PAR-CLIP analysis of neuroblastoma cells in response to amidino-rocaglate treatment

MYCN-amplified neuroblastoma cells exhibit upregulation of translation initiation factors as a result of MYCN-driven transcriptional amplification, including the RNA helicase eIF4A1. Here, we treated MYCN-amplified patient derived xenograft (PDX) neuroblastoma cells with a novel translation initiation inhibitor, amidino-rocaglate CMLD12824, to analyze the impact on the global pattern of eIF4A1 binding to mRNA compared to the naive condition. MYCN-amplified patient derived xenograft (PDX) neuroblastoma cells (COG-N-415) were treated for 1 hour with 10 nM CMLD12824 amidino-rocaglate compound and photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of eIF4A1 was performed to analyze the patterns and changes in eIF4A1 binding of cellular RNAs. Corresponding bulk RNA-sequencing was also performed as control.