Differential Genome-Wide Array-Based Methylation Profiles in Prognostic Subsets of Chronic Lymphocytic Leukemia

Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden.
Blood (Impact Factor: 10.45). 11/2009; 115(2):296-305. DOI: 10.1182/blood-2009-07-232868
Source: PubMed


Global hypomethylation and regional hypermethylation are well-known epigenetic features of cancer; however, in chronic lymphocytic leukemia (CLL), studies on genome-wide epigenetic modifications are limited. Here, we analyzed the global methylation profiles in CLL, by applying high-resolution methylation microarrays (27,578 CpG sites) to 23 CLL samples, belonging to the immunoglobulin heavy-chain variable (IGHV) mutated (favorable) and IGHV unmutated/IGHV3-21 (poor-prognostic) subsets. Overall, results demonstrated significant differences in methylation patterns between these subgroups. Specifically, in IGHV unmutated CLL, we identified methylation of 7 known or candidate tumor suppressor genes (eg, VHL, ABI3, and IGSF4) as well as 8 unmethylated genes involved in cell proliferation and tumor progression (eg, ADORA3 and PRF1 enhancing the nuclear factor-kappaB and mitogen-activated protein kinase pathways, respectively). In contrast, these latter genes were silenced by methylation in IGHV mutated patients. The array data were validated for selected genes using methylation-specific polymerase chain reaction, quantitative reverse transcriptase-polymerase chain reaction, and bisulfite sequencing. Finally, the significance of DNA methylation in regulating gene promoters was shown by reinducing 4 methylated tumor suppressor genes (eg, VHL and ABI3) in IGHV unmutated samples using the methyl-inhibitor 5-aza-2'-deoxycytidine. Taken together, our data for the first time reveal differences in global methylation profiles between prognostic subsets of CLL, which may unfold epigenetic silencing mechanisms involved in CLL pathogenesis.

Download full-text


Available from: Fergus Ryan
  • Source
    • "Genomic DNA (2 μg) of LO2, LO2-X, HepG2, and HepG2.2.15 cells and clinical HCC tissues (n = 2) was modified with sodium bisulfite using an EZ DNA Methylation-Gold Kit (Zymo Research, Orange, CA). Methylationspecific PCR (MSP) and bisulfite-sequencing analysis were then performed as described previously [28]. Amplified bisulfite-sequencing PCR products were cloned into pEASY -T1 vector (Transgen, Beijing, PR China), and five clones from each sample were sequenced. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The infection of hepatitis B virus (HBV) is closely associated with the development of hepatocellular carcinoma (HCC), in which HBV X protein (HBx) plays crucial roles. MicroRNAs are involved in diverse biologic functions and in carcinogenesis by regulating gene expression. In the present study, we aim to investigate the underlying mechanism by which HBx enhances hepatocarcinogenesis. We found that miR-205 was downregulated in 33 clinical HCC tissues in comparison with adjacent noncancerous hepatic tissues. The expression levels of miR-205 were inversely correlated with those of HBx in abovementioned tissues. Then, we demonstrated that HBx was able to suppress miR-205 expression in hepatoma and liver cells. We validated that miR-205 directly targeted HBx mRNA. Ectopic expression of miR-205 downregulated HBx, whereas depletion of endogenous miR-205 upregulated HBx in hepatoma cells. Notably, our data revealed that HBx downregulated miR-205 through inducing hypermethylation of miR-205 promoter in the cells. In terms of function, the forced miR-205 expression remarkably inhibited the HBx-enhanced proliferation of hepatoma cells in vitro and in vivo, suggesting that miR-205 is a potential tumor-suppressive gene in HCC. HBx-transgenic mice showed that miR-205 was downregulated in the liver. Importantly, HBx was able to abrogate the effect of miR-205 on tumor suppression in carcinogenesis. Therefore, we conclude that HBx is able to inhibit tumor suppressor miR-205 to enhance hepatocarcinogenesis through inducing hypermethylation of miR-205 promoter during their interaction. Therapeutically, miR-205 may be useful in the treatment of HCC.
    Full-text · Article · Nov 2013 · Neoplasia (New York, N.Y.)
  • Source
    • "In addition, recent studies implicate that particular epigenetic regulations of some genes, including VHL gene, may play a crucial role in other hematological and non-hematological malignancies. Namely, it was demonstrated that epigenetic changes were found to be involved in pathogenesis of chronic lymphocytic leukemia [29] and endometrial cancer [30]. Moreover, these findings may have an important clinical implication in the era of hypomethylating therapy. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Von Hippel-Lindau disease (VHL disease) is a hereditary cancer predisposition syndrome caused by mutations of the von Hippel-Lindau tumor suppressor gene. The gene product, pVHL, regulates the level of proteins that play a central role in protecting cells against hypoxia. Clinical hallmarks of von Hippel-Lindau disease are the development of central nervous system hemangioblastomas, renal cell carcinoma, pheochromocytoma, neuroendocrine tumors and endolymphatic sac tumors. In this article the case of a 38-year old hemodialyzed patient who became ill with acute myeloid leukemia (AML) three years after being diagnosed with von Hippel-Lindau disease is presented. After cytostatic treatment the patient went into complete hematologic remission but there was still residual disease at the genetic level. After consolidation therapy patient developed bone marrow aplasia and severe pneumonia. Despite intensive treatment the patient died from acute respiratory failure. In this paper we present for the first time a case of von Hippel-Lindau disease associated with acute myeloid leukemia. No evidence of relationship between VHL disease and blood cancers has been demonstrated so far. Despite the fact that there is an increased risk of cancer development in hemodialyzed patients, cancer is a relatively rare cause of death in the dialysed population, and the most common malignancies are genitourinary cancers. It seems likely that development of acute myeloid leukemia in patient with VHL disease can be related to epigenetic alterations of the VHL gene, but further studies are needed.
    Full-text · Article · Aug 2013 · Hereditary Cancer in Clinical Practice
  • Source
    • "Hypermethylated tumor suppressor genes (ABI3, SCGB2A1, VHL, GPX3, IGSF4 and SERPIND5) were identified in unmutated CLL. In mutated cases, hypermethylation genes were involved in cell proliferation and NF-κB pathway (ADORA3, AIRE, CARD15, LOC340061, UNC5CL and LDOC1) and MAPK pathway (PRF1, FABP7) [15]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Lymphoid malignancies, mainly including lymphocytic leukemia and lymphoma, are a group of heterogeneous diseases. Although the clinical outcome of patients has been significantly improved with current immuno-chemotherapy, definitive biomarkers remain to be investigated, particularly those reflecting the malignant behavior of tumor cells and those helpful for developing optimal targeted therapy. Recently, genome-wide analysis reveals that altered genetic methylations play an important role in tumor progression through regulation of multiple cellular transduction pathways. This review describes the pathogenetic effect of the aberrant genetic methylation in lymphoid malignancies, with special emphasis on potential therapeutic strategies targeting key signaling networks.
    Full-text · Article · Aug 2013
Show more