Abstract 1949: A compound screen reveals potential novel therapeutic targets for chordoma: Metabolic stress response and epigenetic control of brachyury
Authors: Cottone Lucia , Hookway Edward , Wells Graham , Ligammari Lorena , Lombard Patrick , Mazitschek Ralph , Sommer Josh , Oppermann Udo , Flanagan Adrienne M. 
Published: August 2018

Abstract
Chordoma is a rare bone cancer, showing notochordal differentiation, that develops in axial skeleton in adults and children. Patients have a median survival of 7 years and radical surgical resection is the main treatment for this morbid disease, which does not respond to cytotoxic chemotherapy. We have previously demonstrated that EGFR inhibitors represent the almost unique family of kinase inhibitors to exert an effect on chordoma cell lines proliferation. However not all cell lines respond to these agents and drug resistance is likely to occur. Genomic studies have revealed that chordomas do not harbor recurrent alterations in kinases whereas chromatin-remodelling genes are altered in at least 20% of cases. The transcription factor brachyury (T) is the diagnostic hallmark of chordoma and is strongly implicated in its pathogenesis. T is regulated during embryonic development at the epigenetic level, suggesting that epigenetic inhibitors may represent a novel therapeutic approach for this disease. In this study, we have undertaken a medium throughput focused compound screen (n=91) using validated small molecule inhibitors of enzymes involved in chromatin biology and metabolic pathways. The alamar blue assay was employed to assess cell viability. Screening revealed activity in a number of compounds targeting the jumonji domain-containing lysine demethylases, including GSK-J4 and KDOBA67, two structurally closely related compounds that mainly target KDM6A (aka UTX) and KMD6B (JMJD3). These compounds were effective in all five chordoma cell lines (UCH1, UCH2, MUG-Chor, UM-Chor, UCH7) tested. In contrast to EGFR inhibitors, these compounds induced downregulation of T at the transcriptional and protein level. Preliminary results suggest this is achieved via the induction of a metabolic stress response as well as through the epigenetic regulation of T, the latter being brought by increased levels of H3K27me3. We also found that Halofuginone, a highly specific inhibitor of the enzyme glutamyl-prolyl tRNA synthetase already tested in phase I autoimmunity clinical trials, induced a metabolic stress response, similar to KDM6 inhibitors, in all chordoma cell lines. Moreover, Halofuginone treatment of a chordoma PDX model demonstrated 44% tumor growth inhibition (p=0.0052). In conclusion, we have identified epigenetic and metabolic pathways that represent potential novel targets for the treatment of chordoma.
Citation Format: Lucia Cottone, Edward Hookway, Graham Wells, Lorena Ligammari, Patrick Lombard, Ralph Mazitschek, Josh Sommer, Udo Oppermann, Adrienne M. Flanagan. A compound screen reveals potential novel therapeutic targets for chordoma: Metabolic stress response and epigenetic control of brachyury [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1949.