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Table 3 Differential expression of genes associated with human arthritis in GWAS studies

From: Kinetics of gene expression and bone remodelling in the clinical phase of collagen-induced arthritis

Gene symbol

Ctrl a

0 to 3d vs. Ctrl b

1 to 2w vs. Ctrl c

3 to 4w vs. Ctrl d

Decline vs. Ctrl e

Protein function

 

log2

Fold change ( P -value)

 

Ankylosing spondylitis

Hapln1

6.72

1.69 (0.15)

3.10 (0.01)

2.89 (0.005)

2.08 (0.01)

Involved in cartilage development and bone formation. Associated with osteophyte formation in OA [ 30 ].

Edil3

5.58

1.53 (0.14)

2.95 (0.003)

3.07 (0.005)

2.33 (0.11)

Integrin ligand with a proposed role in cartilage development and angiogenesis. Inhibitor of the WNT pathway [ 30 ].

Ano6

7.22

2.25 (0.05)

1.88 (0.04)

1.61 (0.14)

1.19 (0.60)

Regulates phosphatidylserine exposure on the cell surface, which is essential for mineralisation of bone and involved in osteoclast formation [ 30 , 31 ].

Psmg1

6.95

2.04 (0.002)

1.91 (0.002)

1.37 (0.03)

1.03 (0.78)

Proteasome Assembly Chaperone 1. The gene is, in addition, associated with inflammatory bowel disease [32].

Rheumatoid arthritis

Anapc4

6.85

1.77 (0.0008)

1.91 (0.0003)

1.45 (0.02)

1.18 (0.45)

An SNP close to this gene was associated with RA susceptibility [33]. The encoded protein is an E3 ubiquitin ligase involved in control of the cell cycle, muscle cell function, and function of neurons [34].

Cd84

5.61

3.07 (0.01)

3.01 (0.004)

2.17 (0.02)

1.51 (0.12)

Membrane protein involved in immune function. High expression of the gene was associated with a positive response to Etanercept treatment [35].

Il6st

9.44

2.41 (0.03)

1.79 (0.06)

1.52 (0.10)

1.09 (0.76)

Signal transducing subunit for cytokines belonging to the IL-6 family. Activates Stat-3, which plays a role in OC and OB differentiation and their interaction [ 36 ].

Ptpn2

6.68

1.74 (0.06)

1.78 (0.02)

1.32 (0.30)

1.46 (0.16)

Protein phosphatase involved in T-cell activation by regulation of the JAK/STAT signalling pathway [33,37,38].

Cdk6

5.88

2.51 (0.10)

2.35 (0.08)

2.11 (0.08)

1.64 (0.21)

Cyclin-dependent kinase involved in proliferation of lymphocytes [39].

Prkcq

7.42

0.48 (0.17)

0.65 (0.26)

0.55 (0.16)

0.61 (0.32)

Kinase involved in activation of NFκB and AP-1 transcription factors [39].

Prkch

7.20

1.36 (0.04)

1.43 (0.07)

1.58 (0.06)

0.99 (0.95)

Serine/threonine kinase. The association with RA is suggestive [38].

Osteoarthritis

Gnl3

7.81

2.41 (0.11)

2.10 (0.08)

2.17 (0.07)

1.47 (0.34)

Nucleostemin. Increased in in vitro cultures of chondrocytes from patients with OA [40].

Glt8d

7.18

1.97 (0.03)

1.99 (0.02)

1.43 (0.05)

1.13 (0.71)

Involved in glycosylation of cartilage proteins [40].

Pla2g

5.96

1.47 (0.16)

1.67 (0.04)

2.06 (0.03)

1.71 (0.04)

Cytosolic phospholipase A2 enzyme. mRNA transcript was abundantly expressed in chondrocytes from OA patients [41].

Ptgs2

6.91

2.66 (0.01)

1.72 (0.07)

1.15 (0.41)

1.56 (0.03)

Cyclooxygenase 2 (COX-2). mRNA transcript was abundantly expressed in chondrocytes from OA patients [41].

Col12a1

8.24

4.56 (0.04)

4.82 (0.01)

2.97 (0.04)

1.74 (0.22)

A SNP close to this gene has been associated with OA susceptibility [ 40 ]. The encoded protein is expressed by OB in areas of bone formation. KO mice have skeletal abnormalities with less mechanical strength and reduced matrix deposition [ 24 ].

  1. aMean log2 expression in non-induced control mice. Mean fold change and P-value in comparison to control: bon day 0 to 3, cin week 1 to 2, din week 3 to 4, ein the declining disease phase. Genes shown in bold are encoding proteins with a known function in cartilage- or bone remodelling. Ctrl, control; GWAS, genome-wide association studies; IL-6, interleukin 6; KO, knockout; NFκB, nuclear factor kappa B; OA, osteoarthritis; OB, osteoblast; OC, osteoclast; RA, rheumatoid arthritis; WNT, wingless-type.