From in silico to the clinic: methods to study proteasome catalysed peptide splicing - AND - Proteasome-Catalyzed peptide splicing and its immunological relevance

Proteasome-Catalyzed peptide splicing and its biological implications – Michele Mishto, PhD

Proteasome generates the epitopes presented on MHC class I molecules that elicit the CD8+ T cell response. Such a response could be used as sword to cut the head of tumours by immunotherapies or to develop vaccines against specific pathogens. In addition to canonical epitopes there have also been a few reported instances of proteasome-generated spliced epitopes. Despite their efficacy in attacking cancer in patients and animal models, these spliced epitopes have been regarded as rare events and substantially neglected. Are we neglecting a relevant portion of the MHC-I immunopeptidome and thus limiting the efficacy of immunotherapies against tumour?
To answer to this question we have performed in silico, in vitro and in vivo experiments aimed to identify and characterize MHC-I-presented spliced epitopes and how they are produced.
The outcome is astonishing. We have found that, indeed, one third of the MHC-I immunopeptidome variety are proteasome-generated spliced peptides and only through these peptides one third of the antigens detected at the cell surface can be represented. The amount of the spliced peptides at the cell surface is comparable to the canonical non- spliced peptides and could trigger similar CD8+ T cell response.
Furthermore, during Listeria monocytogenes infection the production of spliced epitopes by proteasome addresses the CD8+ T cell response toward antigens that would be otherwise neglected by the immune system.
Because of these promising results we can argue that by studying the proteasome-catalysed peptide splicing, its mechanisms and dynamics we could improve the efficacy of anti-cancer immunotherapies such as DNA vaccination and adoptive T cell therapy as well as the development of vaccines against pathogens.
However, we will also need to understand how proteasome-catalysed peptide splicing is impacting the central and peripheral tolerance processes, whether it plays a pivotal role in autoimmunity, and whether its role is limited to the antigen presentation or it goes beyond that.

From in silico to the clinic: methods to study proteasome-catalysed peptide splicing.

Juliane Liepe

The proteasome is a multicomplex enzyme that catalyses protein degradation. It is furthermore regulating the immune response through antigen presentation, where the proteasome produces most of the epitopes presented in the MHC-class I pathway. These epitopes can be generated by simple cut, or cut-and-paste events. Latter so-called proteasome-generated spliced peptides represent more than one third of all peptides bound to MHC-class I molecules. The role of these spliced peptides during an immune response and their potential to represent novel targets for immunotherapy against cancer and viral infection still needs to be explored.
In order to explore this and the complexity of the involved processes an advanced systems biology pipeline is necessary. We here develop and exploit a set of in silico tools to study the details of proteasome-catalysed peptide splicing and its importance in the MHC-class I pathway. This includes algorithms to identify spliced peptides from ex cellulo mass spectrometry data and methods to classify and characterise spliced peptides. Furthermore, we present in silico tools to facilitate a systematic approach to discover novel spliced peptide targets for immunotherapy either against cancer or through vaccine against pathogens.
The proteasome already is a target for therapeutic trails against autoimmune disorders, cancer and infectious diseases, but its full potential still needs to be explored. This research and the in silico tools developed here will aid such translational aspects and advance the ongoing research in systems immunology.