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/ysine-pecific emethylase 1 (LSD1) is highly expressed in Ewing sarcoma cell lines and tumors, with elevated expression levels associated with worse overall survival ( = 0.033), this study has examined biomarkers of sensitivity and mechanisms of cytotoxicity to targeted inhibition using SP-2509 (reversible inhibitor). We report, that innate resistance to SP-2509 was not observed in our Ewing sarcoma cell line cohort ( = 17; IC range, 81 -1,593 nmol/L), in contrast resistance to the next-generation irreversible inhibitor GSK-LSD1 was observed across multiple cell lines (IC > 300 μmol/L). Although 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 genetic depletion. Mechanistically, RNA-seq analysis revealed that SP-2509 imparts robust apoptosis through engagement of the endoplasmic reticulum stress pathway. In addition, 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 inhibitor sensitivity in Ewing sarcoma. .

Catalytic inhibition of KDM1A in Ewing sarcoma is insufficient as a therapeutic strategy

“…14,35 Importantly, in solid tumors, high levels of KDM1A have been associated with metastasis, and inhibition of this demethylase has been shown to attenuate migration and invasion in breast cancer cell lines. 30 38 The discrepancy between our results through inhibition of KDM1A catalytic function and knockdown of the multidomain protein strongly suggests a noncanonical role for KDM1A, independent from its demethylase function.…”

“…This suggests catalytic activity of KDM1A may not contribute to establishing EWS‐FLI1's transcriptional program. Recent findings showed that shRNA‐mediated depletion of KDM1A in Ewing sarcoma cells resulted in severe growth impairment and cell death, confirming their dependency on this demethylase . The discrepancy between our results through inhibition of KDM1A catalytic function and knockdown of the multidomain protein strongly suggests a noncanonical role for KDM1A, independent from its demethylase function.…”

Antiviral Properties of the LSD1 Inhibitor SP-2509

“…In contrast, SP-2509 is over 7,000-fold more selective for LSD1 over MAO-A and MAO-B and is reversible ( 36 ). SP-2509 has been investigated for use as an anti-cancer drug against cancers with high LSD1 expression and poor prognosis, including acute myeloid leukemia ( 36 ), Ewing sarcoma ( 43 ), and advanced prostate cancer ( 37 ). Therefore, SP-2509 or its derivatives may be good candidates for antiviral therapy in the future, especially to treat ACV-resistant strains.…”

A Nonpediatric Extraosseous Ewing Sarcoma of the Pancreas: Differential Diagnosis and Therapeutic Strategies

“…TK216 is a novel small-molecule that directly binds to EWS-FLI1 and inhibits its function by blocking binding to RNA helicase A. TK216 demonstrates potent antiproliferative effects on ES cell lines and xenografts and is currently being tested in clinical trials [24]. Another exciting target is the enzyme lysine-specific demethylase 1 (LSD1) which is highly expressed in ES cell lines, and inhibitors of LSD1 could offer a ray of hope against this lethal disease [25]. In preclinical studies, it has been shown that focal adhesion kinase (FAK) inhibitors and Aurora kinase B inhibitors synergistically impair Ewing sarcoma cell growth and significantly inhibit tumor progression; this treatment approach needs to be validated in clinical trials [26].…”