Selective Inhibition of the m6a RNA Reader, YTHDC1, As a Novel Therapeutic Strategy for MYC-Driven Acute Myeloid Leukemia
Authors: Arora Mansi , Centore Richard , Charles Mark , Chen Yiwen , Watson Matthew , Czekalska Magdalena , Rebmann Marius , Ghandi Mahmoud , Cattin Jerome , Bharatham Nagakumar , Radhakrishnan Prathima , Howarth Alexander , Arter William E , Qamar Seema , Andraghetti Laura , Saar Kadi , Seeber Andrew , Kharas Michael G. , Kulander Martin , Knowles Tuomas , Arora Shilpi 
Published: December 2024

YTHDC1, a prominent m6A RNA epigenetic reader, has emerged as an important target in acute myeloid leukemia (AML) (Cheng et al. 2020, Cancer Cell). YTHDC1 resides within the nucleus, where it is involved in regulating multiple stages of nuclear mRNA processing, including splicing, nuclear export, as well as stability. In AML, YTHDC1 localizes with m6A-marked RNAs in phase-separated assemblies, termed biomolecular condensates, which stabilize oncogenic transcripts such as MYC and BCL2, promoting proliferation, differentiation, and survival of the leukemic cells.
Given the oncogenic role of YTHDC1 in AML, we embarked on a YTHDC1 small molecule inhibitor program with a goal to target MYC-driven cancers. Utilizing our understanding of YTHDC1 condensate behavior alongside our drug discovery expertise, we have identified a series of highly selective YTHDC1 inhibitors that interfere with its interaction with m6A-marked oncogenic RNAs and preclude its phase separation at nanomolar potencies in biochemical and cellular assays. Our inhibitors result in dissolution of YTHDC1 condensates in disease relevant cancer cells in a dose dependent manner. Notably, these inhibitors display exquisite selectivity for YTHDC1 among other YTH family members and exhibit selectivity in dissolving YTHDC1 condensates over other nuclear and cytosolic condensates.
Dissolution of YTHDC1 condensates leads to suppressed oncogenic gene expression, proliferation defects, and induced differentiation and apoptosis in multiple cell models of AML. Compared to the anti-proliferative effects of YTHDC1 inhibition on AML cells, our inhibitors have little effect on the proliferation of primary or immortalized non-cancer cells. Consistent with the role for YTHDC1 in regulating oncogenic gene expression, treatment of AML cells with YTHDC1 inhibitors results in time- and dose-dependent reduction of MYC expression. This is accompanied by reduced expression of MYC pathway genes across multiple cancer cell lines, as assessed by GSEA analyses of RNA-seq data following YTHDC1 inhibition.
Our optimized chemical matter have suitable ADME and PK properties and are well-tolerated, supporting evaluation of efficacy in vivo. Treatment of mice bearing MOLM13 or MV411 AML xenografts with our YTHDC1 inhibitors leads to potent tumor growth inhibition and prolonged survival compared to vehicle-treated control groups. In vivo data demonstrates a good PK/PD/ efficacy correlation. Gene expression profiling of MOLM13 tumors also demonstrate inhibition of MYC target gene sets among the most significant changes upon dosing with YTHDC1 inhibitor. Overall, our data suggests that pharmacological inhibition of YTHDC1 condensates utilizing our optimized small molecule inhibitors presents a viable strategy for treatment of MYC-driven AML.