Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dynamics of gene expression profiling by microarrays and identification of high-risk patients for severe COVID-19 [Array]

ABSTRACT: Dynamics of gene expression profiling by microarrays and identification of high-risk patients for severe COVID-19 [Array]

PROVIDER: PRJNA877669 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals.

Project description:Individuals infected with the SARS-CoV-2 virus present with a wide variety of phenotypes ranging from asymptomatic to severe and even lethal outcomes. Past research has revealed a genetic haplotype on chromosome 3 that entered the human population via introgression from Neanderthals as the strongest genetic risk factor for the severe COVID-19 phenotype. However, the specific variants along this introgressed haplotype that contribute to this risk and the biological mechanisms that are involved remain unclear. Here, we assess the variants present on the risk haplotype for their likelihood of driving the severe COVID-19 phenotype. We do this by first exploring their impact on the regulation of genes involved in COVID-19 infection using a variety of population genetics and functional genomics tools. We then perform an locus-specific massively parallel reporter assay to individually assess the regulatory potential of each allele on the haplotype in a multipotent immune-related cell line. We ultimately reduce the set of over 600 linked genetic variants to identify 4 introgressed alleles that are strong functional candidates for driving the association between this locus and the severe COVID-19. These variants likely drive the locus’ impact on severity by putatively modulating the regulation of two critical chemokine receptor genes: CCR1 and CCR5. These alleles are ideal targets for future functional investigations into the interaction between host genomics and COVID-19 outcomes.

2023-02-09 | GSE176233 | GEO

Dynamics of gene expression profiling by microarrays and identification of high-risk patients for severe COVID-19 [Array]

Project description:The clinical manifestations of SARS-Co-2 infection vary widely, from asymptomatic infection to the development of acute respiratory distress syndrome (ARDS) and death. The host response elicited by SARS-CoV-2 plays a key role in determining the clinical outcome. We hypothesized that determining the dynamic whole blood transcriptomic profile of adult patients hospitalized for COVID-19 and characterizing the subgroup that develops severe disease and ARDS would broaden our understanding of the heterogeneity in clinical outcomes. We recruited 60 hospitalized patients with microbiology-confirmed COVID-19, among whom 19 developed ARDS. Peripheral blood was collected using PAXGene RNA tubes within 24 hours of admission and at day 7. There were 2150 differently expressed genes in patients with ARDS at baseline, and 1963 at day 7. We found a dysregulated inflammatory response in COVID-19 ARDS patients, with an increased expression of genes related to pro-inflammatory molecules and neutrophil and macrophage activation at admission, in addition to the loss of immune regulation. This led in turn to a higher expression of genes related to reactive oxygen species, protein polyubiquitination, and metalloproteinases in latter stages. Some of the most significant differences in gene expression found between patients with and without ARDS corresponded to long non-coding RNA involved in epigenetic control.

2024-12-31 | GSE212865 | GEO

Dynamics of gene expression profiling by microarrays and identification of high-risk patients for severe COVID-19

Project description:Dynamics of gene expression profiling by microarrays and identification of high-risk patients for severe COVID-19

| PRJNA877664 | ENA

Clinical and immunological signatures of severe COVID-19 in previously healthy patients with clonal hematopoiesis

Project description:Many clinical risk factors for severe COVID-19, such as diabetes, hypertension, and high body mass index have been reported. However, searching for additional risk factors should be continued to predict the progression of severe COVID-19 more accurately. We suppose that clonal hematopoiesis of indeterminate potential (CHIP) can also be regarded as one of risk factors. To identify the influence of CHIP in COVID-19 pathogenesis, we performed single-cell RNA-seq using peripheral blood mononuclear cells (PBMCs) obtained from severe COVID-19 patient with CHIP and integrate the data with other published COVID-19 scRNA seq data (GSE149689). After clustering and annotating cell types, we compare the expression profiles between CHIP vs non-CHIP COVID-19 severe patient.

2022-10-19 | GSE182123 | GEO

Small RNA-seq analysis of serum miRNAs in patients with severe COVID-19

Project description:The clinical course of Coronavirus disease 2019 (COVID-19) displays a wide variability, ranging from completely asymptomatic forms to diseases associated with severe clinical outcomes. To reduce the incidence COVID-19 severe outcomes, innovative molecular biomarkers are needed to improve the stratification of patients at the highest risk of mortality and to better customize therapeutic strategies. MicroRNAs associated with COVID-19 outcomes could allow quantifying the risk of severe outcomes and developing models for predicting outcomes, thus helping to customize the most aggressive therapeutic strategies for each patient. Here, we analyzed the circulating miRNA profiles in a set of 12 hospitalized patients with severe COVID-19, with the aim to identify miRNAs associated with in-hospital mortality.

2021-11-24 | GSE189506 | GEO

Temporal dynamics of the host molecular responses underlying severe COVID-19 progression and disease resolution

Project description:Manuscript describes the daily dynamics of transcriptional responses in whole blood, from acute to convalescent phase, in severe and non-severe COVID-19 patients.

2020-12-31 | E-MTAB-9721 | biostudies-arrayexpress

Discovery and systematic assessment of early biomarkers that predict progression to severe COVID-19 disease - 2nd cohort

Project description:In order to identify differentially abundant proteins, human plasma samples from COVID-19 patients with either a mild or moderate (MM) or a critical or severe (CS) disease course from acute phase of infection were analyzed on antibody microarrays 998 different proteins by 1,425 antibodies.

2023-03-15 | E-MTAB-12777 | biostudies-arrayexpress

Immunophenotyping of COVID-19 and Influenza Underscores the Association of Type I IFN Response in Severe COVID-19

Project description:Although most SARS-CoV-2-infected individuals experience mild COVID-19, some patients suffer from severe COVID-19, which is accompanied by acute respiratory distress syndrome and systemic inflammation. To identify factors driving severe progression of COVID-19, we performed single-cell RNA-seq using peripheral blood mononuclear cells (PBMCs) obtained from healthy donors, patients with mild or severe COVID-19, and patients with severe influenza. Patients with COVID-19 exhibited hyper-inflammatory signatures across all types of cells among PBMCs, particularly upregulation of the TNF/IL-1beta-driven inflammatory response as compared to severe influenza. In classical monocytes from patients with severe COVID-19, type I IFN response co-existed with the TNF/IL-1beta-driven inflammation, and this was not seen in patients with milder COVID-19 infection. Based on this, we propose that the type I IFN response exacerbates inflammation in patients with severe COVID-19 infection.

2020-07-06 | GSE149689 | GEO

Discovery and systematic assessment of early biomarkers that predict progression to severe COVID-19 disease - 1st cohort

Project description:In order to identify differentially abundant proteins, human plasma samples from COVID-19 patients with either a mild or moderate (MM) or a critical or severe (CS) disease course from the acute phases of infection were analyzed on antibody microarrays targeting 351 different proteins by 517 antibodies.

2023-04-11 | E-MTAB-12779 | biostudies-arrayexpress

The transcriptional profiles of severe COVID-19

Project description:The study aims at investigating the specifical transcriptional signatures of severe COVID-19

2021-01-15 | GSE164805 | GEO