ATRX in-frame fusions promote endogenous chemoresistance programs but yield immunotherapeutic vulnerabilities in neuroblastoma

High-risk Neuroblastomas (NB) carrying in-frame fusion mutations in the ATRX chromatin remodeler(“ATRX-IFF”) are chemoresistant, and children with these mutations display poor overall survival. There are no specific agents to target these tumors, and the mechanisms driving chemoresistance remain unknown. To gain insight into the mechanisms of chemoresistance, we used scRNAseq in combination with cisplatin to study if cellular plasticity drives chemoresistance. In contrast to non-ATRX-IFF-bearing NBs, ATRX -IFF NBs did not appear to display transcriptionally plastic subpopulations, suggesting that the ATRX -IFF promotes an inherent chemoresistance program. To this end, CRISPR-mediated engineering of ATRX -IFF into the endogenous locus in wildtype cells, results in enhanced chemoresistance to multiple clinically-used agents. Next, to identify potential targetable proteins directly regulated by the ATRX-IFF, we combined chromatin binding assays with cell surface proteomics. Using cell lines and orthotopic PDXs, we identified that the ATRX-IFF binds to, and nucleates a super-enhancer at the PTK7 locus, thereby driving extremely high level cell surface expression of PTK7. PTK7 is a pseudokinase receptor that is targeted by experimental CAR-T cell therapies in active preclinical development. Ongoing work is aimed at understanding the dependency of PTK7 on the ATRX-IFF, and using preclinical CAR-T cell models to target PTK7 in ATRX -IFF NB.