Small-Molecule Targeting of Brachyury Transcription Factor Addiction in Chordoma

Chordoma is a primary bone cancer for which there is no approved therapy1. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors. Here we describe the discovery of therapeutically targetable tumor dependencies in chordoma via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 are potent anti-proliferative agents in chordoma cells. In other cancer types, transcriptional CDK inhibitors have been observed to downregulate highly expressed and enhancer-associated oncogenic transcription factors. In chordoma, we find that the T gene is associated with a 1.5-megabase region containing “super-enhancers” and is the most highly expressed super-enhancer-associated transcription factor. Strikingly, transcriptional CDK inhibition leads to preferential and concentration-dependent downregulation of cellular brachyury protein levels in all chordoma models tested. In vivo, CDK7/12/13-inhibitor treatment significantly reduces chordoma tumor growth. Together, these data demonstrate successful small-molecule targeting of brachyury transcription factor addiction in chordoma, describe a newly identified mechanism of T gene regulation that underlies this therapeutic strategy, and provide a blueprint for applying systematic genetic and chemical screening approaches to identify vulnerabilities in genomically quiet cancers. Chordoma is a primary bone cancer with no approved therapy. The identification of therapeutic targets in this disease has been challenging due to the infrequent occurrence of clinically actionable somatic mutations in chordoma tumors. Here we describe the discovery of therapeutically targetable chordoma dependencies via genome-scale CRISPR-Cas9 screening and focused small-molecule sensitivity profiling. These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation. In other cancer types, transcriptional CDK inhibitors have been observed to down