Fig. 1: HIF-2α is an upstream regulator of gene module governing chondrosarcoma malignancy.

a Three moderately sized modules identified by WGCNA using transcriptome data from chondrosarcoma patients (GSE12475). Cancer-promoting (CP) annotations, significantly associated with each module, were analyzed using IPA. For each module, top ten CP annotations were arranged in the order of –log₁₀(P-value). –log₁₀(P-value) > 2 was used as the cut-off value. A right-tailed Fisher’s exact test was used to determine the statistical significance. b The predicted upstream regulators of the M1 module were color-coded according to the sum of activation z-scores of linked nodes. Edges from EPAS1 are highlighted in red and their thickness indicates significance according to P-value against each annotation (left panel). Representative CP annotations, regulated by EPAS1, were arranged in the order of activation z-score (right panel). A right-tailed Fisher’s exact test was used to determine the statistical significance. c GSEA was performed with the M1 module gene set using transcriptome data obtained from chondrocytes infected with adenovirus (Ad)-Epas1 compared to those infected with Ad-Control (Ctrl) (GSE73659). Normalized enrichment score (NES) and nominal P-value are indicated. d Network connections of M1 module genes visualized by VisANT. The hub genes are located toward the center of the network. e Representative histological and IHC images in normal human cartilage and chondrosarcoma biopsies. Scale bar: 50 μm. f Quantitation of HIF-2α expression in chondrosarcomas with different histological grades: grade I (n = 44), grade II (n = 5) and grade III (n = 16). Significance was calculated by one-way ANOVA. Data represent mean ± SEM. g Patients were grouped by conducting k-means clustering based on collective expression profiles of canonical HIF-2α target genes (Supplementary Fig. 1c). Clinical and prognostic features of patients in Group1 and Group2 are presented by their percentage in each group. 5-year OS; 5-year overall survival. h Kaplan–Meier plot of overall survival of the patients stratified by amplification status of HIF1A (left panel; positive: n = 9; negative: n = 55) and EPAS1 (right panel; positive: n = 24; negative: n = 40) loci. Significance was calculated with the two-sided log-rank test.