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.