Dynamic genome-wide transcriptional response of human monocyte-derived dendritic cells to IL-6 and Il-10
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: David Braun
PROVIDER: E-GEOD-45466 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Dendritic cells (DC) play a vital role in the induction of activation or tolerance of immune response. STAT3 is a master transcriptional regulator of immune response in DCs by positively or negatively regulating DC function, but the mechanisms are unknown. STAT3 is post-translationally modified by acetylation or phosphorylation. While much is understood about transcriptional targets of phosphorylated STAT3, the gene targets and the functional impact of acetylated-STAT3 remain unclear. We aimed to answer the gene targets of acetylated-STAT3 and test the hypothesis that acetylation of STAT3 plays a key role in negative regulation of DCs. We performed genome-wide binding analysis of acetyl-STAT3 by ChIP-Seq coupled with gene expression microarrays. Acetylation of STAT3 induced by SAHA increased its capability to bind to target DNA sites in genome. Theses binding sites were mostly proximal but some were also distal up to over 100 kb from transcription start site. Gene expression array showed 1701 genes up-regulated and 1668 genes down-regulated. Proximal binding of acety-STAT3 showed more effective transcription function than distal binding. In top 500 binding peaks, the frequency of canonical motifs bound by acetyl-STAT3 were significantly higher than that for noncanonical motifs (p<0.00001). Functional analysis revealed that acetyl-STAT3 regulates target genes by upregulating genes that are primarily involved in negative regulation of cytokine production and IL-10 signaling, or downregulating genes that are primarily involved in immune effector process and antigen processing/presentation. Upregulation of IL-10Ra by acetyl-STAT3 contributes to the enhanced sensitivity of IL-10 signaling and negative regulation of DC function. Bone marrow derived dendritic cells were treated with SAHA (500 nm) or diluent for 12 hours. ChIP was performed using antibodies against STAT3, H3K4me3 and matched IgG control. DNA binding profiles were generated by deep sequencing using Illumina HiSeq 2000.
2015-11-05 | E-GEOD-74262 | biostudies-arrayexpress
Project description:Monocytes can give rise to multiple highly specialized cell types to perform a wide array of functions, ranging from pathogen phagocytosis to bone resorption. This differentiation is induced by the binding of cytokines to dedicated receptors on the surface of monocytes, which results in the initiation of genetic programs that enable cells to perform their specialized functions. Given their common background, it is not surprising that monocyte-derived cells share abilities and cellular markers, yet their specialized functions require a dedicated set of proteins. In order to dissect the monocyte differentiation process and to define cell type-specific marker proteins, we differentiated circulating monocytes into dendritic cells, M1 and M2 macrophages, and osteoclasts, and assessed their proteomes by quantitative mass spectrometry throughout the differentiation process. Statistical analysis indicated that monocyte differentiation is a linear process characterized by a common core of proteins that is similarly affected among the distinct differentiation paths. Throughout the specialization process a cluster of RNA-binding and processing proteins was downregulated whereas proteins associated to metabolic processes were increased. Analysis of the specialized cells after 10 days of differentiation uncovered existing and putative novel dendritic cell markers. Combined, we here present a comprehensive proteomic analysis of monocyte differentiation uncovering shared and distinct proteomic features of differentiating monocytes and monocyte-derived cells.
2021-09-09 | PXD016245 | Pride
Project description:The physiological function of the immune system and the response to therapeutic immunomodulators may be sensitive to combinatorial cytokine micro-environments that shape the responses of specific immune cells. Previous work shows that paracrine cytokines released by virus-infected human dendritic cells (DC) can dictate the maturation state of naM-CM-/ve DCs. To understand the effects of paracrine signaling, we systematically studied the effects of combinations cytokines in this complex mixture in generating an antiviral state. After naM-CM-/ve DCs were exposed to either IFNM-NM-2 or to paracrine signaling released by DCs infected by Newcastle Disease Virus (NDV), microarray analysis revealed a large number of genes that were differently regulated by the DC-secreted paracrine signaling. In order to identify the cytokine mechanisms involved, we identified 20 cytokines secreted by NDV infected DCs for which the corresponding receptor gene is expressed in naM-CM-/ve DCs. By exposing cells to all combinations of 19 cytokines (leave-one-out studies) we identified 5 cytokines (IFNM-NM-2, TNFM-NM-1, IL-1M-oM-^AM-", TNFSF15 and IL28) as candidates for regulating DC maturation markers. Subsequent experiments identified IFNM-NM-2, TNFM-NM-1 and IL1M-oM-^AM-" as the major synergistic contributors to this antiviral state. This finding was supported by infection studies in vitro, by T cell activation studies and by in vivo infection studies in mouse. Combination of cytokines can cause response states in DCs that differ from those achieved by the individual cytokines alone. These results suggest that the cytokine microenvironment may act via a combinatorial code to direct the response state of specific immune cells. Further elucidation of this code may provide insight into responses to infection and neoplasia as well as guide the development of combinatorial cytokine immunomodulation for infectious, autoimmune and immunosurveillance-related diseases. Cells exposed to the supernatant of NDV infected cells were compared to NDV infected cells, IFNM-NM-2 treated cells and naM-CM-/ve dendritic cells after 8 hours.
2013-12-15 | E-GEOD-52081 | biostudies-arrayexpress
Project description:The canonical pathway for IL-1? production requires TLR-mediated NF-?B-dependent Il1b gene induction, followed by caspase-containing inflammasome-mediated processing of pro-IL-1?. Here we show that IL-21 unexpectedly induces IL-1? production in conventional dendritic cells (cDCs) via a STAT3-dependent but NF-?B-independent pathway. IL-21 does not induce Il1b expression in CD4+ T cells, with differential histone marks present in these cells versus cDCs. IL-21-induced IL-1? processing in cDCs does not require caspase-1 or caspase-8 but depends on IL-21-mediated death and activation of serine protease(s). Moreover, STAT3-dependent IL-1? expression in cDCs at least partially explains the IL-21-mediated pathologic response occurring during infection with Pneumonia Virus of Mice. These results demonstrate lineage-restricted IL-21-induced IL-1? via a non-canonical pathway and provide evidence for its importance in vivo. Genome-wide transcription factors mapping and binding of STAT3, H3K4me3, H3K27me, H3K4me1, H3K27ac in mouse CD4+ T cells and dendritic cells in WT and Stat3-/- mice. RNA-Seq is performed in mouse CD4+ T cells and dendritic cells in WT mice, with or without indicated cytokines.
2015-07-07 | E-GEOD-61677 | biostudies-arrayexpress
Project description:The dendritic cell (DC) is a master regulator of immune responses. Pathogenic viruses subvert normal immune function in DCs through the expression of immune antagonists. Understanding how these antagonists interact with the host immune system requires knowledge of the underlying genetic regulatory network that operates during an uninhibited antiviral response. In order to isolate and identify this network, we studied DCs infected with Newcastle Disease Virus (NDV), which is able to stimulate innate immunity and DC maturation through activation of RIG-I signaling, but lacks the ability to evade the human interferon response. To analyze this experimental model, we developed a new approach integrating genome-wide expression kinetics and time-dependent promoter analysis. We found that the genetic program underlying the antiviral cell state transition during the first 18-hours post-infection could be explained by a single regulatory network. Gene expression changes were driven by a step-wise multi-factor cascading control mechanism, where the specific transcription factors controlling expression changed over time. Within this network, most individual genes are regulated by multiple factors, indicating robustness against virus-encoded immune evasion genes. In addition to effectively recapitulating current biological knowledge, we predicted, and validated experimentally, antiviral roles for several novel transcription factors. More generally, our results show how a genetic program can be temporally controlled through a single regulatory network to achieve the large-scale genetic reprogramming characteristic of cell state transitions. Total RNA from Monocyte-derived conventional DCs of 2 different donors were infected with Newcastle disease virus (NDV) or as control with allantoic fluid (AF) alon. DC were then harvested at : 0, 1, 2, 6, 10 and 18 hour for control and 1, 2, 4, 6, 8, 10, 12, 14, 16 and 18 hours for NDV infection. Replicates were performed for each of the donors at all timepoints.
2010-03-08 | E-GEOD-18791 | biostudies-arrayexpress
Project description:The interleukin-23 (IL-23) pathway plays a critical role in the pathogenesis of multiple chronic inflammatory disorders, however, inter-individual variability in IL-23-induced signal transduction in circulating human lymphocytes has not been well-defined. In this study, we observed marked, reproducible inter-individual differences in IL-23 responsiveness (measured by STAT3 phosphorylation) in peripheral blood CD8+CD45RO+ memory T and CD3+CD56+ NKT cells. To define mechanisms that might be contributing to the differential IL-23-induced STAT3 activation between individuals, we examined mRNA expression differences in CD8+CD45RO+ memory T cells between IL-23 responsive and non-responsive individuals. We analyzed unstimulated and IL-23 stimulated FACS sorted CD8+CD45RO+ memory T cells from two individuals demonstrating robust IL-23 responsiveness, and two individuals demonstrating low IL-23 responsiveness, using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Affymetrix Expression Console software. No techinical replicates were performed.
2013-03-08 | E-GEOD-42051 | biostudies-arrayexpress
Project description:Talactoferrin alfa (TLF) is a unique recombinant version of human lactoferrin, an important immunomodulatory protein present in exocrine secretions and in the secondary granules of neutrophils. Talactoferrin has demonstrated anti-cancer activity in preclinical studies and in Phase III clinical trials in patients with Renal Cell Cancer and non-small cell lung cancer. We have shown that TLF induces the maturation of human DCs derived from monocytes, suggesting that the linkage of the innate and adaptive immunity through DC maturation is a key immune function mediated by TLF. In this study we used genome-wide expression analysis to explore the mechanisms by which TLF leads to the functional maturation of DC. We show that GMP level recombinant TLF activates human DCs in a Toll-like receptor (TLR) -2 and -4 dependent manner. Human peripheral blood mononuclear cells (PBMCs) were obtained from buffy coats of healthy donors. CD14+ cells were isolated from fresh PBMCs by positive immunoselection with magnetic beads. Immature dendritic cells (i-DC) from four donors were generated using granulocyte-macrophage colony-stimulating factor (GM-CSF) and IL-4. On day 6, cells were harvested in order to have iDC or mDC (conventionally matured DC) by addition of Tumor Necrosis Factor (TNF) -alfa and IL-1beta or TLF-DC (Talactoferrin matured DC) adding Food and Drug Administration-approved, GMP level recombinant TLF generated in eukaryotic cells. After 24 hour culture, cells were harvested and analyzed with Illumina arrays.
2013-12-30 | E-GEOD-26438 | biostudies-arrayexpress
Project description:Myeloma bone disease is characterized by tremendous bone destruction with suppressed bone formation. IL-3 is a multifunctional cytokine that increases myeloma cell growth and osteoclast proliferation while inhibiting osteoblast differentiation. While IL-3 appears to be an attractive therapeutic target for myeloma, attempts at targeting IL-3 have been unsuccessful due to IL-3M-bM-^@M-^Ys effects on normal hematopoiesis. Thus identification of IL-3M-bM-^@M-^Ys downstream effects in MMBD is important for effective targeting of this cytokine in MM. Here we demonstrated that treatment of myeloma patient CD14+ bone marrow monocyte / macrophages with IL-3 induces high levels of Activin A (ActA), a pluripotent TGF-M-NM-2 superfamily member that, like IL-3, modulates MMBD by enhancing osteoclastogenesis and inhibiting osteoblasts. We show that IL-3 induced osteoclastogenesis is mediated by ActA and is RANKL independent. Additionally, IL-3 induced ActA secretion is greatest early in osteoclastogenesis and ActA acts early in osteoclastogenesis. Therefore we suggest that therapies targeting ActA production should block IL-3M-bM-^@M-^Ys effects in myeloma bone disease. Investigate the mediators of IL-3M-bM-^@M-^Ys effects on bone remodeling in myeloma we performed gene expression profiling using Affymetrix GeneChip analysis of IL-3 treated CD14+ peripheral blood from healthy donor.
2014-11-01 | E-GEOD-41992 | biostudies-arrayexpress
Project description:Introduction Disruption of the epithelial barrier can induce eosinophilic esophagitis (EoE), a TH2-mediated food- and aeroallergen associated chronic inflammatory disease 1, 2. The expression of IL-20 subfamily cytokines, IL-19, IL-20 and IL-24, is increased in TH2-mediated diseases, yet their function in EoE is unknown. Methods Combining RNA-sequencing (RNA-seq) and proteome analysis, we have examined the effects of the IL-20 subfamily on esophageal epithelial cells using patient-derived organoids and an experimental EoE mouse model. Results When stimulated with IL-20 subfamily cytokines patient-derived esophageal organoids showed decreased expression of Filaggrin (FLG) and Filaggrin 2 (FLG2) responsible for epithelial cornification. In agreement, EoE patients with active inflammation showed elevated IL-20 subfamily cytokines and decreased FLG and FLG2 expression. Topical corticosteroid treatment in EoE patients restored filaggrin expression, while reducing IL-20 subfamily cytokines. Abolishment of IL-20 subfamily signalling in Il20R2-/- animals attenuated experimental EoE in an OVA-induced mouse model. In the esophageal keratinocyte cell line, KYSE-180, we identified IL-20 subfamily-induced STAT3 and MAPK (ERK1/2) pathway activation. However, Stat3fl/flKrt5cre mice with an epithelium specific deletion of Stat3 developed exacerbated experimental EoE with a pronounced decrease of Flg2. In line, combined stimulation of patient-derived esophageal organoids with IL-20 subfamily cytokines and pharmacological inhibition of STAT3 resulted in aggravated decrease of FLG and FLG2. In addition, pharmacological STAT3 inhibition resulted in reduced transepithelial electrical resistance (TEER) and increased macromolecular flux in patient-derived air liquid interface (ALI) cultures. Whereas, inhibition of the MAPK (ERK1/2) pathway hampered IL-20 subfamily induced TEER reduction and paracellular flux increment. Finally, MAPK (ERK1/2) inhibitor treatment reduced infiltrating CD45+ immune cells in the esophagus and alleviated experimental EoE in mice. Conclusion We discovered a novel regulatory function of the IL-20 subfamily for epithelial barrier integrity. Aberrant IL-20 subfamily signaling disturbs the epithelial barrier function, while abrogation of IL-20 subfamily and ERK1/2 signaling restores epithelial integrity and attenuates experimental EoE. Therefore, we propose that targeting the IL-20 subfamily pathway could present a novel therapeutic strategy for EoE treatment.
2023-05-10 | PXD031509 | Pride
Project description:In order to detect the microRNA expression profile of in vitro generated dendritic cells , purified monocytes from PBMCs were used as dendritic cell (DCs) precursors and were cultured in medium with cocktail for differentiation and maturation to immature dendritic cells (iDCs) and mature dendritic cells (mDCs). microRNA samples were isolated from precursor, iDCs and mDCs and used for microarray-based microRNAs expression profiles. To generate enough amount of immature DC (iDCs) and mature DCs (mDCs), monocytes were differentiated with GM-CSF and rhIL-4 for 2 days and maturated in the presence of TNF-α, IL-1β, IL-6 and PGE2 for another 2 days. With the anticipation to insight developmental-stage-specific microRNAs with potential functions related to monocyte derived DCs, global microRNAs expression profiling was set using microarray technology.microRNA expression profiles were performed in triplicate independent experiments starting for 3 groups of precursor, iDC and mDC generated from different blood donors.
2013-01-28 | E-GEOD-15036 | biostudies-arrayexpress