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Comparative gene expression profiling of serum-free and FBS treated adherent primary pancreatic TIC cultures

ABSTRACT: To induce a differentiated phenotype, primary pancreatic TIC cultures were grown in 10% FBS containing conditions. To analyze gene expression changes upon induction of a differentiated phenotype, total RNA of cells cultured in FBS containing conditions and parallel control cells cultured under serum-free conditions was isolated and comparative gene expression profiling was performed.

ORGANISM(S): Homo sapiens

PROVIDER: GSE59118 | GEO | 2017/05/16

SECONDARY ACCESSION(S): PRJNA254461

REPOSITORIES: GEO

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Comparative gene expression profiling of serum-free and FBS treated adherent primary pancreatic TIC cultures

Project description:To induce a differentiated phenotype, primary pancreatic TIC cultures were grown in 10% FBS containing conditions. To analyze gene expression changes upon induction of a differentiated phenotype, total RNA of cells cultured in FBS containing conditions and parallel control cells cultured under serum-free conditions was isolated and comparative gene expression profiling was performed. RNA was obtained from four different patient derived cultures grown in serum-free or 10% FBS containing culture medium at passage 3 and passage 8

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Project description:Purpose: To understand the changes in RNA expression in tumor-initiating cell (TIC) (spheroid) and non-TIC populations (adherent) in ovarian cancer. Methods: OV90 cells were grown in adherent (non-TIC) or spheroid (TIC) conditions. Total RNA was extracted from each condition and RNAseq was performed and analysed for differential gene expression between the conditions.

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Project description:Purpose: Cyclic mechanical stretch (CMS) promoted proliferation of serum starved mesenchymal stem cells (MSCs) by inhibiting miR-337 expression, similar to FBS. In order to reveal the underlying mechanisms of both CMS and FBS on MSC activation, as well as the regulatory role of miR-337, this research performed high-throughput RNA sequencing (RNA-seq) on MSCs isolated from both wild-type (ET)- and miR-337 knockout- (miR-337-/-) rats. Methods: MSCs isolated form 2-month-old wild-type (WT) and miR-337 knockout (-/-) rats and cultured in vitro to passage 3. After serum starvation for 8h, MSCs were treated with FBS or 10% CMS for another 24h before deep sequencing in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level. Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample. We identified 2472 differentially expressed genes (DEGs) between CMS-stimulated vs. SSt conditions, 2468 DEGs FBS-treated vs. SSt groups. However, only 97 DEGs were identified between CMS and FBS groups, indicating that CMS and FBS groups are more similar to each other and both CMS and FBS groups are quite different from the SSt group. Analysis of DEGs between CMS- or FBS-treated and SSt -treated group revealed that CMS and FBS stimulation activated similar biological processes, of which, PI3K-Akt-mTOR pathway was highly enriched. However, PI3K-Akt-mTOR pathway was not enriched in miR-337-/- MSCs, indicating constitutive activation of this pathway. Conclusions: Our RNA-seq data revealed that both CMS and FBS activates quiescent MSCs through regulating similar genes and pathways. miR-337 is one of the main factors that regulate MSC activation by targeting PI3K-Akt pathway.

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