Third complementarity‐determining region of mutated V_H immunoglobulin genes contains shorter V, D, J, P, and N components than non‐mutated genes

Abstract

SUMMARYThe third complementarity-determining region (CDR3) of immunoglobulin variable genes for the heavy chain (V H ) has been shown to be shorter in length in hypermutated antibodies than in nonhypermutated antibodies. To determine which components of CDR3 contribute to the shorter length, and if there is an effect of age on the length, we analysed 235 cDNA clones from human peripheral blood of V H 6 genes rearranged to immunoglobulin M (IgM) constant genes. There was similar use of diversity (D) and joining (J H ) gene segments between clones from young and old donors, and there was similar use of D segments among the mutated and non-mutated heavy chains. However, in the mutated heavy chains, there was increased use of shorter J H 4 segments and decreased use of longer J H 6 segments compared to the non-mutated proteins. The overall length of CDR3 did not change with age within the mutated and non-mutated categories, but was signi®cantly shorter by three amino acids in the mutated clones compared to the non-mutated clones. Analyses of the individual components that comprise CDR3 indicated that they were all shorter in the mutated clones. Thus, there were more nucleotides deleted from the ends of V H , D, and J H gene segments, and fewer P and N nucleotides added. The results suggest that B cells bearing immunoglobulin receptors with shorter CDR3s have been selected for binding to antigen. A smaller CDR3 may allow room in the antibody binding pocket for antigen to interact with CDRs 1 and 2 as well, so that as the VDJ gene undergoes hypermutation, substitutions in all three CDRs can further contribute to the binding energy.

Immunoglobulin Heavy- And Light-chain Repertoire in Splenic Marginal Zone Lymphoma

“…Analysis of the HCDR3 region was possible in 44/46 rearrangements and revealed that SMZL-HCDR3 composition was comparable to normal PB IgM+ B cells in length (median: 17 aminoacids, range: 8-35), number of Nnucleotides and 5′ and 3′ exonuclease activity at, respectively, the V and J genes. Similar to normal B cells (29), longer HCDR3 regions were observed in SMZL cases with unmutated sequences. The distribution of IGHJ genes was similar to that reported for normal B cells (30): IGHJ4 was the most frequent gene followed by IGHJ6 (23 and 11 sequences, respectively).…”

Evidence for preferential Ig gene usage and differential TdT and exonuclease activities in human naïve and memory B cells

“…Rosner et al reported shorter CDR3 regions in mutated V H 6 genes rearranged to IgM constant genes when compare to un-mutated ones (Rosner et al, 2001). That study found the CDR3 region of mutated genes contained shorter V, D, J, P and N components than non-mutated genes and hypothesized that B cells bearing Ig molecules with shorter CDR3s have been selected for binding to antigen.…”

Characterization of the Human Ig Heavy Chain Antigen Binding Complementarity Determining Region 3 Using a Newly Developed Software Algorithm, JOINSOLVER

“…Different levels of stringency have been applied in the identification of D segments (8,21,25,26). More strict criteria may increase specificity, but at the expense of sensitivity, whereas less strict criteria may do the reverse.…”

“…This is particularly important because it has been claimed in the mouse that the use of inverted D segments and DD fusions predispose to autoantibody formation (9,13). Indeed, even the definition of the D segment is controversial, with some analyses using shorter consecutive nucleotide matches (8,(22)(23)(24)(25)(26), or allowing one mismatch (8,25,26), and others defining the D segment only when a match of 10 consecutive nucleotides is present (20).…”