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bioRxiv · 10.1101/2025.05.16.654522

Fusion transcription factor dosage controls cell state in rhabdomyosarcoma

Hoffman, R. A.·Wang, M.·Sunkel, B. D.·Nguyen, T. H.·Lopez-Nava, J.·Chatterjee, B.·Sun, W.·Barr, F. G.·Stanton, B. Z.
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Abstract

In the fusion-positive subset of rhabdomyosarcoma, the PAX3::FOXO1 oncoprotein is the most common fusion driver. We previously established a human myoblast system for inducible expression of PAX3::FOXO1. In the current study, we modulate PAX3::FOXO1 protein expression to understand the epigenetic and phenotypic functions at different PAX3::FOXO1 levels. Proliferative and oncogenic outcomes depend on PAX3::FOXO1 dosage in this system with transformation dominant at intermediate levels and growth suppression dominant at high levels. After prolonged PAX3::FOXO1 expression, there is dosage-dependent heterogeneity in single cell gene expression profiles. We observe a dosage-specific effect for PAX3::FOXO1 chromatin recognition and identify factors that modulate PAX3::FOXO1 chromatin binding. PAX3::FOXO1 dosage affects expression signatures related to cell cycle, epithelial-mesenchymal transition, and myogenesis. Whereas intermediate PAX3::FOXO1 expression maximizes chromatin binding to modulate gene expression, high PAX3::FOXO1 expression alters S phase progression and increases accessibility behind the replication fork. We conclude that PAX3::FOXO1 exerts dosage-dependent functions to influence epigenetic heterogeneity in fusion-positive rhabdomyosarcoma.

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Hoffman, R. A., Wang, M., Sunkel, B. D., Nguyen, T. H., Lopez-Nava, J., Chatterjee, B., Sun, W., Barr, F. G., Stanton, B. Z.. 2025-05-21. Fusion transcription factor dosage controls cell state in rhabdomyosarcoma. https://doi.org/10.1101/2025.05.16.654522

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