DNA hydroxymethylation is associated with disease severity and persists at enhancers of oncogenic regions in multiple myeloma

Jean-Baptiste Alberge,Mirko Wagner,Michel Attal,Aurélien A Sérandour,Stéphane Minvielle,Florence Magrangeas,Catherine Guérin-Charbonnel,Hervé Avet-Loiseau,Thomas Carell,Loïc Campion,Philippe Moreau,Soline Denié

doi:10.1186/s13148-020-00953-y

Abstract

BackgroundMultiple myeloma (MM) is a heterogeneous plasma cell malignancy that remains challenging to cure. Global hypomethylation correlates with an aggressive phenotype of the disease, while hypermethylation is observed at particular regions of myeloma such as B cell-specific enhancers. The recently discovered active epigenetic mark 5-hydroxymethylCytosine (5hmC) may also play a role in tumor biology; however, little is known about its level and distribution in myeloma. In this study, we investigated the global level and the genomic localization of 5hmC in myeloma cells from 40 newly diagnosed patients, including paired relapses, and of control individuals.ResultsCompared to normal plasma cells, we found global 5hmC levels to be lower in myeloma (P < 0.001). Higher levels of 5hmC were found in lower grades of the International Staging System prognostic index (P < 0.05) and tend to associate with a longer overall survival (P < 0.1). From the hydroxymethylome data, we observed that the remaining 5hmC is organized in large domains overlapping with active chromatin marks and chromatin opening. We discovered that 5hmC strongly persists at key oncogenic genes such as CCND1, CCND2 and MMSET and characterized domains that are specifically hydroxymethylated in myeloma subgroups. Novel 5hmC-enriched domains were found at putative enhancers of CCND2 and MYC in newly diagnosed patients.Conclusions5hmC level is associated with clinical aspects of MM. Mapping 5hmC at a genome-wide level provides insights into the disease biology directly from genomic DNA, which makes it a potent mark to study epigenetics on large patient cohorts.

Highlights

Multiple myeloma (MM) is a plasma cell (PC) neoplasm with an incidence rate of 5/100,000 in Europe and it accounts for approximately 1% of all cancers
5hmC has shown to be in most cases a stable DNA modification and its abundance increases with DNA age [13, 14]. 5hmC is commonly accepted as a DNA mark associated with active chromatin [15,16,17] and is a powerful way to identify active genomic domains associated with a disease directly from genomic DNA or more recently from circulating DNA [18, 19]
We found that 5hmC, but not 5-methylated Cytosine (5mC), is reduced in MM stages II and III compared to Stage I regarding the International Staging System [34], a classification of patients based on beta2microglobulin and albumin levels with a strong prognosis value (Fig. 1b right and Additional file 2: Figure S2B). 5mC and 5hmC global levels were not correlated to the sex or the age of the patients (Additional file 2: Figure S2C–F)

Summary

Introduction

Multiple myeloma (MM) is a plasma cell (PC) neoplasm with an incidence rate of 5/100,000 in Europe and it accounts for approximately 1% of all cancers. Studying DNA epigenetics marks is more adapted to this challenge. Oxidative states of 5-methylated Cytosine (5mC) such as 5hmC, 5fC and 5caC were identified in genomic DNA a decade ago [4,5,6]. 5fC and 5caC are almost undetectable in genomic DNA unless the glycosylase TDG gene is knocked-out [9, 10], whereas 5hmC can be found in all cell types at various levels [11]. The recently discovered active epigenetic mark 5-hydroxymethylCytosine (5hmC) may play a role in tumor biology; little is known about its level and distribution in myeloma. We investigated the global level and the genomic localization of 5hmC in myeloma cells from 40 newly diagnosed patients, including paired relapses, and of control individuals

Methods

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Discussion

Conclusion