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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, 40–43]

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, 41–43, 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

-

-

[113–115]

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, 41–43, 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, 40–43, 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, 41–43, 54]

RASSF1

3p21.3

51

735

28-91

59

75

48 (0-100)(174)

[34, 35, 38, 40–46]

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)

[59–63]

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, 40–43, 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, 33–36, 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.
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Genome Medicine

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