Biology subjects

Zhang, Y.-N.

Publications and source records attributed to Zhang, Y.-N..

9 recordsLinked to original sources

bioRxiv2026

Rationally Engineered Self-Assembling Protein Nanoparticles for Allergen-Specific Peanut Allergy Immunotherapy

Peanut allergy is a prevalent immunoglobulin E (IgE)-mediated food allergy that can cause life-threatening anaphylaxis. Current treatment options provide limited efficacy and variable durability of protection. While allergen-displaying virus-like particles (VLPs) have shown promise, their development is often constrained by limited design flexibility and manufacturing complexity. Here, we develop self-assembling protein nanoparticles (SApNPs) displaying the major allergens Ara h 2 and Ara h 6 as a modular platform for peanut allergy immunotherapy. Using the 60-mer TIP60 scaffold, we engineer nanoparticles by expanding particle size through -helical insertion and replacing the human myosin-X segment with evolutionarily distant catfish homologs, followed by structure-guided and evolution-inspired optimization to enhance thermostability while minimizing human sequence content. Formulated with a Toll-like receptor 9 (TLR9) agonist, these allergen-displaying SApNPs confer robust protection against peanut-induced anaphylaxis in both prophylactic and therapeutic settings. Mechanistically, SApNPs exhibit prolonged lymph node retention, sustained presentation on follicular dendritic cells, and enhanced germinal center responses compared with soluble allergens, promoting allergen-specific IgG and functional T cell responses while limiting IgE escalation. Collectively, these findings establish allergen-displaying SApNPs as a rationally engineered, scalable, and modular platform for peanut allergy treatment with potential applicability to other allergic diseases.

immunology↗

bioRxiv2026

Xenoglycosylation of the HIV-1 Glycan Shield Promotes Cross-Clade Neutralization and Diverse Human Antibody Lineages

Despite advances in HIV-1 envelope glycoprotein (Env)-based vaccine design, eliciting broadly neutralizing antibodies (bNAbs) remains a central challenge. Here, we identify core (1,3)-fucose as a key modulator of neutralizing antibody (NAb) induction and breadth. Uncleaved prefusion-optimized (UFO) trimers and self-assembling protein nanoparticles (SApNPs) produced in High Five (Hi5) insect cells incorporate core (1,3)-fucose into the Env glycan shield. Crystal structures of Hi5-produced BG505 UFO trimers in complex with bNAbs confirm native-like Env architecture and epitope presentation. In wild-type mice, these trimers and SApNPs elicit robust autologous and heterologous NAb responses. We then engineer Chinese hamster ovary (CHO) cells to co-express three insect- and plant-derived core (1,3)-fucosyltransferases. The resulting immunogens carry fucosylated mammalian glycans and elicit cross-clade NAb responses in mice, supporting an important role for core (1,3)-fucose in broadened neutralization. Env-specific IgE responses suggest engagement of associated immune pathways during vaccination. In ATX-Gx humanized mice, core (1,3)-fucosylated, glycan-trimmed Env elicits detectable cross-clade neutralization by week 11. Single-cell analysis identifies distinct human antibody lineages with cross-clade activity and noncanonical Env recognition. Repertoire and functional analyses uncover putatively related lineage members across two animals within the same group. Together, these findings support xenoglycosylation as a promising, germline-agnostic strategy for HIV-1 vaccine design.

immunology↗

bioRxiv2025

Rational design of next-generation filovirus vaccines with glycoprotein stabilization, nanoparticle display, and glycan modification

Filoviruses pose a significant threat to human health due to frequent outbreaks and high mortality. Although two vector-based vaccines are available for Ebola virus, a broadly protective filovirus vaccine remains elusive. Here, we evaluate a general strategy for stabilizing glycoprotein (GP) structures from Ebola, Sudan, and Bundibugyo orthoebolaviruses and Ravn orthomarburgvirus. A 3.2 [A] crystal structure provides atomic-level details of the redesigned Ebola virus GP, while cryo-electron microscopy reveals how a pan-orthoebolavirus neutralizing antibody targets a conserved site on the stabilized Sudan virus GP (3.13 [A] resolution), along with a low-resolution model of antibody-bound Ravn virus GP. A self-assembling protein nanoparticle (SApNP), I3-01v9, is redesigned at the N terminus to enable optimal surface display of filovirus GP trimers. Following detailed in vitro characterization, we examine the lymph node dynamics of Sudan virus GP and GP-presenting SApNPs in mice. Compared with the soluble trimer, SApNPs exhibit [~]112-fold longer retention in lymph node follicles, up to 28-fold greater presentation on follicular dendritic cell dendrites, and up to 3-fold stronger germinal center reactions. Functional antibody responses induced by filovirus GP trimers and SApNPs bearing wild-type and modified glycans are assessed in mice. This study provides a foundation for next-generation filovirus vaccine development. ONE-SENTENCE SUMMARYFilovirus glycoproteins and nanoparticles were rationally designed and characterized in vitro and in vivo to aid filovirus vaccine development.

microbiology↗

bioRxiv2024

A Universal, Single-Component Multilayered Self-Assembling Protein Nanoparticle Vaccine Based on Extracellular Domains of Matrix Protein 2 Against Both Influenza A and B

The development of an effective and broadly protective influenza vaccine against circulating and emerging strains remains elusive. In this study, we evaluated single-component self-assembling protein nanoparticles (1c-SApNPs) presenting the conserved matrix protein 2 ectodomain (M2e) from influenza A and B viruses (IAV and IBV, respectively) as a universal influenza vaccine. We previously designed a tandem antigen comprising three IAV M2e domains of human, avian/swine, and human/swine origins (termed M2ex3). The M2ex3-presenting 1c-SApNPs conferred complete protection in mice against sequential lethal challenges with H1N1 and H3N2. To broaden this protection to counter IBVs, we designed a series of antigens incorporating different arrangements of three IAV M2e domains and three copies of IBV M2e. The tandem repeats of IAV and IBV (termed influenza A-B) M2e arrayed on the I3-01v9a 60-mer 1c-SApNP, when formulated with an oil-in-water emulsion adjuvant, generated greater M2e-specifc immunogenicity and protective efficacy than the soluble influenza A-B M2e trimer, as indicated by higher survival rates and lower weight loss post-challenge. Importantly, one of the influenza A-B M2e SApNP constructs elicited 100% protection against a lethal influenza A (H1N1) challenge in mice and 70% protection against a lethal influenza B (Yamagata lineage) challenge, the latter of which has not been reported in the literature to date. Our study thus provides a truly universal single-component M2e-based vaccine candidate against two major types of influenza virus circulating in humans.

microbiology↗

bioRxiv2024

A tale of two fusion proteins: understanding the metastability of human respiratory syncytial virus and metapneumovirus and implications for rational design of uncleaved prefusion-closed trimers

Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause human respiratory diseases and are major targets for vaccine development. In this study, we designed uncleaved prefusion-closed (UFC) trimers for the fusion (F) proteins of both viruses by examining mutations critical to F metastability. For RSV, we assessed four previous prefusion F designs, including the first and second generations of DS-Cav1, SC-TM, and 847A. We then identified key mutations that can maintain prefusion F in a native-like, closed trimeric form (up to 76%) without introducing any interprotomer disulfide bond. For hMPV, we developed a stable UFC trimer with a truncated F2-F1 linkage and an interprotomer disulfide bond. Tens of UFC constructs were characterized by negative-stain electron microscopy (nsEM), x-ray crystallography (11 RSV-F and one hMPV-F structures), and antigenic profiling. Using an optimized RSV-F UFC trimer as bait, we identified three potent RSV neutralizing antibodies (NAbs) from a phage-displayed human antibody library, with a public NAb lineage targeting sites O and V and two cross-pneumovirus NAbs recognizing site III. In mouse immunization, rationally designed RSV-F and hMPV-F UFC trimers induced robust antibody responses with high neutralizing titers. Our study provides a foundation for future prefusion F-based RSV and hMPV vaccine development. ONE-SENTENCE SUMMARYThe metastability analysis of fusion proteins has informed rational design of uncleaved prefusion-closed trimers for RSV and hMPV vaccine development.

microbiology↗

bioRxiv2023

Single-component multilayered self-assembling protein nanoparticles displaying extracellular domains of matrix protein 2 as a pan-influenza A vaccine

The development of a cross-protective pan-influenza A vaccine remains a significant challenge. In this study, we designed and evaluated single-component self-assembling protein nanoparticles (SApNPs) presenting the conserved extracellular domain of matrix protein 2 (M2e) as vaccine candidates against influenza A viruses. The SApNP-based vaccine strategy was first validated for human M2e (hM2e) and then applied to tandem repeats of M2e from human, avian and swine hosts (M2ex3). Vaccination with M2ex3 displayed on SApNPs demonstrated higher survival rates and lower weight loss compared to the soluble M2ex3 antigen against lethal challenges of H1N1 and H3N2 in mice. M2ex3 I3-01v9a SApNPs formulated with a squalene-based adjuvant were retained in the lymph node follicles over eight weeks and induced long-lived germinal center reactions. Notably, a single low dose of M2ex3 I3-01v9a SApNP formulated with a potent adjuvant, either a Toll-like receptor 9 (TLR9) agonist or a stimulator of interferon genes (STING) agonist, conferred 90% protection against a lethal H1N1 challenge in mice. With the ability to induce robust and durable M2e-specific functional antibody and T cell responses, the M2ex3-presenting I3-01v9a SApNP provides a promising pan-influenza A vaccine candidate. ONE-SENTENCE SUMMARYSingle-component self-assembling protein nanoparticles (SApNPs) displaying tandem M2e elicit robust and durable immunity that may protect against influenza A viruses of diverse origins.

microbiology↗

bioRxiv2022

Single-component multilayered self-assembling protein nanoparticles presenting glycan-trimmed uncleaved prefusion optimized envelope trimers as HIV-1 vaccine candidates

Uncleaved prefusion-optimized (UFO) design can stabilize diverse HIV-1 envelope glycoproteins (Envs). Single-component, self-assembling protein nanoparticles (1c-SApNP) can display 8 or 20 trimeric antigens as multivalent vaccines. Here, we characterized the biophysical, structural, and antigenic properties of 1c-SApNPs that present the BG505 UFO trimer with wildtype and modified glycans. Trimming the glycan shield improved Env recognition by broadly neutralizing antibodies (bNAbs) to the CD4 binding site and other major glycan-containing epitopes. In mice, rabbits, and nonhuman primates, glycan trimming increased the frequency of vaccine responders (FVR) and steered antibody responses away from immunodominant glycan holes and glycan epitopes. The mechanism of vaccine-induced immunity was examined in mice. Compared with the soluble trimer, two large 1c-SApNPs showed 420 times longer retention, 20-32 times greater presentation on follicular dendritic cell dendrites, and up-to-4 times stronger germinal center reactions in lymph node follicles. These findings will inform the next phase of HIV-1 vaccine development. ONE-SENTENCE SUMMARYGlycan trimming of HIV-1 Env immunogens improves the vaccine-induced neutralizing antibody responses in small animals and primates

microbiology↗

bioRxiv2021

Mechanism of a COVID-19 nanoparticle vaccine candidate that elicits a broadly neutralizing antibody response to SARS-CoV-2 variants

Vaccines that induce potent neutralizing antibody (NAb) responses against emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are essential for combating the coronavirus disease 2019 (COVID-19) pandemic. We demonstrated that mouse plasma induced by self-assembling protein nanoparticles (SApNPs) that present 20 rationally designed S2G{Delta}HR2 spikes of the ancestral Wuhan-Hu-1 strain can neutralize the B.1.1.7, B.1.351, P.1, and B.1.617 variants with the same potency. The adjuvant effect on vaccine-induced immunity was investigated by testing 16 formulations for the multilayered I3-01v9 SApNP. Using single-cell sorting, monoclonal antibodies (mAbs) with diverse neutralization breadth and potency were isolated from mice immunized with the receptor binding domain (RBD), S2G{Delta}HR2 spike, and SApNP vaccines. The mechanism of vaccine-induced immunity was examined in mice. Compared with the soluble spike, the I3-01v9 SApNP showed 6-fold longer retention, 4-fold greater presentation on follicular dendritic cell dendrites, and 5-fold stronger germinal center reactions in lymph node follicles. ONE-SENTENCE SUMMARYWith a well-defined mechanism, spike nanoparticle vaccines can effectively counter SARS-CoV-2 variants.

immunology↗

bioRxiv2020

Aglycone polyether ionophores as broad-spectrum agents inhibit multiple enveloped viruses including SARS-CoV-2 in vitro and successfully cure JEV infected mice

Infections with zoonotic viruses, such as flaviviruses, influenza virus, and the SARS-CoV-2 pandemic coronavirus constitute an increasing global risk. Hence, an urgent need exists for the development of broad-spectrum antivirals to prevent such outbreaks. Here, we show that the maduramycin and CP-80,219 aglycone polyether ionophores exhibit effective broad-spectrum antiviral activity, against various viruses, including Japanese encephalitis virus (JEV), Dengue virus (DENV), Zika virus (ZIKV), and Chikungunya virus (CHIKV), while also exhibiting promising activity against PR8 influenza virus and SARS-CoV-2. Moreover, liposome-encapsulated maduramycin and CP-80,219 provide full protection for mice from infection with JEV in vivo. Mechanistic studies suggest that aglycone polyether ionophores primarily inhibit the viral replication step without blocking endosome acidification to promote the fusion between viral and cellular membranes. The successful application of liposomes containing aglycone polyether ionophores in JEV-infected mice offers hope to the development of broad-spectrum antiviral drugs like penicillin back to 1940s.

microbiology↗