Background
Methods
Analysis of PrCa miRNA datasets
Repository | Disease condition | Sample type | miR | Deregulation | Fold change | p value | PMID |
---|---|---|---|---|---|---|---|
GSE65061 | Early/late recurrence | FFPE tissue | 301b | UP4 | 1.7 | 0.026 | 25760964 |
GSE26245 | Recurrent/non-recurrent | FFPE tissue | 130b | UP4 | 1.2 | 0.024 | 21703393 |
GSE26247 | Recurrent/non-recurrent | FFPE tissue | 130b | UP4 | 1.3 | 0.017 | 21703393 |
Personal communication | Metastatic/primary tumor | Frozen tissue | 130b | UP4 | 1.6 | NA | 21765474 |
GSE35813 | PC-3/RWPE-1 | Cell lines | 130b and 301b | UP4 | 1.7 and 1.5 | 0.011 and 0.0091 | 22982408 |
GSE80400 | Tumor/normal | Frozen tissue | 130b | UP4 | 1.9 | 0.14 | 26041889 |
GSE21032, GSE21036, E-TABM-794 | Tumor/normal Recurrent/non-recurrent | Frozen tissue | 130b | UP3 | NA NA | NA 0.004 | 26489476 |
GSE34933, GSE21032, GSE26367 | Tumor/normal | Frozen and FFPE tissue | 130b | UP3 | NA | 0.00000035 | 27179774 |
GSE21036 (PMID 20579941) | Primary tumor/normal Metastatic/primary tumor Metastatic tumor/normal | Frozen tissue | 130b | UP3 | 1.5 1.7 2.6 | < 0.0001 = 0.0002 0.0001 | 28192399 |
GSE55323, GSE26245, GSE26247, GSE65061, GSE62610, GSE46738 | Recurrent/non-recurrent | Frozen and FFPE tissue | 301b | UP3 | NA | 0.0066 | 28651018 |
GSE36803 | Tumor/normal | Frozen tissue | 130b | UP2 | < 1.5 | 0.0019 | 23233736 |
NA | Tumor/normal | FFPE tissue | 130b | UP2 | 2.2 | 0.02 | 27120795 |
NA | Resistant/sensitive to docetaxel | Cell lines | 301b | UP1 | 2.2 | 0.002 | 24714754 |
GSE14857 | Tumor/normal | Frozen tissue | 130b | UP1 | 1.5 | 0.0006 | 19676045 |
E-TABM-794 | Tumor/normal | Frozen tissue | 130b and 301b | UP1 | > 1.5 | < 0.05 | 21765474 |
NA | PrCa patients/Normal control individuals PrCa metastatic/PrCa localized patients | Plasma | 130b | UP1 | 4.7 6.1 | 0.034 0.007 | 22240788 |
E-MTAB-408 | Primary tumor/BPH | Frozen tissue | 130b | UP1 | 2.00 | 0.00019 | 22266859 |
E-MTAB-408 | CRPCs/BPH | Frozen tissue | 130b | UP1 | 2.5 | 0.011 | 22266859 |
NA | C4-2B/RWPE-1 C4-2B/RWPE1 derived exosomes | Cell lines | 130b | UP1 | ~ 2, 3.7 | < 0.05 | 24715691 |
GSE62610 | Recurrent/non-recurrent | FFPE tissue | 301b | UP1 | 2 | 0.025 | 25416653 |
NA | Exosomes/cell line | Cell lines | 130b | UP1 | 8.6 | NA | 27102850 |
NA | Short/long overall survival | FFPE tissue | 301b | UP1 | NA | 0.029 | 27307749 |
NA | Hypoxia/normoxia | Cell lline | 301b | UP1 | > 2 | NA | 27327120 |
NA | Patients/healthy donors | Exosomes | 130b | UP1 | NA | 0.0021 | 28192399 |
NA | Recurrent/non-recurrent | Tissue | 130b | UP1 | NA | 0.018 | 28192399 |
NA | After/before docetaxel | Plasma and serum | 301b | UP1 | 1.6 | 0.04 | 24714754 |
GSE46738 | High/Low pre-operatory PSA levels | FFPE tissue | 130b and 301b | DOWN and UP1 | − 1.3 and 1.2 | < 0.049 and < 0.003 | 25663948 |
GSE55323 | Recurrent/non-recurrent | Tissue | 301b | DOWN4 | − 1.2 | 0.017 | 24967583 |
NA | Tumor/normal | FFPE tissue | 130b | DOWN1 | NA | < 0.0001 | 25154741 |
NA | Gleason 4 or 5/gleason 3 Recurrent/non-recurrent | Serum | 130b | DOWN1 | NA | < 0.05 | 25874774 |
GSE52955 | Tumor/normal | Frozen tissue | 130b and 301b | DOWN1 | NA | < 0.0001 and 0.0014 | 28166834 |
Analysis of prostate transcriptomic and clinical profiles of TCGA-PRAD
Analysis of PrCa DNA methylation data
Statistical analysis
Results
The genomic and epigenomic context of the miR-130b/301b cluster support their coordinated expression in PrCa
The expression of miR-130b and miR-301b increases in PrCa neoplastic tissue and metastasis
The miR-130b and miR-301b are expressed in PrCa and their abundance is positively associated with the DNA methylation of their locus
The expression of miR-130b and miR-301b associates with negative PrCa patient clinical outcome
The correlation between the expression of validated direct targets of miR-130b and miR-301b supports their oncogenic function in PrCa
Gene | PMID | Role in PrCa | miR-130b | miR-301b | ||
---|---|---|---|---|---|---|
r
| p value |
r
| p value | |||
PPARGC1A
|
23868745
|
TSG? (PMC4884178)
|
− 0.3571
|
< 0.0001
|
− 0.3109
|
< 0.0001
|
TP63
a
|
24398967
|
TSG
|
− 0.3313
|
< 0.0001
|
− 0.2286
|
< 0.0001
|
NDRG2
b
|
27327120
|
TSG
|
− 0.2985
|
< 0.0001
|
− 0.2427
|
< 0.0001
|
SLC8A1
c
|
26489476
|
TSG
|
− 0.2884
|
< 0.0001
|
− 0.3174
|
< 0.0001
|
PARVA
c
|
26489476
|
TSG
|
− 0.2846
|
< 0.0001
|
− 0.3113
|
< 0.0001
|
SMAD4
|
24220575
|
TSG
|
− 0.2240
|
< 0.0001
|
− 0.2151
|
0.0002
|
ZBTB4
|
24220575
|
TSG
|
− 0.2231
|
< 0.0001
|
− 0.2829
|
< 0.0001
|
ITGB1
|
24498407
|
TSG
|
− 0.2119
|
< 0.0001
|
− 0.1995
|
0.0006
|
STAT3 | 24040078 | OG | − 0.1423 | 0.0009 | − 0.2049 | 0.0004 |
ZEB1 | 22847613 | OG | − 0.1338 | 0.0018 | − 0.2058 | 0.0004 |
FMR1 | 24021279 | unknown | − 0.1250 | 0.0035 | − 0.1380 | 0.0175 |
CSF1 | 22005523 | OG | − 0.1190 | 0.0055 | − 0.1904 | 0.001 |
PTEN | 24220575 | TSG | − 0.1174 | 0.0062 | − 0.1072 | 0.0654 |
MMP2b | 25154741 | OG | − 0.1094 | 0.0108 | − 0.1286 | 0.027 |
PPARG | 21135128 | TSG | − 0.1072 | 0.0125 | − 0.0358 | 0.5397 |
PDGFRA | 22995917 | OG | − 0.1041 | 0.0152 | − 0.1640 | 0.0047 |
UVRAG | 22228303 | TSG | − 0.0812 | 0.0585 | − 0.0984 | 0.0909 |
RUNX3 | 20176475 | TSG | − 0.0220 | 0.6099 | − 0.1161 | 0.046 |
ARb | 28192399 | TSG | − 0.0201 | 0.6405 | − 0.0772 | 0.1856 |
DEDD2b | 27307749 | TSG | 0.0080 | 0.8522 | 0.0418 | 0.4733 |
DICER1 | 23392577 | unknown | 0.1111 | 0.0096 | 0.0297 | 0.6112 |
TP53INP1
|
18974142
|
OG
|
0.2378
|
< 0.0001
|
0.1746
|
0.0026
|
LMNB1
b
|
28166834
|
OG
|
0.2404
|
< 0.0001
|
0.2071
|
0.0003
|
CCNA2
|
24681352
|
OG
|
0.2947
|
< 0.0001
|
0.2004
|
0.0005
|