Biology subjects

Zhang, K.

Publications and source records attributed to Zhang, K..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

The bacterial swarming factor SwrD forms hexameric rings reminiscent of DNA binding proteins.

Prokaryotic swarming is a collective surface-associated behavior that supports rapid colonization, biofilm formation, and host interactions. Swarming requires enhanced flagellar motor (FM) torque generation under high-load conditions. In many bacteria, this adaptation is achieved through increased stator unit recruitment and coordinated transcriptional regulation of motility genes. Genetic studies have implicated several relatively poorly characterized proteins in swarming, including SwrD, a component of the fla-che operon whose loss impairs torque generation in Bacillus subtilis. Intriguingly, SwrD is conserved in spirochetes that experience high viscous loads but do not exhibit canonical swarming, suggesting a broader functional role in FM regulation. Here, we structurally and biophysically characterize SwrD from B. subtilis and the spirochete Borrelia burgdorferi. In both cases, we show that SwrD assembles into a hexameric ring-like structure featuring a highly charged, disordered peripheral tail. Whereas SwrD displays structural similarities to DNA-binding proteins, key DNA interaction motifs are not conserved in SwrD. Deletion of swrD in B. subtilis results in pronounced swarming defects and altered expression of fla-che operon transcripts. In silico interaction analyses further identify the stator protein MotA as a high-confidence SwrD interactor, but this interaction could not be validated biochemically. Conserved SwrD residues mediate subunit interactions or locate to the hexamer periphery where they may mediate functionally important interactions.

biochemistry↗

bioRxiv2026

Mechanical licensing of functional dendritic cell states for enhanced T cell priming

The plasticity of dendritic cell (DC) functional state is a major hurdle in DC therapy, yet how DCs acquire distinct states independent of ontogeny remains poorly understood. Here, we demonstrate that changes in matrix stress relaxation mechanically educate DCs to adopt distinct, persistent functional states even after the removal of mechanical cues. Stem cell-derived DCs cultured in a fast-relaxing environment exhibited enhanced antigen presentation, faster migration, and higher expression of T cell-recruiting chemokines. Slow-relaxing DCs, biased towards pro-inflammatory cytokine secretion, were enriched for gene signatures associated with lipid accumulation and stress response. These mechanical responses were conserved across human and murine DCs. Using ovalbumin (OVA) as the model antigen, fast-relaxing DCs elicited a CD8+-biased response in vitro, with higher antigen-specific CD8+ T cell activation and proliferation. In vivo adoptive cell transfer of mechanically educated DCs demonstrated that the fast-relaxing matrix licensed DCs to induce a potent draining lymph node T cell response with more antigen-specific T cells and higher restimulation potential. We further showed that DCs sensed matrix stress relaxation through PI3K signaling and actin branching, mediated by the concerted signaling of IL-4 and GM-CSF. Together, these findings demonstrate the role of matrix stress relaxation on the functional state of DCs and suggest a novel approach to enhance ex vivo cellular engineering by targeting mechanical signaling. Graphical AbstractStem cell-derived dendritic cells (DCs) generated ex vivo are engineered using biomaterial platform with tunable matrix stress relaxation. Mechanical education of DCs is licensed by cytokine signaling, actin branching, and PI3K signaling. Fast-relaxing DCs exhibit higher antigen presentation and faster migration, which enhances their capacity to prime and activate antigen-specific CD8+ T cells. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/725170v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@19c68aaorg.highwire.dtl.DTLVardef@19ba1f0org.highwire.dtl.DTLVardef@a49ea5org.highwire.dtl.DTLVardef@1ab7153_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

The P3018S disease variant reveals how dynein's trailing motor sets ensemble velocity.

Mutations in the cytoplasmic dynein heavy chain (DYNC1H1) underlie a range of neurodevelopmental disorders yet how individual variants perturb dynein function remains poorly understood. We characterize the disease-associated P3018S mutation, located in the AAA4 module and within the Lis1-interacting region of the motor. Dynein-dynactin-BicD2 (DDB) complexes containing P3018S dynein move at half the wild-type velocity and generate reduced stall forces but retain the ability to assume the inhibitory phi conformation that Lis1 suppresses, respond to Lis1, and assemble into higher-order force-generating states. Several Schizosaccharomyces species, which lack Lis1, naturally encode a serine at this position, suggesting evolutionary relevance for dynein activation. Using mixed wild-type-mutant assemblies, we find that the dynein occupying the trailing position on dynactin dictates ensemble velocity, and that the leading dyneins LIC enhances trailing-motor velocity by [~]130%, revealing a mechanism for leading-to-trailing motor stimulation within multi-dynein assemblies.

biophysics↗

bioRxiv2026

CAD rewires nucleotide metabolism to drive oxidative stress in myocardial ischemia/reperfusion injury

Myocardial ischemia/reperfusion (I/R) injury is a major determinant of infarct size and clinical outcome, yet effective therapies remain limited. Although metabolic remodeling is central to I/R pathology, the contribution of nucleotide biosynthesis remains unclear. Here, we identify CAD, the multifunctional rate-limiting enzyme of de novo pyrimidine biosynthesis, as a previously unrecognized regulator of myocardial reperfusion injury. CAD activation exacerbated cardiomyocyte death during simulated I/R, whereas CAD knockdown or pharmacological inhibition was protective in vitro. Mechanistically, CAD enhanced dihydroorotate dehydrogenase (DHODH)-dependent electron transfer, increased the CoQH2/CoQ ratio, and promoted complex I reverse electron transport (RET), thereby amplifying mitochondrial ROS. In parallel, CAD suppressed de novo purine synthesis, causing purine insufficiency, DIS3L-dependent RNA decay, and cytosolic ROS. Importantly, cardiomyocyte-specific CAD deletion protected against cardiac I/R injury in vivo. Together, these findings establish CAD as a metabolic hub linking nucleotide flux to dual-compartment ROS signaling and identify nucleotide metabolism as a therapeutic vulnerability in myocardial I/R injury. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/725578v1_ufig1.gif" ALT="Figure 1"> View larger version (87K): org.highwire.dtl.DTLVardef@14c4fedorg.highwire.dtl.DTLVardef@1138ed2org.highwire.dtl.DTLVardef@1057d8borg.highwire.dtl.DTLVardef@17546bd_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Enhanced Radio-sensitization of Glioblastoma Using a Dendrimer-Based Metformin Nano-formulation through Direct Tumor Suppression and Indirect Immune Modulation

Glioblastoma (GBM) is the most common and lethal primary malignant brain tumor in adults, with median survival remaining approximately 12-15 months despite aggressive multimodal therapy. Therapeutic resistance and tumor recurrence are driven in part by limited drug penetration across the blood-brain barrier (BBB) and the persistence of brain cancer stem cells (BCSCs), highlighting the need for brain-penetrant therapeutic platforms capable of achieving sustained intratumoral delivery. Here, we developed a dendrimer-based nanotherapeutic by conjugating metformin to a fourth-generation hydroxyl-terminated polyamidoamine dendrimer (P4-MET) to enhance intracranial bioavailability and therapeutic efficacy in GBM. P4-MET exhibited favorable pharmacokinetic properties, including prolonged retention within the tumor microenvironment, and demonstrated enhanced cytotoxicity against GBM cell lines relative to free metformin (f-MET). Mechanistical studies with transcriptomic profiling by RNA sequencing revealed distinct treatment-associated molecular signatures, identifying BOLA2B as the most significantly differentially expressed gene between treatment groups. Specifically, BOLA2B expression was markedly elevated in f-MET-treated cells but not so following P4-MET treatment. Given the established association of BOLA2B with mTORC1 signaling and GPX4-mediated ferroptosis resistance, these findings suggest that P4-MET may, at least in part, enhance therapeutic efficacy by modulating ferroptosis-associated pathways. In orthotopic GBM models, combination treatment with P4-MET and radiotherapy (RT) significantly prolonged overall survival and increased tumor cell death compared with either monotherapy alone, consistent with a synergistic radiosensitizing effect. Importantly, P4-MET demonstrated minimal systemic toxicity, supporting its favorable therapeutic index and translational potential. Collectively, these findings establish P4-MET as a brain-penetrant nanomedicine platform that improves metformin delivery, modulates ferroptosis-related signaling networks, and potentiates radiotherapeutic response in GBM. This study highlights the potential of dendrimer-enabled metabolic nanotherapies to overcome therapeutic resistance in malignant brain tumors.

cancer biology↗

bioRxiv2026

Sequence-Defined Digital Bottlebrush Polymers for Programmable Oligonucleotide Delivery

Oligonucleotide therapeutics hold transformative potential, yet their clinical translation is hindered by delivery barriers, including rapid renal/hepatic clearance and poor organ specificity. Bottlebrush polymers conjugates have emerged as a promising vector to address these limitations, but conventional architectures with uniform backbones can only achieve an unmodifiable, rigid biodistribution profile. Here, we report a library of sequence-defined "digital" bottlebrush polymers, precisely engineered with controlled placements of chemical motifs that modify physiochemical properties - including lipids, cholesterol, and cationic groups - along a polyphosphodiester backbone. Systematic evaluation of the digital bottlebrush polymer library reveals distinct structure-property relationships and enables organ-biased systemic delivery to several traditionally difficult-to-reach tissues, including muscle and skin. In a mouse model of rheumatoid arthritis, a single dose of a spleen-homing polymer-conjugated antisense oligonucleotide targeting TNF- achieves potent knockdown and drives full functional recovery. These findings establish a versatile design framework for tailoring bottlebrush polymers to specific therapeutic applications.

bioengineering↗

bioRxiv2026

Probabilistic Cardiac Digital Twins for Robust Patient-Specific Modeling

Uncertainty quantification (UQ) in computational heart models is essential for reliable cardiac digital twins (DTs) in personalized medicine, yet remains challenging. Traditional Monte Carlo and stochastic Galerkin methods often become impractical in the high-dimensional, nonlinear state variable and parameter spaces of cardiac electrophysiology and mechanics. This article introduces a framework for learning a joint probability density over cardiac observables and model parameters, enabling the characterization of statistical dependencies across a large number of variables in patient-specific cardiac DTs. By sampling from this density and conditioning on available data, useful predictive distributions can be constructed, allowing uncertainty to be propagated through the model and quantified in terms of variability. Conditional regression can then be performed directly on this learned density, enabling systematic exploration of interdependencies among observables for both predictive inference and model design. The statistical methodology adopts a geometry-aware generative learning framework, recently introduced by the authors, that decouples the learning of data geometry from sampling. First it identifies a low-dimensional latent representation that captures the intrinsic structure of the data and its multiscale geometric features. A stochastic differential equation is then formulated directly in the low-dimensional latent space to generate samples efficiently; these are subsequently mapped back to the high-dimensional space of cardiac states and parameters through a smooth lifting operator. We demonstrate the approach on a ventricular arrhythmia prediction benchmark, where the learned joint probability density enables the construction of predictive distributions over key parameters (e.g., conductivities, fibrosis patterns) through sampling and conditioning. This enables uncertainty to be propagated and quantified through sampling and conditioning on the learned joint density, with substantially fewer model evaluations than conventional UQ methods.

bioengineering↗

bioRxiv2026

Sphk1-S1P signaling drives blood-brain barrier breakdown after intracerebral hemorrhage via HIF-1α-dependent upregulation of Bsg-MMP-9

Blood-brain barrier (BBB) breakdown is a critical pathological event driving secondary brain injury and poor outcomes following intracerebral hemorrhage (ICH). However, the mechanisms governing acute BBB breakdown after ICH remain incompletely understood. Here we demonstrate that the Sphk1-S1P-S1PR3 signaling plays a pivotal role in this process. Sphk1 expression was significantly upregulated in the perihematomal endothelial cells of both ICH patients and mice, with levels positively correlating with BBB dysfunction severity and poor clinical outcomes. Using endothelial-specific genetic gain- and loss-of-function approaches, we found that Sphk1 knockdown attenuated BBB leakage, reduced hematoma volume and brain edema, preserved tight junction integrity, and improved neurological function at 1-day post-ICH, whereas Sphk1 overexpression exacerbated these pathological features. Mechanistically, transcriptomic profiling of perihematomal endothelial cells revealed that prior to its established role in Nlrp3-mediated pyroptosis, Sphk1 promotes early BBB breakdown by regulating the Bsg-MMP-9 axis. Endothelial-specific Bsg deletion completely abrogated the deleterious effects of Sphk1, confirming Bsg as an indispensable intermediary through which Sphk1 signals to MMP-9. ATAC-seq and dual-luciferase assays further demonstrated that Sphk1-generated S1P signals through S1PR3 to activate HIF-1, which directly binds the Bsg promoter to drive its transcription, ultimately promoting MMP-9-mediated tight junction degradation. These findings delineate a complete hierarchical signaling cascade from metabolic enzyme to transcriptional regulation and subsequent barrier injury, establishing the Sphk1-Bsg-MMP-9 axis as a promising therapeutic target for ICH. One sentence summaryThis work identifies an early and pivotal mechanism of blood-brain barrier breakdown after intracerebral hemorrhage, demonstrating that Sphk1-generated S1P signals through S1PR3 to activate HIF-1, which directly transactivates Bsg expression, leading to MMP-9-mediated tight junction degradation, thereby establishing a novel hierarchical axis with therapeutic potential.

cell biology↗

bioRxiv2026

spatiAlytica: Viewer-Grounded Multimodal Agentic System for Interactive Spatial Omics Analysis

Spatial transcriptomics and proteomics map tissue architecture and cellular interactions, but analysis remains limited by programming demands and text-centered AI agents that lack viewer grounding and cross-turn context. We present spatiAlytica, a viewer-centric multimodal interactive agentic system embedded in the Napari viewer that enables non-programmer biologists to perform iterative, hypothesis-driven spatial omics analysis via natural language. spatiAlytica couples viewer-state serialization, agentic memory, biological concept-to-data-field mapping, code generation and debugging, Spatial VQA, and grounded interpretation to support an exploratory analysis and interpretive reasoning workflow. We introduce spatiAlyticaBench, a comprehensive benchmark spanning 222 single-turn spatial analytical coding questions, 178 multi-turn sequential workflow questions, and 7,350 image-grounded reasoning questions. spatiAlytica outperformed strong agentic baselines, while using less time and tokens. Case studies across Kaposis sarcoma, colorectal cancer, and ovarian cancer recapitulated known spatial patterns and uncovered progressive CD8 T-cell dysfunction during KS progression.

bioinformatics↗

bioRxiv2026

Reconstructing True 3D Spatial Omics at Single-Cell Resolution

Capturing the three-dimensional (3D) organization of cells is essential for deciphering complex biological processes, yet comprehensive 3D spatial omics is severely hindered by the destructive nature of physical sectioning and the depth limitations of intact tissue imaging. Current computational methods rely on 2.5D stacking of discrete slices, which inherently disrupts tissue topology and fails to resolve continuous depth-dependent molecular gradients. To bridge this gap, we introduce DO_SCPLOWEEPC_SCPLOWSO_SCPLOWPATIALC_SCPLOW, an Optimal Transport flow matching framework that models tissue evolution as a continuous dynamic vector field. By solving the underlying probability flow ODEs, DO_SCPLOWEEPC_SCPLOWSO_SCPLOWPATIALC_SCPLOW enables the direct extraction of uninterrupted, infinitely resolvable tissue states at arbitrary spatial depths. Using Deep STAR/RIBOmap 3D technologies, we demonstrate that DO_SCPLOWEEPC_SCPLOWSO_SCPLOWPATIALC_SCPLOW achieves improved 3D reconstruction fidelity relative to 2.5D approaches, yielding structures that more closely recapitulate native tissue microenvironments in real-world datasets. Across diverse spatial omics modalities, including spatial proteomics using imaging mass cytometry in human breast cancer and spatial transcriptomics using openST in head and neck squamous cell carcinoma metastatic lymph nodes, DO_SCPLOWEEPC_SCPLOWSO_SCPLOWPATIALC_SCPLOW produces biologically interpretable and high-fidelity reconstructions across datasets. We evaluated the scalability and robustness of DO_SCPLOWEEPC_SCPLOWSO_SCPLOWPATIALC_SCPLOW on a large-scale mouse brain dataset, reconstructing a continuous 3D cellular atlas comprising 39 million cells within 41.6 hours. Systematic downstream characterization validated its ability to recapitulate consistent spatial architectures, cell-type distributions, transcriptomic patterns, and microenvironmental structures across brain regions. Collectively, these results demonstrate DO_SCPLOWEEPC_SCPLOWSO_SCPLOWPATIALC_SCPLOW as a generalizable and efficient solution for true 3D spatial reconstruction across scales and modalities. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/721395v2_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@1a19624org.highwire.dtl.DTLVardef@188361forg.highwire.dtl.DTLVardef@199321corg.highwire.dtl.DTLVardef@a8f411_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

A MinD-like ATPase couples flagellation and cell division in spirochetes

Spirochetes are evolutionarily distinct bacteria defined by their spiral morphology, unique means of motility, and periplasmic flagella (PFs). Because these filaments reside within the periplasm and are mechanically integrated with the cell body, their assembly must be precisely coordinated with cell growth and cytokinesis. However, the mechanism that couples flagellar biogenesis to cell division in spirochetes remains unclear. Using the Lyme disease spirochete Borrelia burgdorferi as a model, we identify FlhG (BB0269), a MinD-like ATPase, as a spatial regulator that links cell division to flagellar patterning. In wild-type cells, 7-11 long helical PFs originate from cell poles and assemble into ribbon-like bundles that wrap around the cell cylinder to drive motility. Deletion of flhG disrupts this ordered architecture, causing marked heterogeneity in flagellar number, defective ribbon assembly, aberrant septation, and severe motility impairment. Mechanistically, FlhG dynamically localizes to the poles and midcell during division, where it directs the positioning of FlhF, a signal recognition particle (SRP) -type GTPase controlling flagellar number and placement, and FliF, the MS-ring protein that nucleates flagellar assembly. Through this spatial regulation, FlhG coordinates flagellar assembly with cytokinetic progression. Together, these findings reveal a spatial regulatory mechanism coupling cell division to flagellation, providing insight into understanding how spirochetes coordinate their distinctive morphogenesis, flagellation and motility. SignificanceSpirochetes such as Borrelia burgdorferi, the causative agent of Lyme disease, rely on periplasmic flagella for motility and cell shape, yet how these structures are coordinated with cell division has remained unclear. We identify a MinD-like ATPase, FlhG, as a spatial regulator that couples flagellar assembly to cytokinesis. In contrast to its homologs in other bacteria, FlhG does not regulate flagellar protein levels but instead directs subcellular positioning of key assembly factors. By dynamically redistributing between the cell poles and division site, FlhG synchronizes flagellar patterning with septum formation. These findings uncover a previously unrecognized mechanism linking cell morphogenesis to the cell cycle and reveal how conserved ATPases can be repurposed to organize complex bacterial architectures.

microbiology↗

bioRxiv2026

Survey of Climate-structured Mycobiomes in Staple Maize: Implications for Endemic Keshan and Kashin-Beck Diseases

Keshan disease (KD) and Kashin-Beck disease (KBD) are geographically restricted disorders in rural China with overlapping environmental and dietary risk factors. Selenium deficiency alone cannot explain their regional heterogeneity. Maize, a dietary staple in endemic areas, represents a key exposure pathway for climate-sensitive foodborne fungi and their metabolites. We profiled maize-associated fungal communities from seven villages across KD-, KBD-, KD-KBD co-endemic, and non-endemic regions using ITS sequencing and integrative bioinformatics. Fungal diversity, composition, trophic structure, and predicted biosynthetic gene cluster potential differed markedly among regions. KD-endemic areas were enriched in saprotrophic taxa such as Penicillium and Aspergillus, KBD-endemic regions favored cold- and humidity-adapted fungi, and KD-KBD co-endemic areas exhibited the highest predicted mycotoxin potential. Fungal patterns were strongly associated with regional temperature and humidity. These findings support a climate-sensitive, foodborne exposome framework, suggesting that variation in maize-associated fungi may contribute to endemic disease risk and highlighting the need for fungal surveillance in public health strategies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/716289v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@2cf23borg.highwire.dtl.DTLVardef@d31e5aorg.highwire.dtl.DTLVardef@6dbcadorg.highwire.dtl.DTLVardef@7e0734_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2026

Seeded aggregation of ANXA11 induces prion-like propagation, TDP-43 co-pathology and nucleocytoplasmic transport defects

Mutations in ANXA11 cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet the mechanisms linking ANXA11 dysfunction to neurodegeneration remain poorly defined. Recent cryo-EM studies revealed heteromeric ANXA11-TDP-43 filaments in patient brains, suggesting a direct pathological connection between these two ALS-associated proteins. However, whether ANXA11 possesses intrinsic amyloidogenic properties and how its aggregation relates to TDP-43 proteinopathy remain unknown. Here, we demonstrate that ANXA11 undergoes liquid-liquid phase separation and subsequently matures into amyloid fibrils through a liquid-to-solid phase transition. ANXA11 fibrils exhibit prion-like properties, including self-templating seeding activity and intercellular propagation in human iPSC-derived neurons. Strikingly, ANXA11 fibrils induces pathological conversion of TDP-43, including hyperphosphorylation, accumulation in detergent-insoluble fractions, and formation of cytoplasmic aggregates. TurboID proximity-labeling proteomics further revealed aggregation-dependent enrichment of nuclear pore complex and nucleocytoplasmic transport factors in the ANXA11 aggregate-proximal proteome. Consistently, ANXA11 aggregation was associated with nuclear envelope abnormalities, altered nucleoporin distribution, impaired mRNA export, and progressive neuronal toxicity in iPSC-derived neurons. Together, these findings establish ANXA11 as an intrinsically amyloidogenic, phase-transition-competent protein whose seeded assemblies propagate between cells, induce TDP-43 co-pathology, and are linked to nucleocytoplasmic transport defects and neuronal injury, thereby providing a mechanistic framework for ANXA11-associated ALS/FTD pathogenesis. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/713853v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1aaad3org.highwire.dtl.DTLVardef@c51d5eorg.highwire.dtl.DTLVardef@10b2891org.highwire.dtl.DTLVardef@1945575_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIANXA11 undergoes liquid-liquid phase separation and matures into amyloid fibrils through a liquid-to-solid phase transition. C_LIO_LIANXA11 fibrils supports homotypic seeding and propagate within SH-SY5Y cells and iPSC-derived neurons. C_LIO_LIANXA11 fibrils induce TDP-43 pathological conversion, including phosphorylation and accumulation in insoluble aggregates. C_LIO_LIANXA11 aggregation is associated with nuclear pore complex remodeling, impaired mRNA export, and neuronal toxicity. C_LI In BriefANXA11 undergoes phase separation and matures into prion-like amyloid fibrils through a liquid-to-solid transition. These seeded assemblies propagate between cells and human neurons, induce TDP-43 pathological conversion, and are associated with remodeling of nuclear pore complexes, impaired mRNA export, and progressive neuronal toxicity. ANXA11 forms seeded amyloid assemblies that spread between cells, induce TDP-43 pathology, and disrupt nucleocytoplasmic transport.

neuroscience↗

bioRxiv2026

Fear Learning Induced Brain Dynamics Predict Individual Extinction Memory Expression following Transcranial Magnetic Stimulation

Fear learning and extinction unfold as time-dependent processes. Herein, we examined how fear learning dynamically reorganizes brain activity immediately after learning, and whether such reorganization can be modulated with TMS application during extinction learning to prospectively predict extinction-memory expression. Eighty-seven healthy adults completed a three-day Pavlovian threat-learning protocol with resting-state fMRI acquired before and after conditioning (Day 1), dorsolateral prefrontal cortex (DLPFC) transcranial magnetic stimulation (TMS) applied during extinction learning (Day 2), and fMRI during extinction recall and renewal (Day 3). Using coactivation pattern analysis with a hidden Markov model within a 24-nodes threat-circuit parcellation, we identified a fear-learning-induced brain state characterized by global threat-circuit coactivation with heightened engagement and transition uncertainty post conditioning, and a progressive increase in engagement across post-conditioning. Critically, conditioning-induced functional connectivity reorganization within this state predicted individual differences in extinction recall- and renewal-related brain activation under TMS-modulated extinction (cross-validated; recall r = 0.47, p = 0.001; renewal r = 0.37, p = 0.01; permutation-tested), but not under natural extinction. Similar associations were observed between neural features and behavioral expression. These findings demonstrate that fear learning reshapes spontaneous brain-state dynamics and that such learning-induced reorganization serves as an interpretable biomarker for neuromodulation-linked extinction-memory expression.

neuroscience↗

bioRxiv2026

A circRNA-based uricase replacement therapy for sustained treatment of hyperuricemia

Hyperuricemia, a major risk factor for gout and kidney disease, arises from the evolutionary loss of human uricase and remains a significant medical challenge due to its high prevalence. However, limited therapeutic options are available for refractory hyperuricemia that typically require long-term treatment. Here we developed a circRNA-based uricase replacement strategy and evaluated its efficacy in uricase-knockout mice as a model for severe hyperuricemia. Lipid nanoparticle-mediated delivery of circRNA enabled efficient in vivo expression of an engineered human-like uricase, which rapidly reduced serum urate levels after a single injection and maintained the urate-lowering effect for up to 10 days. Repeated administration led to sustained urate reduction for 10 weeks, mitigated renal injury, and exhibited favorable biosafety. These findings highlight the therapeutic potential of circRNA-based uricase replacement for the long-term treatment of hyperuricemia and its associated complications.

molecular biology↗

bioRxiv2026

IgG Propels Atherosclerosis by Noncanonically Activating Macrophages

Despite being a central component of adaptive immunity and a highly abundant serum protein, the contribution of IgG to the milieu of atherosclerosis remains unappreciated. Here, we identify a pro-atherogenic role for IgG as it activates an innate immune cascade, independent of its classical antigen-neutralizing function. Analyses of human coronary artery plaques reveal a positive correlation between IgG and cardiovascular and cerebrovascular disease severity. Integrated single-cell plaque analyses localize IgG, coinciding with its recycling receptor FcRn, to pro-inflammatory and foamy macrophages. Genetic ablation of FcRn in myeloid cells prevents IgG from accumulating in mouse atherosclerotic lesions, diminishing plaque size and inflammation. Mechanistically, IgG acts as an endogenous ligand for TLR4, triggering NF-{kappa}B-NLRP3 inflammasome signaling without requiring its antigen-binding domain. Additionally, IgG accelerates macrophage foam cell formation through upregulation of downstream effector LCN2. Our work uncovers a role for previously overlooked adaptive immune molecules in the pathogenesis of atherosclerosis through a noncanonical mechanism linked with innate immunity.

immunology↗

bioRxiv2026

High-resolution retrospective single cell lineage tracing with mutable homopolymers

Retrospective reconstruction of cell lineages from somatic mutations holds substantial promise for understanding development, tissue homeostasis, and disease. Yet, current approaches are often constrained by low marker density, technical noise, and incomplete molecular readouts that limit the resolution and accuracy of inferred lineages. Here, we present RETrace2, a single-cell dual-omic method for simultaneous lineage tracing and cell-type identification. By identifying and targeting highly mutable homopolymers, which we show are approximately twice as informative as conventional microsatellite repeats, combined with technical improvements to increase marker coverage and reduce experimental errors of reading and amplifying homopolymers, RETrace2 can trace lineage continuously at an estimated resolution of fewer than five cell divisions in microsatellite-unstable organisms. Simultaneously, sparse methylation profiles were obtained from the same cells for cell-type identification. We validated the method using in vitro ground-truth models and demonstrated its utility in vivo by reconstructing multi-organ lineage trees from the brain, kidney and liver of Msh2-deficient mice.

genetics↗

bioRxiv2026

Role of desolvation on biomolecular liquid-liquid phase separation

Biomolecular condensates play essential roles in cellular organization and are implicated in diverse pathological processes. Their formation is driven by liquid-liquid phase separation (LLPS), a process that requires coordinated multistep desolvation of biomolecular chains and multivalent inter-chain interactions. Although coarse-grained (CG) models with implicit solvent are widely used to probe LLPS thermodynamics and kinetics, they typically neglect water-mediated desolvation effects, limiting their accuracy and mechanistic interpretability. Here, guided by all-atom simulations and experimental measurements, we develop a desolvation-aware implicit-solvent CG model by incorporating residue-level desolvation terms directly into the pairwise energy function and apply it to investigate LLPS of intrinsically disordered proteins. Incorporating these desolvation interactions reshapes the phase diagram, alleviating dense-phase overcompaction. Notably, we observe an approximately linear correlation between the temperature gap (simulation temperature relative to the critical point) and the extent of conformational expansion accompanying the dilute-to-dense phase transition, a result further supported by theoretical analysis. We also find that desolvation barriers slow early density-fluctuation growth and shorten transient kinetic arrest, whereas solvent-separated contact interactions exert the opposite effects. Both terms further modulate chain mobility within mature condensates through competing packing and energy-landscape effects. Together, this framework enables an efficient representation of desolvation in CG simulations and reveals how desolvation energetics shape both the thermodynamic landscape and kinetic properties of biomolecular LLPS.

biophysics↗