US20070161083A1 - Codon Optimized Recombinant Dermaphagoides Allergens - Google Patents

Codon Optimized Recombinant Dermaphagoides Allergens Download PDF

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US20070161083A1
US20070161083A1 US11/609,575 US60957506A US2007161083A1 US 20070161083 A1 US20070161083 A1 US 20070161083A1 US 60957506 A US60957506 A US 60957506A US 2007161083 A1 US2007161083 A1 US 2007161083A1
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protein
recproder
codon
der
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Alex Bollen
Paul Jacobs
Alain Jacquet
Marc Massaer
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GlaxoSmithKline Biologicals SA
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/43504—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from invertebrates
    • C07K14/43513—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from invertebrates from arachnidae
    • C07K14/43531—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from invertebrates from arachnidae from mites
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • A61P11/06—Antiasthmatics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/08—Antiallergic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides

Definitions

  • the present invention relates to codon optimised polynucleotides which are efficiently expressed in mammalian cells and encode insect proteins from Dermaphagoides dust mite.
  • the optimised codon polynucleotides encode a protein from Dermaphagoides pteronyssinus , such as DerP1 or proDerP1.
  • the present invention also provides methods of preparing pharmaceutical compositions comprising the expression of the codon optimised polynucleotides, and vectors and transformed host cells comprising them.
  • the allergens from the house dust mite Dermatophagoides have long been recognised to be associated with allergic hypersensitivity reactions such as asthma [1].
  • Der p 1 is an immunodominant allergen which elicits the strongest IgE-mediated immune response [2,3].
  • the cysteine proteinase activity of Der p 1 was shown to amplify its potent allergenicity [4,5].
  • the Der p 1 encoding cDNA sequence reveals that, like many mammalian and plant proteinases, Der p 1 is synthesized as an inactive preproenzyme of 320 amino acid residues which is subsequently processed into a 222-amino acid mature form [6,7].
  • the maturation of ProDer p 1 is not known to date but it is thought that the allergen is processed by the cleavage of the 80-residues proregion.
  • Mature Der p 1 was successfully purified from the whole house dust mite culture but with weak overall yield [8]. Recombinant production of allergens represents an efficient way to obtain defined materials with high yields for a variety of experimental procedures such as immunological studies, diagnosis, treatment of IgE-mediated allergic disorders by immunotherapy and understanding structure-function relationships [9]. Previous attempts of Der p 1 expression in bacteria and yeast indicated that the allergen was poorly expressed and mainly under an insoluble form [10-12]. Moreover, recombinant Der p 1 produced in bacteria was shown to have weak IgE binding activity. The recombinant protein expressed in yeast was recognized by specific IgE at, however, a lower level than the natural protein.
  • DerP1 allergens with reduced enzymatic activity that are encoded by the native non-optimised Dermaphagoides gene are described in WO 99/25823.
  • Other recombinant Dermaphagoides allergens include DerP1 (U.S. Pat. No. 6,077,518), DerPII (U.S. Pat. No. 6,132,734), and DerFI and DerFII (U.S. Pat. No. 5,973,132; U.S. Pat. No. 5,958,415; U.S. Pat. No. 5,876,722).
  • the present invention achieves such advantages by providing a polynucleotide sequence which encodes a Dermaphagoides protein, wherein the codon usage pattern of the polynucleotide sequence is altered to resemble that of highly expressed mammalian genes. Accordingly, the cloning and expression of recProDer p 1 has been achieved in Chinese Hamster Ovary cells (CHO) with high efficiency and produces a product which displayed very similar IgE reactivities to native purified DerP1.
  • the DNA code has 4 letters (A, T, C and G) and uses these to spell three letter “codons” which represent the amino acids the proteins encoded in an organism's genes.
  • the linear sequence of codons along the DNA molecule is translated into the linear sequence of amino acids in the protein(s) encoded by those genes.
  • the code is highly degenerate, with 61 codons coding for the 20 natural amino acids and 3 codons representing “stop” signals. Thus, most amino acids are coded for by more than one codon—in fact several are coded for by four or more different codons.
  • codon usage patterns of organisms are highly non-random. Different species show a different bias in their codon selection and, furthermore, utilization of codons may be markedly different in a single species between genes which are expressed at high and low levels. This bias is different in viruses, plants, bacteria, insect and mammalian cells, and some species show a stronger bias away from a random codon selection than others. For example, humans and other mammals are less strongly biased than certain bacteria or viruses. For these reasons, there is a significant probability that a mammalian gene expressed in E. coli or a viral gene expressed in mammalian cells will have an inappropriate distribution of codons for efficient expression.
  • a gene with a codon usage pattern suitable for E. coli expression may also be efficiently expressed in humans. It is believed that the presence in a heterologous DNA sequence of clusters of codons which are rarely observed in the host in which expression is to occur, is predictive of low heterologous expression levels in that host.
  • FIG. 1 Codon usage of ProDer p 1 and highly expressed human (High) genes.
  • Codon usage of a synthetic ProDer p 1 gene (synthetic) after optimisation of codon usage is also represented. Percentage frequencies of individual codons are shown for each corresponding amino acid. The most prevalent codon is shown in bold.
  • FIG. 2 PCR synthesis of ProDer p 1 cDNA.
  • a set of 14 mutually priming oligonucleotides were used for PCR amplification of a synthetic ProDer p 1 cDNA. After one round of amplification, amplified products were submitted to a second PCR amplification using external primers (primers 1 and 14). Oligonucleotides which served as PCR templates for the synthesis are represented by solid bars. Unique restriction sites into the synthetic Proder p 1 cDNA which were used for the cloning into the eukaryotic pEE 14 expression vector are shown above. After each of the two rounds of PCR amplification, electrophoresis on agarose gel of the amplified fragments are also shown.
  • FIG. 3 Expression of synthetic and natural ProDer p 1 in transient transfection assays.
  • FIG. 4 Purification of recProDer p 1.
  • FIG. 5 Carbohydrate analysis of recProDer p 1.
  • Glycosylations of purified allergens were analysed by lectin staining with Galanthus nivalis agglutinin (GNA, Lane 1, 2), Datura stramonium agglutinin (DSA, Lane 3, 4) and Maackia amurensis agglutinin (MAA, Lane 5, 6).
  • Lane 1, 3, 5 purified Der p 1.
  • Lane 2, 4, 6 purified recProDer p 1
  • FIG. 6 Immune recognition of recProDer p 1 by monoclonal antibodies directed to Der p 1.
  • FIG. 7 Correlation between the IgE reactivity of recProDer p 1 and Der p 1.
  • Immunoplates were coated with 500 ng/well of purified Der p 1 or recProDer p 1 and incubated with 95 sera (diluted 1:8) radioallergosorbent positive to D. pteronyssinus .
  • Bound IgE was quantitated by incubation with mouse anti-human IgE and alkaline phosphatase-labelled anti-mouse IgG antibodies, followed by an enzymatic assay. Results are expressed as OD 410 nm values.
  • FIG. 8 Histamine release activity of recProDer p 1
  • Basophils isolated from the peripheral blood of one allergic donor were stimulated with serial dilutions of natural Der p 1 ( ⁇ ) or recProDer p 1 ( ⁇ ).
  • the histamine released from cells was measured by ELISA.
  • the total amount of histamine in basophils was quantified after cell disruption with the detergent IGEPAL CA-630. Results are shown as the ratio of released histamine by allergens to total histamine.
  • the present invention provides a polynucleotide sequence which encodes a Dermatophagoides mite protein, wherein the codon usage pattern of the polynucleotide sequence resembles that of highly expressed mammalian genes.
  • the polynucleotide sequence is a DNA sequence.
  • the codon usage pattern of the polynucleotide sequence is typical of highly expressed human genes.
  • the house dust mite protein in all of the following aspects of the present invention is derived from Dermatophagoides pteronyssinus or Dermatophagoides farinae .
  • the Dermatophagoides pteronyssinus protein is DerP1 or ProDerP1 or DerP2.
  • a synthetic gene comprising a plurality of codons together encoding a Dermatophagoides protein; wherein the selection of the possible codons used for encoding the recombinant insect protein amino acid sequence has been changed to closely mimic the optimised mammalian codon usage, such that the frequency of codon usage in the synthetic gene is substantially the same as a mammalian gene which encodes the same protein.
  • all of the amino acid types present in the protein are optimised such that the codons used to encode that amino acid are used in the same frequency as the known mammalian frequency for that amino acid.
  • optimised codon synthetic genes are used in expression systems that have a protein yield which is greater than 20% higher, and more preferably greater than 50% and most preferably more than 100% higher in yield than the amount of protein produced from the same expression system using a non-optimised native gene for that Dermatophagoides protein.
  • an isolated nucleic acid molecule encoding an Dermaphagoides protein characterised in that the codons present in said polynucleotide which are used to encode each amino acid are selected to appear in substantially the same frequency as set forth in table 1.
  • the meaning of “substantially” is intended to mean that the percentage usage of a particular codon is the figure as appearing in the table ⁇ 20%, more preferably ⁇ 15%, more preferably ⁇ 10%, and ideally ⁇ 5%.
  • x ij is the number of codons of type j in sequence i
  • n is the total number of codons for a particular amino acid k in the sequence
  • x j is the total number of codons of type j in the 2 sequences.
  • the degrees of freedom of the variable is equal to the number of different possible codons minus 1.
  • x ij is the number of codons of type j in sequence i
  • n is the total number of codons for a particular amino acid k in the sequence
  • x j is the total number of codons of type j in the 2 sequences.
  • the degrees of freedom of the variable is equal to the number of different possible codons minus 1.
  • more than 70% of the amino acids are optimised, more preferably more than 80% are optimised and most preferably greater than 90% of the codons are optimised.
  • optimised Dermatophagoides genes express very well in mammalian cells such as CHO cells, but also express very well in yeast cells despite the different codon usage of yeast.
  • the present invention also provides an expression vector which comprises, and is capable of directing the expression of, a polynucleotide sequence according to the first to third aspects of the invention, encoding a Dermatophagoides amino acid sequence wherein the codon usage pattern of the polynucleotide sequence is typical of highly expressed mammalian genes, preferably highly expressed human genes.
  • the vector may be suitable for driving expression of heterologous DNA in bacterial insect or mammalian cells, particularly human cells.
  • Host cells comprising a polynucleotide sequence according to the first aspect of the invention, or an expression vector according the second aspect, is provided.
  • the host cell may be bacterial, e.g. E. coli ; mammalian, e.g. human; or may be an insect cell.
  • Mammalian cells comprising a vector according to the present invention may be cultured cells transfected in vitro or may be transfected in vivo by administration of the vector to the mammal.
  • compositions comprising a recombinant Dermatophagoides protein expressed by the polynucleotides of the present invention, or the codon optimised polynucleotide sequences are also provided.
  • the pharmaceutical compositions comprises a DNA vector according to the second aspect of the present invention.
  • the composition comprises a plurality of particles, preferably gold particles, coated with DNA comprising a vector encoding a polynucleotide sequence which encodes a Dermatophagoides amino acid sequence, wherein the codon usage pattern of the polynucleotide sequence is typical of highly expressed mammalian genes, particularly human genes.
  • the composition comprises a pharmaceutically acceptable excipient and a DNA vector according to the second aspect of the present invention.
  • the composition may also include an adjuvant.
  • the present invention provides a method of making a pharmaceutical composition including the step of altering the codon usage pattern of a wild-type Dermatophagoides nucleotide sequence, or creating a polynucleotide sequence synthetically, to produce a sequence having a codon usage pattern typical of highly expressed mammalian genes and encoding a wild-type Dermatophagoides amino acid sequence or a mutated Dermatophagoides amino acid sequence comprising the wild-type sequence with amino acid changes sufficient to inactivate one or more of the natural functions of the polypeptide.
  • the method further comprising the expression of the synthetic polynucleotide sequence in a mammalian host cell, purification of the expressed recombinant protein, and formulation with pharmaceutically acceptable excipients.
  • Adjuvants are well known in the art (Vaccine Design—The Subunit and Adjuvant Approach, 1995, Pharmaceutical Biotechnology, Volume 6, Eds. Powell, M. F., and Newman, M. J., Plenum Press, New York and London, ISBN 0-306-44867-X).
  • Codon usage patterns for mammals, including humans can be found in the literature (see e.g. Nakamura et. al. Nucleic Acids Research 1996, 24:214-215).
  • the polynucleotides according to the invention have utility in the production by expression of the encoded proteins, which expression may take place in vitro, in vivo or ex vivo.
  • the nucleotides may therefore be involved in recombinant protein synthesis, for example to increase yields, or indeed may find use as therapeutic agents in their own right, utilised in DNA vaccination techniques.
  • cells for example in cell culture, will be modified to include the polynucleotide to be expressed. Such cells include transient, or preferably stable mammalian cell lines.
  • the cell line selected will be one which is not only stable, but also allows for mature glycosylation and cell surface expression of a polypeptide. Expression may be achieved in transformed oocytes.
  • a polypeptide may be expressed from a polynucleotide of the present invention, in cells of a transgenic non-human animal, preferably a mouse.
  • a transgenic non-human animal expressing a polypeptide from a polynucleotide of the invention is included within the scope of the invention.
  • the nucleic acid will be administered to the mammal e.g. human to be vaccinated.
  • the nucleic acid such as RNA or DNA, preferably DNA
  • the polynucleotides may be administered by any available technique.
  • the nucleic acid may be introduced by needle injection, preferably intradermally, subcutaneously or intramuscularly.
  • the nucleic acid may be delivered directly into the skin using a nucleic acid delivery device such as particle-mediated DNA delivery (PMDD).
  • PMDD particle-mediated DNA delivery
  • inert particles such as gold beads
  • a nucleic acid for example by means of discharge under high pressure from a projecting device.
  • particles coated with a nucleic acid molecule of the present invention are within the scope of the present invention, as are delivery devices loaded with such particles).
  • Suitable techniques for introducing the naked polynucleotide or vector into a patient include topical application with an appropriate vehicle.
  • the nucleic acid may be administered topically to the skin, or to mucosal surfaces for example by intranasal, oral, intravaginal or intrarectal administration.
  • the naked polynucleotide or vector may be present together with a pharmaceutically acceptable excipient, such as phosphate buffered saline (PBS). DNA uptake may be further facilitated by use of facilitating agents such as bupivacaine, either separately or included in the DNA formulation.
  • Other methods of administering the nucleic acid directly to a recipient include ultrasound, electrical stimulation, electroporation and microseeding which is described in U.S. Pat. No. 5,697,901.
  • Uptake of nucleic acid constructs may be enhanced by several known transfection techniques, for example those including the use of transfection agents.
  • these agents includes cationic agents, for example, calcium phosphate and DEAE-Dextran and lipofectants, for example, lipofectam and transfectam.
  • the dosage of the nucleic acid to be administered can be altered. Typically the nucleic acid is administered in an amount in the range of 1 pg to 1 mg, preferably 1 pg to 10 ⁇ g nucleic acid for particle mediated gene delivery and 10 ⁇ g to 1 mg for other routes.
  • a nucleic acid sequence of the present invention may also be administered by means of specialised delivery vectors useful in gene therapy. Gene therapy approaches are discussed for example by Verme et al, Nature 1997, 389:239-242. Both viral and non-viral vector systems can be used. Viral based systems include retroviral, lentiviral, adenoviral, adeno-associated viral, herpes viral, Canarypox and vaccinia-viral based systems. Non-viral based systems include direct administration of nucleic acids, microsphere encapsulation technology (poly(lactide-co-glycolide) and, liposome-based systems.
  • Viral and non-viral delivery systems may be combined where it is desirable to provide booster injections after an initial vaccination, for example an initial “prime” DNA vaccination using a non-viral vector such as a plasmid followed by one or more “boost” vaccinations using a viral vector or non-viral based system.
  • a non-viral vector such as a plasmid
  • boost vaccinations using a viral vector or non-viral based system.
  • a nucleic acid sequence of the present invention may also be administered by means of transformed cells.
  • Such cells include cells harvested from a subject.
  • the naked polynucleotide or vector of the present invention can be introduced into such cells in vitro and the transformed cells can later be returned to the subject.
  • the polynucleotide of the invention may integrate into nucleic acid already present in a cell by homologous recombination events.
  • a transformed cell may, if desired, be grown up in vitro and one or more of the resultant cells may be used in the present invention.
  • Cells can be provided at an appropriate site in a patient by known surgical or microsurgical techniques (e.g. grafting, micro-injection, etc.)
  • compositions of the present invention may include adjuvant compounds, or other substances which may serve to increase the immune response induced by the protein which is encoded by the DNA. These may be encoded by the DNA, either separately from or as a fusion with the antigen, or may be included as non-DNA elements of the formulation.
  • adjuvant-type substances which may be included in the formulations of the present invention include ubiquitin, lysosomal associated membrane protein (LAMP), hepatitis B virus core antigen, FLT3-ligand (a cytokine important in the generation of professional antigen presenting cells, particularly dentritic cells) and other cytokines such as IFN- ⁇ and GMCSF.
  • DerF3 is a serine protease from Dermatophagoides farinae (accession D63858NID/g1311456).
  • the codon usage pattern of DerF3 and DP15 are shown in the following table: ⁇ 2 value of ⁇ 2 value of native Limit ⁇ 2 value for native DerF3 DP15 significance (5%) Ala 10.6 3.4 7.81 Cys 4.7 0.5 3.84 Asp 17.5 8.0 3.84 Glu 11.5 8.2 3.84 Phe 4 4.7 3.84 Gly 25.7 11.3 7.81 His 9.6 3.0 3.84 Ile 16.0 8.9 5.99 Lys 14.6 10.2 3.84 Leu 22.4 12.7 11.1 Asn 9.9 15.2 3.84 Pro 9.4 6.3 7.81 Gln 16.1 10.9 3.84 Arg 12 13.7 11.1 Ser 21.1 4.3 11.1 Thr 7.3 3.0 7.81 Val 19 5.9 7.81 Tyr 9.2 12.7 3.84 Values in bold are statistically significant (amino acids that are not codon optimised)
  • Optimised genes may be designed using a Visual Basic program called Calcgene, written by R. S. Hale and G Thompson (Protein Expression and Purification Vol. 12 pp. 185-188 (1998)). For each amino acid residue in the original sequence, a codon was assigned based on the probability of it appearing in highly expressed mammalian or human genes. Details of the program, which works under Microsoft Windows 3.1, can be obtained from the authors. In this article, certain rare codons were excluded from the optimisation process to obviate the possibility of generating clusters of rare codons together which would otherwise prejudice the efficient expression of the gene.
  • the present invention is exemplified but not limited to the following examples.
  • a “humanized” ProDer p 1 gene was synthesized using a set of 14 partially overlapping oligonucleotides. These primers were designed, based on the codon usage of highly expressed human genes, and produced by an 394 DNA/RNA Applied Biosystem synthetizer The degenerately encoded amino acids were not encoded by the most prevalent codons but taking the frequencies of the individual codons into account. For example, histidine residue is encoded by CAC or CAT with a respective frequency of 79% and 21% in highly expressed human genes. Consequently, we attempted to follow the same codon frequency instead of selecting only the CAC codon for each histidine residue in the synthetic ProDer p 1.
  • the native Der p 1 signal sequence was exchanged with the highly efficient leader peptide of the VZV glycoprotein E (gE) to facilitate secretion.
  • the oligonucleotides were the following: 5′ GAAGCTTCGGGCGAATTGCGTGGTTTTAAGTGACT SEQ ID NO. 1 ATATTCGAGGGTCGCCTGTAATATGGGGACAGTTAAT AAACCTGTGGGTGGGGGTATTGATGGGGTTCGGAATT ATCACG 3′ (oligo 1, coding); 5′ GAAGGCTTTCTTGTATTCCTCGAAGGTCTTAATGG SEQ ID NO.
  • GGGACACTAACTGGGGCGACAACGGCTACGGCTACTT CGCCGCCAAC 3′ oligo 13, coding
  • 5′ GCTCTAGACTCGAGGGATCCTTACAGGATCACCAC SEQ ID NO. 14 GTACGGGTACTCCTCGATCATCATCAGGTCGATGTTG GCGGCGAAGTAGC 3′ (oligo 14, non coding).
  • oligonucleotides were incubated together for the amplification of a synthetic ProDer p 1 gene in a PCR reaction.
  • PCR was conducted using High Fidelity Polymerase (Boehringer) with the following conditions: 30 cycles, denaturation at 94° C. for 30 s, annealing at 50° C. for 30 s and elongation at 72° C. for 30 s.
  • the generated products were amplified using the 3′ and 5′ terminal primers (oligo 1 and 14) in the same conditions.
  • the resulting 1080 bp fragment was cloned into a pCRII-TOPO cloning vector (Invitrogen).
  • the resulting plasmid pNIV4845 was used to transform the E. coli strain TOP 10 (Invitrogen).
  • sequences of the natural and codon-optimised genes, together with the encoded amino acid sequence are listed below and are SEQ ID NO.s 15, 16, and 17 respectively.
  • sequences encode the full ProDerP1, and the nucleic acid or amino acid which is underlined indicates the start of the mature DerP1 sequence resulting from the cleavage of the Pro region. SEQ ID NO.
  • the plasmid for stable expression was generated starting from four ProDer p 1 DNA fragments derived from bacterial clones carrying pNIV4845.
  • Clones n°5 and n°20 were respectively submitted to double digestions by HindIII-BssHII and SphI-BglII, to isolate the 228 bp HindIII-BssHII and 272 bp SphI-BglII ProDer p 1 DNA fragments.
  • COS cells (ATCC) were transiently transfected with 10 ⁇ g of pNIV4846 or pNIV4853, a plasmid carrying authentic ProDer p 1 gene, by calcium phosphate coprecipitation.
  • CHO-K1 cells (ATCC) were transfected with pNIV4846 plasmid by lipofection. After a 3-weeks 25 ⁇ M methionylsulphoximin (MSX, Sigma) selection, one round of gene amplification was carried out with 100 ⁇ M MSX.
  • CHO-K1 clone The best producing recombinant CHO-K1 clone was cultured in cell factories in GMEM medium (Invitrogen) supplemented with 2% fetal calf serum (Gibco). Spent culture medium was harvested every 72 h and stored at ⁇ 20° C. until purification.
  • the pool was applied onto a Q sepharose fast flow column (Pharmacia) equilibrated in 20 mM Tris-HCl pH 9.
  • Der p 1 was eluted by addition of 200 mM NaCl in the starting buffer.
  • the Der p 1 purification was achieved by a gel filtration chromatography onto a superdex-75 column (Pharmacia) equilibrated in PBS pH 7.3. Purified Der p 1 was concentrated and stored at ⁇ 20° C.
  • CHO spent culture medium was diluted two times with water and the pH was adjusted to 7.2.
  • the modified supernatant was loaded onto a Q sepharose fast flow column (5 ⁇ 10 cm, Pharmacia) equilibrated in 20 mM Tris-HCl pH 7.2 which is coupled to a hydroxyapatite column (2.6 ⁇ 15 cm, Bio-Rad) conditioned in the same buffer.
  • the flow-through containing recProDer p 1 of both columns was adjusted to pH 9 and applied onto a Q sepharose fast flow column (1.6 ⁇ 10 cm) equilibrated in 20 mM Tris-HCl pH 9.
  • the column was washed with the starting buffer and with the same buffer supplemented with 100 mM NaCl.
  • ProDer p 1 was eluted by a linear NaCl gradient (100-300 mM, 15 column volumes). The recProDer p 1-enriched fractions were pooled and concentrated by ultrafiltration onto a Filtron membrane (Omega variety, cut-off: 10 kD). The recProDer p 1 purification was achieved by a gel filtration chromatography onto a superdex-75 column (1 ⁇ 30 cm, Pharmacia) equilibrated in PBS pH 7.3. Purified recProDer p 1 was concentrated and stored at ⁇ 20° C.
  • Proteins were analyzed by SDS-PAGE on 12.5% polyacrylamide gels. After electrophoresis, proteins were transferred onto nitrocellulose membranes using a semi-dry transblot system (Bio-Rad). Membranes were saturated for 30 min with 0.5% Instagel (PB Gelatins) in TBS-T (50 mM Tris HCl pH 7.5, 150 mM NaCl, 0.1% Tween 80) and incubated with rabbit polyclonal serum raised against Der p 1 peptide 245-267 diluted in blocking solution (1:5000) (Kindly provided by Dr Pestel, Institut Pasteur de Lille, France) [17].
  • TBS-T 50 mM Tris HCl pH 7.5, 150 mM NaCl, 0.1% Tween 80
  • Immunoreactive materials were detected using alkaline phosphatase-conjugated goat anti-rabbit antibodies (Promega, 1:7500) and 5-bromo,4-chloro,3-indolylphosphate (BCIP, Boehringer)/nitroblue tetrazolium (NBT, Sigma) as substrates.
  • alkaline phosphatase-conjugated goat anti-rabbit antibodies Promega, 1:7500
  • BCIP 5-bromo,4-chloro,3-indolylphosphate
  • NBT nitroblue tetrazolium
  • Glycan Differenciation Kit Boehringer
  • Glycan Differenciation Kit Boehringer
  • lectins Galanthus nivalis agglutinin (GNA), Sambucus nigra agglutinin (SNA), Maackia amurensis agglutinin (MAA), Peanut agglutinin (PNA) and Datura stramonium agglutinin (DSA).
  • GAA Galanthus nivalis agglutinin
  • SNA Sambucus nigra agglutinin
  • MAA Maackia amurensis agglutinin
  • PNA Peanut agglutinin
  • DSA Datura stramonium agglutinin
  • Enzymatic assays were performed in 50 mM Tris-HCl pH 7, containing 1 mM EDTA and 20 mM L-cysteine at 25° C. in a total volume of 1 ml.
  • Assays were started by addition of cysteine activated allergen to a final concentration of 100 nM. Before any assay, purified Der p 1 or recProDer p 1 was incubated with a mixture of aprotinin- and p-aminobenzamidine-agarose resins (Sigma) to remove any putative trace of serine protease activity.
  • Total protein concentration was determined by the bicinchoninic acid procedure (MicroBCA, Pierce) with bovine serum albumin as standard.
  • Der p 1 or recProDer p 1 was detected with an ELISA kit using Der p 1 specific monoclonal antibodies 5H8 and 4C1 (Indoor Biotechnologies).
  • the Der p 1 standard (UVA 93/03) used in the assay was at a concentration of 2.5 ⁇ g/ml.
  • Immunoplates were coated overnight with Der p 1 or recProDer p 1 (500 ng/well) at 4° C. Plates were then washed 5 times with 100 ⁇ l per well of TBS-Tween buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% Tween 80) and saturated for 1 hr at 37° C. with 150 ⁇ l of the same buffer supplemented with 1% BSA (Sigma). Sera from allergic patients to D. pteronyssinus and diluted at 1/8 were then incubated for 1 hr at 37° C. Out of the 95 sera used in the experiments, 16 sera ranged in their specific anti- D.
  • pteronyssinus IgE values (RAST assays) from 58.1 kU/L to 99 kU/L and 79 above the upper cut-off value of 100 kU/L. Plates were washed 5 times with TBS-Tween buffer and the allergen-IgE complexes were detected after incubation with a mouse anti-human IgE antibody (Southern Biotechnology Associates) and a goat anti-mouse IgG antibody coupled to alkaline phosphatase (dilution 1/7500 in TBS-Tween buffer, Promega). The enzymatic activity was measured using the p-nitrophenylphosphate substrate (Sigma) dissolved in diethanolamine buffer (pH 9.8). OD 410 nm was measured in a Biorad Novapath ELISA reader.
  • the histamine release was assayed using leukocytes from the peripheral heparinized blood of an allergic donor and by the Histamine-ELISA kit (Immunotech). Basophils were incubated with serial dilutions of recProDer p 1 or Der p 1 for 30 min at 37° C. The total amount of histamine in basophils was quantified after cell disruption with the detergent IGEPAL CA-630 (Sigma).
  • the codon prevalence of ProDer p 1 gene displayed many divergences compared with that used for highly expressed human genes ( FIG. 1 ).
  • oligonucleotides were designed for the construction of a synthetic ProDer p 1 gene to optimise the allergen expression in mammalian cells.
  • the final codon frequency in the synthetic ProDer p 1 gene was very similar to that used in highly expressed mammalian genes.
  • the synthetic ProDer p 1 was assembled from mutually priming oligonucleotides that were subsequently amplified by PCR ( FIG. 2 ). After one round of PCR, amplified products displayed a molecular weight ranging from 3000 to 300 bp. A subsequent amplification with primers complementary to the 5′ end of VZV gE leader peptide and to the 3′ end of synthetic ProDer p 1 gene led to a 1072 bp fragment of excepted size. The amplified fragment was cloned into the pCRII cloning vector. Sequence analysis of recombinant clones revealed the presence of point mutations and deletions in the synthetic ProDer p 1 gene. Finally, the correct coding cassette was obtained after ligation of 4 different fragments isolated from 3 independent bacterial clones, and inserted in the mammalian expression vector pEE14 to give the final plasmid pNIV4846.
  • COS cells were transfected with pNIV4846 and pNIV4853, a pEE14-derived plasmid carrying authentic ProDer p 1 cDNA.
  • the recProDer p 1 expression level of the supernatants was estimated by an ELISA assay, using two anti-Der p 1 monoclonal antibodies.
  • the expression vector carrying the synthetic cDNA directed the recProDer p 1 synthesis more efficiently than the same vector containing the authentic gene.
  • the expression level of humanized ProDer p 1 gene was enhanced up to 450 ng/ml/72 h which represents a 6-fold increase compared with the reference construction (75 ng/ml/72 h). As expected, no recProDer p 1 expression was detected using COS cells transfected by a control vector without any insert.
  • CHO-K1 cells were transfected with pNIV4846 and clones resistant to 25 ⁇ M MSX were selected.
  • the recProDer p 1 level assayed by ELISA indicated that three independent clones secreted recProDer p 1 up to 11 ⁇ g/ml/72 h.
  • Addition of sodium butyrate, a molecule previously reported to enhance expression level of recombinant proteins in culture medium [18] did not influence the recProDer p 1 synthesis.
  • a further amplification of 25 ⁇ M MSX-resistant clones up to 100 ⁇ M MSX increased expression, raising 26 to 34 ⁇ g/ml/72 h recProDer p 1 in culture medium.
  • the clone n°1 was used for recProDer p 1 large-scale production in cell factories and purification. Spent culture medium was collected every 72 h and up to 9 harvests were performed. In these conditions, the best recProDer p 1 expression level raised 15 ⁇ g/ml in the culture medium before purification.
  • recProDer p 1 Purification of recProDer p 1 was achieved by a combination of three chromatographic steps, using anion-exchange, hydroxyapatite and gel filtration media. The final purification yield was about 6 mg of recProDer p 1 per litre of culture medium with a recovery close to 40%. On SDS PAGE, purified recProDer p 1 migrated as three immunoreactive species: two major bands with a respective molecular weight of 41 and 36 kD and one minor band of 38 kD ( FIG. 4 ). This result indicated that the propeptide cleavage, to yield mature Der p 1, did not occur during the expression and purification steps, as natural Der p 1 migrated on SDS PAGE as a 29 kD band. The purity of the product was higher than 90%.
  • recProDer p 1 Carbohydrate analysis of recProDer p 1 was performed by glycan recognition with several specific lectins. Among the five lectins used, only the GNA lectin reacted with the 36 kDa recProDer p 1, pointing to the presence of terminal mannose residues on this molecule, either as high-mannose N-glycan chains or as exposed mannose in hybrid chains ( FIG. 5 ).
  • the 38 and 41 kDa bands were recognized respectively by the DSA and MAA lectins, showing that the 38 kDa molecule carried terminal galactose linked ⁇ (1-4) to N-acetyl-glucosamine in N-glycan chains whereas the carbohydrate structure of the upper band was terminated by sialic acid linked ⁇ (2-3) to galactose.
  • Der p 1 did not react with any lectin confirming that Der p 1 is not glycosylated.
  • recProDer p 1 The enzymatic activity of recProDer p 1 was measured using Cbz-Phe-Arg-AMC and Boc-Gln-Ala-Arg-AMC as substrates [19,20]. As expected, because of the presence of the Pro region, RecProDer p 1 was totally inactive in our assays. In the same experimental conditions, fluorogenic molecules were fully degraded within 4 min by natural Der p 1 used at the same molarity.
  • RecProDer p 1 was tested in ELISA assays to determine whether the recombinant allergen displayed reactivities similar to those of Der p 1 towards specific anti-Der p 1 IgG and anti- Dermatophagoides pteronyssinus IgE. As shown in FIG. 6 , equimolar concentrations of both allergens reacted similarly with two Der p 1 specific monoclonal and conformational antibodies, suggesting that recProDer p 1 displayed the overall structure of the natural allergen. The IgE reactivity of recProDer p 1 and Der p 1 was compared in a direct ELISA wherein immunoplates were directly coated with Der p 1 or recProDer p 1.
  • the ProDer p 1 coding cassette from pNIV4846 (full-length 1-302aa ProDer p 1 cDNA with optimised mammalian codon usage) was amplified by PCR using the following primers: 5′ACTGACAGGCCTCGGCCGAGCTCCATTAA3′ (SEQ ID NO. 18) (StuI restriction site in bold, forward) and 5′CAGTCACCTAGGTCTAGACTCGAGGGGAT3′ (SEQ ID NO. 19) (AvrII restriction site in bold, reverse). The amplified fragment was cloned into the pCR2.1 TOPO cloning vector. The correct ProDer p 1 cassette was verified by DNA sequencing.
  • Recombinant TOPO vector was digested with StuI-AvrII to generate a 918 bp fragment which was introduced into the pPIC9K expression vector restricted with SnaBI-AvrII.
  • the resulting plasmid, pNIV4878 contains the ProDer p 1 cassette downstream to the S. cerevisae ⁇ factor
  • Expression plasmid for the production of unglycosylated ProDer p 1 was derived from pNIV4878 by overlap extension PCR using a set of four primers.
  • the mutated 317 bp AflII-SnaBI fragment was generated by a three-step process.
  • primers 1 and 4 were mixed with pNIV4878 to produce a 200 bp fragment.
  • primers 2 and 3 were mixed with pNIV4878 to produce a 140 bp.
  • the two PCR products were purified onto agarose gel and used as templates for a third round of PCR to obtain a ⁇ 340 bp fragment. This purified fragment was cloned into the pCR2.1 TOPO cloning vector. The mutation was verified by DNA sequencing.
  • Recombinant TOPO vector was digested with AflII-SnaBI to generate a 317 bp fragment which was ligated into the similarly digested pNIV4878.
  • the resulting plasmid, pNIV4883 contains the ProDer p 1 N52Q downstream to the S. cerevisae ⁇ factor
  • Plasmid pNIV4878 was introduced into P. pastoris using the spheroplast transformation method. Transformants were selected for histidinol deshydrogenase (His+) prototrophy. The screening of His+ transformants for geneticin (G418) resistance was performed by plating clones on agar containing increasing concentrations of G418.
  • G418 resistant clones were grown at 30° C. in BMG medium to an OD 600 nm of 2-6. Cells were collected by centrifugation and resuspended to an OD 600 nm of 1 in 100 ml of BMG medium. Proder p 1 expression was induced by daily addition of methanol 0.5% for 6 days. The supernatant was collected by centrifugation and stored at ⁇ 20° C. until purification.
  • codon usage optimisation can induces high-level expression of recProDer p 1, an allergen difficult to produce in CHO cells. This strategy could also be applicable for expression of other allergens and could be extrapolate to other expression systems. Synthetic genes with appropriate codons could thus provide new tools for allergy diagnosis and specific immunotherapy.
  • RecProDer p 1 immobilized on solid phases, could substitute natural Der p 1 in diagnostic test for the detection of specific IgE. Considering the reduced recProDer p 1 anaphylactogenic potential, this recombinant allergen could be used in the future as alternative reagents for immunotherapy to replace the commonly used allergen extracts.

Abstract

The present invention relates to codon optimised polynucleotides which are efficiently expressed in mammalian cells and encode insect proteins from Dermaphagoides dust mite. In particular, the optimised codon polynucleotides encode a protein from Dermaphagoides pteronyssinus, such as DerP1 or proDerP1. The present invention also provides methods of preparing pharmaceutical compositions comprising the expression of the codon optimised polynucleotides, and vectors and transformed host cells comprising them.

Description

  • This application is a continuation of U.S. application Ser. No. 10/297,563 (Allowed) filed 9 Dec. 2002, which is a National Stage Application filed under 35 U.S.C. §371 of PCT/EP01/06483 filed 7 Jun. 2001.
  • The present invention relates to codon optimised polynucleotides which are efficiently expressed in mammalian cells and encode insect proteins from Dermaphagoides dust mite. In particular, the optimised codon polynucleotides encode a protein from Dermaphagoides pteronyssinus, such as DerP1 or proDerP1. The present invention also provides methods of preparing pharmaceutical compositions comprising the expression of the codon optimised polynucleotides, and vectors and transformed host cells comprising them.
  • The allergens from the house dust mite Dermatophagoides have long been recognised to be associated with allergic hypersensitivity reactions such as asthma [1]. Amongst these molecules, Der p 1 is an immunodominant allergen which elicits the strongest IgE-mediated immune response [2,3]. The cysteine proteinase activity of Der p 1 was shown to amplify its potent allergenicity [4,5]. The Der p 1 encoding cDNA sequence reveals that, like many mammalian and plant proteinases, Der p 1 is synthesized as an inactive preproenzyme of 320 amino acid residues which is subsequently processed into a 222-amino acid mature form [6,7]. The maturation of ProDer p 1 is not known to date but it is thought that the allergen is processed by the cleavage of the 80-residues proregion.
  • Mature Der p 1 was successfully purified from the whole house dust mite culture but with weak overall yield [8]. Recombinant production of allergens represents an efficient way to obtain defined materials with high yields for a variety of experimental procedures such as immunological studies, diagnosis, treatment of IgE-mediated allergic disorders by immunotherapy and understanding structure-function relationships [9]. Previous attempts of Der p 1 expression in bacteria and yeast indicated that the allergen was poorly expressed and mainly under an insoluble form [10-12]. Moreover, recombinant Der p 1 produced in bacteria was shown to have weak IgE binding activity. The recombinant protein expressed in yeast was recognized by specific IgE at, however, a lower level than the natural protein.
  • Recombinant DerP1 allergens with reduced enzymatic activity that are encoded by the native non-optimised Dermaphagoides gene are described in WO 99/25823. Other recombinant Dermaphagoides allergens include DerP1 (U.S. Pat. No. 6,077,518), DerPII (U.S. Pat. No. 6,132,734), and DerFI and DerFII (U.S. Pat. No. 5,973,132; U.S. Pat. No. 5,958,415; U.S. Pat. No. 5,876,722).
  • It is clearly desirable to enable the efficient expression of recombinant Dermaphagoides allergens for use in the manufacture of pharmaceuticals, vaccines or diagnostic assays. It is furthermore desirable for the expression systems to produce recombinant allergen at high levels that is also in the same conformation and immunological properties as native Dermaphagoides allergens.
  • The present invention achieves such advantages by providing a polynucleotide sequence which encodes a Dermaphagoides protein, wherein the codon usage pattern of the polynucleotide sequence is altered to resemble that of highly expressed mammalian genes. Accordingly, the cloning and expression of recProDer p 1 has been achieved in Chinese Hamster Ovary cells (CHO) with high efficiency and produces a product which displayed very similar IgE reactivities to native purified DerP1.
  • The DNA code has 4 letters (A, T, C and G) and uses these to spell three letter “codons” which represent the amino acids the proteins encoded in an organism's genes. The linear sequence of codons along the DNA molecule is translated into the linear sequence of amino acids in the protein(s) encoded by those genes. The code is highly degenerate, with 61 codons coding for the 20 natural amino acids and 3 codons representing “stop” signals. Thus, most amino acids are coded for by more than one codon—in fact several are coded for by four or more different codons.
  • Where more than one codon is available to code for a given amino acid, it has been observed that the codon usage patterns of organisms are highly non-random. Different species show a different bias in their codon selection and, furthermore, utilization of codons may be markedly different in a single species between genes which are expressed at high and low levels. This bias is different in viruses, plants, bacteria, insect and mammalian cells, and some species show a stronger bias away from a random codon selection than others. For example, humans and other mammals are less strongly biased than certain bacteria or viruses. For these reasons, there is a significant probability that a mammalian gene expressed in E. coli or a viral gene expressed in mammalian cells will have an inappropriate distribution of codons for efficient expression. However, a gene with a codon usage pattern suitable for E. coli expression may also be efficiently expressed in humans. It is believed that the presence in a heterologous DNA sequence of clusters of codons which are rarely observed in the host in which expression is to occur, is predictive of low heterologous expression levels in that host.
  • There are several examples where changing codons from those which are rare in the host to those which are host-preferred (“codon optimization”) has enhanced heterologous expression levels, for example the BPV (bovine papilloma virus) late genes L1 and L2 have been codon optimised for mammalian codon usage patterns and this has been shown to give increased expression levels over the wild-type HPV sequences in mammalian (Cos-1) cell culture (Zhou et. al. J. Virol 1999. 73, 4972-4982). In this work, every BPV codon which occurred more than twice as frequently in BPV than in mammals (ratio of usage >2), and most codons with a usage ratio of >1.5 were conservatively replaced by the preferentially used mammalian codon. In WO97/31115, WO97/48370 and WO98/34640 (Merck & Co., Inc.) codon optimisation of HIV genes or segments thereof has been shown to result in increased protein expression and improved immunogenicity when the codon optimised sequences are used as DNA vaccines in the host mammal for which the optimisation was tailored. In this work, the sequences consist entirely of optimised codons (except where this would introduce an undesired restriction site, intron splice site etc.) because each viral codon is conservatively replaced with the optimal codon for the intended host.
    • LEGEND TO FIGURES
  • FIG. 1. Codon usage of ProDer p 1 and highly expressed human (High) genes.
  • Codon usage of a synthetic ProDer p 1 gene (synthetic) after optimisation of codon usage is also represented. Percentage frequencies of individual codons are shown for each corresponding amino acid. The most prevalent codon is shown in bold.
  • FIG. 2. PCR synthesis of ProDer p 1 cDNA.
  • A set of 14 mutually priming oligonucleotides were used for PCR amplification of a synthetic ProDer p 1 cDNA. After one round of amplification, amplified products were submitted to a second PCR amplification using external primers (primers 1 and 14). Oligonucleotides which served as PCR templates for the synthesis are represented by solid bars. Unique restriction sites into the synthetic Proder p 1 cDNA which were used for the cloning into the eukaryotic pEE 14 expression vector are shown above. After each of the two rounds of PCR amplification, electrophoresis on agarose gel of the amplified fragments are also shown.
  • FIG. 3. Expression of synthetic and natural ProDer p 1 in transient transfection assays.
  • Supernatants from COS cells transfected with plasmids encoding natural (pNIV 4853) or synthetic ProDer p 1 (pNIV 4846) were assayed for the presence of secreted recProDer p 1 in a Der p 1 ELISA. Supernatant from COS transfected with a plasmid without insert was used as control.
  • FIG. 4. Purification of recProDer p 1.
  • Purified allergens were analyzed by SDS-PAGE and proteins were detected by Coomassie blue staining (panel A), by immunoblotting with rabbit polyclonal serum raised against Der p 1 peptide 245-267 (panel B). Lane 1: purified recProDer p 1. Lane 2: purified Der p 1
  • FIG. 5. Carbohydrate analysis of recProDer p 1.
  • Glycosylations of purified allergens were analysed by lectin staining with Galanthus nivalis agglutinin (GNA, Lane 1, 2), Datura stramonium agglutinin (DSA, Lane 3, 4) and Maackia amurensis agglutinin (MAA, Lane 5, 6). Lane 1, 3, 5: purified Der p 1. Lane 2, 4, 6: purified recProDer p 1
  • FIG. 6. Immune recognition of recProDer p 1 by monoclonal antibodies directed to Der p 1.
  • Reactivity of Der p 1 (●) and recProDer p 1 (▪) towards monoclonal antibodies was assayed in a two-site ELISA. Both allergens were used at the same concentration which was determined in a total protein assay (MicroBCA, Pierce).
  • FIG. 7. Correlation between the IgE reactivity of recProDer p 1 and Der p 1.
  • Immunoplates were coated with 500 ng/well of purified Der p 1 or recProDer p 1 and incubated with 95 sera (diluted 1:8) radioallergosorbent positive to D. pteronyssinus. Bound IgE was quantitated by incubation with mouse anti-human IgE and alkaline phosphatase-labelled anti-mouse IgG antibodies, followed by an enzymatic assay. Results are expressed as OD410 nm values.
  • FIG. 8. Histamine release activity of recProDer p 1
  • Basophils isolated from the peripheral blood of one allergic donor were stimulated with serial dilutions of natural Der p 1 (λ) or recProDer p 1 (ν). The histamine released from cells was measured by ELISA. The total amount of histamine in basophils was quantified after cell disruption with the detergent IGEPAL CA-630. Results are shown as the ratio of released histamine by allergens to total histamine.
    • SUMMARY OF THE INVENTION
  • According to a first aspect, the present invention provides a polynucleotide sequence which encodes a Dermatophagoides mite protein, wherein the codon usage pattern of the polynucleotide sequence resembles that of highly expressed mammalian genes.
  • Preferably the polynucleotide sequence is a DNA sequence. Desirably the codon usage pattern of the polynucleotide sequence is typical of highly expressed human genes. Preferably the house dust mite protein in all of the following aspects of the present invention is derived from Dermatophagoides pteronyssinus or Dermatophagoides farinae. Most preferably, the Dermatophagoides pteronyssinus protein is DerP1 or ProDerP1 or DerP2.
  • Accordingly there is provided in a first aspect of the present invention, a synthetic gene comprising a plurality of codons together encoding a Dermatophagoides protein; wherein the selection of the possible codons used for encoding the recombinant insect protein amino acid sequence has been changed to closely mimic the optimised mammalian codon usage, such that the frequency of codon usage in the synthetic gene is substantially the same as a mammalian gene which encodes the same protein.
  • Preferably in this first aspect, all of the amino acid types present in the protein are optimised such that the codons used to encode that amino acid are used in the same frequency as the known mammalian frequency for that amino acid. In addition, in preferred optimised codon synthetic genes are used in expression systems that have a protein yield which is greater than 20% higher, and more preferably greater than 50% and most preferably more than 100% higher in yield than the amount of protein produced from the same expression system using a non-optimised native gene for that Dermatophagoides protein.
  • Alternatively, in a second aspect of the present invention there is provided an isolated nucleic acid molecule encoding an Dermaphagoides protein, characterised in that the codons present in said polynucleotide which are used to encode each amino acid are selected to appear in substantially the same frequency as set forth in table 1.
    TABLE 1
    Codon usage frequency in mammalian cells
    Amino Frequency
    Acid Codon (percentage used)
    Ala GCG 17
    GCA 13
    GCT 17
    GCC 53
    Arg AGG 18
    AGA 10
    CGG 21
    CGA 6
    CGT 7
    CGC 37
    Asn AAT 22
    AAC 78
    Asp GAT 25
    GAC 75
    Cys TGT 32
    TGC 68
    Gln CAG 88
    CAA 12
    Glu GAG 75
    GAA 25
    Gly GGG 24
    GGA 14
    GGT 12
    GGC 50
    His CAT 21
    CAC 79
    Ile ATA 5
    ATT 18
    ATC 77
    Leu TTG 6
    TTA 2
    CTG 58
    CTA 3
    CTT 5
    CTC 26
    Lys AAG 82
    AAA 18
    Phe TTT 20
    TTC 80
    Pro CCG 17
    CCA 16
    CCT 19
    CCC 48
    Ser AGT 10
    AGC 34
    TCG 9
    TCA 5
    TCT 13
    TCC 28
    Thr ACG 15
    ACA 14
    ACT 14
    ACC 57
    Tyr TAT 26
    TAC 74
    Val GTG 64
    GTA 5
    GTT 7
    GTC 25
  • In this context, the meaning of “substantially” is intended to mean that the percentage usage of a particular codon is the figure as appearing in the table ±20%, more preferably ±15%, more preferably ±10%, and ideally ±5%.
  • Alternatively, in a third aspect of the present invention there is provided, a synthetic gene comprising a plurality of codons together encoding a Dermatophagoides; protein, characterised in that each type of amino acid type has a χ2 value which is not significantly different, at a confidence interval of between 80-99%, to the corresponding χ2 value of that same amino acid type as found in a theoretical mammalian gene; said χ2 value being calculated using the following formula: χ k 2 = ∑ ( x ij - x j / n ) 2 ( x j / n )
  • wherein xij is the number of codons of type j in sequence i, n is the total number of codons for a particular amino acid k in the sequence, and xj is the total number of codons of type j in the 2 sequences. The degrees of freedom of the variable is equal to the number of different possible codons minus 1.
  • Along these same lines, the present invention can also be expressed as providing a synthetic gene comprising a plurality of codons together encoding a Dermatophagoides protein; characterised in that between 60-100% of the different types of amino acids present in the synthetic gene are optimised, characterised in that an amino acid type is considered to be optimised if its χ2 value in the synthetic gene is less that the Limit χ2 value for significance (5%), for that particular amino acid as defined in the following table:
    Amino Acid Limit χ2 value for significance (5%)
    Ala 7.81
    Cys 3.84
    Asp 3.84
    Glu 3.84
    Phe 3.84
    Gly 7.81
    His 3.84
    Ile 5.99
    Lys 3.84
    Leu 11.1
    Asn 3.84
    Pro 7.81
    Gln 3.84
    Arg 11.1
    Ser 11.1
    Thr 7.81
    Val 7.81
    Tyr 3.84

    said χ2 value being calculated using the following formula: χ k 2 = ∑ ( x ij - x j / n ) 2 ( x j / n )
  • wherein xij is the number of codons of type j in sequence i, n is the total number of codons for a particular amino acid k in the sequence, and xj is the total number of codons of type j in the 2 sequences. The degrees of freedom of the variable is equal to the number of different possible codons minus 1. Preferably, more than 70% of the amino acids are optimised, more preferably more than 80% are optimised and most preferably greater than 90% of the codons are optimised.
  • Surprisingly such optimised Dermatophagoides genes express very well in mammalian cells such as CHO cells, but also express very well in yeast cells despite the different codon usage of yeast.
  • The present invention also provides an expression vector is provided which comprises, and is capable of directing the expression of, a polynucleotide sequence according to the first to third aspects of the invention, encoding a Dermatophagoides amino acid sequence wherein the codon usage pattern of the polynucleotide sequence is typical of highly expressed mammalian genes, preferably highly expressed human genes. The vector may be suitable for driving expression of heterologous DNA in bacterial insect or mammalian cells, particularly human cells.
  • Host cells comprising a polynucleotide sequence according to the first aspect of the invention, or an expression vector according the second aspect, is provided. The host cell may be bacterial, e.g. E. coli; mammalian, e.g. human; or may be an insect cell. Mammalian cells comprising a vector according to the present invention may be cultured cells transfected in vitro or may be transfected in vivo by administration of the vector to the mammal.
  • Pharmaceutical compositions comprising a recombinant Dermatophagoides protein expressed by the polynucleotides of the present invention, or the codon optimised polynucleotide sequences are also provided.
  • Preferably the pharmaceutical compositions comprises a DNA vector according to the second aspect of the present invention. In preferred embodiments the composition comprises a plurality of particles, preferably gold particles, coated with DNA comprising a vector encoding a polynucleotide sequence which encodes a Dermatophagoides amino acid sequence, wherein the codon usage pattern of the polynucleotide sequence is typical of highly expressed mammalian genes, particularly human genes. In alternative embodiments, the composition comprises a pharmaceutically acceptable excipient and a DNA vector according to the second aspect of the present invention. The composition may also include an adjuvant.
  • In a further aspect, the present invention provides a method of making a pharmaceutical composition including the step of altering the codon usage pattern of a wild-type Dermatophagoides nucleotide sequence, or creating a polynucleotide sequence synthetically, to produce a sequence having a codon usage pattern typical of highly expressed mammalian genes and encoding a wild-type Dermatophagoides amino acid sequence or a mutated Dermatophagoides amino acid sequence comprising the wild-type sequence with amino acid changes sufficient to inactivate one or more of the natural functions of the polypeptide. The method further comprising the expression of the synthetic polynucleotide sequence in a mammalian host cell, purification of the expressed recombinant protein, and formulation with pharmaceutically acceptable excipients.
  • Methods of preparing a vaccine are provided when the pharmaceutically acceptable excipients comprises an adjuvant. Adjuvants are well known in the art (Vaccine Design—The Subunit and Adjuvant Approach, 1995, Pharmaceutical Biotechnology, Volume 6, Eds. Powell, M. F., and Newman, M. J., Plenum Press, New York and London, ISBN 0-306-44867-X).
  • Codon usage patterns for mammals, including humans can be found in the literature (see e.g. Nakamura et. al. Nucleic Acids Research 1996, 24:214-215).
  • The polynucleotides according to the invention have utility in the production by expression of the encoded proteins, which expression may take place in vitro, in vivo or ex vivo. The nucleotides may therefore be involved in recombinant protein synthesis, for example to increase yields, or indeed may find use as therapeutic agents in their own right, utilised in DNA vaccination techniques. Where the polynucleotides of the present invention are used in the production of the encoded proteins in vitro or ex vivo, cells, for example in cell culture, will be modified to include the polynucleotide to be expressed. Such cells include transient, or preferably stable mammalian cell lines. Particular examples of cells which may be modified by insertion of vectors encoding for a polypeptide according to the invention include mammalian HEK293T, CHO, HeLa, 293 and COS cells. Preferably the cell line selected will be one which is not only stable, but also allows for mature glycosylation and cell surface expression of a polypeptide. Expression may be achieved in transformed oocytes. A polypeptide may be expressed from a polynucleotide of the present invention, in cells of a transgenic non-human animal, preferably a mouse. A transgenic non-human animal expressing a polypeptide from a polynucleotide of the invention is included within the scope of the invention.
  • Where the polynucleotides of the present invention find use as therapeutic agents, e.g. in DNA vaccination, the nucleic acid will be administered to the mammal e.g. human to be vaccinated. The nucleic acid, such as RNA or DNA, preferably DNA, is provided in the form of a vector, such as those described above, which may be expressed in the cells of the mammal. The polynucleotides may be administered by any available technique. For example, the nucleic acid may be introduced by needle injection, preferably intradermally, subcutaneously or intramuscularly. Alternatively, the nucleic acid may be delivered directly into the skin using a nucleic acid delivery device such as particle-mediated DNA delivery (PMDD). In this method, inert particles (such as gold beads) are coated with a nucleic acid, and are accelerated at speeds sufficient to enable them to penetrate a surface of a recipient (e.g. skin), for example by means of discharge under high pressure from a projecting device. (Particles coated with a nucleic acid molecule of the present invention are within the scope of the present invention, as are delivery devices loaded with such particles).
  • Suitable techniques for introducing the naked polynucleotide or vector into a patient include topical application with an appropriate vehicle. The nucleic acid may be administered topically to the skin, or to mucosal surfaces for example by intranasal, oral, intravaginal or intrarectal administration. The naked polynucleotide or vector may be present together with a pharmaceutically acceptable excipient, such as phosphate buffered saline (PBS). DNA uptake may be further facilitated by use of facilitating agents such as bupivacaine, either separately or included in the DNA formulation. Other methods of administering the nucleic acid directly to a recipient include ultrasound, electrical stimulation, electroporation and microseeding which is described in U.S. Pat. No. 5,697,901.
  • Uptake of nucleic acid constructs may be enhanced by several known transfection techniques, for example those including the use of transfection agents. Examples of these agents includes cationic agents, for example, calcium phosphate and DEAE-Dextran and lipofectants, for example, lipofectam and transfectam. The dosage of the nucleic acid to be administered can be altered. Typically the nucleic acid is administered in an amount in the range of 1 pg to 1 mg, preferably 1 pg to 10 μg nucleic acid for particle mediated gene delivery and 10 μg to 1 mg for other routes.
  • A nucleic acid sequence of the present invention may also be administered by means of specialised delivery vectors useful in gene therapy. Gene therapy approaches are discussed for example by Verme et al, Nature 1997, 389:239-242. Both viral and non-viral vector systems can be used. Viral based systems include retroviral, lentiviral, adenoviral, adeno-associated viral, herpes viral, Canarypox and vaccinia-viral based systems. Non-viral based systems include direct administration of nucleic acids, microsphere encapsulation technology (poly(lactide-co-glycolide) and, liposome-based systems. Viral and non-viral delivery systems may be combined where it is desirable to provide booster injections after an initial vaccination, for example an initial “prime” DNA vaccination using a non-viral vector such as a plasmid followed by one or more “boost” vaccinations using a viral vector or non-viral based system.
  • A nucleic acid sequence of the present invention may also be administered by means of transformed cells. Such cells include cells harvested from a subject. The naked polynucleotide or vector of the present invention can be introduced into such cells in vitro and the transformed cells can later be returned to the subject. The polynucleotide of the invention may integrate into nucleic acid already present in a cell by homologous recombination events. A transformed cell may, if desired, be grown up in vitro and one or more of the resultant cells may be used in the present invention. Cells can be provided at an appropriate site in a patient by known surgical or microsurgical techniques (e.g. grafting, micro-injection, etc.)
  • The pharmaceutical compositions of the present invention may include adjuvant compounds, or other substances which may serve to increase the immune response induced by the protein which is encoded by the DNA. These may be encoded by the DNA, either separately from or as a fusion with the antigen, or may be included as non-DNA elements of the formulation. Examples of adjuvant-type substances which may be included in the formulations of the present invention include ubiquitin, lysosomal associated membrane protein (LAMP), hepatitis B virus core antigen, FLT3-ligand (a cytokine important in the generation of professional antigen presenting cells, particularly dentritic cells) and other cytokines such as IFN-γ and GMCSF.
  • Examples of other mite allergens that may be codon optimised according to the methods of the present invention are DerF3 and DP15. DerF3 is a serine protease from Dermatophagoides farinae (accession D63858NID/g1311456). DP15 is major allergen p Dp 15=glutathione S-transferase homolog from Dermatophagoides pteronyssinus (accession S75286/g807137).
  • The codon usage pattern of DerF3 and DP15 are shown in the following table:
    χ2 value of χ2 value of native Limit χ2 value for
    native DerF3 DP15 significance (5%)
    Ala 10.6 3.4 7.81
    Cys 4.7 0.5 3.84
    Asp 17.5 8.0 3.84
    Glu 11.5 8.2 3.84
    Phe 4 4.7 3.84
    Gly 25.7 11.3 7.81
    His 9.6 3.0 3.84
    Ile 16.0 8.9 5.99
    Lys 14.6 10.2 3.84
    Leu 22.4 12.7 11.1
    Asn 9.9 15.2 3.84
    Pro 9.4 6.3 7.81
    Gln 16.1 10.9 3.84
    Arg 12 13.7 11.1
    Ser 21.1 4.3 11.1
    Thr 7.3 3.0 7.81
    Val 19 5.9 7.81
    Tyr 9.2 12.7 3.84

    Values in bold are statistically significant (amino acids that are not codon optimised)
  • Optimised genes may be designed using a Visual Basic program called Calcgene, written by R. S. Hale and G Thompson (Protein Expression and Purification Vol. 12 pp. 185-188 (1998)). For each amino acid residue in the original sequence, a codon was assigned based on the probability of it appearing in highly expressed mammalian or human genes. Details of the program, which works under Microsoft Windows 3.1, can be obtained from the authors. In this article, certain rare codons were excluded from the optimisation process to obviate the possibility of generating clusters of rare codons together which would otherwise prejudice the efficient expression of the gene. In the context of this invention, therefore, either the man skilled in the art can visually check the sequence of the polynucleotide to verify that no clusters of rare codons were present in the optimised gene, or alternatively, one or more rare codons may be excluded from the optimisation process.
    • REFERENCES
    • 1. Platt-Mills and Chapman, J Allergy Clin Immunol 1987; 80:755-775.
    • 2. Chapman et al., J Allergy Clin Immunol 1983; 72: 27-33.
    • 3. Krillis et al., J Allergy Clin Immunol 1984; 74:132-141.
    • 4. Shakib et al., Immunol Today 1998; 19:313-316.
    • 5. Gouch et al., J Exp Med 1999; 12:1897-1901.
    • 6. Chua Ket al., J Exp Med 1988; 167:175-182.
    • 7. Chua et al., Int Arch Allergy Immunol 1993; 101:364-368.
    • 8. Chapman and Platts-Mills, J Immunol 1980; 125:587-592.
    • 9. Chapman et al., Int Arch Allergy Immunol 1997; 113:102-104.
    • 10. Greene et al., J Immunol 1991; 147:3768-3773.
    • 11. Chua et al., J Allergy Clin Immunol 1992; 89:95-102.
    • 12. Scobie et al., Biochem Soc Trans 1994; 22:448S
    • 13. Jacquet et al., Clin Exp Allergy 2000; 30:677-684.
    • 14. Sharp and L1, Nucleic Acids Res 1987; 15:1281-1295.
    • 15. Cherry M: Codon usage and frequency of codon occurrence, In Ausubel F M, Brent R, Kingston R E, Moore D D, Seidman J G, Smith J A, Struhl K (ed.), Current protocols in molecular biology. John Wiley & Sons, Inc., New York, N.Y., 1992, p. A1.8-A1.9.
    • 16. Cockett et al., Biotechnology 1990; 8:662-667
    • 17. Jeannin et al., Mol Immunol 1993; 30:1511-18.
    • 18. Palermo et al., J Biotechnol 1991; 19:35-47.
    • 19. Chambers et al., Biochem Soc Trans 1997; 25:85S.
    • 20. Schulz et al., Mol Pathol 1998; 51:222-224.
    • 21. Hauser H: Heterologous expression of genes in mammalian cells. in Hauser H, Wagner R ed, Mammalian cell biotechnology in protein production. De Gruyter, Berlin, New-York, 1997, p 1-27
    • 22. Holm L, Nucleic Acids Res 1986; 14:3075-3087.
    • 23. Haas et al., Current Biology 1996; 6:315-324.
    • 24. Zhou et al., J Virol 1999; 73:4972-4982.
    • 25. zur Megede et al., J Virol 2000; 74:2628-2635.
    • 26. Smith D, Biotechnol Prog 1996; 12:417-422.
    • 27. Kleber-Janke and Becker, Prot Expr Purif 2000; 19:419-424.
    • 28. Vailes et al., Proceedings of the XVIIth International Congress of Allergology and Clinical Immunology, Sidney, 2000.
    • 29. Bond et al., Mol Immunol 1993; 30:1529-1541.
    • 30. Takahashi et al., Int Arch Allergy Immunol 2000; 122:108-114.
    • 31. Mita et al., Clin Exp Allergy 2000; 30:1582-1590.
  • The present invention is exemplified but not limited to the following examples.
    • EXAMPLE 1, EXPRESSION OF RecProDerP1 IN COS AND CHO CELLS
  • Construction of ProDer p 1 Synthetic Gene
  • A “humanized” ProDer p 1 gene was synthesized using a set of 14 partially overlapping oligonucleotides. These primers were designed, based on the codon usage of highly expressed human genes, and produced by an 394 DNA/RNA Applied Biosystem synthetizer The degenerately encoded amino acids were not encoded by the most prevalent codons but taking the frequencies of the individual codons into account. For example, histidine residue is encoded by CAC or CAT with a respective frequency of 79% and 21% in highly expressed human genes. Consequently, we attempted to follow the same codon frequency instead of selecting only the CAC codon for each histidine residue in the synthetic ProDer p 1. The native Der p 1 signal sequence was exchanged with the highly efficient leader peptide of the VZV glycoprotein E (gE) to facilitate secretion. The oligonucleotides were the following:
    5′GAAGCTTCGGGCGAATTGCGTGGTTTTAAGTGACT SEQ ID NO. 1
    ATATTCGAGGGTCGCCTGTAATATGGGGACAGTTAAT
    AAACCTGTGGGTGGGGGTATTGATGGGGTTCGGAATT
    ATCACG3′ (oligo 1, coding);
    5′GAAGGCTTTCTTGTATTCCTCGAAGGTCTTAATGG SEQ ID NO. 2
    AGCTCGGCCGTGCTCTGACCGGATTCGTTATACGC A
    AGGTACCCGTGATAATTCCGAACCC3′ (oligo 2,
    non coding);
    5′GGAATACAAGAAAGCCTTCAACAAGAGCTATGCCA SEQ ID NO. 3
    CCTTCGAGGACGAGGAGGCCGCGCGCAAGAACTTCCT
    GGAAAGCGTGAAATACGTGCAGAGC3′ (oligo 3,
    coding);
    5′GTCTTAAGGTGTTCGAAAGCCTCGGCGCTCATCAG SEQ ID NO. 4
    GAACCGGTTCTTGAACTCGTCTAAAGACAGGTCGGAC
    AGGTGATTTATAGCCCCGCCGTTGCTCTGCACGTATT
    TCAC3′ (oligo 4, non coding);
    5′CTTTCGAACACCTTAAGACCCAGTTTGATCTCAAC SEQ ID NO. 5
    GCGGAGACCAACGCCTGCAGTATCAACGG CAATGCC
    CCCGCTGAGATTGATCTGCGCC3′ (oligo 5,
    coding);
    5′GACTCTGTCGCGGCCACGCCTGAAAAGGCCCAACA SEQ ID NO. 6
    CCGACCCGCAGCCGCCTTGCATGCGGATGGGAGTCAC
    GGTCCTCATCTGGCGCAGATCAATCTCAG3′
    (oligo 6, non coding);
    5′GTGGCCGCGACAGAGTCGGCATACCTCGCGTATCG SEQ ID NO. 7
    GAATCAGAGCCTGGACCTCGCTGAGCAGGAGCTCGTT
    GACTGCGCCTCCCAAC ACGG3′ (oligo 7,
    coding);
    5′GCTACGTATCGGTAATAGCTTTCCTGCACGACGCC SEQ ID NO. 8
    ATTATGCTGGATGTATTCGATACCTCTGGGAATCGTA
    TCCCCATGACATCCGTGTTGGGAGGCGC3′ (oligo
    8, non coding);
    5′GCTATTACCGATACGTAGCTAGGGAGCAGTCCTGC SEQ ID NO. 9
    CGCCGTCCTAACGCACAGCGCTTCG GCATTTCCAAT
    TATTGCCAGATCTACC3′ (oligo 9, coding);
    5′CCTTGATTCCGATGATGACAGCGATGGCGCTGTGC SEQ ID NO. 10
    GTCTGCGCCAGGGCCTCCCTGATCTTGTTGGCATTAG
    GGGGGTAGATCTGGCAATAATTG3′ (oligo 10,
    non coding);
    5′GTCATCATCGGAATCAAGGATCTGGACGCATTCCG SEQ ID NO. 11
    GCACTATGACGGGCGCACAATCATCCAGCGCGACAAC
    GGATATCAGCCAAACTACC3′ (oligo 11,
    coding);
    5′GTAGTCCACCCCCTGGGCGTTCGAGTAACCCACGA SEQ ID NO. 12
    TGTTGACCGCGTGGTAGTTTGGCTGATATCC3′
    (oligo 12, non coding);
    5′CCAGGGGGTGGACTACTGGATCGTGAGAAACAGTT SEQ ID NO. 13
    GGGACACTAACTGGGGCGACAACGGCTACGGCTACTT
    CGCCGCCAAC3′ (oligo 13, coding);
    5′GCTCTAGACTCGAGGGATCCTTACAGGATCACCAC SEQ ID NO. 14
    GTACGGGTACTCCTCGATCATCATCAGGTCGATGTTG
    GCGGCGAAGTAGC3′ (oligo 14, non
    coding).
  • The oligonucleotides were incubated together for the amplification of a synthetic ProDer p 1 gene in a PCR reaction. Typically, PCR was conducted using High Fidelity Polymerase (Boehringer) with the following conditions: 30 cycles, denaturation at 94° C. for 30 s, annealing at 50° C. for 30 s and elongation at 72° C. for 30 s. The generated products were amplified using the 3′ and 5′ terminal primers (oligo 1 and 14) in the same conditions. The resulting 1080 bp fragment was cloned into a pCRII-TOPO cloning vector (Invitrogen). The resulting plasmid pNIV4845 was used to transform the E. coli strain TOP 10 (Invitrogen).
  • The sequences of the natural and codon-optimised genes, together with the encoded amino acid sequence are listed below and are SEQ ID NO.s 15, 16, and 17 respectively. The sequences encode the full ProDerP1, and the nucleic acid or amino acid which is underlined indicates the start of the mature DerP1 sequence resulting from the cleavage of the Pro region.
    SEQ ID NO. 15, Natural gene
    CGTCCATCATCGATCAAAACTTTTGAAGAATACAAAAAAGCCTTCAACAA
    AAGTTATGCTACCTTCGAAGATGAAGAAGCTGCCCGTAAAAACTTTTTGG
    AATCAGTAAAATATGTTCAATCAAATGGAGGTGCCATCAACCATTTGTCC
    GATTTGTCGTTGGATGAATTCAAAAACCGATTTTTGATGAGTGCAGAAGC
    TTTTGAACACCTCAAAACTCAATTCGATTTGAATGCTGAAACTAACGCCT
    GCAGTATCAATGGAAATGCTCCAGCTGAAATCGATTTGCGACAAATGCGA
    ACTGTCACTCCCATTCGTATGCAAGGAGGCTGTGGTTCATGTTGGGCTTT
    CTCTGGTGTTGCCGCAACTGAATCAGCTTATTTGGCTTACCGTAATCAAT
    CATTGGATCTTGCTGAACAAGAATTAGTCGATTGTGCTTCCCAACACGGT
    TGTCATGGTGATACCATTCCACGTGGTATTGAATACATCCAACATAATGG
    TGTCGTCCAAGAAAGCTACTATCGATACGTTGCACGAGAACAATCATGCC
    GACGACCAAATGCACAACGTTTCGGTATCTCAAACTATTGCCAAATTTAC
    CCACCAAATGTAAACAAAATTCGTGAAGCTTTGGCTCAAACCCACAGCGC
    TATTGCCGTCATTATTGGCATCAAAGATTTAGACGCATTCCGTCATTATG
    ATGGCCGAACAATCATTCAACGCGATAATGGTTACCAACCAAACTATCAC
    GCTGTCAACATTGTTGGTTACAGTAACGCACAAGGTGTCGATTATTGGAT
    CGTACGAAACAGTTGGGATACCAATTGGGGTGATAATGGTTACGGTTATT
    TTGCTGCCAACATCGATTTGATGATGATTGAAGAATATCCATATGTTGTC
    ATTCTCTAA
    SEQ ID NO 16, Synthetic gene
    CGGCCGAGCTCCATTAAGACCTTCGAGGAATACAAGAAAGCCTTCAACAA
    GAGCTATGCCACCTTCGAGGACGAGGAGGCCGCGCGCAAGAACTTCCTGG
    AAAGCGTGAAATACGTGCAGAGCAACGGCGGGGCTATAAATCACCTGTCC
    GACCTGTCTTTAGACGAGTTCAAGAACCGGTTCCTGATGAGCGCCGAGGC
    TTTCGAACACCTTAAGACCCAGTTTGATCTCAACGCGGAGACCAACGCCT
    GCAGTATCAACGGCAATGCCCCCGCTGAGATTGATCTGCGCCAGATGAGG
    ACCGTGACTCCCATCCGCATGCAAGGCGGCTGCGGGTCTTGTTGGGCCTT
    TTCAGGCGTGGCCGCGACAGAGTCGGCATACCTCGCGTATCGGAATCAGA
    GCCTGGACCTCGCTGAGCAGGAGCTCGTTGACTGCGCCTCCCAACACGGA
    TGTCATGGGGATACGATTCCCAGAGGTATCGAATACATCCAGCATAATGG
    CGTCGTGCAGGAAAGCTATTACCGATACGTAGCTAGGGAGCAGTCCTGCC
    GCCGTCCTAACGCACAGCGCTTCGGCATTTCCAATTATTGCCAGATCTAC
    CCCCCTAATGCCAACAAGATCAGGGAGGCCCTGGCGCAGACGCACAGCGC
    CATCGCTGTCATCATCGGAATCAAGGATCTGGACGCATTCCGGCACTATG
    ACGGGCGCACAATCATCCAGCGCGACAACGGATATCAGCCAAACTACCAC
    GCGGTCAACATCGTGGGTTACTCGAACGCCCAGGGGGTGGACTACTGGAT
    CGTGAGAAACAGTTGGGACACTAACTGGGGCGACAACGGCTACGGCTACT
    TCGCCGCCAACATCGACCTGATGATGATCGAGGAGTACCCGTACGTGGTG
    ATCCTGTAA
    SEQ ID NO. 17, protein sequence
    RPSSIKTFEEYKKAFNKSYATFEDEEAARKNFLESVKYVQSNGGAINHLS
    DLSLDEFKNRFLMSAEAFEHLKTQFDLNAETNACSINGNAPAEIDLRQMR
    TVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLAEQELVDCASQHG
    CHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQRFGISNYCQIY
    PPNANKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDNGYQPNYH
    AVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLMMIEEYPYVV
    IL

    Construction of Humanized ProDer p 1 Expression Vector.
  • As the sequencing of eight bacterial clones demonstrated some mutations in the synthetic ProDer p 1 gene, the plasmid for stable expression was generated starting from four ProDer p 1 DNA fragments derived from bacterial clones carrying pNIV4845. Clones n°5 and n°20 were respectively submitted to double digestions by HindIII-BssHII and SphI-BglII, to isolate the 228 bp HindIII-BssHII and 272 bp SphI-BglII ProDer p 1 DNA fragments. Clone n°7 was restricted with BssHII-SphI and BglII-XbaI to generate the 239 bp BssHII-SphI and 329 bp BglII-XbaI ProDer p 1 DNA fragments. These fragments were inserted into the HindIII-XbaI cut pEE14 expression vector (Celltech) [16] to give the final plasmid pNIV4846. The correct recombinants were confirmed by DNA sequencing.
  • Transient Transfections and Selection of RecProDer p 1-Producing Stable CHO-K1 Lines.
  • To determine the expression levels of recProDer p 1, COS cells (ATCC) were transiently transfected with 10 μg of pNIV4846 or pNIV4853, a plasmid carrying authentic ProDer p 1 gene, by calcium phosphate coprecipitation. For stable recProDer p 1 expression, CHO-K1 cells (ATCC) were transfected with pNIV4846 plasmid by lipofection. After a 3-weeks 25 μM methionylsulphoximin (MSX, Sigma) selection, one round of gene amplification was carried out with 100 μM MSX.
  • Expression of the Recombinant Allergen in CHO Cells.
  • The best producing recombinant CHO-K1 clone was cultured in cell factories in GMEM medium (Invitrogen) supplemented with 2% fetal calf serum (Gibco). Spent culture medium was harvested every 72 h and stored at −20° C. until purification.
  • Purification of Natural Der p 1 from Natural Mite Whole Body Extracts.
  • Purification of natural Der p 1 from whole mite culture was performed as previously described [13]. Briefly, D. pteronyssinus extracts were submitted to (NH4)2SO4 precipitation to 60% saturation. The precipitate, collected by ultracentrifugation and resuspended in PBS containing (NH4)2SO4 1M, was applied onto a Resource Phenyl column (Pharmacia) equilibrated in PBS containing (NH4)2SO4 1M. Der p 1 was eluted from the column with water. After the pH and conductivity adjustments of the Der p 1-enriched fractions, the pool was applied onto a Q sepharose fast flow column (Pharmacia) equilibrated in 20 mM Tris-HCl pH 9. Der p 1 was eluted by addition of 200 mM NaCl in the starting buffer. The Der p 1 purification was achieved by a gel filtration chromatography onto a superdex-75 column (Pharmacia) equilibrated in PBS pH 7.3. Purified Der p 1 was concentrated and stored at −20° C.
  • Purification of RecProDer p 1 from CHO Spent Culture Medium.
  • CHO spent culture medium was diluted two times with water and the pH was adjusted to 7.2. The modified supernatant was loaded onto a Q sepharose fast flow column (5×10 cm, Pharmacia) equilibrated in 20 mM Tris-HCl pH 7.2 which is coupled to a hydroxyapatite column (2.6×15 cm, Bio-Rad) conditioned in the same buffer. The flow-through containing recProDer p 1 of both columns was adjusted to pH 9 and applied onto a Q sepharose fast flow column (1.6×10 cm) equilibrated in 20 mM Tris-HCl pH 9. The column was washed with the starting buffer and with the same buffer supplemented with 100 mM NaCl. ProDer p 1 was eluted by a linear NaCl gradient (100-300 mM, 15 column volumes). The recProDer p 1-enriched fractions were pooled and concentrated by ultrafiltration onto a Filtron membrane (Omega serie, cut-off: 10 kD). The recProDer p 1 purification was achieved by a gel filtration chromatography onto a superdex-75 column (1×30 cm, Pharmacia) equilibrated in PBS pH 7.3. Purified recProDer p 1 was concentrated and stored at −20° C.
  • SDS PAGE and Western Blot Analysis
  • Proteins were analyzed by SDS-PAGE on 12.5% polyacrylamide gels. After electrophoresis, proteins were transferred onto nitrocellulose membranes using a semi-dry transblot system (Bio-Rad). Membranes were saturated for 30 min with 0.5% Instagel (PB Gelatins) in TBS-T (50 mM Tris HCl pH 7.5, 150 mM NaCl, 0.1% Tween 80) and incubated with rabbit polyclonal serum raised against Der p 1 peptide 245-267 diluted in blocking solution (1:5000) (Kindly provided by Dr Pestel, Institut Pasteur de Lille, France) [17]. Immunoreactive materials were detected using alkaline phosphatase-conjugated goat anti-rabbit antibodies (Promega, 1:7500) and 5-bromo,4-chloro,3-indolylphosphate (BCIP, Boehringer)/nitroblue tetrazolium (NBT, Sigma) as substrates.
  • Glycan Analysis
  • Carbohydrate analysis was carried out with the Glycan Differenciation Kit (Boehringer) using the following lectins: Galanthus nivalis agglutinin (GNA), Sambucus nigra agglutinin (SNA), Maackia amurensis agglutinin (MAA), Peanut agglutinin (PNA) and Datura stramonium agglutinin (DSA). Briefly, purified proteins were transferred from SDS-PAGE onto nitrocellulose membranes. Membranes were incubated with the different lectins conjugated to digoxigenin. Complexes were detected with anti-digoxigenin antibodies conjugated to alkaline phosphatase.
  • Enzymatic Assays
  • Enzymatic assays were performed in 50 mM Tris-HCl pH 7, containing 1 mM EDTA and 20 mM L-cysteine at 25° C. in a total volume of 1 ml. Hydrolysis of Cbz-Phe-Arg-7-amino-4-methylcoumarin (Cbz-Phe-Arg-AMC) and Boc-Gln-Ala-Arg-7-amino-4-methylcoumarin (Boc-Gln-Ala-Arg-AMC) (Sigma) (both substrates at a final concentration of 100 μM) was monitored using a SLM 8000 spectrofluorimeter with λex=380 nm and λem=460 nm. Assays were started by addition of cysteine activated allergen to a final concentration of 100 nM. Before any assay, purified Der p 1 or recProDer p 1 was incubated with a mixture of aprotinin- and p-aminobenzamidine-agarose resins (Sigma) to remove any putative trace of serine protease activity.
  • Protein Determination
  • Total protein concentration was determined by the bicinchoninic acid procedure (MicroBCA, Pierce) with bovine serum albumin as standard.
  • Der p 1 ELISA
  • Der p 1 or recProDer p 1 was detected with an ELISA kit using Der p 1 specific monoclonal antibodies 5H8 and 4C1 (Indoor Biotechnologies). The Der p 1 standard (UVA 93/03) used in the assay was at a concentration of 2.5 μg/ml.
  • IgE-Binding Activity.
  • Immunoplates were coated overnight with Der p 1 or recProDer p 1 (500 ng/well) at 4° C. Plates were then washed 5 times with 100 μl per well of TBS-Tween buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.1% Tween 80) and saturated for 1 hr at 37° C. with 150 μl of the same buffer supplemented with 1% BSA (Sigma). Sera from allergic patients to D. pteronyssinus and diluted at 1/8 were then incubated for 1 hr at 37° C. Out of the 95 sera used in the experiments, 16 sera ranged in their specific anti-D. pteronyssinus IgE values (RAST assays) from 58.1 kU/L to 99 kU/L and 79 above the upper cut-off value of 100 kU/L. Plates were washed 5 times with TBS-Tween buffer and the allergen-IgE complexes were detected after incubation with a mouse anti-human IgE antibody (Southern Biotechnology Associates) and a goat anti-mouse IgG antibody coupled to alkaline phosphatase (dilution 1/7500 in TBS-Tween buffer, Promega). The enzymatic activity was measured using the p-nitrophenylphosphate substrate (Sigma) dissolved in diethanolamine buffer (pH 9.8). OD410 nm was measured in a Biorad Novapath ELISA reader.
  • For IgE inhibition assays, plates were coated with Der p 1 or recProDer p 1 at the same concentration (0.12 μM). A pool of 20 human sera from allergic patients (RAST value>100 kU/L) was preincubated overnight at 4° C. with various concentrations (3.6-0.002 μM) of Der p 1 or recProDer p 1 as inhibitors and added on ELISA plates. IgE-binding was detected as described above.
  • Histamine Release
  • The histamine release was assayed using leukocytes from the peripheral heparinized blood of an allergic donor and by the Histamine-ELISA kit (Immunotech). Basophils were incubated with serial dilutions of recProDer p 1 or Der p 1 for 30 min at 37° C. The total amount of histamine in basophils was quantified after cell disruption with the detergent IGEPAL CA-630 (Sigma).
    • RESULTS
  • Synthesis of Humanized ProDer p 1 Gene.
  • The codon prevalence of ProDer p 1 gene displayed many divergences compared with that used for highly expressed human genes (FIG. 1). In consequence, oligonucleotides were designed for the construction of a synthetic ProDer p 1 gene to optimise the allergen expression in mammalian cells. As shown in FIG. 1, the final codon frequency in the synthetic ProDer p 1 gene was very similar to that used in highly expressed mammalian genes.
  • The synthetic ProDer p 1 was assembled from mutually priming oligonucleotides that were subsequently amplified by PCR (FIG. 2). After one round of PCR, amplified products displayed a molecular weight ranging from 3000 to 300 bp. A subsequent amplification with primers complementary to the 5′ end of VZV gE leader peptide and to the 3′ end of synthetic ProDer p 1 gene led to a 1072 bp fragment of excepted size. The amplified fragment was cloned into the pCRII cloning vector. Sequence analysis of recombinant clones revealed the presence of point mutations and deletions in the synthetic ProDer p 1 gene. Finally, the correct coding cassette was obtained after ligation of 4 different fragments isolated from 3 independent bacterial clones, and inserted in the mammalian expression vector pEE14 to give the final plasmid pNIV4846.
  • Transient and Stable Expression of RecProDer p 1
  • To compare the expression efficiency of the synthetic ProDer p 1 construct with the original sequence, COS cells were transfected with pNIV4846 and pNIV4853, a pEE14-derived plasmid carrying authentic ProDer p 1 cDNA. The recProDer p 1 expression level of the supernatants was estimated by an ELISA assay, using two anti-Der p 1 monoclonal antibodies. As shown in FIG. 3, the expression vector carrying the synthetic cDNA directed the recProDer p 1 synthesis more efficiently than the same vector containing the authentic gene. The expression level of humanized ProDer p 1 gene was enhanced up to 450 ng/ml/72 h which represents a 6-fold increase compared with the reference construction (75 ng/ml/72 h). As expected, no recProDer p 1 expression was detected using COS cells transfected by a control vector without any insert.
  • CHO-K1 cells were transfected with pNIV4846 and clones resistant to 25 μM MSX were selected. The recProDer p 1 level assayed by ELISA indicated that three independent clones secreted recProDer p 1 up to 11 μg/ml/72 h. Addition of sodium butyrate, a molecule previously reported to enhance expression level of recombinant proteins in culture medium [18], did not influence the recProDer p 1 synthesis. A further amplification of 25 μM MSX-resistant clones up to 100 μM MSX increased expression, raising 26 to 34 μg/ml/72 h recProDer p 1 in culture medium. The clone n°1 was used for recProDer p 1 large-scale production in cell factories and purification. Spent culture medium was collected every 72 h and up to 9 harvests were performed. In these conditions, the best recProDer p 1 expression level raised 15 μg/ml in the culture medium before purification.
  • Purification of RecProDer p 1.
  • Purification of recProDer p 1 was achieved by a combination of three chromatographic steps, using anion-exchange, hydroxyapatite and gel filtration media. The final purification yield was about 6 mg of recProDer p 1 per litre of culture medium with a recovery close to 40%. On SDS PAGE, purified recProDer p 1 migrated as three immunoreactive species: two major bands with a respective molecular weight of 41 and 36 kD and one minor band of 38 kD (FIG. 4). This result indicated that the propeptide cleavage, to yield mature Der p 1, did not occur during the expression and purification steps, as natural Der p 1 migrated on SDS PAGE as a 29 kD band. The purity of the product was higher than 90%.
  • Biochemical Characterization of ProDer p 1
  • All the recProDer p 1 species were submitted to an amino-terminal amino acid sequencing. The N-terminal sequence of 41 and 38 kDa species were identical and started at residue Arg19. The sequence was identified as Arg-Pro-Ser-Ser-Ile, which corresponds to the N-terminal sequence of the Der p 1 propeptide and indicates that cleavage of VZV gE signal peptide proceeded efficiently. Surprisingly, the N-terminal sequence of the 36 kDa band started at residue Ala38 (the obtained sequence was Ala-Thr-Phe-Glu-Asp) showing that, for the 36 kDa molecule, an internal cleavage of the prosequence occurred between Tyr37 and Ala38. Carbohydrate analysis of recProDer p 1 was performed by glycan recognition with several specific lectins. Among the five lectins used, only the GNA lectin reacted with the 36 kDa recProDer p 1, pointing to the presence of terminal mannose residues on this molecule, either as high-mannose N-glycan chains or as exposed mannose in hybrid chains (FIG. 5). The 38 and 41 kDa bands were recognized respectively by the DSA and MAA lectins, showing that the 38 kDa molecule carried terminal galactose linked β(1-4) to N-acetyl-glucosamine in N-glycan chains whereas the carbohydrate structure of the upper band was terminated by sialic acid linked α(2-3) to galactose. As previously showed [13], Der p 1 did not react with any lectin confirming that Der p 1 is not glycosylated.
  • The enzymatic activity of recProDer p 1 was measured using Cbz-Phe-Arg-AMC and Boc-Gln-Ala-Arg-AMC as substrates [19,20]. As expected, because of the presence of the Pro region, RecProDer p 1 was totally inactive in our assays. In the same experimental conditions, fluorogenic molecules were fully degraded within 4 min by natural Der p 1 used at the same molarity.
  • IgG- and IgE-Reactivities of RecProDer p 1
  • RecProDer p 1 was tested in ELISA assays to determine whether the recombinant allergen displayed reactivities similar to those of Der p 1 towards specific anti-Der p 1 IgG and anti-Dermatophagoides pteronyssinus IgE. As shown in FIG. 6, equimolar concentrations of both allergens reacted similarly with two Der p 1 specific monoclonal and conformational antibodies, suggesting that recProDer p 1 displayed the overall structure of the natural allergen. The IgE reactivity of recProDer p 1 and Der p 1 was compared in a direct ELISA wherein immunoplates were directly coated with Der p 1 or recProDer p 1. A set of 95 human sera with positive radioimmunosorbent tests to D. pteronyssinus extract was used at dilution 1:8. IgE titer determinations clearly showed a close correlation of IgE reactivity with both allergens, indicating that recProDer p 1 has very similar IgE binding characteristics compared with Der p 1 (R2=0.8171, P<0.0001) (FIG. 7).
  • Histamine Releasing Activity of RecProDer p 1
  • To compare the allergenic activity of natural Der p 1 and recProDer p 1, basophils from one allergic patient were challenged in vitro with various concentrations of both allergens and the released histamine was measured. Natural Der p 1 was able to induce histamine release from basophils even at a concentration of 1 ng/ml. By contrast, recProDer p 1 could only release histamine at 1000-fold higher concentration (FIG. 8). From this result, recProDer p 1 was shown to be less allergenic that the natural Der p 1.
    • EXAMPLE 2, EXPRESSION OF RecProDerP1 IN Pichia pastoris
  • Construction of ProDer p 1 Expression Vector
  • The ProDer p 1 coding cassette from pNIV4846 (full-length 1-302aa ProDer p 1 cDNA with optimised mammalian codon usage) was amplified by PCR using the following primers: 5′ACTGACAGGCCTCGGCCGAGCTCCATTAA3′ (SEQ ID NO. 18) (StuI restriction site in bold, forward) and 5′CAGTCACCTAGGTCTAGACTCGAGGGGAT3′ (SEQ ID NO. 19) (AvrII restriction site in bold, reverse). The amplified fragment was cloned into the pCR2.1 TOPO cloning vector. The correct ProDer p 1 cassette was verified by DNA sequencing. Recombinant TOPO vector was digested with StuI-AvrII to generate a 918 bp fragment which was introduced into the pPIC9K expression vector restricted with SnaBI-AvrII. The resulting plasmid, pNIV4878, contains the ProDer p 1 cassette downstream to the S. cerevisae α factor
  • Site-Directed Mutagenesis
  • Expression plasmid for the production of unglycosylated ProDer p 1 (N52Q, mature Der p 1 numbering) was derived from pNIV4878 by overlap extension PCR using a set of four primers. The following primers: 5′GGCTTTCGAACACCTTAAGACCCAG3′ (SEQ ID NO. 20) (primer 1, AflII restriction site in bold, forward) and 5′GCTCCCTAGCTACGTA TCGGTAATAGC3′ (SEQ ID NO. 21) (primer 2, SnaBI restriction site in bold, reverse) were used to amplify a 317 bp fragment encoding the ProDer p 1 amino acid sequence 71-176. The following primers 5′CCTCGCGTATCGGCAACAGAGCCTGGACC3′ (SEQ ID NO. 22) (primer 3, mutation N52Q in bold, forward) and 5′GGTCCAGGCTCT GTTGCCGATACGCGAGG3′ (SEQ ID NO. 23) (primer 4, mutation N52Q in bold, reverse) were used to introduce mutation N52Q in the ProDer p 1 sequence.
  • The mutated 317 bp AflII-SnaBI fragment was generated by a three-step process. In PCR n°1, primers 1 and 4 were mixed with pNIV4878 to produce a 200 bp fragment. In PCR n°2, primers 2 and 3 were mixed with pNIV4878 to produce a 140 bp. The two PCR products were purified onto agarose gel and used as templates for a third round of PCR to obtain a ˜340 bp fragment. This purified fragment was cloned into the pCR2.1 TOPO cloning vector. The mutation was verified by DNA sequencing. Recombinant TOPO vector was digested with AflII-SnaBI to generate a 317 bp fragment which was ligated into the similarly digested pNIV4878. The resulting plasmid, pNIV4883, contains the ProDer p 1 N52Q downstream to the S. cerevisae α factor
  • To obtain unglycosylated variants of ProDer p 1 carrying mutations of Der p 1 cysteine residues at position 4, 31 or 65 (mature Der p 1 numbering), overlap extension PCR using the same set of primers were performed with plasmids pNIV4873, pNIV4875 and pNIV4874. The resulting plasmids pNIV4884, 4885 and 4886 encode respectively ProDer p 1 N52Q C4R, N52Q C31R and N52Q C65R.
  • Transformation of P. pastoris
  • Plasmid pNIV4878 was introduced into P. pastoris using the spheroplast transformation method. Transformants were selected for histidinol deshydrogenase (His+) prototrophy. The screening of His+ transformants for geneticin (G418) resistance was performed by plating clones on agar containing increasing concentrations of G418.
  • Production of ProDer p 1 by Recombinant Yeast
  • G418 resistant clones were grown at 30° C. in BMG medium to an OD600 nm of 2-6. Cells were collected by centrifugation and resuspended to an OD600 nm of 1 in 100 ml of BMG medium. Proder p 1 expression was induced by daily addition of methanol 0.5% for 6 days. The supernatant was collected by centrifugation and stored at −20° C. until purification.
  • Purification of ProDer p 1 from Yeast Culture Supernatant
  • Supernatants were diluted 10 times with water and, after pH adjustment to 9, directly loaded onto a Q sepharose column equilibrated in 20 mM Tris-HCl pH 9. The column was washed with the starting buffer. Protein elutions proceeded by step-wise increasing NaCl concentration in the buffer. The ProDer p 1-enriched fractions were pooled and concentrated by ultrafiltration onto a Filtron membrane (Omega serie, cut-off: 10 kD). The ProDer p 1 purification was achieved by a gel filtration chromatography onto a superdex-75 column (1×30 cm, Pharmacia) equilibrated in PBS pH 7.3. Purified ProDer p 1 was concentrated and stored at −20° C. Surprisingly, given the fact that yeast codon usage is significantly different from the human profile, this humanized ProDerP1 expressed very well in this system with a high yield of protein.
  • Discussion
  • The inability to obtain large amounts of Der p 1, the major allergen from D. pteronyssinus is a major obstacle for the development of biochemical and immunological studies. Indeed, whole mite culture is cost effective, the growth rate is slow and the purification yield of native Der p 1 is relatively low, about 1 mg Der p 1 being purified from 1 gram of whole mite culture in our experimental conditions. Moreover, previous attempts of Der p 1 expression in bacteria and yeast indicated that the allergen was poorly expressed and mainly under an insoluble form [10-12].
  • The present study clearly reports that production of recProDer p 1 in mammalian cells is very low indicating that the presence of prosequence is not sufficient to induce high-level recProDer p 1 expression.
  • The codon prevalence of the Proder p 1 gene was different from that most frequently used in highly expressed human genes. To assess the importance of an appropriate codon usage for the recProDer p 1 expression in CHO cells, we decided to engineer a synthetic ProDer p 1 gene based on the mammalian prevalent codons. Our results clearly demonstrate that codon optimisation is beneficial to induce high-level expression of recProDer p 1 in mammalian cells.
  • In summary, codon usage optimisation can induces high-level expression of recProDer p 1, an allergen difficult to produce in CHO cells. This strategy could also be applicable for expression of other allergens and could be extrapolate to other expression systems. Synthetic genes with appropriate codons could thus provide new tools for allergy diagnosis and specific immunotherapy.
  • RecProDer p 1, immobilized on solid phases, could substitute natural Der p 1 in diagnostic test for the detection of specific IgE. Considering the reduced recProDer p 1 anaphylactogenic potential, this recombinant allergen could be used in the future as alternative reagents for immunotherapy to replace the commonly used allergen extracts.

Claims (7)

1. An isolated polynucleotide sequence which encodes a Dermatophagoides mite protein, wherein the codon usage pattern of the polynucleotide sequence resembles that of highly expressed mammalian genes.
2. An isolated polynucleic acid sequence as claimed in claim 1, wherein all of the amino acid types present in the protein are optimised, such that the codons used to encode that amino acid are used in the same frequency as the known mammalian frequency for that amino acid.
3. An isolated polynucleic acid sequence as claimed in claim 1, wherein the yield of protein encoded by the polynucleic acid when expressed by an expression system is greater than 20% higher than the amount of protein produced from the same expression system using a non-optimised native gene for that Dermatophagoides protein.
4. An isolated polynucleic acid sequence encoding a Dermaphagoides protein, characterised in that the codons present in said polynucleotide which are used to encode each amino acid are selected to appear as set forth in the following table
Amino Frequency Acid Codon (percentage used) Ala GCG 17 GCA 13 GCT 17 GCC 53 Arg AGG 18 AGA 10 CGG 21 CGA 6 CGT 7 CGC 37 Asn AAT 22 AAC 78 Asp GAT 25 GAC 75 Cys TGT 32 TGC 68 Gln CAG 88 CAA 12 Glu GAG 75 GAA 25 Gly GGG 24 GGA 14 GGT 12 GGC 50 His CAT 21 CAC 79 Ile ATA 5 ATT 18 ATC 77 Leu TTG 6 TTA 2 CTG 58 CTA 3 CTT 5 CTC 26 Lys AAG 82 AAA 18 Phe TTT 20 TTC 80 Pro CCG 17 CCA 16 CCT 19 CCC 48 Ser AGT 10 AGC 34 TCG 9 TCA 5 TCT 13 TCC 28 Thr ACG 15 ACA 14 ACT 14 ACC 57 Tyr TAT 26 TAC 74 Val GTG 64 GTA 5 GTT 7 GTC 25
5. An isolated polynucleotide comprising SEQ ID NO: 15.
6. An isolated vector comprising the isolated polynucleotide of claim 5.
7. An isolated host cell comprising the vector of claim 6.
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Families Citing this family (14)

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Publication number Priority date Publication date Assignee Title
GB0014288D0 (en) * 2000-06-10 2000-08-02 Smithkline Beecham Biolog Vaccine
GB0120150D0 (en) * 2001-08-17 2001-10-10 Glaxosmithkline Biolog Sa Novel compounds
CA2457890A1 (en) * 2001-08-23 2003-03-06 Merck & Co., Inc. Vaccine using papillomavirus e proteins delivered by viral vector
FR2841906B1 (en) * 2002-07-05 2006-08-18 Stallergenes Sa NUCLEIC ACID MOLECULE ENCODING AN ALLERGENE PREPROPROTEIN OF A MITER OF THE GENUS DERMATOPHAGOIDES OR EUROGLYPHUS AND USE THEREOF FOR THE PRODUCTION OF SAID ALLERGEN IN PLANTS
GB0304424D0 (en) * 2003-02-26 2003-04-02 Glaxosmithkline Biolog Sa Novel compounds
US20050053615A1 (en) * 2003-07-16 2005-03-10 Best Elaine A. Variants of mite group 1 allergens for the treatment of house dust mite allergy
BRPI0507466A (en) * 2004-02-04 2007-07-10 Gen Hospital Corp compositions and methods for modifying polyunsaturated fatty acid content in biological cells
US7527947B2 (en) * 2004-06-14 2009-05-05 Novozymes A/S Signal peptide for producing a polypeptide
EP2410048B1 (en) * 2005-01-24 2016-08-10 DSM IP Assets B.V. Method for producing a compound of interest in a filamentous fungal cell
AU2007207785B2 (en) 2006-01-13 2013-11-14 The Government Of The United States, As Represented By The Secretary Of The Department Of Health And Human Services, National Institutes Of Health Codon optimized IL- 15 and IL- 15R-alpha genes for expression in mammalian cells
EP2388268A1 (en) * 2010-05-18 2011-11-23 Stallergenes S.A. Recombinant Der p 2 expressed in Pichia pastoris as a "natural-like" allergen for immunotherapy and diagnostic purposes
EP2607375A1 (en) 2011-12-21 2013-06-26 The Provost, Fellows, Foundation Scholars, & the other members of Board, of the College of the Holy & Undiv. Trinity of Queen Elizabeth near Dublin Variants of yeast NDI1 gene, and uses thereof in the treatment of disease associated with mitochondrial dysfunction.
CN114107352A (en) * 2012-04-17 2022-03-01 弗·哈夫曼-拉罗切有限公司 Methods of expressing polypeptides using modified nucleic acids
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Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5433948A (en) * 1990-02-13 1995-07-18 Thomas; Wayne R. Cloning and sequencing of allergens of dermatophagoides (house dust mite)
US5968526A (en) * 1994-04-14 1999-10-19 Immulogic Pharamaceutical Corporation T cell epitopes of the major allergens from Dermatophagoides (house dust mite)
US6455686B1 (en) * 1998-04-17 2002-09-24 Heska Corporation Dermatophagoides nucleic acid molecules, proteins and uses thereof
US7173117B2 (en) * 2000-06-10 2007-02-06 Glaxosmithkline Biologicals S.A. Codon optimised recombinant Dermaphagoides allergens

Family Cites Families (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1988010297A1 (en) 1987-06-17 1988-12-29 Princess Margaret Children's Medical Research Foun Cloning of mite allergens
US5697901A (en) 1989-12-14 1997-12-16 Elof Eriksson Gene delivery by microneedle injection
JP2596466B2 (en) 1990-03-03 1997-04-02 アサヒビール株式会社 DNA having transfer information of major allergen of mite and method for producing the allergen
DE69133333T2 (en) * 1991-08-26 2004-07-29 Baxter Healthcare S.A. A bird pox recombinant virus containing an intact FPV-tk gene
AU729231B2 (en) 1996-02-22 2001-01-25 Merck & Co., Inc. Synthetic HIV genes
EP0912607A2 (en) 1996-06-21 1999-05-06 Merck & Co., Inc. Vaccines comprising synthetic genes
AU743616B2 (en) 1997-02-07 2002-01-31 Merck & Co., Inc. Synthetic HIV gag genes
GB9724531D0 (en) 1997-11-19 1998-01-21 Smithkline Biolog Novel compounds

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5433948A (en) * 1990-02-13 1995-07-18 Thomas; Wayne R. Cloning and sequencing of allergens of dermatophagoides (house dust mite)
US5968526A (en) * 1994-04-14 1999-10-19 Immulogic Pharamaceutical Corporation T cell epitopes of the major allergens from Dermatophagoides (house dust mite)
US6455686B1 (en) * 1998-04-17 2002-09-24 Heska Corporation Dermatophagoides nucleic acid molecules, proteins and uses thereof
US7173117B2 (en) * 2000-06-10 2007-02-06 Glaxosmithkline Biologicals S.A. Codon optimised recombinant Dermaphagoides allergens

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