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A time-series analysis of gene expression profiles and phenotype changes in the process of HDF replicative senescence

Authors
Kim, You-Mi; Cho, Hyun Woo; Woo, Hyun Goo; Yoon, Gyesoon
Department
Department of Biochemistry & Molecular Biology
Abstract
Cellular senescence has long been implicated in aging-associated diseases. However, it is not clear which cellular features provide susceptibility to the diseases. To address this, we employed replicative senescence of human diploid fibroblast. The senescence progress was divided into 12 stages according to their population doubling number and resultant doubling time. Typical senescent phenotypes, such as senescence-associated β-galactosidase activity and increase of cellular mass, granularity and intracellular reactive oxygen species, were monitored and compared to gene expression profile which was obtained by cDNA microarray analysis. The heatmap of the gene expression profile revealed four distinct modules (G1, G2, G3 and G4) which are prominently expressed during the senescence process and the functional characterization of each module was performed by Gene Ontology analysis. G1 showed the prominent enrichment of cell cycle-related genes indicating active proliferation activity. This was suppressed at the end of G1 phase (doubling time, 2 days) suggesting the event of the "senescence growth arrest" might occur at this time point. In the young-to-mid-old phase of G2 module, metabolic process-related genes and tRNA/RNA processing were prominently expressed. In the mid-old phase (G3), immune-related functions such as defense response and antigen processing were significantly enriched. In far-old phase (G4), the genes related with cell death and cell growth control were prominently activated. NF-kB pathway-related genes were also activated, which was previously notified to play important role in the aging process. We also examined the enrichment of canonical pathways using KEGG database and analyzed the expression profiles of the genes encoding the SASP proteins. Taken together, our results suggest that senescent phenotypes acquired by multiple doubling may provide different pathologic background according to the senescence stage, implying a potential link to age-associated diseases.
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