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UVB-induced persistent activation of cellular pathways revealed by a loop-designed microarray approach

ABSTRACT: Ultraviolet B (UVB) irradiation has strong biological effects and modulates the expression of many genes. However, the major biological themes affected by UVB remain poorly understood. This work employs a loop-designed microarray approach and applies a log linear model along with multiple hypotheses testing to identify differentially regulated genes at 4, 8, 16, or 24 hours following UVB irradiation. The most prominent biological themes in lists of differentially regulated gene sets were extracted by functional enrichment analysis using DAVID bioinformatics resources 2007. By this approach, we identify that genes that participate in two prime cellular processes – the ribosome pathway and the oxidative phosphorylation pathway - are persistently activated over a period of 24 hours following UVB irradiation. Microarray results were further verified by both mitochondrial activity assay and real-time PCR analysis. These data suggest that the persistent activation of ribosome and oxidative phosphorylation pathways may have a key role in UVB-induced cellular responses. For the first time, the specific cellular pathways that respond to UVB irradiation consistently and persistently can be delineated confidently using a loop-designed microarray approach and functional bioinformatics analysis. The results of this study offer further insight into UVB-induced stress responses. Keywords: UVB, cDNA microarray, loop design, KEGG pathway

ORGANISM(S): Homo sapiens

PROVIDER: GSE7589 | GEO | 2009/04/10

SECONDARY ACCESSION(S): PRJNA100191

REPOSITORIES: GEO

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Project description:The â??small perturbationâ?? approach is critical in studying the â??steady stateâ?? of a biological system. In our experiments, small perturbations were generated by applying a series of repeating intermittent small doses of ultraviolet radiation to a human keratinocyte cell line, HaCaT. The biological response was assessed by monitoring the gene expression profiles using a high reliability and high resolution cDNA microarray system. Following intermittent 10 J/m2 UVB small perturbations, two opposite classes of genes, down-regulated and up-regulated, exhibited an immediate response followed by relaxation between each small perturbation, but were prolonged down- or up-regulated without relaxation while larger doses (233 or 582.5 J/m2) of UVB were applied. A repeated cycle pattern of gene expression following small perturbations is an indication of the existence of steady states. This cycle pattern is suppressed when large perturbations are applied. We believe that this is a universal phenomenon. In our experiments, the functions of up-regulated genes were mainly associated with anti-proliferation, anti-mitogenesis, and apoptosis. On the other hand, down-regulated genes were mainly related to proliferation, mitogenesis, and anti-apoptosis. In conclusion, this study experimentally proves the concept of steady state at the transcription level and demonstrates the feasibility of using small perturbation approaches for investigating steady states. This study could also set a foundation of computational systems biology, which has implicitly used the concept of steady state. Keywords: time course Three UVB exposures are indicated by UV at time points of 0, 8 and 16 hours. T1, T2, T3, T4, T5, and T6 denote the sampling time points. T1, T3 and T5 are allocated 30 minutes after the corresponding UVB irradiation. T2, T4 and T6 are allocated 8 hours after each UVB irradiation. At each sampling time point, two samples (control and UV-irradiated) are collected. See supplementary file Loop_design.pdf for further explanation.

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UVB-induced persistent activation of cellular pathways revealed by a loop-designed microarray approach

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