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CDK9-55 guides the anaphase-promoting complex/cyclosome (APC/C) in choosing the DNA repair pathway choice

Oncogene volume 43, pages 1263–1273 (2024)Cite this article

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Abstract

DNA double-strand breaks (DSBs) contribute to genome instability, a key feature of cancer. DSBs are mainly repaired by homologous recombination (HR) and non-homologous end-joining (NHEJ). We investigated the role of an isoform of the multifunctional cyclin-dependent kinase 9, CDK9-55, in DNA repair, by generating CDK9-55-knockout HeLa clones (through CRISPR-Cas9), which showed potential HR dysfunction. A phosphoproteomic screening in these clones treated with camptothecin revealed that CDC23 (cell division cycle 23), a component of the E3-ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome), is a new substrate of CDK9-55, with S588 being its putative phosphorylation site. Mutated non-phosphorylatable CDC23(S588A) affected the repair pathway choice by impairing HR and favouring error-prone NHEJ. This CDK9 role should be considered when designing CDK-inhibitor-based cancer therapies.

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Fig. 1: CDK9 isoforms regulate DNA damage response.
Fig. 2: Impaired DNA damage response in CDK9-55KO HeLa clones.
Fig. 3: Identification of potential CDK9-55-regulated DDR players though global phosphoproteomic analysis.
Fig. 4: Unaltered APC/C complex formation in HeLa cells carrying the non-phosphorylable mutant CDC23(S588A) in response to camptothecin (CPT).
Fig. 5: CDC23 S588A impairs the HR.
Fig. 6: CDC23 S588A regulates DNA repair pathway choice favouring the non-homologous and joining (NHEJ).

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Data availability

The mass spectrometry proteomics data have been deposited into the MassIVE (http://massive.ucsd.edu) with the accession number MSV000087856.

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Acknowledgements

We are thankful to the Sbarro Health Research Organization (http://www.shro.org) and Italian Ministry of Health Ricerca Corrente 2022 Grant L3/1. This work was supported by Sbarro Health Research Organization and by the Italian Ministry of Health Ricerca Corrente 2022 Grant L3/1. We are grateful to Professor David H. Price, University of Iowa, for the pGEM-T CDK9 55Kda used in pCEFL HA CDK9 55Kda cloning.

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  1. These authors contributed equally: Luigi Alfano, Carmelina Antonella Iannuzzi.

Authors and Affiliations

  1. Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy

    Luigi Alfano, Carmelina Antonella Iannuzzi, Daniela Barone, Cristin Roma & Laura Marra

  2. Breast Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy

    Iris Maria Forte & Michelino De Laurentiis

  3. Department of Medical Biotechnologies, University of Siena, Siena, Italy

    Maria Carmen Ragosta, Maria Cuomo, Giulio Mazzarotti & Antonio Giordano

  4. Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA

    Milena Dell’Aquila, Angela Altieri, Antonella Caporaso, Silvia Boffo & Antonio Giordano

  5. Sbarro Research Health Organization, Candiolo, Torino, Italy

    Paola Indovina

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Contributions

AL contributed to conceptualization, investigation, development of methodology, writing- original draft, funding acquisition; MDA, AA, AC, GM, CR, SB, CAI, IMF, DB, MCR, MC, LM, contributed to investigation, development of methodology, validation; PI contributed to writing - review & editing; AG contributed to conceptualization, supervision, funding acquisition.

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Correspondence to Luigi Alfano or Antonio Giordano.

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Alfano, L., Iannuzzi, C.A., Barone, D. et al. CDK9-55 guides the anaphase-promoting complex/cyclosome (APC/C) in choosing the DNA repair pathway choice. Oncogene 43, 1263–1273 (2024). https://doi.org/10.1038/s41388-024-02982-w

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