Abstract 6355: A characterisation of direct and indirect transcription factor inhibition to target brachyury in chordoma (2022)

Abstract Dysregulated gene programs are a hallmark of cancer, and oncogenic transcription factors (TFs) have emerged as key players that contribute to this cell state. Chordoma is a rare cancer derived from deregulation of the TF brachyury (encoded by the T gene). While brachyury is normally turned off in development and is minimally expressed in healthy tissues, it remains highly expressed and is required in chordoma. TFs like brachyury have been challenging to drug directly, and chordoma represents an ideal system for studying both the biology behind a transcriptional dependency in cancer and how it can therapeutically targeted. Given that chordomas lack targeted therapies, we aim to understand the role of brachyury in the disease, identify therapeutic strategies to target its genetic regulation, and ultimately translate these findings towards the clinic. To achieve this, we sought to compare the consequences of direct and indirect brachyury targeting via targeted protein degradation and transcriptional CDK inhibition. In the absence of a brachyury small molecule, we generated human chordoma cell lines that express only a degradable form of brachyury. With these cell lines, we have mapped the brachyury regulome and have used high resolution microscopy to visualise brachyury genetic regulation. We find that brachyury is an ultra-selective regulator in chordoma, and that brachyury autoregulates through a transcriptional condensate. Both targeted brachyury degradation and transcriptional inhibition with THZ1, a preclinical tool compound inhibiting CDKs 7/12/13, can selectively inhibit T transcription and disrupt the brachyury transcriptional condensate. While these direct and indirect approaches converge to target brachyury, they have distinct phenotypic outcomes; brachyury degradation induces senescence and transcriptional inhibition causes apoptosis. Specifically, brachyury degradation primes cells to treatment with senolytics, which selectively kill senescent chordoma cells. Targeting senescence represents a novel therapeutic strategy in chordoma. Our findings affirm that brachyury is the most promising target in chordoma. We show that while transcriptional inhibition can selectively target brachyury, it mechanistically it contrasts with direct brachyury inhibition. However, these dual therapeutic strategies show that is indeed possible to progress in targeting oncoproteins that have long been considered “undruggable”, and our efforts not only benefit chordoma patients but provide a framework for drugging other transcriptionally addicted cancers. Citation Format: Hadley E. Sheppard, Alessandra Dall’Agnese, Woojun D. Park, M. Shamim Shamim, Julien Dubrulle, Hannah L. Johnson, Fabio Stossi, Josh Sommer, Joan Levy, Tanaz Sharifnia, Mathias Wawer, Behnam Nabet, Paul A. Clemons, Stuart L. Schreiber, Paul Clarke, Rick Young, Charles Y. Lin, Paul Workman. A characterisation of direct and indirect transcription factor inhibition to target brachyury in chordoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6355.