BCR repertoire of B cells with distinct developmental timings
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ABSTRACT:
PROVIDER: PRJNA1052600 | ENA |
REPOSITORIES: ENA
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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
Project description:Inclusion body myositis (IBM) is an autoimmune and degenerative disorder of skeletal muscle. The B cell infiltrates in IBM muscle tissue are predominantly fully differentiated antibody-secreting plasma cells, with scarce naïve or memory B cells. The role of this infiltrate in the disease pathology is not well understood. To better define the humoral response in IBM, we used adaptive immune receptor repertoire sequencing to generate large B cell receptor (BCR) repertoire libraries from IBM muscle biopsies and compared them to those generated from dermatomyositis (DM), polymyositis (PM), and circulating CD27+ memory B cells, derived from healthy controls and antibody secreting cells (ASC) collected following vaccination. The repertoire properties of the IBM infiltrate included: expanded clones that equaled or exceeded the highly clonal vaccine-associated ASC repertoire; reduced somatic mutation selection pressure in the complementary determining regions and framework regions; and enriched usage of class switched IgG and IgA isotypes, with a minor population of IgM expressing cells. These IBM IgM-expressing population revealed unique features, including an elevated somatic mutation frequency and distinct CDR3 physicochemical properties., These findings demonstrate that the IBM muscle BCR repertoire is highly distinct from DM and PM and circulating antigen-experienced subsets, suggesting that it may form through selection by a disease-specific set of antigens.
2023-04-25 | GSE227124 | GEO
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
Project description: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.
2018-01-15 | GSE104111 | GEO
Project description:BCR repertoire analysis of wild-type and Cic-null B-1a cells
| PRJNA689304 | ENA
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
Project description:Immunopeptidome analysis from WT and H2M-KO mice using M5/114, 15G4 and KH74 antibody were analyzed. Details are published in the paper "Regulation of the BCR signalosome by the class II peptide editor, H2-M, affects the development and repertoire of innate-like B cells".
2021-11-29 | MSV000088470 | MassIVE
Project description:We report that a large percentage of thymic B cells undergo class switching intrathymically. Thymic B cell class switching requires cognate T-B interaction. To determine whether B cell specificity was also important for thymic B cell class-switching, we sorted class-switched thymic B cells (CD19+B220+IgM-IgD-), unswitched B cells (CD19+B220+IgM+IgD+) and bulk splenic B cells in 3H9 heavy chain-fixed mice and performed high throughput sequencing analysis of the light chain of these populations. Results of this analysis indicated that class-switched thymic B cells have a distinct repertoire compared with unswitched thymic B cells and splenic B cells. Further reactivity tests indicated that a large part of BCRs enriched in class-switched thymic B cells are autoreactive. These data suggest that autoreactive B cells are selected into class-switched population and expanded in the thymus. Light chain repertoire profiles of class-switched thymic B cells, unswithced thymic B cells and splenic B cells from 3H9 mice were generated by deep sequencing.
2016-08-10 | E-GEOD-85366 | biostudies-arrayexpress
Project description:Erythema migrans (EM) is a skin lesion caused by the spirochete B. burgdorferi (Bb) and is a hallmark initial sign of Lyme disease. Previous studies have demonstrated that T cells and innate immune cells mediate local inflammatory cytokine production that promote the reaction. Despite the established importance of B cells and antibodies in preventing Bb infection and resolving disease, the role of B cells in the skin immune response to Bb is incompletely defined. In this study, we characterized the immunophenotype of EM lesions and used single cell RNA-Seq to investigate B cell receptor (BCR) and T cell receptor (TCR) repertoires in the EM skin lesions and peripheral blood of patients with Lyme disease. We hypothesized that B cells from the circulation, potentially primed by exposure to Bb antigens in regional draining lymph nodes, are recruited into EM lesions and play an active role in the local response to infection. We found that B cells are more abundant in the EM lesion in comparison to autologous uninvolved skin and possess distinct characteristics, including abundant expression of MHCII genes and preferential IgM isotype usage. A subset exhibited low levels of somatic hypermutation despite a gene expression profile more consistent with memory than naïve B cell subsets. Moreover, infiltrating B cells were clonally expanded and a large fraction could be directly traced to circulating relatives. By leveraging single cell gene expression with paired BCR and TCR repertoire sequencing, we demonstrate, for the first time, that B cells are recruited to the skin infection site in early Lyme disease and express a phenotype suggesting that they could play a role in local antigen presentation and antibody production.
2021-06-07 | GSE171215 | GEO
Project description:BCR repertoire sequencing of isotype-switched memory B cells Aim of the study was to explore the differences of Ig repertoires of isotype-switched memory B cells between spleen and bone marrow compartments.
2020-04-24 | GSE139835 | GEO