Nature Communications (Mar 2020)
Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes
- Chloe Chong,
- Markus Müller,
- HuiSong Pak,
- Dermot Harnett,
- Florian Huber,
- Delphine Grun,
- Marion Leleu,
- Aymeric Auger,
- Marion Arnaud,
- Brian J. Stevenson,
- Justine Michaux,
- Ilija Bilic,
- Antje Hirsekorn,
- Lorenzo Calviello,
- Laia Simó-Riudalbas,
- Evarist Planet,
- Jan Lubiński,
- Marta Bryśkiewicz,
- Maciej Wiznerowicz,
- Ioannis Xenarios,
- Lin Zhang,
- Didier Trono,
- Alexandre Harari,
- Uwe Ohler,
- George Coukos,
- Michal Bassani-Sternberg
Affiliations
- Chloe Chong
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center
- Markus Müller
- Vital IT, Swiss Institute of Bioinformatics
- HuiSong Pak
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center
- Dermot Harnett
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology
- Florian Huber
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center
- Delphine Grun
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)
- Marion Leleu
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)
- Aymeric Auger
- Department of Oncology, Centre hospitalier universitaire vaudois (CHUV)
- Marion Arnaud
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center
- Brian J. Stevenson
- Vital IT, Swiss Institute of Bioinformatics
- Justine Michaux
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center
- Ilija Bilic
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology
- Antje Hirsekorn
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology
- Lorenzo Calviello
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology
- Laia Simó-Riudalbas
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)
- Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)
- Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University
- Marta Bryśkiewicz
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University
- Maciej Wiznerowicz
- International Institute for Molecular Oncology
- Ioannis Xenarios
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center
- Lin Zhang
- Center for Research on Reproduction and Women’s Health, University of Pennsylvania
- Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL)
- Alexandre Harari
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center
- Uwe Ohler
- Max Delbrück Centre for Molecular Medicine in the Helmholtz Association, Institute for Medical Systems Biology
- George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center
- Michal Bassani-Sternberg
- Ludwig Institute for Cancer Research, University of Lausanne, Agora Center
- DOI
- https://doi.org/10.1038/s41467-020-14968-9
- Journal volume & issue
-
Vol. 11,
no. 1
pp. 1 – 21
Abstract
Non-canonical HLA-bound peptides from presumed non-coding regions are potential targets for cancer immunotherapy, but their discovery remains challenging. Here, the authors integrate exome sequencing, transcriptomics, ribosome profiling, and immunopeptidomics to identify tumor-specific non-canonical HLA-bound peptides.
