Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies

Goldstein, Leonard D.; Chen, Ying-Jiun J.; Wu, Jing; Chaudhuri, Subhra; Hsiao, Yi-Chun; Schneider, Kellen; Hoi, Kam Hon; Lin, Zhonghua; Guerrero, Steve; Jaiswal, Bijay S.; Stinson, Jeremy; Antony, Aju; Pahuja, Kanika Bajaj; Seshasayee, Dhaya; Modrušan, Zora; Hötzel, Isidro; Seshagiri, Somasekar

doi:10.1038/s42003-019-0551-y

Cited by 126 publications

(95 citation statements)

References 32 publications

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“…In this work we considered only the three CDRs encoded by heavy chain genes. However, the light chain also plays an important role in shaping the BCR paratope [31]. Therefore, it is anticipated that the diversity of light chain CDR configurations would also change along the B-cell differentiation axis.…”

Section: Discussionmentioning

confidence: 99%

Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice

et al. 2020

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Most current analysis tools for antibody next-generation sequencing data work with primary sequence descriptors, leaving accompanying structural information unharnessed. We have used novel rapid methods to structurally characterize the complementary-determining regions (CDRs) of more than 180 million human and mouse B-cell receptor (BCR) repertoire sequences. These structurally annotated CDRs provide unprecedented insights into both the structural predetermination and dynamics of the adaptive immune response. We show that B-cell types can be distinguished based solely on these structural properties. Antigenunexperienced BCR repertoires use the highest number and diversity of CDR structures and these patterns of naïve repertoire paratope usage are highly conserved across subjects. In contrast, more differentiated B-cells are more personalized in terms of CDR structure usage. Our results establish the CDR structure differences in BCR repertoires and have applications for many fields including immunodiagnostics, phage display library generation, and "humanness" assessment of BCR repertoires from transgenic animals. The software tool for structural annotation of BCR repertoires, SAAB+, is available at https://github. com/oxpig/saab_plus.

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Section: Discussionmentioning

confidence: 99%

Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice

et al. 2020

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“…However, the native pairing information of heavy and light chains is essential to fully describe an individual antibody, e.g., for recombinant expression. Although pairing information can be restored to some extent from bulk analyses (i.e., by bioinformatic approaches) [56], the most robust way to achieve these information is either by single cell sorting into multi-well plates [57][58][59][60] or by co-encapsulation of single cells and RNA-capture or barcode beads (e.g., with the 10× Genomics chromium system) in picoliter droplets [23,24,[61][62][63][64][65] (Figure 3, second row). Single cell sorting into multiwell plates is typically limited in throughput to tens of thousands of cells, whereas encapsulation systems allow throughputs of hundreds of thousands of cells.…”

Section: Pairing Of Heavy and Light Chainsmentioning

confidence: 99%

Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies

et al. 2020

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The human antibody repertoire is generated by the recombination of different gene segments as well as by processes of somatic mutation. Together these mechanisms result in a tremendous diversity of antibodies that are able to combat various pathogens including viruses and bacteria, or malignant cells. In this review, we summarize the opportunities and challenges that are associated with the analyses of the B cell receptor repertoire and the antigen-specific B cell response. We will discuss how recent advances have increased our understanding of the antibody response and how repertoire analyses can be exploited to inform on vaccine strategies, particularly against HIV-1.Antibodies are composed of heavy and light chains, both of which are divided into a constant and a variable region ( Figure 1a). The different isotypes for the heavy chain constant regions mediate different effector functions and are grouped into the classes IgM, IgD, and IgE [3]. The variable regions of heavy and light chains form the paratope that contacts the epitope on a particular antigen (e.g., on a bacterial or viral surface protein). Two essential steps act during the lifespan of a B cell to generate B cell receptor diversity: (i) the V(D)J recombination process that builds the naïve (i.e., antigen-inexperienced) B cell repertoire, and (ii) somatic hypermutation (SHM) during the process of affinity maturation that generates high affinity B cell receptors and antibodies (i.e., the antigen-experienced repertoire).lifespan of a B cell to generate B cell receptor diversity: i.) the V(D)J recombination process that 52 builds the naïve (i.e., antigen-inexperienced) B cell repertoire, and ii.) somatic hypermutation (SHM) 53 during the process of affinity maturation that generates high affinity B cell receptors and antibodies 54 (i.e., the antigen-experienced repertoire). 55The initial diversity of the B cell repertoire results from the assembly of the B cell receptor 56 during early B cell development in the bone marrow. The recombination-activating gene (RAG) 1/2 57 enzymes recombine variable (V), diversity (D), and joining (J) gene segments of the immunoglobulin 58 heavy (IgH) chain locus to first assemble the heavy chain variable region, followed by V and J gene 59 segment recombination within the Ig kappa (IgK) and Ig lambda (IgL) loci [4]. Junctional diversity is 60 further increased by RAG1/2 and other enzymes through the generation of palindromic (P) 61 nucleotides, as well as by the terminal deoxynuclotidyl transferase (TdT) through the addition of 62 non-template (N) nucleotides [5] (Figure 1b). Heavy and light chain V genes exclusively encode for 63 two complementarity determining regions (CDR1 and CDR2) that are usually structurally exposed 64 at the tip of the antibody and contribute to antigen recognition. A third CDR (CDR3) is generated by 65 the V(D)J recombination process and is the most variable part within B cell receptors and antibodies. 66The CDRs are interspersed and flanked with framework regions (FWR) that mainly function a...

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“…Enriched S protein speci c B cells were individually co-compartmentalized in droplets with single barcoded hydrogel beads and lysis and reverse transcription reagents using a micro uidic device as described 15 . Droplets of ~1 nL volume were formed at 250 s-1.…”

Section: Single-cell Bcr Sequencingmentioning

confidence: 99%

“…Nevertheless, this method is con ned by the limited throughput. The advent of high throughput single cell sequencing technology demonstrated the potential for obtaining VH-VL pairing information in a high-throughput manner 15,16 . The latest generation of single cell RNA sequencing barcoding technologies developed by companies using droplets (such as 10×Genomics or BioRad) or micro uidics arrays (such as BD Rhapsody or Singleron) can be utilized to identify V gene sequences of a cohort of sorted B cells such as selected B cells using FACS.…”

Section: Introductionmentioning

confidence: 99%

Profiling B cell immune responses to identify neutralizing antibodies from convalescent COVID-19 patients

Huang

Shen²,

Guo

et al. 2020

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The pandemic Coronavirus Disease 2019 (COVID-19) causes noticeable morbidity and mortality worldwide. In addition to vaccine and antiviral drug therapy, the use of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) neutralizing antibodies for treatment purposes is a viable alternative. In this study, we aimed to profile the humoral responses and identify neutralizing antibodies against SARS-CoV-2 using high-throughput single-cell sequencing that tailored to B cell receptor sequencing. From two convalescent patients with high serum titer against SARS-COV-2, we identified seven antibodies specifically binding to SARS-CoV-2. Among these, the most potent antibody, P4A1 was demonstrated to block the binding of spike protein to its receptor angiotensin-converting enzyme 2 (ACE2), and prevent the viral infection in neutralization assays with pseudovirus as well as live virus at nM to sub-nM range. Moreover, antibody P4A1 can also bind strongly to spike protein with N354D/D364Y, R408I, W436R, V367F or D614G mutations respectively, suggesting that the antibody alone or in combination with other antibodies that recognize different variations of SARS-CoV-2, may provide a broad spectrum therapeutic option for COVID-19 patients. Authors Lisu Huang, Bingqing Shen, Yu Guo, and Shu Shen contributed equally to this work.

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Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies

Cited by 126 publications

References 32 publications

Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice

Structural diversity of B-cell receptor repertoires along the B-cell differentiation axis in humans and mice

Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies

Profiling B cell immune responses to identify neutralizing antibodies from convalescent COVID-19 patients

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