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Deep CRISPR mutagenesis characterizes the functional diversity of TP53 mutations

Funk, Julianne S., Klimovich, Maria, Drangenstein, Daniel, Pielhoop, Ole, Hunold, Pascal, Borowek, Anna, Noeparast, Maxim, Pavlakis, Evangelos, Neumann, Michelle, Balourdas, Dimitrios-Ilias, Kochhan, Katharina, Merle, Nastasja, Bullwinkel, Imke, Wanzel, Michael, Elmshäuser, Sabrina, Teply-Szymanski, Julia, Nist, Andrea, Procida, Tara, Bartkuhn, Marek, Humpert, Katharina, Mernberger, Marco, Savai, Rajkumar, Soussi, Thierry, Joerger, Andreas C., Stiewe, Thorsten·2025·Nature Genetics
DOI 10.1038/s41588-024-02039-4

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Abstract

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.

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Metadata

Authors
Funk, J. S., Klimovich, M., Drangenstein, D., Pielhoop, O., Hunold, P., Borowek, A., Noeparast, M., Pavlakis, E., Neumann, M., Balourdas, D.-I., Kochhan, K., Merle, N., Bullwinkel, I., Wanzel, M., Elmshäuser, S., Teply-Szymanski, J., Nist, A., Procida, T., Bartkuhn, M., Humpert, K., Mernberger, M., Savai, R., Soussi, T., Joerger, A. C., & Stiewe, T.
Venue
Nature Genetics
Publisher
Springer Science and Business Media LLC
Published
2025-01
Volume
57
Issue
1
Pages
140-153
ISSN
  • 1061-4036
  • 1546-1718
DOI
10.1038/s41588-024-02039-4
Cited by
103
References
21
Language
en
Licence
Funders
  • Deutsche Forschungsgemeinschaft (STI 182/15-1, STI 182/13-1, GRK2573, 109546710 Project A10, SA 1923/7-1, CRC1213 A10N, JO 1473/1-3)
  • Bundesministerium für Bildung und Forschung (031L0063, DZL)
  • Hessisches Ministerium für Wissenschaft und Kunst (LOEWE iCANx)
  • Von-Behring-Röntgen-Stiftung (65-0004, 66-LV06, 71-0012)
  • José Carreras Leukämie-Stiftung (09 R/2018)
  • Structural Genomics Consortium (SGC): https://www.thesgc.org
  • Institute of Lung Health
  • Deutsche Krebshilfe (TACTIC)

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Funk, J. S., Klimovich, M., Drangenstein, D., Pielhoop, O., Hunold, P., Borowek, A., Noeparast, M., Pavlakis, E., Neumann, M., Balourdas, D.-I., Kochhan, K., Merle, N., Bullwinkel, I., Wanzel, M., Elmshäuser, S., Teply-Szymanski, J., Nist, A., Procida, T., Bartkuhn, M., . . . Stiewe, T. (2025). Deep CRISPR mutagenesis characterizes the functional diversity of TP53 mutations. Nature Genetics. https://doi.org/10.1038/s41588-024-02039-4

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