Allergome-wide peptide microarrays enable epitope deconvolution in allergen-specific immunotherapy

J Allergy Clin Immunol. 2021 Mar;147(3):1077-1086. doi: 10.1016/j.jaci.2020.08.002. Epub 2020 Aug 10.


Background: The interaction of allergens and allergen-specific IgE initiates the allergic cascade after crosslinking of receptors on effector cells. Antibodies of other isotypes may modulate such a reaction. Receptor crosslinking requires binding of antibodies to multiple epitopes on the allergen. Limited information is available on the complexity of the epitope structure of most allergens.

Objectives: We sought to allow description of the complexity of IgE, IgG4, and IgG epitope recognition at a global, allergome-wide level during allergen-specific immunotherapy (AIT).

Methods: We generated an allergome-wide microarray comprising 731 allergens in the form of more than 172,000 overlapping 16-mer peptides. Allergen recognition by IgE, IgG4, and IgG was examined in serum samples collected from subjects undergoing AIT against pollen allergy.

Results: Extensive induction of linear peptide-specific Phl p 1- and Bet v 1-specific humoral immunity was demonstrated in subjects undergoing a 3-year-long AIT against grass and birch pollen allergy, respectively. Epitope profiles differed between subjects but were largely established already after 1 year of AIT, suggesting that dominant allergen-specific antibody clones remained as important contributors to humoral immunity following their initial establishment during the early phase of AIT. Complex, subject-specific patterns of allergen isoform and group cross-reactivities in the repertoires were observed, patterns that may indicate different levels of protection against different allergen sources.

Conclusions: The study highlights the complexity and subject-specific nature of allergen epitopes recognized following AIT. We envisage that epitope deconvolution will be an important aspect of future efforts to describe and analyze the outcomes of AIT in a personalized manner.

Keywords: Allergen; IgE; IgG; IgG(4); allergen-specific immunotherapy; antibody; epitope; linear epitope; peptide microarray.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Allergens / immunology
  • Allergens / metabolism*
  • Antigens, Plant / immunology
  • Antigens, Plant / metabolism*
  • Betula
  • Desensitization, Immunologic / methods*
  • Epitope Mapping
  • Epitopes, B-Lymphocyte / immunology
  • Epitopes, B-Lymphocyte / metabolism*
  • Female
  • Humans
  • Immunoglobulin E / metabolism
  • Immunoglobulin Isotypes / metabolism
  • Male
  • Microarray Analysis
  • Middle Aged
  • Peptides / immunology
  • Peptides / metabolism*
  • Plant Proteins / immunology
  • Plant Proteins / metabolism*
  • Poaceae
  • Pollen / immunology*
  • Rhinitis, Allergic, Seasonal / immunology*
  • Rhinitis, Allergic, Seasonal / therapy


  • Allergens
  • Antigens, Plant
  • Epitopes, B-Lymphocyte
  • Immunoglobulin Isotypes
  • Peptides
  • Plant Proteins
  • Bet v 1 allergen, Betula
  • PHLPI protein, Phleum pratense
  • Immunoglobulin E