The role of the YTHDF m6A readers in neuroblastoma

Neuroblastoma (NB) is the most common extracranial solid tumor diagnosed in the first year of life. The disease is characterized by lack of somatic mutations and high genomic instability including the amplification of MYCN which correlates with poor clinical outcome. These features of NB suggest a pivotal role of transcriptome dynamics in this disease. Analyses of 1089 NB patients show that an overall increase in m6A-regulatory factors correlates with the worst prognosis. Notably, the m6A reader YTHDF1 is upregulated in stage 4 NB corresponding to the highest degree of MYCN amplification. In line with these notions, we observed a positive correlation between MYCN and YTHDF1 by analyzing 33 NB cell lines with different MYCN amplification status. Consistent with this observation, we demonstrated that MYCN knockdown is accompanied by a decrease in all the YTHDF proteins. Furthermore, we demonstrate a loss of proliferating activity in a MYCN-amplified cell line upon knocking out all the YTHDF paralogs and show that the loss in proliferation is mediated by downregulation of DNA replication and chromatin remodeling upon YTHDF depletion. Retinoic acid (RA) is a key agent employed in NB therapy; it induces cell differentiation limiting the proliferation of malignant cells. However, therapeutic protocols adopting RA are limited to maintenance therapy. Thereby, identifying new therapeutic strategies that synergistically enhance RA response is essential to expand the therapeutic window for this drug. Since m6A is a well-known regulator of cellular differentiation, we hypothesized that the protein involved in m6A regulation could act in concert with RA in driving this process. We demonstrate that YTHDF depletion potentiates the response to RA enriching the key processes required for differentiation and that this correlates with an enhanced pro-neural of the YTHDF depleted cells. Together, our findings suggest that targeting the YTHDF family in MYCN-amplified NB represents a promising therapeutic opportunity to control the progression of this disease.