Taken together, these results show for the first time that PAX3-FOXO1 is phosphorylated at Ser201 and Ser205 in primary ARMS tumors, that these phosphorylation events are enriched in cells actively invading the surrounding normal tissue, and that they provide clinical validation for their in vitro effects on ARMS tumor phenotypes. Here, PAX3 is linked to alveolar rhabdomyosarcoma.