Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes

Abstract

The microbiome influences adaptive immunity and molecular mimicry influences T cell reactivity. Here, we evaluated whether the sequence similarity of various antigens to the microbiota dampens or increases immunogenicity of T cell epitopes. Sets of epitopes and control sequences derived from 38 antigenic categories (infectious pathogens, allergens, autoantigens) were retrieved from the Immune Epitope Database (IEDB). Their similarity to microbiome sequences was calculated using the BLOSUM62 matrix. We found that sequence similarity was associated with either dampened (tolerogenic; e.g. most allergens) or increased (inflammatory; e.g. Dengue and West Nile viruses) likelihood of a peptide being immunogenic as a function of epitope source category. Ten-fold cross-validation and validation using sets of manually curated epitopes and non-epitopes derived from allergens were used to confirm these initial observations. Furthermore, the genus from which the microbiome homologous sequences were derived influenced whether a tolerogenic versus inflammatory modulatory effect was observed, with Fusobacterium most associated with inflammatory influences and Bacteroides most associated with tolerogenic influences. We validated these effects using PBMCs stimulated with various sets of microbiome peptides. "Tolerogenic" microbiome peptides elicited IL-10 production, "inflammatory" peptides elicited mixed IL-10/IFNγ production, while microbiome epitopes homologous to self were completely unreactive for both cytokines. We also tested the sequence similarity of cockroach epitopes to specific microbiome sequences derived from households of cockroach allergic individuals and non-allergic controls. Microbiomes from cockroach allergic households were less likely to contain sequences homologous to previously defined cockroach allergens. These results are compatible with the hypothesis that microbiome sequences may contribute to the tolerization of T cells for allergen epitopes, and lack of these sequences might conversely be associated with increased likelihood of T cell reactivity against the cockroach epitopes. Taken together this study suggests that microbiome sequence similarity influences immune reactivity to homologous epitopes encoded by pathogens, allergens and auto-antigens.

Fig 1. HLA class II restricted T cell epitopes vary in similarity to human microbiome sequences.

Epitope (black) and non-epitope (red) maximum BLOSUM score per individual peptide are shown for the Aspergillus (A) and Gluten (B) epitope categories. Median ± interquartile range are shown for each distribution.

Fig 2. Epitopes vary in similarity to microbiome sequences.

Epitope and non-epitope median BLOSUM scores for (A) Allergy, (B) Autoimmunity, (C) Virus, and (D) Bacteria categories. Blue dots indicate non-epitopes being less conserved in the human microbiome, red dots when epitopes are less conserved and black dots indicate categories with no change in conservation when comparing non-epitopes to epitopes. Diagonal line (black) indicate no change in conservation when comparing non-epitopes to epitopes.

Fig 3. Microbiome peptides homologous to dominant epitopes are associated with constitutive IL-10 production.

(A) Combined responses to microbiome derived epitopes for the inflammatory (blue) and tolerogenic (red). (B, C) Combined response to self, pathogen and microbiome derived epitopes for (B) IL-10 and (C) IFNγ. Response is expressed as fold above background. Each dot represents one donor/category combination. IFNγ (dots) and IL-10 (squares). Median ± interquartile range is shown. Two-tailed Mann-Whitney, *, p≤0.05, **, p≤0.01.

Fig 4. Dust allergen epitopes are less conserved in microbiome derived from allergic and non-allergic households.

Maximum BLOSUM score for each epitope/non-epitope per (A) KEGG ontology and (B) proteome in each group. Epitopes (black) and non-epitopes (red) for allergic (left in both graphs) and non-allergic (right in both graphs) households. Two-tailed Mann-Whitney, *, p≤0.05, **, p≤0.01, ****, p≤0.0001.