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

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 cluster of subtype 2 retinoblastomas characterized by DNA hypomethylation and high expression of genes involved in protein synthesis. Subtype 2 retinoblastomas outside the MYCN-driven cluster 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 Samples from primary retinoblastomas (N=59), retinoblastoma cell lines (N=9) were profiled by either Illumina 450K or EPIC beadchip methylation arrays. 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): INF_R_1024 and INF_R_1673.