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Table 1 Gene methylation frequencies in RCC

From: Epigenetics of renal cell carcinoma: the path towards new diagnostics and therapeutics

Gene Locus Mean RCC methylation (%) Number of tumors analyzed Range across multiple studies (%) ccRCC (%) pRCC (%) Adj normal methylation* % (n) References
APAF1 12q23 98 170 97-100 98 - 9 (80) [106, 107]
APC 5q21-22 17 253 14-29 16 32 7 (72) [34, 4043]
BNC1 15q25 46 59 - - - 5 (20) [63]
BTG3 21q11.2-21.1 70 20 - - - 0 (20) [108]
CASP8 2q33-34 6 139 0-16 0 - - [53, 107]
CDH1 16q22.1 35 229 11-80 83 69 87 (62) [33, 4143, 53]
CDH13 16q24.2-24.3 3 40 - - - - [53]
COL14A1 8q24 44 41 - - - 5 (20) [63]
COL15A1 9q22 53 65 - - - 30 (30) [63]
COL1A1 17q21.31-22 57 30 - 65 40 - [106]
CRBP1 3q21-22 9 22 - - - - [54]
CST6 11q13 46 61 - - - 11 (35) [63]
CXCL16 17p13.2 42 62 - 43 40 43 (21) [109]
DAL-1/4.1B 18p11.3 45 55 - 45 - - [110]
DAPK1 9q34.1 35 219 24-41 38 - - [54, 108, 111]
DKK1 10q11.2 44 62 0-52 44 - 8 (62) [63, 65]
DKK2 4q25 58 52 - 58 - 6 (52) [64]
DKK3 11p15.2 50 62 - 53 - 16 (62) [62]
DLC1 8p22-21.3 35 34 - - - 3 (34) [112]
ESR1 6q25.1 69 65 - 67 77 77 (62) [43]
ESR2 14q23.2 53 65 - 56 46 43 (62) [43]
FHIT 3p14.2 53 87 52-53 53 54 52 (0-69) (82) [43, 53]
FLCN 17p11.2 9 120 0-33 21 - - [113115]
GREM1 15q13 24 165 20-41 20 - 15 (79) [63, 101]
GSTP1 11q13 10 177 8-12 6 15 0 (72) [33, 42, 43]
HOXB13 17q21.2 30 50 - - - 0 [102]
IGFBP1 7p14-12 30 30 - 35 20 - [106]
IGFBP3 7p14-12 12 120 3-37 13 40 - [108, 116]
JUP 17q21 91 54 - - 11 11 (54) [100]
KTN19 17q21.2 38 66 - 39 33 14 (22) [109]
LOXL1 15q24 35 23 - - - 24 (17) [63]
LSAMP 3q13.2-21 26 53 - 26 - - [67]
MDRI 7q21.1 86 65 - 87 85 97 (62) [43]
MGMT 10q26 8 225 2-33 2 0 0 (62) [33, 4143, 54]
MT1G 16q13 20 25 - - - - [54]
p14ARF 9p21 33 299 17-68 36 40 20 [33, 34, 40, 43]
p16INK4 9p21 11 407 0-80 10 13 0 (87) [34, 35, 4043, 54, 81]
PDLIM4 5q31 43 41 - - - 0 (22) [63]
PML 15q22 3 90 - 3 - - [107]
PTGS2 1q25.2-25.3 95 65 - 96 92 100 (62) [43]
RARB 3p24 13 206 0-53 2 0 0 (77) [34, 4143, 54]
RASSF1 3p21.3 51 735 28-91 59 75 48 (0-100)(174) [34, 35, 38, 4046]
RASSF5 1q32.1 28 79 19-32 - - - [54, 67]
ROBO1 3p12 18 44 - 18 - - [117]
RPRM 2q23 44 52 - - - 18 (44) [63]
SDHB 1p36.1-35 4 25 - - - - [53]
SFRP1 8p12-11.1 47 234 34-80 50 18 5 (152) [5963]
SFRP2 4q31.3 53 62 - 56 - 10 (62) [62]
SFRP4 7p14-13 53 62 - 56 - 15 (62) [62]
SFRP5 10q24.1 57 62 - 59 - 15 (62) [62]
SLIT2 4q15.2 25 48 - - - 8 (12) [118]
SPINT2 19q13.2 38 118 - 30 45 5 (38) [70]
TIMP3 22q12.1-13.2 51 289 20-78 36 32 14 (104) [34, 4043, 119]
TU3A 3p21.1 39 61 - 42 25 0 (24) [49]
UCHL1 4p14 38 32 - - - 0 (32) [116]
VHL 3p26-25 16 740 8-31 14 16 0 [5, 9, 3336, 40]
WIF1 12q14.3 73 62 - 76   23 (62) [62]
XAF1 17p13.2 12 84 8-50 - - 0 (4) [120, 121]
  1. *Where the range of methylation in adjacent (Adj) normal tissue is high across multiple studies, this range is indicated in parentheses before the number analyzed. Abbreviations: APAF1, apoptotic protease activating factor 1; APC, adenomatous polyposis coli; BNC1, basonuclin 1; BTG3, B-cell translocation gene 3; CASP8, caspase 8; CDH1, cadherin 1; CDH13, cadherin 13; COL, collagen; CRBP, retinol binding protein 1, cellular; CST6, cystatin E/M; CXCL, chemokine (C-X-C motif) ligand; DAL, differentially expressed in adenocarcinoma of the lung; DAPK, death-associated protein kinase; DKK, dickkopf; DLC, deleted in liver cancer; ESR, estrogen receptor; FHIT, fragile histidine triad; FLCN, folliculin; GREM, gremlin; GSTP, glutathione s-transferase protein; HOXB, homeobox family B; IGFBP, insulin-like growth factor binding protein; JUP, junction plakoglobin (also called γ-catenin); KTN, keratin; LOXL, lysyl oxidase-like; LSAMP, limbic system-associated membrane protein; MDRI, multiple drug resistance gene; MGMT, O-6-methylguanine-DNA methyltransferase; MT1G, metallothionein 1G; p14ARF, cyclin-dependent kinase inhibitor 2A alternative reading frame; p16INK4, cyclin-dependent kinase inhibitor 2A; PDLIM4, pdz and lim domain protein 4; PML, promyelocytic leukemia; PTGS, prostaglandin-endoperoxide synthase; RARB, retinoic acid receptor beta; RASSF, RAS association domain family; ROBO, roundabout; RPRM, reprimo; SDHB, Succinate dehydrogenase B; SFRP, secreted frizzled related protein; SLIT2, slit homolog 2; SPINT2, serine peptidase inhibitor, Kunitz type, 2; TIMP, Tissue inhibitor of metalloproteases; UCHL, ubiquitin carboxyl-terminal esterase L1; VHL, von Hippel-Lindau tumor suppressor; WIF, Wnt inhibitory factor; XAF, XIAP associated factor.