The Effect of Interferons on Presentation of Defective Ribosomal Products as HLA Peptides

Dganit Melamed Kadosh,Eilon Barnea,Liran Komov,Arie Admon

doi:10.1016/j.mcpro.2021.100105

Abstract

A subset of class I major histocompatibility complex (MHC)-bound peptides is produced from immature proteins that are rapidly degraded after synthesis. These defective ribosomal products (DRiPs) have been implicated in early alert of the immune system about impending infections. Interferons are important cytokines, produced in response to viral infection, that modulate cellular metabolism and gene expression patterns, increase the presentation of MHC molecules, and induce rapid degradation of proteins and cell-surface presentation of their derived MHC peptides, thereby contributing to the battle against pathogen infections. This study evaluated the role of interferons in the induction of rapid degradation of DRiPs to modulate the repertoire of DRiP-derived MHC peptides. Cultured human breast cancer cells were treated with interferons, and the rates of synthesis and degradation of cellular protein and their degradation products were determined by LC-MS/MS analysis, following the rates of incorporation of heavy stable isotope–labeled amino acids (dynamic stable isotope labeling by amino acids in cell culture, dynamic SILAC) at several time points after the interferon application. Large numbers of MHC peptides that incorporated the heavy amino acids faster than their source proteins indicated that DRiP peptides were abundant in the MHC peptidome; interferon treatment increased by about twofold their relative proportions in the peptidome. Such typical DRiP-derived MHC peptides were from the surplus subunits of the proteasome and ribosome, which are degraded because of the transition to immunoproteasomes and a new composition of ribosomes incorporating protein subunits that are induced by the interferon. We conclude that degradation of surplus subunits induced by the interferon is a major source for DRiP–MHC peptides, a phenomenon relevant to coping with viral infections, where a rapid presentation of MHC peptides derived from excess viral proteins may help alert the immune system about the impending infection.

Highlights

A subset of class I major histocompatibility complex (MHC)-bound peptides is produced from immature proteins that are rapidly degraded after synthesis
The MCF-7 cells were cultured in growth media containing light amino acids for 8 h in the presence of 250 units of IFN-γ or 500 units of IFN-β, followed by shifting to growth media containing the heavy amino acids that were supplemented with the same concentrations of IFN-γ or IFN-β, to continue the exposure to the cytokines
5189 human leukocyte antigen (HLA) peptides derived from 2647 source proteins were assigned H/L ratios by MaxQuant (Fig. 1) and their defective ribosomal products (DRiPs) factor values were calculated using the relative rates of synthesis of each pair of HLA peptide and its source protein (Fig. 2 and supplemental Table S4)

Summary

Graphical Abstract

In Brief Surplus subunits of protein complexes are rapidly degraded, and some of their degradation products are shuttled for presentation by the MHC molecules at the cells’ surface. A subset of class I major histocompatibility complex (MHC)-bound peptides is produced from immature proteins that are rapidly degraded after synthesis These defective ribosomal products (DRiPs) have been implicated in early alert of the immune system about impending infections. Interferons are important cytokines, produced in response to viral infection, that modulate cellular metabolism and gene expression patterns, increase the presentation of MHC molecules, and induce rapid degradation of proteins and cell-surface presentation of their derived MHC peptides, thereby contributing to the battle against pathogen infections. We conclude that degradation of surplus subunits induced by the interferon is a major source for DRiP–MHC peptides, a phenomenon relevant to coping with viral infections, where a rapid presentation of MHC peptides derived from excess viral proteins may help alert the immune system about the impending infection. Dynamic SILAC was exploited to determine whether DRiP processing rates are hastened to alarm the immune system and the antiviral defenses, of impending viral threat, simulated here by IFN-β and IFN-γ treatment

EXPERIMENTAL PROCEDURES

RESULTS

DISCUSSION