The ETS transcription factor ETV6 constrains the transcriptional activity of EWS–FLI to promote Ewing sarcoma

Abstract

Transcription factors (TFs) are frequently mutated in cancer. Paediatric cancers exhibit few mutations genome-wide but frequently harbour sentinel mutations that affect TFs, which provides a context to precisely study the transcriptional circuits that support mutant TF-driven oncogenesis. A broadly relevant mechanism that has garnered intense focus involves the ability of mutant TFs to hijack wild-type lineage-specific TFs in self-reinforcing transcriptional circuits. However, it is not known whether this specific type of circuitry is equally crucial in all mutant TF-driven cancers. Here we describe an alternative yet central transcriptional mechanism that promotes Ewing sarcoma, wherein constraint, rather than reinforcement, of the activity of the fusion TF EWS–FLI supports cancer growth. We discover that ETV6 is a crucial TF dependency that is specific to this disease because it, counter-intuitively, represses the transcriptional output of EWS–FLI. This work discovers a previously undescribed transcriptional mechanism that promotes cancer.

KMAP: Kmer Manifold Approximation and Projection for visualizing DNA sequences

“…The comparison with the established MEME algorithm (Bailey & Elkan, 1994) on a comprehensive benchmark SELEX-seq dataset shows that KMAP generates similar motifs as MEME. Specifically, in the analysis of Ewing Sarcoma (EWS) data, we not only reproduced the original findings (Lu et al, 2023) about GGAA-repeats in the motif of ETS Variant Transcription Factor 6 (ETV6), but also unveiled new insights. We discovered ETV6 could also bind to AGGG repeats and likely inhibited the binding of BACH1, OTX2, ERG1 to the promoter and enhancer regions.…”

Expression of the CIC-DUX4 fusion oncoprotein mimics human CIC-rearranged sarcoma in genetically engineered mouse models

“…To dissect the independent and overlapping roles of ETS1 and PEA3 subfamily genes in CDS, future work will use CRISPR/Cas9 to systematically and combinatorially delete these genes in cell lines and tumors. Of further interest is whether forced overexpression or stabilization of these same factors could be toxic to CDS cells in keeping with the ‘Goldilocks phenomenon’ described in Ewing Sarcoma 38,39 . Lastly, these results indicate that CDS, unlike Ewing Sarcoma, can be modeled in the mouse which is an important breakthrough for the sarcoma research community.…”

Carcinoma-associated fibroblast-like tumor cells remodel the Ewing sarcoma tumor microenvironment

“…The molecular mechanisms that mediate this dissociation remain to be elucidated and this is a key gap in knowledge that the field must now fill. However, given the exciting work from several labs that cell context-specific transcription factors (19)(20)(21), chromatin remodelers (17,18), and nuclear condensates (14,54) influence EWS:FLI1 activity, it is likely that epigenetic mechanisms will be identified as drivers of these hybrid transcriptional states.…”

“…(16)). Genomic loss of STAG2 (17,18), expression of tissue-specific transcription factors (19)(20)(21), activation of the Wnt/β-catenin pathway (22), and other cellintrinsic and cell-extrinsic mechanisms (16), all influence transcriptional activity of EWS::FLI1 and affect the tumorigenic and metastatic properties of EwS cells. Importantly, despite different underlying molecular origins, EWS::FLI1-depleted cells universally show increased expression of mesenchymal lineage genes that are normally repressed by the fusion.…”