Table 1.
Patient characteristics.
Figure 1.
Gene expression profiling was performed on 11 B-cell lymphoma cell lines, with and without epigenetic drug treatment. Genes responding to the epigenetic drugs were further analyzed in B-cell lymphoma patients (n = 480) compared to B cells from healthy donors (n = 5) to see if they were downregulated. These criteria were met by 233 genes. The top 30 genes were selected for Methylation-specific-PCR (MSP) analysis in 18 B-cell lymphoma cell lines. Genes with a methylation frequency above 70% in cell lines were further validated by quantitative MSP (qMSP) in B-cell lymphoma patients (n = 37). The biomarker potential (both for detection and prognostication) of the candidates was subsequently evaluated.
Figure 2.
Gene expression profiles of 30 candidate genes.
Gene expression profiles of 11 B-cell lymphoma cell lines treated (aza/TSA) and untreated (a), 480 B-cell lymphomas (b) and CD19+-B-cells from five healthy donors (c) for the 30 candidate genes for DNA methylation. Genes have been sorted according to the level of downregulation in patients compared to healthy controls.
Table 2.
Methylation status of candidate genes in 18 B-cell lymphoma cell lines.
Figure 3.
Percent promoter methylation of the analyzed genes in the test and validation series.
Each point represents one patient tumor sample. Abbreviations: BL, Burkitt`s lymphoma; DLBCL ABC, activated B-cell like diffuse large B-cell lymphoma; DLBCL GCB, germinal centre B-cell like diffuse large B-cell lymphoma; FL, follicular lymphoma; PBMC, peripheral blood mononuclear cells; PMBL, primary mediastinal B-cell lymphoma PMR, percent methylated reference.
Table 3.
Methylation frequencies and range of PMR values (brackets) assessed by qMSP in the clinical test and validation sets.
Figure 4.
Receiver Operating Characteristics (ROC) curves for individual and combined markers in lymphoma patients versus healthy donors.
The area under the ROC curve (AUC) represents how accurate the individual and combined biomarkers can discriminate between lymphomas and normal controls. A) Individual genes. B) The combined gene panel.