Background
Methods
Patients and samples
Real-time RT-PCR
Gene symbols | Alternate symbols | Gene name | Chromosome location | Genbank accession number |
---|---|---|---|---|
NFKB genes (n = 11)
| ||||
NFKB1
| Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (p105) | 4q24 | NM_003998 | |
NFKB2
| Nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100) | 10q24 | NM_002502 | |
REL
| v-rel reticuloendotheliosis viral oncogene homolog | 2p13-p12 | NM_002908 | |
RELA
| NFKB3 | v-rel reticuloendotheliosis viral oncogene homolog A (p65) | 11q13 | NM_021975 |
RELB
| v-rel reticuloendotheliosis viral oncogene homolog B | 19q13.32 | NM_006509 | |
CHUK
| IKBKA | Conserved helix-loop-helix ubiquitous kinase | 10q24-q25 | NM_001278 |
IKBKB
| Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta | 8p11.2 | NM_001556 | |
IKBKG
| Inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma | Xq28 | NM_003639 | |
NLK
| Nemo like kinase | 17q11.2 | NM_016231 | |
NFKBIA
| Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha | 14q13 | NM_020529 | |
NFKBIB
| Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta | 19q13.1 | NM_1001716 | |
Apoptosis (n = 12)
| ||||
BCL2A1
| BFL1/A1 | Baculoviral IAP repeat-containing 2 | 15q24.3 | NM_004049 |
GADD45B
| Growth arrest and DNA-damage-inducible, beta | 19p13.3 | NM_015675 | |
TNFRSF10B
| TRAILR2, DR5 | Tumor necrosis factor receptor superfamily, member 10b | 8p22-p21 | NM_003842 |
FASLG
| FASL, TNFSF6 | Fas ligand (TNF superfamily, member 6) | 1q23 | NM_000639 |
BIRC4
| XIAP | Baculoviral IAP repeat-containing 4 | Xq25 | NM_001167 |
TNFAIP3
| A20 | Tumor necrosis factor, alpha-induced protein 3 | 6q23 | NM_006290 |
TRAF2
| TNF receptor-associated factor 2 | 9q34 | NM_021138 | |
IER3S
| Immediate early response 3, large transcript | 6p21.3 | NM_003897 | |
IER3L
| Immediate early response 3, short transcript | 6p21.3 | NM_052815 | |
BIRC2
| c-IAP1 | Baculoviral IAP repeat-containing 2 | 11q22 | NM_001166 |
MCL1S
| Myeloid cell leukemia sequence 1 (BCL2-related), short transcript | 1q21 | NM_182763 | |
MCL1L
| Myeloid cell leukemia sequence 1 (BCL2-related), large transcript | 1q21 | NM_021960 | |
Immune response (n = 15)
| ||||
IL1A
| Interleukin 1, alpha | 2q14 | NM_000575 | |
IL1B
| Interleukin 1, beta | 2q14 | NM_000576 | |
IL6
| Interleukin 6 (interferon, beta 2) | 7p21 | NM_000600 | |
IL12B
| Interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40) | 5q31.1-q33.1 | NM_002187 | |
IL15
| Interleukin 15 | 4q31 | NM_000585 | |
CCL2
| MCP-1 | Chemokine (C-C motif) ligand 2 | 17q11.2-q21.1 | NM_002982 |
CCR5
| Chemokine (C-C motif) receptor 5 | 3p21 | NM_000579 | |
TNFRSF11A
| RANK | Tumor necrosis factor receptor superfamily, member 11a, activator of NFKB | 18q22.1 | NM_003839 |
TNFSF11
| RANKL | Tumor necrosis factor (ligand) superfamily, member 11 | 13q14 | NM_003701 |
TNF
| Tumor necrosis factor (TNF superfamily, member 2) | 6p21.3 | NM_000594 | |
IRF7
| Interferon regulatory factor 7 | 11p15.5 | NM_001572 | |
GBP1
| Guanylate binding protein 1, interferon-inducible, 67kDa | 1p22.2 | NM_002053 | |
CD40
| CD40 antigen (TNF receptor superfamily member 5) | 20q12-q13.1 | NM_001250 | |
CD40LG
| CD40 ligand (TNF superfamily, member 5, hyper-IgM syndrome) | Xq26 | NM_000074 | |
CD48
| CD48 molecule | 1q21.3-q22 | NM_001778 | |
Cell Proliferation (n = 8)
| ||||
CSF1
| Colony stimulating factor 1 (macrophage) | 1p21-p13 | NM_000757 | |
CSF1R
| Colony stimulating factor 1 receptor, formerly McDonough feline sarcoma viral (v-fms) oncogene homolog | 5q33-q35 | NM_005211 | |
CSF2
| Colony stimulating factor 2 (granulocyte-macrophage) | 5q31.1 | NM_000758 | |
CCND1
| Cyclin D1 (PRAD1: parathyroid adenomatosis 1) | 11q13 | NM_053056 | |
CCND2
| Cyclin D2 | 12p13 | NM_001759 | |
CCND3
| Cyclin D3 | 6p21.3 | NM_001760 | |
CCNG1
| Cyclin G1 | 5q32-q34 | NM_004060 | |
SOD2
| Mn-SOD | Superoxide dismutase 2, mitochondrial | 6q25.3 | NM_000636 |
Tumor progression (n = 10)
| ||||
MMP9
| Matrix metalloproteinase 9 (gelatinase B, 92 kDa type IV collagenase) | 20q11.2-q13.1 | NM_004994 | |
MMP11
| Matrix metalloproteinase 11 (stromelysin 3) | 22q11.23 | NM_005931 | |
PLAU
| UPA | Plasminogen activator, urokinase | 10q24 | NM_002658 |
CTSB
| Cathepsin B | 8p22 | NM_001908 | |
CXCR4
| Chemokine (C-X-C motif) receptor 4 | 2q21 | NM_003467 | |
CXCL12
| SDF1 | Chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) | 10q11.1 | NM_000609 |
ICAM1
| Intercellular adhesion molecule 1 (CD54), human rhinovirus receptor | 19p13.3-p13.2 | NM_000201 | |
VCAM1
| Vascular cell adhesion molecule 1 | 1p32-p31 | NM_001078 | |
SELE
| ELAM1 | Selectin E (endothelial adhesion molecule 1) | 1q22-q25 | NM_000450 |
TNC
| HXB | Tenascin C (hexabrachion) | 9q33 | NM_002160 |
Angiogenesis (n = 4)
| ||||
IL8
| Interleukin 8 | 4q13-q21 | NM_000584 | |
CXCL1
| GRO1 | Chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha) | 4q21 | NM_001511 |
VEGF
| VEGFA | Vascular endothelial growth factor | 6p12 | NM_003376 |
PTGS2
| COX2 | Prostaglandin-endoperoxide synthetase 2 | 1q25.2-q25.3 | NM_000963 |
Statistical analysis
Results
mRNA expression of the 60 NF-κB-associated genes, ESR1/ERα and MKI67in 35 IBCs and 22 non IBCs
GENES | non IBC (n = 22) | IBC (n = 35) | pb
| Metastases (n = 24) | pc
|
---|---|---|---|---|---|
Upregulated genes in IBC | |||||
CXCL12
| 1,0 (0,3–8,1)a
| 6,2 (0,3–1) |
0,0000048
| 1,5 (0,1–20,1) | 0,2 (NS) |
PTGS2/COX2
| 1,0 (0,2–28,7) | 8,1 (0,2–62,6) |
0,000013
| 8,9 (0,1–397,2) |
0,000018
|
CCND2
| 1,0 (0,2–4,8) | 2,8 (0,5–15,3) |
0,000025
| 0,7 (0,1–15,3) | 0,14 (NS) |
MCL1L
| 1,0 (0,5–7,8) | 2 (0,6–5,8) |
0,000035
| 1,1 (0,2–4,7) | 0,74 (NS) |
TNFAIP3/A20
| 1,0 (0,4–2,7) | 2,6 (0,3–12,8) |
0,000042
| 0,9 (0,2–9,1) | 0,83 (NS) |
GADD45B
| 1,0 (0,1–12,4) | 2,9 (0,1–7,3) |
0,000059
| 1,1 (0,2–7,5) | 0,19 (NS) |
FASLG
| 1,0 (0,1–2,5) | 1,8 (0,3–5,6) |
0,00011
| 0,7 (0,1–7,2) | 0,28 (NS) |
CXCL1/GRO1
| 1,0 (0,1–108,7) | 5,8 (0,2–73,4) |
0,00016
| 5,3 (0,1–149,2) |
0,0026
|
MCL1S
| 1,0 (0,3–3,1) | 2,5 (0,5–9,2) |
0,00018
| 1,4 (0,3–7,0) | 0,12 (NS) |
NFKB1
| 1,0 (0,4–11,1) | 2,1 (0,2–8,0) |
0,00025
| 0,8 (0,2–2,9) | 0,92 (NS) |
CCND3
| 1,0 (0,5–3,5) | 1,5 (0,7–24,4) |
0,00038
| 0,8 (0,3–3,3) | 0,22 (NS) |
SELE
| 1,0 (0,1–3,5) | 3,4 (0,2–212,0) |
0,00053
| 0,7 (0,0–21,7) | 0,15 (NS) |
TNC
| 1,0 (0,1–30,3) | 2,9 (0,3–33,4) |
0,00051
| 0,8 (0,1–16,2) | 0,29 (NS) |
VCAM1
| 1,0 (0,4–4,0) | 2,1 (0,9–16,3) |
0,00051
| 1,1 (0,1–7,0) | 0,92 (NS) |
CD40
| 1,0 (0,3–4,0) | 2,7 (0,2–48,0) |
0,00076
| 0,7 (0,1–9,6) | 0,07 (NS) |
CSF1R
| 1,0 (0,2–3,8) | 2,1 (0,3–25,4) |
0,0012
| 0,6 (0,1–3,1) |
0,028
|
CD48
| 1,0 (0,06–8,39) | 3,07 (0,05–46,98) |
0,0017
| 0,54 (0,02–6,41) |
0,036
|
TNFSF11/RANKL
| 1,0 (0,10–6,0) | 4,2 (0,3–358,3) |
0,0019
| 0,9 (0,1–19,1) | 0,86 (NS) |
IER3L
| 1,0 (0,1–4,8) | 2,7 (0,2–19,2) |
0,0022
| 1,1 (0,1–27,6) | 0,80 (NS) |
TNFRSF11A/RANK
| 1,0 (0,2–3,4) | 1,7 (0,1–30,1) |
0,003
| 1,2 (0,1–14,2) | 0,66 (NS) |
RELA
| 1,0 (0,3–4,5) | 1,3 (0,6–4,5) |
0,0031
| 0,9 (0,3–2,3) | 0,65 (NS) |
CCL2/MCP-1
| 1,0 (0,2–3,6) | 2,1 (0,5–8,0) |
0,0039
| 1,4 (0,1–10,5) | 0,21 (NS) |
IKBKG
| 1,0 (0,4–10,2) | 1,4 (0,6–5,2) |
0,0057
| 0,7 (0,2–3,7) |
0,039
|
TNFRSF10B/TRAILR2
| 1,0 (0,2–2,8) | 1,4 (0,3–5,2) |
0,0067
| 1,1 (0,1–12,3) | 0,76 (NS) |
NFKBIB
| 1,0 (0,5–6,7) | 1,6 (0,4–7,0) |
0,0074
| 0,8 (0,3–5,3) | 0,58 (NS) |
ICAM1
| 1,0 (0,2–4,3) | 1,9 (0,2–19,0) |
0,0083
| 0,9 (0,1–28,1) | 0,38 (NS) |
CD40LG
| 1,0 (0,1–5,0) | 2,6 (0,1–30,3) |
0,0096
| 0,7 (0,1–3,1) |
0,03
|
CSF1
| 1,0 (0,1–3,9) | 1,8 (0,3–11,7) |
0,0096
| 0,6 (0,1–2,9) |
0,044
|
PLAU/UPA
| 1,0 (0,2–16,2) | 2,0 (0,4–17,6) |
0,011
| 0,7 (0,1–18,7) | 0,21 (NS) |
NFKB2
| 1,0 (0,3–3,2) | 1,4 (0,4–10,8) |
0,018
| 0,6 (0,2–4,7) | 0,07(NS) |
IL15
| 1,0 (0,00–7,08) | 1,72 (0,12–9,67) |
0,021
| 1,40 (0,06–8,48) | 0,20 (NS) |
GBP1
| 1,0 (0,17–3,71) | 1,35 (0,34–7,06) |
0,032
| 0,78 (0,13–9,64) | 0,99 (NS) |
REL
| 1,0 (0,3–3,3) | 1,4 (0,2–6,6) |
0,039
| 0,5 (0,2–1,5) |
0,002
|
SOD2
| 1,0 (0,43–3,89) | 1,34 (0,26–7,96) |
0,042
| 1,16 (0,40–4,01) | 0,38 (NS) |
CHUK
| 1,0 (0,4–2,4) | 1,1 (0,5–4,6) |
0,048
| 0,7 (0,2–2,1) | 0,25 (NS) |
Downregulated gene in IBC
| |||||
BIRC4/XIAP
| 1,0 (0,2–4,0) | 0,6 (0,1–1,7) |
0,026
| 0,9 (0,2–15,0) | 0,56 (NS) |
MKI67
| 1,0 (0,4–2,8) | 1,1 (0,2–9,4) | 0,37 (NS) | 1,1 (0,1–1327,8) | 0,46 (NS) |
ESR1/ERa
| 1,0 (0,0–23,2) | 0,2 (0,0–7,9) | 0,070 (NS) | 0,1 (0,0–163,5) | 0,13 (NS) |