SARS-CoV-2 spike protein induces the cytokine release syndrome by stimulating T cells to produce more IL-2
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1010223 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25781527_1.fastq.gz | Fastqsanger.gz | |||
| SRR25781527_2.fastq.gz | Fastqsanger.gz | |||
| SRR25781528_1.fastq.gz | Fastqsanger.gz | |||
| SRR25781528_2.fastq.gz | Fastqsanger.gz | |||
| SRR25781529_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:Cytokine release syndrome (CRS) is one of the leading causes of mortality in COVID-19 patients caused by the SARS-CoV-2 coronavirus. However, the mechanism of CRS induced by SARS-CoV-2 is vague. This study shows that dendritic cells loaded with spike protein of SARS-CoV-2 stimulate T cells to release much more IL-2, which subsequently cooperates with spike protein to facilitate peripheral blood mononuclear cells to release IL-1β, IL-6, and IL-8. The aim of this sequencing is to find the key molecular of IL-2 synergistic spike protein releasing much more inflammatory factors in PBMCs and to explore the molecular mechanism.
2024-09-13 | GSE241843 | GEO
Project description:IntroductionCytokine release syndrome (CRS) is one of the leading causes of mortality in patients with COVID-19 caused by the SARS-CoV-2 coronavirus. However, the mechanism of CRS induced by SARS-CoV-2 is vague.MethodsUsing spike protein combined with IL-2, IFN-γ, and TNF-α to stimulate human peripheral blood mononuclear cells (PBMCs) to secrete CRS-related cytokines, the content of cytokines in the supernatant was detected, and the effects of NK, T, and monocytes were analyzed.ResultsThis study shows that dendritic cells loaded with spike protein of SARS-CoV-2 stimulate T cells to release much more interleukin-2 (IL-2,) which subsequently cooperates with spike protein to facilitate PBMCs to release IL-1β, IL-6, and IL-8. These effects are achieved via IL-2 stimulation of NK cells to release tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ), as well as T cells to release IFN-γ Mechanistically, IFN-γ and TNF-α enhance the transcription of CD40, and the interaction of CD40 and its ligand stabilizes the membrane expression of toll-like receptor 4 (TLR4) that serves as a receptor of spike protein on the surface of monocytes. As a result, there is a constant interaction between spike protein and TLR4, leading to continuous activation of nuclear factor-κ-gene binding (NF-κB). Furthermore, TNF-α also activates NF-κB signaling in monocytes, which further cooperates with IFN-γ and spike protein to modulate NF-κB-dependent transcription of CRS-related inflammatory cytokines.DiscussionTargeting TNF-α/IFN-γ in combination with TLR4 may represent a promising therapeutic approach for alleviating CRS in individuals with COVID-19.
| S-EPMC11445618 | biostudies-literature
Project description:We have generated a wholly defined spike-in dataset for Agilent microarrays consisting of 12 arrays with more than 2000 differentially expressed, and approximately 3600 background, cRNAs. The composition of this “Ag Spike”dataset is identical to that of our previous Platinum Spike dataset (GSE21344) and therefore allows direct cross-platform comparison. Comparison between the Ag Spike and Platinum Spike studies shows high agreement between results obtained using the Affymetrix and Agilent platforms.
2010-10-23 | GSE24866 | GEO
Project description:We have generated a wholly defined spike-in dataset for Agilent microarrays consisting of 12 arrays with more than 2000 differentially expressed, and approximately 3600 background, cRNAs. The composition of this âAg Spikeâdataset is identical to that of our previous Platinum Spike dataset (GSE21344) and therefore allows direct cross-platform comparison. Comparison between the Ag Spike and Platinum Spike studies shows high agreement between results obtained using the Affymetrix and Agilent platforms. We used the same 28 PCR pools that had been used before to generate the Platinum-Spike dataset (GSE21344). These pools contain PCR products from 5725 Drosophila Gene Collection release 1.0 (DGCr1) cDNA clones. We mixed PCR products from all pools together with specified relative abundance to generate two samples representing the A and B conditions. Both samples were in vitro transcribed and then labeled with Cy3 and Cy5 fluorescent dye. Labeled A samples were hybridized with B samples labeled with reverse dye to three Agilent Drosophila Gene Expression microarrays. The process from in vitro transcription to hybridization was repeated twice. At the end we generated 12 arrays that were randomly placed in three independent slides to remove potential systematic error due to array position.
2010-10-23 | E-GEOD-24866 | biostudies-arrayexpress
Project description:Spike-in normalization is a powerful approach to assess global changes in data obtained from genomic mapping of DNA-associated proteins by methods such as ChIP-sequencing (ChIP-seq) or CUT&RUN. While multiple spike-in methods provide detailed documentation, the implementation of these approaches often omit critical quality control steps and veer from the established procedures. Here, we show that proper application of spike-in normalization can increase quantification accuracy across a spectrum of conditions. Next, we outline how misuse of spike-in approaches can create erroneous biological interpretations and provide guidelines to minimize pitfalls when applying this approach to normalize data from protein-DNA interaction results.
2024-08-05 | GSE273915 | GEO
Project description:Purpose: To elucidate how SARS-CoV-2 spike protein affects macrophage inflammatory responses Methods: Peritoneal macrophages were isolated from Myeloid-specific IKKβ knockout mice (IKKβΔMye) and control littermates (IKKβ F/F). Then the macrophages were treated with lentivirus expressing Spike protein for 24 hours Results: Deficiency of IKKβ nearly abolished spike protein-associated geneset scores and DEGs-associated key inflammatory pathways. Conclusions: These results indicate that SARS-CoV-2 Spike protein induces strong inflammatory responses in macrophages, potentially through activation of canonical IKKβ/NF-κB signaling
2022-04-06 | GSE182264 | GEO
Project description:Resistance to anti-spike nanobody.
| PRJEB49553 | ENA
Project description:While the importance of random sequencing errors decreases at higher DNA or RNA sequencing depths, systematic sequencing errors (SSEs) dominate at high sequencing depths and can be difficult to distinguish from biological variants. These SSEs can cause base quality scores to underestimate the probability of error at certain genomic positions, resulting in false positive variant calls, particularly in mixtures such as samples with RNA editing, tumors, circulating tumor cells, bacteria, mitochondrial heteroplasmy, or pooled DNA. Most algorithms proposed for correction of SSEs require a training data set, which is typically either from a part of the data set being M-bM-^@M-^\recalibratedM-bM-^@M-^] (Genome Analysis ToolKit, or GATK) or from a separate data set with special characteristics (SysCall). Here, we combine the advantages of these approaches by adding synthetic RNA spike-in standards to human RNA, and use GATK to recalibrate base quality scores with reads mapped to the spike-in standards. Compared to conventional GATK recalibration that uses reads mapped to the genome, spike-ins improve the accuracy of Illumina base quality scores by a mean of 5 units, and by as much as 13 units M-BM- at CpG sites. In addition, since reads mapping to the genome are not used for recalibration, our method allows run-specific recalibration even for the many species without a comprehensive and accurate SNP database. We also use GATK with the spike-in standards to demonstrate that the Illumina RNA sequencing runs overestimate quality scores for AC, CC, GC, GG, and TC dinucleotides, while SOLiD has less dinucleotide SSEs but more SSEs for certain cycles. We conclude that using these DNA and RNA spike-in standards with GATK improves base quality score recalibration. Four human RNA samples with equimolar ERCC spike-in standards were sequenced on Illumina. Two human brain/liver/muscle RNA mixtures with dynamic range of ERCC spike-in standards were sequenced on SOLiD.
2012-03-03 | E-GEOD-36217 | biostudies-arrayexpress
Project description:This study assessed the N-glycosylation profiles of a full-length trimeric spike protein expressed in either HEK or CHO cells. Glycopeptide analysis was performed using a tandem mass spectrometry workflow and BioPharma Finder™ using HEK and CHO glycan databases for protein characterisation. The results outline important differences in the variety and types of N-glycan generated by the two cell lines across the 22 known N-glycosylation sites of the spike protein. A notable increase in terminal sialylation, as well as the presence of the potentially immunogenic N-glycolylneuraminic acid at a functionally key N-glycosylation site was observed in the CHO derived spike protein. With the potential for the relatively vast and more complex CHO glycan repertoire (182 glycans relative to 39 human glycans) to produce functional implications with CHO expressed spike protein, this study adds valuable knowledge to aid Quality by Design approaches and enable Multi Attribute Monitoring of specific N-glycosylation sites for proteoform analyses. This can further inform antigen development with future variants, to devise updated diagnostic tests and therapeutic vaccine designs
2025-09-15 | PXD054718 | Pride