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: 10.43). 11/2009; 115(2):296-305. DOI: 10.1182/blood-2009-07-232868
Source: PubMed

ABSTRACT 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, Aug 19, 2015
  • 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.
    Neoplasia (New York, N.Y.) 11/2013; 15(11):1282-91. DOI:10.1593/neo.131362 · 5.40 Impact Factor
  • Source
    • "One of the polymorphic CpGs we identified (cg25839227), located ~ 1 kb downstream of the transcription start site of ABI3, has been reported to negatively regulate the metastatic capacity of tumor cells. This CpG site was also found, using the Illumina 27k microarray, to carry differential methylation signatures among different prognostic subsets of chronic lymphocytic leukemia (CLL) [27] "
    [Show abstract] [Hide abstract]
    ABSTRACT: The Illumina Infinium HumanMethylation27 BeadChip (Illumina 27k) microarray is a high-throughput platform capable of interrogating the human DNA methylome. In a search for autosomal sex-specific DNA methylation using this microarray, we discovered autosomal CpG loci showing significant methylation differences between the sexes. However, we found that the majority of these probes cross-reacted with sequences from sex chromosomes. Moreover, we determined that 6-10% of the microarray probes are non-specific and map to highly homologous genomic sequences. Using probes targeting different CpGs that are exact duplicates of each other, we investigated the precision of these repeat measurements and concluded that the overall precision of this microarray is excellent. In addition, we identified a small number of probes targeting CpGs that include single-nucleotide polymorphisms. Overall, our findings address several technical issues associated with the Illumina 27k microarray that, once considered, will enhance the analysis and interpretation of data generated from this platform.
    Genomics 04/2011; 97(4):214-22. DOI:10.1016/j.ygeno.2010.12.004 · 2.79 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: An automatic microprocessor-based audio-frequency CT calibrator, which is based on sample-hold detection, is presented. Due to the use of a nonbalancing differential circuit (without feedback channel), unstable measurement is avoided. The calibrator can be used at frequencies of 50-1500 Hz. Its accuracy is ±1%
    Instrumentation and Measurement Technology Conference, 1988. IMTC-88. Conference Record., 5th IEEE; 05/1988
Show more