High-resolution antibody dynamics of vaccine-induced immune responses

Abstract

The adaptive immune system confers protection by generating a diverse repertoire of antibody receptors that are rapidly expanded and contracted in response to specific targets. Next-generation DNA sequencing now provides the opportunity to survey this complex and vast repertoire. In the present work, we describe a set of tools for the analysis of antibody repertoires and their application to elucidating the dynamics of the response to viral vaccination in human volunteers. By analyzing data from 38 separate blood samples across 2 y, we found that the use of the germ-line library of V and J segments is conserved between individuals over time. Surprisingly, there appeared to be no correlation between the use level of a particular VJ combination and degree of expansion. We found the antibody RNA repertoire in each volunteer to be highly dynamic, with each individual displaying qualitatively different response dynamics. By using combinatorial phage display, we screened selected VH genes paired with their corresponding VL library for affinity against the vaccine antigens. Altogether, this work presents an additional set of tools for profiling the human antibody repertoire and demonstrates characterization of the fast repertoire dynamics through time in multiple individuals responding to an immune challenge.next-generation sequencing | influenza | immunology T he immune system is able to rapidly sense and respond to a vast array of invading organisms. Its arsenal contains systems that are immediately effective against commonly seen patterns (innate immunity) and systems that are capable of responding to novel invaders (adaptive immunity). Given the acute nature and diversity of infections, the immune system must be capable of rapid recognition of a pathogen, amplification of the response, and subsequent contraction of the response after the resolution of the infection. Adaptive immune responses rely on the continuous selection and amplification of specific clones from an enormous library of immune receptors (antibodies and T cell receptors). Specifically, stimulation of B-cell immunity results in the synthesis of antibodies that are secreted into the blood stream or into the mucosa as well as the programming of B memory cells that play a crucial role in the generation of rapid protective responses upon reinfection.Currently, many immunology studies depend on characterizing lymphocyte subsets (e.g., assaying cell-surface receptors) and the ability to correlate them to encoded genetic information (1). Recent advances in next-generation sequencing (NGS) (2) have enabled any DNA-encodable assay to produce massive amounts of data. Indeed, NGS has enabled unprecedented views into the immune repertoire, as its immune receptor diversity is genetically encoded within a complex collection of lymphocytes (3-8).The present study set out to dissect the rapid dynamics of the complete human peripheral antibody response against a controlled immune challenge (vaccination), without the a priori notion of cell state markers or functions...

The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales

“…(a) B-cell lineages in the blood contain both trunks and canopies B-cell repertoire sequencing data were obtained from blood samples of three healthy human donors [18]. As described in §4(a), these sequencing data were processed using the pRESTO pipeline [19] to generate high-quality Ig sequences, which were then submitted to IMGT/HighV-QUEST for germline V(D)J segment identification.…”

“…(a) Repertoire sequencing data B-cell repertoire sequencing data from blood samples of three healthy human donors was obtained from a previous study [18]. In the original publication, a time-series of samples before and after influenza vaccination were sequenced and IgA, IgG and IgM isotypes were identified based on the constant region of the sequences.…”

Automated analysis of high-throughput B-cell sequencing data reveals a high frequency of novel immunoglobulin V gene segment alleles

“…Samples coincide with those used by a previous study (25), and were originally collected and sequenced as part of two other studies (28,29). Sequencing results were preprocessed to remove low-quality reads, annotate and mask primers, assemble paired-end reads, and remove duplicate sequences using the Repertoire Sequencing Toolkit (pRESTO) (30) (clip.med.yale.edu/presto) as previously described (25).…”

“…Highthroughput sequencing of the Ig heavy chain was carried out from blood and tissue samples of seven subjects (Table 1). Three subjects (PGP1, hu420143, and 420IV) were part of an influenza vaccination study (28), and four subjects (M2, M3, M4, and M5) were part of a study on multiple sclerosis (29). One subject (PGP1) was sequenced both on the 454 GS FLX and Illumina MiSeq platforms.…”

Chemical Tools to Monitor and Manipulate the Adaptive Immune System

“…As mentioned above, there is significant interest in mining the adaptive immune response, and especially antibodies, for disease-specific biomarkers. Recently, advances have been made in methods to sort many thousands of individual B cells into small wells allowing native heavy and light pairing to be retained (Laserson et al, 2014; Tan et al, 2014). The CDR sequences of either the heavy or light chain, or both, of each BCR clone can then be determined by sequencing the corresponding cDNA (Georgiou et al, 2014).…”