High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma

Abstract

Methylation of promoter CpG islands has been associated with gene silencing and demonstrated to lead to chromosomal instability. Therefore, some postulate that aberrantly methylated CpG regions may be important bio-markers indicative of cancer development. In this study we used the Illumina GoldenGate Methylation BeadArray Cancer Panel I for simultaneously profiling methylation of 1,505 CpG sites in order to identify methylation differences in 76 liver tissues ranging from normal to pre-neoplastic and neoplastic states. CpG sites for ESR1, GSTM2, and MME were significantly differentially methylated when comparing the pre-neoplastic tissues from patients with concomitant hepatocellular carcinoma (HCC) to the pre-neoplastic tissues from patients without HCC. When comparing paired HCC tissues to their corresponding pre-neoplastic non-tumorous tissues, eight CpG sites, including one CpG site that was hypermethylated (APC) and seven (NOTCH4, EMR3, HDAC9, DCL1, HLA-DOA, HLA-DPA1, and ERN1) that were hypomethylated in HCC, were identified. Our study demonstrates that high-throughput methylation technologies may be used to identify differentially methylated CpG sites that may prove to be important molecular events involved in carcinogenesis.

Genome-wide methylation and expression differences in HPV(+) and HPV(-) squamous cell carcinoma cell lines are consistent with divergent mechanisms of carcinogenesis

“…These differences were marked by overall greater DNA methylation across the genic and other non-repetitive genome in HPV(+) cells compared to HPV(-) cells, also observed in a sample of primary tumors. LINE-1 methylation, a measure of global methylation, was also higher in HPV(+) cell lines and in a larger population of tumor specimens, consistent with the differences of two genes which had both higher methylation and higher expression in HPV(+): ESR1 (due to its significance and differential promoter methylation in other cancers), [28][29][30] and DCC (identified as biologically important in head and neck cancer). 31 Illumina Infinium platform data showed ESR1 and DCC average methylation of 4% and 10% in HPV(-) tumors compared to 82% and 87% respectively in HPV(+) tumors.…”

MethyLight droplet digital PCR for detection and absolute quantification of infrequently methylated alleles

“…The same methylated and unmethylated control DNAs have been used extensively in other DNA methylation studies. [19][20][21] Samples with methylation percentages of 100%, 20%, 4%, 0.8%, 0.16%, 0.032%, 0.006%, and 0% with 20 ng of total DNA were tested at least 4 times in a run in at least 3 independent runs. The operational definition of limits of detection (LOD) is the lowest nonzero concentration in a sample at which replicate measurements give positive qualitative results.…”

Role of histone deacetylase 9 in regulating adipogenic differentiation and high fat diet-induced metabolic disease

“…How HDAC9's molecular actions are functionally linked to the global metabolic state in obesity remains to be ascertained. It should be pointed out that, in addition to adipose tissue, HDAC9 is expressed in other metabolically relevant tissues, including liver, skeletal muscle, and pancreas, [45][46][47] as well as in immune cells. 48 This expression pattern suggests that HDAC9 is globally positioned to influence metabolic disease by influencing multiple target tissues and cells.…”