Fig. 1

CIN shows higher expression levels in non-adherent cells cultured under serum-free conditions than in adherent lines cultured in serum-containing medium. a Molecular characteristics including expression subtype, presence of TP53 mutations and CDKN2A deletion of all cell lines used in this study. Non-adherent cell lines cultured in serum-free medium show more often a proneural expression subtype, while mesenchymal signatures are enriched in adherent, serum-cultured cell lines. Cell lines show high frequencies of TP53 mutations and CDKN2A deletions in both conditions. A more comprehensive overview of molecular characteristics including expression patterns of key glioblastoma subtype genes can be found in Additional file 1: Table S1. b DESeq2 analysis of stem cell markers in non-adherent cell lines cultured in serum-free medium vs. adherent, serum-cultured cell lines. The stem cell marker PROM1 (CD133) is significantly overexpressed (DESeq2, adjusted p-value < 0.001). The stem cell markers SOX2, c-MYC and NES show higher expression values in cells cultured in serum-free medium. However, the differences are not significant. Shown are mean RPKM values + SD of n = 5 cell lines in each group. c DESeq2 analysis of genes regulating cofilin phosphorylation in cells cultured in serum-free medium and serum-cultured cell lines. Chronophin (CIN/PDXP) is overexpressed in glioblastoma cells cultured in serum-free medium, whereas LIMK1 is downregulated (DESeq2, adjusted p-value < 0.01 and p < 0.05, respectively). Shown is the log2 fold change of non-adherent cell lines cultured in serum-free medium versus adherent, serum-cultured cell lines + standard error. d Analysis of the dataset GSE54791. Similar changes as in (c) can be found in independently generated datasets of tumor propagating cells (TPC) and differentiated glioma cells (DGC). CIN is significantly overexpressed in glioblastoma tumor propagating cells, while LIMK2 and ROCK1 are downregulated. The p-values shown are Bonferroni corrected. e Analysis of CIN expression by real-time PCR. The expression of CIN is significantly higher (two-sided Mann-Whitney test, p < 0.05) in cells cultured in serum-free medium. Individual expression values of five non-adherent cell lines cultured in serum-free medium vs. five adherent, serum-cultured cell lines are shown. The expression value in normal human astrocytes was set to one (red dotted line). f Western blot analysis of CIN expression. The expression of CIN is high in all five cell lines cultured in serum-free medium and significantly higher in these lines compared to the adherent, serum-cultured lines (two sided t-test, p = 0.0005)