Biology subjects

Siu, L.

Publications and source records attributed to Siu, L..

3 recordsLinked to original sources

bioRxiv2026

Somatic evolution of a cross-reactive germline antibody that expands its breadth to neutralize new SARS-CoV-2 variants

Rapid antigenic drift of the SARS-CoV-2 receptor-binding domain (RBD) underlies immune escape and continues to challenge the durability of antibody-mediated protection. Among the major classes of RBD-directed antibodies, germline-encoded IGHV3-53 responses are highly potent against early SARS-CoV-2 variants but are generally compromised by Omicron-associated mutations. Here, we identify an intrinsically cross-reactive IGHV3-53 germline antibody that recognizes multiple pre-Omicron variants, including SARS-CoV-2 wild-type, Alpha, and Delta. Notably, we demonstrate that targeted somatic evolution can further expand this breadth to overcome the immune escape of different Omicron variants. Guided by integrated structural and sequence analyses, we introduce four somatic mutations (G26E, T28I, S53P, and Y58F) into the germline antibody, resulting in markedly enhanced binding and neutralization of Omicron BA.1, BA.2, and BA.4/5. High-resolution crystal structures reveal that these mutations re-establish critical interactions disrupted by substitutions on Omicron RBD and optimize affinity at a remodeled epitope interface. Collectively, our findings delineate a structural and mechanistic pathway through which an inherently cross-reactive germline antibody lineage can be adaptively refined to counter highly divergent SARS-CoV-2 variants. This work highlights the underappreciated breadth encoded within the naive B-cell repertoire and provides a conceptual framework for engineering and eliciting antibody responses resilient to future antigenic drift.

immunology↗

bioRxiv2025

UCHL3 regulates subgenomic flaviviral RNA condensates to promote virus propagation

In this study we demonstrate a previously uncharacterised post-translational regulatory mechanism governing flavivirus replication through the deubiquitylating enzyme ubiquitin C-terminal hydrolase L3 (UCHL3). Using activity-based protein profiling, we identified UCHL3 as a key cellular factor activated during Zika virus (ZIKV) and dengue virus (DENV) infections. CRISPR-Cas9 knockout experiments demonstrated that UCHL3 deficiency impairs flavivirus replication and viral protein expression across multiple cellular models. The underlying molecular mechanism involves UCHL3-mediated stabilisation of subgenomic flaviviral RNA (sfRNA)-containing biomolecular condensates. Through biotinylated sfRNA-interactome capture assays, we show that UCHL3 physically interacts with sfRNA-containing ribonucleoprotein complexes alongside G3BP1. Importantly, UCHL3 depletion triggers inappropriate RNase L activation, leading to sfRNA relocalisation from protective P-bodies to degradative compartments, such as RNase L-induced bodies (RLBs) as reported previously, resulting in viral RNA decay. Our rescue experiments confirmed that RNase L knockdown restores viral replication in UCHL3-deficient cells. This pro-viral effect of UCHL3 operates through interferon-independent mechanisms, as demonstrated by persistent replication defects even upon exogenous interferon treatment. This work therefore identifies UCHL3 as a molecular switch controlling the balance between pro-viral and antiviral RNA condensates, representing a promising host dependency factor for broad-spectrum flavivirus intervention strategies.

cell biology↗

bioRxiv2024

The pro-tumoral and anti-tumoral roles of EphA4 on T regulatory cells and tumor associated macrophages during HNSCC tumor progression.

Head and Neck Squamous Cell Carcinoma (HNSCC) is a deadly cancer with poor response to targeted therapy, largely driven by an immunosuppressive tumor microenvironment (TME). Here we examine the immune-modulatory role of the receptor tyrosine kinase EphA4 in HNSCC progression. Within the TME, EphA4 is primarily expressed on regulatory T cells (Tregs) and macrophages. In contrast ephrinB2, an activating ligand of EphA4, is expressed in tumor blood vessels. Using genetically engineered mouse models, we show that EphA4 expressed in Tregs promotes tumor growth, whereas EphA4 expressed in monocytes inhibits tumor growth. In contrast, ephrinB2 knockout in blood vessels reduces both intratumoral Tregs and macrophages. A novel specific EphA4 inhibitor, APY-d3-PEG4, reverses the accelerated tumor growth we had previously reported with EphB4 cancer cell knockout. EphA4 knockout in macrophages not only enhanced their differentiation into M2 macrophage but also increased Treg suppressive activity. APY-d3-PEG4 reversed the accelerated growth seen in the EphA4 knockout of monocytes but conferred no additional benefit when EphA4 was knocked out on Tregs. Underscoring an EphA4-mediated interplay between Tregs and macrophages, we found that knockout of EphA4 in Tregs not only decreases their activation but also reduces tumor infiltration of pro-tumoral M2 macrophages. These data identify Tregs as a primary target of APY-d3-PEG4 and suggest a role for Tregs in regulating macrophage conversion. These data also support the possible anti-cancer therapeutic value of bispecific peptides or antibodies capable of promoting EphA4 blockade in Tregs but not macrophages. SignificanceEphA4 in regulatory T cells has a pro-tumoral effect while EphA4 in macrophages plays an anti-tumoral role underscoring the necessity of developing biologically rational therapeutics.

cancer biology↗