Alterations in DNA methylation/demethylation intermediates predict clinical outcome in chronic lymphocytic leukemia.

Cristina Bagacean,Valerie Olivier,Hussam Saad,Adrian Tempescul,Victor Cristea,Christelle Le Dantec,Pierre-François Cartron,Christian Berthou,Nathalie Douet-Guilbert,Audrey Mohr,Yves Renaudineau,Mihnea Zdrenghea,Anne Bordron

doi:10.18632/oncotarget.20081

Abstract

Cytosine derivative dysregulations represent important epigenetic modifications whose impact on the clinical outcome in chronic lymphocytic leukemia (CLL) is incompletely understood. Hence, global levels of 5-methylcytosine (5-mCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-CaCyt) and 5-hydroxymethyluracil were tested in purified B cells from CLL patients (n = 55) and controls (n = 17). The DNA methylation ‘writers’ (DNA methyltransferases [DNMT1/3A/3B]), ‘readers’ (methyl-CpG-binding domain [MBD2/4]), ‘editors’ (ten-eleven translocation [TET1/2/3]) and ‘modulators’ (SAT1) were also evaluated. Accordingly, patients were stratified into three subgroups. First, a subgroup with a global deficit in cytosine derivatives characterized by hyperlymphocytosis, reduced median progression free survival (PFS = 52 months) and shorter treatment free survival (TFS = 112 months) was identified. In this subgroup, major epigenetic modifications were highlighted including a reduction of 5-mCyt, 5-hmCyt, 5-CaCyt associated with DNMT3A, MBD2/4 and TET1/2 downregulation. Second, the cytosine derivative analysis revealed a subgroup with a partial deficit (PFS = 84, TFS = 120 months), mainly affecting DNA demethylation (5-hmCyt reduction, SAT1 induction). Third, a subgroup epigenetically similar to controls was identified (PFS and TFS > 120 months). The prognostic impact of stratifying CLL patients within three epigenetic subgroups was confirmed in a validation cohort. In conclusion, our results suggest that dysregulations of cytosine derivative regulators represent major events acquired during CLL progression and are independent from IGHV mutational status.

Highlights

The clinical outcome of chronic lymphocytic leukemia (CLL) is heterogeneous with some patients remaining asymptomatic for decades, while others progress rapidly and need therapy soon after diagnosis [24]
Results generated from the present study indicated that: (1) 5-Cyt derivative levels in CLL B cells have a critical impact on disease progression and initial treatment delay in CLL; (2) DNA methylation and active demethylation data analysis classifies CLL patients into 3 subgroups: a worst prognosis subgroup of patients with a defect of both
DNA methylation and active DNA demethylation (Global subgroup) associated with a downregulation of most of the key epigenetic regulators, the Partial subgroup, with an altered active DNA demethylation process associated with SAT1 overexpression, and the Normal subgroup which is epigenetically similar to controls and has a stable disease course; (3) disease progression is associated with dynamic modifications in epigenetic regulator expression, DNMT3A, TET2 and SAT1

Summary

Introduction

The clinical outcome of chronic lymphocytic leukemia (CLL) is heterogeneous with some patients remaining asymptomatic for decades, while others progress rapidly and need therapy soon after diagnosis [24]. Epigenome-wide association studies (EWAS) have contributed to better understanding the significance of DNA methylation in CLL by showing: (1) global DNA hypomethylation combined with local hypermethylation in CLL B cells as observed in other cancers [22]; (2) a link between the methylome profile heterogeneity, an increased genetic complexity and adverse clinical outcome, suggesting some epigenetic modifications as an unfavorable and heritable trait [29, 35]; (3) a distinct DNA methylation signature between the two molecular IGHV subtypes in relation to naïve B cells and unmutated (UM)-CLL, or memory B cells and mutated (M)-CLL [27]; (4) that epigenetic patterns are similar between peripheral blood and lymph node compartments [4], while in contrast, the transcriptome is influenced by the B-cell receptor (BCR) activation in the microenvironment of the lymph node [13]; and (5) aberrant DNA methylation and specific chromatin accessible region overlap with gene loci encoding for risk factors [44]. It has been shown that mice with biallelic loss of the DNA methyltransferase (DNMT)3A develop a lymphoproliferative disease similar to CLL [17]

Methods

Results

Conclusion