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J. Exp. Med.,
Volume 187, Number 1, January 5, 1998 59-70
By
From the * Molecular Immunology Center, Department of Microbiology, University of Texas
Southwestern Medical Center at Dallas, Texas 75235-9140; the During a germinal center reaction, random mutations are introduced into immunoglobulin V
genes to increase the affinity of antibody molecules and to further diversify the B cell repertoire. Antigen-directed selection of B cell clones that generate high affinity surface Ig results in
the affinity maturation of the antibody response. The mutations of Ig genes are typically basepair substitutions, although DNA insertions and deletions have been reported to occur at a low
frequency. In this study, we describe five insertion and four deletion events in otherwise somatically mutated VH gene cDNA molecules. Two of these insertions and all four deletions
were obtained through the sequencing of 395 cDNA clones (~110,000 nucleotides) from
CD38+IgD Oklahoma Medical Research
Foundation, Oklahoma City, Oklahoma 73104; § Schering-Plough Laboratory for Immunological
Research, Dardilly, France; and Baylor Institute for Immunological Research, Dallas, Texas 75235
germinal center, and CD38IgD memory B cell populations from a single human tonsil. No germline genes that could have encoded these six cDNA clones were found after an extensive characterization of the genomic VH4 repertoire of the tonsil donor. These six
insertions or deletions and three additional insertion events isolated from other sources occurred as triplets or multiples thereof, leaving the transcripts in frame. Additionally, 8 of 9 of
these events occurred in the CDR1 or CDR2, following a pattern consistent with selection,
and making it unlikely that these events were artifacts of the experimental system. The lack of
similar instances in unmutated IgD+CD38 follicular mantle cDNA clones statistically associates these events to the somatic hypermutation process (P = 0.014). Close scrutiny of the 9 insertion/deletion events reported here, and of 25 additional insertions or deletions collected from
the literature, suggest that secondary structural elements in the DNA sequences capable of producing loop intermediates may be a prerequisite in most instances. Furthermore, these events
most frequently involve sequence motifs resembling known intrinsic hotspots of somatic hypermutation. These insertion/deletion events are consistent with models of somatic hypermutation involving an unstable polymerase enzyme complex lacking proofreading capabilities, and
suggest a downregulation or alteration of DNA repair at the V locus during the hypermutation
process.
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