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Gene expression profiling of sense and antisense transcripts in liver regeneration by microarray analysis.

ABSTRACT: Liver regeneration is a hyperplastic phenomenon induced by partial hepatectomy (PH) or hepatic damage. A large number of genes have been indicated to be involved in the process of liver regeneration. It was recently reported that natural antisense transcripts are involved in the regulation of gene expression. However, no antisense transcript expressions in liver regeneration have been reported thus far. Therefore, the present study aimed to comprehensively identify up- or downregulated sense and antisense transcripts in liver regeneration using PH mice and a sense/antisense custom-microarray. The results showed that 97 genes were upregulated and 7 genes were downregulated for sense transcripts, whereas 15 genes were upregulated and 2 genes were downregulated for antisense transcripts in regenerating livers as compared to normal livers (P<0.05 and fold change >2.0). Sense and antisense transcripts of the genes, Apoa4, Hp, Fgb and Fgg, exhibited concordant upregulation during the course of liver regeneration. Apoa4, Hp and Fgb transcripts were further investigated by strand-specific reverse transcription-quantitative polymerase chain reaction (RT-qPCR), revealing results consistent with those of the microarray. In conclusion, the up- or downregulated sense and antisense transcripts identified in the present study are suggested to be involved in liver regeneration.

SUBMITTER: Chiba M

PROVIDER: S-EPMC3917095 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

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Gene expression profiling of sense and antisense transcripts in liver regeneration by microarray analysis.

Chiba Mitsuru M Yasue Hiroshi H Ohkohchi Nobuhiro N

Biomedical reports 20130313 3

Liver regeneration is a hyperplastic phenomenon induced by partial hepatectomy (PH) or hepatic damage. A large number of genes have been indicated to be involved in the process of liver regeneration. It was recently reported that natural antisense transcripts are involved in the regulation of gene expression. However, no antisense transcript expressions in liver regeneration have been reported thus far. Therefore, the present study aimed to comprehensively identify up- or downregulated sense and ...[more]

PMID: 24648954

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Project description:BackgroundThe completion of the sequencing of human, mouse and rat genomes and knowledge of cross-species gene homologies enables studies of differential gene expression in animal models. These types of studies have the potential to greatly enhance our understanding of diseases such as liver cancer in humans. Genes co-expressed across multiple species are most likely to have conserved functions. We have used various bioinformatics approaches to examine microarray expression profiles from liver neoplasms that arise in albumin-SV40 transgenic rats to elucidate genes, chromosome aberrations and pathways that might be associated with human liver cancer.ResultsIn this study, we first identified 2223 differentially expressed genes by comparing gene expression profiles for two control, two adenoma and two carcinoma samples using an F-test. These genes were subsequently mapped to the rat chromosomes using a novel visualization tool, the Chromosome Plot. Using the same plot, we further mapped the significant genes to orthologous chromosomal locations in human and mouse. Many genes expressed in rat 1q that are amplified in rat liver cancer map to the human chromosomes 10, 11 and 19 and to the mouse chromosomes 7, 17 and 19, which have been implicated in studies of human and mouse liver cancer. Using Comparative Genomics Microarray Analysis (CGMA), we identified regions of potential aberrations in human. Lastly, a pathway analysis was conducted to predict altered human pathways based on statistical analysis and extrapolation from the rat data. All of the identified pathways have been known to be important in the etiology of human liver cancer, including cell cycle control, cell growth and differentiation, apoptosis, transcriptional regulation, and protein metabolism.ConclusionThe study demonstrates that the hepatic gene expression profiles from the albumin-SV40 transgenic rat model revealed genes, pathways and chromosome alterations consistent with experimental and clinical research in human liver cancer. The bioinformatics tools presented in this paper are essential for cross species extrapolation and mapping of microarray data, its analysis and interpretation.

Dataset Information

Gene expression profiling of sense and antisense transcripts in liver regeneration by microarray analysis.

Publications

Gene expression profiling of sense and antisense transcripts in liver regeneration by microarray analysis.

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