gross examination. Blood was collected from all animals prior to dosing on Day 0, on Days 21 and 42 (21 days after each immunization). Samples were processed to isolate the serum for specific antibody response analyses.
Serum samples from blood collected on Days 21 and 42 from all animals were analyzed individually by ELISA for GI.1 VLP-specific total IgG and IgA antibodies using GI.1 VLP-coated plates. Pre-immune serum samples (Day 0—prior dosing) collected from all animals were pooled by treatment group and each pool was analyzed to insure that they were negative (or below the cut-off value of the analytical test).
Descriptive statistics were performed using GraphPad Prism software (Version 6.05; GraphPad Software, La Jolla, Calif., USA). Antibody titers measured for each group were reported as geometric mean titer (GMT) with 95% confidence intervals (CI). Half of the value of the limit of detection was attributed to antibody titers below the limit of detection of the method specific to the tested antibodies. Therefore, in this study, an animal was considered to be a positive responder if its GMT value for a determined condition was equal or above the limit of detection of the method (LOQ=100). Statistical comparisons between IgG titers of treatment groups were performed using one-way ANOVA followed by a Tukey's test on log 10-transformed data. A comparison between the placebo group and each treatment group was also performed using oneway ANOVA followed by a post hoc Dunnett's test on log 10-transformed data.
The GI.1 VLP-specific total IgG titers that were measured in serum samples from all animals after IM immunization with one dose (Day 21) and two doses (Day 42) of 1 μg or 10 μg of each formulation. Total IgG titers were measured by ELISA using GI.1 VLP-coated plates (LOQ=100). The results are present in
Mouse Immune Response to Norovirus Native VP1 VLPs
As demonstrated in
Similar results area observed with the administration of VP1 fusion proteins, VP1 fusion proteins produced for example, using construct #3360, 3361, 3361, 3363, 3364, 3365, or SEQ ID NO's: 22 to 27, 29 to 43, 49 to 53, and 71, as described herein.
All citations are hereby incorporated by reference.
The present invention has been described with regard to one or more embodiments. However, it will be apparent to persons skilled in the art that a number of variations and modifications can be made to the described subject matter. The scope of the claims should not be limited by the preferred embodiments set forth in the examples, but should be given the broadest interpretation consistent with the description as a whole
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/CA2018/050352 | 3/23/2018 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62475660 | Mar 2017 | US |
