Therapeutic vulnerabilities in the DNA damage response for the treatment of ATRX mutant neuroblastoma

Abstract

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.

ALT Positivity in Human Cancers: Prevalence and Clinical Insights

“…At the same time, a few novel and exciting molecular targets, including ATR, FANCM, and TOP2, have also been identified [ 25 , 27 , 188 , 200 , 201 ]. Recent small molecule screening suggests ATM inhibitor, KU60019; tyrosine kinase inhibitor, sunitinib; and HSP-90 inhibitor, 17-AAG are also promising [ 202 ]. Developing efficacious and targeted therapy for ALT cancers will naturally be the next step.…”

“…A recent in vitro and in vivo study argues combination targeted ALT therapies would maximize therapeutic efficacy [ 202 ]. Such an approach to ALT tumors, which are predominantly high grade and likely to become treatment-resistant, would maximize potential clinical efficacy.…”

“…Such an approach to ALT tumors, which are predominantly high grade and likely to become treatment-resistant, would maximize potential clinical efficacy. To this end, George and colleagues found ATRX-aberrant NB cells are preferentially sensitive to irinotecan, a DNA topoisomerase 1 (TOP1) inhibitor, and Olaparib, a poly ADP ribose polymerase (PARP) inhibitor, respectively [ 202 ]. In combination, the dual therapy enhanced sensitivity but had a greater effect in ATRX-mutant cells.…”

“…In combination, the dual therapy enhanced sensitivity but had a greater effect in ATRX-mutant cells. Furthermore, in a patient-derived xenograft model, one cycle of combination therapy was sufficient to induce sustainable remission and improved overall survival in ATRX-null mice [ 202 ]. Olaparib and irinotecan are already approved for use in clinical medicine, so there is great potential for this combination regiment to be studied in a patient setting.…”

A strike against indolent neuroblastoma

“…Alterations of the chromatin remodeler ATRX are the most common recurrent event in this indolent clinical subtype, which is associated with overall poor survival and lacks effective therapies [3,4]. In this article of EBioMedicine, George et al utilize an isogenic cellular system to screen for compounds that target ATRX-deficient neuroblastoma [5]. Their study sheds light on a promising therapeutic strategy consisting of a combination of olaparib (a PARP inhibitor) and irinotecan (a topoisomerase I inhibitor), both clinical compounds.…”