Abstract 3231: Pharmacological inhibition of the m6A RNA reader, YTHDC1, as a novel approach to targeting biomolecular condensates in cancer
Authors: Centore Richard C. , Charles Mark , Arora Mansi , Chen Yiwen , Watson Matthew , Kelley Charlotte , Czekalska Magdalena , Rebmann Marius , Ghandi Mahmoud , Cattin Jerome , Bharatham Nagakumar , Radhakrishnan Prathima , Howarth Alex , Rudlaff Gale , Arter William E. , Qamar Seema , Saar Kadi , Williamson Douglas , Seeber Andrew , Knowles Tuomas , Arora Shilpi 
Published: March 2024

Epigenetic dysregulation is a hallmark of cancer, and tumors have evolved complex mechanisms to fine-tune oncogenic gene expression. In acute myeloid leukemia (AML), one such regulatory mechanism involves post transcriptional modification of RNAs. The most abundant post transcriptional modification is methylation of adenosine at the N6 position (m6A). This modification is catalyzed by the m6A “writer”, METTL3 and METTL14 complex, and is removed by “erasers” such as FTO and ALKBH5. m6A RNAs can regulate a variety of cellular processes which can impact tumor phenotypes, including RNA stability, splicing, and nuclear export; and METTL3 catalytic inhibitors are currently in clinical development for AML and other cancers (NCT05584111).The m6A “reader”, YTHDC1, has been recognized as a critical contributor to the proliferation and survival of AML cells. As the primary nuclear m6A reader, YTHDC1 localizes with m6A marked RNAs in phase-separated assemblies, termed biomolecular condensates, helping to maintain the stability of oncogenic transcripts such as MYC. Here, we have employed our proprietary microfluidics based screening platform (termed PhaseScanTM) to identify modulators of YTHDC1 biomolecular condensates. Evaluation of early screening hits helped identify that disruption of the interaction between YTHDC1 and m6A RNA is a functionally relevant mechanism of action (MoA) that results in dissolution of YTHDC1 condensates. Using computational and knowledge based approaches, we have identified other structurally distinct inhibitors that occupy the RNA binding pocket of YTHDC1 and disrupt its interaction with m6A RNA at nanomolar potencies. These compounds disrupt cellular YTHDC1 condensates, suppress oncogenic gene expression, and result in anti proliferative and pro-differentiation phenotypes in AML cell lines. Compounds are selective for YTHDC1 over other YTH family members and are also selective in dissolving YTHDC1 condensates over other nuclear and cytosolic condensate systems. Our optimized chemical matter has suitable ADME properties to support in vivo studies. Thus, targeting YTHDC1 biomolecular condensates represents a novel approach to the treatment of AML.

Citation Format: Richard C. Centore, Mark Charles, Mansi Arora, Yiwen Chen, Matthew Watson, Charlotte Kelley, Magdalena Czekalska, Marius Rebmann, Mahmoud Ghandi, Jerome Cattin, Nagakumar Bharatham, Prathima Radhakrishnan, Alex Howarth, Gale Rudlaff, William E. Arter, Seema Qamar, Kadi Saar, Douglas Williamson, Andrew Seeber, Tuomas Knowles, Shilpi Arora. Pharmacological inhibition of the m6A RNA reader, YTHDC1, as a novel approach to targeting biomolecular condensates in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3231.