Overlapping hotspots in CDRs are critical sites for V region diversification

Lirong Wei, Richard Chahwan, Shanzhi Wang, Xiaohua Wang, Phuong T. Pham, Myron F. Goodman, Aviv Bergman, Matthew D. Scharff, Thomas MacCarthy

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Activation-induced deaminase (AID) mediates the somatic hypermutation (SHM) of Ig variable (V) regions that is required for the affinity maturation of the antibody response. An intensive analysis of a published database of somatic hypermutations that arose in the IGHV3-23∗01 human V region expressed in vivo by human memory B cells revealed that the focus of mutations in complementary determining region (CDR)1 and CDR2 coincided with a combination of overlapping AGCT hotspots, the absence of AID cold spots, and an abundance of polymerase eta hotspots. If the overlapping hotspots in the CDR1 or CDR2 did not undergo mutation, the frequency of mutations throughout the V region was reduced. To model this result, we examined the mutation of the human IGHV3-23∗01 biochemically and in the endogenous heavy chain locus of Ramos B cells. Deep sequencing revealed that IGHV3-23∗01 in Ramos cells accumulates AID-induced mutations primarily in the AGCT in CDR2, which was also the most frequent site of mutation in vivo. Replacing the overlapping hotspots in CDR1 and CDR2 with neutral or cold motifs resulted in a reduction in mutations within the modified motifs and, to some degree, throughout the V region. In addition, some of the overlapping hotspots in the CDRs were at sites in which replacement mutations could change the structure of the CDR loops. Our analysis suggests that the local sequence environment of the V region, and especially of the CDR1 and CDR2, is highly evolved to recruit mutations to key residues in the CDRs of the IgV region.

Original languageEnglish (US)
Pages (from-to)E728-E737
JournalProceedings of the National Academy of Sciences of the United States of America
Volume112
Issue number7
DOIs
StatePublished - Feb 17 2015

Fingerprint

Mutation
B-Lymphocytes
Immunoglobulin Variable Region
High-Throughput Nucleotide Sequencing
Mutation Rate
Antibody Formation
Databases
AICDA (activation-induced cytidine deaminase)

Keywords

  • AID
  • Complementarity-determining regions
  • Cytosine deamination
  • IGHV3-23
  • Somatic hypermutation

ASJC Scopus subject areas

  • General

Cite this

Overlapping hotspots in CDRs are critical sites for V region diversification. / Wei, Lirong; Chahwan, Richard; Wang, Shanzhi; Wang, Xiaohua; Pham, Phuong T.; Goodman, Myron F.; Bergman, Aviv; Scharff, Matthew D.; MacCarthy, Thomas.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 112, No. 7, 17.02.2015, p. E728-E737.

Research output: Contribution to journalArticle

Wei, Lirong ; Chahwan, Richard ; Wang, Shanzhi ; Wang, Xiaohua ; Pham, Phuong T. ; Goodman, Myron F. ; Bergman, Aviv ; Scharff, Matthew D. ; MacCarthy, Thomas. / Overlapping hotspots in CDRs are critical sites for V region diversification. In: Proceedings of the National Academy of Sciences of the United States of America. 2015 ; Vol. 112, No. 7. pp. E728-E737.
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