Ferreira et al. utilized circular RNA-derived open-reading frames, which harbor a canonical ATG start codon and span the back-splice junction region, to expand the repertoire of neoantigens to be explored for immunotherapy. A stringent MS-based immunopeptidomics workflow was established and used to identify and verify circRNA-derived HLA-I bound peptides in two melanoma and eight multi-region lung cancer (with paired normal) samples. Six potential lung tumor-specific peptides were observed, with one shared across 5 patients. CircRNA-derived and canonical antigens seemed to follow similar routes of antigen processing and presentation.
Contributed by Ute Burkhardt
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.
Author Info: (1) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Ag
Author Info: (1) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Agora Cancer Research Centre, Lausanne, Switzerland. (2) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Agora Cancer Research Centre, Lausanne, Switzerland. SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland. (3) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Agora Cancer Research Centre, Lausanne, Switzerland. (4) Department of Pathology, University of Michigan, Ann Arbor, MI, USA. (5) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Agora Cancer Research Centre, Lausanne, Switzerland. (6) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Agora Cancer Research Centre, Lausanne, Switzerland. (7) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Agora Cancer Research Centre, Lausanne, Switzerland. (8) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Agora Cancer Research Centre, Lausanne, Switzerland. (9) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Agora Cancer Research Centre, Lausanne, Switzerland. (10) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Agora Cancer Research Centre, Lausanne, Switzerland. (11) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Agora Cancer Research Centre, Lausanne, Switzerland. Center of Experimental Therapeutics, Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. (12) Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. (13) Department of Pathology, University of Michigan, Ann Arbor, MI, USA. Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. (14) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. Agora Cancer Research Centre, Lausanne, Switzerland. SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland. (15) Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland. michal.bassani@chuv.ch. Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. michal.bassani@chuv.ch. Agora Cancer Research Centre, Lausanne, Switzerland. michal.bassani@chuv.ch. Center of Experimental Therapeutics, Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland. michal.bassani@chuv.ch.
