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Methylation analysis of patients with COVID-19 and Clonal Hematopoiesis

ABSTRACT: Methylation analysis of patients with COVID-19 and Clonal Hematopoiesis

PROVIDER: PRJNA865723 | ENA |

REPOSITORIES: ENA

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Methylation analysis of patients with COVID-19 and Clonal Hematopoiesis

Project description:Coronavirus disease 2019 (COVID-19) is associated with significant morbidity and mortality, albeit with considerable heterogeneity among affected individuals. Emerging evidence points towards an important role of preexisting host factors, such as a deregulated inflammatory response at the time of infection. Here, we demonstrate the negative impact of clonal hematopoiesis, a prevalent clonal disorder of ageing individuals, on COVID-19-related cytokine release severity and mortality. In this study we perform use the Illumina MethylationEPIC array to quantify methylation levels in PBMCs from COVID19 patients and patients with clonal hematopoiesis.

2024-08-14 | GSE210430 | GEO

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

TET2 Mutant Clonal Hematopoiesis Enhances Severity of COVID-19 Related Cytokine Release Syndrome and is Associated with Increased Mortality [scMULT]

Project description:Coronavirus disease 2019 (COVID-19) is associated with significant morbidity and mortality, albeit with considerable heterogeneity among affected individuals. Emerging evidence points towards an important role of preexisting host factors, such as a deregulated inflammatory response at the time of infection. Here, we demonstrate the negative impact of clonal hematopoiesis, a prevalent clonal disorder of ageing individuals, on COVID-19-related cytokine release severity and mortality. In this study we perform Multiome single cell sequencing of PBMCs from COVID19 patients and patients with clonal hematopoiesis.

2024-08-14 | GSE210432 | GEO

TET2 Mutant Clonal Hematopoiesis Enhances Severity of COVID-19 Related Cytokine Release Syndrome and is Associated with Increased Mortality [scRNA-seq]

Project description:Coronavirus disease 2019 (COVID-19) is associated with significant morbidity and mortality, albeit with considerable heterogeneity among affected individuals. Emerging evidence points towards an important role of preexisting host factors, such as a deregulated inflammatory response at the time of infection. Here, we demonstrate the negative impact of clonal hematopoiesis, a prevalent clonal disorder of ageing individuals, on COVID-19-related cytokine release severity and mortality. In this study we perform single cell RNA sequencing of PBMCs from COVID19 patients and patients with clonal hematopoiesis.

2024-08-14 | GSE210433 | GEO

Clonal landscape of autoantibody-secreting plasmablasts in COVID-19 patients

Project description:Although severe COVID-19 is often associated with elevated autoantibody titers, the underlying mechanism has been unclear. Here, we investigated repertoires and reactivities of immunoglobulins derived from blood plasmablasts (PBs) in COVID-19 patients. This uncovered robust clonal expansion of PBs secreting cardiolipin (CL)-reactive autoantibodies in humoral response to SARS-CoV-2. About half of the expanded CL-reactive clones were also reactive to SARS-CoV-2 antigens and derived from SARS-CoV-2-specific primary responses as well as seasonal coronavirus-reactive memory responses. One such clone, CoV1804, was reactive to both CL and viral nucleocapsid (N), and exhibited anti-nucleolar activity in human cells. Repertoire analysis identified antibodies sharing genetic features with CoV1804 in COVID-19 patient-derived immunoglobulins from our and other cohorts, thereby constituting a novel public antibody. These public autoantibodies had numerous mutations that enhanced anti-N reactivity. On the other hand, anti-CL reactivity fluctuated through somatic hypermutation, which instead resulted in the acquisition of additional self-reactivities, including anti-nucleolar activity in the progeny. Thus, potentially CL-reactive precursors may have developed multiple reactivities to different self-antigens through clonal expansion driven by viral antigens. Our results unraveled a unique process of autoantibody production during COVID-19 and provide novel insights into the origin of virus-induced autoantibodies.

2024-09-11 | GSE233522 | GEO

Longitudinal clonal IgG cross-reactivity profiles of coronavirus-specific B-cells in COVID-19 patients

Project description:We investigated the kinetics, breadth, magnitude, and level of cross-reactivity of IgG antibodies against SARS-CoV-2 and heterologous seasonal (HCoV-NL63, -229E, -OC43 and -HKU1) and epidemic coronaviruses (SARS-CoV, hCoV-MERS) at the clonal level in patients with mild or severe COVID-19 as well as in disease control patients. We assessed IgG antibody reactivity to nucleocapsid and spike antigens using protein microarray. A cutoff was set at the average plus 3 times the SD of 20 nonreactive cultures with a minimum MFI of 1000.

2022-09-30 | E-MTAB-12161 | biostudies-arrayexpress

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

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

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Clonal hematopoiesis is associated with adverse outcomes in patients with COVID-19

Project description:Clonal hematopoiesis of indeterminate potential (CHIP) is defined as the occurrence of an expanded proportion of mature blood cells derived from a mutant hematopoietic precursor without evidence of hematological malignancies. The principle behind this is that the somatic mutation confers a fitness advantage to the cell in which it arose. Different clinical consequences are linked with this expansion. Early evidence of an association with higher mortality risk was provided. This was not related to higher rates of cancer but was associated in particular with increased cardiovascular mortality. Mechanistically, inflammatory processes are not only related to the development of clonal hematopoiesis, but in turn it is also a driver of inflammation. Besides pulmonary symptoms, COVID-19 evokes complex extra-pulmonary manifestations driving the pathophysiology. Among them, both inflammatory and cardiac-associated mechanisms have been deciphered. With the aim of assessing the impact of clonal hematopoiesis on the pathophysiology of COVID-19, hospitalized patients with severe or critical course were evaluated for the presence of CHIP driver mutations and, more importantly, the association with the clinical picture.

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RNA-seq of RBC depleted whole blood from COVID-19 patients and controls

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

Clonal landscape of autoantibody-secreting plasmablasts in COVID-19 patients

Project description:Clonal landscape of autoantibody-secreting plasmablasts in COVID-19 patients

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