Table 1.
Summary of comprehensive analyses of DNA methylation in human HCC
| Year | Methods (CpG sites analyzed] | Number of cases analyzed | Results | Reference |
|---|---|---|---|---|
| 2008 | MCAMs (6,458 CpG islands] Pyrosequence | 38 cases of HCC | Methylation events were classified into 4 groups according to the progression of methylation from normal liver to HCC | Gao et al. [11] |
| 2009 | BAMCA | 25 cases of HCC 26 of normal liver | Methylation profile of HCC was associated with overall and recurrence-free survival after hepatectomy | Arai et al.[19] |
| 2010 | GoldenGate methylation assaya (1,505 CpG sites] | 38 cases of HCC | Methylation status of 10 CpGs predicts survival of HCC patients | Hernandez-Vargas et al.[24] |
| 2011 | BAMCA Pyrosequence (203 CpG sites] | 34 cases of HCC 45 of normal liver | Methylation status of background liver was associated with survival in patients who underwent liver resection | Nagashio et al.[25] |
| 2011 | HM27 BeadChip (27,578 CpG sites] COBRA (17 CpG sites] | 13 cases of HCC | Methylation was analyzed in HCC cells isolated from HBV-related HCC tissues and 7 potential TSGs were identified | Tao et al.,[20] |
| 2012 | COBRA (27 genes or CpG sites] | 177 cases of HCC 128 cases of hepatitis C | Methylation of 8 TSGs was identified as driver alterations for HCC through the analysis of early HCC and chronic hepatitis C without any history of HCC | Nishida et al.[12] |
| 2012 | HM27 BeadChip (27,578 CpGs] Pyrosequence (24 CpG sites] | 62 cases of HCC | Five methylated genes were identified from the serum, which could constitute a potential tumor marker of HCC | Shen et al.[26] |
| 2012 | HM27 BeadChip (27,578 CpG sites] | 62 cases of HCC | Several miRs showing abnormal methylation and their host genes were identified | Shen et al.[5] |
| 2012 | MeDIP-microarray (27,800 CpG islands] | 162 cases of HCC | Eleven potential TSGs were reported through the MeDIP- microarray and pharmacological unmasking analyses. Functional analyses of MZB1 were performed | Matsumura et al.[22] |
| 2012 | HM27 BeadChip (27,578 CpG sites] | 12 cases of HCC, 15 cases of liver cirrhosis | Methylation differences among HCC, liver cirrhosis, and normal liver were reported. In HCC, many methylated genes were identified as a target of PRC2 in embryonic stem cells | Ammerpohl et al.[15] |
| 2012 | HM27 BeadChip (27,578 CpG sites] | 63 cases of HCC | Methylation, chromosomal alteration, and epigenetically silenced genes were analyzed comprehensively using BeadChip, array CGH, and expression arrays accompanied by pharmacological unmasking | Neumann et al.[16] |
| 2013 | HM450 BeadChip (485,577 CpG sites] | 66 cases of HCC | Genome-wide analyses of hypermethylated and hypomethylated regions in HCC using HM450 BeadChip | Shen et al.[17] |
| 2013 | HM450 BeadChip (485,577 CpG sites] | 45 cases of NAFLD | Methylation differences between mild and advanced NAFLD were reported | Murphy et al.[10] |
| 2013 | HM27 BeadChip (27,578 CpG sites] | 71 cases of HCV-related HCC | Thirteen potential TSGs were reported using comprehensive methylation and expression analyses accompanied by pharmacological unmasking methods | Revill K et al.[23] |
| 2013 | HM450 BeadChip (485,577 CpG sites] | 27 cases of HCC | Genome-wide analyses of hypermethylated and hypomethylated regions in HCC using HM450 BeadChip | Song et al.[18] |
a=Illumina GoldenGate methylation assay using BeadArray technology. MCAMs=methylated CpG island amplification microarrays; BAMCA=bacterial artificial chromosome array-based methylated CpG island amplification; HM27=Illumina Bead Array, HumanMethylation27 BeadChip; CGH=comparative genomic hybridization; COBRA=combined bisulfite restriction analysis; MeDIP-microarray=methylated DNA immunoprecipitation-microarray analysis; HM450=Illumina Bead Array, HumanMethylation450 BeadChip.