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Bulk RNA-seq of wild-type and Nlrp3-/- bone marrow-derived macrophages with or without LPS and ATP costimulation

ABSTRACT: In order to investigate the effect of NLRP3 on the transcription profile of inactive macrophages and active macrophages with LPA and ATP combined stimulation.

ORGANISM(S): Mus musculus

PROVIDER: GSE286554 | GEO | 2025/01/20

REPOSITORIES: GEO

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Bulk RNA-seq of wild-type and Nlrp3-/- bone marrow-derived macrophages with or without LPS and ATP costimulation

Project description:Bulk RNA-seq of wild-type and Nlrp3-/- bone marrow-derived macrophages with or without LPS and ATP costimulation

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Mitochondrial electron transport chain is necessary for NLRP3 inflammasome activation

Project description:The NLRP3 inflammasome is linked to sterile and pathogen-dependent inflammation, and its dysregulation underlies many chronic diseases. Mitochondria have been implicated as regulators of NLRP3 inflammasome through multiple mechanisms including generation of mitochondrial ROS. Here we report that mitochondrial electron transport chain (ETC) complexes I, II, III and V inhibitors all prevent NLRP3 inflammasome activation. Ectopic expression of Saccharomyces cerevisiae NADH dehydrogenase (NDI1) or Ciona intestinalis alternative oxidase (AOX), which can respectively complement the functional loss of mitochondrial complex I or III, without generation of ROS, rescued NLRP3 inflammasome activation in the absence of endogenous mitochondrial complex I or complex III function. Metabolomics revealed phosphocreatine (PCr), which can sustain ATP levels, as a common metabolite that is diminished by mitochondrial ETC inhibitors. PCr depletion decreased ATP levels and NLRP3 inflammasome activation. Thus, mitochondrial ETC sustains NLRP3 inflammasome activation through PCr-dependent generation of ATP but a ROS independent mechanism.

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Acetylomics on rhein treated NLRP3 activated J774A.1 macrophages

Project description:The aim of this project is to observe the effect of 5 μM rhein treatment on the acetylation level of NLRP3 activated macrophages. We primed J774A.1 cells with 100ng/mL LPS for 12 hours followed by 5μM rhein treatment for 30 minutes. Finally, the cells were stimulated with 4 mM ATP for 30 min to trigger the inflammasome assembly. Cell lysates were collected after ATP stimulation by cell scrapers, and acetylomics were performed as described below.

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Tyrosine Phosphorylation of NLRP3 by Src Family Protein Tyrosine Kinase Lyn Suppresses NLRP3 Inflammasome Activation

Project description:The NLRP3 inflammasome is a multi-protein complex that triggers the activation of the inflammatory protein caspase-1 and the maturation of the cytokine IL-1 in response to microbes and other danger signals in host cells. Here, we sought a deeper understanding of how the NLRP3 inflammasome is regulated. We found that inflammasome activation induced the Src family kinase Lyn to phosphorylate NLRP3 at Tyr918, and that this phosphorylation of NLRP3 correlated with a subsequent increase in its ubiquitination, which facilitated its proteasome-mediated degradation. NLRP3 tyrosine phosphorylation and ubiquitination was abrogated in Lyn-deficient macrophages, which produced increased amounts of IL-1. Furthermore, mice lacking Lyn were highly susceptible to LPS-induced septic shock in an NLRP3-dependent manner. Our data demonstrate that Lyn-mediated tyrosine phosphorylation of NLRP3 is a prerequisite for its ubiquitination, thus dampening NLRP3 inflammasome activity.

2022-05-19 | PXD028582 | Pride

Transcriptomics of THP-1 macrophages after treatment with NLRP3-induced EVs

Project description:Inflammasome activation in macrophages induces the release of EVs, however, the effect of these inflammasome-induced EVs on recipient cells is poorly characterized. To characterize the effect EVs released upon LPS + nigericin stimulation, we performed 3' sequencing on the recipient cells (NLRP3 KO THP-1 macrophages and NLRP3 KO THP-1 macrophages that have been reconstituted with NLRP3 to resemble the WT). As controls, RNA isolated from EVs themselves or LPS- or nigericin-treated cells were subjected to 3' sequencing.

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The role of NLRP3 in intra-amniotic inflammation-induced preterm birth

Project description:Macrophages and neutrophils were sorted from the decidua and uterus of Nlrp3+/+ and Nlrp3-/- mice injected with lipopolysaccharide (LPS) or PBS and analyzed using pair-end RNA-sequencing (RNA-seq) to evaluate the effect of Nlrp3 deficiency on the transcriptomes of these innate immune cells in preterm birth.

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Nuclear Receptor Coactivator 6 is a Critical Regulator of NLRP3 Inflammasome Activation and Gouty Arthritis

Project description:Transcriptional coactivators regulate the rate of gene expression in the nucleus, but their role in the extranuclear sites is largely unknown. Here, we demonstrated that nuclear receptor coactivator 6 (NCOA6) translocated to the cytoplasm, then was incorporated to NLRP3 inflammasome complex, and acquired a new function of “activation of inflammation and innate immune response”, beyond its original function of nuclear coactivation, in monocytes and macrophages. Mechanistically, cytoplasmic NCOA6 directly interacted with NACHT domain of NLRP3 and then promoted NLRP3 activity. Genetic ablation of Ncoa6 substantially attenuated severity of mouse models of two NLRP3-dependent diseases, folic-induced acute tubular necrosis and crystal-induced arthritis in mice. Consistent with these findings, NCOA6 was highly expressed in macrophages of gout patients and its signature was significantly enriched in the gout macrophages in transcriptome profiling. Conclusively, NCOA6 is a critical regulator of the NLRP3 inflammasome activation and therefore a promising target for NLRP3-dependent diseases, including gout.

2024-03-05 | GSE207875 | GEO

A key role for NLRP3 signaling in preterm labor and birth driven by the alarmin S100B

Project description:Decidual and uterine macrophages as well as neutrophils from Nlrp3+/+ and Nlrp3-/- mice injected with S100B or PBS were sorted and analyzed using pair-end BGI RNA sequencing (RNA-seq) to evaluate the effect of Nlrp3 deficiency on the transcriptome of these innate immune cells in preterm birth.

2023-06-20 | GSE217041 | GEO

FADD is a new protein secreted unconventionally following classical NLRP3 inflammasome activation

Project description:NLRP3 inflammasome assembles in response to stress or danger signals and leads to unconventional secretion of proinflammatory IL-1. FADD is an NLRP3 inflammasome component. Here we found that classical NLRP3 inflammasome activation in human monocytes/macrophages induced FADD secretion, which required potassium efflux, functional NLRP3 sensor, ASC adaptor and caspase-1 scaffold molecule. FADD is a leaderless protein unconventionally secreted through plasma membrane-derived microvesicles. Blood-derived monocytes from rheumatoid arthritis (RA) patients secreted more FADD following NLRP3 inflammasome activation than those from healthy donors, and we found increased levels of FADD in the sera (ESPOIR cohort) and synovial fluids from RA patients. Levels of synovial FADD correlated with the inflammatory status of the joint. These data reveal that FADD secretion occurs during inflammatory disease in vivo.

2019-02-28 | PXD008168 | Pride

Potential interactors of NLRP3 in NLRP3-inducible THP-1 cells treated with LPS

Project description:The NLRP3-inducible THP-1-cell line was generated by introducing Flag-WT NLRP3 into NLRP3 KO THP-1 cells through a tetracycline (Tet) responsive element (TRE) promoter (Tet-On) lentiviral infection system. Cells were treated with doxycycline (Dox, 200 ng/mL, Sigma-Aldrich, cat# D9891) for 18 h to induce the expression of Flag-NLRP3 in THP-1-derived macrophages, followed by treatment with lipopolysaccharide (LPS, 200 ng/ml, Sigma-Aldrich, cat# L4524) for 3 h. We used the cells without doxycycline treatment as a negative control and mixed the cells from three individual flasks for mass spectrometry. The cells were collected in low-salt lysis buffer (50 mM Tris-HCl (GCRF, China), pH 8.0, 150 mM NaCl (GCRF, China), 1 mM EDTA (Vetec), 1 mM DTT (Sigma-Aldrich) and 0.5% IGEPAL CA630 (Sigma-Aldrich) containing phosphatase inhibitor (Roche) and EDTA-free protease inhibitor (Biosharp)) and incubated on a rocker with ice for 30 min and centrifuged at 12000 g/4 °C for 15 min to obtain cell lysates. The cell lysates were immunoprecipitated with an anti-Flag antibody. The beads were washed three times with low-salt lysis buffer, separated by SDS-PAGE, and then stained with Coomassie Blue. The entire lane was excised and digested with trypsin at 37 °C for 20 h. The enzymatic hydrolysis product was desalted, lyophilized and redissolved in 0.1% FA solution for chromatography-tandem mass spectrometry (LC-MS/MS) identification of peptide mixtures at Applied Protein Technology (aptbiotech, Inc. Shanghai, China) with a Q Exactive mass spectrometer (Thermo Fisher, California, USA). RAW files generated from the spectrometer were subjected to Proteome Discoverer 1.4 software for protein identification.

2022-11-18 | PXD038215 |

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