Transcriptional profiling of SF295 cells following MTF1 knockout by CRISPR/Cas9

SF295 glioblastoma cells were subjected to CRISPR/Cas9-mediated knockout of the MTF1 (metal regulatory transcription factor 1) gene or non-targeted control (GFP). Two guides targeting MTF1 and one guide targeting GFP were cloned into the pXPR_023 all-in-one CRISPR/Cas9 vector. SF295 cells were transduced by lentiviral infection and selected using puromycin. Following selection, RNA was harvested from cell lines growing in culture. Wild-type SF295 cells were also included as a control. Anti-cancer uses of non-oncology drugs have been found on occasion, but such discoveries have been serendipitous and rare. To fully discover activity against multiple tumor types, resource-intensive screening across hundreds of cancer cell lines is needed. We sought to create a public resource containing the growth inhibitory activity of 4,518 drugs tested across 578 human cancer cell lines. To accomplish this, we used PRISM, which involves the molecular barcoding of each cell line, followed by pooling of the barcoded lines. Relative barcode abundance following drug treatment versus controls thus reflects cell viability following drug treatment. We found that an unexpectedly large number of non-oncology drugs selectively inhibited subsets of cancer cell lines. Moreover, the killing activity of the majority of these drugs was predictable based on the molecular features of the cell lines. Mechanistic follow-up of several of these compounds revealed novel mechanisms. These results illustrate the potential of the PRISM drug repurposing resource as a starting point for new oncology therapeutic development. Overall design: Eleven biological samples are included in the study. SF295 wild-type cells (control, duplicate), SF295 GFP sg1 (non-targeting guide control, triplicate), SF295 MTF1 sg1 (triplicate), and SF295 MTF1 sg2 (triplicate).