Background
Methods
Study population
NMD microarray analysis
Patient | Diagnosis age | Gleason score | WHO grade | T* | N †
| M ‡
| Primary PSA§
|
---|---|---|---|---|---|---|---|
015-001** | 53 y 7 m | n.a. | II | T1c | Nx | M0 | n.a. |
043-001** | 50 y 9 m | 6 | II | T2 | Nx | M0 | 3.8 |
232-001** | 70 y 7 m | 7 | II | T1c | Nx | M0 | 6.2 |
232-002** | 75 y 5 m | n.a. | n.a. | T1a | Nx | M0 | 1.3 |
248-006** | 59 y 3 m | 6 | I | T1c | Nx | M0 | 2.9 |
311-003** | 60 y 4 m | 6 | II | T2 | Nx | M0 | 21.9 |
001-002 | 71 y 8 m | n.a. | II | T3 | Nx | M0 | n.a. |
292-010 | 47 y 11 m | 6 | II | T2 | Nx | Mx | 5.2 |
408-002 | 67 y 5 m | 7 | II | T1c | Nx | Mx | 5.5 |
236-006 | 75 y 11 m | n.a. | n.a. | T3 | Nx | Mx | 85 |
402-003 | 67 y 3 m | 6 | I | T2 | Nx | M0 | 13 |
402-001 | 67 y 11 m | 7 | II | T1c | Nx | M0 | 15 |
413-003 | 55 y 3 m | 7 | II | T1c | Nx | M0 | 6.4 |
362-001 | 50 y 7 m | 6 | I | T1b | Nx | M0 | 6.9 |
362-002 | 49 y 4 m | 6 | I | T1c | Nx | Mx | 41.9 |
miRNA microarray analysis
Association analysis
Cell culture and drug treatments
Oligonucleotide array protocol
Mutation screening and genotyping
MicroRNA array protocol
MicroRNA target detection
miRNA expression validation
Statistical analyses
Results
Gene ID | Gene name | Cytogenetic band | Genomic location (strand) | Selection criteria |
---|---|---|---|---|
RBMX
| RNA binding motif protein, X-linked | Xq26.3 | 135 951 351-135 962 939 bp (-) | p < 0.05 |
CSAG2
|
Homo sapiens CSAG family, member 2 | Xq28 | 151 922 445-151 928 738 bp (+) | p < 0.05 |
RAP2C
|
Homo sapiens RAP2C, member of RAS | Xq25 | 131 337 053-131 353 471 bp (-) | p < 0.05, fold change > 1.5 |
SOX3
| SRY (sex determining region Y)-box 3 | Xq27.1 | 139 585 152-139 587 225 bp (-) | p < 0.05 |
MBNL3
| Muscleblind-like 3, (Drosophila) | Xq26.2 | 131 506 029-131 623 996 bp (-) | p < 0.05 |
ZNF75
| Zinc finger protein 75 | Xq26.3 | 134 382 867-134 478 012 bp (-) | p < 0.05 |
MAGEC1
| Melanoma antigen family C, 1 | Xq26 | 140 991 680-140 997 183 bp (+) | p < 0.05 |
MAGEA1
| Melanoma antigen family A, 1 | Xq28 | 152 481 522-152 486 116 bp (-) | p < 0.05, fold change > 1.5 |
MAGEA11
| Melanoma antigen family A, 11 | Xq28 | 148 769 894-148,798,928 bp (+) | location |
MAGEC3
| Melanoma antigen family C, 3 | Xq27.2 | 140 926 102-140 985 618 bp (+) | location |
MAGED1
| Melanoma antigen family D, 1 | Xp11.23 | 51 546 103-51 645 453 bp (+) | p < 0.05 |
U66046
| hypothetical protein FLJ44451 | Xq28 | 148 615 451-148 616 127 bp (-) | p < 0.05 |
SSR4
| signal sequence receptor, delta | Xq28 | 153 058 971-153 063 960 bp (+) | p < 0.05 |
VBP1
| von Hippel-Lindau binding protein 1 | Xq28 | 154 444 550-154 468 098 bp (+) | p < 0.05 |
LDOC1
| leucine zipper, down-regulated in cancer, 1 | Xq27 | 140 269 930-140 271 310 bp (-) | p < 0.05 |
TKTL1
| transketolase-like 1 | Xq28 | 153 524 024-153 558 700 bp (+) | p < 0.05 |
CD40LG
| CD40 ligand | Xq26 | 135 730 336-135 742 549 bp (+) | p < 0.05 |
Gene | Variation* | Amino acid change | dbSNP |
---|---|---|---|
CD40LG
| c.148T > C | p.Leu50Ser | rs1126535 |
LDOC1
| c.-62C > G | - | - |
MAGEA1
| c.-2924G > T | - | - |
c.-264, G > A | - | - | |
c.813C > T | p.Leu271 | rs2233045 | |
c.*17A > G | - | - | |
c.*477C > T | - | - | |
MAGEA11
| c.96+38A > G | - | - |
c.193-64T > C | - | - | |
c.266+10C > T | - | - | |
c.1077 C > T | p.Leu359 | - | |
c.*234T > C | - | - | |
MAGEC1
| c.-2051G > A | - | - |
c.-2008T > C | - | rs1003682 | |
c.2T > C | P.Met1? | - | |
c.5-44T > C | - | - | |
c.74G > A | p.Cys25Tyr | rs176036 | |
c.452C > T | p.Thr151Ile | rs176037 | |
c.1327C > G | p.Leu443Val | rs62611966 | |
c.1401C > G | p.His467Gln | rs176048 | |
c.2125C > T | p.His709Tyr | rs56256227 | |
c.3174G > A | p.Glu1058 | rs12845617 | |
c.*53C > T | - | rs41300301 | |
MAGEC3
| c.-189C > T | - | - |
c.259-66G > A | - | - | |
c.259-15T > C | - | - | |
c.880C > G | p.Leu294Val | - | |
c.958C > T | p.Leu320 | rs176025 | |
MBNL3
| c.923-11G > A | - | - |
RBMX
| c.-1C > A | - | rs2011584 |
SUHW3
| c.1851A > C | p.Gly617 | rs209238 |
c.2161+4C > T | - | - | |
c.2162-41T > C | - | - | |
ZNF75
| c.1434 G > A | p.Thr478 | rs1129093 |
Sample group | Carrier frequency | OR (95% CI) | P |
---|---|---|---|
Male population controls | 7/757 (0.92%) | 1.00 | |
Female population controls | 5/764 (0.65%) | 1.00 | |
Patients with BPH | 2/375 (0.53%) | 1.00 | |
PSA controls | 9/746 (1.21%) | 1.00 | |
Patients with unselected PC | 13/757 (1.72%) | 1.99 (1.00-3.95)* | 0.04* |
2.35 (1.10-5.02)** | 0.02** | ||
Patients with HPC | 4/163 (2.45%) | 2.86 (0.98-8.38)* | 0.04* |
3.38 (1.10-10.40)** | 0.02** |
Mature miRNA1
| p-value | Pre-miR miRBase ID | Location | Possible target site in MAGEC1
| Validation (TaqMan) |
---|---|---|---|---|---|
hsa-miR-296-5p | 0.0049 | MI0000747 | chr 20: intronic (AL136532) | ||
hsa-miR-766
|
0.0157
|
MI0003836
|
chr X: intronic (
SEPT6
)
|
+ (in families 1,15,232,362)
| |
hsa-miR-767-3p
|
0.0189
|
MI0003763
|
chr X: intronic (
GABRA3
)
|
+ (in families
1, 15)
| |
hsa-miR-151-5p
|
0.0312
|
MI0000809
|
chr 8: intronic (
PTK2
)
|
c.5-44T > C
c.*53C > T
|
+ (in family 1)
|
hsa-miR-133a
|
0.0316
|
133a-1: MI0000450
|
chr 18: intronic (
MIB1
)
|
c.74G > A
|
+ (in family 15)
|
133a-2: MI0000451
|
chr 20: intronic (
C20orf166
)
| ||||
hsa-miR-451
|
0.0319
|
MI0001729
|
chr 17: intergenic
|
c.1327C > G
|
+ (in family 1)
|
hsa-miR-23b
|
0.0393
|
MI0000439
|
chr 9: intronic (
C9orf3
)
|
c.452C > T
c.1327C > G
|
+ (in families 1, 15, 413)
|
hsa-miR-223
|
0.0404
|
MI0000300
|
chr X: intergenic
|
+ (in families 1, 15, 362, 413)
| |
hsa-miR-146a* | 0.0404 | MI0000477 | chr 5: intergenic | ||
hsa-miR-342-5p
|
0.0410
|
MI0000805
|
chr 14: intronic (
EVL
)
|
c.452C > T
|
+ (in families 248, 292, 402, 408, 413)
|
hsa-miR-183* | 0.0433 | MI0000273 | chr 7: intergenic | ||
hsa-miR-151-3p
|
0.0438
|
MI0000809
|
chr 8: intronic (
PTK2
)
|
c.5-44T > C
c.*53C > T
|
+ (in families 1, 402)
|
hsa-miR-129-3p | 0.0465 | MI0000473 | chr 11: intergenic | ||
hsa-miR-129* | 0.0477 | MI0000252 | chr 7: intergenic |
Mature miRNA1
| p-value | Pre-miR miRBase ID | Location | Possible target site in MAGEC1
| Validation (TaqMan) |
---|---|---|---|---|---|
hsa-miR-32 | 0.0001 | MI0000090 | chr 9: intronic (C9orf5) | c.*53C > T | + (in families 1, 248) |
hsa-miR-30a | 0.0102 | MI0000088 | chr 6: intronic (C6orf155) | ||
hsa-miR-33a | 0.0184 | MI0000091 | chr 22: intronic (SREBF2) | ||
hsa-miR-345 | 0.0210 | MI0000825 | chr 14: intergenic | ||
hsa-miR-195
|
0.0245
|
MI0000489
|
chr 17: intronic (
AC027763
)
|
c.*53C > T
|
+ (in families 292, 362, 408)
|
hsa-miR-487b
|
0.0279
|
MI0003530
|
chr 14: intergenic
|
c.*53C > T
|
+ (in families 248, 292)
|
hsa-miR-370 | 0.0292 | MI0000778 | chr 14: intergenic | ||
hsa-miR-770-5p
|
0.0305
|
MI0005118
|
chr 14: intronic (
MEG3
)
|
c.3174G > A
|
-
|
hsa-miR-29c
|
0.0330
|
MI0000735
|
chr 1: intergenic
|
c.1327C > G
c.2125C > T
|
+ (in families 1, 248, 362)
|
hsa-miR-34c-3p | 0.0351 | MI0000743 | chr 11: intergenic | ||
hsa-miR-148a | 0.0426 | MI0000253 | chr 7: intergenic | ||
hsa-miR-20b
|
0.0431
|
MI0001519
|
chr X: intergenic
|
+ (in family 1)
| |
hsa-miR-29b | 0.0478 | 29b-1: MI0000105 | chr 7: intronic (AC016831) | ||
29b-2: MI0000107 | chr 1: intergenic | ||||
hsa-miR-212
|
0.0482
|
MI0000288
|
chr 17: intergenic
|
c.3174G > A
|
-
|
hsa-miR-7 | 0.0490 | 7-1: MI0000263 | chr 9: intronic (HNRNPK) | ||
7-2: MI0000264 | chr 15: intergenic | ||||
7-3: MI0000265 | chr 19: intronic (C19orf30) |