Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq for ES2, SUM159 or A549 cells treated with GSK-615

ABSTRACT: GSK-615 was used to treat ES2, SUM159, and A549 cells, and RNA-seq was used to look at how the compound changed gene expression in general. We aimed to predict probable TFs activated with GSK-615 treatment by focusing on the overlapping differentially expressed genes across the three cell lines impacted by GSK-615 in order to find common molecular changes across the three cancer cell lines. The Integrated System for Motif Activity Response Analysis (ISMARA) was then used to look at the DNA-binding motifs of these genes and find the TFs that were present.

INSTRUMENT(S): NA, Illumina TruSeq, Illumina NovaSeq 6000, PureLink RNA Mini Kit

ORGANISM(S): Homo sapiens

SUBMITTER: Boxi Zhang

PROVIDER: E-MTAB-14701 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Cardiac hypertrophy is an important and independent risk factor for the development of cardiac myopathy that may lead to heart failure. Cardiac hypertrophy manifests as an enlargement of the individual cardiomyocytes, which impairs the function of the heart. The only way to cure end-stage cardiac myopathy is by heart transplantation, a possibility limited due to lack of donor hearts. Therefore, early diagnosis of cardiac hypertrophy is needed in order to be able to initiate interventions that may prevent further progression of the disease. The mechanisms underlying the development of cardiac hypertrophy are yet not well understood. To increase the knowledge about mechanisms and regulatory pathways involved in the progression of cardiac hypertrophy, we have developed a human induced pluripotent stem cell (hiPSC)-based in vitro model of cardiac hypertrophy and performed extensive characterization of the model using multi-omics analyses. In a series of experiments, hiPSC-derived cardiomyocytes were stimulated with Endothelin-1 for 8, 24, 48 and 72 hours and their transcriptome and secreted proteome were analyzed thoroughly. The transcriptomic data show many enriched canonical pathways related to cardiac hypertrophy already at the earliest time point, e.g., cardiac hypertrophy signaling, actin cytoskeleton signaling and PI3K/AKT signaling. Cluster analysis of the differentially expressed genes showed that there are numerous clusters of genes that are dysregulated over the time period of 8 to 72h. An integrated transcriptome-secretome analysis enabled the identification of multimodal biomarkers of high relevance for monitoring early cardiac hypertrophy progression. Taken together, the results from this study demonstrate that our in vitro model displays a hypertrophic response on transcriptomic- and secreted proteomic level. The results also provide novel insight into the underlying mechanisms of cardiac hypertrophy and novel putative early cardiac hypertrophy biomarkers have been identified that will be further validated to assess their clinical relevance.

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RNA-seq for ES2, SUM159 or A549 cells treated with GSK-615

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