Biology subjects

Ong, S.-E.

Publications and source records attributed to Ong, S.-E..

At least 19 recordsLinked to original sources

bioRxiv2026

A Modular Platform for Purification of Organelle-associated Mitochondria Reveals Functional Specialization at Organelle Contact Sites

Mitochondria perform diverse metabolic and signaling functions, yet how these activities are spatially organized within the mitochondrial network of cells remains poorly understood. Organelle contact sites are spatially restricted hubs that regulate mitochondrial metabolism, signaling, and dynamics, and are therefore well positioned to influence mitochondrial specialization. Investigation of contact site-associated mitochondrial populations has been hindered by a lack of methods to isolate these subpopulations. Here, we develop Organelle Contact-dependent Affinity Purification (ORCA), a workflow for the isolation and analysis of subpopulations of intact mitochondria and associated proteins defined by their organelle contacts. ORCA revealed distinct proteomes for mitochondria associated with the endoplasmic reticulum, lysosomes, peroxisomes, and the Golgi apparatus, demonstrating that organelle contacts define biochemically specialized mitochondrial populations. Focused analysis of Golgi-associated mitochondria showed enrichment of mitochondrial ribosomes and increased mitochondrial translation, revealing an unexpected role for Golgi-mitochondria contacts in regulating mitochondrial protein homeostasis. ORCA also identified the previously uncharacterized Golgi protein KIAA0930/GMO1 as an evolutionarily conserved regulator of oxidative phosphorylation at Golgi-mitochondria contacts. Together, our findings establish ORCA as a broadly applicable approach for investigating the spatial organization of intracellular organelles and reveal organelle contacts as key determinants of mitochondrial specialization.

cell biology↗

bioRxiv2026

Chemical Genetic Screen Identifies PSD3 as a Direct Substrate of NUAK1 that Regulates Dendritic Spine Maturation

Dysregulation of signaling by Novel (Nua) Kinase 1 (NUAK1) is associated with autism spectrum disorder, tissue fibrosis, and cancer progression. Direct phosphorylation targets of NUAK1 in the brain are unknown, hindering mechanistic understanding of its role in neurodevelopment. Here, we demonstrate that autism-associated NUAK1 variants differentially impact catalytic activity and subcellular distribution. We engineered ATP-analog sensitive NUAK1 and utilized its specificity towards bulky analogs to identify over 30 hitherto unknown direct phosphorylation targets of NUAK1 in the brain. We demonstrate that Pleckstrin Homology and Sec7-domain containing protein 3 (PSD3) is a bona fide phosphorylation target of NUAK1. PSD3, a guanine nucleotide exchange factor (GEF) for ARF6 GTPase, is phosphorylated by NUAK1 at Ser476. In neurons, expression of phosphodeficient PSD3 (S476A) leads to enhanced dendritic spine maturation in an ARF6-dependent fashion. Mechanistically, NUAK1 suppresses ARF6 activation through PSD3 phosphorylation. Abolishing Ser476 phosphorylation leads to aberrant ARF6 activation and increased generation of PI(4,5)P2. Our study reveals direct neuronal substrates of an autism risk gene NUAK1 and further delineates a mechanism through which NUAK1 phosphorylation of PSD3 controls ARF6 activation and dendritic spine maturation.

neuroscience↗

bioRxiv2025

Plasmodium falciparum exploits NUAK1 to establish infection in human erythrocytes

The malaria parasite Plasmodium falciparum continues to demonstrate growing drug resistance, raising the need for innovative treatments. Host-directed therapeutics are emerging as a promising approach for many infectious diseases, but knowledge of critical host factors for malaria is limited. P. falciparum is an obligate intracellular parasite of human erythrocytes, suggesting it has evolved to exploit specific host pathways to establish infection. Here, we report that the AMPK-related kinase NUAK1 is a critical host factor for P. falciparum in erythrocytes and has potential as a therapeutic target. We show that NUAK1 is present in human erythrocytes and undergoes increased phosphorylation in P. falciparum-infected cells. Two highly selective NUAK1 inhibitors, HTH-01-015 and WZ4003, inhibited P. falciparum growth throughout its asexual life cycle, including during erythrocyte invasion. Chemoproteomic profiling confirmed the inhibitors selectivity for human NUAK1. We further show that treatment with the inhibitors reduces phosphorylation of the well-characterized NUAK1 substrate MYPT1 in erythroid cells. Moreover, we find that genetic overexpression of NUAK1 in erythroid cells partially rescues both the signaling and invasion phenotypes elicited by the small molecule inhibitors. These results establish a critical role for the NUAK1 signaling pathway in P. falciparum-infected erythrocytes and highlight its potential as a vulnerable target for host-directed malaria control.

microbiology↗

bioRxiv2025

Xist Repeat A coordinates an assembly of SR proteins to recruit SPEN and induce gene silencing

The lncRNA Xist represents a paradigm to understand the mechanisms of RNA-mediated gene silencing in mammals, which remain largely unresolved. To induce silencing, Xist recruits the RNA-binding protein SPEN through its 5'-proximal Repeat A domain. Yet, how Repeat A recruits SPEN and how SPEN coordinates silencing remain unclear. We report that sequences in Repeat A critical for SPEN recruitment directly bind SR-rich splicing factors. SRSF1, one such factor, is required for optimal SPEN recruitment and its RS-domain recruits SPEN when tethered to Xist. SPEN and SR-protein-binding motifs promote Repeat As association with many proteins, including the m6A machinery and elongating RNA polymerase II. SPEN also represses autosomal genes where its recruitment coincides with SR-protein binding. Our results reveal an unexpectedly essential role for splicing factors in coordinating silencing by Xist and suggest that the sensing of SR-protein-rich assemblies is a general mechanism through which SPEN targets genes for repression.

genetics↗

bioRxiv2024

diaPASEF-Powered Chemoproteomics Enables Deep Kinome Interaction Profiling

Protein-protein interactions (PPIs) underlie most biological functions. Devastating human conditions like cancers, neurological disorders, and infections, hijack PPI networks to initiate disease, and to drive disease progression. Understanding precisely how diseases remodel PPI networks can, therefore, help clarify disease mechanisms and identify therapeutic targets. Protein kinases control most cellular processes through protein phosphorylation. The 518 human kinases, known as the kinome, are frequently dysregulated in disease and highly druggable with ATP-competitive inhibitors. Kinase activity, localization, and substrate recognition are regulated by dynamic PPI networks composed of scaffolding and adapter proteins, other signaling enzymes like small GTPases and E3 ligases, and phospho-substrates. Accordingly, mapping kinase PPI networks can help determine kinome activation states, and, in turn, cellular activation states; this information can be used for studying kinase-mediated cell signaling, and for prioritizing kinases for drug discovery. Previously, we have developed a high-throughput method for kinome PPI mapping based on mass spectrometry (MS)-based chemoproteomics that we named kinobead competition and correlation analysis (kiCCA). Here, we introduce 2nd generation (gen) kiCCA which utilizes data-independent acquisition (dia) with parallel accumulation serial fragmentation (PASEF) MS and a re-designed CCA algorithm with improved selection criteria and the ability to predict multiple kinase interaction partners of the same proteins. Using neuroblastoma cell line models of the noradrenergic-mesenchymal transition (NMT), we demonstrate that 2nd gen kiCCA (1) identified 6.1-times more kinase PPIs in native cell extracts compared to our 1st gen approach, (2) determined kinase-mediated signaling pathways that underly the neuroblastoma NMT, and (3) accurately predicted pharmacological targets for manipulating NMT states. Our 2nd gen kiCCA method is broadly useful for cell signaling research and kinase drug discovery.

biochemistry↗

bioRxiv2024

Nascent transcript O-MAP reveals the molecular architecture of a single-locus subnuclear compartment built by RBM20 and the TTN RNA

Eukaryotic nuclei adopt a highly compartmentalized architecture that influences nearly all genomic processes. Understanding how this architecture impacts gene expression has been hindered by a lack of tools for elucidating the molecular interactions at individual genomic loci. Here, we adapt oligonucleotide-mediated proximity-interactome mapping (O-MAP) to biochemically characterize discrete, micron-scale nuclear neighborhoods. By targeting O-MAP to introns within the TTN pre-mRNA, we systematically map the chromatin loci, RNAs, and proteins within a muscle-specific RNA factory organized around the TTN locus. This reveals an unanticipated compartmental architecture that organizes cis- and trans-interacting chromosomal domains, including a hub of transcriptionally silenced chromatin. The factory also recruits dozens of unique RNA-binding and chromatin-scaffolding factors, including QKI and SAFB, along with their target transcripts. Loss of the cardiac-specific splicing factor RBM20--a master regulator of TTN splicing that is mutated in dilated cardiomyopathy--remodels nearly every facet of this architecture. This establishes O-MAP as a pioneering method for probing single-locus, microcompartment-level interactions that are opaque to conventional tools. Our findings suggest new mechanisms by which coding genes can "moonlight" in nuclear-architectural roles.

genomics↗

bioRxiv2024

Mitochondrial Calcium Signaling Regulates Branched-Chain Amino Acid Catabolism in Fibrolamellar Carcinoma

Metabolic adaptations in response to changes in energy supply and demand are essential for survival. The mitochondrial calcium uniporter plays a key role in coordinating metabolic homeostasis by regulating TCA cycle activation, mitochondrial fatty acid oxidation, and cellular calcium signaling. However, a comprehensive analysis of uniporter-regulated mitochondrial pathways has remained unexplored. Here, we investigate metabolic consequences of uniporter loss- and gain-of-function using uniporter knockout cells and the liver cancer fibrolamellar carcinoma (FLC), which we demonstrate to have elevated mitochondrial calcium levels. Our results reveal that branched-chain amino acid (BCAA) catabolism and the urea cycle are uniporter-regulated metabolic pathways. Reduced uniporter function boosts expression of BCAA catabolism genes, and the urea cycle enzyme ornithine transcarbamylase (OTC). In contrast, high uniporter activity in FLC suppresses their expression. This suppression is mediated by reduced expression of the transcription factor KLF15, a master regulator of liver metabolism. Thus, uniporter responsive calcium signaling plays a central role in FLC-associated metabolic changes, including hyperammonemia. Our study identifies an important role for mitochondrial calcium signaling in metabolic adaptation through transcriptional regulation of metabolism and elucidates its importance for BCAA and ammonia metabolism in FLC.

cell biology↗

bioRxiv2023

Single-cell signaling analysis reveals that Major Vault Protein facilitates RasG12C inhibitor resistance

Recently developed covalent inhibitors for RasG12C provide the first pharmacological tools to target mutant Ras-driven cancers. However, the rapid development of resistance to current clinical Ras G12C inhibitors is common. Presumably, a subpopulation of RasG12C-expressing cells adapt their signaling to evade these inhibitors and the mechanisms for this phenomenon are unclear due to the lack of tools that can measure signaling with single-cell resolution. Here, we utilized recently developed Ras sensors to profile the environment of active Ras and to measure the activity of endogenous Ras in order to pair structure (Ras signalosome) to function (Ras activity), respectively, at a single-cell level. With this approach, we identified a subpopulation of KRasG12C cells treated with RasG12C-GDP inhibitors underwent oncogenic signaling and metabolic changes driven by WT Ras at the golgi and mutant Ras at the mitochondria, respectively. Our Ras sensors identified Major Vault Protein (MVP) as a mediator of Ras activation at both compartments by scaffolding Ras signaling pathway components and metabolite channels. We found that recently developed RasG12C-GTP inhibitors also led to MVP-mediated WT Ras signaling at the golgi, demonstrating that this a general mechanism RasG12C inhibitor resistance. Overall, single-cell analysis of structure-function relationships enabled the discovery of a RasG12C inhibitor-resistant subpopulation driven by MVP, providing insight into the complex and heterogenous rewiring occurring during drug resistance in cancer.

cancer biology↗

bioRxiv2023

Cellular RNA interacts with MAVS to promote antiviral signaling

Immune signaling needs to be well-regulated to promote clearance of pathogens, while preventing aberrant inflammation. Interferons (IFNs) and antiviral genes are activated by the detection of viral RNA by RIG-I-like receptors (RLRs). Signal transduction downstream of RLRs proceeds through a multi-protein complex organized around the central adaptor protein MAVS. Recent work has shown that protein complex function can be modulated by RNA molecules providing allosteric regulation or acting as molecular guides or scaffolds. Thus, we hypothesized that RNA plays a role in organizing MAVS signaling platforms. Here, we show that MAVS, through its central intrinsically disordered domain, directly interacts with the 3' untranslated regions of cellular mRNAs. Importantly, elimination of RNA by RNase treatment disrupts the MAVS signalosome, including newly identified regulators of RLR signaling, and inhibits phosphorylation of the transcription factor IRF3. This supports the hypothesis that RNA molecules scaffold proteins in the MAVS signalosome to induce IFNs. Together, this work uncovers a function for cellular RNA in promoting signaling through MAVS and highlights a generalizable principle of RNA regulatory control of cytoplasmic immune signaling complexes.

immunology↗

bioRxiv2023

Oligonucleotide-directed proximity-interactome mapping (O-MAP): A unified method for discovering RNA-interacting proteins, transcripts and genomic loci in situ.

Throughout biology, RNA molecules form complex networks of molecular interactions that are central to their function, but remain challenging to investigate. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a straightforward method for elucidating the biomolecules near an RNA of interest, within its native cellular context. O-MAP uses programmable oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA, enabling nearby molecules to be enriched by streptavidin pulldown. O-MAP induces exceptionally precise RNA-localized in situ biotinylation, and unlike alternative methods it enables straightforward optimization of its targeting accuracy. Using the 47S pre-ribosomal RNA and long noncoding RNA Xist as models, we develop O-MAP workflows for unbiased discovery of RNA-proximal proteins, transcripts, and genomic loci. This revealed unexpected co-compartmentalization of Xist and other chromatin-regulatory RNAs and enabled systematic characterization of nucleolar-chromatin interactions across multiple cell lines. O-MAP is portable to cultured cells, organoids, and tissues, and to RNAs of various lengths, abundances, and sequence composition. And, O-MAP requires no genetic manipulation and uses exclusively off-the-shelf parts. We therefore anticipate its application to a broad array of RNA phenomena.

molecular biology↗

bioRxiv2022

Designed sensors reveal normal and oncogenic Ras signaling in endomembranes and condensates

Genetically encoded biosensors have accelerated biological discovery, however many important targets such as active Ras (Ras-GTP) are difficult to sense as strategies to match a sensors sensitivity to the physiological range of target are lacking. Here, we use computational protein design to generate and optimize intracellular sensors of Ras activity (LOCKR-based Sensor for Ras activity: Ras-LOCKR-S) and proximity labelers of the signaling environment of Ras (LOCKR-based, Ras activity-dependent Proximity Labeler: Ras-LOCKR-PL). We demonstrate that our tools can measure endogenous Ras activity and environment at subcellular resolution. We illustrate the application of these tools by using them to identify Ras effectors, notably Src-Associated in Mitosis 68 kDa protein (SAM68), enriched in oncogenic EML4-Alk granules. Localizing these sensors to these granules revealed that SAM68 enhances Ras activity specifically at the granules, and SAM68 inhibition sensitizes EML4-Alk-driven cancer cells to existing drug therapies, suggesting a possible therapeutic strategy.

cell biology↗

bioRxiv2022

Neurodevelopmental disorder associated mutations in TAOK1 reveal its function as a plasma membrane remodeling kinase

Mutations in TAOK1, a serine-threonine kinase encoding gene are strongly associated with both autism spectrum disorder (ASD) and neurodevelopmental delay (NDD). However, molecular function of this evolutionarily conserved kinase and the mechanisms through which TAOK1 mutations lead to neuropathology are unknown. Here, we showed that TAOK1 is highly expressed in neurons within the brain, and has a functional role in remodeling the plasma membrane through direct association with phosphoinositides. We characterized four NDD-associated TAOK1 mutations, and demonstrated that these mutations render TAOK1 catalytically dead. Kinase dead TAOK1 mutants were aberrantly trapped in membrane-bound state, which induced exuberant membrane protrusions. Expression of TAOK1 disease mutants in hippocampal neurons led to abnormal growth of the dendritic arbor. The coiled-coil region C-terminal to the kinase domain are predicted to fold into a triple helix. We showed that this triple helix directly bound phospholipids, and was required for both TAOK1 membrane association and induction of aberrant protrusions. Further, TAOK1 mutants were rescued from their membrane-trapped state by exogenous expression of the isolated kinase domain. Utilizing mass-spectrometry, we identified critical residues in the triple helix phosphorylated by TAOK1 that autoregulated its plasma membrane association. These findings define a previously unknown function of TAOK1 as a unique plasma membrane remodeling kinase, and reveal the underlying mechanisms through which TAOK1 dysfunction leads to neurodevelopmental disorders.

neuroscience↗

bioRxiv2022

Proteomic identification of phosphorylation dependent Septin 7 interactors that drive dendritic spine formation

Septins are a family of cytoskeletal proteins that regulate several important aspects of neuronal development. Septin 7 (Sept7) is enriched at the base of dendritic spines in excitatory neurons and mediates both spine formation and spine-synapse maturation. Phosphorylation at a conserved C-terminal tail residue of Sept7 mediates its translocation into the dendritic spine head to allow spine-synapse maturation. The mechanistic basis for postsynaptic stability and compartmentalization conferred by phosphorylated Sept7, however, is not known. We report herein the proteomic identification of Sept7 phosphorylation dependent neuronal interactors. Using Sept7 C-terminal phosphopeptide pulldown and biochemical assays, we show that the 14-3-3 family of proteins specifically interact with Sept7 when phosphorylated at the T426 residue. Biochemically, we validate the interaction between Sept7 and 14-3-3 isoform gamma, and show that 14-3-3 gamma is also enriched in mature dendritic spine head. Further, we demonstrate that interaction of phosphorylated Sept7 with 14-3-3 protects it from dephosphorylation, as expression of a 14-3-3 antagonist significantly decreases phosphorylated Sept7 in neurons. This study identifies 14-3-3 proteins as an important physiological regulator of Sept7 function in neuronal development.

neuroscience↗

bioRxiv2021

Water droplet-in-oil digestion method for single-cell proteomics

Recent advances in single-cell proteomics highlight the promise of sensitive analyses in limited cell populations. However, technical challenges remain for sample recovery, throughput, and versatility. Here, we first report a water droplet-in-oil digestion (WinO) method based on carboxyl-coated beads and phase transfer surfactants for proteomic analysis using limited sample amounts. This method was developed to minimize the contact area between the sample solution and the container to reduce the loss of proteins and peptides by adsorption. This method increased protein and peptide recovery 10-fold as well as the number of quantified transmembrane proteins compared to an in-solution digestion (ISD) method. The proteome profiles obtained from 100 cells using the WinO method highly correlated with those from 10000 cells using the ISD method. We successfully applied the WinO method to single-cell proteomics and quantified 462 proteins. Using the WinO method, samples can be easily prepared in a multi-well plate, making it a widely applicable and suitable method for single-cell proteomics.

systems biology↗

bioRxiv2021

Displacement of PKA catalytic subunit from AKAP signaling islands drives pathology in Cushing's syndrome

Mutations in the catalytic subunit of protein kinase A (PKAc) drive the stress hormone disorder adrenal Cushings syndrome. Here we define mechanisms of action for the PKAc-L205R and W196R variants. Both Cushings mutants are excluded from A kinase anchoring protein (AKAP) signaling islands and consequently diffuse throughout the cell. Kinase-dead experiments show that PKA activity is required for cortisol hypersecretion. However, kinase activation is not sufficient, as only cAMP analog drugs that displace native PKAc from AKAPs enhance cortisol release. Rescue experiments that incorporate mutant PKAc into AKAP signaling islands abolish cortisol overproduction, indicating that kinase anchoring restores normal endocrine function. Phosphoproteomics show that PKAc-L205R and W196R engage different mitogenic signaling pathways. ERK activity is elevated in adrenal-specific PKAc-W196R knock-in mice. Conversely, PKAc-L205R attenuates Hippo signaling, thereby upregulating the YAP/TAZ transcriptional co-activators. Thus, aberrant localization of each Cushings variant promotes the transmission of a distinct downstream pathogenic signal.

molecular biology↗

bioRxiv2021

Multiplexed profiling of kinase interactomes quantifies cellular network plasticity

Cells utilize protein-protein interaction (PPI) networks to receive, transduce, and respond to stimuli. Interaction network rewiring drives devastating diseases like cancers, making PPIs attractive targets for pharmacological intervention. Kinases are druggable nodes in PPI networks but high-throughput proteomics approaches to quantify disease-associated kinome PPI rewiring are lacking. We introduce kinobead competition and correlation analysis (Ki-CCA), a chemoproteomics approach to simultaneously map hundreds of endogenous kinase PPIs. We identified 2,305 PPIs of 300 kinases across 18 diverse cancer lines, quantifying the high plasticity of interaction networks between cancer types, signaling, and phenotypic states; this database of dynamic kinome PPIs provides deep insights into cancer cell signaling. We discovered an AAK1 complex promoting epithelial-mesenchymal transition and drug resistance, and depleting its components sensitized cells to targeted therapy. Ki-CCA enables rapid and highly multiplexed mapping of kinome PPIs in native cell and tissue lysates, without epitope tagged baits, protein labeling, or antibodies.

biochemistry↗

bioRxiv2020

PARprolink: a photoaffinity probe for identifying poly(ADP-ribose)-binding proteins

Post-translational modification of proteins with poly(ADP-ribose) (PAR) is an important component of the DNA damage response. Four PAR synthesis inhibitors have recently been approved for the treatment of breast, ovarian, and prostate cancers. Despite its clinical significance, a molecular understanding of PAR function, including its binding partners, remains incomplete. In this work, we synthesize a PAR photoaffinity probe that captures and isolates endogenous PAR binders. Our method identified dozens of known PAR-binding proteins and hundreds of novel binders involved in DNA repair, RNA processing, and metabolism. PAR binding by eight candidates was confirmed using pull-down and/or electrophoretic mobility shift assays. Using PAR probes of defined lengths, we detected proteins that preferentially bind to 40-mer over 8-mer PAR, indicating that polymer length may regulate the outcome and timing of PAR signaling pathways. This investigation produces the first census of PAR-binding proteins, provides a proteome-wide view of length-selective PAR binding, and associates PAR binding with RNA metabolism and the formation of biomolecular condensates.

molecular biology↗

bioRxiv2019

Kinome-centric pharmacoproteomics identifies signaling pathways underlying cellular responses to targeted cancer drugs

ABSTRACTKinase-dependent signaling networks are frequently dysregulated in cancer, driving disease progression. While kinase inhibition has become an important therapeutic approach many cancers resist drug treatment. Therefore, we need both reliable biomarkers that predict drug responses and new targets to overcome drug resistance. Determining the kinase(s) that control cancer progression in individual cancers can pose a significant challenge. Genomics has identified important, yet limited numbers of kinase driver mutations. Transcriptomics can quantify aberrant gene expression, but it cannot measure the protein phosphorylation that regulates kinase-dependent signaling network activity. Proteomics measures protein expression and phosphorylation and, therefore, quantifies aberrant signaling network activity directly. We developed a kinome-centric pharmacoproteomics platform to study signaling pathways that determine cancer drug response. Using hepatocellular carcinoma (HCC) as our model, we determined kinome activity with kinobead/LC-MS profiling, and screened 299 kinase inhibitors for growth inhibition. Integrating kinome activity with drug responses, we obtained a comprehensive database of predictive biomarkers, and kinase targets that promote drug sensitivity and resistance. Our dataset specified pathway-based biomarkers for the clinical HCC drugs sorafenib, regorafenib and lenvatinib, and we found these biomarkers enriched in human HCC specimens. Strikingly, our database also revealed signaling pathways that promote HCC cell epithelial-mesenchymal transition (EMT) and drug resistance, and that NUAK1 and NUAK2 regulate these pathways. Inhibition of these kinases reversed the EMT and sensitized HCC cells to kinase inhibition. These results demonstrate that our kinome pharmacoproteomics platform discovers both predictive biomarkers for personalized oncology and novel cancer drug targets.

cancer biology↗