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Proc Natl Acad Sci U S A. 2017 Aug 8;114(32):8614-8619. doi: 10.1073/pnas.1709203114. Epub 2017 Jul 26.

Sequence intrinsic somatic mutation mechanisms contribute to affinity maturation of VRC01-class HIV-1 broadly neutralizing antibodies.

Hwang JK1,2,3,4, Wang C1,2,3,4, Du Z1,2,3,4, Meyers RM1,2,3,4, Kepler TB5, Neuberg D6, Kwong PD7, Mascola JR7, Joyce MG7, Bonsignori M8, Haynes BF8, Yeap LS1,2,3,4, Alt FW9,2,3,4.

Author information

1
Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115.
2
Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115.
3
Department of Pediatrics, Harvard Medical School, Boston, MA 02115.
4
Department of Genetics, Harvard Medical School, Boston, MA 02115.
5
Department of Microbiology, Boston University School of Medicine, Boston, MA 02215.
6
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215.
7
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892.
8
Duke Human Vaccine Institute, Department of Medicine, Duke University School of Medicine, Duke University Medical Center, Durham, NC 27710.
9
Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115; alt@enders.tch.harvard.edu.

Abstract

Variable regions of Ig chains provide the antigen recognition portion of B-cell receptors and derivative antibodies. Ig heavy-chain variable region exons are assembled developmentally from V, D, J gene segments. Each variable region contains three antigen-contacting complementarity-determining regions (CDRs), with CDR1 and CDR2 encoded by the V segment and CDR3 encoded by the V(D)J junction region. Antigen-stimulated germinal center (GC) B cells undergo somatic hypermutation (SHM) of V(D)J exons followed by selection for SHMs that increase antigen-binding affinity. Some HIV-1-infected human subjects develop broadly neutralizing antibodies (bnAbs), such as the potent VRC01-class bnAbs, that neutralize diverse HIV-1 strains. Mature VRC01-class bnAbs, including VRC-PG04, accumulate very high SHM levels, a property that hinders development of vaccine strategies to elicit them. Because many VRC01-class bnAb SHMs are not required for broad neutralization, high overall SHM may be required to achieve certain functional SHMs. To elucidate such requirements, we used a V(D)J passenger allele system to assay, in mouse GC B cells, sequence-intrinsic SHM-targeting rates of nucleotides across substrates representing maturation stages of human VRC-PG04. We identify rate-limiting SHM positions for VRC-PG04 maturation, as well as SHM hotspots and intrinsically frequent deletions associated with SHM. We find that mature VRC-PG04 has low SHM capability due to hotspot saturation but also demonstrate that generation of new SHM hotspots and saturation of existing hotspot regions (e.g., CDR3) does not majorly influence intrinsic SHM in unmutated portions of VRC-PG04 progenitor sequences. We discuss implications of our findings for bnAb affinity maturation mechanisms.

KEYWORDS:

HIV-1; activation-induced cytidine deaminase; broadly neutralizing antibodies; intrinsic mutability; somatic hypermutation

PMID:
28747530
PMCID:
PMC5559054
DOI:
10.1073/pnas.1709203114
[Indexed for MEDLINE]
Free PMC Article

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