Journal article

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

Pouya Faridi, Katherine Woods, Simone Ostrouska, Cyril Deceneux, Ritchlynn Aranha, Divya Duscharla, Stephen Q Wong, Weisan Chen, Sri H Ramarathinam, Terry CC Lim Kam Sian, Nathan P Croft, Chen Li, Rochelle Ayala, Jonathan S Cebon, Anthony W Purcell, Ralf B Schittenhelm, Andreas Behren

Cancer Immunology Research | AMER ASSOC CANCER RESEARCH | Published : 2020

Abstract

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..

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Grants

Awarded by Australian National Health and Medical Research Council (NHMRC)


Awarded by Australian NHMRC CJ Martin Early Career Fellowship


Awarded by AustralianNHMRCPractitioner Fellowship


Awarded by NHMRC Principal Research Fellowship


Funding Acknowledgements

The authors acknowledge the Monash Proteomics & Metabolomics Facility for the provision of mass spectrometry instrumentation, training, and technical support, as well as the Monash University Flowcore for flow cytometry instrumentation and assistance. This project was funded, in part, by Ludwig Cancer Research, Melanoma Research Alliance, the Victorian Cancer Agency-supported Melbourne Melanoma Project, Australian National Health and Medical Research Council (NHMRC) project grants 1007381 and 1165490 (to A.W. Purcell), and the Victorian State Government Operational Infrastructure Support Program. A. Behren, P. Faridi, and A.W. Purcell were supported by a grant from La Trobe University (RFA Understanding Disease). C. Li was supported by an Australian NHMRC CJ Martin Early Career Fellowship 1143366. J.S. Cebon was supported by an AustralianNHMRCPractitioner Fellowship 487905. A.W. Purcell was supported by an NHMRC Principal Research Fellowship 1137739. A. Behren is the recipient of a Fellowship from the Victorian Government Department of Health and Human Services acting through the Victorian Cancer Agency. Computational resources were supported by the R@CMon/Monash Node of the NeCTAR Research Cloud, an initiative of the Australian Government's Super Science Scheme and the Education Investment Fund.