High-Resolution Description of Antibody Heavy-Chain Repertoires in Humans

Ramy Arnaout,Sergei B Koralov,Chad Nusbaum,William Lee,Patrick Cahill,Tracey Honan,Klaus Rajewsky,Todd Sparrow,Michael Weiand,Markus Reindl

doi:10.1371/journal.pone.0022365

Ramy Arnaout, Sergei B Koralov + Show 8 more

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https://doi.org/10.1371/journal.pone.0022365

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Abstract

Antibodies' protective, pathological, and therapeutic properties result from their considerable diversity. This diversity is almost limitless in potential, but actual diversity is still poorly understood. Here we use deep sequencing to characterize the diversity of the heavy-chain CDR3 region, the most important contributor to antibody binding specificity, and the constituent V, D, and J segments that comprise it. We find that, during the stepwise D-J and then V-DJ recombination events, the choice of D and J segments exert some bias on each other; however, we find the choice of the V segment is essentially independent of both. V, D, and J segments are utilized with different frequencies, resulting in a highly skewed representation of VDJ combinations in the repertoire. Nevertheless, the pattern of segment usage was almost identical between two different individuals. The pattern of V, D, and J segment usage and recombination was insufficient to explain overlap that was observed between the two individuals' CDR3 repertoires. Finally, we find that while there are a near-infinite number of heavy-chain CDR3s in principle, there are about 3–9 million in the blood of an adult human being.

Highlights

The human adaptive immune system consists of B cells, which secrete antibodies, and T cells, which target infected or otherwise aberrant cells through their T cell receptors (TCRs)
The specificity of adaptive immune responses is encoded in the sequences of recombined antibody and TCR genes
Since the first studies on mice over two decades ago [23,31,46], a central question has been how similar are immune responses between different individuals. This is related to another long-standing question: what is the actual—as opposed to the potential or theoretical [7]—diversity of the adaptive immune response in humans? The answers bear on the feasibility of developing sequenced-based diagnostics to monitor specific immune responses in vaccination, infection, cancer, and autoimmunity, and the general state of the immune system in immunodeficiency states like immunosuppression and aging

Summary

Introduction

The human adaptive immune system consists of B cells, which secrete antibodies, and T cells, which target infected or otherwise aberrant cells through their T cell receptors (TCRs) Both cell types have been of longstanding interest for their roles in vaccines, infections, and autoimmune diseases, as well as cancer [1,2]. The sequence from the V-D to the D-J junction, spanning the entire D segment, is called complementarity determining region (CDR) 3 and encodes part of the heavy chain that makes physical contact with the antigen. It is the single most important determinant of an antibody’s antigen specificity [5,6]. Detailed descriptions of CDR3 diversity are a prerequisite for understanding antibody responses to vaccines and infections and in autoimmunity in fine detail—the level of detail required for rational approaches to development of the generation of diagnostics and therapeutics [1,2]

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