Bias in somatic hypermutation of human V_H genes

Abstract

Translationally silent mutations, which are not antigen selected, of human VH6 Ig gene rearrangements isolated from human spleen were analyzed for bias to gain insight into intrinsic features of the mutation process. Sixty-three clones representing 38 VH6DJ rearrangements had an overall mutation frequency of 4.5%, a replacement/silent (R/S) mutation ratio of 2.1 and 167 unique silent mutations. The silent mutations showed bias in: (i) targeting to CDR1 and CDR2, (ii) an increased frequency of mutations of A compared to T nucleotide bases on the coding strand, and (iii) an increased frequency of transitions versus transversions. Bias of C-->G over C-->A, of G-->C over G-->T and of A-->C over A-->T transversions was also present. Hot spots of mutation were observed, some which corresponded to potential sites of stem-loop formation. The results suggest that the somatic mutation process in man may be targeted to the complementarity determining region for some V genes, exhibits specific base substitutions favoring transitions and specific types of transversions, and may be occurring on only one DNA strand.

Novel Substitution Polymorphisms of Human Immunoglobulin VH Genes in Mexicans

“…The conservation observed herein is consistent with previous reports because this gene has generally been described as demonstrating little polymorphism [50 -52] and few mutations (the only mutation observed in the only allele reported is of the silent type) [53]. Furthermore, this conservation occurs not only at the germline level but also at the somatic level [2,6,54,55]. The importance of this gene for the repertoire [14, 56 -59] and its marked conservation make it possible to consider the presence of dynamic and evolutionary forces acting to maintain the structural and functional characteristics of this gene.…”

Functional Analysis of the Anti-adalimumab Response Using Patient-derived Monoclonal Antibodies

“…R and S mutation frequencies for the framework regions and CDR1 and CDR2 regions were analyzed (Fig. 1B) and indicate an antigen-driven affinity maturation (19), which was confirmed using the Focused test (20); mean R/S ratios are 1.7 and 1.5 for the framework regions of VH and VL, and 8.0 and 4.6 for CDRs of VH and VL, respectively. We were able to express 11 of the above-described monoclonal antibodies in HEK293 cells in large enough quantities to investigate their binding affinity and specificity.…”

The normally expressed κ immunoglobulin light chain gene repertoire and somatic mutations studied by single-sided specific polymerase chain reaction (PCR); frequent occurrence of features often assigned to autoimmunity

“…Of the 69 nucleotides, 22 were guanines, 24 cytosines, 12 thymines, and 11 adenines, of which eight, 18, nine and seven, respectively, were considered as N-additions. Frequent cytosines and guanines among N-additions have been described earlier [12] and would be expected due to the preference for dGTP by the terminal deoxynucleotidyl transferase [26] that would direct the insertion of cytosine in the opposite strand. Terminal deoxynucleotidyl transferase is thought to be at least partly responsible for N-additions [27].…”