MS0621, a novel small-molecule modulator of Ewing sarcoma chromatin accessibility, interacts with an RNA-associated macromolecular complex and influences RNA splicing

Tamara Vital; Aminah Wali; Kyle V Butler; Yan Xiong; Joseph P Foster 2nd; Shelsa S Marcel; Andrew W McFadden; Valerie U Nguyen; Benton M Bailey; Kelsey N Lamb; Lindsey I James; Stephen V Frye; Amber L Mosely; Jian Jin; Samantha G Pattenden; Ian J Davis

doi:10.3389/fonc.2023.1099550

MS0621, a novel small-molecule modulator of Ewing sarcoma chromatin accessibility, interacts with an RNA-associated macromolecular complex and influences RNA splicing

Front Oncol. 2023 Jan 30:13:1099550. doi: 10.3389/fonc.2023.1099550. eCollection 2023.

Authors

Tamara Vital^{1

2}, Aminah Wali^{1

2}, Kyle V Butler^{3

4

5}, Yan Xiong^{3

4

5}, Joseph P Foster 2nd^{2

6}, Shelsa S Marcel^{2

6}, Andrew W McFadden⁷, Valerie U Nguyen⁷, Benton M Bailey⁷, Kelsey N Lamb⁸, Lindsey I James^{7

8}, Stephen V Frye^{7

8}, Amber L Mosely^{9

10}, Jian Jin^{3

4

5}, Samantha G Pattenden^{7

8}, Ian J Davis^{2

7

11}

Affiliations

¹ Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
² Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
³ Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
⁴ Mount Sinai Center for Therapeutics Discovery, Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
⁵ Mount Sinai Center for Therapeutics Discovery, Department of Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
⁶ Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
⁷ Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
⁸ Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
⁹ Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States.
¹⁰ Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States.
¹¹ Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.

Abstract

Ewing sarcoma is a cancer of children and young adults characterized by the critical translocation-associated fusion oncoprotein EWSR1::FLI1. EWSR1::FLI1 targets characteristic genetic loci where it mediates aberrant chromatin and the establishment of de novo enhancers. Ewing sarcoma thus provides a model to interrogate mechanisms underlying chromatin dysregulation in tumorigenesis. Previously, we developed a high-throughput chromatin-based screening platform based on the de novo enhancers and demonstrated its utility in identifying small molecules capable of altering chromatin accessibility. Here, we report the identification of MS0621, a molecule with previously uncharacterized mechanism of action, as a small molecule modulator of chromatin state at sites of aberrant chromatin accessibility at EWSR1::FLI1-bound loci. MS0621 suppresses cellular proliferation of Ewing sarcoma cell lines by cell cycle arrest. Proteomic studies demonstrate that MS0621 associates with EWSR1::FLI1, RNA binding and splicing proteins, as well as chromatin regulatory proteins. Surprisingly, interactions with chromatin and many RNA-binding proteins, including EWSR1::FLI1 and its known interactors, were RNA-independent. Our findings suggest that MS0621 affects EWSR1::FLI1-mediated chromatin activity by interacting with and altering the activity of RNA splicing machinery and chromatin modulating factors. Genetic modulation of these proteins similarly inhibits proliferation and alters chromatin in Ewing sarcoma cells. The use of an oncogene-associated chromatin signature as a target allows for a direct approach to screen for unrecognized modulators of epigenetic machinery and provides a framework for using chromatin-based assays for future therapeutic discovery efforts.

Keywords: Ewing sarcoma (ES); RNA-binding proteins; RNA-processing; SWI/SNF (BAF) complex; chromatin; drug discovery.

Abstract

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