Introduction
Materials and methods
Patients and samples
RNA extraction and amplification
cDNA array hybridisation
Data analysis
Results
Patient and tumour characteristics
Age: median (range) | 49 (28–68) | ||||
---|---|---|---|---|---|
Menopausal status | pre: 25 (58%) | post: 9 (21%) | na: 1 (2%) | HRT: 8 (19%) | |
Histological subtype | lob: 6 (14%) | duct: 34 (79%) | duct/lob: 1 (2%) | medull: 1 (2%) | na: 1 |
ER status | +: 29 (67%) | -: 13 (30%) | na: 1 (2%) | ||
HER-2 status | +: 5 (12%) | -: 36 (84%) | na: 2 (5%) | ||
Inflamm infiltrate | nil: 19 (44%) | mild: 16 (37%) | mod: 6 (14%) | severe: 2 (5%) | |
Grade | 2: 18 (42%) | 3: 24 (56%) | na: 1 (2%) | ||
Percentage invasive tumour: median (range) | 50 (20–95) | ||||
Response | pCR: 4 (9%)* | cCR: 16 (37%) | MRD: 3 (7%) | PR: 8 (19%) | NC: 12 (28%) |
(*7 [16%] had no surgery) | good: 23 (53%) | poor: 20 (47%) | |||
Clinical stage: | |||||
Primary dimension (n) | |||||
2.0–3.0 cm | 15 | ||||
3.1–4.0 cm | 7 | ||||
4.1–5.0 cm | 9 | ||||
>5.0 cm | 11 | ||||
Multifocal | 1 | ||||
Median dimension (range) (cm) | 4 (2–10) | ||||
ER + | ER - | ||||
Skin involvement (n) | 2 | HER2 + | 4 (10%) | 1 (2%) | |
Inflammatory (n) | 2 | ||||
HER2 - | 24 (56%) | 12 (28%) | |||
Nodal involvement (n) | (2 na) | ||||
N0 | 29 | ||||
N1 | 14 | ||||
N2 | 0 | ||||
NA | 0 |
Biopsy characteristics
Basic validation of array data
Effect of percentage tumour on expression profile
Gene name | Genbank accession | Unigene cluster ID | Symbol | Score (d) | q-value (%) |
---|---|---|---|---|---|
ADP-ribosylation factor 1 | AK023803 | Hs.286221 |
ARF1
|
3.11
|
4.13
|
CDC28 protein kinase regulatory subunit 2 | BQ898943 | Hs.83758 |
CKS2
|
2.73
|
4.13
|
TRK-fused gene | NM_006070 | Hs.446568 |
TFG
|
2.65
|
4.13
|
Discs, large homolog 7 (Drosophila) | NM_014750 | Hs.77695 |
DLG7
|
2.60
|
4.13
|
RAB6B, member RAS oncogene family | NM_016577 | Hs.352530 |
RAB6B
|
2.59
|
4.13
|
Epithelial cell transforming sequence 2 oncogene | AY376439 | Hs.293257 |
ECT2
|
2.56
|
4.13
|
FXYD domain containing ion transport regulator 2 | CR627143 | Hs.413137 |
FXYD2
|
2.54
|
4.13
|
Ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila) | NM_004652 | Hs.77578 |
USP9X
|
2.48
|
4.13
|
Pitrilysin metalloproteinase 1 | CR749279 | Hs.528300 |
PITRM1
|
2.46
|
4.13
|
Myeloid differentiation primary response gene (88) | AK124685 | Hs.82116 |
MYD88
|
2.44
|
4.13
|
Baculoviral IAP repeat-containing 5 (survivin) | NM_001012271 | Hs.1578 |
BIRC5
|
2.42
|
4.13
|
Polo-like kinase 4 (Drosophila) | NM_014264 | Hs.172052 |
PLK4
|
2.40
|
4.13
|
2',3'-cyclic nucleotide 3' phosphodiesterase | NM_033133 | Hs.443836 |
CNP
|
2.40
|
4.13
|
Triosephosphate isomerase 1 | BM913099 | Hs.83848 |
TPI1
|
2.39
|
4.13
|
ALL1-fused gene from chromosome 1q | BX649117 | Hs.75823 |
AF1Q
|
2.37
|
4.13
|
Latent transforming growth factor beta binding protein 2 | NM_000428 | Hs.105689 |
LTBP2
|
-3.49
|
1.00
|
LIM domain binding 2 | AL832772 | Hs.4980 |
LDB2
|
-3.43
|
1.00
|
Collagen, type XV, alpha 1 | NM_001855 | Hs.409034 |
COL15A1
|
-3.39
|
1.00
|
Cadherin 5, type 2, VE-cadherin (vascular epithelium) | NM_001795 | Hs.76206 |
CDH5
|
-3.39
|
1.00
|
Forkhead box O1A (rhabdomyosarcoma) | NM_002015 | Hs.170133 |
FOXO1A
|
-3.17
|
1.00
|
TEK tyrosine kinase, endothelial (venous malformations, multiple cutaneous) | BC035514 | Hs.89640 |
TEK
|
-3.02
|
1.00
|
Regulator of G-protein signaling 5 | NM_003617 | Hs.24950 |
RGS5
|
-2.97
|
1.00
|
Fasciculation and elongation protein zeta 1 (zygin I) | NM_022549 | Hs.79226 |
FEZ1
|
-2.90
|
1.00
|
Vascular endothelial growth factor C | NM_005429 | Hs.79141 |
VEGFC
|
-2.90
|
1.00
|
Tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain | NM_003841 | Hs.253829 |
TNFRSF10C
|
-2.82
|
1.00
|
CDNA FLJ25106 fis, clone CBR01467 | AK128814 | Hs.432914 |
-2.79
|
1.00
| |
Alpha-2-macroglobulin | CR749334 | Hs.74561 |
A2M
|
-2.77
|
1.00
|
Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse) | NM_170677 | Hs.362805 |
MEIS2
|
-2.71
|
1.00
|
Tropomodulin 1 | AK096156 | Hs.404289 |
TMOD1
|
-2.70
|
1.00
|
Isoleucine-tRNA synthetase | NM_013417 | Hs.172801 |
IARS
|
-2.63
|
1.00
|
Response prediction using pre-treatment biopsies
Set of samples | Sample size | Minimum error rate | n of genes used in predictor | p value on 'subset' permutation | p value on 'label' permutation |
---|---|---|---|---|---|
All (20%–90%) | 43 | 28% | 3 | Not determined | 0.079 |
High range (50%–95%) | 25 | 12% | 4 | 0.026 | 0.021 |
Low range (20%–50%) | 24 | 13% | 7 | 0.039 | 0.028 |
Mid range (35%–60%) | 24 | 8% | 7 | 0.001 | 0.002 |
Symbol | Genbank accession | Unigene cluster ID | All | Low | Mid | High | Name |
---|---|---|---|---|---|---|---|
ZNF146
| NM_007145 | Hs.444223 | 100 | 100 | 100 | 0 | Zinc finger protein 146 |
RFC3
| CR749565 | Hs.115474 | 100 | 12 | 100 | 0 | Replication factor C (activator 1) 3, 38kDa |
DLD
| NM_000108 | Hs.74635 | 100 | 4 | 100 | 0 | Dihydrolipoamide dehydrogenase |
EIF3S8
| NM_003752 | Hs.534402 | 0 | 100 | 58 | 0 | Eukaryotic translation initiation factor 3, subunit 8 |
SOD1
| BF131654 | Hs.443914 | 0 | 91 | 25 | 0 | Superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (adult)) |
PBEF1
| NM_005746 | Hs.293464 | 25 | 0 | 0 | 88 | Pre-B-cell colony enhancing factor 1 |
CD9
| AK025016 | Hs.387579 | 0 | 100 | 0 | 0 | CD9 antigen (p24) |
TCEB1
| NM_005648 | Hs.435169 | 0 | 100 | 0 | 0 | Transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C) |
IGFBP4
| CR603382 | Hs.1516 | 0 | 0 | 100 | 0 | Insulin-like growth factor binding protein 4 |
STMN1
| BX647885 | Hs.209983 | 0 | 0 | 100 | 0 | Stathmin 1/oncoprotein 18 |
NDRG1
| AK124709 | Hs.318567 | 0 | 0 | 0 | 100 | N-myc downstream regulated gene 1 |
PAM
| NM_000919 | Hs.352733 | 0 | 0 | 0 | 100 | Peptidylglycine alpha-amidating monooxygenase |
ARHE
| X97758 | Hs.6838 | 20 | 0 | 0 | 76 | Ras homolog gene family, member E |
MAPK6
| NM_002748 | Hs.271980 | 95 | 0 | 0 | 0 | Mitogen-activated protein kinase 6 |
SFRS11
| BX640645 | Hs.443458 | 0 | 91 | 0 | 0 | Splicing factor, arginine/serine-rich 11 |
TESK1
| BC038448 | Hs.79358 | 79 | 0 | 0 | 0 | Testis-specific kinase 1 |
THRAP3
| NM_005119 | Hs.250113 | 60 | 0 | 0 | 0 | Thyroid hormone receptor associated protein 3 |
PTPN7
| AK127214 | Hs.402773 | 55 | 0 | 0 | 0 | Protein tyrosine phosphatase, non-receptor type 7 |
PSMC6
| AK127456 | Hs.156171 | 0 | 41 | 0 | 0 | Proteasome (prosome, macropain) 26S subunit, ATPase, 6 |
CD47
| NM_001777 | Hs.446414 | 0 | 0 | 37 | 0 | CD47 antigen (Rh-related antigen, integrin-associated signal transducer) |
REST
| NM_005612 | Hs.401145 | 23 | 0 | 12 | 0 | RE1-silencing transcription factor |
PCNA
| NM_002592 | Hs.78996 | 0 | 0 | 33 | 0 | Proliferating cell nuclear antigen |
CTPS
| BC009408 | Hs.251871 | 0 | 0 | 16 | 0 | CTP synthase |
ARL6IP
| BC010281 | Hs.75249 | 0 | 12 | 0 | 0 | ADP-ribosylation factor-like 6 interacting protein |
CDH1
| NM_004360 | Hs.194657 | 0 | 12 | 0 | 0 | Cadherin 1, type 1, E-cadherin (epithelial) |
ITSN1
| AF064244 | Hs.66392 | 0 | 0 | 0 | 12 | Intersectin 1 (SH3 domain protein) |
GATA4
| NM_002052 | Hs.243987 | 9 | 0 | 0 | 0 | GATA binding protein 4 |
SNRPB
| BM564070 | Hs.83753 | 0 | 8 | 0 | 0 | Small nuclear ribonucleoprotein polypeptides B and B1 |
DLG7
| NM_014750 | Hs.77695 | 0 | 0 | 8 | 0 | Discs, large homolog 7 (Drosophila) |
KCNN3
| BX649146 | Hs.89230 | 0 | 0 | 0 | 8 | Potassium intermediate/small conductance calcium-activated channel |