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Randomized Controlled Trial
. 2013 Dec;98(12):1912-20.
doi: 10.3324/haematol.2013.088740. Epub 2013 Jul 5.

Genome-wide profiling identifies a DNA methylation signature that associates with TET2 mutations in diffuse large B-cell lymphoma

Fazila Asmar  1 , Vasu Punj, Jesper Christensen, Marianne T Pedersen, Anja Pedersen, Anders B Nielsen, Christoffer Hother, Ulrik Ralfkiaer, Peter Brown, Elisabeth Ralfkiaer, Kristian Helin, Kirsten Grønbæk
Affiliations
Randomized Controlled Trial

Genome-wide profiling identifies a DNA methylation signature that associates with TET2 mutations in diffuse large B-cell lymphoma

Fazila Asmar et al. Haematologica. 2013 Dec.

Abstract

The discovery that the Ten-Eleven Translocation (TET) hydroxylases cause DNA demethylation has fundamentally changed the notion of how DNA methylation is regulated. Clonal analysis of the hematopoetic stem cell compartment suggests that TET2 mutations can be early events in hematologic cancers and recent investigations have shown TET2 mutations in diffuse large B-cell lymphoma. However, the detection rates and the types of TET2 mutations vary, and the relation to global methylation patterns has not been investigated. Here, we show TET2 mutations in 12 of 100 diffuse large B-cell lymphomas with 7% carrying loss-of-function and 5% carrying missense mutations. Genome-wide methylation profiling using 450K Illumina arrays identified 315 differentially methylated genes between TET2 mutated and TET2 wild-type cases. TET2 mutations are primarily associated with hypermethylation within CpG islands (70%; P<0.0001), and at CpG-rich promoters (60%; P<0.0001) of genes involved in hematopoietic differentiation and cellular development. Hypermethylated loci in TET2 mutated samples overlap with the bivalent (H3K27me3/H3K4me3) silencing mark in human embryonic stem cells (P=1.5×10(-30)). Surprisingly, gene expression profiling showed that only 11% of the hypermethylated genes were down-regulated, among which there were several genes previously suggested to be tumor suppressors. A meta-analysis suggested that the 35 hypermethylated and down-regulated genes are associated with the activated B-cell-like type of diffuse large B-cell lymphoma in other studies. In conclusion, our data suggest that TET2 mutations may cause aberrant methylation mainly of genes involved in hematopoietic development, which are silenced but poised for activation in human embryonic stem cells.

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Figures

Figure 1.
Figure 1.
TET2 point mutations in primary DLBCL. Distribution and types of TET2 point mutations in primary DLBCL. Twelve mutations were observed in 12 of a total of 100 cases.
Figure 2.
Figure 2.
Hierarchical clustering of β methylation values from 578 CpG sites showing differential methylation in TET2mut and TET2wt samples. These 578 most variable probes were selected as having a FDR-adjusted P<0.05, and a mean β value difference of ≥0.2 between TET2mut and TET2wt samples (explained in the Online Supplementary Design and Methods section). Columns represent samples; rows represent CpG sites. Euclidean distance and complete linkage were used to study the cluster pattern of methylation probes. β values are represented using a pseudocolor scale from 0 to 1 as per color bar. TET2mut samples are separated into two distinct groups, one with higher mean β values and a second group with lower mean β values. Three TET2mut samples, G1, G3, and G8, cannot be distinguished from TET2wt. G18W= Normal CD19+ B cells.
Figure 3.
Figure 3.
Functional gene ontology for differentially methylated TET2 signature genes. Seven top biological functions were identified and ranked by their P value (Y-axis).
Figure 4.
Figure 4.
Relative distribution of the 578 “TET2 signature probes”. Distribution of TET2 signature probes (n=578) in the context of (A) functional genomic distribution classified in different groups: Promoter, Gene body, 3’UTR, and Intergenic and of (B) CpG neighborhood classified into Island, Shore, Shelf, and Other/Open sea. There was a significant enrichment of probes corresponding to promoters and gene bodies, and of probes mapping to CpG islands, determined by Fisher’s exact test (P<0.0001, marked as *). Numbers in parentheses indicate the number of probes in the corresponding genomic region. (C) TET2 differentially methylated loci correspond to the bivalent mark, H3K4me3/H3K27me3 enriched regions. Chip-seq data for hES cells were downloaded from Encode and peak (P<0.01) coordinates were identified if they fell within hypermethylated regions or not. Of the 578 probes a majority of the differentially methylated loci match to the bivalent mark, H3K4me3 and H3K27me3 (53.4%). This enrichment is highly statistically significant from the total number of probes on the 450K platform mapping to these histone marks (H3K27me3 + H3K4me3, P = 1.5×10−30; Fisher’s exact test).
Figure 5.
Figure 5.
Integrated analysis of gene expression and DNA methylation between TET2mut and TET2wt cases. (A) Mean DNA methylation β-value differences between four TET2mut and five TET2wt samples were plotted on the X-axis, and mean log2- transformed gene expression value differences were plotted on the Y-axis to generate a starburst plot for each of the 305 TET2 signature genes. Of these genes, 35 genes were found to be hypermethylated (red dots) and downregulated. (B) The majority of these genes (n=27) were hypermethylated in the promoter regions. (C) A large proportion of 305 hypermethylated genes showed no change (73%) in gene expression.
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References

    1. Baylin SB, Jones PA. A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer. 2011;11(10): 726–34 - PMC - PubMed
    1. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethyl-cytosine in mammalian DNA by MLL partner TET1. Science. 2009;324(5929): 930–5 - PMC - PubMed
    1. Ito S, D’Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature. 2010;466(7310): 1129–33 - PMC - PubMed
    1. Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science. 2011;333 (6047): 1300–3 - PMC - PubMed
    1. Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PA, Rappsilber J, et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature. 2011;473(7347): 343–8 - PMC - PubMed

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