scholarly journals BraCeR: Reconstruction of B-cell receptor sequences and clonality inference from single-cell RNA-sequencing

2017 ◽  
Author(s):  
Ida Lindeman ◽  
Guy Emerton ◽  
Ludvig M. Sollid ◽  
Sarah A. Teichmann ◽  
Michael J.T. Stubbington
Keyword(s):  
B Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
B Lymphocytes ◽  
Antigen Receptor ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Supplementary Note ◽  
Single Cell Rna Sequencing ◽  
Repertoire Sequencing

Reconstruction of antigen receptor sequences from single-cell RNA-sequencing (scRNA-seq) data allows the linking of antigen receptor usage to the full transcriptomic identity of individual B lymphocytes, without having to perform additional targeted repertoire sequencing (Rep-seq). Here we report BraCeR (freely available at https://github.com/teichlab/bracer/), an extension of TraCeR [1], for reconstruction of paired full-length B-cell receptor sequences and inference of clonality from scRNA-seq data (Supplementary Note 1).

scholarly journals An atlas of infiltrated B-lymphocytes in breast cancer revealed by paired single-cell RNA-sequencing and antigen receptor profiling

2019 ◽  
Author(s):  
Qingtao Hu ◽  
Yu Hong ◽  
Pan Qi ◽  
Guangqing Lu ◽  
Xueying Mai ◽  
...  
Keyword(s):  
Breast Cancer ◽  
B Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
B Lymphocytes ◽  
Immune Cells ◽  
Breast Cancer Subtype ◽  
Antigen Receptor ◽  
Tumor Control ◽  
Single Cell Rna Sequencing

AbstractWhile it has been well-recognized that T-cell mediated adaptive cellular immunity plays important roles in cancer immune response and tumor control, the roles of B lymphocytes in tumor development and therapy have only been proposed until recently, and are still mostly controversial. To gain mechanistic insights into the origin and dynamics of tumor infiltrated immune cells, especially B lymphocytes, we combine single-cell RNA-sequencing and antigen receptor lineage analysis to characterize a large number of triple-negative breast cancer (TNBC) infiltrated immune cells and present a comprehensive atlas of infiltrated B-lymphocytes in TNBC, the most aggressive breast cancer subtype. We demonstrate that TNBC infiltrated B cells showed more mature and memory B cell characteristics, as well as high clonality and extensive IgH class switching recombination and somatic hypermutations. The B cell signatures based on single-cell RNA-seq results are significantly associated with improved survival for TNBC patients and provide better prognostication than classic single B cell markers (CD19 or CD20). Further dissection of the mechanisms regulating the functions and dynamic distribution of tumor infiltrated B cell populations will provide new clues for tumor immunotherapy.

scholarly journals Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS

2019 ◽  
Vol 2 (4) ◽  
pp. e201900371 ◽  
Author(s):  
Shaked Afik ◽  
Gabriel Raulet ◽  
Nir Yosef
Keyword(s):  
B Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Single Cells ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Read Length ◽  
Antigen Specificity ◽  
Short Read ◽  
Single Cell Rna Sequencing

RNA sequencing of single B cells provides simultaneous measurements of the cell state and its antigen specificity as determined by the B-cell receptor (BCR). However, to uncover the latter, further reconstruction of the BCR sequence is needed. We present BRAPeS (“BCR Reconstruction Algorithm for Paired-end Single cells” ), an algorithm for reconstructing BCRs from short-read paired-end single-cell RNA sequencing. BRAPeS is accurate and achieves a high success rate even at very short (25 bp) read length, which can decrease the cost and increase the number of cells that can be analyzed compared with long reads. BRAPeS is publicly available at the following link: https://github.com/YosefLab/BRAPeS.

scholarly journals Reconstructing B cell receptor sequences from short-read single cell RNA-sequencir with BRAPeS

2018 ◽  
Author(s):  
Shaked Afik ◽  
Gabriel Raulet ◽  
Nir Yosef
Keyword(s):  
B Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Read Length ◽  
Short Read ◽  
Long Reads ◽  
Single Cell Rna Sequencing ◽  
The Cost

ABSTRACTRNA-sequencing of single B cells provides simultaneous measurements of the cell state and its binding specificity. However, in order to uncover the latter further reconstruction of the B cell receptor (BCR) sequence is needed. We present BRAPeS, an algorithm for reconstructing BCRs from short-read paired-end single cell RNA-sequencing. BRAPeS is accurate and achieves a high success rate even at very short (25bp) read length, which can decrease the cost and increase the number of cells that can be analyzed compared to long reads. BRAPeS is publicly available in the following link: https://github.com/YosefLab/BRAPeS.

scholarly journals Atlas of breast cancer infiltrated B-lymphocytes revealed by paired single-cell RNA-sequencing and antigen receptor profiling

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qingtao Hu ◽  
Yu Hong ◽  
Pan Qi ◽  
Guangqing Lu ◽  
Xueying Mai ◽  
...  
Keyword(s):  
Breast Cancer ◽  
B Cells ◽  
B Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
B Lymphocytes ◽  
Immune Cells ◽  
Antigen Receptor ◽  
Cell Populations ◽  
Single Cell Rna Sequencing

AbstractTo gain mechanistic insights into the functions and developmental dynamics of tumor-infiltrated immune cells, especially B-lymphocytes, here we combine single-cell RNA-sequencing and antigen receptor lineage analysis to characterize a large number of triple-negative breast cancer infiltrated immune cells and report a comprehensive atlas of tumor-infiltrated B-lymphocytes. The single-cell transcriptional profiles reveal significant heterogeneity in tumor-infiltrated B-cell subgroups. The single-cell antigen receptor analyses demonstrate that compared with those in peripheral blood, tumor-infiltrated B-cells have more mature and memory B-cell characteristics, higher clonality, more class switching recombination and somatic hypermutations. Combined analyses suggest local differentiation of infiltrated memory B-cells within breast tumors. The B-cell signatures based on the single-cell RNA-sequencing results are significantly associated with improved survival in breast tumor patients. Functional analyses of tumor-infiltrated B-cell populations suggest that mechanistically, B-cell subgroups may contribute to immunosurveillance through various pathways. Further dissection of tumor-infiltrated B-cell populations will provide valuable clues for tumor immunotherapy.

scholarly journals CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells

2020 ◽  
Author(s):  
Shadi Darvish Shafighi ◽  
Szymon M Kiełbasa ◽  
Julieta Sepúlveda-Yáñez ◽  
Ramin Monajemi ◽  
Davy Cats ◽  
...  
Keyword(s):  
Follicular Lymphoma ◽  
B Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Tumor Heterogeneity ◽  
Single Cells ◽  
Clonal Evolution ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Single Cell Rna Sequencing

ABSTRACTBackgroundDrawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the mutations found in RNA sequencing of the cells. The confidence of the cell-to-clone mapping can be increased by accounting for additional measurements. Follicular lymphoma, a malignancy of mature B cells that continuously acquire mutations in parallel in the exome and in B-cell receptor loci, presents a unique opportunity to align exome-derived mutations with B-cell receptor clonotypes as an independent measure for clonal evolution.ResultsHere, we propose CACTUS, a probabilistic model that leverages the information from an independent genomic clustering of cells and exploits the scarce single cell RNA sequencing data to map single cells to given imperfect genotypes of tumor clones. We apply CACTUS to two follicular lymphoma patient samples, integrating three measurements: whole exome sequencing, single cell RNA sequencing, and B-cell receptor sequencing. CACTUS outperforms a predecessor model by confidently assigning cells and B-cell receptor clonotypes to the tumor clones.ConclusionsThe integration of independent measurements increases model certainty and is the key to improving model performance in the challenging task of charting the genotype-to-phenotype maps in tumors. CACTUS opens the avenue to study the functional implications of tumor heterogeneity, and origins of resistance to targeted therapies.

scholarly journals CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Shadi Darvish Shafighi ◽  
Szymon M. Kiełbasa ◽  
Julieta Sepúlveda-Yáñez ◽  
Ramin Monajemi ◽  
Davy Cats ◽  
...  
Keyword(s):  
Follicular Lymphoma ◽  
B Cell ◽  
Single Cell ◽  
Rna Sequencing ◽  
Tumor Heterogeneity ◽  
Single Cells ◽  
Clonal Evolution ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Sequencing Data

Abstract Background Drawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the mutations found in RNA sequencing of the cells. The confidence of the cell-to-clone mapping can be increased by accounting for additional measurements. Follicular lymphoma, a malignancy of mature B cells that continuously acquire mutations in parallel in the exome and in B cell receptor loci, presents a unique opportunity to join exome-derived mutations with B cell receptor sequences as independent sources of evidence for clonal evolution. Methods Here, we propose CACTUS, a probabilistic model that leverages the information from an independent genomic clustering of cells and exploits the scarce single cell RNA sequencing data to map single cells to given imperfect genotypes of tumor clones. Results We apply CACTUS to two follicular lymphoma patient samples, integrating three measurements: whole exome, single-cell RNA, and B cell receptor sequencing. CACTUS outperforms a predecessor model by confidently assigning cells and B cell receptor-based clusters to the tumor clones. Conclusions The integration of independent measurements increases model certainty and is the key to improving model performance in the challenging task of charting the genotype-to-phenotype maps in tumors. CACTUS opens the avenue to study the functional implications of tumor heterogeneity, and origins of resistance to targeted therapies. CACTUS is written in R and source code, along with all supporting files, are available on GitHub (https://github.com/LUMC/CACTUS).

scholarly journals Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
David S. Fischer ◽  
Meshal Ansari ◽  
Karolin I. Wagner ◽  
Sebastian Jarosch ◽  
Yiqi Huang ◽  
...  
Keyword(s):  
T Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Ex Vivo ◽  
Severe Disease ◽  
Human Leukocyte ◽  
Cell Receptor ◽  
Single Cell Rna Sequencing

AbstractThe in vivo phenotypic profile of T cells reactive to severe acute respiratory syndrome (SARS)-CoV-2 antigens remains poorly understood. Conventional methods to detect antigen-reactive T cells require in vitro antigenic re-stimulation or highly individualized peptide-human leukocyte antigen (pHLA) multimers. Here, we use single-cell RNA sequencing to identify and profile SARS-CoV-2-reactive T cells from Coronavirus Disease 2019 (COVID-19) patients. To do so, we induce transcriptional shifts by antigenic stimulation in vitro and take advantage of natural T cell receptor (TCR) sequences of clonally expanded T cells as barcodes for ‘reverse phenotyping’. This allows identification of SARS-CoV-2-reactive TCRs and reveals phenotypic effects introduced by antigen-specific stimulation. We characterize transcriptional signatures of currently and previously activated SARS-CoV-2-reactive T cells, and show correspondence with phenotypes of T cells from the respiratory tract of patients with severe disease in the presence or absence of virus in independent cohorts. Reverse phenotyping is a powerful tool to provide an integrated insight into cellular states of SARS-CoV-2-reactive T cells across tissues and activation states.

scholarly journals Signatures of B Cell Receptor Repertoire Following Pneumocystis Infection

2021 ◽  
Vol 12 ◽  
Author(s):  
Han Sun ◽  
Hu-Qin Yang ◽  
Kan Zhai ◽  
Zhao-Hui Tong
Keyword(s):  
B Cells ◽  
B Cell ◽  
Single Cell ◽  
Plasma Cells ◽  
Somatic Hypermutation ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Receptor Repertoire ◽  
Elevated Expression ◽  
Pneumocystis Infection

B cells play vital roles in host defense against Pneumocystis infection. However, the features of the B cell receptor (BCR) repertoire in disease progression remain unclear. Here, we integrated single-cell RNA sequencing and single-cell BCR sequencing of immune cells from mouse lungs in an uninfected state and 1–4 weeks post-infection in order to illustrate the dynamic nature of B cell responses during Pneumocystis infection. We identified continuously increased plasma cells and an elevated ratio of (IgA + IgG) to (IgD + IgM) after infection. Moreover, Pneumocystis infection was associated with an increasing naïve B subset characterized by elevated expression of the transcription factor ATF3. The proportion of clonal expanded cells progressively increased, while BCR diversity decreased. Plasma cells exhibited higher levels of somatic hypermutation than naïve B cells. Biased usage of V(D)J genes was observed, and the usage frequency of IGHV9-3 rose. Overall, these results present a detailed atlas of B cell transcriptional changes and BCR repertoire features in the context of Pneumocystis infection, which provides valuable information for finding diagnostic biomarkers and developing potential immunotherapeutic targets.

scholarly journals IVIg modulates BCR signaling through CD22 and promotes apoptosis in mature human B lymphocytes

Blood ◽  
2010 ◽  
Vol 116 (10) ◽  
pp. 1698-1704 ◽  
Author(s):  
Jean-François Séïté ◽  
Divi Cornec ◽  
Yves Renaudineau ◽  
Pierre Youinou ◽  
Rizgar A. Mageed ◽  
...  
Keyword(s):  
B Cell ◽  
B Lymphocytes ◽  
B Lymphocyte ◽  
Cell Receptor ◽  
B Cell Receptor ◽  
Time Dependent ◽  
G1 Phase ◽  
Dependent Manner ◽  
Bcr Signaling ◽  
Sustained Activation

Abstract Among various mechanisms for interactions with B cells, intravenous immunoglobulin (IVIg) may operate through the insertion of its Fc part into the Fc-γ receptor, or the binding of its sialic acid (SA)–bearing glycans to the negatively regulating CD22 lectin. It appeared that IVIg reduces B lymphocyte viability in a dose- and time-dependent manner. Furthermore, we show by confocal microscopy that SA-positive IgG, but not SA-negative IgG bind to CD22. This interaction reduces the strength of B-cell receptor–mediated signaling trough down-regulating tyrosine phosphorylation of Lyn and the B-cell linker proteins, and up-regulating phospholipase Cγ2 activation. This cascade resulted in a sustained activation of Erk 1/2 and arrest of the cell cycle at the G1 phase. These changes may be accounted for the efficacy of IVIg in autoimmune diseases.

Sign in / Sign up

Export Citation Format

Share Document