Structural Comparison of Human Anti-HIV-1 gp120 V3 Monoclonal Antibodies of the Same Gene Usage Induced by Vaccination and Chronic Infection

ABSTRACTElucidating the structural basis of antibody (Ab) gene usage and affinity maturation of vaccine-induced Abs can inform the design of immunogens for inducing desired Ab responses in HIV vaccine development. Analyses of monoclonal Abs (MAbs) encoded by the same immunoglobulin genes at different stages of maturation can help to elucidate the maturation process. We have analyzed four human anti-V3 MAbs with the same VH1-3*01 and VL3-10*01 gene usage. Two MAbs, TA6 and TA7, were developed from a vaccinee in the HIV vaccine phase I trial DP6-001 with a polyvalent DNA prime/protein boost regimen, and two others, 311-11D and 1334, were developed from HIV-infected patients. The somatic hypermutation (SHM) rates in VH of vaccine-induced MAbs are lower than in chronic HIV infection-induced MAbs, while those in VL are comparable. Crystal structures of the antigen-binding fragments (Fabs) in complex with V3 peptides show that these MAbs bind the V3 epitope with a new cradle-binding mode and that the V3 β-hairpin lies along the antigen-binding groove, which consists of residues from both heavy and light chains. Residues conserved from the germ line sequences form specific binding pockets accommodating conserved structural elements of the V3 crown hairpin, predetermining the Ab gene selection, while somatically mutated residues create additional hydrogen bonds, electrostatic interactions, and van der Waals contacts, correlating with an increased binding affinity. Our data provide a unique example of germ line sequences determining the primordial antigen-binding sites and SHMs correlating with affinity maturation of Abs induced by vaccine and natural HIV infection.IMPORTANCEUnderstanding the structural basis of gene usage and affinity maturation for anti-HIV-1 antibodies may help vaccine design and development. Antibodies targeting the highly immunogenic third variable loop (V3) of HIV-1 gp120 provide a unique opportunity for detailed structural investigations. By comparing the sequences and structures of four anti-V3 MAbs at different stages of affinity maturation but of the same V gene usage, two induced by vaccination and another two by chronic infection, we provide a fine example of how germ line sequence determines the essential elements for epitope recognition and how affinity maturation improves the antibody's recognition of its epitope.

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Structural Basis of Antibody Conformation and Stability Modulation by Framework Somatic Hypermutation

Frontiers in Immunology ◽

10.3389/fimmu.2021.811632 ◽

2022 ◽

Vol 12 ◽

Author(s):

Zizhang Sheng ◽

Jude S. Bimela ◽

Phinikoula S. Katsamba ◽

Saurabh D. Patel ◽

Yicheng Guo ◽

...

Keyword(s):

Binding Affinity ◽

Somatic Hypermutation ◽

Affinity Maturation ◽

Structural Basis ◽

Common Mechanism ◽

Bioinformatics Pipeline ◽

Constant Domains ◽

Anti Hiv ◽

Hiv 1

Accumulation of somatic hypermutation (SHM) is the primary mechanism to enhance the binding affinity of antibodies to antigens in vivo. However, the structural basis of the effects of many SHMs remains elusive. Here, we integrated atomistic molecular dynamics (MD) simulation and data mining to build a high-throughput structural bioinformatics pipeline to study the effects of individual and combination SHMs on antibody conformation, flexibility, stability, and affinity. By applying this pipeline, we characterized a common mechanism of modulation of heavy-light pairing orientation by frequent SHMs at framework positions 39H, 91H, 38L, and 87L through disruption of a conserved hydrogen-bond network. Q39LH alone and in combination with light chain framework 4 (FWR4L) insertions further modulated the elbow angle between variable and constant domains of many antibodies, resulting in improved binding affinity for a subset of anti-HIV-1 antibodies. Q39LH also alleviated aggregation induced by FWR4L insertion, suggesting remote epistasis between these SHMs. Altogether, this study provides tools and insights for understanding antibody affinity maturation and for engineering functionally improved antibodies.

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Structural basis for germ-line gene usage of a potent class of antibodies targeting the CD4-binding site of HIV-1 gp120

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1208984109 ◽

2012 ◽

Vol 109 (30) ◽

pp. E2083-E2090 ◽

Cited By ~ 141

Author(s):

Anthony P. West ◽

Ron Diskin ◽

Michel C. Nussenzweig ◽

Pamela J. Bjorkman

Keyword(s):

Binding Site ◽

Germ Line ◽

Structural Basis ◽

Gene Usage ◽

Cd4 Binding Site ◽

Hiv 1

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Genetically identical primate modelling systems for HIV vaccines

Reproduction Fertility and Development ◽

10.1071/rd98057 ◽

1998 ◽

Vol 10 (8) ◽

pp. 651 ◽

Cited By ~ 2

Author(s):

Stephen J. Kent ◽

Ian M. Lewis

Keyword(s):

Immune Responses ◽

Hiv Infection ◽

Vaccine Development ◽

Careful Consideration ◽

Hiv Vaccine ◽

Effective Vaccine ◽

Hiv Vaccines ◽

Major Step ◽

Immunodeficiency Virus ◽

Hiv 1

There is an urgent need for a safe and effective vaccine to prevent human immunodeficiency virus (HIV) infection. Several HIV vaccine candidates have shown promise, but many concerns regarding the safety and efficacy of current vaccines remain. A major hindrance in HIV vaccine development is a poor understanding of precisely what functions HIV vaccines are required to perform in order to protect humans from HIV-1. Only higher primates (i.e. macaques, chimpanzees and humans) are susceptible to HIV-1 or the closely related virus ‘simian immunodeficiency virus’. These species are outbred and there are remarkable genetic differences in both the immune responses to vaccines and their susceptibility to infection. The development of genetically identical macaques would be a major step towards dissecting what immune responses are required to protect from HIV infection. For example, live attenuated HIV-1 vaccines are likely to be highly efficacious, but will induce disease in a substantial proportion of recipients. Defining why a live attenuated vaccine is effective should allow safer vaccines to be developed, retaining only the immunologic properties of an effective vaccine. The reduction in ‘background genetic noise’ obtained by studying genetically identical primates would provide concise answers to critical HIV vaccine issues, by studying a minimal number of animals. Such an approach could potentially be employed in other diseases where non-human primates are the only available model. Small studies can be performed where identical twins are generated by embryo bisection; however, larger studies where multiple immune parameters are simultaneously evaluated would be facilitated by cloning technology. Despite the technical difficulties to be overcome, the potential gains in human health from the development of genetically identical non-human primates are worthy of careful consideration.

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Structural basis for germline gene usage of a potent class of antibodies targeting the CD4 binding site of HIV-1 gp120

Retrovirology ◽

10.1186/1742-4690-9-s2-o33 ◽

2012 ◽

Vol 9 (S2) ◽

Cited By ~ 1

Author(s):

AP West ◽

R Diskin ◽

MC Nussenzweig ◽

PJ Bjorkman

Keyword(s):

Binding Site ◽

Structural Basis ◽

Germline Gene ◽

Gene Usage ◽

Cd4 Binding Site ◽

Hiv 1

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Prevalence of and risk factors for HIV infection in blood donors and various population subgroups in Ethiopia

Epidemiology and Infection ◽

10.1017/s0950268801006604 ◽

2002 ◽

Vol 128 (2) ◽

pp. 221-228 ◽

Cited By ~ 7

Author(s):

R. E. J. H. SENTJENS ◽

Y. SISAY ◽

H. VRIELINK ◽

D. KEBEDE ◽

H. J. ADÈR ◽

...

Keyword(s):

Risk Factors ◽

Hiv Infection ◽

Sexual Behaviour ◽

Blood Donors ◽

Transmitted Disease ◽

Urban Residents ◽

Sexual Transmitted Disease ◽

Low Prevalence ◽

Anti Hiv ◽

Hiv 1

The aim was to determine the prevalence of HIV infection and risk factors for HIV infection in various population subgroups in Ethiopia. Serum panels from blood donors (n = 2610), from various population subgroups in Ethiopia were tested for anti-HIV-1/2 by ELISA. All ELISA repeatedly reactive samples were subjected for confirmation by immunoblot (IB) and anti-HIV-1 and anti-HIV-2 specific ELISAs. 155/2610 (5·9%) blood donors were HIV-1 infected. Of pregnant women, 84/797 (10·5%) were HIV-1 infected, and 1/797 (0·1%) was HIV-2 infected. 1/240 (0·4%) individuals from the rural population were HIV-1 infected. 198/480 (41·3%) female attendees, and 106/419 (25·3%) male attendees at sexual transmitted disease (STD) clinics were HIV-1 infected. One (0·2%) male, and 2 (0·4%) female STD patients were infected with both HIV-1 and HIV-2. It was concluded that the prevalence of HIV-1 infection varied from 0·4% among urban residents to 25·3–41·3% among STD attendees. There is a low prevalence of HIV-2 present in Ethiopian subjects. Risky sexual behaviour is significantly associated with HIV-infection in Ethiopia.

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Ribozyme gene therapy for HIV infection Intracellular immunization of lymphocytes and CD34+ cells with an anti-HIV-1 ribozyme gene

Advanced Drug Delivery Reviews ◽

10.1016/0169-409x(95)00072-f ◽

1995 ◽

Vol 17 (3) ◽

pp. 363-368 ◽

Cited By ~ 8

Author(s):

Flossie Wong-Staal

Keyword(s):

Gene Therapy ◽

Hiv Infection ◽

Intracellular Immunization ◽

Cd34 Cells ◽

Anti Hiv ◽

Hiv 1

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Diagnosis of human immunodeficiency virus (HIV) infection: multicenter evaluation of a newly developed anti-HIV 1 and 2 enzyme immunoassay.

Journal of Clinical Microbiology ◽

10.1128/jcm.32.2.403-406.1994 ◽

1994 ◽

Vol 32 (2) ◽

pp. 403-406

Author(s):

G Hess ◽

F Avillez ◽

M H Lourenco ◽

F D'Agostino ◽

G Cambie ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Hiv Infection ◽

Enzyme Immunoassay ◽

Immunodeficiency Virus ◽

Anti Hiv ◽

Hiv 1

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Structural Basis of the Cross-Reactivity of Genetically Related Human Anti-HIV-1 mAbs: Implications for Design of V3-Based Immunogens

Structure ◽

10.1016/j.str.2009.09.012 ◽

2009 ◽

Vol 17 (11) ◽

pp. 1538-1546 ◽

Cited By ~ 55

Author(s):

Valicia Burke ◽

Constance Williams ◽

Madhav Sukumaran ◽

Seung-Sup Kim ◽

Huiguang Li ◽

...

Keyword(s):

Cross Reactivity ◽

Structural Basis ◽

The Cross ◽

Anti Hiv ◽

Hiv 1

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Highly sensitive and unbiased approach for elucidating antibody repertoires

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1608649113 ◽

2016 ◽

Vol 113 (28) ◽

pp. 7846-7851 ◽

Cited By ~ 31

Author(s):

Sherry G. Lin ◽

Zhaoqing Ba ◽

Zhou Du ◽

Yu Zhang ◽

Jiazhi Hu ◽

...

Keyword(s):

B Cells ◽

B Cell ◽

Germ Line ◽

Variable Region ◽

Cell Receptor ◽

Affinity Maturation ◽

Antigen Binding ◽

Variable Regions ◽

Antibody Repertoires ◽

B Lineage

Developing B lymphocytes undergo V(D)J recombination to assemble germ-line V, D, and J gene segments into exons that encode the antigen-binding variable region of Ig heavy (H) and light (L) chains. IgH and IgL chains associate to form the B-cell receptor (BCR), which, upon antigen binding, activates B cells to secrete BCR as an antibody. Each of the huge number of clonally independent B cells expresses a unique set of IgH and IgL variable regions. The ability of V(D)J recombination to generate vast primary B-cell repertoires results from a combinatorial assortment of large numbers of different V, D, and J segments, coupled with diversification of the junctions between them to generate the complementary determining region 3 (CDR3) for antigen contact. Approaches to evaluate in depth the content of primary antibody repertoires and, ultimately, to study how they are further molded by secondary mutation and affinity maturation processes are of great importance to the B-cell development, vaccine, and antibody fields. We now describe an unbiased, sensitive, and readily accessible assay, referred to as high-throughput genome-wide translocation sequencing-adapted repertoire sequencing (HTGTS-Rep-seq), to quantify antibody repertoires. HTGTS-Rep-seq quantitatively identifies the vast majority of IgH and IgL V(D)J exons, including their unique CDR3 sequences, from progenitor and mature mouse B lineage cells via the use of specific J primers. HTGTS-Rep-seq also accurately quantifies DJH intermediates and V(D)J exons in either productive or nonproductive configurations. HTGTS-Rep-seq should be useful for studies of human samples, including clonal B-cell expansions, and also for following antibody affinity maturation processes.

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