Methylation profile of the promoter CpG islands of 14 “drug-resistance” genes in hepatocellular carcinoma

Abstract

Hypermethylation of promoter CpG islands of both CFTR and GSTpi genes occurs prevalently in HCC, which may correlate with the low expression of these two genes at the mRNA level and has the profound etiological and clinical implications. It is likely to be specific to the early phase of HCC carcinogenesis.

Methylation of multiple genes as molecular markers for diagnosis of a small, well‐differentiated hepatocellular carcinoma

“…[5][6][7] Clinical studies investigating associations between carcinogenesis and abnormal methylation on CpG islands in tumor suppressor genes or genes involved in cell proliferation and death have been conducted in various cancers. [8][9][10][11][12] For HCC, it has been reported that some genes undergo hypermethylation in liver tissues, [13][14][15][16][17][18][19][20][21] supporting the hypothesis that determination of methylation in specific genes may be useful for HCC diagnosis. However, to the best of our knowledge, the diagnosis of HCC, in particular early HCC, based on the methylation levels of a single gene has not been clinically investigated to date.…”

“…The development of the system was essential, as the results reported in previous studies by sequencing were insufficiently validated in clinical samples, and were limited to examination in a few patients and cell lines by non-quantitative sequencing analysis after cloning into plasmid vector DNA. [16][17][18][19][20]37 Moreover, in most reports the methylation status in HCC and non-HCC tissue samples has been evaluated by MSP assay without validation by sequencing, and is largely based on visual judgment of ambiguous PCR products amplified by nonquantitative MSP on agarose gels. 13,15,20,34 Therefore, the methylation status estimated by previous MSP assays may not represent the actual methylation profiles in clinical samples.…”

“…APC, CASP8, CCND2, CFTR, CDKN2A, GSTP1, HIC1, POU3F1, RASSF1A, RUNX3, SPINT2 and TP73 were the genes filtered and were selected from previously reported data. [13][14][15][16][17][18][19][20][21] With the exception of CASP8, all genes were found to contain CpG islands located in their promoter regions by CpG mapping analysis, and the regions including their short CpG-rich stretches were successfully amplified for methylation analysis by sequencing. For CASP8, the region located in intron 3 that contained several CpG dinucleotide sequences was amplified (Table II).…”

“…However, to the best of our knowledge, the diagnosis of HCC, in particular early HCC, based on the methylation levels of a single gene has not been clinically investigated to date. [13][14][15][16][17][18][19][20][21] The aim of the current study was to identify a combination of methylated marker genes suitable for use in the diagnosis of a small HCCs less than 3 cm HCC or a well-differentiated HCC as an early HCC, and to establish a user-friendly methylation-specific PCR (MSP) system to measure methylation status of these HCC gene markers. To achieve the aim, we selected 12 genes (APC, CASP8, CCND2, CFTR, CDKN2A, GSTP1, HIC1, POU3F1, RASSF1A, RUNX3, SPINT2 and TP73) with a clear methylation in >50% (actually 68-100%) of HCC cases examined in studies reported previously as genetic marker candidates for diagnosis of early HCC.…”

“…To achieve the aim, we selected 12 genes (APC, CASP8, CCND2, CFTR, CDKN2A, GSTP1, HIC1, POU3F1, RASSF1A, RUNX3, SPINT2 and TP73) with a clear methylation in >50% (actually 68-100%) of HCC cases examined in studies reported previously as genetic marker candidates for diagnosis of early HCC. [13][14][15][16][17][18][19][20][21] We then analyzed the methylation status of these genes in HCC and non-tumor liver tissues using sequencing and MSP, and evaluated their use, individually and in combination, as a diagnostic tool for the detection of early HCC.…”