Therapeutic Targeting of KDM1A/LSD1 in Ewing Sarcoma with SP-2509 Engages the Endoplasmic Reticulum Stress Response

Abstract

Multi-agent chemotherapeutic regimes remain the cornerstone treatment for Ewing sarcoma, the second most common bone malignancy diagnosed in pediatric and young adolescent populations. We have reached a therapeutic ceiling with conventional cytotoxic agents, highlighting the need to adopt novel approaches that specifically target the drivers of Ewing sarcoma oncogenesis. As KDM1A/<u>l</u>ysine-<u>s</u>pecific <u>d</u>emethylase 1 (LSD1) is highly expressed in Ewing sarcoma cell lines and tumors, with elevated expression levels associated with worse overall survival (<i>P</i> = 0.033), this study has examined biomarkers of sensitivity and mechanisms of cytotoxicity to targeted <i>KDM1A</i> inhibition using SP-2509 (reversible <i>KDM1A</i> inhibitor). We report, that innate resistance to SP-2509 was not observed in our Ewing sarcoma cell line cohort (<i>n</i> = 17; IC₅₀ range, 81 -1,593 nmol/L), in contrast resistance to the next-generation <i>KDM1A</i> irreversible inhibitor GSK-LSD1 was observed across multiple cell lines (IC₅₀ > 300 μmol/L). Although <i>TP53/STAG2/CDKN2A</i> status and basal KDM1A mRNA and protein levels did not correlate with SP-2509 response, induction of KDM1B following SP-2509 treatment was strongly associated with SP-2509 hypersensitivity. We show that the transcriptional profile driven by SP-2509 strongly mirrors <i>KDM1A</i> genetic depletion. Mechanistically, RNA-seq analysis revealed that SP-2509 imparts robust apoptosis through engagement of the endoplasmic reticulum stress pathway. In addition, <i>ETS1/HIST1H2BM</i> were specifically induced/repressed, respectively following SP-2509 treatment only in our hypersensitive cell lines. Together, our findings provide key insights into the mechanisms of SP-2509 cytotoxicity as well as biomarkers that can be used to predict <i>KDM1A</i> inhibitor sensitivity in Ewing sarcoma. <i>Mol Cancer Ther; 17(9); 1902-16. ©2018 AACR</i>.