Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of Dexamethasone in COVID-19 patients

ABSTRACT: Dexamethasone improves the survival of COVID-19 patients in need of supplemental oxygen therapy. Hospitalized COVID-19 patients eligible for dexamethasone therapy were recruited from the general care ward in several centers in Greece and the Netherlands and whole blood transcriptomic analysis was performed before and after starting dexamethasone treatment. Peripheral blood mononuclear cells (PBMCs) were isolated from healthy individuals and COVID-19 patients and stimulated with inactivated SARS-CoV-2 ex vivo in the presence or absence of dexamethasone and their transcriptome was assessed.

ORGANISM(S): Homo sapiens

PROVIDER: GSE227585 | GEO | 2023/07/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Human gut microbiota, COVID-19 patients with mild or severe symptoms.

Project description:Analysis of COVID-19 hospitalized patients, with different kind of symptoms, by human rectal swabs collection and 16S sequencing approach.

2022-09-22 | E-MTAB-12236 | biostudies-arrayexpress

Human plasma proteome immune response to COVID-19

Project description:In this study, we investigated immune responses in a prospective cohort of hospitalized COVID-19 patients (derivation cohort, DC; n = 126) during the spring of 2020. Plasma samples were collected within four days of admission to measure a panel of innate and complement system immune markers. From a subset of this cohort (n = 80), we performed plasma proteomics and developed a predictive survival model based on proteins differentially expressed between survivors (n = 60) and non-survivors (n = 20). Logistic regression analyses were employed to evaluate the predictive value of these biomarkers for 30-day mortality. The developed proteomic prediction model and the regression analyses were subsequently validated using an independent cohort of hospitalized COVID-19 patients (validation cohort, VC) from the autumn/winter of 2020, who received treatment with remdesivir and dexamethasone.

2025-02-18 | PXD055973 | Pride

The difference between neutrophils of HC, COVID-19 patients admitted in ICU and wards.

Project description:We isolated neutrophils from 11 healthy controls, 12 COIVD-19 patients in ICU and 12 COVID-19 patients from ward and submitted the isolated RNA for RNA sequencing. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cohorts. .

2024-06-01 | GSE234207 | GEO

Gene expression profile of peripheral blood mononuclear cells from mild and severe COVID-19 patients, severely ill COVID-19 patients treated with dexamethasone and healthy controls

Project description:The objective of this experiment was to compare the transcriptomic profile (NanoString platform) of peripheral blood mononuclear cells (PBMCs) from COVID-19 patients with mild disease, and patients with severe COVID-19 with and without dexamethasone treatment, and healthy controls. We analyzed PBMCs from 4 mild COVID patients, 3 severe COVID patients,4 severe COVID patients treated with dexamethasone, and 5 healthy controls

2023-03-23 | GSE227341 | GEO

Post-COVID symptoms and endotypes are associated with the inability to modulate the trajectory of immune and hemostatic pathways

Project description:Persistent symptoms after COVID-19 infection can affect almost half of COVID-19 survivors, leading to poor quality of life. Despite its prevalence, the pathophysiology of this phenomenon is poorly understood. We analyzed differences in gene expression between patients with and without post-COVID symptoms in hospital, at follow-up, and longitudinally. As part of the Banque Québécoise de la COVID-19 biobank, 24 adult patients who were hospitalized due to respiratory COVID-19 were enrolled. Whole blood was collected within the first 10 days in hospital and 4-12 weeks after discharge. K-medoids clustering was performed to further separate patients into clusters/endotypes for DE analysis and pathway enrichment. We found that high rates of post-COVID symptoms in hospitalized patients were associated with an inability to mount, and subsequently resolve by 4-12 weeks after discharge, a robust early response involving immune and hemostatic pathways, which was seen in two of three endotypes.

2023-08-15 | GSE222253 | GEO

Proteomic analysis neutrophils from COVID-19 patients

Project description:To go further insight into the involvement of neutrophils in COVID-19 clinical expression, we performed a proteomic analysis of this blood cell type in COVID-19 patients and two non-infected SARS-CoV-2 control groups composed of healthy subjects and ARDS patients hospitalized in intensive care unit (ICU) respectively. All patients were from Guadeloupe and represent a homogeneous population. We have performed a quantitative proteomic study of neutrophiles from French hot spot COVID region, Guadeloupe, confirming the activation of type I IFN pathway and in some target of IFN as TAP proteins, specifically in COVID patients, but not in hospitalized ARDS non-COVID patients and described modification of the NET proteome potentially associated with ARDS.

2022-07-27 | PXD033293 | Pride

A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood

Project description:To elucidate key pathways in the host transcriptome of patients infected with SARS-CoV-2, we used RNA sequencing (RNA Seq) to analyze nasopharyngeal (NP) swab and whole blood (WB) samples from 333 COVID-19 patients and controls, including patients with other viral and bacterial infections. Analyses of differentially expressed genes (DEGs) and pathways was performed relative to other infections (e.g. influenza, other seasonal coronaviruses, bacterial sepsis) in both NP swabs and WB. Comparative COVID-19 host responses between NP swabs and WB were examined. Both hospitalized patients and outpatients exhibited upregulation of interferon-associated pathways, although heightened and more robust inflammatory and immune responses were observed in hospitalized patients with more clinically severe disease. A two-layer machine learning-based classifier, run on an independent test set of NP swab samples, was able to discriminate between COVID-19 and non-COVID-19 infectious or non-infectious acute respiratory illness using complete (>1,000 genes), medium (<100) and small (<20) gene biomarker panels with 85.1%-86.5% accuracy, respectively. These findings demonstrate that SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for differential diagnosis of COVID-19 disease.

2020-12-15 | GSE163151 | GEO

GNPS - Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19

Project description:Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19 Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19 Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19

2022-02-12 | MSV000088828 | GNPS

Dexamethasone modulates immature neutrophils and interferon programming in severe COVID-19

Project description:While critical for host defense, innate immune cells are also pathologic drivers of acute respiratory distress syndrome (ARDS). Innate immune dynamics during COVID-19 ARDS, compared to ARDS from other respiratory pathogens, is unclear. Moreover, mechanisms underlying beneficial effects of dexamethasone during severe COVID-19 remain elusive. Using scRNA-seq and plasma proteomics, we discovered that compared to bacterial ARDS, COVID-19 was associated with expansion of distinct neutrophil states characterized by interferon (IFN) and prostaglandin (PG) signalling. Dexamethasone during severe COVID-19 depleted circulating neutrophils, altered IFNactive neutrophils, downregulated interferon-stimulated gene, and activated IL1R2+ve neutrophils. Dexamethasone also expanded immunosuppressive immature neutrophils and remodeled cellular interactions by changing neutrophils from information receivers into information providers. Male patients had higher proportions of IFNactive neutrophils, preferential steroid-induced immature neutrophil expansion, and possibly different effects on outcome. Our single-cell atlas (www.biernaskielab.ca/COVID_neutrophil) defines COVID-19-enriched neutrophil states and molecular mechanisms of dexamethasone action to develop targeted immunotherapies for severe COVID-19.

2021-10-05 | GSE157789 | GEO

Prior BNT162b vaccination enhances interferon-JAK-STAT regulated antiviral programs in hospitalized COVID-19 patients infected with the SARS-CoV-2 Beta variant

Project description:SARS-CoV-2 infection activates interferon-controlled signaling pathways and elicits a wide spectrum of immune responses and clinical manifestations in human patients. Here, we investigate the impact of prior vaccination on the innate immune response of hospitalized COVID-19 patients infected with the SARS-CoV-2 Beta variant through RNA sequencing of Peripheral Blood Mononuclear Cells. Four patients had received the first dose of BNT162b about 11 days prior to the onset of COVID-19 symptoms and five patients were unvaccinated. Patients had received dexamethasone treatment. Immune transcriptomes were obtained at days 7-13, 20-32 and 42-60 after first symptomology. RNA-seq revealed an enhanced JAK-STAT-mediated immune transcriptome response at day 10 in vaccinated patients as compared to unvaccinated ones. This increase had subsided by day 35. Expression of the genes encoding the antiviral protein oligoadenylate synthetase (OAS) 1, which is inversely correlated with disease severity, and other key antiviral proteins was increased in the vaccinated group. We also investigated the immune transcriptome in naïve individuals receiving their first dose of BNT162b and identified a gene signature shared with the vaccinated COVID-19 patients. Our study demonstrates that RNA-seq can be used to monitor molecular immune responses elicited by the BNT162b vaccine, both in naïve individuals and in COVID-19 patients, and it provides a biomarker-based approach to systems vaccinology.

2022-01-25 | GSE189039 | 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