Table 1

Differentially expressed genes in RASFsn-stimulated chondrocytes (FC ≥ 2; FC ≤ -2; RMA and GCOS)

Functional annotation: gene title (gene symbol)

Accession no.

Chondrocyte mean fold change in expression (GCOS and RMA analysis)

Chondrocyte mean signal intensity (GCOS and RMA analysis)


RASFsn versus NDSFsn stimulation

RASFsn stimulation

NDSFsn stimulation

No stimulation


Inflammation

Cyclooxygenase-2 (COX-2)

NM_000963.1

2.09

4,474.90

1,793.25

108.4

Hydroxysteroid (11-β) dehydrogenase 1 (HSD11B1)

NM_005525

2.41

2,693.41

955.89

1,263.95

Adenosine A2A receptor (ADORA2A)

NM_000675

4.73

249.59

40.13

27.33

Phospholipase A2, group IIA (PLA2G2A)

NM_000300

-2.38

152.32

347.63

787.68

Steroid sulfatase (STS)

AI122754

-3.17

48.36

132.73

412.43

Latexin (LXN)

NM_020169

-5.82

122.35

677.95

610.08

NF-κB signaling pathway

Interleukin-1 receptor antagonist (IL1RN)

U65590

2.10

1,143.23

278.77

48.83

Receptor-interacting serine/threonine kinase 2 (RIPK2)

AF064824.1

2.12

1,190.60

539.58

22.65

Toll-like receptor 2 (TLR2)

NM_003264

2.25

859.07

322.16

57.30

Spermine synthase (SMS)

NM_004595

2.90

165.10

58.99

40.10

Bcl2-related protein A1 (BCL2A1)

NM_004049

4.90

573.95

94.87

14.63

Ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2)

L35594.1

-3.26

810.00

2,175.34

1,273.98

Thioredoxin interacting protein (TXNIP)

AI439556

-3.50

223.27

622.39

670.70

Cytokines/chemokines and receptors

Met proto-oncogene (HGF receptor) (MET)

J02958.1

2.02

823.83

333.01

74.13

Chemokine (C-X-C motif) ligand 1 (Groα)

NM_001511.1

2.08

1,414.49

478.28

28.05

Chemokine (C-X-C motif) ligand 2 (Groβ)

M57731.1

2.51

761.47

237.34

10.08

Interleukin 8 (IL8)

AF043337.1

3.16

5,688.87

1,393.65

38.28

Chemokine (C-X-C motif) ligand 3 (Groγ)

NM_002090

3.78

368.84

58.19

16.68

Chemokine (C-C motif) ligand 20 (MIP-3β)

NM_004591.1

5.25

2,028.88

270.12

14.65

Granulocyte colony-stimulating factor 3 (CSF3)

NM_000759

5.61

180.70

51.59

45.18

Chemokine (C-X-C motif) receptor 4 (CXCR4)

AJ224869

5.66

180.71

27.87

16.10

Interleukin-23, α subunit p19 (IL-23A)

NM_016584

11.00

674.98

43.00

39.33

Immune response

Guanylate binding protein 1, interferon-inducible (GBP1)

BC002666

2.10

450.29

198.92

175.15

2',5'-Oligoadenylate synthetase-related protein p30 (OASL)

AF063612.1

2.38

287.65

98.51

115.65

Interferon-induced protein 44 (IFI44)

NM_006417

2.40

480.29

124.50

238.30

Lymphocyte antigen 6 complex, locus E (LY6E)

NM_002346.1

2.45

569.07

236.97

305.15

Interferon regulatory factor 7 (IRF7)

NM_004030.1

2.48

286.31

93.75

84.93

Interferon-α inducible protein (IFI-6–16)

NM_022873

2.60

550.64

158.67

138.78

Interferon-stimulated gene 20 kDa (ISG20)

U88964

2.61

434.38

153.79

47.20

Interferon-induced protein with tetratricopeptide repeats 3 (IFIT3)

NM_001549

2.69

527.75

137.20

290.03

Pentaxin-related gene, rapidly induced by IL-1β (PTX3)

NM_002852

2.72

340.14

120.25

209.70

Hect domain and RLD 6 (HERC6)

NM_017912.1

3.04

302.12

65.85

117.53

Myxovirus resistance 1, interferon-inducible protein p78 (MX1)

NM_002462

3.09

1,355.03

312.35

557.75

Hect domain and RLD 5 (HERC5)

NM_016323

3.30

608.65

160.90

141.13

2',5'-Oligoadenylate synthetase 1 (OAS1)

NM_002534

4.08

264.81

55.57

70.00

Interferon-α inducible protein, clone IFI-15K (ISG15)

NM_005101.1

4.62

1,943.31

296.19

603.98

Interferon-induced protein 44-like (IFI44L)

NM_006820.1

4.64

691.99

84.63

138.85

Interferon-α inducible protein 27 (IFI27)

NM_005532

5.07

814.69

119.31

154.15

Interferon-induced protein with tetratricopeptide repeats 1 (IFIT1)

NM_001548

5.25

774.38

94.09

361.93

Viperin (cig5)

AI337069

7.14

423.91

34.32

45.65

Collectin sub-family member 12 (COLEC12)

NM_030781

-2.22

648.64

1,347.08

2,518.28

Cell proliferation and differentiation

WNT1 inducible signaling pathway protein 2 (WISP2)

NM_003881

-2.97

206.25

508.11

4,898.73

Inhibitor of DNA binding 3, dominant negative HLH protein (ID3)

NM_002167.1

-3.74

240.35

715.78

1,465.13

Inhibitor of DNA binding 1, dominant negative HLH protein (ID1)

D13889.1

-4.04

742.79

2,479.99

2,376.33

Retinoic acid receptor responder 1 (RARRES1)

NM_002888

-6.10

115.83

538.71

152.20

Fibroblast growth factor 1, acidic (FGF1)

X59065

-8.51

82.49

513.38

70.23

Matrix synthesis

Laminin, β3 (LAMB3)

L25541.1

3.05

636.22

196.21

63.28

EGF-containing fibulin-like ECM protein 1 (EFEMP1)

NM_004105

-3.14

170.34

458.87

331.85

Thrombospondin 2 (THBS2)

NM_003247

-3.28

181.13

489.40

483.68

Spondin 1, extracellular matrix protein (SPON1)

AB051390.1

-4.4

56.04

167.4

69.60

Chondroitin sulfate proteoglycan 2 (CSPG2)

NM_004385

-4.53

235.72

670.67

456.13

Cartilage oligomeric matrix protein (COMP)

NM_000095

-5.08

156.77

655.37

308.43

Others

Metallothionein 1E (MT1E)

BF217861

2.03

1,111.45

554.65

708.38

Solute carrier family 7 member 11 (SLC7A11)

AB040875.1

2.16

692.03

300.52

87.70

Deafness, autosomal dominant 5 (DFNA5)

NM_004403

2.63

1,133.05

379.29

288.20

Phosphoglycerate dehydrogenase (PHGDH)

NM_006623

2.63

171.02

60.04

138.58

Paired immunoglobin-like type 2 receptor α (PILRA)

AJ400843.1

2.82

131.89

32.78

23.75

Calmegin (CLGN)

NM_004362.1

3.20

356.58

87.11

19.30

Neuromedin B (NMB)

NM_021077

3.34

1,163.69

261.33

177.98

Regulator of G-protein signaling 4 (RGS4)

NM_005613.3

3.92

136.81

22.34

42.05

Phosphoinositide-3-kinase, polypeptide 1 (PIK3R1)

AI679268

-3.03

105.59

262.02

182.88

Deiodinase, iodothyronine, type II (DIO2)

U53506.1

-3.10

71.24

193.23

122.88

DEAD (Asp-Glu-Ala-Asp) box polypeptide 10 (DDX10)

NM_004398.2

-3.22

223.36

681.54

252.50

CDK5 regulatory subunit associated protein 2 (CDK5RAP2)

NM_018249

-3.28

250.80

660.54

349.68

Cullin 4B (CUL4B)

AV694732

-3.41

130.55

381.94

83.58

Pyruvate dehydrogenase kinase, isoenzyme 4 (PDK4)

NM_002612.1

-3.65

54.75

179.75

72.75

ATP-binding cassette, sub-family A (ABC1), member 8 (ABCA8)

NM_007168

-3.83

81.80

202.99

141.58

Adlican (DKFZp564I1922)

AF245505.1

-4.90

145.69

486.56

1,835.15


Genes were selected for inclusion if fold change in expression of chondrocytes stimulated with supernatant of a synovial fibroblast cell line derived from a rheumatoid arthritis patient (RASFsn) was ≤-2 (repression) or ≥2 (induction) relative to stimulation with supernatant of a synovial fibroblast cell line derived from a normal donor (NDSFsn) in all specimens (n = 2) as verified by GeneChip Operating Software (GCOS) and Robust Multi-array Analysis (RMA) analyses. Gene expression analysis resulted in 68 differentially expressed genes between RASFsn-stimulated and NDSFsn-stimulated chondrocytes: 44 genes were induced and 24 genes were repressed. Differentially expressed genes were functionally categorized into six rheumatoid arthritis-relevant groups and are listed with accession number, mean fold change in expression and mean signal intensity (generated by GCOS and RMA). Annotation of mean signal intensity of RASFsn-stimulated and NDSFsn-stimulated chondrocytes could facilitate the identification of potential rheumatoid arthritis-specific genes for which further investigation may be required. The mean signal intensity of unstimulated chondrocytes is listed for the determination of baseline expression.

Bcl2, B-cell leukemia 2; cig5, cytomegalovirus-inducible gene 5; ECM, extracellular matrix; Gro, growth-related oncogene; HGF, hepatocyte growth factor; HLH, helix–loop–helix; MIP, macrophage inflammatory protein.

Andreas et al. Arthritis Research & Therapy 2008 10:R9   doi:10.1186/ar2358

Open Data