Biology subjects

Li, Y.

Publications and source records attributed to Li, Y..

At least 181 records · Page 10Linked to original sources

bioRxiv2026

Evaluation of phage activity against diverse Enterococcus faecalis from infective endocarditis

Enterococcus faecalis is a leading cause of infective endocarditis, particularly in older and hospitalized patients. Treatment is challenging due to the intrinsic resistance of E. faecalis to many clinically important antibiotics and the increasing prevalence of multidrug-resistant strains. Bacteriophage (phage)-based therapies, including phage cocktails and phage-antibiotic combinations, offer a promising approach for treating resistant bacterial infections. In this study, we isolated ten novel phages from wastewater by screening on E. faecalis clinical isolates and tested phage activity both individually and in phage-phage and phage-antibiotic combinations against 18 E. faecalis clinical isolates collected from patients with infective endocarditis. We found that 15/18 (83%) isolates were susceptible to at least one phage tested, and that the same proportion of isolates were susceptible to a cocktail of three phages with complementary activities. We also observed improved bacterial growth inhibition and increased killing when phages were combined with ampicillin or daptomycin, two antibiotics commonly used to treat E. faecalis infections. Finally, we found that treatment with the three-phage cocktail improved the survival of Galleria mellonella infected with a pathogenic E. faecalis endocarditis isolate. Overall, these findings suggest that phages could be a helpful addition to the therapeutic repertoire for treating E. faecalis infective endocarditis. ImportanceNew approaches are needed for treating infective endocarditis, a life-threatening heart infection. Here we focus on Enterococcus faecalis, a resilient bacterium that is increasingly resistant to standard-of care antibiotic regimens, and explore the use of phage therapy for treating E. faecalis endocarditis. We found that combining phages together in a cocktail or pairing them with existing antibiotics can effectively kill E. faecalis clinical isolates from patients with infective endocarditis, and that treatment of infected waxworm moth larvae with a phage cocktail improved their survival. The results of this study contribute to the development of phage-based therapeutic approaches for E. faecalis endocarditis, which could ultimately lead to improved outcomes for patients facing this severe infection.

microbiology↗

bioRxiv2026

An Integrated Multi-omics Single Cell Atlas of the Human RPE and Choroid

The retinal pigment epithelium and choroid are critical for supporting the function and maintaining the homeostasis of the outer retina, and their dysfunction underlies a range of inherited and complex ocular diseases. To comprehensively characterize the cellular, transcriptomic, and epigenomic heterogeneity and dynamics within these tissues, we assembled an integrated multi-omics reference atlas comprising 719,813 single-cell/single-nucleus transcriptomes and 234,007 snATAC-seq profiles from 102 ancestrally diverse donors spanning 0 to 99 years of age, including cells from both the macula and periphery. This atlas resolves 48 distinct cell types or states and catalogs 448,567 open chromatin regions. Specifically, we resolved five distinct RPE subpopulations organized along a central-to-peripheral spatial axis, alongside two distinct stress/senescence states. We reconstructed the transcriptomic and epigenetic zonation of endothelial cells and expanded choroidal stromal heterogeneity by characterizing 11 fibroblast and two pericyte types. Age-associated compositional analysis revealed a significant fractional depletion of melanocytes, PI16+ fibroblasts, and venule endothelial cells with age, alongside a modest relative loss of central RPE and a corresponding increase in far-peripheral RPE. Cell-type-specific aging transcriptomics uncovered shared pathways related to inflammatory responses alongside distinct cell-type-specific signatures. Notably, significant age-associated epigenetic changes concentrated in the macula during the transition from early-to-middle adulthood and remained stable into old age, with transcription factors from the AP-1/bZIP family emerging as the dominant enriched motifs. Finally, integrating this atlas with AMD GWAS data provides novel variant-to-gene evidence implicating LIPG and COL4A3 in AMD pathogenesis. Together, this multi-omics atlas serves as both an invaluable community reference and a powerful discovery engine that translates genetic risk signals into localized target cells and candidate mechanisms, laying a foundation for understanding RPE/choroid biology in health and disease.

genomics↗

bioRxiv2026

Conformational dynamics of exopolysaccharides underlie biofilm matrix mechanics in Vibrio cholerae

Polysaccharides remain the least understood biomacromolecules, particularly in terms of the relationship between their chemical structure and physical properties. On the other hand, polysaccharides often serve as the main structural components in biofilms: surface-attached aggregates of bacterial cells encased within a mechanically resilient extracellular matrix. The large chemical space explored by bacteria within biofilms provides excellent opportunities to establish the structure-function relationship for polysaccharides. In this paper, we systematically characterize various polymer properties of Vibrio polysaccharide (VPS), the major exopolysaccharide in biofilms formed by Vibrio cholerae, the causative agent of pandemic cholera. Using a combination of shear rheology, dynamic and static light scattering, and small-angle X-ray scattering, we measure the viscosity, molecular weight, persistence length, radius of gyration, and hydrodynamic radius of this chemically unique biopolymer. Combining all-atom and coarse-grained simulations, we show how the conformational flexibility of a single glycosidic linkage within each VPS monomer can lead to dramatic compaction of the entire polymer chain and nonclassical entanglement behavior. Our comprehensive quantification represents a rare endeavor for bacterial biofilms, whose matrix composition and physical properties remain largely nebulous; it also represents a significant step towards a detailed understanding of the molecular origins of biofilm mechanics.

biophysics↗

bioRxiv2026

Accumulation of Lipid Droplets in Microglia following Neonatal Brain Hypoxia-Ischemia

BackgroundHypoxic-ischemic encephalopathy (HIE) is a major cause of neonatal mortality and neurodevelopmental impairments. Following brain hypoxia-ischemia (HI), microglia face substantial metabolic stress; and upon phagocytosis, they become overloaded with lipids derived from engulfed dead neurons and myelin debris. It is unclear how microglia respond to and process the lipid cargo, and whether lipid accumulation may affect microglia function following neonatal HI. MethodsThe postnatal day 10 mice were subjected to HI using the Vannucci model. Lipid droplets (LD) were assessed by histology and immunofluorescent staining. Single-nucleus RNA sequencing (snRNA-seq) was performed using brain tissue from HI-injured and sham-operated mice at 72 hours after HI. LD-accumulating microglia (LDAM) were identified by a specific LD marker gene perilipin 2 (Plin2). Differential gene expression was analyzed between Plin2-positive and Plin2-negative microglia after HI. Human HIE brain sections were also examined for LD accumulation. The dynamic changes of PLIN2-expressing microglia and infiltrating monocyte-derived macrophages (MDM) at 24 hours, 72 hours and 7 days after HI were compared using flow cytometry. In addition, mouse BV2 microglia were subjected to oxygen-glucose deprivation (OGD) to study phagocytosis and cytokine expression. ResultsLipid droplets accumulated primarily in microglia after HI in neonatal mice and in human HIE brain. LD were not found in astrocytes or neurons. Plin2-expressing LDAM emerged as new microglia clusters after HI. Compared with microglia without LD, LDAM showed a distinct transcriptional profile with upregulation of genes linked to microglial activation, enhanced cholesterol and lipid processing, and a shift towards phagocytic and pro-inflammatory state. Blocking LD biogenesis reduced elevated phagocytosis and IL-1{beta} expression in BV2 cells following OGD. ConclusionOur study revealed that microglia accumulate lipid droplets as part of their metabolic responses to HI in the neonatal brain. Microglial lipid droplet formation is associated with a pro-inflammatory phenotype at early stage after HI, and increased phagocytosis in vitro. The lipid metabolic changes may regulate microglial function and influence HI outcomes.

neuroscience↗

bioRxiv2026

Ribonucleotide Reductase Inhibition Overcomes FLT3 Inhibitor Resistance in Acute Myeloid Leukemia

Internal tandem duplication mutations in FLT3 (FLT3ITD) occur in approximately 30% of patients with acute myeloid leukemia (AML) and are among the most common genetic alterations in this disease. FLT3ITD is a major driver of AML and is associated with poor clinical outcomes. Although FLT3 inhibitors (FLT3is) have significantly improved outcomes for patients with FLT3ITD+ AML, acquired resistance remains a major barrier to durable clinical benefit. Reactivation of RAS/MAPK signaling, often driven by activating NRAS mutations, is a major mechanism of FLT3i resistance in AML; however, effective strategies to overcome this resistance remain lacking. Here, we identify ribonucleotide reductase (RNR) as a critical therapeutic vulnerability in NRAS-driven FLT3i-resistant FLT3ITD+ AML. Activation of RAS signaling through SPRY3 loss or oncogenic NRAS mutations confers robust resistance to FLT3is, whereas pharmacologic inhibition of RNR with multiple inhibitors, as well as siRNA-mediated RNR suppression, reverses FLT3i resistance and restores FLT3i sensitivity across multiple FLT3ITD+ AML models in vitro. In vivo, clofarabine, an FDA-approved RNR inhibitor (RNRi), significantly overcomes NRAS mutation-driven FLT3i resistance. In combination with FLT3 inhibition, clofarabine markedly suppresses the progression of FLT3i-resistant AML and significantly prolongs survival in cell line-derived xenograft (CDX) models. Importantly, the therapeutic efficacy of the gilteritinib/clofarabine combination was independently validated in two genetically distinct patient-derived xenograft (PDX) models harboring different NRAS mutations, demonstrating robust reduction of leukemia burden and confirming the generalizability of RNR inhibition in primary FLT3i-resistant AML. Together, these findings identify a previously unrecognized therapeutic vulnerability in FLT3i-resistant FLT3mut+ AML and establish RNR inhibition as an effective strategy to overcome FLT3i resistance, providing a strong rationale for the clinical evaluation of RNRis in combination with FLT3is in patients with resistant AML. SignificanceAlthough FLT3 inhibitors (FLT3i) are an important therapeutic advance in FLT3ITD+ AML, resistance commonly develops. We identified ribonucleotide reductase (RNR) as a new key vulnerability in NRAS-driven FLT3i-resistant AML and demonstrated that multiple RNRis, including the FDA-approved agent clofarabine, restore FLT3i sensitivity and enhance antileukemic activity, supporting a clinically actionable combination strategy.

cancer biology↗

bioRxiv2026

SpatialJEPA: JEPA-inspired graph-context distillation for spatially aware multiomics integration

Computational frameworks for integrating spatial genomics modalities extend cell-based representation learning across molecular layers, but many paired RNA-ATAC datasets are dissociated and lack spatial coordinates. We introduce SpatialJEPA, a JEPA-inspired teacher-student framework for transferring spatial context from spatial multiomics data to non-spatial multiome data. In contrast to patch- or feature-masking objectives, SpatialJEPA masks spatial context by replacing the teachers spatial neighborhood graph with a self-only identity graph during student training, making the spatial sample appear dissociated to the student. The student learns to match teacher embeddings from this graph-context-restricted view and can therefore be applied to dissociated RNA-ATAC data at inference time. In mouse brain multiomics, the resulting representation supports source-target alignment, recovers spatially organized transcriptomic and chromatin-accessibility programs, and shows concordance with ligand-receptor pathway structure compared with non-spatial references.

molecular biology↗

bioRxiv2026

Pervasive historical introgression across oak phylogeny shapes gene expression

Oaks were once described as the "worst-case scenario" for the biological species concept because of the presumed pervasive hybridization and introgression among species. However, we still lack a full picture of genome-wide introgression across the eight sections of the Quercus phylogeny. Furthermore, we still do not have a complete characterization of what is introgressed and how it functionally influences the recipient species. Firstly, we used 168 whole genomes from 67 Quercus species belonging to the eight sections of the Quercus phylogeny and a super pan-genome to generate a phylogeny and test for ILS and introgression. Introgression was widespread: ancient introgression occurred between ancestors of the eight sections and more recent introgression took place within sections. Secondly, using genome-wide transcriptome, methylome, and chromatin accessibility data from a subset of 19 species sampled from four sections we demonstrated that introgressed genes are more highly and uniformly expressed than non-introgressed ones. This difference in expression level between introgressed and non-introgressed genes mostly results from cis-regulation, and is most likely due to DNA methylation decay in promoter ACRs. In summary, introgression has been a major evolutionary force during the whole evolutionary history of Quercus and had a significant impact on fundamental processes such as gene regulation and expression.

evolutionary biology↗

bioRxiv2026

Effect of Spatial Release from Masking on Listening Effort in Different Semantic Contexts

Humans often communicate and learn in noisy, complex listening environments. Here, we investigated the effects of spatial hearing and semantic context cues on speech intelligibility and listening effort in young adults with typical hearing. The listening task included conditions in which target speech and speech maskers were either spatially co-located or separated. Target sentences were either semantically coherent or anomalous, while the masker comprised a mixture of two coherent sentences. Results showed higher speech intelligibility in spatially separated than co-located conditions, demonstrating a robust spatial release from masking (SRM), which is consistent with prior findings. SRM did not differ between semantically coherent and anomalous sentences, indicating comparable benefits of spatial cues across semantic contexts. However, within each spatial configuration, intelligibility was higher for coherent than anomalous sentences. Listening effort, indexed by peak pupil dilation in pupillometry measurement, was reduced in spatially separated conditions, suggesting a trend toward a release from listening effort. Analysis of the timing of peak pupil dilation revealed a significantly delayed peak dilation for anomalous sentences in the co-located condition compared with coherent sentences in the separated condition, indicating increased processing demands in the absence of spatial and semantic cues. Finally, SRM was correlated with the magnitude of release from listening effort for coherent sentences, but not for anomalous sentences, suggesting that intelligibility and listening effort benefits might co-occur when contextual cues are available.

neuroscience↗

bioRxiv2026

Conditional Deletion of All Neurexins Defines Diversity of Essential Synaptic Organizer Functions for Neurexins

Presynaptic neurexins are key regulators of synapse properties that arguably represent the best-studied synaptic adhesion molecules. Despite thousands of papers, however, no direct comparison of overall neurexin functions in different types of synapses is available. A decade ago, we provided such an analysis but we recently retracted this paper because four images contained microduplications that, although without discernible impact on the paper's conclusions, could not be corrected. As a result, the scientific community lost access to primary data that established the fundamental principle that neurexins perform profoundly different functions in different types of synapses. In the present study, we have therefore reanalyzed the original raw data and expanded their conclusions with new experiments to document, in a single study, the basic contributions of neurexins to different synapses. We used triple conditional knockout mice targeting all neurexins except for Neurexin-1r and applied neuron-specific manipulations combined with slice electrophysiology, two-photon Ca2+-imaging, and immunohistochemistry. With this approach, we focused on excitatory climbing-fiber synapses in the cerebellum and on inhibitory synapses formed by parvalbumin- or somatostatin-positive neurons in the cerebellum, hippocampus, and medial prefrontal cortex. Our results show that pan-neurexin deletions produce dramatically different phenotypes in synapses, ranging from modest to massive impairments in synapse assembly (climbing-fiber and parvalbumin-positive synapses) to severe but selective decreases in action potential-induced presynaptic Ca2+-transients (somatostatin-positive synapses). Thus, neurexins perform powerful but distinct context-dependent roles in different synapses that shape the brain's circuits.

neuroscience↗

bioRxiv2026

CAR T cell foundation model predicts immunotherapy response

Single-cell transcriptomics resolves CAR T-cell states, yet translating heterogeneous cellular signals into patient-level therapeutic response remains challenging. Existing studies primarily identify response-associated genes or cell populations through experimental and statistical analyses, but few predictive frameworks integrate gene-level structure with clinical outcomes. Here, we present gANCHOR, a T-cell foundation model built on a hierarchical hypergraph attention framework combining biologically informed representation learning with patient-level response prediction. By encoding gene-pathway relationships, gANCHOR learns pathway-aware cell embeddings that improve biological conservation and batch robustness. A cell-to-patient attention module then aggregates cellular information to infer therapeutic response. Across benchmark datasets, gANCHOR achieved the strongest overall performance in biological conservation and batch-correction assessments. In response prediction across 161 patients from five CAR T-cell studies, gANCHOR achieved an F1 score of 0.87, outperforming benchmarked single-cell foundation models. gANCHOR also identified reproducible response- and non-response-associated gene programs, providing interpretable biological insights into CAR T-cell efficacy and resistance.

bioinformatics↗

bioRxiv2026

Systematic identification of cell division proteins in haloarchaea and the discovery of a membrane anchor for the Z ring

Most archaea rely on the tubulin-like protein FtsZ for division. In the last decade, several novel cell division proteins have been discovered in the model haloarchaeon Haloferax volcanii which contains two FtsZ proteins, FtsZ1 and FtsZ2. However, the composition of this FtsZ-based archaeal divisome is largely uncharacterized. Here, using in vivo crosslinking coupled with immunoprecipitation and mass spectrometry (CLIP-MS), we identified ten proteins that localize to the division site, including wide-spread proteins predicted to be involved in DNA binding and energy metabolism. Deletion analysis indicate that most of these proteins have a modest or minor impact on cell division, but HVO_0399, renamed as Cell Division Protein C (CdpC), is important for cell division and functions as a membrane anchor for FtsZ1. CdpC consists of three domains, an N-terminal domain (NTD) containing an amphipathic helix critical for membrane binding, a long intrinsically disordered linker, and a C-terminal domain (CTD) that binds FtsZ1 with high affinity and likely promotes its polymerization. Notably, both the NTD and CTD of CdpC harbor a zinc finger that is indispensable for its function. Phylogenetic analysis indicates that CdpC sequences evolved fast across haloarchaea, but exhibited high conservation in domain structure and critical residues found in this study. Overall, our study expands the repertoire of candidate division proteins and establishes CdpC as a membrane anchor for FtsZ1 in haloarchaea. These findings pave the way for in-depth studies of arcaheal cell division and broaden the function of zinc finger proteins in archaea.

microbiology↗

bioRxiv2026

SparseSeg: Target-Conditioned Discovery Segmentation of Cryo-Volume Electron Microscopy Under Sparse Annotation

Cryo-volume electron microscopy (cryo-vEM) enables near-native visualization of cellular ultrastructure, but its broad use is limited by low image contrast and the high cost of dense voxel-level annotation. Existing automated segmentation methods often generalize poorly across cell types, organelles, and imaging conditions. Here, we introduce SparseSeg, a target-conditioned, sparsity-driven segmentation framework that treats organelle segmentation as a discovery process rather than a closed-set classification task. SparseSeg uses a small number of context-specific exemplars to iteratively propagate reliable supervision through the volume. It combines sparse patch-based sampling, a multi-kernel U-Net, and geometry-consistent refinement to expand accurate segmentation while suppressing context-dependent false positives. Across serial cryo-FIB-SEM and conventional vEM datasets, SparseSeg achieves robust segmentation under extreme sparse annotation, including settings with less than 1% labeled slices. This framework reduces annotation burden while preserving morphological fidelity for quantitative cryo-vEM analysis.

bioengineering↗

bioRxiv2026

Glutamine Metabolism Supports α cell Mass and Glucagon Secretion

The liver- cell axis is a finely tuned biological rheostat that regulates whole body amino acid availability. Pancreatic cells secrete glucagon that regulates amino acid catabolism through gluconeogenesis and ureagenesis, yet the mechanisms linking amino acid levels to cell growth and function are not fully understood. Here, we identify glutaminase, the enzyme that catalyzes glutamine catabolism, as a critical cell regulator. Glutaminase is highly enriched in cells across species. cell expression of glutaminase is required for nutrient-dependent mTORC1 activation, suppression of AMPK signaling, and sustained expression of the glutamine transporter SLC38A5. This establishes a feed-forward loop linking glutamine metabolism to amino acid sensing and growth. Reduced glutaminase activity impairs dynamic glucagon secretion in response to low glucose and amino acids. Together, these findings highlight the importance of glutamine metabolism in cell growth and hormone secretion and suggest it may play a role in cell adaptation to hyperaminoacidemia.

physiology↗

bioRxiv2026

Concurrent Stereotactic Body Radiation Therapy and KRAS Inhibition Synergistically Improve Pre-clinical Pancreatic Cancer Treatment

Pancreatic ductal adenocarcinoma (PDAC) is one of the most challenging cancers to treat due to the dismal survival rate, poor post-treatment outcome and profound resistance to a wide range of therapies. With mutant KRAS being a key driver, small molecule inhibitors targeting KRAS or pan-RAS (KRASi) have demonstrated exciting preclinical and early clinical anti-tumor efficacy, and the pan-RAS(ON) inhibitor daraxonrasib (RMC-6236) recently achieved Phase 3 clinically meaningful improvements in patient survival compared to chemotherapy. But resistance to RAS/KRAS inhibitor inevitably develops, which limits and compromises the treatment outcome. In this study, we investigated the combination of stereotactic body radiation therapy (SBRT) and KRAS inhibition (MRTX1133 and daraxonrasib) in the treatment of preclinical PDAC models. We found that this combination strategy synergistically suppresses PDAC cell growth in vitro and enhances tumor control while minimizing local recurrence in orthotopically implanted KPC (LSL-KrasG12D/+;Trp53R172H/+;Pdx1-Cre) murine PDAC tumors in vivo. As radiation therapy (RT) induces ferroptosis in multiple cancer types and mutant KRAS promotes various anti-ferroptotic mechanisms, we tested the role of ferroptosis in promoting tumor-control efficacy. Intriguingly, the addition of a ferroptosis inhibitor, liproxstatin-1, to the combination therapy significantly abrogated the in vivo synergism between SBRT and KRAS inhibition, suggesting that treatment-induced ferroptosis at least partially drives the synergistic efficacy of this combination strategy. Our study indicates that this SBRT-KRASi combination has the potential to overcome treatment resistance and improve outcomes in PDAC patients. These data directly support the design of a planned multi-center Phase 2 clinical trial with this combination strategy in locally advanced PDAC.

cancer biology↗

bioRxiv2026

Deconvolving the spatiotemporal chromatin landscape through the cell cycle

Profiling genomic processes during the cell cycle is challenging because synchronized populations gradually lose synchrony as individual cells progress through the cycle at different rates and divide asymmetrically. Researchers have addressed this challenge by modeling the loss of synchrony and applying sophisticated branching process deconvolution methods to mitigate the effects of imperfect synchrony. Such methods have been used to deconvolve cell cycle transcription, but despite the central role of the chromatin landscape in orchestrating eukaryotic transcription and replication, comparable approaches to deconvolving cell cycle chromatin occupancy have not been developed, because the data are orders of magnitude larger and because DNA replication introduces non-uniform copy number effects across the genome during S phase. We present CyCLOPS, a computational framework that overcomes these technical challenges, enabling deconvolution of the genome-wide chromatin landscape throughout the cell cycle at high spatiotemporal resolution. We apply CyCLOPS to MNase-seq data collected from synchronized yeast populations at 10-minute intervals to produce the first dynamic atlas of genome-wide chromatin occupancy through the cell cycle, profiled at sub-minute resolution. We identify functional groups of cell cycle genes through chromatin-based clustering and uncover chromatin regulatory dynamics, including at non-genic loci. Our atlas reveals that chromatin occupancy and transcription fluctuate largely independently.

bioinformatics↗

bioRxiv2026

Lactylation of Influenza Virus Polymerase Acidic Protein Promotes Viral Replication and Pathogenicity

Influenza virus poses a potential risk of triggering the next global pandemic. In-depth investigation into the mechanisms underlying influenza virus replication and pathogenicity will provide robust support for controlling influenza virus infection. Although post-translational modifications are known to regulate viral infection, the role of lactylation in influenza virus replication remains elusive. In this study, influenza virus ribonucleoprotein complex subunits are found to be lactylated. Specifically, ATAT1 promotes viral polymerase acidic protein (PA) lactylation and enhances viral replication. In contrast, SIRT1 mediates de-lactylation of PA and exerts an inhibitory effect on viral replication. Further investigations reveal lactylation of PA at residues K605 and K609 is essential for viral replication and pathogenicity. Mechanistically, PA K605/609 residues are localized at the interaction interface of the ANP32-mediated polymerase asymmetric dimer; mutation at these residues inhibits polymerase asymmetric dimerization, thereby impairing RNA production during viral genome replication. Collectively, this study uncovers a novel mechanism by which influenza virus hijacks host enzymes to mediate PA lactylation, and expands the molecular regulatory network of influenza virus infection.

microbiology↗

bioRxiv2026

PFOS aggravates atherosclerosis via Bacteroides caecimuris expansion-driven bile acid remodeling and subsequent intestinal FXR-TLR3 signaling cascade

BACKGROUNDPerfluorooctane sulfonate (PFOS) is a widely distributed persistent organic pollutant in the environment and has been associated with an increased risk of atherosclerosis. However, the underlying pathogenic mechanisms remain largely unclear. This study aimed to investigate the effects of PFOS on atherosclerosis and its associated gut-vascular axis. METHODSPseudo-germ-free mouse models and fecal microbiota transplantation (FMT) were used to determine the role of the gut microbiota in PFOS-induced atherosclerosis. Metagenomic sequencing was performed to characterize alterations in gut microbial composition following PFOS exposure, and targeted metabolomics was used to assess bile acid profiles in the ileum and plasma. Transcriptomic analysis of Bacteroides caecimuris (B.caecimuris) was conducted to explore the reasons for the increased abundance of B.caecimuris after PFOS exposure. In addition, intestinal transcriptomics and ChIP-qPCR were performed to validate transcriptional regulation within the FXR-TLR3 signaling axis. RESULTSAmong 127 participants with paired serum and fecal samples, including 82 patients undergoing coronary angiography with Gensini scores (GS score), fecal PFOS levels were significantly associated with lipid profiles and GS score, whereas serum PFOS showed no such association.Mechanistically, PFOS exposure promotes intestinal enrichment of B.caecimuris by upregulating its tolC gene, thereby enhancing efflux capacity.This microbial shift was accompanied by reduced levels of tauro-ursodeoxycholic acid (TUDCA) and aberrant activation of intestinal FXR signaling.Further analyses demonstrated that FXR activation upregulated TLR3 expression and promoted inflammatory responses and atherosclerosis progression via the TLR3-NF-{kappa}B signaling axis. Both intestinal epithelial-specific FXR deficiency (Fxr{Delta}IE) and TUDCA supplementation significantly suppressed pathway activation and alleviated disease phenotypes.Functional experiments identified TLR3 as a key downstream effector of FXR. Overexpression of TLR3 abolished the protective effects observed in Fxr{Delta}IE mice. Moreover, pharmacological inhibition of TLR3 using CU CPT-4a significantly improved established atherosclerotic lesions in vivo. CONCLUSIONSThis study identifies a gut microbiota-driven FXR-TLR3 signaling axis that mediates PFOS-induced atherosclerosis. These findings provide new mechanistic insights into environmentally induced cardiovascular disease and suggest potential targets for risk assessment and therapeutic intervention.

pathology↗

bioRxiv2026

Kidney medulla macrophages maintain a free flow of urine by sensing force

Blockade by sedimentary particles, such as mineral crystals, is a continuous risk the kidney tubule faces. To prevent that, kidney resident macrophages form transepithelial protrusions and remove intratubular sedimentary particles, a behavior particularly prevailing in the medulla over the cortex. However, the molecular mechanisms underlying this characteristic behavior of medulla macrophages are incompletely understood. In this study, we identified that the medulla had higher mechanical stiffness than the cortex in steady state, which was further elevated when kidney stone formed. Increased tissue rigidity was sensed by medulla macrophages via mechanoreceptor Piezo1, which promoted macrophage protrusion formation and their ability to clean the tubules. Loss of Piezo1 expression in kidney macrophages predisposed mice to intratubular accumulation of mineral crystal in steady state and accelerated kidney stone formation during oxalate intake challenge. Signaling via Piezo1 mobilized molecules involved in cell adhesion and protrusion assembly, including Talin2 and focal adhesion kinase (FAK). Finally, we developed a first-of-its-kind cell-based therapy for the treatment of experimental nephrolithiasis by exploiting macrophage Piezo1 activity, and this strategy shows great promise for future translational research.

physiology↗