Background
Methods
Laser capture microdissection and RNA isolation
RNA amplification, microarray target synthesis and hybridization
Microarray data analysis
Validation by immunohistochemistry
Validation by in situhybridization
Validation by PCR
Results
Unsupervised clustering
No | Diagnosis | Grade1
| AC | LN | ER3
| PgR3
| HER-2 | Bcl-2 | E-CD |
---|---|---|---|---|---|---|---|---|---|
1 | IDC | G3 | IDH | N1
| 0 | 0 | 0 | 80% | >90% |
2 | IDC | G2 | none | N1
| 40% | 0 | 0 | 80% | >90% |
3 | IDC | G2 | none | N0
| 10% | 2% | 0 | 70% | >90% |
4 | IDC | G3 | none | N0
| 90% | 50% | 2+ 2
| 100% | >90% |
5 | IDC | G2 | DCIS | N0
| 90% | 1% | 0 | 95% | >90% |
6 | ILC | G2 | LCIS | N0
| 0 | 0 | 0 | 30% | 0 |
7 | ILC | G1 | none | N0
| 80% | 80% | 0 | 100% | 0 |
8 | ILC | G1 | none | N1
| 50% | 0 | 0 | 80% | 0 |
9 | ILC | G2 | LCIS | N1
| 0 | 0 | 0 | <5% | 0 |
10 | ILC | G1 | none | N0
| 50% | 70% | 0 | 80% | 0 |
Genes differentially expressed between normal ductal and lobular cells
Probe Set1
| Gene Symbol | Gene Title | Rank products | Pairwise comparison |
---|---|---|---|---|
Fold-change | Incr/Decr | |||
Regulation of transcription
| ||||
229431_at |
RFXAP↓ | Regulatory factor X-associated protein | -3.1 | 1/6 |
229732_at |
HSZFP36↓ | ZFP-36 for a zinc finger protein | -3.0 | 0/6 |
207117_at |
H-plk↑ | Krueppel-related zinc finger protein | 2.4 | 6/1 |
Protein biosynthesis and modification
| ||||
214130_s_at |
PDE4DIP↓ | Phosphodiesterase 4D interacting protein (myomegalin) | -3.2 | 1/6 |
232752_at |
--- (LOXL1) ↓ | CDNA FLJ10302 fis, clone NT2RM2000042 (lysyl oxidase-like 1) | -1.4 | 1/6 |
Proteolysis and metabolism
| ||||
49452_at |
ACACB↓ | Acetyl-Coenzyme A carboxylase beta | -18 | 0/8 |
220419_s_at |
USP25↓ | Ubiquitin specific peptidase 25 | -2.9 | 1/6 |
220177_s_at |
TMPRSS3↓ | Transmembrane protease, serine 3 | -2.8 | 1/6 |
Ion transport
| ||||
201735_s_at |
CLCN3↓ | Chloride channel 3 | -2.8 | 2/6 |
205044_at |
GABRP↓ | Gamma-aminobutyric acid (GABA) A receptor, pi | -1.8 | 1/6 |
Actin binding
| ||||
212650_at |
EHBP1↑ | EH domain binding protein 1 | 2.6 | 6/0 |
GTPase activity
| ||||
202975_s_at |
RHOBTB3↑ | Rho-related BTB domain containing 3 | 2.5 | 7/1 |
203264_s_at |
ARHGEF9↑ | Cdc42 guanine nucleotide exchange factor (GEF) 9 | 2.6 | 6/0 |
Regulation of cell development, activation, growth and motility
| ||||
209890_at |
TSPAN5↑ | Tetraspanin 5 | 2.6 | 7/0 |
Small leucine-rich proteoglycan (slrp) family
| ||||
211896_s_at |
DCN↑ | Decorin | 2.0 | 7/1 |
Protein kinase cascade
| ||||
211081_s_at |
MAP4K5↓ | Mitogen-activated protein kinase kinase kinase kinase 5 | -2.3 | 1/7 |
Other
| ||||
206157_at |
PTX3↓ | Pentraxin-related gene, rapidly induced by IL-1 beta | -2.8 | 2/7 |
218431_at |
C14orf133↓ | Chromosome 14 open reading frame 133 | -2.7 | 0/7 |
218514_at |
FLJ10587↓ | Hypothetical protein FLJ10587 | -2.6 | 1/7 |
226760_at |
LOC203411↑ | Hypothetical protein LOC203411 | 3.0 | 6/2 |
Genes differentially expressed between tumor cell types and normal cells
Comparison between lobular carcinoma and normal cells
Probe Set1
| Gene Symbol | Gene Title | Fold-change | |||
---|---|---|---|---|---|---|
Tduc | Tlob | |||||
Lobular carcinoma vs normal cells
(↑ – upregulated in Tlob, ↓ – downregulated in Tlob)
|
L
|
D
|
L
|
D
| ||
Extracellular matrix-receptor interaction and focal adhesion (epithelial-mesenchymal transition) | ||||||
227314_at |
ITGA2↓ | Integrin, alpha 2 | n | n | -4.7 | -6.2 |
201438_at |
COL6A3↑ | Collagen, type VI, alpha 3 | n | n | 4.5 | 7.7 |
203083_at |
THBS2↑ | Thrombospondin 2 | n | n | 6.5 | 6.5 |
205713_s_at |
COMP↑ | Cartilage oligomeric matrix protein | n | n | 6.7 | 8.1 |
226237_at |
COL8A1↑ | Collagen, type VIII, alpha 1 | n | n | 8.4 | 5.9 |
225681_at |
CTHRC1↑ | Collagen triple helix repeat containing 1 | n | n | 18.5 | 48.4 |
219087_at |
ASPN↑ | Asporin | n | n | 23.3 | 22.1 |
WNT signalling
| ||||||
223121_s_at 223122_s_at |
SFRP2↑ | Secreted frizzled-related protein 2 | n | n | 5.8 3.9 | 7.4 7.1 |
229802_at |
WISP1↑ | WNT1 inducible signaling pathway protein 1 | n | n | 9.1 | 12.4 |
Actin, calcium and metal ion binding
| ||||||
204455_at |
DST↓ | Dystonin | n | n | -22.2 | -18.3 |
214087_s_at |
MYBPC1↓ | Myosin binding protein C, slow type | n | n | -10.1 | -12.2 |
209301_at |
CA2↓ | Carbonic anhydrase II | n | n | -9.2 | -8.7 |
206509_at |
PIP↓ | Prolactin-induced protein | n | n | -7.0 | -6.3 |
201131_s_at |
CDH1↓ | Cadherin 1, type 1, E-cadherin | n | n | -6.2 | -7.2 |
226777_at |
ADAM12↑ | ADAM metallopeptidase domain 12 | n | n | 5.7 | 5.3 |
213905_x_at |
BGN/SDCCAG33↑ | Biglycan/serologically defined colon cancer antigen 33 | n | n | 8.3 | 7.2 |
Other
| ||||||
227742_at |
CLIC6↓ | Chloride intracellular channel 6 | n | n | -9.3 | -8.2 |
225817_at |
CGNL1↓ | Cingulin-like 1 | n | n | -5.9 | -7.8 |
219850_s_at |
EHF↓ | Ets homologous factor | n | n | -4.1 | -6.3 |
213975_s_at |
LYZ/ILRB1↑ | Lysozyme | n | n | 10.8 | 7.3 |
Ductal carcinoma vs normal cells
(↓ – upregulated in Tduc, ↓ – downregulated in Tduc)
| ||||||
Regulation of transcription
| ||||||
202672_s_at |
ATF3↓ | Activating transcription factor 3 | -4.5 | -7.7 | n | n |
226147_s_at |
PIGR↓ | Polymeric immunoglobulin receptor | -4.8 | -10 | n | n |
Cytokine and growth factor activity
| ||||||
209466_x_at 211737_x_at |
PTN↓ | Pleiotrophin | -5.8 -7.1 | -8.3 -12.5 | n | n |
823_at |
CX3CL1↓ | Chemokine (C-X3-C motif) ligand 1 | -3.6 | -8.3 | n | n |
Ion transport and metabolism
| ||||||
203296_s_at |
ATP1A2↓ | ATPase, Na+/K+ transporting, alpha 2 | -8.2 | -9.6 | n | n |
204259_at |
MMP7↓ | Matrix metallopeptidase 7 | -4.5 | -7.2 | n | n |
212353_at |
SULF1↓ | Sulfatase 1 | 4.6 | 4.0 | n | n |
Other
| ||||||
1553602_at |
LOC118430↓ | Small breast epithelial mucin | -7.1 | -10.4 | n | n |
223623_at |
ECRG4↓ | Esophageal cancer related gene 4 protein | -6.6 | -5.6 | n | n |
206548_at |
FLJ23556↓ | Hypothetical protein FLJ23556 | -6.3 | -11.2 | n | n |
218585_s_at |
DTL↑ | Denticleless homolog (Drosophila) | 3.6 | 4.8 | n | n |
Tumor vs normal cells
(↑ – upregulated in tumor, ↓ – downregulated in tumor)
| ||||||
Extracellular matrix-receptor interaction and focal adhesion (epithelial-mesenchymal transition) | ||||||
224823_at |
MYLK↓ | Myosin, light polypeptide kinase | -3.5 | -3.4 | -5.9 | -5.4 |
204620_s_at 221731_x_at |
CSPG2↑ | Chondroitin sulfate proteoglycan 2 (versican) | 3.0 3.5 | 4.9 5.3 | 4.5 4.0 | 5.8 6.1 |
221729_at |
COL5A2↑ | Collagen, type V, alpha 2 | 3.5 | 4.4 | 9.3 | 11.3 |
211161_s_at |
COL3A1↑ | Collagen, type III, alpha 1 | 4.1 | 3.3 | 9.8 | 14.9 |
212464_s_at |
FN1↑ | Fibronectin 1 | 5.2 | 5.0 | 8.0 | 10.5 |
202311_s_at 202310_s_at |
COL1A1↑ | Collagen, type I, alpha 1 | 5.6 5.1 | 6.0 5.1 | 12.7 10.4 | 13.0 10.8 |
37892_at |
COL11A1↑ | Collagen, type XI, alpha 1 | 6.7 | 7.8 | 6.6 | 5.9 |
202404_s_at |
COL1A2↑ | Collagen, type I, alpha 2 | 6.8 | 10.1 | 30.5 | 18.3 |
Ion and electron transport
| ||||||
205044_at |
GABRP↓ | Gamma-aminobutyric acid (GABA) A receptor, pi | -4.2 | -8.7 | -6.2 | -8.6 |
220230_s_at |
CYB5R2↓ | Cytochrome b5 reductase 2 | -3.6 | -3.8 | -4.3 | -4.2 |
Regulation of transcription
| ||||||
220625_s_at |
ELF5↓ | E74-like factor 5 (ets domain transcription factor) | -4.0 | -4.8 | -5.9 | -8.4 |
209292_at |
ID4↓ | Inhibitor of DNA binding 4 | -2.9 | -5.1 | -10.8 | -4.5 |
Actin and actin-binding proteins
| ||||||
203951_at |
CNN1↓ | Calponin 1, basic, smooth muscle | -6.7 | -6.6 | -6.9 | -7.3 |
243140_at |
ACTA2↓ | Actin, alpha 2, smooth muscle, aorta | -4.0 | -4.1 | -8.7 | -4.0 |
WNT signaling
| ||||||
202037_s_at |
SFRP1↓ | Secreted frizzled-related protein 1 | -7.1 | -8.8 | -8.5 | -7.3 |
Intermediate filament proteins
| ||||||
209351_at |
KRT14↓ | Keratin 14 | -22.9 | -31.0 | -21.9 | -24.0 |
205157_s_at |
KRT17↓ | Keratin 17 | -17.7 | -21.4 | -9.9 | -12.6 |
212730_at |
DMN↓ | Desmuslin | -10.0 | -10.4 | -7.2 | -7.5 |
201820_at |
KRT5↓ | Keratin 5 | -8.9 | -12.7 | -11.3 | -12.1 |
Other
| ||||||
229947_at |
PI15↓ | Peptidase inhibitor 15 | -6.5 | -7.5 | -18.5 | -15.0 |
205380_at |
PDZK1↓ | PDZ domain containing 1 | -4.5 | -5.8 | -4.2 | -6.4 |
213909_at |
LRRC15↑ | Leucine rich repeat containing 15 | 6.2 | 5.7 | 7.3 | 11.8 |
Comparison between ductal carcinoma and normal cells
Comparison between both types of tumor cells and normal cells
Genes differentially expressed between ductal and lobular carcinomas
Probe Set1
| Gene Symbol | Gene Title | Rank products | Pairwise comparison |
---|---|---|---|---|
Fold-change | Incr/Decr | |||
Cell adhesion
| ||||
201131_s_at |
CDH1↓ | Cadherin 1, type 1, E-cadherin (epithelial) | -6.0 | 3/19 |
207169_x_a |
DDR1↓ | Discoidin domain receptor family, member 1 | n | 5/19 |
204776_at |
THBS4↑ | Thrombospondin 4 | n | 19/2 |
219087_at |
ASPN↑ | Asporin (LRR class 1) | 3.9 | 23/0 |
Wnt signalling
| ||||
223168_at |
RHOU↓ | RAS homolog gene family, member U | n | 2/20 |
203230_at |
DVL1↑ | Dishevelled, dsh homolog 1 (Drosophila) | n | 20/0 |
Protein ubiquitination
| ||||
215392_at |
USP3↓ | Ubiquitin specific peptidase 3 | -5.0 | 1/21 |
218247_s_at |
RKHD2↓ | Ring finger and KH domain containing 2 | -4.6 | 0/19 |
1569472_s_at |
TTC3↓ | Tetratricopeptide repeat domain 3 | -4.5 | 0/23 |
Regulation of transcription
| ||||
226115_at |
AHCTF1↓ | AT hook containing transcription factor 1 | -4.0 | 0/22 |
201587_s_at |
IRAK1↓ | Interleukin-1 receptor-associated kinase 1 | n | 2/19 |
202599_s_at |
NRIP1↓ | Nuclear receptor interacting protein 1 | n | 0/19 |
201773_at |
ADNP↓ | Activity-dependent neuroprotector | n | 0/20 |
203637_s_at |
MID1↑ | Midline 1 (Opitz/BBB syndrome) | 4.0 | 20/0 |
235444_at |
FOXP1↑ | Forkhead box P1 | n | 19/4 |
Electron and protein transport
| ||||
204351_at |
S100P↓ | S100 calcium binding protein P | -5.3 | 0/19 |
225177_at |
RAB11FIP1↓ | RAB11 family interacting protein 1 (class I) | -3.5 | 2/21 |
204041_at |
MAOB↑ | Monoamine oxidase B | 3.5 | 20/4 |
212902_at |
SEC24A↑ | SEC24 related gene family, member A | 3.5 | 19/2 |
Cell cycle regulation, cell proliferation and signaling
| ||||
204170_s_at |
CKS2↓ | CDC28 protein kinase regulatory subunit 2 | -4.8 | 2/20 |
207414_s_at |
PCSK6↓ | Proprotein convertase subtilisin/kexin type 6 | n | 4/19 |
209678_s_at |
PRKCI↓ | Protein kinase C, iota | n | 0/22 |
209817_at |
PPP3CB↓ | Protein phosphatase 3, catalytic subunit, beta isoform (calcineurin A beta) | n | 0/24 |
201324_at |
EMP1↑ | Epithelial membrane protein 1 | n | 21/0 |
Metabolism and enzyme activity
| ||||
205509_at |
CPB1↓ | Carboxypeptidase B1 (tissue) | -11.1 | 0/19 |
223746_at |
STK4↓ | Serine/threonine kinase 4 | -4.5 | 2/20 |
225491_at |
SLC1A2↓ | Solute carrier family 1 (glial high affinity glutamate transporter), member 2 | -4.1 | 0/20 |
211379_x_at |
B3GALT3↓ | UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 | -4.0 | 0/20 |
219073_s_at |
OSBPL10↓ | Oxysterol binding protein-like 10 | -4.0 | 1/21 |
229366_at |
CRBN↓ | Cereblon | -3.6 | 0/20 |
226350_at |
CHML↓ | Choroideremia-like (Rab escort protein 2) | n | 0/24 |
217717_s_at |
YWHAB↓ | Tyrosine 3-monooxygenase/tryptophan 5-mono-oxygenase activation protein, beta polypeptide | n | 1/20 |
49452_at |
ACACB↑ | Acetyl-Coenzyme A carboxylase beta | n | 19/0 |
220770_s_at |
LOC63920↑ | Transposon-derived Buster3 transposase-like | 5.3 | 24/0 |
Actin and cytoskeletal protein binding
| ||||
211776_s_at |
EPB41L3↓ | Erythrocyte membrane protein band 4.1-like 3 | -5.3 | 0/21 |
201341_at |
ENC1↓ | Ectodermal-neural cortex (with BTB-like domain) | n | 19/3 |
Nuclear components
| ||||
218585_s_at |
DTL↓ | Denticleless homolog (Drosophila) | -4.6 | 1/19 |
225706_at |
GLCCI1↓ | Glucocorticoid induced transcript 1 | -4.5 | 0/25 |
241863_x_at |
TTC14↓ | Tetratricopeptide repeat domain 14 | -4.4 | 1/20 |
228069_at |
FAM54A↓ | Family with sequence similarity 54, member A | -3.8 | 0/20 |
208576_s_at |
HIST1H3B↓ | Histone 1, H3b | -3.3 | 1/19 |
Other
| ||||
1568838_at | --- ↓ | Full-length cDNA clone CS0DF033YE17 of Fetal brain of Homo sapiens (human) | -5.0 | 1/20 |
226067_at |
C20orf114↓ | Chromosome 20 open reading frame 114 | -4.9 | 0/19 |
1553979_at | --- ↓ | Homo sapiens, clone IMAGE:3906992, mRNA | -4.1 | 0/19 |
230534_at |
MGC15634↓ | Hypothetical protein MGC15634 | -3.6 | 2/20 |
226671_at | --- ↓ | CDNA clone IMAGE:4797120 | -3.8 | 2/20 |
219768_at |
VTCN1↑ | V-set domain containing T cell activation inhibitor 1 | 7.8 | 21/2 |
214657_s_at |
TncRNA↑ | Trophoblast-derived noncoding RNA | 4.5 | 21/0 |
213004_at |
ANGPTL2↑ | Angiopoietin-like 2 | n | 19/4 |
Validation by immunohistochemistry on tissue microarrays
Features | IDC | ILC |
---|---|---|
G1 | 6 (7.5%) | 15 (51.7%) |
G2 | 57 (71.3%) | 11 (37.9%) |
G3 | 17 (21.2%) | 3 (10.3%) |
ER+ | 57 (71.3%) | 19 (65.5%) |
PgR+ | 50 (62.5%) | 17 (58.6%) |
HER-2+ | 12 (15%) | 1 (3.4%) |
Bcl-2+ | 13 (16.3%) | 4 (13.8%) |
N0
| 56 (70%) | 21 (72.4%) |
N1
| 16 (20%) | 6 (20.7%) |
N2
| 8 (10%) | 2 (6.9%) |
Total number of cases | 80 | 29 |
Antibodies | Tumors | Normal tissues (n = 22) | Fisher's pvalue | |
---|---|---|---|---|
Cytokeratin 5/6 |
Ductal carcinomas (n = 80)
| 9 (11.2%) | 22 (100%) | <0.0001 |
Lobular carcinomas (n = 29)
| 3 (10.3%) | <0.0001 | ||
Cytokeratin 17 |
Ductal carcinomas (n = 80)
| 8 (10%) | 22 (100%) | <0.0001 |
Lobular carcinomas (n = 29)
| 2 (6.9%) | <0.0001 |
Antibodies | Ductal carcinomas (n = 80) | Lobular carcinomas (n = 29) | Fisher's pvalue |
---|---|---|---|
E-cadherin | 68 (85%) | 2 (6.7%) | <0.0001 |
DVL1 | 20 (25%) | 28 (96.5%) | <0.0001 |
EMP1 | 13 (16.3%) | 27 (93.1%) | <0.0001 |
DDR1 | 77 (96.2%) | 4 (13.8%) | <0.0001 |