Project description:Caco-2 cells were infected with F. nucleatum (MOI=100:1) or non-infected (control) for 24 hours. Total RNA of cells was extracted using the TRIzol® Reagent (Life Technologies) and cDNA was generated using the PimeScript TMRT Reagent Kit (Takara). We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.
Project description:Caco-2 cells grown on transwells were infected with Japanese encephalitis virus (JEV) and total RNA was isolated from cells at the time when trans-epithelial electrical resistance was reduced by about 50% of uninfected cells
Project description:Common missense mutations (D299G, T399I) have been recently identified in the human TLR4 gene. The aim of this study was to determine how TLR4 and associated mutants affect gene expression in Caco-2 cells. We used microarrays to asses gene expression profiles in Caco-2 stably overexpressing TLR4-WT, TLR4-D299G, TLR4-T399I or untransfected.
Project description:PURPOSE: We generated NAPE-PLD-deleted Caco-2 cells, which is a model of intestinal epithelial cells, using genome editing with the CRISPR/Cas9 system. To explore the molecular events following the deletion of NAPE-PLD in Caco-2 cells, we examined the transcriptomic changes in the NAPE-PLD deleted clone 35 compared with Caco-2 parent cells by RNA-seq. METHODS: mRNA profiles of parent and NAPE-PLD deleted Caco-2 cells were generated using Illumina HiSeq4000 (n=2/each cell). Those raw sequence data were then mapped to the human hg38 reference genome using a custom MOIRAI pipeline with STAR 2.51 for alignment. Then, read counts for each transcript were obtained using featureCounts, and the raw count data were directly analyzed for differential gene expression by using edgeR 3.20.9. RESULTS: Approximately 40 million reads per sample were obtained as raw data. Among a total of 12,331 genes detected in at least in one cell type, 1,019 genes were up-regulated (FDR < 0.01, logFC > 1) and 827 genes were down-regulated (FDR < 0.01, logFC > 1) in clone 35 compared with the parental cells.
Project description:Human astrovirus infection is known to disrupt intestinal barrier function by increasing barrier permeabilty. However, the exact cellular mechanism(s) involved is unknown. We used microarrays to detail the global gene expression changes occuring during astrovirus infection and identify necessary cellular pathways for astrovirus pathogenesis.
Project description:Common missense mutations (D299G, T399I) have been recently identified in the human TLR4 gene. The aim of this study was to determine how TLR4 and associated mutants affect gene expression in Caco-2 cells. We used microarrays to asses gene expression profiles in Caco-2 stably overexpressing TLR4-WT, TLR4-D299G, TLR4-T399I or untransfected. Caco-2 clones stably overexpressing HA-tagged wildtype TLR4-WT, mutant TLR4-D299G or TLR4-T399I were generated. Prior to analysis, cell clones were cultured for 8 days in all experiments. RNA (triplicate) was extracted and hybridized on Affymetrix microarrays.
Project description:Clostridium difficile is an anaerobic spore-forming rod-shaped gram-positive bacterium that can infect both humans and animals. Most studies on the pathogenesis of C. difficile have focused on its toxins and their effect on the host cells. Recently, we utilized microarrays to identify conserved and divergent genes associated with virulence in C. difficile isolates from humans and animals. Our data provided the first clue toward a complex mechanism underlying host adaptation and pathogenesis. Microarray technology offers an efficient high-throughput tool to study the transcriptional profiles of pathogens and infected host cells. Transcriptomes of C. difficile after exposure to environmental and antibiotic stresses and those of human epithelial colorectal Caco-2 cells upon TcdA treatment have been analyzed. To our knowledge, there are still no reports on the transcriptomic study of host-pathogen interactions for C. difficile infection (CDI). In vitro analyses of interplay between host and pathogen are essential to unravel the mechanisms of infection and to investigate the host response to infection. We therefore employed microarrays to study both bacterial and human cellular transcriptome kinetics during CDI to Caco-2 cells. Here we present a large-scale analysis of transcriptional profiles to reveal molecular determinants playing a role in C. difficile pathogenesis and the host response. We found that there were 254 and 224 differentially-expressed genes after CDI in C. difficile and Caco-2 cells, respectively. These genes are clustered according to their functional categories and their potential roles in pathogenesis and host response are discussed. Our results will not only increase our understanding on the host-pathogen interaction, but may also provide targets for drug development. Clostridium difficile: Control vs Infection (time course) mRNA with genomic DNA of tested and reference strains Caco-2 cells: Control vs Infected with Clostridium difficile Time-course experiments of Caco-2 cells infected with C. difficile for 30, 60 and 120 min