Table 3.

DNA methylation in the genomic sequences of specific genes that are associated with the pathogenesis of cholangiocarcinoma

Gene (location)	Function	Epigenetic modification/effect	Outcome	Ref.
p16INK4A or CDKN2A (9p21)	Tumor suppressor gene Regulates cell proliferation and oncogenesis	Promoter region hypermethylation of the p16INK4A results in gene inactivation. Common event in PSC-associated CCA	More frequent in ECC cases. More commonly observed in tumors with vascular invasion. Poor clinical outcome	Ueki et al[115], 2004
p14ARF(9p21)	Encoded by the β transcript of CDKN2A (p16/CDKN2A)	Methylation of p14ARF MF = 38 and 25% (32.35); 40.2% liver fluke CCA (37)	Increased tumorigenesis in CCA	Kim et al[116], 2007
p15INK4b or p15 (9p21)	Effecter of TGF-β-mediated cell cycle arrest	Promoter hypermethylation of p15 gene	Increased tumorigenesis in CCA	Yang et al[117], 2005
p73 gene (1p36.3)	Tumor suppressor gene and related to the p53 gene	Promoter region hypermethylation increased tumorigenesis	Increased tumorigenesis in CCA
TMS1/ASC (16p11.2)	Tumor suppressor gene	Aberrant methylation of the TMS1/ASC cause inactivation of gene	Associated with CCA	Liu et al[118], 2006
FHIT (3p14.2)	Tumor suppressor gene	Promoter hypermethylation of the FHIT gene results in epigenetic silencing of the FHIT promoter region	Development of intrahepatic CCAs	Foja et al[119], 2005
RASSF1A (3p21.3)	Tumor suppressor gene induces cell cycle arrest by inhibiting the accumulation of cyclin D1	Hypermethylation of its CpG island promoter region results in inactivation	Promoter methylation is more common in ECC than	Wong et al[120], 2002
hMLH1 (3p21.3)	DNA mismatch repair gene	Promoter methylation/hypermethylation of the hMLH1 gene	Methylation frequencies vary in sporadic CCA, biliary papillary, neoplasms, and liver fluke-related CCA. Associated with poorly differentiated subtype of CCA with vascular invasion	Yang et al[117], 2005
APC (5q21–q22)	Tumor suppressor gene Controls cell division, cell-cell interactions and cell migration and invasion, and conservation of chromosomal number during cell division	APC gene hypermethylation	Worse clinical outcome in CCA	Yang et al[117], 2005
RAR-β (or HAP, RRB2 and NR1B2) (3p24)	Mediates cellular signaling in embryonic morphogenesis, cell growth and differentiation by regulating gene expression	Gene silencing by promoter region hypermethylation Results in increased tumorigenesis	Increased tumorigenesis in CCA
Epithelial (E) cadherin gene (16q22.1)	Tumor suppressor gene	Hypermethylation of the promoter region of E gene Results in loss of function and contribute to progression of cancer by increasing proliferation, invasion and metastasis	Development of intrahepatic CCA	Lee et al[121], 2002
DAPK (9q34.1)	Tumor suppressor gene Positive mediator of interferon-γ (IFN-γ)-induced programmed cell death	DAPK gene hypermethylation	Associated with poorly differentiated CCAs and with a poor prognosis	Tozawa et al[122], 2004
CHFR gene (12q24.33)	Tumor suppressor gene Delays the entry into the metaphase	Gene silencing by promoter hypermethylation	Increased tumorigenesis in CCA
RUNX3 gene (Ip36)	Tumor suppressor gene Regulate proliferation of the biliary tract epithelium	Methylation of RUNX3 results in gene silencing	Associated with poorer survival
GSTP gene (1q43)	Regulate drug and xenobiotic. metabolism	Promoter region hypermethylation	Hypermethylation more frequent in ICCA than in ECC	Lee et al[121], 2002
MGMT gene (10q26)	Responsible for repairing alkylation. DNA damage inhibits estrogen receptor-mediated cell proliferation	Methylation of discrete regions of the MGMT CpG island, results in heterochromatinization of the MGMT transcription start site and silencing of the gene	Increased frequency of GC to AT transitions in oncogenes and tumor suppressor genes and a poor prognosis	Koga et al[123], 2005
BLU gene (3p21.3)	Tumor suppressor gene	Gene methylation	Increased tumorigenesis in CCA	Tischoff et al[124], 2005
SEMA3B (3p21.3)	Tumor suppressor gene by inducing apoptosis. Plays a critical role in the guidance of growth cones during neuronal development	Methylation of SEMA3B gene	Increased tumorigenesis in CCA
TIMP3 gene (22q12.3)	Plays a role in the induction of apoptosis	CpG island methylation of TIMP3 gene	Associated with worse survival	Lee et al[121], 2002
RIZ1	Tumor suppressor gene	Methylation of RIZ1 Results in chromatin compaction and gene silencing MF = 38% liver fluke CCA (47)	Increased proliferation and migration of CCA cell line	Khaenam et al[125], 2010
OPCML	Tumor suppressor gene	Hypermethylation of OPCML	Increased tumorigenesis in CCA	Sriraksa et al[126], 2011
GSTP1	Tumor suppressor gene	Methylation of GSTP1	Increased tumorigenesis in CCA	Yang et al[117], 2005
COX-2/PTGS2 (1q25.2–q25.3)	Acts both as a dioxygenase and as a peroxidase	Methylation of COX-2 gene	Increased tumorigenesis in CCA	Lee et al[121], 2002
THBS1 gene (15q15)	Mediates cell-to-cell and cell-to-matrix interactions and play roles in platelet aggregation, angiogenesis and tumorigenesis	Hypermethylation in the promoter region of THBS1 gene	Increased tumorigenesis in CCA	Tischoff et al[124], 2005
SOCS3	responsible for sustained IL-6/STAT-3 signaling and enhanced Mcl-1 expression in cholangiocarcinoma	Hypermethylation in the promoter region of SOCS3 gene	Increased tumorigenesis in CCA	Zhang et al[127], 2012

TGF-β: Transforming growth factor-β; CCA: Cholangiocarcinomas; IL: Interleukin; TIMP3: Tissue inhibitors of metalloproteinase 3; SOCS3: Suppressor of cytokine signaling 3; STAT-3: Signal transducer and activator of transcription; THBS1: Thrombospondin 1; SEMA3B: Semaphorin 3B; GSTP1: Glutathione S-transferase pi gene; OPCML: Opioid binding protein/cell adhesion molecule-like gene; MGMT: O6-methylguanine DNA methyltransferase; RIZ1: Retinoblastoma protein-interacting zinc finger gene 1.