The role of proteasome generated spliced peptides in the adaptive immune response

The role of proteasome generated spliced peptides in the adaptive immune response

by Artem Mansurkhodzhaev
Doctoral thesis
Date of Examination:2022-04-20
Date of issue:2022-05-20
Advisor:Dr. Juliane Liepe
Referee:Dr. Juliane Liepe
Referee:Prof. Dr. Henning Urlaub
Referee:Prof. Dr. Patrick Cramer
Referee:Dr. Johannes Soeding
Referee:Dr. Sonja Lorenz
Referee:Dr. Alexander Stein
Persistent Address: http://dx.doi.org/10.53846/goediss-9252

 

 

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Abstract

English

CD8+ T-cells are the crucial component of the adaptive immune system as they survey the cells of the body for the signs of pathogens or tumours and eliminate them when necessary. To do this, T-cells recognise short antigenic peptides pre- sented on the cell surface by Major Histocompatibility Complex class I (MHCI) molecules. The majority of MHCI bound peptides are generated by proteasome through peptide bond hydrolysis. Moreover, proteasome also generates hybrid peptides via proteasome catalysed peptide splicing (PCPS). In the recent years these peptides have been shown to be frequently produced by the proteasome, presented by MHCI molecules and elicit CD8+ T-cell responses, suggesting the importance of spliced peptides for adaptive immune response. However, the mechanisms of spliced peptides generation as well their contribution into adap- tive immunity remain elusive. A particular area of concern is the effect of spliced peptides on the ability of the immune system to distinguish self and non-self and hence the repertoire of circulating CD8+ T-cells. Large sequence variability of spliced peptides could lead to the emergence of a large number of pathogenic peptides that are identical or highly similar to human antigenic peptides. In such cases, such matching pathogenic-human peptides may not be recognised by the T-cells as non-self which enables the immune evasion of pathogens. The mater of molecular mimicry is further complicated by the existence of T-cell receptor cross-reactivity. We showed that proteasome generated spliced peptides sub- stantially enlarge the number of matching viral-human peptides on the theoreti- cal level but owing to the expected frequencies of spliced peptides presented on the cell surface, the practical impact of the spliced peptides on the viral immune evasion is modest, even when considering T-cell cross-reactivity. An alternative scenario would be the failure to eliminate potentially auto-reactive CD8+ T-cells cells and the activation of such cells upon viral or bacterial infection leading to an autoimmune disease such as Type 1 Diabetes (T1D). Accordingly, we explored a potential role of such matching viral-human peptides in T1D and identified pu- tative spliced peptides that could be presented in the pancreas and trigger its autoimmune destruction by self reactive CD8+ T-cells. A special type of MHCI presented peptides that could be viewed in the intersection of self and non-self peptides are the peptides that are derived from the tumor associated antigens. These peptides carry tumor specific mutations which simultaneously make them self and non-self. The knowledge of the impact of such mutations on the pro- cessing of antigens by the proteasome is not only important for a better under- standing of the mechanisms of PCPS but also has implications for discovery of MHCI presented peptides for anti-cancer immunotherapies. We performed a comprehensive comparison of peptide products generation dynamics between the proteasomal digestions of a variety of wild type and mutated polypeptides and discovered that the impacts of the single amino acid exchanges were highly variable and dependent on the physical and chemical properties of amino acid that was replaced. In addition, we identified and quantified a number of potential MHCI binders that were derived from the digestions of the mutated polypeptides, a large fraction of which were spliced peptides.
Keywords: Adaptive immunity; MHC-I; Antigen Presentation Pathway; Proteasome; Epitope; proteasome-catalyzed peptide splicing