Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Early suppression of antiviral host response and protocadherins by SARS-CoV-2 Spike protein in monocyte-derived macrophages

ABSTRACT: Early suppression of antiviral host response and protocadherins by SARS-CoV-2 Spike protein in monocyte-derived macrophages

PROVIDER: PRJNA859179 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR20231403.fastq.gz	Fastqsanger.gz
	SRR20231404.fastq.gz	Fastqsanger.gz
	SRR20231405.fastq.gz	Fastqsanger.gz
	SRR20231406.fastq.gz	Fastqsanger.gz
	SRR20231407.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Early suppression of antiviral host response and protocadherins by SARS-CoV-2 Spike protein in monocyte-derived macrophages

Project description:The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease-19 (COVID-19). The spike protein (S) of SARS-CoV-2 plays a crucial role in mediating viral infectivity; hence, in an extensive effort to curb the pandemic, many urgently approved vaccines rely on the expression of the S protein, aiming to induce a humoral and cellular response to protect against the infection. Given the very limited information about the effects of intracellular expression of the S protein in host cells, we aimed to characterize the early cellular transcriptomic changes induced by expression of the S protein in THP-1 monocyte-derived macrophages (MDMs). The results showed that a wide variety of genes were differentially expressed, products of which are mainly mostly involved in cell adhesion, homeostasis, and most notably, antiviral and immune responses, depicted by significant downregulation of protocadherins and type I alpha interferons. Our study highlights the intrinsic pathogenic role of the S protein and sheds some light on the potential drawbacks of its utilization in the context of vaccination strategies

2022-07-18 | GSE208320 | GEO

B cell epitope mapping of SARS-CoV-2 spike vaccinated rabbits

Project description:This experiment aims to profile polyclonal antibody binding profiles in serum from vaccinated animals relative to antibody function in a virus neutralization assay. Rabbits received three vaccinations with a DNA vaccine encoding the spike protein of the SARS-CoV-2 index strain. Serum samples were selected based on a three-tier (low, intermediate, and high) capacity to cross-neutralize SARS-CoV-2 strains with known neutralization resistance. Following normalization of total anti-spike IgG levels, serum of each animal (n=3) were evaluated for antibody binding to 10mer cyclic constrained peptides spanning the entire spike protein and regions with known SARS-CoV-2 variant of concern spike mutations.

2023-08-31 | E-MTAB-13040 | biostudies-arrayexpress

SARS-CoV-2 spike protein interacts with and activates TLR4

Project description:We here identified that the trimeric spike protein of SARS-CoV-2 could bind to TLR4 directly and robustly activate downstream signaling in monocytes and neutrophils. Moreover, specific TLR4 or NFKB inhibitor, or knockout of MyD88 could significantly block IL-1B induction by spike protein. We thus reveal that spike protein of SARS-CoV-2 functions as a potent stimulus causing TLR4 activation and sepsis related abnormal responses.

2021-02-25 | GSE167480 | GEO

Cytotoxic T cells targeting spike glycoprotein are associated with hybrid immunity to SARS-CoV-2

Project description:mRNA vaccination of individuals with prior SARS-CoV-2 infection provides superior protection against breakthrough infections with variants of concern compared to vaccination in the absence of prior infection. However, the immune mechanisms by which this ‘hybrid immunity’ is generated and maintained are unknown. While genetic variation in spike glycoprotein effectively subverts neutralizing antibodies, spike-specific T cells are generally maintained against SARS-CoV-2 variants. Thus, we comprehensively profiled T cell responses against the S1 and S2 domains of spike glycoprotein in a cohort of SARS-CoV-2-naive or convalescent individuals who received two-dose mRNA vaccine series and were matched by age, sex, and vaccine type. Using flow cytometry, we observed that the overall functional breadth of CD4 T cells as well as polyfunctional Th1 responses were similar between the two groups. However, polyfunctional cytotoxic CD4 T cell responses against both S1 and S2 domains trended higher among convalescent subjects. Multi-modal single-cell RNA sequencing revealed diverse functional programs in spike-specific CD4 and CD8 T cells in both groups. However, convalescent individuals displayed enhanced cytotoxic and antiviral CD8 T cell responses to both S1 and S2 in the absence of cytokine production. Taken together, our data suggest that cytotoxic CD4 and CD8 T cells targeting spike glycoprotein may partially account for hybrid immunity and protection against breakthrough infections with SARS-CoV-2.

2023-03-01 | GSE223236 | GEO

Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs

Project description:In order to identify novel SARS-CoV-2 Spike binding proteins, we carried out a whole genome CRISPR activation screen using the Calabrese Library Set A (Human CRISPR Activation Pooled Library, Addgene #92379).

2022-12-22 | GSE186475 | GEO

Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells

Project description:Immunopeptidomic profiling of HLA-DR diverse monocyte-derived dendritic cells pulsed with SARS-CoV-2 spike (S) protein.

2021-07-09 | PXD021672 | Pride

The SARS-CoV-2 Spike protein modifies the transcriptional profile of human cardiac pericytes

Project description:Human cardiac pericytes express the receptors for SARS-CoV-2 and contribute to microvascular dysfunction in COVID-19 patients. The SARS-CoV-2 capsid Spike protein seems to play a direct role in COVID-19 microangiopathy, but it is not known yet whether the Spike protein alone, without the infectious virus, can induce transcriptional alterations in pericytes. This study investigated the signalling pathways activated by the Spike protein in cultured human cardiac pericytes. We found that 309 RNA transcripts were significantly modulated in pericytes exposed to the Spike protein, with the upregulation of pathways linked to inflammation and viral infection.

2023-05-09 | GSE218644 | GEO

SmartSeq single-cell RNAseq of SARS-CoV-2 spike-specific CD4+ T cells

Project description:We performed longitudinal analysis of three dominant SARS-CoV-2 spike-specific CD4+ T-cell responses carrying single-cell transcriptomic and TCR analysis from ex vivo tetramer+ cells from participants 1-3months post initial infection in 2020 and followed up at 3-4 years, with the aim to characterise the immunodominant CD4+ memory T cell responses 3-4 years post initial infection.

2025-07-31 | E-MTAB-14933 | biostudies-arrayexpress

Pomegranate Peel Extract as an Inhibitor of SARS-CoV-2 Spike Binding to Human ACE2 Receptor (in vitro): A Promising Source of Novel Antiviral Drugs

Project description:Plant extracts are rich in bioactive compounds, such as polyphenols, sesquiterpenes, and triterpenes, which potentially have antiviral activities. As a consequence of the coronavirus disease 2019 pandemic, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus, thousands of scientists have been working tirelessly trying to understand the biology of this new virus and the disease pathophysiology, with the main goal of discovering effective preventive treatments and therapeutic agents. Plant-derived secondary metabolites may play key roles in preventing and counteracting the rapid spread of SARS-CoV-2 infections by inhibiting the activity of several viral proteins, in particular those involved in the virus entry into the host cells and its replication. Using <i>in vitro</i> approaches, we investigated the role of a pomegranate peel extract (PPE) in attenuating the interaction between the SARS-CoV-2 Spike glycoprotein and the human angiotensin-converting enzyme 2 receptor, and on the activity of the virus 3CL protease. Although further studies will be determinant to assess the efficacy of this extract <i>in vivo</i>, our results opened new promising opportunities to employ natural extracts for the development of effective and innovative therapies in the fight against SARS-CoV-2.

2021-10-06 | MTBLS2309 | MetaboLights

Symptomatic SARS-CoV-2 breakthrough infections broaden the repertoire of Spike-reactive CD4 T cells

Project description:SARS-CoV-2 breakthrough infections (BTI) are relatively common, but little is known in terms of differentiating responses associated with asymptomatic BTI (ABTI) versus symptomatic BTI (SBTI). Here, we investigated the impact of ABTI and SBTI on antibody and T cell responses towards Spike. SBTI donors had significantly higher plasma anti-Spike RBD IgG titers compared to both ABTI and SARS-CoV-2 vaccinated donors with no signs of previous infection (VAX) donors. While no impact of ABTI or SBTIs was found in the magnitude of Spike-specific CD4 and CD8 T cell responses, both ABTI and SBTI donors had significantly higher CD4 T cell responses towards non-Spike antigens. In-depth characterization of Spike-specific CD4 and CD8 T cells at scRNA/TCRseq level revealed that ABTI and SBTI induced different alterations of the CD4 compartment. These included a IFNGhigh skewed response among cytokine-producing cells, and a concurrent expansion of type II IFN-responsive TH17-like cells in SBTI. SBTI donors were further found to have an increased CD4 TCR repertoire diversity compared to VAX donors. ABTI-associated alterations of the Spike-specific compartment were intermediate between SBTI and VAX groups, likely reflecting lower antigen exposure and less inflammatory environment during ABTIs versus SBTIs.

2025-12-02 | GSE311993 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data