DOT1L inhibitors block abnormal self-renewal induced by cohesin loss

Katelyn E Heimbruch,Nan Zhu,John Anto Pulikkan,Jessica J Loppnow,Alison E Meyer,Emily Phillips,Sridhar Rao,Kirthi Pulakanti,Michael H Reimer,Joseph B Fisher,Ross L Levine,Adam J Wargolet,Cary T Stelloh,Aaron D Viny

doi:10.1038/s41598-021-86646-9

Abstract

Acute myeloid leukemia (AML) is a high-risk malignancy characterized by a diverse spectrum of somatic genetic alterations. The mechanisms by which these mutations contribute to leukemia development and how this informs the use of targeted therapies is critical to improving outcomes for patients. Importantly, how to target loss-of-function mutations has been a critical challenge in precision medicine. Heterozygous inactivating mutations in cohesin complex genes contribute to AML in adults by increasing the self-renewal capacity of hematopoietic stem and progenitor cells (HSPCs) by altering PRC2 targeting to induce HOXA9 expression, a key self-renewal transcription factor. Here we sought to delineate the epigenetic mechanism underpinning the enhanced self-renewal conferred by cohesin-haploinsufficiency. First, given the substantial difference in the mutational spectrum between pediatric and adult AML patients, we first sought to identify if HOXA9 was also elevated in children. Next, using primary HSPCs as a model we demonstrate that abnormal self-renewal due to cohesin loss is blocked by DOT1L inhibition. In cohesin-depleted cells, DOT1L inhibition is associated with H3K79me2 depletion and a concomitant increase in H3K27me3. Importantly, we find that there are cohesin-dependent gene expression changes that promote a leukemic profile, including HoxA overexpression, that are preferentially reversed by DOT1L inhibition. Our data further characterize how cohesin mutations contribute to AML development, identifying DOT1L as a potential therapeutic target for adult and pediatric AML patients harboring cohesin mutations.

Highlights

Acute myeloid leukemia (AML) is a high-risk malignancy characterized by a diverse spectrum of somatic genetic alterations
It is not known whether HOXA9 upregulation can be identified in pediatric AML and given the significant genetic differences known to exist between adult and pediatric disease[15], determining whether HOXA9 upregulation is a common occurrence in pediatric disease could inform whether treatment strategies identified targeting HOXA9 overexpression could be applicable for use in both pediatric and adult disease
Our group reported that cohesin interacts with the Polycomb Repressive Complex 2 (PRC2) through CTCF and is necessary for proper silencing via trimethylation of H3K27 of the hematopoietic self-renewal transcription factors (TFs) HoxA7 and HoxA911,22

Summary

Introduction

Acute myeloid leukemia (AML) is a high-risk malignancy characterized by a diverse spectrum of somatic genetic alterations. Heterozygous inactivating mutations in cohesin complex genes contribute to AML in adults by increasing the self-renewal capacity of hematopoietic stem and progenitor cells (HSPCs) by altering PRC2 targeting to induce HOXA9 expression, a key self-renewal transcription factor. Other studies demonstrated that haploinsufficiency of individual cohesin genes induces genome-wide changes in chromatin accessibility, resulting in an enrichment for binding sites of myeloid and hematopoietic stem and progenitor (HSPC) self-renewal TFs such as ERG, RUNX1, and GATA2, and STAT58–10. These proposed mechanisms are distinct, collectively they conclude that disrupting cohesin function in HSPCs confers enhanced self-renewal by altering gene expression[21,26,27]. Inhibition of DOT1L in cohesin-depleted murine HSPCs restores normal self-renewal and gene expression, warranting future studies investigating the potential of DOT1L as a therapeutic target for cohesin-mutated AML

Methods

Results

Conclusion