DNA-PK enforces the S/G2 checkpoint in ATM-deficient cells to limit ATR inhibitor efficacy
ATR inhibition has been proposed as a strategy for tumors under replication stress or those harboring ATM deficiency. However, anti-tumor activity is limited by DNA-PK and ATM compensation. Here, we have delineated distinct roles for DNA-PK and ATM during ATR inhibitor exposure. Both kinases are activated in a cell cycle-dependent manner at the S/G2 boundary following ATR inhibition. DNA-PK imposes the S/G2 checkpoint and promotes completion of DNA replication, whereas ATM detects persistent aberrant DNA replication structures with associated DNA damage in late S and G2/M to establish a G2/M checkpoint promoting DNA repair. In ATM-deficient cells and patient tumors, DNA-PK is activated following ATR inhibition and assumes greater versatility by not only enforcing the S/G2 checkpoint but also by detecting aberrant replication structures in S phase in place of ATM, allowing cells to tolerate ATR inhibition. Consequently, DNA-PK inhibition synergizes with ATR inhibition in ATM-deficient cells and enhances ATR inhibitor efficacy in ATM-deficient PDX models. These data support clinical evaluation of combined ATR and DNA-PK inhibition in ATM-deficient cancers.
Authors
- Steffie Revia (ORCID: https://orcid.org/0000-0003-4088-3250)
- Timothy B. Branigan (ORCID: https://orcid.org/0009-0000-7301-8445)
- Jie Hao (ORCID: https://orcid.org/0000-0002-4610-0563)
- Sirisha Mukkavalli (ORCID: https://orcid.org/0000-0002-8875-7985)
- Joachim Albers (ORCID: https://orcid.org/0000-0003-0582-1863)
- Mu-Yan Cai (ORCID: https://orcid.org/0000-0001-5315-8336)
- Kalindi Parmar (ORCID: https://orcid.org/0000-0002-9522-1716)
- Alan D. D’Andrea (ORCID: https://orcid.org/0000-0001-6168-6294)
- Geoffrey Ira Shapiro (ORCID: https://orcid.org/0000-0002-3331-4095)
- Yuqing Jiao (ORCID: https://orcid.org/0009-0005-4257-4867)
- Kelsey McQueen (ORCID: https://orcid.org/0000-0002-2448-0200)
- Ian A. Roundtree (ORCID: https://orcid.org/0000-0002-9791-054X)
- Astrid Zimmermann (ORCID: https://orcid.org/0000-0001-6146-9812)
- Prafulla C. Gokhale (ORCID: https://orcid.org/0000-0002-1974-5921)
- Bose S. Kochupurakkal (ORCID: https://orcid.org/0000-0001-8929-3070)
- Roshen Alharthi
- Gregory Michael Cote (ORCID: https://orcid.org/0000-0003-0181-886X)
Institutions
- Merck KGaA, Darmstadt (Germany) (DE)
- Dana-Farber Cancer Institute (US)
- Merck Healthcare KGaA, Darmstadt (Germany) (DE)
- Mass General Brigham (US)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-10-28
- DOI
- https://doi.org/10.64898/2026.10.25.761677
- Primary Topic
- DNA Repair Mechanisms
- Type
- preprint