Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements

Abstract

B cells produce a diverse antibody repertoire by undergoing gene rearrangements. Pathogen exposure induces the clonal expansion of B cells expressing antibodies that can bind the infectious agent. To assess human B cell responses to trivalent seasonal influenza and monovalent pandemic H1N1 vaccination, we sequenced gene rearrangements encoding the immunoglobulin heavy chain, a major determinant of epitope recognition. The magnitude of B cell clonal expansions correlates with an individual's secreted antibody response to the vaccine, and the expanded clones are enriched with those expressing influenza-specific monoclonal antibodies. Additionally, B cell responses to pandemic influenza H1N1 vaccination and infection in different people show a prominent family of convergent antibody heavy chain gene rearrangements specific to influenza antigens. These results indicate that microbes can induce specific signatures of immunoglobulin gene rearrangements and that pathogen exposure can potentially be assessed from B cell repertoires.

Figure 1. Quantitation of clonal B cells in the blood following vaccination predicts seroconversion

(A) Replicate IGH libraries were generated from peripheral blood B cells for 14 individuals (Table S1) at three time points: pre-vaccination (red arc), day 7 (green arc) and day 21 post-vaccination (purple arc). Replicates are shown as bands within each arc and lines connect clonally related VDJs from independent replicates. Detailed IGH repertoires for each individual are shown in Figure S1A. Figure S1B presents criteria for definition of clonal lineages. (B) Normalized clonality index scores; pre-vaccination (red), 7 days (green) and 21 days post-vaccination (purple). (C) Plasmablast percentages of total B cells (Table S3); pre-vaccination (red) and at days 7 (green) and 21 (purple) post-vaccination. (D) Correlation between metrics and serological antibody response.

Figure 2. Antigen specificity of vaccine-induced B cell clonal populations

(A) B cell lineages with members from mAbs derived from day 7 sorted plasmablasts (blue arc) and deep sequenced IGH from peripheral B cells prior to (red) and at days 7 (green) and 21 (purple) post TIV vaccination. Lines join lineage members. (B) Antigen binding of plasmablast-derived mAbs (Table S2); influenza antigen (green), unknown/untested (yellow), non-influenza antigen (red). Arcs are ‘zoomed’ to shared lineages. 7014 had no shared lineages.

Figure 3. Time course of B cell clonal expansions induced by inactivated H1N1 vaccine

(A) Vaccine induced B cell clonal lineage relationships during H1N1 vaccine response (complete IGH repertoires at Figure S2). Each arc represents a post-vaccination time point sub-divided into expanded (blue) and unexpanded (yellow) compartments. Lines join lineage members at later time points. Orange lines indicate that a lineage was strongly induced at the originating time point (> 0.1% of total IGH). (B) IGHV percentage mutation for strongly induced lineages. Median (red line), quartiles shown as box and whiskers and points are jittered to prevent over-plotting.

Figure 4. Convergent immunoglobulin heavy chain rearrangements identified in H1N1 vaccine responses in different individuals

Multiple sequence alignment of closely related stereotypic H1N1 clones isolated from difference sources. Nucleotide positions are labeled when they differ from the germline genes (top of each block). Nucleotides inferred to be derived from non-templated nucleotide addition during V(D)J rearrangement are not colored. Amino acids positions are labeled when they differ from those in the mAb (bottom of each block). Each block is labeled with the germline, the conserved sequence group (CSG) and the mAb. Members of CSGs are detailed in Table S4. (A) IGH related to 4K8 mAb isolated (Krause et al., 2011) (B) IGH related to 2K11 (Krause et al., 2011) (C) IGH related to CDR3s previously identified by Wrammert et al. (Wrammert et al., 2011). (D) The percentage of total sequences with CDR1 and CDR2 somatic mutation amino acid substitutions in convergent H1N1 clones (upper) compared to 4,784 IGH using IGHV3-7 from the pre-vaccination repertoire of 14 subjects pre-pandemic (lower). The germline sequence is depicted in the white boxes (middle). Asterisks (*) mark amino acid substitutions shared with mAbs 48K or 2K11 (Krause et al., 2011).