Biology subjects

Lee, Y. E.

Publications and source records attributed to Lee, Y. E..

17 recordsLinked to original sources

bioRxiv2026

Developmental and molecular features shaping broad and synergistic actions of human autoantibodies targeting interferon-α

Neutralizing autoantibodies against interferon- (IFN) are associated with severe viral infections but may improve outcomes in IFN-driven autoimmunity. How these antibodies emerge, mature, and function at the molecular level remains unclear. Here, we tracked development of plasma neutralizing activity against all 12 IFNs in multiple human donors over years. Plasma neutralization frequently initiates with narrow IFN specificity, often IFN8, but increases in breadth and potency with individual kinetics. Monoclonal antibody analyses reveal that affinity maturation generates epitope-specific antibody classes, highlighting parallel emergence of subtype-restricted and broadly-reactive antibodies. Biophysical and structural characterization of human antibody-IFN complexes uncovers determinants of initial specificity and breadth development. Strikingly, antibodies engaging non-competing, neutralizing epitopes can act co-operatively to block IFN signaling, and some combinations trigger Fc-effector functions via cell surface IFN:IFNAR2 interactions that may eliminate IFN-responsive cells. Our findings reveal features shaping anti-IFN autoantibody repertoires and unappreciated synergistic mechanisms that amplify their potency and pathogenic potential.

immunology↗

bioRxiv2026

Structure-guided vaccination elicits broadly neutralizing antibodies targeting the HIV-1 silent face

An effective HIV-1 vaccine will likely require broadly neutralizing antibodies (bnAbs) targeting multiple complementary epitopes on the Envelope (Env) glycoprotein. Donor-derived bnAbs targeting the conserved silent face (SF) epitope complement established bnAb classes, but the maturation pathways underlying SF bnAb development and their inducibility via vaccination remain poorly understood. Here, we elicit SF-like bnAbs by vaccination and define pathways by which these responses can be guided toward breadth. Structural analysis of the donor-derived bnAb SF10 revealed that broad neutralization depends on a minimal set of heavy chain mutations despite extensive overall somatic hypermutation. We leveraged these insights to engineer Env immunogens that engage an SF10 precursor and selectively favor breadth-associated mutations during sequential immunization in a new immunoglobulin knock-in mouse model. Vaccination reproducibly elicited heterologous neutralizing serum responses and monoclonal antibodies that acquired key SF-like improbable mutations and broad neutralizing activity. Notably, elicited antibodies combined features of distinct human SF bnAbs, demonstrating that vaccination can access alternative mutational solutions rather than precisely recapitulating a donor-derived maturation pathway. These findings establish the silent face as a tractable vaccine target and expand the bnAb specificities available for multi-epitope HIV-1 vaccine strategies.

immunology↗

bioRxiv2026

Structural basis of diverse antibody recognition of conserved coronavirus spike S2 epitopes that contribute to protective immunity

Conserved epitopes within the coronavirus spike S2 domain elicit broadly reactive antibodies, yet many characterized responses show limited neutralizing and variable protective activity, leaving their contribution to antiviral immunity unclear. Building on our previous mapping of evolutionarily conserved spike coldspots, we isolated human monoclonal antibodies targeting four conserved epitopes in the spike S2 domain: the internal fusion peptide (iFP), the central helix (CH), the connector domain (CD), and a membrane-proximal epitope in the heptad repeat 2 that we term the lower stalk (LS). A crystal structure of an LS-directed antibody defined a previously unresolved mode of antibody recognition of this membrane-proximal epitope, while cryogenic electron microscopy (cryo-EM) structures revealed that genetically diverse CH-specific antibodies use distinct binding modes to converge on conserved features of the prefusion S2 apex. Despite minimal neutralizing activity, CH- and LS-directed antibodies exhibited distinct antiviral functions. LS-directed antibodies mediated Fc{gamma} receptor-dependent effector activity in vitro, whereas the broadly reactive CH-directed antibody ch.007 lacked detectable antibody-dependent cellular cytotoxicity (ADCC) or cellular phagocytosis (ADCP) activity yet protected mice from lethal SARS-CoV-2 MA10 challenge, with protection abrogated by Fc{gamma} receptor-silencing mutations. Together, these findings expand the genetic, structural and functional landscape of human antibody responses to conserved coronavirus S2 epitopes and demonstrate that CH-directed antibodies can contribute to protective immunity through Fc-dependent mechanisms not predicted by in vitro neutralization or conventional in vitro Fc effector assays.

biophysics↗

bioRxiv2026

Structural and mutational analyses define distinct molecular routes to broad SARS-CoV-2 receptor-binding domain recognition

Broadly reactive antibodies elicited by SARS-CoV-2 infection or vaccination can reveal conserved viral vulnerabilities and inform vaccines with broad coronavirus coverage. Here, we characterize two human-derived monoclonal antibodies, B2014 and C5078, that recognize conserved epitopes on the SARS-CoV-2 RBD and retain activity across antigenically distinct variants. Notably, C5078 also recognizes diverse sarbecoviruses and remains active against currently circulating variants, including XFG and NB.1.8.1. Cryo-EM structures reveal that B2014 recognizes an epitope adjacent to the class 3 antibody site, whereas C5078 targets the highly conserved, cryptic site V epitope. Structural analysis defines how C5078 uses affinity-matured interactions to engage conserved RBD residues, providing a molecular basis for its exceptional breadth. Deep mutational scanning across multiple SARS-CoV-2 variant backgrounds further defines potential pathways of antibody escape, explaining the loss of B2014 activity against antigenically evolved variants while revealing a high barrier to escape from C5078. Together, these findings define distinct structural solutions for broad RBD recognition and highlight conserved, mutationally constrained epitopes that may serve as targets for vaccines designed to elicit antibody responses resilient to ongoing SARS-CoV-2 evolution and future sarbecovirus emergence.

biophysics↗

bioRxiv2026

Dissociation kinetics and avidity gate SARS-CoV-2 neutralization by HR2 stem helix antibodies

SARS-CoV-2 evolution has reduced the efficacy of clinical monoclonal antibodies, underscoring the need for therapeutics targeting conserved viral regions. The Spike (S) heptad repeat 2 (HR2) stem helix is highly conserved across SARS-CoV-2 variants and related betacoronaviruses. Although antibodies to this region can neutralize infection, their natural occurrence and evolution remain poorly understood. We previously identified human neutralizing antibodies to a conserved peptide within this region (HR2 coldspot). Here, we show that plasma IgG reactivity to this region remains rare, even after repeated antigen exposure. Longitudinal analysis over 30 months revealed continued somatic hypermutation of HR2-specific antibodies, yet none surpassed the potency or breadth of hr2.016, which emerged shortly after primary infection. Crystal structures of four HR2 stem helix antibodies revealed convergent recognition across distinct antibody lineages. Comparison of hr2.016 with its non-neutralizing clonal relative hr2.086 showed that structural convergence masks distinct binding kinetics. Surface plasmon resonance and molecular dynamics simulations revealed a more stable interaction network for hr2.016, with slower dissociation and prolonged S residence time. Neutralization required the IgG format, supporting an avidity-driven mechanism. Together, these findings define kinetic and avidity constraints governing neutralization at the HR2 stem helix and position hr2.016 as a resilient therapeutic candidate.

immunology↗

bioRxiv2026

Impaired SOX17 Expression Causes Endothelial Dysfunction and Pulmonary Arterial Hypertension by Insufficient Suppression of RUNX1

Genome-wide association studies have identified rare and common mutations associated with increased risk of pulmonary arterial hypertension (PAH), but the mechanism by which impaired SOX17 expression increases PAH risk is not known. Notably, SOX17 plays a critical role in endothelial identity during development by suppressing RUNX1 through binding to its promoter and directing stem and progenitor cells toward an endothelial rather than a hematopoietic cell fate. RUNX1 functions as a key regulator of myeloid differentiation, aberrant angiogenesis and adverse cardiac remodeling. Previously, we found that RUNX1 inhibition reverses pulmonary hypertension (PH) in multiple animal models. Here, we hypothesize that impaired expression of SOX17 in PAH leads to endothelial cell (EC) dysfunction by failing to suppress RUNX1. METHODSHuman pulmonary artery endothelial cells (HPAECs) with stable SOX17 CRISPR/Cas9 knockout or RUNX1 overexpression were generated and examined for endothelial and hematopoietic gene expression, proliferation, migration, apoptosis, and angiogenesis. Immortalized lymphoblastoid cell lines (LCLs) from PAH patients with SOX17 mutations and healthy controls were reprogrammed into induced pluripotent stem cells (iPSCs) and differentiated into ECs. The effect of RUNX1 inhibition on Sugen/hypoxia-PH was examined in rats, SOX17 enhancer knockout (SOX17enhKO) mice, and Cdh5-CreERT2;Runx1(flox/flox);SOX17enhKO triple transgenic mice. SOX17 and RUNX1 expression were analyzed in peripheral blood samples from PAH patients (n=359). RESULTSHPAECs with SOX17 deletion or RUNX1 overexpression exhibited decreased expression of EC markers, enhanced proliferation and migration, defective angiogenesis, and decreased apoptosis. RUNX1 siRNA knockdown or RUNX1 inhibition by Ro5-3335 partially restored the endothelial properties in SOX17 KO HPAECs. ECs differentiated from SOX17 mutant PAH patient iPSCs exhibited upregulated RUNX1 expression and loss of endothelial identity, which was also partially restored by RUNX1 siRNA or Ro5-3335. In addition, SOX17enhKO mice had increased RUNX1 expression and susceptibility to Sugen/hypoxia-induced PH (SuHx-PH). Treatment with RUNX1 inhibitors or inducible endothelial-specific deletion of RUNX1 rescued SuHx-PH susceptibility in SOX17enhKO mice. RUNX1 inhibitors Ro5-3335 and Ro24-7429 also reversed SuHx-PH in wild-type rats. In addition, plasma RUNX1 expression was higher in PAH patients lacking detectable SOX17 expression than in patients with detectable SOX17 expression. CONCLUSIONSImpaired SOX17 expression increases the risk of PAH through insufficient suppression of RUNX1, leading to pulmonary endothelial dysfunction. RUNX1 inhibition mitigates PH associated with SOX17 deficiency and may represent a novel therapeutic strategy for PAH, especially those with rare or common SOX17 mutations.

cell biology↗

bioRxiv2025

Myeloid Specific Ablation of SHIP1 Boosts ex vivo Expansion and Regulatory Function of Myeloid-Derived Suppressor Cells in Inflammatory Arthritis

Myeloid-derived suppressor cells (MDSCs) are a heterogeneous cell population and the immunosuppressive function of MDSCs has been well established in tumor microenvironment. Recent studies show that adoptive transfer of MDSCs can ameliorate collagen-induced inflammatory arthritis (CIA), a mouse model of human rheumatoid arthritis (RA). Src homology 2 domain- containing inositol polyphosphate 5-phosphatase 1 (SHIP1) was previously shown to regulate MDSC differentiation. In this study, we aimed to generate immunosuppressive MDSCs from mouse bone marrow (BM) through genetic modification combined with cytokine treatments, and to investigate the ability of these ex vivo induced BM-MDSCs to suppress inflammatory responses in the CIA mouse model of RA. We found that myeloid specific ablation of SHIP1 increased the ratio of MDSCs and enhanced their regulatory functions in cytokine induced BM culture. MDSCs from LysMcre:SHIP1flox/flox mouse BM culture demonstrated stronger inhibitory effect on T cell proliferation than those from control mouse BM. Ex vivo induced MDSCs from either control mice or mice with myeloid specific ablation of SHIP1 were administered to the CIA mice as a cell-based therapy to treat inflammatory arthritis. Adoptive transfer of either BM-MDSCs significantly reduced disease incidence and severity, but SHIP1 deficient BM-MDSCs exhibited even higher efficacy compared to wild-type BM-MDSCs. Furthermore, pharmacological inhibition of SHIP1 enhanced the expression of immune regulatory genes in BM-derived MDSCs, and adoptive transfer of these cells protected against CIA development. In conclusion, myeloid specific ablation of SHIP1 boosts ex vivo expansion and immune regulatory function of MDSCs in experimental inflammatory arthritis. These ex vivo generated BM-MDSCs may provide novel therapeutic opportunities for the treatment of RA and other inflammatory diseases.

immunology↗

bioRxiv2025

Enabling CAR-T Cell Immunotherapy in Glioblastoma by Modifying Tumor Microenvironment via Oncolytic Adenovirus Encoding Bispecific T Cell Engager

Recent clinical trials show that CAR-T cell therapies can initially blunt tumor growth in glioblastoma (GBM) patients. However, the tumor microenvironment activates mechanisms that inhibit tumor-killing potential of the CAR-T cells and limit their therapeutic efficacy. To counteract this, we have utilized oncolytic adenovirus (OV) Ad5-{Delta}24-RGD as a platform to overexpress a bispecific T cell engager (BiTE) targeting both T cell marker CD3 and GBM specific tumor associated antigen IL-13R2. We first demonstrated that OV-BiTE could enhance recruitment of T cells to GBM in vitro and in vivo. We then showed that intratumoral injection of OV-BiTE followed by infusion of combined EGFR- and EGFRvIII-CAR-T cells was more effective than OV-BiTE supplemented with either CAR-T therapy alone, and led to significant tumor eradication in a GBM xenograft mouse model. In conclusion, our multimodal OV-BiTE & CAR-T cell immunotherapy is capable of overcoming immunosuppressive tumor microenvironment and GBM resistance to treatment. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/667708v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@c55b15org.highwire.dtl.DTLVardef@deffb2org.highwire.dtl.DTLVardef@64ff90org.highwire.dtl.DTLVardef@c65fc2_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIOncolytic adenovirus encoding bispecific T cell engager (OV-BiTE) combines two immunotherapeutic agents into one. C_LIO_LIOV-BiTE strategy modifies tumor microenvironment and enhances recruitment of T cells to glioblastoma (GBM) in vitro and in vivo. C_LIO_LIMultimodal OV-BiTE & CAR-T cell immunotherapy effectively reduced tumor mass in a GBM xenograft mouse model and is superior to either immunotherapy alone. C_LI

cancer biology↗

bioRxiv2024

Bispecific antibodies with broad neutralization potency against SARS-CoV-2 variants of concern

The ongoing emergence of SARS-CoV-2 variants of concern (VOCs) that reduce the effectiveness of antibody therapeutics necessitates development of next-generation antibody modalities that are resilient to viral evolution. Here, we characterized N-terminal domain (NTD) and receptor binding domain (RBD)-specific monoclonal antibodies previously isolated from COVID-19 convalescent donors for their activity against emergent SARS-CoV-2 VOCs. Among these, the NTD-specific antibody C1596 displayed the greatest breadth of binding to VOCs, with cryo-EM structural analysis revealing recognition of a distinct NTD epitope outside of the site i antigenic supersite. Given C1596s favorable binding profile, we designed a series of bispecific antibodies (bsAbs) termed CoV2-biRNs, that featured both NTD and RBD specificities. Notably, two of the C1596-inclusive bsAbs, CoV2-biRN5 and CoV2-biRN7, retained potent in vitro neutralization activity against all Omicron variants tested, including XBB.1.5, EG.5.1, and BA.2.86, contrasting the diminished potency of parental antibodies delivered as monotherapies or as a cocktail. Furthermore, prophylactic delivery of CoV2-biRN5 significantly reduced the viral load within the lungs of K18-hACE2 mice following challenge with SARS-CoV-2 XBB.1.5. In conclusion, our NTD-RBD bsAbs offer promising potential for the design of resilient, next-generation antibody therapeutics against SARS-CoV-2 VOCs. One Sentence SummaryBispecific antibodies with a highly cross-reactive NTD antibody demonstrate resilience to SARS-CoV-2 variants of concern.

immunology↗

bioRxiv2022

Neutralizing monoclonal antibodies elicited by mosaic RBD nanoparticles bind conserved sarbecovirus epitopes

Protection from SARS-related coronaviruses with spillover potential and SARS-CoV-2 variants could prevent and/or end pandemics. We show that mice immunized with nanoparticles co-displaying spike receptor-binding domains (RBDs) from eight sarbecoviruses (mosaic-8 RBD-nanoparticles) efficiently elicit cross-reactive anti-sarbecovirus antibodies against conserved class 1/4 and class 3 RBD epitopes. Monoclonal antibodies (mAbs) identified from initial screening of <10,000 single B-cells secreting IgGs binding two or more sarbecovirus RBDs showed cross-reactive binding and neutralization of SARS-CoV-2 variants and animal sarbecoviruses. Single-particle cryo-EM structures of antibody-spike complexes, including a Fab-Omicron complex, mapped neutralizing mAbs to conserved class 1/4 RBD epitopes and revealed neutralization mechanisms, potentials for intra-spike trimer crosslinking by single IgGs, and induced changes in trimer upon Fab binding. In addition, we identified a mAb resembling Bebtelovimab, an EUA-approved human class 3 anti-RBD mAb. These results support using mosaic RBD-nanoparticles to identify therapeutic pan-sarbecovirus and pan-variant mAbs and to elicit them by vaccination.

immunology↗

bioRxiv2022

Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models

To combat future SARS-CoV-2 variants and spillovers of SARS-like betacoronaviruses (sarbecoviruses) threatening global health, we designed mosaic nanoparticles presenting randomly-arranged sarbecovirus spike receptor-binding domains (RBDs) to elicit antibodies against conserved/relatively-occluded, rather than variable/immunodominant/exposed, epitopes. We compared immune responses elicited by mosaic-8 (SARS-CoV-2 and seven animal sarbecoviruses) and homotypic (only SARS-CoV-2) RBD-nanoparticles in mice and macaques, observing stronger responses elicited by mosaic-8 to mismatched (not on nanoparticles) strains including SARS-CoV and animal sarbecoviruses. Mosaic-8 immunization showed equivalent neutralization of SARS-CoV-2 variants including Omicron and protected from SARS-CoV-2 and SARS-CoV challenges, whereas homotypic SARS-CoV-2 immunization protected only from SARS-CoV-2 challenge. Epitope mapping demonstrated increased targeting of conserved epitopes after mosaic-8 immunization. Together, these results suggest mosaic-8 RBD-nanoparticles could protect against SARS-CoV-2 variants and future sarbecovirus spillovers.

microbiology↗

bioRxiv2022

A naturally arising broad and potent CD4-binding site antibody with low somatic mutation

The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, including insertions and deletions, which make their induction challenging. VRC01-class bNAbs exhibit extraordinary breadth and potency, but also rank among the most highly somatically-mutated bNAbs. Here we describe a VRC01-class antibody isolated from a viremic controller, BG24, that has less than half the mutations of most other relatives of its class, while achieving comparable breadth and potency. A 3.8 [A] X-ray crystal structure of a BG24-BG505 Env trimer complex revealed conserved contacts at the gp120 interface characteristic of the VRC01-class Abs, despite lacking common CDR3 sequence motifs. The existence of moderately-mutated CD4-binding site (CD4bs) bNAbs such as BG24 provides a simpler blueprint for CD4bs antibody induction by a vaccine, raising the prospect that such an induction might be feasible with a germline-targeting approach. TeaserAn anti-HIV-1 antibody with comparable neutralization breadth and potency to similarly-classed antibodies, with half as many mutations.

immunology↗

bioRxiv2022

Conserved Neutralizing Epitopes on the N-Terminal Domain of Variant SARS-CoV-2 Spike Proteins

SARS-CoV-2 infection or vaccination produces neutralizing antibody responses that contribute to better clinical outcomes. The receptor binding domain (RBD) and the N-terminal domain (NTD) of the spike trimer (S) constitute the two major neutralizing targets for the antibody system. Neutralizing antibodies targeting the RBD bind to several different sites on this domain. In contrast, most neutralizing antibodies to NTD characterized to date bind to a single supersite, however these antibodies were obtained by methods that were not NTD specific. Here we use NTD specific probes to focus on anti-NTD memory B cells in a cohort of pre-omicron infected individuals some of which were also vaccinated. Of 275 NTD binding antibodies tested 103 neutralized at least one of three tested strains: Wuhan-Hu-1, Gamma, or PMS20, a synthetic variant which is extensively mutated in the NTD supersite. Among the 43 neutralizing antibodies that were further characterized, we found 6 complementation groups based on competition binding experiments. 58% targeted epitopes outside the NTD supersite, and 58% neutralized either Gamma or Omicron, but only 14% were broad neutralizers. Three of the broad neutralizers were characterized structurally. C1520 and C1791 recognize epitopes on opposite faces of the NTD with a distinct binding pose relative to previously described antibodies allowing for greater potency and cross-reactivity with 7 different variants including Beta, Delta, Gamma and Omicron. Antibody C1717 represents a previously uncharacterized class of NTD-directed antibodies that recognizes the viral membrane proximal side of the NTD and SD2 domain, leading to cross-neutralization of Beta, Gamma and Omicron. We conclude SARS-CoV-2 infection and/or Wuhan-Hu-1 mRNA vaccination produces a diverse collection of memory B cells that produce anti-NTD antibodies some of which can neutralize variants of concern. Rapid recruitment of these cells into the antibody secreting plasma cell compartment upon re-infection likely contributes to the relatively benign course of subsequent infections with SARS-CoV-2 variants including omicron.

immunology↗

bioRxiv2021

Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies

Many anti-SARS-CoV-2 neutralizing antibodies target the ACE2-binding site on viral spike receptor-binding domains (RBDs). The most potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly-emergent zoonotic sarbecoviruses and variants, but usually show only weak neutralization potencies. We characterized two class 4 anti-RBD antibodies derived from COVID-19 donors that exhibited broad recognition and potent neutralization of zoonotic coronavirus and SARS-CoV-2 variants. C118-RBD and C022-RBD structures revealed CDRH3 mainchain H-bond interactions that extended an RBD {beta}-sheet, thus reducing sensitivity to RBD sidechain changes, and epitopes that extended from the cryptic epitope to occlude ACE2 binding. A C118-spike trimer structure revealed rotated RBDs to allow cryptic epitope access and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.

immunology↗

bioRxiv2021

Antibody elicited by HIV-1 immunogen vaccination in macaques displaces Env fusion peptide and destroys a neutralizing epitope

HIV-1 vaccine design aims to develop an immunogen that elicits broadly neutralizing antibodies against a desired epitope, while eliminating responses to off-target regions of HIV-1 Env. Here we report isolation and characterization of Ab1245, an off-target antibody against the Env gp120-gp41 interface, from V3-glycan patch immunogen-primed and boosted macaques. A 3.7[A] cryo-EM structure of an Ab1245-Env complex reveals one Ab1245 Fab binding asymmetrically to Env trimer at the gp120-gp41 interface using its long CDRH3 to mimic regions of gp41. The mimicry includes positioning of a CDRH3 methionine into the gp41 tryptophan clasp, resulting in displacement of the fusion peptide and fusion peptide-proximal region. Despite fusion peptide displacement, Ab1245 is non-neutralizing even at high concentrations, implying that only two fusion peptides per trimer are required for viral-host membrane fusion. These structural analyses facilitate immunogen design to prevent elicitation of Ab1245-like antibodies that block neutralizing antibodies against the fusion peptide.

immunology↗

bioRxiv2020

Mosaic RBD nanoparticles elicit neutralizing antibodies against SARS-CoV-2 and zoonotic coronaviruses

Protection against SARS-CoV-2 and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor-binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles; 4-8 distinct RBDs). Mice immunized with RBD-nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic-RBD-nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs compared to sera from immunizations with homotypic SARS-CoV-2-RBD-nanoparticles or COVID-19 convalescent human plasmas. Moreover, sera from mosaic-RBD-immunized mice neutralized heterologous pseudotyped coronaviruses equivalently or better after priming than sera from homotypic SARS-CoV-2-RBD-nanoparticle immunizations, demonstrating no immunogenicity loss against particular RBDs resulting from co-display. A single immunization with mosaic-RBD-nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses. One sentence summaryNanoparticle strategy for pan-sarbecovirus vaccine 125-character summary for online ToCImmunizing with nanoparticles displaying diverse coronavirus RBDs elicits cross-reactive and neutralizing antibody responses.

immunology↗

bioRxiv2020

Structural classification of neutralizing antibodies against the SARS-CoV-2 spike receptor-binding domain suggests vaccine and therapeutic strategies

The COVID-19 pandemic presents an urgent health crisis. Human neutralizing antibodies (hNAbs) that target the host ACE2 receptor-binding domain (RBD) of the SARS-CoV-2 spike1-5 show therapeutic promise and are being evaluated clincally6-8. To determine structural correlates of SARS-CoV-2 neutralization, we solved 8 new structures of distinct COVID-19 hNAbs5 in complex with SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed classification into categories: (1) VH3-53 hNAbs with short CDRH3s that block ACE2 and bind only to "up" RBDs, (2) ACE2-blocking hNAbs that bind both "up" and "down" RBDs and can contact adjacent RBDs, (3) hNAbs that bind outside the ACE2 site and recognize "up" and "down" RBDs, and (4) Previously-described antibodies that do not block ACE2 and bind only "up" RBDs9. Class 2 comprised four hNAbs whose epitopes bridged RBDs, including a VH3-53 hNAb that used a long CDRH3 with a hydrophobic tip to bridge between adjacent "down" RBDs, thereby locking spike into a closed conformation. Epitope/paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally-occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects, suggesting combinations for clinical use, and providing insight into immune responses against SARS-CoV-2.

molecular biology↗