Alterations of 5-hydroxymethylation in circulating cell-free DNA reflect molecular distinctions of subtypes of non-Hodgkin lymphoma

Brian C.-H Chiu,Wei Zhang,Chang Chen,Chuan He,Sonali M Smith,Girish Venkataraman,Xiaolong Cui,Zhou Zhang,Qiancheng You,Chang Zeng,Rudyard Chiu

doi:10.1038/s41525-021-00179-8

Abstract

The 5-methylcytosines (5mC) have been implicated in the pathogenesis of diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL). However, the role of 5-hydroxymethylcytosines (5hmC) that are generated from 5mC through active demethylation, in lymphomagenesis is unknown. We profiled genome-wide 5hmC in circulating cell-free DNA (cfDNA) from 73 newly diagnosed patients with DLBCL and FL. We identified 294 differentially modified genes between DLBCL and FL. The differential 5hmC in the DLBCL/FL-differentiating genes co-localized with enhancer marks H3K4me1 and H3K27ac. A four-gene panel (CNN2, HMG20B, ACRBP, IZUMO1) robustly represented the overall 5hmC modification pattern that distinguished FL from DLBCL with an area under curve of 88.5% in the testing set. The median 5hmC modification levels in signature genes showed potential for separating patients for risk of all-cause mortality. This study provides evidence that genome-wide 5hmC profiles in cfDNA differ between DLBCL and FL and could be exploited as a non-invasive approach.

Highlights

Non-Hodgkin Lymphoma (NHL) is a heterogeneous group of malignancies that arises within lymphoid cells in the bone marrow or more mature cells in the peripheral lymphoid organs
We investigated epigenetic alterations underlying the molecular distinctions between patients with diffuse large B-cell lymphoma (DLBCL) and follicular lymphoma (FL) using a state-ofthe-art 5hmC-profiling technique in patient-derived cell-free DNA (cfDNA)
We found that 294 genes were differentially modified between DLBCL and FL

Summary

INTRODUCTION

Non-Hodgkin Lymphoma (NHL) is a heterogeneous group of malignancies that arises within lymphoid cells in the bone marrow or more mature cells in the peripheral lymphoid organs. Recent studies on 5hmC revealed the complexes that form between transcription factors and epigenetic regulators during B-cell differentiation[11,12], suggesting a potential role of 5hmC in B-cell malignancies. Studies[13,14,15,16,17] have demonstrated that the 5hmC-Seal technique combined with generation sequencing is a sensitive and robust technique for genome-wide 5hmC distributions in clinical specimens from different sources, such as circulating cell-free DNA (cfDNA) in peripheral blood plasma or genomic DNA from tissue biopsies. We explored the detected subtype-differentiating (e.g., H3K4me[1] and H3K27ac), relative to repressive markers genes for their prognostic value to evaluate their potential clinical implications in NHL.

RESULTS

DISCUSSION

Findings

METHODS