CIC-DUX4 Chromatin Profiling Reveals New Epigenetic Dependencies and Actionable Therapeutic Targets in CIC-Rearranged Sarcomas

Abstract

CIC-DUX4-rearranged sarcoma (CDS) is a rare and aggressive soft tissue tumor that occurs most frequently in young adults. The key oncogenic driver of this disease is the expression of the CIC-DUX4 fusion protein as a result of chromosomal rearrangements. CIC-DUX4 displays chromatin binding properties, and is therefore believed to function as an aberrant transcription factor. However, the chromatin remodeling events induced by CIC-DUX4 are not well understood, limiting our ability to identify new mechanism-based therapeutic strategies for these patients. Here, we generated a genome-wide profile of CIC-DUX4 DNA occupancy and associated chromatin states in human CDS cell models and primary tumors. Combining chromatin profiling, proximity ligation assays, as well as genetic and pharmacological perturbations, we show that CIC-DUX4 operates as a potent transcriptional activator at its binding sites. This property is in contrast with the repressive function of the wild-type CIC protein, and is mainly mediated through the direct interaction of CIC-DUX4 with the acetyltransferase p300. In keeping with this, we show p300 to be essential for CDS tumor cell proliferation; additionally, we find its pharmacological inhibition to significantly impact tumor growth in vitro and in vivo. Taken together, our study elucidates the mechanisms underpinning CIC-DUX4-mediated transcriptional regulation.

Molecular and therapeutic advancements in Capicua (CIC)-rearranged sarcoma

“…Collectively, their findings align with human CDS as they demonstrate multiple shared transcriptional targets including known PEA3 family members that were, in part, associated with p300 transcriptional activation. One interesting observation that is consistent with other findings is that CIC::DUX4 localizes and binds to GGAA-motif sequences on DNA (Kim et al, 2022;Bakaric et al, 2024). These findings indicate that WT CIC and CIC::DUX4 (among other CIC rearrangements) may regulate gene expression through non-consensus (non TGAATGAA-like) like motifs (Thomas et al, 2023).…”

“…Thus, it is reasonable to conceive that CIC::DUX4 attains transcriptional activating capacity through a conserved DUX4 recruitment of p300/CBP, which induces histone H3 acetylation to enable target gene activation (Choi et al, 2016;Bosnakovski et al, 2021). Consistent with this, we and others have observed that global CIC::DUX4 binding overlaps with H3K27ac marks in patient derived CIC::DUX4 cell lines, again suggesting that p300/CBP may in part confer activating capacity (Thomas et al, 2023;Bakaric et al, 2024). Collectively, CIC co-opts the activating capacity of the p300/CBP associated transcription factor, DUX4, to upregulate key target genes including PEA3 family members, cell cycle genes such as CCND2 and CCNE1, and negative MAPK regulators including DUSP4 and DUSP6 that drive malignant phenotypes in aggressive undifferentiated round cell sarcomas (Kawamura-Saito et al, 2006;Yoshimoto et al, 2017;Okimoto et al, 2019;Ponce et al, 2022).…”

Epigenetic determinants of fusion-driven sarcomas: paradigms and challenges

“…P300 inhibitors can disrupt gene signatures driven from CIC-DUX4 activity in URCS, resulting in loss of tumor proliferation (Bosnakovski et al, 2021). Similar effects have been demonstrated through genetic approaches to inactivate P300 function in URCS, and also with targeted protein degradation approaches for P300/CBP (Bakaric et al, 2024).…”