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Table 2 List of the most significantly deregulated miRNAs in MPNSTs relative to plexiform neurofibromas

From: MicroRNAome profiling in benign and malignant neurofibromatosis type 1-associated nerve sheath tumors: evidences of PTEN pathway alterations in early NF1 tumorigenesis

miRNAs

Functionally verified target(s)

Localization

Host gene

Plexiform neurofibromas (n = 41)

MPNSTs (n = 15)

Fold changea

P b

Peripheral nerves (n = 2)c

Significantly down-regulated miRNAs in MPNSTs relative to plexiform neurofibromas (n = 10)

miR-139-5p

 

11q13.4

PDE2A

368.8 [5.6-1523.2]d

71.8 [27.6-247.8]

0.19

< 0.00001

253.1 [149.9-356.3]

miR-150

 

19q13.3

 

1910.1 [4.4-6800.1]

529.6 [105.6-3531.6]

0.28

< 0.0001

1573.4 [1428.9-1717.9]

miR-338-3p

 

17q25.3

AATK

10.7 [0.03-115.4]

2.3 [0.02-29.8]

0.21

< 0.001

125.6 [88.7-162.5]

miR-195

CCND1, CDK6, E2F3[16]CCNE1[17] and RAF1[18]

17p13.1

 

1689.4 [0.03-9958.6]

503.8 [166.6-2233.1]

0.30

< 0.001

689.6 [633.5-745.7]

miR-146a

 

5q34

 

3117.1 [85.4-49237.4]

1252.7 [186.9-65865.7]

0.40

< 0.001

3705.8 [2932.0-4479.5]

miR-95

 

4p16.1

ABLIM2

44.5 [0.02-175.7]

26.6 [3.6-56.2]

0.60

0.001

12.7 [7.5-18.0]

let-7b

RAS[19], CCND1[20] and HMGA2[21]

22q13.3

 

1642.3 [15.8-12746.3]

543.6 [63.9-1531.6]

0.33

0.003

2777.1 [1011.0-4543.1]

miR-186

 

1p13.1

ZRANB2

2030.1 [1.6-3193.4]

1240.9 [727.8-7687.8]

0.61

0.003

2303.1 [1717.4-2889.2]

miR-885-5p

 

3p25.3

ATP2B2

52.4 [0.51-393.3]

20.6 [2.4-62.4]

0.39

0.006

67.2 [46.5-87.9]

miR-200c

ZEB1[22]and ZEB2

12p13.3

 

8.4 [0.51-861.1]

4.8 [0.01-22.4]

0.57

0.008

8.1 [6.1-10.0]

Most significantly upregulated miRNAs in MPNSTs relative to plexiform neurofibromas (n = 28)

miR-135b

APC[23]

1q32.1

 

0.41 [0.02-12.0]

1060.9 [4.2-3562.1]

2616.7

< 10-6

3.4 [0.57-6.3]

miR-449a

CCND1 and HDAC1[24]

5q11.2

CDC20B

0.45 [0.00-11.4]

14.4 [0.28-25.9]

32.30

< 10-6

4.0 [3.4-4.6]

miR-210

HOXA1, HOXA9, HOXA3, and E2F3[25]

11p15.5

 

9.8 [0.05-254.1]

236.0 [3.2-458.5]

24.00

< 10-6

69.2 [19.0-119.4]

miR-301b

PTEN[26]

22q11.2

 

0.81 [0.02-8.2]

17.3 [1.9-121.6]

21.19

< 10-6

0.20 [0.03-0.37]

miR-301a

 

17q22

SKA2

8.7 [0.02-87.8]

173.7 [23.0-592.2]

20.04

< 10-6

3.7 [3.3-4.0]

miR-9

CDH1[27] and CDX2[28]

1q22, 5q14.3 and 15q26.1

 

52.9 [0.03-472.9]

787.6 [2.9-1265.6]

14.90

< 10-6

411.7 [400.8-422.5]

miR-130b

 

22q11.2

 

8.3 [0.02-53.5]

66.2 [23.3-442.7]

7.96

< 10-6

7.0 [5.5-8.6]

miR-454

 

17q22

SKA2

257.3 [0.05-631.7]

1259.4 [494.9-2684.4]

4.90

< 10-6

508.4 [481.2-535.7]

miR-19a

PTEN[29] and CCND1[30]

13q31.3

 

201.3 [0.04-764.3]

749.1 [429.9-2078.0]

3.72

< 10-6

146.9 [141.3-152.5]

miR-106b

PTEN, CCND1, and E2F1[31, 32]

7q22.1

MCM7

126.5 [0.05-483.2]

439.2 [233.9-1795.6]

3.47

< 10-6

81.9 [80.1-83.8]

miR-135a

APC[23]

12q23.1 and 3p21.1

GLYCTK (3p21.1)

0.05 [0.01-4.4]

25.7 [0.01-158.3]

537.54

< 0.00001

65.8 [0.02-131.5]

miR-137

 

1p21.3

 

0.08 [0.01-40.2]

21.4 [0.07-82.0]

258.68

< 0.00001

17.6 [3.1-32.1]

miR-31

 

9p21.3

 

6.4 [0.02-2747.4]

1581.9 [0.02-8261.8]

246.61

< 0.00001

83.0 [13.7-152.4]

miR-129-3p

CDK6

7q32.1 and 11p11.2

 

0.04 [0.00-2.5]

3.8 [0.01-1409.7]

92.36

< 0.00001

0.94 [0.48-1.4]

miR-224

 

Xq28

GABRE

7.0 [0.04-135.0]

120.2 [8.0-748.0]

17.26

< 0.00001

14.7 [9.6-19.9]

miR-10b

NF1, HOXA3 and HOXD10[33, 34]

2q31.1

 

49.1 [0.02-832.3]

649.6 [12.4-1640.1]

14.19

< 0.00001

64.8 [11.7-117.9]

miR-148a

 

7p15.2

 

50.2 [0.04-450.0]

413.6 [3.8-793.2]

8.24

< 0.00001

8.5 [5.2-11.9]

miR-18a

 

13q31.3

 

3.0 [0.02-38.4]

21.2 [6.4-104.6]

7.02

< 0.00001

5.9 [1.4-10.4]

miR-452

 

Xq28

GABRE

9.9 [0.18-82.0]

58.6 [14.6-260.7]

5.93

< 0.00001

19.5 [19.1-19.9]

miR-598

 

8p23.1

XKR6

15.8 [0.04-105.7]

93.3 [5.0-524.7]

5.91

< 0.00001

29.9 [29.0-30.8]

miR-196b

HOXB8[34]

7p15.2

 

29.7 [0.54-526.4]

165.2 [12.5-788.5]

5.56

< 0.00001

124.9 [70.5-179.3]

miR-425

 

3p21.3

DALRD3

16.3 [0.11-116.5]

84.4 [38.3-105.1]

5.18

< 0.00001

19.2 [11.5-27.0]

miR-10a

HOXD10[35]

17q21.3

HOXB3

53.1 [0.04-498.1]

230.1 [67.6-400.7]

4.33

< 0.00001

21.3 [14.2-28.3]

miR-93

 

7q22.1

MCM7

149.2 [0.04-860.2]

607.8 [303.6-2824.3]

4.07

< 0.00001

142.8 [114.4-171.2]

miR-20a

CCND1 and E2F1[31]

13q31.3

 

295.6 [0.02-1269.4]

1064.2 [196.3-3498.9]

3.60

< 0.00001

531.2 [390.0-672.5]

miR-19b

 

13q31.3 and Xq26.2

 

1757.9 [0.99-5939.3]

4761.9 [2678.3-11811.4]

2.71

< 0.00001

3039.0 [2435.6-3642.5]

miR-484

 

Xq26.2

 

1354.6 [70.2-4301.5]

3537.7 [1213.0-8554.1]

2.61

< 0.00001

1047.4 [438.8-1656.1]

miR-192

 

11q13.1

 

38.8 [0.02-95.4]

94.3 [39.7-236.6]

2.43

< 0.00001

27.4 [18.7-36.1]

  1. aMedian expression in MPNSTs/Median expression in plexiform neurofibromas.
  2. bMann- Whitney’s U Test.
  3. cNon tumorigenic controls.
  4. dMedian [range] of miRNAs levels.
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