Automatic Generation of Validated Specific Epitope Sets

Abstract

Accurate measurement of B and T cell responses is a valuable tool to study autoimmunity, allergies, immunity to pathogens, and host-pathogen interactions and assist in the design and evaluation of T cell vaccines and immunotherapies. In this context, it is desirable to elucidate a method to select validated reference sets of epitopes to allow detection of T and B cells. However, the ever-growing information contained in the Immune Epitope Database (IEDB) and the differences in quality and subjects studied between epitope assays make this task complicated. In this study, we develop a novel method to automatically select reference epitope sets according to a categorization system employed by the IEDB. From the sets generated, three epitope sets (EBV, mycobacteria and dengue) were experimentally validated by detection of T cell reactivity ex vivo from human donors. Furthermore, a web application that will potentially be implemented in the IEDB was created to allow users the capacity to generate customized epitope sets.

Figure 1

Diagram of the filtering steps towards the generation of the validated sets of epitopes, including the number of epitopes found in each step.

Figure 2

(a) Web application main page interface. (b) Web application “advanced options” page interface.

Figure 3

Predicted epitope pools induce a detectable ex vivo cytokine response. PBMC from donors with LTBI (MTB donor) or previously exposed to DENV were stimulated with their respective epitope pools and an EBV epitope pool. After ex vivo stimulation, the IFNγ response was measured by ICS using flow cytometry. Gating strategy (a) and representative plots of the responses for both CD4⁺ and CD8⁺ T cells are shown for a MTB donor (b) and DENV donor (c). (d) The ICS IFNγ responses induced by each epitope pool for all donors tested are summarized (n = 10). Statistical difference was determined using a one-tailed Mann-Whitney test. (^∗ P ≤ 0.05; ^∗∗ P ≤ 0.01).