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Table 3 Classification of genes that are differentially expressed in chondrocyte monolayer (baseline) and scaffold culture

From: Chondrogenic differentiation potential of osteoarthritic chondrocytes and their possible use in matrix-associated autologous chondrocyte transplantation

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 **
  1. 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.