Project description:Describe the transcriptomic profile of Golden Hamster olfactory bulb in response to SARS-CoV-2 infection, separating by sexes.

2021-06-19 | E-MTAB-10442 | biostudies-arrayexpress

In severe COVID-19, SARS-CoV-2 induces a chronic, TGF-β-dominated adaptive immune response

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-02-09 | GSE158038 | GEO

Stimulus-specific Immune Modulation by SARS-CoV-2 Nucleocapsid Correlates with Severe COVID-19

Project description:A significant proportion of patients with COVID-19 disease, caused by SARS-CoV-2, develop acute respiratory distress syndrome characterized by pro-inflammatory cytokine secretion and dampened IFN-mediated antiviral response. To uncover the mechanisms by which SARS-CoV-2 drives this dysregulation, we conducted transcriptomic profiling of N-expressing monocyte-derived macrophages treated with different stimuli that activates several pattern recognition receptors. To capture differences in immunoinflammatory responses to different SARS-CoV-2 Nucleocapsids, we performed a comparative proteomics analysis between the hyper inflammatory Delta N protein and less inflammatory Omicron N protein. Both Nucleocapsids expressed in monocyte-derived macrophages were pulled down for affinity purification mass spectrometry (APMS) and their differential protein interactors were identified; revealing Delta N interacts more strongly with stress granule proteins compared to Omicron N, which may explain Delta N pro-inflammatory phenotype. This project was a collaboration between the labs of Dr. Melody Li, Dr. Alexander Hoffmann, and Dr. Mehdi Bouhaddou at UCLA.

2026-06-25 | PXD067631 | Pride

Polymorphisms associated with post-COVID-19 hyperglycemia using the Axiom Human Genotyping SARS-CoV-2 Research Array

Project description:To investigate the association between polymorphisms in innate immune genes and post-COVID-19 hyperglycemia

2025-08-30 | E-MTAB-15470 | biostudies-arrayexpress

Investigation of IgG-reactivity Profiles and Epitope Landscape in Divergent COVID-19 Trajectories and SARS-CoV-2 Variants using SARS-CoV-2 whole proteome peptide microarray

Project description:The objective of the study was to characterize the immunoreactivity profiles of IgG-reactive epitopes in COVID-19 patients with distinct disease trajectories as well as SARS-CoV-2-naïve sera, using a high-density SARS-CoV-2 whole proteome peptide microarray. The microarray comprised of a total of 5347 individual peptides, each consisting of 15 amino acids with an overlap of 13 amino acids printed in duplicate. The microarray also had a panel of the most relevant mutations from SARS-CoV-2 variants of concern like omicron, alpha, beta, gamma, delta, and others. This study consisted of 29 participants, including 10 naïve controls (5 pre-pandemic and 5 SARS-CoV-2 seronegative) and 19 RT-PCR-confirmed COVID-19 patients. The COVID-19 patients were stratified into two distinct cohorts based on their disease trajectories: the severe cohort (S), in which the patients presented moderate COVID-19 symptoms initially but eventually progressed toward severity; and the recovered cohort (R), in which severe COVID-19 patients progressed toward recovery. Our findings contribute to a deeper understanding of the immunopathogenesis of COVID-19 in patients with different disease trajectories, the effect of mutations on immunoreactivity, and potential cross-reactivity due to exposure to common cold viruses.

2025-03-31 | E-MTAB-14495 | biostudies-arrayexpress

IMMUNE DYSREGULATION FOLLOWING INFECTION BY THE NEW CORONAVIRUS SARS-CoV-2 (COVID-19); A NEW DISEASE ENTITY

Project description:Severe pneumonia by the novel coronavirus (COVID-19 infection) is mediated through immune dysregulation. It was studied if this dysregulation persists after recovery and if it is linked to the manifestation of post-covid syndrome (PCS). Patients who had been hospitalized for COVID-19 pneumonia 3 to 6 months ago during two different time periods and matched comparators were the derivation cohort (n=46, September-October 2020) and the validation cohort (n=484, April-July 2021) respectively. Peripheral blood mononuclear cells (PBMCs) were isolated for culture and cytokine stimulation. Patients provided answers to two health questionnaires allowing classification into PCS and were also subject to lung function tests (LFT). The primary endpoint was the modulation of the production of interleukin (IL)-1b and IL-6 from monocytes and among secondary, the modulation of adaptive immune response and the development of PCS. Increased production of IL-1b (p<0.001) and IL-6 (p<0.001) was found in both study periods compared to control. There was increase of pro-inflammatory Th1 responses over anti-inflammatory Th2 responses and attenuation of the T17 response. PCS was manifested in 22% of patients, grouped into three groups of symptoms. Fatigue was associated with the predominance of Th2 responses and abnormal LFT with overproduction of IL-1b and IL-6. Immune dysregulation is apparent after three months post COVID-19 pneumonia with main features the hyper-production of IL-1β and IL-6 by circulating monocytes, the increase of the Th1/Th2 ratio and the attenuation of T17 response.

2025-06-05 | GSE206605 | GEO

COVID-19 tissue atlases reveal SARS-COV-2 pathology and cellular targets

Project description:COVID-19, caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple-organ failure, but little is known about its pathophysiology. Here, we generated single-cell atlases of 23 lung, 16 kidney, 15 liver and 18 heart COVID-19 autopsy donor tissue samples, and spatial atlases of 14 lung donors. Integrated computational analysis uncovered substantial remodeling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of myofibroblasts and putative TP63+ intrapulmonary basal-like progenitor cells. Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells which induced specific host programs. Spatial analysis in lung distinguished inflammatory host responses in lung regions with and without viral RNA. Analysis of the other tissue atlases showed transcriptional alterations in multiple cell types in COVID-19 donor heart tissue, and mapped cell types and genes implicated with disease severity based on COVID-19 GWAS. Our foundational dataset elucidates the biological impact of severe SARS-CoV-2 infection across the body a key step towards new treatments.

2021-04-09 | GSE171668 | GEO

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