DNA methylation in follicular lymphoma

Abstract

Follicular Lymphoma (FL) is a common B cell Non-Hodgkin Lymphoma with a median survival of 8-10 years. Patients frequently undergo transformation to a more aggressive lymphoma and this is associated with drastically reduced survival. The hallmark of FL is the t(14;18) translocation yet this alone is insufficient for lymphomagenesis. While a number of secondary genetic changes have been described, epigenetic studies have lagged behind. Epigenetics refers to mechanisms that alter gene expression without a change in the primary DNA sequence. DNA methylation was quantitatively profiled at 1505 CpG loci in 164 untreated FL as well as 10 pairs of pre- and post-transformation samples and 24 benign haematopoietic controls. Tumour-specific methylation occurred in >100 genes, preferentially occurring within CpG rich areas known as CpG islands and in genes marked by a repressive histone modification in embryonic stem (ES) cells, trimethylated Lysine 27 of Histone H3 (H3K27Me3). Significant inverse correlation with gene expression was identified for a small number of genes. Significant changes in methylation were not seen in FL samples upon transformation. These findings suggested that widespread DNA methylation occurred as an early 'pre-programmed' event in lymphomagenesis rather than being due to silencing of individual tumour suppressor genes. Methylation profiling of a subset of these samples at >27,000 CpG loci revealed aberrant methylation in FL in >700 CpG islands. These hypermethylated genes were enriched for high-density CpG promoters and for a key set of genes with developmental function which were marked by both repressive (H3K27Me3) and activating (H3K4Me3) marks in ES cells. Examination of H3K27me3 expression by immunohistochemistry in pre- and post-transformation biopsy samples showed wide variation in expression. Furthermore, mutations were identified in the histone methylase EZH2 that catalyses H3K27Me3, in 7 of 20 patients. We can conclude therefore that deregulation of DNA and histone methylation are critical inter-related events for FL pathogenesis.