T cell epitope: friend or foe? Immunogenicity of biologics in context

Abstract

Like vaccines, biologic proteins can be very immunogenic for reasons including route of administration, dose frequency and the underlying antigenicity of the therapeutic protein. Because the impact of immunogenicity can be quite severe, regulatory agencies are developing risk-based guidelines for immunogenicity screening. T cell epitopes are at the root of the immunogenicity issue. Through their presentation to T cells, they activate the process of anti-drug antibody development. Preclinical screening for T cell epitopes can be performed in silico, followed by in vitro and in vivo validation. Importantly, screening for immunogenicity is complicated by the discovery of regulatory T cell epitopes, which suggests that immunogenicity testing must now take regulatory T cells into consideration. In this review, we address the application of computational tools for preclinical immunogenicity assessment, the implication of the discovery of regulatory T cell epitopes, and experimental validation of those assessments.

Fig. 1

The same T cell epitope may trigger an effector immune response, characterized by inflammatory cytokines, up regulation of B cell activity, and development of anti-drug antibodies, or a regulatory T cell response characterized by suppressor cytokines, decreased cellular proliferation, and decreased antibody secretion. The “context” of the immune response is the most important factor that determines the T cell phenotype.

Fig. 2

a and b. Stimulation of T helper (Th) cells by antigens involves first activation by interleukin 1 (IL-1) (T1) and then presentation of the antigen at the surface of antigen-presenting cells (usually macrophages, dendritic cells or B cells) (T2) in association with class II major histocompatibility complex molecules (MHC II); for extrinsic (foreign) proteins this requires initial capture of the protein, followed by denaturation and/or degradation so as to associate the molecule or fragments with MHC II. T cells stimulated in this way express receptors for interleukin 2 (IL-2), and secrete various molecules, including factors which stimulate B cells to divide and/or secrete Ig, interferon-gamma and IL-2. (B1) In turn, IL-2 causes proliferation of Th and cytotoxic/suppressor T cells. Encounter of the same antigen by a B cell results in processing and presentation of the epitope at the B cell surface in the context of MHC (B1). Co-stimulatory factors such as B7 interact with the memory B cell (B2), resulting in the secretion of cytokines by the T cell (B3). These cytokines allow the B cell to mature and become a dedicated IgG-producing (isotype switched) memory B cell (B4).

Fig. 3

The influenza HA peptide 306–318 is an epitope known to be promiscuously immunogenic. It has high Z-scores for all 8 alleles in EpiMatrix. The ranking of the EpiMatrix scores (by color) is shown in the Z-score legend. Peptides that have predicted Z-scores above 1.64 (approximately the top 5% of all 9-mers derived from any given protein) have a significant chance of binding to MHC molecules and scores above 2.32 (approximately the top 1%) are highly likely to bind to MHC molecules. A cluster score is calculated by summing the EpiMatrix scores for each of the eight class II alleles. Cluster scores higher than 10 are considered to be significant. The influenza HA peptide shown here has a cluster score of 18. The band-like pattern (EpiBar) showing “hits” for potential binding for all eight class II alleles is characteristic of promiscuous epitopes.

Fig. 4

Summary of the immunogenicity “scale” findings for selected autologous proteins shows how antibody sequences rank, compared to standard controls. EpiMatrix protein immunogenicity scores higher than 20 are considered to be potentially immunogenic. Note that the low-scoring proteins on the lower left side of the scale are known to engender little to no immunogenicity while the higher scoring proteins on the upper left side of the scale are all known immunogens. For monoclonal antibodies, we adjust the antibody scores for the presence of pre-defined regulatory T cell epitopes as we have evidence that the presence of these epitopes decreases the overall immunogenicity of antibodies in the clinic. Discovering these peptide sequences and identifying putative T cell epitopes may potentially be the most important aspect for protein therapeutic development.

Fig. 5

This figure shows the EpiMatrix immunogenicity scale to prospectively predict clinical immunogenicity. It compares novel protein sequences to proteins of known varying immunogenic potential. The new protein therapeutic GDNF was about to be used as treatment for Parkinson's disease or amyotrophic lateral sclerosis (ALS). In EpiMatrix analysis, however, it scores as high as published highly immunogenic peptides from influenza hemagglutinin and tetanus toxin. This might be the cause for the observed side effects during its clinical use as therapeutic.

Fig. 6

We have discovered conserved T cell epitopes in IgG that engage natural regulatory T cells. We hypothesize that antibody-derived Treg epitopes (dark blue epitope on the top) activate regulatory T cells, which leads to suppression of effector T cells that recognize effector epitopes (red epitope on the bottom), like those of IgG hypervariable regions to which central tolerance does not exist. Whether this suppression is mediated by regulatory cytokines alone or by contact-dependent signaling, or both, has yet to be determined . (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)