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Supplementary Figure Legend LEGENDS TO SUPPLEMENTARY FIGURES Supplementary Fig. 1. Cluster analysis of genes essential for tumor cell survival. A, Seventy-one genes were found to be essential for tumor cell survival in both NSCLC and HNSCC. Clustering of these genes using String (version 9.0) resulted in four clusters containing genes involved in RNA processing, ribosome biogenesis, protein modification/ubiquitination and regulation of the G2/M phase of the cell cycle. B, In total 362 genes showed a significantly tumor cell killing phenotype in either the NSCLC and/or HNSCC cell line. Clustering of these genes using String (version 9.0) resulted in three large clusters containing genes involved in RNA processing, ribosome biogenesis and protein modification/ubiquitination. One smaller cluster consisted of 20 genes involved in the regulation of the G2/M phase of the cell cycle (also see Fig. 1B). Supplementary Fig. 2. Deconvolution of genes associated with mitotic spindle formation. SiRNA pools targeting mitotic spindle associated gene expression were deconvoluted in three NSCLC (blue bars) and three HNSCC cell lines (red-orange bars) of each tumor type. Cell viability was measured in triplicate and calculated relative to siCONTROL transfected cells. Bars are median cell viability values and error bars represent the standard deviation. The siRNA pool targeting CDCA8 mRNA (A) gave a significant phenotype in the original HNSCC screen, but could not be confirmed as tumor cell killing after deconvolution. CKAP5 (B), KPNB1 (C), RAN (D) and TPX2 (E) could all be confirmed as tumor cell killing hits with at least 2/4 siRNAs in all six cell lines. In F,G, and H three genes (DLG7, NUTF2 and RCC1) that are associated with mitotic spindle formation via RAN signaling, but that did not reach significance in the original screens, were indeed all negative for tumor cell killing in the deconvolution experiments. 1 Supplementary Fig. 3. KIF11 mRNA targeting siRNAs establish good knockdown of gene expression. A, RNA isolated from KIF11 siRNA transfected SW1573 cells was subjected to quantitative real-time PCR to determine the efficiency of the siRNA transfection and the corresponding mRNA knockdown. Results are calculated relative to siCONTROL siRNA transfected cells. Error bars represent standard deviations of three independent measurements. B, Protein lysates made from KIF11 siRNA transfected SW1573 cells were subjected to western blot analysis. KIF11 protein level was calculated relative to the amount of protein in the siCONTROL lane (negative control), standardized for the loading by beta-actin. Supplementary Fig. 4. Deconvolution of AURKB and AURKC siRNA pools in multiple tumor cell lines and the effect of simultaneous knockdown of the aurora kinase genes on cell viability. A-B, AURKB and AURKC siRNA pools were deconvoluted in three NSCLC (blue bars) and three HNSCC (red-orange bars) cell lines. The siRNA pools showed a minor or no tumor cell killing phenotype, exactly as seen in the initial genome-wide screens. Deconvolution of the pools did not change this observation. Cell viability was measured in triplicate and calculated relative to siCONTROL transfected cells. Bars are median cell viability values and error bars represent the standard deviation. C-D, RNA isolated from two NSCLC (blue bars) and HNSCC cell lines (red-orange bars) was subjected to quantitative real-time PCR to determine the efficiency of mRNA knockdown after AURKA and AURKB siRNA transfection. Results were calculated relative to siCONTROL siRNA transfected cells. Error bars represent standard deviations of three independent experiments. E, AURKA, AURKB and AURKC siRNA pools were transfected in UM-SCC-11B, either separate or in combination. 2 Cell viability is displayed as compared with siCONTROL transfected cells. Error bars represent standard deviations of three independent transfections. F, RNA was isolated from UM-SCC-11B cells transfected with AURKA, AURKB or AURKA+AURKB siRNA pools. mRNA expression levels were measured by RT-PCR and are displayed relative to cells transfected with siCONTROL. Error bars represent the standard deviation of triplicate experiments. Supplementary Fig. 5. KIF11 protein expression in NSCLC and HNSCC cell lines. The KIF11 protein level of four NSCLC and five HNSCC cell lines was determined using western blotting. KIF11 protein levels were calculated relative to the beta-actin loading control. KIF11 protein levels are significantly lower in HNSCC cell lines (p=0.001, t-test) Supplementary Fig. 6. Ispinesib treatment induces G2 arrest in HNSCC cell lines. UM-SCC-22A, VU-SCC-OE and a primary fibroblast culture were treated with ispinesib during 24h, followed by BrdU incubation. The different phases of the cell cycle were examined by FACS analysis (see also Fig. 4B). For both HNSCC cell lines the number of cells in G1 and S phase decreased significantly (p<0.0001, Fisher’s exact probability test), whereas the number of cells in G2/M increased significantly after ispinesib incubation (p<0.0001). For the primary fibroblasts, this shift in overall cell cycle phase was less striking (S phase; p=0.61, G1 and G2/M phase; p<0.05, Fisher’s exact probability test). 3.
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