Ehteda, A. | Search bioRxiv

bioRxiv2025

Selective degradation of oncogenic extrachromosomal DNA by type I-E CRISPR

Extrachromosomal DNA (ecDNA) is a major driver of oncogene amplification, intratumoral heterogeneity and therapy resistance across multiple cancer types, yet there are currently no effective strategies to selectively eliminate it. Here, we show that the type I-E CRISPR system can specifically target and degrade ecDNA in human cancer cell lines (COLO320DM and GBM39). By designing guide RNAs targeting ecDNA-specific breakpoints absent from chromosomal DNA, we achieved efficient depletion of MYC- and EGFR-containing ecDNAs in COLO320DM and GBM39 cells. Loss of ecDNA was accompanied by diminished oncogene signaling, disrupted ecDNA architecture, and impaired tumor cell proliferation, without detectable chromosomal off-target activity. These findings establish a proof-of-concept framework for directly targeting oncogenic ecDNAs and highlight type I-E CRISPR as a promising platform for therapeutic development in ecDNA-driven cancers.

cancer biology↗

bioRxiv2024

Chromatin remodeling with combined FACT and BET inhibition disrupts oncogenic transcription in Diffuse Midline Glioma

Aberrant epigenetic regulation is a hallmark of Diffuse Midline Glioma (DMG), an incurable pediatric brain tumor. The H3K27M driver histone mutation leads to transcriptional dysregulation, indicating that targeting the epigenome and transcription may be key therapeutic strategies against this highly aggressive cancer. One such target is the Facilitates Chromatin Transcription (FACT) histone chaperone. We found FACT to be enriched at developmental gene promoters, coinciding with regions of open chromatin and binding motifs of core DMG regulatory transcription factors. Furthermore, FACT interacted and co-localized with the Bromodomain and Extra-Terminal Domain (BET) protein BRD4 at promoters and enhancers, suggesting functional cooperation between FACT and BRD4 in DMG. In vitro, a combinatorial therapeutic approach using the FACT inhibitor CBL0137, coupled with BET inhibition revealed potent and synergistic cytotoxicity across a range of DMG cultures. These results were recapitulated in vivo, significantly extending survival in three independent orthotopic PDX models of DMG. Mechanistically, we show that CBL0137 treatment decreased chromatin accessibility, synergizing with BET inhibition to cause broad transcriptional collapse, silencing several key oncogenes including MYC, PDGFRA, MDM4 and SOX2, as well as causing alterations to the splicing landscape. Notably, this combination also elicited immune-related effects, including activation of the interferon response and antigen presentation mechanisms in DMG cells and induction of an activated state in macrophages and T cells, as demonstrated in an immunocompetent setting with spatial transcriptomics. Altogether, our data highlights the therapeutic promise of simultaneously targeting FACT and BET proteins in DMG, offering a dual tumor-intrinsic and immune-mediated strategy for combating this devastating pediatric brain tumor.

cancer biology↗