Exploring the MHC-peptide matrix of central tolerance in the human thymus

Abstract

Ever since it was discovered that central tolerance to self is imposed on developing T cells in the thymus through their interaction with self-peptide major histocompatibility complexes on thymic antigen-presenting cells, immunologists have speculated about the nature of these peptides, particularly in humans. Here, to shed light on the so-far unknown human thymic peptide repertoire, we analyse peptides eluted from isolated thymic dendritic cells, dendritic cell-depleted antigen-presenting cells and whole thymus. Bioinformatic analysis of the 842 identified natural major histocompatibility complex I and II ligands reveals significant crosstalk between major histocompatibility complex-class I and II pathways and differences in source protein representation between individuals as well as different antigen-presenting cells. Furthermore, several autoimmune-and tumour-related peptides, from enolase and vimentin for example, are presented in the healthy thymus. 302 peptides are directly derived from negatively selecting dendritic cells, thus providing the first global view of the peptide matrix in the human thymus that imposes self-tolerance in vivo.

T cell epitope redundancy: cross-conservation of the TCR face between pathogens and self and its implications for vaccines and autoimmunity

“…It is not clear whether these HSP-specific T cells are iTreg or nTreg, or even T eff, and how they evolve to adapt a particular phenotype. We have examined these epitopes for epitope redundancy, and did find that the epitopes are not only promiscuous, but they are also highly conserved (across HSP proteins) and that many HSP peptides are found in the thymic and lymph 'peptidomes' [49,50,51].…”

Crossreactivity to vinculin and microbes provides a molecular basis for HLA-based protection against rheumatoid arthritis

“…We therefore proposed that the protective effect of HLA-DRB1*13 is explained by presentation of an HLA-DRB1*13-derived peptide in the context of other (predisposing) HLA class II molecules [19][20][21] .…”

Approach for Identifying Human Leukocyte Antigen (HLA)-DR Bound Peptides from Scarce Clinical Samples

“…Our achieved yields represent a great improvement when compared with two previous studies on BAL cells (23) and dendritic cells from the thymus (17), that offered a yield of 100-and 13-fold lower, respectively. Though, it should be acknowledged that some of the increase is likely because of the improvement in the sensitivity of the instrumentation and using a database searching strategy instead of de novo sequencing.…”

“…Initial problems during the optimization of the procedure described by Wahlströ m et al (23) to the current instrumental set up, where the peptides were separated on columns packed in the emitters and without pre-columns, were associated with frequent loss of spray, most likely due to detergents and polymers. Changing the detergent from the commonly used CHAPS (15)(16)(17)(18)23), to the MS-compatible n-Dodecyl ␤-D-maltoside (DM) (24) increased the spray stability. Moreover, improved washing of protein-G beads prior to elution (e.g.…”

“…Historically, methods for the identification of HLA associated peptide repertoires have been limited because of the complexity and variable nature of endogenous peptides, as well as the limitations in conventional technologies (11)(12)(13)(14)(15)(16)(17)(18). That is, technologies used to analyze peptides associated to HLA class I complexes based on Edman degradation (11) have been subsequently improved to isolate and identify HLA-I peptides with high sensitivity using mass spectrometry (MS) (12), followed by isolation of HLA-II peptides (13).…”