Two opposing gene expression patterns withinATRXaberrant neuroblastoma

Neuroblastoma is the most common extracranial solid tumor in children. A subgroup of high-risk patients is characterized by aberrations in the chromatin remodeller ATRX that is encoded by 35 exons. In contrast to other pediatric cancer whereATRXpoint mutations are most frequent, multi-exon deletions (MEDs) are the most frequent type ofATRXaberrations in neuroblastoma. Of these MEDs 75% are predicted to produce in-frame fusion proteins, suggesting a potential gain-of-function effect compared to nonsense mutations. For neuroblastoma there are only a few patient-derivedATRXaberrant models. Therefore, we created isogenicATRXaberrant models using CRISPR-Cas9 in several neuroblastoma cell lines and one tumoroid and performed total RNA-sequencing on these and on the patient-derived model. Gene set enrichment analysis (GSEA) showed decreased expression of genes related to both ribosome biogenesis and several metabolic process in our isogenicATRXexon 2-10 MED model systems, the patient-derived MED models and in tumor data containing two patients with anATRXexon 2-10 MED. Interestingly, for our isogenicATRXknock-out and exon 2-13 MED models GSEA revealed an opposite expression pattern characterized by increased expression of genes related to ribosome biogenesis and several metabolic process. Our validations confirmed a potential role of ATRX in the regulation of ribosome homeostasis. In this manner we identified two distinct molecular expression patterns withinATRXaberrant neuroblastomas with important implications for the need of distinct treatment regimens.