Abstract
BackgroundFollicular lymphoma (FL) is a form of non-Hodgkin's lymphoma (NHL) that arises from germinal center (GC) B-cells. Despite the significant advances in immunotherapy, FL is still not curable. Beyond transcriptional profiling and genomics datasets, there currently is no epigenome-scale dataset or integrative biology approach that can adequately model this disease and therefore identify novel mechanisms and targets for successful prevention and treatment of FL.Methodology/Principal FindingsWe performed methylation-enriched genome-wide bisulfite sequencing of FL cells and normal CD19+ B-cells using 454 sequencing technology. The methylated DNA fragments were enriched with methyl-binding proteins, treated with bisulfite, and sequenced using the Roche-454 GS FLX sequencer. The total number of bases covered in the human genome was 18.2 and 49.3 million including 726,003 and 1.3 million CpGs in FL and CD19+ B-cells, respectively. 11,971 and 7,882 methylated regions of interest (MRIs) were identified respectively. The genome-wide distribution of these MRIs displayed significant differences between FL and normal B-cells. A reverse trend in the distribution of MRIs between the promoter and the gene body was observed in FL and CD19+ B-cells. The MRIs identified in FL cells also correlated well with transcriptomic data and ChIP-on-Chip analyses of genome-wide histone modifications such as tri-methyl-H3K27, and tri-methyl-H3K4, indicating a concerted epigenetic alteration in FL cells.Conclusions/SignificanceThis study is the first to provide a large scale and comprehensive analysis of the DNA methylation sequence composition and distribution in the FL epigenome. These integrated approaches have led to the discovery of novel and frequent targets of aberrant epigenetic alterations. The genome-wide bisulfite sequencing approach developed here can be a useful tool for profiling DNA methylation in clinical samples.
Highlights
Two major processes that contribute to the epigenome of a cell are DNA methylation and histone modifications
Similar to the ChIP-seq method [17], since methylbinding proteins were used to extract the methylated germinal center (GC)-rich DNA, we observed significant enrichment of sequence reads at CGI regions compared to other genomic regions
We identified 1,878 and 223 genes that were associated with methylated regions of interest (MRIs) in the 59-end of these genes in RL and CD19+ B-cells, respectively (See Table S1 and S2). 59 genes were methylated in both RL and CD19+ B-cells; 1,817 and 164 genes were only methylated in either RL or CD19+ B-cells, respectively
Summary
Two major processes that contribute to the epigenome of a cell are DNA methylation and histone modifications. Given the important role of DNA methylation in tumor initiation and progression, distinct efforts have been made towards the use of DNA methylation as a biomarker in cancer [3,4]. Since this epigenetic change potentially is reversible, demethylating agents are approved for use in the treatment of hematological tumors such as myelodysplastic syndrome [5]. Polycomb (PcG) proteins are multiprotein complexes that epigenetically silence gene expression, including many TSGs [11]. Beyond transcriptional profiling and genomics datasets, there currently is no epigenome-scale dataset or integrative biology approach that can adequately model this disease and identify novel mechanisms and targets for successful prevention and treatment of FL
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