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ABSTRACT: No association of malignant B cell non-Hodgkin lymphomas with ipsilateral SARS-CoV-2 vaccination

PROVIDER: PRJEB54819 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10750225_1.fastq.gz	Fastqsanger.gz
	ERR10750225_2.fastq.gz	Fastqsanger.gz
	ERR10750226_1.fastq.gz	Fastqsanger.gz
	ERR10750226_2.fastq.gz	Fastqsanger.gz
	ERR10750227_1.fastq.gz	Fastqsanger.gz

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Project description:Multiomics and SARS-CoV-2 vaccination

| PRJEB52928 | ENA

scRNA-seq, V(D)J seq, CITE-seq, LIBRA-seq of human CD4+, CD8+ and B lymphocytes PBMCs of 5 donors (3 SARS-CoV-2 experienced and 2 SARS-Cov-2 Naive) before and following two doses of Pfizer/BioNTech BNT162b2 mRNA vaccine

Project description:The experiment aims at characterizing the immune responses elicited by the BNT162b2 vaccine against SARS-CoV-2, initially administered in a two dose regimen (second dose after three weeks followinf the first dose) In particular the transcriptional landscape of circulating T and B lymphocytes has been profiled longitudinnaly by scRNA-seq coupleD with CITE-seq of 19 cell surface markers to better classify T cells subpopulations, LIBRA-seq to assess the Spike-specificity of BCRs and and V(D)J seq to also track T and B cell clones dynamics. Eeach sample was profiled before vaccination (T0), 21 days after the first dose (T1), 2 months after the first dose (1 month after the second dose) (T2). The immune responses were characterized using PBMC from 3 SARS-CoV-2 experienced donors (experiencing SARS-Cov-2 at least 4 months before the first vaccinatin) and 2 SARS-CoV-2 unexperienced donors.

2024-04-18 | E-MTAB-13721 | biostudies-arrayexpress

Class switch towards non-inflammatory, spike-specific IgG4 antibodies after repeated SARS-CoV-2 mRNA vaccination [CITE-Seq]

Project description:RNA vaccines are efficient preventive measures to combat the SARS-CoV-2 pandemic. High levels of neutralizing SARS-CoV-2-antibodies are an important component of vaccine-induced immunity. Shortly after the initial two mRNA vaccine doses, the IgG response mainly consists of the pro-inflammatory subclasses IgG1 and IgG3. Here, we report that several months after the second vaccination, SARS-CoV-2-specific antibodies were increasingly composed of non-inflammatory IgG4, which were further boosted by a third mRNA vaccination and/or SARS-CoV-2 variant breakthrough infections. IgG4 antibodies among all spike-specific IgG antibodies rose on average from 0.04% shortly after the second vaccination to 19.27% late after the third vaccination. This induction of IgG4 antibodies was not observed after homologous or heterologous SARS-CoV-2 vaccination with adenoviral vectors. Single-cell sequencing and flow cytometry revealed substantial frequencies of IgG4-switched B cells within the spike-binding memory B-cell population (median 14.4%; interquartile range (ICR) 6.7-18.1%) compared to the overall memory B-cell repertoire (median 1.3%; ICR 0.9-2.2%) after three immunizations. Importantly, this class switch was associated with a reduced capacity of the spike-specific antibodies to mediate antibody-dependent cellular phagocytosis and complement deposition. Since Fc-mediated effector functions are critical for antiviral immunity, these findings may have consequences for the choice and timing of vaccination regimens using mRNA vaccines, including future booster immunizations against SARS-CoV-2.

2022-12-22 | GSE221319 | GEO

Class switch towards non-inflammatory, spike-specific IgG4 antibodies after repeated SARS-CoV-2 mRNA vaccination [scRNA-Seq]

2022-12-22 | GSE221316 | GEO

Germinal centre-driven maturation of B cell response to SARS-CoV-2 mRNA vaccination

Project description:We used ultrasound-guided fine needle aspiration of the draining ipsilateral axillary lymph nodes to interrogate SARS-CoV-2 mRNA vaccine-induced GC responses in humans.

2022-01-30 | GSE195673 | GEO

Complementarity Determining Regions in SARS-CoV-2 hybrid immunity

Project description:Pre-vaccination SARS-CoV-2 infection can boost protection elicited by COVID-19 vaccination and post-vaccination breakthrough SARS-CoV-2 infection can boost existing immunity conferred by COVID-19 vaccination. Such ‘hybrid immunity’ is effective against SARS-CoV-2 variants. In order to understand ‘hybrid immunity’ at the molecular level we studied the complementarity determining regions (CDR) of anti-RBD (receptor binding domain) antibodies isolated from individuals with ‘hybrid immunity’ as well as from ‘naive’ (notSARS-CoV-2 infected) vaccinated individuals. CDR analysis was done by liquid chromatography/mass spectrometry-mass spectrometry.

2023-02-08 | PXD038849 | Pride

A single intranasal dose of human parainfluenza virus type 3-vectored vaccine induces effective antibody and tissue-resident T cell response in the lungs and protects hamsters against SARS-CoV-2

Project description:Respiratory tract vaccination has an advantage of needle-free delivery and induction of mucosal immune response in the portal of SARS-CoV-2 entry. We utilized human parainfluenza virus type 3 vector to generate constructs expressing the full spike (S) protein of SARS-CoV-2, its S1 subunit, or the receptor-binding domain, and tested them in hamsters as single-dose intranasal vaccines. The construct bearing full-length S induced high titers of neutralizing antibodies specific to S protein domains critical to the protein functions. Robust tissue-resident T cell responses in the lungs were also induced, which represent an additional barrier to infection and should be less sensitive than the antibody responses to mutations present in SARS-CoV-2 variants. Following SARS-CoV-2 challenge, animals were protected from the disease and detectable viral replication. Vaccination prevented induction of gene pathways associated with inflammation. These results indicate advantages of respiratory vaccination against COVID-19 and inform the design of mucosal SARS-CoV-2 vaccines.

2022-05-04 | GSE193288 | GEO

RNA-Sequencing of Saliva Samples from COVID-Infected and Vaccinated Subjects

Project description:SARS-CoV-2 virus is known to infect the oral cavity and can be readily detected using PCR-based testing. In this study, we examined the host transcriptomic response to PCR-confirmed SARS-CoV-2 virus infection, vaccination against SARS-CoV-2, or breakthrough infection following vaccination using RNA-sequencing. The identification of the viral variant for all samples was obtained using full viral genome sequencing. Approximately equal numbers of males and females were used for every major variant lineage. Results indicate strong anti-viral responses in each case, with some differences due to variant strain and vaccination history, as well as age and sex.

2023-09-19 | GSE235262 | GEO

The PDZ-binding motif of SARS-CoV envelope protein is a determinant of viral pathogenesis

Project description:A recombinant SARS-CoV lacking the envelope (E) protein is attenuated in vivo. Here we report that E protein PDZ-binding motif (PBM), a domain involved in protein-protein interactions, is a major virulence determinant in vivo. Elimination of SARS-CoV E protein PBM by using reverse genetics led to attenuated viruses (SARS-CoV-mutPBM) and to a reduction in the deleterious exacerbate immune response triggered during infection with the parental virus (SARS-CoV-wt). Cellular protein syntenin bound E protein PBM during SARS-CoV infection. Syntenin activates p38 MAPK leading to overexpression of inflammatory cytokines, and we have shown that active p38 MAPK was reduced in lungs of mice infected with SARS-CoVs lacking E protein PBM (SARS-CoV-mutPBM) as compared with the parental virus (SARS-CoV-wt), leading to a decreased expression of inflammatory cytokines and to viral attenuation. Therefore, E protein PBM is a virulence factor that activates pathogenic immune response most likely by using syntenin as a mediator of p38 MAPK induced inflammation. Three biological replicates were independently hybridized (one channel per slide) for each sample type (SARS-CoV-wt, SARS-CoV-mutPBM, Mock). Slides were Sure Print G3 Agilent 8x60K Mouse (G4852A-028005)

2014-10-31 | E-GEOD-52920 | biostudies-arrayexpress

Cytokinopathy with aberrant cytotoxic lymphocytes and profibrotic myeloid response in SARS-CoV-2 mRNA vaccine-associated myocarditis

Project description:Rare immune-mediated cardiac tissue inflammation can occur after vaccination, including after SARS-CoV-2 mRNA vaccines, yet the underlying immune cellular and molecular mechanisms driving this pathology remain poorly understood. Here, we investigated the systemic immunopathological landscape underlying such rare cases of myopericarditis occurring after SARS-CoV-2 LNP-mRNA vaccination using peripheral blood single-cell transcriptome and repertoire sequencing, among other multimodal approaches.

2023-05-04 | GSE230227 | GEO

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