Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage

Summary Core regulatory transcription factors (CR TFs) establish enhancers with logical ordering during embryogenesis and development. Here we report that in fusion-positive rhabdomyosarcoma, a cancer of the muscle lineage, the chief oncogene PAX3-FOXO1 is driven by a translocated FOXO1 super enhancer (SE) restricted to a late stage of myogenesis. Using chromatin conformation capture techniques, we demonstrate that the extensive FOXO1 cis-regulatory domain interacts with PAX3. Furthermore, RNA sequencing and chromatin immunoprecipitation sequencing data in tumors bearing rare PAX translocations implicate enhancer miswiring across all fusion-positive tumors. HiChIP of H3K27ac showed connectivity between the FOXO1 SE, additional intra-domain enhancers, and the PAX3 promoter. We show that PAX3-FOXO1 transcription is diminished when this network of enhancers is ablated by CRISPR. Our data reveal a hijacked enhancer network that disrupts the stepwise CR TF logic of normal skeletal muscle development (PAX3 to MYOD to MYOG), replacing it with an “infinite loop” enhancer logic that locks rhabdomyosarcoma in an undifferentiated stage.
Graphical Abstract
Highlights • Muscle lineage enhancer logic is miswired in PAX3-FOXO1-driven rhabdomyosarcoma • PAX7-FOXO1, PAX3-NCOA1, and PAX3-INO80D tumors show evidence of miswired enhancers • FOXO1 super enhancer is myogenically activated and sustains PAX3-FOXO1 expression • Oncogenic translocations select for miswired enhancers around disordered proteins
Biological Sciences; Chromosome Organization; Molecular Mechanism of Gene Regulation; Cancer