US20160289281A1 - Peptide with multiple epitopes - Google Patents

Peptide with multiple epitopes Download PDF

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US20160289281A1
US20160289281A1 US15/095,480 US201615095480A US2016289281A1 US 20160289281 A1 US20160289281 A1 US 20160289281A1 US 201615095480 A US201615095480 A US 201615095480A US 2016289281 A1 US2016289281 A1 US 2016289281A1
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epitope
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Roderick Peter Hafner
Mark Larche
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Circassia Ltd
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Priority claimed from GB0715949A external-priority patent/GB0715949D0/en
Priority claimed from GB0716224A external-priority patent/GB0716224D0/en
Priority claimed from GB0723337A external-priority patent/GB0723337D0/en
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    • C07—ORGANIC CHEMISTRY
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    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
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    • C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
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    • C07K7/08—Linear peptides containing only normal peptide links having 12 to 20 amino acids
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
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    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56966—Animal cells
    • G01N33/56977—HLA or MHC typing
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    • C07K2319/00—Fusion polypeptide

Definitions

  • the present invention relates to peptides comprising multiple MHC Class II-binding T cell epitopes for tolerisation therapy.
  • T-cell antigen recognition requires antigen presenting cells (APCs) to present antigen fragments (peptides) on their cell surface in association with molecules of the major histocompatibility complex (MHC). T cells use their antigen specific T-cell receptors (TCRs) to recognise with high specificity the antigen fragments presented by the APC. Such recognition acts as a trigger to the immune system to generate a range of responses to eradicate the antigen which has been recognized.
  • APCs antigen presenting cells
  • MHC major histocompatibility complex
  • TCRs antigen specific T-cell receptors
  • T cell recognition of the antigen fragments is provided by a smaller subsequence of amino acids within the fragments. This subsequence is known as the T cell epitope.
  • the peptides are presented on MHC Class II molecules, which are recognized by CD4 T cells. Accordingly, interest in allergic and auto- or allo-immune disorders has focused on MHC Class II-binding T cell epitopes.
  • epitopes Given their role in the immune system, there is considerable interest in such epitopes for use as therapeutic agents to modulate the immune systems of subjects. For example, administration of peptide epitopes to subjects has been demonstrated to result in the induction of tolerance to the antigen from which the epitope derives. Therapeutic agents based on such an effect have great potential in the prevention and treatment of allergy, and auto- or allo-immune diseases where the down-regulation of an immune response is desirable.
  • the minimal amino acid sequence of a T cell epitope required for binding to MHC Class II-molecules can be precisely identified and generally comprises approximately nine amino acids.
  • An epitope sequence typically binds specifically to a particular class of MHC Class II molecule, and does not bind to other MHC Class II molecules. Accordingly, the efficacy of a given epitope sequence varies greatly depending on the MHC Class II type of the individual to whom it is administered. To utilise an epitope for, e.g. the induction of tolerance, it is therefore necessary to undertake time-consuming and costly steps to identify the MHC Class II type of the individual to be tolerised.
  • the present inventors have made the finding that by incorporating multiple different epitope sequences, it is possible to produce a peptide which binds to multiple different classes of MHC Class II and is therefore effective when administered to a wider range of individuals, reducing the requirement to identify the MHC Class II type of an individual.
  • Two or more epitope sequences may be combined in a peptide in an overlapping configuration, or as two independent sequences separated by amino acids which are not comprised in either epitope, without producing a peptide large enough to possess significant tertiary structure that would enable it to retain the conformation of an IgG or IgE-cross-linking epitope. Consequently the downstream immune responses to antigen caused by such cross-linking do not occur.
  • the present invention provides:
  • a peptide which has a length of 10 to 25 amino acids comprising a region that comprises at least two different MHC class II-binding T cell epitope sequences, wherein the epitope sequences comprise at least 9 amino acids and derive from an antigenic protein, and wherein each epitope sequence binds to a different MHC class II molecule, and wherein the region is optionally flanked at the N and/or C terminus by additional amino acids which are not part of the epitope sequence.
  • the peptide is typically suitable for use in tolerisation therapy.
  • Polynucleotides, vectors and cells expressing the peptide of the invention, and methods of making the peptide of the invention are also provided.
  • references to inserting, deleting, replacing amino acids herein does not require the actual physical insertion, deletion or replacement of amino acids, and instead a peptide can be synthesized comprising sequence which represents (or is the end result of) the insertion, deletion or replacement having occurred.
  • the MHC Class II-binding T cell epitope comprised in the peptides of the invention is typically the minimal amino acid sequence that is capable of binding to Class II molecules and capable of stimulating T cells when presented in to T cells in association with Class II on the cell surface.
  • the epitope is typically one that binds to a human MHC class II molecule.
  • An MHC Class II molecule consists of two proteins, ⁇ and ⁇ each of which is encoded by a different gene.
  • ⁇ and ⁇ proteins there are three clusters of genes encoding different ⁇ and ⁇ proteins. These are the Human Leukocyte Antigen (HLA) clusters, DR, DQ and DP.
  • HLA Human Leukocyte Antigen
  • DR Human Leukocyte Antigen
  • DQ DQ
  • DP Human Leukocyte Antigen
  • Each cluster comprises multiple different A genes encoding different variant of the ⁇ protein and multiple different B genes encoding different variants of the ⁇ protein.
  • the resulting MHC Class II heterodimers are therefore extremely diverse, and correspondingly so are the T cell epitopes that they bind.
  • the binding site of MHC Class II molecules is composed of two separate proteins which form a cleft.
  • the cleft is open-ended, which in theory allows a peptide of any length to bind.
  • 9 amino acids can occupy the cleft itself.
  • the identities of the up to 9 amino acids which occupy the cleft define whether or not a given peptide will bind to a given MHC Class II molecule and be available for presentation to T cells.
  • These up to 9 amino acids therefore represent the minimal sequence that is required for MHC Class II-binding. It is generally assumed that such a sequence will be capable of stimulating T cells when presented to T cells in association with Class II on the cell surface. However, this may be confirmed experimentally by methods standard in the art.
  • Such methods may typically comprise contacting the epitope with T cells in a sample taken from a subject, under conditions which allow the epitope and the T cells to interact; and then determining whether or not any of the T cells are stimulated. Determining whether or not the T cells are stimulated may be achieved by any suitable method, for example by detecting the production of cytokines by the T cells, wherein cytokine production indicates that T cells have been stimulated. Suitable cytokines include interferon gamma and interleukin 13. Cytokine production may be detected by any suitable method, for example an ELISA, ELISPOT assay or a flow cytometric assay.
  • T cells in a sample from a subject are typically present in a population of peripheral blood mononuclear cells (PBMCs) isolated from a blood or serum sample taken from the subject.
  • PBMCs peripheral blood mononuclear cells
  • the MHC Class II-binding T cell epitope of the invention typically consists of 8 or 9 amino acids, but may consist of 7, 10, 11, 12, 13, 14, 15 or 16 amino acids.
  • the amino acid sequence of the epitope may be broadly defined by further reference to the binding site of MHC Class II molecules. This binding site has specific binding pockets, which corresponding to primary and secondary anchor positions in the sequence of the binding peptide epitope.
  • the binding pockets are defined by amino acid positions in the sequence of the MHC Class II molecule, and are generally not absolutely discriminatory for a specific amino acid in the epitope. Therefore the peptide binding specificity of any given MHC molecule is relatively broad. Thus, peptides binding to the same MHC allotype exhibit some degree of similarity, but there is no requirement for identity.
  • the key anchor positions for binding to the binding pockets are at positions 1, 4, 6, 7 and 9 of the peptide epitope (counting from the most N terminal residue occupying the cleft to the most C terminal).
  • Different HLA-DR alleles which have similar amino acids in their binding pockets therefore typically bind peptides with similar amino acids at positions 1, 4, 6, 7 and 9.
  • the region containing an MHC Class II binding T cell epitope preferably has amino acids at positions corresponding to positions 1, 4, 6, 7 and 9 that allow binding to the widest range of HLA-DR alleles. Examples of characteristic binding properties of different HLA-DR alleles are set out below:
  • DR alleles with Glycine at position 86 of the ⁇ chain show strong preferences for large hydrophobic side chains (Trp, Tyr, Phe) at peptide position 1, whereas Valine at position 86 restricts the pocket size and alters the preferences to small hydrophobic side chains (Val and Ala) at this position.
  • Medium sized hydrophobic amino acids Leu and Be are well accepted in all DR alleles.
  • DR alleles with Gln at position 70, Lysine at position 71, and Arginine or Gln at position 74 of the ⁇ chain have an overall positive charge within pocket 4, which requires negatively charged amino acids Asp and Glu at position 4 of the binding peptide (as in for example, DRB1*0301).
  • DR alleles with this motif are associated with two autoimmune diseases: systematic lupus erythematosus and Hashimoto's thyroiditis.
  • DR alleles with Gln or Arg at position 70, Arg or Lys at position 71 and Glu or Ala at position 74 of the ⁇ chain bind similar peptides to those directly above since the only significant difference is at position 74.
  • pocket 4 increases in size and can accommodate larger amino acids such as Phe, Trp, and Ile (as in for example DRB1*0401, 04, 05).
  • Alleles bearing Glu at position 74 are expected to allow small polar residues, like Ser and Thr at position 4 of the binding peptide.
  • DR alleles with this motif are associated with a susceptibility to rheumatoid arthritis.
  • DR alleles with Asp at position 70, Glu or Arg at position 71, and Leu or Ala at position 74 of the ⁇ chain exclude peptides with negatively charged amino acids at peptide position 4 (for example DRB1*0402). This is due to the presence of Asp at position 70.
  • DR alleles with this motif are associated with the autoimmune diseases Juvenile rheumatoid arthritis (JRA), pemphigus vulgaris, and allergic bronchopulmonary.
  • Polymorphisms at position 9 of the ⁇ chain define the size of binding pocket 9 in all DR alleles. Alleles with Trp at this position accept only small amino acids in position 9 of the binding peptide, e.g. Ala, Val, Gly, Ser, Thr, Pro (as in for example DRB1*0101 and *1501). Glu at position 9, in combination with Asp at position 57, makes pocket 9 negatively charged, facilitating the accommodation of positively charged amino acids, such as Lys (as in for example DRB1*0401 and *0404) and Histine (as in for example DRB1*0402).
  • Lys as in for example DRB1*0401 and *0404
  • Histine as in for example DRB1*0402
  • Asp at position 57 makes a salt-bridged hydrogen bond with Arg at position 76, allowing the pocket to also accommodate aliphatic and polar amino acids.
  • Asp at position 57 is replaced by Ser (for example DRB1*0405) or Ala (DQ8), the hydrogen bonding network is destroyed and Arg at position 76 can strongly attract negatively charged amino acids such as Asp or Glu at position 9 of the binding peptide (as in for example DRB1*0405).
  • An example of a preferred sequence for an epitope therefore has Trp, Tyr, Phe, Val or Ala at position 1; Asp, Glu, Ser or Thr at position 4; and Ala, Val, Gly, Ser, Thr, Pro at position 9.
  • a further example of a preferred sequence for an epitope has a large aromatic or hydrophobic amino acid at position 1, for example Tyr, Phe, Trp, Leu, Ile or Val, and a small, non-charged amino acid at position 6, for example Ser, Thr, Ala, Pro, Val, Ile or Met.
  • Approximately 87.5% of peptides binding to all or a combination of the MHC Class II molecules encoded by the DRB1*0101, *0401 and *0701 alleles contain this motif.
  • preferred epitopes of the invention typically comprise at least 5, 6, 7 or 8 different amino acids.
  • the precise amino sequence of an epitope may be predicted by computer-based algorithms and confirmed by in vitro biochemical analysis. Suitable commercially available algorithms include the EpiMatrix algorithm (EpiVax Inc.). Other algorithms are available at, for example, the website at the ProPed MHC Class-II Binding Peptide Prediction Server. Analysis with these algorithms typically comprises parsing a larger polypeptide sequence into multiple overlapping small peptides. The sequences of these small peptides are then analysed using the algorithm to identify those which are predicted to bind MHC Class II molecules. The overlapping small peptides are typically 9-mers.
  • the candidate peptides which score most highly in this analysis are then assessed for the ability to bind a panel of MHC Class II molecules encoded by different Class II alleles in vitro using standard binding assays.
  • a competitive MHC class II binding assay may be used, wherein each peptide is analysed for its ability to displace a known control binder from each of the human MHC class II allotypes investigated.
  • each peptide is assigned an IC 50 value (the concentration at which 50% inhibition of control peptide binding is achieved). The lower the IC 50 the higher the affinity of a peptide for a given MHC class II allotype.
  • epitope or epitopes in a polypeptide are taken to be those peptides which show the highest binding affinity to MHC Class II molecules.
  • Particularly preferred epitopes show high affinity binding to different Class II molecules encoded by more than one preferably two, more preferably three, four or five MHC Class II alleles.
  • biochemical assays for the identification of a T cell epitope are not typically able to precisely define the position of the minimal epitope sequence within a larger sequence more accurately than to within approximately 12 amino acids, and more typically 15, 20 or more amino acids.
  • the reason for this is that a large sequence must be physically fragmented into smaller overlapping peptides, or smaller overlapping peptides must be manufactured de novo prior to in vitro assessment of the ability of these peptides to bind MHC Class II molecules.
  • the skilled person will recognise that the smaller the overlapping peptide fragments used, the more time-consuming and labour intensive is the process of manufacture.
  • epitopes are often identified as being contained within a larger polypeptide region. It is envisaged that the epitopes of the invention may be defined as such a larger region.
  • the epitope sequences of the invention also comprise functional variants of the epitope sequences.
  • a functional variant epitope sequence is any homologous epitope sequence which is able to stimulate a T cell that specifically recognise the native epitope sequence from which the variant derives, or which is able to induce tolerance to the native epitope sequence in an individual.
  • Such a variant typically has at least 55%, preferably 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% homology to the native epitope sequence. Suitable methods for determining the stimulatory effect of a variant epitope are known in the art.
  • PBMCs peripheral blood mononuclear cells
  • T cell cultures After one week of culture, the T cell cultures are restimulated with autologous antigen presenting cells pulsed with peptides consisting of the native epitope sequence, which produces T cell lines specific for the native epitope sequence.
  • the resulting lines can then be tested to see if they are stimulated by any variant epitope sequence, with stimulation being correlated with, e.g. proliferation or production of cytokines, in particular interferon-gamma, interleukin-13 and interleukin-17.
  • the bioinformatic techniques used to identify epitopes may identify multiple epitopes in the same polypeptide. Each of these multiple epitopes typically binds to different types of MHC Class II molecule. That is, a first epitope may bind Class II molecules encoded by alleles w, x, and y, whereas a second epitope binds Class II molecules encoded by alleles x, y and z. Since the region of the invention comprises at least two different epitope sequences, the peptides of the invention are capable of binding to a large number of different MHC Class II molecules.
  • the multiple different epitope sequences may be comprised in a region as two or more overlapping epitopes. For example, in a sequence of 12 amino acids, one epitope corresponds to amino acids 1 to 9 and a second epitope corresponds to amino acids 4 to 12. A peptide region comprising amino acids 1 to 12 will therefore comprise two overlapping epitope sequences since both epitopes comprise the contiguous sequence of amino acids 4 to 9.
  • a second epitope may comprise the contiguous sequence of 1, 2, 3, 4, 5, 6, 7 or 8 amino acids at the N terminal of a first epitope, with additional amino acids present at the N terminus of this sequence which are not comprised in the first epitope, or may comprise the contiguous sequence of 1, 2, 3, 4, 5, 6, 7 or 8 amino acids at the C terminal of a first epitope, with additional amino acids present at the C terminus of this sequence which are not comprised in the first epitope.
  • a preferred overlap of sequence between any two epitopes typically comprises a contiguous sequence of upto approximately 65% of the amino acids from the N or C terminus either epitope.
  • a second epitope may therefore comprise the contiguous sequence of 6 amino acids at the N terminal of a first epitope, with additional amino acids present at the N terminus of this sequence which are not comprised in the first epitope, or may comprise the contiguous sequence of 6 amino acids at the C terminal of a first epitope, with additional amino acids present at the C terminus of this sequence which are not comprised in the first epitope.
  • the multiple epitopes in the region may be two or more independent sequences.
  • the independent sequences may be consecutive or may be separated by additional amino acids which are not comprised in an epitope.
  • one epitope corresponds to amino acids 1 to 9 and a second epitope corresponds to amino acids 10 to 18.
  • one epitope corresponds to amino acids 1 to 9 and a second epitope corresponds to amino acids 11 to 19.
  • amino acid 10 is not comprised in either epitope.
  • two independent epitope sequences may typically be separated by 1, 2, 3, 4, 5, 6 or 7 additional amino acids which are not comprised in either epitope.
  • the amino acid sequence separating the epitope sequences (“the additional amino acid(s)”) may comprise any amino acid sequence. It is particularly preferred that the additional amino acid(s) comprise a high proportion of hydrophilic amino acids (typically>60%) and comprise no cysteine residues.
  • the sequence of the additional amino acid(s) is identical to or homogolous to the sequence of the amino acid(s) which separates the epitope sequences in the native sequence of the protein from which the epitopes derive. If the additional amino acid(s) are homolgous to the native sequence, homology of greater than 55%, 60%, 75%, 80%, 85%, 90% or 95% with the native sequence is preferred. In an alternative embodiment, the sequence of the additional amino acid(s) is not related to the sequence of the amino acid(s) which separates the epitope sequences in the native sequence of the protein from which the epitopes derive. That is, the region may comprise a fusion protein comprising a first epitope, a sequence of additional amino acids, and at least a second epitope.
  • the multiple epitopes may be present in the region as a combination of overlapping or independent epitope sequences.
  • the region may therefore consist entirely of amino acids which are comprised in at least one epitope.
  • the proportion of amino acids in a region which are comprised in at least one epitope is approximately 70%, 71%, 72%, 73%, 74%, 75%, 80%, 85%, 90% or 95%, or 99%.
  • at least 70% of the amino acids in a region are comprised in at least one epitope.
  • the region therefore typically has a length of approximately 18 amino acids, but may be 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 amino acids in length.
  • the peptides of the invention may consist entirely of the region as defined above. However, the peptides may optionally comprise additional amino acids flanking the N or C termini of the region. These amino acids are not comprised in an epitope. Typically, the proportion of amino acids in a peptide which are comprised in at least one epitope is approximately 70%, 71%, 72%, 73%, 74%, 75%, 80%, 85%, 90% or 95%, or 99%. Preferably, at least 70% of the amino acids in a peptide are comprised in at least one epitope.
  • the residues flanking the region typically result in the peptide having a solubility greater than 3.5 mg/ml in aqueous solution at pH 2.0 to 12.0, or pH 2.0 to 11.0, pH 2.0 to 10.0, pH 2.0 to 9.0, pH 2.0 to 8.0 or pH 2.0 to 7.0.
  • the residues flanking the region are preferably:
  • At both the N and C termini at least one, preferably two, or three amino acids selected from arginine, lysine, histidine, glutamate and aspartate.
  • the peptide may comprise the region as defined above, but incorporating modification of its native sequence. Particularly preferred modifications regions wherein:
  • any hydrophobic residues in the up to one, two, preferably three or four amino acids at the N or C terminus of the native sequence of the region which are not comprised in the epitope are deleted;
  • any two consecutive amino acids comprising the sequence Asp-Gly in the up to three or preferably four amino acids at the N or C terminus of the native sequence of the region which are not comprised in the epitope are deleted.
  • the peptides of the invention typically contain from 10 to 25 amino acids, and may contain 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 amino acids. Peptides longer than 25 amino acids are likely to possess sufficient tertiary structure to cross-link IgG or IgE on cell surfaces resulting in undesirable immune responses such as B cell activation or mast cell degranulation. Peptides shorter than 10 amino acids are unlikely to contain more than one epitope.
  • the peptides of the invention are derived in an intellectual sense from the polypeptide which comprises the epitopes and regions as defined above with additional flanking residues or residues to separate independent epitope sequences. This is done by making use of the amino acid sequence of the region or epitope and synthesising peptides based on the sequence.
  • Peptides may be synthesised using methods well known in the art. Preferred methods include solid-phase peptide synthesis techniques and most preferably preferably an automated or semiautomated peptide synthesizer.
  • an ⁇ -N-carbamoyl protected amino acid and an amino acid attached to the growing peptide chain on a resin are coupled at room temperature in an inert solvent such as dimethylformamide, N-methylpyrrolidinone or methylene chloride in the presence of coupling agents such as dicyclohexylcarbodiimide and 1-hydroxybenzotriazole in the presence of a base such as diisopropyl-ethylamine.
  • an inert solvent such as dimethylformamide, N-methylpyrrolidinone or methylene chloride
  • coupling agents such as dicyclohexylcarbodiimide and 1-hydroxybenzotriazole
  • the ⁇ -N-carbamoyl protecting group is removed from the resulting peptide-resin using a reagent such as trifluoroacetic acid or piperidine, and the coupling reaction repeated with the next desired N-protected amino acid to be added to the peptide chain.
  • a reagent such as trifluoroacetic acid or piperidine
  • Suitable N-protecting groups are well known in the art, and include t-butyloxycarbonyl (tBoc) and fluorenylmethoxycarbonyl (Fmoc).
  • peptide includes not only molecules in which amino acid residues are joined by peptide (—CO—NH—) linkages but also molecules in which the peptide bond is reversed.
  • retro-inverso peptidomimetics may be made using methods known in the art, for example such as those described in Meziere et al (1997) J. Immunol.159, 3230-3237. This approach involves making pseudopeptides containing changes involving the backbone, and not the orientation of side chains. Meziere et al (1997) show that, at least for MHC class II and T helper cell responses, these pseudopeptides are useful.
  • Retro-inverse peptides which contain NH—CO bonds instead of CO—NH peptide bonds, are much more resistant to proteolysis.
  • the peptide bond may be dispensed with altogether provided that an appropriate linker moiety which retains the spacing between the carbon atoms of the amino acid residues is used; it is particularly preferred if the linker moiety has substantially the same charge distribution and substantially the same planarity as a peptide bond.
  • the peptide may conveniently be blocked at its N-or C-terminus so as to help reduce susceptibility to exoproteolytic digestion.
  • the N-terminal amino group of the peptides may be protected by reacting with a carboxylic acid and the C-terminal carboxyl group of the peptide may be protected by reacting with an amine.
  • modifications include glycosylation and phosphorylation.
  • Another potential modification is that hydrogens on the side chain amines of R or K may be replaced with methylene groups (—NH 2 ⁇ -NH(Me) or —N(Me) 2 ).
  • Analogues of peptides according to the invention may also include peptide variants that increase or decrease the peptide's half-life in vivo.
  • analogues capable of increasing the half-life of peptides used according to the invention include peptoid analogues of the peptides, D-amino acid derivatives of the peptides, and peptide-peptoid hybrids.
  • a further embodiment of the variant polypeptides used according to the invention comprises D-amino acid forms of the polypeptide. The preparation of polypeptides using D-amino acids rather than L-amino acids greatly decreases any unwanted breakdown of such an agent by normal metabolic processes, decreasing the amounts of agent which needs to be administered, along with the frequency of its administration.
  • nucleic acid molecule and “polynucleotide” are used interchangeably herein and refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof.
  • Non-limiting examples of polynucleotides include a gene, a gene fragment, messenger RNA (mRNA), cDNA, recombinant polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers.
  • a polynucleotide of the invention may be provided in isolated or purified form.
  • a nucleic acid sequence which “encodes” a selected polypeptide is a nucleic acid molecule which is transcribed (in the case of DNA) and translated (in the case of mRNA) into a polypeptide in vivo when placed under the control of appropriate regulatory sequences.
  • the boundaries of the coding sequence are determined by a start codon at the 5′ (amino) terminus and a translation stop codon at the 3′ (carboxy) terminus.
  • such nucleic acid sequences can include, but are not limited to, cDNA from viral, prokaryotic or eukaryotic mRNA, genomic sequences from viral or prokaryotic DNA or RNA, and even synthetic DNA sequences.
  • a transcription termination sequence may be located 3′ to the coding sequence.
  • Polynucleotides of the invention can be synthesised according to methods well known in the art, as described by way of example in Sambrook et al (1989, Molecular Cloning—a laboratory manual; Cold Spring Harbor Press).
  • the polynucleotide molecules of the present invention may be provided in the form of an expression cassette which includes control sequences operably linked to the inserted sequence, thus allowing for expression of the peptide of the invention in vivo in a targeted subject.
  • These expression cassettes are typically provided within vectors (e.g., plasmids or recombinant viral vectors) which are suitable for use as reagents for nucleic acid immunization.
  • vectors e.g., plasmids or recombinant viral vectors
  • Such an expression cassette may be administered directly to a host subject.
  • a vector comprising a polynucleotide of the invention may be administered to a host subject.
  • the polynucleotide is prepared and/or administered using a genetic vector.
  • a suitable vector may be any vector which is capable of carrying a sufficient amount of genetic information, and allowing expression of a peptide of the invention.
  • the present invention thus includes expression vectors that comprise such polynucleotide sequences.
  • the present invention provides a vector for use in preventing or treating allergy by tolerisation comprising four or more polynucleotide sequences which encode different polypeptides of the invention and optionally one or more further polynucleotide sequences which encode different polypeptides as defined herein.
  • the vector may comprise 4, 5, 6 or 7 polynucleotide sequences which encode different polypeptides of the invention.
  • compositions and products of the invention may comprise a mixture of polypeptides and polynucleotides. Accordingly, the invention provides a composition or product as defined herein, wherein in place of any one of the polypeptide is a polynucleotide capable of expressing said polypeptide.
  • Expression vectors are routinely constructed in the art of molecular biology and may for example involve the use of plasmid DNA and appropriate initiators, promoters, enhancers and other elements, such as for example polyadenylation signals which may be necessary, and which are positioned in the correct orientation, in order to allow for expression of a peptide of the invention.
  • Other suitable vectors would be apparent to persons skilled in the art.
  • a polypeptide of the invention may be provided by delivering such a vector to a cell and allowing transcription from the vector to occur.
  • a polynucleotide of the invention or for use in the invention in a vector is operably linked to a control sequence which is capable of providing for the expression of the coding sequence by the host cell, i.e. the vector is an expression vector.
  • “Operably linked” refers to an arrangement of elements wherein the components so described are configured so as to perform their usual function.
  • a given regulatory sequence such as a promoter
  • operably linked to a nucleic acid sequence is capable of effecting the expression of that sequence when the proper enzymes are present.
  • the promoter need not be contiguous with the sequence, so long as it functions to direct the expression thereof.
  • intervening untranslated yet transcribed sequences can be present between the promoter sequence and the nucleic acid sequence and the promoter sequence can still be considered “operably linked” to the coding sequence.
  • a number of expression systems have been described in the art, each of which typically consists of a vector containing a gene or nucleotide sequence of interest operably linked to expression control sequences. These control sequences include transcriptional promoter sequences and transcriptional start and termination sequences.
  • the vectors of the invention may be for example, plasmid, virus or phage vectors provided with an origin of replication, optionally a promoter for the expression of the said polynucleotide and optionally a regulator of the promoter.
  • a “plasmid” is a vector in the form of an extrachromosomal genetic element.
  • the vectors may contain one or more selectable marker genes, for example an ampicillin resistence gene in the case of a bacterial plasmid or a resistance gene for a fungal vector.
  • Vectors may be used in vitro, for example for the production of DNA or RNA or used to transfect or transform a host cell, for example, a mammalian host cell.
  • the vectors may also be adapted to be used in vivo, for example to allow in vivo expression of the polypeptide.
  • a “promoter” is a nucleotide sequence which initiates and regulates transcription of a polypeptide-encoding polynucleotide. Promoters can include inducible promoters (where expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.), repressible promoters (where expression of a polynucleotide sequence operably linked to the promoter is repressed by an analyte, cofactor, regulatory protein, etc.), and constitutive promoters. It is intended that the term “promoter” or “control element” includes full-length promoter regions and functional (e.g., controls transcription or translation) segments of these regions.
  • a polynucleotide, expression cassette or vector according to the present invention may additionally comprise a signal peptide sequence.
  • the signal peptide sequence is generally inserted in operable linkage with the promoter such that the signal peptide is expressed and facilitates secretion of a polypeptide encoded by coding sequence also in operable linkage with the promoter.
  • a signal peptide sequence encodes a peptide of 10 to 30 amino acids for example 15 to 20 amino acids. Often the amino acids are predominantly hydrophobic.
  • a signal peptide targets a growing polypeptide chain bearing the signal peptide to the endoplasmic reticulum of the expressing cell. The signal peptide is cleaved off in the endoplasmic reticulum, allowing for secretion of the polypeptide via the Golgi apparatus.
  • a peptide of the invention may be provided to an individual by expression from cells within the individual, and secretion from those cells.
  • polynucleotides of the invention may be expressed in a suitable manner to allow presentation of a peptide of the invention by an MHC class II molecule at the surface of an antigen presenting cell.
  • a polynucleotide, expression cassette or vector of the invention may be targeted to antigen presenting cells, or the expression of encoded peptide may be preferentially stimulated or induced in such cells.
  • the polynucleotide, expression cassette or vector will encode an adjuvant, or an adjuvant will otherwise be provided.
  • adjuvant refers to any material or composition capable of specifically or non-specifically altering, enhancing, directing, redirecting, potentiating or initiating an antigen-specific immune response.
  • Polynucleotides of interest may be used in vitro, ex vivo or in vivo in the production of a peptide of the invention. Such polynucleotides may be administered or used in the prevention or treatment of allergy by tolerisation.
  • nucleic acid molecule can be introduced directly into the recipient subject, such as by standard intramuscular or intradermal injection; transdermal particle delivery; inhalation; topically, or by oral, intranasal or mucosal modes of administration.
  • the molecule alternatively can be introduced ex vivo into cells that have been removed from a subject.
  • a polynucleotide, expression cassette or vector of the invention may be introduced into APCs of an individual ex vivo.
  • nucleic acid vaccines Cells containing the nucleic acid molecule of interest are re-introduced into the subject such that an immune response can be mounted against the peptide encoded by the nucleic acid molecule.
  • the nucleic acid molecules used in such immunization are generally referred to herein as “nucleic acid vaccines.”
  • polypeptides, polynucleotides, vectors or cells of the invention may be present in a substantially isolated form. They may be mixed with carriers or diluents which will not interfere with their intended use and still be regarded as substantially isolated. They may also be in a substantially purified form, in which case they will generally comprise at least 90%, e.g. at least 95%, 98% or 99%, of the proteins, polynucleotides, cells or dry mass of the preparation.
  • peptides, polynucleotides, vectors and cells of the invention may be provided to an individual either singly or in combination.
  • Each molecule or cell of the invention may be provided to an individual in an isolated, substantially isolated, purified or substantially purified form.
  • a peptide of the invention may be provided to an individual substantially free from the other peptides.
  • the present invention provides a pharmaceutical formulation for tolerising an individual to a protein from which a peptide of the invention derives, comprising a composition, vector or product according to the invention together with one or more pharmaceutically acceptable carriers or diluents and optionally one or more other therapeutic ingredients.
  • the carrier (s) must be ‘acceptable’ in the sense of being compatible with the other ingredients of the formulation and not deleterious to the recipient thereof.
  • carriers for injection, and the final formulation are sterile and pyrogen free.
  • the present invention provides a pharmaceutical formulation as defined above comprising less than 5% organic solvent.
  • formulation of a composition comprising the peptide, polynucleotide or cell of the invention can be carried out using standard pharmaceutical formulation chemistries and methodologies all of which are readily available to the reasonably skilled artisan.
  • compositions containing one or more molecules or cells of the invention can be combined with one or more pharmaceutically acceptable excipients or vehicles.
  • auxiliary substances such as wetting or emulsifying agents, pH buffering substances and the like, may be present in the excipient or vehicle.
  • excipients, vehicles and auxiliary substances are generally pharmaceutical agents that do not induce an immune response in the individual receiving the composition, and which may be administered without undue toxicity.
  • Pharmaceutically acceptable excipients include, but are not limited to, liquids such as water, saline, polyethyleneglycol, hyaluronic acid, glycerol, and ethanol.
  • Pharmaceutically acceptable salts can also be included therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like.
  • mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like
  • organic acids such as acetates, propionates, malonates, benzoates, and the like.
  • compositions may be prepared, packaged, or sold in a form suitable for bolus administration or for continuous administration.
  • injectable compositions may be prepared, packaged, or sold in unit dosage form, such as in ampoules or in multi-dose containers containing a preservative.
  • Compositions include, but are not limited to, suspensions, solutions, emulsions in oily or aqueous vehicles, pastes, and implantable sustained-release or biodegradable formulations.
  • Such compositions may further comprise one or more additional ingredients including, but not limited to, suspending, stabilizing, or dispersing agents.
  • the active ingredient is provided in dry (for e.g., a powder or granules) form for reconstitution with a suitable vehicle (e.
  • compositions may be prepared, packaged, or sold in the form of a sterile injectable aqueous or oily suspension or solution.
  • This suspension or solution may be formulated according to the known art, and may comprise, in addition to the active ingredient, additional ingredients such as the dispersing agents, wetting agents, or suspending agents described herein.
  • Such sterile injectable formulations may be prepared using a non-toxic parenterally-acceptable diluent or solvent, such as water or 1,3-butane diol, for example.
  • compositions for sustained release or implantation may comprise pharmaceutically acceptable polymeric or hydrophobic materials such as an emulsion, an ion exchange resin, a sparingly soluble polymer, or a sparingly soluble salt.
  • the peptides or polynucleotides of the present invention may be encapsulated, adsorbed to, or associated with, particulate carriers.
  • suitable particulate carriers include those derived from polymethyl methacrylate polymers, as well as PLG microparticles derived from poly(lactides) and poly(lactide-co-glycolides). See, e.g., Jeffery et al. (1993) Pharm. Res. 10:362-368.
  • Other particulate systems and polymers can also be used, for example, polymers such as polylysine, polyarginine, polyornithine, spermine, spermidine, as well as conjugates of these molecules.
  • any of the peptides, polynucleotides or cells mentioned herein will depend upon factors such as the nature of the substance and the method of delivery. Any such substance may be administered in a variety of dosage forms. It may be administered orally (e.g. as tablets, troches, lozenges, aqueous or oily suspensions, dispersible powders or granules), parenterally, subcutaneously, by inhalation, intravenously, intramuscularly, intrasternally, transdermally, intradermally, epicutaneously, sublingually, intranasally, buccally or by infusion techniques. The substance may also be administered as suppositories. A physician will be able to determine the required route of administration for each particular individual.
  • compositions of formulations of the invention will comprise a suitable concentration of each peptide/polynucleotide/cell to be effective without causing adverse reaction.
  • concentration of each peptide in the composition will be in the range of 0.03 to 200 nmol/ml. More preferably in the range of 0.3 to 200 nmol/ml, 3 to 180 nmol/ml, 10 to 150 nmol/ml or 30 to 120 nmol/ml.
  • concentrations are particularly favoured for intradermal administration since an effective dose may be administered in a volume of 60 ⁇ l, preferably 50 ⁇ l, and most preferably 30 ⁇ l.
  • the composition or formulations should have a purity of greater than 95% or 98% or a purity of at least 99%.
  • a composition may therefore be formulated which comprises a molecule and/or cell of the invention and also one or more other therapeutic molecules.
  • a composition of the invention may alternatively be used simultaneously, sequentially or separately with one or more other therapeutic compositions as part of a combined treatment.
  • the present invention relates to peptides, polynucleotides, vectors and cells that are capable of desensitising or tolerising human individuals to proteins from which the peptides of the invention derive.
  • proteins are typically allergens or other antigens to which an immune response is undesirable.
  • antigens include antigens associated with autoimmune diseases, antigens associated with graft-versus-host disease or transplant rejection (herein referred to as alloimmune conditions) and antigens associated with maternal-foetal immune responses, for example Rhesus D Haemolytic Disease of the Newborn.
  • the peptides of the invention are therefore useful in the prevention or treatment an allergic disease, an autoimmune disease, an alloimmune condition or a maternal-foetal immune response.
  • the invention provides compositions, products, vectors and formulations for use in preventing or treating the above conditions.
  • the invention also provides a method of in preventing or treating a subject having the above conditions, comprising administering, either singly or in combination the polypeptides/polynucleotides/cells of the invention as described above.
  • the individual to be treated or provided with the composition or formulation of the invention is preferably human. It will be appreciated that the individual to be treated may be known to be sensitised to the particular allergen or antigen, at risk of being sensitised or suspected of being sensitised. The individual can be tested for sensitisation using techniques well known in the art and as described herein. Alternatively, the individual may have a family history of the conditions described above. It may not be necessary to test an individual for sensitisation to allergens because the individual may display symptoms of allergy when brought into proximity to a suitable allergen source. By proximity is meant 10 metres or less, 5 metres or less, 2 metres or less, 1 metre or less, or 0 metres from the source.
  • Symptoms of allergy can include itchy eyes, runny nose, breathing difficulties, red itchy skin or rash.
  • the individual to be treated may be of any age. However, preferably, the individual may be in the age group of 1 to 90, 5 to 60, 10 to 40, or more preferably 18 to 35.
  • the individual to be treated is from a population that has MHC allele frequencies within the range of frequencies that are representative of the Caucasian population. Reference population allele frequencies for 11 common DRB 1 allele families are shown in Table 1(Data from HLA Facts Book, Parham and Barber).
  • the individual to be treated is from a population that has equivalent MHC allele frequencies as the reference population for the alleles referred to Table 1 (such as for at least 1, 2, 3, 4, 5 or all of the alleles), for example within the ranges of those figures plus or minus 1, 2, 3, 5, 10, 15 or 20%.
  • the individual is from a population where the allele frequencies of the following DRB 1 alleles is:
  • the individual to be treated for allergic disease may have had allergy for at least 2 weeks, 1 month, 6 months, 1 year or 5 years.
  • the individual may suffer from a rash, nasal congestion, nasal discharge and/or coughing caused by the allergy.
  • the individual may or may not have been administered with other compositions/compounds which treat allergy.
  • Suitable allergens from which the region containing a MHC Class II-binding T cell epitope may derive can of course be obtained and/or produced using known methods.
  • Classes of suitable allergens include, but are not limited to, pollens, animal dander (in particular cat dander), grasses, molds, dusts, antibiotics, stinging insect venoms, and a variety of environmental (including chemicals and metals), drug and food allergens.
  • Common tree allergens include pollens from cottonwood, popular, ash, birch, maple, oak, elm, hickory, and pecan trees; common plant allergens include those from mugwort, ragweed, English plantain, sorrel-dock and pigweed; plant contact allergens include those from poison oak, poison ivy and nettles; common grass allergens include rye grass, Timothy, Johnson, Bermuda, fescue and bluegrass allergens; common allergens can also be obtained from molds or fungi such as Alternaria, Fusarium, Hormodendrum, Aspergillus, Micropolyspora, Mucor and thermophilic actinomycetes; epidermal allergens can be obtained from house or organic dusts (typically fungal in origin), from arthropods such as house mites ( Dermatophagoides pteronyssinus ), or from animal sources such as feathers, and dog dander; common food allergens include milk and
  • allergens include, but are not limited to, the major allergen produced by the domestic cat Felis catus ( Felis domesticus ) glycoprotein Fel d1, the major and cryptic epitopes of the Der p I allergen (Hoyne et al. (1994) Immunology 83190-195), bee venom phospholipase A2 (PLA) (Akdis et al. (1996) J. Clin. Invest. 98:1676-1683), birch pollen allergen Bet v 1 (Bauer et al. (1997) Clin. Exp. Immunol.
  • the allergen is selected from the list of allergen sequences and database accession numbers (NCBI Entrez accession numbers) below.
  • NCBI is the National Center for Biotechnology information and is a division of the US National Institutes of Health. Allergen sequences and database accession numbers (NCBI Entrez accession numbers):
  • Hev b 1 (SEQ ID NO: 329) MAEDEDNQQGQGEGLKYLGFVQDAATYAVTTFSNVYLFAKDKSGPLQPGV DIIEGPVKNVAVPLYNRFSYIPNGALKFVDSTVVASVTIIDRSLPPIVKD ASIQVVSAIRAAPEAARSLASSLPGQTKILAKVFYGEN Hev b 3 (SEQ ID NO: 330) MAEEVEEERLKYLDFVRAAGVYAVDSFSTLYLYAKDISGPLKPGVDTIEN VVKTVVTPVYYIPLEAVKFVDKTVDVSVTSLDGVVPPVIKQVSAQTYSVA QDAPRIVLDVASSVFNTGVQEGAKALYANLEPKAEQYAVITWRALNKLPL VPQVANVVVPTAVYFSEKYNDVVRGTTEQGYRVSSYLPLLPTEKITKVFG DEAS
  • Phl p 1 (SEQ ID NO: 345) MASSSSVLLVVVLFAVFLGSAYGIPKVPPGPNITATYGDKWLDAKSTWYGK PTGAGPKDNGGACGYKDVDKPPFSGMTGCGNTPIFKSGRGCGSCFEIKCTKP EACSGEPVVVHITDDNEEPIAPYHFDLSGHAFGAMAKKGDEQKLRSAGELEL QFRRVKCKYPEGTKVTFHVEKGSNPNYLALLVKYVNGDGDVVAVDIKEKG KDKWIELKESWGAIWRIDTPDKLTGPFTVRYTTEGGTKTEAEDVIPEGWKA DTSYESK Phl p 1 (SEQ ID NO: 346) MASSSSVLLVVALFAVFLGSAHGIPKVPPGPNITATYGDKWLDAKSTWYGK PTAAGPKDNGGACGYKDVDKPPFSGMTGCGNTPIFKSGRGCGSCFEIKCTKP EACSGEPVVVHITDDNEEPIAA
  • Bet v 1 (SEQ ID NO: 381) MGVFNYETETTSVIPAARLFKAFILDGDNLFPKVAPQAISSVENIEGNGGPGTI KKISFPEGFPFKYVKDRVDEVDHTNFKYNYSVIEGGPIGDTLEKISNEIKIVAT PDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 130975 Bet v 2 (SEQ ID NO: 382) MSWQTYVDEHLMCDIDGQASNSLASAIVGHDGSVWAQSSSFPQFKPQEITGI MKDFEEPGHLAPTGLHLGGIKYMVIQGEAGAVIRGKKGSGGITIKKTGQALV FGIYEEPVTPGQCNMVVERLGDYLIDQGL 1168696 Bet v 3 (SEQ ID NO: 383) MPCSTEAMEKAGHGHASTPRKRSLSNSSFRLRSESLNTLRLRRIFDLFDKNSD GIITVDELSRALNLLGLETDLSELEST
  • Eur m 1 (variant) (SEQ ID NO: 407) TYACSINSVSLPSELDLRSLRTVTPIRMQGGCGSCWAFSGVASTESA YLAYRNMSLDLAEQELVDCASQNGCHGDTIPRGIEYIQQNGVVQEHY YPYVAREQSCHRPNAQRYGLKNYCQISPPDSNKIRQALTQTHTAVAV IIGIKDLNAFRHYDGRTIMQHDNGYQPNYHAVNIVGYGNTQGVDYWI VRNSWDTTWGDNGYGYFAANINL
  • SEQ ID NO: 408 TYACSINSVSLPSELDLRSLRTVTPIRMQGGCGSCWAFSGVASTESA YLAYRNMSLDLAEQELVDCASQNGCHGDTIPRGIEYIQQNGVVQEHY YPYVAREQSCHRPNAQRYGLKNYCQISPPDSNKIRQALTQTHTAVAV IIGIKDLNAFRHYDGRTIMQHDNGYQP
  • T cell epitopes are derived from the allergens: cat dander protein Fel d1; House dust mite proteins Der P1, Der P2 and Der P7; Ragweed protein amb a 1.1, a 1.2, a1.3 or a1.4; Rye grass proteins lol p1 and lol p5; Timothy grass proteins phl p1 and phl p5; Bermuda grass protein Cyn d 5; Alternaria alternate proteins Alt a 1, Alt a 2 and Enolase (Alt a 6); Birch protein Bet v1 and P14; German Cockroach proteins Bla g 1, Bla g 2, Bla g 3, Bla g 4, Bla g 5 and Bla g 6; Mugwort protein Art v 1; Russian thistle protein Sal k 1 and Sal k 2; peanut Ara h1, Ara h2, Ara h3, Ara h4, Ara h5, Ara h6, plant profilins or lipid transfer proteins or a human leukocyte antigen.
  • Suitable autoimmune antigens from which the MHC Class II-binding T cell epitope may derive can of course be obtained and/or produced using known methods.
  • Suitable autoimmune antigens include the major antigens in the following autoimmune diseases: Acute disseminated encephalomyelitis (ADEM); Addison's disease; Ankylosing spondylitis; Antiphospholipid antibody syndrome (APS); Aplastic anemia; Autoimmune hepatitis; Autoimmune Oophoritis; Coeliac disease; Crohn's disease; Diabetes mellitus type 1; Gestational pemphigoid; Goodpasture's syndrome; Graves' disease; Guillain-Barré syndrome (GBS); Hashimoto's disease; Idiopathic thrombocytopenic purpura; Kawasaki's Disease; Lupus erythematosus; Multiple sclerosis; Myasthenia gravis; Opsoclonus myoclonus syndrome (OMS); Optic neuritis
  • eptiopes may be derived from antigens involved with maternal-foetal immunes responses, for example Rhesus D antigens involved in Rhesus D Haemolytic Disease of the Newborn.
  • MHC Class I molecules alsowise referred to as human leukocyte antigens-HLA
  • HLA-A2 human leukocyte antigens-HLA
  • ⁇ 3 domain and/or transmembrane domain of MHC Class I molecules most preferably from the human MHC Class I molecule HLA-A2.
  • the epitopes may be of proteins which are administered to the individual, for example for therapy. Such proteins may act as neoantigens in the individual, such as for example in the situation where the individual does not express the protein.
  • the therapeutic protein may be factor IIX or salcatonin.
  • Particularly suitable proteins from which to derive the epitope sequences of the invention are those which have a low frequency of epitopes per amino acid residue, i.e. the ratio of amino acids in the minimal binding sequence of an epitope, relative to the total number of amino acids in the protein (“the epitope ratio”) is low.
  • a protein with a low frequency of epitopes per amino acid residue typically has an epitope ratio of 1:35, 1:40, 1:45, 1:50, 1:55, 1:60 or 1:65.
  • These proteins are preferred sources of epitope sequences of the invention because a high proportion of the different epitope sequences derived from such proteins typically overlap.
  • the percentage of epitope sequences which overlap with at least one other epitope sequence is greater than 60%, 65%, 70%, 80% or 90%.
  • the aim of this study is to identify peptides with strong affinities for the seven most common human MHC Class II HLA-DRB1* allotypes (covering in total around 63% of the allotypes found in the average Caucasian population).
  • HLM House Dust Mite
  • Der p 1, Der p 2 and Der p 7 in vitro binding assays have been performed on a subset of peptides from these allergenic proteins.
  • Peptides for testing in the binding assays were initially identified by an in silico approach known as “peptide threading” (carried out by Biovation, Ltd.,Aberdeen, Scotland, UK).
  • the assay employed is a competitive MHC class II binding assay, wherein each peptide is analysed for its ability to displace a known control binder from each of the human MHC class II allotypes investigated.
  • the allotypes and control peptides used in this study are shown in the table below.
  • a peptide that has an IC50 value that is parity to the control peptide has an identical binding affinity, while peptides with a ratio less than one have a higher affinity and those with a ratio greater than one have a lower affinity.
  • Solubility in aqueous solution is an essential criterion for a peptide to be an effective therapeutic agent. Therefore, as a consequence of the solubility screen we will have eliminated very hydrophobic peptides with a high frequency of large hydrophobic amino acid residues in multiple binding registers. This is a characteristic of promiscuous HLA-DRB1* binders.
  • the data from the binding assays is shown in Table 3B. The relative binding of each peptide is shown for each of the allotypes in the study. The data shows that 24 of the 44 peptides tested bound to one or more of the MHC Class II allotypes.
  • the % purity of the peptides is indicated in Table 3A. This is of significance as purities were seen to vary from 60-90%. This would have a considerable effect on the ability of a peptide to compete if it is relatively impure.
  • HDM23A and HDM32 show low affinity binding; however, they are of reduced purity (66.7% and 68.7% respectively) compared to other HDM peptides. Therefore, if purity is taken into consideration, they may in fact have an equivalent affinity to a peptide of a higher purity.
  • the assay was also carried out under less stringent conditions. All the Der p binding peptides were seen to have a high ratio when tested against this allotype, showing they were low affinity binders compared to the control peptide.
  • the DQA1*0102/DQB1*0602 binding assay uses a peptide from the B-chain of human insulin which is of lower affinity compared to those used in the DR assays. This dictates that the DQ assay is very sensitive and tends to produce very low ratio values for the strongest binders to this MHC Class II allotype. This sensitivity also accounts for the relatively higher number of DQ binding peptides within the panel screened.
  • HDM 21B RGKPFQLEAVFEANQNT SEQ ID NO: 26 identified as binders to all or a combination of these 3 allotypes, 14 (87.5%) contain this motif, which suggests that these are promiscuous binders with a range of affinities for the 1-4-7 allotypes.
  • a range of peptides have been shown to have the capacity to bind the MHC Class II allotypes and are considered to represent T cell epitopes.
  • the inventors were able to identify sequences comprising T cell epitopes which are close together in the overall protein sequence and therefore construct peptides which comprise overlapping epitopes. A number of such sequences will be apparent to the skilled person when considering Tables 1A and 1B. Specific illustrative examples include:
  • HDM01 (residues 112-124) and HDM02 (118-130). Providing a combination of these two sequences, the inventors devised a longer sequence spanning residues 112 to 130. In order to reduce dimer formation by this longer peptide, the cysteine at position 129 is replaced with serine to give new peptide HDM01A:
  • HDM34 (residues 74-88) and HDM35 (79-91). Providing a combination of these two sequences, the inventors devised a longer sequence spanning residues 72 to 89. Residues 72 and 73 were added, and residues 90 and 91 removed in order to improve solubility for the new peptide, HDM207:
  • Table 1C presents results from a cytokine release assay performed on four house dust mite allergic individuals for HDM01A compared to HDM01 and HDM02, and on three house dust mite allergic individuals for HDM34, HDM35 and HDM207.
  • Cytokine secretion profiles from PBMC's were analysed in response to the peptide stimulation using the above peptides.
  • Supernatants from the cytokine release assay were tested for the presence of 2 cytokines, IFN- ⁇ and IL-13, using either an ELISA assay or a multiplex bead array assay.
  • a typical cytokine release assay requires 40 ⁇ 10 6 PBMC's per subject.
  • 250 ⁇ l of a 200 ⁇ g/ml solution of the appropriate antigen or peptide concentration is distributed into the appropriate wells of 48 well plates. Plates are the incubated in a humidified 5% CO 2 incubator at 37° C. for a maximum of 4 hours.
  • 250 ⁇ l of a 5 ⁇ 10 6 cell/ml PBMC suspension is then added to each well and the plates returned to the incubator for 5 days. Following stimulation, samples of culture supernatant are harvested for testing by ELISA or multiplex bead assay according to standard protocols.
  • the new peptides HDM01A and HDM207 give rise to significantly higher cytokine production in all patients tested than the original “single epitope” peptides from which they derive.
  • Peptides HDM19 to 26A are from Der p2; peptide HDM37 is from Der f2.
  • Peptides HDM 28 to 49 are from Der p 7.
  • the sequence of Der p 1 from which the “residues in parent” positions are derived is the publically available sequence with NCBI Accession No. P08176.
  • the corresponding sequences for Der p 2 and Der p 7 are NCBI Accession Nos. P49278 and P49273, respectively.
  • the Timothy Grass pollen allergen Phl p 5 Accession number 2003342A was analysed by methods analogous to those used in Example 1. A number of peptides sequences containing MHC Class II binding epitopes were identified. As above, the inventors were able to identify sequences comprising T cell epitopes which are close together in the overall protein sequence and therefore construct peptides which comprise overlapping epitopes.
  • Tim10B which consists of residues 260 to 277 of Phl p5. This peptide was constructed by extending peptide Tim10C (residues 268 to 276 of Phl p5) to include a second, third and fourth T cell epitope (As confirmed in the further in silico analysis of Phl p 5 in Example 5). Production of IL13 in response to both peptides was measured as in Example 1. As shown in FIG. 1 , Tim 10B demonstrates consistently greater cytokine production in the panel of subjects tested than the “single epitope” peptide Tim 10C.
  • Tim 10B 260 KYTVFETALKKAITAMSE 277 (SEQ ID NO: 50)
  • Tim 10C 268 LKKAITAMS 276 (SEQ ID NO: 51)
  • the peptides listed in this Example were identified as containing T cell epitopes by an in silico MHC binding analysis.
  • the peptides identified have strong affinities for the seven most common human MHC Class II HLA-DRB1* allotypes (covering in total around 63% of the allotypes found in the average Caucasian population).
  • binding potential for HLA DR1, DR2, DR3, DR4, DR7, DR8, DR11, DR13 and DR15 is assessed.
  • Putative MHC ligands are selected by scoring each 9-mer frame in a protein sequence. This score is derived by comparing the sequence of the 9-mer to the matrix of amino acid sequences known to bind to each MHC allele. Retrospective studies have demonstrated that EpiMatrix accurately predicts published MHC ligands (Jesdale et al., in Vaccines '97 (Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 1997)). Successful prediction of peptides which bind to multiple MHC molecules has also been confirmed.
  • the tables shown below show Epivax data for consecutive 9-mers in specific regions of each of the above allergen proteins.
  • the regions are identified by “Frame start” and “Frame stop” values, which refer to the amino acid positions in the published sequences of each protein (the protein concerned and the relevant public database accession number for its sequence is shown at the top of each table). Flanking amino acids, added to stabilize the cluster during in-vitro testing, are shown underlined.
  • Epivax also analysed hydrophobicity of peptides containing epitopes. Scores of greater than 1 are considered to be unsuitable for administration and/or manufacture.
  • Example 3 The peptides listed in this Example were identified as in Example 3.
  • Example 3 The peptides listed in this Example were identified as in Example 3.
  • Phl P 1 Accession No. P43213 Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO 142 GDEQKLRSA 150 ⁇ .62 ⁇ .54 ⁇ 1.14 -2.14 ⁇ 1.22 ⁇ .15 .20 ⁇ 1.31 0 146 143 DEQKLRSAG 151 ⁇ .71 .34 ⁇ 1.29 ⁇ 1.40 1.88 .74 .42 ⁇ .25 1 147 144 EQKLRSAGE 152 1.04 .00 1.00 ⁇ .03 1.42 .61 ⁇ .03 ⁇ .85 0 148 145 QKLRSAGEL 153 .85 .25 ⁇ .69 2.11 1.23 .54 .
  • Example 3 The peptides listed in this Example were identified as in Example 3.
  • ALT A 1 Accession No. AAD00097 Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ ID Start Sequence Stop Hydrophobicity Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits NO 40 Q LLMLSAKR 48 .06 1.52 0 232 41 LLMLSAKRM 49 .87 2.83 1.44 2.17 1.46 1.71 1.47 1.33 3 233 42 LMLSAKRMK 50 .01 1.62 2.04 1.49 1 234 43 MLSAKRMKV 51 .06 1.29 1.49 1.65 1.83 1.28 2.34 3 235 44 LSAKRMKVA 52 .04 0 236 45 SAKRMKVAF 53 ⁇ .07 0 237 46 AKRMKVAFK 54 ⁇ .41 1.67 1.38 1 238 47 KRMKVAF
  • AAM90320 Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ ID Start Sequence Stop Hydrophobicity Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits NO 53 T YYNSLGFN 61 ⁇ .12 0 261 54 YYNSLGFNI 62 .03 2.47 2.66 1.94 3 262 55 YNSLGFNIK 63 ⁇ .26 1.48 0 263 56 NSLGFNIKA 64 .09 0 264 57 SLGFNIKAT 65 .40 0 265 58 LGFNIKATN 66 .10 1.72 2.04 1.82 1.62 3 266 59 GFNIKATNG 67 ⁇ .37 0 267 60 FNIKATNGG 68 ⁇ .37 1.58 1.92 2.97 1.50 1.48 1.55

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Abstract

The present invention relates to peptides comprising multiple MHC Class II-binding T cell epitopes for tolerisation therapy.

Description

    RELATED APPLICATIONS
  • This application is a continuation of U.S. patent application Ser. No. 12/673,386 (allowed), filed on Mar. 11, 2010, which is a national stage filing under 35 U.S.C. 371 of International Patent Application No. PCT/GB2008/002780, filed Aug. 15, 2008, which claims the benefit of British Patent Application No. 0715949.4, filed Aug. 15, 2007, British Patent Application No. 0716224.1, filed Aug. 20, 2007, and British Priority Application No. 0723337.2, filed Nov. 28, 2007.
    • FIELD OF THE INVENTION
  • The present invention relates to peptides comprising multiple MHC Class II-binding T cell epitopes for tolerisation therapy.
    • BACKGROUND OF THE INVENTION
  • T-cell antigen recognition requires antigen presenting cells (APCs) to present antigen fragments (peptides) on their cell surface in association with molecules of the major histocompatibility complex (MHC). T cells use their antigen specific T-cell receptors (TCRs) to recognise with high specificity the antigen fragments presented by the APC. Such recognition acts as a trigger to the immune system to generate a range of responses to eradicate the antigen which has been recognized.
  • Most of the specificity of T cell recognition of the antigen fragments is provided by a smaller subsequence of amino acids within the fragments. This subsequence is known as the T cell epitope. In the case of extracellular allergens and auto- or allo-antigens, the peptides are presented on MHC Class II molecules, which are recognized by CD4 T cells. Accordingly, interest in allergic and auto- or allo-immune disorders has focused on MHC Class II-binding T cell epitopes.
  • Given their role in the immune system, there is considerable interest in such epitopes for use as therapeutic agents to modulate the immune systems of subjects. For example, administration of peptide epitopes to subjects has been demonstrated to result in the induction of tolerance to the antigen from which the epitope derives. Therapeutic agents based on such an effect have great potential in the prevention and treatment of allergy, and auto- or allo-immune diseases where the down-regulation of an immune response is desirable.
    • SUMMARY OF THE INVENTION
  • The minimal amino acid sequence of a T cell epitope required for binding to MHC Class II-molecules can be precisely identified and generally comprises approximately nine amino acids. An epitope sequence typically binds specifically to a particular class of MHC Class II molecule, and does not bind to other MHC Class II molecules. Accordingly, the efficacy of a given epitope sequence varies greatly depending on the MHC Class II type of the individual to whom it is administered. To utilise an epitope for, e.g. the induction of tolerance, it is therefore necessary to undertake time-consuming and costly steps to identify the MHC Class II type of the individual to be tolerised.
  • The present inventors have made the finding that by incorporating multiple different epitope sequences, it is possible to produce a peptide which binds to multiple different classes of MHC Class II and is therefore effective when administered to a wider range of individuals, reducing the requirement to identify the MHC Class II type of an individual. Two or more epitope sequences may be combined in a peptide in an overlapping configuration, or as two independent sequences separated by amino acids which are not comprised in either epitope, without producing a peptide large enough to possess significant tertiary structure that would enable it to retain the conformation of an IgG or IgE-cross-linking epitope. Consequently the downstream immune responses to antigen caused by such cross-linking do not occur.
  • Accordingly, the present invention provides:
  • a peptide which has a length of 10 to 25 amino acids, the peptide comprising a region that comprises at least two different MHC class II-binding T cell epitope sequences, wherein the epitope sequences comprise at least 9 amino acids and derive from an antigenic protein, and wherein each epitope sequence binds to a different MHC class II molecule, and wherein the region is optionally flanked at the N and/or C terminus by additional amino acids which are not part of the epitope sequence. The peptide is typically suitable for use in tolerisation therapy. Polynucleotides, vectors and cells expressing the peptide of the invention, and methods of making the peptide of the invention are also provided.
    • DETAILED DESCRIPTION OF THE INVENTION
  • It is to be understood that references to inserting, deleting, replacing amino acids herein does not require the actual physical insertion, deletion or replacement of amino acids, and instead a peptide can be synthesized comprising sequence which represents (or is the end result of) the insertion, deletion or replacement having occurred.
    • Amino Acids
  • The table below shows the properties of amino acids.
  •
    Ala aliphatic, hydrophobic, neutral Met hydrophobic,
    neutral
    Cys polar, hydrophobic, neutral Asn polar, hydrophilic,
    neutral
    Asp polar, hydrophilic, charged (−) Pro hydrophobic,
    neutral
    Glu polar, hydrophilic, charged (−) Gln polar, hydrophilic,
    neutral
    Phe aromatic, hydrophobic, neutral Arg polar, hydrophilic,
    charged (+)
    Gly aliphatic, neutral Ser polar, hydrophilic,
    neutral
    His aromatic, polar, hydrophilic, Thr polar, hydrophilic,
    charged (+) neutral
    Ile aliphatic, hydrophobic, neutral Val aliphatic, hydrophobic,
    neutral
    Lys polar, hydrophilic, charged(+) Trp aromatic, hydrophobic,
    neutral
    Leu aliphatic, hydrophobic, neutral Tyr aromatic, polar,
    hydrophobic
    • MHC Class II-Binding T Cell Epitopes
  • The MHC Class II-binding T cell epitope comprised in the peptides of the invention is typically the minimal amino acid sequence that is capable of binding to Class II molecules and capable of stimulating T cells when presented in to T cells in association with Class II on the cell surface. The epitope is typically one that binds to a human MHC class II molecule.
  • An MHC Class II molecule consists of two proteins, α and β each of which is encoded by a different gene. In humans, there are three clusters of genes encoding different α and β proteins. These are the Human Leukocyte Antigen (HLA) clusters, DR, DQ and DP. Each cluster comprises multiple different A genes encoding different variant of the α protein and multiple different B genes encoding different variants of the β protein. The resulting MHC Class II heterodimers are therefore extremely diverse, and correspondingly so are the T cell epitopes that they bind.
  • The binding site of MHC Class II molecules is composed of two separate proteins which form a cleft. The cleft is open-ended, which in theory allows a peptide of any length to bind. However, only 9 amino acids can occupy the cleft itself. The identities of the up to 9 amino acids which occupy the cleft define whether or not a given peptide will bind to a given MHC Class II molecule and be available for presentation to T cells. These up to 9 amino acids therefore represent the minimal sequence that is required for MHC Class II-binding. It is generally assumed that such a sequence will be capable of stimulating T cells when presented to T cells in association with Class II on the cell surface. However, this may be confirmed experimentally by methods standard in the art.
  • Such methods may typically comprise contacting the epitope with T cells in a sample taken from a subject, under conditions which allow the epitope and the T cells to interact; and then determining whether or not any of the T cells are stimulated. Determining whether or not the T cells are stimulated may be achieved by any suitable method, for example by detecting the production of cytokines by the T cells, wherein cytokine production indicates that T cells have been stimulated. Suitable cytokines include interferon gamma and interleukin 13. Cytokine production may be detected by any suitable method, for example an ELISA, ELISPOT assay or a flow cytometric assay. Particularly preferred methods include Multiplex bead array assays as described in, for example de Jager et al; Clinical and Diagnostic Laboratory Immunology, 2003, Vol 10(1) p. 133-139 The T cells in a sample from a subject are typically present in a population of peripheral blood mononuclear cells (PBMCs) isolated from a blood or serum sample taken from the subject.
  • The MHC Class II-binding T cell epitope of the invention typically consists of 8 or 9 amino acids, but may consist of 7, 10, 11, 12, 13, 14, 15 or 16 amino acids. The amino acid sequence of the epitope may be broadly defined by further reference to the binding site of MHC Class II molecules. This binding site has specific binding pockets, which corresponding to primary and secondary anchor positions in the sequence of the binding peptide epitope. The binding pockets are defined by amino acid positions in the sequence of the MHC Class II molecule, and are generally not absolutely discriminatory for a specific amino acid in the epitope. Therefore the peptide binding specificity of any given MHC molecule is relatively broad. Thus, peptides binding to the same MHC allotype exhibit some degree of similarity, but there is no requirement for identity.
  • For the most common human MHC Class II type, HLA-DR, the key anchor positions for binding to the binding pockets are at positions 1, 4, 6, 7 and 9 of the peptide epitope (counting from the most N terminal residue occupying the cleft to the most C terminal). Different HLA-DR alleles which have similar amino acids in their binding pockets therefore typically bind peptides with similar amino acids at positions 1, 4, 6, 7 and 9. Accordingly, the region containing an MHC Class II binding T cell epitope preferably has amino acids at positions corresponding to positions 1, 4, 6, 7 and 9 that allow binding to the widest range of HLA-DR alleles. Examples of characteristic binding properties of different HLA-DR alleles are set out below:
  • DR alleles with Glycine at position 86 of the β chain show strong preferences for large hydrophobic side chains (Trp, Tyr, Phe) at peptide position 1, whereas Valine at position 86 restricts the pocket size and alters the preferences to small hydrophobic side chains (Val and Ala) at this position. Medium sized hydrophobic amino acids Leu and Be are well accepted in all DR alleles.
  • DR alleles with Gln at position 70, Lysine at position 71, and Arginine or Gln at position 74 of the β chain have an overall positive charge within pocket 4, which requires negatively charged amino acids Asp and Glu at position 4 of the binding peptide (as in for example, DRB1*0301). DR alleles with this motif are associated with two autoimmune diseases: systematic lupus erythematosus and Hashimoto's thyroiditis.
  • DR alleles with Gln or Arg at position 70, Arg or Lys at position 71 and Glu or Ala at position 74 of the β chain bind similar peptides to those directly above since the only significant difference is at position 74. However, when Ala is present at position 74, pocket 4 increases in size and can accommodate larger amino acids such as Phe, Trp, and Ile (as in for example DRB1*0401, 04, 05). Alleles bearing Glu at position 74 are expected to allow small polar residues, like Ser and Thr at position 4 of the binding peptide. DR alleles with this motif are associated with a susceptibility to rheumatoid arthritis.
  • DR alleles with Asp at position 70, Glu or Arg at position 71, and Leu or Ala at position 74 of the β chain exclude peptides with negatively charged amino acids at peptide position 4 (for example DRB1*0402). This is due to the presence of Asp at position 70. DR alleles with this motif are associated with the autoimmune diseases Juvenile rheumatoid arthritis (JRA), pemphigus vulgaris, and allergic bronchopulmonary.
  • Polymorphisms at position 9 of the β chain define the size of binding pocket 9 in all DR alleles. Alleles with Trp at this position accept only small amino acids in position 9 of the binding peptide, e.g. Ala, Val, Gly, Ser, Thr, Pro (as in for example DRB1*0101 and *1501). Glu at position 9, in combination with Asp at position 57, makes pocket 9 negatively charged, facilitating the accommodation of positively charged amino acids, such as Lys (as in for example DRB1*0401 and *0404) and Histine (as in for example DRB1*0402). In most MHC class II alleles, Asp at position 57 makes a salt-bridged hydrogen bond with Arg at position 76, allowing the pocket to also accommodate aliphatic and polar amino acids. In cases where Asp at position 57 is replaced by Ser (for example DRB1*0405) or Ala (DQ8), the hydrogen bonding network is destroyed and Arg at position 76 can strongly attract negatively charged amino acids such as Asp or Glu at position 9 of the binding peptide (as in for example DRB1*0405).
  • An example of a preferred sequence for an epitope therefore has Trp, Tyr, Phe, Val or Ala at position 1; Asp, Glu, Ser or Thr at position 4; and Ala, Val, Gly, Ser, Thr, Pro at position 9. A further example of a preferred sequence for an epitope has a large aromatic or hydrophobic amino acid at position 1, for example Tyr, Phe, Trp, Leu, Ile or Val, and a small, non-charged amino acid at position 6, for example Ser, Thr, Ala, Pro, Val, Ile or Met. Approximately 87.5% of peptides binding to all or a combination of the MHC Class II molecules encoded by the DRB1*0101, *0401 and *0701 alleles contain this motif. Furthermore, since T cell epitopes derived from allergens and autoimmune antigens do not typically contain a large number of repeats of a given amino acid or amino acids, preferred epitopes of the invention typically comprise at least 5, 6, 7 or 8 different amino acids.
  • The precise amino sequence of an epitope may be predicted by computer-based algorithms and confirmed by in vitro biochemical analysis. Suitable commercially available algorithms include the EpiMatrix algorithm (EpiVax Inc.). Other algorithms are available at, for example, the website at the ProPed MHC Class-II Binding Peptide Prediction Server. Analysis with these algorithms typically comprises parsing a larger polypeptide sequence into multiple overlapping small peptides. The sequences of these small peptides are then analysed using the algorithm to identify those which are predicted to bind MHC Class II molecules. The overlapping small peptides are typically 9-mers.
  • The candidate peptides which score most highly in this analysis are then assessed for the ability to bind a panel of MHC Class II molecules encoded by different Class II alleles in vitro using standard binding assays. For example a competitive MHC class II binding assay may be used, wherein each peptide is analysed for its ability to displace a known control binder from each of the human MHC class II allotypes investigated. In such an assay each peptide is assigned an IC50 value (the concentration at which 50% inhibition of control peptide binding is achieved). The lower the IC50 the higher the affinity of a peptide for a given MHC class II allotype.
  • The epitope or epitopes in a polypeptide are taken to be those peptides which show the highest binding affinity to MHC Class II molecules. Particularly preferred epitopes show high affinity binding to different Class II molecules encoded by more than one preferably two, more preferably three, four or five MHC Class II alleles.
  • It will be appreciated that biochemical assays for the identification of a T cell epitope are not typically able to precisely define the position of the minimal epitope sequence within a larger sequence more accurately than to within approximately 12 amino acids, and more typically 15, 20 or more amino acids. The reason for this is that a large sequence must be physically fragmented into smaller overlapping peptides, or smaller overlapping peptides must be manufactured de novo prior to in vitro assessment of the ability of these peptides to bind MHC Class II molecules. The skilled person will recognise that the smaller the overlapping peptide fragments used, the more time-consuming and labour intensive is the process of manufacture. Hence epitopes are often identified as being contained within a larger polypeptide region. It is envisaged that the epitopes of the invention may be defined as such a larger region.
  • In all cases, it is envisaged that the epitope sequences of the invention also comprise functional variants of the epitope sequences. A functional variant epitope sequence is any homologous epitope sequence which is able to stimulate a T cell that specifically recognise the native epitope sequence from which the variant derives, or which is able to induce tolerance to the native epitope sequence in an individual. Such a variant typically has at least 55%, preferably 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 99% homology to the native epitope sequence. Suitable methods for determining the stimulatory effect of a variant epitope are known in the art. For example, a sample of peripheral blood mononuclear cells (PBMCs) can be stimulated with the protein from which the native epitope derives at various cell densities. After one week of culture, the T cell cultures are restimulated with autologous antigen presenting cells pulsed with peptides consisting of the native epitope sequence, which produces T cell lines specific for the native epitope sequence. The resulting lines can then be tested to see if they are stimulated by any variant epitope sequence, with stimulation being correlated with, e.g. proliferation or production of cytokines, in particular interferon-gamma, interleukin-13 and interleukin-17.
    • Regions Containing at Least Two MHC Class II-Binding T Cell Epitopes
  • As set out above, the bioinformatic techniques used to identify epitopes may identify multiple epitopes in the same polypeptide. Each of these multiple epitopes typically binds to different types of MHC Class II molecule. That is, a first epitope may bind Class II molecules encoded by alleles w, x, and y, whereas a second epitope binds Class II molecules encoded by alleles x, y and z. Since the region of the invention comprises at least two different epitope sequences, the peptides of the invention are capable of binding to a large number of different MHC Class II molecules.
  • The multiple different epitope sequences may be comprised in a region as two or more overlapping epitopes. For example, in a sequence of 12 amino acids, one epitope corresponds to amino acids 1 to 9 and a second epitope corresponds to amino acids 4 to 12. A peptide region comprising amino acids 1 to 12 will therefore comprise two overlapping epitope sequences since both epitopes comprise the contiguous sequence of amino acids 4 to 9.
  • The overlap of sequence between any two epitopes may typically comprise a contiguous sequence of upto approximately 10%, 20%, 30%, 40%, 50%, 60%, 65%, 70%, 80% or 90% of the amino acids from the N or C terminus either epitope. Therefore, assuming an epitope length of 9 amino acids, a second epitope may comprise the contiguous sequence of 1, 2, 3, 4, 5, 6, 7 or 8 amino acids at the N terminal of a first epitope, with additional amino acids present at the N terminus of this sequence which are not comprised in the first epitope, or may comprise the contiguous sequence of 1, 2, 3, 4, 5, 6, 7 or 8 amino acids at the C terminal of a first epitope, with additional amino acids present at the C terminus of this sequence which are not comprised in the first epitope.
  • A preferred overlap of sequence between any two epitopes typically comprises a contiguous sequence of upto approximately 65% of the amino acids from the N or C terminus either epitope. For an epitope length of 9 amino acids, a second epitope may therefore comprise the contiguous sequence of 6 amino acids at the N terminal of a first epitope, with additional amino acids present at the N terminus of this sequence which are not comprised in the first epitope, or may comprise the contiguous sequence of 6 amino acids at the C terminal of a first epitope, with additional amino acids present at the C terminus of this sequence which are not comprised in the first epitope.
  • Alternatively, the multiple epitopes in the region may be two or more independent sequences. The independent sequences may be consecutive or may be separated by additional amino acids which are not comprised in an epitope. As an example of the former case, in a sequence of 18 amino acids, one epitope corresponds to amino acids 1 to 9 and a second epitope corresponds to amino acids 10 to 18. As an example of the latter case, in a sequence of 19 amino acids, one epitope corresponds to amino acids 1 to 9 and a second epitope corresponds to amino acids 11 to 19. In this example, amino acid 10 is not comprised in either epitope. In general terms, two independent epitope sequences may typically be separated by 1, 2, 3, 4, 5, 6 or 7 additional amino acids which are not comprised in either epitope.
  • The amino acid sequence separating the epitope sequences (“the additional amino acid(s)”) may comprise any amino acid sequence. It is particularly preferred that the additional amino acid(s) comprise a high proportion of hydrophilic amino acids (typically>60%) and comprise no cysteine residues.
  • In one preferred embodiment, the sequence of the additional amino acid(s) is identical to or homogolous to the sequence of the amino acid(s) which separates the epitope sequences in the native sequence of the protein from which the epitopes derive. If the additional amino acid(s) are homolgous to the native sequence, homology of greater than 55%, 60%, 75%, 80%, 85%, 90% or 95% with the native sequence is preferred. In an alternative embodiment, the sequence of the additional amino acid(s) is not related to the sequence of the amino acid(s) which separates the epitope sequences in the native sequence of the protein from which the epitopes derive. That is, the region may comprise a fusion protein comprising a first epitope, a sequence of additional amino acids, and at least a second epitope.
  • Alternatively the multiple epitopes may be present in the region as a combination of overlapping or independent epitope sequences.
  • It will be appreciated that the region may therefore consist entirely of amino acids which are comprised in at least one epitope. Typically, the proportion of amino acids in a region which are comprised in at least one epitope is approximately 70%, 71%, 72%, 73%, 74%, 75%, 80%, 85%, 90% or 95%, or 99%. Preferably, at least 70% of the amino acids in a region are comprised in at least one epitope.
  • The region therefore typically has a length of approximately 18 amino acids, but may be 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 amino acids in length.
    • Peptides
  • The peptides of the invention may consist entirely of the region as defined above. However, the peptides may optionally comprise additional amino acids flanking the N or C termini of the region. These amino acids are not comprised in an epitope. Typically, the proportion of amino acids in a peptide which are comprised in at least one epitope is approximately 70%, 71%, 72%, 73%, 74%, 75%, 80%, 85%, 90% or 95%, or 99%. Preferably, at least 70% of the amino acids in a peptide are comprised in at least one epitope.
  • The residues flanking the region typically result in the peptide having a solubility greater than 3.5 mg/ml in aqueous solution at pH 2.0 to 12.0, or pH 2.0 to 11.0, pH 2.0 to 10.0, pH 2.0 to 9.0, pH 2.0 to 8.0 or pH 2.0 to 7.0. The residues flanking the region are preferably:
  • at the N terminus, at least one, two, three, four, five or six contiguous amino acids corresponding to the at least one, two, three, four, five or six contiguous amino acids immediately N terminal to the region in the natural sequence of the protein from which the region derives; or
  • at the C terminus, at least one, two, three, four, five or six contiguous amino acids corresponding to the at least one, two, three, four, five or six contiguous amino acids immediately C terminal to the epitope sequence in the natural sequence of the protein from which the region derives; or
  • at both the N and C termini, at least one, preferably two, or three amino acids selected from arginine, lysine, histidine, glutamate and aspartate.
  • Further, the peptide may comprise the region as defined above, but incorporating modification of its native sequence. Particularly preferred modifications regions wherein:
  • any cysteine residues in the native sequence of the region are replaced with serine; and/or
  • any hydrophobic residues in the up to one, two, preferably three or four amino acids at the N or C terminus of the native sequence of the region which are not comprised in the epitope are deleted; and/or
  • any two consecutive amino acids comprising the sequence Asp-Gly in the up to three or preferably four amino acids at the N or C terminus of the native sequence of the region which are not comprised in the epitope are deleted.
  • The peptides of the invention typically contain from 10 to 25 amino acids, and may contain 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 amino acids. Peptides longer than 25 amino acids are likely to possess sufficient tertiary structure to cross-link IgG or IgE on cell surfaces resulting in undesirable immune responses such as B cell activation or mast cell degranulation. Peptides shorter than 10 amino acids are unlikely to contain more than one epitope.
    • Peptide Synthesis
  • The peptides of the invention are derived in an intellectual sense from the polypeptide which comprises the epitopes and regions as defined above with additional flanking residues or residues to separate independent epitope sequences. This is done by making use of the amino acid sequence of the region or epitope and synthesising peptides based on the sequence. Peptides may be synthesised using methods well known in the art. Preferred methods include solid-phase peptide synthesis techniques and most preferably preferably an automated or semiautomated peptide synthesizer. Typically, using such techniques, an α-N-carbamoyl protected amino acid and an amino acid attached to the growing peptide chain on a resin are coupled at room temperature in an inert solvent such as dimethylformamide, N-methylpyrrolidinone or methylene chloride in the presence of coupling agents such as dicyclohexylcarbodiimide and 1-hydroxybenzotriazole in the presence of a base such as diisopropyl-ethylamine. The α-N-carbamoyl protecting group is removed from the resulting peptide-resin using a reagent such as trifluoroacetic acid or piperidine, and the coupling reaction repeated with the next desired N-protected amino acid to be added to the peptide chain. Suitable N-protecting groups are well known in the art, and include t-butyloxycarbonyl (tBoc) and fluorenylmethoxycarbonyl (Fmoc).
  • The term “peptide” includes not only molecules in which amino acid residues are joined by peptide (—CO—NH—) linkages but also molecules in which the peptide bond is reversed. Such retro-inverso peptidomimetics may be made using methods known in the art, for example such as those described in Meziere et al (1997) J. Immunol.159, 3230-3237. This approach involves making pseudopeptides containing changes involving the backbone, and not the orientation of side chains. Meziere et al (1997) show that, at least for MHC class II and T helper cell responses, these pseudopeptides are useful. Retro-inverse peptides, which contain NH—CO bonds instead of CO—NH peptide bonds, are much more resistant to proteolysis.
  • Similarly, the peptide bond may be dispensed with altogether provided that an appropriate linker moiety which retains the spacing between the carbon atoms of the amino acid residues is used; it is particularly preferred if the linker moiety has substantially the same charge distribution and substantially the same planarity as a peptide bond. It will also be appreciated that the peptide may conveniently be blocked at its N-or C-terminus so as to help reduce susceptibility to exoproteolytic digestion. For example, the N-terminal amino group of the peptides may be protected by reacting with a carboxylic acid and the C-terminal carboxyl group of the peptide may be protected by reacting with an amine. Other examples of modifications include glycosylation and phosphorylation. Another potential modification is that hydrogens on the side chain amines of R or K may be replaced with methylene groups (—NH2→-NH(Me) or —N(Me)2).
  • Analogues of peptides according to the invention may also include peptide variants that increase or decrease the peptide's half-life in vivo. Examples of analogues capable of increasing the half-life of peptides used according to the invention include peptoid analogues of the peptides, D-amino acid derivatives of the peptides, and peptide-peptoid hybrids. A further embodiment of the variant polypeptides used according to the invention comprises D-amino acid forms of the polypeptide. The preparation of polypeptides using D-amino acids rather than L-amino acids greatly decreases any unwanted breakdown of such an agent by normal metabolic processes, decreasing the amounts of agent which needs to be administered, along with the frequency of its administration.
    • Polynucleotides, Vectors and Cells
  • The terms “nucleic acid molecule” and “polynucleotide” are used interchangeably herein and refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Non-limiting examples of polynucleotides include a gene, a gene fragment, messenger RNA (mRNA), cDNA, recombinant polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide of the invention may be provided in isolated or purified form. A nucleic acid sequence which “encodes” a selected polypeptide is a nucleic acid molecule which is transcribed (in the case of DNA) and translated (in the case of mRNA) into a polypeptide in vivo when placed under the control of appropriate regulatory sequences. The boundaries of the coding sequence are determined by a start codon at the 5′ (amino) terminus and a translation stop codon at the 3′ (carboxy) terminus. For the purposes of the invention, such nucleic acid sequences can include, but are not limited to, cDNA from viral, prokaryotic or eukaryotic mRNA, genomic sequences from viral or prokaryotic DNA or RNA, and even synthetic DNA sequences. A transcription termination sequence may be located 3′ to the coding sequence.
  • Polynucleotides of the invention can be synthesised according to methods well known in the art, as described by way of example in Sambrook et al (1989, Molecular Cloning—a laboratory manual; Cold Spring Harbor Press).
  • The polynucleotide molecules of the present invention may be provided in the form of an expression cassette which includes control sequences operably linked to the inserted sequence, thus allowing for expression of the peptide of the invention in vivo in a targeted subject. These expression cassettes, in turn, are typically provided within vectors (e.g., plasmids or recombinant viral vectors) which are suitable for use as reagents for nucleic acid immunization. Such an expression cassette may be administered directly to a host subject. Alternatively, a vector comprising a polynucleotide of the invention may be administered to a host subject. Preferably the polynucleotide is prepared and/or administered using a genetic vector. A suitable vector may be any vector which is capable of carrying a sufficient amount of genetic information, and allowing expression of a peptide of the invention.
  • The present invention thus includes expression vectors that comprise such polynucleotide sequences. Thus, the present invention provides a vector for use in preventing or treating allergy by tolerisation comprising four or more polynucleotide sequences which encode different polypeptides of the invention and optionally one or more further polynucleotide sequences which encode different polypeptides as defined herein. The vector may comprise 4, 5, 6 or 7 polynucleotide sequences which encode different polypeptides of the invention.
  • Furthermore, it will be appreciated that the compositions and products of the invention may comprise a mixture of polypeptides and polynucleotides. Accordingly, the invention provides a composition or product as defined herein, wherein in place of any one of the polypeptide is a polynucleotide capable of expressing said polypeptide.
  • Expression vectors are routinely constructed in the art of molecular biology and may for example involve the use of plasmid DNA and appropriate initiators, promoters, enhancers and other elements, such as for example polyadenylation signals which may be necessary, and which are positioned in the correct orientation, in order to allow for expression of a peptide of the invention. Other suitable vectors would be apparent to persons skilled in the art. By way of further example in this regard we refer to Sambrook et al.
  • Thus, a polypeptide of the invention may be provided by delivering such a vector to a cell and allowing transcription from the vector to occur. Preferably, a polynucleotide of the invention or for use in the invention in a vector is operably linked to a control sequence which is capable of providing for the expression of the coding sequence by the host cell, i.e. the vector is an expression vector.
  • “Operably linked” refers to an arrangement of elements wherein the components so described are configured so as to perform their usual function. Thus, a given regulatory sequence, such as a promoter, operably linked to a nucleic acid sequence is capable of effecting the expression of that sequence when the proper enzymes are present. The promoter need not be contiguous with the sequence, so long as it functions to direct the expression thereof. Thus, for example, intervening untranslated yet transcribed sequences can be present between the promoter sequence and the nucleic acid sequence and the promoter sequence can still be considered “operably linked” to the coding sequence.
  • A number of expression systems have been described in the art, each of which typically consists of a vector containing a gene or nucleotide sequence of interest operably linked to expression control sequences. These control sequences include transcriptional promoter sequences and transcriptional start and termination sequences. The vectors of the invention may be for example, plasmid, virus or phage vectors provided with an origin of replication, optionally a promoter for the expression of the said polynucleotide and optionally a regulator of the promoter. A “plasmid” is a vector in the form of an extrachromosomal genetic element. The vectors may contain one or more selectable marker genes, for example an ampicillin resistence gene in the case of a bacterial plasmid or a resistance gene for a fungal vector. Vectors may be used in vitro, for example for the production of DNA or RNA or used to transfect or transform a host cell, for example, a mammalian host cell. The vectors may also be adapted to be used in vivo, for example to allow in vivo expression of the polypeptide.
  • A “promoter” is a nucleotide sequence which initiates and regulates transcription of a polypeptide-encoding polynucleotide. Promoters can include inducible promoters (where expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.), repressible promoters (where expression of a polynucleotide sequence operably linked to the promoter is repressed by an analyte, cofactor, regulatory protein, etc.), and constitutive promoters. It is intended that the term “promoter” or “control element” includes full-length promoter regions and functional (e.g., controls transcription or translation) segments of these regions.
  • A polynucleotide, expression cassette or vector according to the present invention may additionally comprise a signal peptide sequence. The signal peptide sequence is generally inserted in operable linkage with the promoter such that the signal peptide is expressed and facilitates secretion of a polypeptide encoded by coding sequence also in operable linkage with the promoter.
  • Typically a signal peptide sequence encodes a peptide of 10 to 30 amino acids for example 15 to 20 amino acids. Often the amino acids are predominantly hydrophobic. In a typical situation, a signal peptide targets a growing polypeptide chain bearing the signal peptide to the endoplasmic reticulum of the expressing cell. The signal peptide is cleaved off in the endoplasmic reticulum, allowing for secretion of the polypeptide via the Golgi apparatus. Thus, a peptide of the invention may be provided to an individual by expression from cells within the individual, and secretion from those cells.
  • Alternatively, polynucleotides of the invention may be expressed in a suitable manner to allow presentation of a peptide of the invention by an MHC class II molecule at the surface of an antigen presenting cell. For example, a polynucleotide, expression cassette or vector of the invention may be targeted to antigen presenting cells, or the expression of encoded peptide may be preferentially stimulated or induced in such cells.
  • In some embodiments, the polynucleotide, expression cassette or vector will encode an adjuvant, or an adjuvant will otherwise be provided. As used herein, the term “adjuvant” refers to any material or composition capable of specifically or non-specifically altering, enhancing, directing, redirecting, potentiating or initiating an antigen-specific immune response.
  • Polynucleotides of interest may be used in vitro, ex vivo or in vivo in the production of a peptide of the invention. Such polynucleotides may be administered or used in the prevention or treatment of allergy by tolerisation.
  • Methods for gene delivery are known in the art. See, e.g., U.S. Pat. Nos. 5,399,346, 5,580,859 and 5,589,466. The nucleic acid molecule can be introduced directly into the recipient subject, such as by standard intramuscular or intradermal injection; transdermal particle delivery; inhalation; topically, or by oral, intranasal or mucosal modes of administration. The molecule alternatively can be introduced ex vivo into cells that have been removed from a subject. For example, a polynucleotide, expression cassette or vector of the invention may be introduced into APCs of an individual ex vivo. Cells containing the nucleic acid molecule of interest are re-introduced into the subject such that an immune response can be mounted against the peptide encoded by the nucleic acid molecule. The nucleic acid molecules used in such immunization are generally referred to herein as “nucleic acid vaccines.”
  • The polypeptides, polynucleotides, vectors or cells of the invention may be present in a substantially isolated form. They may be mixed with carriers or diluents which will not interfere with their intended use and still be regarded as substantially isolated. They may also be in a substantially purified form, in which case they will generally comprise at least 90%, e.g. at least 95%, 98% or 99%, of the proteins, polynucleotides, cells or dry mass of the preparation.
    • Formulations and Compositions
  • The peptides, polynucleotides, vectors and cells of the invention may be provided to an individual either singly or in combination. Each molecule or cell of the invention may be provided to an individual in an isolated, substantially isolated, purified or substantially purified form. For example, a peptide of the invention may be provided to an individual substantially free from the other peptides.
  • Whilst it may be possible for the peptides, polynucleotides or compositions according to the invention to be presented in raw form, it is preferable to present them as a pharmaceutical formulation. Thus, according to a further aspect of the invention, the present invention provides a pharmaceutical formulation for tolerising an individual to a protein from which a peptide of the invention derives, comprising a composition, vector or product according to the invention together with one or more pharmaceutically acceptable carriers or diluents and optionally one or more other therapeutic ingredients. The carrier (s) must be ‘acceptable’ in the sense of being compatible with the other ingredients of the formulation and not deleterious to the recipient thereof. Typically, carriers for injection, and the final formulation, are sterile and pyrogen free. The high solubility of the peptide of the invention results in there being little or no requirement for the organic solvents usual in pharmaceutical compositions. Accordingly, the present invention provides a pharmaceutical formulation as defined above comprising less than 5% organic solvent. Subject to this limitation, formulation of a composition comprising the peptide, polynucleotide or cell of the invention can be carried out using standard pharmaceutical formulation chemistries and methodologies all of which are readily available to the reasonably skilled artisan.
  • For example, compositions containing one or more molecules or cells of the invention can be combined with one or more pharmaceutically acceptable excipients or vehicles. Auxiliary substances, such as wetting or emulsifying agents, pH buffering substances and the like, may be present in the excipient or vehicle. These excipients, vehicles and auxiliary substances are generally pharmaceutical agents that do not induce an immune response in the individual receiving the composition, and which may be administered without undue toxicity. Pharmaceutically acceptable excipients include, but are not limited to, liquids such as water, saline, polyethyleneglycol, hyaluronic acid, glycerol, and ethanol. Pharmaceutically acceptable salts can also be included therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulfates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. A thorough discussion of pharmaceutically acceptable excipients, vehicles and auxiliary substances is available in Remington's Pharmaceutical Sciences (Mack Pub. Co., N.J. 1991).
  • Such compositions may be prepared, packaged, or sold in a form suitable for bolus administration or for continuous administration. Injectable compositions may be prepared, packaged, or sold in unit dosage form, such as in ampoules or in multi-dose containers containing a preservative. Compositions include, but are not limited to, suspensions, solutions, emulsions in oily or aqueous vehicles, pastes, and implantable sustained-release or biodegradable formulations. Such compositions may further comprise one or more additional ingredients including, but not limited to, suspending, stabilizing, or dispersing agents. In one embodiment of a composition for parenteral administration, the active ingredient is provided in dry (for e.g., a powder or granules) form for reconstitution with a suitable vehicle (e. g., sterile pyrogen-free water) prior to parenteral administration of the reconstituted composition. The pharmaceutical compositions may be prepared, packaged, or sold in the form of a sterile injectable aqueous or oily suspension or solution. This suspension or solution may be formulated according to the known art, and may comprise, in addition to the active ingredient, additional ingredients such as the dispersing agents, wetting agents, or suspending agents described herein. Such sterile injectable formulations may be prepared using a non-toxic parenterally-acceptable diluent or solvent, such as water or 1,3-butane diol, for example. Other acceptable diluents and solvents include, but are not limited to, Ringer's solution, isotonic sodium chloride solution, and fixed oils such as synthetic mono-or di-glycerides. Other parentally-administrable compositions which are useful include those which comprise the active ingredient in microcrystalline form, in a liposomal preparation, or as a component of a biodegradable polymer systems. Compositions for sustained release or implantation may comprise pharmaceutically acceptable polymeric or hydrophobic materials such as an emulsion, an ion exchange resin, a sparingly soluble polymer, or a sparingly soluble salt.
  • Alternatively, the peptides or polynucleotides of the present invention may be encapsulated, adsorbed to, or associated with, particulate carriers. Suitable particulate carriers include those derived from polymethyl methacrylate polymers, as well as PLG microparticles derived from poly(lactides) and poly(lactide-co-glycolides). See, e.g., Jeffery et al. (1993) Pharm. Res. 10:362-368. Other particulate systems and polymers can also be used, for example, polymers such as polylysine, polyarginine, polyornithine, spermine, spermidine, as well as conjugates of these molecules.
  • The formulation of any of the peptides, polynucleotides or cells mentioned herein will depend upon factors such as the nature of the substance and the method of delivery. Any such substance may be administered in a variety of dosage forms. It may be administered orally (e.g. as tablets, troches, lozenges, aqueous or oily suspensions, dispersible powders or granules), parenterally, subcutaneously, by inhalation, intravenously, intramuscularly, intrasternally, transdermally, intradermally, epicutaneously, sublingually, intranasally, buccally or by infusion techniques. The substance may also be administered as suppositories. A physician will be able to determine the required route of administration for each particular individual.
  • The compositions of formulations of the invention will comprise a suitable concentration of each peptide/polynucleotide/cell to be effective without causing adverse reaction. Typically, the concentration of each peptide in the composition will be in the range of 0.03 to 200 nmol/ml. More preferably in the range of 0.3 to 200 nmol/ml, 3 to 180 nmol/ml, 10 to 150 nmol/ml or 30 to 120 nmol/ml. Such concentrations are particularly favoured for intradermal administration since an effective dose may be administered in a volume of 60 μl, preferably 50 μl, and most preferably 30 μl. The composition or formulations should have a purity of greater than 95% or 98% or a purity of at least 99%.
  • A composition may therefore be formulated which comprises a molecule and/or cell of the invention and also one or more other therapeutic molecules. A composition of the invention may alternatively be used simultaneously, sequentially or separately with one or more other therapeutic compositions as part of a combined treatment.
    • Therapeutic Methods and Individual to be Treated
  • The present invention relates to peptides, polynucleotides, vectors and cells that are capable of desensitising or tolerising human individuals to proteins from which the peptides of the invention derive. Such proteins are typically allergens or other antigens to which an immune response is undesirable. Examples of such antigens include antigens associated with autoimmune diseases, antigens associated with graft-versus-host disease or transplant rejection (herein referred to as alloimmune conditions) and antigens associated with maternal-foetal immune responses, for example Rhesus D Haemolytic Disease of the Newborn. The peptides of the invention are therefore useful in the prevention or treatment an allergic disease, an autoimmune disease, an alloimmune condition or a maternal-foetal immune response. The invention provides compositions, products, vectors and formulations for use in preventing or treating the above conditions. The invention also provides a method of in preventing or treating a subject having the above conditions, comprising administering, either singly or in combination the polypeptides/polynucleotides/cells of the invention as described above.
  • The individual to be treated or provided with the composition or formulation of the invention is preferably human. It will be appreciated that the individual to be treated may be known to be sensitised to the particular allergen or antigen, at risk of being sensitised or suspected of being sensitised. The individual can be tested for sensitisation using techniques well known in the art and as described herein. Alternatively, the individual may have a family history of the conditions described above. It may not be necessary to test an individual for sensitisation to allergens because the individual may display symptoms of allergy when brought into proximity to a suitable allergen source. By proximity is meant 10 metres or less, 5 metres or less, 2 metres or less, 1 metre or less, or 0 metres from the source. Symptoms of allergy can include itchy eyes, runny nose, breathing difficulties, red itchy skin or rash. The individual to be treated may be of any age. However, preferably, the individual may be in the age group of 1 to 90, 5 to 60, 10 to 40, or more preferably 18 to 35. Preferably, the individual to be treated is from a population that has MHC allele frequencies within the range of frequencies that are representative of the Caucasian population. Reference population allele frequencies for 11 common DRB 1 allele families are shown in Table 1(Data from HLA Facts Book, Parham and Barber).
  • TABLE 1
    DRB1
    1 3 4 7 8 11 12 13 14 15 16
    % 6.4 14.7 15.7 8.8 3.4 8.3 3.9 14.7 2.9 17.6 2.5
    Reference 9.4 11.1 12.8 13.2 3.7 13.4 2.3 10.2 3.2 10.7 3.6
    population %

    Reference frequencies were obtained by analysis of multiple studies reporting frequencies and the figures shown are mean values. Preferably therefore, the individual to be treated is from a population that has equivalent MHC allele frequencies as the reference population for the alleles referred to Table 1 (such as for at least 1, 2, 3, 4, 5 or all of the alleles), for example within the ranges of those figures plus or minus 1, 2, 3, 5, 10, 15 or 20%.
  • Preferably the individual is from a population where the allele frequencies of the following DRB 1 alleles is:
    • 4—at least 9%
    • 7—at least 10%
    • 11—at least 8%.
  • The individual to be treated for allergic disease may have had allergy for at least 2 weeks, 1 month, 6 months, 1 year or 5 years. The individual may suffer from a rash, nasal congestion, nasal discharge and/or coughing caused by the allergy. The individual may or may not have been administered with other compositions/compounds which treat allergy.
    • Allergens and Antigens
  • Suitable allergens from which the region containing a MHC Class II-binding T cell epitope may derive can of course be obtained and/or produced using known methods. Classes of suitable allergens include, but are not limited to, pollens, animal dander (in particular cat dander), grasses, molds, dusts, antibiotics, stinging insect venoms, and a variety of environmental (including chemicals and metals), drug and food allergens. Common tree allergens include pollens from cottonwood, popular, ash, birch, maple, oak, elm, hickory, and pecan trees; common plant allergens include those from mugwort, ragweed, English plantain, sorrel-dock and pigweed; plant contact allergens include those from poison oak, poison ivy and nettles; common grass allergens include rye grass, Timothy, Johnson, Bermuda, fescue and bluegrass allergens; common allergens can also be obtained from molds or fungi such as Alternaria, Fusarium, Hormodendrum, Aspergillus, Micropolyspora, Mucor and thermophilic actinomycetes; epidermal allergens can be obtained from house or organic dusts (typically fungal in origin), from arthropods such as house mites (Dermatophagoides pteronyssinus), or from animal sources such as feathers, and dog dander; common food allergens include milk and cheese (diary), egg, wheat, nut (e.g., peanut), seafood (e.g., shellfish), pea, bean and gluten allergens; common environmental allergens include metals (nickel and gold), chemicals (formaldehyde, trinitrophenol and turpentine), Latex, rubber, fiber (cotton or wool), burlap, hair dye, cosmetic, detergent and perfume allergens; common drug allergens include local anesthetic and salicylate allergens; antibiotic allergens include penicillin, tetracycline and sulfonamide allergens; and common insect allergens include bee, wasp and ant venom, and cockroach calyx allergens. Particularly well characterized allergens include, but are not limited to, the major allergen produced by the domestic cat Felis catus (Felis domesticus) glycoprotein Fel d1, the major and cryptic epitopes of the Der p I allergen (Hoyne et al. (1994) Immunology83190-195), bee venom phospholipase A2 (PLA) (Akdis et al. (1996) J. Clin. Invest. 98:1676-1683), birch pollen allergen Bet v 1 (Bauer et al. (1997) Clin. Exp. Immunol. 107:536-541), and the multi-epitopic recombinant grass allergen rKBG8.3 (Cao et al. (1997) Immunology90:46-51). These and other suitable allergens are commercially available and/or can be readily prepared as extracts following known techniques.
  • Preferably, the allergen is selected from the list of allergen sequences and database accession numbers (NCBI Entrez accession numbers) below. NCBI is the National Center for Biotechnology information and is a division of the US National Institutes of Health. Allergen sequences and database accession numbers (NCBI Entrez accession numbers):
    • House Dust Mite Dermatophagoides Pteronyssinus
  • DerP 1
    (SEQ ID NO: 316)
    MKIVLAIASLLALSAVYARPSSIKTFEEYKKAFNKSYATFEDEEAARKNFLES
    VKYVQSNGGAINHLSDLSLDEFKNRFLMSAEAFEHLKTQFDLNAETNACSIN
    GNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESAYLAYRNQSLDLA
    EQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESYYRYVAREQSCRRPNAQ
    RFGISNYCQIYPPNVNKIREALAQTHSAIAVIIGIKDLDAFRHYDGRTIIQRDN
    GYQPNYHAVNIVGYSNAQGVDYWIVRNSWDTNWGDNGYGYFAANIDLM
    MIEEYPYVVIL
    DerP 2
    (SEQ ID NO: 317)
    MMYKILCLSLLVAAVARDQVDVKDCANHEIKKVLVPGCHGSEPCIIHRGKPF
    QLEAVFEANQNTKTAKIEIKASIDGLEVDVPGIDPNACHYMKCPLVKGQQYD
    IKYTWNVPKIAPKSENVVVTVKVMGDDGVLACAIATHAKIRD
    DerP 3
    (SEQ ID NO: 318)
    MIIYNILIVLLLAINTLANPILPASPNATIVGGEKALAGECPYQISLQSSSHFCG
    GTILDEYWILTAAHCVAGQTASKLSIRYNSLKHSLGGEKISVAKIFAHEKYDS
    YQ1DNDIALIKLKSPMKLNQKNAKAVGLPAKGSDVKVGDQVRVSGWGYLE
    EGSYSLPSELRRVDIAVVSRKECNELYSKANAEVTDNMICGGDVANGGKDS
    CQGDSGGPVVDVKNNQVVGIVSWGYGCARKGYPGVYTRVGNFIDWIESKR
    SQ 
    DerP 4
    (SEQ ID NO: 319)
    KYXNPHFIGXRSVITXLME 
    DerP 5
    (SEQ ID NO: 320)
    MKFIIAFFVATLAVMTVSGEDKKHDYQNEFDFLLMERIHEQIKKGELALFYL
    QEQINHFEEKPTKEMKDKIVAEMDTIIAMIDGVRGVLDRLMQRKDLDIFEQY
    NLEMAKKSGDILERDLKKEEARVKKIEV 
    DerP 6
    (SEQ ID NO: 321)
    AIGXQPAAEAEAPFQISLMK 
    DerP7
    (SEQ ID NO: 322)
    MMKLLLIAAAAFVAVSADPIHYDKITEEINKAVDEAVAAIEKSETFDPMKVP
    DHSDKFERHIGIIDLKGELDMRNIQVRGLKQMKRVGDANVKSEDGVVKAHL
    LVGVHDDVVSMEYDLAYKLGDLHPNTHVISDIQDFVVELSLEVSEEGNMTL
    TSFEVRQFANVVNHIGGLSILDPIFAVLSDVLTAIFQDTVRAEMTKVLAPAFK
    KELERNNQ 
    DerP9
    (SEQ ID NO: 323)
    IVGGSNASPGDAVYQIAL
    • Dermatophagoides Farinae
  • Der f 1
    (SEQ ID NO: 324)
    MKFVLAIASLLVLTVYARPASIKTFEFKKAFNKNYATVEEEEVARKN
    FLESLKYVEANKGAINHLSDLSLDEFKNRYLMSAEAFEQLKTQFDLN
    AETSACRINSVNVPSELDLRSLRTVTPIRMQGGCGSCWAFSGVAATE
    SAYLAYRNTSLDLSEQELVDCASQHGCHGDTIPRGIEYIQQNGVVEE
    RSYPYVAREQRCRRPNSQHYGISNYCQIYPPDVKQIREALTQTHTAI
    AVIIGIKDLRAFQHYDGRTIIQHDNGYQPNYHAVNIVGYGSTQGDDY
    WIVRNSWDTTWGDSGYGYFQAGNNLMMIEQYPYVVIM
    Der f 2
    (SEQ ID NO: 325)
    MISKILCLSLLVAAVVADQVDVKDCANNEIKKVMVDGCHGSDPCIIH
    RGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFMK
    CPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATH
    GKIRD
    Der f 3
    (SEQ ID NO: 326)
    MMILTIVVLLAANILATPILPSSPNATIVGGVKAQAGDCPYQISLQS
    SSHFCGGSILDEYWILTAAHCVNGQSAKKLSIRYNTLKHASGGEKIQ
    VAEIYQHENYDSMTIDNDVALIKLKTPMTLDQTNAKPVPLPAQGSDV
    KVGDKIRVSGWGYLQEGSYSLPSELQRVDIDVVSREQCDQLYSKAGA
    DVSENMICGGDVANGGVDSCQGDSGGPVVDVATKQIVGIVSWGYGCA
    RKGYPGVYTRVGNFVDWIESKRSQ
    Der f 4
    (SEQ ID NO: 327)
    AVGGQDADLAEAPFQISLLK
    Der f 7
    (SEQ ID NO: 328)
    MMKFLLIAAVAFVAVSADPIHYDKITEEINKAIDDAIAAIEQSETID
    PMKVPDHADKFERHVGIVDFKGELAMRNIEARGLKQMKRQGDANVKG
    EEGIVKAHLLIGVHDDIVSMEYDLAYKLGDLHPTTHVISDIQDFVVA
    LSLEISDEGNITMTSFEVRQFANVVNHIGGLSILDPIFGVLSDVLTA
    IFQDTVRKEMTKVLAPAFKRELEKN
    • Additional Mite Allergen Sequences (NCBI Entrez Accession):
  • 1170095; 1359436; 2440053; 666007; 487661; 1545803; 84702; 84699; 625532; 404370; 1091577; 1460058; 7413; 9072; 387592.
    • Cat Felis Sequences (NCBI Entrez Accession):
  • 539716; 539715; 423193; 423192; 423191; 423190; 1364213; 1364212; 395407; 163827; 163823; 163825; 1169665; 232086; 1169666.
    • Latex Hevea Sequences:
  • Hev b 1
    (SEQ ID NO: 329)
    MAEDEDNQQGQGEGLKYLGFVQDAATYAVTTFSNVYLFAKDKSGPLQPGV
    DIIEGPVKNVAVPLYNRFSYIPNGALKFVDSTVVASVTIIDRSLPPIVKD
    ASIQVVSAIRAAPEAARSLASSLPGQTKILAKVFYGEN 
    Hev b 3
    (SEQ ID NO: 330)
    MAEEVEEERLKYLDFVRAAGVYAVDSFSTLYLYAKDISGPLKPGVDTIEN
    VVKTVVTPVYYIPLEAVKFVDKTVDVSVTSLDGVVPPVIKQVSAQTYSVA
    QDAPRIVLDVASSVFNTGVQEGAKALYANLEPKAEQYAVITWRALNKLPL
    VPQVANVVVPTAVYFSEKYNDVVRGTTEQGYRVSSYLPLLPTEKITKVFG
    DEAS
    • Additional Hevea Sequences (NCBI Entrez Accession):
  • 3319923; 3319921; 3087805; 1493836; 1480457; 1223884; 3452147; 3451147; 1916805; 232267; 123335; 2501578; 3319662; 3288200; 1942537; 2392631; 2392630; 1421554; 1311006; 494093; 3183706; 3172534; 283243; 1170248; 1708278; 1706547; 464775; 266892; 231586; 123337; 116359; 123062; 2213877; 542013; 2144920; 1070656; 2129914; 2129913; 2129912; 100135; 82026; 1076559; 82028; 82027; 282933; 280399; 100138; 1086972; 108697; 1086976; 1086978; 1086978; 1086976; 1086974; 1086972; 913758; 913757; 913756; 234388; 1092500; 228691; 1177405; 18839; 18837; 18835; 18833; 18831; 1209317; 1184668; 168217; 168215; 168213; 168211; 168209; 348137.
    • Rye Grass Lolium Sequences:
  • 126385 Lol p 1
    (SEQ ID NO: 331)
    MASSSSVLLVVALFAVFLGSAHGIAKVPPGPNITAEYGDKWLDAKSTWYGK
    PTGAGPKDNGGACGYKNVDKAPFNGMTGCGNTPIFKDGRGCGSCFEIKCTK
    PESCSGEAVTVTITDDNEEPIAPYHFDLSGHAFGSMAKKGEEQNVRSAGELE
    LQFRRVKCKYPDDTKPTFHVEKASNPNYLAILVKYVDGDGDVVAVDIKEKG
    KDKWIELKESWGAVWRIDTPDKLTGPFTVRYTTEGGTKSEFEDVIPEGWKA
    DTSYSAK 
    126386  Lol p 2a
    (SEQ ID NO: 332)
    AAPVEFTVEKGSDEKNLALSIKYNKEGDSMAEVELKEHGSNEWLALKKNG
    DGVWEIKSDKPLKGPFNFRFVSEKGMRNVFDDVVPADFKVGTTYKPE 
    126387 Lol p 3
    (SEQ ID NO: 333)
    TKVDLTVEKGSDAKTLVLNIKYTRPGDTLAEVELRQHGSEEWEPMTKKGNL
    WEVKSAKPLTGPMNFRFLSKGGMKNVFDEVIPTAFTVGKTYTPEYN 
    2498581 Lol p 5a
    (SEQ ID NO: 334)
    MAVQKYTVALFLRRGPRGGPGRSYAADAGYTPAAAATPATPAATPAGGWR
    EGDDRRAEAAGGRQRLASRQPWPPLPTPLRRTSSRSSRPPSPSPPRASSPTSA
    AKAPGLIPKLDTAYDVAYKAAEAHPRGQVRRLRHCPHRSLRVIAGALEVHA
    VKPATEEVLAAKIPTGELQIVDKIDAAFKIAATAANAAPTNDKFTVFESAFNK
    ALNECTGGAMRPTSSSPPSRPRSSRPTPPPSPAAPEVKYAVFEAALTKAITAM
    TQAQKAGKPAAAAATAAATVATAAATAAAVLPPPLLVVQSLISLLIYY 
    2498582 Lol p 5b
    (SEQ ID NO: 335)
    MAVQKHTVALFLAVALVAGPAASYAADAGYAPATPATPAAPATAATPATP
    ATPATPAAVPSGKATTEEQKLIEKINAGFKAAVAAAAVVPPADKYKTFVETF
    GTATNKAFVEGLASGYADQSKNQLTSKLDAALKLAYEAAQGATPEAKYDA
    YVATLTEALRVIAGTLEVHAVKPAAEEVKVGAIPAAEVQLIDKVDAAYRTA
    ATAANAAPANDKFTVFENTFNNAIKVSLGAAYDSYKFIPTLVAAVKQAYAA
    KQATAPEVKYTVSETALKKAVTAMSEAEKEATPAAAATATPTPAAATATAT
    PAAAYATATPAAATATATPAAATATPAAAGGYKV 
    455288 Lol p isoform 9
    (SEQ ID NO: 336)
    MAVQKHTVALFLAVALVAGPAASYAADAGYAPATPATPAAPATAATPATP
    ATPATPAAVPSGKATTEEQKLIEKINAGFKAAVAAAAVVPPADKYKTFVETF
    GTATNKAFVEGLASGYADQSKNQLTSKLDAALKLAYEAAQGATPEAKYDA
    YVATLTEALRVIAGTLEVHAVKPAAEEVKVGAIPAAEVQLIDKVDAAYRTA
    ATAANAAPANDKFTVFENTFNNAIKVSLGAAYDSYKFIPTLVAAVKQAYAA
    KQATAPEVKYTVSETALKKAVTAMSEAEKEATPAAAATATPTPAAATATAT
    PAAAYATATPAAATATATPAAATATPAAAGGYKV 
    1582249 Lol p 11
    (SEQ ID NO: 337)
    DKGPGFVVTGRVYCDPCRAGFETNVSHNVEGATVAVDCRPFDGGESKLKA
    EATTDKDGWYKIEIDQDHQEEICEVVLAKSPDKSCSEIEEFRDRARVPLTSNX
    GIKQQGIRYANPIAFFRKEPLKECGGILQAY 
    • Additional Lolium Sequences (NCBI Entrez Accession):
  • 135480; 417103; 687261; 687259; 1771355; 2388662; 631955; 542131; 542130; 542129; 100636; 626029; 542132; 320616; 320615; 320614; 100638; 100634; 82450; 626028; 100639; 283345; 542133; 1771353; 1763163; 1040877; 1040875; 250525; 551047; 515377; 510911; 939932; 439950; 2718; 168316; 168314; 485371; 2388664; 2832717; 2828273; 548867.
    • Olive Tree Olive Sequences
  • 416610 Ole e 1
    (SEQ ID NO: 338)
    EDIPQPPVSQFHIQGQVYCDTCRAGFITELSEFIPGASLRLQCKDKE
    NGDVTFTEVGYTRAEGLYSMLVERDHKNEFCEITLISSGRKDCNEIP
    TEGWAKPSLKFKLNTVNGTTRTVNPLGFFKKEALPKCAQVYNKLGMY
    PPNM
    • Parietaria Parietaria Sequences:
  • 2497750 Par j P2
    (SEQ ID NO: 339)
    MRTVSMAALVVIAAALAWTSSAEPAPAPAPGEEACGKVVQDIMPCLHFVKG
    EEKEPSKECCSGTKKLSEEVKTTEQKREACKCIVRATKGISGIKNELVAEVPK
    KCDIKTTLPPITADFDCSKIQSTIFRGYY 
    1352506 Par j P5
    (SEQ ID NO: 340)
    MVRALMPCLPFVQGKEKEPSKGCCSGAKRLDGETKTGPQRVHACECIQTAM
    KTYSDIDGKLVSEVPKHCGIVDSKLPPIDVNMDCKTVGVVPRQPQLPVSLRH
    GPVTGPSDPAHKARLERPQIRVPPPAPEKA
    1532056 Par j P8
    (SEQ ID NO: 341)
    MRTVSMAALVVIAAALAWTSSAELASAPAPGEGPCGKVVHHIMPCLKFVKG
    EEKEPSKSCCSGTKKLSEEVKTTEQKREACKCIVAATKGISGIKNELVAEVPK
    KCGITTTLPPITADFDCSKIESTIFRGYY 
    1532058 Par j P9
    (SEQ ID NO: 342)
    MRTVSAPSAVALVVIVAAGLAWTSLASVAPPAPAPGSEETCGTVVRALMPC
    LPFVQGKEKEPSKGCCSGAKRLDGETKTGLQRVHACECIQTAMKTYSDIDG
    KLVSEVPKHCGIVDSKLPPIDVNMDCKTLGVVPRQPQLPVSLRHGPVTGPSD
    PAHKARLERPQIRVPPPAPEKA
    2497749 Par j P9
    (SEQ ID NO: 343)
    MRTVSARSSVALVVIVAAVLVWTSSASVAPAPAPGSEETCGTVVGALMPCL
    PFVQGKEKEPSKGCCSGAKRLDGETKTGPQRVHACECIQTAMKTYSDIDGK
    LVSEVPKHCGIVDSKLPPIDVNMDCKTLGVLHYKGN 
    1086003 Par j 1
    (SEQ ID NO: 344)
    MVRALMPCLPFVQGKEKEPSKGCCSGAKRLDGETKTGPQRVHACECIQTAM
    KTYSDIDGKLVSEVPKHCGIVDSKLPPIDVNMDCKTVGVVPRQPQLPVSLRH
    GPVTGPSRSRPPTKHGWRDPRLEFRPPHRKKPNPAFSTLG 
    • Additional Parietaria Sequences (NCBI Entrez Accession):
  • 543659; 1836011; 1836010; 1311513; 1311512; 1311511; 1311510; 1311509; 240971.
    • Timothy Grass Phleum Sequences:
  • Phl p 1
    (SEQ ID NO: 345)
    MASSSSVLLVVVLFAVFLGSAYGIPKVPPGPNITATYGDKWLDAKSTWYGK
    PTGAGPKDNGGACGYKDVDKPPFSGMTGCGNTPIFKSGRGCGSCFEIKCTKP
    EACSGEPVVVHITDDNEEPIAPYHFDLSGHAFGAMAKKGDEQKLRSAGELEL
    QFRRVKCKYPEGTKVTFHVEKGSNPNYLALLVKYVNGDGDVVAVDIKEKG
    KDKWIELKESWGAIWRIDTPDKLTGPFTVRYTTEGGTKTEAEDVIPEGWKA
    DTSYESK 
    Phl p 1
    (SEQ ID NO: 346)
    MASSSSVLLVVALFAVFLGSAHGIPKVPPGPNITATYGDKWLDAKSTWYGK
    PTAAGPKDNGGACGYKDVDKPPFSGMTGCGNTPIFKSGRGCGSCFEIKCTKP
    EACSGEPVVVHITDDNEEPIAAYHFDLSGIAFGSMAKKGDEQKLRSAGEVEI
    QFRRVKCKYPEGTKVTFHVEKGSNPNYLALLVKFSGDGDVVAVDIKEKGKD
    KWIALKESWGAIWRIDTPEVLKGPFTVRYTTEGGTKARAKDVIPEGWKADT
    AYESK 
    Phlp 2
    (SEQ ID NO: 347)
    MSMASSSSSSLLAMAVLAALFAGAWCVPKVTFTVEKGSNEKHLAVLVKYE
    GDTMAEVELREHGSDEWVAMTKGEGGVWTFDSEEPLQGPFNFRFLTEKGM
    KNVFDDVVPEKYTIGATYAPEE 
    Phl p 5
    (SEQ ID NO: 348)
    ADLGYGGPATPAAPAEAAPAGKATTEEQKLIEKINDGFKAALAAAAGVPPA
    DKYKTFVATFGAASNKAFAEGLSAEPKGAAESSSKAALTSKLDAAYKLAYK
    TAEGATPEAKYDAYVATLSEALRIIAGTLEVHAVKPAAEEVKVIPAGELQVIE
    KVDSAFKVAATAANAAPANDKFTVFEAAFNNAIKASTGGAYESYKFIPALE
    AAVKQAYAATVATAPEVKYTVFETALKKAFTAMSEAQKAAKPATEATATA
    TAAVGAATGAATAATGGYKV 
    Phl p 5
    (SEQ ID NO: 349)
    ADLGYGGPATPAAPAEAAPAGKATTEEQKLIEKINDGFKAALAAAAGVPPA
    DKYKTFVATFGAASNKAFAEGLSAEPKGAAESSSKAALTSKLDAAYKLAYK
    TAEGATPEAKYDAYVATLSEALRIIAGTLEVHAVKPAAEEVKVIPAGELQVIE
    KVDSAFKVAATAANAAPANDKFTVFEAAFNNAIKASTGGAYESYKFIPALE
    AAVKQAYAATVATAPEVKYTVFETALKKAITAMSEAQKAAKPATEATATA
    TAAVGAATGAATAATGGYKV 
    Phl p 5b
    (SEQ ID NO: 350)
    AAAAVPRRGPRGGPGRSYTADAGYAPATPAAAGAAAGKATTEEQKLIEDIN
    VGFKAAVAAAASVPAADKFKTFEAAFTSSSKAAAAKAPGLVPKLDAAYSV
    AYKAAVGATPEAKFDSFVASLTEALRVIAGALEVHAVKPVTEEPGMAKIPA
    GELQIIDKIDAAFKVAATAAATAPADDKFTVFEAAFNKAIKESTGGAYDTYK
    CIPSLEAAVKQAYAATVAAAPQVKYAVFEAALTKAITAMSEVQKVSQPATG
    AATVAAGAATTAAGAASGAATVAAGGYKV 
    Phl p 5a
    (SEQ ID NO: 351)
    ADLGYGPATPAAPAAGYTPATPAAPAGADAAGKATTEEQKLIEKINAGFKA
    ALAGAGVQPADKYRTFVATFGPASNKAFAEGLSGEPKGAAESSSKAALTSK
    LDAAYKLAYKTAEGATPEAKYDAYVATLSEALRIIAGTLEVHAVKPAAEEV
    KV1PAGELQVIEKVDAAFKVAATAANAAPANDKFTVFEAAFNDEIKASTGG
    AYESYKFIPALEAAVKQAYAATVATAPEVKYTVFETALKKAITAMSEAQKA
    AKPAAAATATATAAVGAATGAATAATGGYKV 
    Phl p 5
    (SEQ ID NO: 352)
    MAVQKYTVALFLAVALVAGPAASYAADAGYAPATPAAAGAEAGKATTEE
    QKLIEDINVGFKAAVAAAASVPAADKFKTFEAAFTSSSKAATAKAPGLVPKL
    DAAYSVSYKAAVGATPEAKFDSFVASLTEALRVIAGALEVHAVKPVTEEPG
    MAK1PAGELQIIDKIDAAFKVAATAAATAPADTVFEAAFNKAIKE STGGAYD
    TYKCIPSLEAAVKQAYAATVAAAPQVKYAVFEAALTKAITAMSEVQKVSQP
    ATGAATVAAGAATTAAGAASGAATVAAGGYKV 
    Phl p 5
    (SEQ ID NO: 353)
    MAVQKYTVALFLAVALVAGPAASYAADAGYAPATPAAAGAEAGKATTEE
    QKLIEDINVGFKAAVAAAASVPAADKFKTFEAAFTSSSKAATAKAPGLVPKL
    DAAYSVAYKAAVGATPEAKFDSFVASLTEALRVIAGALEVHAVKPVTEDPA
    WPKIPAGELQIIDKIDAAFKVAATAAATAPADDKFTVFEAAFNKAIKE STGG
    AYDTYKCIPSLEAAVKQAYAATVAAAPQVKYAVFEAALTKAITAMSEVQK
    VSQPATGAATVAAGAATTATGAASGAATVAAGGYKV 
    Phl p 5
    (SEQ ID NO: 354)
    ADAGYAPATPAAAGAEAGKATTEEQKLIEDINVGFKAAVAAAASVPAADKF
    KTFEAAFTSSSKAATAKAPGLVPKLDAAYSVAYKAAVGATPEAKFDSFVAS
    LTEALRVIAGALEVHAVKPVTEEPGMAKIPAGELQIIDKIDAAFKVAATAAA
    TAPADDKFTVFEAAFNKAIKESTGGAYDTYKCIPSLEAAVKQAYAATVAAA
    PQVKYAVFEAALTKAITAMSEVQKVSQPATGAATVAAGAATTAAGAASGA
    ATVAAGGYKV 
    Phl p 5
    (SEQ ID NO: 355)
    SVKRSNGSAEVHRGAVPRRGPRGGPGRSYAADAGYAPATPAAAGAEAGKA
    TTEEQKLIEDINVGFKAAVAAAASVPAADKFKTFEAAFTSSSKAATAKAPGL
    VPKLDAAYSVAYKAAVGATPEAKFDSFVASLTEALRVIAGALEVHAVKPVT
    EEPGMAK1PAGELQIIDKIDAAFKVAATAAATAPADDKFTVFEAAFNKAIKES
    TGGAYDTYKCIPSLEAAVKQAYAATVAAAPQVKYAVFEAALTKAITAMSEV
    QKVSQPATGAATVAAGAATTAAGAASGAATVAAGGYKV 
    Phl p 5
    (SEQ ID NO: 356)
    MAVHQYTVALFLAVALVAGPAGSYAADLGYGPATPAAPAAGYTPATPAAP
    AGAEPAGKATTEEQKLIEKINAGFKAALAAAAGVPPADKYRTFVATFGAAS
    NKAFAEGLSGEPKGAAESSSKAALTSKLDAAYKLAYKTAEGATPEAKYDAY
    VATVSEALRIIAGTLEVHAVKPAAEEVKVIPAGELQVIEKVDAAFKVAATAA
    NAAPANDKFTVFEAAFNDAIKASTGGAYESYKFIPALEAAVKQAYAATVAT
    APEVKYTVFETALKKAITAMSEAQKAAKPAAAATATATAAVGAATGAATA
    ATGGYKV 
    Phl p 5
    (SEQ ID NO: 357)
    ADLGYGGPATPAAPAEAAPAGKATTEEQKLIEKINDGFKAALAAAAGVPPA
    DKYKTFVATFGAASNKAFAEGLSAEPKGAAESSSKAALTSKLDAAYKLAYK
    TAEGATPEAKYDAYVATLSEALRIIAGTLEVHAVKPAAEEVKVIPAGELQVIE
    KVDSAFKVAATAANAAPANDKFTVFEAAFNNAIKASTGGAYESYKFIPALE
    AAVKQAYAATVATAPEVKYTVFETALKKAFTAMSEAQKAAKPATEATATA
    TAAVGAATGAATAATGGYKV 
    Phl p5b
    (SEQ ID NO: 358)
    AAAAVPRRGPRGGPGRSYTADAGYAPATPAAAGAAAGKATTEEQKLIEDIN
    VGFKAAVAAAASVPAADKFKTFEAAFTSSSKAAAAKAPGLVPKLDAAYSV
    AYKAAVGATPEAKFDSFVASLTEALRVIAGALEVHAVKPVTEEPGMAKIPA
    GELQIIDKIDAAFKVAATAAATAPADDKFTVFEAAFNKAIKESTGGAYDTYK
    CIPSLEAAVKQAYAATVAAAPQVKYAVFEAALTKAITAMSEVQKVSQPATG
    AATVAAGAATTAAGAASGAATVAAGGYKV 
    Phl p5a
    (SEQ ID NO: 359)
    ADLGYGPATPAAPAAGYTPATPAAPAGADAAGKATTEEQKLIEKINAGFKA
    ALAGAGVQPADKYRTFVATFGPASNKAFAEGLSGEPKGAAESSSKAALTSK
    LDAAYKLAYKTAEGATPEAKYDAYVATLSEALRIIAGTLEVHAVKPAAEEV
    KV1PAGELQVIEKVDAAFKVAATAANAAPANDKFTVFEAAFNDEIKASTGG
    AYESYKFIPALEAAVKQAYAATVATAPEVKYTVFETALKKAITAMSEAQKA
    AKPAAAATATATAAVGAATGAATAATGGYKV 
    Phl p 5
    (SEQ ID NO: 360)
    AVPRRGPRGGPGRSYAADAGYAPATPAAAGAEAGKATTEEQKLIEDINVGF
    KAAVAAAASVPAGDKFKTFEAAFTSSSKAATAKAPGLVPKLDAAYSVAYK
    AAVGATPEAKFDSFVASLTEALRVIAGALEVHAVKPVTEEPGMAK1PAGELQ
    IIDKIDAAFKVAATAAATAPADDKFTVFEAAFNKAIKESTGGAYDTYKCIPSL
    EAAVKQAYAATVAAAPQVKYAVFEAALTKAITAMSEVQKVSQPATGAATV
    AAGAATTATGAASGAATVAAGGYKV 
    Phl p 5b
    (SEQ ID NO: 361)
    MAVPRRGPRGGPGRSYTADAGYAPATPAAAGAAAGKATTEEQKLIEDINVG
    FKAAVAARQRPAADKFKTFEAASPRHPRPLRQGAGLVPKLDAAYSVAYKA
    AVGATPEAKFDSFVASLTEALRVIAGALEVHAVKPVTEEPGMAKIPAGELQII
    DK1DAAFKVAATAAATAPADDKFTVFEAAFNKAIKESTGGAYDTYKCIPSLE
    AAVKQAYAATVAAAAEVKYAVFEAALTKAITAMSEVQKVSQPATGAATVA
    AGAATTAAGAASGAATVAAGGYKV 
    Phl p 5
    (SEQ ID NO: 362)
    MAVHQYTVALFLAVALVAGPAASYAADLGYGPATPAAPAAGYTPATPAAP
    AEAAPAGKATTEEQKLIEKINAGFKAALAAAAGVQPADKYRTFVATFGAAS
    NKAFAEGLSGEPKGAAESSSKAALTSKLDAAYKLAYKTAEGATPEAKYDAY
    VATLSEALRIIAGTLEVHAVKPAAEEVKVIPAGELQVIEKVDAAFKVAATAA
    NAAPANDKFTVFEAAFNDAIKASTGGAYESYKFIPALEAAVKQAYAATVAT
    APEVKYTVFETALKKAITAMSEAQKAAKPAAAATATATAAVGAATGAATA
    ATGGYKV 
    Phlp 5
    (SEQ ID NO: 363)
    EAPAGKATTEEQKLIEKINAGFKAALARRLQPADKYRTFVATFGPASNKAFA
    EGLSGEPKGAAESSSKAALTSKLDAAYKLAYKTAEGATPEAKYDAYVATLS
    EALRIIAGTLEVHAVKPAAEEVKVIPAAELQVIEKVDAAFKVAATAANAAPA
    NDKFTVFEAAFNDEIKASTGGAYESYKFIPALEAAVKQAYAATVATAPEVK
    YTVFETALKKAITAMSEAQKAAKPPPLPPPPQPPPLAATGAATAATGGYKV
    Phl p 5
    (SEQ ID NO: 364)
    MAVHQYTVALFLAVALVAGPAASYAADLGYGPATPAAPAAGYTPATPAAP
    AEAAPAGKATTEEQKLIEKINAGFKAALAAAAGVQPADKYRTFVATFGAAS
    NKAFAEGLSGEPKGAAESSSKAALTSKLDAAYKLAYKTAEGATPEAKYDAY
    VATLSEALRIIAGTLEVHAVKPAAEEVKVIPAGELQVIEKVDAAFKVAATAA
    NAAPANDKFTVFEAAFNDAIKASTGGAYESYKFIPALEAAVKQAYAATVAT
    APEVKYTVFETALKKAITAMSEAQKAAKPAAAATATATAAVGAATGAATA
    ATGGYKV 
    Phl p 5b
    (SEQ ID NO: 365)
    MAVPRRGPRGGPGRSYTADAGYAPATPAAAGAAAGKATTEEQKLIEDINVG
    FKAAVAARQRPAADKFKTFEAASPRHPRPLRQGAGLVPKLDAAYSVAYKA
    AVGATPEAKFDSFVASLTEALRVIAGALEVHAVKPVTEEPGMAKIPAGELQII
    DKIDAAFKVAATAAATAPADDKFTVFEAAFNKAIKESTGGAYDTYKCIPSLE
    AAVKQAYAATVAAAAEVKYAVFEAALTKAITAMSEVQKVSQPATGAATVA
    AGAATTAAGAASGAATVAAGGYKV 
    Phl p 5a
    (SEQ ID NO: 366)
    ADLGYGPATPAAPAAGYTPATPAAPAGADAAGKATTEEQKLIEKINAGFKA
    ALAGAGVQPADKYRTFVATFGPASNKAFAEGLSGEPKGAAESSSKAALTSK
    LDAAYKLAYKTAEGATPEAKYDAYVATLSEALRIIAGTLEVHAVKPAAEEV
    KVIPAGELQVIEKVDAAFKVAATAANAAPANDKFTVFEAAFNDEIKASTGG
    AYESYKFIPALEAAVKQAYAATVATAPEVKYTVFETALKKAITAMSEAQKA
    AKPPPLPPPPQPPPLAATGAATAATGGYKV 
    Phl p 5
    (SEQ ID NO: 367)
    MAVHQYTVALFLAVALVAGPAASYAADLGYGPATPAAPAAGYTPATPAAP
    AEAAPAGKATTEEQKLIEKINAGFKAALAAAAGVQPADKYRTFVATFGAAS
    NKAFAEGLSGEPKGAAESSSKAALTSKLDAAYKLAYKTAEGATPEAKYDAY
    VATLSEALRIIAGTLEVHAVKPAAEEVKVIPAGELQVIEKVDAAFKVAATAA
    NAAPANDKFTVFEAAFNDAIKASTGGAYESYKFIPALEAAVKQAYAATVAT
    APEVKYTVFETALKKAITAMSEAQKAAKPAAAATATATAAVGAATGAATA
    ATGGYKV 
    Phl p 6
    (SEQ ID NO: 368)
    MAAHKFMVAMFLAVAVVLGLATSPTAEGGKATTEEQKLIEDVNASFRAAM
    ATTANVPPADKYKTFEAAFTVSSKRNLADAVSKAPQLVPKLDEVYNAAYN
    AADHAAPEDKYEAFVLHFSEALRIIAGTPEVHAVKPGA
    Phl p 6
    (SEQ ID NO: 369)
    SKAPQLVPKLDEVYNAAYNAADHAAPEDKYEAFVLHFSEALHIIAGTPEVH
    AVKPGA
    Phl p 6
    (SEQ ID NO: 370)
    ADKYKTFEAAFTVSSKRNLADAVSKAPQLVPKLDEVYNAAYNAADHAAPE
    DKYEAFVLHFSEALHIIAGTPEVHAVKPGA
    Phl p 6
    (SEQ ID NO: 371)
    TEEQKLIEDVNASFRAAMATTANVPPADKYKTLEAAFTVSSKRNLADAVSK
    APQLVPKLDEVYNAAYNAADHAAPEDKYEAFVLHFSEALRIIAGTPEVHAV
    KPGA
    Phl p 6
    (SEQ ID NO: 372)
    MAAHKFMVAMFLAVAVVLGLATSPTAEGGKATTEEQKLIEDINASFRAAM
    ATTANVPPADKYKTFEAAFTVSSKRNLADAVSKAPQLVPKLDEVYNAAYN
    AADHAAPEDKYEAFVLHFSEALHIIAGTPEVHAVKPGA
    Phl p 6
    (SEQ ID NO: 373)
    MVAMFLAVAVVLGLATSPTAEGGKATTEEQKLIEDVNASFRAAMATTANV
    PPADKYKTFEAAFTVSSKRNLADAVSKAPQLVPKLDEVYNAAYNAADHAA
    PEDKYEAFVLHFSEALRIIAGTPEVHAVKPGA
    Phlp 7
    (SEQ ID NO: 374)
    MADDMERIFKRFDTNGDGKISLSELTDALRTLGSTSADEVQRMMAEIDTDG
    DGFIDFNEFISFCNANPGLMKDVAKVF 
    Phl p 11
    (SEQ ID NO: 375)
    MSWQTYVDEHLMCEIEGHHLASAAILGHDGTVWAQSADFPQFKPEEITGIM
    KDFDEPGHLAPTGMFVAGAKYMVIQGEPGRVIRGKKGAGGITIKKTGQALV
    VGIYDEPMTPGQCNMVVERLGDYLVEQGM

    Additional Phleum sequences (NCBI entrez accession):
    458878; 548863; 2529314; 2529308; 2415702; 2415700; 2415698; 542168; 542167; 626037; 542169; 541814; 542171; 253337; 253336; 453976; 439960.
    • Wasp (and Related) Vespula Sequences:
  • 465054 ALLERGEN VES V 5
    (SEQ ID NO: 376)
    MEISGLVYLIIIVTIIDLPYGKANNYCKIKCLKGGVHTACKYGSLKPNCGNKV
    VVSYGLTKQEKQDILKEHNDFRQKIARGLETRGNPGPQPPAKNMKNLVWN
    DELAYVAQVWANQCQYGHDTCRDVAKYQVGQNVALTGSTAAKYDDPVK
    LVKMWEDEVKDYNPKKKFSGNDFLKTGHYTQMVWANTKEVGCGSIKYIQE
    KWHKHYLVCNYGPSGNFMNEELYQTK 
    1709545 ALLERGEN VES M 1
    (SEQ ID NO: 377)
    GPKCPFNSDTVSIIIETRENRNRDLYTLQTLQNHPEFKKKTITRPVVFITHGFTS
    SASEKNFINLAKALVDKDNYMVISIDWQTAACTNEYPGLKYAYYPTAASNT
    RLVGQYIATITQKLVKDYKISMANIRLIGHSLGAHVSGFAGKRVQELKLGKY
    SEIIGLDPARPSFDSNHCSERLCETDAEYVQIIHTSNYLGTEKILGTVDFYMNN
    GKNNPGCGRFFSEVCSHTRAVIYMAECIKHECCLIGIPRSKSSQPISRCTKQEC
    VCVGLNAKKYPSRGSFYVPVESTAPFCNNKGKII 
    1352699 ALLERGEN VES V 1
    (SEQ ID NO: 378)
    MEENMNLKYLLLFVYFVQVLNCCYGHGDPLSYELDRGPKCPFNSDTVSIIIE
    TRENRNRDLYTLQTLQNHPEFKKKTITRPVVFITHGFTSSASETNFINLAKAL
    VDKDNYMVISIDWQTAACTNEAAGLKYLYYPTAARNTRLVGQYIATITQKL
    VKHYKISMANIRLIGHSLGAHASGFAGKKVQELKLGKYSEIIGLDPARPSFDS
    NHCSERLCETDAEYVQIIHTSNYLGTEKTLGTVDFYMNNGKNQPGCGRFFSE
    VCSHSRAVIYMAECIKHECCLIGIPKSKSSQPISSCTKQECVCVGLNAKKYPSR
    GSFYVPVESTAPFCNNKGKII 
    1346323 ALLERGEN VES V 2
    (SEQ ID NO: 379)
    SERPKRVFNIYWNVPTFMCHQYDLYFDEVTNFNIKRNSKDDFQGDKIAIFYD
    PGEFPALLSLKDGKYKKRNGGVPQEGNITIHLQKFIENLDKIYPNRNFSGIGVI
    DFERWRPIFRQNWGNMKIHKNFSIDLVRNEHPTWNKKMIELEASKRFEKYA
    RFFMEETLKLAKKTRKQADWGYYGYPYCFNMSPNNLVPECDVTAMHEND
    KMSWLFNNQNVLLPSVYVRQELTPDQRIGLVQGRVKEAVRISNNLKHSPKV
    LSYWWYVYQDETNTFLTETDVKKTFQEIVINGGDGIIIWGSSSDVNSLSKCK
    RLQDYLLTVLGPIAINVTEAVN 
    549194 ALLERGEN VES VI
    (SEQ ID NO: 380)
    5KVNYCKIKCLKGGVHTACKYGTSTKPNCGKMVVKAYGLTEAEKQEILKV
    HNDFRQKVAKGLETRGNPGPQPPAKNMNNLVWNDELANIAQVWASQCNY
    GHDTCKDTEKYPVGQNIAKRSTTAALFDSPGKLVKMWENEVKDFNPNIEWS
    KNNLKKTGHYTQMVWAKTKEIGCGSVKYVKDEWYTHYLVCNYGPSGNFR
    NEKLYEKK 
    • Additional Vespula Sequences (NCBI Entrez Accession):
  • 549193; 549192; 549191; 549190; 549189; 117414; 126761; 69576; 625255; 627189; 627188; 627187; 482382; 112561; 627186; 627185; 1923233; 897645; 897647; 745570; 225764; 162551.
    • Tree Allergen Sequences (Mainly Birch) Sequences:
  • 114922 Bet v 1
    (SEQ ID NO: 381)
    MGVFNYETETTSVIPAARLFKAFILDGDNLFPKVAPQAISSVENIEGNGGPGTI
    KKISFPEGFPFKYVKDRVDEVDHTNFKYNYSVIEGGPIGDTLEKISNEIKIVAT
    PDGGSILKISNKYHTKGDHEVKAEQVKASKEMGETLLRAVESYLLAHSDAYN 
    130975 Bet v 2
    (SEQ ID NO: 382)
    MSWQTYVDEHLMCDIDGQASNSLASAIVGHDGSVWAQSSSFPQFKPQEITGI
    MKDFEEPGHLAPTGLHLGGIKYMVIQGEAGAVIRGKKGSGGITIKKTGQALV
    FGIYEEPVTPGQCNMVVERLGDYLIDQGL
    1168696 Bet v 3
    (SEQ ID NO: 383)
    MPCSTEAMEKAGHGHASTPRKRSLSNSSFRLRSESLNTLRLRRIFDLFDKNSD
    GIITVDELSRALNLLGLETDLSELESTVKSFTREGNIGLQFEDFISLHQSLNDSY
    FAYGGEDEDDNEEDMRKSILSQEEADSFGGFKVFDEDGDGYISARELQMVL
    GKLGFSEGSEIDRVEKMIVSVDSNRDGRVDFFEFKDMMRSVLVRSS
    809536 Bet v 4
    (SEQ ID NO: 384)
    MADDHPQDKAERERIFKRFDANGDGKISAAELGEALKTLGSITPDEVKHMM
    AEIDTDGDGFISFQEFTDFGRANRGLLKDVAKIF 
    543675 Que a I-Quercus alba = oak trees (fragment)
    (SEQ ID NO: 385)
    GVFTXESQETSVIAPAXLFKALFL
    543509 Car b I-Carpinus betulus = hornbeam trees (fragment)
    (SEQ ID NO: 386)
    GVFNYEAETPSVIPAARLFKSYVLDGDKLIPKVAPQAIXK 
    543491 Aln g I-Alnus glutinosa = alder trees (fragment)
    (SEQ ID NO: 387)
    GVFNYEAETPSVIPAARLFKAFILDGDKLLPKVAPEAVSSVENI 
    1204056 Rubisco
    (SEQ ID NO: 388)
    VQCMQVWPPLGLKKFETLSYLPPLSSEQLAKEVDYLLRKNLIPCLEFELEHG
    FVYREHNRSPGYYDGRYWTMWKLPMFGCNDSSQVLKELEECKKAYPSAFI
    RIIGFDDK 

    Additional tree allergen sequences (NCBI entrez accession number):
    131919; 128193; 585564; 1942360; 2554672; 2392209; 2414158; 1321728; 1321726; 1321724; 1321722; 1321720; 1321718; 1321716; 1321714; 1321712; 3015520; 2935416; 464576; 1705843; 1168701; 1168710; 1168709; 1168708; 1168707; 1168706; 1168705; 1168704; 1168703; 1168702; 1842188; 2564228; 2564226; 2564224; 2564222; 2564220; 2051993; 1813891; 1536889; 534910; 534900; 534898; 1340000; 1339998; 2149808; 66207; 2129477; 1076249; 1076247; 629480; 481805; 81443; 1361968; 1361967; 1361966; 1361965; 1361964; 1361963; 1361962; 1361961; 1361960; 1361959; 320546; 629483 ; 629482; 629481; 541804; 320545; 81444; 541814; 629484; 474911; 452742; 1834387; 298737; 298736; 1584322; 1584321; 584320; 1542873; 1542871; 1542869; 1542867; 1542865; 1542863; 1542861; 1542859; 1542857; 1483232; 1483230; 1483228; 558561; 551640; 488605; 452746; 452744; 452740; 452738; 452736; 452734; 452732; 452730; 452728; 450885; 17938; 17927; 17925; 17921; 297538; 510951; 289331; 289329; 166953.
    • Peanut
  • Peanut sequences
  • 1168391 Ara h 1
    (SEQ ID NO: 389)
    MRGRVSPLMLLLGILVLASVSATHAKSSPYQKKTENPCAQRCLQSCQ
    QEPDDLKQKACESRCTKLEYDPRCVYDPRGHTGTTNQRSPPGERTRG
    RQPGDYDDDRRQPRREEGGRWGPAGPREREREEDWRQPREDWRRPSH
    QQPRKIRPEGREGEQEWGTPGSHVREETSRNNPFYFPSRRFSTRYGN
    QNGRIRVLQRFDQRSRQFQNLQNHRIVQIEAKPNTLVLPKHADADNI
    LVIQQGQATVTVANGNNRKSFNLDEGHALRIPSGFISYILNRHDNQN
    LRVAKISMPVNTPGQFEDFFPASSRDQSSYLQGFSRNTLEAAFNAEF
    NEIRRVLLEENAGGEQEERGQRRWSTRSSENNEGVIVKVSKEHVEEL
    TKHAKSVSKKGSEEEGDITNPINLREGEPDLSNNFGKLFEVKPDKKN
    PQLQDLDMMLTCVEIKEGALMLPHFNSKAMVIVVVNKGTGNLELVAV
    RKEQQQRGRREEEEDEDEEEEGSNREVRRYTARLKEGDVFIMPAAHP
    VAINTASSELHLLGFGINAENNHRIFLAGDKDNVIDQIEKQAKDLAF
    PGSGEQVEKLIKNQKESHFVSARPQSQSQSPSSPEKESPEKEDQEEE
    NQGGKGPLLSILKAFN
    • Ragweed Ambrosia Sequences
  • 113478 Amb a 1
    (SEQ ID NO: 390)
    MGIKHCCYILYFTLALVTLLQPVRSAEDLQQILPSANETRSLTTCGT
    YNIIDGCWRGKADWAENRKALADCAQGFAKGTIGGKDGDIYTVTSEL
    DDDVANPKEGTLRFGAAQNRPLWIIFARDMVIRLDRELAINNDKTID
    GRGAKVEIINAGFAIYNVKNIIIHNIIMHDIVVNPGGLIKSHDGPPV
    PRKGSDGDAIGISGGSQIWIDHCSLSKAVDGLIDAKHGSTHFTVSNC
    LFTQHQYLLLFWDFDERGMLCTVAFNKFTDNVDQRMPNLRHGFVQVV
    NNNYERWGSYALGGSAGPTILSQGNRFLASDIKKEVVGRYGESAMSE
    SINWNWRSYMDVFENGAIFVPSGVDPVLTPEQNAGMIPAEPGEAVLR
    LTSSAGVLSCQPGAPC
    113479 Amb a 2
    (SEQ ID NO: 391)
    MGIKHCCYILYFTLALVTLVQAGRLGEEVDILPSPNDTRRSLQGCEA
    HNIIDKCWRCKPDWAENRQALGNCAQGFGKATHGGKWGDIYMVTSDQ
    DDDVVNPKEGTLRFGATQDRPLWIIFQRDMIIYLQQEMVVTSDKTID
    GRGAKVELVYGGITLMNVKNVIIHNIDIHDVRVLPGGRIKSNGGPAI
    PRHQSDGDAIHVTGSSDIWIDHCTLSKSFDGLVDVNWGSTGVTISNC
    KFTHHEKAVLLGASDTHFQDLKMHVTLAYNIFTNTVHERMPRCRFGF
    FQIVNNFYDRWDKYAIGGSSNPTILSQGNKFVAPDFIYKKNVCLRTG
    AQEPEWMTWNWRTQNDVLENGAIFVASGSDPVLTAEQNAGMMQAEPG
    DMVPQLTMNAGVLTCSPGAPC
    113477 Amb a 1.3
    (SEQ ID NO: 392)
    MGIKQCCYILYFTLALVALLQPVRSAEGVGEILPSVNETRSLQACEA
    LNIIDKCWRGKADWENNRQALADCAQGFAKGTYGGKWGDVYTVTSNL
    DDDVANPKEGTLRFAAAQNRPLWIIFKNDMVINLNQELVVNSDKTID
    GRGVKVEIINGGLTLMNVKNIIIHNINIHDVKVLPGGMIKSNDGPPI
    LRQASDGDTINVAGSSQIWIDHCSLSKSFDGLVDVTLGSTHVTISNC
    KFTQQSKAILLGADDTHVQDKGMLATVAFNMFTDNVDQRMPRCRFGF
    FQVVNNNYDRWGTYAIGGSSAPTILCQGNRFLAPDDQIKKNVLARTG
    TGAAESMAWNWRSDKDLLENGAIFVTSGSDPVLTPVQSAGMIPAEPG
    EAAIKLTSSAGVFSCHPGAPC
    113476 Amb a 1.2
    (SEQ ID NO: 393)
    MGIKHCCYILYFTLALVTLLQPVRSAEDVEEFLPSANETRRSLKACE
    AHNIIDKCWRCKADWANNRQALADCAQGFAKGTYGGKHGDVYTVTSD
    KDDDVANPKEGTLRFAAAQNRPLWIIFKRNMVIHLNQELVVNSDKTI
    DGRGVKVNIVNAGLTLMNVKNIIIHNINIHDIKVCPGGMIKSNDGPP
    ILRQQSDGDAINVAGSSQIWIDHCSLSKASDGLLDITLGSSHVTVSN
    CKFTQHQFVLLLGADDTHYQDKGMLATVAFNMFTDHVDQRMPRCRFG
    FFQVVNNNYDRWGTYAIGGSSAPTILSQGNRFFAPDDIIKKNVLART
    GTGNAESMSWNWRTDRDLLENGAIFLPSGSDPVLTPEQKAGMIPAEP
    GEAVLRLTSSAGVLSCHQGAPC
    113475 Amb a 1.1
    (SEQ ID NO: 394)
    MGIKHCCYILYFTLALVTLLQPVRSAEDLQEILPVNETRRLTTSGAY
    NIIDGCWRGKADWAENRKALADCAQGFGKGTVGGKDGDIYTVTSELD
    DDVANPKEGTLRFGAAQNRPLWIIFERDMVIRLDKEMVVNSDKTIDG
    RGAKVEIINAGFTLNGVKNVIIHNINMHDVKVNPGGLIKSNDGPAAP
    RAGSDGDAISISGSSQIWIDHCSLSKSVDGLVDAKLGTTRLTVSNSL
    FTQHQFVLLFGAGDENIEDRGMLATVAFNTFTDNVDQRMPRCRHGFF
    QVVNNNYDKWGSYAIGGSASPTILSQGNRFCAPDERSKKNVLGRHGE
    AAAESMKWNWRTNKDVLENGAIFVASGVDPVLTPEQSAGMIPAEPGE
    SALSLTSSAGVLSCQPGAPC
    • Cedar Sequences
  • 493634 Cry j IB precursor
    (SEQ ID NO: 395)
    MDSPCLVALLVFSFVIGSCFSDNPIDSCWRGDSNWAQNRMKLADCAV
    GFGSSTMGGKGGDLYTVTNSDDDPVNPPGTLRYGATRDRPLWIIFSG
    NMNIKLKMPMYIAGYKTFDGRGAQVYIGNGGPCVFIKRVSNVIIHGL
    YLYGCSTSVLGNVLINESFGVEPVHPQDGDALTLRTATNIWIDHNSF
    SNSSDGLVDVTLTSTGVTISNNLFFNHHKVMSLGHDDAYSDDKSMKV
    TVAFNQFGPNCGQRMPRARYGLVHVANNNYDPWTIYAIGGSSNPTIL
    SEGNSFTAPNESYKKQVTIRIGCKTSSSCSNWVWQSTQDVFYNGAYF
    VSSGKYEGGNIYTKKEAFNVENGNATPHLTQNAGVLTCSLSKRC
    493632 Cry j IA precursor
    (SEQ ID NO: 396)
    MDSPCLVALLVLSFVIGSCFSDNPIDSCWRGDSNWAQNRMKLADCAV
    GFGSSTMGGKGGDLYTVTNSDDDPVNPAPGTLRYGATRDRPLWIIFS
    GNMNIKLKMPMYIAGYKTFDGRGAQVYIGNGGPCVFIKRVSNVIIHG
    LHLYGCSTSVLGNVLINESFGVEPVHPQDGDALTLRTATNIWIDHNS
    FSNSSDGLVDVTLSSTGVTISNNLFFNHHKVMLLGHDDAYSDDKSMK
    VTVAFNQFGPNCGQRMPRARYGLVHVANNNYDPWTIYAIGGSSNPTI
    LSEGNSFTAPNESYKKQVTIRIGCKTSSSCSNWVWQSTQDVFYNGAY
    FVSSGKYEGGNIYTKKEAFNVENGNATPQLTKNAGVLTCSLSKRC
    1076242 Cry j II precursor- Japanese cedar
    (SEQ ID NO: 397)
    MAMKLIAPMAFLAMQLIIMAAAEDQSAQIMLDSVVEKYLRSNRSLRK
    VEHSRHDAINIFNVEKYGAVGDGKHDCTEAFSTAWQAACKNPSAMLL
    VPGSKKFVVNNLFFNGPCQPHFTFKVDGIIAAYQNPASWKNNRIWLQ
    FAKLTGFTLMGKGVIDGQGKQWWAGQCKWVNGREICNDRDRPTAIKF
    DFSTGLIIQGLKLMNSPEFHLVFGNCEGVKIIGISITAPRDSPNTDG
    IDIFASKNFHLQKNTIGTGDDCVAIGTGSSNIVIEDLICGPGHGISI
    GSLGRENSRAEVSYVHVNGAKFIDTQNGLRIKTWQGGSGMASHIIYE
    NVEMINSENPILINQFYCTSASACQNQRSAVQIQDVTYKNIRGTSAT
    AAAIQLKCSDSMPCKDIKLSDISLKLTSGKIASCLNDNANGYFSGHV
    IPACKNLSPSAKRKESKSHKHPKTVMVENMRAYDKGNRTRILLGSRP
    PNCTNKCHGCSPCKAKLVIVHRIMPQEYYPQRWICSCHGKIYHP
    1076241 Cry j II protein- Japanese cedar
    (SEQ ID NO: 398)
    MAMKFIAPMAFVAMQLIIMAAAEDQSAQIMLDSDIEQYLRSNRSLRK
    VEHSRHDAINIFNVEKYGAVGDGKHDCTEAFSTAWQAACKKPSAMLL
    VPGNKKFVVNNLFFNGPCQPHFTFKVDGIIAAYQNPASWKNNRIWLQ
    FAKLTGFTLMGKGVIDGQGKQWWAGQCKWVNGREICNDRDRPTAIKF
    DFSTGLIIQGLKLMNSPEFHLVFGNCEGVKIIGISITAPRDSPNTDG
    IDIFASKNFHLQKNTIGTGDDCVAIGTGSSNIVIEDLICGPGHGISI
    GSLGRENSRAEVSYVHVNGAKFIDTQNGLRIKTWQGGSGMASHIIYE
    NVEMINSENPILINQFYCTSASACQNQRSAVQIQDVTYKNIRGTSAT
    AAAIQLKCSDSMPCKDIKLSDISLKLTSGKIASCLNDNANGYFSGHV
    IPACKNLSPSAKRKESKSHKHPKTVMVKNMGAYDKGNRTRILLGSRP
    PNCTNKCHGCSPCKAKLVIVHRIMPQEYYPQRWMCSRHGKIYHP
    541803 Cry j I precursor- Japanese cedar
    (SEQ ID NO: 399)
    MDSPCLVALLVLSFVIGSCFSDNPIDSCWRGDSNWAQNRMKLADCAV
    GFGSSTMGGKGGDLYTVTNSDDDPVNPPGTLRYGATRDRPLWIIFSG
    NMNIKLKMPMYIAGYKTFDGRGAQVYIGNGGPCVFIKRVSNVIIHGL
    HLYGCSTSVLGNVLINESFGVEPVHPQDGDALTLRTATNIWIDHNSF
    SNSSDGLVDVTLSSTGVTISNNLFFNHHKVMLLGHDDAYSDDKSMKV
    TVAFNQFGPNCGQRMPRARYGLVHVANNNYDPWTIYAIGGSSNPTIL
    SEGNSFTAPNESYKKQVTIRIGCKTSSSCSNWVWQSTQDVFYNGAYF
    VSSGKYEGGNIYTKKEAFNVENGNATPQLTKNAGVLTCSLSKRC
    541802 Cry j I precursor- Japanese cedar
    (SEQ ID NO: 400)
    MDSPCLVALLVFSFVIGSCFSDNPIDSCWRGDSNWAQNRMKLADCAV
    GFGSSTMGGKGGDLYTVTNSDDDPVNPAPGTLRYGATRDRPLWIIFS
    GNMNIKLKMPMYIAGYKTFDGRGAQVYIGNGGPCVFIKRVSNVIIHG
    LYLYGCSTSVLGNVLINESFGVEPVHPQDGDALTLRTATNIWIDHNS
    FSNSSDGLVDVTLTSTGVTISNNLFFNHHKVMSLGHDDAYSDDKSMK
    VTVAFNQFGPNCGQRMPRARYGLVHVANNNYDPWTIYAIGGSSNPTI
    LSEGNSFTAPNESYKKQVTIRIGCKTSSSCSNWVWQSTQDVFYNGAY
    FVSSGKYEGGNIYTKKEAFNVENGNATPHLTQNAGVLTCSLSKRC
    • Dog Canis Sequences:
  • Can f 1
    (SEQ ID NO: 401)
    MKTLLLTIGFSLIAILQAQDTPALGKDTVAVSGKWYLKAMTADQEVP
    EKPDSVTPMILKAQKGGNLEAKITMLTNGQCQNITVVLHKTSEPGKY
    TAYEGQRVVFIQPSPVRDHYILYCEGELHGRQIRMAKLLGRDPEQSQ
    EALEDFREFSRAKGLNQEILELAQSETCSPGGQ
    Serum albumin fragment
    (SEQ ID NO: 402)
    EAYKSEIAHRYNDLGEEHFRGLVL
    Serum albumin fragment
    (SEQ ID NO: 403)
    LSSAKERFKCASLQKFGDRAFKAWSVARLSQRFPKADFAEISKVVTD
    LTKVHKECCHGDLLECADDRADLAKYMCENQDSISTKLKECCDKPVL
    EKSQCLAEVERDELPGDLPSLAADFVEDKEVCKNYQEAKDVFLGTFL
    YEYSRRHPEYSVSLLLRLAKEYEATLEKCCATDDPPTCYAKVLDEFK
    PLVDEPQNLVKTNCELFEKLGEYGFQNALLVRYTKKAPQVSTPTLVV
    EVSRKLGKVGTKCCKKPESERMSCADDFLS
    Can f 2
    (SEQ ID NO: 404)
    MQLLLLTVGLALICGLQAQEGNHEEPQGGLEELSGRWHSVALASNKS
    DLIKPWGHFRVFIHSMSAKDGNLHGDILIPQDGQCEKVSLTAFKTAT
    SNKFDLEYWGHNDLYLAEVDPKSYLILYMINQYNDDTSLVAHLMVRD
    LSRQQDFLPAFESVCEDIGLHKDQIVVLSDDDRCQGSRD
    • Additional Dog Allergen Protein (NCBI Entrez Accession):
  • 1731859
    • Horse Equus Sequences:
  • 1575778 Equ c 1
    (SEQ ID NO: 405)
    MKLLLLCLGLILVCAQQEENSDVAIRNFDISKISGEWYSIFLASDVK
    EKIEENGSMRVFVDVIRALDNSSLYAEYQTKVNGECTEFPMVFDKTE
    EDGVYSLNYDGYNVFRISEFENDEHIILYLVNFDKDRPFQLFEFYAR
    EPDVSPEIKEEFVKIVQKRGIVKENIIDLTKIDRCFQLRGNGVAQA
    3121755 Equ c 2
    (SEQ ID NO: 406)
    SQXPQSETDYSQLSGEWNTIYGAASNIXK
    • Euroglyphus (Mite) Euroglyphus Sequences:
  • Eur m 1 (variant)
    (SEQ ID NO: 407)
    TYACSINSVSLPSELDLRSLRTVTPIRMQGGCGSCWAFSGVASTESA
    YLAYRNMSLDLAEQELVDCASQNGCHGDTIPRGIEYIQQNGVVQEHY
    YPYVAREQSCHRPNAQRYGLKNYCQISPPDSNKIRQALTQTHTAVAV
    IIGIKDLNAFRHYDGRTIMQHDNGYQPNYHAVNIVGYGNTQGVDYWI
    VRNSWDTTWGDNGYGYFAANINL
    Eur m 1 (variant)
    (SEQ ID NO: 408)
    TYACSINSVSLPSELDLRSLRTVTPIRMQGGCGSCWAFSGVASTESA
    YLAYRNMSLDLAEQELVDCASQNGCHGDTIPRGIEYIQQNGVVQEHY
    YPYVAREQSCHRPNAQRYGLKNYCQISPPDSNKIRQALTQTHTAVAV
    IIGIKDLNAFRHYDGRTIMQHDNGYQPNYHAVNIVGYGNTQGVDYWI
    VRNSWDTTWGDNGYGYFAANINL
    Eur m 1 (variant)
    (SEQ ID NO: 409)
    ETNACSINGNAPAEIDLRQMRTVTPIRMQGGCGSCWAFSGVAATESA
    YLAYRNQSLDLAEQELVDCASQHGCHGDTIPRGIEYIQHNGVVQESY
    YRYVAREQSCRRPNAQRFGISNYCQIYPPNANKIREALAQTHSAIAV
    IIGIKDLDAFRHYDGRTIIQRDNGYQPNYHAVNIVGYSNAQGVDYWI
    VRNSWDTNWGDNGYGYFAANIDL
    Eur m 1 (variant)
    (SEQ ID NO: 410)
    ETSACRINSVNVPSELDLRSLRTVTPIRMQGGCGSCWAFSGVAATES
    AYLAYRNTSLDLSEQELVDCASQHGCHGDTIPRGIEYIQQNGVVEER
    SYPYVAREQQCRRPNSQHYGISNYCQIYPPDVKQIREALTQTHTAIA
    VIIGIKDLRAFQHYDGRTIIQHDNGYQPNYHAVNIVGYGSTQGVDYW
    IVRNSWDTTWGDSGYGYFQAGNNL
    • Poa (Grass) Sequences
  • 113562 POLLEN ALLERGEN POA P 9
    (SEQ ID NO: 411)
    MAVQKYTVALFLVALVVGPAASYAADLSYGAPATPAAPAAGYTPAAP
    AGAAPKATTDEQKMIEKINVGFKAAVAAAGGVPAANKYKTFVATFGA
    ASNKAFAEALSTEPKGAAVDSSKAALTSKLDAAYKLAYKSAEGATPE
    AKYDDYVATLSEALRIIAGTLEVHGVKPAAEEVKATPAGELQVIDKV
    DAAFKVAATAANAAPANDKFTVFEAAFNDAIKASTGGAYQSYKFIPA
    LEAAVKQSYAATVATAPAVKYTVFETALKKAITAMSQAQKAAKPAAA
    ATGTATAAVGAATGAATAAAGGYKV
    113561 POA P 9
    (SEQ ID NO: 412)
    MAVHQYTVALFLAVALVAGPAASYAADVGYGAPATLATPATPAAPAA
    GYTPAAPAGAAPKATTDEQKLIEKINAGFKAAVAAAAGVPAVDKYKT
    FVATFGTASNKAFAEALSTEPKGAAAASSNAVLTSKLDAAYKLAYKS
    AEGATPEAKYDAYVATLSEALRIIAGTLEVHAVKPAGEEVKAIPAGE
    LQVIDKVDAAFKVAATAANAAPANDKFTVFEAAFNDAIKASTGGAYQ
    SYKFIPALEAAVKQSYAATVATAPAVKYTVFETALKKAITAMSQAQK
    AAKPAAAVTATATGAVGAATGAVGAATGAATAAAGGYKTGAATPTAG
    GYKV
    113560 POA P 9
    (SEQ ID NO: 413)
    MDKANGAYKTALKAASAVAPAEKFPVFQATFDKNLKEGLSGPDAVGF
    AKKLDAFIQTSYLSTKAAEPKEKFDLFVLSLTEVLRFMAGAVKAPPA
    SKFPAKPAPKVAAYTPAAPAGAAPKATTDEQKLIEKINVGFKAAVAA
    AAGVPAASKYKTFVATFGAASNKAFAEALSTEPKGAAVASSKAVLTS
    KLDAAYKLAYKSAEGATPEAKYDAYVATLSEALRIIAGTLEVHGVKP
    AAEEVKAIPAGELQVIDKVDAAFKVAATAANAAPANDKFTVFEAAFN
    DAIKASTGGAYQSYKFIPALEAAVKQSYAATVATAPAVKYTVFETAL
    KKAITAMSQAQKAAKPAAAVTGTATSAVGAATGAATAAAGGYKV
    • Cockroach Sequences
  • 2833325 Cr p 1
    (SEQ ID NO: 414)
    MKTALVFAAVVAFVAARFPDHKDYKQLADKQFLAKQRDVLRLFHRVH
    QHNILNDQVEVGIPMTSKQTSATTVPPSGEAVHGVLQEGHARPRGEP
    FSVNYEKHREQAIMLYDLLYFANDYDTFYKTACWARDRVNEGMFMYS
    FSIAVFHRDDMQGVMLPPPYEVYPYLFVDHDVIHMAQKYWMKNAGSG
    EHHSHVIPVNFTLRTQDHLLAYFTSDVNLNAFNTYYRYYYPSWYNTT
    LYGHNIDRRGEQFYYTYKQIYARYFLERLSNDLPDVYPFYYSKPVKS
    AYNPNLRYHNGEEMPVRPSNMYVTNFDLYYIADIKNYEKRVEDAIDF
    GYAFDEHMKPHSLYHDVHGMEYLADMIEGNMDSPNFYFYGSIYHMYH
    SMIGHIVDPYHKMGLAPSLEHPETVLRDPVFYQLWKRVDHLFQKYKN
    RLPRYTHDELAFEGVKVENVDVGKLYTYFEQYDMSLDMAVYVNNVDQ
    ISNVDVQLAVRLNHKPFTYNIEVSSDKAQDVYVAVFLGPKYDYLGRE
    YDLNDRRHYFVEMDRFPYHVGAGKTVIERNSHDSNIIAPERDSYRTF
    YKKVQEAYEGKSQYYVDKGHNYCGYPENLLIPKGKKGGQAYTFYVIV
    TPYVKQDEHDFEPYNYKAFSYCGVGSERKYPDNKPLGYPFDRKIYSN
    DFYTPNMYFKDVIIFHKKYDEVGVQGH
    2231297 Cr p 2
    (SEQ ID NO: 415)
    INEIHSIIGLPPFVPPSRRHARRGVGINGLIDDVIAILPVDELKALF
    QEKLETSPDFKALYDAIRSPEFQSIISTLNAMQRSEHHQNLRDKGVD
    VDHFIQLIRALFGLSRAARNLQDDLNDFLHSLEPISPRHRHGLPRQR
    RRSARVSAYLHADDFHKIITTIEALPEFANFYNFLKEHGLDVVDYIN
    EIHSIIGLPPFVPPSRRHARRGVGINGLIDDVIAILPVDELKALFQE
    KLETSPDFKALYDAIRSPEFQSIISTLNAMPEYQELLQNLRDKGVDV
    DHFIRVDQGTLRTLSSGQRNLQDDLNDFLALIPTDQILAIAMDYLAN
    DAEVQELVAYLQSDDFHKIITTIEALPEFANFYNFLKEHGLDVVDYI
    NEIHSIIGLPPFVPPSQRHARRGVGINGLIDDVIAILPVDELKALFQ
    EKLETSPDFKALYDAIDLRSSRA
    1703445 Bla g 2
    (SEQ ID NO: 416)
    MIGLKLVTVLFAVATITHAAELQRVPLYKLVHVFINTQYAGITKIGN
    QNFLTVFDSTSCNVVVASQECVGGACVCPNLQKYEKLKPKYISDGNV
    QVKFFDTGSAVGRGIEDSLTISNLTTSQQDIVLADELSQEVCILSAD
    VVVGIAAPGCPNALKGKTVLENFVEENLIAPVFSIHHARFQDGEHFG
    EIIFGGSDWKYVDGEFTYVPLVGDDSWKFRLDGVKIGDTTVAPAGTQ
    AIIDTSKAIIVGPKAYVNPINEAIGCVVEKTTTRRICKLDCSKIPSL
    PDVTFVINGRNFNISSQYYIQQNGNLCYSGFQPCGHSDHFFIGDFFV
    DHYYSEFNWENKTMGFGRSVESV
    1705483 Bla g 4
    (SEQ ID NO: 417)
    AVLALCATDTLANEDCFRHESLVPNLDYERFRGSWIIAAGTSEALTQ
    YKCWIDRFSYDDALVSKYTDSQGKNRTTIRGRTKFEGNKFTIDYNDK
    GKAFSAPYSVLATDYENYAIVEGCPAAANGHVIYVQIRFSVRRFHPK
    LGDKEMIQHYTLDQVNQHKKAIEEDLKHFNLKYEDLHSTCH
    2326190 Bla g 5
    (SEQ ID NO: 418)
    YKLTYCPVKALGEPIRFLLSYGEKDFEDYRFQEGDWPNLKPSMPFGK
    TPVLEIDGKQTHQSVAISRYLGKQFGLSGKDDWENLEIDMIVDTISD
    FRAAIANYHYDADENSKQKKWDPLKKETIPYYTKKFDEVVKANGGYL
    AAGKLTWADFYFVAILDYLNHMAKEDLVANQPNLKALREKVLGLPAI
    KAWVAKRPPTDL
    • Additional Cockroach Sequences (NCBI Entrez Accession Numbers):
  • 2580504; 1580797; 1580794; 1362590; 544619; 544618; 1531589; 1580792; 1166573; 1176397; 2897849.
    • Allergen (General) Sequences: NCBI Accession Numbers
  • 2739154; 3719257; 3703107; 3687326; 3643813; 3087805; 1864024; 1493836; 1480457; 2598976; 2598974; 1575778; 763532; 746485; 163827; 163823; 3080761; 163825; 3608493; 3581965; 2253610; 2231297; 2897849; 3409499; 3409498; 3409497; 3409496; 3409495; 3409494; 3409493; 3409492; 3409491; 3409490; 3409489; 3409488; 3409487; 3409486; 3409485; 3409484; 3409483; 3409482; 3409481; 3409480; 3409479; 3409478; 3409477; 3409476; 3409475; 3409474; 3409473; 3409472; 3409471; 3409470; 3409469; 3409468; 3409467; 3409466; 3409465; 3409464; 3409463; 3409462; 3409461; 3409460; 3409459; 3409458; 3409457; 3409456; 3318885; 3396070 ; 3367732; 1916805; 3337403; 2851457; 2851456; 1351295; 549187; 136467; 1173367; 2499810; 2498582; 2498581; 1346478; 1171009; 126608; 114091; 2506771; 1706660; 1169665; 1169531; 232086; 416898; 114922; 2497701; 1703232; 1703233; 1703233; 1703232; 3287877; 3122132; 3182907; 3121758; 3121756; 3121755; 3121746; 3121745; 3319925; 3319923; 3319921; 3319651; 3318789; 3318779; 3309647; 3309047; 3309045; 3309043; 3309041; 3309039; 3288200; 3288068; 2924494; 3256212; 3256210; 3243234; 3210053; 3210052; 3210051; 3210050; 3210049; 3210048; 3210047; 3210046; 3210045; 3210044; 3210043; 3210042; 3210041; 3210040; 3210039; 3210038; 3210037; 3210036; 3210035; 3210034; 3210033; 3210032; 3210031; 3210030; 3210029; 3210028; 3210027; 3210026; 3210025; 3210024; 3210023; 3210022; 3210021; 3210020; 3210019; 3210018; 3210017; 3210016; 3210015; 3210014; 3210013; 3210012; 3210011; 3210010; 3210009; 3210008; 3210007; 3210006; 3210005; 3210004; 3210003; 3210002; 3210001; 3210000; 3209999; 3201547; 2781152; 2392605; 2392604; 2781014; 1942360; 2554672; 2392209; 3114481; 3114480; 2981657; 3183706; 3152922 ; 3135503 ; 3135501; 3135499; 3135497; 2414158; 1321733; 1321731; 1321728; 1321726; 1321724; 1321722; 1321720; 1321718; 1321716; 1321714; 1321712; 3095075; 3062795; 3062793; 3062791; 2266625; 2266623; 2182106; 3044216; 2154736; 3021324; 3004467; 3005841; 3005839; 3004485; 3004473; 3004471; 3004469; 3004465; 2440053; 1805730; 2970629 ; 2959898; 2935527 ; 2935416; 809536; 730091; 585279; 584968; 2498195; 2833325; 2498604; 2498317; 2498299; 2493414; 2498586; 2498585; 2498576; 2497749; 2493446; 2493445; 1513216 ; 729944; 2498099; 548449; 465054; 465053; 465052; 548671; 548670; 548660; 548658; 548657; 2832430; 232084; 2500822; 2498118; 2498119; 2498119; 2498118; 1708296; 1708793; 416607; 416608; 416608; 416607; 2499791; 2498580; 2498579; 2498578; 2498577; 2497750; 1705483; 1703445; 1709542; 1709545; 1710589; 1352699; 1346568; 1346323; 1346322; 2507248; 11352240; 1352239; 1352237; 1352229; 1351935; 1350779; 1346806; 1346804; 1346803; 1170095; 1168701; 1352506; 1171011; 1171008; 1171005; 1171004; 1171002; 1171001; 1168710; 1168709; 1168708; 1168707; 1168706; 1168705; 1168704; 1168703; 1168702; 1168696; 1168391; 1168390; 1168348; 1173075; 1173074; 1173071; 1169290; 1168970; 1168402; 729764; 729320; 729979; 729970; 729315; 730050; 730049; 730048; 549194; 549193; 549192; 549191; 549190; 549189; 549188; 549185; 549184; 549183; 549182; 549181; 549180; 549179; 464471; 585290; 416731; 1169666; 113478; 113479; 113477; 113476; 113475; 130975; 119656; 113562; 113561; 113560; 416610; 126387; 126386; 126385; 132270; 416611; 416612; 416612; 416611; 730035; 127205; 1352238; 125887; 549186; 137395; 730036; 133174; 114090; 131112; 126949; 129293; 124757; 129501; 416636; 2801531; 2796177; 2796175; 2677826; 2735118; 2735116; 2735114; 2735112; 2735110; 2735108; 2735106 ; 2735104; 2735102 ; 2735100 ; 2735098 ; 2735096 ; 2707295 ; 2154730; 2154728; 1684720; 2580504 ; 2465137; 2465135; 2465133; 2465131; 2465129; 2465127; 2564228; 2564226; 2564224; 2564222; 2564220; 2051993; 1313972; 1313970; 1313968; 1313966; 2443824 ; 2488684; 2488683; 2488682; 2488681; 2488680; 2488679; 2488678; 2326190 ; 2464905; 2415702; 2415700; 2415698; 2398759; 2398757; 2353266 ; 2338288 ; 1167836; 414703 ; 2276458 ; 1684718 ; 2293571 ; 1580797 ; 1580794 ; 2245508 ; 2245060; 1261972; 2190552 ; 1881574 ; 511953 ; 1532058; 1532056; 1532054; 1359436; 666007; 487661; 217308; 1731859; 217306; 217304; 1545803; 1514943; 577696; 516728; 506858; 493634; 493632; 2154734; 2154732; 543659; 1086046; 1086045; 2147643; 2147642; 1086003; 1086002; 1086001; 543675; 543623; 543509; 543491; 1364099; 2147108; 2147107; 1364001; 1085628; 631913; 631912; 631911; 2147092; 477301; 543482; 345521; 542131; 542130; 542129; 100636; 2146809; 480443; 2114497; 2144915; 72355; 71728; 319828; 1082946; 1082945; 1082944; 539716; 539715; 423193; 423192; 423191; 423190; 1079187; 627190; 627189; 627188; 627187; 482382; 1362656; 627186; 627185; 627182; 482381; 85299; 85298; 2133756; 2133755; 1079186; 627181; 321044; 321043; 112559; 112558; 1362590; 2133564; 1085122; 1078971; 627144; 627143; 627142; 627141; 280576; 102835; 102834; 102833; 102832; 84703; 84702; 84700; 84699; 84698; 84696; 477888; 477505; 102575; 102572; 478272; 2130094; 629813; 629812; 542172; 542168; 542167; 481432; 320620; 280414; 626029; 542132; 320615; 320614; 100638; 100637; 100635; 82449; 320611; 320610; 280409; 320607; 320606; 539051; 539050; 539049; 539048; 322803; 280407; 100501; 100498; 100497; 100496; 1362137; 1362136; 1362135; 1362134; 1362133; 1362132; 1362131; 1362130; 1362129; 1362128; 100478; 2129891; 1076531; 1362049; 1076486; 2129817; 2129816; 2129815; 2129814; 2129813; 2129812; 2129805; 2129804; 2129802; 2129801; 2129800; 2129799; 479902; 479901; 2129477; 1076247; 629480; 1076242; 1076241; 541803; 541802; 280372; 280371; 1361968; 1361967; 1361966; 1361965; 1361964; 1361963; 1361962; 1361961; 1361960; 1361959; 320546; 2119763; 543622; 541804; 478825; 478824; 478823; 421788; 320545; 81444; 626037; 626028; 539056; 483123; 481398; 481397; 100733; 100732; 100639; 625532; 1083651; 322674; 322673; 81719; 81718; 2118430; 2118429; 2118428; 2118427; 419801; 419800; 419799; 419798; 282991; 100691; 322995; 322994; 101824; 626077; 414553 ; 398830 ; 1311457; 1916292 ; 1911819; 1911818; 1911659; 1911582; 467629; 467627; 467619 ; 467617 ; 915347; 1871507; 1322185; 1322183; 897645 ; 897647 ; 1850544 ; 1850542 ; 1850540 ; 288917; 452742; 1842045 ; 1839305; 1836011; 1836010; 1829900; 1829899; 1829898; 1829897; 1829896; 1829895; 1829894; 1825459 ; 1808987 ; 159653 ; 1773369 ; 1769849; 1769847; 608690 ; 1040877 ; 1040875; 1438761; 1311513; 1311512; 1311511; 1311510; 1311509; 1311689; 1246120; 1246119; 1246118; 1246117; 1246116; 1478293; 1478292; 1311642; 1174278; 1174276; 1086972; 1086974; 1086976; 1086978; 1086978; 1086976; 1086974; 1086972; 999009; 999356; 999355; 994866; 994865; 913758; 913757; 913756; 913285; 913283; 926885; 807138; 632782; 601807; 546852; 633938; 544619; 544618; 453094; 451275; 451274; 407610; 407609; 404371; 409328; 299551; 299550; 264742; 261407; 255657; 250902; 250525; 1613674; 1613673; 1613672; 1613671; 1613670; 1613304; 1613303; 1613302; 1613240; 1613239; 1613238; 1612181; 1612180; 1612179; 1612178; 1612177; 1612176; 1612175; 1612174; 1612173; 1612172; 1612171; 1612170; 1612169; 1612168; 1612167; 1612166; 1612165; 1612164; 1612163; 1612162; 1612161; 1612160; 1612159; 1612158; 1612157; 1612156; 1612155; 1612154; 1612153; 1612152; 1612151; 1612150; 1612149; 1612148; 1612147; 1612146; 1612145; 1612144; 1612143; 1612142; 1612141; 1612140; 1612139; 1093120; 447712; 447711; 447710; 1587177; 158542; 1582223; 1582222; 1531589 ; 1580792 ; 886215; 1545897; 1545895; 1545893; 1545891; 1545889; 1545887; 1545885; 1545883; 1545881; 1545879; 1545877; 1545875; 166486 ; 1498496 ; 1460058; 972513; 1009442 ; 1009440 ; 1009438 ; 1009436 ; 1009434 ; 7413 ; 1421808 ; 551228; 452606 ; 32905; 1377859 ; 1364213; 1364212; 395407; 22690 ; 22688 ; 22686; 22684 ; 488605 ; 17680 ; 1052817 ; 1008445 ; 1008443 ; 992612; 706811 ; 886683; 747852 ; 939932 ; 19003 ; 1247377 ; 1247375; 1247373; 862307 ; 312284 ; 999462; 999460 ; 999458 ; 587450 ; 763064 ; 886209 ; 1176397 ; 1173557 ; 902012; 997915; 997914; 997913; 997912; 997911; 997910; 99790; 997908; 997907; 997906; 997905; 997904; 997903; 997902; 997901; 997900; 997899; 997898; 997897; 997896; 997895; 997894; 997893; 997892; 910984; 910983; 910982; 910981; 511604 ; 169631 ; 169629 ; 169627 ; 168316 ; 168314 ; 607633 ; 555616; 293902 ; 485371 ; 455288 ; 166447 ; 166445 ; 166443 ; 166435 ; 162551 ; 160780; 552080 ; 156719 ; 156715 ; 515957 ; 515956 ; 515955 ; 515954 ; 515953 ; 459163; 166953 ; 386678 ; 169865.
  • Particularly preferred T cell epitopes are derived from the allergens: cat dander protein Fel d1; House dust mite proteins Der P1, Der P2 and Der P7; Ragweed protein amb a 1.1, a 1.2, a1.3 or a1.4; Rye grass proteins lol p1 and lol p5; Timothy grass proteins phl p1 and phl p5; Bermuda grass protein Cyn d 5; Alternaria alternate proteins Alt a 1, Alt a 2 and Enolase (Alt a 6); Birch protein Bet v1 and P14; German Cockroach proteins Bla g 1, Bla g 2, Bla g 3, Bla g 4, Bla g 5 and Bla g 6; Mugwort protein Art v 1; Russian thistle protein Sal k 1 and Sal k 2; peanut Ara h1, Ara h2, Ara h3, Ara h4, Ara h5, Ara h6, plant profilins or lipid transfer proteins or a human leukocyte antigen.
  • Suitable autoimmune antigens from which the MHC Class II-binding T cell epitope may derive can of course be obtained and/or produced using known methods. Suitable autoimmune antigens include the major antigens in the following autoimmune diseases: Acute disseminated encephalomyelitis (ADEM); Addison's disease; Ankylosing spondylitis; Antiphospholipid antibody syndrome (APS); Aplastic anemia; Autoimmune hepatitis; Autoimmune Oophoritis; Coeliac disease; Crohn's disease; Diabetes mellitus type 1; Gestational pemphigoid; Goodpasture's syndrome; Graves' disease; Guillain-Barré syndrome (GBS); Hashimoto's disease; Idiopathic thrombocytopenic purpura; Kawasaki's Disease; Lupus erythematosus; Multiple sclerosis; Myasthenia gravis; Opsoclonus myoclonus syndrome (OMS); Optic neuritis; Ord's thyroiditis; Pemphigus; Pernicious anaemia; Polyarthritis in dogs; Primary biliary cirrhosis; Rheumatoid arthritis; Reiter's syndrome; Sjögren's syndrome; Takayasu's arteritis; Temporal arteritis (also known as “giant cell arteritis”); Warm autoimmune hemolytic anemia; Wegener's granulomatosis.
  • Other preferred eptiopes may be derived from antigens involved with maternal-foetal immunes responses, for example Rhesus D antigens involved in Rhesus D Haemolytic Disease of the Newborn.
  • Other preferred epitopes may be derived from antigens involved in graft-versus-host disease or transplant rejection (alloimmune responses), for example from MHC Class I molecules (otherwise referred to as human leukocyte antigens-HLA), preferably from the α3 domain and/or transmembrane domain of MHC Class I molecules, most preferably from the human MHC Class I molecule HLA-A2.
  • The epitopes may be of proteins which are administered to the individual, for example for therapy. Such proteins may act as neoantigens in the individual, such as for example in the situation where the individual does not express the protein. The therapeutic protein may be factor IIX or salcatonin.
  • Particularly suitable proteins from which to derive the epitope sequences of the invention are those which have a low frequency of epitopes per amino acid residue, i.e. the ratio of amino acids in the minimal binding sequence of an epitope, relative to the total number of amino acids in the protein (“the epitope ratio”) is low. A protein with a low frequency of epitopes per amino acid residue typically has an epitope ratio of 1:35, 1:40, 1:45, 1:50, 1:55, 1:60 or 1:65. These proteins are preferred sources of epitope sequences of the invention because a high proportion of the different epitope sequences derived from such proteins typically overlap. In general, the percentage of epitope sequences which overlap with at least one other epitope sequence, as a proportion of the total number of epitopes in a protein with a low epitope ratio as defined above, is greater than 60%, 65%, 70%, 80% or 90%.
  • The following Examples illustrate the invention:
    • EXAMPLE 1 House Dust Mite Peptides from Der p 1, Der p2 and Der p 7 MHC Class II Binding Search
  • The aim of this study is to identify peptides with strong affinities for the seven most common human MHC Class II HLA-DRB1* allotypes (covering in total around 63% of the allotypes found in the average Caucasian population). In order to identify binding peptides in the House Dust Mite (HDM) allergens, Der p 1, Der p 2 and Der p 7, in vitro binding assays have been performed on a subset of peptides from these allergenic proteins. Peptides for testing in the binding assays were initially identified by an in silico approach known as “peptide threading” (carried out by Biovation, Ltd.,Aberdeen, Scotland, UK). This is a bioinformatic analysis of consecutive peptides from a sequence for the potential to be accommodated within the binding groove of MHC class II HLA-DR molecules. This subset of peptides was pre-screened for solubility in an aqueous, acidic milieu and a final panel of 44 peptides selected for testing in an in vitro MHC Class II binding assay.
    • Methods
  • The assay employed is a competitive MHC class II binding assay, wherein each peptide is analysed for its ability to displace a known control binder from each of the human MHC class II allotypes investigated. The allotypes and control peptides used in this study are shown in the table below.
  • Control Peptides used in the In Vitro Binding Assays
  • Allotype Control Peptide Sequence
    DRB1*0101 Influenza PKYVKQNTLKLAT
    haemagglutinin (SEQ ID NO: 1)
    307-319
    DRB1*0301 Myco. tuberculosis/ AKTIAYDEEARRGLE
    leprae hsp 65 2-16 (SEQ ID NO: 2)
    DRB1*0401 Influenza PKYVKQNTLKLAT
    haemagglutinin (SEQ ID NO: 1)
    307-319
    DRB1*0701 Influenza PKYVKQNTLKLAT
    haemagglutinin (SEQ ID NO: 1)
    307-319
    DRB1*1101 Influenza PKYVKQNTLKLAT
    haemagglutinin (SEQ ID NO: 1)
    307-319
    DRB1*1301 HLA-DQB1*0603 21-36 TERVRLVTRHIYNREE
    (SEQ ID NO: 3)
    DRB1*1501 Human myelin basic ENPVVHFFKNIVTPR
    protein 85-99 (SEQ ID NO: 4)
    DQB1*0602 Human Insulin B 1-15 FVNQHLCGSHLVEAL
    (SEQ ID NO: 5)

    Each of the 44 HDM peptides (which are shown in Tables A and B) were analysed in the competition assay and screened for relative binding compared to the control peptide. Due to the nature of the competitive assay the data for each peptide is represented as a ratio of its own IC50 to that of the control peptide. Thus, a peptide that has an IC50 value that is parity to the control peptide has an identical binding affinity, while peptides with a ratio less than one have a higher affinity and those with a ratio greater than one have a lower affinity.
    • Results
  • Solubility in aqueous solution is an essential criterion for a peptide to be an effective therapeutic agent. Therefore, as a consequence of the solubility screen we will have eliminated very hydrophobic peptides with a high frequency of large hydrophobic amino acid residues in multiple binding registers. This is a characteristic of promiscuous HLA-DRB1* binders. The data from the binding assays is shown in Table 3B. The relative binding of each peptide is shown for each of the allotypes in the study. The data shows that 24 of the 44 peptides tested bound to one or more of the MHC Class II allotypes. A range of cross-reactivity is seen with 5 peptides binding only one allotype, 8 peptides binding two, 9 peptides binding three and two peptides binding four different MHC Class II allotypes (red). It would also be expected that such peptides would have the ability to bind similar allotypes that have not been tested through the homology of MHC structures. This can be seen in the cross-reactivity of peptides for DRB1*0101, *0401, *0701 and *1101 in several cases here. Also shown is the solubility status of the peptide at the highest concentrations in the aqueous solution of the binding assay. The value illustrates the lowest concentration at which an insoluble white precipitate is seen. There appears to be no significant nonspecific effect of the formation of precipitate in the assays. Several peptides that precipitate at high concentrations also bind to MHC class II; however, several also show no ability to compete with the control peptides. It is to be expected that peptides liable to form precipitates may exhibit high affinity and promiscuous binding due to the presence of many hydrophobic residues.
  • The % purity of the peptides is indicated in Table 3A. This is of significance as purities were seen to vary from 60-90%. This would have a considerable effect on the ability of a peptide to compete if it is relatively impure. For example, HDM23A and HDM32 show low affinity binding; however, they are of reduced purity (66.7% and 68.7% respectively) compared to other HDM peptides. Therefore, if purity is taken into consideration, they may in fact have an equivalent affinity to a peptide of a higher purity.
  • It can be seen that some MHC Class II allotypes bind to more peptides than others; this is probably to be expected as there is variability between the pocket positions in the different MHC class II binding grooves. There are however, also a number of well-characterised differences between the affinities of the various control peptides. Clearly a high affinity control peptide will be more difficult to displace by the competing HDM peptide resulting in the identification of fewer binding peptides. This can be illustrated by the data presented here. For example, the Influenza Haemagglutinin 307-319 control peptide, has varying affinity according to the allotype, where DRB1*0101>*0401>*0701>* 1101. This is reflected in the number of binders to each of the allotypes, where DRB1*0101 has the lowest number of binders (5) and DRB1*1101 has the highest(14). Furthermore, the binding assay for DRB1*1501 is very stringent due to the high affinity of Myelin Basic Protein 85-99 for this allotype. In the high stringency screen the Fel d 1 peptide EQVAQYKALPVVLENA (SEQ ID NO:6), that was tested in an earlier study, gave a ratio of 0.97 indicating that high affinity binders could be identified at this stringency.
  • In addition, to identify lower affinity binders, the assay was also carried out under less stringent conditions. All the Der p binding peptides were seen to have a high ratio when tested against this allotype, showing they were low affinity binders compared to the control peptide. The DQA1*0102/DQB1*0602 binding assay uses a peptide from the B-chain of human insulin which is of lower affinity compared to those used in the DR assays. This dictates that the DQ assay is very sensitive and tends to produce very low ratio values for the strongest binders to this MHC Class II allotype. This sensitivity also accounts for the relatively higher number of DQ binding peptides within the panel screened. Finally, on closer analysis, the peptides identified as ligands for the DRB1*0101,*0401, *0701 superfamily, are found to incorporate a motif that is characteristic of promiscuous binders to this family of allotypes where: P1=Y, F, W, L, I, V, or M (Large aromatic or hydrophobic residue), P6=S, T, C, A, P, V, I, M (small, non-charged residue) Out of the 16 peptides (e.g. HDM 21B RGKPFQLEAVFEANQNT SEQ ID NO: 26) identified as binders to all or a combination of these 3 allotypes, 14 (87.5%) contain this motif, which suggests that these are promiscuous binders with a range of affinities for the 1-4-7 allotypes.
    • Conclusions
  • A range of peptides have been shown to have the capacity to bind the MHC Class II allotypes and are considered to represent T cell epitopes. Thus the inventors were able to identify sequences comprising T cell epitopes which are close together in the overall protein sequence and therefore construct peptides which comprise overlapping epitopes. A number of such sequences will be apparent to the skilled person when considering Tables 1A and 1B. Specific illustrative examples include:
  • HDM01 (residues 112-124) and HDM02 (118-130). Providing a combination of these two sequences, the inventors devised a longer sequence spanning residues 112 to 130. In order to reduce dimer formation by this longer peptide, the cysteine at position 129 is replaced with serine to give new peptide HDM01A:
  • (SEQ ID NO: 7)
    IDLRQMRTVTPIR MQGGSG

    (HDM01=underlined, HDM02=bold).
  • HDM34 (residues 74-88) and HDM35 (79-91). Providing a combination of these two sequences, the inventors devised a longer sequence spanning residues 72 to 89. Residues 72 and 73 were added, and residues 90 and 91 removed in order to improve solubility for the new peptide, HDM207:
  • (SEQ ID NO: 8)
    DMRNIQVRGLKQMKRVG D

    (HDM34=underlined, HDM35=bold).
  • Evidence that these new peptides are suitable for tolerisation to house dust mite allergens is shown in Table 1C. Table 1C presents results from a cytokine release assay performed on four house dust mite allergic individuals for HDM01A compared to HDM01 and HDM02, and on three house dust mite allergic individuals for HDM34, HDM35 and HDM207.
  • Cytokine secretion profiles from PBMC's were analysed in response to the peptide stimulation using the above peptides. Supernatants from the cytokine release assay were tested for the presence of 2 cytokines, IFN-γ and IL-13, using either an ELISA assay or a multiplex bead array assay.
  • A typical cytokine release assay requires 40×106 PBMC's per subject. In more detail, 250 μl of a 200 μg/ml solution of the appropriate antigen or peptide concentration is distributed into the appropriate wells of 48 well plates. Plates are the incubated in a humidified 5% CO2 incubator at 37° C. for a maximum of 4 hours. 250 μl of a 5×106 cell/ml PBMC suspension is then added to each well and the plates returned to the incubator for 5 days. Following stimulation, samples of culture supernatant are harvested for testing by ELISA or multiplex bead assay according to standard protocols.
  • As can be seen, the new peptides HDM01A and HDM207 give rise to significantly higher cytokine production in all patients tested than the original “single epitope” peptides from which they derive.
  • TABLE 1A
    Residues
    in parent % Solubility Precipitation SEQ
    Peptide Sequence molecule purity test in assay ID NO
    HDM01 IDLRQMRTVTPIR 112-124 79.2 YES None  9
    HDM02 RTVTPIRMQGGCG 118-130 79.6 YES None 10
    HDM03C RNQSLDLAEQELVDCASQH 149-167 60.1 YES None 11
    HDM05 EYIQHNGVVQESY 179-191 77.5 YES None 12
    HDM06 RYVAREQSCRRPN 193-205 79.7 YES None 13
    HDM07 PNVNKIREALAQT 220-232 88.6 YES None 14
    HDM08 NKIREALAQTHSA 223-235 87.6 YES None 15
    HDM09A REALAQTHSAIAVI 226-239 69.6 YES 1000 μM 16
    (2.9 mg/ml)
    HDM11 IGIKDLDAFRHYD 240-252 77.6 YES None 17
    HDM12 KDLDAFRHYDGRT 243-255 72.9 YES None 18
    HDM13 RTIIQRDNGYQPNY 254-267 70.7 NO None 19
    HDM16A RNSWDTNWGDNGYG 287-300 70.0 YES None 20
    HDM17 NSVNVPSELDLRSLRT 105-120 74.5 YES None 21
    HDM19 DQVDVKDCANHEIKK 18-32 81.4 YES None 22
    HDM20 CIIHRGKPFQLEA 44-56 77.4 YES None 23
    HDM21 KPFQLEAVFEANQNT 50-64 88.7 YES  200 μM 24
    (0.3 mg/ml)
    HDM21A KPFQLEAVFEANQNTK 50-65 90.1 YES 5000 μM 25
    (9.3 mg/ml)
    HDM21B RGKPFQLEAVFEANQNT 48-64 82.6 YES 1000 μM 26
    (1.98 mg/ml) 
    HDM22A EAVFEANQNTKTAK 55-68 90.3 YES None 27
    HDM23A DGLEVDVPGIDPNACH 76-88 66.7 YES None 28
    HDM26A DGVLACAIATHAKIR 131-145 1000 μM 29
    (1.5 mg/ml)
    HDM27 AKIEIKASLDGLE 67-79 65.9 YES 1000 μM 30
    (1.4 mg/ml)
    HDM28 KAVDEAVAAIEKS 31-43 86.8 YES 1000 μM 31
    (1.3 mg/ml)
    HDM29 ETFDPMKVPDHSD 44-56 84.7 YES None 32
    HDM29A ETFDPMKVPDHSDK 44-57 91.7 YES None 33
    HDM29B KSETFDPMKVPDHSD 42-56 92.5 YES 1000 μM 34
    (1.7 mg/ml)
    HDM30 DKFERHIGIIDLK 56-68 81.4 YES 5000 μM 35
    (7.9 mg/ml)
    HDM31 IGIIDLKGELDMRN 62-75 1000 μM 36
    (1.8 mg/ml)
    HDM31A HIGIIDLKGELDMRN 61-75 66.4 YES 1000 μM 37
    (1.7 mg/ml)
    HDM32 IDLKGELDMRNIQ 65-77 68.7 YES 5000 μM 38
    (7.7 mg/ml)
    HDM32A IDLKGELDMRNIQVR 65-79 85.2 YES 5000 μM 39
    (9.0 mg/ml)
    HDM33 LDMRNIQVRGLKQ 71-83 70.3 YES None 40
    HDM34 RNIQVRGLKQMKRVG 74-88 74.7 YES None 41
    HDM35 RGLKQMKRVGDAN 79-91 84.0 YES None 42
    HDM36 KRVGDANVKSEDG 85-97 82.9 YES None 43
    HDM37 ANVKSEDGVVKAH  90-102 76.5 YES None 44
    HDM39 DDVVSMEYDLAYK 109-121 84.9 NO* None 45
    HDM39A HDDVVSMEYDLAYKL 108-121 80.9 YES 1000 μM 46
    (1.8 mg/ml)
    HDM40A VSMEYDLAYKLGDLH 112-124 66.9 YES 1000 μM 47
    (1.8 mg/ml)
    HDM48 TAIFQDTVRAEMTK 187-200 79.1 YES 1000 μM 48
    (1.6 mg/ml)
    HDM49 DTVRAEMTKVLAP 192-204 69.5 YES None 49
    Peptides HDM01 to 116A are from Der p1;
    peptide HDM17 is from Der f1.
    Peptides HDM19 to 26A are from Der p2;
    peptide HDM37 is from Der f2.
    Peptides HDM 28 to 49 are from Der p 7.
    The sequence of Der p 1 from which the “residues in parent” positions are derived is the publically available sequence with NCBI Accession No. P08176.
    The corresponding sequences for Der p 2 and Der p 7 are NCBI Accession Nos. P49278 and P49273, respectively.
  • TABLE 1B
    DQA1*
    0102
    DRB1 DRB1* DRB1* DRB1* DRB1* DRB1* DRB1* DQB1*
    Peptide *0101 0301 0401 0701 1101 1301 1501 0602
    HDM01 19.23 16
    HDM02 80 0.03
    HDM03C 0.16
    HDM05
    HDM06 30.36 0.86
    HDM07
    HDM08
    HDM09A 0.49 21.15 200
    HDM11
    HDM12
    HDM13
    HDM16A
    HDM17
    HDM19
    HDM20 1.1 28 242.11 2.37
    HDM21 92 11.15 11.73
    HDM21A 200 52.17 10.27
    HDM21B 13.5 0.78 4.1
    HDM22A 328.6 80
    HDM23A 347 0.76
    HDM26A 42.3 16.28 0.61
    HDM27
    HDM28
    HDM29
    HDM29A
    HDM29B
    HDM30 6.2
    HDM31
    HDM31A
    HDM32A
    HDM33 46.51 41.5 263.16
    HDM34 3.38 3.7 769.23
    HDM35 1.26
    HDM36
    HDM37
    HDM39
    HDM39A 76.19 0.71 0.1
    HDM40A 2.29 6
    HDM48 211.26 15.71 13.57
    HDM49 671.43 1.7
    HDM50
    HDM51 20.93 30.91
  • TABLE 1C
    (cytokine levels shown in pg/ml)
    Subject Cytokine HDM01 HDM02 HDM01A
    1 Il-13 73 61 502
    IFN-γ 139 350 459
    2 Il-13 47 11 82
    IFN-γ 63 58 166
    3 Il-13 26 24 57
    IFN-γ 0 22 44
    4 Il-13 81 37 135
    IFN-γ 31 0 44
    HDM34 HDM35A HDM207
    A Il-13 0 0 11
    IFN-γ 0 0 72
    B Il-13 0 0 169
    IFN-γ 26 20 341
    C Il-13 4 25 676
    IFN-γ 113 247 609
    • EXAMPLE 2 Grass Peptides
  • The Timothy Grass pollen allergen Phl p 5 Accession number 2003342A was analysed by methods analogous to those used in Example 1. A number of peptides sequences containing MHC Class II binding epitopes were identified. As above, the inventors were able to identify sequences comprising T cell epitopes which are close together in the overall protein sequence and therefore construct peptides which comprise overlapping epitopes.
  • A specific example is peptide Tim10B, which consists of residues 260 to 277 of Phl p5. This peptide was constructed by extending peptide Tim10C (residues 268 to 276 of Phl p5) to include a second, third and fourth T cell epitope (As confirmed in the further in silico analysis of Phl p 5 in Example 5). Production of IL13 in response to both peptides was measured as in Example 1. As shown in FIG. 1, Tim 10B demonstrates consistently greater cytokine production in the panel of subjects tested than the “single epitope” peptide Tim 10C.
  •
    Tim 10B 260 KYTVFETALKKAITAMSE 277
    (SEQ ID NO: 50)
    Tim 10C 268 LKKAITAMS 276
    (SEQ ID NO: 51)
    • EXAMPLE 3
  • Peptides Comprising Multiple Epitopes from House Dust Mite Allergens Der Pl
  • The peptides listed in this Example were identified as containing T cell epitopes by an in silico MHC binding analysis. The peptides identified have strong affinities for the seven most common human MHC Class II HLA-DRB1* allotypes (covering in total around 63% of the allotypes found in the average Caucasian population).
  • In order to identify additional binding peptides in the House dust mite allergen der p 1, the inventors used an in silico approach known as “peptide threading” using the commercially available EpiMatrix algorithm (EpiVax Inc.) This is a bioinformatic analysis of peptides from a sequence for the potential to be accommodated within the binding groove of MHC class II HLA-DR molecules. EpiMatrix is a matrix-based algorithm that ranks amino acid segments from any polypeptide sequence by estimated probability of binding to each of the selected MHC molecules. (De Groot et al., AIDS Research and Human Retroviruses 13:539-41 (1997)). The procedure for developing matrix motifs was published by Schafer et al, 16 Vaccine 1998 (1998). In this Example, binding potential for HLA DR1, DR2, DR3, DR4, DR7, DR8, DR11, DR13 and DR15 is assessed. Putative MHC ligands are selected by scoring each 9-mer frame in a protein sequence. This score is derived by comparing the sequence of the 9-mer to the matrix of amino acid sequences known to bind to each MHC allele. Retrospective studies have demonstrated that EpiMatrix accurately predicts published MHC ligands (Jesdale et al., in Vaccines '97 (Cold Spring Harbor Press, Cold Spring Harbor, N.Y., 1997)). Successful prediction of peptides which bind to multiple MHC molecules has also been confirmed. The tables shown below show Epivax data for consecutive 9-mers in specific regions of each of the above allergen proteins. The regions are identified by “Frame start” and “Frame stop” values, which refer to the amino acid positions in the published sequences of each protein (the protein concerned and the relevant public database accession number for its sequence is shown at the top of each table). Flanking amino acids, added to stabilize the cluster during in-vitro testing, are shown underlined. Epivax also analysed hydrophobicity of peptides containing epitopes. Scores of greater than 1 are considered to be unsuitable for administration and/or manufacture.
  • The “Z-score” under each HLA allele indicates the potential of a given 9-mer to bind to that HLA allele. All scores in the Top 5% (Z-Score>=1.64) are considered “Hits”. “Hits” in each 9 mer scoring above 1.64 are considered to comprise T cell epitopes (summarised in the “Hits” column). Thus the inventors were able to identify sequences which are close together in the overall protein sequence and therefore construct peptides which comprise overlapping epitopes. Examples of such sequences are provided beneath the Table for the relevant section of each protein. Where such sequences comprise greater than two epitopes, it will be appreciated that any fragment of these sequences comprising at least two overlapping epitopes would also be suitable.
  •
    DER P 1: Accession No, P08176
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hit ID NO
    51 LESVKYVQS 59 1.31 0 52
    52 ESVKYVQSN 60 0 53
    53 SVKYVQSNG 61 1.37 0 54
    54 VKYVQSNGG 62 1.43 1.84 1.97 1.63 1.53 1.28 2.37 3 55
    55 KYVQSNGGA 63 0 56
    56 YVQSNGGAI 64 2.24 2.88 1.45 2.04 3 57
    57 VQSNGGAIN 65 1.54 0 58
    58 QSNGGAINH 66 0 59
    Suitable sequence HDM_1_ME1 = VK YVQSNGGAI (SEQ ID NO: 60) (residues 54-64) [epitope 1 = bold, epitope 2 = underlined]
    DER P 1: Accession No. P08176
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    72 LDEFKNRFL 80 0 61
    73 DEFKNRFLM 81 1.61 1.49 0 62
    74 EFKNRFLMS 82 0 63
    75 FKNRFLMSA 83 2.19 2.20 2.28 3 64
    76 KNRFLMSAE 84 0 65
    77 NRFLMSAEA 85 2.21 2.26 1.87 3 66
    78 RFLMSAEAF 86 0 67
    79 FLMSAEAFE 87 1.53 1.56 1.28 0 68
    Suitable sequence HDM_1_ME3 = LRQ MRTVTP IRM QGGCGS_ (SEQ ID NO: 81) (residues 114-131) [epitope 1 = bold,
    epitope 2 = underlined, epitope 3 = italic]
    DER P 1: Accession No. P08176
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    114 LRQMRTVTP 122 2.44 2.22 2.66 1.37 1.77 2.45 1.78 6 70
    115 RQMRTVTPI 123 0 71
    116 QMRTVTPIR 124 0 72
    117 MRTVTPIRM 125 1.78 2.04 1.37 2.16 1.97 2.36 5 73
    118 RTVTPIRMQ 126 0 74
    119 TVTPIRMQG 127 1.28 0 75
    120 VTPIRMQGG 128 0 76
    121 TPIRMQGGC 129 0 77
    122 PIRMQGGCG 130 1.29 0 78
    123 IRMQGGCGS 131 2.85 2.26 1.36 1.98 2.22 1.65 5 79
    124 RMQGGCGSC 132 0 80
    Suitable sequence HDM_1_ME3 = LRQ MRTVTP IRM QGGCGS_ (SEQ ID NO: 81) (residues 114-131) [epitope 1 = bold,
    epitope 2 = underlined, epitope 3 = italic]
    DER P 1: Accession No. P08176
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    144 AYLAYRNQS 152 1.95 1.39 1 82
    145 YLAYRNQSL 153 1.95 1.52 1.81 1.81 3.13 4 83
    146 LAYRNQSLD 154 2.22 1 84
    147 AYRNQSLDL 155 1.42 1.79 1.67 2 85
    148 YRNQSLDLA 156 1.52 1.80 1.87 1.69 1.36 3 86
    149 RNQSLDLAE 157 0 87
    Suitable sequence HDM_1_ME4 = A
    Figure US20160289281A1-20161006-P00001
    DLA (SEQ ID NO: 88) (residues 144−156) [epitope 1 = bold, 
    epitope 2 = underlined, epitope 3 = italic, epitope 4 = grey background, epitope 5 = last 9 amino acids]
    DER P 1: Accession No. P08176
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    190 SYYRYVARE 198 0 89
    191 YYRYVAREQ 199 1.96 1.51 1.41 2.67 2.08 1.38 1.49 3 90
    192 YRYVAREQS 200 1.90 2.57 1.85 1.90 2.92 3.69 2.31 7 91
    193 RYVAREQSC 201 0 92
    194 YVAREQSCR 202 1.29 1.28 2.24 1.68 2 93
    195 VAREQSCRR 203 0 94
    196 AREQSCRRP 204 0 95
    197 REQSCRRPN 205 0 96
    198 EQSCRRPNA 206 2.03 1.29 1.71 2 97
    199 QSCRRPNAQ 207 0 98
    Suitable sequence HDM_1_ME5 = Y
    Figure US20160289281A1-20161006-P00002
    SCRRPNA (SEQ ID NO: 99) (residues 191-206) [epitope 1 = bold, epitope 2 =
    underlined, epitope 3 = italic, epitope 4 = grey background]
    DER P 1: Accession No. P08176
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    298 GYGYFAANI 306 0 100
    299 YGYFAANID 307 1.44 2.74 1.65 2 101
    300 GYFAANIDL 308 1.40 1.78 1.94 2 102
    301 YFAANIDLM 309 1.55 1.53 0 103
    302 FAANIDLMM 310 1.41 1.50 1.87 1.46 1.74 1.83 3 104
    303 AANIDLMMI 311 0 105
    304 ANIDLMMIE 312 0 106
    Suitable sequence HDM_1_ME6 = YGYFAANIDLMM (SEQ ID NO: 107) (residues 299-310) [epitope 1 = bold, epitope 2 =
    underlined, epitope 3 = italic, epitope 4 = grey background]
    • EXAMPLE 4 Peptides Comprising Multiple Epitopes from Birch Pollen Allergens
  • The peptides listed in this Example were identified as in Example 3.
  •
    BET V 1: Accession No. 1FM4A
    Frame Frame Hydro- DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop phobicity Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    14 PAARMFKAF 22 .07 0 108
    15 AARMFKAFI 23 1.00 1.41 1.86 1.33 1.91 2 109
    16 ARMFKAFIL 24 1.22 2.26 1.99 1.68 3.25 4 110
    17 RMFKAFILD 25 .14 0 111
    Suitable sequence BET_1_ME1 = A ARMFKAFIL (SEQ ID NO: 112) (residues 15-24) [epitope 1 = bold, epitope 2 = underlined]
    BET V 1: CAA04829.1
    Frame Frame Hydro- DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop phobicity Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    2 VFNYEIGAT 10 .09 2.11 1 113
    3 FNYEIGATS 11 −.12 2.27 2.09 1.46 2 114
    4 NYEIGATSV 12 .03 0 115
    5 YEIGATSVI 13 .92 2.11 1.91 1.87 1.77 1.69 5 116
    6 EIGATSVIP 14 .19 0 117
    7 IGATSVIPA 15 .32 1.90 1.42 1.45 1 118
    8 GATSVIPAA 16 .25 0 119
    Suitable sequence BET_1_ME2 = V
    Figure US20160289281A1-20161006-P00003
    VIPA (SEQ ID NO: 120) (residues 2-15) [epitope 1 = bold, epitope 2 = underlined,
    epitope 3 = italic, epitope 4 = grey background]
    BET V 1: Accession No. P43186
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    63 SPFKYVKER 71 −.86 −1.47 −1.35 −.95 −.31 −1.42 −.48 −1.14 0 121
    64 PFKYVKERV 72 −.85 .85 −1.38 −.65 .85 −.16 1.15 .85 0 122
    65 FKYVKERVD 73 .71 .71 .05 .62 2.34 1.79 1.15 .15 2 123
    66 KYVKERVDE 74 −.77 .51 −1.53 −.65 2.29 .47 .86 −.47 1 124
    67 YVKERVDEV 75 1.89 .79 2.27 1.72 .09 .42 −.83 −.09 3 125
    68 VKERVDEVD 76 −1.55 −.39 −.95 −.52 1.50 −.80 .28 .19 0 126
    69 KERVDEVDH 77 −.75 −.15 .00 −.26 .20 .99 −.28 −.35 0 127
    Suitable sequence BET_1_ME3 = F
    Figure US20160289281A1-20161006-P00004
    V (SEQ ID NO: 314) (residues 65-75) [epitope 1 = bold, epitope 2 = underlined,
    epitope 3 = italic]
    BET V 1: Accession No. P43186
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    79 NFKYSYSMI 87 −.16 −.59 −1.04 −.25 −.18 −1.28 −.47 1.09 0 128
    80 FKYSYSMIE 88 .81 .41 1.87 1.30 1.46 1.32 −.15 1.43 1 129
    81 KYSYSMIEG 89 −1.13 −.38 −.95 −1.37 .65 −1.20 .13 .41 0 130
    82 YSYSMIEGG 90 .26 .69 1.34 1.35 .56 .82 −.05 −.51 0 131
    83 SYSMIEGGA 91 .21 .42 −.24 −.94 .28 1.51 −1.01 .48 0 132
    84 YSMIEGGAL 92 .11 .67 .28 1.26 −.63 1.93 3 133
    85 SMIEGGALG 93 1.26 .23 .75 −1.29 .23 .14 −.86 −.68 0 134
    Suitable sequence BET_1_ME4 = FKYS YSMIEGGAL (SEQ ID NO: 135) (residues 80-92) [epitope 1 = bold, epitope 2 = underlined]
    BET V 1: Accession No. P43177
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    143 ALLRAVESY 151 −.81 .35 −.34 .29 −.06 −.84 1.00 −.32 0 136
    144 LLRAVESYL 152 1.26 1.52 .46 1.47 .78 .46 .90 1.73 1 137
    145 LRAVESYLL 153 1.91 1.66 1.36 1.73 1.51 6 138
    146 RAVESYLLA 154 .65 −.01 .83 −.65 −.88 −.23 −.76 .09 0 139
    147 AVESYLLAH 155 −1.28 −.03 .05 −.69 −.71 .28 −.36 −.38 0 140
    148 VESYLLAHS 156 −.53 .94 −.18 -2.13 1.08 .59 1.28 1.06 0 141
    149 ESYLLAHSD 157 .75 −1.02 .25 .44 1.28 .13 −.18 −1.41 0 142
    150 SYLLAHSDA 158 .44 .48 .81 −.78 .66 1.33 .17 .28 0 143
    151 YLLAHSDAY 159 1.61 1.73 1.83 1.48 .14 .13 .88 .83 2 144
    Suitable sequence BET_1_ME5 = L
    Figure US20160289281A1-20161006-P00005
    AHSDAY (SEQ ID NO: 145) (residues 144−151) [epitope 1 = bold, epitope 2 = underlined, 
    epitope 3 = italic]
    • EXAMPLE 5 Peptides Comprising Multiple Epitopes from Timothy Grass Pollen Allergens
  • The peptides listed in this Example were identified as in Example 3.
  •
    Phl P 1: Accession No. P43213
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    142 GDEQKLRSA 150 −.62 −.54 −1.14 -2.14 −1.22 −.15 .20 −1.31 0 146
    143 DEQKLRSAG 151 −.71 .34 −1.29 −1.40 1.88 .74 .42 −.25 1 147
    144 EQKLRSAGE 152 1.04 .00 1.00 −.03 1.42 .61 −.03 −.85 0 148
    145 QKLRSAGEL 153 .85 .25 −.69 2.11 1.23 .54 .74 2.14 2 149
    146 KLRSAGELE 154 −.07 −.03 −.17 .56 −.13 −.63 −.74 −.84 0 150
    147 LRSAGELEL 155 1.80 1.91 1.14 2.02 1.17 .86 1.89 2.40 5 151
    148 RSAGELELQ 156 −1.14 .12 −.35 −.95 −.18 −.28 −1.20 −.57 0 152
    Suitable sequence Phl_1_ME1 = DE
    Figure US20160289281A1-20161006-P00006
    EL (SEQ ID NO: 153) (residues 143-155) 
    [epitope 1 = bold, epitope 2 = underlined, epitope 3 = italic]
    Phl P 1: Accession No. P43213
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    181 NYLALLVKY 189 .08 1.23 −.26 −.23 −.14 −.20 .89 .20 0 154
    182 YLALLVKYV 190 2.74 −.32 1.97 2.80 1.32 1.50 .23 .48 3 155
    183 LALLVKYVN 191 1.27 1.27 −.08 −.19 2.09 1.78 .99 .97 2 156
    184 ALLVKYVNG 192 .65 .48 .31 .38 .43 .57 .33 .98 0 157
    Suitable sequence Phl_1_ME2 = Y LALLVKYVN (SEQ ID NO: 158) (residues 182-191) [epitope 1 = bold, epitope 2 = underlined]
    Phl P 1: Accession No. P43213
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    215 SWGAIWRID 223 −.68 −1.26 −1.15 −.21 .08 −1.12 −.91 −1.80 0 159
    216 WGAIWRIDT 224 1.95 1.28 1.03 2.16 1.37 1.93 .83 1.35 3 160
    217 GAIWRIDTP 225 −1.73 −1.00 .04 −.45 −1.91 −.96 −.46 −1.40 0 161
    218 AIWRIDTPD 226 −1.52 −1.01 −1.25 −1.34 .35 −1.57 −.66 .32 0 162
    219 IWRIDTPDK 227 .79 .96 1.81 .21 .13 1.44 .52 .69 1 163
    220 WRIDTPDKL 228 1.97 2.87 2.36 2.86 1.13 .63 .28 1.09 4 164
    221 RIDTPDKLT 229 −.75 -2.52 −1.02 −.36 −1.45 −1.27 −1.42 −.12 0 165
    Suitable sequence Phl_1_ME3 = WGA
    Figure US20160289281A1-20161006-P00007
    L (SEQ ID NO: 166) (residues 216-228) 
    [epitope 1 = bold, epitope 2 = underlined, epitope 3 = italic]
    Phl P 1: Accession No. P43213
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    142 GDEQKLRSA 150 −.62 −.54 −1.14 -2.14 −1.22 −.15 .20 −1.31 0 167
    143 DEQKLRSAG 151 −.71 .34 −1.29 −1.40 1.88 .74 .42 −.25 1 168
    144 EQKLRSAGE 152 1.04 .00 1.00 −.03 1.42 .61 −.03 −.85 0 169
    145 QKLRSAGEL 153 .85 .25 −.69 2.11 1.23 .54 .74 2.14 2 170
    146 KLRSAGELE 154 −.07 −.03 −.17 .56 −.13 −.63 −.74 −.84 0 171
    147 LRSAGELEL 155 1.80 1.91 1.14 2.02 1.17 .86 1.89 2.40 5 172
    148 RSAGELELQ 156 −1.14 .12 −.35 −.95 −.18 −.28 −1.20 −.57 0 173
    Suitable sequence Phl_1_ME4 = (residues 143-155) [epitope 1 = bold, epitope 2 = underlined, epitope 3 = italic]
    Phl P 5: Accession No. 2003342A
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits NO
    69 KINAGFKAA 77 .34 −.85 .04 −.03 −.48 −.24 −.55 −.41 0 174
    70 INAGFKAAL 78 1.39 2.68 −.06 −.20 1.06 1.08 1.32 1.38 1 175
    71 NAGFKAALA 79 1.10 −.02 .67 −1.09 .41 .72 .23 .50 0 176
    72 AGFKAALAA 80 .67 .42 .52 −.36 .93 .68 1.11 1.15 0 177
    73 GFKAALAAA 81 .26 .83 .22 −1.54 .06 .51 .51 −.07 0 178
    74 FKAALAAAA 82 3.20 2.30 2.70 1.16 1.80 2.26 1.93 1.53 6 179
    75 KAALAAAAG 83 1.74 .29 1.03 −.47 1.34 1.29 .25 −.64 1 180
    76 AALAAAAGV 84 1.74 .84 .69 .63 .24 .26 .52 .51 1 181
    77 ALAAAAGVQ 85 1.05 .43 .84 1.31 1.09 1.08 −.09 1.39 0 182
    Suitable sequence Phl_5_ME1 = INAG
    Figure US20160289281A1-20161006-P00008
    GV (SEQ ID NO: 183) (residues 70-84) [epitope 1 = bold, epitope 2 =
    underlined, epitope 3 = italic, epitope 4 = grey background]
    Phl P 5: Accession No. 2003342A
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    89 KYRTFVATF 97 .31 −.73 .91 .36 −.58 −.03 −.25 −.91 0 184
    90 YRTFVATFG 98 2.56 1.50 2.20 1.06 1.84 1.45 1.32 2.45 4 185
    91 RTFVATFGA 99 1.13 .96 1.02 .76 .59 1.08 1.23 1.74 1 186
    92 TFVATFGAA 100 −.30 −.25 −.40 −.34 −.54 −.03 −.74 .03 0 315
    93 FVATFGAAS 101 2.41 .66 2.30 .87 1.30 1.96 1.09 1.34 3 187
    94 VATFGAASN 102 1.00 .22 .20 −.81 .98 .25 .45 1.07 0 188
    Suitable sequence Phl_5_ME2 = Y
    Figure US20160289281A1-20161006-P00009
    AS (SEQ ID NO: 189) (residues 90-101) 
    [epitope 1 = bold, epitope 2 = underlined, epitope 3 = italic]
    Phl P 5: Accession No. 2003342A
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    126 TSKLDAAYK 134 .83 −.45 .60 −.78 .26 .86 −.47 −1.50 0 190
    127 SKLDAAYKL 135 1.53 2.11 1.00 1.99 .61 .03 −.16 1.07 2 191
    128 KLDAAYKLA 136 .44 −1.45 −.32 −.26 −1.06 −.83 −1.13 −.32 0 192
    129 LDAAYKLAY 137 .53 2.43 .00 −.42 .69 .59 2.39 1.24 2 193
    130 DAAYKLAYK 138 −1.58 −.35 −1.07 -2.56 .28 −.30 .03 −.49 0 194
    131 AAYKLAYKT 139 .54 −.12 −.68 −.01 .70 .09 .05 .80 0 195
    132 AYKLAYKTA 140 1.09 −.95 .16 .08 −.27 .33 −.38 −.04 0 196
    133 YKLAYKTAE 141 1.65 2.54 1.18 .69 2.43 1.44 1.79 1.30 4 197
    134 KLAYKTAEG 142 .38 .66 .85 −1.04 1.73 .49 1.01 .72 1 198
    135 LAYKTAEGA 143 .64 1.05 .61 .12 1.26 .93 1.35 .61 0 199
    Suitable sequence Phl_5_ME3 = SK
    Figure US20160289281A1-20161006-P00010
    KTAEG (SEQ ID NO: 200) (residues 127-142) [epitope 1 = bold, epitope 2 =
    underlined, epitope 3 = italic, epitope 4 = grey background]
    Phl P 5: Accession No. 2003342A
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    192 KVDAAFKVA 200 .00 −1.20 −.30 −.37 −.82 −.58 −.89 −.73 0 201
    193 VDAAFKVAA 201 .90 2.21 .46 −.23 .91 1.28 1.84 1.53 2 202
    194 DAAFKVAAT 202 .48 −.86 .42 −.65 −.18 −.26 −.59 .03 0 203
    195 AAFKVAATA 203 .70 .50 .26 −1.24 1.02 .90 .86 .09 0 204
    196 AFKVAATAA 204 1.13 .81 .68 −.03 −.78 .50 .28 1.14 0 205
    197 FKVAATAAN 205 2.18 1.37 2.22 .91 1.95 1.38 1.03 .89 3 206
    198 KVAATAANA 206 2.23 1.24 1.72 .20 .84 1.29 .91 .57 2 207
    199 VAATAANAA 207 1.63 1.24 1.78 1.50 .63 .94 1.23 2.07 2 208
    200 AATAANAAP 208 .33 .10 .73 −1.15 −.38 −.33 −.20 −.12 0 209
    Suitable sequence Phl_5_ME4 = VDAAFKVAATAANAA (SEQ ID NO: 210) (residues 193-207) [epitope 1 = bold, epitope 2 =
    underlined, epitope 3 = italic, epitope 4 = grey background]
    Phl P 5: Accession as 2003342A
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    234 SYKFIPALE 242 .10 −.05 −.16 −1.19 1.21 −.12 .19 −.10 0 211
    235 YKFIPALEA 243 3.30 1.48 3.23 2.19 1.37 2.79 1.24 2.12 5 212
    236 KFIPALEAA 244 −1.07 −.16 −.36 −.59 −.58 −.16 .31 −.52 0 213
    237 FIPALEAAV 245 1.33 1.18 .76 .60 .94 .96 .84 .47 0 214
    238 IPALEAAVK 246 1.26 .59 1.04 −.36 .69 1.29 .54 −.55 0 215
    239 PALEAAVKQ 247 1.37 .40 1.65 .90 .74 .92 −.70 .20 1 216
    240 ALEAAVKQA 248 .50 −.89 .43 −.03 −.94 −.71 −.58 −.17 0 217
    241 LEAAVKQAY 249 .95 2.96 .15 −.19 1.07 .99 1.71 1.41 2 218
    242 EAAVKQAYA 250 .83 .63 .22 −.67 .51 1.62 .47 −.66 0 219
    Suitable sequence Phl_5_ME5 = YKFIPALEAAVKQAY (SEQ ID NO: 220) (residues 235-249) [epitope 1 = bold, epitope 2 =
    underlined, epitope 3 = italic]
    Phl P 5: Accession No. 2003342A
    Frame Frame DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ
    Start Sequence Stop Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits ID NO
    260 KYTVFETAL 268 .18 .07 −.69 .38 −.89 −.24 −.44 .55 0 221
    261 YTVFETALK 269 1.27 .76 2.24 .19 1.77 1.87 .98 .70 3 222
    262 TVFETALKK 270 1.34 .66 1.84 .52 .44 .87 −.11 .09 1 223
    263 VFETALKKA 271 −.26 −.71 −.35 −.32 −.39 .18 .33 .53 0 224
    264 FETALKKAI 272 1.66 1.28 .09 1.25 1.50 1.16 1.52 1.32 1 225
    265 ETALKKAIT 273 1.19 .67 .08 −.69 1.38 1.82 .62 −.43 1 226
    266 TALKKAITA 274 .51 −.01 .23 −.09 .89 .16 .48 .62 0 227
    267 ALKKAITAM 275 −.55 .17 −.37 −.50 −.39 −.70 .15 .32 0 228
    268 LKKAITAMS 276 2.13 2.14 2.85 .58 1.67 2.00 1.77 1.25 6 229
    269 KKAITAMSE 277 .70 −.73 .82 −.09 .93 .99 −1.11 .57 0 230
    Suitable sequence Phl_5_ME6 = YTVFETALKKAITAMS (SEQ ID NO: 231) (residues 261-276) [epitope 1 = bold, epitope 2 = underlined, 
    epitope 3 = italic, epitope 4 = grey background, epitope 5 = last 9 amino acids]
    • EXAMPLE 6 Peptides Comprising Multiple Epitopes from Alternaria Allergens
  • The peptides listed in this Example were identified as in Example 3.
  •
    ALT A 1: Accession No. AAD00097
    Frame  Frame  DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ ID 
    Start Sequence Stop Hydrophobicity Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits NO
    40 QLLMLSAKR 48 .06 1.52 0 232
    41 LLMLSAKRM 49 .87 2.83 1.44 2.17 1.46 1.71 1.47 1.33 3 233
    42 LMLSAKRMK 50 .01 1.62 2.04 1.49 1 234
    43 MLSAKRMKV 51 .06 1.29 1.49 1.65 1.83 1.28 2.34 3 235
    44 LSAKRMKVA 52 .04 0 236
    45 SAKRMKVAF 53 −.07 0 237
    46 AKRMKVAFK 54 −.41 1.67 1.38 1 238
    47 KRMKVAFKL 55 −.19 1.81 1.79 1.81 1.37 1.96 4 239
    48 RMKVAFKLD 56 −.14 0 240
    49 MKVAFKLDI 57 .86 1.82 2.87 1.74 1.49 2.82 2.60 5 241
    50 KVAFKLDIE 58 .05 0 242
    Figure US20160289281A1-20161006-C00001
    Figure US20160289281A1-20161006-C00002
    Sequences ALT_1_ME1 and ALT_1_ME2 may also be combined to create ALT_1_ME3 = LLMLSAKRMKVAFKLDI (SEQ ID NO: 245) containing 6 epitopes
    77 GFKRCLQFT 85 −.03 0 246
    78 FKRCLQFTL 86 .34 1.63 1.84 2.35 1.96 3 247
    79 KRCLQFTLY 87 −.11 0 248
    80 RCLQFTLYR 88 −.18 1.31 0 249
    81 CLQFTLYRP 89 .14 0 250
    82 LQFTLYRPR 90 −.63 1.31 1.73 1 251
    83 QFTLYRPRD 91 −1.44 2.03 1 252
    84 FTLYRPRDL 92 −.63 1.92 1.65 1.57 1.92 1.97 4 253
    85 TLYRPRDLL 93 −.52 0 254
    86 LYRPRDLLS 94 −.53 1.28 1.71 1 255
    87 YRPRDLLSL 95 −.53 1.37 2.34 2.46 1.58 1.93 2.44 4 256
    88 RPRDLLSLL 96 .01 0 257
    Figure US20160289281A1-20161006-C00003
    Figure US20160289281A1-20161006-C00004
    Sequences ALT_1_ME4 and ALT_1_ME5 may also be combined to create ALT_1_ME6 = FKRCLQFTLYRPRDLLSL (SEQ ID NO: 260)(residues 78-95)containing 6 epitopes 
    ALT A 2: Accession No. AAM90320
    Frame  Frame  DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ ID 
    Start Sequence Stop Hydrophobicity Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits NO
    53 TYYNSLGFN  61 −.12 0 261
    54 YYNSLGFNI  62 .03 2.47 2.66 1.94 3 262
    55 YNSLGFNIK  63 −.26 1.48 0 263
    56 NSLGFNIKA  64 .09 0 264
    57 SLGFNIKAT  65 .40 0 265
    58 LGFNIKATN  66 .10 1.72 2.04 1.82 1.62 3 266
    59 GFNIKATNG  67 −.37 0 267
    60 FNIKATNGG  68 −.37 1.58 1.92 2.97 1.50 1.48 1.55 2 268
    61 NIKATNGGT  69 −.76 0 269
    62 IKATNGGTL  70 .06 1.96 2.71 2.94 3 270
    63 KATNGGTLD  71 −.18 0 271
    Figure US20160289281A1-20161006-C00005
    115 DITYVATAT 123 .13 0 273
    116 ITYVATATL 124 1.41 2.04 1.81 1.54 1.65 1.73 1.62 1.59 4 274
    117 TYVATATLP 125 .73 0 275
    118 YVATATLPN 126 .42 2.17 2.84 2.45 2.11 1.74 1.92 6 276
    119 VATATLPNY 127 .42 2.10 1.87 2 277
    120 ATATLPNYC 128 .23 0 278
    Figure US20160289281A1-20161006-C00006
    146 AYITLVTLP 154 .33 0 280
    147 YITLVTLPK 155 .90 1.80 2.79 1.47 1.67 2.15 4 281
    148 ITLVTLPKS 156 .96 1.70 2.21 1.63 1.66 3 282
    149 TLVTLPKSS 157 .08 0 283
    Figure US20160289281A1-20161006-C00007
    ALT A 6: Accession No. Q9HDT3
    Frame  Frame  DRB1*0101 DRB1*0301 DRB1*0401 DRB1*0701 DRB1*0801 DRB1*1101 DRB1*1301 DRB1*1501 SEQ ID 
    Start Sequence Stop Hydrophobicity Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Z-Score Hits NO
    188 EVYQKLKAL 196 −.06 0 285
    189 VYQKLKALA 197 .31 1.90 2.13 2.02 2.21 4 286
    190 YQKLKALAK 198 −.59 2.57 2.63 1.84 1.92 2.40 5 287
    191 QKLKALAKK 199 −.88 0 288
    192 KLKALAKKT 200 −.57 1.74 1.47 1 289
    193 LKALAKKTY 201 −.28 1.49 1.97 1.69 1.87 2.45 4 290
    194 KALAKKTYG 202 −.16 1.44 0 291
    Figure US20160289281A1-20161006-C00008
    236 GYTGKIKIA 244 .00 0 293
    237 YTGKIKIAM 245 .28 1.57 2.68 1.60 2.02 2 294
    238 TGKIKIAMD 246 .03 0 295
    239 GKIKIAMDV 247 .58 1.40 1.65 1 296
    240 KIKIAMDVA 248 .82 0 297
    241 IKIAMDVAS 249 1.17 1.56 1.88 2.15 1.39 1.52 2.28 3 298
    242 KIAMDVASS 250 .58 1.53 1.92 1.63 1 299
    243 IAMDVASSE 251 .62 2.53 1.54 1 300
    244 AMDVASSEF 252 .09 0 301
    Figure US20160289281A1-20161006-C00009
    364 AFGAGWGVM 372 .25 0 303
    365 FGAGWGVMV 373 1.42 2.11 1.55 1.90 2 304
    366 GAGWGVMVS 374 1.02 1.47 0 305
    367 AGWGVMVSH 375 .71 0 306
    368 GWGVMVSHR  376 .01 0 307
    369 WGVMVSHRS  377 −.03 2.54 3.16 1.50 1.56 2.57 3 308
    370 GVMVSHRSG  378 .02 1.44 1.97 1.59 1 309
    371 VMVSHRSGE  379 −.32 1.85 1 310
    372 MVSHRSGET 380 −.87 2.20 1.65 2 311
    373 VSHRSGETE  381 −.31 0 312
    Figure US20160289281A1-20161006-C00010

Claims (4)

1. (canceled)
2. A composition comprising a peptide which has a length of 10 to 25 amino acids and which comprises a region having the sequence of SEQ ID NO: 60 or SEQ ID NO: 81.
3. A composition according to claim 2 which additionally comprises a pharmaceutically acceptable carrier and an adjuvant.
4. A composition according to claim 2 which additionally comprises an effective amount of a preservative and a pharmaceutically acceptable carrier.
US15/095,480 2007-08-15 2016-04-11 Peptide with multiple epitopes Abandoned US20160289281A1 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
US15/095,480 US20160289281A1 (en) 2007-08-15 2016-04-11 Peptide with multiple epitopes

Applications Claiming Priority (9)

Application Number Priority Date Filing Date Title
GB0715949A GB0715949D0 (en) 2007-08-15 2007-08-15 Peptide with improved solubility
GB0715949.4 2007-08-15
GB0716224.1 2007-08-20
GB0716224A GB0716224D0 (en) 2007-08-20 2007-08-20 Peptides for vaccine
GB0723337.2 2007-11-28
GB0723337A GB0723337D0 (en) 2007-11-28 2007-11-28 Peptide with reduced dimer formation
PCT/GB2008/002778 WO2009022154A2 (en) 2007-08-15 2008-08-15 Peptide with multiple epitopes
US67338610A 2010-03-11 2010-03-11
US15/095,480 US20160289281A1 (en) 2007-08-15 2016-04-11 Peptide with multiple epitopes

Related Parent Applications (2)

Application Number Title Priority Date Filing Date
PCT/GB2008/002778 Continuation WO2009022154A2 (en) 2007-08-15 2008-08-15 Peptide with multiple epitopes
US12/673,386 Continuation US9340580B2 (en) 2007-08-15 2008-08-15 Peptide with multiple epitopes

Publications (1)

Publication Number Publication Date
US20160289281A1 true US20160289281A1 (en) 2016-10-06

Family

ID=40134075

Family Applications (7)

Application Number Title Priority Date Filing Date
US12/673,412 Active 2030-04-21 US8652485B2 (en) 2007-08-15 2008-08-15 Peptide for vaccine
US12/673,386 Expired - Fee Related US9340580B2 (en) 2007-08-15 2008-08-15 Peptide with multiple epitopes
US12/673,334 Active 2030-01-07 US8551493B2 (en) 2007-08-15 2008-08-15 Peptide with reduced dimer formation
US13/974,603 Abandoned US20130336999A1 (en) 2007-08-15 2013-08-23 Peptide with reduced dimer formation
US14/150,045 Abandoned US20140186403A1 (en) 2007-08-15 2014-01-08 Peptide for vaccine
US15/095,480 Abandoned US20160289281A1 (en) 2007-08-15 2016-04-11 Peptide with multiple epitopes
US15/294,973 Active - Reinstated US9744222B2 (en) 2007-08-15 2016-10-17 Peptide for vaccine

Family Applications Before (5)

Application Number Title Priority Date Filing Date
US12/673,412 Active 2030-04-21 US8652485B2 (en) 2007-08-15 2008-08-15 Peptide for vaccine
US12/673,386 Expired - Fee Related US9340580B2 (en) 2007-08-15 2008-08-15 Peptide with multiple epitopes
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