Identification of Antigen-Specific B-Cell Receptor Sequences from the Total B-Cell Repertoire

ABSTRACTMemory B cell reserves can generate protective antibodies against repeated SARS-CoV-2 infections, but with an unknown reach from original infection to antigenically drifted variants. We charted memory B cell receptor-encoded monoclonal antibodies (mAbs) from 19 COVID-19 convalescent subjects against SARS-CoV-2 spike (S) and found 7 major mAb competition groups against epitopes recurrently targeted across individuals. Inclusion of published and newly determined structures of mAb-S complexes identified corresponding epitopic regions. Group assignment correlated with cross-CoV-reactivity breadth, neutralization potency, and convergent antibody signatures. mAbs that competed for binding the original S isolate bound differentially to S variants, suggesting the protective importance of otherwise-redundant recognition. The results furnish a global atlas of the S-specific memory B cell repertoire and illustrate properties conferring robustness against emerging SARS-CoV-2 variants.

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Transplanted Long-Term Cultured Pre-Bi Cells Expressing Calpastatin Are Resistant to B Cell Receptor–Induced Apoptosis

Journal of Experimental Medicine ◽

10.1084/jem.194.3.247 ◽

2001 ◽

Vol 194 (3) ◽

pp. 247-254 ◽

Cited By ~ 15

Author(s):

Antonio Ruiz-Vela ◽

Fernando Serrano ◽

Manuel A. González ◽

José Luis Abad ◽

Antonio Bernad ◽

...

Keyword(s):

B Cells ◽

B Cell ◽

Cell Receptor ◽

B Cell Receptor ◽

Scid Mice ◽

Cell Repertoire ◽

Clonal Deletion ◽

B Cell Repertoire ◽

Induced Apoptosis

Long-term cultured pre-B cells are able to differentiate into immunoglobulin (Ig)M-positive B cells (IgM+ cells) when transplanted into severe combined immunodeficient (SCID) mice. Based on previous studies, here we report the development of a reconstitution assay in nonobese diabetic/SCID (NOD/SCID) mice using pre-B cells, which allows us to study the role of calpains (calcium-activated endopeptidases) during B cell development as well as in B cell clonal deletion. Using this model, we show that calpastatin (the natural inhibitor of calpains) inhibits B cell receptor–induced apoptosis in IgM+ cells derived from transplanted mice. We thus hypothesize an important function for calpain in sculpting the B cell repertoire.

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A public antibody class recognizes a novel S2 epitope exposed on open conformations of SARS-CoV-2 spike

10.1101/2021.12.01.470767 ◽

2021 ◽

Author(s):

Mathieu Claireaux ◽

Tom G Caniels ◽

Marlon de Gast ◽

Julianna Han ◽

Denise Guerra ◽

...

Keyword(s):

B Cells ◽

B Cell ◽

Cell Receptor ◽

Memory B Cells ◽

B Cell Receptor ◽

Cell Repertoire ◽

Fold Enrichment ◽

B Cell Repertoire ◽

High Fraction ◽

Antibody Class

AbstractDelineating the origins and properties of antibodies elicited by SARS-CoV-2 infection and vaccination is critical for understanding their benefits and potential shortcomings. Therefore, we investigated the SARS-CoV-2 spike (S)-reactive B cell repertoire in unexposed individuals by flow cytometry and single-cell sequencing. We found that ∼82% of SARS-CoV-2 S-reactive B cells show a naive phenotype, which represents an unusually high fraction of total human naive B cells (∼0.1%). Approximately 10% of these naive S-reactive B cells shared an IGHV1-69/IGKV3-11 B cell receptor pairing, an enrichment of 18-fold compared to the complete naive repertoire. A proportion of memory B cells, comprising switched (∼0.05%) and unswitched B cells (∼0.04%), was also reactive with S and some of these cells were reactive with ADAMTS13, which is associated with thrombotic thrombocytopenia. Following SARS-CoV-2 infection, we report an average 37-fold enrichment of IGHV1-69/IGKV3-11 B cell receptor pairing in the S-reactive memory B cells compared to the unselected memory repertoire. This class of B cells targets a previously undefined non-neutralizing epitope on the S2 subunit that becomes exposed on S proteins used in approved vaccines when they transition away from the native pre-fusion state because of instability. These findings can help guide the improvement of SARS-CoV-2 vaccines.

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Inferring processes underlying B-cell repertoire diversity

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2014.0243 ◽

2015 ◽

Vol 370 (1676) ◽

pp. 20140243 ◽

Cited By ~ 94

Author(s):

Yuval Elhanati ◽

Zachary Sethna ◽

Quentin Marcou ◽

Curtis G. Callan ◽

Thierry Mora ◽

...

Keyword(s):

B Cell ◽

Somatic Hypermutation ◽

Cell Receptor ◽

Statistical Properties ◽

Cell Repertoire ◽

Vdj Recombination ◽

Site Model ◽

Human B Cells ◽

B Cell Repertoire ◽

Repertoire Diversity

We quantify the VDJ recombination and somatic hypermutation processes in human B cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the statistical properties of the naive repertoire, first after its initial generation via VDJ recombination and then after selection for functionality. We also infer statistical properties of the somatic hypermutation machinery (exclusive of subsequent effects of selection). Our main results are the following: the B-cell repertoire is substantially more diverse than T-cell repertoires, owing to longer junctional insertions; sequences that pass initial selection are distinguished by having a higher probability of being generated in a VDJ recombination event; somatic hypermutations have a non-uniform distribution along the V gene that is well explained by an independent site model for the sequence context around the hypermutation site.

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Inferring processes underlying B-cell repertoire diversity.

10.1101/015115 ◽

2015 ◽

Cited By ~ 3

Author(s):

Yuval Elhanati ◽

Zachary Sethna ◽

Quentin Marcou ◽

Curtis G Callan ◽

Thierry Mora ◽

...

Keyword(s):

B Cell ◽

Somatic Hypermutation ◽

Cell Receptor ◽

Statistical Properties ◽

Cell Repertoire ◽

Vdj Recombination ◽

Site Model ◽

Human B Cells ◽

B Cell Repertoire ◽

Repertoire Diversity

We quantify the VDJ recombination and somatic hypermutation processes in human B-cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the statistical properties of the naive repertoire, first after its initial generation via VDJ recombination and then after selection for functionality. We also infer statistical properties of the somatic hypermutation machinery (exclusive of subsequent effects of selection). Our main results are the following: the B-cell repertoire is substantially more diverse than T-cell repertoires, due to longer junctional insertions; sequences that pass initial selection are distinguished by having a higher probability of being generated in a VDJ recombination event; somatic hypermutations have a non-uniform distribution along the V gene that is well explained by an independent site model for the sequence context around the hypermutation site.

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Identification of Variable and Joining germline genes and alleles for Rhesus macaque from B-cell receptor repertoires

10.1101/254599 ◽

2018 ◽

Cited By ~ 1

Author(s):

Wei Zhang ◽

Xinyue Li ◽

Longlong Wang ◽

Jianxiang Deng ◽

Liya Lin ◽

...

Keyword(s):

B Cell ◽

Rhesus Macaque ◽

Rhesus Macaques ◽

Cell Receptor ◽

B Cell Receptor ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Cell Repertoire ◽

Germline Genes ◽

Novel Alleles

AbstractThe Rhesus macaque is a valuable preclinical animal model to estimate vaccine effectiveness, and is also important for understanding antibody maturation and B-cell repertoire evolution responding to vaccination; however, incomplete mapping of rhesus immunoglobulin germline genes hinders the research efforts. To address this deficiency, we sequenced B-cell receptor (BCR) repertoires of 75 India Rhesus macaques. Using a bioinformatic method that has been validated with BCR repertoire analysis of three human donors, we were able to infer rhesus Variable (V) and Joint(J) germline alleles, identifying a total of 122 V and 20 J germline alleles. Importantly, 91 V and 13 J alleles were novel, and 40 V and 13 J genes were found at a novel genome region that has not been previously recorded. The novelty of these newly identified alleles was supported by two observations. Firstly, 50 V and 5 J novel alleles were observed in whole genome sequencing data of 10 Rhesus macaques. Secondly, using alignment reference including the novel alleles, the mutation rate of rearranged repertoires was significant declined in 9 other irrelevant samples, and all our identified novel V and J alleles were 100% identity mapped by rearranged repertoire data. These newly identified novel alleles, along with previous reported alleles, provide an important reference for future investigations of rhesus immune repertoire evolution, in response to vaccination or infection. In addition, the method outlined in our study offered an example to future efforts in identifying novel immunoglobulin alleles.

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A Novel Mechanism for B Cell Repertoire Maturation Based on Response by B Cell Precursors to Pre–B Receptor Assembly

Journal of Experimental Medicine ◽

10.1084/jem.187.2.259 ◽

1998 ◽

Vol 187 (2) ◽

pp. 259-264 ◽

Cited By ~ 84

Author(s):

R. Wasserman ◽

Y.-S. Li ◽

S.A. Shinton ◽

C.E. Carmack ◽

T. Manser ◽

...

Keyword(s):

B Cell ◽

Heavy Chain ◽

Light Chain ◽

Fetal Liver ◽

Cell Receptor ◽

Cell Repertoire ◽

Surrogate Light Chain ◽

B Cell Repertoire ◽

Cell Progression ◽

B Cell Precursors

The expression of different sets of immunoglobulin specificities by fetal and adult B lymphocytes is a long-standing puzzle in immunology. Recently it has become clear that production of immunoglobulin μ heavy chain and subsequent assembly with a surrogate light chain to form the pre-B cell receptor complex is critical for development of B cells. Here we show that instead of promoting pre–B cell progression as in adult bone marrow, this complex inhibits pre–B cell growth in fetal liver. Curiously, we identify a fetal-associated VH11 μ heavy chain that allows continued pre-B proliferation in fetal liver. Interestingly, this heavy chain does not associate efficiently with a surrogate light chain, providing a previously unrecognized mechanism for skewing the expression of distinctive VH genes toward fetal through early neonatal life.

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