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Título: 

Supplementary material for article Broad Transcriptomic Impact of Sorafenib and Its Relation to the Antitumoral Properties in Liver Cancer Cells

Autor: Contreras, Laura CSIC; Rodríguez-Gil, Alfonso CSIC; Muntané, Jordi CSIC ORCID; Cruz, Jesús de la CSIC ORCID
Fecha de publicación: 25-feb-2022
Editor: Multidisciplinary Digital Publishing Institute
Citación: Contreras, Laura; Rodríguez-Gil, Alfonso; Muntané, Jordi; Cruz, Jesús de la; 2022; Supplementary material for article Broad Transcriptomic Impact of Sorafenib and Its Relation to the Antitumoral Properties in Liver Cancer Cells [Dataset]; Multidisciplinary Digital Publishing Institute; https://doi.org/10.3390/cancers14051204/s1
Descripción: Table S1. List of DEGs in Sfb-treated HepG2 and SNU423 cells. See supplementary Table S1 Excel file. Table S2. List of DEGs with log2(FC) higher than 1.5 or lower than -1.5 in Sfb-treated HepG2 and SNU423 cells. See supplementary Table S2 Excel file. Table S3. List of pathways activated or inhibited upon a Sfb treatment in HepG2 cells. See supplementary Table S3 Excel file. Figure S1. Quantitative RT-PCR validation of RNA-Seq data for HepG2 cells. A selection of down-regulated and up-regulated genes were assessed for gene expression through qPCR. Cells were grown for 24 h and then treated with 10 μM Sorafenib for 12 h before RNA extraction. The table compared the fold expression obtained by RNA-Seq versus the relative expression calculated by RT-PCR. Note that the corresponding mRNA levels quantified by RT-PCR from untreated cells (control) were arbitrarily set at 1.0. The ACTB, BAX, BIRC3, CEBP, CPEB4, DUSP1, EIF4E2, EPOP, FEN1, GADD45B, IDI1, PCNA, SMAD7, TPI and VEGFA genes were analysed. Expression levels were relativized to levels of 28S rRNA of each sample. Values are the mean ± S.D. values of at least three independent experiments performed in triplicate. Statistical significances were analysed by the Student's test (*p< 0.05, **p< 0.01, *** p< 0.001, ****p< 0.0001). Values for upregulated genes are shown in red, while those for downregulated genes are shown in green. Figure S2. Quantitative RT-PCR validation of RNA-Seq data for SNU423 cells. A selection of down-regulated and up-regulated genes were assessed for gene expression through qPCR. Cells were grown for 24 h and then treated with 10 μM Sorafenib for 12 h before RNA extraction. The table compared the fold expression obtained by RNA-Seq versus the relative expression calculated by RT-PCR. Note that the corresponding mRNA levels quantified by RT-PCR from untreated cells (control) were arbitrarily set at 1.0. The BIM, BOP1, BIRC3, CPEB4, DUSP1, EIF4E2, EPOP, GADD45B, IDI1, PHB, PCNA, SMAD7 and TPI genes were analysed. Expression levels were relativized to levels of 28S rRNA of each sample. Values are the mean ± S.D. values of at least three independent experiments performed in triplicate. Statistical significances were analysed by the Student's test (*p< 0.05, **p< 0.01, ***p< 0.001, ****p< 0.0001). Values for upregulated genes are shown in red, while those for downregulated genes are shown in green. Figure S3. Sorafenib lead to translation inhibition in HCC cells. Polysome profiles in HepG2 and SNU423 cells treated or not with Sorafenib (10 μM, 12 h). Cell extracts and polysome profile analysis were performed following the procedure described in Material and Methods. Ten A260 units of each extract were resolved in 7 to 50% sucrose gradients. The A254 was continuously monitored. Sedimentation is from left to right. The identity of the different peaks is indicated. Figure S4. Cholesterol biosynthesis pathway in humans. This outline shows the cholesterol biosynthesis process with those enzymes whose genes were down-regulated by Sfb in red as suggested by our RNA-Seq analysis. The log2(FC) for each one is indicated in brackets. Figure S5. Categories with opposite NES values in HepG2 and SNU423 cell lines. Reactome categories which show NES in opposite directions in the two cell lines analysed with the GSEA. NES and False Discovery Rate (FDR) q-Value are shown for each category. Panel (A) shows categories with FDR lower than 0.3 for HepG2 cells and its value in SNU423 cell line whereas panel (B) shows categories with FDR more significative for SNU423 cells and its respective value for HepG2 cells. Figure S6. Uncropped Western Blots.
Versión del editor: https://doi.org/10.3390/cancers14051204/s1
URI: http://hdl.handle.net/10261/331254
DOI: 10.3390/cancers14051204/s1
Referencias: Contreras, Laura; Rodríguez-Gil, Alfonso; Muntané, Jordi; Cruz, Jesús de la. Broad Transcriptomic Impact of Sorafenib and Its Relation to the Antitumoral Properties in Liver Cancer Cells. https://doi.org/10.3390/cancers14051204 . http://hdl.handle.net/10261/303956
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