Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides.
Details
Serval ID
serval:BIB_6C0EA9079104
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides.
Journal
Nature communications
ISSN
2041-1723 (Electronic)
ISSN-L
2041-1723
Publication state
Published
Issued date
15/03/2024
Peer-reviewed
Oui
Volume
15
Number
1
Pages
2357
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Publication Status: epublish
Abstract
Circular RNAs (circRNAs) are covalently closed non-coding RNAs lacking the 5' cap and the poly-A tail. Nevertheless, it has been demonstrated that certain circRNAs can undergo active translation. Therefore, aberrantly expressed circRNAs in human cancers could be an unexplored source of tumor-specific antigens, potentially mediating anti-tumor T cell responses. This study presents an immunopeptidomics workflow with a specific focus on generating a circRNA-specific protein fasta reference. The main goal of this workflow is to streamline the process of identifying and validating human leukocyte antigen (HLA) bound peptides potentially originating from circRNAs. We increase the analytical stringency of our workflow by retaining peptides identified independently by two mass spectrometry search engines and/or by applying a group-specific FDR for canonical-derived and circRNA-derived peptides. A subset of circRNA-derived peptides specifically encoded by the region spanning the back-splice junction (BSJ) are validated with targeted MS, and with direct Sanger sequencing of the respective source transcripts. Our workflow identifies 54 unique BSJ-spanning circRNA-derived peptides in the immunopeptidome of melanoma and lung cancer samples. Our approach enlarges the catalog of source proteins that can be explored for immunotherapy.
Keywords
Humans, RNA, Circular/metabolism, RNA, Messenger, Peptides, Histocompatibility Antigens Class I
Pubmed
Web of science
Open Access
Yes
Create date
22/03/2024 13:20
Last modification date
09/08/2024 15:00