High-throughput antibody sequencing reveals genetic evidence of global regulation of the naïve and memory repertoires that extends across individuals

Abstract

Vast diversity in the antibody repertoire is a key component of the adaptive immune response. This diversity is generated centrally through the assembly of variable, diversity and joining gene segments, and peripherally by somatic hypermutation and class-switch recombination. The peripheral diversification process is thought to only occur in response to antigenic stimulus, producing antigenselected memory B cells. Surprisingly, analyses of the variable, diversity and joining gene segments have revealed that the naïve and memory subsets are composed of similar proportions of these elements. Lacking, however, is a more detailed study, analyzing the repertoires of naïve and memory subsets at the level of the complete V(D)J recombinant. This report presents a thorough examination of V(D)J recombinants in the human peripheral blood repertoire, revealing surprisingly large repertoire differences between circulating B-cell subsets and providing genetic evidence for global control of repertoire diversity in naïve and memory circulating B-cell subsets.

Structures of Preferred Human IgV Genes–Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation

“…High-throughput Ab sequencing of naive versus IgM memory versus IgG memory repertoires revealed that IGHV3-30 and IGHV3-23 are the most commonly used heavy variable genes, both of which are dominant in the S. pneumoniae 23F human Ab response (10,48). Interestingly, IGHJ4 usage increased in memory subsets, and those containing IGHJ4 paired with IGHV3-30 found increased usage of IGHD3 family members, the same combination used in KE5.…”

Expression of Immunoglobulin Receptors with Distinctive Features Indicating Antigen Selection by Marginal Zone B Cells from Human Spleen

“…Selective antigenic pressures underlying the emergence of stereotyped gene rearrangements have been proposed both in zebra fish and humans (46,47). Furthermore, stereotyped B cell receptors (BCRs) are frequent in clones from different patients with chronic lymphocytic leukemia (CLL) (30,48,49) and also mantle cell lymphoma (MCL) (34) and splenic marginal zone lymphoma (SMZL) (32,50), suggesting stimulation/ selection by common antigens during lymphomagenesis.…”

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

“…For example, antigen experience has been reported to result in decreased length and hydrophobicity of the heavy-chain third complementarity-determining region (CDR-H3) and to alter CDR-H3 amino acid content relative to the naive repertoire (8,9). Analysis of the VH repertoire in identical twins provided evidence that germline gene use is genetically predetermined (10), but other studies demonstrated that VH gene use for a particular B-cell subset among different donors is more closely related than are different B-cell subsets within an individual (8,9,11). However, because of technical limitations (13), these and other studies were confined to analysis of the heavy and light chain repertoires separately.…”

“…Specifically, additional information is needed regarding how a history of pathogen and environmental exposure modulates the sequence and conformational properties of naive antibodies to yield a mature antibody repertoire that confers effective protection. High-throughput DNA sequencing of the heavy-chain variable (VH) gene repertoire from human donors has begun to delineate repertoire-wide differences among antibodies encoded by different B-cell subsets (8)(9)(10)(11)(12)(13)(14). For example, antigen experience has been reported to result in decreased length and hydrophobicity of the heavy-chain third complementarity-determining region (CDR-H3) and to alter CDR-H3 amino acid content relative to the naive repertoire (8, 9).…”