How the Proteasome Modulates the Immunopeptidome

The immunopeptidome is the repertoire of short peptides presented by the Major Histocompatibility Complex class I and class II (MHC I and MHC II) transmembrane proteins. Several key features distinguish these two antigen presentation pathways. For example, MHC class I proteins are ubiquitously expressed by all nucleated cell types, while MHC class II proteins are only expressed by immune antigen-presenting cells (APCs). Peptides loaded onto MHC I proteins (8-10 amino acids) are processed by the proteasome; in contrast, peptides loaded onto MHC II proteins (10-25 amino acids) undergo proteolysis within lysosomes or phagosomes. Finally, MHC I and MHC II bound peptides are specifically recognized by CD8 and CD4 T cells, respectively.

Reprinted from “MHC Class I and II Pathways”, by (2020). Retrieved from

Both MHC I and MHC II class peptides may be leveraged for cancer immunotherapy strategies (Janeway et al. 2001). These strategies are based on identifying novel antigens or “neoantigens,” which arise in cancer cells in association with somatic mutations. For example, identified MHC I neoantigen peptides may support the development of personalized vaccines to promote CD8 T cell-mediated tumor cell killing (Bianchi et al. 2020).

Multiple Proteasomes Shape the MHC I Immunopeptidome

The proteasome is a multi-protein complex, consisting of a 20S core catalytic unit and associated regulatory subunits, such as 19S, PA28, and PA200. Together, this complex mediates ubiquitinated-protein degradation. The proteasome’s activity is not only determined by associated regulatory subunits but is also influenced by its 20S core components. Several 20S core subsets, which differ in β subunit composition, give rise to constitutive, immune, and intermediate proteasomes. Among these, the immunoproteasome predominates in lymphoid tissues. However, in non-immune cells, proinflammatory cytokines such as IFN (α, β and γ) and TNF induce the immunoproteasome (Murata et al. 2018, Kors et al. 2020). Because tumors possess an inflammatory microenvironment, a standing question in the field pertains to the role of inflammation in modulating the proteasome’s composition and activity, and consequently, how it shapes peptide presentation and the immunopeptidome.

Lessons from the Melanoma Immunopeptidome

The influence of proinflammatory cytokines in modulating the melanoma immunopeptidome has been more recently highlighted by Faridi et al. 2020. In this study, investigators isolated HLA class I bound peptides from a melanoma cell line untreated or treated with IFNγ. Investigators identified two main groups of HLA class I bound peptides, linear (>90%) and cis-spliced peptides (~7%), irrespective of INFγ treatment conditions. Consistent with previous work, treatment with INFγ induced the immunoproteasome and led to an expanded immunopeptidome, providing the opportunity to identify new epitopes with therapeutic potential.

Significantly, investigators identified changes in the composition of the immunopeptidome, indicated by changes in the proportion of specific melanoma-associated peptides in the presence of INFγ. Additionally, the study was successful in identifying new cis-spliced immunogenic melanoma epitopes. Because some of these newly identified cis-spliced peptides were recognized in vitro by T cells derived from different melanoma patients, investigators are hopeful for their potential as targets for immunotherapy.


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