Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage.

Berkley E Gryder,Rossella Rota,Silvia Pomella,Nicholas G Aboreden,Benjamin Z Stanton,Beat Schäfer,Christopher R Vakoc,Young Song,Marco Wachtel,Javed Khan,Wardah Mohammed,Kenneth Chang,Winston Ewert,Osama El Demerdash,Jun S Wei

doi:10.1016/j.isci.2020.101103

Abstract

SummaryCore 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.

Highlights

Control of the expression of the core regulatory transcription factors (CR TFs) that guide developmental decision making are directed by logical enhancer elements (Boyer et al, 2005; Chen et al, 2008; Lee and Young, 2013; Vermunt et al, 2019)
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

Summary

Introduction

Control of the expression of the core regulatory transcription factors (CR TFs) that guide developmental decision making are directed by logical enhancer elements (Boyer et al, 2005; Chen et al, 2008; Lee and Young, 2013; Vermunt et al, 2019). These genomic elements, when heavily activated, become super enhancers (SEs) with unusually large deposits of active histone marks, chromatin regulators, and transcriptional coactivators (Hnisz et al, 2013). We test the hypothesis that the chromosomal translocation event resulted in novel enhancer/ promoter interactions to maintain robust expression of the oncogenic fusion protein in FP-RMS

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