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Table 2 Dominant gene signatures induced by transforming growth factor-β1 in the mesenchymal MDA-MB-231 CN and MDA-MB-231 H2 cell lines

From: HER-2 overexpression differentially alters transforming growth factor-β responses in luminal versus mesenchymal human breast cancer cells

Sequence namea

Sequence descriptionb

Fold Δ MB-231 CNc

Fold Δ MB-231 H2d

Gene ontologye

ANGPTL4

Angiopoietin-like 4

 

3.34

Angiogenesis

EDN1

Endothelin 1 (ET-1)

2.87

2.45

Angiogenesis

VEGF

Vascular endothelial growth factor

 

2.16 (4)

Angiogenesis

DAAM1

Dishevelled associated activator of morphogenesis 1

 

3.58

Cytoskeleton regulation

FSCN1

Fascin homolog 1, actin-bundling protein

 

2.71

Cytoskeleton regulation

KRT7

Keratin 7

 

1.71

Cytoskeleton regulation

KRTHB1

Keratin, hair, basic, 1

 

1.70

Cytoskeleton regulation

MYO10

Myosin X

2.13

2.16

Cytoskeleton regulation

NEDD9

Neural precursor cell, developmentally down-regulated 9

 

2.56

Cytoskeleton regulation

PLEK2

Pleckstrin 2

4.62

3.80

Cytoskeleton regulation

PODXL

Podocalyxin-like

3.07

1.92

Cytoskeleton regulation

PDLIM4

LIM domain protein, Reversion-induced LIM protein (RIL)

 

1.95

Cytoskeleton regulation

SMTN

Smoothelin

 

2.02

Cytoskeleton regulation

SPAG4

Sperm associated antigen 4

 

2.60

Cytoskeleton regulation

TAGLN

Transgelin

2.21

3.35

Cytoskeleton regulation

TPM1

Tropomyosin 1 (alpha)

1.90 (3)

2.42 (3)

Cytoskeleton regulation

TUBA3

Tubulin, alpha 3

 

2.04

Cytoskeleton regulation

COL1A1

Collagen, type I, alpha 1

10.10

18.47 (2)

ECM/adhesion

COL4A1

Collagen, type IV, alpha 1

5.08 (2)

3.94 (2)

ECM/adhesion

COL4A2

Collagen, type IV, alpha 2

3.10 (2)

2.40 (2)

ECM/adhesion

COL5A1

Collagen, type V, alpha 1

 

3.71 (3)

ECM/adhesion

COL6A3

Collagen, type VI, alpha 3

 

20.61

ECM/adhesion

COL7A1

Collagen, type VII, alpha 1

 

3.74 (2)

ECM/adhesion

FN1

Fibronectin 1

 

2.22 (4)

ECM/adhesion

ITGA2

Integrin, alpha 2 (CD49B, alpha 2, VLA-2 receptor)

 

1.85

ECM/adhesion

ITGA5

Integrin, alpha 5 (fibronectin receptor)

 

2.58

ECM/adhesion

ITGB1

Integrin, beta 1 (fibronectin, receptor, beta)

 

3.13

ECM/adhesion

LAMC2

Laminin, gamma 2

 

7.84 (2)

ECM/adhesion

MFAP2

Microfibrillar-associated protein 2

 

2.15

ECM/adhesion

SDC1

Syndecan 1

 

2.25 (2)

ECM/adhesion

THBS1

Thrombospondin 1

5.15 (4)

3.03 (4)

ECM/adhesion

CLDN4

Claudin 4

 

1.78

ECM/adhesion

ADAM19

A disintegrin and metalloproteinase domain 19

2.42

3.12

Protease and inhibitors

FURIN

Furin (paired basic amino acid cleaving enzyme)

2.57

2.56

Protease and inhibitors

MMP14

Matrix metalloproteinase 14 (membrane-inserted)

2.19

1.85 (2)

Protease and inhibitors

PRSS3

Protease, serine, 3 (mesotrypsin)

 

3.19 (2)

Protease and inhibitors

PLAU

Plasminogen activator, urokinase

2.02 (2)

2.76 (2)

Protease and inhibitors/ECM

PLAUR

Plasminogen activator, urokinase receptor

 

1.70

Protease and inhibitors/ECM

SERPINE1

PAI-1 plasminogen activator inhibitor type 1

5.80 (2)

3.74 (3)

Protease and inhibitors/ECM

BMP1

Bone morphogenetic protein 1

 

2.29

Secreted factor

FSTL3

Follistatin-like 3 (secreted glycoprotein)

2.31

3.00

Secreted factor

IL11

Interleukin 11

2.78

2.13 (2)

Secreted factor

JAG1

Jagged 1 (Alagille syndrome)

1.98

1.99

Secreted factor

LTBP2

Latent transforming growth factor-β binding protein 2

2.44

3.12

Secreted factor

LTBP3

Latent transforming growth factor-β binding protein 3

 

3.26

Secreted factor

STC1

Stanniocalcin 1

2.99 (2)

2.01 (3)

Secreted factor

TGFB1

Transforming growth factor, beta 1

5.77

3.98 (2)

Secreted factor

WNT5B

Wingless-type MMTV integration site family, 5B

1.80

5.82

Secreted factor

CGB

Chorionic gonadotropin, beta polypeptide

18.25

45.95

Secreted factor

ARHB

RhoB

2.83

1.91

Signal transduction

ARHD

ras homolog gene family, member D

 

9.26

Signal transduction

CSF1R

Colony stimulating factor 1 receptor, (v-fms) oncogene

 

7.16

Signal transduction

EPHB2

EphB2

5.09

6.30 (4)

Signal transduction

MADH7

MAD, mothers against decapentaplegic homolog 7

2.16

5.79

Signal transduction

MAPK13

Mitogen-activated protein kinase 13

 

2.28

Signal transduction

MAPK8IP3

Mitogen-activated protein kinase 8 interact. protein 3

 

2.02

Signal transduction

PIK3CD

Phosphoinositide-3-kinase, catalytic, delta polypeptide

 

2.46

Signal transduction

RAB31

RAB31, member RAS oncogene family

 

1.82

Signal transduction

RALB

v-ral simian leukemia viral oncogene homolog B

 

1.93

Signal transduction

SGNE1

Secretory granule, neuroendocrine protein 1

 

10.38

Signal transduction

SPEC1

Small protein effector 1 of Cdc42

1.92

1.97

Signal transduction

TMEPAI

Transmembrane, prostate androgen induced RNA

7.85

9.08

Signal transduction

ABL1

v-abl Abelson murine leukemia viral oncogene 1

 

1.95

Signal transduction

NET1

Neuroepithelial cell transforming gene 1

 

2.25 (2)

Signal transduction

PINK1

phosphatase and tensin homolog (PTEN) induced putative kinase 1

 

1.98 (2)

Signal transduction

PORCN

Likely ortholog of mouse porcupine homolog, PPN

 

2.49

Signal transduction

PTPRK

Protein tyrosine phosphatase, receptor type, K

1.85

2.29

Signal transduction

JUN

v-jun sarcoma virus 17 oncogene homolog (avian)

 

1.98 (2)

Transcription factor

JUNB

jun B proto-oncogene

2.01

8.34

Transcription factor

MONDOA

Mlx interactor

 

2.26

Transcription factor

SOX4

SOX4 gene for SRY (sex determining region Y)-box 4

 

1.97

Transcription factor

BHLHB2

Basic helix-loop-helix domain containing, class B, 2

4.26 (2)

4.61 (2)

Transcription factor

SNAI2

Snail homolog 2 (Drosophila)

 

2.37

Transcription factor

  1. a,b The primary sequence names and descriptions for the differentially regulated genes (defined as greater or equal to 1.7-fold changed with a p-value of < 0.01) were extracted using Rosetta Resolver. Genes from the dominant ontology classes are shown and thus genes with unknown function or those not in well represented ontology classes are not listed. The complete set of differentially expressed genes can be found in Additional files 6, 7, 8, 9. c Fold change in expression of the induced or repressed genes in the MDA-MB-231 CN cell line after a 24 h exposure to 2 ng/ml recombinant TGF-β1 compared to the diluent treated controls. The number in parentheses after the fold change indicates the number of affected elements that were averaged to calculate the fold difference. d Fold change in expression of the induced or repressed genes in the MDA-MB-231 H2 cell line after a 24 h exposure to 2 ng/ml recombinant TGF-β1 compared to the diluent treated controls. The number in parentheses to the right of the fold change indicates the number of affected elements that were averaged to calculate the fold difference. e The gene ontology annotation was curated from the Summary Function and GO fields downloaded from SOURCE [105].
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Breast Cancer Research

ISSN: 1465-542X

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