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Gene expression changes during serum starvation-induced quiescence in human fibroblasts

ABSTRACT: We report a comparison of gene expression profiling microarray datasets generated from proliferating and serum-starved quiescent human normal diploid fibroblasts. 4 biological replicates of proliferative and quiescent fibroblasts were subjected to 4 individual dye-swap experiments. Data from these arrays were used in a publication to compare reproducibility between microarrays and RNA-seq; RNA-seq (2 replicates of each proliferative and quiescent fibroblasts) are available through the GEO (accession #: GSE65145). Correlations between both the microarrays and the RNA-seq dataset showed only moderate concordance (r =0.42) in genes exhibiting a ≥5-fold change. Examination of gene expression profiles from prolfierating and quiescent normal human fibroblasts using microarray technology

ORGANISM(S): Homo sapiens

PROVIDER: GSE66780 | GEO | 2015/10/15

SECONDARY ACCESSION(S): PRJNA277961

REPOSITORIES: GEO

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Project description:Background: Although quiescence—reversible cell-cycle arrest—is a key part in the life history and fate of many mammalian cell types, the mechanisms of gene regulation in quiescent cells are poorly understood. We sought to clarify the role of microRNAs as regulators of the cellular functions of quiescent human fibroblasts. Results: Using microarrays, we discovered that the expression of the majority of profiled microRNAs differed between proliferating and quiescent fibroblasts. Fibroblasts induced into quiescence by contact inhibition or serum starvation had similar microRNA profiles, indicating common changes induced by distinct quiescence signals. By analyzing the gene expression patterns of microRNA target genes with quiescence, we discovered a strong regulatory function for miR-29, which is downregulated with quiescence. Using microarrays and immunoblotting, we confirmed that miR-29 targets genes encoding collagen and other extracellular matrix proteins and that those target genes are induced in quiescence. In addition, overexpression of miR-29 resulted in more rapid cell cycle re-entry from quiescence. We also found that let-7 and miR-125 were upregulated in quiescent cells. Overexpression of either one alone resulted in slower cell cycle re-entry from quiescence, while the combination of both together slowed cell cycle re-entry even further. Conclusions: microRNAs regulate key aspects of fibroblast quiescence including the proliferative state of the cells as well as their gene expression profiles, in particular, the induction of extracellular matrix proteins in quiescent fibroblasts. microRNAs in human neonatal dermal fibroblasts in 3 cell cycle conditions (proliferating, 4 days serum starved, 7 days contact inhibited) were analyzed by one color microarray. 3 separate fibroblast cell lines from different human donors were analyzed for each condition, with two separate labeling and hybridization samples for each cell line. In total, 18 samples were hybridized to the microRNA microarray.

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Gene expression changes during serum starvation-induced quiescence in human fibroblasts

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