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

Abstract

Oncogenic fusion proteins generated by chromosomal translocations play major roles in cancer. Among them, fusions between EWSR1 and transcription factors generate oncogenes with powerful chromatin regulatory activities, capable of establishing complex gene expression programs in permissive precursor cells. Here we define the epigenetic and 3D connectivity landscape of Clear Cell Sarcoma, an aggressive cancer driven by the EWSR1-ATF1 fusion gene. We find that EWSR1-ATF1 displays a distinct DNA binding pattern that requires the EWSR1 domain and promotes ATF1 retargeting to new distal sites, leading to chromatin activation and the establishment of a 3D network that controls oncogenic and differentiation signatures observed in primary CCS tumors. Conversely, EWSR1-ATF1 depletion results in a marked reconfiguration of 3D connectivity, including the emergence of regulatory circuits that promote neural crest-related developmental programs. Taken together, our study elucidates the epigenetic mechanisms utilized by EWSR1-ATF1 to establish regulatory networks in CCS, and points to precursor cells in the neural crest lineage as candidate cells of origin for these tumors.

Inflammatory and Nested Testicular Sex Cord Tumor

“…In recent years, it has become clear that most individual gene fusions are nonspecific, being identified in neoplasms with widely different histopathologic and clinical characteristics 22. The phenotypic and biological features of tumors driven by gene fusions are likely determined by multiple factors, such as the cell of origin, the tumor microenvironment, and the presence of concurrent genomic and epigenomic alterations 23,24. This is apparently the case for neoplasms driven by EWSR1::ATF1 , a fusion that has been identified in multiple tumor types, including clear cell sarcoma of soft tissue, malignant gastrointestinal neuroectodermal tumor (also known as clear cell sarcoma-like tumor of the gastrointestinal tract), clear cell carcinoma of salivary gland, hyalinizing clear cell carcinoma of the thymus and lung, clear cell odontogenic carcinoma, myoepithelial tumors, intracranial myxoid mesenchymal tumor, primary pulmonary myxoid sarcoma, and subsets of mesothelioma, angiosarcoma, and angiomatoid fibrous histiocytoma 25–41.…”

“…In animal models, EWSR1::ATF1 is, in and of itself, sufficient to promote oncogenesis 24. The resulting fusion protein predictably consists of an N-terminal portion that contains the transactivation domain of EWSR1 and a C-terminal portion that contains the DNA-binding domain of ATF1 23,49. The latter is a conserved leucine zipper (shared by other frequent fusion partners of EWSR1 such as CREB1 and CREM ) that binds to sequences known as cAMP response element motifs 23.…”

MS0621, a novel small-molecule modulator of Ewing sarcoma chromatin accessibility, interacts with an RNA-associated macromolecular complex and influences RNA splicing

“…Interestingly, although MS1360 pulled down both the EWSR1::ATF1 fusion protein and the parental ATF1 transcription factor in SU-CCS-1 cells, ATF1, which was present in the other cell lines, was not pulled down. The inclusion of ATF1 in the MS1360-interacting complex in SU-CCS-1 cells may reflect the contribution of the EWSR1 domain to the fusion ( 20 ). These data demonstrate that MS0621 interacts with a complex enriched with proteins involved in transcription and co-transcriptional processes.…”

An absolute approach to using whole exome DNA and RNA workflow for cancer biomarker testing

“…However, case 4BC-146 revealed the presence of rare fusions of EWSR1::ATF1 in NSCLC patient ( Figure 4C ). In this case, the outcome from the NGS is more toward understanding the molecular drivers associated with disease onset and its phenotype, since EWSR1 fusions do not have targeted therapy drugs approved ( 47 ). These data elucidate the importance of RNA exome sequencing to identify rare/novel driver mutations associated with the disease ( 59 ).…”