New Member of the V1V2-Directed CAP256-VRC26 Lineage That Shows Increased Breadth and Exceptional Potency

ABSTRACT The epitopes defined by HIV-1 broadly neutralizing antibodies (bNAbs) are valuable templates for vaccine design, and studies of the immunological development of these antibodies are providing insights for vaccination strategies. In addition, the most potent and broadly reactive of these bNAbs have potential for clinical use. We previously described a family of 12 V1V2-directed neutralizing antibodies, CAP256-VRC26, isolated from an HIV-1 clade C-infected donor at years 1, 2, and 4 of infection (N. A. Doria-Rose et al., Nature 509:55–62, 2014, http://dx.doi.org/10.1038/nature13036). Here, we report on the isolation and characterization of new members of the family mostly obtained at time points of peak serum neutralization breadth and potency. Thirteen antibodies were isolated from B cell culture, and eight were isolated using trimeric envelope probes for differential single B cell sorting. One of the new antibodies displayed a 10-fold greater neutralization potency than previously published lineage members. This antibody, CAP256-VRC26.25, neutralized 57% of diverse clade viral isolates and 70% of clade C isolates with remarkable potency. Among the viruses neutralized, the median 50% inhibitory concentration was 0.001 μg/ml. All 33 lineage members targeted a quaternary epitope focused on V2. While all known bNAbs targeting the V1V2 region interact with the N160 glycan, the CAP256-VRC26 antibodies showed an inverse correlation of neutralization potency with dependence on this glycan. Overall, our results highlight the ongoing evolution within a single antibody lineage and describe more potent and broadly neutralizing members with potential clinical utility, particularly in areas where clade C is prevalent. IMPORTANCE Studies of HIV-1 broadly neutralizing antibodies (bNAbs) provide valuable information for vaccine design, and the most potent and broadly reactive of these bNAbs have potential for clinical use. We previously described a family of V1V2-directed neutralizing antibodies from an HIV-1 clade C-infected donor. Here, we report on the isolation and characterization of new members of the family mostly obtained at time points of peak serum neutralization breadth and potency. One of the new antibodies, CAP256-VRC26.25, displayed a 10-fold greater neutralization potency than previously described lineage members. It neutralized 57% of diverse clade viral isolates and 70% of clade C isolates with remarkable potency: the median 50% inhibitory concentration was 0.001 μg/ml. Our results highlight the ongoing evolution within a single antibody lineage and describe more potent and broadly neutralizing members with potential clinical utility, particularly in areas where clade C is prevalent.

[1]  B. Haynes,et al.  HIV‐1 neutralizing antibodies: understanding nature's pathways , 2013, Immunological reviews.

[2]  Florian Klein,et al.  Antibodies in HIV-1 Vaccine Development and Therapy , 2013, Science.

[3]  Chaim A. Schramm,et al.  Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus , 2013, Nature.

[4]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[5]  J. Mascola,et al.  Human antibodies that neutralize HIV-1: identification, structures, and B cell ontogenies. , 2012, Immunity.

[6]  L. Morris,et al.  HIV broadly neutralizing antibody targets , 2015, Current opinion in HIV and AIDS.

[7]  Thomas B Kepler,et al.  B-cell–lineage immunogen design in vaccine development with HIV-1 as a case study , 2012, Nature Biotechnology.

[8]  Chaim A. Schramm,et al.  Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies , 2014, Nature.

[9]  P. Casali,et al.  CD40 Engagement Triggers Switching to IgA1 and IgA2 in Human B Cells Through Induction of Endogenous TGF-β: Evidence for TGF-β But Not IL-10-Dependent Direct Sμ→Sα and Sequential Sμ→Sγ, Sγ→Sα DNA Recombination , 1998, The Journal of Immunology.

[10]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[11]  John P. Moore,et al.  Cryo-EM Structure of a Fully Glycosylated Soluble Cleaved HIV-1 Envelope Trimer , 2013, Science.

[12]  T. Kepler,et al.  High-throughput isolation of immunoglobulin genes from single human B cells and expression as monoclonal antibodies. , 2009, Journal of virological methods.

[13]  J. Mascola,et al.  Immunotypes of a Quaternary Site of HIV-1 Vulnerability and Their Recognition by Antibodies , 2011, Journal of Virology.

[14]  John P. Moore,et al.  Asymmetric recognition of the HIV-1 trimer by broadly neutralizing antibody PG9 , 2013, Proceedings of the National Academy of Sciences.

[15]  L. Morris,et al.  Multiple Pathways of Escape from HIV Broadly Cross-Neutralizing V2-Dependent Antibodies , 2013, Journal of Virology.

[16]  B. Korber,et al.  Prevalence of broadly neutralizing antibody responses during chronic HIV-1 infection , 2014, AIDS.

[17]  C. Gray,et al.  Establishing a Cohort at High Risk of HIV Infection in South Africa: Challenges and Experiences of the CAPRISA 002 Acute Infection Study , 2008, PloS one.

[18]  J. Mascola,et al.  Efficient protein boosting after plasmid DNA or recombinant adenovirus immunization with HIV-1 vaccine constructs. , 2007, Vaccine.

[19]  Mario Roederer,et al.  Rational Design of Envelope Identifies Broadly Neutralizing Human Monoclonal Antibodies to HIV-1 , 2010, Science.

[20]  Adi Doron-Faigenboim,et al.  FastML: a web server for probabilistic reconstruction of ancestral sequences , 2012, Nucleic Acids Res..

[21]  Jens Meiler,et al.  Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth. , 2015, The Journal of clinical investigation.

[22]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[23]  Ron Diskin,et al.  Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding , 2011, Science.

[24]  Young Do Kwon,et al.  Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection , 2015, Cell.

[25]  Renate Kunert,et al.  Cardiolipin Polyspecific Autoreactivity in Two Broadly Neutralizing HIV-1 Antibodies , 2005, Science.

[26]  J. Sodroski,et al.  Soluble Mimetics of Human Immunodeficiency Virus Type 1 Viral Spikes Produced by Replacement of the Native Trimerization Domain with aHeterologous Trimerization Motif: Characterization and Ligand Binding Analysis , 2005, Journal of Virology.

[27]  Terri Wrin,et al.  Human Immunodeficiency Virus Type 1 Elite Neutralizers: Individuals with Broad and Potent Neutralizing Activity Identified by Using a High-Throughput Neutralization Assay together with an Analytical Selection Algorithm , 2009, Journal of Virology.

[28]  R. Wyatt,et al.  Cleavage-independent HIV-1 Env trimers engineered as soluble native spike mimetics for vaccine design. , 2015, Cell reports.

[29]  J. Mascola,et al.  High throughput HIV-1 microneutralization assay , 2013 .

[30]  Jerome H. Kim,et al.  Prospects for a globally effective HIV-1 vaccine. , 2015, Vaccine.

[31]  Young Do Kwon,et al.  Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9 , 2011, Nature.

[32]  Dennis R. Burton,et al.  A Limited Number of Antibody Specificities Mediate Broad and Potent Serum Neutralization in Selected HIV-1 Infected Individuals , 2010, PLoS pathogens.

[33]  L. Morris,et al.  The Neutralization Breadth of HIV-1 Develops Incrementally over Four Years and Is Associated with CD4+ T Cell Decline and High Viral Load during Acute Infection , 2011, Journal of Virology.

[34]  John P. Moore,et al.  Recombinant HIV envelope trimer selects for quaternary-dependent antibodies targeting the trimer apex , 2014, Proceedings of the National Academy of Sciences.

[35]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[36]  Richard T. Wyatt,et al.  Breadth of Human Immunodeficiency Virus-Specific Neutralizing Activity in Sera: Clustering Analysis and Association with Clinical Variables , 2009, Journal of Virology.

[37]  S. Tangye,et al.  IL-21-Induced Isotype Switching to IgG and IgA by Human Naive B Cells Is Differentially Regulated by IL-41 , 2008, The Journal of Immunology.

[38]  John P. Moore,et al.  A Next-Generation Cleaved, Soluble HIV-1 Env Trimer, BG505 SOSIP.664 gp140, Expresses Multiple Epitopes for Broadly Neutralizing but Not Non-Neutralizing Antibodies , 2013, PLoS pathogens.

[39]  Baoshan Zhang,et al.  Broad and potent neutralization of HIV-1 by a gp41-specific human antibody , 2012, Nature.

[40]  Michel C Nussenzweig,et al.  Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning. , 2008, Journal of immunological methods.

[41]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[42]  Lynn Morris,et al.  Viral variants that initiate and drive maturation of V1V2-directed HIV-1 broadly neutralizing antibodies , 2015, Nature Medicine.

[43]  Gwo-Yu Chuang,et al.  A Short Segment of the HIV-1 gp120 V1/V2 Region Is a Major Determinant of Resistance to V1/V2 Neutralizing Antibodies , 2012, Journal of Virology.

[44]  S. Zolla-Pazner,et al.  The V1/V2 Domain of gp120 Is a Global Regulator of the Sensitivity of Primary Human Immunodeficiency Virus Type 1 Isolates to Neutralization by Antibodies Commonly Induced upon Infection , 2004, Journal of Virology.

[45]  D. Burton,et al.  Incomplete Neutralization and Deviation from Sigmoidal Neutralization Curves for HIV Broadly Neutralizing Monoclonal Antibodies , 2015, PLoS pathogens.

[46]  J. Mascola,et al.  Isolation of human monoclonal antibodies from peripheral blood B cells , 2013, Nature Protocols.

[47]  T. Kepler,et al.  Analysis of a Clonal Lineage of HIV-1 Envelope V2/V3 Conformational Epitope-Specific Broadly Neutralizing Antibodies and Their Inferred Unmutated Common Ancestors , 2011, Journal of Virology.

[48]  David C Montefiori,et al.  Measuring HIV neutralization in a luciferase reporter gene assay. , 2009, Methods in molecular biology.

[49]  Tongqing Zhou,et al.  Structure and immune recognition of trimeric prefusion HIV-1 Env , 2014, Nature.

[50]  Pham Phung,et al.  Broad neutralization coverage of HIV by multiple highly potent antibodies , 2011, Nature.

[51]  Randy J Read,et al.  Recent developments in the PHENIX software for automated crystallographic structure determination. , 2004, Journal of synchrotron radiation.

[52]  Baoshan Zhang,et al.  Structural basis for diverse N-glycan recognition by HIV-1–neutralizing V1–V2–directed antibody PG16 , 2013, Nature Structural &Molecular Biology.

[53]  John P. Moore,et al.  Crystal Structure of a Soluble Cleaved HIV-1 Envelope Trimer , 2013, Science.

[54]  L. Morris,et al.  The Antibody Response against HIV-1. , 2012, Cold Spring Harbor perspectives in medicine.

[55]  J. Mascola,et al.  Broadly neutralizing antibodies and the search for an HIV-1 vaccine: the end of the beginning , 2013, Nature Reviews Immunology.

[56]  N. Harindranath,et al.  CD40 ligand and appropriate cytokines induce switching to IgG, IgA, and IgE and coordinated germinal center and plasmacytoid phenotypic differentiation in a human monoclonal IgM+IgD+ B cell line. , 1998, Journal of immunology.

[57]  L. Morris,et al.  Potent and Broad Neutralization of HIV-1 Subtype C by Plasma Antibodies Targeting a Quaternary Epitope Including Residues in the V2 Loop , 2011, Journal of Virology.

[58]  John R Mascola,et al.  Antibody responses to envelope glycoproteins in HIV-1 infection , 2015, Nature Immunology.

[59]  Tongqing Zhou,et al.  Delineating Antibody Recognition in Polyclonal Sera from Patterns of HIV-1 Isolate Neutralization , 2013, Science.

[60]  P. Casali,et al.  CD40 engagement triggers switching to IgA1 and IgA2 in human B cells through induction of endogenous TGF-beta: evidence for TGF-beta but not IL-10-dependent direct S mu-->S alpha and sequential S mu-->S gamma, S gamma-->S alpha DNA recombination. , 1998, Journal of immunology.

[61]  Pham Phung,et al.  Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target , 2009, Science.

[62]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[63]  Dennis R. Burton,et al.  Variable Loop Glycan Dependency of the Broad and Potent HIV-1-Neutralizing Antibodies PG9 and PG16 , 2010, Journal of Virology.

[64]  N. Doria-Rose,et al.  Strategies to guide the antibody affinity maturation process. , 2015, Current opinion in virology.

[65]  Xuesong Yu,et al.  Factors Associated with the Development of Cross-Reactive Neutralizing Antibodies during Human Immunodeficiency Virus Type 1 Infection , 2008, Journal of Virology.

[66]  Adam Godzik,et al.  Clustering of highly homologous sequences to reduce the size of large protein databases , 2001, Bioinform..

[67]  Gwo-Yu Chuang,et al.  Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-120 interface , 2014, Nature.