Differential Epigenetic Effects of BMI Inhibitor PTC-028 on Fusion-Positive Rhabdomyosarcoma Cell Lines from Distinct Metastatic Sites

• Published in: Regenerative engineering and translational medicine 2022-09, Vol.8 (3), p.446-455
• Main Authors: Shields, Cara E., Schnepp, Robert W., Haynes, Karmella A.
• Format: Article
• Language: English
• Subjects: AfroBiotech 2020 Topical Edition; Biomaterials; Biomedical Engineering and Bioengineering; Biosynthesis; Cancer; Cell cycle; Chemistry and Materials Science; Cholesterol; Encyclopedias; Epigenetics; Gene expression; Gene sequencing; Genes; Genomes; Heterogeneity; Kinases; Materials Science; Original Research; Pediatrics; Proteins; Regenerative Medicine/Tissue Engineering; Ribonucleic acid; RNA
• ISSN: 2364-4133; 2364-4141
• DOI: 10.1007/s40883-021-00244-9

Purpose This study aims to deepen our understanding of the novel potential therapeutic target BMI1 (B lymphoma Mo-MLV insert region 1 homolog) in the rare pediatric cancer fusion-positive rhabdomyosarcoma (FP-RMS) and identify gene expression changes that may underlie the loss of cell viability and proliferation that were induced by genetic and pharmacological inhibition of BMI1 in our previous study. Methods FP-RMS cell lines Rh28 and Rh30 were treated with DMSO (vehicle control) or PTC-028, a BMI1 inhibitor, and RNA was collected after 24 or 48 h from three biological replicates. RNA-seq was performed, and differentially expressed gene sets were analyzed by Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment, and OncoPPi protein–protein interaction data. Results Many differentially expressed genes in Rh28 and Rh30 belonged to common pathways including downregulation of cell cycle progression, the DNA damage response, and cholesterol biosynthesis. In Rh30 + PTC-028, the majority of the differentially expressed TEAD-motif-containing, Hippo-regulated genes became downregulated. We identified two potential kinases of LATS1/2, EPHA2 and PDGFRA, that become upregulated in PTC-028-treated Rh28 and Rh30 cells. Conclusion Expression profiling of FP-RMS-derived cell lines suggests that gene expression underlies heterogeneity of FP-RMS. In spite of this heterogeneity, epigenetic intervention through BMI1 elicits an anti-cancer response. Lay summary Rhabdomyosarcoma (RMS) is a rare pediatric cancer that afflicts hundreds of patients every year. Currently, there are no targeted therapies available for patients with RMS. Our previous work identified a druggable epigenetic protein, BMI1, as a potential therapeutic target. In this study, we investigate the influence of BMI1 inhibitor PTC-028 on developmental pathways and cellular processes through RNA-sequencing. We show that BMI1 inhibition elicits both overlapping and distinct responses in RMS cell lines, indicating inherent differences in these cell lines, though BMI1 inhibition remains an effective therapy. Future works should include epigenetic profiling and additional cell lines and/or patient samples to further understand the influence of BMI1 inhibition in RMS cells.