Faridi, Pouya

Woods, Katherine

Ostrouska, Simone

Deceneux, Cyril

Aranha, Ritchlynn

Duscharla, Divya

Wong, Stephen Q

Chen, Weisan

Ramarathinam, Sri H

Lim Kam Sian, Terry C C

Croft, Nathan P

Li, Chen

Ayala, Rochelle

Cebon, Jonathan S

Purcell, Anthony W

Schittenhelm, Ralf B

Behren, Andreas

2020-09-16

Antigen recognition by CD8+ T cells is governed by the pool of peptide antigens presented on the cell surface in the context of HLA class I complexes. Studies have shown not only a high degree of plasticity in the immunopeptidome, but also that a considerable fraction of all presented peptides is generated through proteasome-mediated splicing of noncontiguous regions of proteins to form novel peptide antigens. Here, we used high-resolution mass spectrometry combined with new bioinformatic approaches to characterize the immunopeptidome of melanoma cells in the presence or absence of IFNγ. In total, we identified more than 60,000 peptides from a single patient-derived cell line (LM-MEL-44) and demonstrated that IFNγ induced changes in the peptidome, with an overlap of only approximately 50% between basal and treated cells. Around 6% to 8% of the peptides were identified as cis-spliced peptides, and 2,213 peptides (1,827 linear and 386 cis-spliced peptides) were derived from known melanoma-associated antigens. These peptide antigens were equally distributed between the constitutive- and IFNγ-induced peptidome. We next examined additional HLA-matched patient-derived cell lines to investigate how frequently these peptides were identified and found that a high proportion of both linear and spliced peptides was conserved between individual patient tumors, drawing on data amassing to more than 100,000 peptide sequences. Several of these peptides showed in vitro immunogenicity across multiple patients with melanoma. These observations highlight the breadth and complexity of the repertoire of immunogenic peptides that can be exploited therapeutically and suggest that spliced peptides are a major class of tumor antigens.

Cancer Immunology Research 2020; 8(10): 1322-1334

Cancer Immunology Research

0000-0003-3474-3104

0000-0001-7582-3990

0000-0002-5221-9771

0000-0002-2787-1282

0000-0002-2128-5127

0000-0001-8538-8857

0000-0002-3898-950X

0000-0003-0532-8331

0000-0001-8738-1878

0000-0001-5329-280X

https://ahro.austin.org.au/austinjspui/handle/1/24971

Spliced Peptides and Cytokine-Driven Changes in the Immunopeptidome of Melanoma.

Journal Article