1. RNA-seq data analysis of stimulated hepatocellular carcinoma cells treated with epigallocatechin gallate and fisetin reveals target genes and action mechanisms
- Author
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Fragiskos N. Kolisis, Heleni Loutrari, Panagiotis C. Agioutantis, and Vasilios Kotsikoris
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TF, transcription factor ,Hepatocellular carcinoma ,EMT, epithelial to mesenchymal transition ,RNA-Seq ,DMSO, dimethyl sulfoxide ,MMP9, Matrix Metallopeptidase 9 ,Biochemistry ,Transcriptome ,chemistry.chemical_compound ,0302 clinical medicine ,Structural Biology ,Gene expression ,MMP11, Matrix Metallopeptidase 11 ,CTGF, Connective Tissue Growth Factor ,CLIC3, Chloride Intracellular Channel 3 ,0303 health sciences ,HSPA2, Heat Shock Protein Family A (Hsp70) Member 2 ,ECM, extracellular matrix ,SEM, standard error of mean ,Epigallocatechin gallate ,3. Good health ,Computer Science Applications ,030220 oncology & carcinogenesis ,Research Article ,STIM, stimulated ,Biotechnology ,Reactome Pathways ,lcsh:Biotechnology ,DEGs, differentially expressed genes ,ADAM, a disintegrin and metalloproteinase with thrombospondin motifs ,RNA-sequencing ,Biophysics ,FIS, fisetin ,Biology ,SERPINE1, Serpin Family E Member 1 ,MEM, minimum essential medium ,03 medical and health sciences ,ADAMTS9, ADAM metallopeptidase with thrombospondin type 1 motif 9 ,lcsh:TP248.13-248.65 ,HSPB1, Heat Shock Protein Family B (Small) Member 1 ,GO, Gene Ontology ,RT-qPCR, reverse transcription-quantitative real time PCR ,Transcription factors ,Genetics ,PDGFRB, Platelet Derived Growth Factor Receptor Beta ,Transcription factor ,Gene ,PI3K/AKT/mTOR pathway ,ComputingMethodologies_COMPUTERGRAPHICS ,030304 developmental biology ,Tumor microenvironment ,Fisetin ,Gene Ontology ,chemistry ,Cancer research ,MMPs, matrix metalloproteinases ,HCC, hepatocellular carcinoma ,SD, standard deviation ,EGCG, epigallocatechin gallate - Abstract
Graphical abstract, Hepatocellular carcinoma (HCC) is an essentially incurable inflammation-related cancer. We have previously shown by network analysis of proteomic data that the flavonoids epigallocatechin gallate (EGCG) and fisetin (FIS) efficiently downregulated pro-tumor cytokines released by HCC through inhibition of Akt/mTOR/RPS6 phospho-signaling. However, their mode of action at the global transcriptome level remains unclear. Herein, we endeavor to compare gene expression alterations mediated by these compounds through a comprehensive transcriptome analysis based on RNA-seq in HEP3B, a responsive HCC cell line, upon perturbation with a mixture of prototypical stimuli mimicking conditions of tumor microenvironment or under constitutive state. Analysis of RNA-seq data revealed extended changes on HEP3B transcriptome imposed by test nutraceuticals. Under stimulated conditions, EGCG and FIS significantly modified, compared to the corresponding control, the expression of 922 and 973 genes, respectively, the large majority of which (695 genes), was affected by both compounds. Hierarchical clustering based on the expression data of shared genes demonstrated an almost identical profile in nutraceutical-treated stimulated cells which was virtually opposite in cells exposed to stimuli alone. Downstream enrichment analyses of the co-modified genes uncovered significant associations with cancer-related transcription factors as well as terms of Gene Ontology/Reactome Pathways and highlighted ECM dynamics as a nodal modulation point by nutraceuticals along with angiogenesis, inflammation, cell motility and growth. RNA-seq data for selected genes were independently confirmed by RT-qPCR. Overall, the present systems approach provides novel evidence stepping up the mechanistic understanding of test nutraceuticals, thus rationalizing their clinical exploitation in new preventive/therapeutic modalities against HCC.
- Published
- 2020
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