Biology subjects

Wong, C.-H.

Publications and source records attributed to Wong, C.-H..

8 recordsLinked to original sources

bioRxiv2026

Differential Acceptance Specificity of Human Fucosyltransferases toward GDP-azidofucose and GDP-alkynylfucose as Glycosylation Probes

Described here is the synthesis and assembly of a new-generation mRNA-bifunctional lipid nanoparticle (mRNA-BLNP3) for selective delivery of mRNA to antigen-presenting cells (APCs). Compared to mRNA-BLNP1 and BLNP2 (BioRxiv,doi.org/10.1101/2023.12.26.572282), the mRNA-BLNP3, incorporating a glycolipid with the lipid moiety designed to target the CD1d receptor on dendritic cells (DCs) and the sugar head group targeting the mannose-binding receptors on APCs is more selective with stronger target-specific immune responses. It was shown that vaccination in mice with mRNA-BLNP1 elicited enhanced cytokine induction and antibody responses compared to traditional mRNA-LNPs, and the mRNA-BLNP2 vaccine, incorporating a mannose-glycolipid, further improved DC targeting. However, BLNP3, incorporating the glycolipid with an aryl-mannose head group targeting the mannose receptor on APCs and the same lipid moiety targeting the Cd1d receptor on DCs, showed superior lymph node targeting in vivo with reduced liver accumulation, enhanced mRNA expression in DCs and macrophages, and increased DC maturation. Immunization in mice with mRNA-BLNP3 elicited enhanced humoral and cellular immune responses compared to mRNA-BLNP1 and mRNA-BLNP2, with higher antigen-specific IgG titers and granzyme B-producing CD8 T cells, demonstrating that BLNP3 is a promising bifunctional lipid nanoparticle for delivery of mRNA vaccines with improved efficacy and safety.

biochemistry↗

bioRxiv2025

An Atlas of Extrachromosomal DNA Structures Illuminates Its Evolution and Biogenesis in Cancer

Extrachromosomal circular DNA (ecDNA) is a prevalent driver of oncogene amplification across diverse types of cancers. Leveraging single-molecule long-read sequencing and a de novo circular genome assembler, ecLego3, we charted a comprehensive atlas of ecDNA structures from longitudinal pairs of primary and recurrent glioblastoma (GBM). Our approach resolved 23 ecDNA genomes representing major oncogenes associated with GBM pathogenesis and revealed a dynamic configuration characterized by pronounced structural variation and multi-species co-existence within individual tumors. Evolutionary trajectories were shaped by hierarchical accrual of structural variants, predominated by deletions and inversions, giving rise to novel oncogene isoforms and enhancer repositioning. Such structural plasticity promotes intratumor heterogeneity and tumor fitness. Multiomic analyses at single cell resolution linked ecDNA abundance and structure to transcriptional output, uncovering non-linear scaling and synergistic co-selection among multiple ecDNA species. Comparative profiling revealed locus-dependent configuration, a contraction of ecDNA diversity upon recurrence, and convergent structural architectures across patients, implicating repeat-mediated genomic rearrangements and replication stress in ecDNA biogenesis. These findings elucidate ecDNA-driven mechanisms of tumor adaptation and highlight new molecular vulnerabilities, informing potential biomarkers and therapeutic strategies for high-grade gliomas.

cancer biology↗

bioRxiv2023

Synthesis and Assembly of mRNA-Bifunctional Lipid Nanoparticle (BLNP) for Selective Delivery of mRNA Vaccines to Dendritic Cells

Described here is the synthesis and assembly of a new-generation mRNA-bifunctional lipid nanoparticle (mRNA-BLNP3) for selective delivery of mRNA to antigen-presenting cells (APCs). Compared to mRNA-BLNP1 and BLNP2 (BioRxiv,doi.org/10.1101/2023.12.26.572282), the mRNA-BLNP3, incorporating a glycolipid with the lipid moiety designed to target the CD1d receptor on dendritic cells (DCs) and the sugar head group targeting the mannose-binding receptors on APCs is more selective with stronger target-specific immune responses. It was shown that vaccination in mice with mRNA-BLNP1 elicited enhanced cytokine induction and antibody responses compared to traditional mRNA-LNPs, and the mRNA-BLNP2 vaccine, incorporating a mannose-glycolipid, further improved DC targeting. However, BLNP3, incorporating the glycolipid with an aryl-mannose head group targeting the mannose receptor on APCs and the same lipid moiety targeting the Cd1d receptor on DCs, showed superior lymph node targeting in vivo with reduced liver accumulation, enhanced mRNA expression in DCs and macrophages, and increased DC maturation. Immunization in mice with mRNA-BLNP3 elicited enhanced humoral and cellular immune responses compared to mRNA-BLNP1 and mRNA-BLNP2, with higher antigen-specific IgG titers and granzyme B-producing CD8+ T cells, demonstrating that BLNP3 is a promising bifunctional lipid nanoparticle for delivery of mRNA vaccines with improved efficacy and safety.

biochemistry↗

bioRxiv2023

Use of phase plate cryo-EM reveals conformation diversity of therapeutic IgG with 50 kDa Fab fragment resolved below 6 angstrom

While cryogenic electron microscopy (cryo-EM) is fruitfully used for harvesting high-resolution structures of sizable macromolecules, its application to small or flexible proteins composed of domains like immunoglobulin (IgG) remain challenging. Here, we applied single particle cryo-EM to Rituximab, a therapeutic IgG mediating cancer cell toxicity, to explore its solution conformations. We found Rituximab molecules exhibited aggregates in cryo-EM specimens contrary to its solution behavior, and utilized a non-ionic detergent to successfully disperse them as isolated particles amenable to single particle analysis. As the detergent adversely reduced the protein-to-solvent contrast, we employed phase plate contrast to mitigate the impaired protein visibility. Assisted by phase plate imaging, we obtained a canonical three-arm IgG structure with other structures displaying variable arm densities co-existing in solution, affirming high flexibility of arm-connecting linkers. Furthermore, we showed phase plate imaging enables reliable structure determination of Fab to sub-nanometer resolution from ab initio, yielding a characteristic two-lobe structure that could be unambiguously docked with crystal structure. Our findings revealed conformation diversity of IgG and demonstrated phase plate was viable for cryo-EM analysis of small proteins without symmetry. This work helps extend cryo-EM boundaries, providing a valuable imaging and structural analysis framework for macromolecules with similar challenging features.

biochemistry↗

bioRxiv2023

Cell-based production of Fc-GlcNAc and Fc-alpha-2,6 sialyl glycan enriched antibody with improved effector functions through glycosylation pathway engineering

Glycosylation of antibody plays an important role in Fc-mediated killing of tumor cells and virus-infected cells through effector functions such as antibody-dependent cellular cytotoxicity (ADCC), antibody dependent cell-mediated phagocytosis (ADCP) and vaccinal effect. Previous studies showed that therapeutical humanized antibodies with 2-6 sialyl complex type (SCT) glycan attached to Fc-Asn297 exhibited optimal binding to the Fc receptors on effector cells associated with ADCC, ADCP and vaccinal effect. However, the production of antibodies with homogeneous Fc-SCT needs multiple in vitro enzymatic and purification steps. In this study, we report two different approaches to shorten the processes to produce SCT-enriched antibodies. First, we expressed a bacterial endoglycosidase in GNT1-KO EXPI293 cells to trim all N-glycans to mono-GlcNAc glycoforms for in vitro transglycosylation to generate homogeneous SCT antibody. Second, we engineered the glycosylation pathway of HEK293 cells through knockout of the undesired glycosyltransferases and expression of the desired glycosyltransferases to produce SCT enriched antibodies with similar binding affinity to Fc receptors and ADCC activity to homogenous SCT antibody.

biochemistry↗

bioRxiv2023

Synthesis of Dendritic Cell-Targeted Polymeric Nanoparticles for Selective Delivery of mRNA Vaccines to Elicit Enhanced Immune Responses

Recent development of SARS-CoV-2 spike mRNA vaccines to control the pandemic is a breakthrough in the field of vaccine development. mRNA vaccines are generally formulated with lipid nanoparticles (LNPs) which are composed of several lipids with specific ratios; however, they generally lack selective delivery. To develop a simpler method selective delivery of mRNA, we reported here the synthesis of biodegradable copolymers decorated with guanidine and zwitterionic groups and an aryltrimannoside ligand as polymeric nanoparticles (PNPs) for encapsulation and selective delivery of an mRNA to dendritic cells (DCs). A representative DC-targeted SARS-CoV-2 spike mRNA-PNP vaccine was shown to elicit a stronger protective immune response in mice as compared to the mRNA-LNP and mRNA-PNP vaccines without the selective delivery design. It is anticipated that this technology will be generally applicable to development of DC-targeted mRNA vaccines with enhanced immune response. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/566827v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@df68faorg.highwire.dtl.DTLVardef@1651a76org.highwire.dtl.DTLVardef@ac5b8borg.highwire.dtl.DTLVardef@1ae1475_HPS_FORMAT_FIGEXP M_FIG C_FIG Dendritic cell-targeted mRNA-PNP vaccines

biochemistry↗

bioRxiv2021

Impact of Glycosylation on SARS-CoV-2 Infection and Broadly Protective Vaccine Design

A major challenge to end the pandemic caused by SARS-CoV-2 is to develop a broadly protective vaccine. As the key immunogen, the spike protein is frequently mutated with conserved epitopes shielded by glycans. Here, we reveal that spike glycosylation has site-differential effects on viral infectivity and lung epithelial cells generate spike with more infective glycoforms. Compared to the fully glycosylated spike, immunization of spike protein with N-glycans trimmed to the monoglycosylated state (Smg) elicits stronger immune responses and better protection for hACE2 transgenic mice against variants of concern. In addition, a broadly neutralizing monoclonal antibody was identified from the Smg immunized mice, demonstrating that removal of glycan shields to better expose the conserved sequences is an effective and simple approach to broad-spectrum vaccine development. One-Sentence SummaryRemoving glycan shields to expose conserved epitopes is an effective approach to develop a broad-spectrum SARS-CoV-2 vaccine.

microbiology↗

bioRxiv2017

Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome

Acquired genomic structural variants (SVs) are major hallmarks of the cancer genome. Their complexity has been challenging to reconstruct from short-read sequencing data. Here, we exploit the long-read sequencing capability of the nanopore platform using our customized pipeline, Picky, to reveal SVs of diverse architecture in a breast cancer model. From modest sequencing coverage, we identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses and uncovered repetitive DNA as the major source of variation. Examination of the genome-wide breakpoints at nucleotide-resolution uncovered micro-insertions as the common structural features associated with SVs. Breakpoint density across the genome is associated with propensity for inter-chromosomal connectivity and transcriptional regulation. Furthermore, an over-representation of reciprocal translocations from chromosomal double-crossovers was observed through phased SVs. The comprehensive characterization of SVs using the robust long-read sequencing approach in cancer cohorts will facilitate strategies to monitor genome stability during tumor evolution and improve therapeutic intervention.

genomics↗