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Ohnmacht AJ, Stahler A, Stintzing S, Modest DP, Holch JW, Westphalen CB, Hölzel L, Schübel MK, Galhoz A, Farnoud A, Ud-Dean M, Vehling-Kaiser U, Decker T, Moehler M, Heinig M, Heinemann V, Menden MP. The Oncology Biomarker Discovery framework reveals cetuximab and bevacizumab response patterns in metastatic colorectal cancer. Nat Commun 2023; 14:5391. [PMID: 37666855 PMCID: PMC10477267 DOI: 10.1038/s41467-023-41011-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/17/2023] [Indexed: 09/06/2023] Open
Abstract
Precision medicine has revolutionised cancer treatments; however, actionable biomarkers remain scarce. To address this, we develop the Oncology Biomarker Discovery (OncoBird) framework for analysing the molecular and biomarker landscape of randomised controlled clinical trials. OncoBird identifies biomarkers based on single genes or mutually exclusive genetic alterations in isolation or in the context of tumour subtypes, and finally, assesses predictive components by their treatment interactions. Here, we utilise the open-label, randomised phase III trial (FIRE-3, AIO KRK-0306) in metastatic colorectal carcinoma patients, who received either cetuximab or bevacizumab in combination with 5-fluorouracil, folinic acid and irinotecan (FOLFIRI). We systematically identify five biomarkers with predictive components, e.g., patients with tumours that carry chr20q amplifications or lack mutually exclusive ERK signalling mutations benefited from cetuximab compared to bevacizumab. In summary, OncoBird characterises the molecular landscape and outlines actionable biomarkers, which generalises to any molecularly characterised randomised controlled trial.
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Affiliation(s)
- Alexander J Ohnmacht
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Arndt Stahler
- Charité Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Hematology, Oncology, and Cancer Immunology, Charitéplatz 1, 10117, Berlin, Germany
| | - Sebastian Stintzing
- Charité Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Hematology, Oncology, and Cancer Immunology, Charitéplatz 1, 10117, Berlin, Germany
- German Cancer Consortium (DKTK), partner sites Berlin and Munich, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Dominik P Modest
- Charité Universitätsmedizin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Hematology, Oncology, and Cancer Immunology, Charitéplatz 1, 10117, Berlin, Germany
| | - Julian W Holch
- German Cancer Consortium (DKTK), partner sites Berlin and Munich, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Medicine III and Comprehensive Cancer Center Munich, University Hospital, Ludwig-Maximilians University Munich, 81377, Munich, Germany
| | - C Benedikt Westphalen
- Department of Medicine III and Comprehensive Cancer Center Munich, University Hospital, Ludwig-Maximilians University Munich, 81377, Munich, Germany
| | - Linus Hölzel
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
| | - Marisa K Schübel
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Ana Galhoz
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Ali Farnoud
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
| | - Minhaz Ud-Dean
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
| | | | | | - Markus Moehler
- Department of Medicine I and Research Center for Immunotherapy (FZI), Johannes Gutenberg-University Clinic, 55131, Mainz, Germany
| | - Matthias Heinig
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
| | - Volker Heinemann
- Department of Medicine III and Comprehensive Cancer Center Munich, University Hospital, Ludwig-Maximilians University Munich, 81377, Munich, Germany.
| | - Michael P Menden
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany.
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany.
- Department of Biochemistry and Pharmacology, University of Melbourne, Victoria, 3010, Australia.
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