MYCN-driven de-differentiation profile identifies a subgroup of aggressive retinoblastoma II

Retinoblastoma are childhood eye tumors arising from retinal precursor cells. Two distinct retinoblastoma subtypes with different clinical behavior have been described based on gene expression and methylation profiling. Using consensus clustering of DNA methylation analysis from retinoblastomas, we identified a MYCN-driven of subtype 2 retinoblastomas characterized by DNA hypomethylation and high expression of genes involved in protein synthesis. Subtype 2 retinoblastomas outside the MYCN-driven were characterized by high expression of genes from mesodermal development, including NKX2-5. Knockdown of MYCN expression in retinoblastoma cell models caused growth arrest and reactivated a subtype 1-specific photoreceptor signature. These molecular changes suggest that removing the driving force of MYCN oncogenic activity rescues molecular circuitry driving subtype 1 biology. The MYCN-RB gene signature generated from the cell models better identified MYCN-driven retinoblastoma than MYCN amplification and could identify cases that may benefit from MYCN-targeted therapy. MYCN drives tumor progression in a molecularly defined retinoblastoma subgroup, and inhibiting MYCN activity could restore a more differentiated and less aggressive tumor biology Overall design: RNA-sequencing data from primary retinoblastomas (N=50), retinoblastoma cell lines (N=8) and MYCN-KD retinoblastoma cell line models (N=4) were generated. The data from primary retinoblastomas were integrated with the previously published data from two relapse retinoblastomas ** (van Tilburg et al., 2021; Heipertz et al., 2022; Peterziel et al., 2022; Worst et al., 2016) Pseudoalignments to hg38 (GRCh38) and quantification were performed using the kallisto/sleuth pipeline