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. 2016 Oct 4;17(2):596-608.
doi: 10.1016/j.celrep.2016.09.018.

Insights Into the Pathogenesis of Anaplastic Large-Cell Lymphoma Through Genome-wide DNA Methylation Profiling

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Free PMC article

Insights Into the Pathogenesis of Anaplastic Large-Cell Lymphoma Through Genome-wide DNA Methylation Profiling

Melanie R Hassler et al. Cell Rep. .
Free PMC article

Abstract

Aberrant DNA methylation patterns in malignant cells allow insight into tumor evolution and development and can be used for disease classification. Here, we describe the genome-wide DNA methylation signatures of NPM-ALK-positive (ALK+) and NPM-ALK-negative (ALK-) anaplastic large-cell lymphoma (ALCL). We find that ALK+ and ALK- ALCL share common DNA methylation changes for genes involved in T cell differentiation and immune response, including TCR and CTLA-4, without an ALK-specific impact on tumor DNA methylation in gene promoters. Furthermore, we uncover a close relationship between global ALCL DNA methylation patterns and those in distinct thymic developmental stages and observe tumor-specific DNA hypomethylation in regulatory regions that are enriched for conserved transcription factor binding motifs such as AP1. Our results indicate similarity between ALCL tumor cells and thymic T cell subsets and a direct relationship between ALCL oncogenic signaling and DNA methylation through transcription factor induction and occupancy.

Keywords: DNA methylation; NPM-ALK; anaplastic large-cell lymphoma.

Figures

Figure 1
Figure 1. DNA Methylation of ALCL versus Normal CD3+ T Cells
(A) Venn diagram showing significant MVPs (based on M values and adjusted p < 0.01) among indicated groups in comparisons of ALK+, ALK−, and normal CD3+. Numbers indicate unique MVPs of selected segments; numbers in parentheses indicate total number of MVPs of the three group comparisons: ALK+ versus CD3+, ALK− versus CD3+, and ALK+ versus ALK−. (B) Hierarchical clustering of the top 31,580 differentially methylated CpG sites detected between ALK+ and control T cells (color key indicates percentage of methylation, from red = 100% methylation to green = 0% methylation). Sample annotation: blue, tumor; yellow, normal CD3+; red, ALK+ ALCL; green, ALK− ALCL. (C) Hierarchical clustering of the top 5,453 MVPs detected in control T cells versus ALK− ALCL (color key and sample annotation as in B). (D) Number and distribution of MVPs between CD3+ T cells and ALK+ or ALK− ALCL found at specific genomic regions and regions around CpG islands. Hypomethylated MVPs are shown at the top; hypermethylated MVPs are at the bottom. Differentially methylated sites were obtained after filtering the data (filtering criteria: adjusted p value < 0.01 and β-value difference > |0.2|). See also Figures S1 and S2.
Figure 2
Figure 2. Comparison of Different Developmental Stages of Thymocytes with ALCL Tumor Cells
(A) Left panel: principal-component analysis of thymic T cell subsets in comparison to ALK+ and ALK− tumor cells and peripheral CD3+ T cells (p < 9.4e–6, q value = 9.46e–4). Right panel: thymic developmental stages from ETPs (CD34+/CD1a) to SP CD4+ or CD8+ cells. (B) Hierarchical clustering of the top 1% of all probes of thymic subsets, ALK+ and ALK− tumor cells, and peripheral CD3+ T cells (4,817 CpG sites) (p < 9.4e–6, q value = 9.46e–4). Data were normalized using Qlucore software, as described in the Supplemental Experimental Procedures. Global normalization was used to center the β values for each sample to a mean of 0 (variance = 1) to adjust for differences in signal intensities of the different Infinium BeadChips. Color key from green = −2 (0% methylation) to red = +2 (100% methylation).
Figure 3
Figure 3. Silencing of T-Cell-Specific TFs in ALCL
(A) Serial stages of thymic T cell development are driven by specific TFs. DN, double negative. (B) Gene expression differences of indicated TFs between ALK+ and ALK− ALCL compared to CD3+ T cells. (C) DNA methylation levels of promoter regions of indicated genes as determined by quantitative methylation ms-qPCR in 28 ALK+ ALCL, 3 ALK− ALCL, 15 AITL, and 18 PTCL-NOS tumor samples, with 6 healthy CD3+ samples as controls. Samples were analyzed by one-way ANOVA (p < 0.05) followed by pairwise comparisons to the control group using unpaired t tests. Values are shown as mean ± SEM. See also Figure S3.
Figure 4
Figure 4. Genomic and Epigenomic Features of Differentially Methylated CpG Sites
(A) Epiexplorer analysis using indicated genomic features of hypermethylated (red) and hypomethylated (green) CpG sites for ALK+ and ALK− ALCL compared to CD3+ T cells in relation to all CpG sites on the Illumina 450k array (black). (B) Epigenetic switching is detected at the HOXD cluster in ALK+ and ALK− ALCL at regions that show H3K27me3 and EZH2 occupancy by ChIP-seq in ESCs and in GM12878 lymphoblastoid cells. Top tracks (blue): differential methylation of ALK+/ALK− ALCL versus CD3+ T cells. Middle tracks: University of California Santa Cruz (UCSC) gene annotation track, where green boxes are CpG islands. Lower tracks: enrichment of EZH2 and H3K27me3 in lymphoblastoid cells (red) and ESCs (green). (C) ChIP interrogating repressive histone marks (H3K9me3, H3K27me3) and active histone marks (H3K4me3) at HOXA9 and HOXD3 gene promoters in ALK+ SU-DHL-1 cells. GAPDH is shown as control for an active region, SAT2 is control for a heterochromatic region, NCR is control for a negative control region, and PLAU is control positive control for H3K27me3 occupancy. H3global indicates a control ChIP for global H3 occupancy. Values are means ± SD. Each value is the mean of three replicates. See also Figure S4.
Figure 5
Figure 5. Characterization of DMRs
(A) Identification of DMRs, calculated from mean β values of all CpGs annotated to a distinct genomic region, between ALK+ (left) and ALK− (right) versus CD3+ T cells (p value < 0.05; β-value difference ≥ 0.15). TSS includes CpGs within either 200 or 1,500 bp of the TSS. Hypermethylated DMRs are depicted in red; hypomethylated DMRs are in green. (B) GO term analysis using the DAVID web-based tool. Significant GO terms (adjusted p < 0.05) are highly similar in ALK+ and ALK− tumors. (C) Correlation of genes with differentially methylated promoters with gene expression profiles of ALK+ and ALK− ALCL and T cells. Blue, genes downregulated in ALCL versus T cells; red, genes upregulated in ALCL versus T cells. Hypermethylated TSS, genes showing higher methylation in both groups within their promoters; hypomethylated TSS, genes with lower methylation in their promoters in both groups. See also Tables S1, S2, and S3.
Figure 6
Figure 6. Canonical Pathways Are Affected by Differentially Methylated Genes
(A) Multiple genes of the TCR pathway are hypermethylated in ALK+ and ALK− ALCL (red, significantly hypermethylated genes; green, significantly hypomethylated genes; adjusted p value < 0.05; β-value difference ≥ 0.15). The pathway was generated through the use of QIAGEN’s IPA. (B) DNA sequence motif identified by unbiased motif search in regions adjacent to hypomethylated CpGs in ALK+ and ALK− ALCL (top) compared to the AP1 consensus motif (bottom). (C) ChIP for JUNB occupancy at hypomethylated ALCL promoters with putative AP1 binding sites. PDGFRβ, positive control. ChIP was normalized to a negative control region in the 3′ end of the PDGFRβ; gene containing no AP1 motif. Values are means ± SEM. Each value is the mean of three replicates. See also Figures S5–S8.

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