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Increased breadth of HIV-1 neutralization achieved by diverse antibody clones each with limited neutralization breadth.
Chukwuma VU, Kose N, Sather DN, Sapparapu G, Falk R, King H, Singh V, Lampley R, Malherbe DC, Ditto NT, Sullivan JT, Barnes T, Doranz BJ, Labranche CC, Montefiori DC, Kalams SA, Haigwood NL, Crowe JE
(2018) PLoS One 13: e0209437
MeSH Terms: Antibodies, Neutralizing, Antibody Diversity, B-Lymphocytes, Cells, Cultured, Epitope Mapping, Epitopes, HIV Antibodies, HIV Infections, HIV-1, Humans, Hybridomas, Neutralization Tests, env Gene Products, Human Immunodeficiency Virus
Show Abstract · Added March 31, 2019
Broadly neutralizing antibodies (bNAbs) are rarely elicited by current human immunodeficiency virus type 1 (HIV-1) vaccine designs, but the presence of bNAbs in naturally infected individuals may be associated with high plasma viral loads, suggesting that the magnitude, duration, and diversity of viral exposure may contribute to the development of bNAbs. Here, we report the isolation and characterization of a panel of human monoclonal antibodies (mAbs) from two subjects who developed broadly neutralizing autologous antibody responses during HIV-1 infection. In both subjects, we identified collections of mAbs that exhibited specificity only to a few autologous envelopes (Envs), with some mAbs exhibiting specificity only to a subset of Envs within the quasispecies of a particular sample at one time point. Neutralizing antibodies (NAbs) isolated from these subjects mapped mostly to epitopes in the Env V3 loop region and the CD4 binding site. None of the individual neutralizing mAbs recovered exhibited the cumulative breadth of neutralization present in the serum of the subjects. Surprisingly, however, the activity of polyclonal mixtures comprising individual mAbs that each possessed limited neutralizing activity, could achieve increased breadth of neutralizing activity against autologous isolates. While a single broadly neutralizing antibody targeting one epitope can mediate neutralization breadth, the findings presented here suggest that a cooperative polyclonal process mediated by diverse antibodies with more limited breadth targeting multiple epitopes also can achieve neutralization breadth against HIV-1.
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Integrating linear optimization with structural modeling to increase HIV neutralization breadth.
Sevy AM, Panda S, Crowe JE, Meiler J, Vorobeychik Y
(2018) PLoS Comput Biol 14: e1005999
MeSH Terms: Algorithms, Amino Acid Motifs, Antibodies, Neutralizing, Computational Biology, Epitopes, HIV Antibodies, HIV Infections, HIV-1, Humans, Linear Models, Machine Learning, Regression Analysis, Software, Support Vector Machine
Show Abstract · Added March 14, 2018
Computational protein design has been successful in modeling fixed backbone proteins in a single conformation. However, when modeling large ensembles of flexible proteins, current methods in protein design have been insufficient. Large barriers in the energy landscape are difficult to traverse while redesigning a protein sequence, and as a result current design methods only sample a fraction of available sequence space. We propose a new computational approach that combines traditional structure-based modeling using the Rosetta software suite with machine learning and integer linear programming to overcome limitations in the Rosetta sampling methods. We demonstrate the effectiveness of this method, which we call BROAD, by benchmarking the performance on increasing predicted breadth of anti-HIV antibodies. We use this novel method to increase predicted breadth of naturally-occurring antibody VRC23 against a panel of 180 divergent HIV viral strains and achieve 100% predicted binding against the panel. In addition, we compare the performance of this method to state-of-the-art multistate design in Rosetta and show that we can outperform the existing method significantly. We further demonstrate that sequences recovered by this method recover known binding motifs of broadly neutralizing anti-HIV antibodies. Finally, our approach is general and can be extended easily to other protein systems. Although our modeled antibodies were not tested in vitro, we predict that these variants would have greatly increased breadth compared to the wild-type antibody.
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14 MeSH Terms
Recent Abacavir Use Increases Risk of Type 1 and Type 2 Myocardial Infarctions Among Adults With HIV.
Elion RA, Althoff KN, Zhang J, Moore RD, Gange SJ, Kitahata MM, Crane HM, Drozd DR, Stein JH, Klein MB, Eron JJ, Silverberg MJ, Mathews WC, Justice AC, Sterling TR, Rabkin CS, Mayor AM, Klein DB, Horberg MA, Bosch RJ, Eyawo O, Palella FJ, North American AIDS Cohort Collaboration on Research and Design of IeDEA
(2018) J Acquir Immune Defic Syndr 78: 62-72
MeSH Terms: Adult, Aged, Antirheumatic Agents, CD4 Lymphocyte Count, Cohort Studies, Dideoxynucleosides, Female, HIV Infections, Humans, Male, Middle Aged, Myocardial Infarction, North America, Risk Assessment, Risk Factors
Show Abstract · Added March 14, 2018
BACKGROUND - There is persistent confusion as to whether abacavir (ABC) increases the risk of myocardial infarction (MI), and whether such risk differs by type 1 (T1MI) or 2 (T2MI) MI in adults with HIV.
METHODS - Incident MIs in North American Cohort Collaboration on Research and Design participants were identified from 2001 to 2013. Discrete time marginal structural models addressed channeling biases and time-dependent confounding to estimate crude hazard ratio (HR) and adjusted hazard ratio (aHR) and 95% confidence intervals; analyses were performed for T1MI and T2MI separately. A sensitivity analysis evaluated whether Framingham risk score (FRS) modified the effect of ABC on MI occurrence.
RESULTS - Eight thousand two hundred sixty-five adults who initiated antiretroviral therapy contributed 29,077 person-years and 123 MI events (65 T1MI and 58 T2MI). Median follow-up time was 2.9 (interquartile range 1.4-5.1) years. ABC initiators were more likely to have a history of injection drug use, hepatitis C virus infection, hypertension, diabetes, impaired kidney function, hyperlipidemia, low (<200 cells/mm) CD4 counts, and a history of AIDS. The risk of the combined MI outcome was greater for persons who used ABC in the previous 6 months [aHR = 1.84 (1.17-2.91)]; and persisted for T1MI (aHR = 1.62 [1.01]) and T2MI [aHR = 2.11 (1.08-4.29)]. FRS did not modify the effect of ABC on MI (P = 0.14) and inclusion of FRS in the MSM did not diminish the effect of recent ABC use on the combined outcome.
CONCLUSIONS - Recent ABC use was associated with MI after adjustment for known risk factors and for FRS. However, screening for T1MI risks may not identify all or even most persons at risk of ABC use-associated MIs.
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15 MeSH Terms
Adipose Tissue is Enriched for Activated and Late-Differentiated CD8+ T Cells and Shows Distinct CD8+ Receptor Usage, Compared With Blood in HIV-Infected Persons.
Koethe JR, McDonnell W, Kennedy A, Abana CO, Pilkinton M, Setliff I, Georgiev I, Barnett L, Hager CC, Smith R, Kalams SA, Hasty A, Mallal S
(2018) J Acquir Immune Defic Syndr 77: e14-e21
MeSH Terms: Adipose Tissue, Adult, Anti-HIV Agents, Blood Cells, CD8-Positive T-Lymphocytes, Cohort Studies, Female, HIV Infections, Humans, Male, Middle Aged, Receptors, Antigen, T-Cell, Sequence Analysis, DNA, Sustained Virologic Response, T-Lymphocyte Subsets
Show Abstract · Added March 14, 2018
BACKGROUND - Adverse viral and medication effects on adipose tissue contribute to the development of metabolic disease in HIV-infected persons, but T cells also have a central role modulating local inflammation and adipocyte function. We sought to characterize potentially proinflammatory T-cell populations in adipose tissue among persons on long-term antiretroviral therapy and assess whether adipose tissue CD8 T cells represent an expanded, oligoclonal population.
METHODS - We recruited 10 HIV-infected, non-diabetic, overweight or obese adults on efavirenz, tenofovir, and emtricitabine for >4 years with consistent viral suppression. We collected fasting blood and subcutaneous abdominal adipose tissue to measure the percentage of CD4 and CD8 T cells expressing activation, exhaustion, late differentiation/senescence, and memory surface markers. We performed T-cell receptor (TCR) sequencing on sorted CD8 cells. We compared the proportion of each T-cell subset and the TCR repertoire diversity, in blood versus adipose tissue.
RESULTS - Adipose tissue had a higher percentage of CD3CD8 T cells compared with blood (61.0% vs. 51.7%, P < 0.01) and was enriched for both activated CD8HLA-DR T cells (5.5% vs. 0.9%, P < 0.01) and late-differentiated CD8CD57 T cells (37.4% vs. 22.7%, P < 0.01). Adipose tissue CD8 T cells displayed distinct TCRβ V and J gene usage, and the Shannon Entropy index, a measure of overall TCRβ repertoire diversity, was lower compared with blood (4.39 vs. 4.46; P = 0.05).
CONCLUSIONS - Adipose tissue is enriched for activated and late-differentiated CD8 T cells with distinct TCR usage. These cells may contribute to tissue inflammation and impaired adipocyte fitness in HIV-infected persons.
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15 MeSH Terms
Cancer-Attributable Mortality Among People With Treated Human Immunodeficiency Virus Infection in North America.
Engels EA, Yanik EL, Wheeler W, Gill MJ, Shiels MS, Dubrow R, Althoff KN, Silverberg MJ, Brooks JT, Kitahata MM, Goedert JJ, Grover S, Mayor AM, Moore RD, Park LS, Rachlis A, Sigel K, Sterling TR, Thorne JE, Pfeiffer RM, North American AIDS Cohort Collaboration on Research and Design of the International Epidemiologic Databases to Evaluate AIDS, North American AIDS Cohort Collaboration on Research and Design of the International Epidemiologic Databases to Evaluate AIDS
(2017) Clin Infect Dis 65: 636-643
MeSH Terms: Adolescent, Adult, CD4 Lymphocyte Count, Female, HIV Infections, Humans, Male, Middle Aged, Neoplasms, North America, Proportional Hazards Models, Retrospective Studies, Viral Load, Young Adult
Show Abstract · Added March 14, 2018
Background - Cancer remains an important cause of morbidity and mortality in people with human immunodeficiency virus (PWHIV) on effective antiretroviral therapy (ART). Estimates of cancer-attributable mortality can inform public health efforts.
Methods - We evaluated 46956 PWHIV receiving ART in North American HIV cohorts (1995-2009). Using information on incident cancers and deaths, we calculated population-attributable fractions (PAFs), estimating the proportion of deaths due to cancer. Calculations were based on proportional hazards models adjusted for age, sex, race, HIV risk group, calendar year, cohort, CD4 count, and viral load.
Results - There were 1997 incident cancers and 8956 deaths during 267145 person-years of follow-up, and 11.9% of decedents had a prior cancer. An estimated 9.8% of deaths were attributable to cancer (cancer-attributable mortality rate 327 per 100000 person-years). PAFs were 2.6% for AIDS-defining cancers (ADCs, including non-Hodgkin lymphoma, 2.0% of deaths) and 7.1% for non-AIDS-defining cancers (NADCs: lung cancer, 2.3%; liver cancer, 0.9%). PAFs for NADCs were higher in males and increased strongly with age, reaching 12.5% in PWHIV aged 55+ years. Mortality rates attributable to ADCs and NADCs were highest for PWHIV with CD4 counts <100 cells/mm3. PAFs for NADCs increased during 1995-2009, reaching 10.1% in 2006-2009.
Conclusions - Approximately 10% of deaths in PWHIV prescribed ART during 1995-2009 were attributable to cancer, but this fraction increased over time. A large proportion of cancer-attributable deaths were associated with non-Hodgkin lymphoma, lung cancer, and liver cancer. Deaths due to NADCs will likely grow in importance as AIDS mortality declines and PWHIV age.
Published by Oxford University Press for the Infectious Diseases Society of America 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.
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14 MeSH Terms
CD4:CD8 Ratio and CD8 Count as Prognostic Markers for Mortality in Human Immunodeficiency Virus-Infected Patients on Antiretroviral Therapy: The Antiretroviral Therapy Cohort Collaboration (ART-CC).
Trickey A, May MT, Schommers P, Tate J, Ingle SM, Guest JL, Gill MJ, Zangerle R, Saag M, Reiss P, Monforte AD, Johnson M, Lima VD, Sterling TR, Cavassini M, Wittkop L, Costagliola D, Sterne JAC, Antiretroviral Therapy Cohort Collaboration (ART-CC)
(2017) Clin Infect Dis 65: 959-966
MeSH Terms: Adolescent, Adult, Aged, Anti-HIV Agents, Biomarkers, CD4-CD8 Ratio, CD4-Positive T-Lymphocytes, CD8-Positive T-Lymphocytes, Cause of Death, Europe, Female, HIV Infections, Humans, Lymphocyte Count, Male, Middle Aged, North America, Prognosis, Proportional Hazards Models, Viral Load, Young Adult
Show Abstract · Added March 14, 2018
Background - We investigated whether CD4:CD8 ratio and CD8 count were prognostic for all-cause, AIDS, and non-AIDS mortality in virologically suppressed patients with high CD4 count.
Methods - We used data from 13 European and North American cohorts of human immunodeficiency virus-infected, antiretroviral therapy (ART)-naive adults who started ART during 1996-2010, who were followed from the date they had CD4 count ≥350 cells/μL and were virologically suppressed (baseline). We used stratified Cox models to estimate unadjusted and adjusted (for sex, people who inject drugs, ART initiation year, and baseline age, CD4 count, AIDS, duration of ART) all-cause and cause-specific mortality hazard ratios for tertiles of CD4:CD8 ratio (0-0.40, 0.41-0.64 [reference], >0.64) and CD8 count (0-760, 761-1138 [reference], >1138 cells/μL) and examined the shape of associations using cubic splines.
Results - During 276526 person-years, 1834 of 49865 patients died (249 AIDS-related; 1076 non-AIDS-defining; 509 unknown/unclassifiable deaths). There was little evidence that CD4:CD8 ratio was prognostic for all-cause mortality after adjustment for other factors: the adjusted hazard ratio (aHR) for lower vs middle tertile was 1.11 (95% confidence interval [CI], 1.00-1.25). The association of CD8 count with all-cause mortality was U-shaped: aHR for higher vs middle tertile was 1.13 (95% CI, 1.01-1.26). AIDS-related mortality declined with increasing CD4:CD8 ratio and decreasing CD8 count. There was little evidence that CD4:CD8 ratio or CD8 count was prognostic for non-AIDS mortality.
Conclusions - In this large cohort collaboration, the magnitude of adjusted associations of CD4:CD8 ratio or CD8 count with mortality was too small for them to be useful as independent prognostic markers in virally suppressed patients on ART.
© The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.
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21 MeSH Terms
Brief Report: Weight Gain in Persons With HIV Switched From Efavirenz-Based to Integrase Strand Transfer Inhibitor-Based Regimens.
Norwood J, Turner M, Bofill C, Rebeiro P, Shepherd B, Bebawy S, Hulgan T, Raffanti S, Haas DW, Sterling TR, Koethe JR
(2017) J Acquir Immune Defic Syndr 76: 527-531
MeSH Terms: Adult, Benzoxazines, Cohort Studies, Female, HIV Infections, HIV Integrase Inhibitors, Humans, Male, Middle Aged, Retrospective Studies, Reverse Transcriptase Inhibitors, Weight Gain
Show Abstract · Added March 14, 2018
BACKGROUND - With the introduction of integrase strand transfer inhibitor (INSTI)-based antiretroviral therapy, persons living with HIV have a potent new treatment option. Recently, providers at our large treatment clinic noted weight gain in several patients who switched from efavirenz/tenofovir disoproxil fumarate/emtricitabine (EFV/TDF/FTC) to dolutegravir/abacavir/lamivudine (DTG/ABC/3TC). In this study, we evaluated weight change in patients with sustained virologic suppression who switched from EFV/TDF/FTC to an INSTI-containing regimen.
METHODS - We performed a retrospective observational cohort study among adults on EFV/TDF/FTC for at least 2 years who had virologic suppression. We assessed weight change over 18 months in patients who switched from EFV/TDF/FTC to an INSTI-containing regimen or a protease inhibitor (PI)-containing regimen versus those on EFV/TDF/FTC over the same period. In a subgroup analysis, we compared patients switched to DTG/ABC/3TC versus raltegravir- or elvitegravir-containing regimens.
RESULTS - A total of 495 patients were included: 136 who switched from EFV/TDF/FTC to an INSTI-containing regimen and 34 switched to a PI-containing regimen. Patients switched to an INSTI-containing regimen gained an average of 2.9 kg at 18 months compared with 0.9 kg among those continued on EFV/TDF/FTC (P = 0.003), whereas those switched to a PI regimen gained 0.7 kg (P = 0.81). Among INSTI regimens, those switched to DTG/ABC/3TC gained the most weight at 18 months (5.3 kg, P = 0.001 compared with EFV/TDF/FTC).
CONCLUSION - Adults living with HIV with viral suppression gained significantly more weight after switching from daily, fixed-dose EFV/TDF/FTC to an INSTI-based regimen compared with those remaining on EFV/TDF/FTC. This weight gain was greatest among patients switching to DTG/ABC/3TC.
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12 MeSH Terms
Outcomes of HIV-positive patients with cryptococcal meningitis in the Americas.
Crabtree Ramírez B, Caro Vega Y, Shepherd BE, Le C, Turner M, Frola C, Grinsztejn B, Cortes C, Padgett D, Sterling TR, McGowan CC, Person A
(2017) Int J Infect Dis 63: 57-63
MeSH Terms: Adult, Americas, Anti-Retroviral Agents, CD4 Lymphocyte Count, Female, Follow-Up Studies, HIV Infections, Humans, Male, Meningitis, Cryptococcal, Middle Aged, Patient Compliance, Retrospective Studies, Treatment Outcome
Show Abstract · Added March 14, 2018
BACKGROUND - Cryptococcal meningitis (CM) is associated with substantial mortality in HIV-infected patients. Optimal timing of antiretroviral therapy (ART) in persons with CM represents a clinical challenge, and the burden of CM in Latin America has not been well described. Studies suggest that early ART initiation is associated with higher mortality, but data from the Americas are scarce.
METHODS - HIV-infected adults in care between 1985-2014 at participating sites in the Latin America (the Caribbean, Central and South America network (CCASAnet)) and the Vanderbilt Comprehensive Care Clinic (VCCC) and who had CM were included. Survival probabilities were estimated. Risk of death when initiating ART within the first 2 weeks after CM diagnosis versus initiating between 2-8 weeks was assessed using dynamic marginal structural models adjusting for site, age, sex, year of CM, CD4 count, and route of HIV transmission.
FINDINGS - 340 patients were included (Argentina 58, Brazil 138, Chile 28, Honduras 27, Mexico 34, VCCC 55) and 142 (42%) died during the observation period. Among 151 patients with CM prior to ART 56 (37%) patients died compared to 86 (45%) of 189 with CM after ART initiation (p=0.14). Patients diagnosed with CM after ART had a higher risk of death (p=0.03, log-rank test). The probability of survival was not statistically different between patients who started ART within 2 weeks of CM (7/24, 29%) vs. those initiating between 2-8 weeks (14/53, 26%) (p=0.96), potentially due to lack of power.
INTERPRETATION - In this large Latin-American cohort, patients with CM had very high mortality rates, especially those diagnosed after ART initiation. This study reflects the overwhelming burden of CM in HIV-infected patients in Latin America.
Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.
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14 MeSH Terms
Increased Risk of Myocardial Infarction in HIV-Infected Individuals in North America Compared With the General Population.
Drozd DR, Kitahata MM, Althoff KN, Zhang J, Gange SJ, Napravnik S, Burkholder GA, Mathews WC, Silverberg MJ, Sterling TR, Heckbert SR, Budoff MJ, Van Rompaey S, Delaney JAC, Wong C, Tong W, Palella FJ, Elion RA, Martin JN, Brooks JT, Jacobson LP, Eron JJ, Justice AC, Freiberg MS, Klein DB, Post WS, Saag MS, Moore RD, Crane HM
(2017) J Acquir Immune Defic Syndr 75: 568-576
MeSH Terms: Adult, Anti-HIV Agents, Antiretroviral Therapy, Highly Active, CD4 Lymphocyte Count, Comorbidity, Female, HIV Infections, Humans, Incidence, Male, Middle Aged, Myocardial Infarction, North America, Proportional Hazards Models, Risk Assessment, Risk Factors, Viral Load
Show Abstract · Added March 14, 2018
BACKGROUND - Previous studies of cardiovascular disease (CVD) among HIV-infected individuals have been limited by the inability to validate and differentiate atherosclerotic type 1 myocardial infarctions (T1MIs) from other events. We sought to define the incidence of T1MIs and risk attributable to traditional and HIV-specific factors among participants in the North American AIDS Cohort Collaboration on Research and Design (NA-ACCORD) and compare adjusted incidence rates (IRs) to the general population Atherosclerosis Risk in Communities (ARIC) cohort.
METHODS - We ascertained and adjudicated incident MIs among individuals enrolled in 7 NA-ACCORD cohorts between 1995 and 2014. We calculated IRs, adjusted incidence rate ratios (aIRRs), and 95% confidence intervals of risk factors for T1MI using Poisson regression. We compared aIRRs of T1MIs in NA-ACCORD with those from ARIC.
RESULTS - Among 29,169 HIV-infected individuals, the IR for T1MIs was 2.57 (2.30 to 2.86) per 1000 person-years, and the aIRR was significantly higher compared with participants in ARIC [1.30 (1.09 to 1.56)]. In multivariable analysis restricted to HIV-infected individuals and including traditional CVD risk factors, the rate of T1MI increased with decreasing CD4 count [≥500 cells/μL: ref; 350-499 cells/μL: aIRR = 1.32 (0.98 to 1.77); 200-349 cells/μL: aIRR = 1.37 (1.01 to 1.86); 100-199 cells/μL: aIRR = 1.60 (1.09 to 2.34); <100 cells/μL: aIRR = 2.19 (1.44 to 3.33)]. Risk associated with detectable HIV RNA [<400 copies/mL: ref; ≥400 copies/mL: aIRR = 1.36 (1.06 to 1.75)] was significantly increased only when CD4 was excluded.
CONCLUSIONS - The higher incidence of T1MI in HIV-infected individuals and increased risk associated with lower CD4 count and detectable HIV RNA suggest that early suppressive antiretroviral treatment and aggressive management of traditional CVD risk factors are necessary to maximally reduce MI risk.
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17 MeSH Terms
Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing Antibody that Lacks a Protruding Loop.
Cale EM, Gorman J, Radakovich NA, Crooks ET, Osawa K, Tong T, Li J, Nagarajan R, Ozorowski G, Ambrozak DR, Asokan M, Bailer RT, Bennici AK, Chen X, Doria-Rose NA, Druz A, Feng Y, Joyce MG, Louder MK, O'Dell S, Oliver C, Pancera M, Connors M, Hope TJ, Kepler TB, Wyatt RT, Ward AB, Georgiev IS, Kwong PD, Mascola JR, Binley JM
(2017) Immunity 46: 777-791.e10
MeSH Terms: Amino Acid Sequence, Antibodies, Neutralizing, B-Lymphocytes, Binding Sites, Complementarity Determining Regions, HIV Antibodies, HIV Envelope Protein gp120, HIV Infections, HIV-1, Humans, Models, Molecular, Peptide Fragments, Phylogeny, Protein Binding, Protein Conformation, Protein Interaction Domains and Motifs, Protein Multimerization, Vaccines, Virus-Like Particle, env Gene Products, Human Immunodeficiency Virus
Show Abstract · Added March 14, 2018
Most HIV-1-specific neutralizing antibodies isolated to date exhibit unusual characteristics that complicate their elicitation. Neutralizing antibodies that target the V1V2 apex of the HIV-1 envelope (Env) trimer feature unusually long protruding loops, which enable them to penetrate the HIV-1 glycan shield. As antibodies with loops of requisite length are created through uncommon recombination events, an alternative mode of apex binding has been sought. Here, we isolated a lineage of Env apex-directed neutralizing antibodies, N90-VRC38.01-11, by using virus-like particles and conformationally stabilized Env trimers as B cell probes. A crystal structure of N90-VRC38.01 with a scaffolded V1V2 revealed a binding mode involving side-chain-to-side-chain interactions that reduced the distance the antibody loop must traverse the glycan shield, thereby facilitating V1V2 binding via a non-protruding loop. The N90-VRC38 lineage thus identifies a solution for V1V2-apex binding that provides a more conventional B cell pathway for vaccine design.
Copyright © 2017 Elsevier Inc. All rights reserved.
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19 MeSH Terms