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BCR heavy and light chain repertoire sequencing of pertitoneal cavity B-1a cells from wild-type and Igll1 knockout mice

ABSTRACT: We report that B-1a cells develop in a surrogate light chain independent context. As a consequence, the precursor B-1a cell population avoids a pre-BCR positive selection stage. To confirm that the B-1a cells generated in this manner repersent a bonafide B-1a cell compartment, we did NGS on BCR rearrangements to assess the repertoire diversity. We find that as a whoile, B-1a cell repertoire that develop in Igll1 kncokout mice are similar compared to wild-type. This supports our findings that B-1a cells develop properly in the absence of surrogate light chain.

ORGANISM(S): Mus musculus

PROVIDER: GSE104111 | GEO | 2018/01/15

SECONDARY ACCESSION(S): PRJNA408276

REPOSITORIES: GEO

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BCR heavy and light chain repertoire sequencing of pertitoneal cavity B-1a cells from wild-type and Igll1 knockout mice

Project description:BCR heavy and light chain repertoire sequencing of pertitoneal cavity B-1a cells from wild-type and Igll1 knockout mice

| PRJNA408276 | ENA

BCR repertoire analysis of wild-type and Cic-null B-1a cells

Project description:Purpose: B-1a cells have a distinct BCR repertoire compared with that of B-2 cells. To examine whether CIC loss affects the BCR repertoire in B-1a cells, we analyzed mRNA sequences of immunoglobulin heavy (Igh) and light (Igk and Igl) chain genes in B-1a cells from 12-week-old control and Cicf/f;Cd19-Cre mice. Methods: Peritoneal cavity B-1a cells (IgM+, CD19+, CD5+, CD43+) were sorted by a MoFlo-XDP (Beckman Coulter). Total RNA was extracted using TRIzol Reagent (GeneAll), according to the manufacturer’s instructions. Long Read iR-Profile Reagent System (iRepertoire) was used to generate NGS libraries covering BCR chains including Igh, Igk, and Igl. Briefly, nested inside and outside primers selectively amplified all V- and C- regions and incorporated communal adaptors. Following clean up, only target amplicons, which contain 5’ and 3’ communal adaptors, were exponentially amplified. Amplified libraries were multiplexed for sequencing on the Illumina Miseq platform. Sequence reads were de-multiplexed according to the barcode sequences. Results: Trimmed reads were mapped to germline V, D and J reference sequences downloaded from the IMGT database. IgH diversity and the usage of variable (V) segments in heavy (Ighv) chain and light (Igkv and Iglv) chain genes were comparable between control and Cic-null B-1a cells. Analysis of non-templated (N)-nucleotide addition at V(D)J junctions revealed that Cic-null B-1a cells have a higher proportion of zero to two N-nucleotides-containing-BCRs than control cells. Conclusions: Our study presents the first comparative BCR repertoire analysis of wild-type and Cic-null B-1a cells. We concluded that CIC deficiency does not dramatically alter the BCR repertoire in B-1a cells.

2021-12-16 | GSE164147 | GEO

BCR repertoire of B cells with distinct developmental timings

Project description:B cells are known to have different properties and BCR repertoires depending on the time of development. Our objective is to investigate the BCR repertoire of B cells across embryonic, neonatal, and adult stages, particularly in cells with a RAG2 expression history. We focus on sequencing and analyzing the immunoglobulin heavy chain (IGH) genes of these cells to understand their BCR diversity and specificity. Additionally, we explore the relationship between B-1a cells and bone marrow IgM+ plasmablasts/plasma cells, aiming to shed light on the development and function of B-1a cells in the immune system.

2023-12-17 | GSE250175 | GEO

Mus musculus strain:SLC KO and C57BL/6

Project description:Analysis of IgH repertoire selection in the absence of surrogate light chain

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Essential role of the transcription factor Bhlhe41 in regulating the self-renewal and BCR repertoire of B-1a cells

Project description:The innate-like B-1a cells provide a first line of defense against pathogens, and yet little is known about their transcriptional control. Here we identified an essential role of the transcription factor Bhlhe41, with a lesser contribution of Bhlhe40, in controlling late stages of B-1a cell differentiation. Bhlhe41/Bhlhe40 mutant B-1a cells were strongly reduced and had an abnormal cell-surface phenotype and altered B-cell receptor (BCR) repertoire, as exemplified by loss of the phosphatidylcholine-specific Vh12/Vk4 BCR. Expression of a pre-rearranged Vh12/Vk4 BCR failed to rescue the mutant phenotype and revealed enhanced proliferation accompanied with increased cell death, implicating Bhlhe41 in controlling the self-renewal of B-1a cells. Bhlhe41 directly repressed the expression of cell cycle regulators and inhibitors of BCR signaling, while activating pro-survival cytokine signaling.

2017-01-19 | GSE93764 | GEO

Antibody from Single Human VH-rearranging Mouse Potently Neutralizes All SARS-CoV-2 Variants Through BA.5 by Inhibiting Membrane Fusion

Project description:Here, we describe a mouse model in which the primary B cell receptor (BCR) repertoire is generated solely through V(D)J recombination of a human VH1-2 heavy chain (HC) and, substantially, a human Vk1-33 light chain (LC). Thus, primary humanized BCR repertoire diversity in these mice derives from immensely diverse HC and LC antigen-contact complementarity-region-3 (CDR3) sequences generated de novo by non-templated junctional modifications during V(D)J recombination. We assayed the V usage and CDR3 diversity in this mouse model by HTGTS-repertoire sequencing. Immunizing this human VH1-2/Vk1-33-rearranging model with prototype SARS-CoV-2 spike protein immunogens elicited several VH1-2/Vk1-33-based nAbs. Of these, SP1-77 potently and broadly neutralized all SARS-CoV-2 variants through BA.5. Cryo-EM studies revealed that SP1-77 binds RBD away from the ACE2 receptor-binding-motif via a striking CDR3-dominated mode of recognition. Lattice-light-sheet-microscopy-based studies confirmed that SP1-77 did not block ACE2-mediated viral attachment or subsequent endocytosis, but rather blocked membrane fusion. The SP1-77 binding epitope and neutralization mechanism may offer additional strategies for designing vaccines that robustly neutralize emerging SARS-CoV-2 variants.

2022-07-28 | GSE197255 | GEO

The endogenous retrovirus Mtv8 which resides within the V kappa locus does not influence the mouse immunoglobulin repertoire

Project description:The vast diversity of mammalian adaptive antigen receptors allows for robust and efficient immune responses against a wide number of pathogens. The antigen receptor repertoire is built during the recombination and hypermutation of B and T cell receptor (B-, TCR) loci. V(D)J recombination rearranges these antigen receptor loci which are organized as an array of separate V, (D), and J gene segments. Which gene segments are recombined, and thus which particular antigen receptors are present in the host repertoire, depends on the three-dimensional architecture of the recombining locus. The endogenous retrovirus (ERV) mouse mammary tumor provirus (Mtv8) resides on mouse chromosome 6 interposed within the large array of light chain kappa (IgK) V gene segments. It was unknown, however, whether Mtv8 influences the BCR repertoire, as ERVs can contribute to changes in genomic architecture by driving high levels of local transcription. We generated Mtv8-deficient mice to determine if the ERV influenced V(D)J recombination and found no significant difference in the peripheral BCR repertoire of Mtv8-deficient mice compared to wildtype controls. Thus, Mtv8, the endogenous retrovirus in the Igk locus, does not influence BCR repertoires.

2023-11-27 | GSE248410 | GEO

Characterization of B-cell receptor repertoire associated with asymptomatic and symptomatic infections of SARS-CoV-2

Project description:The immune responses to SARS-CoV-2 infections are very complex and remain to be further characterized. In this study, we performed the single-cell B-cell receptor (BCR) sequencing (scBCR-seq) of the PBMC samples from the healthy controls and SARS-CoV-2 infected individuals with various clinical presentations, and subsequently analyzed the abundance, diversity and difference of BCR repertoire in different groups of COVID-19 patients and the healthy controls, respectively. We identified a number of unique heavy or light chain VDJ genes pairs and combinational preference in each group, such as IGKV3-7 enriched in the asymptomatic subjects, whereas IGHV3-23-IGHJ4, IGHV1-18–IGLV3-19, IGHV1-18–IGLV3-21, and IGHV1-1–IGLV3-25 enriched in the recovery patients from the severe diseases. These findings may advance our understanding of the B-cell mediated immune responses to SARS-CoV-2 infections and help develop novel vaccine candidates and therapeutic antibodies against COVID-19.

2022-09-15 | GSE180118 | GEO

Project description:BCR repertoire

| PRJNA771191 | ENA

Transcription profiling of mouse bone marrow with Aiolos and OBF-1 deletions from 7 week old mice

Project description:The chromatin regulator Aiolos and the transcriptional coactivator OBF-1 have been implicated in regulating aspects of B cell maturation and activation. Mice lacking either of these factors have a largely normal early B cell development. However, when both factors are eliminated simultaneously a block is uncovered at the transition between pre-B and immature B cells, indicating that these proteins exert a critical function in developing B lymphocytes. In mice deficient for Aiolos and OBF-1, the numbers of immature B cells are reduced, small pre-BII cells are increased and a significant impairment in immunoglobulin light chain DNA rearrangement is observed. We identified genes whose expression is deregulated in the pre-B cell compartment of these mice. In particular, we found that components of the pre-BCR, such as the surrogate light chain genes l5l5 and VpreB, fail to be efficiently silenced in double-mutant mice. Strikingly, developmentally regulated nuclear repositioning of the l5l5 gene is impaired in pre-B cells lacking OBF-1 and Aiolos. These studies uncover a novel role for OBF-1 and Aiolos in controlling the transcription and nuclear organization of genes involved in pre-BCR function. OBF-1 or Aiolos or both were deleted and the gene expression profiles for these animals investigated using Affymetrix arrays Experiment Overall Design: Two control wildtype animals, then duplicates for each of the single Aiolos or OBF-1 mutants and further duplicates for the Aiolos/OBF-1 double mutants

2008-11-13 | E-GEOD-12356 | biostudies-arrayexpress

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