Project description:Gene level expression estimate using the Whole Transcript (WT) Assay approach of the Gene 1.0 ST Array System for Mouse. This assay was done to identify the RIPK1-dependent gene expression changes in mouse BMDMs. Cost-effective gene-level analysis based on whole-transcript coverage. We analyzed Bone Marrow Derived Macrophages (BMDMs) under 4 different conditions (Control, LPS, LPS/zVAD, LPS/zVAD/Nec-1) to assess inflammatory changes in RIPK1 kinase dependent manner compared to LPS, LPS/zVAD plus RIPK1 inhibitor Nec-1 and control.
Project description:We report the genome-wide RNA sequencing analysis in Il10-/- bone marrow-derived macrophages (BMDMs) stimulated by lipopolysaccharide (LPS) where IL-10 effect in macrophage inflammatory response was examined in IL-10-deficient BMDMs upon LPS stimulation with addition of exogenous IL-10.
Project description:Lactic acid (LA) has emerged as an important modulator of immune cell function. We performed ATAC-seq to profile the chromatin landscape of bone marrow-derived macrophages (BMDMs) upon lipopolysaccharide (LPS) stimulation with or without LA. Additionally, we also report the genome-wide RNA sequencing analysis in bone marrow-derived macrophages (BMDMs) where LA effect in macrophage inflammatory response was examined in BMDMs upon lipopolysaccharide (LPS) stimulation in the presence or absence of LA. To further examine LA effect due to low pH, hydrochloric acid (HCl) was used to adjust similar pH conditions (i.e. pH 6.5) as in media with LA.
Project description:Wild type and Irg1 knockout mouse bone marrow derived macrophages (BMDMs) were processed with a redox proteomics workflow and analyzed by LC-MS/MS with TMT based quantification.
Project description:<p>Macrophages play a critical role in the inflammatory response and tumor development. Macrophages are primarily divided into pro-inflammatory M1-like and anti-inflammatory M2-like macrophages based on their activation status and functions. <em>In vitro</em> macrophage models could be derived from mouse bone marrow cells stimulated with two types of differentiation factors: GM-CSF (GM-BMDMs) and M-CSF (M-BMDMs), to represent M1-and M2-like macrophages, respectively. Since macrophage differentiation requires coordinated metabolic reprogramming and transcriptional rewiring in order to fulfill their distinct roles, we combined both transcriptome and metabolome analysis, coupled with experimental validation, to gain insight into the metabolic status of GM-and M-BMDMs. The data revealed higher levels of the tricarboxylic acid cycle (TCA cycle), oxidative phosphorylation (OXPHOS), fatty acid oxidation (FAO), and urea and ornithine production from arginine in GM-BMDMs, and a preference for glycolysis, fatty acid storage, bile acid metabolism, and citrulline and nitric oxide (NO) production from arginine in M-BMDMs. Correlation analysis with the proteomic data showed high consistency in the mRNA and protein levels of metabolic genes. Similar results were also obtained when compared to RNA-seq data of human monocyte derived macrophages from the GEO database. Furthermore, canonical macrophage functions such as inflammatory response and phagocytosis were tightly associated with the representative metabolic pathways. In the current study, we identified the core metabolites, metabolic genes, and functional terms of the two distinct mouse macrophage populations. We also distinguished the metabolic influences of the differentiation factors GM-CSF and M-CSF, and wish to provide valuable information for <em>in vitro</em> macrophage studies. </p>
Project description:Unprogrammed macrophage polarization, is associated with diabetic wound ulcers. Nevertheless, development of corresponding drugs is still a challenge. Here, exosomes are isolated from naive bone marrow-derived macrophages (BMDMs) (M0-Exos), inflammatory BMDMs (M1-Exos), and anti-inflammatory BMDMs (M2-Exos), with the aim of pinpointing the exosomes functionality and identify global miRNAs expression profiles.
Project description:Gene expression in bone marrow-derived macrophages (BMDMs) from WT and mice lacking the transcriptional repressor Kruppel-like factor 3 (KLF3). We cultured BMDMs from bone marrow for 7-10 days then treated cells with 100 ng/mL lipopolysaccharide (LPS) or vehicle (PBS) for 0 h or 8 h, followed by RNA extraction. We aimed to investigate deregulated genes and pathways in macrophages lacking KLF3, during the inflammatory response to endotoxin (LPS).
Project description:Macrophages play critical roles in inflammation and tissue homeostasis, and their functions are regulated by various autocrine, paracrine, and endocrine factors. We have previously shown that CTRP6, a secreted protein of the C1q family, targets both adipocytes and macrophages to promote obesity-linked inflammation in adipose tissue. However, the gene programs and signaling pathways directly regulated by CTRP6 in macrophage remain unknown. Here, we combine transcriptomic and phosphoproteomic analyses to show that CTRP6 activates inflammatory gene programs and signaling pathways in bone marrow-derived macrophages (BMDMs). Treatment of BMDMs with CTRP6 upregulates proinflammatory, and suppresses the anti-inflammatory, gene expression. We show that CTRP6 activates p44/42-MAPK, p38-MAPK, and NF-κB signalings to promote inflammatory cytokine secretion from BMDMs, and that pharmacologic inhibition of these signaling pathways largely abolish the effects of CTRP6. Pretreatment of BMDMs with CTRP6 further augments LPS-induced inflammatory signaling and cytokine secretion from BMDMs. Consistent with the metabolic phenotype of proinflammatory M1-like macrophages, CTRP6 treatment induces a shift toward aerobic glycolysis and lactate production, reduces oxidative metabolism, and elevates mitochondrial ROS production in BMDMs. We use a Ctrp6 knockout mouse model to further confirm the physiologic relevance of our in vitro findings. BMDMs from CTRP6-deficient mice are less inflammatory at baseline and show a marked suppression of LPS-induced inflammatory gene expression and cytokine secretion. Loss of CTRP6 in mice also dampens LPS-induced inflammation and hypothermia. Collectively, we provide mechanistic evidence that CTRP6 regulates macrophage function, and neutralizing CTRP6 activity may have beneficial effects in reducing inflammation.
Project description:Identification of pro- and anti-inflammatory pathways induced in M-CSF differentiated bone-marrow derived macrophages (BMDMs) after 3 h stimulation with two different TLR2 agonists, Helicobacter hepaticus polysacharide and Pam3CSK4 (75 ng/ml), using TSB (Tryptone Soya Broth) medium as a control
