Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

MiRNA expression profiling of human monocyte-derived dendritic cells (moDCs) during maturation

ABSTRACT: miRNA expression profiling of human monocyte-derived dendritic cells (moDCs) during maturation. Immature, 4h and 16h LPS-activated moDCs were used. In this study were analysed 2 biological samples of RNA extracted from 4h-post LPS stimulation moDCs and 2 bfrom 16h-post LPS stimulation. The RNA from 0h-post LPS stimulation were used as reference sample. Were also performed dye-swaps of each biological sample as technical replicates.

ORGANISM(S): Homo sapiens

SUBMITTER: Manuel Santos

PROVIDER: E-GEOD-13369 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

MicroRNA-155 modulates the interleukin-1 signaling pathway in activated human monocyte-derived dendritic cells.

Ceppi Maurizio M Pereira Patricia M PM Dunand-Sauthier Isabelle I Barras Emmanuèle E Reith Walter W Santos Manuel A MA Pierre Philippe P

Proceedings of the National Academy of Sciences of the United States of America 20090204 8

In response to inflammatory stimulation, dendritic cells (DCs) have a remarkable pattern of differentiation (maturation) that exhibits specific mechanisms to control immunity. Here, we show that in response to Lipopolysaccharides (LPS), several microRNAs (miRNAs) are regulated in human monocyte-derived dendritic cells. Among these miRNAs, miR-155 is highly up-regulated during maturation. Using LNA silencing combined to microarray technology, we have identified the Toll-like receptor/interleukin- ...[more]

PMID: 19193853

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Project description:Dendritic cells (DCs) are the sentinels of the mammalian immune system and they undergo a complex maturation process mediated by activation upon pathogen detection. Recent studies described the analysis of activated DCs by transcriptional profiling, but translation regulation was never taken in account. Therefore, the nature of the mRNAs being translated at various stages of DC activation was determined with the help of translational profiling, which is the sucrose gradient fractionation of polysomal-bound mRNAs combined to microarrays analysis. Total and polysomal-bound mRNA populations were compared in immature (0h) and LPS-stimulated (4h and 16h) human monocyte-derived DCs with the help of Affymetrix microarrays. Biostatistical analysis indicated that 296 mRNA molecules are translationally regulated during DC-activation. The most abundant biological process among the regulated mRNAs was protein biosynthesis, indicating the existence of a negative feedback loop regulating translation. Interestingly, a cluster of 17 ribosomal proteins were part of the regulated mRNAs, indicating that translation may be fine-tuned by particular components of the translational machinery. Our observations highlight the importance of translation regulation during the immune response, and may favour the identification of novel gene clusters or protein networks relevant for immunity. Our study also provides information on the possible absence of correlation between gene expression and real protein production in DCs. To identify translationally regulated mRNA molecules, gene expression derived from the polysome-bound mRNAs was compared by Affymetrix microarrays analysis to the gene expression derived from unfractionated total mRNAs derived from whole-cell lysates, as recently described on several reports (Johannes 1999, Rajasekhar 2003, Bushell 2006, Lü 2006, Parent 2008). Polysomal RNA (P) and total RNA (T) were isolated from MoDCs generated from four different blood donors. Since three timepoints (0h, 4h and 16h) were chosen for each blood donor and RNA type, twenty-four RNA samples were totally analyzed by microarrays.

Project description:Human monocyte-derived dendritic cells (moDCs) have been used as an in vitro model for studying tolerance and immunity. However, the underlying metabolic states of tolerogenic (dexamethasone and vitamin D3-treated), immature and immunogenic (mature, LPS-treated) moDCs have not been completely characterized. Through transcriptomic analyses, we determined that tolerogenic moDCs exhibit augmented catabolic pathways with respect to oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO) and glycolysis. Functionally, tolerogenic moDCs showed the highest mitochondrial membrane potential, production of reactive oxygen species and superoxide, and increased mitochondrial spare respiratory capacity. Tolerogenic and mature moDCs manifested differential FAO gene expression with FAO activity being significantly higher in tolerogenic and immature moDCs than in mature. In addition, tolerogenic and mature moDCs demonstrated similar levels of glycolytic rate, but not glycolytic capacity and reserve, which were more pronounced in tolerogenic and immature moDCs. Finally, tolerogenic and immature moDCs, but not mature moDCs, showed high plasticity to compensate the intracellular ATP content after inhibition of different energetic metabolic pathways. Overall, tolerogenic moDCs exhibit a metabolic signature of increased, stable OXPHOS programing and high plasticity for metabolic adaptation. These findings provide a framework for future research of metabolic properties of human DCs. Total RNA of sixteen samples from four moDC types (tolerogenic, LPS-tolerogenic, immature and mature) were extracted by Trizol (Invitrogen) followed by a clean-up procedure using RNeasy Micro Kit (Qiagen). All RNA samples had an integrity number ≥9.6 assessed by Agilent Bioanalyzer. Total RNA samples were amplified using TargetAmp™ and the biotinilated cRNA was prepared by Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre). After the hybridization to the Illumina Human HT-12 v4 Beadchips for 17 h at 58°C, the arrays were washed, stained (Illumina Wash Protocol) and then scanned using BeadArray Scanner 500GX. Array data were extracted at the probe level without background correction using Illumina GenomeStudio software. These raw data were quantile normalized and log2 transformed. Technical replicates were obtained from the hybridization in duplicate of three samples. Pearson correlation analysis showed high correlation between the technical replicates (r>0.99). Differentially expressed genes (DEGs) were identified using Limma16 with Benjamini-Hochberg multiple testing correction (p<0.05). DEGs were further clustered into different groups according to the patterns of expression change among the different moDC types using STEM software17. The analysis was performed in R v.2.12.2 (http://www.R-project.org) with Bioconductor 2.12 (http://www.bioconductor.org) and enabled by Pipeline Pilot (www.accelrys.com).

Project description:Allergic contact dermatitis (ACD) is the most prevalent form of immunotoxicity in humans. Dendritic cells (DC) play a central role in the pathogenesis of ACD, particularly during the sensitization phase to a specific allergen. Upon activation, DCs maturate and migrate to draining lymph nodes which is accompanied by major metabolic and phenotypic alterations that facilitate the presentation of the captured antigen to prime naïve T cells. Nevertheless, knowledge on the molecular effects during maturation of DCs in the context of ACD remain scarce. Here, we present a global proteomic analysis of monocyte-derived dendritic cells (MoDC) treated with NiSO4, the most prominent cause of ACD. Proteomic alterations induced after treatment with NiSO4 were compared to the bacterial trigger lipopolysaccharide (LPS). Both substances possess a similar TLR4 binding capacity, which may help to identify allergy-specific effects compared to bacterial activation. MoDCs treated for 24 h with 2.5 µg/ ml LPS displayed a very strong immunological response, characterized by upregulation of DC activation markers, secretion of proinflammatory cytokines and stimulation of T cell proliferation. Similar immunological responses were observed after treatment with 400 µM NiSO4 but less pronounced. Both triggered TLR4 and TREM1 pathways. However, NiSO4 in addition, also activated hypoxic and apoptotic pathways, which might have overshadowed initial signaling. Moreover, our proteomic data support the importance of Nrf2 as a key player in mediating sensitization since many Nrf2 targets genes were strongly upregulated on protein level selectively after treatment with NiSO4. Strikingly, NiSO4 stimulation induced cellular hypocholesterolemia which was counteracted by the induction of genes and proteins relevant for cholesterol biosynthesis. Our proteomic study allowed for the first time to better characterize some of the fundamental differences between NiSO4 and LPS-triggered activation of MoDCs, providing an important contribution to the molecular understanding of contact allergy.

Dataset Information

MiRNA expression profiling of human monocyte-derived dendritic cells (moDCs) during maturation

Publications

MicroRNA-155 modulates the interleukin-1 signaling pathway in activated human monocyte-derived dendritic cells.

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