PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma [pcHiC_HiC]

Alveolar rhabdomyosarcoma (ARMS) patients harboring PAX3-FOXO1 and PAX7-FOXO1 fusion proteins exhibit a greater incidence of tumor relapse, metastasis, and poor survival outcome, thereby underscoring the urgent need to develop effective therapies to treat this subtype of childhood cancer. To uncover mechanisms that contribute to tumor initiation, we develop a muscle progenitor model and use epigenomic approaches to unravel genome rewiring events mediated by PAX3/7 fusion proteins. Among the key targets of PAX3/7 fusion proteins, we identify a cohort of oncogenes, FGF receptors, tRNA-modifying enzymes, and genes essential for mitochondrial metabolism and protein translation, which we successfully targeted in preclinical trials. We identify leucine usage as a key factor driving the growth of aggressive PAX-fusion tumors, as limiting its bioavailability impaired oxidative phosphorylation and mitochondrial metabolism, delaying tumor progression and improving survival in vivo. Our data provide a compelling list of actionable targets and suggest promising new strategies to treat this tumor. Overall design: Human induced pluripotent stem cells (iPS) were differentiated to muscle progenitors through the inducible expression of Pax7 with doxycycline. Next, we introduce the expression of the oncogenic fusion proteins Pax3-FOXO1 or Pax7-FOXO1 (Flag tagged) using lentiviruses and stopped Pax7 expression for 3 days to study the roles of the fusion proteins in gene regulation. We extracted RNA for gene expression analysis by RNA-seq. We performed Cut&Run followed by sequencing using antibodies against Falg, H3K4me1, H3K4me3 and H3K27ac. Finally, we extracted DNA to perform promoter-capture HiC (pcHiC) and HiC to explore the changes in chromatin topology exerted by the expression of the fusion proteins.