KDM3B inhibitors disrupt the oncogenic activity of PAX3-FOXO1 in fusion-positive rhabdomyosarcoma
Yong Kim, Berkley E. Gryder, Ranuka Sinniah, Megan L. Peach, Jack F. Shern, Abdalla Abdelmaksoud, Silvia Pomella, Girma M. Woldemichael, Benjamin Z. Stanton, David Milewski, Joseph J. Barchi, John S. Schneekloth, Raj Chari, Joshua T. Kowalczyk, Shilpa R. Shenoy, Jason R. Evans, Young Song, Chaoyu Wang, Xinyu Wen, Hsien-Chao Chou, Vineela Gangalapudi, Dominic Esposito, Jane Jones, Lauren Procter, Maura O’Neill, Lisa M. Jenkins, Nadya I. Tarasova, Jun S. Wei, James B. McMahon, Barry R. O’Keefe, Robert G. Hawley, Javed Khan
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS) is an aggressive pediatric sarcoma driven primarily by the PAX3-FOXO1 fusion oncogene, for which therapies targeting PAX3-FOXO1 are lacking. Here, we screen 62,643 compounds using an engineered cell line that monitors PAX3-FOXO1 transcriptional activity identifying a hitherto uncharacterized compound, P3FI-63. RNA-seq, ATAC-seq, and docking analyses implicate histone lysine demethylases (KDMs) as its targets. Enzymatic assays confirm the inhibition of multiple KDMs with the highest selectivity for KDM3B. Structural similarity search of P3FI-63 identifies P3FI-90 with improved solubility and potency. Biophysical binding of P3FI-90 to KDM3B is demonstrated using NMR and SPR. P3FI-90 suppresses the growth of FP-RMS in vitro and in vivo through downregulating PAX3-FOXO1 activity, and combined knockdown of KDM3B and KDM1A phenocopies P3FI-90 effects. Thus, we report KDM inhibitors P3FI-63 and P3FI-90 with the highest specificity for KDM3B. Their potent suppression of PAX3-FOXO1 activity indicates a possible therapeutic approach for FP-RMS and other transcriptionally addicted cancers.