Biology subjects

Huan, Y. W.

Publications and source records attributed to Huan, Y. W..

8 recordsLinked to original sources

bioRxiv2026

Mutational fitness landscapes of diverse human influenza H1N1 neuraminidases

While neuraminidase (NA) is emerging as a promising influenza vaccine target, it evolves rapidly and undergoes antigenic drift. However, our understanding of its evolutionary constraints remains limited. Here, we systematically quantified the replication fitness effects of >6,000 mutations for each of three antigenically diverse H1N1 NAs using deep mutational scanning. Moderate correlations among H1N1 NA fitness landscapes revealed mutations with strain-dependent replication fitness effects. Additionally, cross-subtype comparison between N1 and N2 NAs uncovered similar epistatic effects that were enriched in the C-terminal interprotomer interface. We also showed that NA mutational fitness strongly correlated between in vivo and in vitro. Characterization of 40 individually constructed NA mutants further demonstrated that NA mutational fitness depended more on its surface protein expression than on its total protein expression or endoplasmic reticulum stress induction. Overall, the large dataset generated in this work provides critical insights into the evolutionary constraints of NA.

microbiology↗

bioRxiv2026

TRIM21 is a molecular rheostat for influenza A virus replication

TRIM21 is a multifunctional E3 ubiquitin ligase and intracellular antibody receptor, yet its role during viral infection remains unclear, with reports describing both antiviral and proviral activities. Here, we show that TRIM21 regulates influenza infection in an expression-dependent manner by functioning as a molecular rheostat rather than a binary restriction factor. This graded activity of TRIM21, which leads to both suppression and promotion of influenza replication, couples linkage-specific ubiquitination of viral nucleoprotein with modulation of innate immune signaling. Additionally, loss of TRIM21 unmasks a compensatory antiviral program centered on PRKDC, which is a ubiquitination target of TRIM21. This positions PRKDC as a latent restriction factor selectively engaged when primary TRIM21 control is lost. Together, these findings reveal a hierarchical and plastic antiviral network in which TRIM21 sets an adjustable threshold for host defense while restraining secondary restriction pathways. This framework highlights the sophisticated layers of regulation of the host ubiquitin-mediated antiviral immunity.

cell biology↗

bioRxiv2026

Structural insights into antibody responses against influenza A virus in its natural reservoir

While influenza A virus undergoes rapid antigenic drift in humans, at least some subtypes, such as H3, have relatively stable antigenicity in natural waterfowl reservoirs, despite the presence of immune pressure. However, the underlying mechanisms remain poorly understood. This study identified and characterized 187 antibodies to H3 hemagglutinin from experimentally infected mallard ducks, 18 of which were further analyzed by cryo-EM. Compared with human H3 antibodies, duck H3 antibodies exhibited higher glycan-binding propensity, more balanced immunodominance hierarchy, and targeted distinct epitopes. Other unique features of duck H3 antibodies included a convergent CDR H3-independent heavy chain-only binding mode and an N-glycosylated CDR H3 as decoy receptor. By annotating duck immunoglobulin germline genes, we also demonstrated the importance of gene conversion in duck H3 antibodies. Overall, our findings provide insights into how millennia of coevolution have shaped the interplay between influenza A virus antigenic drift and antibody responses in the natural reservoir.

immunology↗

bioRxiv2025

Structure basis for distinct protective mechanisms of IGHV3-23 antibodies targeting influenza hemagglutinin stem

Characterization of antibodies targeting the conserved stem domain of influenza hemagglutinin (HA) is critical for developing broadly protective countermeasures against influenza virus. From a phage display human antibody library, this study discovers three group 1 HA-specific stem antibodies, namely HB31, HB34, and HB315, all of which are encoded by IGHV3-23. While HB31 and HB34 have minimal neutralization activity in vitro, their Fc-mediated effector functions lead to better in vivo protection than the potently neutralizing HB315. Consistently, cryo-EM analysis suggests that HB31 and HB34 have a higher Fc accessibility than HB315, based on their epitopes and approaching angles. HB31 and HB34 engage a pocket in the upper HA stem that is rarely targeted by known HA stem antibodies, whereas the epitope of HB315 involves the lower stem. Overall, our findings provide insights not only into the structure-function relationship of HA stem antibodies, but also into the design of next-generation influenza therapeutics.

immunology↗

bioRxiv2025

Evolution of antibody cross-reactivity to influenza H5N1 neuraminidase from an N2-specific germline

The ongoing spread of highly pathogenic avian influenza H5N1 clade 2.3.4.4b virus in animals and its occasional spillover to humans have raised concerns about a potential H5N1 pandemic. Although recent studies have shown that pre-existing human antibodies can recognize H5N1 neuraminidase, the molecular basis of how this cross-reactivity develops remains poorly understood. In this study, we used a phage display antibody library derived from 245 healthy donors to isolate an antibody, HB420, that cross-reacts with neuraminidases of human H3N2 and avian H5N1 clade 2.3.4.4b viruses and confers protection in vivo. Cryo-EM analysis reveals that HB420 targets the neuraminidase active site by mimicking sialic acid binding through a single Asp residue. Furthermore, the inferred germline of HB420 is N2-specific but acquires cross-reactivity to H5N1 neuraminidase through somatic hypermutation. Overall, our findings provide insights into how neuraminidase antibody evolves breadth, which has important implications for the development of broadly protective influenza vaccines.

immunology↗

bioRxiv2024

Deep mutational scanning of influenza A virus NEP reveals pleiotropic mutations in its N-terminal domain

The influenza A virus nuclear export protein (NEP) is a multifunctional protein that is essential for the viral life cycle and has very high sequence conservation. However, since the open reading frame of NEP largely overlaps with that of another influenza viral protein, non-structural protein 1, it is difficult to infer the functional constraints of NEP based on sequence conservation analysis. Besides, the N-terminal of NEP is structurally disordered, which further complicates the understanding of its function. Here, we systematically measured the replication fitness effects of >1,800 mutations of NEP. Our results show that the N-terminal domain has high mutational tolerance. Additional experiments demonstrate that N-terminal domain mutations pleiotropically affect viral transcription and replication dynamics, host cellular responses, and mammalian adaptation of avian influenza virus. Overall, our study not only advances the functional understanding of NEP, but also provides insights into its evolutionary constraints.

cell biology↗

bioRxiv2022

P1 bacteriophage-enabled delivery of CRISPR-Cas9 antimicrobial activity against Shigella flexneri

The discovery of clustered, regularly interspaced, short palindromic repeats (CRISPR) and the Cas9 RNA-guided nuclease provides unprecedented opportunities to selectively kill specific populations or species of bacteria. However, the use of CRISPR-Cas9 to clear bacterial infections in vivo is hampered by the inefficient delivery of cas9 genetic constructs into bacterial cells. Here, we use a broad-host-range P1-derived phagemid to deliver the CRISPR-Cas9 chromosomal-targeting system into Escherichia coli and the dysentery-causing Shigella flexneri to achieve DNA sequence-specific killing of targeted bacterial cells. We show that genetic modification of the helper P1 phage DNA packaging site (pac) significantly enhances the purity of packaged phagemid and improves the Cas9-mediated killing of S. flexneri cells. We further demonstrate that P1 phage particles can deliver chromosomal-targeting cas9 phagemids into S. flexneri in vivo using a zebrafish larvae infection model, where it significantly reduces the bacterial load and promotes host survival. Our study highlights the potential of combining a P1 bacteriophage-based delivery with the CRISPR chromosomal-targeting system to achieve DNA sequence-specific cell lethality and efficient clearance of bacterial infection.

microbiology↗

bioRxiv2022

The host range and the role of O-antigen in P1 transduction with its alternative S' tail fibre

Enterobacteria phage P1 expresses two types of tail fibre, S and S. Despite the wide usage of phage P1 for transduction, the host range and the receptor for its alternative S tail fibre was never determined. Here, a {Delta}S-cin {Delta}pac E. coli P1 lysogenic strain was generated to allow packaging of phagemid DNA into P1 phage having either S or S tail fibre. P1(S) could transduce phagemid DNA into Shigella flexneri 2a 2457O, Shigella flexneri 5a M90T and Escherichia coli O3 efficiently. Mutational analysis of the O-antigen assembly genes and LPS inhibition assays indicated that P1(S) transduction requires at least one O-antigen unit. E. coli O111:B4 LPS produced a high neutralising effect against P1(S) transduction, indicating that this E. coli strain could be a host for P1(S). Mutations in the O-antigen modification genes of S. flexneri 2a 2457O and S. flexneri 5a M90T did not cause significant changes to P1(S) transduction efficiency. A higher transduction efficiency of P1(S) improved the delivery of a cas9 antimicrobial phagemid into both S. flexneri 2457O and M90T. These findings provide novel insights into P1 tropism-switching, by identifying the host range of P1(S) and demonstrating its potential for delivering a sequence-specific Cas9 antimicrobial into clinically relevant S. flexneri.

microbiology↗