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Table 1 List of genes known to be modified by the methylation status in renal cell cancer (references in the text)

From: Role of DNA methylation in renal cell carcinoma

Gene Function Promoter methylation in renal cancer tissue compared to normal tissue Gene expression in renal cancer tissue compared to normal tissue Effect of hypomethylating agent on gene expression
TCF-21 Tumor suppressor gene involved in specification of differentiation ↑↑
PCDH17 Tumor suppressor gene involved in calcium-dependent cell adhesion ↑↑ ?
LRRC3B Tumor suppressor gene involved in cell adhesion and apoptosis ↑↑ ?
SFRP1 Wnt antagonist tumor suppressor ↑↑↑ ↓↓ ?
RAP1GAP Tumor suppressor (inactivates Rap-mediated invasion and metastasis) ↑↑
RASSF1 Tumor suppressor (cell-cycle control, microtubule stabilization) ↑↑↑ ↓↓ ↑↑
UNC5C Tumor suppressor (induction of apoptosis) ↑↑ ↓↓ ↑↑
KILLIN Tumor suppressor (cell-cycle arrest, regulated by p53) ↑↑↑ ↓↓ ↑↑
KRT19 Organization of myofibrils and maintaining structural integrity of epithelial cells ↑↑ ↓↓ ↑↑
HOXA5 Tumor suppressor (upregulates p53) ? ?
MSH-2 DNA mismatch repair
miR-9-1 and miR-9-3 Targeted suppression of gene transcription and translation ?
DKK Tumor suppressor Wnt direct inhibitor ↑↑ ↑ (Transfection of gene inhibits cell proliferation and invasion, and increases apoptosis)
SFRP5 Tumor suppressor Wnt antagonist ↑↑↑ ↓↓ ↑↑ (Transfection of gene inhibits anchorage independent colony formation ability and invasion and increases apoptosis)
GATA-3 TBRIII signaling. inihibitor of cell proliferation ↑↑↑ ↓↓ ↑↑
TIMP-3 VEGF-3 antagonist, matrix metalloproteinase inhibitor ↑↑ ↓↓ ?
GREM-1 gene TGF-β signaling inhibition ↑↑ ↓↓ ↑↑
WIF-1 Wnt antagonist ↑↑↑ ↓↓ ↑↑ (Transfection of gene reduced cell viability, suppressed colony formation, and increased apoptosis)
UCHL1 Ubiquitination of proteins ↑↑
BTG3 E2F1 inhibition → negative regulation of cell cycle ↑↑↑ ↓↓ ↑↑
TU3A Tumor suppressor, mechanism unknown ↑↑
14-3-3 sigma Causes G2 phase block for DNA repair
p16 Cyclin kinase-dependent inhibition → causes cell-cycle arrest ?
SFRP2 Wnt antagonist ↑↑↑ ↓↓ ↑↑
FHIT Tumor suppressor, induction of apoptosis ↑↑ ↓↓ ?
XAF-1 Pro-apoptotic gene, inhibitor of “inhibition of apoptosis” protein ↑↑
APAF 1 Pro-apoptotic gene, activation of caspase 9 ↑↑↑↑ ↓↓↓ ↑↑
DAPK-1 Mediation of IFN-γ induced apoptosis ?
DLC-1 Inhibitor of RhoAGTPase ?
DLK-1 Pro-apoptotic gene ↑↑ ↓↓ ↑↑ (Transfection decreases cell proliferation, increases cell apoptosis)
HOX-B-13 Pro-apoptotic gene ↑↑↑ ↓↓ ↑↑ (Transfection decreases cell proliferation)
DAL-1 Protein 4.1-related tumor suppressor gene ↑↑
SPINT-2 Tumor suppressor: inhibits HGF which activates Ras pathway ↑↑ ? (Transfection decreases cell proliferation)
Gamma-catenin Involved in cell-cell adhesion. Loss of function correlates with poorer prognosis in cancer ↑↑↑ ↓↓ ↑↑
Connexin-32 Gap junction protein. May be involved in the increased incidence of RCC in maintenance hemodialysis patients ↑↑ ↓↓ ?
Ecad Tumor suppressor: encodes for cell-cell adhesion glycoprotein ↑↑ ↓↓ ↑↑
HLA-G Tumor promoter: involved in helping tumor cells evade immunosurveillance ?
IL-8 Tumor promoter: promotes angiogenesis and metastasis ↓ (genomic hypomethylation) ?
CA9/G250 Tumor promoter: expressed in hypoxic tumors, produces bicarbonate which neutralizes the surrounding acidic pH and aids cancer progression ↓↓ ↑↑
CYTIP Promotes metastasis. Helps tumor cells evade cell death cytokines ↑↑ ?