Expression and ChIP-seq analysis LPS stimulated THP-1 cells
ABSTRACT: This SuperSeries is composed of the following subset Series: GSE32141: Expression analysis LPS stimulated THP-1 cells in four paired samples GSE32324: ChIP-seq analysis LPS stimulated THP-1 cells Refer to individual Series
Macrophages play a critical role in innate immunity, and the expression of early response genes orchestrate much of the initial response of the immune system. Macrophages undergo extensive transcriptional reprogramming in response to inflammatory stimuli such as Lipopolysaccharide (LPS).To identify gene transcription regulation patterns involved in early innate immune responses, we used two genome-wide approaches--gene expression profiling and chromatin immunoprecipitation-sequencing (ChIP-seq) ...[more]
Project description:Macrophages play a critical role in innate immunity, and the expression of early response genes orchestrate much of the initial response of the immune system. Macrophages undergo extensive transcriptional reprogramming in response to inflammatory stimuli such as Lipopolysaccharide (LPS). To identify gene transcription regulation patterns involved in early innate immune responses, we used two genome-wide approaches - gene expression profiling and chromatin immunoprecipitation-sequencing (ChIP-seq) analysis. We examined the effect of 2 hrs LPS stimulation on early gene expression and its relation to chromatin remodeling (H3 acetylation; H3Ac) and promoter binding of Sp1 and RNA polymerase II phosphorylated at serine 5 (S5P RNAPII), which is a marker for transcriptional initiation. Our results indicate novel and alternative gene regulatory mechanisms for certain proinflammatory genes. We identified two groups of up-regulated inflammatory genes with respect to chromatin modification and promoter features. One group, including highly up-regulated genes such as tumor necrosis factor (TNF), was characterized by H3Ac, high CpG content and lack of TATA boxes. The second group, containing inflammatory mediators (interleukins and CCL chemokines), was up-regulated upon LPS stimulation despite lacking H3Ac in their annotated promoters, which were low in CpG content but did contain TATA boxes. Genome-wide analysis showed that few H3Ac peaks were unique to either +/-LPS condition. However, within these, an unpacking/expansion of already existing H3Ac peaks was observed upon LPS stimulation. In contrast, a significant proportion of S5P RNAPII peaks (approx 40%) was unique to either condition. Furthermore, data indicated a large portion of previously unannotated TSSs, particularly in LPS-stimulated macrophages, where only 28% of unique S5P RNAPII peaks overlap annotated promoters. The regulation of the inflammatory response appears to occur in a very specific manner at the chromatin level for specific genes and this study highlights the level of fine-tuning that occurs in the immune response. 4 pairs of THP-1 cells either stimulated with LPS or not This submission represents transcriptome component of study.
Project description:In this study we performed an RNA-seq analysis of lipopolysaccharide (LPS) and palmitate (PAL) stimulated THP-1 macrophages to study the gene regulatory mechanisms underlying classical innnate immune response and chronical inflammatory response caused by metabolic stress. This analysis was done to complement single-cell transcriptome analyses of the same cell models.
Project description:In this study we performed single-cell transcriptome analysis of THP-1 macrophages, stimulated with high levels of free fatty acids (palmitate, PAL) typical for obese adipose tissue microenvironment or lipopolysaccharide (LPS), representing a classical stimulus activating innate immune response. Analysing full transcriptomes of individual cells, we were able to distinguish 3 macrophage transcriptional states and decipher gene regulatory pathways underlying macrophage state identity in both stimulations.
Project description:To better understand the interaction of TGFbeta and Toll-like-receptor 4 (TLR4) signaling in monocytes, we performed microarray analysis. We identified a unique set of genes whose expressions in monocytes were regulated by simultaneous stimulation of TLR4 and TGFβ signaling. THP-1 cells, a human monocytic cell line, were stimulated for 24 hours with PBS as control, LPS (100ng/ml), TGFbeta1 (1ng/ml) or LPS (100ng/ml) + TGFbeta1 (1ng/ml). After 24 hours of stimulation, total RNA was isolated and prepared for genome wide analyses using Illumina HumanRef8 V3.0 Beadchips. In total 32 arrays were analyzed including 8 samples of PBS-stimulated monocytes, 8 samples of LPS-stimulated monocytes, 8 samples of TGFbeta1 stimulated monocytes and 8 samples of monocytes stimulated with LPS + TGFbeta1.
Project description:The role of synovial tissue fibroblasts and macrophages interactions in driving chronic inflammation and resolution of arthritis is unknown. In this project, we used bulk RNAseq to investigate the impact of different phenotypes of macrophages on activation of synovial fibroblasts.
Project description:microRNA signatures with diagnosis, distant metastasis and prognosis for nasopharyngeal carcinoma 62 nasopharyngeal carcinoma and 6 non-cancer nasopharyngitis fresh tissues were detected by microRNA microarray
Project description:Toll-like receptors are among the first sensors that detect and drive immune responses to pathogens. Macrophages that encounter a pathogen are usually not stimulated through one TLR but by a combination of these receptors engaged by distinct ligands produced by the microbe. As a first step to understanding the integrated signaling under such complex conditions, we have investigated the differences in the phosphoprotein signaling cascades triggered by individual TLR4, TLR2 and TLR7 ligands using a single responding cell population. We performed a global quantitative and early post-stimulation kinetic analysis of the mouse macrophage phosphoproteome using stable isotope labeling with amino acids coupled to phosphopeptide enrichment and high-resolution mass spectrometry.
Project description:To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish asthma and normal subjects. We analyzed gene expression patterns of the peripheral blood cells from asthma patients compared with those from normal subjects using microarray analyses. In addition, we analyzed gene expression patterns of the LPS or HDM-treated THP1 cells compared with those from non-treated THP1 cells. And we analyzed the microarray data through clustering analysis, signaling pathway analysis and others. Ten milliliters of peripheral blood of five mild asthma, five severe asthma and five normal subjects were centrifuged at 4000 rpm for 20 min to collect 0.4 mL of the buffy coat fraction for in vivo study. To induce an inflammatory response, for in vitro study, the THP1 cells were seeded in 12-well plates at a density of 1 × 106 cells/well in RPMI 1640 medium containing 0.5% fetal bovine serum and stimulated for 24 hrs with LPS or HDM extract. After stimulation the THP1 cells were harvested using a cell scraper and lysed for total RNA extraction. Total RNA was extracted from the buffy coat fractions and RNA was reverse transcribed into cDNA for microarray analysis