EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma

Chimeric proteins resulting from chromosomal translocations play a major role as driver oncogenes in cancer. Among them, fusions between EWSR1 and transcription factors (TFs) generate oncogenes with powerful chromatin regulatory activities, capable of establishing complex gene expression programs. Specific fusion partners are implicated in distinct tumor types, suggesting that the oncogenic activity of EWSR1 fusions is determined by their DNA binding properties and the chromatin environment of precursor cells. Here we combined functional epigenomics with nuclear topology mapping to define the epigenetic and 3D connectivity landscape of Clear Cell Sarcoma (CCS), one of the most aggressive forms of human cancer, which is driven by the EWSR1-ATF1 fusion gene. We find that EWSR1-ATF1 displays a distinctive DNA binding pattern that depends on the EWSR1 prion-like domain and is divergent from wild type ATF1. EWSR1-ATF1 promotes ATF1 retargeting to new distal sites, leading to chromatin activation and the establishment of a 3D network that controls oncogenic and differentiation signatures shared with primary CCS tumors. Conversely, EWSR1-ATF1 depletion results in a marked reconfiguration of 3D connectivity, including the emergence of a new set of connections controlling neural crest-related developmental programs. Accordingly, interrogation of more than 160’000 single cell expression profiles from the human skin atlas reveals that loss of EWSR1-ATF1 expression induces a differentiated cell state that resembles cells in the Schwann cell-melanocytic axis. Taken together, our study uncovers the cooperativity network of EWSR1-ATF1, delineates the molecular underpinnings of its epigenetic function in CCS, and points to precursor cells in the neural crest lineage as candidate cells of origin for these tumors.