Molecular-level analysis of the serum antibody repertoire in young adults before and after seasonal influenza vaccination.

Lee J¹, Boutz DR², Chromikova V³, Joyce MG⁴, Vollmers C⁵, Leung K⁴, Horton AP², DeKosky BJ¹, Lee CH¹, Lavinder JJ¹, Murrin EM¹, Chrysostomou C¹, Hoi KH⁶, Tsybovsky Y⁷, Thomas PV⁴, Druz A⁴, Zhang B⁴, Zhang Y⁴, Wang L⁴, Kong WP⁴, Park D¹, Popova LI⁸, Dekker CL⁹, Davis MM^10,¹¹, Carter CE¹², Ross TM¹², Ellington AD^2,¹³, Wilson PC⁸, Marcotte EM^2,¹³, Mascola JR⁴, Ippolito GC¹³, Krammer F³, Quake SR^5,^10,¹⁴, Kwong PD⁴, Georgiou G^1,^2,^6,¹³.

Author information

1: Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA.
2: Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA.
3: Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
4: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, Maryland, USA.
5: Department of Bioengineering, Stanford University, Stanford, California, USA.
6: Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA.
7: Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.
8: Department of Medicine, Section of Rheumatology, Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA.
9: Department of Pediatrics, Stanford University, Stanford, California, USA.
10: Howard Hughes Medical Institute, Stanford University, Stanford, California, USA.
11: Department of Microbiology and Immunology, Stanford University, Stanford, California, USA.
12: Center for Vaccines and Immunology, Department of Infectious Diseases, University of Georgia, Athens, Georgia, USA.
13: Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.
14: Department of Applied Physics, Stanford University, Stanford, California, USA.

Abstract

Molecular understanding of serological immunity to influenza has been confounded by the complexity of the polyclonal antibody response in humans. Here we used high-resolution proteomics analysis of immunoglobulin (referred to as Ig-seq) coupled with high-throughput sequencing of transcripts encoding B cell receptors (BCR-seq) to quantitatively determine the antibody repertoire at the individual clonotype level in the sera of young adults before and after vaccination with trivalent seasonal influenza vaccine. The serum repertoire comprised between 40 and 147 clonotypes that were specific to each of the three monovalent components of the trivalent influenza vaccine, with boosted pre-existing clonotypes accounting for ∼60% of the response. An unexpectedly high fraction of serum antibodies recognized both the H1 and H3 monovalent vaccines. Recombinant versions of these H1 + H3 cross-reactive antibodies showed broad binding to hemagglutinins (HAs) from previously circulating virus strains; several of these antibodies, which were prevalent in the serum of multiple donors, recognized the same conserved epitope in the HA head domain. Although the HA-head-specific H1 + H3 antibodies did not show neutralization activity in vitro, they protected mice against infection with the H1N1 and H3N2 virus strains when administered before or after challenge. Collectively, our data reveal unanticipated insights regarding the serological response to influenza vaccination and raise questions about the added benefits of using a quadrivalent vaccine instead of a trivalent vaccine.

Comment in

Understanding immune responses to the influenza vaccine. [Nat Med. 2016]

PMID:: 27820605
PMCID:: PMC5301914
DOI:: 10.1038/nm.4224

[Indexed for MEDLINE]

Free PMC Article

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Figure 1

Delineation of the serological repertoire to IIV3. (a) Experimental design. For the sequencing of B cell receptor (BCR)-encoding transcripts (BCR-seq), we used peripheral B cells isolated 7 d after vaccination to sequence the V_H repertoires for constructing custom databases of each donor for heavy chain peptide identification and the paired heavy and light chain (V_H:V_L) repertoire for acquiring the endogenous light-chain information for the heavy chains. From sera of the donors, antibodies specific to each IIV1 were isolated through IIV1-immobilized column purification, and the purified immunoglobulins were subsequently analyzed proteomically (Ig-seq). Representative serum antibodies were recombinantly expressed for characterization. (b) Representative serological repertoire (rep.) (of n = 36 that we analyzed) (donor 1, day 28 anti–H1 A/CA09). Each bar represents a unique clonotype, and the y axis indicates the relative abundance (fraction), as determined by proteomic analysis. (c) Heat maps of the relative amounts of antibody clonotypes (each column indicates distinct clonotype) comprising the serological repertoire to each IIV1 at different time points for donor 1. The amount of each clonotype is determined by multiplying its relative abundance by the serum titer for that sample. Relative amounts are determined by normalizing the amounts to day 28 serum titers (Online Methods). Similar analyses were done for all of the donors (n = 4). (d) Predominance of pre-existing antibody clonotypes (Abs) in serum after vaccination. Each data point (see key) corresponds to the fraction of pre-existing Abs in the serological repertoire to an IIV1 for a specific donor. Averages are calculated as mean, with error-bars indicating s.e.m. (n = 12 for each group). Vic, Victoria. (e) Correlation between ELISA serum titer to IIV1 and the number of clonotypes in the respective serum repertoires. Each data point corresponds to titers and the number of clonotypes in the serological repertoire specific to an IIV1 for a donor at each time point (n = 36). (f) Inverse correlation between pre-vaccination ELISA serum titers and the frequency of vaccine-elicited clonotypes at day 28. Frequency is calculated as the number of vaccine-elicited clonotypes divided by the total number of unique clonotypes at day 28. For e,f, statistical analyses were performed using two-sided nonparametric Spearman rank correlation test.