Linear Epitope Binding Patterns of Grass Pollen-Specific Antibodies in Allergy and in Response to Allergen-Specific Immunotherapy

Abstract

Allergic diseases affect many individuals world-wide and are dependent on the interaction between allergens and antibodies of the IgE isotype. Allergen-specific immunotherapy (AIT) can alter the development of the disease, e.g., through induction of allergen-specific IgG that block allergen-IgE interactions. The knowledge of epitopes recognized by allergy-causing and protective antibodies are limited. Therefore, we developed an allergome-wide peptide microarray, aiming to track linear epitope binding patterns in allergic diseases and during AIT. Here, we focused on immune responses to grass pollen allergens and found that such epitopes were commonly recognized before initiation of AIT and that AIT commonly resulted in increased antibody production against additional epitopes already after 1 year of treatment. The linear epitope binding patterns were highly individual, both for subjects subjected to and for individuals not subjected to AIT. Still, antibodies against some linear epitopes were commonly developed during AIT. For example, the two rigid domains found in grass pollen group 5 allergens have previously been associated to a diversity of discontinuous epitopes. Here, we present evidence that also the flexible linker, connecting these domains, contains regions of linear epitopes against which antibodies are developed during AIT. We also describe some commonly recognized linear epitopes on Phl p 2 and suggest how antibodies against these epitopes may contribute to or prevent allergy in relation to a well-defined stereotyped/public IgE response against the same allergen. Finally, we identify epitopes that induce cross-reactive antibodies, but also antibodies that exclusively bind one of two highly similar variants of a linear epitope. Our findings highlight the complexity of antibody recognition of linear epitopes, with respect to both the studied individuals and the examined allergens. We expect that many of the findings in this study can be generalized also to discontinuous epitopes and that allergen peptide microarrays provide an important tool for enhancing the understanding of allergen-specific antibodies in allergic disease and during AIT.

Linear epitopes of bony fish β-parvalbumins

“…Their anti-β-parvalbumin antibody repertoires were largely established at the time of sampling and little evolution was observed over time, although with some fluctuations. Past studies of immune responses to peptide-defined epitopes of aeroallergens (grass allergens and PR-10-type allergens like Bet v 1) in the same cohort in response to vaccination identified an early establishment of a dominant, individualized epitope reactivity profile that remained relatively stable throughout the final years of the study ( 20 , 21 ). The epitope recognition of pre-existing aeroallergen-specific humoral immunity similarly remained stable over time.…”

“…We proposed that allergen-specific B cell clones expanded early during a response and remained dominant over time. Epitopes recognized by aeroallergen-specific IgE were commonly also recognised by the IgG population of the same subject ( 20 , 21 ), suggesting that there might be a clonal relationship between dominant antibodies over time. Sequencing of antibody-encoding genes, several of which encoded antibodies with defined aeroallergen specificity of these allergic subjects, demonstrated that IgE-encoding allergen-specific clones not uncommonly were maintained during an extended period of time, even throughout the entire 3-year study period ( 23 , 24 ).…”

“…The study was performed according to the Declaration of Helsinki, approved by the regional ethical board at Lund University, and written informed consent was obtained from study participants. These samples were analysed for their ability to recognise linear allergen epitopes ( 20 , 21 ). Eight of these subjects (Donors 1-8) had, in a study unrelated to the present research question, undergone specific immunotherapy to treat aeroallergen allergy.…”

“…Importantly, peptide arrays can be scaled to cover a large diversity of allergens in a high-throughput format. Such technology is used by us in efforts to identify epitopes of several other allergens ( 20 , 21 ). As an alternative high-throughput technology, a recent study employed immunoprecipitation of allergen peptides displayed on T7 phage and subsequent sequencing-based deconvolution of genes encoding peptides bound by human antibodies, to enable identification of epitopes recognized by human antibodies ( 22 ).…”

Statistical Analysis and Tokenization of Epitopes to Construct Artificial Neoepitope Libraries

“…Furthermore, the identification of patterns in epitopes provides valuable insights for designing therapies and vaccines based on the antibody–antigen interaction, for example, using high-throughput data from epitope libraries to train ML algorithms to better predict epitopes involved in specific antibody–antigen interactions. Consequently, better strategies can be employed to neutralize pathogens and boost the humoral and immune response. , In the diagnostics field, the COVID-19 pandemic has shown that the rapid development of reliable antibody/antigen detecting devices is paramount for the early detection and control of new infectious pathogens. The fast production of such devices can help in evaluating the exposure to pathogens and levels of immunization after treatments or vaccination.…”