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Genome-wide characterization of a novel necrotic granuloma model of latent tuberculosis infection and reactivation in mice

ABSTRACT: We sought to develop and characterize a novel paucibacillary model in mice, which develop necrotic lung granulomas following infection with Mycobacterium tuberculosis. Paucibacillary infection was established, recapitulating the sterilizing activities of human LTBI regimens. TNF neutralization led to increased lung bacillary load, disrupted granuloma architecture with expanded necrotic foci and reduced tissue hypoxia, and accelerated animal mortality. TNF-neutralized mouse lungs and sera showed significant upregulation of IFNγ, IL-1β, IL-6, IL-10, CCL2, CCL3, and matrix metalloproteinase genes

ORGANISM(S): Mus musculus

PROVIDER: GSE55183 | GEO | 2014/02/20

SECONDARY ACCESSION(S): PRJNA238823

REPOSITORIES: GEO

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Genome-wide characterization of a novel necrotic granuloma model of latent tuberculosis infection and reactivation in mice

Project description:We sought to develop and characterize a novel paucibacillary model in mice, which develop necrotic lung granulomas following infection with Mycobacterium tuberculosis. Paucibacillary infection was established, recapitulating the sterilizing activities of human LTBI regimens. TNF neutralization led to increased lung bacillary load, disrupted granuloma architecture with expanded necrotic foci and reduced tissue hypoxia, and accelerated animal mortality. TNF-neutralized mouse lungs and sera showed significant upregulation of IFN?, IL-1?, IL-6, IL-10, CCL2, CCL3, and matrix metalloproteinase genes Six weeks after aerosol-immunization with recombinant M. bovis BCG overexpressing the 30-kilodalton antigen, C3HeB/FeJ mice were aerosol-infected with M. tuberculosis H37Rv. Six weeks later, mice were treated with one of three standard regimens for latent TB infection (LTBI) or TNF-neutralizing antibody. Mouse lungs were analyzed by histology, positron emission tomography/computed tomography, whole-genome microarrays, and RT-PCR. Lungs and sera were studied by multiplex enzyme-linked immunosorbent assays

2014-02-20 | E-GEOD-55183 | biostudies-arrayexpress

Microarray transcription profiling of healthy and PVYNTN infected potato tuber tissues (necrotic and non-necrotic)

Project description:To extend our understanding of systemic necrosis in susceptible potato tubers infected with the necrotic strain of Potato virus Y (PVYNTN) gene expression was compared between healthy and infected non-necrotic and necrotic (both non-necrotic and necrotic tissue) potato tubers.

2018-05-16 | E-MTAB-5776 | biostudies-arrayexpress

Prunus necrotic ringspot virus

Project description:Prunus necrotic ringspot virus Variation

| PRJNA326695 | ENA

RNA sequencing of necrotic core and non-necrotic rim of tumors from 4T1 cell xenografts into rat

Project description:The goal of this experiment was to determine differences in RNA expression between the central necrotic tumor core and the non-necrotic rim region in orthotopic xenograft models of 4T1 cells transplanted into immunocompromised rat hosts. These samples are derived from tissues obtained from 4T1 spheroids transplanted orthotopically into the mammary fat pads of SRG OncoRats. 4T1 cells were cultured as spheroids in suspension for 24-hours prior to transplantation in 2% matrigel. 600,000 cells in a 1:1 mixture of matrigel and DMEM/F12 were transplanted orthotopically into the right T4 fat pads of SRG rats. At day 27 post transplanation, primary tumors and lungs were collected. The primary tumors were cut in half to expose the cross-section, and the tumors were dissected to isolate the necrotic core region and the non-necrotic rim region. Samples were snap frozen and sent to Genewiz-Azenta for RNA extraction, library prep, and next-gen sequencing.

2024-01-01 | GSE223419 | GEO

Monocyte-derived macrophages orchestrate multiple cell-type interactions to repair necrotic liver lesions

Project description:The liver can fully regenerate after partial resection and its underlying mechanisms have been extensively studied. The liver can also rapidly regenerate after injury with most studies focusing on hepatocyte proliferation; however, how hepatic necrotic lesions during acute or chronic liver diseases are eliminated and repaired remains obscure. Here we demonstrate that monocyte-derived macrophages (MoMFs) are rapidly recruited to and encapsulate necrotic areas during immune-mediated liver injury, and this feature is essential in repairing necrotic lesions. At the early stage of injury, infiltrating MoMFs activate the JAG1-NOTCH2 axis to induce cell death-resistant SOX9+ hepatocytes near the necrotic lesions, which acts as a barrier from further injury. Subsequently, necrotic environment (hypoxia and dead cells) induces a cluster of C1q+MoMFs that promote necrotic removal and liver repair, while Pdgfb+MoMFs activate hepatic stellate cells (HSCs) to express a-smooth muscle actin and induce a strong contraction signal (YAP, pMLC) to squeeze and finally eliminate the necrotic lesions. In conclusion, MoMFs play a key role in repairing the necrotic lesions not only by removing necrotic tissues but also by inducing cell death resistant hepatocytes to form a perinecrotic capsule and by activating a-smooth actin expressing HSCs to facilitate necrotic lesion resolution.

2023-06-06 | GSE229498 | GEO

Prunus necrotic ringspot virus

Project description:cherry and Prunus necrotic ring spot virus (PNRSV)

| PRJNA245552 | ENA

Quantitative Phospho-proteomic Analysis of TNFα/NFκB Signaling Reveals a Role for RIPK1 Phosphorylation in Suppressing Necrotic Cell Death

Project description:TNFα is a potent inducer of inflammation due to its ability to promote gene expression, inpart via the NFκB pathway. Moreover, in some contexts, TNFα promotes Caspase-dependent apoptosis or RIPK1/RIPK3/MLKL-dependent necrosis. Engagement of the TNF Receptor Signaling Complex (TNF-RSC), which contains multiple kinase activities, promotes phosphorylation of several downstream components, including TAK1, IKKα/IKKβ, IκBα and NFκB. However, immediate downstream phosphorylation events occurring in response to TNFα signaling are poorly understood at a proteome-wide level. Here we use Tandem mass tagging-based proteomics to quantitatively characterize acute TNFα-mediated alterations in the proteome and phosphoproteome with or without inhibition of the cIAP-dependent survival arm of the pathway with a SMAC mimetic. We identify and quantify over 8,000 phosphorylated peptides, among which are numerous known sites in the TNF-RSC, NFκB, and MAP kinase signaling systems, as well as numerous previously unrecognized phosphorylation events. Functional analysis of S320 phosphorylation in RIPK1 demonstrates a role for this event in suppressing its kinase activity, association with CASPASE-8 and FADD proteins, and subsequent necrotic cell death during inflammatory TNFα stimulation. This study provides a resource for further elucidation of TNFα-dependent signaling pathways.

2017-05-30 | PXD006055 | Pride

Necrocide 1 Mediates Necrotic Cell Death and Immunogenic Response in Human Cancer Cells

Project description:Many anticancer agents induce apoptosis, mitotic catastrophe or cellular senescence. Here, we report the functional characterization of an experimental inducer of tumor necrosis factor (TNF)-independent necrosis, necrocide-1 (NC1). NC1 (but not its stereoisomer) killed a panel of human cancer cells (but not normal cells) at nanomolar concentrations and with a non-apoptotic, necrotic morphotype, both in vitro and in vivo. NC1-induced killing was not inhibited by caspase blockers, anti-apoptotic BCL2 overexpression or TNFα neutralization, suggesting that NC1 elicits a bona fide necrotic pathway. However, pharmacological or genetic inhibition of necroptosis, pyroptosis and ferroptosis failed to block NC1-mediated cell death. Instead, NC1 elicited reactive oxygen species (ROS) production by mitochondria, and elimination of mitochondrial DNA, quenching of mitochondrial ROS, as well as blockade of mitochondrial permeability transition with cyclosporine A, interfered with NC1-induced cell death. NC1 induced hallmarks of immunogenic cell death incurring calreticulin (CALR) exposure, ATP secretion and high mobility group box 1 (HMGB1) release. Taken together, these data identify a previously uncharacterized signaling cascade leading to an immunogenic variant of mitochondrion-regulated necrosis, supporting the notion that eliciting regulated necrosis may constitute a valid approach for anticancer therapy.

2023-05-01 | GSE226801 | GEO

Prunus necrotic ringspot virus

Project description:Prunus necrotic ringspot virus Amplicon sequencing and variation analysis

| PRJNA326662 | ENA

Label-free proteomic analysis of apoptotic, necrotic and necroptotic DAMPs from HNSCC cells

Project description:Necroptosis is a newly discovered form of programmed cell death (PCD) showing necrotic features, including membrane permeabilization and the release of damage-associated molecular patterns (DAMPs). Studies have revealed both its tumorigenic role and therapeutic potential in various cancers, yet its impact on head and neck squamous cell carcinoma (HNSCC) is poorly understood. To investigate the differential composition of necroptotic DAMPs, SCC25 cells treated by TNF-α+Smac mimetic (TS), TNF-α+Smac mimetic+zVAD-fmk (TSZ) and Freeze-Thaw (FT) to induce apoptosis, necroptosis and necrosis respectively. Mass spectrum analysis was used to compare the differential compositions among DAMPs derived from apoptosis (TS), necroptosis (TSZ) and necrosis (FT).

2022-07-16 | PXD035379 | iProX

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