Global transcriptional responses to KI-MS2-008 treatment and Myc inactivation via doxycycline addition

The Myc/Max heterodimer has crucial roles in normal cellular processes such as cell proliferation, metabolism, apoptosis, and differentiation, but its activity is often deregulated in a majority of human cancers. In an effort to explore alternative modes of Myc perturbation, we identified KI-MS2-008 as a small molecule that binds Max and modulates Myc-driven transcription, and in some cellular contexts, KI-MS2-008 treatment leads to a decrease in c-Myc protein levels. As the Myc/Max heterodimer controls many cellular processes, we expected that treatment with this small molecule would cause changes in the transcriptome. We found that treatment with 10 µM KI-MS2-008 resulted in global alterations in the transcriptome, mimicking direct Myc inactivation with doxycycline in P493-6, a B cell line with a Tet-Off system for c-Myc expression. We also discovered enrichment of various Myc target gene sets in the genes downregulated in response to KI-MS2-008 treatment in P493-6 cells. This trend was also observed in ST486 cells, but not in P3HR1 cells, which were chosen as non-engineered B cell lines that were sensitive and insensitive, respectively, toward KI-MS2-008 in cell viability assays. Overall design: RNA-seq characterizing three B cell lines: P493-6 (an engineered, KI-MS2-008 sensitive cell line), ST486 (a non-engineered, KI-MS2-008 sensitive cell line), and P3HR1 (a non-engineered, KI-MS2-008 insensitive cell line). P493-6 cells were treated with 0.1 µg/mL doxycycline, 1 µM KI-MS2-008, 10 µM KI-MS2-008, or 0.4% DMSO for 45 minutes or 8 hours. ST486 cells were treated with 1 µM KI-MS2-008, 10 µM KI-MS2-008 or 0.4% DMSO for 45 minutes or 8 hours. P3HR1 cells were treated with 10 µM KI-MS2-008 or 0.4% DMSO for 8 hours. 4 replicates were performed for each condition.

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Struntz NB, Chen A, Deutzmann A, Wilson RM, Stefan E, Evans HL, Ramirez MA, Liang T, Caballero F, Wildschut MHE, Neel DV, Freeman DB, Pop MS, McConkey M, Muller S, Curtin BH, Tseng H, Frombach KR, Butty VL, Levine SS, Feau C, Elmiligy S, Hong JA, Lewis TA, Vetere A, Clemons PA, Malstrom SE, Ebert BL, Lin CY, Felsher DW, Koehler AN