GENE CONVERSION CONTRIBUTES TO HUMAN ANTIBODY DIVERSITY. ♦ 61

The naïve antibody/B-cell receptor (BCR) repertoires of different individuals ought to exhibit significant functional commonality, given that most pathogens trigger an effective antibody response to immunodominant epitopes. Sequence-based repertoire analysis has so far offered little evidence for this phenomenon. For example, a recent study estimated the number of shared (‘public’) antibody clonotypes in circulating baseline repertoires to be around 0.02% across ten unrelated individuals. However, to engage the same epitope, antibodies only require a similar binding site structure and the presence of key paratope interactions, which can occur even when their sequences are dissimilar. Here, we search for evidence of geometric similarity/convergence across human antibody repertoires. We first structurally profile naïve (‘baseline’) antibody diversity using snapshots from 41 unrelated individuals, predicting all modellable distinct structures within each repertoire. This analysis uncovers a high (much greater than random) degree of structural commonality. For instance, around 3% of distinct structures are common to the ten most diverse individual samples (‘Public Baseline’ structures). Our approach is the first computational method to find levels of BCR commonality commensurate with epitope immunodominance and could therefore be harnessed to find more genetically distant antibodies with same-epitope complementarity. We then apply the same structural profiling approach to repertoire snapshots from three individuals before and after flu vaccination, detecting a convergent structural drift indicative of recognising similar epitopes (‘Public Response’ structures). We show that Antibody Model Libraries derived from Public Baseline and Public Response structures represent a powerful geometric basis set of low-immunogenicity candidates exploitable for general or target-focused therapeutic antibody screening.

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Gene Conversion of Sialic Acid Binding Domains in CD33-Related Siglecs by Adjacent Pseudogenes: A Novel Mechanism To Change Sialic Acid Binding Specificity.

Blood ◽

10.1182/blood.v104.11.1471.1471 ◽

2004 ◽

Vol 104 (11) ◽

pp. 1471-1471

Author(s):

Toshiyuki Hayakawa ◽

Takashi Angata ◽

Elliott H. Margulies ◽

Tarjei Mikkelsen ◽

Eric D. Green ◽

...

Keyword(s):

Immune Response ◽

Sialic Acid ◽

Gene Conversion ◽

Gene Cluster ◽

Innate Immune Response ◽

Binding Specificity ◽

Sialic Acids ◽

Innate Immune ◽

Antibody Diversity ◽

Sialic Acid Binding

Abstract Siglecs (sialic acid-binding immunoglobulin superfamily lectins) are a family of cell surface receptors involved in regulating the immune response. The CD33-Related Siglecs (CD33rSiglecs, namely Siglec-3, -5 through -11 and -XII in humans) are a subgroup of these molecules found primarily on cells of the innate immune system. All are type-1 transmembrane proteins with an N-terminal sialic acid-recognizing V-set domain followed by a variable number of C-2 set domains, a transmembrane region and a cytosolic C-terminal domain that includes two tyrosine-based signaling motifs. Available data suggest an inhibitory signaling role in the innate immune response, mediated by recognition of host sialic acids as “self”. Nine of the 13 known primate Siglec genes along with 14 Siglec pseudogenes comprise the CD33-related Siglec gene cluster on human chromosome 19. Gene conversion is a mechanism for copying part of a genomic sequence into another, contributing to genetic diversity. Pseudogenes are known to play role in generating functional diversity of related genes (e.g., antibody diversity via gene conversion in chickens). We recently analyzed genomic sequences of the CD33-related Siglec gene cluster in three primates (human, chimpanzee and baboon) and found evidence for rapid evolution in this gene family (Angata et al., PNAS, in press). Additional evolutionary studies using distance-based phylogenetic trees shows evidence for three partial gene conversions between Siglec genes and adjacent Siglec pseudogenes. All three involve the coding regions for extracellular domains that mediate sialic acid recognition, and two involve a pseudogene converting a known Siglec gene. Functional analyses using recombinant proteins show marked differences in sialic acid-binding properties between the converted Siglec and its non-converted ortholog. These findings suggest that gene conversion with pseudogenes has contributed to the rapid functional evolution of the Siglecs, and provides a novel mechanism for changing sialic acid binding specificity. We hypothesize that this mechanism allows for rapid evolutionary adjustments in the recognition of endogenous sialic acids as “self”, a potential factor in controlling the innate immune response.

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Germ line maintenance of the pseudogene donor pool for somatic immunoglobulin gene conversion in chickens.

Molecular and Cellular Biology ◽

10.1128/mcb.13.2.821 ◽

1993 ◽

Vol 13 (2) ◽

pp. 821-830 ◽

Cited By ~ 26

Author(s):

W T McCormack ◽

E A Hurley ◽

C B Thompson

Keyword(s):

Gene Conversion ◽

Light Chain ◽

Germ Line ◽

Sequence Information ◽

Immunoglobulin Gene ◽

Donor Pool ◽

Region Gene ◽

Antibody Diversity ◽

Meiotic Gene ◽

V Gene

Somatic immunoglobulin diversity is generated in avian species by sequential gene conversion of variable (V) gene segments of the immunoglobulin heavy- and light-chain loci during B-cell development. The germ line pools of donor sequence information for somatic V-region gene conversion are found in families of V pseudogenes, located 5' of the single functional V gene of each locus. The sequence relationships among the pseudogenes (psi VL) and functional VL1 gene of the chicken light-chain alleles in three inbred strains were compared to determine the extent of diversity within the germ line pseudogene cluster. Numerous differences were observed. For example, compared with the previously reported CB allele and the G4 allele, the S3 allele contains two intact pseudogenes between psi VL16 and psi VL18. These two adjacent psi VL gene segments (psi VL17a and psi VL17b) could have given rise to the psi VL17 segment of the G4 and CB alleles by homologous recombination. The majority of other sequence polymorphisms among the psi VL alleles appear to be the result of meiotic gene conversion. The incidence of untemplated mutations within psi VL segments is significantly lower than the incidence of mutation within the pseudogene flanking regions. Together with the observations that most psi VL segments have open reading frames and lack stop codons, these data support the hypothesis that the psi VL cluster resembles a functional multigene family maintained by evolutionary selection for its functional role in generating somatic antibody diversity. Meiotic gene conversion events within the psi VL cluster serve both to introduce diversity by the exchange of short segments between family members and to prevent the accumulation of random mutations.

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Germ line maintenance of the pseudogene donor pool for somatic immunoglobulin gene conversion in chickens

Molecular and Cellular Biology ◽

10.1128/mcb.13.2.821-830.1993 ◽

1993 ◽

Vol 13 (2) ◽

pp. 821-830

Author(s):

W T McCormack ◽

E A Hurley ◽

C B Thompson

Keyword(s):

Gene Conversion ◽

Light Chain ◽

Germ Line ◽

Sequence Information ◽

Immunoglobulin Gene ◽

Donor Pool ◽

Region Gene ◽

Antibody Diversity ◽

Meiotic Gene ◽

V Gene

Somatic immunoglobulin diversity is generated in avian species by sequential gene conversion of variable (V) gene segments of the immunoglobulin heavy- and light-chain loci during B-cell development. The germ line pools of donor sequence information for somatic V-region gene conversion are found in families of V pseudogenes, located 5' of the single functional V gene of each locus. The sequence relationships among the pseudogenes (psi VL) and functional VL1 gene of the chicken light-chain alleles in three inbred strains were compared to determine the extent of diversity within the germ line pseudogene cluster. Numerous differences were observed. For example, compared with the previously reported CB allele and the G4 allele, the S3 allele contains two intact pseudogenes between psi VL16 and psi VL18. These two adjacent psi VL gene segments (psi VL17a and psi VL17b) could have given rise to the psi VL17 segment of the G4 and CB alleles by homologous recombination. The majority of other sequence polymorphisms among the psi VL alleles appear to be the result of meiotic gene conversion. The incidence of untemplated mutations within psi VL segments is significantly lower than the incidence of mutation within the pseudogene flanking regions. Together with the observations that most psi VL segments have open reading frames and lack stop codons, these data support the hypothesis that the psi VL cluster resembles a functional multigene family maintained by evolutionary selection for its functional role in generating somatic antibody diversity. Meiotic gene conversion events within the psi VL cluster serve both to introduce diversity by the exchange of short segments between family members and to prevent the accumulation of random mutations.

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Evidence of Antibody Repertoire Functional Convergence through Public Baseline and Shared Response Structures

10.1101/2020.03.17.993444 ◽

2020 ◽

Cited By ~ 2

Author(s):

Matthew I. J. Raybould ◽

Claire Marks ◽

Aleksandr Kovaltsuk ◽

Alan P. Lewis ◽

Jiye Shi ◽

...

Keyword(s):

Computational Method ◽

Basis Set ◽

Human Antibody ◽

Base Line ◽

Antibody Diversity ◽

Public Response ◽

Flu Vaccination ◽

Functional Convergence ◽

Before And After ◽

Antibody Repertoires

The antibody repertoires of different individuals ought to exhibit significant functional commonality, given that most pathogens trigger a successful immune response in most people. Sequence-based approaches have so far offered little evidence for this phenomenon. For example, a recent study estimated the number of shared (‘public’) antibody clonotypes in circulating baseline repertoires to be around 0.02% across ten unrelated individuals. However, to engage the same epitope, antibodies only require a similar binding site structure and the presence of key paratope interactions, which can occur even when their sequences are dissimilar. Here, we investigate functional convergence in human antibody repertoires by comparing the anti-body structures they contain. We first structurally profile base-line antibody diversity (using snapshots from 41 unrelated individuals), predicting all modellable distinct structures within each repertoire. This analysis uncovers a high (much greater than random) degree of structural commonality. For instance, around 3% of distinct structures are common to the ten most diverse individual samples (‘Public Baseline’ structures). Our approach is the first computational method to provide support for the long-assumed levels of baseline repertoire functional commonality. We then apply the same structural profiling approach to repertoire snapshots from three individuals before and after flu vaccination, detecting a convergent structural drift indicative of recognising similar epitopes (‘Public Response’ structures). Antibody Model Libraries derived from Public Baseline and Public Response structures represent a powerful geometric basis set of low-immunogenicity candidates exploitable for general or target-focused therapeutic antibody screening.

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Human antibody diversity

Immunotechnology ◽

10.1016/s1380-2933(97)88968-3 ◽

1996 ◽

Vol 2 (4) ◽

pp. 263

Keyword(s):

Human Antibody ◽

Antibody Diversity

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Probing Human Antibody Diversity in HIV Infection

Idiotypes in Medicine: Autoimmunity, Infection and Cancer ◽

10.1016/b978-044482807-1/50028-4 ◽

1997 ◽

pp. 293-301

Author(s):

Saoussen Karray ◽

Moncef Zouali

Keyword(s):

Hiv Infection ◽

Human Antibody ◽

Antibody Diversity

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Heavy Chain CDR 3 and Junctional Length Biases in Human Antibody Repertoires Associated with Heavy and Light Chain Germline Utilization

10.1101/664714 ◽

2019 ◽

Author(s):

Kannan Sankar ◽

Kam Hon Hoi ◽

Isidro Hötzel

Keyword(s):

B Cell ◽

Heavy Chain ◽

Length Distribution ◽

Sequence Diversity ◽

Segment Length ◽

Human Antibody ◽

Antibody Diversity ◽

Nucleotide Insertion ◽

Antibody Repertoires ◽

Selection Of

AbstractAntibody variable domain sequence diversity is generated by recombination of germline segments. The third complementarity-determining region of the heavy chain (CDR H3) is the region of highest sequence diversity and is formed by the joining of heavy chain VH, DH and JH germline segments combined with random nucleotide trimming and additions between these segments. We show that CDR H3 length distribution is biased in human antibody repertoires as a function of VH, VL and JH germline segment utilization. Most length biases are apparent in the naïve B cell compartment, with a significant bias towards shorter CDR H3 sequences observed in association with a subset of VH and VL germlines in the antigen experienced compartment. Similar biases were not observed in nonproductive heavy chain recombination products, indicating selection of the repertoire during B cell maturation as a major driver of the length biases. Some VH-associated CDR H3 length biases are dependent on utilization of specific JH germline segments in a manner not directly linked to JH segment length in the germline, but are rather associated with selection of differentially trimmed JH segments in the naïve compartment. In addition, DH segment and N-region random nucleotide insertion lengths within CDR H3 in the naïve compartment were also biased by specific VH/JH germline combinations, indicating a complex set of constraints between germline segments selected during repertoire maturation. Our findings reveal biases in the antibody diversity landscape shaped by VH, VL, and JH germline features with implications for mechanisms of naïve and immune repertoire selection.

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