Single Cell RNA-Seq of PBMC from COVID-19 patients and Control subjects
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PROVIDER: PRJNA702537 | ENA |
REPOSITORIES: ENA
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Project description:Single Cell RNA-Seq of PBMC from COVID-19 patients and control patients using 10x genomics 5' DGE
2021-02-17 | GSE166992 | GEO
Project description:The COVID-19 is a mild to moderate respiratory tract infection in the majority, but also can cause life-threatening respiratory failure or persistent debilitating symptoms in a subset of patients. However, the mechanism of protective immunity in mild cases and the pathogenesis of severe COVID-19 remain unclear. On the other hand, it has been proposed that the potent anti-inflammatory effects of corticosteroids are beneficial to decrease the fatality rate in severe COVID-19 patients but its specific mechanism is still in debate.
2023-03-24 | GSE188172 | GEO
Project description:The pathophysiologic significance of redox imbalance is unquestionable as numerous reports and topic reviews indicate alterations in redox parameters during corona virus disease 2019 (COVID-19). However, a more comprehensive understanding of redox-related parameters in the context of COVID-19-mediated inflammation and pathophysiology is required. COVID-19 subjects (n=64) and control subjects (n=19) were enrolled, and blood was drawn within 72 hours of diagnosis. Serum multiplex assay and buffy coat cell mRNA sequencing was performed. Oxidant/free radical (electron paramagnetic resonance (EPR) spectroscopy, nitrite-nitrate assay) and antioxidant (ferrous reducing ability of serum assay and high-performance liquid chromatography) were performed. Multivariate analyses were performed to evaluate potential of indicated parameters to predict clinical outcome. Significantly greater levels of multiple inflammatory and vascular markers were quantified in the subjects admitted to the ICU compared to non-ICU subjects. Gene set enrichment analyses indicated significant enhancement of oxidant related pathways and biochemical assays confirmed a significant increase in free radical production and uric acid reduction in COVID-19 subjects. Multivariate analyses confirmed a positive association between serum levels of VCAM-1, ICAM-1 and a negative association between the abundance of one electron oxidants (detected by ascorbate radical formation) and mortality in COVID subjects while IL-17c and TSLP levels predicted need for intensive care in COVID-19 subjects.
2022-09-21 | GSE211979 | GEO
Project description:Immune characteristics associated with Coronavirus Disease-2019 (COVID-19) severity are currently unclear. We characterized bronchoalveolar lavage fluid (BALF) immune cells from patients with varying severity of COVID-19 disease and from healthy subjects using single-cell RNA-sequencing. Proinflammatory monocyte-derived macrophages were abundant in the BALF from severe COVID-9 patients. Moderate cases were characterized by the presence of highly clonally expanded tissue-resident CD8+ T cells. This atlas of the bronchoalveolar immune-microenvironment suggests potential mechanisms underlying pathogenesis and recovery in COVID-19.
2020-04-22 | GSE145926 | GEO
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
Project description:Saliva, a biofluid enriched in biological omic constituents, has emerged as a promising source for exosomal biomarkers due to its easy accessibility. Despite the understanding of the coronavirus disease-19 (COVID-19), the role of Salivary Extracellular Vesicles (sEVs) in COVID-19 remains poorly understood. Exploring the proteomic cargo of sEVs could prove valuable for diagnostic and prognostic purposes in assessing COVID-19. The proteomic cargo of sEVs from COVID-19 (+) subjects and their healthy close contacts (HCC) was explored. Nine COVID-19 positive (+) patients and eleven in-house close contact patients identified by real-time quantitative polymerase chain reaction (RT-qPCR) of nasopharyngeal swabs were included. In-house close contacts were defined as individuals with a negative RT-qPCR result sharing a residence with a confirmed COVID-19 case. sEVs were isolated by ultracentrifugation from unstimulated saliva samples, and subsequently characterized through nanoparticle tracking, transmission electron microscopy, and western-blot analyses. The proteomic cargo of sEVs was processed by LC-MS/MS. sEVs were morphologically compatible with EVs, with the presence of Syntenin-1 and CD81 EVs markers. The sEVs proteome showed 1,417 proteins: 1,288 in COVID-19 (+) cases and 1,382 in HCC. 35 proteins were found exclusively and 89 were more abundant in sEVs from COVID-19 (+) subjects. “Coronavirus disease response”, “complement and coagulation cascades”, and “PMN extracellular trap formation” were the most enriched KEGG pathways in COVID-19 (+) cases. The most represented biological processes were “Hemoglobin and haptoglobin binding” and “oxygen carrier activity”, and the best-denoted molecular functions were “regulated exocytosis and secretion” and “leucocyte and PMN mediated immunity”. We suggest that sEVs proteomic cargo in COVID-19 is related to immune response processes, oxygen transport, and antioxidant mechanisms. In contrast, in HCC, sEVs signature profiles are mainly associated with epithelial homeostasis.
2024-05-21 | PXD047446 | Pride
Project description:Red blood cells (RBC) depleted whole blood from COVID-19 patients and controls was harvested and processed in order to performed 10X single cell RNA-seq. For COVID-19 patients 2 samples 10 days a part were analyzed.
2020-08-21 | E-MTAB-9221 | biostudies-arrayexpress
Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections cause coronavirus disease 2019 (COVID-19) and are associated with inflammation and coagulopathy and high incidence of thrombosis. Myeloid cells (Mϕ) help coordinate the initial immune response in COVID-19. Although we appreciate that Mϕ lie at the nexus of inflammation and thrombosis, the mechanisms that unite the two in COVID-19 remain largely unknown. In this study, we employed systems biology approaches including proteomics, transcriptomics, and mass cytometry to define the circulating proteome and circulating immune cell phenotypes in subjects with COVID-19. In a cohort of COVID-19 subjects (n=35), circulating markers of inflammation (CCL23, IL-6) and vascular dysfunction (ACE2, tissue factor [TF]) were elevated in subjects with severe compared with mild COVID-19. Additionally, although the total white blood cell (WBC) counts were similar between COVID-19 groups, CD14+ monocytes from severe COVID-19 subjects expressed more TF. At baseline, transcriptomics demonstrated increased IL-6, CCL3, ACOD1, C5AR1, C5AR2, and TF in severe COVID-19 subjects compared with controls. Using “stress” transcriptomics, we found that circulating immune cells from severe COVID-19 subjects had evidence of profound immune paralysis with greatly reduced transcriptional activation and release of inflammatory markers in response to Toll-like receptor (TLR) activation. Finally, sera from severe (but not mild) COVID-19 subjects activated human monocytes and induced TF expression. Taken together, these observations further elucidate the pathological mechanisms that underlie immune dysfunction and coagulation abnormalities in COVID-19, contributing to our growing understanding of SARS-CoV-2 infections that could also be leveraged to develop novel diagnostic and therapeutic strategies.
2024-01-23 | GSE247186 | GEO
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
Project description:We isolated PBMC from healthy, moderate ( Oxygen supply < 10L/min), and severe (Oxygen supply >= 10L/min) COVID-19 patients after their admission to Intensive Care Units (ICU), at two timepoints (Day-1 and Day-4); and performed both CD14+ Monocyte enrichment followed by a Pan-DC kit to retrieve all Antigen Presenting Cell (APC) subsets from these age-matched patients. We performed single cell RNA sequencing using 10X technology on the single cell suspensions and constracted a high-resolution map of 81,643 Antigen Presenting Cells (APC) from the three COVID-19 severity groups. We were able to retrieve all the known six APC subsets and deciphered the altered pathways and ati-viral mechanisms, correlated with the disease severity.
2021-05-10 | GSE169346 | GEO