Biology subjects

Wong, Y. Y.

Publications and source records attributed to Wong, Y. Y..

9 recordsLinked to original sources

bioRxiv2025

Oncogenic virus hijacks SOX18 pioneer function to enhance viral persistence

Kaposis sarcoma herpesvirus (KSHV) establishes lifelong oncogenic infection in lymphatic endothelial cells (LECs) by ensuring episomal maintenance of its genome via the viral protein LANA. Efficient viral genome maintenance typically involves host DNA replication and episome tethering, but the extent of cell-type-specific regulation remains unclear. Here, we identify that KSHV hijacks the pioneering function of the endothelial-specific transcription factor SOX18 to facilitate persistence of viral episomes. Upon infection, LANA co-opts SOX18 to recruit the SWI/SNF chromatin-remodeling complex via its ATPase subunit BRG1, enhancing chromatin accessibility and enabling efficient viral genome persistence. Disruption of SOX18 or BRG1--genetically or pharmacologically--leads to reduced episome load and attenuated hallmarks of virus infection. This work highlights how viruses can harness lineage-specific transcriptional regulators to establish persistent nuclear retention of their episome into the host genome.

molecular biology↗

bioRxiv2025

Inhibiting SOX18 with propranolol restores vascular integrity in NR2F2-driven malformations

Translating genomic discoveries into therapies for rare genetic disorders remains a significant challenge, particularly for variants of unknown significance (VUS) where molecular mechanisms are unclear. This is particularly relevant in vascular malformations, where venous differentiation remains poorly understood, and the role of transcription factors in specifying venous identity is only beginning to be elucidated. Here, we combine live-cell single-molecule imaging with genomics-based approaches to uncover a biophysical mechanism of transcription factor antagonism that underpins venous identity. We show that SOX18 and NR2F2 antagonistically co-regulate venous differentiation through dynamic feedback between their nuclear populations. This interaction is disrupted in vascular malformation syndrome caused by a de novo heterozygous NR2F2 mutation, presenting with aberrant vascular integrity and bleeding. Treatment with an FDA-approved drug--known to inhibit SOX18--led to marked clinical improvement in the proband. To dissect the molecular mechanism underlying this mutation and the drug response, we used human embryonic stem cells (hESCs) engineered to carry the probands NR2F2 variant. These cells exhibited impaired hESC to venous differentiation with no effect on artery EC differentiation. In silico modelling and live-cell molecular imaging revealed that the NR2F2 variant is hyper-mobile, fails to form homodimers, and cannot recruit SOX18, thereby disrupting a critical transcriptional antagonism that underpins venous endothelial identity. We demonstrate that targeted pharmacological inhibition of SOX18 restores this regulatory balance in hESC-derived venous endothelial cells, rescuing both gene expression and NR2F2 binding dynamics at the single-molecule level. Together, this study uncovers a biophysical mechanism of transcription factor antagonism that governs venous differentiation and offers a framework for developing targeted therapies for rare vascular malformations.

developmental biology↗

bioRxiv2024

Anti-phase clustering of regulatory factors shapes gene bursting

Stem cell self-renewal relies on finely tuned transcriptional oscillations of pluripotency genes, yet the sequence by which transcription factors (TFs) govern "on" and "off" states remains unclear. Here, we integrate trimodal single-molecule imaging - SOX2 mobility, Nanog locus diffusion, and real-time Nanog mRNA synthesis using the STREAMING-tag reporter - to visualise endogenous regulatory dynamics in living cells. We identify two SOX2 binding modes linked to transcriptional priming and termination and show coordinated temporal activity of SOX2, OCT4, BRD4, and MED22 at the Nanog locus. Live-cell and fixed-cell measurements reveal that local RNA fluctuations modulate SOX2 visiting-frequency rates. During the active elongation, high nascent enhancer and mRNA levels transiently sequester SOX2 through non-specific interactions, reducing its effective repetitive rebinding and limiting interference with elongating polymerase. After transcript release, declining RNA density permits SOX2 re-engagement, with high-visiting frequency with longer residency and increased locus mobility. These dynamics reveal RNA-dependent feedback that alternately buffers and primes transcriptional re-initiation.

molecular biology↗

bioRxiv2023

Plasma membrane abundance dictates phagocytic capacity and functional crosstalk in myeloid cells

Professional phagocytes like neutrophils and macrophages tightly control what they eat, how much they eat, and when they move after eating. We show that plasma membrane abundance is a key arbiter of these cellular behaviors. Neutrophils and macrophages lacking the G-protein subunit G{beta}4 exhibit profound plasma membrane expansion due to enhanced production of sphingolipids. This increased membrane allocation dramatically enhances phagocytosis of bacteria, fungus, apoptotic corpses, and cancer cells. G{beta}4 deficient neutrophils are also defective in the normal inhibition of migration following cargo uptake. In G{beta}4 knockout mice, myeloid cells exhibit enhanced phagocytosis of inhaled fungal conidia in the lung but also increased trafficking of engulfed pathogens to other organs. These results reveal an unexpected, biophysical control mechanism lying at the heart of myeloid functional decision-making.

cell biology↗

bioRxiv2023

Topographical analysis of immune cell interactions reveals a biomechanical signature for immune cytolysis

Immune cells live intensely physical lifestyles characterized by structural plasticity, mechanosensitivity, and force exertion. Whether specific immune functions require stereotyped patterns of mechanical output, however, is largely unknown. To address this question, we used super-resolution traction force microscopy to compare cytotoxic T cell immune synapses with contacts formed by other T cell subsets and macrophages. T cell synapses were globally and locally protrusive, which was fundamentally different from the coupled pinching and pulling of macrophage phagocytosis. By spectrally decomposing the force exertion patterns of each cell type, we associated cytotoxicity with compressive strength, local protrusiveness, and the induction of complex, asymmetric interfacial topographies. These features were further validated as cytotoxic drivers by genetic disruption of cytoskeletal regulators, direct imaging of synaptic secretory events, and in silico analysis of interfacial distortion. We conclude that T cell-mediated killing and, by implication, other effector responses are supported by specialized patterns of efferent force.

immunology↗

bioRxiv2021

Progesterone receptor-A isoform interaction with RUNX transcription factors controls chromatin remodelling at promoters during ovulation

Progesterone receptor (PGR) plays diverse roles in reproductive tissues and thus coordinates mammalian fertility. In the ovary, acutely induced PGR is the key determinant of ovulation through transcriptional control of a unique set of genes that culminates in follicle rupture. However, the molecular mechanisms for PGRs specialised function in ovulation is poorly understood. To address this, we assembled a detailed genomic profile of PGR action through combined ATAC-seq, RNA-seq and ChIP-seq analysis in wildtype and isoform-specific PGR null mice. We demonstrated the unique action of PGR-A isoform in the ovary through a transcriptional complex involving physical interaction with RUNX and JUN/FOS transcription factors. The assembly of this unique complex directs targeting of PGR binding to proximal promoter regions and enables chromatin accessibility, leading to ovulatory gene induction. This PGR signalling mechanism is specific to ovulation and provides potential targets for infertility treatments as well as new contraceptives that block ovulation.

molecular biology↗

bioRxiv2020

NK cells promote cancer immunoediting through tumor-intrinsic loss of interferon-stimulated gene expression

Natural killer (NK) cells are innate lymphocytes that constantly patrol host tissues against transformed cells in a process known as cancer immunosurveillance. Previous evidence in mice has demonstrated that NK cell-derived IFN-{gamma} can promote immunoevasion by sculpting the immunogenicity of developing tumors in a process known as cancer immunoediting. This process involves the elimination of highly immunogenic "unedited" tumor cells followed by the eventual escape of less immunogenic "edited" tumor cell variants that are able to escape recognition or elimination by the immune system. Here, we show that NK cell-edited fibrosarcomas decrease the expression of 17 conserved IFN-{gamma}-inducible genes compared to unedited tumor cells. High expression of 3 of these identified genes (Psmb8, Trim21, Parp12) in human tumor samples correlates with enhanced survival in breast cancer, melanoma, and sarcoma patients. While NK cell-edited fibrosarcomas displayed resistance to IFN-{gamma} growth suppression in vitro, functional knockouts of individual interferon stimulated genes (ISGs) were not required for outgrowth of unedited tumor cell lines in vitro and in vivo compared to complete loss of IFN signaling. Furthermore, knockout of IFN-{gamma}-intrinsic signaling via deletion of Ifngr in edited B16 F10 and E0771 LMB metastatic cancer cell lines did not impact host survival following lung metastasis. Together, these results suggest that unedited tumors can be selected for decreased IFN-{gamma} signaling to evade immune responses in vivo, and as a consequence, tumor-extrinsic IFN signaling may be more important for potentiating durable anti-tumor responses to advanced solid tumors.

immunology↗

bioRxiv2020

3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk

BackgroundGenome-wide association and fine-mapping studies have enabled the discovery of single nucleotide polymorphisms (SNPs) and other variants that are significantly associated with many autoimmune diseases including type 1 diabetes (T1D). However, many of the SNPs lie in non-coding regions, limiting the identification of mechanisms that contribute to autoimmune disease progression. MethodsAutoimmunity results from a failure of immune tolerance, suggesting that regulatory T cells (Treg) are likely a significant point of impact for this genetic risk, as Treg are critical for immune tolerance. Focusing on T1D as a model of defective function of Treg in autoimmunity, we designed a SNPs filtering workflow called 3 Dimensional Functional Annotation of Accessible Cell Type Specific SNPs (3DFAACTS-SNP) that utilises overlapping profiles of Treg-specific epigenomic data (ATAC-seq, Hi-C and FOXP3-ChIP) to identify regulatory elements potentially driving the effect of variants associated with T1D, and the gene(s) that they control. ResultsUsing 3DFAACTS-SNP we identified 36 SNPs with plausible Treg-specific mechanisms of action contributing to T1D from 1,228 T1D fine-mapped variants, identifying 119 novel interacting regions resulting in the identification of 51 candidate target genes. We further demonstrated the utility of the workflow by applying it to three other fine-mapped/meta-analysed SNP autoimmune datasets, identifying 17 Treg-centric candidate variants and 35 interacting genes. Finally, we demonstrate the broad utility of 3DFAACTS-SNP for functional annotation of any genetic variation using all common (>10% allele frequency) variants from the Genome Aggregation Database (gnomAD). We identified 7,900 candidate variants and 3,245 candidate target genes, generating a list of potential sites for future T1D or autoimmune research. ConclusionsWe demonstrate that it is possible to further prioritise variants that contribute to T1D based on regulatory function and illustrate the power of using cell type specific multi-omics datasets to determine disease mechanisms. The 3DFAACTS-SNP workflow can be customised to any cell type for which the individual datasets for functional annotation have been generated, giving broad applicability and utility.

bioinformatics↗

bioRxiv2020

Early metazoan origin and multiple losses of a novel clade of RIM pre-synaptic calcium channel scaffolding protein homologues

The precise localization of CaV2 voltage-gated calcium channels at the synapse active zone requires various interacting proteins, of which, Rab3 interacting molecule or RIM is considered particularly important. In vertebrates, RIM interacts with CaV2 channels in vitro via a PDZ domain that binds to the extreme C-termini of the channels at acidic ligand motifs of D/E-D/E/H-WC-COOH, and knockout of RIM in vertebrates and invertebrates disrupts CaV2 channel synaptic localization and synapse function. Here, we describe a previously uncharacterized clade of RIM proteins bearing homologous domain architectures as known RIM homologues, but some notable differences including key amino acids associated with PDZ domain ligand specificity. This novel RIM emerged near the stem lineage of metazoans and underwent extensive losses, but is retained in select animals including the early-diverging placozoan Trichoplax adhaerens, and molluscs. RNA expression and localization studies in Trichoplax and the mollusc snail Lymnaea stagnalis indicate differential regional/tissue type expression, but overlapping expression in single isolated neurons from Lymnaea. Ctenophores, the most early-diverging animals with synapses, are unique among animals with nervous systems in that they lack the canonical RIM, bearing only the newly identified homologue. Through phylogenetic analysis, we find that CaV2 channel D/E-D/E/H-WC-COOH like PDZ ligand motifs were present in the common ancestor of cnidarians and bilaterians, and delineate some deeply conserved C-terminal structures that distinguish CaV1 from CaV2 channels, and CaV1/CaV2 from CaV3 channels.

evolutionary biology↗