DNA methylation, microRNAs, and their crosstalk as potential biomarkers in hepatocellular carcinoma

Table 1 List of genes commonly silenced by DNA hypermethylation in primary hepatocellular carcinoma tumor samples

Gene	Cellular function	Freq	Ref.
14-3-3 ε	Cell cycle, mitogenic signaling	89%	[47]
APC	Cell proliferation, migration, apoptosis	44%-71%	[48-52]
ARHI	Cell proliferation and invasion	47%	[53]
ASS	Cell cycle and cell invasion	-	[54]
BASP1	Apoptosis	50%	[55]
BLU	Apoptosis	81%	[56]
CADM1	Cell adhesion and cell differentiation	41%	[57]
CASP8	Apoptosis	34%	[58]
CAV1	Cell cycle and proliferation	56%	[59]
CCND2	Cell cycle	24%-68%	[48,50]
CDH1	Cell adhesion and metastasis	34%	[52]
CDKN2A	Cell cycle	30%-70%	[49,50,60,61]
CFTR	Intercellular transport	77%-98%	[50,62]
CHFR	Cell cycle, protein degradation	35%	[63]
COX-2	Immune response, cell migration	35%	[64]
CSRP1	Cell proliferation and differentiation	56%	[59]
DKK1	Cell proliferation	36%	[52]
DKK3	Cell differentiation, embryonic development	-	[65]
DLC-1	Cell proliferation	24%-35%	[52,66]
DLEC1	Cell proliferation	71%	[67]
E2F1	Cell proliferation, migration, and differentiation	71%	[68]
FAM43B	Cell proliferation	60%	[69]
FBLN1	Cell adhesion and migration	50%	[70]
FHIT	Cell proliferation and apoptosis	65%	[56]
GSTP1	Cell metabolism and detoxification	70%-76%	[50,60,61,71]
HAI-2/PB	Cell proliferation and invasion	80%	[72]
HDPR1	Cell proliferation, differentiation, cellular signaling	51%	[73]
HINT1	Apoptosis	55%	[74]
IGFBP-3	Cell proliferation and growth	33%	[75]
KL	Cell proliferation and growth	81%	[76]
KLK10	Cell proliferation, survival, and cellular signaling	55%	[77]
LIFR	Signal transduction	48%	[78]
MAGE-A1	Cell differentiation, embryonic development	53%	[79]
MAGE-A3	Cell differentiation, embryonic development	74%	[79]
MAT1A	Cell metabolism	85%	[80]
MT1G	Cell proliferation and apoptosis	60%	[81]
MTM1	Cell differentiation	100%	[82]
MTSS1	Cell migration and metastasis	80%	[83]
MUC2	Immune system	62%	[84]
NORE1B	Cell proliferation and growth	62%	[85]
NQO1	Cell metabolism	50%	[86]
OXGR1	Cell growth and metabolism	78%	[77]
p14ARF	Cell proliferation and apoptosis	40%-42%	[68,71]
p15INK4B	Cell cycle	22%-61%	[71,87]
P16	Cell cycle	37%-83%	[48,71,87]
P21	Cell cycle	63%	[68]
P27	Cell cycle	48%	[68]
P300	Cell proliferation and differentiation	68%	[68]
P53	Cell proliferation, apoptosis, and DNA repair	14%	[68]
P73	DNA repair and apoptosis	35%	[71]
PCDH10	Cell adhesion and migration	76%	[88]
PER3	DNA repair	60%	[89]
PRDM2	Cell metabolism	-	[90]
PTEN	Cell proliferation and migration	16%-22%	[87,91]
RASSF1A	Cell proliferation, migration, and apoptosis	64%-88%	[48,51]
RB	Cell cycle, apoptosis	24%-32%	[68,87]
RECK	Cell invasion and metastasis	55%	[92]
RELN	Cell adhesion	37%	[93]
RIZ1	Cell proliferation and apoptosis	29%-67%	[48,94,95]
RUNX-3	Apoptosis	38%-48%	[50-52]
SFRP1	Cell proliferation and differentiation	37%-45%	[51,52,96]
SFRP2	Cell proliferation and differentiation	48%-54%	[97]
SFRP5	Cell proliferation and differentiation	39%	[96]
SLIT2	Cell migration	83%	[98]
SOCS1	Cell growth and survival	39%-72%	[9,48,90,99]
SOX1	Cell proliferation	57%	[100]
SOX17	Cell differentiation and embryonic development	82%	[101]
SPARC	Cell growth and invasion	75%	[102]
SPINT2	Cell proliferation and growth	60%	[50]
SRD5A2	Cell proliferation and androgenic physiology	50%	[55]
Survivin	Apoptosis and cell proliferation	33%	[58]
TFPI2	Matrix remodelling	47%	[103]
TIP30	Apoptosis and metastasis	47%	[104]
UCHL1	Cell metabolism and protein degradation	44%	[105]
UNC5C	Cell migration	26%	[106]
Vimentin	Cell migration and signaling	56%	[107]
WIF-1	Cell proliferation	49%-61%	[52,65,108]
WT1	Cell proliferation and survival	54%	[68]
ZHX2	Cell proliferation, differentiation, and development	47%	[109]

Freq: Frequency of hypermethylation.