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Cancer Immunol Immunother. 2019 Jun 20. doi: 10.1007/s00262-019-02358-0. [Epub ahead of print]

Editing the immunopeptidome of melanoma cells using a potent inhibitor of endoplasmic reticulum aminopeptidase 1 (ERAP1).

Author information

1
National Centre for Scientific Research Demokritos, Patriarchou Gregoriou and Neapoleos 27, Agia Paraskevi, 15341, Athens, Greece.
2
Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
3
Centro de Biologia Molecular Severo Ochoa (Consejo Superior de Investigaciones Cientificas, Universidad Autonoma), Madrid, Spain.
4
Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
5
Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece.
6
National Centre for Scientific Research Demokritos, Patriarchou Gregoriou and Neapoleos 27, Agia Paraskevi, 15341, Athens, Greece. stratos@rrp.demokritos.gr.

Abstract

The efficacy of cancer immunotherapy, including treatment with immune-checkpoint inhibitors, often is limited by ineffective presentation of antigenic peptides that elicit T-cell-mediated anti-tumor cytotoxic responses. Manipulation of antigen presentation pathways is an emerging approach for enhancing the immunogenicity of tumors in immunotherapy settings. ER aminopeptidase 1 (ERAP1) is an intracellular enzyme that trims peptides as part of the system that generates peptides for binding to MHC class I molecules (MHC-I). We hypothesized that pharmacological inhibition of ERAP1 in cells could regulate the cellular immunopeptidome. To test this hypothesis, we treated A375 melanoma cells with a recently developed potent ERAP1 inhibitor and analyzed the presented MHC-I peptide repertoire by isolating MHC-I, eluting bound peptides, and identifying them using capillary chromatography and tandem mass spectrometry (LC-MS/MS). Although the inhibitor did not reduce cell-surface MHC-I expression, it induced qualitative and quantitative changes in the presented peptidomes. Specifically, inhibitor treatment altered presentation of about half of the total 3204 identified peptides, including about one third of the peptides predicted to bind tightly to MHC-I. Inhibitor treatment altered the length distribution of eluted peptides without change in the basic binding motifs. Surprisingly, inhibitor treatment enhanced the average predicted MHC-I binding affinity, by reducing presentation of sub-optimal long peptides and increasing presentation of many high-affinity 9-12mers, suggesting that baseline ERAP1 activity in this cell line is destructive for many potential epitopes. Our results suggest that chemical inhibition of ERAP1 may be a viable approach for manipulating the immunopeptidome of cancer.

KEYWORDS:

Aminopeptidase; Enzyme; Inhibitor; MHC; Melanoma; Proteomics

PMID:
31222486
DOI:
10.1007/s00262-019-02358-0

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