Biology subjects

Chen, P.

Publications and source records attributed to Chen, P..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Isolation of folate-producing probiotics and its regulatory effects on homocysteine metabolism and gut microbiota composition

BackgroundFolate deficiency is a global nutritional problem associated with multiple adverse health outcomes, including impaired one-carbon metabolism and elevated homocysteine levels (hyperhomocysteinemia). Gut microbiota-mediated folate biosynthesis has emerged as a promising strategy for improving host folate status. This study aimed to isolate folate-producing probiotic strains, clarify their folate synthesis mechanisms, and evaluate their regulatory effects on folate metabolism and gut microbiota in folate-deficient mice. MethodsHigh-throughput cultivation and screening were performed to isolate folate-producing probiotics. Whole-genome sequencing, pathway reconstruction, and metabolite profiling in fermented milk were used to explore folate biosynthesis pathways and potential microbial cross-feeding interactions. A folate-deficient mouse model was established to evaluate the effects of a probiotic cocktail on serum folate, homocysteine (Hcy) levels, and gut microbiota composition using microbiological assays, biochemical analyses, qPCR, 16S rRNA gene sequencing, alpha diversity analysis, principal coordinates analysis (PCoA), and Linear discriminant analysis Effect Size (LEfSe) analysis. ResultsOver 1,000 bacterial isolates were obtained, and over 10 strains, mainly belonging to Lactobacillus, Bifidobacterium, and Bacillus, showed folate production levels above 100 ng/mL. Genomic analysis revealed that most selected probiotic strains lacked genes involved in para-aminobenzoic acid (pABA) biosynthesis but retained downstream folate synthesis modules, suggesting a potential dependence on pABA-producing gut commensals for precursor supply through microbial cross-feeding. In fermented milk, probiotic strains mainly produced bioactive folates (5-MeTHF and THF), with strain-specific production capacities; L. plantarum, W. coagulans, and B. animalis subsp. lactis significantly increased 5-MeTHF levels in fermented milk. In vivo, high-dose probiotic intervention significantly elevated serum folate (p<0.01) and reduced Hcy (p<0.05) in folate-deficient mice, while medium-dose intervention showed no significant effects. The probiotic strains colonized the mouse gut in a dose-dependent manner: high-dose group exhibited >4,000-fold increase in relative abundance (Bifidobacteriaceae and Bacillaceae enriched), medium-dose group only enriched Bacillaceae, and low-dose group showed no effective colonization. High dose probiotic treatment enhanced gut microbial species diversity (increased Shannon index) and restored folate deficiency-induced gut microbiota dysbiosis (PCoA clustering closer to normal group). ConclusionThis study screened high folate-producing probiotic strains and demonstrated their ability to synthesize active 5-MeTHF, which may rely on microbial cross-feeding in gut microbiota. Furthermore, we demonstrated that folate-producing probiotic intervention significantly improves folate status and Hcy metabolism and restores gut microbiota homeostasis in folate-deficient mice. These findings suggensted that such probiotics could serve as a safer, more physiological intervention for folate deficiency and hyperhomocysteinemia, especially in populations with MTHFR polymorphisms.

microbiology↗

bioRxiv2026

HYPER-Net: Physics-Conditioned Self-Supervised Reconstruction for Fourier Light-Field Microscopy

The rapid convergence of optical innovation and machine intelligence is reshaping biological imaging by enabling platforms that jointly advance image formation and computational reconstruction for highspeed, high-resolution volumetric microscopy. However, broadly accessible three-dimensional imaging at high spatiotemporal resolution remains limited by the reliance of existing supervised methods on large modality-matched training datasets, the computational burden of conventional iterative reconstruction, and sensitivity to optical mismatch arising from small deviations in the spatial-angular point spread functions. Here, we introduce HYPER-Net, a physics-conditioned self-supervised framework for Fourier light-field microscopy that integrates scan-free volumetric acquisition with fast, robust three-dimensional reconstruction. HYPER-Net incorporates experiment-specific point-spread functions into the learning process in two complementary roles: as the forward operator that enforces measurement consistency and as a conditioning signal that adaptively modulates intermediate feature representations. This design reduces reliance on paired experimental ground-truth volumes, improves robustness to system variation, and enables generalizable reconstruction across diverse biological contexts. Using human colon organoids, embryonic Xenopus laevis hearts, hiPSC-derived cardiac spheroids, and freely moving Caenorhabditis elegans, we demonstrate high-fidelity volumetric imaging of tissue morphology, cardiac function, calcium-contraction coupling, and locomotion-associated neural and muscular dynamics. These results position HYPER-Net as a versatile framework for rapid volumetric imaging and quantitative analysis of dynamic biological systems across basic research and biomedical applications.

bioengineering↗

bioRxiv2026

A Novel Central-Peripheral Interface: The Auditory Nerve Glial Transition Zone Exhibits Enhanced Age-Related Immune and Glial Cell Dysfunction

Age-related hearing loss (ARHL) is a rapidly growing public health concern, affecting two-thirds of adults over 65 years old, with no effective therapeutics available. As the aging population grows at an unprecedented rate, the burden of ARHL will only increase. The causes of ARHL are multifactorial, but an understudied major contributor is glial dysfunction. The auditory nerve (AN) conducts sound from the cochlea to the brainstem and holds a diverse population of immune cells and myelinating glia. As the AN fibers bundle together within the cochlea to project to the brainstem, they are first myelinated by Schwann cells in the peripheral AN, then myelinated by oligodendrocytes in the central AN. The region where myelination shifts from Schwann cells to oligodendrocytes is the glial transition zone (GTZ), located in the cochlear modiolus, creating a unique biological niche. While central-peripheral interfaces are recognized in other cranial nerves, the AN GTZ is understudied. This region integrates the peripheral and central microenvironments within the confined bony cochlea, positioning it as a niche for glial dysfunction in pathological conditions, such as aging. We hypothesize that the GTZ is a site of enhanced glial dysfunction contributing to age-related AN demyelination, an important contributor to ARHL. We evaluated this in an ARHL mouse model combining RNA-sequencing, quantitative immunohistochemistry, and 3D high-resolution imaging. We examined the AN GTZ from human temporal bone donors. RNA-sequencing of the AN revealed age-associated increases in abnormal myelination/glial function and inflammation. There was a significant age-dependent increase in Iba1+ macrophages/microglia, with accumulation at the AN GTZ, and an increase in cellular volume and surface area, suggesting greater age-related activation. Macrophages/microglia contained significantly more internalized myelin debris in the AN (peripheral, central, and GTZ) with aging. More importantly, we found structurally intact myelin within macrophages/microglia only at the GTZ, suggesting a unique microenvironment at the GTZ altering phagocytic activity in aging. Together, our data suggest that the GTZ, a previously unrecognized central-peripheral interface, is a critical site of immune-glial interactions and especially vulnerable to age-related demyelination and neuroinflammation. This study highlights the GTZ as a potential target for preserving AN myelination and mitigating ARHL.

neuroscience↗

bioRxiv2026

Hydrogel Fiber Endomicroscopy

Multimode fibers enable minimally invasive, high-resolution imaging through ultrathin probes, thereby enhancing diagnostic precision and facilitating real-time monitoring in delicate anatomical regions. In this work, we introduce HYFEN, a hydrogel-based endomicroscopic imaging platform for flexible, biocompatible, and subcellular-scale fluorescence microscopy. HYFEN leverages the unique properties of hydrogel materials, adaptive optics, and pixel-wise image enhancement to address challenges associated with silica-based fibers, including mode scrambling, limited field of view, and mechanical rigidity. The technique achieves precise mode threading, rapid diffraction-limited focusing at kilohertz speeds, and high-fidelity fluorescence signal acquisition with subcellular resolution. Notably, the approach extends fluorescence imaging under enhanced fiber dimensions and bending conditions that are unachievable with conventional modalities. Together, these advances establish HYFEN as a versatile platform for next-generation biointerfacing and minimally invasive imaging across biomedical and clinical settings.

bioengineering↗

bioRxiv2026

Syndecan-1 Promotes Alveolar Type 2 Epithelial Cell Senescence during Lung Fibrosis.

Idiopathic pulmonary fibrosis (IPF) is an age-related, progressive, and fatal interstitial lung disease for which effective therapies remain limited. Alveolar type 2 (AT2) epithelial cells serve as facultative stem cells essential for alveolar repair; however, AT2 cell senescence disrupts epithelial regeneration and contributes to fibrotic remodeling in IPF. Syndecan-1 is a transmembrane heparan sulfate proteoglycan predominantly expressed by lung epithelial cells, but its role in AT2 dysfunction during fibrosis is poorly defined. Here, we demonstrate that syndecan-1 is robustly upregulated in AT2 cells in IPF and other fibrotic lung diseases, as well as in murine bleomycin-induced lung fibrosis. Syndecan-1 expression was further enhanced with aging and associated with increased fibrotic burden in aged mice. Using integrated human transcriptomic analyses, mouse genetic models, and epithelial cell-based systems, we show that excess syndecan-1 promotes cell-autonomous epithelial senescence and impairs AT2 progenitor function. Elevated syndecan-1 reduced AT2 renewal capacity, disrupted differentiation, and diminished surfactant protein C level, whereas genetic loss of syndecan-1 attenuated senescence and preserved epithelial function following injury. Together, these findings identify syndecan-1 as a critical epithelial regulator of AT2 senescence and maladaptive repair in pulmonary fibrosis and support targeting syndecan-1-driven epithelial dysfunction as a potential therapeutic strategy.

cell biology↗

bioRxiv2026

Stochastic Evolutionary Control in Heterogeneous Populations

Therapeutic resistance, which poses a central challenge in cancer and infectious disease treatment, arises from the evolutionary dynamics of heterogeneous populations as a natural consequence of the evolutionary tendency towards higher fitness. Here we introduce SHEPHERD (Stochastic Heterogeneity-informed Evolutionary Policy Hampering the Expansion of Resistance to Drugs), which integrates Wright-Fisher (WF) population genetics modeling with Markov Decision Processes (MDPs) to design optimal adaptive drug policies which reduce the fitness of evolving disease, mitigating resistance. While MDPs have been applied to evolutionary control under the strong-selection, weak-mutation (SSWM) assumption--where populations are effectively homogeneous--SHEPHERD operates beyond this regime, effectively capturing the full stochastic dynamics of genetically heterogeneous populations experiencing mutation and selection of a wide array of strengths. Using synthetic multi-drug fitness landscapes, we show the benefit of the optimized SHEPHERD protocol for in silico disease systems with three, four, and eight genotypes: the long-term mean fitness of the disease is reduced compared to any single-drug or two-drug periodic regimen. Although these examples specifically model drug resistance, we discuss the potential broad applicability of our approach to calculating strategies for controlling a wide class of evolving populations. We further analyze the sensitivity of SHEPHERD strategies to different levels of genotypic frequency discretization and temporal resolution, demonstrating robustness once moderate resolution is achieved, but strong dependence on the timing of drug updates. Although current results rely on synthetic landscapes due to the lack of empirical multi-genotype, multi-drug measurements outside the SSWM regime, our study establishes a foundation for applying MDP optimization to broad classes of evolutionary dynamics, highlighting both the opportunities and the computational challenges of controlling evolution.

evolutionary biology↗

bioRxiv2026

Discovering macroscale functional organization on the structure of brain-like recurrent neural networks

Linking structure and function is a central topic in both neurobiology and artificial intelligence. Human brain functions are organized across the macroscale cortex into parcellations, modules, and hierarchies that can be inferred from intrinsic structural architecture, providing an interpretable and clinically meaningful framework for linking structure to function. While artificial neural networks have been successfully aligned with human cognition at the representational level, it remains unclear whether the structural principles linking brain anatomy and function can extend to artificial neural networks, and whether imposing brain-like structural constraints can induce comparable functional organization to that observed in the human brain. Here, we introduce BrainRNN, a brain-like recurrent neural network architecture inspired by macroscale human cortical structure. We show that under structural constraints, BrainRNNs selectively regulate the distribution of connectivity and recruit more activated units in association regions for higher-order cognitive capacity. Moreover, we demonstrate structure-function coupling in BrainRNNs and show that structural constraints enable macroscale functional organization, including functional modules and gradients, to emerge along topographic and topological axes, closely mirroring empirical findings in the human cortex. Together, these results demonstrate how multiple brain-like structural constraints jointly shape functional organization and enable function to be inferred from structure, highlighting the potential of structurally grounded artificial intelligence for neuroscientific research.

neuroscience↗

bioRxiv2026

Efficient replication of influenza D virus in the human airway underscores zoonotic potential

Influenza D virus (IDV), primarily found in livestock species, has demonstrated cross-species transmission potential, yet its threat to humans remains poorly understood. Here, we curated a panel of IDV isolates collected during field surveillance from 2011 to 2020 from swine and cattle to assess their ability to infect human airway cells as a proxy for zoonotic threat assessment. Using lung epithelial cell lines, primary well-differentiated airway epithelial cultures, and precision-cut lung slices, we demonstrated that IDV efficiently propagates in cells and tissues from the human respiratory tract, reaching titers comparable to human influenza A virus (IAV). Infection kinetics in primary porcine airway cultures and respiratory tissues mirrored those from human, suggesting similar infectivity across species. To define host responses to IDV infection, we evaluated innate immune sensing and downstream interferon signaling in human respiratory cells. IDV infection resulted in markedly reduced activation of interferon regulatory factor (IRF) signaling and diminished induction of interferon lambda 1 and interferon-stimulated genes compared to IAV, indicating inefficient activation of innate immune sensing pathways. However, IDV replication was potently restricted in interferon-pretreated cells, demonstrating sensitivity to interferon-mediated antiviral effector mechanisms once an antiviral state was established. Together, these findings show that IDV can efficiently infect the human airway while limiting innate immune sensing, a feature that may facilitate zoonotic spillover. Our study highlights the need for enhanced surveillance of IDV at the animal-human interface and provides a foundation for further investigation into its biology and potential for causing human infection and disease. SIGNIFICANCE STATEMENTInfluenza D virus (IDV) is a poorly understood virus type in the Orthomyxoviridae family. Although initially considered incapable of infecting humans, high seropositivity rates among cattle and swine workers suggest that zoonotic infections may already be occurring. However, the extent of human compatibility--and the potential for spillover--remains poorly understood. Our study demonstrates that IDV replicates efficiently in multiple human respiratory models while largely evading innate immune defenses, raising concern that only minimal evolutionary changes may be required for sustained human transmission. These findings underscore the need for further investigation into IDV biology and zoonotic risk. Such studies are critical for identifying viruses with the potential to adapt to humans before they become public health threats.

microbiology↗

bioRxiv2026

Near completely reversing the γ- to β-globin switch by enhancer release, retargeting and reinforcing

The {gamma}- to {beta}-globin switch is intricately regulated during human ontogeny, and this process is manipulated for therapeutic approaches to treat {beta}-hemoglobinopathies by activating {gamma}-globin expression. Several genetic strategies to reactivate HbF have partially reversed the {gamma}- to {beta}-globin switch and ameliorated the clinical symptoms of {beta}-hemoglobinopathies. However, whether the {gamma}- to {beta}-globin switch can be completely reversed remains unknown. Completely reversing the {gamma}- to {beta}-globin switch requires a thorough redirection of the locus control region (LCR) from interacting with the {beta}-globin gene (HBB) to interacting with the {gamma}-globin gene (HBG). Here, we found that disrupting the KLF1-mediated HBB-LCR interaction by mutating the CACCC motif in HBB leads to the release of the LCR and its retargeting to other {beta}-like globin genes. Moreover, simultaneously disrupting the KLF1-mediated HBB-LCR interaction and the epigenetic repression of HBG by combined editing of the CACCC motif in HBB and the TGACCA motif in HBG reinforces the HBG-LCR interaction, resulting in almost exclusive {gamma}-globin expression while nearly absent {beta}-globin expression, achieving near complete reversal of the {gamma}- to {beta}-globin switch. This finding demonstrates the comprehensive regulation of the {gamma}- to {beta}-globin switch by gene competition and gene silencing mechanisms. This finding also suggests that silenced genes can be fully activated through the redirection of enhancer-promoter contacts and that the specificity of enhancer-promoter contact within chromosomal domains is achieved through the transcription factor clusters binding to enhancers and promoters. Combined editing of the CACCC&TGACCA motifs also offer a more optimal therapeutic strategy for {beta}-hemoglobinopathies.

molecular biology↗

bioRxiv2026

Differential Acceptance Specificity of Human Fucosyltransferases toward GDP-azidofucose and GDP-alkynylfucose as Glycosylation Probes

Described here is the synthesis and assembly of a new-generation mRNA-bifunctional lipid nanoparticle (mRNA-BLNP3) for selective delivery of mRNA to antigen-presenting cells (APCs). Compared to mRNA-BLNP1 and BLNP2 (BioRxiv,doi.org/10.1101/2023.12.26.572282), the mRNA-BLNP3, incorporating a glycolipid with the lipid moiety designed to target the CD1d receptor on dendritic cells (DCs) and the sugar head group targeting the mannose-binding receptors on APCs is more selective with stronger target-specific immune responses. It was shown that vaccination in mice with mRNA-BLNP1 elicited enhanced cytokine induction and antibody responses compared to traditional mRNA-LNPs, and the mRNA-BLNP2 vaccine, incorporating a mannose-glycolipid, further improved DC targeting. However, BLNP3, incorporating the glycolipid with an aryl-mannose head group targeting the mannose receptor on APCs and the same lipid moiety targeting the Cd1d receptor on DCs, showed superior lymph node targeting in vivo with reduced liver accumulation, enhanced mRNA expression in DCs and macrophages, and increased DC maturation. Immunization in mice with mRNA-BLNP3 elicited enhanced humoral and cellular immune responses compared to mRNA-BLNP1 and mRNA-BLNP2, with higher antigen-specific IgG titers and granzyme B-producing CD8 T cells, demonstrating that BLNP3 is a promising bifunctional lipid nanoparticle for delivery of mRNA vaccines with improved efficacy and safety.

biochemistry↗

bioRxiv2026

Hyperactivated YAP1 Drives an Invasive EMT Subtype of Cervical Squamous Cell Carcinoma

Cervical cancer (CVC) is classically understood as an HPV-driven disease in which high-risk HPV infects cervical basal epithelial cells, induces neoplastic transformation, and drives upward epithelial expansion, pathogenic events underlying the success of cytology- and HPV-based screening. With widespread HPV vaccination and screening, the WHO has launched the CVC elimination initiative and believes that CVC will be the first cancer that would be eliminated as a public health problem. However, statistics showed that CVC remains the most common gynecologic malignancy worldwide, and in the United States, where HPV testing and Pap smears have reached near-maximal implementation, the CVC mortality rate has plateaued for more than two decades. These epidemiologic trends suggest the existence of a subset of CVC that can escape current screening strategies. Here, we demonstrate that hyperactivation of YAP1 caused by disruption of Hippo-YAP signaling is sufficient to induce a subtype of HPV-independent invasive CVC that lacks surface lesions and therefore evades HPV- and cytology-based detection. Using single-cell RNA sequencing combined with high-resolution spatial transcriptomics, we define the cellular architecture, molecular pathways, and immune microenvironment underlying this invasive subtype. We show that YAP1-driven tumors adopt an EMT-high transcriptional state and selectively recruit immunosuppressive myeloid-derived suppressor cells that functionally interact with cancer cells to promote invasion and progression. Our findings suggest that targeting the disrupted Hippo signaling may offer a new strategy to prevent the subset of invasive CVC that current HPV- and Pap-based programs cannot detect, an essential step toward achieving global CVC elimination.

cancer biology↗

bioRxiv2025

Temporal boundary gating of auditory sensitivity

Perception unfolds over time, but whether continuous sounds are sampled with uniform sensitivity is unknown. We combine human psychophysics, EEG and rodent neurophysiology to show that local auditory change detection is strongly gated by stimulus boundaries. In humans, brief perturbations inserted at different temporal positions within 0.5-1-s tones revealed an inverted U-shaped sensitivity profile: detection was attenuated near sound onset and offset and maximal mid-epoch, with EEG change responses showing a closely matching dependence on change timing. Electrocorticography in awake rats exhibited homologous temporal weighting, and analogous profiles for amplitude changes and visual motion demonstrated cross-feature and cross-modal generality. To uncover circuit mechanisms, we recorded single units along the inferior colliculus-medial geniculate body-auditory cortex pathway together with laminar local field potentials in A1. Onset-locked suppression of change responses emerged in midbrain and was progressively amplified in thalamus and cortex, whereas the full start-end profile was expressed in granular-layer alpha-gamma power. A simple biophysically grounded model in which onset responses saturate and cortical populations integrate over finite temporal windows recapitulates this pattern, explaining how stimulus boundaries disrupt prospective and retrospective integration and thereby degrade change detection near the beginning and end of sounds.

neuroscience↗

bioRxiv2025

HypoxamicroRNA-210 protects against hepatic steatosis by inhibiting CIDEC expression

Background and AimsMetabolic dysfunction-associated steatotic liver disease (MASLD) is a major global health burden. Although hypoxia is known to contribute to MASLD pathogenesis, the role of hypoxia signaling remains poorly defined. We investigated whether HypoxamicroRNA-210 (miR-210), a key hypoxia-inducible microRNA, regulates hepatic lipid metabolism and MASLD development. MethodsSerum miR-210 levels were quantified in MASLD patients and matched controls. Human hepatic spheroids and HepG2 cells were exposed to fatty acids to assess miR-210 induction and lipid accumulation. miR-210 knockout mice were fed a Western diet to evaluate hepatic steatosis and transcriptomic changes using RNA sequencing. RNA pull-down and 3UTR-driven luciferase reporter assays were employed to identify miR-210 targets. Functional effects of miR-210 mimic were examined in knockout mice, db/db mice, and in vitro human hepatic spheroid models. ResultsSerum miR-210 levels were significantly reduced in MASLD patients compared with matched controls. Consistently, human hepatic spheroids did not appropriately increase miR-210 expression in response to fatty acid-induced intracellular hypoxia. This blunted miR-210 response contributed to hepatic lipid accumulation, as loss of miR-210 in a mouse model of MASLD led to increased hepatic lipid deposition and activation of lipid metabolic pathways. We identified CIDEC as a direct miR-210 target mediating its inhibitory effects on hepatic lipid accumulation, and restoring miR-210 expression suppressed CIDEC and reduced hepatic lipid content in knockout mice on a Western diet. Moreover, miR-210 attenuated lipid accumulation in both in vitro human hepatic spheroids and in vivo db/db mice models of MASLD. ConclusionsmiR-210 protects against hepatic steatosis by inhibiting CIDEC expression, suggesting miR-210-CIDEC axis as a promising therapeutic target for reducing hepatic lipid accumulation and preventing MASLD progression. Impact and ImplicationsThis study addresses a critical gap in understanding how hypoxia signaling shapes MASLD and uncovers a novel pathogenic mechanism of hepatic steatosis arising from fatty acids-induced dysregulation of miR-210. Impaired hypoxia responses, via blunted miR-210 induction, contribute to hepatic lipid accumulation through upregulation of CIDEC, a newly identified target of miR-210. These findings establish miR-210 as a novel regulator of hepatic lipid homeostasis and underscore its therapeutic potential. Interventions aimed at restoring miR-210 function in the liver may offer a promising strategy to ameliorate hepatic steatosis and prevent MASLD progression.

molecular biology↗

bioRxiv2025

Echoes as Signal, Not Noise: Reverberation Sharpens Sensitivity to Temporal Structure

Sensitivity to temporal structure is fundamental to hearing, yet how natural reverberation shapes this sensitivity is unclear. Here we identify echo-facilitated temporal sensitivity (EFTS), a principle whereby the auditory system exploits echoes to selectively enhance responses to rapid temporal changes. Using transitional click trains with subtle inter-click-interval (ICI) shifts, we first show that increasing echo strength systematically enlarges the sound-level step at ICI transitions in both recorded and simulated stimuli, sharpening the physical boundary between segments of distinct temporal structure. In humans, psychophysical detection of ICI changes improves monotonically with echo level in both simulated and real free-field environments, while a late EEG change response scales with echo strength as onset responses remain comparatively stable. In awake rats, electrocorticography over auditory cortex reveals parallel echo-dependent enhancement of transition-evoked activity. Single units exhibit echo-level-dependent amplification of change-related firing and improved neurometric discriminability. Laminar local field potential and current source density analyses further show that echo-dependent divergence emerges first in granular and infragranular layers before propagating to supragranular cortex, consistent with thalamocortical drive followed by intracortical amplification. Together, these findings establish EFTS as a cross-species mechanism that reframes echoes as structured signals the brain uses to sharpen temporal integration in everyday listening.

neuroscience↗

bioRxiv2025

Revealing the antibiotic resistome in the global hadal trenches by large-scale cultivation and metagenomics

The global hadal trenches that reside more than 6000 meters below the sea level, represent one of Earths most remote ecosystems, potentially harboring a microbial reservoir for antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). However, the global hadal environments remain the least investigated ecosystem for ARB/ARG compositions and distribution. This study took three-fold approaches to investigate the ARB/ARGs in the global hadal trench sediments, i.e., large-scale cultivation to isolate and verify ARB/ARGs from Challenger Deep sediments, metagenomic analysis of sediment samples from Challenger Deep over a six-year period, and comparative study of resistomes across six hadal trenches through metagenomic analysis. The Challenger Deep sediments had a consistent average ARG abundance of 0.02 copy/cell over a six-year period, whereas some ARG subtypes fluctuated and showed distinct temporal dynamics. Large-scale screening of ARB via microbial cultivation using 13 classes of antibiotics led to enriching distinct ARB, for which eleven genera were identified by metagenomic sequencing as major host for ARGs. The global hadal trench sediments showed a variable ARG abundance, which was significantly lower than those from environments in proximity to human activities, representing a relatively pristine reservoir. Phylogenetic analysis suggested the hadal ARGs underwent niche-specific selections and formed hadal trench-specific clusters that diverged from human-associated lineages, which can be outward transported when disturbed. The study established the hadal trench sediments, as a relatively pristine reservoir of natural ARGs, providing a crucial environmental baseline for assessing their impacts on the ecosystems and public health risks.

microbiology↗

bioRxiv2025

Single-cell atlas reveals alveolar macrophage-specific Oncostatin-M drives pulmonary fibrosis via fibroblast activation in PCV2d infection

A hallmark of pulmonary fibrosis is the aberrant activation of lung fibroblasts into pathological fibroblasts that produce excessive extracellular matrix(1). Clarifying the cell-specific mechanisms by which viruses induce this process is crucial for developing effective strategies to intervene in disease progression. Here, we demonstrate that alveolar macrophage subsets specifically express tumor suppressor M (Osm) after infection by PCV2d infection and related intervention experiments in mice, combined with single-cell transcriptome sequencing (scRNA-seq). Through validation using histopathological analyses and an in vitro macrophage-fibroblast co-culture model, these alveolar macrophage-derived oncostatin M (Osm) were confirmed to specifically drive fibroblast activation. Vaccine intervention experiments further confirmed that targeted inhibition of oncostatin M (Osm) expression in alveolar macrophages significantly attenuated fibroblast activation and extracellular matrix deposition, thereby mitigating pulmonary fibrosis progression. Therefore, subgroup-specific secretion of oncostatin M (Osm) by alveolar macrophages represents a key driver mediating PCV2d infection-induced pulmonary fibrosis, and targeting this pathway offers a potential therapeutic strategy for viral-induced pulmonary fibrosis.

genomics↗

bioRxiv2025

IgG-Bridging-Seeded Synergistic Aggregation of SARS-CoV-2 Spikes Underlies Potent Neutralization by A Low-Affinity Antibody

Mechanistic studies of viral neutralization typically prioritize high-affinity antibodies, relegating low-affinity binders to the sidelines. We report P5-1C8, a Class 1 SARS-CoV-2 antibody that exemplifies this underexplored "low-affinity yet high-potency" phenotype, retaining strong neutralization of Omicron JN.1 despite markedly weakened trimer binding (KD = 225 nM; IC50 = 0.06 nM). Structural and biophysical analyses reveal that P5-1C8 engages WT and BA.1 spikes through canonical intra-spike bivalency, but with JN.1 it induces aggregation. Using virion-like nanoparticles displaying multiple spikes, we show that IgG remains bound with no detectable dissociation and triggers pronounced aggregation. Coarse-grained molecular dynamics delineate the stepwise pathway in which weak IgG-spike contacts seed aggregation via transient inter-spike bridging. Together, these findings establish the first mechanistic framework demonstrating how weak-binding antibodies can nonetheless achieve potent neutralization through higher-order aggregation, thereby expanding the conceptual landscape of antibody function and opening new directions for antibody evaluation and design. Graphical AbstractLow-affinity antibodies are frequently disregarded in discovery pipelines. This work reports P5-1C8, a Class 1 SARS-CoV-2 antibody with weak trimer binding (KD-to-IC50 > 3,700-fold) yet potent neutralization of Omicron JN.1. Structural, biophysical, functional and coarse-grained simulations collectively demonstrate that transient inter-spike IgG bridging seeds higher-order aggregation, which in turn drives neutralization and provides a mechanistic framework. O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/691454v1_ufig1.gif" ALT="Figure 1000"> View larger version (79K): org.highwire.dtl.DTLVardef@1d4f132org.highwire.dtl.DTLVardef@1274400org.highwire.dtl.DTLVardef@e186a6org.highwire.dtl.DTLVardef@4f1870_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Antimetastatic Sulfonate-Functionalized Mesoporous Silica Nanoparticles Enhance Irinotecan Stability and Delivery for Colorectal Cancer Treatment

Metastatic colorectal cancer (mCRC) remains a leading cause of cancer-related mortality, with Irinotecan (IRI) serving as a backbone chemotherapeutic despite its dose-limiting toxicities, instability of the active lactone form, and lack of intrinsic antimetastatic activity. To overcome these barriers, we developed sulfonate-functionalized mesoporous silica nanoparticles (MSNs), referred to as (SO3-)-MSN-PEG/TA, as a multifunctional nanocarrier for IRI delivery. This nanoformulation markedly enhanced drug loading efficiency and preserved over 90% of the lactone form for up to six months, enabling sustained release and improved pharmacological stability. In vitro studies demonstrated superior cellular uptake, enhanced apoptosis, and a reduced IC50 compared to free IRI. Beyond drug delivery, (SO3-)-MSN-PEG/TA exhibited intrinsic antimetastatic activity by modulating focal adhesion kinase (FAK)/paxillin signaling, thereby impairing cell migration and suppressing angiogenesis, along with efficient tumor accumulation through the enhanced permeability and retention (EPR) effect. Pharmacokinetic analysis further revealed that IRI@(SO3-)-MSN-PEG/TA prolonged systemic retention, maintaining higher IRI plasma concentrations compared with free IRI. IRI@(SO3-)-MSN-PEG/TA significantly inhibited both primary tumor growth and metastatic dissemination in orthotopic and heterotopic colorectal cancer models, while markedly reducing systemic toxicities and preserving bone marrow cellularity relative to free IRI and liposomal IRI (Onivyde). Collectively, this dual-functional nanomedicine provides an innovative therapeutic strategy that not only augments IRI efficacy but also confers metastasis suppression and favorable pharmacokinetics, addressing critical unmet needs in mCRC treatment. These findings highlight the translational potential of IRI@(SO3-)-MSN-PEG/TA as a safer and more effective therapy for mCRC.

bioengineering↗