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Systematic compositional analysis of extracellular vesicles produced by cells undergoing apoptosis, necroptosis or necroptosis

ABSTRACT: Systematic compositional analysis of extracellular vesicles produced by cells undergoing apoptosis, necroptosis or necroptosis

PROVIDER: PRJNA917299 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25573205_1.fastq.gz	Fastqsanger.gz
	SRR25573205_2.fastq.gz	Fastqsanger.gz
	SRR25573206_1.fastq.gz	Fastqsanger.gz
	SRR25573206_2.fastq.gz	Fastqsanger.gz
	SRR25573207_1.fastq.gz	Fastqsanger.gz

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Systematic compositional analysis of extracellular vesicles produced by cells undergoing apoptosis, necroptosis or necroptosis

Project description:Formation of extracellular vesicles (EVs) has emerged as a novel paradigm in cell-to-cell communication in health and disease. We performed a comparative analysis of steady-state (ssEVs) and cell death-associated EVs (cdEVs) following apoptosis (apoEVs), necroptosis (necEVs), and ferroptosis (ferEVs) using the same cell line. For each EV type, we systematically determined the biophysical and biochemical characteristics, the protein cargo, and the presence of methylated ribosomal RNA. The cell death EVs showed distinctive rRNA methylation patterns compared to ssEVs.

2023-09-30 | GSE221999 | GEO

Systematic compositional analysis of exosomal extracellular vesicles produced by cells undergoing apoptosis, necroptosis and ferroptosis.

Project description:Formation of extracellular vesicles (EVs) has emerged as a novel paradigm in cell-to-cell communication in health and disease. EVs are notably produced during cell death but it had remained unclear whether different modalities of regulated cell death (RCD) influence the biogenesis and composition of EVs. To this end, we performed a comparative analysis of steady-state (ssEVs) and cell death-associated EVs (cdEVs) following TNF-induced necroptosis (necEVs), anti-Fas-induced apoptosis (apoEVs), and ML162-induced ferroptosis (ferEVs) using the same cell line. For each RCD condition, we determined the biophysical and biochemical characteristics of the cell death-associated EVs (cdEVs), the protein cargo, and the presence of methylated ribosomal RNA. We found that the global protein content of all cdEVs was increased compared to steady-state EVs. Qualitatively, the isolated exosomal ssEVs and cdEVs, contained a largely overlapping protein cargo including some quantitative differences in particular proteins. All cdEVs were enriched for proteins involved in RNA splicing and nuclear export, and showed distinctive rRNA methylation patterns compared to ssEVs. Interestingly, necEVs and apoEVs, but strikingly not ferEVs, showed enrichment of proteins involved in ribosome biogenesis. Altogether, our work documents quantitative and qualitative differences between ssEVs and cdEVs.

| S-EPMC10560658 | biostudies-literature

Quantitative analysis of phosphoproteome in necroptosis reveals a role of TRIM28 phosphorylation in promoting necroptosis-induced cytokine production

Project description:Necroptosis is a form of regulated necrotic cell death which promotes inflammation. In cells undergoing necroptosis, the activated RIPK1 kinase mediates the formation of RIPK1/RIPK3/MLKL complex to promote MLKL oligomerization and execution of necroptosis. RIPK1 kinase activity also promotes cell-autonomous activation of proinflammatory cytokine production in necroptosis. However, the signaling pathways downstream of RIPK1 kinase in necroptosis and how RIPK1 kinase activation controls inflammatory response induced by necroptosis are still largely unknown. Here we quantitatively measured the temporal dynamics of over 7000 confident phosphosites during necroptosis using mass spectrometry. Our study defined a RIPK1-dependent phosphorylation pattern in late necroptosis that is associated with a proinflammatory component marked by p-S473 TRIM28. We show that the activation of p38 MAPK mediated by oligomerized MLKL promotes the phosphorylation of S473 TRIM28, which in turn mediates inflammation during late necroptosis. Taken together, our study illustrates a mechanism by which p38 MAPK may be activated by oligomerized MLKL to promote inflammation in necroptosis.

2021-04-01 | GSE171214 | GEO

Systematic comparative analysis of extracellular vesicles following apoptosis, necroptosis and ferroptosis

Project description:The formation of extracellular vesicles (EVs) has emerged as a novel paradigm in cell-to-cell communication during health and disease. According to the type of cell death modalities, the intercellular functions of EVs may be influenced by their biogenesis and composition. To identify a possible EV cargo signature, we performed a comparative analysis of steady-state (ssEVs) and cell death-associated EVs (cdEVs) following apoptosis (apoEVs), necroptosis (necEVs) and ferroptosis (ferEVs) in the same cell type. We determined the physical and biochemical characteristics, the protein cargo by mass spectrometry.

2023-10-12 | PXD039297 | Pride

RIPK1 dephosphorylation and kinase activation by PPP1R3G/PP1γ promote apoptosis and necroptosis

Project description:Receptor-interacting protein kinase 1(RIPK1) is a key regulator of inflammation and cell death. Many sites on RIPK1, including serine 25, are phosphorylated to inhibit its kinase activity and cell death. How these inhibitory phosphorylation sites are dephosphorylated is poorly understood. Using a sensitized CRISPR whole genome knockout screen, we discover that protein phosphatase 1 regulatory subunit 3G (PPP1R3G) is required for RIPK1-dependent apoptosis and necroptosis. Mechanistically, PPP1R3G recruits its catalytic subunit protein phosphatase 1 gamma (PP1g) to Complex I to remove inhibitory phosphorylations of RIPK1. A PPP1R3G mutant which does not bind PP1g fails to rescue RIPK1 activation and cell death. Furthermore, chemical prevention of RIPK1 inhibitory phosphorylations or mutation of serine 25 of RIPK1 to alanine largely restores cell death in PPP1R3G-knockout cells. Finally, Ppp1r3g-/- mice are protected from tumor necrosis factor-induced systemic inflammatory response syndrome, confirming the important role of PPP1R3G in regulating apoptosis and necroptosis in vivo.

2021-10-26 | GSE176422 | GEO

RNA-Seq Analyses of the apoptosis and necroptosis in MEF

Project description:Purpose: we used next generation sequencing to analyze gene expression profiles of MEF treated with PBS (control), TNF-ɑ + Cycloheximide (TC) or TNF-ɑ + Cycloheximide+ z-VAD-fmk (TCZ). The goals of this study are to compare the different gene expression profiles between MEF treated with TC compared to PBS treatment and MEF treated with TCZ compared to PBS treatment. Methods: In MEF, the combination of TNF-α and cycloheximide (TC) induces apoptosis, whereas the addition of z-VAD-fmk (TCZ) to this regimen promotes necroptosis, using High-seq 2000 Illumina sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: By comparing the RPKM values between the two groups, a total 492 DEGs (342 upregulated and 150 downregulated) were identified in MEF treated with TC compared to PBS treatment, and a total 424 DEGs (242 upregulated and 182 downregulated) were identified in MEF treated with TCZ compared to PBS treatment. Next, we compared all identified DEGs in MEF between TC and TCZ treatment. We found that 252 DEGs overlapped between TC and TCZ treatment, whereas 240 DEGs were only present in TC treatment and 172 DEGs were only present in TCZ treatment. Conclusions: we firstly identified 492 DEGs in apoptotic MEF, and as well as 424 DEGs in necroptotic MEF. And we performed the enriched molecular pathway, molecules, transcription factors and signaling networks by IPA analysis. We revealed that apoptosis and necroptosis may share certain common canonical pathways and transcription factors.

2020-01-09 | GSE143294 | GEO

Sublethal necroptosis signaling promotes inflammation and liver cancer

Project description:We developed a genetic mouse model of chronic necroptosis activation in hepatocytes (in the presence of basal NF-kB activity) that lead to hepatocellular carcinoma. Blocking Necroptosis (RIP3) or NF-kB-(IKKβ) activation in those mice blocked hepatocarcinogenesis.

2023-07-03 | GSE166875 | GEO

RNA-Seq Analyses of the apoptosis and necroptosis in MEF

Project description:RNA-Seq Analyses of the apoptosis and necroptosis in MEF

| PRJNA599928 | ENA

Prior Knowledge Transfer Across Transcriptional Datasets Using Compositional Statistics [Tumor]

Project description:An expert-pathologist-reviewed epithelial ovarian cancer reference library (n = 50) used to assign the histopathology of epithelial ovarian cell lines using compositional statistics and random gene-sets

2016-11-08 | GSE73551 | GEO

ZBP1 is a cytosolic RNA virus sensor driving activation of the NLRP3 inflammasome, pyroptosis, necroptosis and apoptosis

Project description:The innate immune system recognizes nucleic acids as a signature of microbial infection and initiates host-protective responses, including the production of type I IFN and proinflammatory cytokines. Z-DNA binding protein 1 (ZBP1, also known as DLM-1 or DAI) was previously identified as a dsDNA binding protein, triggering DNA-mediated activation of innate immune responses. However, mice or cells lacking ZBP1 produce normal levels of type I IFN in response to dsDNA. Therefore, the classification of ZBP1 as a true DNA sensor remains to be resolved. Here, we report that the single stranded RNA virus, influenza A virus (IAV) is a trigger of the cytosolic sensor ZBP1. Sensing of IAV infection by ZBP1 engages a novel NLRP3 inflammasome pathway that is not defined by the conventions of the canonical and non-canonical NLRP3 inflammasome pathways. Surprisingly, IAV-induced cell death was not prevented by the absence of the NLRP3 inflammasome. Instead, we identified parallel contributions from pyroptosis, necroptosis and apoptosis in the execution of ZBP1-dependent cell death, mediated by the kinase RIPK3. Overall, the ability of ZBP1 to sense IAV infection signifies a point of divergence for IAV-induced programmed cell death pathways and inflammasome activation. We used microarrays to explore the gene expression profiles differentially expressed in influenza-infected bone marrow derived macrophages (BMDM) isolated from Ifnar1-/- and wild-type mice.

2016-08-11 | E-GEOD-77611 | biostudies-arrayexpress

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