Biology subjects

Liu, F.

Publications and source records attributed to Liu, F..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Atypical p38 Kinase Signaling in Retinal Vascular Damage and Recovery

Despite the life-changing impact of anti-VEGF therapies, vascular retinopathies continue to affect millions of patients worldwide. To better understand disease progression, it is essential to define alternative mechanisms that contribute to retinal vascular dysregulation. Mitogen-activated protein kinase (MAPK) p38 plays a significant role in regulating vascular homeostasis, angiogenesis, and retinal disease progression, yet effective therapeutic targeting remains elusive. An alternative atypical p38 signaling pathway is mediated by interaction with the adaptor protein TGF-beta activated kinase 1, binding protein 1 (TAB1). Atypical p38 can be activated by ischemia or by inflammatory G protein-coupled receptors (GPCRs) to regulate inflammation and vascular homeostasis. However, atypical signaling has not been investigated in the context of vascular retinopathies, specifically oxygen-induced retinopathy (OIR). Here, we utilized a genetic knock-in mouse to block atypical p38 activity (Tab1KI) to explore retinal damage during OIR. We report that Tab1KI mice display significantly reduced vaso-obliteration and limited neovascularization relative to wild-type C57BL6 controls. Retinal RNAseq analysis revealed distinct transcriptional regulation in the Tab1KI mouse. Suppression of atypical p38 reduced Mef2c signaling, which in turn enhanced microglial activation and inflammation. Despite the upregulation of proangiogenic markers, the increase in endothelial markers does not correlate with the dysregulated growth of blood vessels. Instead, Mef2c suppression reduces pathological angiogenesis, while increasing physiological vascular regrowth. The combined data suggest that the selective inhibition of atypical p38 signaling could block the enhanced pathogenic neovascular tuft formation without impacting blood vessel repair. Further investigation will clarify how atypical p38 controls neovascular responses, potentially revealing new treatment strategies for vascular retinopathies. NEW AND NOTEWORTHYMAPK p38 drives ocular injury and inflammation, but the contribution of Tab1-dependent atypical p38 in retinal injury has not been investigated. Using a mouse genetic knock-in model to block atypical p38 during oxygen-induced retinal injury, we show that atypical p38 enhances vascular damage and neovascular tufting. Blockade of atypical p38 protects mice from retinal vascular damage.

cell biology↗

bioRxiv2025

Genetic Insights of Image-Based Traits: Analysis Pipeline for AI-based Phenotyping, Combined-GWAS, and Federated Learning with Application to the Human Face

Biological images capture rich morphological information and understanding their genetic basis is crucial for elucidating underlying molecular mechanisms, relevant in biomedical, evolutionary, and forensic research and applications. However, progress in understanding the genetic basis of image-based complex traits is hindered by key limitations in the current methodology, regarding both, the degree of which the large image complexity is captured with the phenotyping methods and how the analysis methods deal with the underlying large genetic complexity. Here, we present a robust, scalable, privacy-preserving computer pipeline for analysing image-based complex traits and unveiling their genetic basis by integrating (i) AI-based phenotyping for large-scale extraction of image-based traits across cohorts in a federated learning framework, without sharing individual images; (ii) Combined-GWAS (C-GWAS) for identifying genetic variants underlying the numerous AI-derived image-based traits; and (iii) Explainable AI (XAI)-based image visualization of the identified genetic association effects. In its first application to the example of the human face, we analysed 3D facial images and genomic data from two European cohorts (N=7,309), extracted 200 AI-derived facial traits, identified 43 significantly face associated genetic loci, including 12 novel ones, and replicated 70% of them in an independent European dataset (N=8,246). XAI-based visualization of the identified genetic effects shows the involvement of many of these loci in different parts of the face. Our study provides a privacy-aware and extensible pipeline for investigating the genetic basis of image-based complex traits implemented in a computationally efficient python package available at GitLab and its first application yielded new insights into the genetic architecture of facial shape variation.

genetics↗

bioRxiv2025

An AI-based and coding-free protocol for forests Leaf Area Index (LAI) calculation

O_LISeasonal and spatial variations in leaf area index (LAI) are challenging to detect in tropical forests due to dynamic lighting conditions and the subtle differences in the variation. Many existing LAI software tools offer one-click processing of all images through auto-threshold segmentation (e.g., HemispheR, HemiPy and Hemisfer), but they produce results with large discrepancies. Some software (e.g. CAN-EYE) requires manual tuning of each image, making large-scale analysis impractical. C_LIO_LIWe analysed 19,000 images from four tropical forest subtypes and found that using coding-free AI software to process hemispherical images can significantly improve the consistency of leaf-sky segmentation, thereby enhancing LAI outcomes. C_LIO_LIThe results show that replacing the auto-threshold with AI substantially reduced inter-software disagreement and delineated correct seasonal and spatial patterns. CAN-EYE was able to identify seasonal patterns but produced less accurate results than the CAN-EYE-AI integrated approach due to subjective user bias. C_LIO_LIThe high consistency achieved through AI integration enables reliable cross-site and cross-operator comparisons. As users can customise the AI model according to local images and combine the AI model with other LAI software, our integrated, affordable, and coding-free method offers wide applicability and high consistency of LAI measurements, facilitating the advancement of tropical forest monitoring and research. C_LI Data/Code for peer review statementOne of the key features of this method is coding-free. The method is explained in Protocolv20251118.docx. We have uploaded R codes for drawing figures in a zip pack. These codes and the protocol will be deposited in the Zenodo (or figshare) database under accession link [TBC]. Since Zenodo allows authors to archive updated versions after publication, we may update the protocol by uploading a revised version to Zenodo. Please check the Zenodo archive for any new versions. In the protocol, we note that users can use Image_conversion_20220407.m and lets_change_values.R instead of the Renormalise function of ilastik to modify values in the classification output images. These codes are not essential for users following our protocol, but could be useful for integrating ilastik with other LAI software not covered in this paper. Additionally, the protocol mentions that Gather_LAI_fapar_from_caneye.R can be used to consolidate output Excel files, eliminating the need to manually open each file. Field measurements of LAI and GCC are available on request.

ecology↗

bioRxiv2025

Self-limiting population suppression gene drive in the West Nile vector mosquito, Culex quinquefasciatus

Culex mosquitoes transmit major pathogens including West Nile virus, encephalitis, filariasis, and avian malaria, threatening public health, poultry, and ecosystems. We engineered a CRISPR-based population suppression gene drive targeting a conserved exon of the doublesex (dsx) gene. The drive incorporates a recoded dsxM segment to preserve male function while converting genetic females into sterile intersexes, enabling male-biased propagation and removal of fertile females. It achieves super-Mendelian inheritance ([~]71%) and generates partially dominant sterile resistance alleles via end-joining, resulting in intersex phenotypes with reduced fertility and hatchability. Modeling predicts that this RIDD (Release of Insects carrying a Dominant-sterile Drive) system can suppress populations at low intrinsic growth rates and release ratios, outperforming SIT and fs-RIDL strategies in persistence and efficiency, with further gains achievable through improved cleavage rates. This study establishes a self-limiting gene drive framework for Culex suppression, highlightling the potential of targeting conserved sex-determination pathways for sustainable vector control.

genetics↗

bioRxiv2025

Dual-Mode Microfluidic Immunostaining (Dumi) Device for Diagnostic Biomarkers Detection and Tumor Microenvironment Evaluation

The limited availability of tissue samples from rare tumors poses a major barrier to advances in precise diagnosis, prognostic evaluation, and therapeutic research--challenges exemplified by primary central nervous system diffuse large B-cell lymphoma (PCNS-DLBCL). However, both immunohistochemical (IHC) subtyping and preliminary studies of the tumor microenvironment (TME) using multiplex immunolabeling rely on conventional staining workflows that consume numerous serial sections per case, leading to irreversible depletion of precious samples from rare tumors. Here, we developed a dual-mode microfluidic immunostaining (Dumi) device, which integrates diagnostic and research workflows into a single, automated platform. Clinical validation shows that > 90% reduction in section usage, complete detection of subtyping diagnostic biomarkers on just 1-2 slides, and displays the TME maps incorporating six immune markers for analysis research. This microfluidic innovative offers an efficient, cost-effective, and multifunctional alternative immunostaining methods, overcoming the limitations of scarce tissue resources and providing a clinically accessible solution to the diagnostic and therapeutic challenges with rare tumors. TeaserDumi device enables multiplex IHC & TME mapping on 1-2 slides, reducing tissue use by >90% for rare tumors like PCNS-DLBCL.

bioengineering↗

bioRxiv2025

Autophagy-driven Presynaptic Reorganization as a Molecular Signature of Brain Resilience.

Neural circuits must remain functionally stable while responding flexibly to changing demands, stressors, and aging-related decline. While this balance is thought to be maintained through plasticity programs that integrate molecular, metabolic, and activity-dependent signals to reconfigure synapses structurally and functionally, direct mechanistic models of how such adaptations are orchestrated remain scarce. Here, we show that targeted impairment of autophagy in the Drosophila mushroom body (MB), a key sleep-regulatory and integrative center in the fly brain, triggers a brain-wide remodeling at presynaptic active zones (AZ). Quantitative proteomics revealed a specific upregulation of AZ scaffold proteins (including BRP, RIM, and Unc13A), accompanied by reduced levels of calcium channel subunits and increased Shaker-type potassium channels. These changes occurred largely independent of transcription and highlight a coordinated, excitability-tuning response centered on the AZ. Behaviorally, MB-specific autophagy impairment increased sleep and modestly extended lifespan. These adaptations resembled a previously described resilience program termed PreScale, which promotes restorative sleep homeostasis in response to sleep deprivation and early, still reversible brain aging. Conversely, overexpression of Atg5 in the MB delayed the onset of PreScale. Notably, autophagic disruption confined to MB neurons also caused widespread, non-cell autonomous accumulation of Ref(2)P and ATG8a-positive aggregates across the brain, revealing systemic propagation of proteostatic stress. Together, our findings identify MB autophagy as a key regulator of synaptic architecture and sleep-associated resilience. Such early acting programs may actively preserve circuit function and behavioral output by regulating synaptic plasticity, and define a genetically tractable model for how local stress signals can orchestrate brain-wide adaptation via post-transcriptional synaptic reprogramming.

neuroscience↗

bioRxiv2025

O-GlcNAcylation-Ubiquitin Crosstalk of METTL1 Drives m7G Epitranscriptomic Collapse and Lipid Metabolic Reprogramming in Diabetic Cardiomyopathy

BackgroundMetabolic remodelling and memory in cardiomyocytes is a pivotal mechanism underlying cardiomyopathy pathogenesis. Clinical observations demonstrate persistent progression of hyperglycaemia-induced multiorgan damage following blood glucose stabilization, which is predominantly mediated through epigenetic regulation. While prior studies have identified epigenetic contributions to hyperglycaemic myocardial injury, the involvement of RNA methylation-particularly N7-methylguanosine (m7G) modification-in this regulatory network remains undefined. MethodsClinical specimens were collected from diabetic patients, and cardiomyocyte-specific METTL1 and ob/ob knockout murine models were established in parallel. Multiomic profiling (proteomics, glycoproteomics, ubiquitinomics, m7G-MeRIP sequencing, and metabolomics) was systematically conducted. The molecular mechanisms governing METTL1 regulation via O-GlcNAcylation and ubiquitination were elucidated through integrated in vitro and in vivo assays. A DUB siRNA library and computational strategies combining molecular docking with molecular dynamics simulations were employed for screening drugs targeting METTL1 O-GlcNAcylation, followed by in vivo therapeutic validation. ResultsComparative analysis of diabetic murine and human samples revealed strong METTL1 downregulation in cardiomyopathy contexts. Tamoxifen-inducible METTL1 knockout mice presented exacerbated diabetic cardiomyopathy phenotypes, confirming its cardioprotective function. Multiomic integration demonstrated that METTL1-mediated m7G modification critically regulates cardiomyocyte fatty acid metabolism. Mechanistically, hyperglycaemia was found to induce O-GlcNAcylation at the METTL1-T268 residue, suppressing m7G methyltransferase activity by 38% (p < 0.01). Subsequent investigations revealed that USP5 deubiquitinase activity is impaired under hyperglycaemic conditions, leading to accelerated METTL1 degradation. Notably, administration of the first-in-class small drug HIT106265621 significantly attenuated cardiomyopathy-associated pathological alterations in ob/ob mice in vivo. ConclusionHyperglycaemia promotes METTL1 O-GlcNAcylation, which impedes USP5-mediated deubiquitination, consequently reducing cardiomyocyte METTL1 protein levels and m7G modification. METTL1 deficiency drives diabetic cardiomyopathy progression through fatty acid metabolic dysregulation, inflammatory activation, and myocardial hypertrophy. Pharmacological inhibition of the OGT-METTL1 interaction using HIT106265621 has therapeutic potential for metabolic cardiomyopathy intervention.

pathology↗

bioRxiv2025

Functionalization of lipid nanoemulsions with humanized antibodies using plug-and-play cholesterol anchor for targeting cancer cells

Lipid NEs are promising green nanocarriers for diagnostic and therapeutic applications, but their functionalization with biomolecules, such as antibodies, remains a challenge due to liquid nature of their core. Here, we developed an original plug-and-play strategy to graft an antibody (trastuzumab) at the surface of NEs, using components generally recognized as safe (GRAS). We synthesized a reactive derivative of cholesterol and a Biotin-PEG3000-Lysine linker, which can react within one-pot formulation to form an amphiphilic carbamate Biotin-PEG3000-Cholesterol. The cholesterol ensures anchorage of the linker, which effectively exposes biotin moiety at the surface of NEs for further antibody grafting using a biotin-neutravidin coupling. The reaction between the Biotin-PEG3000-Lysine linker and NPC-Chol was confirmed by 1H-NMR and absorption spectroscopy. The obtained biotinylated 50-nm NEs loaded with a near-infrared dye were successfully targeted to neutravidin-coated glass surfaces and imaged at the single-droplet level. The biotinylated NEs bearing the trastuzumab antibody targeted specifically HER2-amplified breast cancer models HCC-1954 and SKBR3, in contrast to control MDA-MB-231 (HER2-low) cells. Altogether, our study proposes an efficient methodology for grafting antibodies to the surface of NEs, which offers new opportunities of application of these green nanocarriers in biomedicine.

pharmacology and toxicology↗

bioRxiv2025

Multiparametric Correlative Topographical and Volumetric Fluorescence Microscopy

Live-cell imaging of cell surface topography and intracellular architecture is essential for understanding cellular function. However, conventional approaches often involve trade-offs between resolution, invasiveness, and volumetric coverage. Here, we present an integrated Scanning Ion Conductance Microscope and single-objective Oblique Plane Microscope (SICM-OPM) system that enables simultaneous non-contact topographical imaging and volumetric fluorescence imaging within the same live cell. Beyond correlative live imaging, the platform supports nanomechanical mapping with tens-of-nanometres resolution, fluorescence-guided localised molecular delivery via the SICM, and benefits from reduced photobleaching due to light-sheet excitation. We demonstrate this platforms capabilities by visualising imipramine-induced T-tubule remodelling in live cardiomyocytes, revealing subsurface detubulation while surface morphology remains preserved. Additionally, we show precision delivery of fluorescent cargos--including dextrans and -synuclein--into diatom and mammalian cells, alongside localised stiffness mapping to evaluate mechanical responses. We believe this technique opens new avenues for correlative structural, functional, and biophysical studies in live cells, with broad relevance to cell biology, neurodegeneration, and mechanobiology.

biophysics↗

bioRxiv2025

Sephin1 alleviates white matter injury by protecting oligodendrocyte after intracerebral hemorrhage

BackgroundWhite matter injury (WMI) caused by intracerebral hemorrhage (ICH) is a major neuropathological feature closely associated with neurological impairments such as motor and sensory dysfunction. Oligodendrocytes (OLs), which are responsible for repairing WMI, also suffer severe death resulting from the compression of hematoma and secondary neuroinflammation after ICH. Sephin1, a selective inhibitor of PPP1R15A, has been shown to reduce general protein synthesis and protect OLs by prolonging the integrated stress response (ISR). We aimed to evaluate the effectiveness of Sephin1 in protecting OLs in experimental ICH mice and primary OLs and microglia co-cultures. MethodsWe first determined the performance of ICH mice treated with Sephin1 or vehicle in multiple behavioral tests. To investigate dynamic changes in the number of OLs surrounding the hematoma after ICH, we labeled and tracked apoptotic, proliferating, and mature OLs using immunofluorescence staining. ResultsSephin1 treatment improved long-term neurological function after ICH, which was accompanied by a significant alleviation of WMI in the perihematomal region. Our data indicated that Sephin1 dramatically increased the population of OLs in the perihematomal region after ICH by inhibiting OL apoptosis and promoting OL proliferation. Moreover, Sephin1 treatment attenuated neuroinflammation after ICH by inhibiting microglial polarization to the M1 phenotype. In vitro, a co-culture model of primary OLs and microglia demonstrated that Sephin1 preserved the viability of OLs under pro-inflammatory conditions. ConclusionsOur observations suggest that Sephin1 is a promising therapeutic drug to preserve the OLs and alleviate WMI around the hematoma in ICH, highlighting its translational potential to improve long-term neurological recovery in hemorrhagic stroke.

neuroscience↗

bioRxiv2025

Genomic analysis identifies Campylobacter concisus genomospecies 2 as a novel species and proposes the name Campylobacter oralis

Campylobacter concisus comprises two distinct genomospecies (GS) based on core genome analysis. Here we conducted further analysis and demonstrated that C. concisus GS2 strains belong to a novel Campylobacter species. A total of 245 C. concisus genomes including 85 GS1 and 160 GS2 strains were analysed. DNA-DNA hybridization (DDH) values between strains of GS1 and GS2 C. concisus were from 42.8% to 66%. Average Nucleotide Identity (ANI) between GS1 and GS2 C. concisus strains were from 87.8% to 89.7%. The average GC contents of GS1 and GS2 C. concisus strains were 37.3% and 39.2% respectively. GS1 and GS2 specific genes have been identified. GS1 and GS2 C. concisus strains can also be differentiated based on core genome, 23S rRNA polymorphisms and protein profiles. Their morphology appears different under certain conditions. In conclusion, ANI and DDH values clearly support that C. concisus GS2 as a novel Campylobacter species, for which we propose the name Campylobacter oralis. The identification of C. concisus and C. oralis specific genes, along with differences in their protein profiles, morphology, core genome and 23S rRNA phylogeny, further support this classification.

microbiology↗

bioRxiv2025

Integrative structural interactomics reveals protein organization and structure in a giant virus

Giant viruses are large DNA viruses that infect unicellular and multicellular eukaryotes and form exceptionally large extracellular particles. (Meta)genomics and (meta)transcriptomics have provided insight into their diverse coding repertoire, but many of the proteins remain to be characterized as they lack homology with known proteins. Here, we integrated cross-linking mass spectrometry, quantitative proteomics, computational tools and cryo-EM data to characterize the protein architecture of intact melbournevirus particles. Based on this, we allocated 88 viral proteins to different virion sub-compartments and proposed topologies of 25 inner membrane proteins. We assigned eight components of the capsid in cryo-EM data, including proteins that tether the capsid shell to the membrane, reflecting key points in virion maturation. The data provide a valuable resource and demonstrate the power of an integrative approach to gain system-level structural insights into a poorly characterized biological system.

biochemistry↗

bioRxiv2025

DR5 CAR-T cells target solid tumors and suppress MDSCs with minimal toxicity

Chimeric antigen receptor (CAR) T cell therapies have poor efficacy in solid tumors due to limited target specificity and an immunosuppressive tumor microenvironment. We investigated death receptor 5 (DR5) as a CAR target based on its high expression in both solid tumors and myeloid- derived suppressor cells (MDSCs). We engineered agonistic DR5-specific CAR constructs and evaluated their activity in multiple models, demonstrating DR5-expression-dependent tumor killing, confirmed by knockout and overexpression experiments. DR5-targeting single-chain variable fragments retained their pro-apoptotic activity when expressed on non-effector cells or extracellular vesicles. Among multiple CAR designs, we identified a construct with optimized binding affinity that maintained T cell viability while preserving strong tumor and MDSC-killing potency. To assess safety and efficacy in an immunocompetent setting, we also developed a murine DR5-targeted CAR. In multiple xenograft and syngeneic mouse models, DR5 CAR-T cells reduced tumor growth, prolonged survival, and did not cause detectable toxicity. In patient- derived organoids and tissue slices, DR5 CAR-T cells infiltrated tumor tissues, reduced MDSCs, boosted CD8+ T cell activity, and inhibited tumor growth. These findings support DR5-targeted CAR-T therapy as a promising strategy for treating solid tumors, which combines direct tumor cytotoxicity with immune activation and minimizes off-target effects. TeaserDR5 CAR-T cells eliminate tumor cells and MDSCs and activate tumor-resident CD8+ T cells within the TME.

cancer biology↗

bioRxiv2025

HSV-1 orchestrates host RAP80 ubiquitination by ICP0 and UL36USP to promote viral survival

Herpes simplex virus 1 (HSV-1) is a widespread human pathogen that establishes lifelong infections, ubiquitination is crucial for HSV - 1 to interact with the host and regulate its life activities. But the mechanisms of how HSV-1 dynamically modulates host proteins at different infection stages to promote its own survival remains challenging. Here we identified DNA damage response protein RAP80 as a critical target of HSV-1 ubiquitination enzymes ICP0 and UL36USP throughout HSV-1s infection cycle. In early stages, RAP80 inhibits HSV-1 transcription by directly binding to the viral genome, blocking viral protein ICP4 binding to transcription factors. This interaction is regulated by phase separation via an intricate interplay between RAP80 and ICP0/ICP4. As infection progresses, the viral E3 ligase ICP0 degrades RAP80, dissolving phase separation, and allowing the formation of a mature viral replication compartment. In late infection stages, RAP80 is deubiquitinated by the viral deubiquitinase UL36USP, which restores cellular homeostasis and promotes HSV-1 survival. This process involves modulating the R-loop-cGAS-apoptosis pathway. These findings underscore the dynamic interplay between viral and host factors and the complex mechanisms used by HSV-1 to subvert host defenses, offering practical implications for the future development of antiviral strategies.

molecular biology↗

bioRxiv2025

Altered susceptibility of rare yeast species causing vulvovaginal candidiasis at acidic vaginal environment

This study evaluated potency of antifungals against the rare emerging yeast causing VVC under the influence of acid pH (4.5). The antifungal susceptibility was evaluated by CLSI-M27A4 for 25 isolates represented 11 rare yeast species recovered from VVC patients. Among 11 yeast species (25 isolates), Clavispora lusitaniae (n=9) was the most common species, followed by Cyberlindnera fabianii (n=4), Kodamaea ohmeri, Candida metapsilosis and Candida bracarensis (n=2, respectively), Pichia norvegensis, Kluyveromyces marxianus, Diutina rugosa, Tricholoma matsutake, Candida nivariensis and Candida africana (n=1, respectively). The antifungal agents most affected by a lower pH were terconazole (4-fold higher, MIC >0.5-8mg/L) to all 11 yeast species; followed by amphotericin B (3-fold higher, MIC >2mg/L) to 9 species except K. ohmeri and D. rugose; nystatin (2-fold higher, MIC >2 - 4 mg/L) to 9 species except C. nivariensis and C.africana; micafungin (2-fold higher, MIC >0.125 - 1 mg/L) to 8 species except C. metapsilosis, D. rugosa and Tricholoma matsutake by acid pH, respectively. 5-flucytosine was not affected by pH to all tested yeast species, and maintained activity at low PH. The rare yeast species tested shared high MICs of terconazole, amphotericin B, nystatin at pH4.5 compared with those at pH7.0. The in vitro antifungal susceptibility at pH 7.0 did not consistently predict the activity of antifungals against those rare yeast species at vaginal acidic pH. Further investigations assessing the clinical utility of antifungal susceptibility testing should take these findings into consideration.

microbiology↗

bioRxiv2025

Secondary structure transitions and dual PIP2 binding define cardiac KCNQ1-KCNE1 channel gating

The KCNQ1+KCNE1 potassium channel complex forms the slow delayed rectifier current (IKs) critical for cardiac repolarization. Loss-of-function variants in KCNQ1 and KCNE1 cause long QT syndrome types 1 and 5 (LQT1/LQT5), accounting for over one-third of clinical LQTS cases. Despite prior structural work on KCNQ1 and KCNQ1+KCNE3, the structural basis of KCNQ1+KCNE1 remains unresolved. Using cryo-EM and electrophysiology, we determined high-resolution (2.5-3.4 [A]) structures of human KCNQ1+KCNE1 in both closed and open states. KCNE1 occupies a pivotal position at the interface of three KCNQ1 subunits, inducing seven "helix-to-loop" transitions in KCNQ1 transmembrane segments. These structural rearrangements: 1) stabilize the closed pore and the conformation of the intermediate voltage-sensing domain, thereby determining channel gating, ion permeation, and single channel conductance; 2) enable a dual-PIP2 modulation mechanism, where one PIP2 occupies the canonical site, while the second PIP2 bridges the S4-S5 linker, KCNE1, and the adjacent S6, stabilizing channel opening; 3) create a fenestration capable of binding compounds specific for KCNQ1+KCNE1 (e.g., AC-1). Together, these findings reveal a previously unrecognized large-scale secondary structural transition during ion channel gating that fine-tunes IKs function and provides a foundation for targeted LQTS therapy development.

biophysics↗

bioRxiv2025

3'UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages

Acid resistance is crucial for enterobacteria to withstand host acidic environments during infection, including the gastrointestinal tract and macrophage phagosomes. A key acid resistance mechanism of the facultative intracellular pathogen Salmonella is expression of the arginine decarboxylase AdiA. While AdiA confers acid resistance via an H+-consuming reaction, we discover that the 3'-untranslated region (UTR) of adiA mRNA is processed by RNase E into a regulatory small RNA, AdiZ. Through RNA-RNA interactome profiling and transcriptomic analysis, followed by in vitro structural probing and in vivo validations, we demonstrate that AdiZ directly base-pairs with and negatively regulates ptsG, pykF, and dmsA mRNAs involved in glucose uptake, glycolysis, and anaerobic respiration, respectively. Intriguingly, AdiZ is induced and facilitates Salmonella survival within macrophages, where acidic and hypoxic stresses prevail. Thus, simultaneous expression of AdiA and AdiZ from a single mRNA ties arginine-dependent acid resistance to metabolic reprogramming of Salmonella in the host intracellular niches. HIGHLIGHTSO_LISalmonella adiA transcript expresses both acid resistance enzyme and sRNA AdiZ C_LIO_LIAdiZ derived from the adiA 3'UTR is induced under an acidic and anaerobic condition C_LIO_LIAdiZ base-pairs with mRNAs to modulate glucose metabolism and anaerobic respiration C_LIO_LIAdiZ promotes Salmonella survival in acidic and hypoxic macrophage vacuoles C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/658255v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@10aec22org.highwire.dtl.DTLVardef@14b5f2org.highwire.dtl.DTLVardef@1b53c8dorg.highwire.dtl.DTLVardef@19a8540_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

IL-17A-driven Macrophage Disorder Promotes Plaque Instability in Psoriatic Atherosclerosis

Psoriasis is a common chronic inflammatory skin disease that predisposes individuals to cardiovascular diseases such as atherosclerosis. However, the underlying mechanisms linking these conditions have not yet been fully elucidated. Recent studies have indicated that the inflammatory cytokine IL-17A plays a significant role in both diseases. The aim of this study was to investigate how psoriasis affects the stability of atherosclerotic plaques via the IL-17A/IL-17RA pathway. We performed single-cell sequencing on patients with both psoriasis and atherosclerosis to analyze changes in the immune microenvironment within their carotid plaques and psoriatic lesions. We found that IL-17A significantly upregulated the expression of pro-inflammatory factors (e.g., CXCL8) in macrophages of psoriatic atherosclerosis patients, leading to weakening of the fibrous cap structure of plaques. Additionally, IL-17A further exacerbated plaque instability by interfering with macrophage lipid metabolism, particularly sphingolipid metabolism. Finally, using in vitro experiments and animal models, we demonstrated that IL-17A enhances pro-inflammatory and metabolic abnormalities in macrophages by downregulating PPAR{gamma}. Therapeutic strategies targeting IL-17A may contribute to the simultaneous mitigation of psoriasis and atherosclerosis-associated cardiovascular risk, providing new directions for clinical intervention.

cell biology↗