Array-based DNA methylation profiling in follicular lymphoma

Abstract

Quantitative methylation profiling was performed using the Illumina GoldenGate Assay in untreated Follicular Lymphoma (FL) (164), paired pre- and post-transformation FL (20), benign haematopoietic (24) samples and purified B & T cells from two FL cases. Methylation values allowed separation of untreated FL samples from controls with one exception based primarily on tumour-specific gains of methylation typically occurring within CpG islands. Genes which are targets for epigenetic repression in stem cells by Polycomb Repressor Complex 2 were significantly overrepresented among hypermethylated genes. Methylation profiles were conserved in sequential FL and t-FL biopsies suggesting that widespread methylation represents an early event in lymphomagenesis and may not contribute substantially to transformation. Significant (p<0.05) correlation between FL methylation values and reduced gene expression was demonstrated for up to 28% of loci. Methylation changes occurred predominantly in B cells with variability in the amount of non-malignant tissue between samples preventing conclusive correlation with survival. This represents an important caveat in attributing prognostic relevance to methylation and future studies in cancer will optimally require purified tumour populations to address the impact of methylation on clinical outcome.

Methylation profiling of mediastinal gray zone lymphoma reveals a distinctive signature with elements shared by classical Hodgkin's lymphoma and primary mediastinal large B-cell lymphoma

“…28,30 Furthermore, we have recently demonstrated that matched formalin-fixed paraffin-embedded and frozen surgical pathology replicates showed the complete preservation of the cancer methylome, 31 and that immunohistochemistry studies of formalin-fixed paraffin-embedded tissue specimens do not alter the DNA methylation profile. 25 Here, we performed pyrosequencing for four different CpG sites from three different genes (CDH1, FAT, SLIT2) and demonstrated a high accuracy of the methylation array (Online Supplementary Table S2).…”

EZH2 Y641 mutations in follicular lymphoma

“…2 Indeed, DNA-methylation profiling studies in FL by our group and others have shown that PRC2 gene targets in stem cells are significantly overrepresented among the hypermethylated genes in these tumours, linking these two epigenetic mechanisms in FL. 3 The spectrum of cancers with EZH2 mutation is also increasing, with mutations in myeloid disorders leading to reduced or complete loss of H3K27me3 expression consistent with a tumour suppressor role for EZH2. [4][5][6] Deregulation of the EZH2-H3K27me3 pathway may also occur by other mechanisms, with over-expression of EZH2 associated with poor outcome in a range of solid tumours.…”

“…As EZH2 has been implicated in direct control of DNA methylation, 10 we went on to test whether mutation had an effect on DNA methylation, using our previously generated FL methylation profiles of paired FL and t-FL samples. 3 Average methylation values across 1264 CpG loci differed by no more than 2% between EZH2 wild-type and EZH2 mutated samples. Although we cannot rule out the possibility of minor effects on methylation, the absence of any major differences suggests that EZH2 mutations have no effect on DNA-methyltransferase recruitment.…”

“…3 Accordingly, (i) Igf1 signaling negatively regulates lifespan in worms, flies and mammals, and (ii) Igf1 and Ins level in blood is regulated positively by caloric uptake. Although Ins is secreted after calorie uptake from pancreatic islands, Igf1 (known also as somatomedin-C) is secreted from liver into peripheral blood in growth hormone (GH) dependent manner.…”

Epigenetic Dysregulation in Follicular Lymphoma

“…Despite this, hypermethylation of tumor suppressor genes has been demonstrated in numerous studies including FL [56,57], with a significant overlap noted between hypermethylated CpGs and PRC2 target genes in embryonic stem cells [58]. Although initial reports suggested conservation of methylation profiles between paired pre-and post-transformation samples [58], the introduction of higher resolution platforms, suggests measurable differences in relapsed and more aggressive tumors [59,60].…”