Table 3.
Classification of genes that are differentially expressed in chondrocyte monolayer (baseline) and scaffold culture
| Functional annotation Gene title (Gene symbol) |
Accession number | Fold change Scaffold vs Monolayer |
|
|---|---|---|---|
| Normal donors | OA donors | ||
| Extracellular matrix | |||
| Aggrecan (ACAN) | [GenBank:X17406] | 2.0 | 3.4 ** |
| Asporin (ASPN) | [GenBank:NM_017680] | 18.8 * | 6.0 * |
| Biglycan (BGN) | [GenBank:NM_001711] | 12.5 | 12.7 * |
| Cartilage intermediate layer protein 2 (CILP2) | [GenBank:BC034926] | 78.2 * | 71.3 * |
| Collagen, type II, alpha 1 (COL2A1) | [GenBank:X06268] | 87.1 | 519.9 ** |
| Collagen, type XI, alpha 1 (COL11A1) | [GenBank:BG028597] | 10.4 ** | 5.9 * |
| Collagen, type IX, alpha 2 (COL9A2) | [GenBank:AI733465] | 4.3 | 8.1 |
| Cartilage link protein 1 (CRTL1) | [GenBank:NM_001884] | 2.5 | 1.8 |
| Cartilage oligomeric matrix protein (COMP) | [GenBank:NM_000095] | 128.0 ** | 794.2 *** |
| Dermatopontin (DPT) | [GenBank:AL049798] | 69.7 ** | 44.2 *** |
| Fibromodulin (FMOD) | [GenBank:NM_002023] | 5.1 | 8.4 * |
| Fibronectin 1 (FN1) | [GenBank:AJ276395] | 5.7 * | 34.6 *** |
| TIMP metalloproteinase inhibitor 4 (TIMP4) | [GenBank:NM_003256] | 14.1 * | 25.4 * |
| Tenascin C (TNC) | [GenBank:BF434846] | 3.3 | 3.5 * |
| Cell adhesion and receptors | |||
| Epidermal growth factor receptor (EGFR) | [GenBank:AW157070] | -3.0 ** | -1.9 |
| Fibroblast growth factor receptor 2 (FGFR2) | [GenBank:NM_022969] | -7.4 * | -4.3 |
| Laminin, alpha 2 (LAMA2) | [GenBank:AK026829] | 5.7 * | 4.8 |
| Laminin, alpha 4 (LAMA4) | [GenBank:NM_002290] | -6.6 * | -8.6 ** |
| Transforming growth factor, beta receptor I (TGFBR1) | [GenBank:AV700621] | 4.2 | 20.0 *** |
| Thrombospondin 3 (THBS3) | [GenBank:L38969] | 8.2 ** | 8.5 * |
| Growth factors | |||
| Bone morphogenetic protein 1 (BMP1) | [GenBank:NM_001199] | 2.1 * | 1.8 |
| Fibroblast growth factor 9 (FGF9) | [GenBank:NM_002010] | -9.0 | -3.0 |
| Insulin-like growth factor 1 (IGF1) | [GenBank:AI972496] | 8.3 | 6.0 |
| Insulin-like growth factor 2 (IGF2) | [GenBank:X07868] | 114.9 ** | 43.5 ** |
| Transforming growth factor, beta 1 (TGFB1) | [GenBank:BC000125] | 3.0 * | 2.4 * |
| Transcription factors | |||
| Distal-less homeobox 5 (DLX5) | [GenBank:NM_005221] | 5.1 * | 25.6 * |
| Homeobox A11 (HOXA11) | [GenBank:H94842] | 6.5 | 2.3 * |
| Homeobox A13 (HOXA13) | [GenBank:BG289306] | 5.2 | 2.0 |
| Runt-related transcription factor 2 (RUNX2) | [GenBank:AL353944] | 4.0 | 4.2 * |
| SIX homeobox 1 (SIX1) | [GenBank:N79004] | 1.6 * | 1.3 |
| SIX homeobox 4 (SIX4) | [GenBank:AI554514] | 1.8 | 2.3 |
| SRY (sex determining region Y)-box 9 (SOX9) | [GenBank:NM_000346] | 4.4 ** | 11.8 ** |
| Wingless-type MMTV integration site family, member 5B (WNT5B) | [GenBank:AW007350] | 3.0 | 7.0 |
| Enzymes | |||
| ADAM metalloproteinase with thrombospondin type 1 motif, 12 (ADAMTS12) | [GenBank:W74476] | -13.7 ** | -2.4 |
| ADAM metalloproteinase with thrombospondin type 1 motif, 2 (ADAMTS2) | [GenBank:NM_021599] | 3.1 | 4.7 ** |
| ADAM metalloproteinase with thrombospondin type 1 motif, 5 (ADAMTS5) | [GenBank:BF060767] | -8.8 * | -7.6 ** |
| Matrix metalloproteinase 1 (MMP1) | [GenBank:NM_002421] | -10.6 ** | -59.7 |
| Matrix metalloproteinase 2 (MMP2) | [GenBank:NM_004530] | 1.9 * | 3.4 * |
| Matrix metalloproteinase 7 (MMP7) | [GenBank:NM_002423] | 109.7 *** | 107.2 ** |
One hundred and seven genes associated with skeletal development and extracellular matrix formation were found differentially expressed in chondrocytes obtained from normal donors cultured in monolayer (baseline) and scaffolds. The expression patterns of these genes were compared with those of differentiating osteoarthritic (OA) chondrocytes to assess the chondrogenic capacity of these cells. Only genes are presented that belong to the shown functional categories. For the complete list see Additional data file 2. * P < 0.05; ** P < 0.01; *** P < 0.001.