Loss-of-function mutations in the histone methyltransferase EZH2 promote chemotherapy resistance in AML

Julia Kempf ,Kerstin Völse,Maike Roas,Tobias Herold,Moreno Festini,Klaus H Metzeler,Gunnar Schotta,Manuela Scholz,Heinrich Leonhardt,Irmela Jeremias,Oliver Weigert,Binje Vick,Lucas E Wange,Sebastian Bultmann,Sabrina Weser,Michael D Bartoschek,Wolfgang Hiddemann,Raphael Mattes,Enes Ugur,Karsten Spiekermann

doi:10.1038/s41598-021-84708-6

Abstract

Chemotherapy resistance is the main impediment in the treatment of acute myeloid leukaemia (AML). Despite rapid advances, the various mechanisms inducing resistance development remain to be defined in detail. Here we report that loss-of-function mutations (LOF) in the histone methyltransferase EZH2 have the potential to confer resistance against the chemotherapeutic agent cytarabine. We identify seven distinct EZH2 mutations leading to loss of H3K27 trimethylation via multiple mechanisms. Analysis of matched diagnosis and relapse samples reveal a heterogenous regulation of EZH2 and a loss of EZH2 in 50% of patients. We confirm that loss of EZH2 induces resistance against cytarabine in the cell lines HEK293T and K562 as well as in a patient-derived xenograft model. Proteomics and transcriptomics analysis reveal that resistance is conferred by upregulation of multiple direct and indirect EZH2 target genes that are involved in apoptosis evasion, augmentation of proliferation and alteration of transmembrane transporter function. Our data indicate that loss of EZH2 results in upregulation of its target genes, providing the cell with a selective growth advantage, which mediates chemotherapy resistance.

Highlights

Acute myeloid leukaemia (AML) is a heterogeneous haematological malignancy, characterised by clonal expansion of abnormal, undifferentiated myeloid precursor cells
In our previous study[35], examining diagnosis/relapse pairs of 50 cytogenetically normal (CN) acute myeloid leukaemia (AML) patients, we found mutations in epigenetic modifiers, including Enhancer of zeste homolog 2 (EZH2), frequently gained at relapse, suggesting epigenetic mechanisms to be involved in disease progression in a subset of patients
We found EZH2 loss-of-function mutations to be involved in the development of resistance against cytarabine and observed upregulation of EZH2 target genes due to loss of H3K27 trimethylation

Summary

Introduction

Acute myeloid leukaemia (AML) is a heterogeneous haematological malignancy, characterised by clonal expansion of abnormal, undifferentiated myeloid precursor cells. EZH2 has been found to serve a dual purpose, as either tumour suppressor or oncogene, Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, LMU Munich, Planegg Martinsried, Germany. EZH2 loss-of-function mutations seem to be rare in A ML28, loss of EZH2 by other mechanisms have been frequently reported and appear to play a major role in disease progression[29,30]. In our previous study[35], examining diagnosis/relapse pairs of 50 cytogenetically normal (CN) AML patients, we found mutations in epigenetic modifiers, including EZH2, frequently gained at relapse, suggesting epigenetic mechanisms to be involved in disease progression in a subset of patients. We found EZH2 loss-of-function mutations to be involved in the development of resistance against cytarabine and observed upregulation of EZH2 target genes due to loss of H3K27 trimethylation

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Results

Conclusion