Biology subjects

Wong, L. H.

Publications and source records attributed to Wong, L. H..

7 recordsLinked to original sources

bioRxiv2026

HRS dephosphorylation at membrane contact sites promotes sorting within multivesicular endosomes

HRS is a receptor tyrosine kinase substrate and component of the ESCRT machinery. It enables sorting of ubiquitylated cargo into multivesicular endosomes (MVEs) for lysosomal degradation but also functions in receptor recycling. We show that co-depletion of its ESCRT-0 binding partners, STAM1 and STAM2, recapitulates defects in EGF receptor (EGFR) sorting onto intraluminal vesicles (ILVs) but does not mirror the increased MVE size evident after HRS depletion. Using mutagenesis of the endogenous gene or introduction of APEX2-tagged HRS variants, we find that HRS Y329/334 phosphorylation is dispensable for EGFR sorting and MVE size control. AnnexinA1 mediates endosomal contact with the ER and promotes EGF-stimulated ILV formation. We show that reduced ILV formation on AnnexinA1 depletion is accompanied by increased HRS phosphorylation, likely through reduced HRS dephosphorylation by ER-localised PTP1B. Conversely, Y329/334 mutation renders ILV formation insensitive to AnnexinA1 depletion. Our data suggest that rapid HRS dephosphorylation at ER:MVE contacts promotes efficient ILV formation.

cell biology↗

bioRxiv2025

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model

Deep learning models that predict functional genomic measurements from DNA sequence are powerful tools for deciphering the genetic regulatory code. Existing methods trade off between input sequence length and prediction resolution, thereby limiting their modality scope and performance. We present AlphaGenome, which takes as input 1 megabase of DNA sequence and predicts thousands of functional genomic tracks up to single base pair resolution across diverse modalities - including gene expression, transcription initiation, chromatin accessibility, histone modifications, transcription factor binding, chro- matin contact maps, splice site usage, and splice junction coordinates and strength. Trained on human and mouse genomes, AlphaGenome matches or exceeds the strongest respective available external models on 24 out of 26 evaluations on variant effect prediction. AlphaGenomes ability to simultaneously score variant effects across all modalities accurately recapitulates the mechanisms of clinically-relevant variants near the TAL1 oncogene. To facilitate broader use, we provide tools for making genome track and variant effect predictions from sequence.

bioinformatics↗

bioRxiv2023

Y chromosome damage underlies testicular abnormalities in ATR-X syndrome

ATR-X (alpha thalassemia, mental retardation, X-linked) syndrome is a severe developmental disorder affecting males caused by mutations in the chromatin remodelling gene ATRX. Genital abnormalities in affected boys include hypospadias and ambiguous genitalia, and patients show small poorly formed testes with only a few seminiferous tubules. Our mouse model recapitulated these testicular defects when Atrx was specifically deleted in Sertoli cells (ScAtrxKO). ScAtrxKO mice develop small testes with fewer and discontinuous tubules due to G2/M arrest and apoptosis of Sertoli cells. Here, we investigated the mechanism underlying the Sertoli cell defects in ATR-X syndrome. In healthy male control mice, Sertoli cell nuclei contain a single novel "GATA4 PML nuclear body (NB)" that strongly expresses the transcription factor GATA4, as well as ATRX and its binding partner DAXX. The GATA4 PML NB co-localizes with heterochromatin protein HP1 and PH3 (a marker of chromosome condensation), and with the short arm of the Y chromosome (Yp). In contrast, ScAtrxKO Sertoli cells contain a single giant GATA4 PML NB, frequently associated with DNA double-strand breaks in G2/M-arrested Sertoli cells that underwent apoptosis. HP1 and PH3 were absent from the giant GATA4 foci suggesting a local failure in heterochromatin formation and chromosome condensation. Our data indicate that in Sertoli cells, ATRX protects a chromosomal region of Yp from DNA damage, probably during replication stress, and thus protects Sertoli cells from cell death. We discuss Y chromosome damage as a novel mechanism for testicular failure and the potential role of GATA4 during this process. Disclosure SummaryThe authors have nothing to disclose.

developmental biology↗

bioRxiv2022

A conditional histone H3.3 mutation in mice orthologous to a driver of paediatric diffuse instrinsic pontine glioma

Most paediatric diffuse intrinsic pontine gliomas carry a lysine- to methionine-27 (K27M) mutation in the histone variant H3.3 encoded by the H3.3 histone A (H3F3A) gene. To establish a pre-clinical model of the disease we made a Cre/loxP conditional H3.3K27M mutation at the orthologous H3f3a locus in mice. Importantly, expression of the mutant transcript is under endogenous H3f3a regulatory control. This system is distinct from others in which H3.3M27 is ectopically expressed, thereby providing a resource for the development of pDIPG models with orthologous regulation of mutant H3.3. Mice in which expression of the mutant transcript was induced with a nestin-cre transgene developed as dwarfs in the presence of intact growth hormone signaling.

genetics↗

bioRxiv2021

Massively parallel characterization of CYP2C9 variant enzyme activity and abundance

CYP2C9 encodes a cytochrome P450 enzyme responsible for metabolizing up to 15% of small molecule drugs, and CYP2C9 variants can alter the safety and efficacy of these therapeutics. In particular, the anti-coagulant warfarin is prescribed to over 15 million people annually and polymorphisms in CYP2C9 can affect patient response leading to an increased risk of hemorrhage. We developed Click-seq, a pooled yeast-based activity assay to test thousands of variants. Using Click-seq, we measured the activity of 6,142 missense variants expressed in yeast. We also measured the steady-state cellular abundance of 6,370 missense variants expressed in a human cell line using Variant Abundance by Massively Parallel sequencing (VAMP-seq). These data revealed that almost two-thirds of CYP2C9 variants showed decreased activity, and that protein abundance accounted for half of the variation in CYP2C9 function. We also measured activity scores for 319 previously unannotated human variants, many of which may have clinical relevance.

genomics↗

bioRxiv2021

Cholesteryl Hemiazelate Induces Lysosome Dysfunction and Exocytosis in Macrophages

OBJECTIVEA key event in atherogenesis is the formation of lipid-loaded macrophages, lipidotic cells, which exhibit irreversible accumulation of undigested modified low-density lipoproteins in lysosomes. This event culminates with the loss of cell homeostasis, inflammation and cell death. In this study we propose to identify the chemical etiological factors and understanding the molecular and cellular mechanisms responsible for the impairment of lysosome function in macrophages. APPROACH AND RESULTSUsing shotgun lipidomics we have discovered that a family of oxidized lipids (cholesteryl hemiesters, ChE), end products of oxidation of polyunsaturated cholesteryl esters, occurs at higher concentrations in the plasma of two cohorts of cardiovascular disease patients than in the plasma of a control cohort. Macrophages exposed to the most prevalent ChE, cholesteryl hemiazelate (ChA) exhibit lysosome enlargement, peripheral lysosomal positioning, lysosome dysfunction and lipidosis which are irreversible. The transcriptomic profile of macrophages exposed to ChA indicates that the lysosome pathway is deeply affected and is well correlated with lysosome phenotypic and functional changes. Interestingly, the dysfunctional peripheral lysosomes are more prone to fuse with the plasma membrane, secreting their undigested luminal content into the extracellular milieu with potential consequences to the pathology. CONCLUSIONWe identify ChA not only as one of the molecules involved in the etiology of irreversible lysosome dysfunction culminating with lipidosis but also as a promoter of exocytosis of the dysfunctional lysosomes. The latter event is a new mechanism that may be important in the pathogenesis of atherosclerosis.

cell biology↗

bioRxiv2020

Histone demethylome map reveals combinatorial gene regulatory functions in embryonic stem cells

Epigenetic regulators and transcription factors establish distinct regulatory networks for gene regulation to maintain the embryonic stem cell (ESC) state. Although much has been learned regarding individual epigenetic regulators, their combinatorial functions remain elusive. Here, we report previously unknown combinatorial functions of histone demethylases (HDMs) in gene regulation of mouse ESCs. Generation of a histone demethylome (HDMome) map of 20 well-characterized HDMs based on their genome-wide binding revealed co-occupancy of HDMs in different combinations: KDM1A-KDM4B-KDM6A and JARID2-KDM2B-KDM4A-KDM4C-KDM5B largely co-occupy at enhancers and promoters, respectively. Mechanistic studies uncover that KDM1A-KDM6A combinatorially modulates P300/H3K27ac, H3K4me2 deposition and OCT4 recruitment that directs the OCT4/CORE regulatory network for target gene expression; while co-operative actions of JARID2-KDM2B-KDM4A-KDM4C-KDM5B control H2AK119ub1 and bivalent marks of polycomb-repressive complexes that facilitate the PRC regulatory network for target gene repression. Thus, combinatorial functions of HDMs differentially impact gene expression programs in mESCs.

genomics↗