#EWS::FLI1
(1/5) Excited to share our new paper in Advanced Science! We combine genome editing, super-resolution microscopy, and single-molecule tracking to investigate the endogenous oncogenic fusion transcription factor EWS::FLI1 in Ewing sarcoma cells. advanced.onlinelibrary.wiley.com/doi/full/10....
Dynamic Regulation of Endogenous Transcription Factor Hubs at Single‐Molecule Resolution
This study combines single-molecule microscopy and genome editing to characterize the dynamic behaviors of endogenous oncofusion transcription factor EWS::FLI1 in Ewing sarcoma cells. EWS::FLI1 forms...
advanced.onlinelibrary.wiley.com
July 16, 2026 at 2:08 AM
Modelling EWS::FLI1 protein fluctuations reveal determinants of tumor plasticity in Ewing sarcoma

link.springer.com/article/10.1...
Modelling EWS::FLI1 protein fluctuations reveal determinants of tumor plasticity in Ewing sarcoma - EMBO Molecular Medicine
Tumor cell plasticity drives metastasis and therapy resistance, yet its regulation by oncoprotein dosage dynamics remains poorly understood. In Ewing sarcoma (EwS), variations in EWS::FLI1 (EF) fusion...
link.springer.com
January 4, 2026 at 8:00 PM
📢 Thrilled to share our latest paper, KDM6 Demethylases Contribute to EWSR1::FLI1-Driven Oncogenic Reprogramming in Ewing Sarcoma, from my PhD, is now published in Cancer Research!

Explore our findings🔬🧬: aacrjournals.org/cancerres/ar...

#Epigenetics #Cancer #EwingSarcoma

Huge thanks to the team!
KDM6 Demethylases Contribute to EWSR1::FLI1-Driven Oncogenic Reprogramming in Ewing Sarcoma
Abstract. Ewing Sarcoma (EwS) is a highly aggressive tumor arising in bones and soft tissues driven by the fusion oncoprotein EWSR1::FLI1. This aberrant transcription factor binds to GGAA microsatelli...
aacrjournals.org
October 14, 2025 at 7:38 PM
Our latest study is now online! A great collaboration between the @fgh-lab.bsky.social and @enriquedealava.bsky.social Labs, driven by the outstanding work of J. Olmedo-Pelayo at @ibis-investigacion.bsky.social Check it out!
EWS::FLI1-DHX9 interaction promotes Ewing sarcoma sensitivity to DNA topoisomerase 1 poisons by altering R-loop metabolism - Oncogene
Oncogene - EWS::FLI1-DHX9 interaction promotes Ewing sarcoma sensitivity to DNA topoisomerase 1 poisons by altering R-loop metabolism
www.nature.com
July 29, 2025 at 8:36 AM
EWS::FLI1-DHX9 interaction promotes Ewing #sarcoma sensitivity to DNA topoisomerase 1 poisons by altering R-loop metabolism

www.nature.com/articles/s41...
EWS::FLI1-DHX9 interaction promotes Ewing sarcoma sensitivity to DNA topoisomerase 1 poisons by altering R-loop metabolism - Oncogene
Oncogene - EWS::FLI1-DHX9 interaction promotes Ewing sarcoma sensitivity to DNA topoisomerase 1 poisons by altering R-loop metabolism
www.nature.com
July 29, 2025 at 11:47 AM
Phase 1/2 trial: Trabectedin + low-dose irinotecan in 37 relapsed Ewing sarcoma patients shows potential to counter EWS:FLI1 activity. PMID:41991689, Nat Med 2026, @NatureMedicine https://doi.org/10.1038/s41591-026-04340-7 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
Trabectedin and low-dose irinotecan to target EWS::FLI1 in Ewing sarcoma: a phase 1/2 trial | Nature Medicine
Ewing sarcoma (ES) is a bone and soft tissue sarcoma that is absolutely dependent on the EWS::FLI1 transcription factor for cell survival. No compound has been shown to reverse EWS::FLI1 activity in patients, and outcomes for relapsed patients remain poor. Trabectedin above a threshold concentration reverses the activity of EWS::FLI1 and is potentiated by low-dose irinotecan in vivo. This open-label phase 1/2 trial of trabectedin with irinotecan (SARC037) enrolled 37 relapsed/refractory patients with ES. The primary objectives were to determine the safety, tolerability, recommended phase 2 dose (RP2D; phase 1) and objective response rate (ORR; phase 2) of trabectedin administered as a 1-hour infusion in combination with low-dose irinotecan in patients with ES. The secondary objectives were to determine the progression-free survival (PFS), 6-month PFS, duration of response and 18F-fluorothymidine positron emission tomography (18F-FLT PET) avidity of ES tumors. The RP2D was trabectedin 1
doi.org
May 22, 2026 at 5:10 AM
Subversion of mRNA degradation pathways by EWSR1::FLI1 represents a therapeutic vulnerability in Ewing #sarcoma

www.nature.com/articles/s41...
Subversion of mRNA degradation pathways by EWSR1::FLI1 represents a therapeutic vulnerability in Ewing sarcoma - Nature Communications
The EWSR1::FLI1 fusion protein is the oncogenic driver of Ewing sarcoma (EwS). Here, the authors find that EWSR1::FLI1 plays a non-canonical role in mRNA decay via interactions with the CCR4-NOT deade...
www.nature.com
July 21, 2025 at 6:33 PM
🎉Congratulations to Veveeyan Suresh, from the Kovar group, who successfully defended his PhD thesis entitled "Regulation, dynamics and functional impact of EWS::FLI1 oncoprotein dosages in Ewing sarcoma".
August 25, 2026 at 9:33 AM
Ewing sarcoma tumor fitness depends on three snoRNA host genes–SNHG1, SNHG12, and SNHG30–that regulate chemical modification of ribosomal RNA. Blocking them slowed tumor growth, pointing to a strategy to target the unique EWS-FLI1 biology sustaining Ewing sarcoma. academic.oup.com/narcancer/ar...
SNHG family lncRNAs promote Ewing sarcoma cell fitness through intronic snoRNA-guided rRNA modifications
Abstract. Over 90% of Ewing sarcomas (EWS) are driven by the EWS–FLI1 fusion oncoprotein. EWS–FLI1 acts as a pioneer transcription factor, altering the exp
academic.oup.com
August 29, 2026 at 7:11 PM
Rewiring the fusion oncoprotein EWS/FLI1 in Ewing sarcoma with bivalent small molecules https://www.biorxiv.org/content/10.1101/2025.03.14.643353v1
March 17, 2025 at 7:50 PM
New publication "Chimeric protein EWS::FLI1 drives cell proliferation in Ewing Sarcoma via aberrant expression of KCNN1/SK1 and dysregulation of calcium signaling" @natureportfolio.bsky.social fruitful collaborative project with CRCI2NA @insermgrandouest.bsky.social
www.nature.com/articles/s41...
Chimeric protein EWS::FLI1 drives cell proliferation in Ewing Sarcoma via aberrant expression of KCNN1/SK1 and dysregulation of calcium signaling - Oncogene
Oncogene - Chimeric protein EWS::FLI1 drives cell proliferation in Ewing Sarcoma via aberrant expression of KCNN1/SK1 and dysregulation of calcium signaling
www.nature.com
January 20, 2025 at 2:48 PM
Preprint out of induced proximity between EWS/FLI1 with BCL6 leads to cell death by a new TCIP called EB-TCIP. Work out from teams at Stanford and DFCI and co-led by the lab of Kimberly Stegmaier!
www.biorxiv.org/content/10.1...
Rewiring the fusion oncoprotein EWS/FLI1 in Ewing sarcoma with bivalent small molecules
Deregulated transcription is a defining hallmark of cancer, especially pediatric malignancies, which are frequently driven by fusion transcription factors. Targeting transcription factors directly has...
www.biorxiv.org
March 22, 2025 at 8:10 PM
(3/5) Hub formation is a neomorphic behavior of EWS::FLI1 not conferred by its parental proteins, EWSR1 and FLI1. During mitosis, EWS::FLI1 hubs dissolve, but EWS::FLI1 molecules continue to dynamically associate with mitotic chromosomes.
July 16, 2026 at 2:08 AM
(4/5) Nascent RNA destabilizes EWS::FLI1 hubs without affecting their dimensions. LY2835219 and trabectedin, compounds previously reported to affect EWS::FLI1 function, disrupt and mislocalize endogenous EWS::FLI1 hubs, respectively, highlighting their therapeutic potential.
July 16, 2026 at 2:08 AM
Check out our new lab paper out in @natcomms.nature.com
doi.org/10.1038/s414...

EWSR1::FLI1, the main oncogenic driver of Ewing sarcoma and a notoriously challenging drug target, has mostly been studied for its role in transcriptional deregulation 🧬

But it turns out not to be its only function...
Subversion of mRNA degradation pathways by EWSR1::FLI1 represents a therapeutic vulnerability in Ewing sarcoma - Nature Communications
The EWSR1::FLI1 fusion protein is the oncogenic driver of Ewing sarcoma (EwS). Here, the authors find that EWSR1::FLI1 plays a non-canonical role in mRNA decay via interactions with the CCR4-NOT deade...
doi.org
July 26, 2025 at 8:42 AM
Rewiring the fusion oncoprotein EWS/FLI1 in Ewing sarcoma with bivalent small molecules https://www.biorxiv.org/content/10.1101/2025.03.14.643353v1
March 17, 2025 at 7:50 PM
pubpeer.com/publications...
Answers like these …, one wonders if the experiments have even been done…
PubPeer - CRM1 Inhibition Promotes Cytotoxicity in Ewing Sarcoma Cells...
There are comments on PubPeer for publication: CRM1 Inhibition Promotes Cytotoxicity in Ewing Sarcoma Cells by Repressing EWS-FLI1–Dependent IGF-1 Signaling (2016)
pubpeer.com
December 5, 2024 at 2:16 PM
New preprint: Hunting for MSI in long-read data with Owl 🦉

Owl is an MSI caller purpose-built for #PacBio HiFi and integrated into our somatic workflow.

Data:
• Low baseline (~1–5%)
• 15–18% MSI-H instability
• Links GGAA repeats to EWS::FLI1 fusion

Preprint here: bit.ly/4beWECU
March 12, 2026 at 4:30 PM
👉EWS::FLI1 modulates R-loop metabolism via DHX9, driving increased vulnerability to TOP1-targeting agents.
👉Targeting TOP1 in EWS cells destabilizes the genome and provokes strong replication stress and cell death in EwS cells and tumors

Grateful to all collaborators who made this work possible!
July 29, 2025 at 8:36 AM
CK2 inhibitor CX-4945 targets EWS-FLI1 protein abundance and shows anti-tumor activity in metastatic mouse models of Ewing Sarcoma https://www.biorxiv.org/content/10.1101/2025.09.24.677357v1
September 26, 2025 at 11:48 PM
Dynamic modelling of EWS::FLI1 fluctuations reveals molecular determinants of phenotypic tumor plasticity and prognosis in Ewing sarcoma https://www.biorxiv.org/content/10.1101/2025.04.03.647002v1
April 9, 2025 at 3:49 AM
RRIDs were included in this paper. Thanks for making your methods matter! #OpenScience #reproducibility #ReproducibleResearch
RUNX2 Represses the EWS-FLI1-mediated Transcription in Ewing’s Sarcoma Cells
doi.org
February 1, 2026 at 8:01 AM
RRIDs were included in this in EMBO Molecular Medicine paper. Thanks for making your methods matter! #BetterScience #accelerateopenscience #OpenResearch
Modelling EWS::FLI1 protein fluctuations reveal determinants of tumor plasticity in Ewing sarcoma - EMBO Molecular Medicine
Tumor cell plasticity drives metastasis and therapy resistance, yet its regulation by oncoprotein dosage dynamics remains poorly understood. In Ewing sarcoma (EwS), variations in EWS::FLI1 (EF) fusion oncoprotein activity have been associated with epithelial-mesenchymal plasticity (EMP). Using degron technology, we precisely modulated endogenous EF in EwS cells and linked phenotypic states to distinct oncoprotein dosages. Strikingly, modest EF depletion promoted a pro-metastatic phenotype that diminished upon near-complete EF loss, revealing a paradoxical effect of submaximal EF inhibition. Nascent RNA-sequencing uncovered distinct gene clusters with heterogenous transcriptional responses to graded EF loss. Genes most sensitive to subtle EF depletion harbored GGAA microsatellites within EF-bound enhancers, while chromatin profiling uncovered candidate cofactors regulating EF-repressed EMP programs. Transient EF depletion followed by rapid restoration, modelling oncoprotein fluctuations
doi.org
February 21, 2026 at 8:07 AM