The influence of T cell development on pathogen specificity and autoreactivity

T cells orchestrate adaptive immune responses upon activation. T cell activation requires sufficiently strong binding of T cell receptors on their surface to short peptides derived from foreign proteins bound to protein products of the major histocompatibility (MHC) gene products, which are displayed on the surface of antigen presenting cells. T cells can also interact with peptide-MHC complexes, where the peptide is derived from host (self) proteins. A diverse repertoire of relatively self-tolerant T cell receptors is selected in the thymus. We study a model, computationally and analytically, to describe how thymic selection shapes the repertoire of T cell receptors, such that T cell receptor recognition of pathogenic peptides is both specific and degenerate. We also discuss the escape probability of autoimmune T cells from the thymus.Comment: 12 pages, 7 figure

A single-amino-acid variant of the H60 CD8 epitope generates specific immunity with diverse TCR recruitment

TCR of CD8 T cells recognizes peptides of 8–9 amino acids in length (epitope) complexed with MHC class I. Peptide ligands differing from an epitope by one or two amino acids are thought to modulate the immune response specific to that epitope. H60 is a minor histocompatibility antigen for which the specific CD8 T-cell response dominates during alloresponse after MHC-matched allogeneic transplantation. In the present study, we developed a transgenic mouse (designated H60H Tg) expressing a variant of H60, designated H60H, in which the arginine residue at position 4 of the H60 epitope sequence (LTFNYRNL) is replaced by a histidine residue (LTFHYRNL). Immunization of female C57BL/6 mice with splenocytes from male H60H Tg induced a CD8 T cell primary response and memory response after re-challenge. The response was CD4 help-dependent, demonstrating the potency of H60H as a cellular antigen. The response induced by the H60H cellular antigen was comparable to that induced by H60 in its peak magnitude and overall immune kinetics. H60H challenge recruited broadly diverse TCRs to the specific response, shaping a TCR repertoire different from that of the natural H60 epitope. However, some of the TCRs did overlap between the H60H- and H60-specific CD8 T cells, suggesting that H60H might modulate the H60-specific response. These results may provide a basis for the modulation of the H60-specific CD8 T-cell response

Modelling the Human Immune System by Combining Bioinformatics and Systems Biology Approaches

Over the past decade a number of bioinformatics tools have been developed that use genomic sequences as input to predict to which parts of a microbe the immune system will react, the so-called epitopes. Many predicted epitopes have later been verified experimentally, demonstrating the usefulness of such predictions. At the same time, simulation models have been developed that describe the dynamics of different immune cell populations and their interactions with microbes. These models have been used to explain experimental findings where timing is of importance, such as the time between administration of a vaccine and infection with the microbe that the vaccine is intended to protect against. In this paper, we outline a framework for integration of these two approaches. As an example, we develop a model in which HIV dynamics are correlated with genomics data. For the first time, the fitness of wild type and mutated virus are assessed by means of a sequence-dependent scoring matrix, derived from a BLOSUM matrix, that links protein sequences to growth rates of the virus in the mathematical model. A combined bioinformatics and systems biology approach can lead to a better understanding of immune system-related diseases where both timing and genomic information are of importance