Endogenous EWSR1-FLI1 degron alleles enable control of fusion oncoprotein expression in tumor cell lines and xenografts

McGinnis, J. H.; Enriquez, A. B.; Vandiver, F.; Bai, X.; Kim, J.; Kilgore, J.; Saha, P.; O'Hara, R.; Xie, Y.; Banaszynski, L.; Williams, N. S.; McFadden, D. G.

doi:10.1101/2024.10.27.620498

bioRxiv · 10.1101/2024.10.27.620498

Endogenous EWSR1-FLI1 degron alleles enable control of fusion oncoprotein expression in tumor cell lines and xenografts

McGinnis, J. H.·Enriquez, A. B.·Vandiver, F.·Bai, X.·Kim, J.·Kilgore, J.·Saha, P.·O'Hara, R.·Xie, Y.·Banaszynski, L.·Williams, N. S.·McFadden, D. G.

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Abstract

Pediatric malignancies frequently harbor chromosomal translocations that induce expression of fusion oncoproteins. The EWSR1-FLI1 fusion oncoprotein acts as a neomorphic transcription factor and is the dominant genetic driver of Ewings sarcoma. Interrogation of the mechanisms by which EWSR1-FLI1 drives tumorigenesis has been limited by a lack of model systems to precisely and selectively control its expression in patient-derived cell lines and xenografts. Here, we report the generation of a panel of patient-derived EWS cell lines in which inducible protein degrons were engineered into the endogenous EWSR1-FLI1 locus. These alleles enabled rapid and efficient depletion of EWSR1-FLI1. Complete suppression of EWSR1-FLI1 induced a reversible cell cycle arrest at the G1-S checkpoint, and we identified a core set of transcripts downstream of EWSR1-FLI1 across multiple cell lines and degron systems. Additionally, depletion of EWSR1-FLI1 potently suppressed tumor growth in xenograft models validating efforts to directly target EWSR1-FLI1 in Ewings sarcoma.

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McGinnis, J. H., Enriquez, A. B., Vandiver, F., Bai, X., Kim, J., Kilgore, J., Saha, P., O'Hara, R., Xie, Y., Banaszynski, L., Williams, N. S., McFadden, D. G.. 2024-10-29. Endogenous EWSR1-FLI1 degron alleles enable control of fusion oncoprotein expression in tumor cell lines and xenografts. https://doi.org/10.1101/2024.10.27.620498

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