Evaluation of gene expression alterations in alveolar rhabdomyosarcoma upon CHD4 and PAX3-FOXO1 silencing

The goal of this study was to explore in detail how the chromatin remodeler and NuRD subunit CHD4 controls the oncogenic signature of the tumor driver and fusion protein PAX3-FOXO1 in fusion-positive (alveolar) rhabdomyosarcoma. To this aim, we established RH4 cell lines (alveolar rhabdomyosarcoma cell lines) stably expressing doxycycline-inducible shRNAs targeting CHD4 and PAX3-FOXO1. Then, we performed RNA-seq experiments 24hrs and 48hrs after doxycycline-mediated silencing of CHD4 and PAX3-FOXO1. RH4 cells expressing a scramble shRNA upon doxycycline treatment were used as negative controls.