Introduction
Materials and methods
Cells, culture treatments, and RNA extraction
Microarray analysis and gene signature derivations
Gene signatures and clinical parameters for 394 estrogen receptor positive primary breast tumors
Ox-E/ER gene signature functional analysis and prognostic validation
Results
Defining gene signatures responsive to estrogen/estrogen receptor modulation and oxidative stress
Gene signature enrichment and estrogen receptor-positive breast cancer clinical features
Comparison | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
PR- over PR+
| ERBB2- over ERBB2+
| Age | ||||||||
Gene set | NES | Nominal P
| FWER P
| NES | Nominal P
| FWER P
| NES | Nominal P
| FWER P
| |
Modulation of E2 and ER | Estrogen/ER induced | -1.03 | 0.42 | 0.91 | 1.06 | 0.36 | 0.87 |
-1.60
|
0.02
|
0.18
|
Estrogen/ER repressed | -1.14 | 0.27 | 0.81 | -0.99 | 0.46 | 0.90 |
1.67
|
0.01
|
0.11
| |
Modulation of oxidative stress | Ox induced | 1.15 | 0.28 | 0.78 |
-1.61
|
0.04
|
0.19
| -1.45 | 0.07 | 0.36 |
Ox repressed |
-1.53
|
0.02
|
0.24
| 1.19 | 0.20 | 0.75 | 1.18 | 0.21 | 0.74 | |
Ox-E/ER Ox-induced | 0.90 | 0.54 | 0.95 | -1.43 | 0.11 | 0.40 | -1.45 | 0.09 | 0.37 | |
Ox-E/ER Ox repressed |
-1.75
|
0.00
|
0.07
| 1.36 | 0.11 | 0.53 | -1.13 | 0.29 | 0.81 | |
Modulation of ER and oxidative stress | Ox' induced | 1.17 | 0.24 | 0.75 |
-1.66
|
0.02
|
0.13
| -1.21 | 0.19 | 0.71 |
Ox' repressed |
-1.54
|
0.04
|
0.23
| 1.21 | 0.21 | 0.73 |
1.71
|
0.01
|
0.09
| |
Ox'-E/ER Ox induced | -1.30 | 0.15 | 0.61 | -1.04 | 0.40 | 0.86 | -1.19 | 0.24 | 0.75 | |
Ox'-E/ER Ox repressed | -1.39 | 0.11 | 0.44 | 0.94 | 0.54 | 0.93 | 1.49 | 0.07 | 0.32 | |
Literaturea
| MAPK induced | 1.16 | 0.28 | 0.77 | -0.98 | 0.48 | 0.91 | -0.74 | 0.78 | 0.98 |
MAPK repressed | -1.17 | 0.25 | 0.77 | 1.09 | 0.33 | 0.83 | 0.99 | 0.46 | 0.92 | |
Luminal markers |
-1.69
|
0.03
|
0.10
|
1.68
|
0.02
|
0.11
|
1.85
|
0.00
|
0.01
| |
Sustained estrogen-induced | 1.00 | 0.45 | 0.90 | -1.26 | 0.18 | 0.64 | -1.07 | 0.36 | 0.85 | |
Proliferation markers |
1.92
|
0.00
|
0.01
|
-1.95
|
0.00
|
0.01
|
-1.70
|
0.04
|
0.09
|
Comparison | |||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
LN- over LN+
| Grade 3 over grade 1 | Grade 3 over grade 2 | Grade 2 over grade 1 | ||||||||||
Gene set | NES | Nominal P
| FWER P
| NES | Nominal P
| FWER P
| NES | Nominal P
| FWER P
| NES | Nominal P
| FWER P
| |
Modulation of E2 and ER | Estrogen/ER induced | -1.38 | 0.07 | 0.47 | 1.40 | 0.07 | 0.45 | 1.14 | 0.27 | 0.78 | 1.27 | 0.15 | 0.63 |
Estrogen/ER repressed | 1.35 | 0.11 | 0.52 |
-1.51
|
0.05
|
0.28
| -1.27 | 0.16 | 0.62 | -1.21 | 0.18 | 0.69 | |
Modulation of oxidative stress | Ox induced | 1.14 | 0.30 | 0.79 | 1.44 | 0.08 | 0.38 | 1.55 | 0.06 | 0.23 | 0.78 | 0.75 | 0.98 |
Ox repressed | 1.03 | 0.42 | 0.87 | -1.32 | 0.11 | 0.57 |
-1.51
|
0.03
|
0.29
| -0.88 | 0.65 | 0.95 | |
Ox-E/ER Ox induced | 1.10 | 0.36 | 0.82 | 1.11 | 0.34 | 0.80 | 1.11 | 0.35 | 0.82 | -0.98 | 0.46 | 0.90 | |
Ox-E/ER Ox repressed | 1.24 | 0.20 | 0.69 | -1.00 | 0.44 | 0.90 | -1.34 | 0.12 | 0.54 | -0.42 | 1.00 | 1.00 | |
Modulation of ER and oxidative stress | Ox' induced | 1.00 | 0.44 | 0.89 |
1.50
|
0.05
|
0.30
| 1.53 | 0.06 | 0.25 | 0.82 | 0.70 | 0.97 |
Ox' repressed | 0.99 | 0.47 | 0.90 |
-1.74
|
0.01
|
0.06
|
-1.70
|
0.01
|
0.09
| -1.19 | 0.21 | 0.73 | |
Ox'-E/ER Ox induced | 1.03 | 0.42 | 0.87 | 0.91 | 0.52 | 0.93 | 0.75 | 0.77 | 0.98 | -1.43 | 0.12 | 0.40 | |
Ox'-E/ER Ox repressed | 1.24 | 0.20 | 0.68 |
-1.65
|
0.02
|
0.12
| -1.35 | 0.13 | 0.53 | -1.48 | 0.06 | 0.32 | |
Literaturea
| MAPK induced | 0.99 | 0.45 | 0.90 | 0.81 | 0.70 | 0.98 | 0.95 | 0.52 | 0.92 | -0.55 | 0.96 | 1.00 |
MAPK repressed | -1.09 | 0.31 | 0.81 | 1.06 | 0.38 | 0.84 | -1.02 | 0.44 | 0.88 | 1.17 | 0.27 | 0.75 | |
Luminal markers | 1.19 | 0.32 | 0.73 |
-1.71
|
0.02
|
0.08
|
-1.77
|
0.01
|
0.05
| -0.81 | 0.65 | 0.97 | |
Sustained estrogen-induced | -1.20 | 0.23 | 0.69 |
1.79
|
0.00
|
0.03
| 1.33 | 0.11 | 0.54 |
1.63
|
0.02
|
0.14
| |
Proliferation markers |
-1.76
|
0.02
|
0.06
|
2.02
|
0.00
|
0.00
|
1.97
|
0.00
|
0.00
|
1.90
|
0.00
|
0.01
|
Oxidative stress associations with tumor proliferation
Pathway analysis of the Ox-E/ER gene signature
Affymetrix probe set ID | UniGene symbol | E/ER sensitivity | Oxidant sensitivity | Fold change | ||||
---|---|---|---|---|---|---|---|---|
E deprivation | ER-α knockdown | 8 hours diamide | 8 hours H2O2
| 8 hours menadione | ||||
213245_at | ADCY1 | E/ER Induced | Repressed | 0.38 | 0.46 | 0.56 | 0.36 | 0.57 |
212136_at | ATP2B4 | E/ER Induced | Repressed | 0.54 | 0.52 | 0.53 | 0.50 | 0.55 |
203685_at | BCL2 | E/ER Induced | Repressed | 0.25 | 0.39 | 0.66 | 0.43 | 0.56 |
213605_s_at | C6orf216 | E/ER Induced | Repressed | 0.47 | 0.48 | 0.53 | 0.63 | 0.60 |
219174_at | CCDC2 | E/ER Induced | Repressed | 0.49 | 0.66 | 0.64 | 0.61 | 0.47 |
206280_at | CDH18 | E/ER Induced | Repressed | 0.37 | 0.49 | 0.45 | 0.37 | 0.36 |
204135_at | DOC1 | E/ER Induced | Repressed | 0.48 | 0.50 | 0.46 | 0.51 | 0.26 |
214240_at | GAL | E/ER Induced | Induced | 0.27 | 0.42 | 1.84 | 1.82 | 2.04 |
210640_s_at | GPR30 | E/ER Induced | Repressed | 0.19 | 0.60 | 0.46 | 0.36 | 0.27 |
211829_s_at | GPR30 | E/ER Induced | Repressed | 0.29 | 0.44 | 0.43 | 0.35 | 0.33 |
204237_at | GULP1 | E/ER Induced | Repressed | 0.44 | 0.56 | 0.65 | 0.62 | 0.49 |
204235_s_at | GULP1 | E/ER Induced | Repressed | 0.46 | 0.64 | 0.64 | 0.60 | 0.48 |
215913_s_at | GULP1 | E/ER Induced | Repressed | 0.50 | 0.64 | 0.61 | 0.59 | 0.53 |
207719_x_at | KIAA0470 | E/ER Induced | Repressed | 0.59 | 0.63 | 0.57 | 0.61 | 0.58 |
207358_x_at | MACF1 | E/ER Induced | Repressed | 0.52 | 0.51 | 0.66 | 0.61 | 0.61 |
203037_s_at | MTSS1 | E/ER Induced | Repressed | 0.50 | 0.63 | 0.59 | 0.39 | 0.32 |
214156_at | MYRIP | E/ER Induced | Repressed | 0.40 | 0.51 | 0.48 | 0.38 | 0.36 |
212462_at | MYST4 | E/ER Induced | Repressed | 0.52 | 0.53 | 0.63 | 0.66 | 0.36 |
215643_at | SEMA3D | E/ER Induced | Repressed | 0.36 | 0.39 | 0.51 | 0.35 | 0.39 |
220038_at | SGK3 | E/ER Induced | Repressed | 0.15 | 0.34 | 0.61 | 0.32 | 0.32 |
207586_at | SHH | E/ER Induced | Repressed | 0.16 | 0.32 | 0.59 | 0.53 | 0.37 |
216504_s_at | SLC39A8 | E/ER Induced | Repressed | 0.37 | 0.55 | 0.66 | 0.49 | 0.61 |
209921_at | SLC7A11 | E/ER Induced | Induced | 0.37 | 0.38 | 1.68 | 11.09 | 8.82 |
217678_at | SLC7A11 | E/ER Induced | Induced | 0.37 | 0.52 | 2.18 | 13.46 | 11.81 |
201195_s_at | SLC7A5 | E/ER Induced | Induced | 0.35 | 0.51 | 1.60 | 1.72 | 1.78 |
212353_at | SULF1 | E/ER Induced | Repressed | 0.36 | 0.45 | 0.52 | 0.44 | 0.46 |
203998_s_at | SYT1 | E/ER Induced | Repressed | 0.57 | 0.54 | 0.52 | 0.53 | 0.49 |
208161_s_at | ABCC3 | E/ER Repressed | Induced | 7.30 | 4.63 | 1.78 | 2.29 | 3.11 |
209641_s_at | ABCC3 | E/ER Repressed | Induced | 7.91 | 3.94 | 1.79 | 2.50 | 3.46 |
203196_at | ABCC4 | E/ER Repressed | Induced | 3.08 | 4.16 | 1.93 | 1.93 | 2.31 |
206561_s_at | AKR1B10 | E/ER Repressed | Induced | 2.93 | 3.00 | 3.26 | 5.25 | 9.07 |
203180_at | ALDH1A3 | E/ER Repressed | Induced | 9.43 | 8.26 | 3.07 | 5.80 | 6.94 |
205965_at | BATF | E/ER Repressed | Induced | 2.35 | 2.02 | 1.51 | 1.98 | 2.07 |
207996_s_at | C18orf1 | E/ER Repressed | Repressed | 5.71 | 2.07 | 0.49 | 0.36 | 0.47 |
213618_at | CENTD1 | E/ER Repressed | Induced | 3.27 | 2.17 | 1.65 | 2.18 | 3.28 |
218182_s_at | CLDN1 | E/ER Repressed | Induced | 2.48 | 2.64 | 2.77 | 5.43 | 5.28 |
221059_s_at | COTL1 | E/ER Repressed | Induced | 2.45 | 1.81 | 1.56 | 1.59 | 1.82 |
209101_at | CTGF | E/ER Repressed | Induced | 8.30 | 4.15 | 1.78 | 3.68 | 15.15 |
217028_at | CXCR4 | E/ER Repressed | Repressed | 3.22 | 2.82 | 0.47 | 0.56 | 0.30 |
205749_at | CYP1A1 | E/ER Repressed | Induced | 3.28 | 0.55 | 6.75 | 8.96 | 33.02 |
210757_x_at | DAB2 | E/ER Repressed | Repressed | 3.25 | 1.51 | 0.51 | 0.60 | 0.43 |
201279_s_at | DAB2 | E/ER Repressed | Repressed | 3.45 | 1.67 | 0.47 | 0.56 | 0.39 |
201278_at | DAB2 | E/ER Repressed | Repressed | 4.26 | 1.99 | 0.47 | 0.53 | 0.45 |
201280_s_at | DAB2 | E/ER Repressed | Repressed | 4.89 | 2.30 | 0.42 | 0.42 | 0.32 |
201694_s_at | EGR1 | E/ER Repressed | Induced | 5.77 | 4.42 | 1.73 | 3.03 | 2.52 |
219850_s_at | EHF | E/ER Repressed | Repressed | 4.14 | 3.96 | 0.43 | 0.35 | 0.35 |
220625_s_at | ELF5 | E/ER Repressed | Repressed | 2.27 | 2.12 | 0.49 | 0.53 | 0.39 |
220624_s_at | ELF5 | E/ER Repressed | Repressed | 2.38 | 2.35 | 0.54 | 0.53 | 0.38 |
201324_at | EMP1 | E/ER Repressed | Induced | 15.49 | 8.23 | 1.55 | 1.80 | 2.49 |
202949_s_at | FHL2 | E/ER Repressed | Induced | 1.63 | 1.56 | 2.15 | 3.87 | 5.07 |
213144_at | GOSR2 | E/ER Repressed | Induced | 1.81 | 1.86 | 1.93 | 1.95 | 1.72 |
212444_at | GPCR5A | E/ER Repressed | Induced | 3.73 | 2.33 | 1.51 | 2.51 | 1.65 |
203108_at | GPRC5A | E/ER Repressed | Induced | 2.46 | 2.07 | 1.57 | 2.58 | 1.70 |
203424_s_at | IGFBP5 | E/ER Repressed | Repressed | 2.81 | 1.99 | 0.52 | 0.48 | 0.47 |
211959_at | IGFBP5 | E/ER Repressed | Repressed | 3.11 | 2.23 | 0.48 | 0.40 | 0.41 |
203287_at | LAD1 | E/ER Repressed | Induced | 1.70 | 1.86 | 1.79 | 1.81 | 2.20 |
216641_s_at | LAD1 | E/ER Repressed | Induced | 1.72 | 1.94 | 1.65 | 1.56 | 2.21 |
218574_s_at | LMCD1 | E/ER Repressed | Induced | 3.47 | 1.60 | 1.58 | 1.64 | 2.44 |
209679_s_at | LOC57228 | E/ER Repressed | Induced | 3.49 | 2.47 | 1.82 | 1.73 | 2.17 |
209373_at | MALL | E/ER Repressed | Induced | 7.87 | 5.99 | 2.21 | 3.06 | 4.35 |
211026_s_at | MGLL | E/ER Repressed | Induced | 2.52 | 2.78 | 3.26 | 2.66 | 4.96 |
217996_at | PHLDA1 | E/ER Repressed | Induced | 2.80 | 3.15 | 1.67 | 3.40 | 6.33 |
204284_at | PPP1R3C | E/ER Repressed | Repressed | 3.24 | 2.66 | 0.41 | 0.27 | 0.18 |
212636_at | QKI | E/ER Repressed | Repressed | 8.56 | 5.16 | 0.60 | 0.62 | 0.44 |
219562_at | RAB26 | E/ER Repressed | Repressed | 1.99 | 3.66 | 0.62 | 0.59 | 0.64 |
215321_at | RPIB9 | E/ER Repressed | Repressed | 1.72 | 1.88 | 0.66 | 0.46 | 0.56 |
213413_at | SBLF | E/ER Repressed | Repressed | 6.25 | 3.13 | 0.52 | 0.51 | 0.53 |
220979_s_at | ST6GALNAC5 | E/ER Repressed | Repressed | 2.87 | 1.55 | 0.64 | 0.61 | 0.66 |
205547_s_at | TAGLN | E/ER Repressed | Induced | 2.67 | 4.49 | 4.18 | 3.94 | 8.73 |
201506_at | TGFBI | E/ER Repressed | Induced | 4.45 | 2.24 | 1.63 | 2.11 | 2.81 |
218368_s_at | TNFRSF12A | E/ER Repressed | Induced | 1.91 | 1.61 | 1.74 | 2.14 | 2.31 |
218856_at | TNFRSF21 | E/ER Repressed | Induced | 4.72 | 2.65 | 1.69 | 4.21 | 5.40 |
214581_x_at | TNFRSF21 | E/ER Repressed | Induced | 5.81 | 3.41 | 2.08 | 5.43 | 6.63 |
216920_s_at | TRGC2///TRGV9///LOC442532///LOC442670///TARP | E/ER Repressed | Repressed | 2.08 | 1.61 | 0.63 | 0.53 | 0.49 |
215806_x_at | TRGC2///TRGV9///LOC442532///LOC442670///TARP | E/ER Repressed | Repressed | 2.44 | 1.62 | 0.65 | 0.59 | 0.52 |