Comparison of Gene Expression Profiles between Keratinocytes, Melanocytes and Fibroblasts

BACKGROUND: The skin has many important functions such as protection, preservation, temperature regulation, and vitamin D synthesis. It is composed of a variety of cell types including keratinocytes, melanocytes and fibroblasts. OBJECTIVE: We attempted to compare the gene expression profiles between keratinocytes, melanocytes and fibroblast, using cDNA microarray. METHODS: Keratinocytes, melanocytes and fibroblasts were primary cultured from five foreskin specimens. Total RNAs were extracted and pooled to reduce the individual variations, and then used for cDNA microarray. RESULTS: Total 12,028 genes were selected as the reliable genes whose expression was detected in at least one of the three cell types. By comparing the relative expression levels with cutoff limitation as a fourfold change, we obtained 126 fibroblast-specific, 179 keratinocyte-specific and 173 melanocyte-specific genes, many of which are known to be characteristically expressed in each cell type. In addition, we identified many genes whose skin-specific functions have not yet been determined. CONCLUSION: Our data provide important information on which to base further investigation into the specification of skin cell types.

Gene Expression Analysis of the Human Astrocytoma Cell after Abeta25-35 Stimulation Followed by Ibuprofen Administration

BACKGROUND: The molecular events leading to the development of sporadic late-onset Alzheimer's disease (AD) have not been defined. A number of mechanism for the protective effects of non-steroidal anti-inflammatory drugs (NSAIDs) in AD have been proposed. We investigated the ibuprofen effect of global gene expression on the amyloid-beta25-35 (Abeta25-35)-stimulated human astrocytoma cell. METHODS: U373MG, a human astrocytoma cell line, was incubated with 25 microM of aggregated Abeta25-35 or aggregated Abeta25-35 plus 100 microM ibuprofen at 37degrees C for 24 hours. Cells treated with ibuprofen alone were used as the negative control. Differential gene expression analysis was carried out with the Illumina human whole genome microarray. Real-time reverse transcriptase polymerase chain reaction (RT-PCR) was also done to validate the gene expression changes. After Welch's t-test, the significant subset of outlier genes were identified by an expression change cut-off 1.5 fold, p<0.05. Kyoto Encyclopedia of Genes and Genomes database was used for cellular signaling pathway analysis. RESULTS: A total of 371 differentially expressed genes were identified from 16,692 detectable signals in Abeta25-35 peptide stimulated U373MG cells- 182 up-regulated genes with 21 biological pathways including biosynthesis of steroid, peroxisome proliferator-activated receptor signaling pathway and focal adhesion and 189 down-regulated genes with 14 biological pathways including transforming growth factor-beta signaling pathway, axon guidance and mitogen activated protein kinase signaling pathway. Ibuprofen suppressed the up-regulated expression of immunity/inflammation (especially, SERPINE1), signal pathway, metabolism and cancer-related genes. The expression of microarray data was confirmed by real-time RT-PCR. CONCLUSION: Aggregated Abeta25-35 induces expression of widespread transcriptional alterations, namely 21 functional groups 182 up-regulated genes and 14 functional groups 189 down-regulated genes in U373MG cells. Ibuprofen, a commonly used NSAID, suppressed Abeta25-35-induced increase of global changes in transcription of sets of genes especially immunity/inflammation, signal pathway, metabolism and cancer-related genes.

Microarray Applications in Cancer Research / Journal of the Korean Cancer Association, 대한암학회지

DNA microarray technology permits simultaneous analysis of thousands of DNA sequences for genomic research and diagnostics applications. Microarray technology represents the most recent and exciting advance in the application of hybridization-based technology for biological sciences analysis. This review focuses on the classification (oligonucleotide vs. cDNA) and application (mutation-genotyping vs. gene expression) of microarrays. Oligonucleotide microarrays can be used both in mutation-genotyping and gene expression analysis, while cDNA microarrays can only be used in gene expression analysis. We review microarray mutation analysis, including examining the use of three oligonucleotide microarrays developed in our laboratory to determine mutations in RET, beta-catenin and K-ras genes. We also discuss the use of the Affymetrix GeneChip in mutation analysis. We review microarray gene expression analysis, including the classifying of such studies into four categories: class comparison, class prediction, class discovery and identification of biomarkers.

Immunodeficiency Virus Type 1 Infection of H9 Cells

Human immunodeficiency virus type 1 (HIV-1) virus causes severe defect in the immune system and affects the host cell gene expression profoundly. The gene expression pattern will be characterized by changes in cellular mRNA levels that are dependent on both the stage of infection and the biological state of the infected cells. The expression levels of 7,404 cellular RNA transcripts were assessed in H9 cells at different time points after HIV-1 IIIB infection. In total 7 time-points, 959/7,404 (13%) genes were a 2-fold or greater expressed. 387 of 959 genes (40.4%) were up-regulated, and other 572 genes (59.6%) were down-regulated. Three hundred seventeen genes were up-regulated a 2-fold or greater at 72 hr postinfection and 2 to 139 genes were up-regulated at the other time-points. In contrast, 126 to 349 genes were down-regulated a 2-fold or greater in all time-points, excepting 6 hr postinfection. Twenty-three genes were up-regulated a 2-fold or greater over at least four of seven time-points, which were mostly ribosomal proteins and MHCs. Especially, MHCs including HLA-DRA were steadily up-regulated from 24 hr postinfection. Thirty genes were down-regulated a 2-fold or greater in all the time-points, which were mainly related with synthesis and metabolism. These results show that host cell gene expression was altered by HIV-1 infection according to time-points and will provide a framework for studies on interactions between host and HIV-1 infection.