Table 3

Down-regulated genes in cancer cells grown as a co-culture with CAFs

No

Fold change

Gene ID

Gene name

Molecular function

Biological process

1

2.17

EPS8L1

Epidermal growth factor receptor kinase substrate 8-like protein 1

intracellular signaling cascade; cell motion; signal transduction

2

2.17

OR4X1

Olfactory receptor 4X1

3

2.18

C2orf61

Uncharacterized protein C2orf61

4

2.18

DSN1

Kinetochore-associated protein DSN1 homolog

5

2.18

PFAS

Phosphoribosylformylglycinamidine synthase

ligase activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

6

2.18

SLC5A2

Sodium/glucose cotransporter 2

carbohydrate transmembrane transporter activity; cation transmembrane transporter activity

cation transport; extracellular transport; amino acid transport; carbohydrate metabolic process; cellular amino acid and derivative metabolic process

7

2.18

TMEM138

Transmembrane protein 138

8

2.19

FOLR1

Folate receptor alpha

receptor activity;transmembrane transporter activity

vitamin transport

9

2.19

MFN2

Mitofusin-2

hydrolase activity, acting on ester bonds; phosphatase activity

intracellular protein transport; organelle organization; mitochondrion organization

10

2.19

NDRG3

Protein NDRG3

11

2.19

UNC13D

Protein unc-13 homolog D

intracellular protein transport; exocytosis

12

2.20

GOLPH3

Golgi phosphoprotein 3

13

2.20

SLC22A13

Solute carrier family 22 member 13

ATPase activity, coupled to transmembrane movement of substances; ligase activity; carbohydrate transmembrane transporter activity; cation transmembrane transporter activity

cation transport; anion transport; extracellular transport; carbohydrate transport; carbohydrate metabolic process

14

2.20

USP54

Inactive ubiquitin carboxyl-terminal hydrolase 54

ubiquitin-protein ligase activity

protein metabolic process

15

2.22

NMI

N-myc-interactor

DNA binding; transcription factor activity; transcription cofactor activity

response to interferon-gamma; intracellular signaling cascade; signal transduction; cellular defense response

16

2.22

PDCD1

Programmed cell death protein 1

17

2.22

SNRPN

Small nuclear ribonucleoprotein-associated protein N

RNA splicing factor activity, transesterification mechanism; RNA binding

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

18

2.23

SPSB1

SPRY domain-containing SOCS box protein 1

19

2.24

ADAMTS15

A disintegrin and metalloproteinase with thrombospondin motifs 15

peptidase activity; protein binding; peptidase inhibitor activity

fertilization; signal transduction; cell-matrix adhesion; cell-cell adhesion; protein metabolic process; signal transduction; ectoderm development; mesoderm development; skeletal system development; angiogenesis; nervous system development; muscle organ development

20

2.24

MTRF1L

Peptide chain release factor 1-like, mitochondrial

translation factor activity, nucleic acid binding; translation release factor activity

protein metabolic process

21

2.24

TOMM7

Mitochondrial import receptor subunit TOM7 homolog

transmembrane transporter activity

intracellular protein transport

22

2.25

ATG7

Autophagy-related protein 7

ligase activity

intracellular signaling cascade; coenzyme metabolic process; protein metabolic process; signal transduction

23

2.25

C19orf52

Uncharacterized protein C19orf52

24

2.25

USF2

Upstream stimulatory factor 2

DNA binding; transcription factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; lipid metabolic process

25

2.26

POGK

Pogo transposable element with KRAB domain

DNA binding

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; ectoderm development; nervous system development

26

2.26

ZNF804B

Zinc finger protein 804B

27

2.27

CD274

Programmed cell death 1 ligand 1

ubiquitin-protein ligase activity; receptor activity; DNA binding; receptor binding; transcription factor activity; transcription cofactor activity

immune system process; neurotransmitter secretion; intracellular protein transport; exocytosis; signal transduction; synaptic transmission; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; protein metabolic process; cell-cell signaling; organelle organization; establishment or maintenance of chromatin architecture; mesoderm development; mammary gland development; response to stress; cellular defense response

28

2.27

FAM132B

Protein FAM132B

29

2.27

STK32C

Serine/threonine-protein kinase 32 C

kinase activity

cell cycle; intracellular signaling cascade; protein metabolic process; cell cycle; signal transduction

30

2.28

CADM4

Cell adhesion molecule 4

receptor activity

31

2.28

GLIPR2

Golgi-associated plant pathogenesis-related protein 1

immune system process

32

2.28

GPR160

Probable G-protein coupled receptor 160

33

2.29

GALNT2

Polypeptide N-acetylgalactosaminyltransferase 2 soluble form

transferase activity, transferring glycosyl groups

carbohydrate metabolic process; protein metabolic process

34

2.29

KRT20

Keratin, type I cytoskeletal 20

structural constituent of cytoskeleton

cellular component morphogenesis; cellular component morphogenesis; ectoderm development; cellular component morphogenesis

35

2.29

PTPN6

Tyrosine-protein phosphatase non-receptor type 6

hydrolase activity, acting on ester bonds; phosphatase activity; receptor activity

immune system process; intracellular protein transport; mitosis; cell surface receptor linked signal transduction; intracellular signaling cascade; cell-matrix adhesion; cell-cell adhesion; protein metabolic process; cytokinesis; cell motion; mitosis; signal transduction; nervous system development; cellular glucose homeostasis

36

2.29

SOHLH1

Spermatogenesis- and oogenesis-specific basic helix-loop-helix-containing protein 1

37

2.31

CENPM

Centromere protein M

38

2.31

HPCAL1

Hippocalcin-like protein 1

calcium ion binding; calmodulin binding; small GTPase regulator activity

visual perception; sensory perception; cell surface receptor linked signal transduction; signal transduction

39

2.31

TMEM81

Transmembrane protein 81

40

2.32

HOXA1

Homeobox protein Hox-A1

DNA binding; transcription factor activity

female gamete generation; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; segment specification; ectoderm development; gut mesoderm development; embryonic development; skeletal system development; angiogenesis; nervous system development; muscle organ development

41

2.32

SMO

Smoothened homolog

G-protein coupled receptor activity; receptor binding

cell surface receptor linked signal transduction; cell-cell signaling

42

2.33

LAMP2

Lysosome-associated membrane glycoprotein 2

lysosomal transport; intracellular protein transport; protein metabolic process

43

2.33

RNF121

RING finger protein 121

ubiquitin-protein ligase activity

protein metabolic process

44

2.34

PLA2G2E

Group IIE secretory phospholipase A2

hydrolase activity, acting on ester bonds

signal transduction; lipid metabolic process; signal transduction

45

2.34

POU6F2

POU domain, class 6, transcription factor 2

DNA binding; transcription factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

46

2.34

PPP2R4

Serine/threonine-protein phosphatase 2A regulatory subunit B'

protein binding;phosphatase activator activity; phosphatase regulator activity

protein metabolic process

47

2.34

STX5

Syntaxin-5

SNAP receptor activity

neurotransmitter secretion; intracellular protein transport; exocytosis; endocytosis; synaptic transmission; cell-cell signaling

48

2.35

DMC1

Meiotic recombination protein DMC1/LIM15 homolog

hydrolase activity; DNA binding

immune system process; meiosis; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; meiosis; response to stress

49

2.35

ERRFI1

ERBB receptor feedback inhibitor 1

signal transduction;signal transduction

50

2.36

TSPYL4

Testis-specific Y-encoded-like protein 4

protein binding; phosphatase inhibitor activity; phosphatase regulator activity

apoptosis; cell cycle; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; protein metabolic process; cell cycle; organelle organization; establishment or maintenance of chromatin architecture

51

2.37

USF1

Upstream stimulatory factor 1

DNA binding; transcription factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; lipid metabolic process

52

2.40

ARFGAP3

ADP-ribosylation factor GTPase-activating protein 3

nucleic acid binding; protein binding; small GTPase regulator activity

cell surface receptor linked signal transduction; cell adhesion

53

2.40

CNBP

Cellular nucleic acid-binding protein

nucleic acid binding

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; lipid metabolic process

54

2.40

NKD1

Protein naked cuticle homolog 1

55

2.41

MRPL51

39S ribosomal protein L51, mitochondrial;

structural constituent of ribosome; nucleic acid binding

protein metabolic process

56

2.41

OPRK1

Kappa-type opioid receptor

G-protein coupled receptor activity

sensory perception; cell surface receptor linked signal transduction; synaptic transmission; cell motion; signal transduction; cell-cell signaling

57

2.41

PTX3

Pentraxin-related protein PTX3

immune response; response to stress; defense response to bacterium

58

2.42

GPRC5B

G-protein coupled receptor family C group 5 member B

G-protein coupled receptor activity

cell surface receptor linked signal transduction; signal transduction

59

2.42

NGLY1

Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase

hydrolase activity

protein metabolic process

60

2.43

CAPN12

Calpain-12

peptidase activity; calcium ion binding; calmodulin binding; calcium-dependent phospholipid binding

induction of apoptosis; intracellular signaling cascade; protein metabolic process; signal transduction

61

2.43

POLD1

DNA polymerase delta catalytic subunit

DNA-directed DNA polymerase activity; hydrolase activity, acting on ester bonds; nucleic acid binding

cell cycle; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; cell cycle

62

2.44

TBC1D8

TBC1 domain family member 8

hydrolase activity; protein binding; small GTPase regulator activity

intracellular protein transport; exocytosis; cellular component morphogenesis

63

2.45

DHRS11

Dehydrogenase/reductase SDR family member 11

oxidoreductase activity

visual perception; sensory perception; lipid metabolic process

64

2.46

LZTR1

Leucine-zipper-like transcriptional regulator 1

structural constituent of cytoskeleton; DNA binding; chromatin binding; protein binding; small GTPase regulator activity; transcription factor activity

spermatogenesis; immune system process; intracellular protein transport; vesicle-mediated transport; cell cycle; nitrogen compound metabolic process; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; protein metabolic process

65

2.46

OR6V1

Olfactory receptor 6 V1

66

2.47

C12orf65

Uncharacterized protein C12orf65

translation factor activity, nucleic acid binding; translation release factor activity

protein metabolic process

67

2.47

C2orf56

Protein midA homolog, mitochondrial

68

2.47

RBM42

RNA-binding protein 42

RNA splicing factor activity, transesterification mechanism; DNA binding; RNA binding

spermatogenesis; neurological system process; cell cycle; nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; protein metabolic process; ectoderm development; nervous system development

69

2.48

DPM2

Dolichol phosphate-mannose biosynthesis regulatory protein

70

2.48

TDRD12

Tudor domain-containing protein 12

RNA helicase activity; translation factor activity, nucleic acid binding; translation initiation factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; protein metabolic process

71

2.53

CCDC85B

Coiled-coil domain-containing protein 85B

72

2.54

MATN1

Cartilage matrix protein

extracellular matrix structural constituent

immune system process; sensory perception of sound;sensory perception; signal transduction; cell-cell adhesion; cellular component morphogenesis; mesoderm development; skeletal system development; blood coagulation

73

2.55

FLYWCH1

FLYWCH-type zinc finger-containing protein 1

74

2.55

PLA2G2D

Group IID secretory phospholipase A2

hydrolase activity, acting on ester bonds

signal transduction; lipid metabolic process; signal transduction

75

2.56

TMEM38A

Trimeric intracellular cation channel type A

76

2.58

RGS11

Regulator of G-protein signaling 11

protein binding;small GTPase regulator activity

cell surface receptor linked signal transduction; signal transduction; dorsal/ventral axis specification

77

2.61

BAHD1

Bromo adjacent homology domain-containing 1 protein

DNA binding

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

78

2.67

CHD5

Chromodomain-helicase-DNA-binding protein 5

DNA helicase activity; nucleic acid binding

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; organelle organization; establishment or maintenance of chromatin architecture

79

2.67

CHD5

Tryptophan-rich protein;

structural constituent of ribosome; nucleic acid binding

protein metabolic process

80

2.67

CYP39A1

Cytochrome P450 39A1

oxidoreductase activity

respiratory electron transport chain; lipid metabolic process

81

2.68

SUDS3

Sin3 histone deacetylase corepressor complex component SDS3

cell cycle

82

2.69

C16orf62

UPF0505 protein C16orf62

83

2.69

FLOT2

Flotillin-2

intracellular protein transport; vesicle-mediated transport

84

2.69

NINJ1

Ninjurin-1

neurological system process; cell adhesion; cell adhesion; ectoderm development; nervous system development

85

2.70

FAM84A

Protein FAM84A

86

2.71

PAF1

RNA polymerase II-associated factor 1 homolog

87

2.71

PAF1

Peroxisome assembly factor 1

protein metabolic process

88

2.77

POLR2F

DNA-directed RNA polymerases I, II, and III subunit

DNA-directed RNA polymerase activity; nucleic acid binding

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

89

2.78

C12orf34

Uncharacterized protein C12orf34

90

2.80

GGT6

Gamma-glutamyltransferase 6 light chain

acyltransferase activity; peptidase activity

cellular amino acid and derivative metabolic process; protein metabolic process

91

2.83

TSC22D4

TSC22 domain family protein 4

DNA binding; transcription factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

92

2.84

CLRN2

Clarin-2

93

2.92

KCNS1

Potassium voltage-gated channel subfamily S member 1

cation transmembrane transporter activity; voltage-gated potassium channel activity; cation channel activity

muscle contraction; blood circulation; neuronal action potential propagation; cation transport; signal transduction; synaptic transmission; signal transduction; cell-cell signaling

94

2.94

OR51T1

Olfactory receptor 51 T1

95

2.96

OR51I1

Olfactory receptor 51I1

96

3.01

ZNF135

Zinc finger protein 135

DNA binding;transcription factor activity

nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

97

3.03

QDPR

Dihydropteridine reductase

oxidoreductase activity

cellular amino acid and derivative metabolic process

98

3.11

C9

Complement component C9b

peptidase activity; receptor activity

complement activation; signal transduction; cell-cell adhesion; protein metabolic process; signal transduction; response to stimulus

99

3.16

VDAC1

Voltage-dependent anion-selective channel protein 1

voltage-gated ion channel activity; anion channel activity

anion transport

100

3.85

FDX1L

Adrenodoxin-like protein, mitochondrial

oxidoreductase activity

respiratory electron transport chain; ferredoxin metabolic process; vitamin metabolic process; lipid metabolic process; protein metabolic process

The list of down-regulated genes in cancer cells grown as a co-culture with carcinoma-associated fibroblasts (CAFs). Gene ID, name, molecular function and biological process are listed according to the Panther Database classification www.pantherdb.org webcite. The analyzed genes were significantly down-regulated at the level of p < 0.05, fold change > 2.0.

Król et al. BMC Veterinary Research 2012 8:35   doi:10.1186/1746-6148-8-35