Memory B Cell Activation, Broad Anti-influenza Antibodies, and Bystander Activation Revealed by Single-Cell Transcriptomics

Felix Horns, Cornelia L Dekker, Stephen R Quake, Felix Horns, Cornelia L Dekker, Stephen R Quake

Abstract

Antibody memory protects humans from many diseases. Protective antibody memory responses require activation of transcriptional programs, cell proliferation, and production of antigen-specific antibodies, but how these aspects of the response are coordinated is poorly understood. We profile the molecular and cellular features of the antibody response to influenza vaccination by integrating single-cell transcriptomics, longitudinal antibody repertoire sequencing, and antibody binding measurements. Single-cell transcriptional profiling reveals a program of memory B cell activation characterized by CD11c and T-bet expression associated with clonal expansion and differentiation toward effector function. Vaccination elicits an antibody clone, which rapidly acquired broad high-affinity hemagglutinin binding during affinity maturation. Unexpectedly, many antibody clones elicited by vaccination do not bind vaccine, demonstrating non-specific activation of bystander antibodies by influenza vaccination. These results offer insight into how molecular recognition, transcriptional programs, and clonal proliferation are coordinated in the human B cell repertoire during memory recall.

Keywords: antibody repertoires; human antibody memory; infectious disease; influenza; single-cell transcriptomics; vaccination.

Conflict of interest statement

Declaration of Interests The authors declare no competing interests.

Copyright © 2019. Published by Elsevier Inc.

Figures

Figure 1.. Experimental Design and Workflow for…
Figure 1.. Experimental Design and Workflow for Studying B Cell Response to Influenza Vaccination Using Integrated Single-Cell and Antibody Repertoire Sequencing
(A) Study design. 2011–2012 seasonal trivalent influenza vaccine was administered, and peripheral blood samples were collected for analysis at the indicated days before and after vaccination. (B) Experiment workflow. Antibody heavy-chain repertoire sequencing (Rep-seq) was performed on samples from all time points. Single-cell transcriptional profiling and antibody heavy- and light-chain sequencing were performed on samples from d7 and d9 after vaccination.
Figure 2.. Clone Dynamics during B Cell…
Figure 2.. Clone Dynamics during B Cell Response to Influenza Vaccination
(A) Comparison of clonal abundance measurements across platforms, showing cells detected by single-cell sequencing and sequences detected by Rep-seq within each clone. Color indicates density of clones. ND, not detected. (B) Population dynamics of B cell clones. Each line represents a clone. Colored lines indicate vaccine-responsive clones (>50-fold expansion from D0 to D7 and >0.1% of repertoire at D7, as in Horns et al., 2019), according to the key in (C). Gray lines indicate non-vaccine-responsive clones. (C) Repertoire-wide distribution of the extent of clonal expansion after vaccination. Histogram shows the fold change from D0 to D7 of clones annotated as not vaccine responsive, which composed a substantial fraction of the repertoire at D7 (>0.1%) and had ≥1 cell detected by single-cell sequencing. Clones identified as vaccine responsive are indicated by markers (stars indicate vaccine binding, and circles indicate not vaccine binding). Dashed line shows the extent of expansion used as cutoff for identifying vaccine-responsive clones. Inf indicates undefined fold change arising because zero cells in the clone were detected at D0. D0, day of vaccination; D7, 7 days after vaccination; ND, not detected. See also Figure S1.
Figure 3.. Characterization of Gene Expression in…
Figure 3.. Characterization of Gene Expression in Single B Cells Isolated from Peripheral Blood after Influenza Vaccination
(A–C) Principal-component analysis and t-distributed stochastic neighbor embedding (tSNE) separates cells into distinct clusters. Each dot is a cell, colored by type or state revealed by gene expression profile (A), antibody isotype as revealed by single-cell antibody heavy-chain sequencing (B), or clonal population dynamics as revealed by Rep-seq (C). (D) Differential expression analysis identifies markers of distinct B cell states. Genes of immunological interest are labeled. (E–G) Gene expression distributions in distinct B cell states of established immune activation-related genes (E), transcription factors (F), and signaling receptors (G). See also Figure S2, Table S1, and Table S2.
Figure 4.. Binding of Influenza Vaccine-Responsive Antibodies…
Figure 4.. Binding of Influenza Vaccine-Responsive Antibodies to Vaccine
Binding of 21 monoclonal antibodies from 5 clones to the trivalent inactivated influenza vaccine from the 2011–2012 season was measured using enzyme-linked immunosorbent assay (ELISA), revealing that many vaccine-responsive antibodies do not bind vaccine. Ab, antibody; OD, optical density; hIgG1, human IgG1. See also Figure S3.
Figure 5.. Reconstructing Evolution of a Broadly…
Figure 5.. Reconstructing Evolution of a Broadly Binding High-Affinity Anti-influenza Antibody Clone
(A) Binding of antibodies from the L3 clone to a panel of influenza hemagglutinin (HA) variants was measured using ELISA. OD, optical density; hIgG1, human IgG1. (B) Evolutionary history of L3 depicted as a maximum-likelihood phylogeny based on heavy-chain sequence. Markers indicate antibodies detected by single-cell sequencing (N1–N7) or repertoire sequencing (R1–R7), or reconstructed ancestral sequences (germline and A1–A4). (C) Dissociation constants (KDs) of binding between L3 antibody variants and H1 (A/California/7/2009) and H3 (A/Perth/16/2009) hemagglutinin variants, as determined by biolayer interferometry. L3 antibodies include extant sequences (N1–N7), reconstructed ancestral sequences (germline and A1–A4), and engineered variants having the L3N6 sequences, but with heavy chain reverted to the inferred germline sequence (germline immunoglobulin heavy chain [IGH]), light chain reverted to the inferred germline sequence (germline immunoglobulin kappa chain [IGK]), or a light chain sequence substituted from a different clone (IGK swap). Jitter was added to germline and germline IGH to improve visualization of the data points. (D) Dissociation constants of binding between L3 antibodies compared with extent of somatic hypermutation. (E) Dissociation constants of binding between L3 antibodies and H1 variants from childhood (A/New Caledonia/20/1999) and adulthood (A/California/7/2009). Dashed line indicates equal KD for binding to both variants. Uncertainty of fitted parameters was smaller than the size of the markers used for plotting; therefore, error bars are not shown. See also Figure S4 and Figure S5.

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