Chordoma preclinical models exhibit resistance to BAF complex inhibitor FHD-286, alone or in combination with gemcitabine

To evaluate BRG1(SMARCA4)/BRM(SMARCA2) as a potential therapeutic target, chordoma cell lines were treated with FHD-286. A panel of 4 chordoma cell lines were seeded in a white-walled 96-well plate so that at the start of treatment, 36 hours after plating, the confluence was 15%. The assay endpoint for each cell line was the amount of time for untreated cells to reach 80-90% confluence. Cell line-specific seeding densities and assay durations can be found through the link at the bottom of this page. CH22, UM-Chor1, U-CHCF365, and U-CH2 cell lines were plated in 100uL of (4:1) IMDM:RPMI 1640 + 10% FBS + 1% NEAA + 1% GlutaMAX. Cells were treated in triplicate with a 3-fold serial dilution of each drug with a top concentration of 5 uM to the lowest concentration of 0.762 nM. At the assay endpoint, cell viability was measured using CellTiter-Glo 2.0 Cell Viability Assay. Representative dose-response curves of the mean +/- the standard deviation are shown. The data was normalized to the DMSO-only control. Experiments for treatment with FHD-286 were repeated in all lines to ensure reproducibility. The absolute EC50 of all lines toward the single agent FHD-286 was >1 uM.To evaluate if exacerbating replication stress induces sensitivity to BAF complex inhibition, cells were plated as noted above except for the addition of either 2.5 nM gemcitabine to CH22 and U-CHCF365 and 25 nM gemcitabine to U-CH2 and UM-Chor1 to the FHD-286 titration. The FHD-286 titration + gemcitabine addition was normalized to the gemcitabine only treatment instead of to the DMSO only control. Gemcitabine did not significantly increase sensitivity to FHD-286.