The challenges of modelling antibody repertoire dynamics in HIV infection
Abstract
Antibody affinity maturation by somatic hypermutation of B-cell immunoglobulin variable region genes has been studied for decades in various model systems using well-defined antigens. While much is known about the molecular details of the process, our understanding of the selective forces that generate affinity maturation are less well developed, particularly in the case of a co-evolving pathogen such as HIV. Despite this gap in understanding, high-throughput antibody sequence data are increasingly being collected to investigate the evolutionary trajectories of antibody lineages in HIV-infected individuals. Here, we review what is known in controlled experimental systems about the mechanisms underlying antibody selection and compare this to the observed temporal patterns of antibody evolution in HIV infection. In addition, we describe how our current understanding of antibody selection mechanisms leaves questions about antibody dynamics in HIV infection unanswered. Without a mechanistic understanding of antibody selection in the context of a co-evolving viral population, modelling and analysis of antibody sequences in HIV-infected individuals will be limited in their interpretation and predictive ability.
- Authors:
-
- Univ. of California, Berkeley, CA (United States)
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1233536
- Report Number(s):
- LA-UR-15-21720
Journal ID: ISSN 0962-8436
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences
- Additional Journal Information:
- Journal Volume: 370; Journal Issue: 1676; Journal ID: ISSN 0962-8436
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; HIV; evolution; immunology
Citation Formats
Luo, Shishi, and Perelson, Alan S. The challenges of modelling antibody repertoire dynamics in HIV infection. United States: N. p., 2015.
Web. doi:10.1098/rstb.2014.0247.
Luo, Shishi, & Perelson, Alan S. The challenges of modelling antibody repertoire dynamics in HIV infection. United States. https://doi.org/10.1098/rstb.2014.0247
Luo, Shishi, and Perelson, Alan S. Mon .
"The challenges of modelling antibody repertoire dynamics in HIV infection". United States. https://doi.org/10.1098/rstb.2014.0247. https://www.osti.gov/servlets/purl/1233536.
@article{osti_1233536,
title = {The challenges of modelling antibody repertoire dynamics in HIV infection},
author = {Luo, Shishi and Perelson, Alan S.},
abstractNote = {Antibody affinity maturation by somatic hypermutation of B-cell immunoglobulin variable region genes has been studied for decades in various model systems using well-defined antigens. While much is known about the molecular details of the process, our understanding of the selective forces that generate affinity maturation are less well developed, particularly in the case of a co-evolving pathogen such as HIV. Despite this gap in understanding, high-throughput antibody sequence data are increasingly being collected to investigate the evolutionary trajectories of antibody lineages in HIV-infected individuals. Here, we review what is known in controlled experimental systems about the mechanisms underlying antibody selection and compare this to the observed temporal patterns of antibody evolution in HIV infection. In addition, we describe how our current understanding of antibody selection mechanisms leaves questions about antibody dynamics in HIV infection unanswered. Without a mechanistic understanding of antibody selection in the context of a co-evolving viral population, modelling and analysis of antibody sequences in HIV-infected individuals will be limited in their interpretation and predictive ability.},
doi = {10.1098/rstb.2014.0247},
journal = {Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences},
number = 1676,
volume = 370,
place = {United States},
year = {Mon Jul 20 00:00:00 EDT 2015},
month = {Mon Jul 20 00:00:00 EDT 2015}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 5 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
The promise and challenge of high-throughput sequencing of the antibody repertoire
journal, January 2014
- Georgiou, George; Ippolito, Gregory C.; Beausang, John
- Nature Biotechnology, Vol. 32, Issue 2
Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus
journal, April 2013
- Liao, Hua-Xin; Lynch, Rebecca; Zhou, Tongqing
- Nature, Vol. 496, Issue 7446
B-cell–lineage immunogen design in vaccine development with HIV-1 as a case study
journal, May 2012
- Haynes, Barton F.; Kelsoe, Garnett; Harrison, Stephen C.
- Nature Biotechnology, Vol. 30, Issue 5
Consistent Viral Evolutionary Changes Associated with the Progression of Human Immunodeficiency Virus Type 1 Infection
journal, December 1999
- Shankarappa, Raj; Margolick, Joseph B.; Gange, Stephen J.
- Journal of Virology, Vol. 73, Issue 12
Germinal Centers
journal, April 2012
- Victora, Gabriel D.; Nussenzweig, Michel C.
- Annual Review of Immunology, Vol. 30, Issue 1
Clonal selection in the germinal centre by regulated proliferation and hypermutation
journal, May 2014
- Gitlin, Alexander D.; Shulman, Ziv; Nussenzweig, Michel C.
- Nature, Vol. 509, Issue 7502
Generation of antibody diversity in the immune response of BALB/c mice to influenza virus hemagglutinin.
journal, May 1984
- McKean, D.; Huppi, K.; Bell, M.
- Proceedings of the National Academy of Sciences, Vol. 81, Issue 10
A Theory of Germinal Center B Cell Selection, Division, and Exit
journal, July 2012
- Meyer-Hermann, Michael; Mohr, Elodie; Pelletier, Nadége
- Cell Reports, Vol. 2, Issue 1
Manipulating the Selection Forces during Affinity Maturation to Generate Cross-Reactive HIV Antibodies
journal, February 2015
- Wang, Shenshen; Mata-Fink, Jordi; Kriegsman, Barry
- Cell, Vol. 160, Issue 4
B cell follicle sanctuary permits persistent productive simian immunodeficiency virus infection in elite controllers
journal, January 2015
- Fukazawa, Yoshinori; Lum, Richard; Okoye, Afam A.
- Nature Medicine, Vol. 21, Issue 2
The dysfunction of T follicular helper cells
journal, September 2014
- Cubas, Rafael; Perreau, Matthieu
- Current Opinion in HIV and AIDS, Vol. 9, Issue 5
T follicular helper cells and HIV/SIV-specific antibody responses
journal, May 2014
- Petrovas, Constantinos; Koup, Richard A.
- Current Opinion in HIV and AIDS, Vol. 9, Issue 3
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
journal, May 2008
- Keele, B. F.; Giorgi, E. E.; Salazar-Gonzalez, J. F.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 21
Modeling sequence evolution in acute HIV-1 infection
journal, November 2009
- Lee, Ha Youn; Giorgi, Elena E.; Keele, Brandon F.
- Journal of Theoretical Biology, Vol. 261, Issue 2
The HIV-1 Envelope Glycoproteins: Fusogens, Antigens, and Immunogens
journal, June 1998
- Wyatt, R.
- Science, Vol. 280, Issue 5371
Initial B-Cell Responses to Transmitted Human Immunodeficiency Virus Type 1: Virion-Binding Immunoglobulin M (IgM) and IgG Antibodies Followed by Plasma Anti-gp41 Antibodies with Ineffective Control of Initial Viremia
journal, October 2008
- Tomaras, G. D.; Yates, N. L.; Liu, P.
- Journal of Virology, Vol. 82, Issue 24, p. 12449-12463
HIV-1 Envelope gp41 Antibodies Can Originate from Terminal Ileum B Cells that Share Cross-Reactivity with Commensal Bacteria
journal, August 2014
- Trama, Ashley M.; Moody, M. Anthony; Alam, S. Munir
- Cell Host & Microbe, Vol. 16, Issue 2
Antibody neutralization and escape by HIV-1
journal, March 2003
- Wei, Xiping; Decker, Julie M.; Wang, Shuyi
- Nature, Vol. 422, Issue 6929
Limited Neutralizing Antibody Specificities Drive Neutralization Escape in Early HIV-1 Subtype C Infection
journal, September 2009
- Moore, Penny L.; Ranchobe, Nthabeleng; Lambson, Bronwen E.
- PLoS Pathogens, Vol. 5, Issue 9
Rapid evolution of the neutralizing antibody response to HIV type 1 infection
journal, March 2003
- Richman, D. D.; Wrin, T.; Little, S. J.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 7
The Antibody Response against HIV-1
journal, November 2011
- Overbaugh, J.; Morris, L.
- Cold Spring Harbor Perspectives in Medicine, Vol. 2, Issue 1
Endocytosis and Recycling of Immune Complexes by Follicular Dendritic Cells Enhances B Cell Antigen Binding and Activation
journal, June 2013
- Heesters, Balthasar A.; Chatterjee, Priyadarshini; Kim, Young-A.
- Immunity, Vol. 38, Issue 6
Evolution of an HIV glycan–dependent broadly neutralizing antibody epitope through immune escape
journal, October 2012
- Moore, Penny L.; Gray, Elin S.; Wibmer, C. Kurt
- Nature Medicine, Vol. 18, Issue 11
Viral Escape from HIV-1 Neutralizing Antibodies Drives Increased Plasma Neutralization Breadth through Sequential Recognition of Multiple Epitopes and Immunotypes
journal, October 2013
- Wibmer, Constantinos Kurt; Bhiman, Jinal N.; Gray, Elin S.
- PLoS Pathogens, Vol. 9, Issue 10
Cooperation of B Cell Lineages in Induction of HIV-1-Broadly Neutralizing Antibodies
journal, July 2014
- Gao, Feng; Bonsignori, Mattia; Liao, Hua-Xin
- Cell, Vol. 158, Issue 3
Independent Expansion of Epitope-Specific Plasma Cell Responses upon HIV-1 Envelope Glycoprotein Immunization
journal, June 2013
- Forsell, Mattias N. E.; Soldemo, Martina; Dosenovic, Pia
- The Journal of Immunology, Vol. 191, Issue 1
Works referencing / citing this record:
Host-pathogen coevolution and the emergence of broadly neutralizing antibodies in chronic infections
preprint, January 2015
- Nourmohammad, Armita; Otwinowski, Jakub; Plotkin, Joshua B.
- arXiv