Fig. 4: SURF2 depletion up-regulates the p53 pathway.

RNA-seq analyses of SURF2 depletion. U2OS cells were treated by scramble siRNAs or by siRNAs against SURF2 for 96 h. mRNA expression levels were compared between the two conditions, and experiments were repeated (n = 3). a Volcano plot showing significantly differentially expressed genes. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called differentially expressed genes indicated: up-regulated genes (red) and down-regulated (blue) or unaffected (gray). Genes from the TP53 pathway are highlighted yellow. b Gene set enrichment analysis (GSEA) in SURF2 depleted genes or in the control condition (siSCR). ES; enrichment score. GSEA P-values were derived from permutation testing and corrected for multiple testing using the False Discovery Rate (FDR) method. Enrichment score (ES) and FDR value were applied to sort SURF2 depleted and control cells genes-enriched after gene set permutations were performed 1000 times for the analysis. Gene Network Analysis was based on DEGs (log2foldchange  >  1). c Western-blot analyses showing the accumulation of different proteins in 20 µg of cellular extracts produced from U2OS cells treated with scrambled siRNAs (siSCR) or with siRNAs directed against SURF2 (siSurf2). d Quantification of signals obtained by western-blot analysis and normalized to actin signals in each condition (c) from independent biological replicates (p53, n = 5; SURF2, n = 5; p21 n = 5; MDM2, n = 3; RPL5, n = 3; RPL11, n = 3). Two-tailed t-test analysis was used for statistics. Data are presented as mean values +/− SD. Significant differences are indicated by stars (p-value \(\le\)0.05*; \(\le\)0.01**;\(\,\le\)0.001*** and \(\le\)0.0001****) or with the precise p-value on the graph (p). e Co-depletion experiment. Western-blot analyses showing the accumulation of different proteins in 20 µg of cellular extracts issued from U2OS cells treated with a combination of different siRNAs: scrambled (siSCR); RPL5 (siRPL5); RPL11 (siRPL11) or SURF2 (siSurf2). f Quantification of signals obtained by western-blot analysis and normalized to GAPDH signals in each condition (h) (n = 3). Data are presented as mean values +/− SD. A one-way ANOVA test was used for statistics. Significant differences are indicated by stars (p-value \(\le\)0.05*; \(\le\)0.01** and \(\le\)0.001***) or with the precise p-value on the graph (p). Source data are provided as a Source Data file.