Figure 5

Transcriptomic analysis. (a) Principal component analysis comparing the gene expression profiles of two chondrosarcoma (CS) biopsies, two chondrogenic 3D pellets and five cell lines in monolayer was performed using 190 genes of interest. (b) Hierarchical clustering analysis (centroid linkage method, uncentered correlation) was performed using a subset of 78 genes differentially expressed between CS cell lines and the group containing CS biopsies and chondrogenic 3D pellets. Genes for which the difference was significant are indicated (*P<0.05; Mann–Whitney test). (c) Expression levels of indicated genes were confirmed in CH03, CH34, and CH56 biopsies, chondrogenic 3D pellets or cells in monolayer. Statistical analysis was performed using t-test (for CH34 and CH56 pellets and cells, *P<0.05 and **P<0.001 compared with the original biopsy; for CH03 cells, ^###P<0.001 compared with CH03 pellet). (d) The expression levels of COL2A1, COMP, and ACAN were determined in indicated tumor biopsies, cell lines in monolayer or chondrogenic 3D pellets as well as normal human mesenchymal stem cell (MSC). Statistical analysis was performed using t-test (for CH34 and CH56 pellets and cells, **P<0.01 compared with the original biopsy; for CH03 cells, ^##P<0.01 and ^###P<0.001 compared with CH03 pellet).