Biology subjects

Su, M.

Publications and source records attributed to Su, M..

At least 19 recordsLinked to original sources

bioRxiv2026

The S1B-Targeting PEDV Neutralizing Antibody C62 Prematurely Activates S-trimer and Mimics Receptor Function

Porcine epidemic diarrhea virus (PEDV) causes devastating enteric disease in piglets, yet the mechanistic basis of antibody-mediated neutralization remains poorly understood. Here, we determined the structure of PEDV HNXX-strain spike domain B (S1B) simultaneously bound by C62, a neutralizing porcine monoclonal antibody against PEDV G2 strains, and N34, a non-neutralizing porcine PEDV antibody. The structure reveals that C62 targets a conserved, cryptic epitope that is accessible only when S1B adopts an "up" conformation. Functionally, we showed that C62 has substantially stronger activity than N34 in triggering S-trimer disassembly and inducing the formation of proteinase K-resistant, post-fusion-like S2 structures. Despite the weaker triggering activity of N34, both C62 and N34 can function as artificial receptors. Notably, although the C62 epitope is conserved across both G1 and G2 strains, C62 exhibits G2-strain-biased neutralizing activity. We further showed that differences in cell-surface membrane fusion activity among PEDV spikes correlate with distinct viral entry pathways and are jointly determined by the S1A and S1B sequences. Together, our findings identify a strain-specific vulnerable site on the PEDV S-trimer and provide insight into how cell-surface membrane fusion activity may influence viral entry pathway selection and antibody neutralization efficacy.

microbiology↗

bioRxiv2026

Tirzepatide attenuates atherosclerosis through weight loss-independent anti-inflammatory mechanisms

BackgroundAtherosclerosis is a chronic inflammatory vascular disorder with persistent residual inflammation even after standard lipid-lowering therapy. Mounting evidence from bench to bedside suggests that diabetes and obesity accelerate atherosclerosis development. Tirzepatide (TZP), a dual Glucagon-Like Peptide-1 Receptor/Glucose-Dependent Insulinotropic Polypeptide Receptor (GLP-1R/GIPR) agonist approved for treating diabetes and obesity, has demonstrated proven cardiometabolic efficacy in large cardiovascular outcome trials. However, it remains largely uncertain whether TZP attenuates atherosclerosis independent of its anti-diabetic and anti-obese effects through direct actions on the vasculature. MethodsWe established atherosclerotic mouse models under diabetic, obese, and non-diabetic/non-obese conditions. Analysis of covariance (ANCOVA) and pair-feeding experiments were applied to experimentally decouple weight-dependent metabolic improvement from intrinsic vasculoprotection. Molecular and cell biological assays in human umbilical vein endothelial cells (HUVECs) and human aortic endothelial cells (HAECs) were performed to dissect the underlying signaling mechanisms. ResultsTZP markedly reduced aortic plaque burden and inflammation, restrained necrotic core enlargement, and improved plaque stability across all experimental mouse models. Both ANCOVA and pair-feeding experiments confirmed that these atheroprotective effects were independent of food intake and body weight loss. Furthermore, TZP attenuated systemic and vascular inflammation in Tumor Necrosis Factor- (TNF)-treated C57BL/6J mice, and this protection occurred without changes in body weight or blood glucose levels. Mechanistically, TZP directly targeted endothelial cells and activated the cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA)/endothelial nitric oxide synthase (eNOS) pathway, increased eNOS phosphorylation and nitric oxide bioavailability, consequently downregulating the expression of the pro-inflammatory adhesion molecules Vascular Cell Adhesion Molecule-1 (VCAM-1) and Intercellular Adhesion Molecule-1 (ICAM-1). ConclusionsTZP arrests atherosclerosis progression through weight loss-independent anti-inflammatory mechanisms. These findings implicate TZP as a promising therapeutic drug for mitigating residual vascular inflammation in patients with atherosclerotic cardiovascular disease (ASCVD), irrespective of glycemic status or obesity. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LITirzepatide exerts direct anti-atherosclerotic effects in preclinical mouse models of atherosclerosis under diabetic, obese, and non-obese conditions. C_LIO_LITirzepatide directly targets endothelial GLP-1R/GIPR and downstream cAMP/PKA/eNOS signaling pathway to suppress NF-{kappa}B-driven vascular inflammation, thereby uncovering a previously unrecognized vasculoprotective mechanism underlying its cardiovascular benefits C_LI What Are the Clinical Implications?O_LITirzepatide exerts direct vascular protective effects independent of body weight reduction, suggesting that its cardiovascular benefits may extend beyond glycemic control and obesity management. C_LIO_LITirzepatide may represent a promising therapeutic drug for addressing residual vascular inflammation in ASCVD patients, including those without overt diabetes or obesity C_LI

physiology↗

bioRxiv2026

Host, diet, microbiome, and xenobiotic plasma metabolites associate with kidney cell-type transcriptional programs in CKD

BackgroundChronic kidney disease (CKD) is associated with widespread alterations in the circulating metabolome, including metabolites influenced by diet and the gut microbiome that may represent modifiable disease pathways. However, the extent to which metabolites from distinct origins are associated with kidney cell-type-specific injury programs remains incompletely characterized. MethodsWe analyzed plasma metabolomics data from 240 Kidney Precision Medicine Project (KPMP) participants (207 CKD, 33 healthy reference) and validated findings in an independent cohort (n=883). We applied unsupervised clustering to identify metabotypes and elastic net classification to generate a continuous metabotype score. We classified metabolites by origin (host-derived, diet-derived, microbiome-dependent, xenobiotic) and trained random forest models to predict filtration markers and structural injury. In 66 participants with matched kidney single-cell RNA sequencing, we regressed podocyte and proximal tubule pseudobulk expression against plasma metabolites and computed hub scores quantifying transcriptional connectivity. ResultsTwo reproducible metabotypes separated CKD from healthy states (elastic net CV AUC=0.984 discovery, 0.997 validation), with the metabotype score strongly correlating with eGFR ({rho}=-0.79). Although they represented a minor subset of the circulating metabolome, diet-and microbiome-dependent metabolites such as myo-inositol, guaiacol sulfate, and indole derivatives were among the strongest metabotype-defining features. Metabolites improved prediction of filtration markers beyond clinical covariates, most notably for BUN ({Delta}R{superscript 2}=+0.29), driven by urea, guanidinosuccinate, and the microbiome-derived arabitol/xylitol. Plasma metabolites were associated with interstitial fibrosis (415 metabolites) and tubular atrophy (505 metabolites) and distinguished opposing proximal tubule transcriptional programs. Across kidney cell types, environmental xenobiotics (PFHxS, halogenated benzoic acids) activated aryl hydrocarbon receptor, inflammatory, and fibrotic programs in podocytes, while endogenous metabolites engaged inflammatory and oxidative stress programs in proximal tubule. ConclusionPlasma metabotypes capture metabolic heterogeneity beyond eGFR, with metabolites of distinct origins associated with cell-type-specific kidney injury programs, supporting plasma metabolomics as a noninvasive approach for molecular patient stratification in CKD. Key PointsO_LIUnsupervised clustering defined reproducible plasma metabotypes spanning host-, diet-, microbiome-, and xenobiotic-derived metabolites that separated CKD from healthy reference states. C_LIO_LIDiet- and microbiome-dependent metabolites were among the strongest metabotype-defining features and showed the strongest associations with podocyte and proximal tubule gene expression. C_LIO_LIMetabolites of distinct origins associated with different cell-type transcriptional programs in podocytes and proximal tubule. C_LI

Systems Biology↗

bioRxiv2026

Desert hedgehog enhances endothelial resilience and prevents atherosclerosis by mitigating PAI-1 signaling

BACKGROUNDAtherosclerotic cardiovascular disease remains the leading cause of death worldwide. Most current pharmacotherapies target conventional risk factors that promote atherosclerosis (e.g., hyperlipidemia) rather than intrinsic resilience factors that protect against atherosclerosis in the face of risk factors. Here, we investigated the role of desert hedgehog (DHH), a canonical ligand of the hedgehog signaling pathway, as a novel resilience factor that restrains endothelial mesenchymal transition (EndoMT) and protects against atherosclerosis. METHODSSingle-cell RNA sequencing (scRNA-seq) was performed on atheroprone and atheroprotective regions of the ApoE knockout mouse aorta to identify mechanoresponsive genes associated with atherosclerosis. Endothelial cell-specific Dhh knockout mice were subjected to partial carotid ligation and hypercholesterolemic conditions to investigate the role of endothelial Dhh in atherosclerosis progression. scRNA-seq, bulk RNA sequencing, endothelial lineage tracing, immunoprecipitation-coupled mass spectrometry, and surface plasmon resonance were used to in-vestigate the role and mechanism of DHH in EndoMT. Pharmacological interventions and recombinant DHH administration were performed in vivo to evaluate therapeutic potential of DHH targeting. DHH expression was also examined in human atherosclerotic arteries and serum samples from patients with coronary artery disease. RESULTSDHH protein expression was enriched in arterial endothelium from mice, porcine, and humans. However, DHH expression was significantly reduced in atherosclerotic arteries and serum from patients with coronary artery disease. scRNA-seq of atheroprone and atheroresistant region of mouse aorta identified Dhh as a novel mechanoresponsive gene enriched in aortic regions exposed to unidirectional laminar flow. Endothelial cell-specific Dhh knockout (DhhecKO) mice exhibited increased atherosclerotic lesion area, large necrotic cores, and reduced collagen content following partial carotid ligation. Similarly, under hypercholesterolemic conditions, both male and female DhhecKO mice showed aggravated atherosclerosis progression. scRNA-seq of DhhecKO mouse aortas revealed an increased proportion of endothelial cells undergoing mesenchymal transition, indicating enhanced EndoMT. These findings were corroborated by bulk RNA-sequencing of DHH depleted HUVECs and endothelial lineage tracing in inducible DhhecKO mice. Mechanistically, DHH directly interacted with plasminogen activator inhibitor type 1 (PAI-1) and suppressed PAI-1-induced EndoMT. PAI-1 promoted EndoMT in ECs through activation of canonical TGF-{beta} signaling (SMAD2/3) and noncanonical AKT/ERK1/2 signaling via interaction with low-density lipoprotein receptor-related protein (LRP1). Neutralization of PAI-1 or inhibition of LRP1, AKT/ERK1/2, or SMAD3 signaling abolished DHH deficiency-induced EndoMT. DHH competitively inhibited PAI-1 binding to LRP1, thereby attenuating downstream pro-EndoMT signaling. Intriguingly, treatment with PAI-1 inhibitor TM5275 mitigated endothelial Dhh deficiency induced EndoMT in vivo. Of translational relevance, recombinant mouse DHH protein administration reduced atherosclerosis progression, stabilized plaque, and decreased the expression of EndoMT markers in ApoE knockout mice. CONCLUSIONSDesert hedgehog (DHH) is an intrinsic endothelial cell-enriched resilience factor that protects against EndoMT and atherosclerosis by preventing PAI-1 signaling. The present study implicates endothelial DHH as a potential therapeutic target for atherosclerotic cardiovascular disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/729715v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@194c8a3org.highwire.dtl.DTLVardef@1004d52org.highwire.dtl.DTLVardef@d47c73org.highwire.dtl.DTLVardef@368866_HPS_FORMAT_FIGEXP M_FIG C_FIG Desert hedgehog (DHH) is an intrinsic endothelial cell-enriched resilience factor that protects against EndoMT and atherosclerosis by preventing PAI-1 binding to LRP1 and downstream AKT/ERK, as well as SMAD2/3 signaling. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIDHH was identified as a flow-responsive resilience gene that is downregulated by disturbed flow in endothelial cells. C_LIO_LIEndothelial-specific deletion of Dhh promoted endothelial-to-mesenchymal transition (En-doMT) and atherosclerosis. C_LIO_LIDHH directly interacts with PAI-1 and preclude PAI-1 mediated pro-EndoMT signaling. C_LI What Are the Clinical Implications?O_LIDHH maintains endothelial homeostasis during atherosclerosis. C_LIO_LITargeting endothelial DHH-PAI-1 axis may represent a potential therapeutic strategy to reduce EndoMT and limit plaque progression. C_LIO_LILower circulating DHH level may serve as a potential biomarker of endothelial dysfunction and plaque vulnerability in atherosclerotic disease. C_LI

biochemistry↗

bioRxiv2026

Phage-based microbiome manipulation reveals ecological interactions within gut communities

Mechanistic understanding of gut ecology is limited by the availability of tools for precise manipulation of microbiome composition. Here, we isolate lytic phages to enable targeted removal of gut commensal Escherichia fergusonii (Ef) from complex, undefined stool-derived in vitro communities. A single phage drove resistance without fitness cost in monoculture, but resistant Ef exhibited reduced fitness in communities, enabling expansion of closely related Proteobacteria. Resistance arose via reversible promoter inversion linked to outer-membrane function. A phage cocktail overcame resistance to achieve Ef knockout across communities with minimal collateral effects. Using knockout communities, we show that Ef is necessary and sufficient for preventing Salmonella invasion. Replacement with an Ef transposon-mutant library revealed that community-specific fitness defects are enriched in genes involved in outer-membrane assembly. Disruption of these genes sensitized Ef to antagonistic community members, highlighting interspecies warfare as a key driver of microbiome ecology. These results establish phage-mediated perturbation as a framework for linking species to community-level function and for enabling precision microbiome engineering.

microbiology↗

bioRxiv2025

Mast cell extracellular granules are bioactive condensates driven by heparin and polyamine

Biomolecular condensates are membraneless bodies that organize biochemical reactions typically within cells. However, the roles of condensates in extracellular space--where conditions differ substantially from intracellular space--remain poorly understood. Here, we report mast cell extracellular granules (MCEGs), a stable membraneless entity, are condensates assembled via electrostatic interactions between glycosaminoglycans and polyamines. Disrupting polyamine synthesis or trafficking blocks MCEG formation and compromises the storage of proteases and cytokines. Granules reconstituted with heparin and spermine are sufficient to enrich mediators such as CPA3 and TNF, maintaining an elevated pH and higher concentrations of calcium and zinc compared to the extracellular milieu. This unique environment enhances CPA3 enzymatic activity. Furthermore, the granules increase TNF binding and its bioactivity toward endothelial cells. Together, we reveal MCEGs as functionally active biomolecular condensates with distinct biochemical and immunological properties; MCEGs are formed through sugar-metabolite interactions, expanding the mechanisms of condensate assembly beyond classical protein-protein and protein-RNA interactions.

cell biology↗

bioRxiv2025

Exploring use of ozone nanobubbles for removal of cyanobacteria and co-occurring antimicrobial resistance genes in water supply and reuse systems

Harmful cyanobacterial blooms present persistent risks to both drinking water security and wastewater reuse, driving the need for advanced treatment strategies. Treatment barrier(s) need to be capable of simultaneously controlling cyanobacteria, cyanotoxins, and co-occurring contaminants like bloom-associated antimicrobial resistance genes (ARGs) particularly in the case of recycling treated wastewater. Ozone nanobubble technology has emerged as a promising innovation, offering extended oxidative stability and enhanced interfacial reactivity compared to conventional ozonation. Hence this research objectives were to (a) assess the removal performance of ozone nanobubbles in eliminating cyanobacteria and their co-occurring contaminants in comparison to conventional ozone systems, and (b) investigate the repeatability of the results in varying background water qualities, ozone decay and the potential for by-products formation Ozonation using nanobubbles enhanced oxidation performance by 19%-34% in the drinking water reservoir compared to conventional ozonation while keeping the ozone concentration below 2mg/l. Lower oxidation efficiencies were observed in treated wastewater compared to drinking water sources, reflecting the higher content of organic matter and suspended solids, and oxidant demand characteristic of recycled water systems. Despite these challenges, ozone nanobubbles consistently outperformed conventional ozonation in reducing both cyanobacterial biomass and cell viability, underscoring their potential as an advanced "polishing" step for algal management in wastewater reuse applications. By exploring fate of ARGs alongside cyanobacteria and toxin removal, this work extends beyond traditional ozonation trials. It provides valuable field-based evidence that bridges the divide between laboratory efficacy and full-scale operational performance. Future studies should build on this by exploring combined or sequential treatment barriers that enhance DNA degradation, thereby addressing both cellular and genetic risks in water supply and reuse systems. Observing the action of nanobubbles under dynamic, real-world water quality conditions is currently challenging; however, this studys novel field trials demonstrate potential nanobubble applications and provide valuable insights to guide future investigations. The results reinforce the broader applicability of ozone nanobubble technology for multi-target contaminant control in water reservoirs.

microbiology↗

bioRxiv2025

Type one protein phosphatases (TOPPs) catalyze EIN2 dephosphorylation to regulate ethylene signaling in Arabidopsis

TOPPs (Type one protein phosphatases) widely modulate plant hormone signaling and stress responses in plants, but their roles in ethylene signal transduction remain unknown. This study reveals a reciprocal regulatory relationship between TOPPs and EIN2 (Ethylene insensitive 2)-mediated ethylene signaling. We identified that ethylene can induce TOPPs expression, and topp1/4/5 triple mutants exhibited partial ethylene insensitivity with reduced EIN3 protein levels and ERF1 (Ethylene response factor 1) expression. Mechanistically, TOPPs genetically act upstream of EIN2, physically interacting with its carboxyl-terminal domain (EIN2-C) to dephosphorylate the critical S655 residue. This site-specific dephosphorylation promotes EIN2 stability and EIN2-C nuclear accumulation, thereby activating ethylene responses. Notably, transgenic plants expressing phosphorylation-deficient EIN2S655A displayed constitutive ethylene responses and improved salt tolerance. Further investigation showed that EIN3/EIL1 (EIN3 like 1) transcriptionally activates TOPPs expression by binding to their promoter, amplifying ethylene signaling accordingly. Together, our finding establishes TOPPs play an important regulatory role in ethylene signal transduction and elucidate a dephosphorylation-switch mechanism in controlling EIN2 function, providing critical insight into the role of EIN2 post-translational modifications in plant stress adaptation.

plant biology↗

bioRxiv2025

Programmable Aptamer-Embedded Circular RNAs for Targeted Antigen-Presenting Cells Immunotherapy

The targeted delivery of mRNA to specific cell types in vivo remains a major unmet need in mRNA-based therapeutics. Conventional strategies rely on nanocarriers engineered with various modifications. However, these exogenous materials could cause adverse reactions, and their complex manufacturing processes often hinder clinical application. By leveraging the innate programmability of RNA sequences, we herein report a carrier-free, scalable, and programmable aptamer-embedded circular RNAs (Apt-circRNAs) design that confers targeting capability through the strategic incorporation of different aptamers at varying densities, while retaining circular RNA stability and protein production capability. Experimental results show that antigen-loaded Apt-circRNAs enable targeted delivery to antigen-presenting cells (APCs), drive endogenous antigen expression, activate antigen-specific T cells, and elicit potent immune responses that mediate clearance of both early-and late-stage tumors in mouse models. In humanized models of colorectal cancer, the combination of Apt-circRNA and PD-1 blockade produced synergistic antitumor effects and significantly reshaped the tumor microenvironment. In a first-in-human (FIH) clinical trial, Apt-circRNA vaccine encoding KRAS G12D/G12V neoantigens exhibited a favorable safety profile and induced robust immune activation, T cell mobilization, and neoantigen-specific immune responses. With this study, we have established a new paradigm in carrier-free, APC-targeted RNA vaccine design, offering a safe and effective platform for next-generation cancer immunotherapy.

bioengineering↗

bioRxiv2025

Controlling malaria mosquito reproduction via the octopamine beta2 receptor

Mosquito reproduction in a broad sense involves multiple steps from acoustic recognition of mating partners to egg hatching. We show that the octopamine receptor AgOct{beta}2R controls different aspects of this process in a sexually dimorphic manner. AgOct{beta}2R knockout males present auditory defects that impair their ability to inseminate females, whilst knockout females are sterile. These phenotypes suggest AgOct{beta}2R as a target to impair mosquito reproduction at multiple levels. We test the reproductive effects of the insecticide amitraz, an AgOct{beta}2R agonist, showing that amitraz exposure reduces insemination in the lab but not in the field and has no effects on female sterility, excluding its applicability as a mating disruptor. Pharmacological assays reveal that AgOct{beta}2R sensitivity to amitraz is reduced compared to other arthropods, but its responses can be altered by modifying residues in the binding pocket. Together, our results establish AgOct{beta}2R as a promising target to disrupt mosquito reproduction but emphasize the necessity of developing new tools to exploit this approach.

neuroscience↗

bioRxiv2025

Paracrine Signals from HIV-1 Infected Immune Cells Reprogram Cervical Cancer Pathways

Persistent infection with human papillomavirus (HPV) is the primary cause of cervical cancer worldwide. Notably, women co-infected with HPV and human immunodeficiency virus type 1 (HIV-1) have a six-fold higher lifetime risk of developing cervical cancer compared to those without HIV, even when adhering to antiretroviral therapy (ART) and achieving T-cell reconstitution. While chronic HIV-1 infection is known to cause inflammation, how paracrine signals from immune cells alter signaling in cervical cells remain poorly understood. To address this, we conducted global transcriptomics analysis on cervical swabs from Kenyan women with HPV, stratified by HIV-1 and cancer status. Strikingly, women with HIV-1 showed cancer-like gene expression patterns in non-cancerous cervical epithelial cells. Complementary global mass spectrometry (MS) proteomics of cervical cells exposed to the secretome of HIV-1 infected primary CD4+ T-cells revealed altered expression of proteins in MAPK, PI3K-AKT, and {beta}-catenin signaling pathways. Integrative network analyses of transcriptomic and proteomic datasets revealed that HIV-1 altered gene expression in key pathways known to drive cervical cancer, including genes commonly mutated in HIV-1-naive disease. Notably, IRS-1, a key PI3K-AKT pathway activator, was found to be consistently upregulated in both participant samples and cell culture models, as were interferon-stimulated genes. Phosphoproteomics MS analysis confirmed PI3K-AKT pathway activation in cervical cells exposed to conditioned media from HIV-1-infected T-cells. Together, our findings uncover how HIV-1 reshapes cervical cell signaling via paracrine mechanisms and highlights the PI3K pathway as a potential therapeutic target in HIV-associated cervical cancer.

cancer biology↗

bioRxiv2025

SF3B1K700E Drives Oncogenic Alternative Splicing of Cell Cycle Checkpoint Genes in Cancer

Pre-mRNA splicing plays a crucial role in maintaining cellular homeostasis, with strict regulation required for processes such as cell cycle progression. SF3B1, a core component of the spliceosome, has emerged as a key player in alternative splicing regulation and is frequently mutated in cancer. Among these mutations, SF3B1K700E disrupts normal splicing patterns and deregulates cell cycle control. Here we profiled K562 erythroleukaemia cells expressing either wild-type or SF3B1K700E by RNA-seq and uncovered 763 high-confidence splicing alterations enriched for G2/M regulators, including ARPP19, ENSA, STAG2 and ECT2. Notably, increased inclusion of ARPP19 exon 2 produces the ARPP19-long isoform, which sustains PP2A-B55 inhibition and promotes mitotic progression. A core subset of the K700E-linked splicing changes re-appeared after siRNA-mediated SF3B1 depletion in HeLa cells, underscoring a mutation-dependent spliceosomal signature that transcends cell type. Pharmacological inhibition of DYRK1A (INDY) or broad serine/threonine phosphatases (okadaic acid) shifted ARPP19 exon 2 inclusion in the same direction as SF3B1K700E, pointing to a kinase-phosphatase signaling axis that influences these splice events. Functionally, ectopic expression of ARPP19-long accelerated mitotic exit, and high ARPP19-long abundance associated with poorer overall survival in the TCGA-AML cohort. Our findings highlight a connection between SF3B1-dependent splicing, cell cycle progression, and tumorigenesis, offering new insights into the molecular mechanisms underlying cancer-associated splicing dysregulation.

molecular biology↗

bioRxiv2025

FASN Inactivation-induced Progranulin (GRN) Expression Promotes Lysosome-dependent Cell Death to Suppress Leukemogenesis

Cancer cells rely on lipogenesis in addition to exogenous lipid uptake, and fatty acid synthase (FASN) is aberrantly overexpressed in myeloid leukemia. However, the precise role of FASN in leukemogenesis in vivo remains elusive. Here, we demonstrated that FASN is essential for leukemogenesis. Ablation of FASN impeded leukemic cell growth, survival, clonogenicity in vitro, and the leukemic burden in vivo. Conditional knockout of FASN barely affected hematopoiesis but significantly attenuated the leukemic progression of MLL-AF9 transplants. By screening a library of platensimycin derivatives, we identified compound MS-C19 as a potent FASN inhibitor. Pharmacological targeting of FASN by MS-C19 suppressed leukemic cell growth and clonogenicity in clinical AML blasts. Mechanistically, both MS-C19 treatment and FASN deficiency triggered the activation of lysosomal and inflammatory gene expression. Loss of FASN led to lysosomal membrane permeabilization and subsequent lysosome-associated cell death, but not lysosome biogenesis. We further identified that GRN, a lysosomal and neuroinflammatory gene, was potently transcribed by TFEB upon FASN loss. Depletion of GRN significantly reversed the inhibitory effects caused by FASN knockdown. Our work demonstrates that FASN is a therapeutic target for myeloid leukemia, and inactivation of FASN by the lead compound MS-C19 provides an alternative approach for leukemic intervention. Key PointsO_LIGenetic ablation of FASN induces apoptosis, impedes leukemia cell growth, and improves the survival of leukemic xenografts. C_LIO_LITargeting FASN by the compound MS-C19, a derivative of the natural microbe antibiotic platensimycin, reduces the cell survival of leukemic cell lines, the clinical leukemic blasts, and MLL-AF9 transformed murine leukemic cells. C_LIO_LIFASN inhibition induces lysosome-dependent cell death that relies on Progranulin (GRN) expression. C_LI

cancer biology↗

bioRxiv2025

The Golgi Rim is a Precise Tetraplex of Golgin Proteins that Can Self-Assemble into Filamentous Bands

Golgin proteins have long been suspected to be organizers of the Golgi stack. Using three-dimensional super-resolution microscopy, we comprehensively localize the human golgin family at the rim of the Golgi apparatus at 10-20 nm resolution in situ. Unexpectedly, we find that the golgins are precisely organized into a tetraplex with four discrete layers, each containing a specific set of rim golgins. We observe no golgins inside the stack between its membrane-bound cisternae. Biochemically characterizing most of the golgins as isolated proteins, we find that they form anti-parallel dimers and further self-assemble into bands of multi-micron-long filaments. Based on our findings, we propose an "outside-in" physical model, the Golgin Organizer Hypothesis, in which the Golgi stack of cisternae and its overall ribbon morphology directly result from bending circumferential bands of rim golgin filaments onto a membrane surface, explaining stack formation without the need for special "stacking proteins."

cell biology↗

bioRxiv2025

Probing the substrate binding-induced conformational change of a ZIP metal transporter using a sandwich ELISA

Zrt-/Irt-like proteins (ZIPs), a family of divalent metal transporters, are crucial for maintaining the homeostasis of zinc, an essential trace element involved in numerous biological processes. While extensive research on the prototypical ZIP from Bordetella bronchiseptica (BbZIP) have suggested an elevator transport mechanism, the dynamic conformational changes during the transport cycle have not been thoroughly studied. In this work, we developed a sandwich ELISA using a custom anti-BbZIP monoclonal antibody to investigate the conformational change induced by the metal binding to the transport site. This was achieved by determining the accessibility of a cysteine residue introduced at a position exposed to the solvent only when the transporter adopts an outward-facing conformation. This assay allowed us to report the dissociation constants of BbZIP for Zn2+ and Cd2+ at low and sub-micromolar levels, respectively. Notably, the installation of a positive charge at the M2 site drastically reduced metal binding at the M1 site, consistent with an auxiliary role for the M2 site in metal transport. We also demonstrated that this assay can be used to rapidly screen variants for subsequent structural study. We anticipate that other transporters where substrate binding induces large conformational changes can also be studied using this method.

biochemistry↗

bioRxiv2025

Plat safeguards maternally aged oocytes against programmed cell death through activating the Erk1/2 pathway

The decline in oocytes quality and developmental potential with female reproductive aging is well recognized, yet the underlying mechanisms remain insufficiently investigated. In this study, through an integrative analysis of transcriptomes and morphologies of individual oocytes from young and aged mice, morphologically defective aged oocytes are identified with distinct transcriptomic features. Further analysis demonstrates that both apoptotic and ferroptotic pathways are activated in the defective aged oocytes, and simultaneously blocking both pathways reverses the defective morphology to the largest extent. The Plat gene, which encodes tissue-type plasminogen activator (tPA), is downregulated with oocyte aging, and Plat knockdown increases oocytes susceptibility to both apoptosis and ferroptosis. Mechanistically, tPA functions as an upstream signaling molecule for Erk1/2 activation by interacting with particular phosphorylation kinases such as Alk. Consequently, Plat loss downregulates Erk1/2 pathway activity in oocytes, leading to degeneration through programmed cell death. Supplementing exogenous tPA in in vitro oocyte maturation cultures reduces defect rate of aged oocytes, thereby improving oocyte quality and developmental potential. Collectively, Plat plays a pivotal role in protecting aged mouse oocytes from programmed cell death, and tPA supplementation may serve as a potential clinical strategy to enhance oocyte quality in females of advanced maternal age.

developmental biology↗

bioRxiv2024

UTX Epigenetically Imposes a Cytolytic Effector Program in Autoreactive Stem-like CD8+ T cell Progenitors

Type 1 Diabetes Mellitus (T1D) is a chronic disease caused by an unremitting autoimmune attack on pancreatic beta cells. This autoimmune chronicity is mediated by stem-like progenitor CD8+ T cells that continually repopulate the pool of beta cell-specific cytolytic effectors. Factors governing the conversion of progenitors to effectors, however, remain unclear. T1D has been linked to a chromosomal region (Xp13-p11) that contains the epigenetic regulator UTX, which suggests a key role for UTX in T1D pathogenesis. Here, we show that T cell-specific UTX deletion in NOD mice protects against T1D development. In T cells of NOD mice and T1D patients, UTX ablation resulted in the accumulation of CD8+ progenitor cells with concomitant deficiency of effectors, suggesting a key role for UTX in poising progenitors for transition to effectors. Mechanistically, UTXs role in T1D was independent of its inherent histone demethylase activity but instead relied on binding with transcription factors (TCF1 and STAT3) to co-regulate genes important in the maintenance and differentiation of progenitor CD8+ T cells. Together, these findings identify a critical role for UTX in T1D and the UTX:TCF1:STAT3 complex as a therapeutic target for terminating the long-lived autoimmune response.

immunology↗

bioRxiv2024

Structural and Mechanistic Insights into Symmetry Conversion in Plant GORK K+ Channel Regulation

GORK is a shaker-like potassium channel in plants that contains ankyrin (ANK) repeats. In guard cells, activation of GORK causes K+ efflux, reducing turgor pressure and closing stomata. However, how GORK is regulated remains largely elusive. Here, we solved the cryo-EM structure of Arabidopsis GORK, revealing an unusual symmetry reduction (from C4 to C2) feature within its tetrameric assembly. This symmetry reduction in GORK channel is driven by ANK dimerization, which disrupts the coupling between transmembrane helices and cytoplasmic domains, thus maintaining GORK in an autoinhibited state. Electrophysiological and structural analyses further confirmed that ANK dimerization inhibits GORK, and its removal restores C4 symmetry, converting GORK to an activatable state. This dynamic switching between C2 and C4 symmetry, mediated by ANK dimerization, presents a GORK target site that guard cells regulate to switch the plant K+ channel between inhibited and activatable states, thus controlling stomatal movement in response to environmental stimuli.

plant biology↗