RNA-seq of porcine peripheral blood mononuclear cells treated with lipopolysaccharide and dexamethasone
Ontology highlight
ABSTRACT: RNA-seq analysis was performed following the treatment of porcine PBMCs with lipopolysaccharide and dexamethasone for two hours to investigate responses to acute activation of immune and glucocorticoid receptor signaling and their crosstalk.
Project description:The objective of this study was to compare the transcriptomes of uninfected DH82 cells, a canine histiocytic sarcoma cell line, with DH82 cells, persistently infected with the Onderstepoort strain of canine distemper virus in order to identify effects of canine distemper virus infection upon the transcriptome of this tumor cell line and hereby draw conclusions on possible paramyxovirus-induced oncolytic mechanisms
Project description:The opportunistic pathogenic mold Aspergillus fumigatus is an increasing cause of morbidity and mortality in immunocompromised and, in part, immunocompetent patients. Like bacteria or yeast, A. fumigatus can grow in multicellular communities by the formation of a hyphal network encased in an extracellular matrix. Here, we describe the proteome and transcriptome of planktonic and biofilm-grown A. fumigatus mycelium after 24h and 48h. A biofilm- and time-dependent regulation of many proteins and genes of the primary metabolism indicates a developmental stage of the young biofilm at 24h, which demands energy. At a matured biofilm phase, metabolic activity seems to be reduced. However, genes encoding hydrophobins and proteins involved in the biosynthesis of secondary metabolites were significantly upregulated. In particular, proteins of the gliotoxin secondary metabolite gene cluster were induced in biofilm cultures. This was confirmed by RT-PCR and by detection of this immunologically active mycotoxin in culture supernatants using HPLC analysis. The enhanced production of gliotoxin by in vitro formed biofilms reported here may play also a significant role under in vivo conditions. It may confer A. fumigatus protection from the host immune system and also enable its survival and persistence in chronic lung infections such as aspergilloma. Comparison of biofilm and submers cultures at 24h and 48h after induction.
Project description:Human cell cultures A549 and HepG2/C3 were exposed to 0-100 micromolar Tris(1,3-dichloro-2-propyl)phosphate (TDCIPP) in 0.5% DMSO or to 0.5% DMSO alone for 24 h. RNA was prepared and labeled with Cy3. Agilent SurePrint G3 Human GE v2 8x60k Microarrays, Agilent design ID 039494, were used to profile transcriptional responses to TDCIPP.
Project description:In a whole-transcriptome study, cellular responses of DCs confronted with the fungi A. fumigatus, C. albicans or the bacterial cell wall component LPS were investigated. Therefore DCs of four independent donors were harvested after 6 and 12 hours co-culture with A. fumigatus, C. albicans and LPS and analyzed with Affymetrix whole genome expression arrays. In general, transcriptomic analysis revealed a clustering of the A. fumigatus and C. albicans stimulated DCs. However, LPS and fungi-dependent gene expression showed more common similarities compared to the untreated control. Stimulation with LPS induced a differential regulation of 2793 and 2863 genes after 6 /12h, while confrontation with A. fumigatus and C. albicans resulted in 743/1076 and 1729/974 differentially regulated genes, respectively. Kruppel-like factor 4 (KLF4) was identified as the only transcription factor that was down-regulated in DCs by both fungi but induced by stimulation with LPS. Human DCs were generated from 4 independent, healthy blood donors. moDCs were either left untreated or co-cultivated with Aspergillus fumigatus 46645 germ tubes or Candida albicans SC5314 (MOI1) and or LPS (1µg/ml) for 6h.
Project description:Unstimulated (M0), M1-polarized (GM-CSF, LPS, IFNγ-stimulated), and M2-polarized (M-CSF, IL-4-stimulated) canine blood-derived macrophages were generated in vitro and investigated for differences in their transcriptome to create a basis for future investigations upon the role of macrophage polarization in dogs, a species, which has emerging importance for translational research.
Project description:Monocytes are key players in inflammatory processes which are triggered by lipopolysaccharide (LPS), the major outer membrane component of gram-negative bacteria. The present study in human monocytic THP-1 cells was designed in order to identify LPS-inducible genes which are down-regulated by the reduced form of CoQ10 (ubiquinol, Q10H2). For this purpose, THP-1 cells were incubated with 10 µM Q10H2 for 24 h. Subsequently, cells were stimulated for 4 h with 1µg/ml LPS and the resulting gene expression levels were determined using microarrays. 14 LPS-inducible genes were identified to be significantly (p < 0.05) down-regulated by Q10H2 pre-treatment between a factor of 1.32 and 1.65. The strongest effect of Q10H2 incubation was found for the nuclear receptor coactivator 2 gene (NCOA2). Gene Ontology (GO) terms revealed for the Q10H2-sensitive genes an involvement in e.g. signal transduction processes (CENTD1, NCOA2, PSD3, PPP2R5C), transcriptional regulation (NCOA2, POU2F1, ETV3) and cell proliferation pathways (CCDC100, EPS15). In conclusion, we provide evidence in THP-1 cells that the reduced form of CoQ10 (Q10H2) modulates LPS-induced gene expression. Whole genome expression profiles were analysed from monocytes pre-incubated with the reduced form of CoQ10 (ubiquinol, Q10H2) before subsequent stimulation with LPS. Stimulated (+LPS) and unstimulated (-LPS) monocytes were used as positive and negative controls, respectively. For every experimental group (3 groups in total), three Affymetrix Human Genome U133 Plus 2.0 arrays were used, thus resulting in the analysis of 9 microarrays.
Project description:Genetic TNFAIP3 (A20) inactivation is a classical somatic lymphoma lesion and the genomic trait in haploinsufficiency of A20 (HA20). Single-cell sequencing reveals “pre-lymphoma” transcription signatures in lymphocytes of HA20 patients.
Project description:Postnatal neural progenitors of the enteric nervous system are a potential source for future cell replacement therapies of developmental dysplasia like Hirschrpung’s disease. However, little is known about the molecular mechanisms driving the homeostasis and differentiation of this cell pool. In this work, we conducted Affymetrix gene chip experiments to identify differences in gene regulation between proliferation and early differentiation of enteric neural progenitors. We detected a total of 1333 regulated genes that were linked to different groups of cellular mechanisms involved in cell cycle, apoptosis, neural proliferation, and differentiation. As expected, we found a strong inhibition of cell cycle progression as well as an enhanced expression of neuronal and glial markers. We further found a marked inactivation of the canonical Wnt pathway during the beginning of cellular differentiation. Taken together, this data illustrated the various mechanisms taking place during the proliferation and early differentiation of enteric neural progenitor cells. We analyzed 2 groups with 3 samples each: 1 group consistent of cells proliferating für 11 days and 1 group of enterospheres proliferating for 9 days and differentiating for 2 days before RNA extraction
Project description:Differentiation assays with neural progenitor cells of the enteric nervous system (ENS) showed elongated neurite outgrowth under influence of 3,5,3'-Triiodothyronine (concentrations 50 nm and 100 nm). For analysis, neural cells were stained with TUJ1 (beta-Tubulin III). Microarray analysis should enlighten these results on a genetical basis and give hints about the regulation pathways. We analyzed 2 groups with 3 samples each: 1 group consistent of cells treated with 100 nm T3 for 1 day and 1 control group consistens of cells without T3 treatment
Project description:This study investigates the effects of exercise and genetic predisposition on the transcriptomic profile of the pituitary gland of long-term selected marathon (DUhTP) and non-inbred (DUC) mice. In the exercise group, mice underwent treadmill training for three weeks. For the sedentary control group, mice were kept under minimal physical activities. For the 3-week training program, the mice were running five days per week (Monday to Friday) starting at age of 49 days after birth (Walz et. al. 2021). All mice used in this experiment were male and sacrificed at day 70 of life for tissue sampling.