Therapeutic vulnerabilities in the DNA damage response for the treatment of ATRX mutant neuroblastoma
Sally L George,
Federica Lorenzi,
David King,
Sabine Hartlieb,
James Campbell,
Helen Pemberton,
Umut H Toprak,
Karen Barker,
Jennifer Tall,
Barbara Martins da Costa,
Marlinde L van den Boogaard,
M Emmy M Dolman,
Jan J Molenaar,
Helen E Bryant,
Frank Westermann,
Christopher J Lord,
Louis Chesler
Affiliations
Sally L George
Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT United Kingdom; Corresponding author.
Federica Lorenzi
Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
David King
Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, United Kingdom
Sabine Hartlieb
Neuroblastoma Genomics, Hopp Children`s Cancer Center Heidelberg (KiTZ) & German Cancer Research Center (DKFZ), Heidelberg, Germany
James Campbell
Bioinformatics Core Facility, The Institute of Cancer Research, London, United Kingdom
Helen Pemberton
CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research London, SW3 6JB, United Kingdom
Umut H Toprak
Neuroblastoma Genomics, Hopp Children`s Cancer Center Heidelberg (KiTZ) & German Cancer Research Center (DKFZ), Heidelberg, Germany
Karen Barker
Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
Jennifer Tall
Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
Barbara Martins da Costa
Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom
Marlinde L van den Boogaard
Princess Maxima Center for Pediatric Cancer, Utrecht, The Netherlands
M Emmy M Dolman
Princess Maxima Center for Pediatric Cancer, Utrecht, The Netherlands
Jan J Molenaar
Princess Maxima Center for Pediatric Cancer, Utrecht, The Netherlands
Helen E Bryant
Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Beech Hill Road, Sheffield S10 2RX, United Kingdom
Frank Westermann
Neuroblastoma Genomics, Hopp Children`s Cancer Center Heidelberg (KiTZ) & German Cancer Research Center (DKFZ), Heidelberg, Germany
Christopher J Lord
CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research London, SW3 6JB, United Kingdom
Louis Chesler
Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, United Kingdom; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, Sutton, Surrey SM2 5PT United Kingdom
Background: In neuroblastoma, genetic alterations in ATRX, define a distinct poor outcome patient subgroup. Despite the need for new therapies, there is a lack of available models and a dearth of pre-clinical research. Methods: To evaluate the impact of ATRX loss of function (LoF) in neuroblastoma, we utilized CRISPR-Cas9 gene editing to generate neuroblastoma cell lines isogenic for ATRX. We used these and other models to identify therapeutically exploitable synthetic lethal vulnerabilities associated with ATRX LoF. Findings: In isogenic cell lines, we found that ATRX inactivation results in increased DNA damage, homologous recombination repair (HRR) defects and impaired replication fork processivity. In keeping with this, high-throughput compound screening showed selective sensitivity in ATRX mutant cells to multiple PARP inhibitors and the ATM inhibitor KU60019. ATRX mutant cells also showed selective sensitivity to the DNA damaging agents, sapacitabine and irinotecan. HRR deficiency was also seen in the ATRX deleted CHLA-90 cell line, and significant sensitivity demonstrated to olaparib/irinotecan combination therapy in all ATRX LoF models. In-vivo sensitivity to olaparib/irinotecan was seen in ATRX mutant but not wild-type xenografts. Finally, sustained responses to olaparib/irinotecan therapy were seen in an ATRX deleted neuroblastoma patient derived xenograft. Interpretation: ATRX LoF results in specific DNA damage repair defects that can be therapeutically exploited. In ATRX LoF models, preclinical sensitivity is demonstrated to olaparib and irinotecan, a combination that can be rapidly translated into the clinic. Funding: This work was supported by Christopher's Smile, Neuroblastoma UK, Cancer Research UK, and the Royal Marsden Hospital NIHR BRC.