Deep CRISPR mutagenesis characterizes the functional diversity of TP53 mutations
The mutational landscape of TP53, a tumor suppressor mutated in about half of all cancers, includes over 2,000 known missense mutations. To fully leverage TP53 mutation status for personalized medicine, a thorough understanding of the functional diversity of these mutations is essential. We conducted a deep mutational scan using saturation genome editing with CRISPR-mediated homology-directed repair to engineer 9,225 TP53 variants in cancer cells. This high-resolution approach, covering 94.5% of all cancer-associated TP53 missense mutations, precisely mapped the impact of individual mutations on tumor cell fitness, surpassing previous deep mutational scan studies in distinguishing benign from pathogenic variants. Our results revealed even subtle loss-of-function phenotypes and identified promising mutants for pharmacological reactivation. Moreover, we uncovered the roles of splicing alterations and nonsense-mediated messenger RNA decay in mutation-driven TP53 dysfunction. These findings underscore the power of saturation genome editing in advancing clinical TP53 variant interpretation for genetic counseling and personalized cancer therapy.
Authors
- Michelle M. Neumann (ORCID: https://orcid.org/0000-0002-9546-7433)
- Tara Procida
- Julia Teply‐Szymanski (ORCID: https://orcid.org/0000-0002-3880-1968)
- Maria Klimovich
- Marek Bartkuhn (ORCID: https://orcid.org/0000-0001-6872-9082)
- Evangelos Pavlakis (ORCID: https://orcid.org/0000-0002-7971-609X)
- Julianne Funk (ORCID: https://orcid.org/0000-0002-1848-7975)
- Katharina Humpert
- Nastasja Merle (ORCID: https://orcid.org/0000-0003-4957-8463)
- Daniel Drangenstein
- Andrea Nist (ORCID: https://orcid.org/0000-0002-7524-6801)
- Sabrina Elmshäuser
- Rajkumar Savai (ORCID: https://orcid.org/0000-0003-1538-2091)
- Thorsten Stiewe (ORCID: https://orcid.org/0000-0003-0134-7826)
- Imke Bullwinkel
- Marco Mernberger
- Dimitrios-Ilias Balourdas (ORCID: https://orcid.org/0000-0002-1790-2268)
- Katharina Kochhan
- Thierry Soussi (ORCID: https://orcid.org/0000-0001-8184-3293)
- Anna Borowek
- Andreas C. Joerger (ORCID: https://orcid.org/0000-0002-1232-0138)
- Amir Noeparast (ORCID: https://orcid.org/0000-0002-3216-5630)
- Pascal Hunold (ORCID: https://orcid.org/0000-0002-7087-5908)
- Michael Wanzel (ORCID: https://orcid.org/0000-0001-6879-3383)
- Ole Pielhoop
Institutions
- Goethe University Frankfurt (DE)
- Uppsala University Hospital (SE)
- Inserm (FR)
- Philipps University of Marburg (DE)
- Justus-Liebig-Universität Gießen (DE)
- Science for Life Laboratory (SE)
- Sorbonne Université (FR)
- Max Planck Institute for Heart and Lung Research (DE)
- German Center for Lung Research (DE)
- Universities of Giessen and Marburg Lung Center (DE)
- Centre de Recherche Saint-Antoine (FR)
- Cardio-Pulmonary Institute (DE)
Publication Details
- Journal
- Nature Genetics
- Published
- 2025-01-01
- DOI
- https://doi.org/10.1038/s41588-024-02039-4
- Citations
- 62
- Primary Topic
- CRISPR and Genetic Engineering
- Type
- article
- Field-Weighted Citation Impact
- 45.94
Funders
- Von-Behring-Röntgen-Stiftung
- Deutsche Forschungsgemeinschaft
- Bundesministerium für Bildung und Forschung
- Hessisches Ministerium für Wissenschaft und Kunst
- José Carreras Leukämie-Stiftung
- Deutsche Krebshilfe