Allergen nomenclature*

Terminology/Terminologie Allergen nomenclature* IUIS/WHO Allergen Nomenclature Subcommittee1 The revised nomenclature for allergens is presented together with proposed nomenclatures for (a) aller- gen genes, mRNAs and cDNAs, and (b) recombinant and synthetic peptides of allergenic interest. Introduction Rapid advances have been made in the past few years on allergen characterization and sequence deter- mination by chemical and molecular biological approaches. This is indicated by the list of allergens with known partial or complete amino acid sequen- ces in Table 1. A number of other important aller- gens are known in addition to those in Table 1 but their sequences are as yet not known. A useful source for known allergens is the Allergen Database (ALBE) in which are compiled their known bio- chemical and immunological properties together with their sequence data if known (1). To take into account these advances, a revision of the current allergen nomenclature system (2) is given below. As in the current nomenclature system, the proposed revisions are for allergens which induce IgE-mediated (atopic) allergy in humans. In addition to the expected thorough immunochemical character- ization of any newly discovered allergen, investiga- tors are urged to obtain partial, or preferably com- plete, sequence data before using the official nomenclature system. Also it is expected that inves- tigators would screen a reasonable population size so as to establish the frequency of response in patients to the newly discovered allergens. Investigators frequently refer to allergens as major or minor ones. The generally accepted mean- * A resum6 in French of this article appears on page 802. Requests for reprints should be addressed to the Chairman of the IUIS Nomenclature Committee, Professor Michel Kazatchki- ne, Unit6 d'Immunologie, H6pital Broussais, 96 rue Didot, 75014 Paris, France. I Members of this Nomenclature Subcommittee: Te Piao King (Chairman), Donald Hoffman, Henning Lowenstein, David G. Marsh, Thomas A.E. Platts-Mills and Wayne Thomas. Reprint No. 5531 ing of this terminology is that an allergen is desig- nated as either major or minor depending on whether greater or less than 50% of patients tested have the corresponding allergen-specific IgEs (cf. 3-5). The revised nomenclature for allergens is given below together with the proposed nomenclatures for (a) allergen genes, mRNAs and cDNAs and (b) recombinant and synthetic peptides of allergenic interest. Revised nomenclature (1) Allergens Allergens are designated according to the accepted taxonomic name of their source as follows: the first three letters of the genus, space, the first letter of the species, space, and an Arabic number. The numbers are assigned to the allergens in the order of their identification, and the same number is generally used to designate homologous allergens of related species. As two examples, Lol p 1 refers to the first pollen allergen identified from Lolium perenne, rye grass, and Cyn d 1 refers to the homologous pollen allergen from Cynodon dactylon, Bermuda grass. In some instances, the above system of the first 3 letters of a genus and the first letter of a species has to be modified to include an additional letter for designation of the exact genus or species. For exam- ple, 4 of the many vespids which can cause insect allergy are Vespula vulgaris, Vespula vidua, Vespula consobrina and Vespa crabo. The homologous major venom allergens, antigen 5s, from Vespula vulgaris and Vespula vidua are both designated as Ves v 5 in the existing nomenclature, and those from Vespula consobrina and Vespa crabo are designated as Ves c 5. To avoid these ambiguities, antigen 5s from Ves- pula vulgaris and Vespula vidua will be designated Bulletin of the World Health Organization, 1994, 72 (5): 797-806 797 IUIS/WHO Allergen Nomenclature Subcommittee Table 1: Some allergens with known amino acid sequences Allergen Allergens; systematic MW source and original names (kDa) A. Weed pollens Asterales Ambrosia artemisiifolia (short ragweed) Amb a 1; antigen E 38 Ambrosia trifida (giant ragweed) Artemisia vulgaris (mugwort) B. Grass pollens Poales: Cynodon dactylon (Bermuda grass) Dactylis glomerata (orchard grass) Lolium perenne (rye grass) Phleum pratense (timothy) Poa pratensis (Kentucky blue grass) Sorghum halepense (Johnson grass) C. Tree pollens Fagales: Alnus glutinosa (alder) Betula verrucosa (birch) Carpinus betulus (hornbeam) Corylus avelana (hazel) Quercus alba (white oak) Pinales: Cryptomeria japonica (sugi) Juniper sabinoides Amb a 2; antigen K Amb a 3; Ra3 Amb a 5; Ra5 Amb a 6; Ra6 Amb a 7; Ra7 Amb a ? Amb t 5; Ra5G Art v 2 Cyn d 1 Dac g 1; AgDgl Dac g 2 Dac g 5 Lol p 1; group Lol p 2; group 11 Lol p 3; group IlIl Lol p 5 Lol p 9; Lol p lb Phi p 1 Phl p 5; Ag25 Poa p 1; group Poa p 5 Poa p 9 Sor h 1 Aln g 1 Bet v 1 Bet v 2; profilin Car b 1 Cor a 1 Que a 1 Cry j 1 Cry j 2 Jun s 1 38 11 5 10 12 11 4.4 35 32 32 11 27 11 11 31 31/35 27 32 33 31 32/34 17 17 15 17 17 17 41-45 Sequence dataa, b C C C C C p C C p C p C p C C C p C C C p p C C C C C C C P C C C WHO Bulletin OMS. Vol 72 1994 Referencesa 8, 20 8, 21 22 11, 23 24, 25 26 27 9, 10, 28 29 30, 31 32 33 34 35, 36 37 38 34 39 40, 41 42-45 46 34 47 48 49 50 51 52 53 54 55, 56 57, 58 59 798 Allergen nomenclature (Table 1: continued) Juniper virginiana Oleales: Olea europea (olive) D. Mites Dermatophagoides pteronyssinus (mite) Dermatophagoides microceras (mite) Dermatophagoides farinae (mite) Lepidoglyphus destructor (storage mite) E. Animals Canis domesticusc Felis domesticus (cat saliva) Mus musculus (mouse urine) Rattus norvegius (rat urine) F. Fungi Aspergillus fumigatus Candida albicans Alternaria alternata Trichophyton tonsurans G. Insects Apis mellifera (honey bee) Bombus pennsylvanicus (bumble bee) Blattaria germanica (cockroach) Chironomus thummi thummi (midges) Dolichovespula maculata (white face hornet) Dolichovespula arenaria (yellow hornet) Jun v 1 Ole e 1 Der p 1; antigen P1 Der p 2 Der p 3; trypsin Der p 4; amylase Der p 5 Der p 6; chymotrypsin Der p 7 Der m 1 Der f 1 Der f 2 Der f 3 Lep d ? Can d 1 Can d 2 Fel d 1; cat-1 Mus m 1; MUP Rat n 1 Asp f 1 Aspf ? Asp f ? Cand a ? Alt a 1 Tri t 1 Api m 1; phospholipase A2 Api m 2; hyaluronidase Api m 4; melittin Bom p 1; phospholipase Bom p 4; protease Bla g 2 Chi t 1; hemoglobin Dol m 1; phospholipase Al Dol m 2; hyaluronidase Dol m 5; antigen 5 Dol a 5; antigen 5 C 58 C 59, 60 25 14 28/30 60 14 25 22-28 25 25 14 30 15 38 19 17 18 90 55 40 28 30 16 44 3 16 20 16 35 44 23 23 C C p p C p C p C C p p C C C C C C p p C p p C C C p p C C C C C C 61 62 63 64 65 66 67 68 69 70, 71 72 73 74 74 15 75, 76 77, 78 79 80 81 82 83-85 86 87 88 89 90 90 91 92 93 94 95, 96 97 WHO Bulletin OMS. Vol 72 1994 799 IUIS/WHO Allergen Nomenclature Subcommittee (Table 1: continued) Polistes annularis (wasp) Polistes exclamans (wasp) Polistes fuscatus (wasp) Polistes metricus (wasp) Vespula flavopilosa (yellowjacket) Vespula germanica (yellowjacket) Vespula maculifrons (yellowjacket) Vespula pennsylvanica (yellowjacket) Vespula squamosa (yellowjacket) Vespula vidua (wasp) Vespula vulgaris (yellowjacket) Vespa crabo Solenopsis invicta (fire ant) H. Foods Gadus callarias (cod) Gallus domesticus (chicken) Penaeus aztecus (brown shrimp) Brassica juncea (oriental mustard) Hordeum vulgare (barley) Sinapis alba (yellow mustard) I. Others Ascaris suum Hevea brasiliensis Pol a 1; phospholipase Al Pol a 2; hyaluronidase Pol a 5; antigen 5 Pol e 1; phospholipase Al Pol e 5; antigen 5 Pol f 5; antigen 5 Pol m 5; antigen 5 Ves f 5; antigen 5 Ves g 5; antigen 5 Ves m 1; phospholipase Al Ves m 2; hyaluronidase Ves m 5; antigen 5 Ves p 5; antigen 5 Ves s 5; antigen 5 Ves vi 5 Ves v 1; phopholipase Al Ves v 2; hyaluronidase Ves v 5; antigen 5 Vesp c 1; phospholipase Vesp c 5.0101; antigen 5 Vesp c 5.0102; antigen 5 Sol 2 Sol 3 Sol 4 Gad c 1; allergen M Gal d 1; ovomucoid Gal d 2; ovalbumin Gal d 3; conalbumin (Ag22) Gal d 4; lysozyme Pen a 1 Pen a 2; tropomyosin Bra j 1; 25 albumin Hor v 1; BMAI-1 Sin a 1; 25 albumin Asc s 1 Hev b 1; elongation factor 5 44 23 34 23 23 23 23 23 33.5 44 23 23 23 23 35 44 23 34 23 23 13 24 13 12 28 44 78 14 36 34 14 15 14 10 58 p p C p C C 98 98 97 100 97 99 P 99 C C C p C C C C C p C p C C C C C 99 99 101 102 97 99 99 99 98 98 97 100 99 99 103, 104 103 103 C 105 C C C C 106, 106, 106, 106, P 108 p 109 C 110 C 111 C 112 P 113 P 114 107 107 107 107 a References are those where partial (P) or complete (C) amino acid sequence data are available. Original references describing the initial characterization studies are not given because of limited space. We apolo- gize to our colleagues whose allergen sequence data we may have overlooked for inclusion in this Table. b Sequence data for group 5 and 9 allergens from several grass pollens indicate that they are highly homol- ogous proteins. Comparison of complete sequence data of group 5 and 9 allergens from a single grass spe- cies will clarify whether these two groups are the same protein. c Canis domesticus is also designated as Canis familiaris. WHO Bulletin OMS. Vol 72 1994800 Allergen nomenclature as Ves v 5 and Ves vi 5 respectively, and those from Vespula consobrina and Vespa crabo as Ves c 5 and Vesp c 5. In the examples given, the modified nomenclature is used for the allergens from Vespula vidua and Vespa crabo, as the allergens from Vespu- la vulgaris were characterized prior to those for Ves- pula vidua and Vespa crabo. Another example is for allergens from the domestic dog (Canis domesticus) and the mold Can- dida albicans. To avoid ambiguity, the modified system is used to designate Can d and Cand a aller- gens from these two sources respectively. In the current nomenclature system (2) the let- ters are italicized and the numerals are Roman numerals. In the revised system, only letters of nor- mal type and Arabic numbers are used. The proposed changes conform to the accepted nomenclature used in bacterial genetics (6) and HLA system (7) in that italicized and normal characters are used to represent genotypes and phenotypes respectively. (2) Allergens and isoallergens An allergen from a single species may consist of sev- eral closely similar molecules. These similar mole- cules are designated as isoallergens when they share the following common biochemical properties: (a) similar molecular size; (b) identical biological func- tion, if known, e.g. enzymatic action; and (c) >67% identity of amino acid sequences. It is recognized that the recommended >67% sequence identity for 2 allergens to be assigned to the same group is only a guide. There are likely to be borderline cases. As an example, the ragweed aller- gens Amb a 1 and 2 share 65% amino acid sequence identity (8). These allergens were assigned to differ- ent groups because of their different immunochemi- cal properties before their sequences were known. Allergens from different species of the same or different genus which share the above-mentioned common biochemical properties are considered to belong to the same group and the sequence identity requirement can be <67% as is the case for allergens of the same species. For example, Amb a 5 and Amb t 5 from short and giant ragweed pollens have about 45% sequence identity (9), and also have similar ter- tiary structures (10, 11). Another example is the minor pollen allergens Amb a 10, Poa p 10 and Lol p 10 from ragweed (12), Kentucky bluegrass (13) and rye grass (14). Although their sequences are not known, they are assigned to the same allergen group as they clearly have the same biological function of cytochrome c. (3) Isoallergens and variants cDNA cloning of allergens often show nucleotide mutations which are either silent or which can lead to single or multiple amino acid substitutions. In the revised system, members of an allergen group which have >67% amino acid sequence identity are desig- nated as isoallergens. Each isoallergen may have multiple forms of closely similar sequences, which are designated as variants. Isoallergens and their variants belonging to the same allergen group are designated by suffixes of a period followed by four Arabic numerals. The first two numerals 01 to 99 refer to a particular isoaller- gen, and the two subsequent numerals 01 to 99 refer to a particular variant of a particular isoallergen designated by the preceding two numerals. In cases where there is only one known isoallergen but there are several variants, the system of a suffix of 4 numerals will still apply. These numerals will be chosen in the order of the identification of allergens and/or their cDNAs irrespective of the physicochem- ical properties of the allergens. In cases of silent mutations, there can be more than one suffix of 4 numerals designating the same allergen and in that case the suffix with the lowest number will be used to designate the allergen of interest. The addition of suffixes of 4 numerals to desig- nate isoallergens and their variants will permit their unambiguous designation. In many cases it is un- necessary to specify the isoallergen or variant and the corresponding suffixes may be deleted; for example, Bet v 1 represents any Bet v 1 allergen and Bet v 1.0101 represents variant number 1 of isoallergen Bet v 1. Two other examples of this nomenclature system are given below. On cDNA cloning, Amb a I showed multiple polymorphic forms which differ from each other by 12-24% in their sequences (8). Four such forms of Amb a I are known and they are designated as Amb a 1.01, 1.02, 1.03 and 1.04. Each isoallergen of the Amb a I group is found to have 1 to 3 variants with >97% of sequence identity. These variants of the Amb a 1.01 group will be designated as Amb a 1.0101, 1.0102 and etc. In contrast to Amb a I, only two forms of Amb a II were found on cDNA cloning. These forms differ in two polymorphic sites and they have >99% amino acid sequence identity. They are designated as Amb a 2.0101 and 2.0102. Nomenclature for allergen genes, mRNAs and cDNAs At present the genomic structures of allergens are known in at least two cases; cat allergen Fel d 1 and mouse urinary allergen Mus m 1. Knowledge of the genomic structure can provide an understanding of how the different polymorphic forms are generated by differential splicing and/or exon usage. By adopt- WHO Bulletin OMS. Vol 72 1994 801 IUIS/WHO Allergen Nomenclature Subcommittee ing the revised nomenclature for allergens, we can reserve the italicized characters to designate an aller- gen gene. Normal characters are used for designation of mRNAs and cDNAs. For example, Fel d 1 is a protein consisting of two polypeptide chains (15) which are encoded by two separate genes (16). The two allergen genes for chains 1 and 2 of Fel d 1 will be represented by Fel d JA and Fel d IB respectively. Allelic forms of mRNAs and cDNAs of the Fel d JA gene are des- ignated as mRNA or cDNA Fel d 1A.0101 where the numerals are to correspond to those of the polymor- phic allergens. Nomenclature for recombinant and synthetic peptides of allergenic interest There is interest in the possible use of fragments of allergens as reagents to modulate allergen-specific immune responses. Such fragments may be prepared by recombinant technology or by chemical synthesis. Therefore it is useful to establish a generally accept- ed nomenclature for such peptides of allergenic interest. The nomenclature for recombinant and synthetic peptides of allergenic interest is to be based on the nomenclature for naturally occurring allergens since it is well accepted by the scientific and the clinical communities. An allergen which is prepared by recombinant (r) or chemical synthetic (s) means is to be differentiated from a natural (n) allergen by the addition of the prefix of r or s followed by a suffix of the amino acid residue positions which are given in parenthesis. For examples, a recombinant hornet venom allergen Dol m 5.0201 which contains the entire sequence of 204 residues will be designated as rDol m 5.0201, and a recombinant or synthetic pep- tide of residue 151-165 of Dol m 5.0201 will be des- ignated as r or sDol m 5.0201 (151-165) respectively. Natural allergens may contain post-translational modifications as many proteins do. These modifica- tions include glycosylation, acylation, methylation, etc. Recombinant or synthetic allergen, designated by the prefix r or s, is taken to indicate that it does not contain the post-translational modification of the natural allergen. If the recombinant or synthetic allergen does contain the exact same modification as that of the natural allergen, it will be designated with a prefix of m or sn. For example, the honey bee venom allergen phospholipase A2, Api m 1, is a glycoprotein with an oligosaccharide attached at the asparagine residue number 13 (17, 18). A synthe- tic peptide of residues 1-20 of Api m 1 without the oligosaccharide at residue 13 will be designated as sApi m 1 (1-20), and a synthetic peptide of residue 1-20 with the exact same oligosaccharide of the natu- ral allergen will be designated as snApi m 1 (1-20). For recombinant or synthetic fragments which are derivatives of sequences contained within the native allergen structure, an additional suffix enclosed in square brackets will be used to indicate that the peptide referred to is an analogue. Substitu- tions or modifications of amino acid residues are given with the standard one-letter code and super- script numbers indicate the residue positions at which modifications occur. The one-letter codes for L-amino acids are given in upper case letters and those for D-amino acids are in lower case letters. The modifications which can be substitution, insertion or deletion are specified in parenthesis within the brackets. Obviously when there are many changes, it will not be practical to follow this nomenclature but to give the fully modified sequences. Examples of these analogues of sDol m 5.0201 (151-165) are given below: Unmodified: sDol m 5.0201 (151-165) Substitution: sDol m 5.0201 (151-165) [K 153] - L-lysine residue at position 153 of sDol m 5.0201 (151-165) is substituted with D-lysine Insertion: sDol m 5.0201 (151-165) [+K 153] - one residue of L-lysine is inserted between posi- tions 153-154 Deletion: sDol m 5.0201 (151-165) [-K 153] - L-lysine residue at position 153 is deleted N-terminal modification: sDol m 5.0201 (151- 165) [N-Ac] - N-terminal amino group is acetylated C-terminal modification: sDol m 5.0201 (151- 165) [C-NH2] - C-terminal carboxyl group is in the form of car- boxamide The nomenclature proposed above is very simi- lar to that used for synthetic peptides representative of immunoglobulin sequences (19). Acknowledgement We thank Drs Martin Chapman, Irwin Griffith, Shayam Mohaptra, Rosalia Rodriguez and Alec Sehon for review- ing this article. Resume Nomenclature des allergbnes La nomenclature des allergenes a e mise a jour en tenant compte des progres rapides realises ces dernieres annees dans la caract6risation des allergenes et la determination de leur sequence WHO Bulletin OMS. Vol 72 1994802 Allergen nomenclature en acides amines par des techniques biochimiques et de biologie moleculaire. La nouvelle nomenclature est presentee dans un tableau concernant les allerg6nes, les isoaller- genes et leurs variants (pollens, acariens, autres allergenes, animaux, mycophytes, insectes, ali- ments, divers). La nomenclature concerne egale- ment a) les genes, les ARNm et les ADNc des allerg6nes et b) les peptides synthetiques et recombinants importants en allergologie. References 1. Marsh DG, Freidhoff LR. ALBE, An allergen data- base. IUIS, Baltimore, MD, Edition 1.0. 2. Marsh DG et al. Allergen nomenclature. Bulletin of the World Health Organization, 1986, 64: 767-770. 3. King TP, PS Norman, Cornell JT. 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