Fig. 2

Unsupervised hierarchal clustering comparing FLS and FLS cultured in conditioned media from Ch after 6 h in culture and differentially expressed genes in these cells. There are 247 differentially expressed genes in CFLS vs CFLS cultured in conditioned media from chondrocytes (CFLS-Ch) and 31 genes are differentially expressed in JFLS vs conditioned media from chondrocytes (JFLS-Ch) (1% FDR) (a). Using a manually curated list of genes specific to TGFβ and BMP signaling pathways, we examined changes in gene expression over 24 h using linear expression values. CFLS-Ch have decreased expression of BMPR1b (p = 0.003), BMPR2 (p = 0.002), GDF5 (p = 0.030), SMAD5 (p = 0.023), and SMAD7 (p = 0.035) compared with CFLS (b). JFLS-Ch have decreased expression of TGFBI compared with JFLS (p = 0.016) (c). Using a manually curated list of genes specific to Ch differentiation and maturation, changes in the log ratio of the fold change of linear gene expression over 24 h revealed that CFLS-Ch downregulate COLX (p = 0.037), VEGFA (p = 0.034), COL1A1 (p = 0.031), and COL1A2 (p = 0.036) compared with CFLS (d). CFLS-Ch overexpress MMP2 (p = 0.048), FGFR2 (p = 0.050), and IGF1 (p = 0.027) compared with CFLS (d). JFLS-Ch have decreased expression of MMP9 (p = 0.038), COL1A1 (p = 0.042), SOX6 (p = 0.049), and MMP2 (p = 0.050) compared with untreated JFLS. JFLS-Ch upregulate expression of MATN3 (p = 0.023) when compared with JFLS (e)