Biology subjects

Yuan, S.

Publications and source records attributed to Yuan, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

CYB5R3 Controls Sex-Specific Stress Erythropoiesis via Heme-Biosynthesis

Cytochrome b5 reductase 3 (CYB5R3) or met-hemoglobin reductase is an oxidoreductase that maintains hemoprotein and cellular redox balance, yet its contribution to erythropoiesis under stress conditions remains unclear. Motivated by prior observations that the hypomorphic CYB5R3 T117S blunts hydroxyurea-induced fetal hemoglobin responses in patients with sickle cell disease, we tested whether CYB5R3 contributes to the regulation of erythropoiesis. Hematopoietic lineage-specific CYB5R3 knockout mice exhibited markedly impaired erythropoietic induction in response to chronic hypoxia compared to controls, with males showing a more pronounced deficit, and splenectomy further exacerbating this impairment. Genetic deletion of CYB5R3 in human CD34 progenitors reduced globin expression and disrupted terminal erythroid differentiation. Meanwhile, CYB5R3 knockdown in K562 cells produced a heme-deficient state whereby only exogenous heme but not hydroxyurea, iron, or upstream precursors restored globin synthesis. Transcriptomic profiling revealed coordinated downregulation of erythroid transcription factors and multiple enzymes in the heme biosynthetic pathway, which was reversed with heme treatment. Together, these results reveal an unexpected function for CYB5R3 beyond met-hemoglobin reduction, positioning it as a central metabolic regulator of sex-specific stress erythropoiesis and unveiling a heme-restricted vulnerability that may augment disease severity in anemia, hemoglobinopathies, and individuals carrying CYB5R3 loss-of-function variants. Key pointsO_LICYB5R3 is required for effective stress erythropoietic induction, with a more pronounced impact in males. C_LIO_LIErythroid-specific CYB5R3 deficiency creates a heme-limited state, impairing erythroblast differentiation and maturation. C_LI

molecular biology↗

bioRxiv2025

An Integrated Single-Cell Atlas Reveals Hepatic Stellate Cell Heterogeneity and Spatiotemporal Dynamics after Liver Injury

BackgroundHepatic stellate cells (HSCs) orchestrate fibrosis-free repair after acute liver injury (ALI) and sustain fibrogenesis in chronic liver injury (CLI). However, the heterogeneity and spatiotemporal dynamics of HSCs across these different injury models remain elusive. This study sought to construct a cross-etiological HSC atlas to delineate HSC states and transitions during liver injury. MethodsWe integrated 86,072 single-cell transcriptomes from 84 mouse samples across four etiologies and validated findings using multi-omics data from 277 mouse and 798 human samples. Cellular dynamics were characterized through clustering, trajectory inference, spatial analysis, and multicellular coordination network analysis. Experimental validation included liver injury models and gain-of-functional assays in primary mouse HSCs and LX-2 cells. ResultsWe established a cross-etiological, spatiotemporally resolved HSC atlas comprising 11 subpopulations. Trajectory analysis delineated a continuous quiescence-activation-attenuation (QAA) trajectory, recapitulating the in vivo full spectrum of state transitions and being supported by sequential pathway activation validated in vitro. In ALI, HSCs spatiotemporally completed the QAA trajectory around injury zones, whereas collagen-producing S100a6 HSCs pathologically accumulated in mouse and human CLI due to trajectory dysregulation. Notably, the atlas identified a previously unrecognized apoptosis-prone Mrc2 HSC subtype strongly co-localized with p53 in both mice and humans. Overexpression of transcription factors confirmed that Hbp1, Tbx20, Atoh8, and Plagl1 enriched in Mrc2+ HSCs promoted HSC apoptosis. Finally, we revealed the microenvironment of distinct cellular modules which coordinated HSC progression along the QAA trajectory. A 531-gene signature derived from the inflammatory-fibrotic cellular module significantly correlated with fibrosis stage and hepatocellular carcinoma risk in human cohorts. ConclusionsWe established a comprehensive HSC atlas and delineates HSC heterogeneity and spatiotemporal dynamic across etiologies. Dysregulation of the QAA trajectory underlies fibrotic progression, providing a resource for identifying antifibrotic targets.

cell biology↗

bioRxiv2025

Isolation of the first cultured representative from a deep-branching phylum in serpentinite-hosted ecosystems

Serpentinization drives abiotic synthesis of organics (e.g., hydrocarbon) potentially conducive to the emergence of life, making serpentinite-hosted systems and associated microbial community key windows into nature of lifes origin. Although cultivation-independent studies uncovered the Candisdatus Bipolaricaulota widely distributed in serpentinizing environments, cultivation of this phylum has been unsuccessful. Here we cultured the first pure strain, J31, of Ca. Bipolaricaulota from the Lost City hydrothermal field, a well-characterized marine serpentinite system, using hydrocarbons as the primary nutrient source. As an early-branching bacterial lineage, strain J31 exhibits an unusual morphology composed of a central rod and elongated Toga-like extensions at both ends, and divides by binary fission. Strain J31 absorbs hexadecane through Toga ends via coordinated processes resembling inhalation and swallowing, after which hexadecane is efficiently transported to the central rod in the vesicle-like structures and subsequently converted into membrane lipids to support Toga synthesis and cellular growth. Hydrocarbon-degrading capability is widespread among the globally distributed members of Ca. Bipolaricaulota. Strain J31 colonizes serpentine minerals, facilitating the utilization of hydrocarbons derived from serpentines and promoting the release of soluble iron and silicon, thereby linking microbial activity to geochemical cycling. Thus, our study presents a novel strategy for cultivating deep-branching bacteria and offers insights into the metabolic foundations of early life on Earth--and potentially on other rocky planets undergoing serpentinization.

microbiology↗

bioRxiv2025

MillionFull enables massive, full-length enzyme sequence-fitness data collection at low cost for machine learning-guided enzyme engineering

Machine learning holds great promise for accelerating enzyme optimization, but its power is fundamentally constrained by the limited availability of sequence-fitness data. Here, we introduce MillionFull, a low-cost method that enables high-throughput full-length sequence- fitness mapping for enzymes of arbitrary length. Each run yields on the order of 10-10 data points, capturing sequence-function relationships at unprecedented scale. By overcoming the data bottleneck, MillionFull provides a foundation for dramatically advancing AI-driven enzyme engineering.

synthetic biology↗

bioRxiv2025

Endothelial CYB5R3 couples store-operated calcium entry to TRPV2 activation and vascular fitness

NADH-cytochrome b5 reductase 3 (CYB5R3) is a flavoprotein that governs nitric oxide (NO) signaling and supports NADPH oxidase 4-derived hydrogen peroxide production via coenzyme Q reduction in endothelium. While CYB5R3 expression is decreased during aging, the downstream consequences of CYB5R3 loss are not understood. Here, we demonstrate that depletion of CYB5R3 in primary human aortic endothelial cells activates a Ca2+ influx network characterized by the upregulation of calcium release-activated calcium (CRAC) channel subunits ORAI2 and ORAI3, as well as the non-selective cation channel transient receptor potential vanilloid 2 (TRPV2). When endoplasmic-reticulum Ca2+ stores were depleted, CYB5R3-deficient cells had increased Ca2+ entry through the plasma membrane, part of which was insensitive to classical store-operated Ca2+ entry (SOCE) blockers and was mediated by TRPV2, as demonstrated by genetic knockdown and pharmacologic inhibition. Mechanistically, loss of CYB5R3 increased Ca2+-dependent NO production through elevated CRAC channel activity, which oxidatively inhibited the protein tyrosine phosphatase non-receptor type 1 (PTPN1). This prevented TRPV2 dephosphorylation, thereby maintaining Janus kinase 1 (JAK1)-dependent channel activation downstream of SOCE. It also enhanced the responsiveness of TRPV2 to physiological heat stimuli. Thus, CYB5R3 normally acts as a brake, limiting NO-dependent PTPN1 oxidation and restraining TRPV2 activity. In vivo, endothelial-specific Cyb5r3 deletion enhanced acetylcholine-induced vasorelaxation and improved exercise capacity, demonstrating a physiological function for this pathway in vascular adaptation. Together, these findings identify a CYB5R3-NO-SOCE- PTPN1-TRPV2 signaling axis that couples endothelial redox balance to Ca2+ dynamics and vascular function. SIGNIFICANCEEndothelial cells rely on receptor-regulated Ca2+ signals to produce vasodilators and control vascular function; however, the molecular mechanisms coordinating these pathways are incompletely understood. We identify CYB5R3 as a key redox switch that couples store-operated Ca2+ entry to the non-selective cation channel TRPV2. Loss of CYB5R3 enhances TRPV2 activity downstream of SOCE through NO-dependent oxidative inhibition of the phosphatase PTPN1, sustaining Janus kinase-mediated TRPV2 channel activation. This novel mechanism expands the physiological scope of CYB5R3 by redefining how redox enzymes intersect with Ca2+ signaling, linking endothelial CYB5R3 to vascular relaxation and exercise capacity in vivo. This positions CYB5R3 as a central regulator of vascular function with broad implications for cardiovascular health and disease.

cell biology↗

bioRxiv2025

CYB5R4 sustains endothelial proliferation and ischemia-induced angiogenesis by maintaining RRM2-dependent nucleotide balance

Angiogenesis is essential for revascularization in peripheral artery disease (PAD), yet pro-angiogenic therapies remain inconsistent. Here, we identify a cytosolic reductase, CYB5R4, as an intrinsic regulator of endothelial proliferation and ischemia-induced angiogenesis. In mice, global haploinsufficiency or inducible endothelial deletion of Cyb5r4 delayed perfusion recovery after femoral artery ligation and reduced capillary expansion. CYB5R4 is known to promote stearoyl-CoA desaturase (SCD) activity and is required for the de novo synthesis of monounsaturated fatty acids. In human endothelial cells, CYB5R4 silencing impaired proliferation with G1-S arrest that was not rescued by monounsaturated fatty acids and differed from the loss of SCD, indicating an SCD-independent mechanism. RNA sequencing with Bayesian network inference highlighted the ribonucleotide-reductase subunit RRM2 as a key downstream mediator. RRM2 overexpression partially restored proliferation. Integrated untargeted metabolomics and targeted nucleotide quantification revealed an imbalanced nucleotide pool in CYB5R4-deficient cells. These findings support a model in which CYB5R4 sustains endothelial proliferation and ischemia-driven angiogenesis by maintaining RRM2-dependent nucleotide balance. Targeting the CYB5R4-RRM2 axis may improve therapeutic angiogenesis in PAD.

molecular biology↗

bioRxiv2025

UHRF1 restricts HCoV-229E infection through epigenetic silencing of the viral receptor APN

The emergence of SARS-CoV-2 has posed significant threats to global health, particularly for the older population. Similarly, common human coronaviruses, such as HCoV-229E, which typically cause mild cold-like symptoms, have also been linked to severe diseases, underscoring the need to understand virus-host interactions and identify host factors contributing to viral pathogenesis and disease progression. In this study, we performed a genome-wide CRISPR knockout screen using HCoV-229E and identified Ubiquitin-like with PHD and RING finger domain 1 (UHRF1) as a potent restriction factor. Mechanistically, UHRF1 suppressed HCoV-229E infection by downregulating the expression of its cell entry receptor, aminopeptidase N (APN), through promoter hypermethylation. Focused CRISPR activation screens of UHRF1-downregulated genes confirmed the critical role of APN in HCoV-229E infection and identified additional genes (e.g., SIGLEC1, PLAC8, and heparan sulfate biosynthesis genes) contributing to the restrictive functions of UHRF1. Transcriptomic and single-cell RNA sequencing analysis revealed that UHRF1 expression decreases with age, negatively correlating with increased APN expression. This age-related decline in UHRF1 was further validated in primary alveolar macrophages isolated from elderly individuals, which exhibited heightened susceptibility to HCoV-229E infection compared to those from younger individuals. Our findings highlight UHRF1 as a key age-related host defense factor against coronavirus infection and provide novel insights into the epigenetic regulation of viral entry receptors.

microbiology↗

bioRxiv2025

Huntingtin preserves mitochondrial genome integrity in neurons, which is impaired in Huntingtons disease

Huntingtin (HTT) function is enigmatic, as the native protein plays critical roles in neuronal health, while mutant HTT (mHTT), carrying an expanded polyglutamine stretch, triggers neurotoxicity and contributes to the pathogenesis of Huntingtons disease (HD). We recently found that HTT is part of a nuclear transcription-coupled DNA repair (TCR) complex with DNA repair enzymes including polynucleotide-kinase-3-phosphatase (PNKP). This complex resolves DNA lesions during transcription to maintain genome integrity, while in HD, mHTT impairs the activity of this complex, resulting in accumulation of DNA lesions. Using molecular, cellular biology and computational methods, we find that HTT has a role in assembling a functional DNA repair complex in mitochondria. Together with mitochondrial RNA polymerase and transcription factors, HTT resolves mitochondrial DNA lesions to preserve mitochondrial genome integrity and function. Pathogenic mHTT impairs this activity, resulting in persistent DNA lesions and reduced mitochondrial function in HD. Importantly, restoring activity of this complex in a Drosophila HD model through ectopic HTT or PNKP expression significantly improves mitochondrial genome integrity and ameliorates motor deficits. HIGHLIGHTSO_LIHTT organizes a functional, multifactorial mitochondrial DNA repair complex C_LIO_LIMutant HTT impairs the mitochondrial DNA repair complex causing DNA damage accumulation C_LIO_LIHTT-associated repair complex resolves mitochondrial DNA lesions and DNA integrity C_LIO_LIRestoring repair activity in HD flies rescues mitochondrial DNA integrity and motor defects C_LI

neuroscience↗

bioRxiv2025

Two Spag6 genes control sperm formation and male fertility in mice

Sperm-associated antigen 6 (SPAG6) is the mammalian orthologue of Chlamydomonas PF16, a central axonemal protein essential for flagellar motility. In mice, two homologous genes have been identified: the ancestral Spag6 on chromosome 2 and the evolutionary derived Spag6l on chromosome 16. Although Spag6 knockout mice (Spag6-/-) are phenotypically normal, the surviving Spag6l-/- males are infertile. To further investigate the roles of SPAG6 and SPAG6L, we generated compound mutants by crossing the two knockout lines. Compound heterozygous Spag6+/-; Spag6l+/- mice are fertile, while all Spag6-/-; Spag6l+/- males are infertile despite grossly normal appearance. Histological and ultrastructural analyses revealed defective spermiogenesis, including abnormal chromatin condensation, malformed acrosome and manchette, and disorganized mitochondrial and fibrous sheath. Both SPAG6 and SPAG6L bind to SPINK2, a key regulator of acrosome function, but SPAG6 has an approximately 10-fold higher binding affinity than SPAG6L. Moreover, SPAG6 modulates testicular AKAP4 and SPAG16L levels, which are critical components of the fibrous sheath and central apparatus respectively. Notably, SPAG6 suppresses tubulin acetylation, whereas SPAG6L enhances this post-translational modification, suggesting antagonistic roles in microtubule assembly. Overall, our findings demonstrate that SPAG6 and SPAG6L coordinately regulate sperm formation and male fertility during evolution.

developmental biology↗

bioRxiv2025

Discovery of an Achiral Small Molecule TREM2 Agonist with Im-proved Pharmacokinetic Profile and Validated Target Engagement

The triggering receptor expressed on myeloid cells 2 (TREM2) is a lipid-sensing immunoreceptor on microglia that has emerged as a therapeutic target for Alzheimers disease. Here, we report the discovery of C1, an achiral structural analog of VG-3927--the first small molecule TREM2 agonist to enter clinical development. C1 was synthesized via a modular and enantioselective-free route using sequential Suzuki couplings, enabling rapid scaffold diversification. Compared to VG-3927, the stereochemically simplified derivative (C1) exhibits superior microglial phagocytosis and validated target engagement. C1 induces TREM2 activation in HEK293-hTREM2/DAP12 cells, and its direct binding to TREM2 was confirmed using both microscale thermophoresis (MST) and surface plasmon resonance (SPR). Importantly, C1 also demonstrates a superior pharmacokinetic profile to VG-3927, including enhanced metabolic stability in human and mouse microsomes, favorable PAMPA permeability, and a LogD7.4 compatible with CNS penetration. Docking studies suggested a potential binding mode of C1 at the extracellular domain of TREM2, revealing key polar and hydrophobic interactions. These findings position C1 as a synthetically accessible and pharmacokinetically favorable lead for the development of TREM2-targeted therapies

pharmacology and toxicology↗

bioRxiv2025

Discovery of a First-in-Class SLIT2 Binder Disrupting the SLIT2/ROBO1 Axis via DNA-Encoded Library (DEL) Screening

The SLIT2/ROBO1 signaling axis plays a critical role in neural development, immune regulation, and tumor progression, including glioblastoma. However, small molecule inhibitors targeting this protein-protein interaction remain unexplored. Herein, we report the discovery and validation of DEL-S1, a first-in-class small molecule that binds to SLIT2 and disrupts its interaction with ROBO1. Using a DNA-encoded library (DEL) screen of 4.2 billion compounds, DEL-S1 was identified and confirmed to bind SLIT2 via temperature-related intensity change (TRIC) assay. Functional inhibition of the SLIT2/ROBO1 complex by DEL-S1 was demonstrated using a Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) assay, yielding an IC50 of 68.8 {+/-} 12.5 {micro}M. Molecular docking and molecular dynamics (MD) simulations revealed key interaction hotspots at the SLIT2 binding interface and confirmed that DEL-S1 impairs SLIT2/ROBO1 complex formation by inducing conformational rearrangements. DEL-S1 exhibited favorable ADME properties, including satisfactory plasma and microsomal stability, low cytotoxicity, and minimal hERG liability. To facilitate structure-activity relationship (SAR) exploration, we designed and implemented a modular, one-pot synthetic route leveraging cyanuric chloride reactivity, enabling rapid derivatization of the triazine scaffold of DEL-S1. This strategy yielded structurally diverse analogs, including water-soluble carboxylate derivatives with preserved SLIT2/ROBO1 inhibitory activity. Together, this work establishes a novel chemical scaffold targeting SLIT2 and introduces a flexible synthetic platform to support further optimization toward therapeutic development.

biochemistry↗

bioRxiv2025

Tau Oligomerization Drives Neurodegeneration via Nuclear Membrane Invagination and Lamin B Receptor Binding in Alzheimer's disease

The microtubule-associated protein tau aggregates into oligomeric complexes that highly correlate with Alzheimers disease (AD) progression. Increasing evidence suggests that nuclear membrane disruption occurs in AD and related tauopathies, but whether this is a cause or consequence of neurodegeneration remains unclear. Using the optogenetically inducible 4R1N Tau::mCherry::Cry2Olig (optoTau) system in iPSC-derived neurons, we demonstrate that tau oligomerization triggers nuclear rupture and nuclear membrane invagination. Pathological tau accumulates at sites of invagination, inducing structural abnormalities in the nuclear envelope and piercing into the nuclear space. These findings were confirmed in the humanized P301S tau (PS19) transgenic mouse model, where nuclear envelope disruption appeared as an early-onset event preceding neurodegeneration. Further validation in post-mortem AD brain tissues revealed nuclear lamina disruption correlating with pathological tau emergence in early-stage patients. Notably, electron microscopy shows that tau-induced nuclear invagination triggers global chromatin reorganization, potentially driving aberrant gene expression and protein translation associated with AD. These findings suggest that nuclear membrane disruption is an early and possibly causative event in tau-mediated neurodegeneration, establishing a mechanistic link between tau oligomerization and nuclear stress. Further investigation into nuclear destabilization could inform clinical strategies for mitigating AD pathogenesis.

neuroscience↗

bioRxiv2025

Development of noninvasive imaging to measure spontaneous pain in mice

Objectively measuring pain in laboratory animals is essential for pain research and analgesic development. Despite the development of various behavioral tests to measure evoked pain in animal models, measuring spontaneous pain remains challenging. To address this unmet need, we developed a novel imaging approach to detect spontaneous nociception in animal pain models. To do this, we generated a Bacterial Artificial Chromosomes transgenic mouse that expresses Redquorin under the murine synapsin 1 promoter. Redquorin is a fusion protein consisting of chimera and a 2x tandem dimer Tomato Aequorin (tdTA), which emits long wavelength bioluminescence from activated neurons in the presence of coelenterazine. This luminescence can penetrate tissues and form a projected image on the body surface that can be detected with a spectrum In Vivo Imaging System, thus creating a Nociceptive Neuronal Activity Imaging mouse. We used the tdTA mice to image bioluminescence in the spinal regions as a surrogate of spontaneous pain induced by capsaicin, the HIV-1 envelope glycoprotein gp120, and spinal nerve ligation. Results show that Redquorin-emitted bioluminescence is a sensitive optical surrogate to measure spontaneous pain. This approach offers a new method to measure spontaneous pain in animal models for basic and translational research.

neuroscience↗

bioRxiv2025

Metabolic modulation of intratumoral cholesterol with gut microbiota for the treatment of colorectal cancer

Excess cholesterol is positively correlated with colorectal cancer (CRC). Current therapeutic strategies for modulating cholesterol levels in CRC are limited and often come with complications. Here, we demonstrated that microbiome shunting of intestinal cholesterol to anticancer metabolites is a safe and applicable therapeutic approach for CRC. By screening major microbial metabolic products of cholesterol, we found that 4-cholesten-3-one (4-C-3) was selectively depleted in fecal samples and tumor tissues of patients with CRC. 4-C-3 exhibits strong antitumor effects on human CRC cell lines, patient-derived organoids, and patient-derived xenograft (PDX) models. Mechanistically, 4-C-3 suppresses CRC tumorigenesis by dually targeting the epidermal growth factor receptor (EGFR) and Kirsten rat sarcoma viral oncogene homologue (KRAS). 4-C-3 directly binds to EGFR, blocking its signal transduction by inhibiting the binding of EGFR ligands. Additionally, 4-C-3 inhibits oncogenic KRAS variants, such as KRASG12D, by suppressing nucleotide exchange activity and effector engagement. By targeting both EGFR and KRAS, 4-C-3 reduces primary resistance to anti-EGFR therapies caused by KRAS mutations in CRC. As a proof-of-concept study, we showed that delivery of 4-C-3 by Oscillibacter ruminantium, a 4-C-3- producing commensal bacterium that is reduced in CRC patients, or a nonpathogenic Escherichia coli strain engineered to specifically convert intestinal cholesterol into 4-C-3, removed intratumoral cholesterol and led to rapid tumor regression in multiple models of CRC. These results suggest that microbial therapies for restoring intestinal cholesterol homeostasis represent a new therapeutic avenue for CRC.

cancer biology↗

bioRxiv2025

The Role of Ribose Modifications on the Structural Stability of Nucleotide Analogs with α-thiotriphosphate at the Active Site of SARS-CoV-2 RdRp

As a promising drug target, RNA-dependent RNA polymerase (RdRp) has attracted much attention recently due to its notable conserved active site, especially in the context of COVID-19 spreading. To inhibit the function of RdRp, nucleotide analog is a common choice for acting as a chain terminator or RNA corruptor. Although some nucleotide analogs have shown the ability to terminate the extension of a nascent strand of SARS-CoV-2, most of them are likely to be excised due to the proofreading of SARS-CoV-2 nsp14/nsp10. A previous experimental study found that introducing sulfur modification into analogs phosphate moieties (-thiotriphosphate; "thio" modification) can break the bottleneck. For instance, Sofosbuvir with -thiotriphosphate modification successfully escaped from the excision of nsp14/10. However, it is unknown how the -thiotriphosphate affects the structural stability of nucleotide analogs with different ribose modifications at the active site of SARS-CoV-2 RdRp. Thus, in this study, we performed extensive molecular dynamics simulations on four nucleotide analogs with -thiotriphosphate to elucidate what kind of ribose modification combined with "thio" modification would benefit the analogs structural stability at the active site. We found that the "thio" modification led to the torsion of phosphate moieties, profoundly affecting the overall conformation of analogs and surrounding residues, determining the Watson-Crick base pairing and catalytic efficiency. Interestingly, chemical modification on the ribose, especially the 1 and 3-ribose positions, increases the structural stability of analogs through hydrogen bond interactions. Our results revealed nucleotide analogs structural and dynamical features with "thio" modification at the active site, which may contribute to future drug design or repurposing aimed at the SARS-CoV-2 RdRp.

bioinformatics↗

bioRxiv2025

MsyB-HU Interaction Modulates a Two-Tiered Bacterial Stress Response by Regulating DNA Supercoiling

Bacteria respond to stressful conditions through multiple pathways, including changes in gene expression patterns and mutations for adaptation. DNA supercoiling is a fundamental regulatory principle of bacterial gene expression, controlled antagonistically by DNA gyrase and topoisomerase I. Nucleoid-associated proteins, such as HU, also regulate supercoiling through interactions with DNA. Here, we identify Escherichia coli protein MsyB as a HU inhibitor and a {beta}-clamp binder. MsyB is fine-tuned under various stressful conditions, where it modulates the population of DNA-bound HU by forming a HU-MsyB complex. Consequently, the balance between DNA-bound HU and MsyB-bound HU adjusts the DNA supercoiling state, thereby influencing transcription for adaptation. Additionally, under prolonged starvation during the stationary phase, sustained high level of MsyB increases DNA exposure to damaging factors, acting as a damage inducer. The HU/MsyB/{beta}-clamp interaction suggests a model in which MsyB coordinates with HU and the {beta}-clamp to facilitate damage acquisition and error-prone DNA repair. Thus, MsyB-dependent supercoiling regulation represents a novel two-tiered bacterial stress response mechanism in gene expression and adaptive mutation. Our findings reveal a previously unrecognized regulatory mechanism of bacterial supercoiling, positioning HU as a promising antibiotic target.

microbiology↗

bioRxiv2025

Circulating extracellular vesicles from HIV-1 gp120-treated mice act as endogenous algogens, mediating and maintaining HIV-associated chronic pain

HIV-associated chronic pain (HIV-PAIN) remains prevalent in the post combined antiretroviral therapy era, affecting 30-60% of HIV patients worldwide. The underlying mechanism responsible for the development and maintenance of chronic pain remains unclear. gp120 is a causal factor of the HIV-PAIN and functions as an exogenous algogen. The pain experienced by human HIV-PAIN has been modeled in mice (referred to as mHIV-PAIN) using intrathecal (i.t.) injections of gp120. gp120 is a relatively short-term, static, exogenous algogen that is exhaustible in vivo. In authentic infection, HIV virions serve as the primary source of exogenous gp120, which initiates the early phase of clinical HIV-PAIN. Interestingly, while the source of replenishing gp120 decreases after antiretroviral therapy by suppressing viremia, the prevalence of chronic HIV-PAIN remains stable. To induce chronic pain in mice, gp120 needs to be repeatedly applied by the i.t. route. This raises a key question: Is an endogenous inexhaustible algogen responsible for maintaining the chronicity of HIV-PAIN? In the present study, we isolated circulating small extracellular vesicles (sEV) from mice using our mHIV-PAIN model that is i.t. injected with gp120. We refer to such sEV as gp120-sEV herein. We observed that gp120 is absent in gp120-sEV. Following transfusion of gp120-sEV intrathecally, naive recipient mice exhibit an extensive pain phenotype, including cold pain tested with we newly invented dry ice vapor cold test. RNA-sequence analysis suggests that gp120-sEVs induced expression of genes related to nociception and neuroinflammation pathways. These findings provide direct evidence that circulating sEV function as endogenous long-term "dynamic" algogens that enhance initial pain and extend the chronification of HIV-PAIN in mice, suggesting that chronic HIV-PAIN requires an exogenous algogen (gp120) paired with endogenous algogen (gp120-sEV), and that these components work synchronically to initiate and extend pain chronification. This double algogen concept provides a new insight into the pathogenesis of HIV-PAIN chronification. Our new mechanistic understanding will also assist in identifying new therapeutics to alleviate HIV-PAIN by targeting pathological gp120-sEV.

neuroscience↗

bioRxiv2024

In Situ Integration of Porous Polyethylene Nanomembrane with Wound Exudates for Scarless Healing

Achieving scarless wound repair through innovative material designs, such as hydrogels infused with growth factors and cells, has been extensively explored. In this study, we introduce a scarless healing material called pgPE, which is based on a porous and biologically inert ultra-high molecular weight polyethylene (UHMWPE) nanomembrane. This highly flexible nanomembrane conforms closely to the wound site and effectively absorbs wound-associated species into its nanopores, forming pgPE in situ. The resulting pgPE creates an ideal environment that fosters physiological metabolism while acting as a barrier against pathogens. Our findings demonstrate that pgPE facilitates complete skin reconstruction, including the regeneration of hair follicles. Additionally, we characterized the immune microenvironment and hypoxic conditions, revealing that pgPE alleviates hypoxia and modulates immune responses, thereby promoting healing towards a scar-free outcome. The integration of wound-associated species within pgPE has been evidenced through three-dimensional Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) analysis of postmortem samples. This study highlights the potential of personalized solutions that align with physiological systems for enhanced wound healing.

bioengineering↗