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5,856 results for “B cell”
Profiling of linear B-cell epitopes against human coronaviruses in pooled sera sampled early in the COVID-19 pandemic
<p>Background: Antibodies play a key role in the immune defence against infectious pathogens. Understanding the underlying process of B cell recognition is not only of fundamental interest; it supports important applications within diagnostics and therapeutics. Whereas the nature of conformational B cell epitope recognition is inherently complicated, linear B cell epitopes offer a straightforward approach that potentially can be reduced to one of peptide recognition.</p> <p>Methods: Using an overlapping peptide approach representing the entire proteomes of the seven main coronaviruses known to infect humans, we analysed sera pooled from eight PCR-confirmed COVID-19 convalescents and eight pre-pandemic controls. Using a high-density peptide microarray platform, 13-mer peptides overlapping by 11 amino acids were in situ synthesised and incubated with the pooled primary serum samples, followed by development with secondary fluorochrome-labelled anti-IgG and -IgA antibodies. Interactions were detected by fluorescence detection. Strong Ig interactions encompassing consecutive peptides were considered to represent "high-fidelity regions" (HFRs). These were mapped to the coronavirus proteomes using a 60% homology threshold for clustering.</p> <p>Results: We identified 333 human coronavirus derived HFRs. Among these, 98 (29%) mapped to SARS-CoV-2, 144 (44%) mapped to one or more of the four circulating common cold coronaviruses (CCC), and 54 (16%) cross-mapped to both SARS-CoV-2 and CCCs. The remaining 37 (11%) mapped to either SARS-CoV or MERS-CoV. Notably, the COVID-19 serum was skewed towards recognising SARS-CoV-2-mapped HFRs, whereas the pre-pandemic was skewed towards recognising CCC-mapped HFRs. In terms of absolute numbers of linear B cell epitopes, the primary targets are the ORF1ab protein (60%), the spike protein (21%), and the nucleoprotein (15%) in that order; however, in terms of epitope density, the order would be reversed.</p> <p>Conclusion: We identified linear B cell epitopes across coronaviruses, highlighting pan-, alpha-, beta-, or SARS-CoV-2-corona-specific B cell recognition patterns. These findings could be pivotal in deciphering past and current exposures to epidemic and endemic coronavirus. Moreover, our results suggest that pre-pandemic anti-CCC antibodies may cross-react against SARS-CoV-2, which could explain the highly variable outcome of COVID-19. Finally, the methodology used here offers a rapid and comprehensive approach to high-resolution linear B-cell epitope mapping, which could be vital for future studies of emerging infectious diseases.</p>
PM_035422_B_Celles
<u>File Name</u>: PM_035422_B_Celles.jpg <br><u>Sublocation</u>: Celles-les-Dinant, Eglise Saint-Hadelin <br><u>Location</u>: Houyet <br><u>Province</u>: Namur <br><u>Country</u>: Belgium <br><u>Header</u>: Église paroissiale (Eglise Saint-Hadelin). Extérieur. Le site. <br><u>Description</u>: Parish church (Eglise Saint-Hadelin) Exterior The site <br><u>Keywords</u>: Belgium, Celles-les-Dinant (Houyet), Cultural heritage, Europe, Historic site, Houyet, Monuments, Namur, Romanesque, Styles, Thematic <br><br><u>Author</u>: Photo: Paul M.R. Maeyaert <br><u>Copyright</u>: Paul M.R. Maeyaert <br>
PM_035425_B_Celles
<u>File Name</u>: PM_035425_B_Celles.jpg <br><u>Sublocation</u>: Celles-les-Dinant, L'Hermitage Saint-Hadelin <br><u>Location</u>: Houyet <br><u>Province</u>: Namur <br><u>Country</u>: Belgium <br><u>Header</u>: Abbaye (L'Hermitage Saint-Hadelin). Extérieur. Façade ouest et entrée. 19ème siècle ( ?). <br><u>Description</u>: Abbey (L'Hermitage Saint-Hadelin) Exterior West facade and entrance 19th century (?) <br><u>Keywords</u>: Belgium, Celles-les-Dinant (Houyet), Cultural heritage, Europe, Houyet, Monuments, Namur, Neo-Romanesque, Romanesque, Styles <br><br><u>Author</u>: Photo: Paul M.R. Maeyaert <br><u>Copyright</u>: Paul M.R. Maeyaert <br>
PM_035415_B_Celles
<u>File Name</u>: PM_035415_B_Celles.jpg <br><u>Sublocation</u>: Celles-les-Dinant, Eglise Saint-Hadelin <br><u>Location</u>: Houyet <br><u>Province</u>: Namur <br><u>Country</u>: Belgium <br><u>Header</u>: Église paroissiale (Eglise Saint-Hadelin). Intérieur. La nef. 11ème siècle (1040 ?). <br><u>Description</u>: Parish church (Eglise Saint-Hadelin) Interior The nave 11th century (1040 ?) <br><u>Keywords</u>: Belgium, Celles-les-Dinant (Houyet), Cultural heritage, Europe, Houyet, Monuments, Namur, Romanesque, Styles <br><br><u>Author</u>: Photo: Paul M.R. Maeyaert <br><u>Copyright</u>: Paul M.R. Maeyaert <br>
Raw data to: "Vectored antibody gene delivery restores host B and T cell control of persistent viral infection"
<p>Raw data underlying the publication by Ertuna et al. entitled "Vectored antibody gene delivery restores host B and T cell control of persistent viral infection"</p>
Coloc summary results for "Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets"
<p>Text files containing coloc results between MS GWAS loci and CD4 T and B cell cis-eQTLs from DICE. These results accompany the paper "<strong>Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets"</strong></p>
Single Cell Phenotypic Profiling to Identify a Set of Immune Cell Protein Biomarkers for Relapsed and Refractory Diffuse Large B Cell Lymphoma: A Single-Center Study
<p>Diffuse large B-cell lymphoma (DLBCL) is the most common invasive type of non-Hodgkin lymphoma. Cell-of-origin (COO) classification is related to patients’ prognoses. Primary drug resistance in treatment for DLBCL has been observed. The specific serum biomarkers in these patients who suffer from relapsed and refractory (R/R)-DLBCL remains unclear. In the current study, using single-cell RNA sequencing (scRNA-seq) and mass cytometry (CyTOF), we determined and verified immune cell biomarkers at the mRNA and protein levels in single-cell resolution from 18 diagnostic peripheral blood mononuclear cell (PBMC) specimens collected from patients with R/R DLBCL. As controls, five PBMC specimens from healthy volunteers were obtained. We identified a panel of 35 surface marker genes for the features of R/R DLBCL unique cell cluster by scRNA-seq of eight R/R DLBCL patient samples and validated its efficiency in an external cohort consisting of 10 R/R DLBCL patients by CyTOF. The cell clustering and dimension reduction were compared among R/R DLBCL samples in CyTOF Space with COO as well as the C-MYC expression designation. Immune cells from each patient occupied unique regions in the 32-dimensional phenotypic space with no apparent clustering of samples into discrete subtypes. Significant heterogeneity observed in subgroups was mainly attributed to individual differences among samples and not to expression differences in a single, homogeneous immune cell subpopulation. The marker panel showed reliability in labeling R/R DLBCL without any influence from COO stratification and C-MYC expression designation. Furthermore, we compared all the markers between R/R DLBCL and normal samples. A total of 12 biomarkers were significantly overexpressed in R/R DLBCL relative to the normal samples. Therefore, we further optimized the diagnostic biomarker panel of R/R DLBCL comprising CD82, CD55, CD36, CD63, CD59, IKZF1, CD69, CD163, CD14, CD226, CD84, and CD31. In summary, we developed a novel set of biomarkers for the diagnoses of patients with R/R DLBCL. Detections procedures at single-cell resolution provide precise biomarkers which may substantially overcome intertumoral and intratumoral heterogeneity among primary samples. The findings confirmed that each case was unique and may comprise multiple, genetically distinct subclones.</p> <p>Here we uploaded the dataset of CyTOF for external validation. For more detailed information, please contact Dr zheng (zenki_zheng@163.com)</p> <p> </p>
A B cell actomyosin arc network couples integrin co-stimulation to mechanical force-dependent immune synapse formation
<p>B-cell activation and immune synapse (IS) formation with membrane-bound antigens are actin-dependent processes that scale positively with the strength of antigen-induced signals. Importantly, ligating the B-cell integrin, LFA-1, with ICAM-1 promotes IS formation when antigen is limiting. Whether the actin cytoskeleton plays a specific role in integrin-dependent IS formation is unknown. Here we show using super-resolution imaging of mouse primary B cells that LFA-1: ICAM-1 interactions promote the formation of an actomyosin network that dominates the B-cell IS. This network is created by the formin mDia1, organized into concentric, contractile arcs by myosin 2A, and flows inward at the same rate as B-cell receptor (BCR): antigen clusters. Consistently, individual BCR microclusters are swept inward by individual actomyosin arcs. Under conditions where integrin is required for synapse formation, inhibiting myosin impairs synapse formation, as evidenced by reduced antigen centralization, diminished BCR signaling, and defective signaling protein distribution at the synapse. Together, these results argue that a contractile actomyosin arc network plays a key role in the mechanism by which LFA-1 co-stimulation promotes B-cell activation and IS formation.</p>
Supplementary data for article "Reduced B-cell antigenicity of Omicron lowers host serologic response"
<p>This repository contains five supplementary data files for the research article "<strong>Reduced B-cell antigenicity of Omicron lowers host serologic response</strong>". For more information, please refer to the article preprint https://doi.org/10.1101/2022.02.15.480546 and upcoming article at Cell Reports.</p> <p> </p> <ol> <li><strong>Table_hCoV229E.xlsx:</strong> list of hCoV229E RBD sequences, with associated isolate and collection date identifiers, and ScanNet antigenicity score for reproducing <strong>Figure 3A</strong>. Aligned sequences and templates are also provided.</li> <li><strong>table_artificial_variants.csv</strong>: List of artificial RBD sequences generated by an evolutionary-based sequence generative model for reproducing <strong>Figure 3B</strong>, <strong>Supplementary Figure S6H</strong>.</li> <li><strong>MSA_RBD.fasta:</strong> Multiple Sequence Alignment of RBD sequences and sample weights used for training the sequence generative model used in <strong>Figure 3B</strong>, <strong>Supplementary Figures S2C, S6</strong>.</li> <li><strong>table_antibody_hit_rate_RBD.csv</strong>: Empirical epitope distribution for the RBD, as determined from the Protein Data Bank and raw data for <strong>Supplementary Figure S1</strong>).</li> <li><strong>RBD_virtual_DMS.xlsx</strong>: virtual Deep Mutational Scan performed with ScanNet and the sequence generative model shown in <strong>Supplementary Figure S2</strong>.</li> </ol> <p> </p> <p> </p>
Single-cell transcriptomic analysis of B cells reveals new insights into atypical memory B cells in COVID-19
<p><span>Here, we performed single-cell RNA sequencing of S1 and RBD protein-specific B cells from convalescent COVID-19 patients with different clinical manifestations. This study aimed to evaluate the role and developmental pathway of atypical memory B cells in response to SARS-CoV-2 infection. The results revealed a proinflammatory signature across B cell subsets associated with disease severity, as evidenced by the upregulation of genes such as <em>GADD45B</em>, <em>MAP3K8</em>, and <em>NFKBIA</em> in critical and severe individuals. Furthermore, the analysis of atypical memory B cells suggested a developmental pathway similar to that of conventional memory B cells through germinal centers, as indicated by the expression of several genes involved in germinal center processes, including <em>CXCR4</em>, <em>CXCR5</em>, <em>BCL2</em>, and <em>MYC</em>. Additionally, the upregulation of genes characteristic of the immune response in COVID-19, such as <em>ZFP36</em> and <em>DUSP1</em>, suggested that the differentiation and activation of atypical memory B cells may be influenced by exposure to SARS-CoV-2 and that these genes may contribute to the immune response for COVID-19 recovery. Our study contributes to a better understanding of atypical memory B cells in COVID-19 and the role of other B cell subsets across different clinical manifestations.</span></p>
Data for Isotype-aware Inference of B cell Clonal Lineage Trees from Single-cell Sequencing Data
<p>This is the accompanying data to the manuscript titled<em> Isotype-aware Inference of B cell Clonal Lineage Trees from Single-cell Sequencing Data</em>. To reproduce the TRIBAL output please use this <a href="https://doi.org/10.5281/zenodo.12741290">code repository</a> as the arguments and codebase may have changed since release. </p>
Partis post-processed B cell receptor repertoires from BioProject PRJNA349143
<p>These files correspond to partis annotations of several datasets found in BioProject PRJNA349143. (DOI: 10.5281/zenodo.821659).</p>
Pandemic, epidemic, endemic: B cell repertoire analysis reveals unique anti-viral responses to SARS-CoV-2, Ebola and Respiratory Syncytial Virus
<p>VDJ gene usage, and associated amino acid sequences and properties, from healthy controls as well as patients with COVID-19, RSV or Ebola and Yellow fever vaccine recipients.</p>
Supplementary Figures -B Cell Epitopes Mapping of the Vibrio cholera Toxins A, B, and P and an ELISA assay
<p>Figure S1- List of <em>Vibrio cholerae</em> [toxin A (P01555), B (P01556), and P (P29485)] synthetic peptides and position in the cellulose membrane of Spot synthesis.</p> <p>Figure S2- Purification of the peptide B (Vc/TxB-11) by HPLC using an XBridge BEH C18 (2.7 μ, 5 cm x 4.6 mm) column coupled to a Water HPLC system at a flow rate of 1.2 ml min<sup>-1 </sup>using mobile phases A [0.05% formic acid in water (18 MΩ × cm)] and B [(0.05% formic acid in ACN (acetonitrile acid)] (v/v) in water. Detection at 200-300 nm using a diode array.</p> <p>Figure S3- Mass spectrometry. The peptide B (Vc/TxB-11) was solubilized in deionized water to a final concentration of 10 µg/ml and then added formic acid to a final concentration of 0.1%. The mass spectrometer used was the Water UPLC model Acquity-I Class. The samples were electronically injected by the equipment at 1 µl/min. The range used for ion detection ranged from 1000-11500 m/z.</p>
Frozen feather and motif files for Distinct stage-specific transcriptional states of B cells derived from human tonsillar tissue.
<p>Frozen feather and motif files for manuscript "Distinct stage-specific transcriptional states of B cells derived from human tonsillar tissue" by Espinoza DA, et al. Data was downloaded from cisTarget database from aertslab.org.</p>
B-cell receptor data from intratumoural B cells in melanoma patients
<p>This record contains data used in the Crescioli et al. analysis of B-cell response in melanoma, specifically analysis concerning high-throughput BCR repertoire.</p> <p>Files:</p> <p>"Visium_all_Aug22_comboDatBoth.txt": IMGT/HighV-Quest output of the high-throughput intratumoural BCR repertoire from n=5 melanoma tumours. In tab-separated text file format.</p> <p>"HV_EB_COV_MEL_comb_Oct22.RDS": A R data object (readable into R with "readRDS(...)") containing combined data from the melanoma (MEL) data with analogous high-throughput BCR repertoire data from healthy volunteers (HV), Ebola convalescent patients (EB) and hospitalised COVID-19 patients (COV). HV, EB and COV data are taken from <a href="https://dx.doi.org/10.5281/zenodo.5146019">https://dx.doi.org/10.5281/zenodo.5146019</a>. Here the sequences are filtered to contain only unique combinations of isotype and IMGT-numbered V-domain DNA sequence (to remove redundancies due to e.g. capturing BCR transcripts from plasma cells).</p> <p>"BM_Master_Light_Useasreftrue_140325_withPepStats_8.csv". IMGT/HighV-Quest output of the Bone Marrow light chain repertoire data. <a href="https://doi.org/10.3389/fimmu.2016.00388">Published in Townsend et al. Front Immunol 7:388 (2016)</a>. Used here for the comparison of gene conversion frequencies against the melanoma light chain repertoire.</p> <p>"BM_Master_Light_Useasreftrue_140325_withPepStats_8_Vgapped.fasta". The IMGT-gapped V-gene sequence from the Townsend et al. (see above) Bone Marrow light chain repertoire data. This is the raw input to BrepConvert. Provided here for this dataset; same sequences for the melanoma/healthy data are already in the RDS object ("HV_EB_COV_MEL_comb_Oct22.RDS").</p> <p>"2_IMGT-gapped-nt-sequences_visa.txt", "2_IMGT-gapped-nt-sequences_visb.txt": Raw output of IMGT/HighV-Quest containing IMGT-gapped nucleotide sequences. These files were parsed to extract the IMGT-gapped V-gene sequence for BrepConvert analysis.</p> <p>"BrepConvert.zip": BrepConvert gene conversion analysis results for Healthy and Melanoma repertoires.</p> <p>See code in <a href="https://github.com/josef0731/melanoma-ig">https://github.com/josef0731/melanoma-ig</a> for ways to use these input files for reproducing the analyses.</p> <p> </p>
Efficient isolation of rare B cells using next-generation antigen barcoding
<p><strong>ABSTRACT:</strong> The ability to efficiently isolate antigen-specific B cells in high throughput will greatly accelerate the discovery of therapeutic monoclonal antibodies (<strong>mAbs</strong>) and catalyze rational vaccine development. Traditional mAb discovery is a costly and labor-intensive process, although recent advances in single-cell genomics using emulsion microfluidics allow simultaneous processing of thousands of individual cells. Here we present a streamlined method for isolation and analysis of large numbers of antigen-specific B cells, including next generation antigen barcoding and an integrated computational framework for B cell multi-omics. We demonstrate the power of this approach by recovering thousands of antigen-specific mAbs, including the efficient isolation of extremely rare precursors of VRC01-class and IOMA-class broadly neutralizing HIV mAbs.</p> <p> </p>
Data from: Hemin treatment drives viral reactivation and plasma cell differentiation of EBV latently infected B cells
<p>Epstein-Barr virus (EBV) and <em>Plasmodium falciparum</em> have a well described role in the development of endemic Burkitt lymphoma (BL), yet the mechanisms involved remain unknown. A major hallmark of malarial disease is hemolysis and bystander eryptosis of red blood cells, which causes release of free heme in large quantities into peripheral blood. We hypothesized that heme released during malaria infection drives differentiation of latently infected EBV-positive B cells, resulting in viral reactivation and release of infectious virus. To test this hypothesis, we used the EBV-positive Mutu I B-cell line and treated with hemin (the oxidized form of heme) and evaluated for evidence of EBV reactivation. Hemin treatment resulted in the expression of EBV immediate early, early and late lytic gene transcripts. In addition, expression of CD138, a marker of plasma cells was co-expressed with the late lytic protein gp350 on hemin treated Mutu I cells. Finally, DNase-resistant EBV DNA indicative of virion production was detected in supernatant. To assess the transcriptional changes induced by hemin treatment, RNA sequencing was performed on mock- and hemin-treated Mutu I cells, and a shift from mature B cell transcripts to plasma cell transcripts was identified. To identify the mechanism of hemin-induced B cell differentiation, we measured levels of the plasma cell transcriptional repressor, BACH2, that contains specific heme binding sites. Hemin treatment caused significant degradation of BACH2 by 24 hours post-treatment in four BL cell lines (two EBV positive, two EBV negative). Knockdown of BACH2 in Mutu I cells using siRNAs significantly increased CD138+gp350+ cells to levels similar to treatment with hemin. This suggested that hemin induced BACH2 degradation was responsible for plasma cell differentiation and viral reactivation. Together, these data support a model where EBV reactivation can occur during malaria infection via heme modulation, providing a mechanistic link between malaria and EBV. </p>
Data and results for "Germline-encoded specificities and the predictability of the B cell response"
<p>Data and results for Vieira et al., <a href="https://www.biorxiv.org/content/10.1101/2022.09.16.508315v4">Germline-encoded specificities and the predictability of the B cell response</a></p> <p>Code for the analyses is available at <a href="https://github.com/cobeylab/v_gene_selection/">https://github.com/cobeylab/v_gene_selection/</a></p> <p> </p>
Quantification of hair cell number, ribeye b and nuclei in the zebrafish inner ear endorgans
<p>The three otolithic endorgans of the inner ear are known to be involved in sound detection in different teleost fishes, yet their relative roles for auditory-vestibular functions within the same species remain unclear. In zebrafish (<em>Danio</em> <em>rerio</em>), saccule and utricle are thought to play key functions in encoding auditory and vestibular information, respectively, but the biological function of the lagena is not clear. We hypothesized that the zebrafish saccule serves as a <span>primary </span>auditory endorgan, <span>making it more vulnerable to noise exposure</span>, and that lagena might have an auditory function given its connectivity to the saccule and dominant vestibular function of the utricle.</p> <p>In this study, we compared the impact of acoustic trauma (continuous white noise at 168 dB for 24 h) between the sensory epithelia of the three otolithic endorgans. Noise treatment caused hair cell loss in both the saccule and lagena but not in the utricle. This effect was identified immediately after acoustic treatment and did not increase 24 h post trauma. Furthermore, hair cell loss was accompanied by a reduction in presynaptic activity measured based on Ribeye b presence but mainly in the saccule, supporting its main contribution for noise-induced hearing loss.</p> <p>Our findings support the hypothesis that the saccule plays a major role in sound detection and that lagena is also acoustically affected extending the species hearing dynamic range.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.