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Gene expression analyses of HCT116 p53+/+ and HCT116 p53-/- cells knocked down for RPS19 or BYSL

ABSTRACT: Gene expression analyses of HCT116 p53+/+ and HCT116 p53-/- cells knocked down for RPS19 or BYSL

PROVIDER: PRJNA1078819 | ENA |

REPOSITORIES: ENA

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Project description:A gene expression array was used to measure differential expresion of mRNAs upon knockdown of RPS19 or BYSL in HCT116 TP53+/+ and HCT116 TP53-/- cells. Two independent experiments were performed to analyze the eight conditions subject to analyses: HCT116 TP53+/+ and HCT116 TP53-/- cells harvested 24 h (si-ctrl and si-RPS19) and 48 h (si-ctrl and si-BYSL) after si-RNA transfection. Each experiment included three biological replicates of each condition. In silico gene set expression analyses (GSEA) revealed multiple gene sets that were differentially enriched in at least two of the RPS19 and/or BYSL knockdown conditions. Out of those, the upregulated gene sets showing the highest enrichment score in TP53+/+ cells included the signatures for p53-regulated genes and for oxidative phosphorylation. Our GSEAs also revealed that the siRNA-mediated depletion of either RPS19 or BYSL is associated with a marked downmodulation of gene signatures linked to the signaling of the mammalian target of rapamycin complex 1 (mTORC1) and the activation of the unfolded protein response (UPR). These two gene sets become downregulated at similar levels irrespectively of the p53 presence in the HCT116 cells, thus indicating that their expression must be under the control of other transcriptional regulators. Interestingly, these two gene signatures have not ever been pointed as relevant in DBA or any other ribosomopathy patients. We noticed that many of the genes commonly downregulated by the knockdowns of the RPS19 and BYSL transcripts are direct targets of the transcription factor ATF4. This led us to perform a GSEA analysis of a list of 41 genes (AmTOR signature) whose expression is commonly induced by ATF4 downstream of mTORC1 and phosphorylated IF2-alpha in normal and stressed cells, respectively. It was found that the mRNAs for ATF4 and most of the AmTOR signature genes display a similar downregulation in both TP53+/+ and TP53-/- HCT116 cells upon depletion of either the RPS19 or the BYSL transcript.

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Gene expression analyses of HCT116 p53+/+ and HCT116 p53-/- cells knocked down for RPS19 or BYSL

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