High-Throughput Screening of Epigenetic Inhibitors in Chordoma and Chondrosarcoma

Background: Chordoma and chondrosarcoma are rare tumors of the central nervous system. Once thought of as related tumors, genetic and molecular profiling has resulted in their independent classification. Chordomas have a 5-year survival rate of 61%, while chondrosarcoma have 5-year survival rates of 29 to 90% depending on grade. Adjuvant therapy for chordomas and CNS chondrosarcoma are highly debated. The poor patient outcomes and lack of therapeutic options for these patients require additional research to identify novel therapies to treat these tumors. Some genetic studies have found a high incidence of mutations in epigenetic and cell cycle genes, suggesting epigenetic dysregulation may play a role in these diseases and offer a therapeutic target. We sought to address the need for additional therapies for these tumors by profiling their sensitivity to epigenetic inhibition.

Methods: One chondrosarcoma and two chordomas were resected and collected via our neural tissue bank. Four chordoma cell lines were provided by the Chordoma Foundation. We screened the tumors using the Caymen Chemical Epigenetic Inhibitor Library. Drugs were dosed at a concentration of 5 μm in triplicate, and cell viability was assay 72 hours later via MTS. Any compound that significantly reduced cell viability compared with an untreated control was considered for further evaluation.

Results: One chondrosarcoma and six chordomas were screened in this study. Notably, we are actively screening additional chordoma cell lines from the Chordoma Foundation. Chordoma and chondrosarcoma have nonoverlapping drug sensitivity profiles, further marking the differences between these tumors. The chondrosarcoma was sensitive to inhibition of bromodomain (BET) proteins, Jumonji domains, and DNA methyltransferase activity by OTX015, JIB-04, and SGI102, respectively. No single agent was able to significantly reduce chordoma viability across all tumors; however, four of the six tumors were sensitive to histone deacetylase (HDAC) inhibition by HC toxin or panobinostat, and three tumors were sensitive to G9a inhibition by UNC0631 or BIX01294. G9a regulates Histone-Three-Lysine-residue-9 (H3K9) methylation. One of the chordomas was sensitive to both HDAC and G9a inhibition. Collectively, inhibition of HDAC activity and G9a has potential as a treatment for patients with chordoma.

Conclusion: Chordoma and chondrosarcoma have unrelated sensitivity profiles to epigenetic inhibition, although both tumors have the potential to be treated via inhibition of epigenetic mechanisms. Chordoma are sensitive to HDAC and G9a inhibition, suggesting a combinatorial treatment may be beneficial to patients with chordoma.